Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008933.1 Hibiscus syriacus cultivar Beakdansim tig00112249_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: 2862162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1677484 original size:58 final size:58
Alignment explanation
Indices: 1677394--1677507 Score: 228
Period size: 58 Copynumber: 2.0 Consensus size: 58
1677384 GGGATAAGCT
1677394 CACTAACTAGAGAACTGATATAAAGGATGAAGAAATGTACGTAGCAATTATATTCCCC
1 CACTAACTAGAGAACTGATATAAAGGATGAAGAAATGTACGTAGCAATTATATTCCCC
1677452 CACTAACTAGAGAACTGATATAAAGGATGAAGAAATGTACGTAGCAATTATATTCC
1 CACTAACTAGAGAACTGATATAAAGGATGAAGAAATGTACGTAGCAATTATATTCC
1677508 AGAAATGAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (58 bp):
CACTAACTAGAGAACTGATATAAAGGATGAAGAAATGTACGTAGCAATTATATTCCCC
Found at i:1680368 original size:22 final size:24
Alignment explanation
Indices: 1680343--1680386 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1680333 CAATTCATTT
1680343 ATCTT-TTCTT-TATCTTGTTTTA
1 ATCTTATTCTTATATCTTGTTTTA
*
1680365 ATCTTATTTTTATATCTTGTTT
1 ATCTTATTCTTATATCTTGTTT
1680387 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 4 0.21
24 10 0.53
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (24 bp):
ATCTTATTCTTATATCTTGTTTTA
Found at i:1683548 original size:305 final size:293
Alignment explanation
Indices: 1683055--1683800 Score: 1032
Period size: 305 Copynumber: 2.5 Consensus size: 293
1683045 AAAAATATGG
** *
1683055 AAAGGCATGAACCCATAAACCAACTAAAGTCAATAACATTCT--AA-TTTATGCAAATCATTAAA
1 AAAGGCATGAAAGCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAAATCATTAAA
* *
1683117 AATATGAAAAATAACAGTAACAACCCACATTGCAGTTCTGTTAATTCATAATCAAGTTCAATTGG
66 AATATGAAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAATTAATAATCAAGTTCAATTGG
* **
1683182 TCCTTTGTTAACTGCCTTTCGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACATGAAAAGGTCA
131 TCCCTTACTAACTGCCTTTCGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACATGAAAAGGTCA
* *
1683247 AATATTTATAGATGATAGCTTTCACACTGGAGAAGATGATGATTCAACATTTATATCTAATACAA
196 AATATTTAGAGATGATAGCTTTCACACTGGAGAAGATGATGATT---C-GTTATATCTAATACAA
*
1683312 TGAACCATAGATACGGGACTAAAGACCAAAACCATTA
257 TGAACCATAGATACGGGACTAAAGACCAAAACCATGA
1683349 AAAGGCATGAAAGCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAAATCATTAAA
1 AAAGGCATGAAAGCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAAATCATTAAA
* *
1683414 AATATGAAGAAAAAAAAAATAACAGTAACAACTCACATAGCAGTTCTGTTAATTAAGAATCAAGT
66 AATAT---G-----AAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAATTAATAATCAAGT
* *
1683479 TCAATTGGTCCCTTACTAACTGCCTTTTGCTTAGTCCTGTAGCAATCTGCAACTAGAGCACATGA
123 TCAATTGGTCCCTTACTAACTGCCTTTCGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACATGA
*
1683544 AAAGGTCAGATATTTAGAGATGATAGCTTTCACACTGGAGAAGATGATGATTCGTTATATCTAAT
188 AAAGGTCAAATATTTAGAGATGATAGCTTTCACACTGGAGAAGATGATGATTCGTTATATCTAAT
*
1683609 ACAATGAACCATAGATACGGGACTAAAGACCTAAACCATGA
253 ACAATGAACCATAGATACGGGACTAAAGACCAAAACCATGA
1683650 AAAGGCATGAAAAATATGGAAAGGCATGAACCCATAAACCAACTCAAGTCAATAACATTCTAAAA
1 AAAGGC---------AT-G-AA---A-G----CATAAACCAACTCAAGTCAATAACATTCTAAAA
1683715 TTTTATGC-AATCATTAAAAATATGAAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAATT
47 TTTTATGCAAATCATTAAAAATATGAAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAATT
1683779 AATAATCAAGTTCAATTGGTCC
112 AATAATCAAGTTCAATTGGTCC
1683801 ATCGATCTTT
Statistics
Matches: 403, Mismatches: 19, Indels: 43
0.87 0.04 0.09
Matches are distributed among these distances:
294 39 0.10
296 2 0.00
297 23 0.06
300 1 0.00
301 56 0.14
302 1 0.00
305 157 0.39
310 2 0.00
311 61 0.15
312 2 0.00
315 1 0.00
316 2 0.00
319 15 0.04
320 41 0.10
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (293 bp):
AAAGGCATGAAAGCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAAATCATTAAA
AATATGAAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAATTAATAATCAAGTTCAATTGG
TCCCTTACTAACTGCCTTTCGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACATGAAAAGGTCA
AATATTTAGAGATGATAGCTTTCACACTGGAGAAGATGATGATTCGTTATATCTAATACAATGAA
CCATAGATACGGGACTAAAGACCAAAACCATGA
Found at i:1685316 original size:335 final size:335
Alignment explanation
Indices: 1684706--1685376 Score: 1342
Period size: 335 Copynumber: 2.0 Consensus size: 335
1684696 ACACTGGAGA
1684706 AGATGATGATTCAACATTTATATCTAATACAATGAACCATAGATACGGGACTAAAGACCAAAACC
1 AGATGATGATTCAACATTTATATCTAATACAATGAACCATAGATACGGGACTAAAGACCAAAACC
1684771 ATGAAAAGGCATGAAAAAATTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAA
66 ATGAAAAGGCATGAAAAAATTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAA
1684836 TTTTATGCAAATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAA
131 TTTTATGCAAATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAA
1684901 TTCAGAATCAAGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAA
196 TTCAGAATCAAGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAA
1684966 CTAGAGCACATGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTGGAAAAATATTTGGAA
261 CTAGAGCACATGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTGGAAAAATATTTGGAA
1685031 AGGCACCCAT
326 AGGCACCCAT
1685041 AGATGATGATTCAACATTTATATCTAATACAATGAACCATAGATACGGGACTAAAGACCAAAACC
1 AGATGATGATTCAACATTTATATCTAATACAATGAACCATAGATACGGGACTAAAGACCAAAACC
1685106 ATGAAAAGGCATGAAAAAATTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAA
66 ATGAAAAGGCATGAAAAAATTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAA
1685171 TTTTATGCAAATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAA
131 TTTTATGCAAATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAA
1685236 TTCAGAATCAAGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAA
196 TTCAGAATCAAGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAA
1685301 CTAGAGCACATGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTGGAAAAATATTTGGAA
261 CTAGAGCACATGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTGGAAAAATATTTGGAA
1685366 AGGCACCCAT
326 AGGCACCCAT
1685376 A
1 A
1685377 AACCAACTCA
Statistics
Matches: 336, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
335 336 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (335 bp):
AGATGATGATTCAACATTTATATCTAATACAATGAACCATAGATACGGGACTAAAGACCAAAACC
ATGAAAAGGCATGAAAAAATTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAA
TTTTATGCAAATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAA
TTCAGAATCAAGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAA
CTAGAGCACATGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTGGAAAAATATTTGGAA
AGGCACCCAT
Found at i:1685536 original size:235 final size:235
Alignment explanation
Indices: 1685118--1685975 Score: 1436
Period size: 235 Copynumber: 3.6 Consensus size: 235
1685108 GAAAAGGCAT
1685118 GAAAAA-A-TTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAA
1 GAAAAATATTTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAA
*
1685181 ATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTGCAGTTCTGTTAATTCAGAATCA
66 ATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTTCAGTTCTGTTAATTCAGAATCA
1685246 AGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACA
131 AGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACA
1685311 TGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTG
196 TGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTG
1685351 GAAAAATATTTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAA
1 GAAAAATATTTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAA
*
1685416 ATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTTCAGTTTTGTTAATTCAGAATCA
66 ATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTTCAGTTCTGTTAATTCAGAATCA
1685481 AGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACA
131 AGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACA
1685546 TGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTG
196 TGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTG
1685586 GAAAAATATTTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAA
1 GAAAAATATTTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAA
*
1685651 ATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTTCAGTTTTGTTAATTCAGAATCA
66 ATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTTCAGTTCTGTTAATTCAGAATCA
1685716 AGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACA
131 AGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACA
1685781 TGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTG
196 TGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTG
*
1685821 GAAAAAATGATGATTCAACATTTATATGAAAAGGCATGAACCCATAAACCAACTCAAGTCAATAA
1 G---AAA--A--A-T----A--T-T-TGGAAAGGC----ACCCATAAACCAACTCAAGTCAATAA
* * *
1685886 AATTCTAAAATTTTATGCAAATCATTAAAAATATG--AAAAACAACAGTAACAACTCACATTTTA
46 CATTCTAAAATTTTATGCAAATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTTCA
*
1685949 GTTCTGTTAATTCAGAATCAAGGTCAA
111 GTTCTGTTAATTCAGAATCAAGTTCAA
1685976 ATTTTATGTA
Statistics
Matches: 595, Mismatches: 8, Indels: 24
0.95 0.01 0.04
Matches are distributed among these distances:
233 6 0.01
234 1 0.00
235 460 0.77
238 3 0.01
240 1 0.00
242 1 0.00
243 1 0.00
247 1 0.00
249 1 0.00
250 1 0.00
251 8 0.01
253 51 0.09
255 60 0.10
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (235 bp):
GAAAAATATTTGGAAAGGCACCCATAAACCAACTCAAGTCAATAACATTCTAAAATTTTATGCAA
ATCATTAAAAATATGAAAAAAATAACAGTAACAACTCACATTTCAGTTCTGTTAATTCAGAATCA
AGTTCAATTGGTCCCTTGCTAACTGCCTTTTGCTTAGTCCTGCAGCAATCTGCAACTAGAGCACA
TGAAAAGGTCAAATATTTAGAGATGATAGCTTTCACACTG
Found at i:1686817 original size:172 final size:172
Alignment explanation
Indices: 1686531--1686875 Score: 690
Period size: 172 Copynumber: 2.0 Consensus size: 172
1686521 AAATAGGGAC
1686531 AATGTGGTCCGCATGCCATGCATTGTCCTCAGAAGGTAAATTAGGAAATTAGTTCAAAGAAAATA
1 AATGTGGTCCGCATGCCATGCATTGTCCTCAGAAGGTAAATTAGGAAATTAGTTCAAAGAAAATA
1686596 TTGTGGTCTAGAAAGTAACAGTGAATGACTCAACTTATGTGGACATTTTCCCACAAAGTTGTTCA
66 TTGTGGTCTAGAAAGTAACAGTGAATGACTCAACTTATGTGGACATTTTCCCACAAAGTTGTTCA
1686661 ATACTTGATATGTAAAGGAGGTTTCTTTACATGAAAACTCAA
131 ATACTTGATATGTAAAGGAGGTTTCTTTACATGAAAACTCAA
1686703 AATGTGGTCCGCATGCCATGCATTGTCCTCAGAAGGTAAATTAGGAAATTAGTTCAAAGAAAATA
1 AATGTGGTCCGCATGCCATGCATTGTCCTCAGAAGGTAAATTAGGAAATTAGTTCAAAGAAAATA
1686768 TTGTGGTCTAGAAAGTAACAGTGAATGACTCAACTTATGTGGACATTTTCCCACAAAGTTGTTCA
66 TTGTGGTCTAGAAAGTAACAGTGAATGACTCAACTTATGTGGACATTTTCCCACAAAGTTGTTCA
1686833 ATACTTGATATGTAAAGGAGGTTTCTTTACATGAAAACTCAA
131 ATACTTGATATGTAAAGGAGGTTTCTTTACATGAAAACTCAA
1686875 A
1 A
1686876 CTGTCTTTGC
