Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007173.1 Hibiscus syriacus cultivar Beakdansim tig00018827_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: 1357898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:167413 original size:113 final size:114
Alignment explanation
Indices: 167238--167889 Score: 590
Period size: 113 Copynumber: 5.5 Consensus size: 114
167228 GCTAGATCGA
*
167238 GTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
167303 ACTTTTTGCTCGAATTC-ATCTCTTGATGGATAAACATTTGCCAGAAGT
66 ACTTTTTGCTCGAATTCTATCTCTAGATGGATAAACATTTGCCAGAAGT
* *
167351 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* ** * * * * *
167416 ACCTTTTGCTCG-ACGCTATCAC-AGAAGGAGATAGATCGGCATCAACTTTTCTAGGTAA-A
66 ACTTTTTGCTCGAATTCTATCTCTAG-ATG-GATA-A-----A-C-A-TTTGCCA-G-AAGT
167475 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
167540 ACTTTTTGCTCGAATTC-ATCTCTTGATGGATCAACATTTGCCAGAAGT
66 ACTTTTTGCTCGAATTCTATCTCTAGATGGATAAACATTTGCCAGAAGT
* *
167588 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTTA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
** * * * **
167653 A-TCTTTTGCTCG-ACGCTATCAC-AGAAGGAGATATATCGGCACCAACTTTTCCAGAGAAA
66 ACT-TTTTGCTCGAATTCTATCTCTAG-ATG-GATA-A-----A-C-A-TTTGCCAGA-AGT
* * * *
167712 GTTCATAATGAGAAGAACTTATATGAAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
167776 ACCTTTTGCAT--AATTCTATCACATAAGCAGATAGATTAGCATAAACCTTT-CCAGAAGT
66 ACTTTTTGC-TCGAATTCTAT--C-T---C---TAGA-T-GGATAAACATTTGCCAGAAGT
* *
167834 GTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
167890 GCTTATTTAA
Statistics
Matches: 438, Mismatches: 54, Indels: 84
0.76 0.09 0.15
Matches are distributed among these distances:
112 9 0.02
113 159 0.36
114 12 0.03
115 3 0.01
116 1 0.00
117 1 0.00
120 2 0.00
121 2 0.00
122 30 0.07
123 90 0.21
124 112 0.26
125 6 0.01
126 1 0.00
127 1 0.00
129 1 0.00
132 2 0.00
133 5 0.01
134 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (114 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACTTTTTGCTCGAATTCTATCTCTAGATGGATAAACATTTGCCAGAAGT
Found at i:167652 original size:237 final size:237
Alignment explanation
Indices: 167237--167977 Score: 1023
Period size: 237 Copynumber: 3.1 Consensus size: 237
167227 TGCTAGATCG
167237 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
167302 AACTTTTTGCTCGAATTCATCTCTTGATGGATAAACATTTGCCAGAAGTGTTCATAATGAGAAGA
66 AACTTTTTGCTCGAATTCATCTCTTGATGGATAAACATTTGCCAGAAGTGTTCATAATGAGAAGA
*
167367 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCGACGC
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGACGC
* *
167432 TATCACAGAAGGAGATAGATCGGCATCAACTTTTCTAG-GTAA
196 TATCACAGAAGGAGATAGATCGGCACCAACTTTTCCAGAG-AA
*
167474 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
167539 AACTTTTTGCTCGAATTCATCTCTTGATGGATCAACATTTGCCAGAAGTGTTCATAATGAGAAGA
66 AACTTTTTGCTCGAATTCATCTCTTGATGGATAAACATTTGCCAGAAGTGTTCATAATGAGAAGA
* *
167604 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTTAATCTTTTGCTCGACGC
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGACGC
*
167669 TATCACAGAAGGAGATATATCGGCACCAACTTTTCCAGAGAA
196 TATCACAGAAGGAGATAGATCGGCACCAACTTTTCCAGAGAA
* * *
167711 AGTTCATAATGAGAAGAACTTATATGAAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
167775 AACCTTTTGCAT--AATTCTATCACATAAGCAGATAGATTAGCATAAACCTTT-CCAGAAGTGTT
66 AACTTTTTGC-TCGAATTC-AT--C-T---C---TTGA-T-GGATAAACATTTGCCAGAAGTGTT
* * * * *
167837 CATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTTAACA
118 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACC
* * * * * * **
167902 TTTTGAAT-GACTCTATCACAGAAGGAAATAGGTC--CA-CATCATCCCCAGCAGAA
183 TTTTG-CTCGACGCTATCACAGAAGGAGATAGATCGGCACCAACTTTTCCAG-AGAA
167955 AGTTCATAATGAGAAGAACTCAT
1 AGTTCATAATGAGAAGAACTCAT
167978 CTAAAGAAAG
Statistics
Matches: 454, Mismatches: 34, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
235 5 0.01
236 44 0.10
237 255 0.56
238 2 0.00
239 1 0.00
242 1 0.00
243 8 0.02
244 28 0.06
245 3 0.01
246 97 0.21
247 10 0.02
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (237 bp):
AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTTGCTCGAATTCATCTCTTGATGGATAAACATTTGCCAGAAGTGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGACGC
TATCACAGAAGGAGATAGATCGGCACCAACTTTTCCAGAGAA
Found at i:167808 original size:123 final size:122
Alignment explanation
Indices: 167588--167984 Score: 424
Period size: 123 Copynumber: 3.2 Consensus size: 122
167578 TGCCAGAAGT
* *
167588 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTTA
1 GTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTTA
* * * * * * *
167653 ATCTTTTGC-TCGACGCTATCACAGAAGGAGATATATCGGCACCAACTTTTCCAGAGAAA
65 ACCTTTTGCAT-GACTCTATCACAGAAGCAGATAGATCAGCACAAACCTTTCCAGA-AAA
* * * *
167712 GTTCATAATGAGAAGAACTTATATGAAGAGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTTAA
* * * * * **
167777 CCTTTTGCATAATTCTATCACATAAGCAGATAGATTAGCATAAACCTTTCCAGAAGT
66 CCTTTTGCATGACTCTATCACAGAAGCAGATAGATCAGCACAAACCTTTCCAGAAAA
* *
167834 GTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTTA
1 GTTCATAATGAGAAGAACTCATCTGAA-GAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTTA
* * * * * * * **
167899 ACATTTTGAATGACTCTATCACAGAAGGAAATAGGTC--CAC-ATCATCCCCAGCAGAAA
65 ACCTTTTGCATGACTCTATCACAGAAGCAGATAGATCAGCACAAACCTTTCCAG-A-AAA
*
167956 GTTCATAATGAGAAGAACTCATCTAAAGA
1 GTTCATAATGAGAAGAACTCATCTGAAGA
167985 AAGAGAAAAA
Statistics
Matches: 226, Mismatches: 43, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
120 7 0.03
121 5 0.02
122 53 0.23
123 134 0.59
124 27 0.12
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (122 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTTAA
CCTTTTGCATGACTCTATCACAGAAGCAGATAGATCAGCACAAACCTTTCCAGAAAA
Found at i:168140 original size:3 final size:3
Alignment explanation
Indices: 168132--168203 Score: 90
Period size: 3 Copynumber: 23.0 Consensus size: 3
168122 TTACCCATTT
* *
168132 TTA TTA TTA TTTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
168178 TTA TTA TATA TTA TTTA TTA ATA TTA
1 TTA TTA T-TA TTA -TTA TTA TTA TTA
168204 CAAAACCCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
3 51 0.85
4 9 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:173616 original size:28 final size:28
Alignment explanation
Indices: 173574--173629 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
173564 AATAAAAATT
*
173574 ATAATATTTAAATTATTAATTAATATAA
1 ATAATATTTAAATTATTAATTAACATAA
** *
173602 ATAATATTTTTATTATTATTTAACATAA
1 ATAATATTTAAATTATTAATTAACATAA
173630 TGATATAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
ATAATATTTAAATTATTAATTAACATAA
Found at i:175819 original size:33 final size:34
Alignment explanation
Indices: 175790--175853 Score: 96
Period size: 32 Copynumber: 1.9 Consensus size: 34
175780 CAAAATTCCT
*
175790 AAACACTTTAATTACATTCT-AA-CCTAAATTCA
1 AAACACTTCAATTACATTCTAAACCCTAAATTCA
*
175822 AAATACTTCAATTACATTCTAAACCCTAAATT
1 AAACACTTCAATTACATTCTAAACCCTAAATT
175854 AAAGTATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 18 0.64
33 2 0.07
34 8 0.29
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (34 bp):
AAACACTTCAATTACATTCTAAACCCTAAATTCA
Found at i:175889 original size:33 final size:35
Alignment explanation
Indices: 175850--175921 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 35
175840 CTAAACCCTA
175850 AATTAAAGTATTCTAGAATTTA-GGTTTAAAAT-T
1 AATTAAAGTATTCTAGAATTTAGGGTTTAAAATGT
* * * *
175883 AATTAAATTATTTTGGAATTTAGGGTTTAGAATGT
1 AATTAAAGTATTCTAGAATTTAGGGTTTAAAATGT
175918 AATT
1 AATT
175922 GAGGATGTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 19 0.58
34 9 0.27
35 5 0.15
ACGTcount: A:0.39, C:0.01, G:0.15, T:0.44
Consensus pattern (35 bp):
AATTAAAGTATTCTAGAATTTAGGGTTTAAAATGT
Found at i:183913 original size:245 final size:238
Alignment explanation
Indices: 183478--183965 Score: 845
Period size: 245 Copynumber: 2.0 Consensus size: 238
183468 AAGGACTTAA
183478 CCACTATTTTATGCTAATACAAGGAGGCAATAGAATGGACCATCGCAATATAAAAGGGTTGAGTC
1 CCACTATTTTATGCTAATACAAGGAGGCAATAGAATGGACCATCGCAATATAAAAGGGTTGAGTC
183543 CATCCACTTGCATGCATAAATTAAAACCGAAACCGAAGAAGGTGCAAAACCAAGTGAAAGTCAAC
66 CATCCACTTGCATGCATAAATT--AA-C-AAACCGAAGAAGGTGCAAAACCAAGTGAAAGTCAAC
183608 GCCGGCTAAATCCACCAATGATGGAAGTGGTAAAAAATGAGATACAAAAATCCTAGATACATATA
127 GCCGGCTAAATCCACCAATGATGGAAGTGGTAAAAAATGAGATACAAAAATCCTAGATACATATA
183673 TTATATATCCAATTTCGGATAGCAATGGGTAAGTCCGATACATGTAGTTC
192 TTATATATCCAATTTCGGATAG--ATGGGTAAGTCCGAT-CATGTAGTTC
183723 CCACTATTTTATGCTAATACAAGGAGGCAATAGAATGGACCATCGCTAATATAAAAGGGTTGAGT
1 CCACTATTTTATGCTAATACAAGGAGGCAATAGAATGGACCATCGC-AATATAAAAGGGTTGAGT
183788 CCATCCACTTGCATGCATAAAATT-A-AAACCGAAGAAGGTGCAAAACCAACACGTGAAAGTCAA
65 CCATCCACTTGCATGCAT-AAATTAACAAACCGAAGAAGGTGCAAAACC-A-A-GTGAAAGTCAA
183851 CGCCGGCTAAATCCACCAATGATGGAAGTGGTAAAAAATGAGATACAAAAAATCCTAGATACATA
126 CGCCGGCTAAATCCACCAATGATGGAAGTGGTAAAAAATGAGATAC-AAAAATCCTAGATACATA
183916 TATTATATATCCAATTTCGGATAGATGGGTAAGTCCGATCATGTAGTTC
190 TATTATATATCCAATTTCGGATAGATGGGTAAGTCCGATCATGTAGTTC
183965 C
1 C
183966 TAAAAAACAG
Statistics
Matches: 237, Mismatches: 0, Indels: 15
0.94 0.00 0.06
Matches are distributed among these distances:
241 22 0.09
242 12 0.05
243 16 0.07
244 58 0.24
245 88 0.37
246 36 0.15
247 5 0.02
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23
Consensus pattern (238 bp):
CCACTATTTTATGCTAATACAAGGAGGCAATAGAATGGACCATCGCAATATAAAAGGGTTGAGTC
CATCCACTTGCATGCATAAATTAACAAACCGAAGAAGGTGCAAAACCAAGTGAAAGTCAACGCCG
GCTAAATCCACCAATGATGGAAGTGGTAAAAAATGAGATACAAAAATCCTAGATACATATATTAT
ATATCCAATTTCGGATAGATGGGTAAGTCCGATCATGTAGTTC
Found at i:190709 original size:29 final size:30
Alignment explanation
Indices: 190670--190726 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
190660 GTGCCCATCA
*
190670 TACCTCAACAGTGTTTAACCGTTCATCTTT
1 TACCTCAACAGTATTTAACCGTTCATCTTT
**
190700 TACCT-AACAGTATTTAACTTTTCATCT
1 TACCTCAACAGTATTTAACCGTTCATCT
190727 AATTAACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.42
Consensus pattern (30 bp):
TACCTCAACAGTATTTAACCGTTCATCTTT
Found at i:191283 original size:79 final size:79
Alignment explanation
Indices: 191194--191663 Score: 690
Period size: 79 Copynumber: 5.9 Consensus size: 79
191184 TTTTAGGCTT
* * * * **
191194 ATAATGCACCCGTATGCATTTCAGCTATGGCATCCTTTCATGCTAGTAATATACCCATATGCATT
1 ATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
*
191259 ATTCTTTTATGCCG
66 ATTATTTTATGCCG
* * * *
