Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015079.1 Kokia drynarioides strain JFW-HI SEQ_130123, 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: 413849
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 252 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:197446 original size:11 final size:11
Alignment explanation
Indices: 197407--197450 Score: 61
Period size: 11 Copynumber: 3.7 Consensus size: 11
197397 TAATTATTAT
197407 TTTTTCAATATA
1 TTTTT-AATATA
197419 TTTTTAATTATTA
1 TTTTTAA-TA-TA
197432 TTTTTAATATA
1 TTTTTAATATA
197443 TTTTTAAT
1 TTTTTAAT
197451 TTATCGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 12 0.40
12 9 0.30
13 9 0.30
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTAATATA
Found at i:197592 original size:17 final size:18
Alignment explanation
Indices: 197561--197594 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
197551 GAATATTACA
*
197561 ACAATATAAATTAAATTT
1 ACAATATAAAATAAATTT
197579 ACAA-ATAAAATAAATT
1 ACAATATAAAATAAATT
197595 CTAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
ACAATATAAAATAAATTT
Found at i:198377 original size:62 final size:61
Alignment explanation
Indices: 198272--198751 Score: 372
Period size: 61 Copynumber: 7.9 Consensus size: 61
198262 GAAAAGTTGA
* * * * *
198272 TGTCGGCCAATGC-ATGGCTAACACAAAAAATATTTGAATTTTTTTATTAGATAGAAAGGTGG
1 TGTCGGTC-ATGCAATGGCTAACACCAAAAA-ATTTGAATTTTTTTATCAGATAAAAAGGTAG
** * * *
198334 TGTTAGTCATGCAATGGCCAACACCAAAAAATTTGATTTTTTTTATCAGAT-AATAGGTAG
1 TGTCGGTCATGCAATGGCTAACACCAAAAAATTTGAATTTTTTTATCAGATAAAAAGGTAG
* ** ** *
198394 TGTC-GTCCAATGC-AT-GCCAACATAAAAAAAAATTAAAATTTTTTTATCAGAT-AAAACGTAG
1 TGTCGGT-C-ATGCAATGGCTAAC--ACCAAAAAATTTGAATTTTTTTATCAGATAAAAAGGTAG
* * * * *
198455 TGTCGGCCATGCAATGGCTAATACCAAAAAAATTTAAATTTTTTTATCAAATTAAAAAGGTGG
1 TGTCGGTCATGCAATGGCTAACACC-AAAAAATTTGAATTTTTTTATCAGA-TAAAAAGGTAG
* * *
198518 TGTCGGTCATGCAATGGTTAACACCAAAGAATTTGAATTTTTTTATCAAATTAAAAAGGTAG
1 TGTCGGTCATGCAATGGCTAACACCAAAAAATTTGAATTTTTTTATCAGA-TAAAAAGGTAG
* * * *
198580 TGTTGGTCATGCAATGGTTAACACCAAAAAATTTGAA-TTTTTTAT-ATGACAAAAAGG-GG
1 TGTCGGTCATGCAATGGCTAACACCAAAAAATTTGAATTTTTTTATCA-GATAAAAAGGTAG
* * * * * ** * * **
198639 CGTCAGCCATGCAATGACCAACATAAAAAAAATTG-A-TTTTTTACCAGATAAAAAAGAAAG
1 TGTCGGTCATGCAATGGCTAACACCAAAAAATTTGAATTTTTTTATCAGAT-AAAAAGGTAG
* ** * * *
198699 TATCGACCATGCAATTGCCAACACCAAAAAATTTGAA-TTTTTTATCTGATAAA
1 TGTCGGTCATGCAATGGCTAACACCAAAAAATTTGAATTTTTTTATCAGATAAA
198752 TTTTTTTTTA
Statistics
Matches: 339, Mismatches: 63, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
58 10 0.03
59 41 0.12
60 55 0.16
61 109 0.32
62 95 0.28
63 29 0.09
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (61 bp):
TGTCGGTCATGCAATGGCTAACACCAAAAAATTTGAATTTTTTTATCAGATAAAAAGGTAG
Found at i:213007 original size:6 final size:6
Alignment explanation
Indices: 212996--213024 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
212986 AGGATTCTGC
212996 GGCTGA GGCTGA GGCTGA GGCTGA GGCTG
1 GGCTGA GGCTGA GGCTGA GGCTGA GGCTG
213025 GGAGGGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.17, G:0.52, T:0.17