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 173 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (172 bp):
AATGTGGTCCGCATGCCATGCATTGTCCTCAGAAGGTAAATTAGGAAATTAGTTCAAAGAAAATA
TTGTGGTCTAGAAAGTAACAGTGAATGACTCAACTTATGTGGACATTTTCCCACAAAGTTGTTCA
ATACTTGATATGTAAAGGAGGTTTCTTTACATGAAAACTCAA
Found at i:1687867 original size:297 final size:297
Alignment explanation
Indices: 1687328--1687926 Score: 1128
Period size: 297 Copynumber: 2.0 Consensus size: 297
1687318 AAATCCAGTG
1687328 ACATATGTGACAAATGGTATACAAGAAAAGAGTAATTGGTTCTTACTTGCATGGTTTTTTGGCAG
1 ACATATGTGACAAATGGTATACAAGAAAAGAGTAATTGGTTCTTACTTGCATGGTTTTTTGGCAG
1687393 AGTTTGTCGAGTGGTTCATCAGTCAGGGTCCAACCATGAGTACATTCTTTCTCCTTTTTACTTTA
66 AGTTTGTCGAGTGGTTCATCAGTCAGGGTCCAACCATGAGTACATTCTTTCTCCTTTTTACTTTA
*
1687458 ACTACGCCGTAGATGGACCTTTTTATAGACAACATTTGGAGGTAAAGAAACATTTATCTCACAAA
131 ACTACGCCGTAGATGGACCTTTTTATAGACAACATTGGGAGGTAAAGAAACATTTATCTCACAAA
*
1687523 AAACCTATCAGCAGTCCCTGCAACAGAATTACAAAGAAACGCCTTAAGTCATTCATAATGAAAGA
196 AAACCTATCAGCAGTCCCTGCAACAGAATTACAAAGAAACACCTTAAGTCATTCATAATGAAAGA
1687588 AATAAGATATCCCGGAGACA-AATACATGTTCATTCAT
261 AATAAGATATCCCGGAG-CAGAATACATGTTCATTCAT
1687625 ACATATGTGACAAATGGTATACAAGAAAAGAGTAATTGGTTCTTACTTGCATGGTTTTTTGGCAG
1 ACATATGTGACAAATGGTATACAAGAAAAGAGTAATTGGTTCTTACTTGCATGGTTTTTTGGCAG
* * *
1687690 AGTTTTTTGAGTGGTTCATCAGTCAGGGTCCAACCCTGAGTACATTCTTTCTCCTTTTTACTTTA
66 AGTTTGTCGAGTGGTTCATCAGTCAGGGTCCAACCATGAGTACATTCTTTCTCCTTTTTACTTTA
1687755 ACTACGCCGTAGATGGACCTTTTTATAGACAACATTGGGAGGTAAAGAAACATTTATCTCACAAA
131 ACTACGCCGTAGATGGACCTTTTTATAGACAACATTGGGAGGTAAAGAAACATTTATCTCACAAA
*
1687820 AAGCCTATCAGCAGTCCCTGCAACAGAATTACAAAGAAACACCTTAAGTCATTCATAATGAAAGA
196 AAACCTATCAGCAGTCCCTGCAACAGAATTACAAAGAAACACCTTAAGTCATTCATAATGAAAGA
1687885 AATAAGATATCCCGGAGCAGAATACATGTTCATTCAT
261 AATAAGATATCCCGGAGCAGAATACATGTTCATTCAT
1687922 ACATA
1 ACATA
1687927 CCCCACTGTT
Statistics
Matches: 295, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
296 2 0.01
297 293 0.99
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (297 bp):
ACATATGTGACAAATGGTATACAAGAAAAGAGTAATTGGTTCTTACTTGCATGGTTTTTTGGCAG
AGTTTGTCGAGTGGTTCATCAGTCAGGGTCCAACCATGAGTACATTCTTTCTCCTTTTTACTTTA
ACTACGCCGTAGATGGACCTTTTTATAGACAACATTGGGAGGTAAAGAAACATTTATCTCACAAA
AAACCTATCAGCAGTCCCTGCAACAGAATTACAAAGAAACACCTTAAGTCATTCATAATGAAAGA
AATAAGATATCCCGGAGCAGAATACATGTTCATTCAT
Found at i:1689262 original size:34 final size:34
Alignment explanation
Indices: 1689224--1689304 Score: 153
Period size: 34 Copynumber: 2.4 Consensus size: 34
1689214 CAAAGAAACG
*
1689224 ATAAAAATAATTTGCTTTTAAATATTCCTTTTGT
1 ATAAAAACAATTTGCTTTTAAATATTCCTTTTGT
1689258 ATAAAAACAATTTGCTTTTAAATATTCCTTTTGT
1 ATAAAAACAATTTGCTTTTAAATATTCCTTTTGT
1689292 ATAAAAACAATTT
1 ATAAAAACAATTT
1689305 TGAAATGACC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (34 bp):
ATAAAAACAATTTGCTTTTAAATATTCCTTTTGT
Found at i:1690621 original size:34 final size:34
Alignment explanation
Indices: 1690540--1690621 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 34
1690530 CAAAGAAACG
* *
1690540 ATAAAAATAATTTGCTTTTAAATATTCCTTTTGT
1 ATAAAAACAATTTTCTTTTAAATATTCCTTTTGT
1690574 ATAAAAACAATTTTCTTTTAAATATTCCTTTTGT
1 ATAAAAACAATTTTCTTTTAAATATTCCTTTTGT
1690608 ATAAAAACAATTTT
1 ATAAAAACAATTTT
1690622 GAAATGACCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.48
Consensus pattern (34 bp):
ATAAAAACAATTTTCTTTTAAATATTCCTTTTGT
Found at i:1693281 original size:532 final size:531
Alignment explanation
Indices: 1691760--1693358 Score: 3155
Period size: 530 Copynumber: 3.0 Consensus size: 531
1691750 CTTCTAAAAT
1691760 CCATCAGATATGAAACAGAAACTCCTACCCGTTTTATCATAAAATGTAAACGTAATTACTGATAT
1 CCATCAGATATGAAACAGAAACTCCTACCCGTTTTATCATAAAATGTAAACGTAATTACTGATAT
1691825 ATGTAAGGCATCAAGTACTCTATTGAAACACCAAGTTTCTTAATCAAATGTAAGCAGAAATTAGA
66 ATGTAAGGCATCAAGTACTCTATTGAAACACCAAGTTTCTTAATCAAATGTAAGCAGAAATTAGA
1691890 ACTTGTAAATTCCACAACTACTCCAAAATCATAACTTATGTCCCAAGTACCATTCTAACTGCATT
131 ACTTGTAAATTCCACAACTACTCCAAAATCATAACTTATGTCCCAAGTACCATTCTAACTGCATT
1691955 TTAAAGTAATATTATAGTTAAAAAGTGATCAAATATGGAAGGCGAAACTCAAATAACTAAACAGC
196 TTAAAGTAATATTATAGTTAAAAAGTGATCAAATATGGAAGGCGAAACTCAAATAACTAAACAGC
1692020 AGCTAATGCAGTAGAAAATTCAATAAAGCACATATCAGTAAAGGGAGTTGGGACTTTTTAAACTC
261 AGCTAATGCAGTAGAAAATTCAATAAAGCACATATCAGTAAAGGGAGTTGGGACTTTTTAAACTC
1692085 ACAATGGTATTTTAATTCACTGAAAATAAAAATTAGACTGACGAATAAAAATACCAAGAAAACAA
326 ACAATGGTATTTTAATTCACTGAAAATAAAAATTAGACTGACGAATAAAAATACCAAGAAAACAA
1692150 GTTAAATGAGAAGAAATCATAAGCAAAGCACCATTACCATATAAAAGAAGATTAAGACATCCAAT
391 GTTAAATGAGAAGAAATCATAAGCAAAGCACCATTACCATATAAAAGAAGATTAAGACATCCAAT
1692215 AACACATGTGGAATATGGAGAAAACAGATGCCCGTGAAACCCCCTATAACAAAAACAAATAA-TT
456 AACACATGTGGAATATGGAGAAAACAGATGCCCGTGAAACCCCCTATAACAAAAACAAATAATTT
1692279 TTTTTTTGCAA
521 TTTTTTTGCAA
1692290 CCATCAGATATGAAACAGAAACTCCTACCCGTTTTATCATAAAATGTAAACGTAATTACTGATAT
1 CCATCAGATATGAAACAGAAACTCCTACCCGTTTTATCATAAAATGTAAACGTAATTACTGATAT
1692355 ATGTAAGGCATCAAGTACTCTATTGAAACACCAAGTTTCTTAATCAAATGTAAGCAGAAATTAGA
66 ATGTAAGGCATCAAGTACTCTATTGAAACACCAAGTTTCTTAATCAAATGTAAGCAGAAATTAGA
1692420 ACTTGTAAATTCCACAACTACTCCAAAATCATAACTTATGTCCCAAGTACCATTCTAACTGCATT
131 ACTTGTAAATTCCACAACTACTCCAAAATCATAACTTATGTCCCAAGTACCATTCTAACTGCATT
1692485 TTAAAGTAATATTATAGTTAAAAAGTGATCAAATATGGAAGGCGAAACTCAAATAACTAAACAGC
196 TTAAAGTAATATTATAGTTAAAAAGTGATCAAATATGGAAGGCGAAACTCAAATAACTAAACAGC
1692550 AGCTAATGCAGTAGAAAATTCAATAAAGCACATATCAGTAAAGGGAGTTGGGACTTTTTAAACTC
261 AGCTAATGCAGTAGAAAATTCAATAAAGCACATATCAGTAAAGGGAGTTGGGACTTTTTAAACTC
1692615 ACAATGGTATTTTAATTCACTGAAAATAAAAATTAGACTGACGAATAAAAATACCAAGAAAACAA
326 ACAATGGTATTTTAATTCACTGAAAATAAAAATTAGACTGACGAATAAAAATACCAAGAAAACAA
1692680 GTTAAATGAGAAGAAATCATAAGCAAAGCACCATTACCATATAAAAGAAGATTAAGACATCCAAT
391 GTTAAATGAGAAGAAATCATAAGCAAAGCACCATTACCATATAAAAGAAGATTAAGACATCCAAT
1692745 AACACATGTGGAATATGGAGAAAACAGATGCCCGTGAAACCCCCTATAACAAAAACAAATAATTT
456 AACACATGTGGAATATGGAGAAAACAGATGCCCGTGAAACCCCCTATAACAAAAACAAATAATTT
1692810 TTTTTTTGCAA
521 TTTTTTTGCAA
1692821 CCATCAGATATGAAACAGAAACTCCTACCCGTTTTATCATAAAAATGTAAACGTAATTACTGATA
1 CCATCAGATATGAAACAGAAACTCCTACCCGTTTTATCAT-AAAATGTAAACGTAATTACTGATA
1692886 TATGTAAGGCATCAAGTACTCTATTGAAACACCAAGTTTCTTAATCAAATGTAAGCAGAAATTAG
65 TATGTAAGGCATCAAGTACTCTATTGAAACACCAAGTTTCTTAATCAAATGTAAGCAGAAATTAG
1692951 AACTTGTAAATTCCACAACTACTCCAAAATCATAACTTATGTCCCAAGTACCATTCTAACTGCAT
130 AACTTGTAAATTCCACAACTACTCCAAAATCATAACTTATGTCCCAAGTACCATTCTAACTGCAT
1693016 TTTAAAGTAATATTATAGTTAAAAAGTGATCAAATATGGAAGGCGAAACTCAAATAACTAAACAG
195 TTTAAAGTAATATTATAGTTAAAAAGTGATCAAATATGGAAGGCGAAACTCAAATAACTAAACAG
*
1693081 CAGCTAATGCAGTAGAAAATTCAATACAGCACATATCAGTAAAGGGAGTTGGGACTTTTTAAACT
260 CAGCTAATGCAGTAGAAAATTCAATAAAGCACATATCAGTAAAGGGAGTTGGGACTTTTTAAACT
1693146 CACAATGGTATTTTAATTCACTGAAAATAAAAATTAGACTGACGAATAAAAATACCAAGAAAACA
325 CACAATGGTATTTTAATTCACTGAAAATAAAAATTAGACTGACGAATAAAAATACCAAGAAAACA
1693211 AGTTAAATGAGAAGAAATCATAAGCAAAGCACCATTACCATATAAAAGAAGATTAAGACATCCAA
390 AGTTAAATGAGAAGAAATCATAAGCAAAGCACCATTACCATATAAAAGAAGATTAAGACATCCAA
1693276 TAACACATGTGGAATATGGAGAAAACAGATGCCCGTGAAACCCCCTATAACAAAAACAAATAATT
455 TAACACATGTGGAATATGGAGAAAACAGATGCCCGTGAAACCCCCTATAACAAAAACAAATAA--
1693341 TTTTTTTTTTGCAA
518 TTTTTTTTTTGCAA
1693355 CCAT
1 CCAT
1693359 GTTACAAACT
Statistics
Matches: 1064, Mismatches: 1, Indels: 4
1.00 0.00 0.00
Matches are distributed among these distances:
530 517 0.49
531 53 0.05
532 476 0.45
534 18 0.02
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (531 bp):
CCATCAGATATGAAACAGAAACTCCTACCCGTTTTATCATAAAATGTAAACGTAATTACTGATAT
ATGTAAGGCATCAAGTACTCTATTGAAACACCAAGTTTCTTAATCAAATGTAAGCAGAAATTAGA
ACTTGTAAATTCCACAACTACTCCAAAATCATAACTTATGTCCCAAGTACCATTCTAACTGCATT
TTAAAGTAATATTATAGTTAAAAAGTGATCAAATATGGAAGGCGAAACTCAAATAACTAAACAGC
AGCTAATGCAGTAGAAAATTCAATAAAGCACATATCAGTAAAGGGAGTTGGGACTTTTTAAACTC
ACAATGGTATTTTAATTCACTGAAAATAAAAATTAGACTGACGAATAAAAATACCAAGAAAACAA
GTTAAATGAGAAGAAATCATAAGCAAAGCACCATTACCATATAAAAGAAGATTAAGACATCCAAT
AACACATGTGGAATATGGAGAAAACAGATGCCCGTGAAACCCCCTATAACAAAAACAAATAATTT
TTTTTTTGCAA
Found at i:1698481 original size:16 final size:16
Alignment explanation
Indices: 1698460--1698492 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1698450 TTTATATATA
1698460 TATTAAGACGATGTTG
1 TATTAAGACGATGTTG
1698476 TATTAAGACGATGTTG
1 TATTAAGACGATGTTG
1698492 T
1 T
1698493 CAATCTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (16 bp):
TATTAAGACGATGTTG
Found at i:1699522 original size:37 final size:37
Alignment explanation
Indices: 1699449--1699523 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
1699439 ACTGTAAGAT
* *
1699449 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
1699486 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
1699523 A
1 A
1699524 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:1701578 original size:31 final size:32
Alignment explanation
Indices: 1701543--1701620 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 32
1701533 CCTGATGTTT
1701543 ACTTTTTGTTTCATTTTAATACTC-GA-CGTTA
1 ACTTTTTGTTTCATTTTAATAC-CAGACCGTTA
* *
1701574 ACTTTTTGTTTCATTTTAGTACCATACCGTTA
1 ACTTTTTGTTTCATTTTAATACCAGACCGTTA
1701606 ACTTTTTGTTTCATT
1 ACTTTTTGTTTCATT
1701621 CTAGTAACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 1 0.02
31 22 0.51
32 20 0.47
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.54
Consensus pattern (32 bp):
ACTTTTTGTTTCATTTTAATACCAGACCGTTA
Found at i:1701610 original size:32 final size:31
Alignment explanation
Indices: 1701543--1701626 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 31
1701533 CCTGATGTTT
*
1701543 ACTTTTTGTTTCATTTTAATACTCGACGTTA
1 ACTTTTTGTTTCATTTTAGTACTCGACGTTA
*
1701574 ACTTTTTGTTTCATTTTAGTAC-CATACCGTTA
1 ACTTTTTGTTTCATTTTAGTACTC-GA-CGTTA
*
1701606 ACTTTTTGTTTCATTCTAGTA
1 ACTTTTTGTTTCATTTTAGTA
1701627 ACTAAATTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
30 1 0.02
31 22 0.46
32 25 0.52
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (31 bp):
ACTTTTTGTTTCATTTTAGTACTCGACGTTA
Found at i:1704039 original size:29 final size:30
Alignment explanation
Indices: 1703977--1704032 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 30
1703967 TATTGTATTT
*
1703977 TTTTAATAATTATTTTATAATATTGAATAA
1 TTTTAATAATTATTTTATAATATTAAATAA
*
1704007 TTTTAATAATTA-TTTATAATTTTAAA
1 TTTTAATAATTATTTTATAATATTAAA
1704033 ATATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TTTTAATAATTATTTTATAATATTAAATAA
Found at i:1704383 original size:14 final size:14
Alignment explanation
Indices: 1704366--1704426 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