191273 ATAATGCACCCATATACATTTTAGTTATGACATCCTTTCATGCAAATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
* *
191338 ATTCTTTTATGCCA
66 ATTATTTTATGCCG
* *
191352 ATAATGCACCCATATGCATTTCAACTACGACATCCTTTCATGCCAATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
*
191417 ATTATTTTATGTCG
66 ATTATTTTATGCCG
*
191431 ATAATGCACCCATATGCAATTCAGCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
*
191496 ATTATTTTATGTCG
66 ATTATTTTATGCCG
* * * *
191510 ATAATGCACCCATATGCAATTCAGCTATGGCATCCTTTCATGCCAATAATGTACCCATATACATT
1 ATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
*
191575 ATTCTTTTATGCCG
66 ATTATTTTATGCCG
* * *
191589 ATAATGCACCCATATTCATTTTCA-CTATGGCATCCTTTCATGCCAATAATGTACCCATATGCAT
1 ATAATGCACCCATATGCA-TTTCAGCTATGACATCCTTTCATGCCAATAATGCACCCATATGCAT
191653 TATTATTTTAT
65 TATTATTTTAT
191664 TCGTTTGTTC
Statistics
Matches: 359, Mismatches: 31, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
79 355 0.99
80 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (79 bp):
ATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
ATTATTTTATGCCG
Found at i:191323 original size:45 final size:43
Alignment explanation
Indices: 191262--191658 Score: 254
Period size: 45 Copynumber: 9.8 Consensus size: 43
191252 ATGCATTATT
* * *
191262 CTTTTATGCCGATAATGCACCCATATACATTTTAGTTATGACATC
1 CTTTCATGCCAATAATGCACCCATATGCATTTTA--TATGACATC
*
191307 CTTTCATGCAAATAATGCACCCATATGCA--TTAT-T--C-T-
1 CTTTCATGCCAATAATGCACCCATATGCATTTTATATGACATC
* *
191343 -TTT-ATGCCAATAATGCACCCATATGCATTTCAACTACGACATC
1 CTTTCATGCCAATAATGCACCCATATGCATTT-TA-TATGACATC
191386 CTTTCATGCCAATAATGCACCCATATGCA--TTAT-T---AT-
1 CTTTCATGCCAATAATGCACCCATATGCATTTTATATGACATC
* * * *
191422 -TTT-ATGTCGATAATGCACCCATATGCAATTCAGCTATGACATC
1 CTTTCATGCCAATAATGCACCCATATGCATTTTA--TATGACATC
191465 CTTTCATGCCAATAATGCACCCATATGCA--TTAT-T---AT-
1 CTTTCATGCCAATAATGCACCCATATGCATTTTATATGACATC
* * * * *
191501 -TTT-ATGTCGATAATGCACCCATATGCAATTCAGCTATGGCATC
1 CTTTCATGCCAATAATGCACCCATATGCATTTTA--TATGACATC
* *
191544 CTTTCATGCCAATAATGTACCCATATACA--TTAT-T--C-T-
1 CTTTCATGCCAATAATGCACCCATATGCATTTTATATGACATC
* * *
191580 -TTT-ATGCCGATAATGCACCCATATTCATTTTCACTATGGCATC
1 CTTTCATGCCAATAATGCACCCATATGCATTTT-A-TATGACATC
*
191623 CTTTCATGCCAATAATGTACCCATATGCATTATTAT
1 CTTTCATGCCAATAATGCACCCATATGCATT-TTAT
191659 TTTATTCGTT
Statistics
Matches: 278, Mismatches: 29, Indels: 91
0.70 0.07 0.23
Matches are distributed among these distances:
34 88 0.32
35 12 0.04
36 7 0.03
37 8 0.03
38 6 0.02
39 3 0.01
40 3 0.01
41 6 0.02
42 7 0.03
43 8 0.03
44 13 0.05
45 115 0.41
46 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (43 bp):
CTTTCATGCCAATAATGCACCCATATGCATTTTATATGACATC
Found at i:191360 original size:34 final size:34
Alignment explanation
Indices: 191307--191608 Score: 190
Period size: 34 Copynumber: 7.9 Consensus size: 34
191297 TTATGACATC
* *
191307 CTTTCATGCAAATAATGCACCCATATGCATTATT
1 CTTTTATGCCAATAATGCACCCATATGCATTATT
191341 CTTTTATGCCAATAATGCACCCATATGCATTTCAACTACGACAT
1 CTTTTATGCCAATAATGCACCCATATGCA-TT--A-T------T
*
191385 CCTTTCATGCCAATAATGCACCCATATGCATTATT
1 -CTTTTATGCCAATAATGCACCCATATGCATTATT
* * *
191420 ATTTTATGTCGATAATGCACCCATATGCAATTCAGCTAT
1 CTTTTATGCCAATAATGCACCCATATGC-ATT-A--T-T
191459 GACATCCTTTCATGCCAATAATGCACCCATATGCATTATT
1 --C-T--TTT-ATGCCAATAATGCACCCATATGCATTATT
* * *
191499 ATTTTATGTCGATAATGCACCCATATGCAATTCAGCTAT
1 CTTTTATGCCAATAATGCACCCATATGC-ATT-A--T-T
* *
191538 GGCATCCTTTCATGCCAATAATGTACCCATATACATTATT
1 --C-T--TTT-ATGCCAATAATGCACCCATATGCATTATT
* *
191578 CTTTTATGCCGATAATGCACCCATATTCATT
1 CTTTTATGCCAATAATGCACCCATATGCATT
191609 TTCACTATGG
Statistics
Matches: 214, Mismatches: 21, Indels: 66
0.71 0.07 0.22
Matches are distributed among these distances:
34 95 0.44
35 15 0.07
36 2 0.01
37 3 0.01
38 4 0.02
39 2 0.01
40 2 0.01
41 3 0.01
42 3 0.01
43 2 0.01
44 15 0.07
45 68 0.32
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (34 bp):
CTTTTATGCCAATAATGCACCCATATGCATTATT
Found at i:192232 original size:21 final size:21
Alignment explanation
Indices: 192203--192259 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
192193 ATACTACCTC
192203 ATCAGTATCGATACTGATTGA
1 ATCAGTATCGATACTGATTGA
*
192224 ATCAATATCGATACTGATTGA
1 ATCAGTATCGATACTGATTGA
192245 ATCAGTATCGATACT
1 ATCAGTATCGATACT
192260 ACTTAGTTAA
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:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
ATCAGTATCGATACTGATTGA
Found at i:203602 original size:3 final size:3
Alignment explanation
Indices: 203596--203709 Score: 97
Period size: 3 Copynumber: 37.0 Consensus size: 3
203586 TAATATTATT
* * *
203596 TAA TAA TAT TAA TAA TAA TAA TATA TAA TAA GAA CATA TATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TA-A TAA TAA
* * * * *
203644 TAG TAG T-A TTA TATA TAA TTA TATA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
203690 TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
203710 GTAAGACCAT
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
2 3 0.03
3 75 0.81
4 15 0.16
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:205006 original size:22 final size:22
Alignment explanation
Indices: 204975--205051 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
204965 ACATACAGTA
*
204975 AATCTTTCATCTTTGAAAAAAG
1 AATCTATCATCTTTGAAAAAAG
*
204997 AATCTATCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAAAG
*
205019 AATCTATCATATTT-ATAAAAAG
1 AATCTATCATCTTTGA-AAAAAG
*
205041 AATATATCATC
1 AATCTATCATC
205052 GTTGCAGAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAAAG
Found at i:210536 original size:9 final size:9
Alignment explanation
Indices: 210522--210546 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
210512 AAAAGTTAGT
210522 AAAATAATA
1 AAAATAATA
210531 AAAATAATA
1 AAAATAATA
210540 AAAATAA
1 AAAATAA
210547 ATTTATTATT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAATA
Found at i:212387 original size:29 final size:28
Alignment explanation
Indices: 212325--212398 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
212315 GTTAGTTGCT
*
212325 TCCTCTTTTTTTGTTTTTTCTGTCTCCC
1 TCCTCTTTTTTTGTTTTTTCTATCTCCC
* *
212353 TTCTCTTTTTCTTTTTTTTTCTATCGT-CC
1 TCCTCTTTTT-TTGTTTTTTCTATC-TCCC
*
212382 TCCTCTTCTTTTGTTTT
1 TCCTCTTTTTTTGTTTT
212399 GCAGGATCCG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
28 15 0.39
29 22 0.58
30 1 0.03
ACGTcount: A:0.01, C:0.26, G:0.05, T:0.68
Consensus pattern (28 bp):
TCCTCTTTTTTTGTTTTTTCTATCTCCC
Found at i:212783 original size:3 final size:3
Alignment explanation
Indices: 212775--212898 Score: 167
Period size: 3 Copynumber: 40.7 Consensus size: 3
212765 TTATTTATTA
* * *
212775 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAAT AAT AAG AAG AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* *
212822 AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
212870 AAT AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
212899 ATTTAAATGA
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
3 101 0.94
4 6 0.06
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:213175 original size:76 final size:76
Alignment explanation
Indices: 213026--213516 Score: 786
Period size: 76 Copynumber: 6.4 Consensus size: 76
213016 GATGGAAATG
* * * *
213026 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC-GAAGGTTTTTGAAAACATCAAAAATC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTG-AGG-CTTTGAAAACATCAAAAAGC
213090 TCCCGAAGGCTTT
64 TCCCGAAGGCTTT
* * *
213103 TTGGAAACATCATGCACTGCAGGATTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTC
213168 CCGAAGGCTTT
66 CCGAAGGCTTT
* * **
213179 TTGAAAACATCATGCACTGTAGGACTTACAGATGACCCTGAGGCTTTGAGAACATCAAAAAAATC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTC
*
213244 CTGAAGGCTTT
66 CCGAAGGCTTT
*
213255 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGCTTTGAGAACATCAAAAAGCTC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTC
213320 CCGAAGGCTTT
66 CCGAAGGCTTT
* *
213331 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTT
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTC
213396 CCGAAGGCTTT
66 CCGAAGGCTTT
* *
213407 TTGAAAACATCATGCACTGTAGGACTTACAGATGACCCTGAGGCTTTGATAACATCAAAAAGCTC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTC
213472 CCGAAGGCTTT
66 CCGAAGGCTTT
* *
213483 TTGGAGACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCATGCACTGCAGGACTTACAGATG
213517 TGGGAAATAG
Statistics
Matches: 385, Mismatches: 28, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
76 347 0.90
77 37 0.10
78 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (76 bp):
TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTC
CCGAAGGCTTT
Found at i:216653 original size:114 final size:115
Alignment explanation
Indices: 216453--216902 Score: 699
Period size: 115 Copynumber: 3.9 Consensus size: 115
216443 GATCATGCAG
* * * * * *
216453 TTCATCTTTCAATTCCAATGATCGG-TTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* * * ** *
216517 AACACTTCCAGAAAATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGATCTCCTTATTCCTACTACAAGAAAA
*
216567 TTCATCTTTCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACTAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
216631 AACACTTCCAGAATATGCTATTGGATCTCCTTATTCCTACTACAAGAAAA
66 AACACTTCCAGAAGATGCTATTGGATCTCCTTATTCCTACTACAAGAAAA
* *
216681 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTTATACCAAACCATATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
216746 AACACTTCCAGAAGATGCTATTGGATCTCTTTATTCCTACTACAAGAAAA
66 AACACTTCCAGAAGATGCTATTGGATCTCCTTATTCCTACTACAAGAAAA
216796 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
216861 AACACTTCCAGAAGATGCTATT-GAGTCTTCTTATTTCTACTA
66 AACACTTCCAGAAGATGCTATTGGA-TCTCCTTATTCCTACTA
216903 TGAGAACGTG
Statistics
Matches: 311, Mismatches: 23, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
114 128 0.41
115 183 0.59
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGATCTCCTTATTCCTACTACAAGAAAA
Found at i:219044 original size:1 final size:1
Alignment explanation
Indices: 219038--219088 Score: 57
Period size: 1 Copynumber: 51.0 Consensus size: 1
219028 CTTGATTCAA
* * * * *
219038 TTTTTTTCTTTTTCTTTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
219089 CTTTCTTTGC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.06, G:0.04, T:0.90
Consensus pattern (1 bp):
T
Found at i:219058 original size:15 final size:14
Alignment explanation
Indices: 219038--219096 Score: 75
