Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009141.1 Hibiscus syriacus cultivar Beakdansim tig00112649_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: 919200
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:220453 original size:91 final size:93
Alignment explanation
Indices: 220317--220508 Score: 307
Period size: 92 Copynumber: 2.1 Consensus size: 93
220307 ATCCCTAGTA
* * * * *
220317 GAGTCTCCAAGCTGTCGTCACTGTTTTTCGTCAGGGTGGGGAAAAA-TTGTATGACTTAGGGGTT
1 GAGTCGCCAAACTGTCGTCACTCTTTTTCGCCAGGGTGGGGAAAAACTTGTATGACTTAGGGGGT
*
220381 TTTCTTTGAAAATGTTTTGAAATGTTGG
66 TTTCTTTGAAAAGGTTTTGAAATGTTGG
*
220409 GAGTCGCCAAACTGTCGTCAC-CTTTTTCGCCCGGGTGGGGAAAAACTTGTATGACTTAGGGGGT
1 GAGTCGCCAAACTGTCGTCACTCTTTTTCGCCAGGGTGGGGAAAAACTTGTATGACTTAGGGGGT
220473 TTTCTTTGAAAAGGTTTTGAAATGTTGG
66 TTTCTTTGAAAAGGTTTTGAAATGTTGG
220501 GAGTCGCC
1 GAGTCGCC
220509 GCCAATCATT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 21 0.23
92 71 0.77
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.34
Consensus pattern (93 bp):
GAGTCGCCAAACTGTCGTCACTCTTTTTCGCCAGGGTGGGGAAAAACTTGTATGACTTAGGGGGT
TTTCTTTGAAAAGGTTTTGAAATGTTGG
Found at i:222657 original size:2 final size:2
Alignment explanation
Indices: 222650--222686 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
222640 TTTCTTTCTT
222650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
222687 TTGTTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:229165 original size:15 final size:15
Alignment explanation
Indices: 229110--229155 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
229100 ATATAACATT
229110 TATTCACATAGAACA
1 TATTCACATAGAACA
*
229125 TATTCGCATAGAACA
1 TATTCACATAGAACA
229140 TATTCACATAGAACA
1 TATTCACATAGAACA
229155 T
1 T
229156 TTACTCATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:229201 original size:57 final size:57
Alignment explanation
Indices: 229140--229271 Score: 151
Period size: 57 Copynumber: 2.3 Consensus size: 57
229130 GCATAGAACA
* * *
229140 TATTCACATAGAACATTTACTCATAGTATTTCCCATAT-A-ATTATTTAATTTATCATT
1 TATTCACATAGAACATATACTCATAGTATTT--CATATAACATTATTCAAATTATCATT
* * * *
229197 TATTCATACAGAACATATACTTATAGTGTTTCATATAACATTATTCAAATTATCATT
1 TATTCACATAGAACATATACTCATAGTATTTCATATAACATTATTCAAATTATCATT
* *
229254 TGTTCCCATAGAACATAT
1 TATTCACATAGAACATAT
229272 TTACAAAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
55 5 0.08
56 1 0.02
57 56 0.90
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (57 bp):
TATTCACATAGAACATATACTCATAGTATTTCATATAACATTATTCAAATTATCATT
Found at i:234176 original size:23 final size:24
Alignment explanation
Indices: 234111--234168 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
234101 GAAATTGTTG
* * * *
234111 CATAGAATTTGCACCGAAATGCCA
1 CATAGAATATGCACAGAAGTACCA
234135 CATAGAATATGCACAGAAGTACCA
1 CATAGAATATGCACAGAAGTACCA
234159 CATAG-ATATG
1 CATAGAATATG
234169 TCTCGAAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (24 bp):
CATAGAATATGCACAGAAGTACCA
Found at i:235496 original size:94 final size:94
Alignment explanation
Indices: 235335--235523 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
235325 GCATTAATTA
235335 AAAACCAACTCAAAAATTTAAGAAACAATCAACTTTAAAATCACTTACCTTAGCATGGAGGTTCA
1 AAAACCAACTCAAAAATTTAAGAAACAATCAACTTTAAAATCACTTACCTTAGCATGGAGGTTCA
235400 CGTTGAAGAATGAAGAAGTGAAGATGAAG
66 CGTTGAAGAATGAAGAAGTGAAGATGAAG
235429 AAAACCAACTCAAAAATTTAAGAAACAATCAACTTTAAAATCACTTACCTTAGCATGGAGGTTCA
1 AAAACCAACTCAAAAATTTAAGAAACAATCAACTTTAAAATCACTTACCTTAGCATGGAGGTTCA
235494 CGTTGAAGAATGAAGAAGTGAAGATGAAG
66 CGTTGAAGAATGAAGAAGTGAAGATGAAG
235523 A
1 A
235524 GAAGAGTTTC
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (94 bp):
AAAACCAACTCAAAAATTTAAGAAACAATCAACTTTAAAATCACTTACCTTAGCATGGAGGTTCA
CGTTGAAGAATGAAGAAGTGAAGATGAAG
Found at i:240418 original size:3 final size:3
Alignment explanation
Indices: 240410--240453 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
240400 TTTTGTCCCG
* *
240410 TTA TTA TTA TTA TTA GTA TTA GTA TTCA -TA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT
240454 TAAAAATACT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:252937 original size:329 final size:328
Alignment explanation
Indices: 252286--252943 Score: 1174
Period size: 329 Copynumber: 2.0 Consensus size: 328
252276 TATGGAGACA
*
252286 AGCTCCACACCCCTCCTGATCCATTGCATGTAATGACTGCTCCATGGCCATTCTCTATGTGGGGC
1 AGCTCCACACCCCTCCTCATCCATTGCATGTAATGACTGCTCCATGGCCATTCTCTATGTGGGGC
* * *
252351 ATGTATGTTATTAGGCAAATTTCACCCAAAGCTTCTAATGGCCACCGTTTCATATTTGTGGCAAT
66 ATGGATGCTATTAGGCAAATTTCACCCAAAGCTTCTAATGGCCACCGTTTCATATTCGTGGCAAT
* * *
252416 GTACTACTTAACTAAGTGGGTAGAACGGCCTCCTATGCAAATGTCACTCAACCAGCAGTTTGCAA
131 ATACTACTTAACTAAGTGGGTAGAAAGGCCTCCTATGCAAATGTCACTCAACCAGCACTTTGCAA
*
252481 GTTCTTGAAGAGAGAAATTATCTATCGGTATGGGCTACCAGAAAGGATCATCACCGACAATGCCT
196 GTTCTTAAAGAGAGAAATTATCTATCGGTATGGGCTACCAGAAAGGATCATCACCGACAATGCCT
* *
252546 TGAATTTAAACAATAAGATGATGGAATAAGTATGTAAACAGTTCCAGATTAAACATCATAATTCA
261 TGAATTTAAACAATAAGATAATGAAATAAGTATGTAAACAGTTCCAGATTAAACATCATAATTCA
252611 ACC
326 ACC
252614 AGCTCCACACCCCTCCTCATCCATTGCATGTAATGACTGCTCCATGGCCATTCTCTATGTGGGGC
1 AGCTCCACACCCCTCCTCATCCATTGCATGTAATGACTGCTCCATGGCCATTCTCTATGTGGGGC
252679 ATGGATGCTATTAGGCAAATTTCACCCAAAGCTTCTAATGGCCACCGTTTCATATTCGTGGCAAT
66 ATGGATGCTATTAGGCAAATTTCACCCAAAGCTTCTAATGGCCACCGTTTCATATTCGTGGCAAT
252744 ATACTACTTAACTAAGTGGGTAGAAGAGGCCTCCTATGCAAATGTCACTCAACCAGCACTTTGCA
131 ATACTACTTAACTAAGTGGGTAGAA-AGGCCTCCTATGCAAATGTCACTCAACCAGCACTTTGCA
* * *
252809 AGTT-TGTAAAGAGATAAATTATCTGTTGGTATGGGCTACCAGAAAGGATCATCACCGACAATGC
195 AGTTCT-TAAAGAGAGAAATTATCTATCGGTATGGGCTACCAGAAAGGATCATCACCGACAATGC
252873 CTTGAATTTAAACAATAAGATAATGAAATAAGTATGTAAACAGTTCCAGATTAAACATCATAATT
259 CTTGAATTTAAACAATAAGATAATGAAATAAGTATGTAAACAGTTCCAGATTAAACATCATAATT
252938 CAACC
324 CAACC
252943 A
1 A
252944 CTTATTGCCC
Statistics
Matches: 315, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
328 151 0.48
329 164 0.52
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (328 bp):
AGCTCCACACCCCTCCTCATCCATTGCATGTAATGACTGCTCCATGGCCATTCTCTATGTGGGGC
ATGGATGCTATTAGGCAAATTTCACCCAAAGCTTCTAATGGCCACCGTTTCATATTCGTGGCAAT
ATACTACTTAACTAAGTGGGTAGAAAGGCCTCCTATGCAAATGTCACTCAACCAGCACTTTGCAA
GTTCTTAAAGAGAGAAATTATCTATCGGTATGGGCTACCAGAAAGGATCATCACCGACAATGCCT
TGAATTTAAACAATAAGATAATGAAATAAGTATGTAAACAGTTCCAGATTAAACATCATAATTCA
ACC
Found at i:253573 original size:26 final size:26
Alignment explanation
Indices: 253544--253619 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 26
253534 GAAAAAAATG
*
253544 AAAAA-GAAAAAACGAGAGAAAAGAAAA
1 AAAAATGAAAAAA--AGAAAAAAGAAAA
253571 AAAAATGAAAAAAAGAAAAAAGAAAA
1 AAAAATGAAAAAAAGAAAAAAGAAAA
* *
253597 AGAAAA-G-AATAAATAAAAAAGAA
1 A-AAAATGAAAAAAAGAAAAAAGAA
253620 TGTTCAAGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.32
26 14 0.32
27 9 0.20
28 7 0.16
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.04
Consensus pattern (26 bp):
AAAAATGAAAAAAAGAAAAAAGAAAA
Found at i:253583 original size:18 final size:17
Alignment explanation
Indices: 253535--253619 Score: 86
Period size: 17 Copynumber: 5.0 Consensus size: 17
253525 AAGTGGACTG
253535 AAAAAAATGAAAAAGAA
1 AAAAAAATGAAAAAGAA
**
253552 AAAACGA-GAGAAAAGAA
1 AAAAAAATGA-AAAAGAA
253569 AAAAAAATGAAAAA-AA
1 AAAAAAATGAAAAAGAA
*
253585 GAAAAAA-GAAAAAGAA
1 AAAAAAATGAAAAAGAA
*
253601 AAGAATAAATAAAAAAGAA
1 AA-AA-AAATGAAAAAGAA
253620 TGTTCAAGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
15 6 0.11
16 13 0.24
17 23 0.42
18 5 0.09
19 8 0.15
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAAATGAAAAAGAA
Found at i:253615 original size:19 final size:17
Alignment explanation
Indices: 253535--253619 Score: 71
Period size: 19 Copynumber: 4.6 Consensus size: 17
253525 AAGTGGACTG
*
253535 AAAAAAATGAAAAAGAAA
1 AAAAAAAAG-AAAAGAAA
** *
253553 AAACGAGAGAAAAGAAA
1 AAAAAAAAGAAAAGAAA
*
253570 AAAAAATGAAAAAAAGAAA
1 AAAAAA--AAGAAAAGAAA
253589 AAAGAAAAAGAAAAGAATA
1 AAA-AAAAAGAAAAGAA-A
253608 AATAAAAAAGAA
1 AA-AAAAAAGAA
253620 TGTTCAAGAT
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
17 12 0.23
18 14 0.26
19 23 0.43
20 4 0.08
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAAAAGAAAAGAAA
Found at i:254962 original size:30 final size:30
Alignment explanation
Indices: 254926--254987 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
254916 TAGTGACTGC
*
254926 GAACAAGTCTGCCCCGATTCAATCTTCCCT
1 GAACAAGTCTACCCCGATTCAATCTTCCCT
*
254956 GAACAAGTCTATCCCGATTCAATCTTCCCT
1 GAACAAGTCTACCCCGATTCAATCTTCCCT
254986 GA
1 GA
254988 GTGTCAGCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.34, G:0.13, T:0.27
Consensus pattern (30 bp):
GAACAAGTCTACCCCGATTCAATCTTCCCT
Found at i:255082 original size:160 final size:163
Alignment explanation
Indices: 254808--255114 Score: 476
Period size: 160 Copynumber: 1.9 Consensus size: 163
254798 AATCGAACTT
* *
254808 GATTTAATCTTCCCTGAGTGACAGCGAAATGGATCAACTCCCCCAGATCTGATATTCCCTTTAGA
1 GATTCAATCTTCCCTGAGTGACAGCGAAATGGATCAACT-CCCCAGATCTGATATTCCCTTCAGA
* * * *
254873 ATAAGTGAAATAGATCCCTCTCATCTAAGATTTGATATTCCCTTAGTGACTGC-GAACAAGTCTG
65 ATAAGCGAAACAGATCCCTCTCATCTAAGATTTGATATTCCCCTAGTGACAGCGGAACAAGTCTG
254937 CCCCGATTCAATCTTCCCTGAACAAGTCTATCCC
130 CCCCGATTCAATCTTCCCTGAACAAGTCTATCCC
* *
254971 GATTCAATCTTCCCTGAGTGTCAGCGGAATGGATCAACT-CCCAGATCTG-TATTCCCTTCAGAA
1 GATTCAATCTTCCCTGAGTGACAGCGAAATGGATCAACTCCCCAGATCTGATATTCCCTTCAGAA
* * *
255034 TAAGCGAAACAGATCCCTGTCATCTAAGGTTTGATATTCCCCTAGTGACAGCGGAACAAGTCTTC
66 TAAGCGAAACAGATCCCTCTCATCTAAGATTTGATATTCCCCTAGTGACAGCGGAACAAGTCTGC
*
255099 CCCGATTCGATCTTCC
131 CCCGATTCAATCTTCC
255115 TAAGTGACAG
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
160 59 0.45
161 36 0.27
163 36 0.27
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (163 bp):
GATTCAATCTTCCCTGAGTGACAGCGAAATGGATCAACTCCCCAGATCTGATATTCCCTTCAGAA
TAAGCGAAACAGATCCCTCTCATCTAAGATTTGATATTCCCCTAGTGACAGCGGAACAAGTCTGC
CCCGATTCAATCTTCCCTGAACAAGTCTATCCC
Found at i:255300 original size:133 final size:130
Alignment explanation
Indices: 254956--255338 Score: 449
Period size: 133 Copynumber: 2.9 Consensus size: 130
254946 AATCTTCCCT
* *
254956 GAACAAGTCTATCCCGATTCAATCTTCCCTGAGTG-TCAGCGGAATGGATCAACT-CCCAGATCT
1 GAACAAGTCTACCCCGATTCAATCTTTCCTGAGTGAT-AGCGGAATGGATCAACTCCCCAGATCT
* * * * *
255019 G-TATTCCCTTCAGAATAAGCGAAACA-GATC-CCTGTCATCTAAGGTTTGATATTCCCCTAGTG
65 GATATTCCCTTCAGAAGAAGCG-AACATG-TCTTCT-T-TTCCAAGATTTGATATT-CCCTAGTG
255081 ACAGCG
125 ACAGCG
* * * * *
255087 GAACAAGTCTTCCCCGATTCGATC-TTCCTAAGTGACAGCGGAATGGATCAACTCCCCATATCTG
1 GAACAAGTCTACCCCGATTCAATCTTTCCTGAGTGATAGCGGAATGGATCAACTCCCCAGATCTG
255151 ATATTCCCTTCAGAAGAAGCAGAACATGTCATTCTTTTCCAAGATTTGATATTCCCTGAGTGACA
66 ATATTCCCTTCAGAAGAAGC-GAACATGTC-TTCTTTTCCAAGATTTGATATTCCCT-AGTGACA
255216 GCG
128 GCG
* *
255219 GAACAAGTCTACCCCAATTCAATCTTTCCTGAGTGATAGCTGAATGGATCAACTCCCCCAGATCT
1 GAACAAGTCTACCCCGATTCAATCTTTCCTGAGTGATAGCGGAATGGATCAACT-CCCCAGATCT
* *
255284 GATATT-CCTTCAGAAGAATTG-GAACATGTCTCTCTTTTCCTAGATCTGATATTCC
65 GATATTCCCTTCAGAAGAA--GCGAACATGTCT-TCTTTTCCAAGATTTGATATTCC
255339 TTCAGAAGAA
Statistics
Matches: 218, Mismatches: 21, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
130 25 0.11
131 34 0.16
132 70 0.32
133 71 0.33
134 17 0.08
135 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (130 bp):
GAACAAGTCTACCCCGATTCAATCTTTCCTGAGTGATAGCGGAATGGATCAACTCCCCAGATCTG
ATATTCCCTTCAGAAGAAGCGAACATGTCTTCTTTTCCAAGATTTGATATTCCCTAGTGACAGCG
Found at i:255332 original size:47 final size:47
Alignment explanation
Indices: 255278--255387 Score: 175
Period size: 47 Copynumber: 2.3 Consensus size: 47
255268 CAACTCCCCC
** * *
255278 AGATCTGATATTCCTTCAGAAGAATTGGAACATGTCTCTCTTTTCCT
1 AGATCTGATATTCCTTCAGAAGAAGCGGAACATGTCCCTCTTTTCCA
255325 AGATCTGATATTCCTTCAGAAGAAGCGGAACATGTCCCTCTTTTCCA
1 AGATCTGATATTCCTTCAGAAGAAGCGGAACATGTCCCTCTTTTCCA
*
255372 AGATTTGATATTCCTT
1 AGATCTGATATTCCTT
255388 AGTGACAACG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (47 bp):
AGATCTGATATTCCTTCAGAAGAAGCGGAACATGTCCCTCTTTTCCA
Found at i:255507 original size:133 final size:134