1704356 GAGAATCTAC
*
1704366 TTATATTGTTATAA
1 TTATATTATTATAA
1704380 TTATATTATTATAA
1 TTATATTATTATAA
*
1704394 -TATATATAATATAA
1 TTATAT-TATTATAA
*
1704408 TTTTATT-TTAATAA
1 TTATATTATT-ATAA
1704422 -TATAT
1 TTATAT
1704427 AATAAATTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 10 0.26
14 25 0.64
15 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TTATATTATTATAA
Found at i:1704413 original size:25 final size:25
Alignment explanation
Indices: 1704385--1704434 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1704375 TATAATTATA
1704385 TTATTATAAT-ATATATAATATAATT
1 TTATTATAATAATATATAATA-AATT
*
1704410 TTATTTTAATAATATATAATAAATT
1 TTATTATAATAATATATAATAAATT
1704435 AGTAATACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATTATAATAATATATAATAAATT
Found at i:1704557 original size:14 final size:14
Alignment explanation
Indices: 1704530--1704595 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
1704520 TAATAAAATA
1704530 TAATATTCAT-ATTT
1 TAATATT-ATAATTT
1704544 TAATATTATAATTTT
1 TAATATTATAA-TTT
* *
1704559 TAATGTTTTAA---
1 TAATATTATAATTT
*
1704570 TAATATTATTATTT
1 TAATATTATAATTT
1704584 TAATA-TATAATT
1 TAATATTATAATT
1704596 AATATAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
11 8 0.20
13 8 0.20
14 13 0.32
15 12 0.29
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (14 bp):
TAATATTATAATTT
Found at i:1704596 original size:16 final size:17
Alignment explanation
Indices: 1704564--1704596 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1704554 ATTTTTAATG
*
1704564 TTTTAATAATATTATTA
1 TTTTAATAATATAATTA
1704581 TTTTAAT-ATATAATTA
1 TTTTAATAATATAATTA
1704597 ATATAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAATAATATAATTA
Found at i:1704598 original size:25 final size:27
Alignment explanation
Indices: 1704543--1704605 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
1704533 TATTCATATT
* * *
1704543 TTAATATTATAATTTTTAATGTTTTAA
1 TTAATATTATTATTTTTAATGATATAA
1704570 -TAATATTATTA-TTTTAAT-ATATAA
1 TTAATATTATTATTTTTAATGATATAA
*
1704594 TTAATATAATTA
1 TTAATATTATTA
1704606 ATAATATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 4 0.13
25 17 0.55
26 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAATATTATTATTTTTAATGATATAA
Found at i:1704607 original size:37 final size:36
Alignment explanation
Indices: 1704566--1704665 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 36
1704556 TTTTAATGTT
*
1704566 TTAATAATATTATTATTTTAATATATAATTAATATAA
1 TTAATAATATT-TTATTTTAATAAATAATTAATATAA
1704603 TTAATAATATATGGTTCTTATTTTAATAAATAATTAATATAA
1 TTAAT-A-ATA---TT-TTATTTTAATAAATAATTAATATAA
*
1704645 TTTATAATAATTTTATTTTAA
1 TTAATAAT-ATTTTATTTTAA
1704666 AGAAATATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
37 14 0.26
38 3 0.06
39 3 0.06
40 2 0.04
41 2 0.04
42 30 0.56
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (36 bp):
TTAATAATATTTTATTTTAATAAATAATTAATATAA
Found at i:1704652 original size:23 final size:22
Alignment explanation
Indices: 1704580--1704654 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 22
1704570 TAATATTATT
*
1704580 ATTTTAATATATAATTAATATA
1 ATTTTAATAAATAATTAATATA
*** * *
1704602 A--TTAAT-AATATATGGTTCTT
1 ATTTTAATAAATA-ATTAATATA
1704622 ATTTTAATAAATAATTAATATA
1 ATTTTAATAAATAATTAATATA
1704644 ATTTATAATAA
1 ATTT-TAATAA
1704655 TTTTATTTTA
Statistics
Matches: 37, Mismatches: 11, Indels: 9
0.65 0.19 0.16
Matches are distributed among these distances:
19 3 0.08
20 10 0.27
22 14 0.38
23 10 0.27
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (22 bp):
ATTTTAATAAATAATTAATATA
Found at i:1704726 original size:14 final size:15
Alignment explanation
Indices: 1704707--1704748 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1704697 AAAGTTGTAT
**
1704707 ATAATATTTTAAT-A
1 ATAATATTGAAATAA
1704721 ATAATATTGAAATAA
1 ATAATATTGAAATAA
1704736 ATAATATT-AAATA
1 ATAATATTGAAATA
1704749 TATTATTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
ATAATATTGAAATAA
Found at i:1707190 original size:64 final size:63
Alignment explanation
Indices: 1707076--1707215 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 63
1707066 TATAAAATAG
* * * * *
1707076 TCATTAAATTTATCGAACTGTTATAAGATGATGATTAGATTTTATCGAATTATTACAAAATGA
1 TCATTAAATTTATCAAACTATTATAAGATGATCATTAAATATTATCGAATTATTACAAAATGA
* * * * *
1707139 TCATTGAATTTTATCAAACTATTATAA-ATTGATCATTAAATATTATTGAATTGTTATAAAATTA
1 TCATT-AAATTTATCAAACTATTATAAGA-TGATCATTAAATATTATCGAATTATTACAAAATGA
*
1707203 TTATTAAATTTAT
1 TCATTAAATTTAT
1707216 TGAAATTTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
63 13 0.21
64 50 0.79
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (63 bp):
TCATTAAATTTATCAAACTATTATAAGATGATCATTAAATATTATCGAATTATTACAAAATGA
Found at i:1707196 original size:32 final size:31
Alignment explanation
Indices: 1707076--1707215 Score: 113
Period size: 32 Copynumber: 4.4 Consensus size: 31
1707066 TATAAAATAG
*
1707076 TCATTAAATTTATCGAACTGTTATAAGA-TGA
1 TCATTAAATTTATCGAACTATTATAA-ATTGA
* * * * *
1707107 TGATTAGATTTTATCGAATTATTACAAAATGA
1 TCATTA-AATTTATCGAACTATTATAAATTGA
* *
1707139 TCATTGAATTTTATCAAACTATTATAAATTGA
1 TCATT-AAATTTATCGAACTATTATAAATTGA
* * *
1707171 TCATTAAATATTATTGAATTGTTATAAAATT-A
1 TCATTAAAT-TTATCGAACTATTAT-AAATTGA
*
1707203 TTATTAAATTTAT
1 TCATTAAATTTAT
1707216 TGAAATTTTA
Statistics
Matches: 88, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
31 13 0.15
32 69 0.78
33 6 0.07
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (31 bp):
TCATTAAATTTATCGAACTATTATAAATTGA
Found at i:1707204 original size:22 final size:22
Alignment explanation
Indices: 1707117--1707212 Score: 63
Period size: 22 Copynumber: 4.5 Consensus size: 22
1707107 TGATTAGATT
* * * *
1707117 TTATCGAATTATTACAAAATGA
1 TTATTGAATTGTTATAAAATTA
* * *
1707139 TCATTGAATT-TTATCAAACTA
1 TTATTGAATTGTTATAAAATTA
* * *
1707160 TTA-TAAATTGATCATTAAA-TA
1 TTATTGAATTG-TTATAAAATTA
1707181 TTATTGAATTGTTATAAAATTA
1 TTATTGAATTGTTATAAAATTA
*
1707203 TTATTAAATT
1 TTATTGAATT
1707213 TATTGAAATT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
20 5 0.09
21 20 0.36
22 31 0.55
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (22 bp):
TTATTGAATTGTTATAAAATTA
Found at i:1708782 original size:20 final size:20
Alignment explanation
Indices: 1708757--1708797 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1708747 CGTTGCAGAC
1708757 ATGACGGATGCTACTATGAT
1 ATGACGGATGCTACTATGAT
*
1708777 ATGACGGATGCTATTATGAT
1 ATGACGGATGCTACTATGAT
1708797 A
1 A
1708798 AGCCGCGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (20 bp):
ATGACGGATGCTACTATGAT
Found at i:1718583 original size:36 final size:36
Alignment explanation
Indices: 1718538--1718734 Score: 281
Period size: 36 Copynumber: 5.5 Consensus size: 36
1718528 ACGAAAGAAT
*
1718538 GCATC-GCACTTCCGATTCAAGTTGAACGGAGGGAA
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAGGGAA
* *
1718573 GCGTCGGCACTTTCGATTCAAGTCGAACGGAGGGAA
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAGGGAA
*
1718609 GCGTCGGCACTTCCGATTCAAGTCGAACGGAGGGAA
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAGGGAA
*
1718645 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAA
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAGGGAA
* * * *
1718681 GCATCAGCACTTCCGATTCAAGTTGAACGGAAGGAT
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAGGGAA
* *
1718717 GTATC-GCACTTTCGATTC
1 GCATCGGCACTTCCGATTC
1718735 GAGTGTTCAT
Statistics
Matches: 150, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
35 16 0.11
36 134 0.89
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (36 bp):
GCATCGGCACTTCCGATTCAAGTCGAACGGAGGGAA
Found at i:1722871 original size:31 final size:31
Alignment explanation
Indices: 1722833--1722894 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1722823 GTCGCCGGTA
1722833 ATTCCATGCACACACTCCTTTATTTTAGTAT
1 ATTCCATGCACACACTCCTTTATTTTAGTAT
* * *
1722864 ATTCCATGCGCACATTCCTTTATTTTGGTAT
1 ATTCCATGCACACACTCCTTTATTTTAGTAT
1722895 GATCGGTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.44
Consensus pattern (31 bp):
ATTCCATGCACACACTCCTTTATTTTAGTAT
Found at i:1723681 original size:31 final size:31
Alignment explanation
Indices: 1723643--1723718 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
1723633 TAAACTATCA
* * *
1723643 GTTTTAGTATTTAAACTGTTAGTTATGATCC
1 GTTTTAGTACTTAAACTATCAGTTATGATCC
* *
1723674 GTTTTAGTACTTAAACTATCAGTTTTGGTCC
1 GTTTTAGTACTTAAACTATCAGTTATGATCC
1723705 GTTTTAGTACTTAA
1 GTTTTAGTACTTAA
1723719 CTTTTAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (31 bp):
GTTTTAGTACTTAAACTATCAGTTATGATCC
Found at i:1724005 original size:15 final size:15
Alignment explanation
Indices: 1723985--1724028 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1723975 TAAACGCGTA
1723985 ATTTACCTAAAGTAT
1 ATTTACCTAAAGTAT
*
1724000 ATTTACTTAAAGTAT
1 ATTTACCTAAAGTAT
*
1724015 ATTTACCCAAAGTA
1 ATTTACCTAAAGTA
1724029 ATAGTTGCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (15 bp):
ATTTACCTAAAGTAT
Found at i:1726231 original size:12 final size:12
Alignment explanation
Indices: 1726214--1726238 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1726204 TCGAAAGAAA
1726214 GTATTCGAATAT
1 GTATTCGAATAT
1726226 GTATTCGAATAT
1 GTATTCGAATAT
1726238 G
1 G
1726239 GAAGAATCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (12 bp):
GTATTCGAATAT
Found at i:1727184 original size:60 final size:60
Alignment explanation
Indices: 1727117--1727244 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
1727107 GCATCATCTG
* * *
1727117 TCCCCAAAATATGAATCTCATTCTAAATTGATCCCTAAAATTTTGAATATTCCAATTTCA
1 TCCCCAAAATATGAATCTCATTCTAAATTGATCCCTAAAATTTTAAAGACTCCAATTTCA
* ** * * * *
1727177 TCCCCAAACTATGGCTCTTATTCTAAATTGGTCCCTAAACTTTTAAAGCCTCCAATTTCA
1 TCCCCAAAATATGAATCTCATTCTAAATTGATCCCTAAAATTTTAAAGACTCCAATTTCA
*
1727237 TCCGCAAA
1 TCCCCAAA
1727245 TTCATCCAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (60 bp):
TCCCCAAAATATGAATCTCATTCTAAATTGATCCCTAAAATTTTAAAGACTCCAATTTCA
Found at i:1731438 original size:2 final size:2
Alignment explanation
Indices: 1731425--1731473 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1731415 GGTTTTTCTT
* *
1731425 TA TA TC TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1731466 TA TA TA TA
1 TA TA TA TA
1731474 CACGCACACA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1732215 original size:59 final size:59
Alignment explanation
Indices: 1732148--1732261 Score: 228
Period size: 59 Copynumber: 1.9 Consensus size: 59
1732138 GGTGGACCAA
1732148 TTGTAAGTACCTTAAAAATATTAATTAATCTGATATTCTGATGACCAACTCCATACAAT