Consensus pattern (6 bp):
GGCTGA
Found at i:217233 original size:11 final size:11
Alignment explanation
Indices: 217217--217241 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
217207 AAGTATAATA
217217 AAATAATTAAG
1 AAATAATTAAG
217228 AAATAATTAAG
1 AAATAATTAAG
217239 AAA
1 AAA
217242 AATACTGGAA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (11 bp):
AAATAATTAAG
Found at i:217912 original size:11 final size:10
Alignment explanation
Indices: 217881--217915 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
217871 ATTAAAAAAT
217881 AAAATTATAA
1 AAAATTATAA
217891 AAAATTATAA
1 AAAATTATAA
*
217901 AGAATATATAA
1 AAAAT-TATAA
217912 AAAA
1 AAAA
217916 ATTAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (10 bp):
AAAATTATAA
Found at i:218511 original size:23 final size:23
Alignment explanation
Indices: 218467--218548 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
218457 TTAATGTTCA
* *
218467 CGAAAATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-TGAACATTAAT
* *
218490 CAAACATGTTCATGAACATTAAA
1 CGAACATGTTCATGAACATTAAT
*
218513 CGAACATATTCATGAACATATAAT
1 CGAACATGTTCATGAACAT-TAAT
*
218537 TGAACATGTTCA
1 CGAACATGTTCA
218549 CGAAAAATGT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 4 0.08
23 31 0.65
24 13 0.27
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (23 bp):
CGAACATGTTCATGAACATTAAT
Found at i:219790 original size:5 final size:5
Alignment explanation
Indices: 219782--219806 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
219772 CATAAAATAA
219782 GTTTG GTTTG GTTTG GTTTG GTTTG
1 GTTTG GTTTG GTTTG GTTTG GTTTG
219807 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (5 bp):
GTTTG
Found at i:221601 original size:100 final size:100
Alignment explanation
Indices: 221423--221616 Score: 334
Period size: 100 Copynumber: 1.9 Consensus size: 100
221413 TTTGTCTATA
*
221423 TGCCAAAGCACAGGGTGCATAGCAGAGATTTCATACTATGAGGTCTACATGGATAGGTGCTAGGA
1 TGCCAAAGCACAGGCTGCATAGCAGAGATTTCATACTATGAGGTCTACATGGATAGGTGCTAGGA
*
221488 TCTTTTAGAAGTCAAAACCAAAGAAATTTAAAAAT
66 TATTTTAGAAGTCAAAACCAAAGAAATTTAAAAAT
* *
221523 TGCCAAAGCACAGGCTGCATAGCAGAGATTTCATACTATGAGGTCTACATGGATGGGTGCTATGA
1 TGCCAAAGCACAGGCTGCATAGCAGAGATTTCATACTATGAGGTCTACATGGATAGGTGCTAGGA
* *
221588 TATTTTAGTAGTCAAAACTAAAGAAATTT
66 TATTTTAGAAGTCAAAACCAAAGAAATTT
221617 CAATTTTGGA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 88 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (100 bp):
TGCCAAAGCACAGGCTGCATAGCAGAGATTTCATACTATGAGGTCTACATGGATAGGTGCTAGGA
TATTTTAGAAGTCAAAACCAAAGAAATTTAAAAAT
Found at i:222326 original size:26 final size:27
Alignment explanation
Indices: 222271--222332 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 27
222261 GGGTTGTTAT
222271 TTATTATTTATTTATCATCATCATGTTCC
1 TTATTATTTATTTATCATCATCA--TTCC
222300 TTATTATTTATTTATCATCATCA-TCC
1 TTATTATTTATTTATCATCATCATTCC
222326 TTATTAT
1 TTATTAT
222333 GATGATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 10 0.30
29 23 0.70
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.56
Consensus pattern (27 bp):