Alignment explanation
Indices: 255327--255606 Score: 385
Period size: 134 Copynumber: 2.1 Consensus size: 134
255317 CTTTTCCTAG
* *
255327 ATCTGATA-TTCCTTCAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGATATT-CCTTAG
1 ATCTGATATTTCCTTCAAAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAG
* *
255390 TGACAA-CGGAACAAGTCTGCCCCAATTCAATCTTCCCTGAGTGACAACGGAATGGATCAAC-TC
66 TGA-AAGCAGAACAAGTCTGCCCCAATTCAATCTTCCCTAAGTGACAACGGAATGGATCAACAT-
255453 CCCCAA
129 CCCCAA
* *
255459 ATCTGATATTTTCTTCAAAATAAGCGGAACA-GATCCCTCTCTTT-CAAGATTTGATATTCCCTG
1 ATCTGATATTTCCTTCAAAAGAAGCGGAACATG-TCCCTCT-TTTCCAAGATTTGATATTCCCTG
* * *
255522 AGTGAAAGCAGAATAAGTCTGCCCCGATTCAATCTTCCCTAAGTGACAGCGGAATGGATCAACAT
64 AGTGAAAGCAGAACAAGTCTGCCCCAATTCAATCTTCCCTAAGTGACAACGGAATGGATCAACAT
*
255587 CCCCAG
129 CCCCAA
255593 ATCTGATA-TTCCTT
1 ATCTGATATTTCCTT
255607 GAGTGACAGT
Statistics
Matches: 131, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
132 9 0.07
133 47 0.36
134 74 0.56
135 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (134 bp):
ATCTGATATTTCCTTCAAAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAG
TGAAAGCAGAACAAGTCTGCCCCAATTCAATCTTCCCTAAGTGACAACGGAATGGATCAACATCC
CCAA
Found at i:255516 original size:180 final size:180
Alignment explanation
Indices: 255146--255518 Score: 518
Period size: 180 Copynumber: 2.1 Consensus size: 180
255136 AACTCCCCAT
*
255146 ATCTGATATTCCCTTCAGAAGAAGCAGAACATGTCATTCTTTTCCAAGATTTGATATTCCCTGAG
1 ATCTGATATT-CCTTCAGAAGAAGCAGAACATGTCACTCTTTTCCAAGATTTGATATTCCCTGAG
* * * * *
255211 TGACAGCGGAACAAGTCTACCCCAATTCAATCTTTCCTGAGTGATAGCTGAATGGATCAACTCCC
65 TGACAACGGAACAAGTCTACCCCAATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCC
* * ** * *
255276 CCAGATCTGATATTCCTTCAGAAGAATTGGAACATGTCTCTCTTTTCCTAG
130 CCAAATCTGATATTCCTTCAAAAGAAGCGGAACATGTCCCTCTTTTCCAAG
* * *
255327 ATCTGATATTCCTTCAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGATATT-CCTTAGT
1 ATCTGATATTCCTTCAGAAGAAGCAGAACATGTCACTCTTTTCCAAGATTTGATATTCCCTGAGT
*
255391 GACAACGGAACAAGTCTGCCCCAATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCCC
66 GACAACGGAACAAGTCTACCCCAATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCCC
* *
255456 CAAATCTGATATTTTCTTCAAAATAAGCGGAACA-GATCCCTCTCTTT-CAAG
131 CAAATCTGATA-TTCCTTCAAAAGAAGCGGAACATG-TCCCTCT-TTTCCAAG
*
255507 ATTTGATATTCC
1 ATCTGATATTCC
255519 CTGAGTGAAA
Statistics
Matches: 170, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
179 76 0.45
180 81 0.48
181 13 0.08
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (180 bp):
ATCTGATATTCCTTCAGAAGAAGCAGAACATGTCACTCTTTTCCAAGATTTGATATTCCCTGAGT
GACAACGGAACAAGTCTACCCCAATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCCC
CAAATCTGATATTCCTTCAAAAGAAGCGGAACATGTCCCTCTTTTCCAAG
Found at i:255581 original size:313 final size:312
Alignment explanation
Indices: 255013--255606 Score: 804
Period size: 313 Copynumber: 1.9 Consensus size: 312
255003 ATCAACTCCC
* * * *
255013 AGATCTGTATTCCCTTCAGAATAAGCGAAACAGATCCCTGTCATCTAAGGTTTGATATTCCCCTA
1 AGATCTGTATTCCCTTCAGAAGAAGCGAAACAGATCCCTCTCATCCAAGATTTGATATTCCCCTA
* * * * *
255078 GTGACAGCGGAACAAGTCTTCCCCGATTCGATCTTCCTAAGTGACAGCGGAATGGATCAACTCCC
66 GTGACAACGGAACAAGTCTGCCCCAATTCAATCTTCCTAAGTGACAACGGAATGGATCAACTCCC
* * *
255143 CATATCTGATATTCCCTTCAGAAGAAGCAGAACATGTCATTCTTTTCCAAGATTTGATATTCCCT
131 CAAATCTGATATTCCCTTCAAAAGAAGCAGAACATGTCACTCTTTTCCAAGATTTGATATTCCCT
* * * * * *
255208 GAGTGACAGCGGAACAAGTCTACCCCAATTCAATCTTTCCTGAGTGATAGCTGAATGGATCAAC-
196 GAGTGAAAGCAGAACAAGTCTACCCCAATTCAATCTTCCCTAAGTGACAGCGGAATGGATCAACA
255272 TCCCCCAGATCTGATATTCCTTCAGAAGAATTGGAACATGTCTCTCTTTTCCT
261 T-CCCCAGATCTGATATTCCTTCAGAAGAATTGGAACATGTCTCTCTTTTCCT
* ** *
255325 AGATCTGATATT-CCTTCAGAAGAAGCGGAACATG-TCCCTCTTTTCCAAGATTTGATATT-CCT
1 AGATCTG-TATTCCCTTCAGAAGAAGCGAAACA-GATCCCTCTCATCCAAGATTTGATATTCCCC
*
255387 TAGTGACAACGGAACAAGTCTGCCCCAATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACT
64 TAGTGACAACGGAACAAGTCTGCCCCAATTCAATCTT-CCTAAGTGACAACGGAATGGATCAACT
** * * *
255452 CCCCCAAATCTGATATTTTCTTCAAAATAAGCGGAACA-GATCCCTCTCTTT-CAAGATTTGATA
128 -CCCCAAATCTGATATTCCCTTCAAAAGAAGCAGAACATG-TCACTCT-TTTCCAAGATTTGATA
* * *
255515 TTCCCTGAGTGAAAGCAGAATAAGTCTGCCCCGATTCAATCTTCCCTAAGTGACAGCGGAATGGA
190 TTCCCTGAGTGAAAGCAGAACAAGTCTACCCCAATTCAATCTTCCCTAAGTGACAGCGGAATGGA
255580 TCAACATCCCCAGATCTGATATTCCTT
255 TCAACATCCCCAGATCTGATATTCCTT
255607 GAGTGACAGT
Statistics
Matches: 244, Mismatches: 31, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
311 35 0.14
312 71 0.29
313 134 0.55
314 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (312 bp):
AGATCTGTATTCCCTTCAGAAGAAGCGAAACAGATCCCTCTCATCCAAGATTTGATATTCCCCTA
GTGACAACGGAACAAGTCTGCCCCAATTCAATCTTCCTAAGTGACAACGGAATGGATCAACTCCC
CAAATCTGATATTCCCTTCAAAAGAAGCAGAACATGTCACTCTTTTCCAAGATTTGATATTCCCT
GAGTGAAAGCAGAACAAGTCTACCCCAATTCAATCTTCCCTAAGTGACAGCGGAATGGATCAACA
TCCCCAGATCTGATATTCCTTCAGAAGAATTGGAACATGTCTCTCTTTTCCT
Found at i:259173 original size:19 final size:19
Alignment explanation
Indices: 259146--259197 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
259136 CTACTAATTT
*
259146 AGTACTGATACTTTCAAAG-
1 AGTATTGATACTTT-AAAGA
*
259165 AGTATTGATACCTTAAAGA
1 AGTATTGATACTTTAAAGA
259184 AGAATATTGATACT
1 AG--TATTGATACT
259198 GCCCTTTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.15
19 14 0.52
21 9 0.33
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (19 bp):
AGTATTGATACTTTAAAGA
Found at i:262297 original size:29 final size:30
Alignment explanation
Indices: 262232--262299 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
262222 GTCATACATT
* *
262232 ATATTAGATATTTTAGCAAAGTATAGATATC
1 ATATTAGATATTTTAACAAAG-ATAGATACC
*
262263 ACATTAGATATTTTAACAAAG-TAGATACC
1 ATATTAGATATTTTAACAAAGATAGATACC
262292 ATATTAGA
1 ATATTAGA
262300 GTTTAAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 14 0.42
31 19 0.58
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (30 bp):
ATATTAGATATTTTAACAAAGATAGATACC
Found at i:266473 original size:80 final size:80
Alignment explanation
Indices: 266347--266503 Score: 305
Period size: 80 Copynumber: 2.0 Consensus size: 80
266337 TTAAACCTTA
266347 TCACTTTGCTTAGTTAAATCTCAATGTATACTATTTATTTTTATTTAGTTTGTACATGAATAAAC
1 TCACTTTGCTTAGTTAAATCTCAATGTATACTATTTATTTTTATTTAGTTTGTACATGAATAAAC
266412 TACTAGCCTTTAATT
66 TACTAGCCTTTAATT
*
266427 TCACTTTGCTTAGTTAAATCTCTATGTATACTATTTATTTTTATTTAGTTTGTACATGAATAAAC
1 TCACTTTGCTTAGTTAAATCTCAATGTATACTATTTATTTTTATTTAGTTTGTACATGAATAAAC
266492 TACTAGCCTTTA
66 TACTAGCCTTTA
266504 CTTTTATCCA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (80 bp):
TCACTTTGCTTAGTTAAATCTCAATGTATACTATTTATTTTTATTTAGTTTGTACATGAATAAAC
TACTAGCCTTTAATT
Found at i:269730 original size:54 final size:54
Alignment explanation
Indices: 269660--270158 Score: 675
Period size: 54 Copynumber: 9.3 Consensus size: 54
269650 TTTGGGGTGA
* * * * * *
269660 ACACGTAGTGCTGATACGGGCATTCATAAACATATTATGAATTATGTGGGTTGT
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGC
** * **
269714 ACACTTAGTGTTGATACAGTCGTTCATAAA-TTAATTATGAATTCCGTGGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTT-ATTATGAATTATGTGGGTTGC
* * *
269768 ACACTTAGTGCGGATACGGTCGATCATAAACTTATTATGAATTTTGTGGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGC
* * **
269822 ACACTTAGTACCGATACAGTCGTTCATAAAC-TATTATGAATTACATGGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGC
** **
269875 ACACTTAGTGCTTATACGGTCGTTCATAAACTTATTATGAATTCCGTGGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGC
* * *
269929 AAACTTAGTGCTGATACGGTCGTTCATAAACTTATTATGAATTTTGTGGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGC
269983 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGC
* * * *
270037 ACACTTAGAGCCGATACAGTCATTCATAAACTTATTATGAATT-TGTAGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGC
270090 ACACTTAGTGCCGATA-GGTCGTTCATAAACTTATTATGAATT-TCGTGGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTAT-GTGGGTTGC
*
270143 ACACTTAGTGTCGATA
1 ACACTTAGTGCCGATA
270159 TTACACATAG
Statistics
Matches: 397, Mismatches: 44, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
52 25 0.06
53 94 0.24
54 276 0.70
55 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (54 bp):
ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGC
Found at i:269958 original size:161 final size:162
Alignment explanation
Indices: 269682--270151 Score: 725
Period size: 161 Copynumber: 2.9 Consensus size: 162
269672 GATACGGGCA
*
269682 TTCATAAACATATTATGAATTATGTGGGTTGTACACTTAGTG-TTGATACAGTCGTTCATAAA-T
1 TTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGCTT-ATACAGTCGTTCATAAACT
* *
269745 TAATTATGAATTCCGTGGGTTGCACACTTAGTGCGGATACGGTCGATCATAAACTTATTATGAAT
65 T-ATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAAT
269810 TTTGTGGGTTGCACACTTAGTACCGATACAGTCG
129 TTTGTGGGTTGCACACTTAGTACCGATACAGTCG
** *
269844 TTCATAAAC-TATTATGAATTACATGGGTTGCACACTTAGTGCTTATACGGTCGTTCATAAACTT
1 TTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGCTTATACAGTCGTTCATAAACTT
* *
269908 ATTATGAATTCCGTGGGTTGCAAACTTAGTGCTGATACGGTCGTTCATAAACTTATTATGAATTT
66 ATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTT
* *
269973 TGTGGGTTGCACACTTAGTGCCGATACGGTCG
131 TGTGGGTTGCACACTTAGTACCGATACAGTCG
* * ** *
270005 TTCATAAACTTATTATGAATTATGTGGGTTGCACACTTAGAGCCGATACAGTCATTCATAAACTT
1 TTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGCTTATACAGTCGTTCATAAACTT
* *
270070 ATTATGAATT-TGTAGGTTGCACACTTAGTGCCGATA-GGTCGTTCATAAACTTATTATGAATTT
66 ATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTT
*
270133 CGTGGGTTGCACACTTAGT
131 TGTGGGTTGCACACTTAGT
270152 GTCGATATTA
Statistics
Matches: 284, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
160 45 0.16
161 168 0.59
162 71 0.25
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (162 bp):
TTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGCTTATACAGTCGTTCATAAACTT
ATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTT
TGTGGGTTGCACACTTAGTACCGATACAGTCG
Found at i:269959 original size:27 final size:27
Alignment explanation
Indices: 269877--269962 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
269867 TGGGTTGCAC
*
269877 ACTTAGTGCTTATACGGTCGTTCATAA
1 ACTTAGTGCTGATACGGTCGTTCATAA
** * * *
269904 ACTTA-TTATGAATTCCGTGGGTTGC--AA
1 ACTTAGTGCTG-ATACGGT-CGTT-CATAA
269931 ACTTAGTGCTGATACGGTCGTTCATAA
1 ACTTAGTGCTGATACGGTCGTTCATAA
269958 ACTTA
1 ACTTA
269963 TTATGAATTT
Statistics
Matches: 42, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
25 1 0.02
26 5 0.12
27 29 0.69
28 6 0.14
29 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (27 bp):
ACTTAGTGCTGATACGGTCGTTCATAA
Found at i:270036 original size:215 final size:215
Alignment explanation
Indices: 269660--270152 Score: 733
Period size: 215 Copynumber: 2.3 Consensus size: 215
269650 TTTGGGGTGA
* * * * * * *
269660 ACACGTAGTGCTGATACGGGCATTCATAAACATATTATGAATTATGTGGGTTGTACACTTAGTGT
1 ACACTTAGTGCTGATACGGTCGTTCATAAACTTATTATGAATTACGTGGGTTGCACACTTAGTGC
*
269725 TGATACAGTCGTTCATAAATTAATTATGAATTCCGTGGGTTGCACACTTAGTGCGGATACGGTCG
66 TGATACAGTCGTTCATAAATTAATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* *
269790 ATCATAAACTTATTATGAATTTTGTGGGTTGCACACTTAGTA-CCGATACAGTCGTTCATAAAC-
131 ATCATAAACTTATTATGAATTATGTGGGTTGCACACTTAG-AGCCGATACAGTCATTCATAAACT
*
269853 TATTATGAATTACATGGGTTGC
195 TATTATGAATT-CATAGGTTGC
* * *
269875 ACACTTAGTGCTTATACGGTCGTTCATAAACTTATTATGAATTCCGTGGGTTGCAAACTTAGTGC
1 ACACTTAGTGCTGATACGGTCGTTCATAAACTTATTATGAATTACGTGGGTTGCACACTTAGTGC
* **
269940 TGATACGGTCGTTCATAAACTT-ATTATGAATTTTGTGGGTTGCACACTTAGTGCCGATACGGTC
66 TGATACAGTCGTTCATAAA-TTAATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTC
*
270004 GTTCATAAACTTATTATGAATTATGTGGGTTGCACACTTAGAGCCGATACAGTCATTCATAAACT
130 GATCATAAACTTATTATGAATTATGTGGGTTGCACACTTAGAGCCGATACAGTCATTCATAAACT
**
270069 TATTATGAATTTGTAGGTTGC
195 TATTATGAATTCATAGGTTGC
* *
270090 ACACTTAGTGCCGATA-GGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACACTTAGTG
1 ACACTTAGTGCTGATACGGTCGTTCATAAACTTATTATGAATTACGTGGGTTGCACACTTAGTG
270153 TCGATATTAC
Statistics
Matches: 251, Mismatches: 24, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