1 TTGTAAGTACCTTAAAAATATTAATTAATCTGATATTCTGATGACCAACTCCATACAAT
1732207 TTGTAAGTACCTTAAAAATATTAATTAATCTGATATTCTGATGACCAACTCCATA
1 TTGTAAGTACCTTAAAAATATTAATTAATCTGATATTCTGATGACCAACTCCATA
1732262 ATTAACCCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.36
Consensus pattern (59 bp):
TTGTAAGTACCTTAAAAATATTAATTAATCTGATATTCTGATGACCAACTCCATACAAT
Found at i:1732901 original size:10 final size:10
Alignment explanation
Indices: 1732886--1732957 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
1732876 GGGTCTCCAA
1732886 CGTTTATGTT
1 CGTTTATGTT
1732896 CGTTTATGTT
1 CGTTTATGTT
1732906 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
1732917 ATGTTCGTGTT
1 -CGTTTATGTT
1732928 CGTTTATGTT
1 CGTTTATGTT
1732938 CG----TGTT
1 CGTTTATGTT
1732944 CGTTTATGTT
1 CGTTTATGTT
1732954 CGTT
1 CGTT
1732958 ATTTATTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
6 6 0.12
10 31 0.65
11 7 0.15
12 4 0.08
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1732917 original size:16 final size:16
Alignment explanation
Indices: 1732892--1732956 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1732882 CCAACGTTTA
1732892 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1732908 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
1732924 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1732940 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1732956 T
1 T
1732957 TATTTATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1733045 original size:16 final size:16
Alignment explanation
Indices: 1733024--1733056 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1733014 AAAAAAATTT
*
1733024 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
1733040 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
1733056 T
1 T
1733057 CTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:1734299 original size:61 final size:63
Alignment explanation
Indices: 1734192--1734315 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 63
1734182 GTTATCAATA
1734192 ATTAAGAAAAATTATGAATAAATAGAGCGGAATGATTACAAGGTAGTATTTGTT-AGAAGTTT
1 ATTAAGAAAAATTATGAATAAATAGAGCGGAATGATTACAAGGTAGTATTTGTTCAGAAGTTT
* *
1734254 ATTAAGAAAAATTATGAATAAATAGAGTGG-ATGATTACAATGTAGTATTTGTTCAGAAGTTT
1 ATTAAGAAAAATTATGAATAAATAGAGCGGAATGATTACAAGGTAGTATTTGTTCAGAAGTTT
1734316 TCTTAGTTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 22 0.37
62 37 0.63
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (63 bp):
ATTAAGAAAAATTATGAATAAATAGAGCGGAATGATTACAAGGTAGTATTTGTTCAGAAGTTT
Found at i:1737341 original size:49 final size:49
Alignment explanation
Indices: 1737282--1737563 Score: 272
Period size: 49 Copynumber: 5.7 Consensus size: 49
1737272 AACTGCTCTA
* * *
1737282 TAATGAAAGTTAAATGCATAATGGTGCGTTTTTTGCAGAAATGTACCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTTGCAGAAATGTGCCAC
*
1737331 TAATGCAAGTTAAATGC-TAAAT-GTGC-TTTTTTGACAGAAAGATTGAAAGATGTCAC
1 TAATGCAAGTTAAATGCAT-AATGGTGCATTTTTTG-CAG-AA-A-T----G-TGCCAC
*
1737387 TAATGCAAGTTAAATGCATAATGGTGCATTTTTTGCATAAATGTGCCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTTGCAGAAATGTGCCAC
* *
1737436 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTTGCATAAATGTG-CAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTTGCAGAAATGTGCCAC
* * * * * *
1737484 TAATGCGAGTTAAATGCAT-ATCAGTGCA-TTTTGGTAGAAAGGTGTCAC
1 TAATGCAAGTTAAATGCATAAT-GGTGCATTTTTTGCAGAAATGTGCCAC
* *
1737532 TAATG-ACAGTTAAATGTATAACGGTGCATTTT
1 TAATGCA-AGTTAAATGCATAATGGTGCATTTT
1737564 AGCATAAAAG
Statistics
Matches: 198, Mismatches: 17, Indels: 36
0.79 0.07 0.14
Matches are distributed among these distances:
47 20 0.10
48 58 0.29
49 74 0.37
50 2 0.01
51 1 0.01
54 1 0.01
55 2 0.01
56 26 0.13
57 7 0.04
58 7 0.04
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (49 bp):
TAATGCAAGTTAAATGCATAATGGTGCATTTTTTGCAGAAATGTGCCAC
Found at i:1737489 original size:48 final size:48
Alignment explanation
Indices: 1737384--1737571 Score: 220
Period size: 48 Copynumber: 3.9 Consensus size: 48
1737374 TGAAAGATGT
*
1737384 CACTAATGCAAGTTAAATGCATAATGGTGCATTTTTTGCATAAATGTGC
1 CACTAATGCAAGTTAAATGCATAAAGGTGCA-TTTTTGCATAAATGTGC
1737433 CACTAATGCAAGTTAAATGCATAAAGGTGCATTTTTTGCATAAATGTG-
1 CACTAATGCAAGTTAAATGCATAAAGGTGCA-TTTTTGCATAAATGTGC
* * * * * * *
1737481 CACTAATGCGAGTTAAATGCATATCA-GTGCATTTTGGTAGAAAGGTGT
1 CACTAATGCAAGTTAAATGCATA-AAGGTGCATTTTTGCATAAATGTGC
* * *
1737529 CACTAATG-ACAGTTAAATGTATAACGGTGCATTTTAGCATAAA
1 CACTAATGCA-AGTTAAATGCATAAAGGTGCATTTTTGCATAAA
1737572 AGATGTCACT
Statistics
Matches: 121, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
47 12 0.10
48 61 0.50
49 48 0.40
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (48 bp):
CACTAATGCAAGTTAAATGCATAAAGGTGCATTTTTGCATAAATGTGC
Found at i:1741823 original size:16 final size:17
Alignment explanation
Indices: 1741804--1741840 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1741794 TTAGTAATAA
1741804 AAAATATA-GAAAAATT
1 AAAATATATGAAAAATT
1741820 AAAATATATGAAAAATT
1 AAAATATATGAAAAATT
1741837 AAAA
1 AAAA
1741841 ATTTTAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (17 bp):
AAAATATATGAAAAATT
Found at i:1741823 original size:17 final size:18
Alignment explanation
Indices: 1741803--1741842 Score: 66
Period size: 16 Copynumber: 2.3 Consensus size: 18
1741793 ATTAGTAATA
1741803 AAAAATATA-GAAAAATT
1 AAAAATATATGAAAAATT
1741820 -AAAATATATGAAAAATT
1 AAAAATATATGAAAAATT
1741837 AAAAAT
1 AAAAAT
1741843 TTTAGGGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 8 0.38
18 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAAATATATGAAAAATT
Found at i:1749414 original size:24 final size:24
Alignment explanation
Indices: 1749382--1749428 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1749372 AAACTGATTG
1749382 TAATTGTTGTGGGGTTGTAATTTT
1 TAATTGTTGTGGGGTTGTAATTTT
*
1749406 TAATTGTTGTGGGGTTTTAATTT
1 TAATTGTTGTGGGGTTGTAATTT
1749429 CTTTATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (24 bp):
TAATTGTTGTGGGGTTGTAATTTT
Found at i:1750736 original size:30 final size:30
Alignment explanation
Indices: 1750702--1750780 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
1750692 GATCTAATCT
1750702 CATGCAGATGTCAGAATGGAGAATTTATCC
1 CATGCAGATGTCAGAATGGAGAATTTATCC
* * *
1750732 CATGCAAATATCAGAAAT-GAGAGTTTATCC
1 CATGCAGATGTCAG-AATGGAGAATTTATCC
** *
1750762 CATATAGATGTAAGAATGG
1 CATGCAGATGTCAGAATGG
1750781 GGAACGTCCC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 3 0.08
30 33 0.85
31 3 0.08
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (30 bp):
CATGCAGATGTCAGAATGGAGAATTTATCC
Found at i:1754781 original size:2 final size:2
Alignment explanation
Indices: 1754776--1754803 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1754766 CATGTGTGTG
1754776 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
1754804 AGTCAGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1757098 original size:2 final size:2
Alignment explanation
Indices: 1757091--1757117 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1757081 GTTAACCCCA
1757091 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1757118 AATAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1758222 original size:17 final size:18
Alignment explanation
Indices: 1758200--1758234 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1758190 AAAATATTTA
1758200 TTAAAAAA-TAAAATAAT
1 TTAAAAAATTAAAATAAT
1758217 TTAAAAAATTAAAATAAT
1 TTAAAAAATTAAAATAAT
1758235 CCCTTCGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAAATTAAAATAAT
Found at i:1763498 original size:156 final size:158
Alignment explanation
Indices: 1763304--1763611 Score: 451
Period size: 156 Copynumber: 2.0 Consensus size: 158
1763294 TTAAAAAACA
* * * *
1763304 AACTTACAATAAATAATGAATTTAAAAAATAATAAAAATATGAAAAATTAAGGGATTAAATTGAA
1 AACTTAAAATAAATAATGAATTTAAAAAATAAGAAAAATATGAAAAATCAAGGGACTAAATTGAA
*
1763369 AAATAAAAATATTATTATC-AAAAAGA-G-ATTGAAAGTACATATGTATTCTACAATGATTTATG
66 AAATAAAAAAATTATTA-CAAAAAAGAGGAATTGAAAGTACATATGTATTCTACAATGATTTATG
*
1763431 AACATGTGATTCAAATTTAGTAAGAGATG
130 AACATGTAATTCAAATTTAGTAAGAGATG
* * *
1763460 AACTTAAAATAAATGATGAATTTTATAAATAAGAAAAATATGAAAAATCAAGGGACTAAATTGAA
1 AACTTAAAATAAATAATGAATTTAAAAAATAAGAAAAATATGAAAAATCAAGGGACTAAATTGAA
* * *
1763525 AAATAAAAAAATTGTTACAAAAAAGAGGAATTGAAAGTACATATGTATTCTACGATGATTTATGG
66 AAATAAAAAAATTATTACAAAAAAGAGGAATTGAAAGTACATATGTATTCTACAATGATTTATGA
** *
1763590 GTATGTAATTCAAATTTGGTAA
131 ACATGTAATTCAAATTTAGTAA
1763612 AAAAAAATAG
Statistics
Matches: 134, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
155 1 0.01
156 80 0.60
157 1 0.01
158 52 0.39
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (158 bp):
AACTTAAAATAAATAATGAATTTAAAAAATAAGAAAAATATGAAAAATCAAGGGACTAAATTGAA
AAATAAAAAAATTATTACAAAAAAGAGGAATTGAAAGTACATATGTATTCTACAATGATTTATGA
ACATGTAATTCAAATTTAGTAAGAGATG
Found at i:1769180 original size:20 final size:20
Alignment explanation
Indices: 1769155--1769192 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1769145 TAGGTTCGAG
*
1769155 TATCGATATTGGATGAATAA
1 TATCGATATTGAATGAATAA
1769175 TATCGATATTGAATGAAT
1 TATCGATATTGAATGAAT
1769193 TGGGTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (20 bp):
TATCGATATTGAATGAATAA
Found at i:1772207 original size:29 final size:29
Alignment explanation
Indices: 1772175--1772232 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1772165 GTACAATTAG
*
1772175 GAAATTGAAAACTTTTAAAGTTCAGTGAA
1 GAAATTGAAAACTTTTAAAGTTCACTGAA
1772204 GAAATTGAAAACTTTTAAAGTTCACTGAA
1 GAAATTGAAAACTTTTAAAGTTCACTGAA
1772233 CAAAATAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.31
Consensus pattern (29 bp):
GAAATTGAAAACTTTTAAAGTTCACTGAA
Found at i:1773369 original size:446 final size:443
Alignment explanation
Indices: 1772533--1773426 Score: 1542
Period size: 446 Copynumber: 2.0 Consensus size: 443
1772523 CTCTGTATTA
* *
1772533 TAAATGTATATCACATATAAAAAAATATGAAGAAATACATATGTATTGTATATGGTTACAAAATA
1 TAAATGTATATCACATATAAAAAAATATGAAGAAATACATATATATTGTATATAGTTACAAAATA
* * *
1772598 ACCATTTAAATTGGAATGAAATAATATCATAATATTATAAATATTTATATTTAAATTTAAGCAGA
66 ACCATTTAAATTGAAATAAAATAATATCATAATATTATAAATATTTATAATTAAATTTAAGCAGA
1772663 AACTAGAAAATTTAACTTGACTCGAATTTTATAAATTCGACTCAACTCGATAAAATTTTAAGTCA
131 AACTAGAAAATTTAACTTGACTCGAATTTTATAAATTCGACTCAACTCGATAAAATTTTAAGTCA
* * *
1772728 ACTTCGAGTTGTAAAATAGAATTCGACAACTCGAATAATTCAAAAAATTTTAACTCGACTCACTT
196 ACTTCGAGTTGTAAAATAAAATTCGACAACTCGAATAATTCAAAAAAATTTAACTCGACTCACTC
* * * *
1772793 TAACGCTGACCCCTAATTGGAATGCTTCTGAATTCTACACAGCCATTTCTCTTTTTCTTTTTAGC