Period size: 14 Copynumber: 4.2 Consensus size: 14
219028 CTTGATTCAA
*
219038 TTTTTTTCTTTTTC
1 TTTTTTTTTTTTTC
*
219052 TTTTTTTTTTGTT-
1 TTTTTTTTTTTTTC
*
219065 TTGTTTTTTTTTTC
1 TTTTTTTTTTTTTC
219079 TTTTTTTTTTCTTTC
1 TTTTTTTTTT-TTTC
219094 TTT
1 TTT
219097 GCTGGATGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
13 11 0.29
14 20 0.53
15 7 0.18
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:219060 original size:11 final size:11
Alignment explanation
Indices: 219038--219092 Score: 76
Period size: 11 Copynumber: 5.0 Consensus size: 11
219028 CTTGATTCAA
219038 TTTTTTTCTTT
1 TTTTTTTCTTT
219049 TTCTTTTT-TTT
1 TT-TTTTTCTTT
* *
219060 TTGTTTTGTTT
1 TTTTTTTCTTT
219071 TTTTTTTCTTT
1 TTTTTTTCTTT
219082 TTTTTTTCTTT
1 TTTTTTTCTTT
219093 CTTTGCTGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
10 4 0.10
11 30 0.77
12 5 0.13
ACGTcount: A:0.00, C:0.07, G:0.04, T:0.89
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:219395 original size:2 final size:2
Alignment explanation
Indices: 219388--219429 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
219378 ACAACAAATG
219388 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
219430 TAAAGGATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:225161 original size:29 final size:28
Alignment explanation
Indices: 225099--225172 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
225089 GTTAGTTGCT
225099 TCCTCTTTTTTTGTTTTTTCTGTCTCCC
1 TCCTCTTTTTTTGTTTTTTCTGTCTCCC
* *
225127 TTCTCTTTTTCTTTTTTTTTCTGTCGT-CC
1 TCCTCTTTTT-TTGTTTTTTCTGTC-TCCC
*
225156 TCCTCTTCTTTTGTTTT
1 TCCTCTTTTTTTGTTTT
225173 GCAGGATCCG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 15 0.38
29 23 0.59
30 1 0.03
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.68
Consensus pattern (28 bp):
TCCTCTTTTTTTGTTTTTTCTGTCTCCC
Found at i:225557 original size:3 final size:3
Alignment explanation
Indices: 225549--225642 Score: 143
Period size: 3 Copynumber: 30.7 Consensus size: 3
225539 TTATTTATTA
* *
225549 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAAT AAT AAG AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
*
225596 AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
225643 ATTTAAATGA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
3 77 0.93
4 6 0.07
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:227680 original size:3 final size:3
Alignment explanation
Indices: 227669--227780 Score: 86
Period size: 3 Copynumber: 36.7 Consensus size: 3
227659 ATTATTTAAG
* *
227669 AAT ATT AAT AAT AAT AAT ATAT AAT AAT AAC ATAT ATAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT A-AT AAT AAT AAT
* * * * * *
227717 AGT -AT AAT ATAT AAT TAT ACT ACT -AT TAT TAT GAAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
227762 AAT AAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
227781 GTAAGACCGG
Statistics
Matches: 91, Mismatches: 11, Indels: 14
0.78 0.09 0.12
Matches are distributed among these distances:
2 4 0.04
3 73 0.80
4 14 0.15
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:232259 original size:11 final size:11
Alignment explanation
Indices: 232243--232268 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
232233 TCATTTAAAC
232243 ATTTTACATCA
1 ATTTTACATCA
232254 ATTTTACATCA
1 ATTTTACATCA
232265 ATTT
1 ATTT
232269 CCTCATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTTACATCA
Found at i:237283 original size:23 final size:23
Alignment explanation
Indices: 237224--237289 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
237214 CTGAATGATT
*
237224 CAGTGCTGACTGATTCAACAAAA
1 CAGTGCTGACTGATTCAGCAAAA
*
237247 CAGTGATGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
* *
237270 CAGTGCTAAATGATTCAGCA
1 CAGTGCTGACTGATTCAGCA
237290 TCAAAGTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (23 bp):
CAGTGCTGACTGATTCAGCAAAA
Found at i:237943 original size:20 final size:20
Alignment explanation
Indices: 237920--237957 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
237910 TTTCCAAATT
*
237920 CGCAACGCGAATTTGTAAAA
1 CGCAACGCGAATTCGTAAAA
237940 CGCAACGCGAATTCGTAA
1 CGCAACGCGAATTCGTAA
237958 TTCAGAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
CGCAACGCGAATTCGTAAAA
Found at i:238126 original size:20 final size:20
Alignment explanation
Indices: 238101--238167 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
238091 GCGTTGCGAT
*
238101 TTTCGCGTTTCGAATTTGAC
1 TTTCGCATTTCGAATTTGAC
238121 TTTCGCATTGT-GAATTTGAC
1 TTTCGCATT-TCGAATTTGAC
*
238141 TTTCGCATTGCGAATTTGAC
1 TTTCGCATTTCGAATTTGAC
238161 TTTCGCA
1 TTTCGCA
238168 ACAATCGCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 42 0.98
21 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.43
Consensus pattern (20 bp):
TTTCGCATTTCGAATTTGAC
Found at i:240461 original size:24 final size:24
Alignment explanation
Indices: 240426--240472 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
240416 GTGGCATTTT
*
240426 CTTCTCTCTTTTTTTCTTCAGGGA
1 CTTCTCTCTTTTCTTCTTCAGGGA
240450 CTTCT-TCTTTTTCTTCTTCAGGG
1 CTTCTCTC-TTTTCTTCTTCAGGG
240473 TTATATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.06, C:0.26, G:0.13, T:0.55
Consensus pattern (24 bp):
CTTCTCTCTTTTCTTCTTCAGGGA
Found at i:240677 original size:24 final size:24
Alignment explanation
Indices: 240650--240696 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
240640 ATCATTAAAA
240650 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
240674 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
240697 TTTTGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:241346 original size:21 final size:20
Alignment explanation
Indices: 241296--241346 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
241286 TGGGGAAGGA
* *
241296 TGAAAAATTGCGTTGCGAAT
1 TGAAAAATCGAGTTGCGAAT
* *
241316 TCAGAAATCGAGTTGCGAATT
1 TGAAAAATCGAGTTGCGAA-T
241337 TGAAAAATCG
1 TGAAAAATCG
241347 CAATGCGAAC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (20 bp):
TGAAAAATCGAGTTGCGAAT
Found at i:241400 original size:19 final size:19
Alignment explanation
Indices: 241360--241408 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
241350 TGCGAACTCA
*
241360 GTTGCGAAATTGGAATTCGC
1 GTTGCG-AATTCGAATTCGC
241380 GTTGCGAATTCGAGATT-GC
1 GTTGCGAATTCGA-ATTCGC
241399 GTTGCGAATT
1 GTTGCGAATT
241409 TGTTGGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (19 bp):
GTTGCGAATTCGAATTCGC
Found at i:245266 original size:63 final size:63
Alignment explanation
Indices: 245167--245377 Score: 248
Period size: 63 Copynumber: 3.4 Consensus size: 63
245157 CATCCCCTCC
* * * * *
245167 CCTCTTCTTTACATTCTGATTGCAAACATTGTCCCCTTCCTTCAAAAACTTTTCCTCTGTTCT
1 CCTCTTCTTTCCATTCTGTTTGCTAACATTTTCCCCTTCCTTCAAAAACTTTTCCTCTGTTAT
* *
245230 CCTCTTCTTTCCATTCTTTTTGCTTACATTTTCCCCTTCCTTCAAAAACTTTTCCTCTGTTAT
1 CCTCTTCTTTCCATTCTGTTTGCTAACATTTTCCCCTTCCTTCAAAAACTTTTCCTCTGTTAT
* * * * ** * * *
245293 CCTATTCTTTCAATTCTGTTTACTGATGTTTTCCCCTTCCATCAAAAGCTTTTCCTC--TAAT
1 CCTCTTCTTTCCATTCTGTTTGCTAACATTTTCCCCTTCCTTCAAAAACTTTTCCTCTGTTAT
*
245354 -CTCTTCTTTCCATTTTGTTTGCTA
1 CCTCTTCTTTCCATTCTGTTTGCTA
245378 TCCCCTTCCA
Statistics
Matches: 126, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
60 19 0.15
61 3 0.02
63 104 0.83
ACGTcount: A:0.17, C:0.30, G:0.06, T:0.48
Consensus pattern (63 bp):
CCTCTTCTTTCCATTCTGTTTGCTAACATTTTCCCCTTCCTTCAAAAACTTTTCCTCTGTTAT
Found at i:250239 original size:23 final size:22
Alignment explanation
Indices: 250191--250308 Score: 84
Period size: 21 Copynumber: 5.4 Consensus size: 22
250181 TTATGTTATA
*
250191 ATAATATATGGTTTTT-AAGAATAT
1 ATAATATA--GTTTTTGAA-AACAT
250215 ATAATATAGTTTTTTGAAAACAT
1 ATAATATAG-TTTTTGAAAACAT
* *
250238 ATTATATAG-TTTTGAAAATAT
1 ATAATATAGTTTTTGAAAACAT
* *
250259 AT-ATCATTGTTTTTGAAAACGT
1 ATAAT-ATAGTTTTTGAAAACAT
* *
250281 ATTATTTAGTTTTT-AAAA-AT
1 ATAATATAGTTTTTGAAAACAT
*
250301 ATTATATA
1 ATAATATA
250309 TATTATGCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
20 10 0.13
21 20 0.25
22 20 0.25
23 19 0.24
24 10 0.13
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (22 bp):
ATAATATAGTTTTTGAAAACAT
Found at i:250275 original size:22 final size:22
Alignment explanation
Indices: 250195--250308 Score: 103
Period size: 22 Copynumber: 5.3 Consensus size: 22
250185 GTTATAATAA
* *
250195 TATATGGTTTTT-AAGAATATAT
1 TATATAGTTTTTGAA-AACATAT
*
250217 AATATAGTTTTTTGAAAACATAT
1 TATATAG-TTTTTGAAAACATAT
*
250240 TATATAG-TTTTGAAAATATA-
1 TATATAGTTTTTGAAAACATAT
* *
250260 TATCATTGTTTTTGAAAACGTAT
1 TAT-ATAGTTTTTGAAAACATAT
*
250283 TATTTAGTTTTT-AAAA-ATAT
1 TATATAGTTTTTGAAAACATAT
250303 TATATA
1 TATATA
250309 TATTATGCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.15
21 19 0.25
22 23 0.31
23 20 0.27
24 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (22 bp):
TATATAGTTTTTGAAAACATAT
Found at i:256268 original size:12 final size:12
Alignment explanation
Indices: 256251--256275 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
256241 AACAAGACAT
256251 ATTTTCTCGAAG
1 ATTTTCTCGAAG
256263 ATTTTCTCGAAG
1 ATTTTCTCGAAG
256275 A
1 A
256276 ACATATTGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTTTCTCGAAG
Found at i:257610 original size:72 final size:72
Alignment explanation
Indices: 257534--257830 Score: 203
Period size: 72 Copynumber: 4.1 Consensus size: 72
257524 ACCAAGATTG
* * * *
257534 ACTTAAACCGTGAAAGGGAGTAATCTCATCTGACTTTCCCATGAAGGGGAGTTATCTAAAGAATC
1 ACTTAAACCATGAAAGGGAGTCATCTCACCTGACTTTCCCATGAAGGGGAGTTATCCAAAGAATC
* *
257599 GAGATCA
66 AAGACCA
** * * * **
257606 ACTTAAATTAT-ATAGGGGAGTCGTCTCACCTGGCTTTCCTGTGAAGGGGAGTTATCCAAAGAAT
1 ACTTAAACCATGA-AAGGGAGTCATCTCACCTGACTTTCCCATGAAGGGGAGTTATCCAAAGAAT
257670 CATA-ACCA
65 CA-AGACCA
* * * * * * * * * *
257678 ACATAAACCACG-AAGGAGAGTCATCTTACCTAACTTTCTCGTGAAGGGAACTCATCTAAAGAAT
1 ACTTAAACCATGAAAGG-GAGTCATCTCACCTGACTTTCCCATGAAGGGGAGTTATCCAAAGAAT
*
257742 CAAGA-TA
65 CAAGACCA
* * ** * *
257749 GACTTAAACC-TCGAAGGGGTGTCATCTCATTTGCCTTTCCCATTAA--GGAGTATCATCCAAAG
1 -ACTTAAACCAT-GAAAGGGAGTCATCTCACCTGACTTTCCCATGAAGGGGAGT-T-ATCCAAAG
*
257811 ATTCAAGACCA
62 AATCAAGACCA
257822 ACTTAAACC
1 ACTTAAACC
257831 GCGAAGCCTA
Statistics
Matches: 167, Mismatches: 47, Indels: 22
0.71 0.20 0.09
Matches are distributed among these distances:
70 3 0.02
71 6 0.04
72 153 0.92
73 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (72 bp):
ACTTAAACCATGAAAGGGAGTCATCTCACCTGACTTTCCCATGAAGGGGAGTTATCCAAAGAATC
AAGACCA