214 46 0.18
215 192 0.76
216 13 0.05
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (215 bp):
ACACTTAGTGCTGATACGGTCGTTCATAAACTTATTATGAATTACGTGGGTTGCACACTTAGTGC
TGATACAGTCGTTCATAAATTAATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
ATCATAAACTTATTATGAATTATGTGGGTTGCACACTTAGAGCCGATACAGTCATTCATAAACTT
ATTATGAATTCATAGGTTGC
Found at i:284474 original size:54 final size:54
Alignment explanation
Indices: 284392--284778 Score: 416
Period size: 54 Copynumber: 7.3 Consensus size: 54
284382 CTTTGGGGTG
* * *
284392 CACACGTAGTGTTGATACGGTCGTTCATAAACATATTATGAATTCTATGGGTTA
1 CACACTTAGTGTTGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTA
* * * *
284446 CACACATAGTGTTGATACGTTTGTTCATAAACTTTTTATGAATTCTGTGGGTTA
1 CACACTTAGTGTTGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTA
* * * * *
284500 CACACTTAGTGATGATGCGGTCGTTCATTAACTTATTATGAATTTTGTGGGTTG
1 CACACTTAGTGTTGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTA
* * * *
284554 CATACTTAGTGTCGATGCGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTG
1 CACACTTAGTGTTGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTA
* ** **
284608 CACAGTTAGAATTGATACGGTCGTTC----A--TA--ATGAATTCTGTGGGTGG
1 CACACTTAGTGTTGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTA
*** **
284654 CACACTTAGTGCCAATACGGTCGTTCATAAACTTATTATGAATTAC-GTGGGTGG
1 CACACTTAGTGTTGATACGGTCGTTCATAAACTTATTATGAATT-CTGTGGGTTA
** *
284708 CACACTTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATT-TCGTGGGTTG
1 CACACTTAGTGTTGATACGGTCGTTCATAAACTTATTATGAATTCT-GTGGGTTA
*
284762 CACACTTAGTGTCGATA
1 CACACTTAGTGTTGATA
284779 GTACACATAG
Statistics
Matches: 284, Mismatches: 38, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
46 36 0.13
48 2 0.01
50 2 0.01
52 2 0.01
54 241 0.85
55 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (54 bp):
CACACTTAGTGTTGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTA
Found at i:284581 original size:108 final size:108
Alignment explanation
Indices: 284380--284778 Score: 462
Period size: 108 Copynumber: 3.8 Consensus size: 108
284370 TCATTGTAAG
* * * * * *
284380 TTCTTTGGGGTGCACACGTAGTGTTGATACGGTCGTTCATAAACATATTATGAATTCTATGGGTT
1 TTCTGTGGGTTGCACACTTAGTGATGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTT
* * * * * *
284445 ACACACATAGTGTTGATACGTTTGTTCATAAACTTTTTATGAA
66 GCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAA
* * * *
284488 TTCTGTGGGTTACACACTTAGTGATGATGCGGTCGTTCATTAACTTATTATGAATTTTGTGGGTT
1 TTCTGTGGGTTGCACACTTAGTGATGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTT
* *
284553 GCATACTTAGTGTCGATGCGGTCGTTCATAAACTTATTATGAA
66 GCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAA
* *
284596 TTCTGTGGGTTGCACAGTTAG-AATTGATACGGTCGTTC----A--TA--ATGAATTCTGTGGGT
1 TTCTGTGGGTTGCACACTTAGTGA-TGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGT
* * *
284652 GGCACACTTAGTGCCAATACGGTCGTTCATAAACTTATTATGAA
65 TGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAA
*
284696 TTAC-GTGGGTGGCACACTTAGTGCA-GATACGGTCGTTCATAAACTTATTATGAATT-TCGTGG
1 TT-CTGTGGGTTGCACACTTAGTG-ATGATACGGTCGTTCATAAACTTATTATGAATTCT-GTGG
284758 GTTGCACACTTAGTGTCGATA
63 GTTGCACACTTAGTGTCGATA
284779 GTACACATAG
Statistics
Matches: 244, Mismatches: 34, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
100 83 0.34
101 1 0.00
102 3 0.01
104 2 0.01
106 2 0.01
107 2 0.01
108 151 0.62
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (108 bp):
TTCTGTGGGTTGCACACTTAGTGATGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTT
GCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAA
Found at i:284697 original size:154 final size:154
Alignment explanation
Indices: 284483--284770 Score: 427
Period size: 154 Copynumber: 1.9 Consensus size: 154
284473 TAAACTTTTT
* ** * * **
284483 ATGAATTCTGTGGGTTACACACTTAGTGATGATGCGGTCGTTCATTAACTTATTATGAATTTTGT
1 ATGAATTCTGTGGGTGACACACTTAGTGACAATACGGTCGTTCATAAACTTATTATGAATTACGT
* * *
284548 GGGTTGCATACTTAGTGTC-GATGCGGTCGTTCATAAACTTATTATGAA-TTCTGTGGGTTGCAC
66 GGGTGGCACACTTAGTG-CAGATACGGTCGTTCATAAACTTATTATGAATTTC-GTGGGTTGCAC
*
284611 AGTTAGAATTGATACGGTCGTTCATA
129 ACTTAGAATTGATACGGTCGTTCATA
* *
284637 ATGAATTCTGTGGGTGGCACACTTAGTGCCAATACGGTCGTTCATAAACTTATTATGAATTACGT
1 ATGAATTCTGTGGGTGACACACTTAGTGACAATACGGTCGTTCATAAACTTATTATGAATTACGT
284702 GGGTGGCACACTTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACAC
66 GGGTGGCACACTTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACAC
284767 TTAG
131 TTAG
284771 TGTCGATAGT
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
153 1 0.01
154 115 0.97
155 3 0.03
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (154 bp):
ATGAATTCTGTGGGTGACACACTTAGTGACAATACGGTCGTTCATAAACTTATTATGAATTACGT
GGGTGGCACACTTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACAC
TTAGAATTGATACGGTCGTTCATA
Found at i:284711 original size:100 final size:100
Alignment explanation
Indices: 284537--284737 Score: 278
Period size: 100 Copynumber: 2.0 Consensus size: 100
284527 TTAACTTATT
* * * * * *
284537 ATGAATTTTGTGGGTTGCATACTTAGTGTCGATGCGGTCGTTCATAAACTTATTATGAATTCTGT
1 ATGAATTCTGTGGGTGGCACACTTAGTGCCAATACGGTCGTTCATAAACTTATTATGAATTCTGT
* * **
284602 GGGTTGCACAGTTAGAATTGATACGGTCGTTCATA
66 GGGTGGCACACTTAGAACAGATACGGTCGTTCATA
284637 ATGAATTCTGTGGGTGGCACACTTAGTGCCAATACGGTCGTTCATAAACTTATTATGAATTAC-G
1 ATGAATTCTGTGGGTGGCACACTTAGTGCCAATACGGTCGTTCATAAACTTATTATGAATT-CTG
**
284701 TGGGTGGCACACTTAGTGCAGATACGGTCGTTCATA
65 TGGGTGGCACACTTAGAACAGATACGGTCGTTCATA
284737 A
1 A
284738 ACTTATTATG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
100 87 0.99
101 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (100 bp):
ATGAATTCTGTGGGTGGCACACTTAGTGCCAATACGGTCGTTCATAAACTTATTATGAATTCTGT
GGGTGGCACACTTAGAACAGATACGGTCGTTCATA
Found at i:286530 original size:26 final size:26
Alignment explanation
Indices: 286494--286549 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
286484 ATTATCAACT
*
286494 ATATTTTTAAAGGATG-TTAATTCGAA
1 ATATTTTTAAAGGATGATT-ATTCAAA
286520 ATATTTTTAAAGGATGATTATTCAAA
1 ATATTTTTAAAGGATGATTATTCAAA
286546 ATAT
1 ATAT
286550 GATTTTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (26 bp):
ATATTTTTAAAGGATGATTATTCAAA
Found at i:287898 original size:22 final size:21
Alignment explanation
Indices: 287873--287951 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 21
287863 AAGTTAAAAC
287873 TTTTTCAATGAAAAGACTTAAT
1 TTTTTC-ATGAAAAGACTTAAT
*
287895 TTTTTGAT-AAAAGAACTTAAT
1 TTTTTCATGAAAAG-ACTTAAT
* *
287916 TGTTTTCATGAAATGATTTAATT
1 T-TTTTCATGAAAAGACTTAA-T
*
287939 TTTTTCATAAAAA
1 TTTTTCATGAAAA
287952 TAATTGTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.11
21 10 0.21
22 26 0.55
23 6 0.13
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (21 bp):
TTTTTCATGAAAAGACTTAAT
Found at i:288023 original size:61 final size:62
Alignment explanation
Indices: 287942--288060 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 62
287932 TTTAATTTTT
* * *
287942 TTCATAAAAATAATTGTTGAATAGATATGATTGAACGG-TGAAACTTTAAATAAAAAATTAA
1 TTCATAAAAAGAATTGTTGAATAGATATGATTAAACGGATGAAACTTTAAACAAAAAATTAA
* * * *
288003 TTCATGAAAAGAATTGTTGAATATATATGATTAAATGGATGTAACTTTAAACAAAAAA
1 TTCATAAAAAGAATTGTTGAATAGATATGATTAAACGGATGAAACTTTAAACAAAAAA
288061 AATAAATCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 33 0.66
62 17 0.34
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (62 bp):
TTCATAAAAAGAATTGTTGAATAGATATGATTAAACGGATGAAACTTTAAACAAAAAATTAA
Found at i:288875 original size:20 final size:20
Alignment explanation
Indices: 288852--288931 Score: 151
Period size: 20 Copynumber: 4.0 Consensus size: 20
288842 TGAAAATCGT
288852 ATTGCGATAGTACTGTTTAC
1 ATTGCGATAGTACTGTTTAC
288872 ATTGCGATAGTACTGTTTAC
1 ATTGCGATAGTACTGTTTAC
*
288892 ATTGCGATAGTATTGTTTAC
1 ATTGCGATAGTACTGTTTAC
288912 ATTGCGATAGTACTGTTTAC
1 ATTGCGATAGTACTGTTTAC
288932 CTATATTGGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTGCGATAGTACTGTTTAC
Found at i:288997 original size:20 final size:20
Alignment explanation
Indices: 288968--289008 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
288958 TTGAAAATCG
*
288968 CATTGTGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
*
288988 CATTGCGATAGTATTGTTTA
1 CATTGCGATAGTACTGTTTA
289008 C
1 C
289009 CTATATCGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (20 bp):
CATTGCGATAGTACTGTTTA
Found at i:289006 original size:117 final size:117
Alignment explanation
Indices: 288796--289008 Score: 363
Period size: 117 Copynumber: 1.8 Consensus size: 117
288786 GAAATTCGCG
** * * *
288796 TTGCGATAGTTGTGTTTACTTATATTGGTAATTAGCGTTGCGAATTTGAAAATCGTATTGCGATA
1 TTGCGATAGTACTGTTTACCTATATTGGTAATTAGCGTTACGAATTTGAAAATCGCATTGCGATA
288861 GTACTGTTTACATTGCGATAGTACTGTTTACATTGCGATAGTATTGTTTACA
66 GTACTGTTTACATTGCGATAGTACTGTTTACATTGCGATAGTATTGTTTACA
*
288913 TTGCGATAGTACTGTTTACCTATATTGGTAATTAGCGTTACGAATTTGAAAATCGCATTGTGATA
1 TTGCGATAGTACTGTTTACCTATATTGGTAATTAGCGTTACGAATTTGAAAATCGCATTGCGATA
*
288978 GTACTGTTTACATTGCGATAGTATTGTTTAC
66 GTACTGTTTACATTGCGATAGTACTGTTTAC
289009 CTATATCGGT
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 89 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (117 bp):
TTGCGATAGTACTGTTTACCTATATTGGTAATTAGCGTTACGAATTTGAAAATCGCATTGCGATA
GTACTGTTTACATTGCGATAGTACTGTTTACATTGCGATAGTATTGTTTACA
Found at i:289020 original size:77 final size:77
Alignment explanation
Indices: 288890--289086 Score: 304
Period size: 77 Copynumber: 2.5 Consensus size: 77
288880 AGTACTGTTT
* * * *
288890 ACATTGCGATAGTATTGTTTACATTGCGATAGTACTGTTTACCTATATTGGTAATTAGCGTTACG
1 ACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATATCGGTAATTAACGTTACA
*
288955 AATTTGAAAATC
66 AATTTGAAAAAC
* * *
288967 GCATTGTGATAGTACTGTTTACATTGCGATAGTATTGTTTACCTATATCGGTAATTAACGTTACA
1 ACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATATCGGTAATTAACGTTACA
289032 AATTTGAAAAAC
66 AATTTGAAAAAC
*
289044 ACATTGCGATAGTACTGTTTACATTGCGATATTTACTGTTTAC
1 ACATTGCGATAGTACTGTTTACATTGCGATA-GTACTGTTTAC
289087 ATTGCGATAG
Statistics
Matches: 107, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
77 98 0.92
78 9 0.08
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (77 bp):
ACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATATCGGTAATTAACGTTACA
AATTTGAAAAAC
Found at i:289082 original size:21 final size:20
Alignment explanation
Indices: 289044--289126 Score: 130
Period size: 20 Copynumber: 4.1 Consensus size: 20
289034 TTTGAAAAAC
289044 ACATTGCGATAGTACTGTTT
1 ACATTGCGATAGTACTGTTT
*
289064 ACATTGCGATATTTACTGTTT
1 ACATTGCGATA-GTACTGTTT
289085 ACATTGCGATAGTACTGTTT
1 ACATTGCGATAGTACTGTTT
* *
289105 ACATTACGATAGTACTATTT
1 ACATTGCGATAGTACTGTTT
289125 AC
1 AC
289127 TTCACAATGC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 39 0.67
21 19 0.33
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (20 bp):
ACATTGCGATAGTACTGTTT
Found at i:289918 original size:2 final size:2
Alignment explanation
Indices: 289911--289944 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
289901 TAATATGGCC
289911 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
289945 CCCAAACGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:290424 original size:133 final size:133
Alignment explanation
Indices: 290177--290511 Score: 388
Period size: 133 Copynumber: 2.5 Consensus size: 133
290167 ACTTCCCTGT
* * * * *
290177 TCTTCAGGGAAGATTGAATTGGACTTGATTTGCTTCACTGCTCTTTAGGAATACCAAATCTAAAA
1 TCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTTAGGAACACCAAATTTGAAA
* * * * * * **
290242 TAAAGAGGATCTACTCCACTATTGTTTAATGGAGATCAGACTCGTAGAATTGTGATCCACTTCGT
66 GAAAGAGAATCTACTCCACTACTCTTTAAGGGAGATCAGACTCGTAGAATTGTGATCCACTCCAC
290307 TGC
131 TGC
*
290310 TCTTTAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTTAGGAACACCAAATTTGAAA
1 TCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTTAGGAACACCAAATTTGAAA
* * * *
290375 G-AAGAAGAAT-TGCTTCACTACTCTTTAGGGGAGATCAGACTCAAG-AGAATTTTGATCCACTC
66 GAAAG-AGAATCTACTCCACTACTCTTTAAGGGAGATCAGACTC--GTAGAATTGTGATCCACTC
290437 CACTGC
128 CACTGC
* * * * * * *
290443 TCTTCAGGGAAGATTGAATCAAATTTGATTTGATTCGCTACTCTTCAGGAAGACCAAATCTTGAA