261 TAACGCTCACACCTAATTGGAATGCTTCTGAATTCTACACAACCATTTCTCTTTTTCATTTTAGC
1772858 CTCCTTATCTCATCATCTAGTCATTCCTAGCCACTGCTATCCACATCACCATCATAATGTTCTTC
326 CTCCTTATCTCATCATCTAGTCATTCCTAGCCACTGCTATCCACATCACCATCATAATGTTCTTC
*
1772923 ATCTACCACACTAGAATAATTAACACATTCGAACCCACCACTACTATGGA-CAT
391 ATCTACCACACTAGAAAAATTAACACATTCGAACCCACCACTACTAT-GACCAT
* *
1772976 TAAATGTATATTACATATAAAAAAATATGAAGAAATACATATATATTTTATATAGTTACAAAA-A
1 TAAATGTATATCACATATAAAAAAATATGAAGAAATACATATATATTGTATATAGTTACAAAATA
*
1773040 ACTATTTAAATTGAAATAAAATAATATCATAATATTATAAATATTTATAATTAAATTTAAGCAGA
66 ACCATTTAAATTGAAATAAAATAATATCATAATATTATAAATATTTATAATTAAATTTAAGCAGA
1773105 AACTAGAAAATTTAACTTGACTCGACTCGAATTTTATAAATTCGACTCAACTCGATAAAATTTTA
131 AACTAGAAAATTTAAC-T---T-GACTCGAATTTTATAAATTCGACTCAACTCGATAAAATTTTA
*
1773170 AGTCAACTTCGAGTTGTAAAATAAAATTCGACAACTCGAATAATTCAAAAAAATTTAGCTCGACT
191 AGTCAACTTCGAGTTGTAAAATAAAATTCGACAACTCGAATAATTCAAAAAAATTTAACTCGACT
1773235 CACTCTAACGCTCA-ACCTAATTGGAATGCTTCTGAATTCTACACAACCATTTCTCTTTTTCATT
256 CACTCTAACGCTCACACCTAATTGGAATGCTTCTGAATTCTACACAACCATTTCTCTTTTTCATT
*
1773299 TTAGCCTCCTTATCTCATCATCTAGTCATTCCTAGCCACTGCTATCCACATCACCATCATAATTT
321 TTAGCCTCCTTATCTCATCATCTAGTCATTCCTAGCCACTGCTATCCACATCACCATCATAATGT
*
1773364 TCTTCATCTACCACACTAGAAAAATTAACACCTTCGAACCCACCACTACTATGACCAT
386 TCTTCATCTACCACACTAGAAAAATTAACACATTCGAACCCACCACTACTATGACCAT
1773422 TAAAT
1 TAAAT
1773427 TCACTGTCAC
Statistics
Matches: 426, Mismatches: 19, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
442 78 0.18
443 60 0.14
445 2 0.00
446 170 0.40
447 116 0.27
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (443 bp):
TAAATGTATATCACATATAAAAAAATATGAAGAAATACATATATATTGTATATAGTTACAAAATA
ACCATTTAAATTGAAATAAAATAATATCATAATATTATAAATATTTATAATTAAATTTAAGCAGA
AACTAGAAAATTTAACTTGACTCGAATTTTATAAATTCGACTCAACTCGATAAAATTTTAAGTCA
ACTTCGAGTTGTAAAATAAAATTCGACAACTCGAATAATTCAAAAAAATTTAACTCGACTCACTC
TAACGCTCACACCTAATTGGAATGCTTCTGAATTCTACACAACCATTTCTCTTTTTCATTTTAGC
CTCCTTATCTCATCATCTAGTCATTCCTAGCCACTGCTATCCACATCACCATCATAATGTTCTTC
ATCTACCACACTAGAAAAATTAACACATTCGAACCCACCACTACTATGACCAT
Found at i:1776524 original size:37 final size:36
Alignment explanation
Indices: 1776481--1776615 Score: 152
Period size: 35 Copynumber: 3.7 Consensus size: 36
1776471 ATTAATATAG
*
1776481 TATAGTTTTTGAAAA-TATTTTTGAAAAAAATATAATA
1 TATAG-TTTTGAAAACGATTTTTG-AAAAAATATAATA
** *
1776518 TATAGTTTTTAGAAAACGGGTTTTG-AAAAATATATTA
1 TATAG-TTTT-GAAAACGATTTTTGAAAAAATATAATA
*
1776555 TATAGTTTTGAAAACGATTTTTGAAAATATATAATA
1 TATAGTTTTGAAAACGATTTTTGAAAAAATATAATA
1776591 TATAG-TTTGAAAATCG-TTTTTGAAA
1 TATAGTTTTGAAAA-CGATTTTTGAAA
1776616 TCATTATATT
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
35 29 0.34
36 21 0.24
37 26 0.30
38 5 0.06
39 5 0.06
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.42
Consensus pattern (36 bp):
TATAGTTTTGAAAACGATTTTTGAAAAAATATAATA
Found at i:1779554 original size:17 final size:17
Alignment explanation
Indices: 1779534--1779566 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1779524 ATATTTATTT
*
1779534 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
1779551 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
1779567 TACTATCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:1779795 original size:25 final size:24
Alignment explanation
Indices: 1779729--1779792 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 24
1779719 AAAAATACAA
* *
1779729 AATATTTTAACTACTTAAATTTATT
1 AATATTTT-ATTAATTAAATTTATT
1779754 AATATTTTATTAAATTAAACTTT-TT
1 AATATTTTATT-AATTAAA-TTTATT
1779779 ACATATTATTATTA
1 A-ATATT-TTATTA
1779793 TTATTAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
24 2 0.06
25 17 0.52
26 9 0.27
27 5 0.15
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (24 bp):
AATATTTTATTAATTAAATTTATT
Found at i:1782491 original size:20 final size:20
Alignment explanation
Indices: 1782463--1782501 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1782453 TTCCACCATA
1782463 TGCAACTATATGCTCCTAAT
1 TGCAACTATATGCTCCTAAT
* *
1782483 TGCATCTATATGGTCCTAA
1 TGCAACTATATGCTCCTAA
1782502 ATGAGCTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (20 bp):
TGCAACTATATGCTCCTAAT
Found at i:1789343 original size:16 final size:16
Alignment explanation
Indices: 1789316--1789349 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1789306 TATAACGAAT
1789316 AAATAGATAATAACTAA
1 AAATAGATAATAA-TAA
1789333 AAATA-ATAATAATAA
1 AAATAGATAATAATAA
1789348 AA
1 AA
1789350 TAAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
AAATAGATAATAATAA
Found at i:1789366 original size:17 final size:20
Alignment explanation
Indices: 1789317--1789357 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1789307 ATAACGAATA
*
1789317 AATAGATAAT-AACTAAAAAT
1 AATA-ATAATAAAATAAAAAT
1789337 AATAATAATAAAATAAAAAT
1 AATAATAATAAAATAAAAAT
1789357 A
1 A
1789358 TATATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
AATAATAATAAAATAAAAAT
Found at i:1789989 original size:20 final size:20
Alignment explanation
Indices: 1789952--1789990 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1789942 TGAATGGTGC
*
1789952 CGGCCACCGTTGAACGGCGT
1 CGGCCACCGTTCAACGGCGT
*
1789972 CGGCCACCGTTCATCGGCG
1 CGGCCACCGTTCAACGGCG
1789991 ACAAAACTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.38, G:0.33, T:0.15
Consensus pattern (20 bp):
CGGCCACCGTTCAACGGCGT
Found at i:1801027 original size:24 final size:24
Alignment explanation
Indices: 1800977--1801041 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
1800967 AATCTTATAT
* *
1800977 GGCACTACGGTGC-ATTTCTACGC
1 GGCACTACAGTGCAAATTCTACGC
* *
1801000 GGCACTTCAGTGCAAATTCTACGT
1 GGCACTACAGTGCAAATTCTACGC
1801024 GGCACTACAGTGCAAATT
1 GGCACTACAGTGCAAATT
1801042 TATACGAGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 11 0.31
24 25 0.69
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (24 bp):
GGCACTACAGTGCAAATTCTACGC
Found at i:1801740 original size:19 final size:19
Alignment explanation
Indices: 1801716--1801753 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1801706 CAACTTATAT
*
1801716 TTTTAT-GAATTTATATGTA
1 TTTTATCGAAGTTAT-TGTA
1801735 TTTTATCGAAGTTATTGTA
1 TTTTATCGAAGTTATTGTA
1801754 GCAGTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (19 bp):
TTTTATCGAAGTTATTGTA
Found at i:1802135 original size:23 final size:28
Alignment explanation
Indices: 1802080--1802134 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1802070 GTTAATATCC
1802080 TGTTTATTTATGGGAATTGTGGATGTTA
1 TGTTTATTTATGGGAATTGTGGATGTTA
*
1802108 TGTTTATTTATGGGAATTGTGTATGTT
1 TGTTTATTTATGGGAATTGTGGATGTT
1802135 TTATCGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (28 bp):
TGTTTATTTATGGGAATTGTGGATGTTA
Found at i:1802144 original size:28 final size:28
Alignment explanation
Indices: 1802085--1802144 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1802075 TATCCTGTTT
* **
1802085 ATTTATGGGAATTGTGGATGTTATGTTT
1 ATTTATGGGAATTGTGGATGTTATATCG
* *
1802113 ATTTATGGGAATTGTGTATGTTTTATCG
1 ATTTATGGGAATTGTGGATGTTATATCG
1802141 ATTT
1 ATTT
1802145 TATTTGCTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.02, G:0.25, T:0.52
Consensus pattern (28 bp):
ATTTATGGGAATTGTGGATGTTATATCG
Found at i:1802810 original size:9 final size:9
Alignment explanation
Indices: 1802793--1802837 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
1802783 TTCTCATCCG
1802793 ACTGAGCAT
1 ACTGAGCAT
1802802 A-TCGAGCAT
1 ACT-GAGCAT
1802811 ACTGAGCAT
1 ACTGAGCAT
* *
1802820 ACAGAGTAT
1 ACTGAGCAT
1802829 ACTGAGCAT
1 ACTGAGCAT
1802838 GGACCTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 1 0.03
9 28 0.93
10 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (9 bp):
ACTGAGCAT
Found at i:1802814 original size:18 final size:18
Alignment explanation
Indices: 1802793--1802837 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1802783 TTCTCATCCG
1802793 ACTGAGCATATC-GAGCAT
1 ACTGAGCATA-CAGAGCAT
*
1802811 ACTGAGCATACAGAGTAT
1 ACTGAGCATACAGAGCAT
1802829 ACTGAGCAT
1 ACTGAGCAT
1802838 GGACCTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (18 bp):
ACTGAGCATACAGAGCAT
Found at i:1809049 original size:30 final size:30
Alignment explanation
Indices: 1809013--1809231 Score: 149
Period size: 30 Copynumber: 7.3 Consensus size: 30
1809003 ATTCTTGACA
* * *
1809013 TTGCATGTGACTTCGTTCCCCATCATGATT
1 TTGCATGGGACTTCGTTCCCTATCCTGATT
* * * *
1809043 TTGCATGGGATTTCATTCCCTGTCCCGATT
1 TTGCATGGGACTTCGTTCCCTATCCTGATT
* *
1809073 CTGCATGGGACTTCGTTCCTTATCCTGATT
1 TTGCATGGGACTTCGTTCCCTATCCTGATT
* * *
1809103 TTGCATGAGACTTCGTTCTCTGTCCTGATT
1 TTGCATGGGACTTCGTTCCCTATCCTGATT
* * * *
1809133 TTGTATTGGACCTT-GTT-CCTCGTCCCGATT
1 TTGCATGGGA-CTTCGTTCCCT-ATCCTGATT
* * **
1809163 CTGCATAGGACCTT-GTTCCCCGT-CTCGATT
1 TTGCATGGGA-CTTCGTTCCCTATCCT-GATT
* * **
1809193 CTACATGGGACTTCGTTCCCCGTCCTGATT
1 TTGCATGGGACTTCGTTCCCTATCCTGATT
*
1809223 CTGCATGGG
1 TTGCATGGG
1809232 TACCTCTTCA
Statistics
Matches: 152, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
29 6 0.04
30 139 0.91
31 7 0.05
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (30 bp):
TTGCATGGGACTTCGTTCCCTATCCTGATT
Found at i:1809085 original size:60 final size:60
Alignment explanation
Indices: 1809014--1809231 Score: 206
Period size: 60 Copynumber: 3.6 Consensus size: 60
1809004 TTCTTGACAT
* * * * *
1809014 TGCATGTGACTTCGTTCCCCATCATGATTTTGCATGGGATTTCATTCCCTGTCCCGATTC
1 TGCATGGGACTTCGTTCCCCATCCTGATTCTGCATGGGACTTCGTTCCCTGTCCCGATTC
** * * * * *
1809074 TGCATGGGACTTCGTTCCTTATCCTGATTTTGCATGAGACTTCGTTCTCTGTCCTGATTT
1 TGCATGGGACTTCGTTCCCCATCCTGATTCTGCATGGGACTTCGTTCCCTGTCCCGATTC
* * * * * * * *
1809134 TGTATTGGACCTT-GTTCCTCGTCCCGATTCTGCATAGGACCTT-GTTCCCCGTCTCGATTC
1 TGCATGGGA-CTTCGTTCCCCATCCTGATTCTGCATGGGA-CTTCGTTCCCTGTCCCGATTC
* *
1809194 TACATGGGACTTCGTTCCCCGTCCTGATTCTGCATGGG
1 TGCATGGGACTTCGTTCCCCATCCTGATTCTGCATGGG
1809232 TACCTCTTCA
Statistics
Matches: 126, Mismatches: 29, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
59 3 0.02
60 117 0.93
61 6 0.05
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (60 bp):
TGCATGGGACTTCGTTCCCCATCCTGATTCTGCATGGGACTTCGTTCCCTGTCCCGATTC
Found at i:1812737 original size:138 final size:138
Alignment explanation
Indices: 1812481--1812740 Score: 414
Period size: 138 Copynumber: 1.9 Consensus size: 138
1812471 TAAGTGATGT
**
1812481 CAAATGATTGAGGCAAGGAAGTTCATCCAAACTTTTGCATGACCTACAGTCAAGGATTTTAAGGT
1 CAAATGATCAAGGCAAGGAAGTTCATCCAAACTTTTGCATGACCTACAGTCAAGGATTTTAAGGT
* * **
1812546 TGTTGGCTCCTAATAGATTTGGAATCTTACTTAAATTCTTGCAACCAGAAAGGTCAAGTCTTTCA
66 TGATGGCTCCCAATAGATTTGGAATCTTACTTAAATTCTTGCAAAAAGAAAGGTCAAGTCTTTCA