Found at i:259041 original size:24 final size:23
Alignment explanation
Indices: 259014--259181 Score: 136
Period size: 24 Copynumber: 7.4 Consensus size: 23
259004 TTATGTTATA
*
259014 ATAATATATAGTTTTTAAGAATAT
1 ATAATATATAGTTTTTAA-AACAT
*
259038 ATAATATACT--TTTTGAAAACAT
1 ATAATATA-TAGTTTTTAAAACAT
259060 AT--TATATAGTTTTTAAAACAT
1 ATAATATATAGTTTTTAAAACAT
* *
259081 ATAGTATATAGTTTTTGAAAAGAT
1 ATAATATATAGTTTTT-AAAACAT
* *
259105 ATAGTATATAGTTTTTGAAA-AT
1 ATAATATATAGTTTTTAAAACAT
**
259127 AT-ATAGTATTCTTTTTGAAAACAT
1 ATAATA-TATAGTTTTT-AAAACAT
* * *
259151 AT--TATACAGTTTTGAAAGCAT
1 ATAATATATAGTTTTTAAAACAT
259172 ATAATATATA
1 ATAATATATA
259182 TATAGTTTTT
Statistics
Matches: 118, Mismatches: 15, Indels: 23
0.76 0.10 0.15
Matches are distributed among these distances:
19 1 0.01
20 4 0.03
21 23 0.19
22 24 0.20
23 31 0.26
24 34 0.29
25 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (23 bp):
ATAATATATAGTTTTTAAAACAT
Found at i:259050 original size:22 final size:22
Alignment explanation
Indices: 259019--259179 Score: 157
Period size: 22 Copynumber: 7.2 Consensus size: 22
259009 TTATAATAAT
*
259019 ATATAGTTTTT-AAGAATATATA
1 ATATAGTTTTTGAA-AACATATA
* *
259041 ATATACTTTTTGAAAACATATT
1 ATATAGTTTTTGAAAACATATA
259063 ATATAGTTTTT-AAAACATATA
1 ATATAGTTTTTGAAAACATATA
*
259084 GTATATAGTTTTTGAAAAGATATA
1 --ATATAGTTTTTGAAAACATATA
*
259108 GTATATAGTTTTTGAAAATATATA
1 --ATATAGTTTTTGAAAACATATA
* ** *
259132 GTATTCTTTTTGAAAACATATT
1 ATATAGTTTTTGAAAACATATA
* *
259154 ATACAG-TTTTGAAAGCATATA
1 ATATAGTTTTTGAAAACATATA
259175 ATATA
1 ATATA
259180 TATATAGTTT
Statistics
Matches: 116, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
21 26 0.22
22 45 0.39
23 13 0.11
24 32 0.28
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.43
Consensus pattern (22 bp):
ATATAGTTTTTGAAAACATATA
Found at i:259188 original size:27 final size:27
Alignment explanation
Indices: 259058--259201 Score: 81
Period size: 24 Copynumber: 6.0 Consensus size: 27
259048 TTTTGAAAAC
*
259058 ATATTATATAGTTTTT-AAAACATATA
1 ATATTATACAGTTTTTGAAAACATATA
* *
259084 GTA-TAT--AGTTTTTGAAAAGATATA
1 ATATTATACAGTTTTTGAAAACATATA
*
259108 GTA-TAT--AGTTTTTG-AAA-ATAT-
1 ATATTATACAGTTTTTGAAAACATATA
* *
259129 ATAGTATTC--TTTTTGAAAAC-----
1 ATATTATACAGTTTTTGAAAACATATA
*
259149 ATATTATACAG-TTTTGAAAGCATATA
1 ATATTATACAGTTTTTGAAAACATATA
*
259175 ATATATATATAGTTTTTGAAAACATAT
1 ATAT-TATACAGTTTTTGAAAACATAT
259202 GTAATAAATA
Statistics
Matches: 95, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
20 7 0.07
21 11 0.12
22 13 0.14
23 13 0.14
24 23 0.24
25 3 0.03
26 6 0.06
27 6 0.06
28 13 0.14
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (27 bp):
ATATTATACAGTTTTTGAAAACATATA
Found at i:259212 original size:28 final size:28
Alignment explanation
Indices: 259160--259271 Score: 78
Period size: 28 Copynumber: 4.1 Consensus size: 28
259150 TATTATACAG
*
259160 TTTTGAAAGCATATAATATATATATAGT
1 TTTTGAAAACATATAATATATATATAGT
**
259188 TTTTGAAAACATATGTAATA-A-ATATAAC
1 TTTTGAAAACATA--TAATATATATATAGT
* *
259216 TCTTG-AAA-A-AT-GTAT-TATATAGT
1 TTTTGAAAACATATAATATATATATAGT
*
259239 TTTTGAAAATATA-ATATATATTATATAGT
1 TTTTGAAAACATATA-ATATA-TATATAGT
259268 TTTT
1 TTTT
259272 AATATATATA
Statistics
Matches: 64, Mismatches: 9, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
22 2 0.03
23 10 0.16
24 3 0.05
25 2 0.03
26 2 0.03
27 6 0.09
28 21 0.33
29 13 0.20
30 5 0.08
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (28 bp):
TTTTGAAAACATATAATATATATATAGT
Found at i:259316 original size:19 final size:18
Alignment explanation
Indices: 259289--259350 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
259279 ATAGTAAACA
*
259289 TATTATTATTATTTTACTT
1 TATTTTTATTATTTTA-TT
*
259308 TATTTTTATTTTTTTATT
1 TATTTTTATTATTTTATT
* *
259326 TACTTTTCATT-TTTATTTT
1 TA-TTTTTATTATTT-TATT
259345 TATTTT
1 TATTTT
259351 CAGGTCCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.30
19 26 0.70
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTTTATTATTTTATT
Found at i:259339 original size:7 final size:6
Alignment explanation
Indices: 259306--259350 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
259296 ATTATTTTAC
*
259306 TTTATT TTTATT TTT-TT ATTTACTT TTCATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT -TTTA-TT TTTATT TTTATT TTTATT TT
259351 CAGGTCCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 2 0.06
6 27 0.79
7 3 0.09
8 2 0.06
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:259346 original size:23 final size:21
Alignment explanation
Indices: 259291--259349 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 21
259281 AGTAAACATA
*
259291 TTATTATTATTTTACTTTATTT
1 TTATTTTTA-TTTACTTTATTT
259313 TTATTTTTTTATTTACTTTTCATTT
1 TTA--TTTTTATTTAC-TTT-ATTT
259338 TTATTTTTATTT
1 TTATTTTTATTT
259350 TCAGGTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 3 0.09
23 14 0.44
24 8 0.25
25 7 0.22
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATTTTTATTTACTTTATTT
Found at i:259351 original size:18 final size:18
Alignment explanation
Indices: 259300--259352 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
259290 ATTATTATTA
*
259300 TTTTACTTTATTTTTATTT
1 TTTTA-TTTATTTTCATTT
259319 TTTTATTTACTTTTCATTT
1 TTTTATTTA-TTTTCATTT
259338 TTATT-TTTATTTTCA
1 TT-TTATTTATTTTCA
259353 GGTCCAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 10 0.32
19 19 0.61
20 2 0.06
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTATTTTCATTT
Found at i:262118 original size:22 final size:22
Alignment explanation
Indices: 262093--262158 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
262083 GTTGCCAAAC
262093 TTCCTAAAGGAATGGAT-ATTTT
1 TTCCTAAAGG-ATGGATCATTTT
*
262115 TTCC-AAAGGATTGATCATTTT
1 TTCCTAAAGGATGGATCATTTT
* *
262136 TTCATAAGGGATGGATCATTTT
1 TTCCTAAAGGATGGATCATTTT
262158 T
1 T
262159 CAAAGGGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.13
21 13 0.34
22 20 0.53
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (22 bp):
TTCCTAAAGGATGGATCATTTT
Found at i:262159 original size:21 final size:21
Alignment explanation
Indices: 262098--262166 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
262088 CAAACTTCCT
*
262098 AAAGGAATGGAT-ATTTTTTCC
1 AAAGGGATGGATCATTTTTT-C
*
262119 AAA-GGATTGATCATTTTTTC
1 AAAGGGATGGATCATTTTTTC
262139 ATAAGGGATGGATCA-TTTTTC
1 A-AAGGGATGGATCATTTTTTC
262160 AAAGGGA
1 AAAGGGA
262167 ATGATCCTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 14 0.33
21 19 0.45
22 9 0.21
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (21 bp):
AAAGGGATGGATCATTTTTTC
Found at i:262172 original size:20 final size:20
Alignment explanation
Indices: 262112--262178 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
262102 GAATGGATAT
*
262112 TTTTTCCAAA-GGATTGATCA
1 TTTTT-CAAAGGGAATGATCA
262132 TTTTTTCATAAGGG-ATGGATCA
1 -TTTTTCA-AAGGGAAT-GATCA
*
262154 TTTTTCAAAGGGAATGATCC
1 TTTTTCAAAGGGAATGATCA
262174 TTTTT
1 TTTTT
262179 GAAAAAGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 16 0.40
21 17 0.43
22 7 0.17
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (20 bp):
TTTTTCAAAGGGAATGATCA
Found at i:262172 original size:42 final size:42
Alignment explanation
Indices: 262099--262178 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
262089 AAACTTCCTA
*
262099 AAGGAATGGATATTTTTTCCAAAGGATTGATCATTTTTTCAT
1 AAGGAATGGATATTTTTTCCAAAGGAATGATCATTTTTTCAT
* *
262141 AAGGGATGGATCA-TTTTT-CAAAGGGAATGATCCTTTTT
1 AAGGAATGGAT-ATTTTTTCCAAA-GGAATGATCATTTTT
262179 GAAAAAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 4 0.12
42 28 0.85
43 1 0.03
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (42 bp):
AAGGAATGGATATTTTTTCCAAAGGAATGATCATTTTTTCAT
Found at i:262218 original size:21 final size:21
Alignment explanation
Indices: 262133--262219 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 21
262123 GATTGATCAT
* ** *
262133 TTTTTCATAAGGGATGGATCA
1 TTTTTCAAAAGGGATATATCC
262154 TTTTTC-AAAGGGA-ATGATCC
1 TTTTTCAAAAGGGATAT-ATCC
* * * *
262174 TTTTTGAAAAAGAATCA-ATGC
1 TTTTTCAAAAGGGAT-ATATCC
262195 TTTTTCAAAAGGGATATATCC
1 TTTTTCAAAAGGGATATATCC
262216 TTTT
1 TTTT
262220 ACTAGAAAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
20 15 0.31
21 33 0.67
23 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.39
Consensus pattern (21 bp):
TTTTTCAAAAGGGATATATCC
Found at i:263246 original size:17 final size:16
Alignment explanation
Indices: 263205--263246 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
263195 AAATACCATT
263205 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
263221 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
263238 TAAAA-AATT
1 TAAAATAATT
263247 GATATGCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:265037 original size:3 final size:3
Alignment explanation
Indices: 265024--265067 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
265014 TGGACTTGTC
265024 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
265068 TTATTATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:265072 original size:3 final size:3
Alignment explanation
Indices: 265066--265101 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
265056 ATAATAATAA
265066 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
265102 ACTGGGACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:266941 original size:21 final size:22
Alignment explanation
Indices: 266915--266971 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
266905 TTGGAGAGAG
*
266915 AAAATCAAGAATAAAGGAGTA-
1 AAAATCAAGAATAAAGGAATAT
* *
266936 AAAATCAATAACAAAGGAATAT
1 AAAATCAAGAATAAAGGAATAT
*
266958 AAAATGAAGAATAA
1 AAAATCAAGAATAA
266972 GAGTTTCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.65, C:0.05, G:0.14, T:0.16
Consensus pattern (22 bp):
AAAATCAAGAATAAAGGAATAT
Found at i:273591 original size:2 final size:2
Alignment explanation
Indices: 273584--273609 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
273574 AATGCACTCA
273584 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
273610 CAGTAAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:288492 original size:20 final size:20
Alignment explanation
Indices: 288467--288514 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
288457 TATATCAAGT
*
288467 CACTTGAGGAGTATGTGGAA
1 CACTTGAGGAGCATGTGGAA
288487 CACTTGAGGAGCATGTGGAA
1 CACTTGAGGAGCATGTGGAA
288507 CACTTGAG
1 CACTTGAG
288515 AAAGGTGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.23