TTATTATTTATTTATCATCATCATTCC
Found at i:222332 original size:29 final size:29
Alignment explanation
Indices: 222271--222371 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 29
222261 GGGTTGTTAT
* *
222271 TTATTATTTATTTATCATCATCATGTTCC
1 TTATTATTTATTTATCATCATCATCTTCA
222300 TTATTATTTATTTATCATCATCATCCTT-A
1 TTATTATTTATTTATCATCATCAT-CTTCA
*
222329 TTATGATGATTTATTATTTATTTATCATCATCTTCA
1 TTAT--T-A--T-TTATTTA-TCATCATCATCTTCA
222365 TTATTAT
1 TTATTAT
222372 CAAGGAGAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
29 28 0.47
30 2 0.03
31 2 0.03
32 1 0.02
33 1 0.02
34 2 0.03
35 10 0.17
36 14 0.23
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.56
Consensus pattern (29 bp):
TTATTATTTATTTATCATCATCATCTTCA
Found at i:225161 original size:42 final size:42
Alignment explanation
Indices: 225081--225197 Score: 114
Period size: 42 Copynumber: 2.7 Consensus size: 42
225071 TCGAGTCATA
* * *
225081 AGTCTTCCTTTTTAAATATAATTTCATTCTCATCTCGAGACA-T
1 AGTCTTCC-ATTTACATA-AATTTCATGCTCATCTCGAGACACT
* *
225124 GAGTCTTCC-TTTA-ATAATATTCTCATGCTCATTTCGAGTCACT
1 -AGTCTTCCATTTACATAA-ATT-TCATGCTCATCTCGAGACACT
225167 AGTCTTCCATTTACATAAATTTACATGCTCA
1 AGTCTTCCATTTACATAAATTT-CATGCTCA
225198 AACCGAGGCA
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
40 1 0.02
41 6 0.09
42 29 0.45
43 16 0.25
44 12 0.19
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (42 bp):
AGTCTTCCATTTACATAAATTTCATGCTCATCTCGAGACACT
Found at i:226297 original size:22 final size:21
Alignment explanation
Indices: 226264--226311 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
226254 CTCTTTCTCT
*
226264 CATTTTTTCTCTTGAAAAACAC
1 CATTTTTCCTCTT-AAAAACAC
* *
226286 TATTTTTCCTCTTCAAAACAC
1 CATTTTTCCTCTTAAAAACAC
226307 CATTT
1 CATTT
226312 ATAAACATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.29, C:0.25, G:0.02, T:0.44
Consensus pattern (21 bp):
CATTTTTCCTCTTAAAAACAC
Found at i:226360 original size:3 final size:3
Alignment explanation
Indices: 226347--226376 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
226337 AAGAATTAGT
*
226347 TTC TGC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
226377 ACCTTGTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:228907 original size:3 final size:3
Alignment explanation
Indices: 228899--228924 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
228889 TTTGCCTTTT
228899 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
228925 TGATTCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:230521 original size:18 final size:20
Alignment explanation
Indices: 230498--230541 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
230488 ATATATATAA
230498 TTTAAACAAA-TA-ACATTT
1 TTTAAACAAATTATACATTT
* *
230516 TTTAAAGAAATTATATATTT
1 TTTAAACAAATTATACATTT
230536 TTTAAA
1 TTTAAA
230542 TAATTAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 11 0.50
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
TTTAAACAAATTATACATTT
Found at i:233452 original size:21 final size:20
Alignment explanation
Indices: 233422--233461 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
233412 TTTATTTTTT