1812611 AGAGATTC
131 AGAGATTC
*
1812619 CAAATGATCAAGGCAAGGAAGTTCATCCAACCTTTTGCATGACCTACAGTCAAGGATTTTAAGGT
1 CAAATGATCAAGGCAAGGAAGTTCATCCAAACTTTTGCATGACCTACAGTCAAGGATTTTAAGGT
* * *
1812684 TGATGGCTCCCGATAGATTTGGCATCTTCCTTAAATTCTTGCAAAAA-AGAAGGTCAA
66 TGATGGCTCCCAATAGATTTGGAATCTTACTTAAATTCTTGCAAAAAGA-AAGGTCAA
1812741 TTTTCTTCAA
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
137 1 0.01
138 110 0.99
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (138 bp):
CAAATGATCAAGGCAAGGAAGTTCATCCAAACTTTTGCATGACCTACAGTCAAGGATTTTAAGGT
TGATGGCTCCCAATAGATTTGGAATCTTACTTAAATTCTTGCAAAAAGAAAGGTCAAGTCTTTCA
AGAGATTC
Found at i:1816470 original size:26 final size:26
Alignment explanation
Indices: 1816396--1816470 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
1816386 TTAACTATTT
*
1816396 CAATAATTAAAATTTAT-TTTAATAA
1 CAATAATTAAAATTTATATTTTATAA
* *
1816421 CAAAAATTCAAAA--TAAATTATTATAA
1 CAATAATT-AAAATTTATATT-TTATAA
**
1816447 TTATAATTAAAATTTATATTTTAT
1 CAATAATTAAAATTTATATTTTAT
1816471 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
24 2 0.05
25 13 0.34
26 18 0.47
27 5 0.13
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
CAATAATTAAAATTTATATTTTATAA
Found at i:1818896 original size:65 final size:62
Alignment explanation
Indices: 1818759--1818898 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 62
1818749 CAATATTGCC
*
1818759 ATAAGATTGTAATTGATAAAAATTAATGAGAATAAAACAGACATATGAAAATAATTGAAACG
1 ATAAGATTGTAATTGATAAAAATTAATGAGAATAAAACAGACATATGAAAACAATTGAAACG
** * * *
1818821 ATAAGATTGTAACTT-ATAAAAATGATAATGAGAATTGAATAGACATTTGAATAACAATTGAACC
1 ATAAGATTGTAA-TTGATAAAAAT--TAATGAGAATAAAACAGACATATGAA-AACAATTGAAAC
1818885 G
62 G
*
1818886 ATAAGGTTGTAAT
1 ATAAGATTGTAAT
1818899 CGGTTAAGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
62 20 0.30
63 2 0.03
64 23 0.34
65 22 0.33
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.29
Consensus pattern (62 bp):
ATAAGATTGTAATTGATAAAAATTAATGAGAATAAAACAGACATATGAAAACAATTGAAACG
Found at i:1824155 original size:29 final size:31
Alignment explanation
Indices: 1824113--1824179 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
1824103 TAAATTTATC
1824113 ATTAAATTGTATCAA-ATTGTTAAAAAA-TT
1 ATTAAATTGTATCAATATTGTTAAAAAAGTT
* *
1824142 ATTAAATT-TCATCAATTTTTTTAAAAAATGTT
1 ATTAAATTGT-ATCAATATTGTTAAAAAA-GTT
1824174 ATTAAA
1 ATTAAA
1824180 ATATTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 13 0.41
30 10 0.31
32 8 0.25
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (31 bp):
ATTAAATTGTATCAATATTGTTAAAAAAGTT
Found at i:1830553 original size:28 final size:28
Alignment explanation
Indices: 1830471--1830568 Score: 90
Period size: 28 Copynumber: 3.4 Consensus size: 28
1830461 ACAATAAATG
*
1830471 ACTTTTATAAATTACAATATACA-ACACAA
1 ACTTTTATAAATTACAATA-AAAGACA-AA
* * * * *
1830500 ATTTTTATAAATCACATTTAAGGACAAA
1 ACTTTTATAAATTACAATAAAAGACAAA
*
1830528 ACTTTTATAAATTACACTAAAAGACAAA
1 ACTTTTATAAATTACAATAAAAGACAAA
1830556 ACATTTTAGTAAA
1 AC-TTTTA-TAAA
1830569 AGGACAAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
28 28 0.51
29 23 0.42
30 4 0.07
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (28 bp):
ACTTTTATAAATTACAATAAAAGACAAA
Found at i:1830623 original size:29 final size:29
Alignment explanation
Indices: 1830568--1830651 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 29
1830558 ATTTTAGTAA
*
1830568 AAGGACAAAAACTTTTTAAAAAATTAAAATT
1 AAGGAC-AAAACTTTTT-ATAAATTAAAATT
1830599 AAGGACAAAACTTTTTATAAATTAAAATT
1 AAGGACAAAACTTTTTATAAATTAAAATT
* *
1830628 AAGGATAAAACCTTTTATAAATTA
1 AAGGACAAAACTTTTTATAAATTA
1830652 TAATAGATAC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
29 34 0.68
30 10 0.20
31 6 0.12
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (29 bp):
AAGGACAAAACTTTTTATAAATTAAAATT
Found at i:1830672 original size:29 final size:29
Alignment explanation
Indices: 1830575--1830680 Score: 119
Period size: 29 Copynumber: 3.6 Consensus size: 29
1830565 TAAAAGGACA
* *
1830575 AAAACTTTTTAAAAAATTAAAATTAAGGAC
1 AAAACTTTTT-ATAAATTAAAATTAAGGAT
1830605 AAAACTTTTTATAAATTAAAATTAAGGAT
1 AAAACTTTTTATAAATTAAAATTAAGGAT
* *
1830634 AAAACCTTTTATAAATTATAA-T-A-GAT
1 AAAACTTTTTATAAATTAAAATTAAGGAT
1830660 ACCACAACTTTTTATAAATTA
1 A--A-AACTTTTTATAAATTA
1830681 CATTAAAGGA
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.06
27 1 0.01
28 2 0.03
29 51 0.75
30 10 0.15
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAACTTTTTATAAATTAAAATTAAGGAT
Found at i:1832300 original size:16 final size:16
Alignment explanation
Indices: 1832276--1832333 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
1832266 GATCTGAAAT
1832276 AAATAAATTTATAAAA
1 AAATAAATTTATAAAA
* *
1832292 AAATTAATTTTTAATAA
1 AAATAAATTTATAA-AA
*
1832309 AGATAAAATTTAATTAAAA
1 AAAT-AAATTT-A-TAAAA
1832328 AAATAA
1 AAATAA
1832334 TATATAAAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 12 0.38
17 5 0.16
18 7 0.22
19 5 0.16
20 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAATAAATTTATAAAA
Found at i:1839592 original size:3 final size:3
Alignment explanation
Indices: 1839586--1839628 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1839576 CTACTACTAC
1839586 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1839629 TTACGAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1841257 original size:41 final size:41
Alignment explanation
Indices: 1841200--1841283 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
1841190 AGAATGTACT
* *
1841200 CTTTTTATCTTTTTAGGATTAGGGAGGTATTTAACGATACA
1 CTTTTCATCTTTTTAGGATTAGGGAGGTATTTAACGAGACA
1841241 CTTTTCATCTTTTTAGGATTAGGGAGGTATTTAACGAGACA
1 CTTTTCATCTTTTTAGGATTAGGGAGGTATTTAACGAGACA
1841282 CT
1 CT
1841284 ATCCTTGACT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (41 bp):
CTTTTCATCTTTTTAGGATTAGGGAGGTATTTAACGAGACA
Found at i:1843332 original size:100 final size:97
Alignment explanation
Indices: 1843149--1843345 Score: 367
Period size: 100 Copynumber: 2.0 Consensus size: 97
1843139 CAGTCTACCT
1843149 GCGTATTTCTAAGAGAGGGGACATTCCTCTTGTGGTCCTTTGTACCTTACGTTTTCATTTTAGTC
1 GCGTATTTCTAAGAGAGGGGACATTCCTCTTGTGGTCCTTTGTACCTTACGTTTTCATTTTAGTC
1843214 CCTAGATTGAAATTTTCATGTTTATAATTTCA
66 CCTAGATTGAAATTTTCATGTTTATAATTTCA
1843246 GCGTATTTCTAAGAGAGGGGACATTCCTCTTTGTGGTCCTTTGTACCTTACGTTTATTCATTTTA
1 GCGTATTTCTAAGAGAGGGGACATTCCTC-TTGTGGTCCTTTGTACCTTACG-TT-TTCATTTTA
1843311 GTCCCTAGATTGAAATTTTCATGTTTATAATTTCA
63 GTCCCTAGATTGAAATTTTCATGTTTATAATTTCA
1843346 TTCTTTTATT
Statistics
Matches: 97, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
97 29 0.30
98 22 0.23
99 2 0.02
100 44 0.45
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (97 bp):
GCGTATTTCTAAGAGAGGGGACATTCCTCTTGTGGTCCTTTGTACCTTACGTTTTCATTTTAGTC
CCTAGATTGAAATTTTCATGTTTATAATTTCA
Found at i:1846424 original size:14 final size:13
Alignment explanation
Indices: 1846404--1846539 Score: 63
Period size: 14 Copynumber: 10.6 Consensus size: 13
1846394 AATCGATACC
1846404 TTTTGCATTTTCA
1 TTTTGCATTTTCA
*
1846417 TCTTTGCATTTTTA
1 T-TTTGCATTTTCA
* *
1846431 CGTTTGTATTTAT-A
1 -TTTTGCATTT-TCA
* *
1846445 TTTT-TATTTT-T
1 TTTTGCATTTTCA
*
1846456 TTTTGCATTTGCA
1 TTTTGCATTTTCA
*
1846469 TCTTTGCATTTTTA
1 T-TTTGCATTTTCA
* *
1846483 TGTTTGTATTTACA
1 T-TTTGCATTTTCA
1846497 TTTT-CATTTT--
1 TTTTGCATTTTCA
*
1846507 TTTT-CATTTACA
1 TTTTGCATTTTCA
*
1846519 -TTTGCATTTGCA
1 TTTTGCATTTTCA
1846531 TCTTTGCAT
1 T-TTTGCAT
1846540 AATTATGTTT
Statistics
Matches: 94, Mismatches: 18, Indels: 21
0.71 0.14 0.16
Matches are distributed among these distances:
10 9 0.10
11 8 0.09
12 20 0.21
13 8 0.09
14 48 0.51
15 1 0.01
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.62
Consensus pattern (13 bp):
TTTTGCATTTTCA
Found at i:1846482 original size:52 final size:52
Alignment explanation
Indices: 1846404--1846510 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
1846394 AATCGATACC
* * *
1846404 TTTTGCATTTTCATCTTTGCATTTTTACGTTTGTATTTATATTTTTATTTTT
1 TTTTGCATTTGCATCTTTGCATTTTTACGTTTGTATTTACATTTTCATTTTT
*
1846456 TTTTGCATTTGCATCTTTGCATTTTTATGTTTGTATTTACATTTTCATTTTT
1 TTTTGCATTTGCATCTTTGCATTTTTACGTTTGTATTTACATTTTCATTTTT
1846508 TTT
1 TTT
1846511 CATTTACATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.15, C:0.10, G:0.08, T:0.66
Consensus pattern (52 bp):
TTTTGCATTTGCATCTTTGCATTTTTACGTTTGTATTTACATTTTCATTTTT
Found at i:1850006 original size:9 final size:9
Alignment explanation
Indices: 1849994--1850018 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1849984 TTTATTTGAT
1849994 ATTCATTAA
1 ATTCATTAA
1850003 ATTCATTAA
1 ATTCATTAA
1850012 ATTCATT
1 ATTCATT
1850019 GTTTATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTCATTAA
Found at i:1853770 original size:23 final size:23
Alignment explanation
Indices: 1853704--1853772 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
1853694 TATCTCATTC
*
1853704 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAATAG
* **
1853727 AAGA-T-TTTAT-C-T--AATTC
1 AAGATTGTTTTTCCTTGAAATAG
1853744 AAGATTGTTTTTCCTTGAAATAG
1 AAGATTGTTTTTCCTTGAAATAG
1853767 AAGATT
1 AAGATT
1853773 TTATCTCGCT
Statistics
Matches: 33, Mismatches: 7, Indels: 12
0.63 0.13 0.23
Matches are distributed among these distances:
17 6 0.18
18 1 0.03
19 5 0.15
20 2 0.06
21 5 0.15
22 1 0.03
23 13 0.39
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAATAG
Found at i:1853860 original size:40 final size:40
Alignment explanation
Indices: 1853686--1853862 Score: 264
Period size: 40 Copynumber: 4.4 Consensus size: 40
1853676 CATTTAATAC
**
1853686 GAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACA
1 GAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACA
*** *
1853726 GAAGATTTTATCTAATTCAAGATTGTTTTTCCTTGAAATA
1 GAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACA
*
1853766 GAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTCAAACA
1 GAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACA
*
1853806 GAAGACTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACA
1 GAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACA
* *
1853846 AAATATTTTATCTCGCT
1 GAAGATTTTATCTCGCT
1853863 TCAGATAGTT
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 125 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (40 bp):
GAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACA
Found at i:1853920 original size:37 final size:38
Alignment explanation
Indices: 1853833--1853920 Score: 90
Period size: 37 Copynumber: 2.3 Consensus size: 38
1853823 CAAGATTGTT
* *
1853833 TTTCCTTGAAACAAAATATTTTATCTCGCTTCAGATAG