1 TCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTTAGGAACACCAAAT-TTGAA
290508 AGAA
65 AGAA
290512 TAAAAATTTG
Statistics
Matches: 171, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
132 29 0.17
133 133 0.78
134 8 0.05
135 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (133 bp):
TCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTTAGGAACACCAAATTTGAAA
GAAAGAGAATCTACTCCACTACTCTTTAAGGGAGATCAGACTCGTAGAATTGTGATCCACTCCAC
TGC
Found at i:290579 original size:133 final size:133
Alignment explanation
Indices: 290309--290584 Score: 283
Period size: 133 Copynumber: 2.1 Consensus size: 133
290299 CACTTCGTTG
* * * * *
290309 CTCTTTAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTTAGGAACACCAAATTTGAA
1 CTCTTCAGGGAAGATTGAATCAAACTTGATTTGATTCACTACTCTTCAGGAACACCAAATTTGAA
* * * *
290374 AGAAGAAGAATTGCTTCACTACTCTTTAGGGGAGATCAGACTCAAGAGAATTTTGATCCACTCCA
66 AGAAGAAAAATTGCTTCACTACTCTTTAGGGGAGATCAGAATCAACAGAAATTTGATCCACTCCA
**
290439 CTG
131 CCA
* * *
290442 CTCTTCAGGGAAGATTGAATCAAATTTGATTTGATTCGCTACTCTTCAGGAAGACCAAATCTTGA
1 CTCTTCAGGGAAGATTGAATCAAACTTGATTTGATTCACTACTCTTCAGGAACACCAAAT-TTGA
* * * * * * **
290507 AAGAATAAAAATTTG-TTC-C-ATTTTTTCGGGTA-ATCAGATATCTTACAGAAATTTGATTTAC
65 AAGAAGAAAAA-TTGCTTCACTACTCTTTAGGGGAGATCAGA-ATC-AACAGAAATTTGATCCAC
290568 TCCACCA
127 TCCACCA
290575 CTCTTC-GGGA
1 CTCTTCAGGGA
290585 GGAGCTAAAT
Statistics
Matches: 117, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
131 6 0.05
132 15 0.13
133 77 0.66
134 16 0.14
135 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (133 bp):
CTCTTCAGGGAAGATTGAATCAAACTTGATTTGATTCACTACTCTTCAGGAACACCAAATTTGAA
AGAAGAAAAATTGCTTCACTACTCTTTAGGGGAGATCAGAATCAACAGAAATTTGATCCACTCCA
CCA
Found at i:291911 original size:6 final size:6
Alignment explanation
Indices: 291895--291955 Score: 52
Period size: 7 Copynumber: 9.3 Consensus size: 6
291885 TGATTTATTT
291895 TTTTTC ATTTTTC -TTTTC TTTTTCC TTTTTCC TTTTTCC TTTTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTT-C TTTTT-C TTTTT-C --TTTTTC
*
291942 ATTTTC TTTTTC TT
1 TTTTTC TTTTTC TT
291956 CCATCCTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
5 5 0.10
6 16 0.33
7 21 0.44
8 1 0.02
9 5 0.10
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:291911 original size:14 final size:14
Alignment explanation
Indices: 291894--291952 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 14
291884 TTGATTTATT
291894 TTTTTTCATTTTTC
1 TTTTTTCATTTTTC
291908 --TTTTC-TTTTTC
1 TTTTTTCATTTTTC
* *
291919 CTTTTTCCTTTTTCC
1 TTTTTTCATTTTT-C
291934 TTTTTTTCA-TTTTC
1 -TTTTTTCATTTTTC
291948 TTTTT
1 TTTTT
291953 CTTCCATCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
11 6 0.16
12 5 0.13
13 10 0.26
14 6 0.16
15 5 0.13
16 6 0.16
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTCATTTTTC
Found at i:291918 original size:18 final size:19
Alignment explanation
Indices: 291895--291930 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
291885 TGATTTATTT
291895 TTTTTCATTTTT-CTTTTC
1 TTTTTCATTTTTCCTTTTC
*
291913 TTTTTCCTTTTTCCTTTT
1 TTTTTCATTTTTCCTTTT
291931 TCCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTCATTTTTCCTTTTC
Found at i:291946 original size:7 final size:7
Alignment explanation
Indices: 291895--291938 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
291885 TGATTTATTT
*
291895 TTTTTCA
1 TTTTTCC
291902 TTTTT-C
1 TTTTTCC
291908 -TTTT-C
1 TTTTTCC
291913 TTTTTCC
1 TTTTTCC
291920 TTTTTCC
1 TTTTTCC
291927 TTTTTCC
1 TTTTTCC
291934 TTTTT
1 TTTTT
291939 TTCATTTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
5 5 0.15
6 4 0.12
7 25 0.74
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCC
Found at i:302848 original size:18 final size:18
Alignment explanation
Indices: 302825--302871 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
302815 TATAATTTAT
*
302825 CCCGAAGTACCACTATGC
1 CCCGAAGGACCACTATGC
*
302843 CCCGAAGGACCACTATGT
1 CCCGAAGGACCACTATGC
*
302861 CCAGAAGGACC
1 CCCGAAGGACC
302872 GCATATCACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.36, G:0.21, T:0.13
Consensus pattern (18 bp):
CCCGAAGGACCACTATGC
Found at i:306853 original size:9 final size:9
Alignment explanation
Indices: 306830--306870 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
306820 TTCTGATTTG
306830 CTTTCTTTTT
1 CTTT-TTTTT
306840 C-TTTTTTT
1 CTTTTTTTT
306848 CTTTTTTTT
1 CTTTTTTTT
*
306857 ATTTTTTTT
1 CTTTTTTTT
306866 CTTTT
1 CTTTT
306871 GGCTTTCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 6 0.21
9 21 0.75
10 1 0.04
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.85
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:311576 original size:28 final size:28
Alignment explanation
Indices: 311536--311591 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
311526 ACCACTGTTG
*
311536 CTTTCAAGCACTGACTCGACGATATAAT
1 CTTTCAAGCACTGACTCGACAATATAAT
* * *
311564 CTTTCAAGTACTGGCTTGACAATATAAT
1 CTTTCAAGCACTGACTCGACAATATAAT
311592 GTAAACGAAG
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:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (28 bp):
CTTTCAAGCACTGACTCGACAATATAAT
Found at i:315657 original size:32 final size:30
Alignment explanation
Indices: 315615--315687 Score: 101
Period size: 32 Copynumber: 2.4 Consensus size: 30
315605 AGAGTCGAGG
* *
315615 GTTACCTATGTCCTTCGGGACATATGGGCA
1 GTTACCTATGTCCTTCGAGACATATGGACA
*
315645 GGATTACCTATGTCCTTTGAGACATATGGACA
1 -G-TTACCTATGTCCTTCGAGACATATGGACA
315677 GTTACCTATGT
1 GTTACCTATGT
315688 TCTTATGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 10 0.26
31 2 0.05
32 26 0.68
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGAGACATATGGACA
Found at i:316596 original size:25 final size:25
Alignment explanation
Indices: 316568--316628 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
316558 ACTGTCTTGC
* *
316568 TAATAGAATTACGATTATTATGTTA
1 TAATAGAATTAAGATTATTACGTTA
316593 TAATAGAATTAAGATTATTACGTTA
1 TAATAGAATTAAGATTATTACGTTA
316618 TAATAGAATTA
1 TAATAGAATTA
316629 TGATGATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.41
Consensus pattern (25 bp):
TAATAGAATTAAGATTATTACGTTA
Found at i:320146 original size:18 final size:19
Alignment explanation
Indices: 320116--320151 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
320106 CGATAAAATG
320116 AATTAATGATAATGATATT
1 AATTAATGATAATGATATT
*
320135 AATTAA-GATAATTATAT
1 AATTAATGATAATGATAT
320152 ACATGTGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
AATTAATGATAATGATATT
Found at i:323954 original size:32 final size:30
Alignment explanation
Indices: 323913--324001 Score: 108
Period size: 32 Copynumber: 2.9 Consensus size: 30
323903 GAGTCGATGG
323913 TTACCTATGTCCTTCGAGACATATGGACAGGA
1 TTACCTATGTCCTTCGAGACATATGGACA--A
* *
323945 TTACCTATGTCCTTCGGGACATATAGACAA
1 TTACCTATGTCCTTCGAGACATATGGACAA
* *
323975 TTACTTATGTTCTTC-AGAACATATGGA
1 TTACCTATGTCCTTCGAG-ACATATGGA
324002 TAGTGGTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.02
30 22 0.44
32 27 0.54
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (30 bp):
TTACCTATGTCCTTCGAGACATATGGACAA
Found at i:324018 original size:24 final size:22
Alignment explanation
Indices: 323986--324044 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 22
323976 TACTTATGTT
* *
323986 CTTCAGAACATATGGATAGTGGTC
1 CTTCGGAACATATGCATA--GGTC
324010 CTTCGGAACATATGCATAGGTC
1 CTTCGGAACATATGCATAGGTC
* *
324032 ATTCGGGACATAT
1 CTTCGGAACATAT
324045 TTCACATGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 15 0.48
24 16 0.52
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (22 bp):
CTTCGGAACATATGCATAGGTC
Found at i:324036 original size:22 final size:23
Alignment explanation
Indices: 323991--324044 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
323981 ATGTTCTTCA
* *
323991 GAACATATGGATAGTGGTCCTTCG
1 GAACATATGCATAG-GGTCATTCG
324015 GAACATATGCATA-GGTCATTCG
1 GAACATATGCATAGGGTCATTCG
*
324037 GGACATAT
1 GAACATAT
324045 TTCACATGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 15 0.56
24 12 0.44
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (23 bp):
GAACATATGCATAGGGTCATTCG
Found at i:325912 original size:16 final size:16
Alignment explanation
Indices: 325891--325922 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
325881 TTAAGGGGTC
*
325891 AATTTAAAATTTTAAA
1 AATTTAAAAGTTTAAA
325907 AATTTAAAAGTTTAAA
1 AATTTAAAAGTTTAAA
325923 TTAAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTTAAAAGTTTAAA
Found at i:330115 original size:21 final size:24
Alignment explanation
Indices: 330086--330159 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
330076 TGTATACTTC
*
330086 TCTTCGATT-TGT-GCTTACTGCT
1 TCTTCGATTGTCTGGCTTACTGCT
330108 TCTT-GATTGGTCTGGCTTACTGCT
1 TCTTCGATT-GTCTGGCTTACTGCT
330132 TCTTC-ATTGTTCTGG-TATACTGCT
1 TCTTCGATTG-TCTGGCT-TACTGCT
330156 TCTT
1 TCTT
330160 TGTTGTTCCT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
21 4 0.09
22 4 0.09
23 4 0.09
24 33 0.73
ACGTcount: A:0.09, C:0.22, G:0.19, T:0.50
Consensus pattern (24 bp):
TCTTCGATTGTCTGGCTTACTGCT
Found at i:330125 original size:24 final size:24
Alignment explanation
Indices: 330098--330159 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
330088 TTCGATTTGT
*
330098 GCTTACTGCTTCTTGATTGGTCTG
1 GCTTACTGCTTCTTCATTGGTCTG
*
330122 GCTTACTGCTTCTTCATTGTTCTG
1 GCTTACTGCTTCTTCATTGGTCTG
330146 G-TATACTGCTTCTT
1 GCT-TACTGCTTCTT
330160 TGTTGTTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.48
Consensus pattern (24 bp):
GCTTACTGCTTCTTCATTGGTCTG
Found at i:330165 original size:24 final size:24
Alignment explanation
Indices: 330098--330167 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
330088 TTCGATTTGT
*
330098 GCTTACTGCTTC-TTGATTGGTCTG
1 GCTTACTGCTTCTTTG-TTGTTCTG
**
330122 GCTTACTGCTTCTTCATTGTTCTG
1 GCTTACTGCTTCTTTGTTGTTCTG
330146 G-TATACTGCTTCTTTGTTGTTC
1 GCT-TACTGCTTCTTTGTTGTTC
330168 CTGTTCTGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 1 0.03
24 37 0.95
25 1 0.03
ACGTcount: A:0.09, C:0.21, G:0.20, T:0.50
Consensus pattern (24 bp):
GCTTACTGCTTCTTTGTTGTTCTG
Found at i:331929 original size:3 final size:3
Alignment explanation
Indices: 331921--331946 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
331911 TGCTGGTGAT
331921 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
331947 AACCCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:339803 original size:67 final size:67
Alignment explanation
Indices: 339679--339812 Score: 171
Period size: 67 Copynumber: 2.0 Consensus size: 67
339669 ACAACTTCGA
** * * * *
339679 GAATTGACACGTAAGATGGAGGAAAAAGATAAGGTCATGAAAGAAGCTTCTGTCCAAGCAAACAA
1 GAATTGACACAAAAGATGCAGGAAAAAGACAAGGCCATGAAAGAAGCTTCTGGCCAAGCAAACAA
339744 TG
66 TG
* * *
339746 GAATTGACACAAAAGATGCAGGAAAAAGACAATGCCATGAAAGAAG-TTGTTGGCCAAGCAAATA
1 GAATTGACACAAAAGATGCAGGAAAAAGACAAGGCCATGAAAGAAGCTT-CTGGCCAAGCAAACA
339810 ATG
65 ATG
339813 TGGCTCATAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 2 0.04
67 55 0.96
ACGTcount: A:0.45, C:0.13, G:0.25, T:0.17
Consensus pattern (67 bp):
GAATTGACACAAAAGATGCAGGAAAAAGACAAGGCCATGAAAGAAGCTTCTGGCCAAGCAAACAA
TG
Found at i:342497 original size:18 final size:18
Alignment explanation
Indices: 342474--342518 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
342464 GATGCAATTA
342474 GTATCGATATTGATGTGG
1 GTATCGATATTGATGTGG
342492 GTATCGATATTGATGTGG
1 GTATCGATATTGATGTGG
342510 GTATCGATA
1 GTATCGATA
342519 CCATGGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (18 bp):
GTATCGATATTGATGTGG
Found at i:343011 original size:54 final size:54
Alignment explanation
Indices: 342937--343247 Score: 307
Period size: 54 Copynumber: 5.8 Consensus size: 54
342927 TTATAGAATG
* * * *
342937 GGCACTATGTGTTCAACTTAAGAAATTCATAATAGGTTTATAAATTTTTATATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTCATATT
* * *
342991 GGCACTGTGTGTCCAACTTAAGAAATTCATAACAAGTTTATAAATTTTCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTCATATT
* **
343045 GACACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTTGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTCATATT
* ** * * * *
343099 GGCATTGTGTGTTTAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATAGT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTCATATT
** ** * * * *** * *
343153 GGCACTAAGTGTGCAACCCATGAAATTCATAATATGTTTATGAATGACCTTATC
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTCATATT
** ** * *
343207 GGCACTAAGTGTGCAACCCATGAAATTCATAATATGTTTAT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTAT
343248 GAACGACCGT
Statistics
Matches: 224, Mismatches: 33, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 224 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (54 bp):
GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTCATATT
Found at i:343072 original size:108 final size:108
Alignment explanation
Indices: 342939--343193 Score: 339
Period size: 108 Copynumber: 2.4 Consensus size: 108
342929 ATAGAATGGG
* *
342939 CACTATGTGTTCAACTTAAGAAATTCATAATAGGTTTATAAATTTTTATATTGGCACTGTGTGTC
1 CACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTTATATTGGCACTGTGTGTC
* * * *
343004 CAACTTAAGAAATTCATAACAAGTTTATAAATTTTCGTATTGA
66 CAACCTAAGAAATTCATAACAAGTTTATAAATTTCCATAGTGA
* * * *
343047 CACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTTGTATTGGCATTGTGTGTT
1 CACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTTATATTGGCACTGTGTGTC
* * * *
343112 TAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATAGTGG
66 CAACCTAAGAAATTCATAACAAGTTTATAAATTTCCATAGTGA
* ** * *
343155 CACTAAGTGTGCAACCCATGAAATTCATAATATGTTTAT
1 CACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTAT
343194 GAATGACCTT
Statistics
Matches: 127, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
108 127 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.39
Consensus pattern (108 bp):
CACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTTATATTGGCACTGTGTGTC
CAACCTAAGAAATTCATAACAAGTTTATAAATTTCCATAGTGA
Found at i:343222 original size:162 final size:162
Alignment explanation
Indices: 342944--343247 Score: 356
Period size: 162 Copynumber: 1.9 Consensus size: 162
342934 ATGGGCACTA
* * ** * ** *
342944 TGTGTTCAACTTAAGAAATTCATAATAGGTTTATAAATTTTTATATTGGCACTGTGTGTCCAACT
1 TGTGTTCAACCTAAGAAATTCATAATAAGTTTATAAATTTCCATAGTGGCACTAAGTGTCCAACC
* *** * ** **
343009 TAAGAAATTCATAACAAGTTTATAAATTTTCGTATTGACACTGTGTGTGCAACTTAAGAAATTCA
66 CAAGAAATTCATAACAAGTTTATAAATGACCGTATCGACACTAAGTGTGCAACCCAAGAAATTCA
343074 TAATAAGTTTATAAATTTTTGTATTGGCATTG
131 TAATAAGTTTATAAATTTTTGTATTGGCATTG
* * *
343106 TGTGTTTAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATAGTGGCACTAAGTGTGCAACC
1 TGTGTTCAACCTAAGAAATTCATAATAAGTTTATAAATTTCCATAGTGGCACTAAGTGTCCAACC
* * * * * * *
343171 CATGAAATTCATAATATGTTTATGAATGACCTTATCGGCACTAAGTGTGCAACCCATGAAATTCA
66 CAAGAAATTCATAACAAGTTTATAAATGACCGTATCGACACTAAGTGTGCAACCCAAGAAATTCA
*
343236 TAATATGTTTAT
131 TAATAAGTTTAT
343248 GAACGACCGT
Statistics
Matches: 114, Mismatches: 28, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
162 114 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (162 bp):
TGTGTTCAACCTAAGAAATTCATAATAAGTTTATAAATTTCCATAGTGGCACTAAGTGTCCAACC
CAAGAAATTCATAACAAGTTTATAAATGACCGTATCGACACTAAGTGTGCAACCCAAGAAATTCA
TAATAAGTTTATAAATTTTTGTATTGGCATTG
Found at i:343347 original size:54 final size:54
Alignment explanation
Indices: 343120--343338 Score: 309
Period size: 54 Copynumber: 4.1 Consensus size: 54
343110 TTTAACCTAA
* *** *
343120 GAAATTCATAATAAGTTTATGAATTTCCATAGT-GGCACTAAGTGTGCAACCCAT
1 GAAATTCATAATATGTTTATGAACGACCGTA-TCGGCACTAAGTGTGCAACCCAT
* *
343174 GAAATTCATAATATGTTTATGAATGACCTTATCGGCACTAAGTGTGCAACCCAT
1 GAAATTCATAATATGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCAT
*
343228 GAAATTCATAATATGTTTATGAACGACCGTATCGACACTAAGTGTGCAACCCACT
1 GAAATTCATAATATGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCA-T
* *
343283 -AAATTCATAATATGTTTATGAACGACCGTATCGGCACTACGTGTGCACCCCA-
1 GAAATTCATAATATGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCAT
343335 GAAA
1 GAAA
343339 ACTTATAATG
Statistics
Matches: 152, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
53 4 0.03
54 147 0.97
55 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (54 bp):
GAAATTCATAATATGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCAT
Found at i:344938 original size:29 final size:29
Alignment explanation
Indices: 344905--345391 Score: 175
Period size: 29 Copynumber: 14.9 Consensus size: 29
344895 TTGTTATTCA
* * *
344905 TGACTCCCTCGCGAAGAGGAGTTAATCCT
1 TGACTTCCTCGTGAAGAGGAGTCAATCCT
*
344934 TGACTTCCTCGTGAAGAGAAGTCAATCTTTGTAATTCT
1 TGACTTCCTCGTGAAGAGGAGTCAATC---------CT
* **
344972 TGACTCCCTCACGAAGAGGAGTCAATCCT
1 TGACTTCCTCGTGAAGAGGAGTCAATCCT
*
345001 TGACTTCCTCGTGAAGAGAAGTCAATCCT
1 TGACTTCCTCGTGAAGAGGAGTCAATCCT
* * *
345030 TGACTTCCTCGTGAAGAGAATTCAATCTTT
1 TGACTTCCTCGTGAAGAGGAGTCAATC-CT
*
345060 ATTATTCCTAACTCCCTCGTGAAGAGGAGTCAATCCT
1 -TGA---CT---T-CCTCGTGAAGAGGAGTCAATCCT
** * * * *
345097 TGACTTTATTGTGAAAAGAAGTCAATCAT
1 TGACTTCCTCGTGAAGAGGAGTCAATCCT
345126 TGTTATTCTTGAATCCCTCGTGAAGAGGAGTCAATCCT
1 TG--A--C-T---T-CCTCGTGAAGAGGAGTCAATCCT
* *
345164 TGACTTCCTTGTGAAGAGAAGTCAATCTTTGTTATTCT
1 TGACTTCCTCGTGAAGAGGAGTCAATC---------CT
*
345202 TGACTCCCTCGTGAAGAGGAGTCAATCCT
1 TGACTTCCTCGTGAAGAGGAGTCAATCCT
* *
345231 TGACTTCCTCGTTAAGAGAAGTCAATCTTTGTTATTCT
1 TGACTTCCTCGTGAAGAGGAGTCAATC---------CT
*
345269 TGACTCCCTCGTGAAGAGGAGTCAATCAC-
1 TGACTTCCTCGTGAAGAGGAGTCAATC-CT
* * * **
345298 TGACTTCCTCGTAAAAAGAAGTCAAACTTTT
1 TGACTTCCTCGTGAAGAGGAGTC-AA-TCCT
* * *
345329 TTATTCATGACTCCATTGTGAAGAGGAGCCAATCCT
1 TGA--C-T---TCC-TCGTGAAGAGGAGTCAATCCT
*
345365 TGACTTCCTCGTGAAGAGAAGTCAATC
1 TGACTTCCTCGTGAAGAGGAGTCAATC
345392 TTTGTTCTTC
Statistics
Matches: 342, Mismatches: 61, Indels: 110
0.67 0.12 0.21
Matches are distributed among these distances:
29 175 0.51
30 9 0.03
31 6 0.02
33 6 0.02
34 6 0.02
36 7 0.02
37 8 0.02
38 125 0.37
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (29 bp):
TGACTTCCTCGTGAAGAGGAGTCAATCCT
Found at i:344959 original size:67 final size:67
Alignment explanation
Indices: 344865--345027 Score: 247
Period size: 67 Copynumber: 2.4 Consensus size: 67
344855 GAATCTTCAA
* * * * * *
344865 CTTGAC-TCTCTCGCGAAGAGGATTCAATCTTTGTTATTCATGACTCCCTCGCGAAGAGGAGTTA
1 CTTGACTTC-CTCGTGAAGAGAAGTCAATCTTTGTAATTCATGACTCCCTCACGAAGAGGAGTCA
344929 ATC
65 ATC
*
344932 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTAATTCTTGACTCCCTCACGAAGAGGAGTCAA
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTAATTCATGACTCCCTCACGAAGAGGAGTCAA
344997 TC
66 TC
344999 CTTGACTTCCTCGTGAAGAGAAGTCAATC
1 CTTGACTTCCTCGTGAAGAGAAGTCAATC
345028 CTTGACTTCC
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
67 86 0.98
68 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (67 bp):
CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTAATTCATGACTCCCTCACGAAGAGGAGTCAA
TC
Found at i:345074 original size:96 final size:96
Alignment explanation
Indices: 344905--345123 Score: 303
Period size: 96 Copynumber: 2.3 Consensus size: 96
344895 TTGTTATTCA
* * * * *
344905 TGACTCCCTCGCGAAGAGGAGTTAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTAATT
1 TGACTTCCTCGTGAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTATAATT
* *
344970 CTTGACTCCCTCACGAAGAGGAGTCAATCCT
66 CCTAACTCCCTCACGAAGAGGAGTCAATCCT
* *
345001 TGACTTCCTCGTGAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAATTCAATCTTTATTATT
1 TGACTTCCTCGTGAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTATAATT
**
345066 CCTAACTCCCTCGTGAAGAGGAGTCAATCCT
66 CCTAACTCCCTCACGAAGAGGAGTCAATCCT
** * *
345097 TGACTTTATTGTGAAAAGAAGTCAATC
1 TGACTTCCTCGTGAAGAGAAGTCAATC
345124 ATTGTTATTC
Statistics
Matches: 108, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 108 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (96 bp):
TGACTTCCTCGTGAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTATAATT
CCTAACTCCCTCACGAAGAGGAGTCAATCCT
Found at i:345078 original size:67 final size:67
Alignment explanation
Indices: 345001--346583 Score: 1861
Period size: 67 Copynumber: 23.9 Consensus size: 67
344991 AGTCAATCCT
* * * *
345001 TGACTTCCTCGTGAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAATTCAATCTTTATTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
345066 CC
66 CC
* ** * * *
345068 TAACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTTATTGTGAAAAGAAGTCAATCATTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
345133 CT
66 CC
* *
345135 TGAATCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTTGTGAAGAGAAGTCAATCTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
345200 CT
66 CC
*
345202 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTTAAGAGAAGTCAATCTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
345267 CT
66 CC
* * * *
345269 TGACTCCCTCGTGAAGAGGAGTCAATCAC-TGACTTCCTCGTAAAAAGAAGTCAAACTTTTTTAT
1 TGACTCCCTCGTGAAGAGGAGTCAATC-CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTAT
*
345333 TCA
65 TCC
* * * *
345336 TGACTCCATTGTGAAGAGGAGCCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTCTT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
345401 CT
66 CC
* * ** * * * * *
345403 TTATTCCCTCGCAAAGAGGATTAAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTATAATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
345468 CT
66 CC
* * *
345470 TGACTCCCTCGCGAAGAGGAGTCAATCCTTAACTTCCTCATGAAGAGAAGTCAATCTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
345535 CC
66 CC
* ** * * * * * **
345537 TGAATCCCTAATGAAGATGAGTCAATCCTTGACTTGCTTGTGAAAAGAAATCAATAATTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
345602 CC
66 CC
** * * * *
345604 TGACTCATTCATGAAGACGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTCAATCCTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
**
345669 TT
66 CC
* * *
345671 TGACTCCCTCATGAATATGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
345736 CC
66 CC
* * * * * * * * *
345738 TGACTCCCTTGTTAAGAGGAGTCAATCATCGACTTCCTTGAGAAGATAAATCAATATTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
345803 CC
66 CC
* * * *
345805 TGACTCACTCGTGAAGAGGAGTCAATCCTTGACTTCCTCATGAAAACAAGTCAATCTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
345870 CT
66 CC
* *
345872 TAACTCCCTCGTGAAGAGGAGTCAATCCTTGAATTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
345937 CT
66 CC
** * * *
345939 TGACTCCCTCGCAAAAAGGATTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATTTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
**
346004 AT
66 CC
* * * * * *
346006 TGACTCCTTCGTGGAGA-GAGTCAATCCTCGACTTTCTCGTAAAGAGAAGTCAGTCTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
346070 CC
66 CC
* * * *
346072 TAACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTTGTGAAGAAAAGTCAATCTTTTTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
346137 CC
66 CC
* * *
346139 TGACTCCCTCGTGAAGAGGAGTCAATCATTGACTTCCTTGTGAAGAGAATTCAATCTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
346204 CC
66 CC
* ** * * * *
346206 TGGCTCCCTCACGAAGATGAGTCAATCATTGACTTTCTCGTGAAGAGAAGTCAATCTTTTTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
346271 CC
66 CC
* * * * ** * * ** * *
346273 TGGCTCTCTCGTAAAAAATAGTCAATCATTAACTTCCTC-ACAGAGAGGAGTCAATCCTTG--A-
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGA-AGAGAAGTCAATCTTTGTTAT
346334 --C
65 TCC
* * * *
346335 T---T-CCTCGCGGAGATGAGTCAATCCATT-ACTTCCTCGTGAAGAGTAGTCAATCTTTGTTAT
1 TGACTCCCTCGTGAAGAGGAGTCAATCC-TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTAT
346395 T-C
65 TCC
* *
346397 ---C-CCCTCGTGAAGAGGAGTCAATCCTCGACTTTCTCGTGAAGAGAAGTCAATCTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
346458 CC
66 CC
* * *
346460 TGAATCCCTCGTGAAGAGGAGTCAATCCTTGAGTTCCTCGTGAAGATAAGTCAATCTTTGTTATT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
346525 CC
66 CC
* * *
346527 TGACTCCCTCGCGAAGAGGAGTCAATCCTTGACTTCCTCATGAAGAGAAATCAATCT
1 TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCT
346584 CTAAGTATGG
Statistics
Matches: 1287, Mismatches: 211, Indels: 36
0.84 0.14 0.02
Matches are distributed among these distances:
58 37 0.03
59 4 0.00
60 1 0.00
61 1 0.00
62 54 0.04
63 1 0.00
65 1 0.00
66 57 0.04
67 1130 0.88