Consensus pattern (20 bp):
CACTTGAGGAGCATGTGGAA
Found at i:289149 original size:61 final size:61
Alignment explanation
Indices: 289051--289165 Score: 203
Period size: 61 Copynumber: 1.9 Consensus size: 61
289041 TAACTCTAAA
*
289051 GTGTATACCCAAGACACTTAGTGCAGGTGGTGGGCACGACCTTATGTGTCATAGTACTAGT
1 GTGTATACCCAAGACACTTAGTGCAGGTGGTGGGCACGAACTTATGTGTCATAGTACTAGT
* *
289112 GTGTATACCCAAGACACTTAGTGCATGTGGTGTGCACGAACTTATGTGTCATAG
1 GTGTATACCCAAGACACTTAGTGCAGGTGGTGGGCACGAACTTATGTGTCATAG
289166 CATTACGATG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (61 bp):
GTGTATACCCAAGACACTTAGTGCAGGTGGTGGGCACGAACTTATGTGTCATAGTACTAGT
Found at i:290652 original size:25 final size:25
Alignment explanation
Indices: 290592--290658 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 25
290582 TAGAAAATAT
* *
290592 AAATATTATTTTTAA-TATAGTTTTA
1 AAATATT-TTTTTAATTATAATGTTA
* *
290617 AAATCTATTTTTAATTATAATGTTA
1 AAATATTTTTTTAATTATAATGTTA
* *
290642 TAATATTTTTTTTATTA
1 AAATATTTTTTTAATTA
290659 ATATGGGGTA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
24 7 0.21
25 26 0.79
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (25 bp):
AAATATTTTTTTAATTATAATGTTA
Found at i:293713 original size:15 final size:15
Alignment explanation
Indices: 293693--293749 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
293683 ACGGATGTTA
293693 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
293708 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
*
293724 GCAGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
293740 CGGGTACCCG
1 CGGGTACCCG
293750 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:293720 original size:32 final size:32
Alignment explanation
Indices: 293684--293749 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
293674 TGTCCCGACA
*
293684 CGGATGTTACGGGTACCCGGTAATCGGGTACC
1 CGGATGTTACAGGTACCCGGTAATCGGGTACC
* *
293716 CGGATTTTGCAGGTACCCGGTAATCGGGTACC
1 CGGATGTTACAGGTACCCGGTAATCGGGTACC
293748 CG
1 CG
293750 ATACCCGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (32 bp):
CGGATGTTACAGGTACCCGGTAATCGGGTACC
Found at i:301608 original size:18 final size:16
Alignment explanation
Indices: 301552--301594 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
301542 GATTAAGCGT
301552 TGAATGATTCAAATAC
1 TGAATGATTCAAATAC
301568 TGAATGATTCAAATAC
1 TGAATGATTCAAATAC
301584 TGAATGATTCA
1 TGAATGATTCA
301595 GAAGCTCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (16 bp):
TGAATGATTCAAATAC
Found at i:304829 original size:63 final size:63
Alignment explanation
Indices: 304751--304873 Score: 237
Period size: 63 Copynumber: 2.0 Consensus size: 63
304741 TACAAAGCTT
304751 GAACAAATGGAAGATTTCAGAGAACCAAAATAGAAGATCCAGCAATTGATCATACTAGTTAGA
1 GAACAAATGGAAGATTTCAGAGAACCAAAATAGAAGATCCAGCAATTGATCATACTAGTTAGA
*
304814 GAACAAATGGAAGATTTCAGAGAACCAAAATAGAAGATCCAGTAATTGATCATACTAGTT
1 GAACAAATGGAAGATTTCAGAGAACCAAAATAGAAGATCCAGCAATTGATCATACTAGTT
304874 TCGTCATTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.22
Consensus pattern (63 bp):
GAACAAATGGAAGATTTCAGAGAACCAAAATAGAAGATCCAGCAATTGATCATACTAGTTAGA
Found at i:306861 original size:31 final size:30
Alignment explanation
Indices: 306778--306864 Score: 92
Period size: 27 Copynumber: 2.9 Consensus size: 30
306768 AACTTATTAA
*
306778 ATATATTTTATTATTAAATTAATTTAAAAAT
1 ATATATTTTA-TGTTAAATTAATTTAAAAAT
*
306809 ATTTTATTTT-TGTT---TTAATTTAAAAAT
1 A-TATATTTTATGTTAAATTAATTTAAAAAT
*
306836 ATATATTTTATGTTAAAATTTATTTAAAA
1 ATATATTTTATGTT-AAATTAATTTAAAA
306865 GTATGATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
26 7 0.15
27 18 0.39
30 3 0.07
31 11 0.24
32 7 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
ATATATTTTATGTTAAATTAATTTAAAAAT
Found at i:311544 original size:34 final size:36
Alignment explanation
Indices: 311497--311598 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
311487 TTTCGTCCTA
311497 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* *
311532 -TAGGATTTAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
311567 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
311599 GTTATACTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 28 0.47
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:312029 original size:18 final size:17
Alignment explanation
Indices: 311990--312032 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
311980 ATTATATGGA
311990 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
312006 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
312024 TATTATTAT
1 TATTATTAT
312033 GTATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:316266 original size:15 final size:16
Alignment explanation
Indices: 316226--316308 Score: 55
Period size: 15 Copynumber: 5.2 Consensus size: 16
316216 AGATCCAATC
* *
316226 AAGAACAAAAAAGA-A
1 AAGAAAAAAAAAAACA
** *
316241 AAGAAGCAAAAAAGCA
1 AAGAAAAAAAAAAACA
316257 AA-AAAAAAAAAAACA
1 AAGAAAAAAAAAAACA
* *
316272 AAGAAAAAGAGAAAC-
1 AAGAAAAAAAAAAACA
*
316287 AAGAACAAAAACAAAAAA
1 AAGAA-AAAAA-AAAACA
316305 AAGA
1 AAGA
316309 GCAAAAATCA
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
15 27 0.53
16 17 0.33
17 3 0.06
18 4 0.08
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAACA
Found at i:316984 original size:22 final size:22
Alignment explanation
Indices: 316959--317013 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
316949 GCTATCCCAT
316959 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
316981 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
317003 CAAACCTTTGA
1 CAAACCTTTGA
317014 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:317453 original size:18 final size:18
Alignment explanation
Indices: 317430--317465 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
317420 TCAACATCAA
* *
317430 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
317448 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
317466 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:317933 original size:36 final size:36
Alignment explanation
Indices: 317893--318087 Score: 168
Period size: 36 Copynumber: 5.4 Consensus size: 36
317883 ACTCATGATT
* * *
317893 GTTTTTCTTAAAACAATATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAATATTTGTCTCTCTTGAGACA
* ** * *
317929 GTTT-TCACTAGTAGAGT-TTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAATATTTGTCTCTCTTGAGACA
* *
317964 GTTTCCCTTGAAACAA-ATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAATA-TTTGTCTCTCTTGAGACA
* *
318000 GTTTCTCTTGAAACAA-ATTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAATATTT-GTCTCTCTTGAGACA
*
318036 GTTTCCCTTGAAATA-AAT-TTTGTCTCTCTTGAGACA
1 GTTTCTCTT-AAA-ACAATATTTGTCTCTCTTGAGACA
* *
318072 GTTTCCCTTGAAACAA
1 GTTTCTCTTAAAACAA
318088 AATATTTGAA
Statistics
Matches: 130, Mismatches: 20, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
34 1 0.01
35 32 0.25
36 89 0.68
37 7 0.05
38 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
GTTTCTCTTAAAACAATATTTGTCTCTCTTGAGACA
Found at i:317988 original size:71 final size:73
Alignment explanation
Indices: 317903--318226 Score: 239
Period size: 72 Copynumber: 4.6 Consensus size: 73
317893 GTTTTTCTTA
* * * * * * *
317903 AAAC-AATATTTGTCTCGCTTGAGACCGTTTTCACTAG-TA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAAAT-TTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
317965 TTTCCCTTG
65 TTTCCCTTG
* *
317974 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
318038 TTCCCTTG
66 TTCCCTTG
* * * * *
318046 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
318102 TTTTCTTTG
65 TTTCCCTTG
* * ** * * * * *
318111 AAACAAATTTCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
318175 TTTCTCTTG
65 TTTCCCTTG
* * *
318184 AAAC-AATTTTCGTCTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
318227 ATCTTTGAAT
Statistics
Matches: 204, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
64 2 0.01
65 46 0.23
66 5 0.02
70 7 0.03
71 22 0.11
72 81 0.40
73 39 0.19
74 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:318047 original size:72 final size:71
Alignment explanation
Indices: 317946--318226 Score: 317
Period size: 72 Copynumber: 4.0 Consensus size: 71
317936 CTAGTAGAGT
* *
317946 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
318011 AACAAA
66 AACAAA
*
318017 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
318082 AAACAAA
65 AAACAAA
* * * * * * **
318089 -----ATAT-TTGA-ATATGTTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
1 TTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
318147 GAACTAAGT
65 AAAC-AA-A
* * *
318156 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTG
318220 AAACAAA
65 AAACAAA
318227 ATCTTTGAAT
Statistics
Matches: 171, Mismatches: 27, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
64 2 0.01
65 46 0.27
66 5 0.03
71 3 0.02
72 74 0.43
73 39 0.23
74 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (71 bp):
TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAA
Found at i:318186 original size:102 final size:102
Alignment explanation
Indices: 318001--318189 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
317991 CTTGAGACAG
*
318001 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
318066 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
318103 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
*
318167 TGAGACAGTTTCTCTTGAAACAA
65 TGAGACAGTTTCCCTTGAAACAA
318190 TTTTCGTCTA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 34 0.43
102 45 0.57
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:318211 original size:36 final size:36
Alignment explanation
Indices: 318103--318225 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
318093 TTGAATATGT
* *
318103 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
318138 TTTCTTTTGGAACTAAGTTTT-GTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
*
318175 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAG
*
318211 TTTCCCTTGAAACAA
1 TTTCTCTTGAAACAA
318226 AATCTTTGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
35 9 0.12
36 37 0.48
37 28 0.36
38 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:318218 original size:138 final size:137
Alignment explanation
Indices: 317965--318289 Score: 454
Period size: 138 Copynumber: 2.4 Consensus size: 137
317955 CTTGAGACAG
*
317965 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
*
318030 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
*