1 TTTCCTTGAAACAAAATATTTTATCTCCCTTCAGACAG
* * * *
1853871 TTTCCCTCGAAAC-AAA-GTTTTGTCTCCCTTGAGACAG
1 TTT-CCTTGAAACAAAATATTTTATCTCCCTTCAGACAG
1853908 TTTCTCTTGAAAC
1 TTTC-CTTGAAAC
1853921 CTATTTCGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
36 1 0.02
37 26 0.63
38 6 0.15
39 8 0.20
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (38 bp):
TTTCCTTGAAACAAAATATTTTATCTCCCTTCAGACAG
Found at i:1854368 original size:20 final size:20
Alignment explanation
Indices: 1854306--1854369 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
1854296 TTAATGGAGA
*
1854306 GTTCATAATGTGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * ***
1854326 -ATC-CAATGAGGAAGAAGAA
1 GTTCATAATGA-GAAGAACTT
1854345 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1854365 GTTCA
1 GTTCA
1854370 ACCTTGCATC
Statistics
Matches: 30, Mismatches: 11, Indels: 6
0.64 0.23 0.13
Matches are distributed among these distances:
18 4 0.13
19 8 0.27
20 13 0.43
21 5 0.17
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1854564 original size:136 final size:135
Alignment explanation
Indices: 1854384--1854727 Score: 552
Period size: 136 Copynumber: 2.6 Consensus size: 135
1854374 TGCATCAGTG
*
1854384 TTTCCAAAGGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGGGAGAAGAAGTTCATAATGAG
*
1854449 AAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGAGGAA
65 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGAA
*
1854514 TTGACA
130 TCGACA
*
1854520 TTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAA-AGAGGGAGAAGAAGTTCATAATGAG
* *
1854585 AAGAGATTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
65 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGAA
1854650 TCGACA
130 TCGACA
* * *
1854656 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCGTCCTAA-A-GGAG-A-AAGTTCATAATGAGA
1 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGGAGAAGAAGTTCATAATGAGA
*
1854717 AGAACTTGTTC
66 AGAGCTTGTTC
1854728 CTTTCAAATC
Statistics
Matches: 195, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
131 24 0.12
132 1 0.01
133 4 0.02
134 1 0.01
135 3 0.02
136 162 0.83
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (135 bp):
TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGGAGAAGAAGTTCATAATGAGA
AGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGAAT
CGACA
Found at i:1854849 original size:242 final size:242
Alignment explanation
Indices: 1854530--1854969 Score: 663
Period size: 242 Copynumber: 1.8 Consensus size: 242
1854520 TTTCCAATGG
* *
1854530 AGAGTTCATAATGAGAATAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAAGAGATTGT
1 AGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGAGAAGAGATTGT
* *
1854595 TCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGATCGACATTTC
66 TCAACCTATCACTCGATTCAC-A-ATTTCGAATCAGTGACGCCTCGCTTGAGGAATCGACATTT-
* *
1854660 CAATGAAGAGTTCATAATGAGAAGAACTCGTCCTAA-AGG-AGA-AAGTTCATAATGAGAAGAAC
128 CAATGAAGAGTTCATAATGAGAAGAACTCATCC-AAGAGGAAAAGAAGTTCATAATGAGAAGAAC
1854722 TTGTTCCTTTCAAATCTATCACAGAAGGAGGTGGATCAACATTTTTAGTGA
192 TTGTTCCTTTCAAATCTATCACAGAAGGAGGTGGATCAACATTTTTAGTGA
* *
1854773 AGAGTTCATAATGAGAAGAACTCATCCAA-AGAGGAAGAAGGAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGAGAAGAGATTGT
* * * * * *
1854837 TTAACCTATCACTCGATTCACATTTTCGAATCAGTGATGTCTCGCTTGAGGAATTGACATTTTAA
66 TCAACCTATCACTCGATTCACAATTTCGAATCAGTGACGCCTCGCTTGAGGAATCGACATTTCAA
* *
1854902 TGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAAAGAAGTTCATAATGAGAAGAATTTG
131 TGAAGAGTTCATAATGAGAAGAACTCATCCAA-GAGGAAAAGAAGTTCATAATGAGAAGAACTTG
1854967 TTC
195 TTC
1854970 AACCTTGCAT
Statistics
Matches: 177, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
238 2 0.01
239 30 0.17
240 38 0.21
241 3 0.02
242 76 0.43
243 28 0.16
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (242 bp):
AGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGAGAAGAGATTGT
TCAACCTATCACTCGATTCACAATTTCGAATCAGTGACGCCTCGCTTGAGGAATCGACATTTCAA
TGAAGAGTTCATAATGAGAAGAACTCATCCAAGAGGAAAAGAAGTTCATAATGAGAAGAACTTGT
TCCTTTCAAATCTATCACAGAAGGAGGTGGATCAACATTTTTAGTGA
Found at i:1858556 original size:18 final size:18
Alignment explanation
Indices: 1858529--1858571 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1858519 TCCCTTTTTC
*
1858529 CTTT-TTTTTTTCATCTT
1 CTTTCTTTTTTCCATCTT
* *
1858546 TTTTCTTTTTTCCTTCTT
1 CTTTCTTTTTTCCATCTT
1858564 CTTTCTTT
1 CTTTCTTT
1858572 GCTGGATGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (18 bp):
CTTTCTTTTTTCCATCTT
Found at i:1858566 original size:21 final size:21
Alignment explanation
Indices: 1858522--1858567 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1858512 CAATTTCTCC
**
1858522 CTTTTTCCTTTTTTTTTTCAT
1 CTTTTTCCTTTTTTCCTTCAT
* *
1858543 CTTTTTTCTTTTTTCCTTCTT
1 CTTTTTCCTTTTTTCCTTCAT
1858564 CTTT
1 CTTT
1858568 CTTTGCTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (21 bp):
CTTTTTCCTTTTTTCCTTCAT
Found at i:1868117 original size:23 final size:23
Alignment explanation
Indices: 1868082--1868131 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1868072 TCATCTAGGG
* *
1868082 AAAAAATTATCTATAATTAAGTAT
1 AAAAAATTATCTA-AAATAAATAT
*
1868106 AAAAGATT-TCTAAAATAAATAT
1 AAAAAATTATCTAAAATAAATAT
1868128 AAAA
1 AAAA
1868132 TGTTGTTCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.52
23 4 0.17
24 7 0.30
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (23 bp):
AAAAAATTATCTAAAATAAATAT
Found at i:1870025 original size:11 final size:11
Alignment explanation
Indices: 1870009--1870033 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1869999 AACCATAGCA
1870009 TAAACTTGGAT
1 TAAACTTGGAT
1870020 TAAACTTGGAT
1 TAAACTTGGAT
1870031 TAA
1 TAA
1870034 TTACAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
TAAACTTGGAT
Found at i:1872122 original size:16 final size:16
Alignment explanation
Indices: 1872092--1872136 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1872082 TGTTTATGTC
1872092 TATTC-TAAA-TTTAA
1 TATTCTTAAATTTTAA
1872106 TATTCTTAAATTTTAA
1 TATTCTTAAATTTTAA
1872122 TATT-TTATAATTTTA
1 TATTCTTA-AATTTTA
1872137 CCTTATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.18
15 7 0.25
16 16 0.57
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTCTTAAATTTTAA
Found at i:1873194 original size:48 final size:49
Alignment explanation
Indices: 1873108--1873200 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 49
1873098 AAATTAATAA
* * * *
1873108 AAAAATATATTTTACTGGAACTTATCACATCGATGTGACGAGTTTGAAT
1 AAAAATATATTTTACTGAAACTCATCACATCCACGTGACGAGTTTGAAT
* *
1873157 AAAAATAT-TTTTATTGAAACTCATCACCTCCACGTGACGAGTTT
1 AAAAATATATTTTACTGAAACTCATCACATCCACGTGACGAGTTT
1873201 CATAAACACT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
48 30 0.79
49 8 0.21
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (49 bp):
AAAAATATATTTTACTGAAACTCATCACATCCACGTGACGAGTTTGAAT
Found at i:1878099 original size:60 final size:57
Alignment explanation
Indices: 1877933--1878106 Score: 190
Period size: 61 Copynumber: 2.9 Consensus size: 57
1877923 TTGCATTATA
1877933 CATCCTCAAAATATGACCCTCATTTTAAATTAGTCCTCAAACTTTTGAACATTCTAATT
1 CATCCTC-AAATATGA-CCTCATTTTAAATTAGTCCTCAAACTTTTGAACATTCTAATT
* * * **
1877992 TATCCTTAAATCATGACTCTCAATTTAAATCGGTCC-CTAGGAA-TTTTGAACATTCTAAATT
1 CATCCTCAAAT-ATGAC-CTCATTTTAAATTAGTCCTC-A--AACTTTTGAACATTCT-AATT
*
1878053 CATCCTGAAACTATGATCCTCATTTTAAATTAGTCCTCAAACTTTTGAACATTC
1 CATCCTCAAA-TATGA-CCTCATTTTAAATTAGTCCTCAAACTTTTGAACATTC
1878107 CAATAATATC
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
58 6 0.06
59 27 0.28
60 25 0.26
61 34 0.36
62 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (57 bp):
CATCCTCAAATATGACCTCATTTTAAATTAGTCCTCAAACTTTTGAACATTCTAATT
Found at i:1878298 original size:60 final size:60
Alignment explanation
Indices: 1878191--1878303 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
1878181 AATTAGGACC
* * * *
1878191 ATAGTTTAGGGATGGAATTAGAATGATTAAAAGTTTAGAGAACAATTTCGAATAAGAATT
1 ATAGTTTAGGGATGAAACTAGAATGATTAAAAATTTAGAGAACAATTTAGAATAAGAATT
* **
1878251 ATAGTTTAGGGATGAAACTAGAATGTTTAAAAATTT-GAGGATTAATTTAGAAT
1 ATAGTTTAGGGATGAAACTAGAATGATTAAAAATTTAGA-GAACAATTTAGAAT
1878304 GATGATCATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 2 0.04
60 43 0.96
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (60 bp):
ATAGTTTAGGGATGAAACTAGAATGATTAAAAATTTAGAGAACAATTTAGAATAAGAATT
Found at i:1878315 original size:60 final size:60
Alignment explanation
Indices: 1878190--1878317 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
1878180 AAATTAGGAC
* * * *
1878190 CATAGTTTAGGGATGGAATTAGAATGATTAAAAGTTTAGAGAACAATTTCGAATAAGAAT
1 CATAGTTTAGGGATGAAACTAGAATGATTAAAAATTTAGAGAACAATTTAGAATAAGAAT
* * ** *
1878250 TATAGTTTAGGGATGAAACTAGAATGTTTAAAAATTT-GAGGATTAATTTAGAATGATG-AT
1 CATAGTTTAGGGATGAAACTAGAATGATTAAAAATTTAGA-GAACAATTTAGAAT-AAGAAT
1878310 CATAGTTT
1 CATAGTTT
1878318 GAGGATGTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 2 0.04
60 52 0.93
61 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (60 bp):
CATAGTTTAGGGATGAAACTAGAATGATTAAAAATTTAGAGAACAATTTAGAATAAGAAT
Found at i:1882421 original size:60 final size:59
Alignment explanation
Indices: 1882265--1882423 Score: 137
Period size: 60 Copynumber: 2.6 Consensus size: 59
1882255 TAAAACATTC
* * * * *
1882265 AAAAGTTTG-GGAACTAATATAGAATTAGGGCCACAGTTTAGGGATGAAATTAGAATGATT
1 AAAAGTTTGAGG-ATTAATTTAGAA-TAGGACCATAGTTTAGGGATGAAACTAGAATGATT
* * **
1882325 AAAAGTTT-A-GAGTTCAATTTCGAATAAGAGTTATAGTTTAGGGATGAAACTAGAATG-TT
1 AAAAGTTTGAGGA-TT-AATTTAGAATAGGA-CCATAGTTTAGGGATGAAACTAGAATGATT
*
1882384 CGAAAGTTTGAGGATTAATTTAGAATGAGGACCATAGTTT
1 -AAAAGTTTGAGGATTAATTTAGAAT-AGGACCATAGTTT
1882424 GAGGACGTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
58 1 0.01
59 7 0.09
60 61 0.79
61 6 0.08
62 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.31
Consensus pattern (59 bp):
AAAAGTTTGAGGATTAATTTAGAATAGGACCATAGTTTAGGGATGAAACTAGAATGATT
Found at i:1887501 original size:14 final size:14
Alignment explanation
Indices: 1887482--1887520 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
1887472 TTATGTTTGT
1887482 TTATGTTCGTTCGG
1 TTATGTTCGTTCGG
1887496 TTATGTTCGTTCGG
1 TTATGTTCGTTCGG
1887510 TTATGTTCGTT
1 TTATGTTCGTT
1887521 TATGTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.54
Consensus pattern (14 bp):
TTATGTTCGTTCGG
Found at i:1887537 original size:24 final size:24
Alignment explanation
Indices: 1887490--1887540 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1887480 GTTTATGTTC
* *
1887490 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