68 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (67 bp):
TGACTCCCTCGTGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
CC
Found at i:345136 original size:163 final size:163
Alignment explanation
Indices: 344865--345190 Score: 483
Period size: 163 Copynumber: 2.0 Consensus size: 163
344855 GAATCTTCAA
* * * *
344865 CTTGACTCTCTCGCGAAGAGGATTCAATCTTTGTTATTCATGACTCCCTCGCGAAGAGGAGTTAA
1 CTTGACTCTCTCGCGAAGAGAATTCAATCTTTATTATTCATAACTCCCTCGCGAAGAGGAGTCAA
* * * *
344930 TCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTAATTCTTGACTCCCTCACGAAGAGGAGTC
66 TCCTTGACTTCATCGTGAAAAGAAGTCAATCATTGTAATTCTTGAATCCCTCACGAAGAGGAGTC
344995 AATCCTTGACTTCCTCGTGAAGAGAAGTCAATC
131 AATCCTTGACTTCCTCGTGAAGAGAAGTCAATC
* * *
345028 CTTGACT-TCCTCGTGAAGAGAATTCAATCTTTATTATTCCTAACTCCCTCGTGAAGAGGAGTCA
1 CTTGACTCT-CTCGCGAAGAGAATTCAATCTTTATTATTCATAACTCCCTCGCGAAGAGGAGTCA
* * * **
345092 ATCCTTGACTTTATTGTGAAAAGAAGTCAATCATTGTTATTCTTGAATCCCTCGTGAAGAGGAGT
65 ATCCTTGACTTCATCGTGAAAAGAAGTCAATCATTGTAATTCTTGAATCCCTCACGAAGAGGAGT
*
345157 CAATCCTTGACTTCCTTGTGAAGAGAAGTCAATC
130 CAATCCTTGACTTCCTCGTGAAGAGAAGTCAATC
345191 TTTGTTATTC
Statistics
Matches: 145, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
162 1 0.01
163 144 0.99
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (163 bp):
CTTGACTCTCTCGCGAAGAGAATTCAATCTTTATTATTCATAACTCCCTCGCGAAGAGGAGTCAA
TCCTTGACTTCATCGTGAAAAGAAGTCAATCATTGTAATTCTTGAATCCCTCACGAAGAGGAGTC
AATCCTTGACTTCCTCGTGAAGAGAAGTCAATC
Found at i:345149 original size:38 final size:37
Alignment explanation
Indices: 345107--345296 Score: 151
Period size: 38 Copynumber: 5.5 Consensus size: 37
345097 TGACTTTATT
*
345107 GTGAAAAGAAGTCAATCATTGTTATTCTTGAATCCCTC
1 GTGAAGAGAAGTCAATCATTGTTATTCTTG-ATCCCTC
* * *
345145 GTGAAGAGGAGTCAATCCTTG--A--C-T--T-CCTT
1 GTGAAGAGAAGTCAATCATTGTTATTCTTGATCCCTC
*
345174 GTGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTC
1 GTGAAGAGAAGTCAATCATTGTTATTCTTGA-TCCCTC
* *
345212 GTGAAGAGGAGTCAATCCTTG--A--C-T--T-CCTC
1 GTGAAGAGAAGTCAATCATTGTTATTCTTGATCCCTC
* *
345241 GTTAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTC
1 GTGAAGAGAAGTCAATCATTGTTATTCTTGA-TCCCTC
*
345279 GTGAAGAGGAGTCAATCA
1 GTGAAGAGAAGTCAATCA
345297 CTGACTTCCT
Statistics
Matches: 119, Mismatches: 15, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
29 44 0.37
30 2 0.02
31 2 0.02
33 4 0.03
34 4 0.03
36 2 0.02
37 2 0.02
38 59 0.50
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (37 bp):
GTGAAGAGAAGTCAATCATTGTTATTCTTGATCCCTC
Found at i:345674 original size:38 final size:37
Alignment explanation
Indices: 345632--346102 Score: 97
Period size: 38 Copynumber: 13.9 Consensus size: 37
345622 GAGTCAATCA
*
345632 TTGACTTCCTCGTGAAGAGAAGTCAATCCTTGTTATTT
1 TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTA-TT
* *
345670 TTGACTCCCTCATGAATATG-AGTCAATCC--------
1 TTGACTCCCTCGTGAAGA-GAAGTCAATCCTTGTTATT
* *
345699 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
1 TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
* * * *
345736 CCTGACTCCCTTGTTAAGAGGAGTCAAT-C-----A--
1 -TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
* * * * * * **
345766 TCGACTTCCTTGAGAAGATAAATCAATATTTGTTATT
1 TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
* * *
345803 CCTGACTCACTCGTGAAGAGGAGTCAATCC--------
1 -TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
* * * * *
345833 TTGACTTCCTCATGAAAACAAGTCAATCTTTGTTATT
1 TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
* *
345870 CTTAACTCCCTCGTGAAGAGGAGTCAATCCTTG--A--
1 -TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
* *
345904 ---A-TTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
1 TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
** * * *
345937 CTTGACTCCCTCGCAAAAAGGATTCAATCC--------
1 -TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
* **
345967 TTGACTTCCTCGTGAAGAGAAGTCAATTTTTGTTATT
1 TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
* * * *
346004 ATTGACTCCTTCGTGGAGAG-AGTCAATCCTCG--A-C
1 -TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
* * *
346038 TT---T--CTCGTAAAGAGAAGTCAGTCTTTGTTATT
1 TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
* * *
346070 CCTAACTCCCTCGTGAAGAGGAGTCAATCCTTG
1 -TTGACTCCCTCGTGAAGAGAAGTCAATCCTTG
346103 ACTTCCTTGT
Statistics
Matches: 291, Mismatches: 85, Indels: 114
0.59 0.17 0.23
Matches are distributed among these distances:
28 9 0.03
29 117 0.40
30 2 0.01
31 2 0.01
32 1 0.00
33 3 0.01
35 2 0.01
36 2 0.01
37 10 0.03
38 142 0.49
39 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (37 bp):
TTGACTCCCTCGTGAAGAGAAGTCAATCCTTGTTATT
Found at i:345848 original size:29 final size:29
Alignment explanation
Indices: 345812--345927 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 29
345802 TCCTGACTCA
*
345812 CTCGTGAAGAGGAGTCAATCCTTGACTTC
1 CTCGTGAAGAGAAGTCAATCCTTGACTTC
* * * *
345841 CTCATGAAAACAAGTCAATCTTTGTTATTCTTAACTCC
1 CTCGTGAAGAGAAGTCAATCCTTG--A--C-T---T-C
* *
345879 CTCGTGAAGAGGAGTCAATCCTTGAATTC
1 CTCGTGAAGAGAAGTCAATCCTTGACTTC
345908 CTCGTGAAGAGAAGTCAATC
1 CTCGTGAAGAGAAGTCAATC
345928 TTTGTTATTC
Statistics
Matches: 66, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
29 39 0.59
30 1 0.02
31 1 0.02
33 2 0.03
34 1 0.02
36 1 0.02
37 1 0.02
38 20 0.30
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (29 bp):
CTCGTGAAGAGAAGTCAATCCTTGACTTC
Found at i:346181 original size:29 final size:29
Alignment explanation
Indices: 346139--346194 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
346129 TTTTTATTCC
*
346139 TGACTCCCTCGTGAAGAGGAGTCAATCAT
1 TGACTCCCTCGTGAAGAGAAGTCAATCAT
* * *
346168 TGACTTCCTTGTGAAGAGAATTCAATC
1 TGACTCCCTCGTGAAGAGAAGTCAATC
346195 TTTGTTATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (29 bp):
TGACTCCCTCGTGAAGAGAAGTCAATCAT
Found at i:346370 original size:29 final size:30
Alignment explanation
Indices: 346292--346370 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
346282 CGTAAAAAAT
*
346292 AGTCAAT-CATTAACTTCCTCACAGAGAGG
1 AGTCAATCCATTAACTTCCTCGCAGAGAGG
* * *
346321 AGTCAATCC-TTGACTTCCTCGCGGAGATG
1 AGTCAATCCATTAACTTCCTCGCAGAGAGG
346350 AGTCAATCCATT-ACTTCCTCG
1 AGTCAATCCATTAACTTCCTCG
346371 TGAAGAGTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 41 0.93
30 3 0.07
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (30 bp):
AGTCAATCCATTAACTTCCTCGCAGAGAGG
Found at i:346382 original size:29 final size:28
Alignment explanation
Indices: 346316--346448 Score: 90
Period size: 29 Copynumber: 4.5 Consensus size: 28
346306 TTCCTCACAG
* * *
346316 AGAGGAGTCAATCCTTGACTTCCTCGCGG
1 AGAGTAGTCAATCCTT-ACTTCCTCGTGA
346345 AGA-TGAGTCAATCCATTACTTCCTCGTGA
1 AGAGT-AGTCAATCC-TTACTTCCTCGTGA
*
346374 AGAGTAGTCAATCTTTGTTA-TTCCCCCTCGTGA
1 AGAGTAGTCAATC---CTTACTT---CCTCGTGA
* * *
346407 AGAGGAGTCAATCCTCGACTTTCTCGTGA
1 AGAGTAGTCAATCCT-TACTTCCTCGTGA
*
346436 AGAGAAGTCAATC
1 AGAGTAGTCAATC
346449 TTTGTTATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
29 52 0.62
30 6 0.07
31 4 0.05
32 2 0.02
33 20 0.24
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (28 bp):
AGAGTAGTCAATCCTTACTTCCTCGTGA
Found at i:346483 original size:38 final size:37
Alignment explanation
Indices: 346429--346553 Score: 122
Period size: 38 Copynumber: 3.5 Consensus size: 37
346419 CCTCGACTTT
346429 CTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGAATCC
1 CTCGTGAAGAGAAGTCAATCTTTGTTATTCCTG-ATCC
* * *
346467 CTCGTGAAGAGGAGTCAATCCTTG--A-----G-TTC
1 CTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGATCC
*
346496 CTCGTGAAGATAAGTCAATCTTTGTTATTCCTGACTCC
1 CTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGA-TCC
* *
346534 CTCGCGAAGAGGAGTCAATC
1 CTCGTGAAGAGAAGTCAATC
346554 CTTGACTTCC
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
29 23 0.34
31 2 0.03
36 2 0.03
38 41 0.60
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (37 bp):
CTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGATCC
Found at i:346798 original size:40 final size:40
Alignment explanation
Indices: 346681--346826 Score: 132
Period size: 40 Copynumber: 3.6 Consensus size: 40
346671 TCTTTCAGAT
* *
346681 TTGGTCTTCCTGAAGAGCAGTGAA-CTAAATCAAGTTCGAT
1 TTGGTCTTCCTGAAGAGCAGCGAAGC-AAATCAAGTTCGAA
* * * *
346721 TTGGTCCTCCTGAAGAGCAACAAAGCAAATAAAGTTCGAA
1 TTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGAA
* * * * **
346761 TTGGTCTTCCTAAAGTGCAGCGAAGGAAATCATGTTCGGT
1 TTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGAA
** *
346801 TTAATCTTCCCTGAAGAGCAACGAAG
1 TTGGTCTT-CCTGAAGAGCAGCGAAG
346827 TGGATCAAAT
Statistics
Matches: 83, Mismatches: 21, Indels: 3
0.78 0.20 0.03
Matches are distributed among these distances:
40 68 0.82
41 15 0.18
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (40 bp):
TTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGAA
Found at i:347232 original size:15 final size:16
Alignment explanation
Indices: 347212--347245 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
347202 TAGAATTTCC
347212 TTTTGTTTAG-TTTAT
1 TTTTGTTTAGTTTTAT
*
347227 TTTTGTTTTGTTTTAT
1 TTTTGTTTAGTTTTAT
347243 TTT
1 TTT
347246 GGTTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.09, C:0.00, G:0.12, T:0.79
Consensus pattern (16 bp):
TTTTGTTTAGTTTTAT
Found at i:347279 original size:23 final size:21
Alignment explanation
Indices: 347252--347321 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 21
347242 TTTTGGTTAT
347252 ATATAGTATAGTTTTGAAAAT-
1 ATATA-TATAGTTTTGAAAATA
347273 A-A-ATATAGTTTTGAAAAATA
1 ATATATATAGTTTTG-AAAATA
*
347293 TATATATCATAGTTTTAAAAATA
1 -ATATAT-ATAGTTTTGAAAATA
347316 A-ATATA
1 ATATATA
347322 ATATTAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
18 10 0.24
19 6 0.14
20 2 0.05
21 6 0.14
22 2 0.05
23 8 0.19
24 8 0.19
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (21 bp):
ATATATATAGTTTTGAAAATA
Found at i:347304 original size:24 final size:23
Alignment explanation
Indices: 347269--347321 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
347259 ATAGTTTTGA
*
347269 AAATAAAT-ATAGTTTTGAAAAAT
1 AAATATATCATAGTTTT-AAAAAT
*
347292 ATATATATCATAGTTTTAAAAAT
1 AAATATATCATAGTTTTAAAAAT
347315 AAATATA
1 AAATATA
347322 ATATTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (23 bp):
AAATATATCATAGTTTTAAAAAT
Found at i:347338 original size:16 final size:17
Alignment explanation
Indices: 347307--347339 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
347297 TATCATAGTT
347307 TTAAAAATAAATATAATA
1 TTAAAAAT-AATATAATA
347325 TTAAAAAT-ATATAAT
1 TTAAAAATAATATAAT
347340 TTATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATAATATAATA
Found at i:347349 original size:41 final size:42
Alignment explanation
Indices: 347249--347337 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
347239 TTATTTTGGT
* * *
347249 TATATATAGT-ATAGTTTTGAAAATAAATATAGTTTTGAAAAA
1 TATATATA-TCATAGTTTTAAAAATAAATATAATATTGAAAAA
347291 TATATATATCATAGTTTTAAAAATAAATATAATATT-AAAAA
1 TATATATATCATAGTTTTAAAAATAAATATAATATTGAAAAA
347332 TATATA
1 TATATA
347338 ATTTATGGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 12 0.28
42 31 0.72
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (42 bp):
TATATATATCATAGTTTTAAAAATAAATATAATATTGAAAAA
Found at i:350597 original size:14 final size:15
Alignment explanation
Indices: 350570--350598 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
350560 TAATAAATAT
350570 AAATAACATGATAAA
1 AAATAACATGATAAA
350585 AAATAAC-TGATAAA
1 AAATAACATGATAAA
350599 TGTGTAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (15 bp):
AAATAACATGATAAA
Found at i:350987 original size:38 final size:38
Alignment explanation
Indices: 350921--351341 Score: 451
Period size: 38 Copynumber: 11.3 Consensus size: 38
350911 TTTATACTAT
350921 AAAATCAATTTTTG-AAA-ATATATATTATATAGTTTTG
1 AAAA-CAATTTTTGAAAATATATATATTATATAGTTTTG
** *
350958 AAAACGGTTTTCGAAAATATATATATTATATAGTTTTG
1 AAAACAATTTTTGAAAATATATATATTATATAGTTTTG
**** *
350996 -AATTTTTTTTTGAAAACATATATATAATATATAGTTTTTG
1 AAAACAATTTTTG-AAA-ATATATATATTATATAG-TTTTG
*
351036 AAAAC-ATTTTTGAAAATATATATAATATATAGTTTTTG
1 AAAACAATTTTTGAAAATATATATATTATATAG-TTTTG