318095 GAATATG
131 GAATATA
* * * * * * * *
318102 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * *
318167 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAATAT
*
318231 TTGAATTTA
129 TTGAATATA
* * * *
318240 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
318290 CAAAATCTTC
Statistics
Matches: 162, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
137 50 0.31
138 112 0.69
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:318288 original size:65 final size:67
Alignment explanation
Indices: 318184--318341 Score: 196
Period size: 67 Copynumber: 2.4 Consensus size: 67
318174 GTTTCTCTTG
** * * **
318184 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCC
1 AAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCC
318246 CTA
65 CTA
* *
318249 AAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
318314 TA
66 TA
*
318316 AAACATAATTTTGTTTCCCTTGAGAC
1 AAACA-AATTTTGTCTCCCTTGAGAC
318342 CGTTTCTCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 24 0.30
66 8 0.10
67 29 0.36
68 19 0.24
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:318318 original size:67 final size:65
Alignment explanation
Indices: 318175--318341 Score: 192
Period size: 65 Copynumber: 2.5 Consensus size: 65
318165 CTTGAGACAG
* * ** * * **
318175 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTT
318239 A
65 A
* *
318240 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTG-AA-ACAAAATCTTCAAATT
318305 TA
64 TA
*
318307 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGAC
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGAC
318342 CGTTTCTCAT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 30 0.35
66 8 0.09
67 29 0.34
68 19 0.22
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (65 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTTA
Found at i:319190 original size:105 final size:105
Alignment explanation
Indices: 318993--319724 Score: 1034
Period size: 105 Copynumber: 7.0 Consensus size: 105
318983 ATATCGTGGC
* * * *
318993 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCT
*
319057 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGAATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
319099 ACTCCAGACAACGTAAGTTCAACTTCACGGCGAAGGGACCGCTGCCTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
319164 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
319204 ACTCCAGACAACGCAAGTTCAACTTCATGACAAAGGGACCGTTGCTTGT---CAACAACTTCTTA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
319266 ATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
319306 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
319371 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
319411 ACTCCATACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
319476 ATCTCAGAGCCAATTTCAATTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
319516 ATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
**
319577 A-TTCAGATTCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
319616 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCT
** * * * *
319680 CGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTAG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
319722 ACT
1 ACT
319725 TGGAACAATG
Statistics
Matches: 566, Mismatches: 49, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
99 2 0.00
100 79 0.14
101 3 0.01
102 99 0.17
103 4 0.01
104 3 0.01
105 296 0.52
106 78 0.14
107 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:319358 original size:207 final size:208
Alignment explanation
Indices: 318993--319725 Score: 971
Period size: 207 Copynumber: 3.5 Consensus size: 208
318983 ATATCGTGGC
* * * * *
318993 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCG-CTGCTTGT--AC-AACAACTTCT
* * *
319057 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGTAAGTTCAAC
62 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAAC
* *
319122 TTCACGGCGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
127 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
319187 ACAACGAAGGATATTGG
192 ACAACGAAGGATATTGG
* * *
319204 ACTCCAGACAACGCAAGTTCAACTTCATGACAAAGGGACCGTTGCTTGT-CAACAACTTCTTAAT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGTACAACAACTTCTCAAT
*
319268 TTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCA
66 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCA
* *
319333 CGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAA
131 CGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
319398 CGAAGGATATTGG
196 CGAAGGATATTGG
* * * *
319411 ACTCCATACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGT--ACAACAACTTCTCA
* *
319476 ATCTCAGAGCCAATTTCAATTTCACAACGAAGGATATTGGA-TTCCAGACAACGCAAGTTCAACT
64 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTT-CAGACAACGCAAGTTCAACT
**
319540 TCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCAATTTCAACTTCA
128 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCA
319600 CAACGAAGGATATTGG
193 CAACGAAGGATATTGG
* * * * * * *
319616 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCG-CTGCTTGT--AC-AACAACTTCT
** * * * *
319680 CGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTAGACTT
62 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTT
319726 GGAACAATGC
Statistics
Matches: 469, Mismatches: 45, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
204 2 0.00
205 79 0.17
206 45 0.10
207 195 0.42
208 3 0.01
209 4 0.01
210 100 0.21
211 39 0.08
212 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (208 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGTACAACAACTTCTCAAT
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
CGAAGGATATTGG
Found at i:319564 original size:312 final size:310
Alignment explanation
Indices: 318993--319724 Score: 1119
Period size: 312 Copynumber: 2.3 Consensus size: 310
318983 ATATCGTGGC
*
318993 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCC
* *
319058 AATTTCAGAGCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGTAAGTTCAACT
66 AA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * *
319123 TCACGGCGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCA
130 TCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
* *
319188 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACAAAGGGACCGTTGCTTGT
195 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGT
**
319253 CAACAACTTCTTAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
260 CAACAAAAT-TTAA-TTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
* * *
319306 ACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTC
1 AC-TCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTC
* *
319368 CCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAATGCAAGTTCAA
64 CCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* *
319433 CTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAATTT
128 CTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTT
* *
319498 CACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTT
193 CACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTT
* ** *
319563 GTCAACAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGATATTGG
258 GTCAACAAAATTTAATTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
*
319616 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCC
** * * *
319681 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTAGACT
66 AATT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
319725 TGGAACAATG
Statistics
Matches: 380, Mismatches: 32, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
309 4 0.01
310 80 0.21
311 51 0.13
312 197 0.52
313 44 0.12
314 4 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (310 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCC
AATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCAC
AACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGTC
AACAAAATTTAATTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
Found at i:320303 original size:34 final size:36
Alignment explanation
Indices: 320259--320360 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
320249 TTTCGTCCTA
320259 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
320294 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
320329 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
320361 GTTATACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:320791 original size:18 final size:17
Alignment explanation
Indices: 320752--320794 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
320742 ATTATATGGA
320752 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
320768 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
320786 TATTATTAT
1 TATTATTAT
320795 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:337989 original size:32 final size:32
Alignment explanation
Indices: 337953--338037 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
337943 AGGTAGAACA
337953 CTTAGTGTTCGAGAGAAACTAGGTGAGTGATC
1 CTTAGTGTTCGAGAGAAACTAGGTGAGTGATC
*
337985 CTTAGTGTTTGAGAGAAACTAGGTGAGTGATC
1 CTTAGTGTTCGAGAGAAACTAGGTGAGTGATC
338017 CTTAGTGTTCGAGAGAAACTA
1 CTTAGTGTTCGAGAGAAACTA
338038 AGGGAGGATC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (32 bp):
CTTAGTGTTCGAGAGAAACTAGGTGAGTGATC
Found at i:338525 original size:18 final size:19
Alignment explanation
Indices: 338502--338538 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
338492 CCATTCACAC
338502 ACATTC-CATTTTGACATA
1 ACATTCTCATTTTGACATA
*
338520 ACATTCTCATTTTTACATA
1 ACATTCTCATTTTGACATA
338539 CCACCACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (19 bp):
ACATTCTCATTTTGACATA
Found at i:359209 original size:12 final size:12
Alignment explanation
Indices: 359188--359217 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
359178 AGATGAGCCT
359188 GAGCAACCCGAG
1 GAGCAACCCGAG
*
359200 GAGCAGCCCGAG
1 GAGCAACCCGAG
359212 GAGCAA
1 GAGCAA
359218 GCACAACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.33, C:0.30, G:0.37, T:0.00
Consensus pattern (12 bp):
GAGCAACCCGAG
Found at i:367937 original size:27 final size:27
Alignment explanation
Indices: 367905--367972 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
367895 GGATAAACAT
367905 TTTTGCATATGCATTTGCATCTTT-GCA
1 TTTTGCATATGCATTT-CATCTTTAGCA
* *
367932 TTTTGCATCA-ACATTTCATTTTTAAGCA
1 TTTTGCAT-ATGCATTTCATCTTT-AGCA
367960 TTTT-CATATGCAT
1 TTTTGCATATGCAT
367973 CATTCATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
26 7 0.21