233422 AACTTTAAAA-ATTATAAAAG
1 AACTTTAAAATATT-TAAAAG
233442 AACTATTAAAATATTTAAAA
1 AACT-TTAAAATATTTAAAA
233462 ATTTTCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 11 0.61
22 3 0.17
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AACTTTAAAATATTTAAAAG
Found at i:236190 original size:35 final size:35
Alignment explanation
Indices: 236148--236253 Score: 212
Period size: 35 Copynumber: 3.0 Consensus size: 35
236138 AATCATGCTG
236148 ATACAACTGTTGAATGAGCTGCCAAGAGATGTGAT
1 ATACAACTGTTGAATGAGCTGCCAAGAGATGTGAT
236183 ATACAACTGTTGAATGAGCTGCCAAGAGATGTGAT
1 ATACAACTGTTGAATGAGCTGCCAAGAGATGTGAT
236218 ATACAACTGTTGAATGAGCTGCCAAGAGATGTGAT
1 ATACAACTGTTGAATGAGCTGCCAAGAGATGTGAT
236253 A
1 A
236254 ATTTGTACAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 71 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (35 bp):
ATACAACTGTTGAATGAGCTGCCAAGAGATGTGAT
Found at i:240024 original size:3 final size:3
Alignment explanation
Indices: 240016--240045 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
240006 CATTTAACCC
240016 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
240046 AAAACAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:240613 original size:20 final size:21
Alignment explanation
Indices: 240573--240614 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
240563 TTAAAAATTA
*
240573 TTTCCTATTTTCTTTTCTTTT
1 TTTCCTATTTCCTTTTCTTTT
*
240594 TTTCTTATTTCCTTTT-TTTT
1 TTTCCTATTTCCTTTTCTTTT
240614 T
1 T
240615 CCATTATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTCCTATTTCCTTTTCTTTT
Found at i:240738 original size:17 final size:18
Alignment explanation
Indices: 240716--240749 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
240706 AATTTAAGAA
*
240716 TATTTT-TTGTTTTTTCT
1 TATTTTATTCTTTTTTCT
240733 TATTTTATTCTTTTTTC
1 TATTTTATTCTTTTTTC
240750 AGGTATTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (18 bp):
TATTTTATTCTTTTTTCT
Found at i:243811 original size:420 final size:417
Alignment explanation
Indices: 243035--243873 Score: 1534
Period size: 420 Copynumber: 2.0 Consensus size: 417
243025 AAATAGGTTA
*
243035 ATTTTCAACTTTAGCCCTTTTAATATGATTAAATTTGAGATTTAATTCTTATATTTTAGTTTCAT
1 ATTTTCAACTTTAGCCCTTTTAATATGATTAAATTTGAGATTTAATTCTTATATTTTAATTTCAT
243100 TTTTAGTCCTACTATGCTTAAATTTGAGATTTAATCTTTATACTTTAATTTCAAACATCATTTGG
66 TTTTAGTCCTACTATGCTTAAATTTGAGATTTAATCTTTATACTTTAATTTCAAACATCATTTGG
* * *
243165 TCTCTGTATTTTTATAATTTTTTAAATTACTTCGAATAGTTAATATTGTTAACTTTTCAATTAAA
131 TCTCTATATTTTCATAATTTTTTAAATTACTTCAAATAGTTAATATTGTTAACTTTTCAATTAAA
243230 ATGTTATGTGATTACATATAATTTGAACATGAACTTTTAAAATCATAAAGTAAAGTGATTAAATT
196 ATGTTATGTGATTACATATAATTTGAACATGAACTTTTAAAATCATAAAGTAAAGTGATTAAATT
243295 CTTGAAAATAAAAGTTAGGGGACTAAATTCCTAATGTACGAAGTGTAGAGACTTAAAGTCATGGT
261 CTTGAAAATAAAAGTTAGGGGACTAAATTCCTAATGTACGAAGTGTAGAGACTTAAAGTCATGGT
*
243360 TGTTTAAACCTAACTGTATCGACTGGTTGGACTAGGAACTTGTCAAGATATTGATCCGAAGAGAA
326 TGTTTAAACCTAACCGTATCGACTGGTTGGACTAGGAACTTGTCAAGATATTGATCCGAAGAGAA
*
243425 GTACCAGACTGATTAACCTGCGAATTG
391 GCACCAGACTGATTAACCTGCGAATTG
243452 ATTTTCAACTTTAGCCCTTTTAATATGATTAAATTTGAGATTTAATTCTTATATTTTAATTTCAT