1887514 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
1887538 GTT
1 GTT
1887541 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:1887538 original size:38 final size:38
Alignment explanation
Indices: 1887465--1887540 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
1887455 CGTTCGTGAA
* * *
1887465 CGTTCGGTTATGTTTGTTTATGTTCGTTCGGTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTTCATTCAGTTATGTT
*
1887503 CGTTCGGTTATGTTCGTTTATGTTCATTCATTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTTCATTCAGTTATGTT
1887541 TAACCCAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.11, C:0.12, G:0.22, T:0.55
Consensus pattern (38 bp):
CGTTCGGTTATGTTCGTTTATGTTCATTCAGTTATGTT
Found at i:1888492 original size:16 final size:16
Alignment explanation
Indices: 1888467--1888531 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
1888457 CCAACGTTTA
1888467 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
* *
1888483 TGTTCATTTATGTTCG
1 TGTTCGTTTATATTCG
*
1888499 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
1888515 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
1888531 T
1 T
1888532 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:1888622 original size:16 final size:16
Alignment explanation
Indices: 1888601--1888633 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1888591 AAAAAAAATT
1888601 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1888617 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1888633 T
1 T
1888634 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1890845 original size:79 final size:79
Alignment explanation
Indices: 1890706--1890857 Score: 286
Period size: 79 Copynumber: 1.9 Consensus size: 79
1890696 TAATCACGTT
*
1890706 CCGAGTCGTCGAAATTGCCGATTAGTTTCTAATTTACTTTTAACTAATAACCCTGATTTTTAACC
1 CCGAGTCGTCGAAATTGCCGATTAGTTTCTAATTTACTTTTAACTAATAAACCTGATTTTTAACC
1890771 ACTTATTTCTAGTC
66 ACTTATTTCTAGTC
*
1890785 CCGAGTCGTCGAAATTGCCGATTAGTTTCTAATTTACTTTTAACTAATAAACCTGTTTTTTAACC
1 CCGAGTCGTCGAAATTGCCGATTAGTTTCTAATTTACTTTTAACTAATAAACCTGATTTTTAACC
1890850 ACTTATTT
66 ACTTATTT
1890858 ATAATATATT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (79 bp):
CCGAGTCGTCGAAATTGCCGATTAGTTTCTAATTTACTTTTAACTAATAAACCTGATTTTTAACC
ACTTATTTCTAGTC
Found at i:1891399 original size:25 final size:25
Alignment explanation
Indices: 1891348--1891400 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1891338 TTTTAGGTGT
* * *
1891348 AAAAATATAATTTTTATTTATTTAA
1 AAAAATATAAATTTTAGTTATTAAA
1891373 AAAAATATGAAATTTTAGTT-TTAAA
1 AAAAATAT-AAATTTTAGTTATTAAA
1891398 AAA
1 AAA
1891401 CCAACAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AAAAATATAAATTTTAGTTATTAAA
Found at i:1892512 original size:3 final size:3
Alignment explanation
Indices: 1892504--1892535 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
1892494 GATCATCTAC
1892504 ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
1892536 GTGTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1895331 original size:13 final size:13
Alignment explanation
Indices: 1895313--1895343 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1895303 ATATTGAATT
1895313 TTCTTTTTTAATC
1 TTCTTTTTTAATC
1895326 TTC-TTTTTAATC
1 TTCTTTTTTAATC
1895338 TTCTTT
1 TTCTTT
1895344 ATTCTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (13 bp):
TTCTTTTTTAATC
Found at i:1896479 original size:9 final size:9
Alignment explanation
Indices: 1896465--1896541 Score: 55
Period size: 10 Copynumber: 7.9 Consensus size: 9
1896455 GGCTCCTGGA
1896465 AACCGGTTT
1 AACCGGTTT
1896474 AACCGGTTTT
1 AACCGG-TTT
1896484 CAACCGGTTCT
1 -AACCGGTT-T
*
1896495 GACCGGTTT
1 AACCGGTTT
*
1896504 GACCGGTTTT
1 AACCGG-TTT
*
1896514 CAACCGGTTCG
1 -AACCGGTT-T
*
1896525 AACCGATTT
1 AACCGGTTT
*
1896534 GACCGGTT
1 AACCGGTT
1896542 CGAACCGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
9 19 0.35
10 24 0.44
11 12 0.22
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1896490 original size:20 final size:21
Alignment explanation
Indices: 1896465--1896503 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1896455 GGCTCCTGGA
1896465 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
1896485 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
1896504 GACCGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:1896502 original size:30 final size:30
Alignment explanation
Indices: 1896465--1896541 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
1896455 GGCTCCTGGA
*
1896465 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGGTTTTCAACCGGTTC-G
1896496 -ACCGGTTTGACCGGTTTTCAACCGGTTCG
1 AACCGGTTTGACCGGTTTTCAACCGGTTCG
*
1896525 AACCGATTTGACCGGTT
1 AACCGGTTTGACCGGTT
1896542 CGAACCGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTTCAACCGGTTCG
Found at i:1896510 original size:19 final size:19
Alignment explanation
Indices: 1896467--1896556 Score: 78
Period size: 19 Copynumber: 4.6 Consensus size: 19
1896457 CTCCTGGAAA
*
1896467 CCGGTTTAACCGGTTTTC-AA
1 CCGGTTTGACCGG--TTCGAA
*
1896487 CCGGTTCTGACCGGTTTG-A
1 CCGGTT-TGACCGGTTCGAA
*
1896506 CCGGTTTTCAACCGGTTCGAA
1 CCGG-TTT-GACCGGTTCGAA
*
1896527 CCGATTTGACCGGTTCGAA
1 CCGGTTTGACCGGTTCGAA
1896546 CC-GTTTGACCG
1 CCGGTTTGACCG
1896557 ACCCGACCCG
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
18 8 0.14
19 21 0.36
20 19 0.33
21 10 0.17
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCGAA
Found at i:1896578 original size:17 final size:17
Alignment explanation
Indices: 1896556--1896610 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
1896546 CCGTTTGACC
*
1896556 GACCCGACCCGATCGTT
1 GACCCGACCCGACCGTT
1896573 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1896590 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1896607 GACC
1 GACC
1896611 GTTGACTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1901690 original size:50 final size:50
Alignment explanation
Indices: 1901632--1901732 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
1901622 AATGGGAGCG
1901632 TATTACTATGGATTTTGTTACTGGCTTGCCTATGACTCCTTCGAAAAAGA
1 TATTACTATGGATTTTGTTACTGGCTTGCCTATGACTCCTTCGAAAAAGA
1901682 TATTACTATGGATTTTGTTACTGGCTTGCCTATGACTCCTTCGAAAAAGA
1 TATTACTATGGATTTTGTTACTGGCTTGCCTATGACTCCTTCGAAAAAGA
1901732 T
1 T
1901733 TCAGTTTGGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (50 bp):
TATTACTATGGATTTTGTTACTGGCTTGCCTATGACTCCTTCGAAAAAGA
Found at i:1903495 original size:10 final size:9
Alignment explanation
Indices: 1903460--1903550 Score: 83
Period size: 10 Copynumber: 9.3 Consensus size: 9
1903450 GCTGCTGGAA
*
1903460 ACCGGTTTA
1 ACCGGTTTG
*
1903469 ACCGGTTTTCA
1 ACCGG-TTT-G
1903480 ACCGGTTCTG
1 ACCGGTT-TG
1903490 ACCGGTTTG
1 ACCGGTTTG
*
1903499 ACCGGTTTCCA
1 ACCGGTTT--G
1903510 ACCGGTTTG
1 ACCGGTTTG
1903519 AACCGGTTTG
1 -ACCGGTTTG
*
1903529 ACCGGTCTG
1 ACCGGTTTG
1903538 AACCGGTTTG
1 -ACCGGTTTG
1903548 ACC
1 ACC
1903551 AGCCTGACAC
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
9 26 0.37
10 29 0.41
11 15 0.21
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1903496 original size:30 final size:29
Alignment explanation
Indices: 1903460--1903550 Score: 121
Period size: 30 Copynumber: 3.1 Consensus size: 29
1903450 GCTGCTGGAA
*
1903460 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGGTTTTCAACCGGTT-TG
*
1903490 ACCGGTTTGACCGGTTTCCAACCGGTTTG
1 ACCGGTTTGACCGGTTTTCAACCGGTTTG
* *
1903519 AACCGGTTTGACCGG-TCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTTCAACCGGTTTG
1903548 ACC
1 ACC
1903551 AGCCTGACAC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.05
29 13 0.24
30 39 0.71
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.30
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTTCAACCGGTTTG
Found at i:1903504 original size:19 final size:19
Alignment explanation
Indices: 1903459--1903550 Score: 105
Period size: 19 Copynumber: 4.7 Consensus size: 19
1903449 GGCTGCTGGA
* *
1903459 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TTTG
1903479 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTTTG
*
1903499 -ACCGGTTTCCAACCGGTTTG
1 AACCGGTTT--GACCGGTTTG
*
1903519 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTTTG
1903538 AACCGGTTTGACC
1 AACCGGTTTGACC
1903551 AGCCTGACAC
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.02
19 28 0.44
20 20 0.32
21 14 0.22
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTG
Found at i:1903557 original size:19 final size:19
Alignment explanation
Indices: 1903517--1903557 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1903507 CCAACCGGTT
* *
1903517 TGAACCGGTTTGACCGGTC
1 TGAACCGGTTTGACCAGCC
1903536 TGAACCGGTTTGACCAGCC
1 TGAACCGGTTTGACCAGCC
1903555 TGA
1 TGA
1903558 CACGACCCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.24
Consensus pattern (19 bp):
TGAACCGGTTTGACCAGCC
Found at i:1903585 original size:22 final size:21
Alignment explanation
Indices: 1903553--1903615 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
1903543 GTTTGACCAG
*
1903553 CCTGACACGACCCGATCGTTGA
1 CCTGACCCGACCCGA-CGTTGA
1903575 CCTGACCCGA--C--CGTTGA
1 CCTGACCCGACCCGACGTTGA
*
1903592 CCCGACCCGACCCGACCGTTGA
1 CCTGACCCGACCCGA-CGTTGA
1903614 CC
1 CC
1903616 GTTGACTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
17 15 0.44
19 1 0.03
20 1 0.03
22 17 0.50
ACGTcount: A:0.19, C:0.44, G:0.22, T:0.14
Consensus pattern (21 bp):
CCTGACCCGACCCGACGTTGA
Found at i:1903592 original size:12 final size:12
Alignment explanation
Indices: 1903577--1903615 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1903567 ATCGTTGACC
1903577 TGACCCGACCGT
1 TGACCCGACCGT
1903589 TGACCCGACC--
1 TGACCCGACCGT
*
1903599 CGACCCGACCGT
1 TGACCCGACCGT
1903611 TGACC
1 TGACC
1903616 GTTGACTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:1903615 original size:17 final size:17
Alignment explanation
Indices: 1903555--1903603 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
1903545 TTGACCAGCC
* *
1903555 TGACACGACCCGATCGT
1 TGACCCGACCCGACCGT
*
1903572 TGACCTGACCCGACCGT
1 TGACCCGACCCGACCGT
1903589 TGACCCGACCCGACC
1 TGACCCGACCCGACC
1903604 CGACCGTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.20, C:0.43, G:0.22, T:0.14
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1909428 original size:9 final size:9
Alignment explanation
Indices: 1909412--1909441 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1909402 GATGAAAACG
1909412 ACAACATCA
1 ACAACATCA
*
1909421 ATAACATCA
1 ACAACATCA
1909430 ACAACATCA
1 ACAACATCA
1909439 ACA
1 ACA
1909442 CCAAGATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (9 bp):
ACAACATCA
Done.