*
351074 AAAACAA-TTTTGAAAATATATATAATATATAGTTTTTG
1 AAAACAATTTTTGAAAATATATATATTATATAG-TTTTG
* * *
351112 AAAA-TATTTTTGAAAATGTATATAATATATAGTTTTG
1 AAAACAATTTTTGAAAATATATATATTATATAGTTTTG
* *
351149 AAAATATTTTTTG-AAA-ATATATATTATATAGTTTT-
1 AAAACAATTTTTGAAAATATATATATTATATAGTTTTG
351184 AAAACAATTTTTG-AAA-ATATATATTATATAGTTTT-
1 AAAACAATTTTTGAAAATATATATATTATATAGTTTTG
*
351219 AAAACAATTTTCG-AAA-ATATATATTATATAGTTTT-
1 AAAACAATTTTTGAAAATATATATATTATATAGTTTTG
* *
351254 AAAATAATTTTTGAAAATATATATATTATATGGTTTTG
1 AAAACAATTTTTGAAAATATATATATTATATAGTTTTG
** * **
351292 AAAACAATTTTT-AAAGGCATATATAATATATAGTTTAA
1 AAAACAATTTTTGAAA-ATATATATATTATATAGTTTTG
*
351330 AAAATAATTTTT
1 AAAACAATTTTT
351342 TATATATTAT
Statistics
Matches: 339, Mismatches: 32, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
35 78 0.23
36 26 0.08
37 48 0.14
38 154 0.45
39 20 0.06
40 11 0.03
41 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (38 bp):
AAAACAATTTTTGAAAATATATATATTATATAGTTTTG
Found at i:351162 original size:13 final size:13
Alignment explanation
Indices: 351144--351168 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
351134 TAATATATAG
351144 TTTTGAAAATATT
1 TTTTGAAAATATT
351157 TTTTGAAAATAT
1 TTTTGAAAATAT
351169 ATATTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTTGAAAATATT
Found at i:359125 original size:36 final size:36
Alignment explanation
Indices: 359079--359456 Score: 206
Period size: 38 Copynumber: 10.2 Consensus size: 36
359069 ATTAAAATCA
359079 ATTTTTGAAAATATATATTATATAGTTTTGAAAATG
1 ATTTTTGAAAATATATATTATATAGTTTTGAAAATG
* *
359115 GTTTTCGAAAATATATATATTATATAGTTTTG--AATG
1 ATTTTTG-AAA-ATATATATTATATAGTTTTGAAAATG
* * *
359151 TTTTTTGAAAACATATATAATATATAGTTTTTGAAAA-C
1 ATTTTTG-AAA-ATATATATTATATAG-TTTTGAAAATG
* *
359189 ATTTTTGAAAATATATATAATATATAGTTTTTAAAA-C
1 ATTTTTGAAAATATATAT--TATATAGTTTTGAAAATG
*
359226 AATTTTGAATATATATATATATATATA-TATATAT-ATAATAT-
1 ATTTTTGAA-A-ATATATAT-TATATAGT-T-T-TGA-AA-ATG
* * * *
359267 AGTTTCTGAAAATAT-TTTTGA-AAATGTATAT-AATATAT-
1 A-TTTTTGAAAATATATATT-ATATA-GT-TTTGAA-A-ATG
* * **
359305 AGTTTTGAAAATATATATTATAAAGTTTT-AAAACA
1 ATTTTTGAAAATATATATTATATAGTTTTGAAAATG
**
359340 ATTTTTGAAAATATATATTATATAGTTTT-AAAACA
1 ATTTTTGAAAATATATATTATATAGTTTTGAAAATG
* **
359375 ATTTTTGAAAAAATATATATTATATGGTTTTGAAAACA
1 ATTTTTG--AAAATATATATTATATAGTTTTGAAAATG
* * * *
359413 ATTTTTAAAAGCATATATAATATATTGTTTTAAAAATG
1 ATTTTTGAAA--ATATATATTATATAGTTTTGAAAATG
*
359451 TTTTTT
1 ATTTTT
359457 TATATATTAT
Statistics
Matches: 283, Mismatches: 31, Indels: 54
0.77 0.08 0.15
Matches are distributed among these distances:
34 1 0.00
35 41 0.14
36 46 0.16
37 65 0.23
38 96 0.34
39 15 0.05
40 10 0.04
41 3 0.01
42 6 0.02
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.46
Consensus pattern (36 bp):
ATTTTTGAAAATATATATTATATAGTTTTGAAAATG
Found at i:359199 original size:74 final size:72
Alignment explanation
Indices: 359080--359219 Score: 201
Period size: 74 Copynumber: 1.9 Consensus size: 72
359070 TTAAAATCAA
* ** *
359080 TTTTTGAAAATATATATTATATAGTTTTGAAAATGGTTTTCGAAAATATATATATTATATAGTTT
1 TTTTTGAAAATATATAATATATAGTTTTGAAAATCATTTTCGAAAATATATATAATATATAGTTT
359145 TGAATGT
66 TGAATGT
*
359152 TTTTTGAAAACATATATAATATATAGTTTTTGAAAA-CATTTTTGAAAATATATATAATATATAG
1 TTTTTG-AAA-ATATATAATATATAG-TTTTGAAAATCATTTTCGAAAATATATATAATATATAG
359216 TTTT
63 TTTT
359220 TAAAACAATT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
72 6 0.10
73 3 0.05
74 42 0.70
75 9 0.15
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (72 bp):
TTTTTGAAAATATATAATATATAGTTTTGAAAATCATTTTCGAAAATATATATAATATATAGTTT
TGAATGT
Found at i:359241 original size:2 final size:2
Alignment explanation
Indices: 359234--359267 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
359224 ACAATTTTGA
359234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
359268 GTTTCTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:359319 original size:23 final size:24
Alignment explanation
Indices: 359282--359337 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
359272 CTGAAAATAT
*
359282 TTTTGAAAATGTATATAATATATAG
1 TTTTGAAAA-GTATATAATATAAAG
*
359307 TTTTGAAAA-TATATATTATAAAG
1 TTTTGAAAAGTATATAATATAAAG
359330 TTTT-AAAA
1 TTTTGAAAA
359338 CAATTTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 16 0.55
25 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (24 bp):
TTTTGAAAAGTATATAATATAAAG
Found at i:359353 original size:35 final size:35
Alignment explanation
Indices: 359307--359447 Score: 192
Period size: 35 Copynumber: 3.9 Consensus size: 35
359297 TAATATATAG
*
359307 TTTTGAAAATATATATTATAAAGTTTTAAAACAAT
1 TTTTGAAAATATATATTATATAGTTTTAAAACAAT
359342 TTTTGAAAATATATATTATATAGTTTTAAAACAAT
1 TTTTGAAAATATATATTATATAGTTTTAAAACAAT
*
359377 TTTTGAAAAAATATATATTATATGGTTTTGAAAACAAT
1 TTTTG--AAAATATATATTATATAGTTTT-AAAACAAT
* * *
359415 TTTTAAAAGCATATATAATATATTGTTTTAAAA
1 TTTTGAAA--ATATATATTATATAGTTTTAAAA
359448 ATGTTTTTTT
Statistics
Matches: 96, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
35 39 0.41
36 3 0.03
37 25 0.26
38 29 0.30
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTTGAAAATATATATTATATAGTTTTAAAACAAT
Found at i:359456 original size:38 final size:36
Alignment explanation
Indices: 359312--359448 Score: 145
Period size: 37 Copynumber: 3.8 Consensus size: 36
359302 TATAGTTTTG
* *
359312 AAAATATATATTATAAAGTTTTAAAACAA-TTTTT-G
1 AAAATATATATTATATAGTTTTAAAA-AATTTTTTAA
*
359347 AAAATATATATTATATAGTTTTAAAACAATTTTTGAA
1 AAAATATATATTATATAGTTTTAAAA-AATTTTTTAA
*
359384 AAAATATATATTATATGGTTTTGAAAACAA-TTTTTAA
1 AAAATATATATTATATAGTTTT-AAAA-AATTTTTTAA
* * *
359421 AAGCATATATAATATATTGTTTTAAAAA
1 AA-AATATATATTATATAGTTTTAAAAA
359449 TGTTTTTTTA
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
35 28 0.31
36 5 0.06
37 33 0.37
38 24 0.27
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (36 bp):
AAAATATATATTATATAGTTTTAAAAAATTTTTTAA
Found at i:359488 original size:4 final size:4
Alignment explanation
Indices: 359479--359526 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
359469 TAATATTATT
*
359479 TTTA TTTA TTTA TTTA TTTA TTT- TATTA -TTA TTCA TTT- TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA
359524 TTT
1 TTT
359527 TCATTTTAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 10 0.27
4 27 0.73
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:359496 original size:27 final size:27
Alignment explanation
Indices: 359451--359523 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
359441 TTTAAAAATG
*
359451 TTTT-TTTATATATTATATTAATATTAT
1 TTTTATTTATTTATT-TATTAATATTAT
* *
359478 TTTTATTTATTTATTTATTTATTTTAT
1 TTTTATTTATTTATTTATTAATATTAT
* *
359505 TATTATTCATTT-TTTATTA
1 TTTTATTTATTTATTTATTA
359524 TTTTCATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
26 6 0.15
27 24 0.62
28 9 0.23
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTATTTATTTATTTATTAATATTAT
Found at i:359506 original size:36 final size:37
Alignment explanation
Indices: 359455--359526 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
359445 AAAATGTTTT
359455 TTTATATATTATATTAATATT-A-TTTTTATTTATTTA
1 TTTATATATTATATTAATATTCATTTTTTA-TTATTTA
* * *
359491 TTTATTTATTTTATTATTATTCATTTTTTATTATTT
1 TTTATATATTATATTAATATTCATTTTTTATTATTT
359527 TCATTTTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 18 0.58
37 7 0.23
38 6 0.19
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (37 bp):
TTTATATATTATATTAATATTCATTTTTTATTATTTA
Found at i:359525 original size:33 final size:30
Alignment explanation
Indices: 359451--359526 Score: 73
Period size: 33 Copynumber: 2.4 Consensus size: 30
359441 TTTAAAAATG
*
359451 TTTTT-TTATATATTATATTAATATTATTT
1 TTTTTATTATTTATTATATTAATATTATTT
* *
359480 TTATTTATTTATTTATTTATTTTATTATTATTCAT
1 TT-TTTA-TTATTTA-TTATATTAATATTATT--T
359515 TTTTTATTATTT
1 TTTTTATTATTT
359527 TCATTTTAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 2 0.05
30 3 0.08
32 6 0.16
33 20 0.53
34 4 0.11
35 3 0.08
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTTTATTATTTATTATATTAATATTATTT
Found at i:359529 original size:16 final size:17
Alignment explanation
Indices: 359499--359533 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
359489 TATTTATTTA
359499 TTTTATTATTATTCATT
1 TTTTATTATTATTCATT
359516 TTTTATTATT-TTCATT
1 TTTTATTATTATTCATT
359532 TT
1 TT
359534 AGGTCCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTATTATTCATT
Found at i:359534 original size:14 final size:15
Alignment explanation
Indices: 359492--359525 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
359482 ATTTATTTAT
*
359492 TTATTTATTTTATTA
1 TTATTCATTTTATTA
359507 TTATTCATTTT-TTA
1 TTATTCATTTTATTA
359521 TTATT
1 TTATT
359526 TTCATTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTCATTTTATTA
Found at i:364175 original size:20 final size:21
Alignment explanation
Indices: 364136--364177 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
364126 TTTAATTGAA
* *
364136 TTATTTATATTTATTTTTATT
1 TTATTTATATCTATTATTATT
364157 TTATTT-TATCTATTATTATT
1 TTATTTATATCTATTATTATT
364177 T
1 T
364178 ATAAATAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATTTATATCTATTATTATT
Found at i:364239 original size:15 final size:15
Alignment explanation
Indices: 364219--364247 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
364209 TTTATTATTA
364219 ATATTTAATGATTTT
1 ATATTTAATGATTTT
364234 ATATTTAATGATTT
1 ATATTTAATGATTT
364248 AGTAATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
ATATTTAATGATTTT
Found at i:364241 original size:22 final size:24
Alignment explanation
Indices: 364190--364248 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
364180 AAATAGTCAA
*
364190 ATTTAAAATTTACATAGAATTTAT
1 ATTTAATATTTACATAGAATTTAT
*
364214 -TATTAATATTTA-AT-GATTTTAT
1 AT-TTAATATTTACATAGAATTTAT
364236 ATTTAATGATTTA
1 ATTTAAT-ATTTA
364249 GTAATGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 12 0.40
23 9 0.30
24 9 0.30
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (24 bp):
ATTTAATATTTACATAGAATTTAT
Found at i:364262 original size:16 final size:16
Alignment explanation
Indices: 364241--364272 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
364231 TTTATATTTA
364241 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
364257 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
364273 TATTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
ATGATTTAGTAATGAT
Found at i:364284 original size:24 final size:24
Alignment explanation
Indices: 364239--364464 Score: 121
Period size: 24 Copynumber: 9.4 Consensus size: 24
364229 ATTTTATATT
* *
364239 TAATGATTTAGTAATGATATGATTTAG
1 TAATGA-TTATTAAT-A-ATGATTTAA
*
364266 TAATGATTATTAATAATGA-TTAC
1 TAATGATTATTAATAATGATTTAA
* * *
364289 TTATTAATATT--TAATGATTTGATA
1 TAATGATTATTAATAATGATTT-A-A
*
364313 TTTAATGATTTAATAATAATGA-TTAA
1 --TAATGA-TTATTAATAATGATTTAA
*
364339 TAATGATTTATTATTAAT-ATTTAA
1 TAATGA-TTATTAATAATGATTTAA
* * *
364363 TGAT--TTGA-TACTAATGATTTAG
1 TAATGATT-ATTAATAATGATTTAA
* * *
364385 TAATGATTAGTAATAATAAAATT-A
1 TAATGATTATTAATAAT-GATTTAA
* *
364409 TAATAATTACTAATAATGATTTAA
1 TAATGATTATTAATAATGATTTAA
* *
364433 TAATGATTACTAATAATTATTTAA
1 TAATGATTATTAATAATGATTTAA
364457 TAAT-ATTA
1 TAATGATTA
364465 AATATTTAAA
Statistics
Matches: 157, Mismatches: 26, Indels: 36
0.72 0.12 0.16
Matches are distributed among these distances:
21 14 0.09
22 11 0.07
23 21 0.13
24 77 0.49
25 4 0.03
26 12 0.08
27 10 0.06
28 2 0.01
29 6 0.04
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (24 bp):
TAATGATTATTAATAATGATTTAA
Found at i:364302 original size:7 final size:8
Alignment explanation
Indices: 364292--364368 Score: 60
Period size: 7 Copynumber: 10.2 Consensus size: 8
364282 TGATTACTTA
364292 TTAAT-AT
1 TTAATGAT
364299 TTAATGAT
1 TTAATGAT
*
364307 TTGAT-AT
1 TTAATGAT
364314 TTAATGAT
1 TTAATGAT
364322 TTAAT-A-
1 TTAATGAT
*
364328 ATAATGAT
1 TTAATGAT
364336 TAATAATGAT
1 T--TAATGAT
*
364346 TT-ATTA-
1 TTAATGAT
364352 TTAAT-AT
1 TTAATGAT
364359 TTAATGAT
1 TTAATGAT
364367 TT
1 TT
364369 GATACTAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
6 7 0.12
7 23 0.41