27 19 0.56
28 8 0.24
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.49
Consensus pattern (27 bp):
TTTTGCATATGCATTTCATCTTTAGCA
Found at i:369232 original size:15 final size:14
Alignment explanation
Indices: 369214--369369 Score: 88
Period size: 15 Copynumber: 10.7 Consensus size: 14
369204 AAATAAAGAG
369214 AAAGAAAAAAGAAGC
1 AAAGAAAAAAGAA-C
*
369229 AAAGAAAGAAA-AAA
1 AAAGAAA-AAAGAAC
369243 AAGAGAAAAGAAGAAAC
1 AA-AGAAAA-AAG-AAC
* *
369260 AAA-AAAACAGTGAGC
1 AAAGAAAA-A-AGAAC
* *
369275 AAAGAGAAAATAAGC
1 AAAGAAAAAAGAA-C
*
369290 AAAGAAAAAAAGCAC
1 AAAG-AAAAAAGAAC
**
369305 AAAGAGCAAAGAA-
1 AAAGAAAAAAGAAC
*
369318 AAAGAAAAGA-AAC
1 AAAGAAAAAAGAAC
*
369331 AAAGAGAAAAGAAGAC
1 AAAGAAAAAAG-A-AC
369347 AAAGAAAAAAGAA-
1 AAAGAAAAAAGAAC
369360 AAAGAAAAAA
1 AAAGAAAAAA
369370 ACGAAGAAAA
Statistics
Matches: 107, Mismatches: 21, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
12 2 0.02
13 25 0.23
14 11 0.10
15 39 0.36
16 26 0.24
17 4 0.04
ACGTcount: A:0.74, C:0.06, G:0.19, T:0.01
Consensus pattern (14 bp):
AAAGAAAAAAGAAC
Found at i:369238 original size:23 final size:20
Alignment explanation
Indices: 369208--369265 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
369198 AAATCAAAAT
*
369208 AAAG-AGAAAGAAAAAAGAAGC
1 AAAGAAGAAA-AAAAAAG-AGA
369229 AAAGAA-AGAAAAAAAAGAGA
1 AAAGAAGA-AAAAAAAAGAGA
369249 AAAGAAGAAACAAAAAA
1 AAAGAAGAAA-AAAAAA
369266 ACAGTGAGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
20 10 0.31
21 19 0.59
22 3 0.09
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAAAAAAAAGAGA
Found at i:369256 original size:19 final size:21
Alignment explanation
Indices: 369218--369264 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
369208 AAAGAGAAAG
*
369218 AAAAAAGAAGCAAAGAAAGAA
1 AAAAAAGAAGAAAAGAAAGAA
369239 AAAAAAG-AGAAAAG-AAGAA
1 AAAAAAGAAGAAAAGAAAGAA
369258 ACAAAAA
1 A-AAAAA
369265 AACAGTGAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 7 0.29
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAGAAAAGAAAGAA
Found at i:369279 original size:23 final size:22
Alignment explanation
Indices: 369218--369279 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
369208 AAAGAGAAAG
*
369218 AAAAAAGA-AGCAAAGAAAGAA
1 AAAAAAGAGAGCAAAGAAACAA
**
369239 AAAAAAGAGAAAAGAAGAAACAA
1 AAAAAAGAGAGCA-AAGAAACAA
*
369262 AAAAACAGTGAGCAAAGA
1 AAAAA-AGAGAGCAAAGA
369280 GAAAATAAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 8 0.25
22 2 0.06
23 17 0.53
24 5 0.16
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (22 bp):
AAAAAAGAGAGCAAAGAAACAA
Found at i:369297 original size:13 final size:13
Alignment explanation
Indices: 369272--369379 Score: 55
Period size: 13 Copynumber: 7.8 Consensus size: 13
369262 AAAAACAGTG
369272 AGCAAAGAGAAAATA
1 AGCAAAGA-AAAA-A
369287 AGCAAAGAAAAAA
1 AGCAAAGAAAAAA
*
369300 AGCACAAAGAGCAAAGA
1 AG--CAAAGA--AAAAA
369317 A--AAAGAAAAGAA
1 AGCAAAGAAAA-AA
369329 A-CAAAGAGAAAAGA
1 AGCAAAGA-AAAA-A
369343 AGACAAAG-AAAAA
1 AG-CAAAGAAAAAA
*
369356 AGAAAAAGAAAAAA
1 AG-CAAAGAAAAAA
*
369370 A-CGAAGAAAA
1 AGCAAAGAAAA
369380 CAATGACAAG
Statistics
Matches: 77, Mismatches: 5, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
11 3 0.04
12 9 0.12
13 22 0.29
14 19 0.25
15 14 0.18
16 5 0.06
17 5 0.06
ACGTcount: A:0.73, C:0.07, G:0.19, T:0.01
Consensus pattern (13 bp):
AGCAAAGAAAAAA
Found at i:369324 original size:41 final size:42
Alignment explanation
Indices: 369279--369376 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
369269 GTGAGCAAAG
* * **
369279 AGAAAATAAGCAAAGA-AAAA-AAGCACAAAGAGCAAAGAAAA
1 AGAAAAGAAACAAAGAGAAAAGAAG-ACAAAGAAAAAAGAAAA
369320 AGAAAAGAAACAAAGAGAAAAGAAGACAAAGAAAAAAGAAAA
1 AGAAAAGAAACAAAGAGAAAAGAAGACAAAGAAAAAAGAAAA
*
369362 AGAAAA-AAACGAAGA
1 AGAAAAGAAACAAAGA
369377 AAACAATGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 22 0.44
42 25 0.50
43 3 0.06
ACGTcount: A:0.73, C:0.07, G:0.18, T:0.01
Consensus pattern (42 bp):
AGAAAAGAAACAAAGAGAAAAGAAGACAAAGAAAAAAGAAAA
Found at i:370645 original size:68 final size:61
Alignment explanation
Indices: 370507--370661 Score: 170
Period size: 68 Copynumber: 2.4 Consensus size: 61
370497 TATCAGTATC
* * * *
370507 CTTTTAGT-TGTTTCTCTTGAAACAAATTTTGTCTCTCGAGACAGTTTCTTTTAAAAAACT
1 CTTTGAGTATGTTTCTCTTGAAACAAATTTTGTCTCTCGAGACAATTTATTTTAAAAAAAT
*
370567 CTTTGAGTATGTTTCTC-TGAAAACAATTTTTTGTCTCTCTTGAGACAATTTATTTTGAGAAACA
1 CTTTGAGTATGTTTCTCTTG-AAACAA-ATTTTGTCTCTC--GAGACAATTTATTTT---AAA-A
370631 AAAT
58 AAAT
*
370635 CTTTGAGTATGTTTCTTTTGAAACAAA
1 CTTTGAGTATGTTTCTCTTGAAACAAA
370662 ACCATCTTTG
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
60 9 0.12
61 14 0.18
62 11 0.14
64 13 0.17
67 3 0.04
68 26 0.33
69 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (61 bp):
CTTTGAGTATGTTTCTCTTGAAACAAATTTTGTCTCTCGAGACAATTTATTTTAAAAAAAT
Found at i:370680 original size:32 final size:32
Alignment explanation
Indices: 370633--370694 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
370623 GAGAAACAAA
*
370633 ATCTTTGAGTATGTTTCTTTTGAAACAAAACC
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAACC
* *
370665 ATCTTTGCGTCTGTTTCCTTTGAAACAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAA
370695 TACATATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (32 bp):
ATCTTTGAGTATGTTTCCTTTGAAACAAAACC
Found at i:370781 original size:29 final size:30
Alignment explanation
Indices: 370739--370796 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
370729 TTGTCTCTTT
*
370739 TGAGACAGCTTCTCTTG-AAGCATTATCTA
1 TGAGACAGCTTCTCTTGAAACCATTATCTA
* *
370768 TGAGTCAGTTTCTCTTGAAACCATTATCT
1 TGAGACAGCTTCTCTTGAAACCATTATCT
370797 CTAAAGATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (30 bp):
TGAGACAGCTTCTCTTGAAACCATTATCTA
Found at i:371002 original size:42 final size:42
Alignment explanation
Indices: 370810--371062 Score: 160
Period size: 48 Copynumber: 5.8 Consensus size: 42
370800 AAGATGGTCT
* * *
370810 GTCGTCCTTATCACGTAGGAACTGTGTCATCCCTCG--ACCA
1 GTCGTCCTCATCACGTAGGAACCGTGTCATCCCTAGATACCA
* * *
370850 GACCTCCTCATCACGTA-GAAGCCGTGTCACCCCT-GATAACCA
1 GTCGTCCTCATCACGTAGGAA-CCGTGTCATCCCTAGAT-ACCA
* *
370892 G-CAGTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGATGGATC-
1 GTC-GTCCTCATCACGTAGGAACCGTG---TCATCCCT--AGAT--ACCA
* * * *
370940 GTCGTCCTAATCGCGAAGGAACCATGTCATCCCT-GATAACCA
1 GTCGTCCTCATCACGTAGGAACCGTGTCATCCCTAGAT-ACCA
* **
370982 GTCGTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGATGGCA
1 GTCGTCCTCATCACGTAGGAACCGTG---TCATCCCT--AGATACCA
*
371029 TGTCGTCCTCATCACGTAGGAACCATGTCATCCC
1 -GTCGTCCTCATCACGTAGGAACCGTGTCATCCC
371063 CCAACCCACC
Statistics
Matches: 165, Mismatches: 26, Indels: 39
0.72 0.11 0.17
Matches are distributed among these distances:
39 4 0.02
40 25 0.15
41 3 0.02
42 48 0.29
43 3 0.02
45 26 0.16
47 2 0.01
48 51 0.31
49 3 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (42 bp):
GTCGTCCTCATCACGTAGGAACCGTGTCATCCCTAGATACCA
Found at i:371034 original size:90 final size:90
Alignment explanation
Indices: 370874--371062 Score: 310
Period size: 90 Copynumber: 2.1 Consensus size: 90
370864 GTAGAAGCCG
*
370874 TGTCACCCCTGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGATGGAT
1 TGTCATCCCTGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGATGGAT
*
370939 CGTCGTCCTAATCGCGAAGGAACCA
66 CGTCGTCCTAATCACGAAGGAACCA
370964 TGTCATCCCTGATAACCAGTC-GTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGATGGC
1 TGTCATCCCTGATAACCAG-CAGTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGATGG-
* *
371028 AT-GTCGTCCTCATCACGTAGGAACCA
64 ATCGTCGTCCTAATCACGAAGGAACCA
371054 TGTCATCCC
1 TGTCATCCC
371063 CCAACCCACC
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
90 90 0.97
91 3 0.03
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (90 bp):
TGTCATCCCTGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGATGGAT
CGTCGTCCTAATCACGAAGGAACCA
Found at i:371440 original size:3 final size:3
Alignment explanation
Indices: 371419--371457 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
371409 CTACAAAAAC
371419 ATT ATT -TT AATT A-T ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
371458 ACAAAACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 27 0.82
4 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:373105 original size:30 final size:31
Alignment explanation
Indices: 373071--373176 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 31
373061 TTGTTTTTGT
373071 TATTTTAGTCCTTTAAATGTATATATTTT-C
1 TATTTTAGTCCTTTAAATGTATATATTTTAC
* * * *
373101 TA-TTTAGACCCTTAAGTTTATAT-TTTTAC
1 TATTTTAGTCCTTTAAATGTATATATTTTAC
* * * *
373130 TATTTTAGCCCTTT-AA-GTTTCTATTTTGC
1 TATTTTAGTCCTTTAAATGTATATATTTTAC
* *
373159 CATTATAGTCCTTTAAAT
1 TATTTTAGTCCTTTAAAT
373177 TTTGGTTTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 9
0.71 0.17 0.11
Matches are distributed among these distances:
28 7 0.12
29 37 0.65
30 13 0.23
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTTTAGTCCTTTAAATGTATATATTTTAC
Found at i:373186 original size:59 final size:59
Alignment explanation
Indices: 373109--373268 Score: 182
Period size: 60 Copynumber: 2.7 Consensus size: 59
373099 TCTATTTAGA
* * *
373109 CCCTTAAGTTTATATTTTTACTATTTTAGCCCTTTAAGTTTCTATT-TTGCCATTATAGT
1 CCCTTAAATTTCTGTTTTTACTATTTTAGCCCTTTAAGTTTCTATTATT-CCATTATAGT
* * *
373168 CCTTTAAATTT-TGGTTTTTACTTTTTTAGCCCTTTACA-TTTCTATTAATTCCATTTTAGT
1 CCCTTAAATTTCT-GTTTTTACTATTTTAGCCCTTTA-AGTTTCTATT-ATTCCATTATAGT
** *
373228 CCCTTAAATTTCTGTTTTTGTTATTTTCGCCCTTTAAGTTT
1 CCCTTAAATTTCTGTTTTTACTATTTTAGCCCTTTAAGTTT
373269 ATGTTTTTGC
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
58 1 0.01
59 39 0.46
60 42 0.49
61 3 0.04
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.55
Consensus pattern (59 bp):
CCCTTAAATTTCTGTTTTTACTATTTTAGCCCTTTAAGTTTCTATTATTCCATTATAGT
Found at i:373254 original size:30 final size:30
Alignment explanation
Indices: 372928--373288 Score: 163
Period size: 30 Copynumber: 12.1 Consensus size: 30
372918 TTACTGGTTA
* **
372928 AGTCCCTTAAGTTTAC-G-TTTTGCTACGTT
1 AGTCCCTTAAATTT-CTGTTTTTGCTATTTT
* * **
372957 AGTACCTTTAAGTTTCTGTTTGAGCTATTTT
1 AGT-CCCTTAAATTTCTGTTTTTGCTATTTT
* * *
372988 AGTCCTTTAAATTTCT-TCTTGTGTTATTTT
1 AGTCCCTTAAATTTCTGT-TTTTGCTATTTT
* * * *
373018 TGTCCTTTAACTTTCTGTTTTTGTTA-TTT
1 AGTCCCTTAAATTTCTGTTTTTGCTATTTT
* * *
373047 AGTCTCTTAAGAGTT-TGTTTTTGTTATTTT
1 AGTCCCTTAA-ATTTCTGTTTTTGCTATTTT
* * * *
373077 AGTCCTTTAAATGTATATATTTT-CTA-TTT
1 AGTCCCTTAAATTTCTGT-TTTTGCTATTTT
* * * * *
373106 AGACCCTTAAGTTTATATTTTTACTATTTT
1 AGTCCCTTAAATTTCTGTTTTTGCTATTTT
* * * *
373136 AG-CCCTTTAAGTTTCT-ATTTTGCCATTAT
1 AGTCCC-TTAAATTTCTGTTTTTGCTATTTT
* * *
373165 AGTCCTTTAAATTT-TGGTTTTTACTTTTTT
1 AGTCCCTTAAATTTCT-GTTTTTGCTATTTT
* * * *
373195 AG-CCCTTTACATTTCTATTAATT-CCATTTT
1 AGTCCC-TTAAATTTCTGTT-TTTGCTATTTT
*
373225 AGTCCCTTAAATTTCTGTTTTTGTTATTTT
1 AGTCCCTTAAATTTCTGTTTTTGCTATTTT
* * * *
373255 CG-CCCTTTAAGTTTATGTTTTTGCTATTTA
1 AGTCCC-TTAAATTTCTGTTTTTGCTATTTT
373285 AGTC
1 AGTC
373289 TTTTAAATCA
Statistics
Matches: 255, Mismatches: 55, Indels: 42
0.72 0.16 0.12
Matches are distributed among these distances:
28 5 0.02
29 76 0.30
30 151 0.59
31 23 0.09
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (30 bp):
AGTCCCTTAAATTTCTGTTTTTGCTATTTT
Found at i:374086 original size:16 final size:16
Alignment explanation
Indices: 374054--374100 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
374044 ATATTTTTGA
* *
374054 CTTAAAAATGATTTTT
1 CTTAAAATTGTTTTTT
374070 CTCT-AAATTGTTTTTT
1 CT-TAAAATTGTTTTTT
374086 CTTAAAATTGTTTTT
1 CTTAAAATTGTTTTT
374101 AAAAGATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.28, C:0.09, G:0.06, T:0.57
Consensus pattern (16 bp):
CTTAAAATTGTTTTTT
Found at i:382173 original size:6 final size:6
Alignment explanation
Indices: 382129--382172 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
382119 CCTAAATATG
* *
382129 TGCATA TGCATA TGCATA TGCATA TGCATA TGTATA TGTATA TG
1 TGCATA TGCATA TGCATA TGCATA TGCATA TGCATA TGCATA TG
382173 TTTGTATGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (6 bp):
TGCATA
Found at i:382242 original size:2 final size:2
Alignment explanation
Indices: 382235--382263 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
382225 AAGGTGCTGC
382235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
382264 AACTGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:387504 original size:15 final size:16
Alignment explanation
Indices: 387476--387508 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
387466 AAAATCTTTC
387476 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
387492 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
387507 TT
1 TT
387509 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:389642 original size:15 final size:16
Alignment explanation
Indices: 389619--389651 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
389609 TCATTTATGC
389619 ATAAATTTT-AATTTT
1 ATAAATTTTAAATTTT
*
389634 ATAACTTTTAAATTTT
1 ATAAATTTTAAATTTT
389650 AT
1 AT
389652 TTTTTATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATTTTAAATTTT
Found at i:390929 original size:2 final size:2
Alignment explanation
Indices: 390924--390963 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
390914 AAAAAAGGAA
390924 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
390964 CAAAGTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:391395 original size:2 final size:2
Alignment explanation
Indices: 391388--391418 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
391378 TATTAAAGAA
391388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
391419 GTAAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:391495 original size:18 final size:17
Alignment explanation
Indices: 391472--391514 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
391462 ATATATACAT
391472 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
391490 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
391507 ATAA-AATA
1 ATAATAATA
391515 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:391971 original size:34 final size:34
Alignment explanation
Indices: 391928--391996 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
391918 GAATCCTAGC
391928 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
391962 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
391996 A
1 A
391997 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:392846 original size:105 final size:105
Alignment explanation
Indices: 392545--393310 Score: 1087
Period size: 105 Copynumber: 7.3 Consensus size: 105
392535 CATTGTTCCA
* * * * ** * *
392545 AGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
392610 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
392651 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
392711 AGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
392751 AATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
392816 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTATGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
392856 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
392921 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
392961 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
393026 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
393066 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
393131 AACGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
393171 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
393236 CAGTC-GTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
393277 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
393311 CGCAGATGGC
Statistics
Matches: 601, Mismatches: 48, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
99 1 0.00
100 81 0.13
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 403 0.67
106 79 0.13
107 4 0.01
109 21 0.03
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:394004 original size:31 final size:31
Alignment explanation
Indices: 393969--394096 Score: 73
Period size: 31 Copynumber: 3.9 Consensus size: 31
393959 GGGAAATAAA
393969 CTCAAA-GATTTTGTGTTTCAAGAGAAACTGT
1 CTCAAACGATTTTGTGTTTCAAGAGAAACT-T
** * *
394000 CTCAAGGGAGACGAAATT-TGTTTCAAGGGAAACAAT
1 CTC-A---A-ACGATTTTGTGTTTCAAGAGAAAC-TT
* *
394036 CTCAAA-GGTTTTGTGTTTCCAGAGAAACATT
1 CTCAAACGATTTTGTGTTTCAAGAGAAAC-TT
* * *
394067 TTCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1 CTCAAACG-ATTTTGTGTTTCAAGAGAAAC
394097 AATTTCAAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
30 3 0.04
31 24 0.32
32 3 0.04
33 19 0.26
35 2 0.03
36 19 0.26
37 4 0.05
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (31 bp):
CTCAAACGATTTTGTGTTTCAAGAGAAACTT
Found at i:394004 original size:67 final size:67
Alignment explanation
Indices: 393872--394063 Score: 249
Period size: 67 Copynumber: 2.8 Consensus size: 67
393862 GTCTTAAAAA
* * * * *
393872 AGACAGAATTCGTTTCAAGGGAAACAATCTTAAAGATATATGTTGTTTCATGAGAAACGGCCTCA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGGCCTCA
393937 AGGG
64 AGGG
* * * * *
393941 AGACAAAATTTGTTTTAAGGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAG
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAG
394006 GG
66 GG
* * *
394008 AGACGAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCCAGAGAAAC
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
394064 ATTTTCAAAG
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
67 73 0.68
68 3 0.03
69 31 0.29
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (67 bp):
AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAG
GG
Found at i:394123 original size:36 final size:33
Alignment explanation
Indices: 394018--394132 Score: 153
Period size: 33 Copynumber: 3.5 Consensus size: 33
394008 AGACGAAATT
* *
394018 TGTTTCAAGGGAAACAATCTCAAAGG--TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
* *
394049 TGTTTCCAGAGAAACATTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
394082 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG--T-TTTTTG
394118 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
394133 TGTATCAAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
31 22 0.30
33 29 0.40
35 1 0.01
36 21 0.29
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:394273 original size:36 final size:36
Alignment explanation
Indices: 394173--394287 Score: 167
Period size: 37 Copynumber: 3.1 Consensus size: 36
394163 CAAGGATTGA
*
394173 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
394210 TGTTTTAAGAAAAACATGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
*
394247 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
394283 TGTTT
1 TGTTT
394288 AATGTAAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 24 0.35
37 28 0.41
38 17 0.25
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:394337 original size:30 final size:30
Alignment explanation
Indices: 394301--394359 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
394291 GTAAAACATA
*
394301 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
*
394331 TTCAAAGTTTATGTTTCAATAGAAACTGT
1 TTCAAAGTTTATGTTTCAAGAGAAACTGT
394360 CTCAAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:394392 original size:36 final size:36
Alignment explanation
Indices: 394342--394427 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
394332 TCAAAGTTTA
** * *
394342 TGTTTCAATAGAAACTGTCTCAA-AGGAGGCAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGA-GAGACAAAATT
394378 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
**
394414 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
394428 TGTTTATGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 42 0.98
37 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:394498 original size:93 final size:95
Alignment explanation
Indices: 394337--394609 Score: 363
Period size: 93 Copynumber: 2.8 Consensus size: 95
394327 TGTTTTCAAA
* * *
394337 GTTTATGTTTCAATAGAAACTGTCTCAAAGGAGGCAAAA-TTTGTTTCAAGGGAAACTATCTCAA
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
394401 GAGAGACAAAATTCATTTCAAGGG-A-AAT
66 GAGAGACAAAATTCATTTCAAGGGAATAAT
*
394429 GTTTATGTCTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
394494 GAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAAT
66 GAGAGACAAAATTCATTTCAAGGG-AA-----T-AAT
* * *
394531 GTTTATGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTCTGTTTCGAGGGAAACTATCTC
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT-TGTTTCAAGGGAAACTATCTC
* *
394596 AAGCGAGATAAAAT
64 AAGAGAGACAAAAT
394610 CTTGTTTTAA
Statistics
Matches: 159, Mismatches: 10, Indels: 12
0.88 0.06 0.07
Matches are distributed among these distances:
92 35 0.22
93 49 0.31
95 1 0.01
102 39 0.25
103 3 0.02
104 32 0.20
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (95 bp):
GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
GAGAGACAAAATTCATTTCAAGGGAATAAT
Done.