8 18 0.32
10 8 0.14
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (8 bp):
TTAATGAT
Found at i:364305 original size:76 final size:74
Alignment explanation
Indices: 364213--364356 Score: 218
Period size: 76 Copynumber: 1.9 Consensus size: 74
364203 ATAGAATTTA
* * *
364213 TTATTAATATTTAATGATTTTATATTTAATGATTTAGTAATGATATGATTTAGTAATGA-TTATT
1 TTATTAATATTTAATGATTTGATATTTAATGATTTAATAAT-A-ATGA-TTAATAATGATTTATT
364277 AATAATGATTAC
63 AATAATGATTAC
*
364289 TTATTAATATTTAATGATTTGATATTTAATGATTTAATAATAATGATTAATAATGATTTATTATT
1 TTATTAATATTTAATGATTTGATATTTAATGATTTAATAATAATGATTAATAATGATTTATTAAT
364354 AAT
66 AAT
364357 ATTTAATGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
73 9 0.14
74 14 0.22
75 1 0.02
76 39 0.62
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.51
Consensus pattern (74 bp):
TTATTAATATTTAATGATTTGATATTTAATGATTTAATAATAATGATTAATAATGATTTATTAAT
AATGATTAC
Found at i:364329 original size:26 final size:26
Alignment explanation
Indices: 364224--364329 Score: 80
Period size: 26 Copynumber: 4.2 Consensus size: 26
364214 TATTAATATT
* *
364224 TAATGATTTTATATTTAATGATTTAG
1 TAATGATTTGATATTTAATGATTTAA
*
364250 TAATGATATGAT-TTAGTAATGATTATTAA
1 TAATGATTTGATATT--TAATGA-T-TTAA
***
364279 TAATGATTACTTA-TTAAT-A-TT--
1 TAATGATTTGATATTTAATGATTTAA
364300 TAATGATTTGATATTTAATGATTTAA
1 TAATGATTTGATATTTAATGATTTAA
364326 TAAT
1 TAAT
364330 AATGATTAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
21 10 0.17
22 5 0.08
23 3 0.05
24 2 0.03
25 2 0.03
26 15 0.25
27 10 0.17
28 1 0.02
29 12 0.20
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (26 bp):
TAATGATTTGATATTTAATGATTTAA
Found at i:364334 original size:14 final size:14
Alignment explanation
Indices: 364224--364388 Score: 55
Period size: 15 Copynumber: 11.1 Consensus size: 14
364214 TATTAATATT
* *
364224 TAATGATTTTATATT
1 TAATGATTTAATA-A
*
364239 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
364253 TGATATGATTTAGTAA
1 T-A-ATGATTTAATAA
* *
364269 TGATTA-TTAATAA
1 TAATGATTTAATAA
* * *
364282 TGATTACTTATTAATATT
1 TAATGA--T-TTAATA-A
* *
364300 TAATGATTTGATATT
1 TAATGATTTAATA-A
364315 TAATGATTTAATAA
1 TAATGATTTAATAA
364329 TAATGA-TTAATAA
1 TAATGATTTAATAA
* * *
364342 TGATTTATTATTAATATT
1 T-AATGA-T-TTAATA-A
* *
364360 TAATGATTTGATAC
1 TAATGATTTAATAA
*
364374 TAATGATTTAGTAA
1 TAATGATTTAATAA
364388 T
1 T
364389 GATTAGTAAT
Statistics
Matches: 116, Mismatches: 22, Indels: 25
0.71 0.13 0.15
Matches are distributed among these distances:
13 20 0.17
14 25 0.22
15 36 0.31
16 15 0.13
17 15 0.13
18 5 0.04
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.49
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:364339 original size:60 final size:59
Alignment explanation
Indices: 364234--364388 Score: 206
Period size: 60 Copynumber: 2.6 Consensus size: 59
364224 TAATGATTTT
* * *
364234 ATATTTAATGATTT-AGTAATGATATGATTTAGTAATGATTATTAATAATGA-TTACTTATTA
1 ATATTTAATGATTTGA-T-ATTA-ATGATTTAGTAATAATGATTAATAATGATTTA-TTATTA
*
364295 ATATTTAATGATTTGATATTTAATGATTTAATAATAATGATTAATAATGATTTATTATTA
1 ATATTTAATGATTTGATA-TTAATGATTTAGTAATAATGATTAATAATGATTTATTATTA
*
364355 ATATTTAATGATTTGATACTAATGATTTAGTAAT
1 ATATTTAATGATTTGATATTAATGATTTAGTAAT
364389 GATTAGTAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
59 14 0.16
60 50 0.59
61 20 0.24
62 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.48
Consensus pattern (59 bp):
ATATTTAATGATTTGATATTAATGATTTAGTAATAATGATTAATAATGATTTATTATTA
Found at i:364367 original size:45 final size:46
Alignment explanation
Indices: 364208--364457 Score: 169
Period size: 45 Copynumber: 5.4 Consensus size: 46
364198 TTTACATAGA
* * *
364208 ATTTATTATTAATATTTAATGATTTTATATTTAATGATTTAGTAATG
1 ATTTATTATTAATATTTAATGATTTAATA-ATAATGATTTAATAATG
* * * *
364255 A--TATGATT--TA-GTAATGA-TTATTAATAATGATTACTTATTAAT-
1 ATTTATTATTAATATTTAATGATTTAATAATAATGA-T--TTAATAATG
* *
364297 ATTTAATGATTTGATATTTAATGATTTAATAATAATGA-TTAATAATG
1 ATTT-ATTA-TTAATATTTAATGATTTAATAATAATGATTTAATAATG
* * *
364344 ATTTATTATTAATATTTAATGATTTGATACTAATGATTTAGTAATG
1 ATTTATTATTAATATTTAATGATTTAATAATAATGATTTAATAATG
* * * * *
364390 ATTAGTAATAATAAAATTATAAT-AATTACTAATAATGATTTAATAATG
1 ATT--TATTATTAATATT-TAATGATTTAATAATAATGATTTAATAATG
* *
364438 A-TTACTAATAATTATTTAAT
1 ATTTATTATTAA-TATTTAAT
364458 AATATTAAAT
Statistics
Matches: 162, Mismatches: 24, Indels: 36
0.73 0.11 0.16
Matches are distributed among these distances:
40 6 0.04
41 5 0.03
42 7 0.04
43 9 0.06
44 1 0.01
45 47 0.29
46 26 0.16
47 6 0.04
48 33 0.20
49 10 0.06
50 12 0.07
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (46 bp):
ATTTATTATTAATATTTAATGATTTAATAATAATGATTTAATAATG
Found at i:364493 original size:20 final size:20
Alignment explanation
Indices: 364468--364509 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
364458 AATATTAAAT
364468 ATTTAAATAGAATTTATTCA
1 ATTTAAATAGAATTTATTCA
*
364488 ATTTAAATCGAATTTATTCA
1 ATTTAAATAGAATTTATTCA
364508 AT
1 AT
364510 ATAACTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTAAATAGAATTTATTCA
Found at i:364540 original size:22 final size:23
Alignment explanation
Indices: 364495--364554 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
364485 TCAATTTAAA
* *
364495 TCGAATTTATTCA-ATATAACTAG
1 TCGAATTTATT-ATTTATAAATAG
364518 TCGAATTTA-TATTTATAAATAG
1 TCGAATTTATTATTTATAAATAG
364540 TCGAATTTATTATTT
1 TCGAATTTATTATTT
364555 TTACATTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 18 0.55
23 14 0.42
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (23 bp):
TCGAATTTATTATTTATAAATAG
Found at i:365173 original size:15 final size:15
Alignment explanation
Indices: 365153--365181 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
365143 TATCATTACT
365153 AAATCATTAAATATC
1 AAATCATTAAATATC
365168 AAATCATTAAATAT
1 AAATCATTAAATAT
365182 TACTAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:366854 original size:17 final size:17
Alignment explanation
Indices: 366818--366857 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
366808 GTCCAAGGTC
** *
366818 TAAATTAATAATTTTGA
1 TAAATTAATAAGATTAA
366835 TAAATTAATAAGATTAA
1 TAAATTAATAAGATTAA
366852 TAAATT
1 TAAATT
366858 TCCGAAAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TAAATTAATAAGATTAA
Found at i:367827 original size:9 final size:9
Alignment explanation
Indices: 367813--367838 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
367803 TCTCTCGGTT
367813 CAACAAACA
1 CAACAAACA
367822 CAACAAACA
1 CAACAAACA
367831 CAACAAAC
1 CAACAAAC
367839 TTGTGTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (9 bp):
CAACAAACA
Found at i:368825 original size:2 final size:2
Alignment explanation
Indices: 368818--368882 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
368808 TATTTACATG
368818 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
368860 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
368883 TTATTTATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:370139 original size:16 final size:16
Alignment explanation
Indices: 370118--370160 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
370108 GATTAAGCGC
370118 TGAATGATTCAAATGT
1 TGAATGATTCAAATGT
370134 TGAATGATTCAAATGT
1 TGAATGATTCAAATGT
370150 TGAATGATTCA
1 TGAATGATTCA
370161 GAGGCTATGT
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:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (16 bp):
TGAATGATTCAAATGT
Found at i:373187 original size:5 final size:5
Alignment explanation
Indices: 373151--373175 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
373141 ATTTATTTAA
373151 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
373176 AATAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:391797 original size:107 final size:109
Alignment explanation
Indices: 391558--391799 Score: 305
Period size: 107 Copynumber: 2.2 Consensus size: 109
391548 TCACTACATA
*
391558 TGACCAAAATGCAAAAACACACTAAACTTAGAGGGACTAAACAACAAATAACCCTATAAACACAT
1 TGACCAAAATGCAAAAACACGCTAAACTTAGAGGGACTAAACAACAAATAACCCTATAAACACAT
*
391623 AACATGCACGAAAAAAGGTAAATACCAGATTCGGTCCATTCAGG
66 AACATGCACGAAAAAAGGTAAATACCAGATTCGGCCCATTCAGG
* ** ** * * *
391667 TGATCGCAATGCAAAAA-TTGCTAAATTTAGAGGGGCTAAAC-ACAAATAA-CCTAGTAAATACA
1 TGACCAAAATGCAAAAACACGCTAAACTTAGAGGGACTAAACAACAAATAACCCTA-TAAACACA
* * *
391729 TAACATGCACGAAAAAA-GTAAATACCATATT-TGCCCCTTACAGG
65 TAACATGCACGAAAAAAGGTAAATACCAGATTCGGCCCATT-CAGG
*
391773 TGACCAAAATGCAAAAACGCGCTAAAC
1 TGACCAAAATGCAAAAACACGCTAAAC
391800 CTAAGGGGAC
Statistics
Matches: 111, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
105 5 0.05
106 35 0.32
107 38 0.34
108 19 0.17
109 14 0.13
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.19
Consensus pattern (109 bp):
TGACCAAAATGCAAAAACACGCTAAACTTAGAGGGACTAAACAACAAATAACCCTATAAACACAT
AACATGCACGAAAAAAGGTAAATACCAGATTCGGCCCATTCAGG
Found at i:391807 original size:106 final size:109
Alignment explanation
Indices: 391558--391807 Score: 305
Period size: 106 Copynumber: 2.3 Consensus size: 109
391548 TCACTACATA
* *
391558 TGACCAAAATGCAAAAACACACTAAACTTAGAGGGACTAAACAACAAATAACCCTATAAACACAT
1 TGACCAAAATGCAAAAACACGCTAAACTTAGAGGGGCTAAACAACAAATAACCCTATAAACACAT
*
391623 AACATGCACGAAAAAAGGTAAATACCAGATTCGGTCCATTCAGG
66 AACATGCACGAAAAAAGGTAAATACCAGATTCGGCCCATTCAGG
* ** ** * *
391667 TGATCGCAATGCAAAAA-TTGCTAAATTTAGAGGGGCTAAAC-ACAAATAA-CCTAGTAAATACA
1 TGACCAAAATGCAAAAACACGCTAAACTTAGAGGGGCTAAACAACAAATAACCCTA-TAAACACA
* * *
391729 TAACATGCACGAAAAAA-GTAAATACCATATT-TGCCCCTTACAGG
65 TAACATGCACGAAAAAAGGTAAATACCAGATTCGGCCCATT-CAGG
* *
391773 TGACCAAAATGCAAAAACGCGCTAAACCTA-AGGGG
1 TGACCAAAATGCAAAAACACGCTAAACTTAGAGGGG
391808 ACCTATGCAT
Statistics
Matches: 118, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
105 5 0.04
106 40 0.34
107 40 0.34
108 19 0.16
109 14 0.12
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (109 bp):
TGACCAAAATGCAAAAACACGCTAAACTTAGAGGGGCTAAACAACAAATAACCCTATAAACACAT
AACATGCACGAAAAAAGGTAAATACCAGATTCGGCCCATTCAGG
Found at i:392614 original size:20 final size:20
Alignment explanation
Indices: 392591--392634 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
392581 ATTTTAAGTA
*
392591 ATAATAATAATAAATAAA-AT
1 ATAAGAATAA-AAATAAATAT
*
392611 ATAAGAATAAGAATAAATAT
1 ATAAGAATAAAAATAAATAT
392631 ATAA
1 ATAA
392635 AAAATGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
ATAAGAATAAAAATAAATAT
Found at i:393186 original size:202 final size:201
Alignment explanation
Indices: 392758--393191 Score: 459
Period size: 202 Copynumber: 2.1 Consensus size: 201
392748 GACTTATTCA
* * * *
392758 CATTATGAACCCTTCCATTGGAAATTTTGATCCACCTCTTTCTGTGATGGATTCAACTAAAGTGA
1 CATTATGAACCCTT--ATTGGAAATGTTGATCCACCTCTTTCTGTAATGGAATCAACTAAAGCGA
* * * *
392823 GTATGATGATCCAACTCCATATGCGATGGATGAGAAAAGGTTGATGCTGTTCCAACTCCTTATAT
64 GTAGGATGATCCAACTCCAAATGAGATGGATGAGAAAAGATTGATGCTGTTCCAACTCCTTATAT
* *
392888 GATGAAAACAAGATAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCATCAGATAA
129 GACGAAAACAAGATAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATAA
392953 GTTCTTCT
194 GTTCTTCT
* * *
392961 CTTTATGTATACTCC--ACTGGAAATGTTGATCCA-CTTTCTTCTGTAATGGAATCAAAC-AAAG
1 CATTATG-A-AC-CCTTATTGGAAATGTTGATCCACCTCT-TTCTGTAATGGAATC-AACTAAAG
* * ** * *
393022 CGA-TGAGGATG-TCTAACTCCAAATGAGATGGATGAGCCAATTATTGGTGTTGTTCCAACTCCT
61 CGAGT-AGGATGATCCAACTCCAAATGAGATGGATGAG-AAAAGATTGATGCTGTTCCAACTCCT
* * * * * * * *
393085 TATGTGACG-GAACAAGCTAAGGTTGAGCAAGTTCTTCTCATTATGAACTTTCTTCTCTCTCGTT
124 TATATGACGAAAACAAGATAAAGTTGAACAAGTTCTTCTCATTATGAAC-TTCTTCTCCCTCATC
* *
393149 GGATGAGTTCTTCT
188 AGATAAGTTCTTCT
393163 CATTATGAACCCTATATTGGAAATGTTGA
1 CATTATGAACCCT-TATTGGAAATGTTGA
393192 GCCAAGTTCT
Statistics
Matches: 189, Mismatches: 31, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
199 2 0.01
200 2 0.01
201 61 0.32
202 110 0.58
203 9 0.05
204 1 0.01
205 2 0.01
206 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (201 bp):
CATTATGAACCCTTATTGGAAATGTTGATCCACCTCTTTCTGTAATGGAATCAACTAAAGCGAGT
AGGATGATCCAACTCCAAATGAGATGGATGAGAAAAGATTGATGCTGTTCCAACTCCTTATATGA
CGAAAACAAGATAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATAAGT
TCTTCT
Done.