1 ATTTTCAACTTTAGCCCTTTTAATATGATTAAATTTGAGATTTAATTCTTATATTTTAATTTCAT
243517 TTTTAGTCCTACTATGCTTAAATTTGAGATTTAATCTTTATACTTTAATTTCAAACATCATTTGG
66 TTTTAGTCCTACTATGCTTAAATTTGAGATTTAATCTTTATACTTTAATTTCAAACATCATTTGG
*
243582 TCTCTATATTTTCATAATTTTTTAAATTATTTCAAATAGTTAATAATATTGTTAACTTTTCAATT
131 TCTCTATATTTTCATAATTTTTTAAATTACTTCAAATAG-T--TAATATTGTTAACTTTTCAATT
*
243647 AAAATGTTATGTGGTTACATATAATTTGAACATGAACTTTTAAAATCATAAAGTAAAGTGATTAA
193 AAAATGTTATGTGATTACATATAATTTGAACATGAACTTTTAAAATCATAAAGTAAAGTGATTAA
*
243712 ATTCTTGAAAATAAAAGTTAGGGGACTAAATTCCTAATGTACGAAGTGTAGAGACTTAGAGTCAT
258 ATTCTTGAAAATAAAAGTTAGGGGACTAAATTCCTAATGTACGAAGTGTAGAGACTTAAAGTCAT
* * *
243777 GGTTGTTTAAATCTAACCGTATTGACTGGTTGGACTGGGAACTTGTCAAGATATTGATCCGAAGA
323 GGTTGTTTAAACCTAACCGTATCGACTGGTTGGACTAGGAACTTGTCAAGATATTGATCCGAAGA
*
243842 GAAGCATCAGACTGATTAACCTGCGAATTG
388 GAAGCACCAGACTGATTAACCTGCGAATTG
243872 AT
1 AT
243874 ACGGACCAAT
Statistics
Matches: 406, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
417 164 0.40
418 1 0.00
420 241 0.59
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (417 bp):
ATTTTCAACTTTAGCCCTTTTAATATGATTAAATTTGAGATTTAATTCTTATATTTTAATTTCAT
TTTTAGTCCTACTATGCTTAAATTTGAGATTTAATCTTTATACTTTAATTTCAAACATCATTTGG
TCTCTATATTTTCATAATTTTTTAAATTACTTCAAATAGTTAATATTGTTAACTTTTCAATTAAA
ATGTTATGTGATTACATATAATTTGAACATGAACTTTTAAAATCATAAAGTAAAGTGATTAAATT
CTTGAAAATAAAAGTTAGGGGACTAAATTCCTAATGTACGAAGTGTAGAGACTTAAAGTCATGGT
TGTTTAAACCTAACCGTATCGACTGGTTGGACTAGGAACTTGTCAAGATATTGATCCGAAGAGAA
GCACCAGACTGATTAACCTGCGAATTG
Found at i:244918 original size:16 final size:16
Alignment explanation
Indices: 244897--244951 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
244887 ATTTTTTAAT
244897 AATAATGTTTAACAAA
1 AATAATGTTTAACAAA
* **
244913 AATAATCATCTTATACAGT
1 AATAAT-GT-TTA-ACAAA
244932 AATAATGTTTAACAAA
1 AATAATGTTTAACAAA
244948 AATA
1 AATA
244952 GTTATGTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 13 0.43
17 4 0.13
18 4 0.13
19 9 0.30
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (16 bp):
AATAATGTTTAACAAA
Found at i:244918 original size:19 final size:19
Alignment explanation
Indices: 244894--244961 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
244884 ACCATTTTTT
244894 AATAATAATGTTTAACAAA
1 AATAATAATGTTTAACAAA
* *
244913 AATAATCAT-CTTATAC---
1 AATAATAATGTTTA-ACAAA
*
244929 AGTAATAATGTTTAACAAA
1 AATAATAATGTTTAACAAA
* *
244948 AATAGTTATGTTTA
1 AATAATAATGTTTA
244962 TAAAATAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
16 9 0.25
17 3 0.08
18 3 0.08
19 21 0.58
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (19 bp):
AATAATAATGTTTAACAAA
Found at i:245718 original size:22 final size:22
Alignment explanation
Indices: 245680--245724 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
245670 TCAAACAATC
* *
245680 TAATTATATTTTAAAATTAATT
1 TAATTATATATTAAAATAAATT
245702 TAATTAATATATT-AAATAAATT
1 TAATT-ATATATTAAAATAAATT
245724 T
1 T
245725 TATAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATTATATATTAAAATAAATT
Found at i:245901 original size:2 final size:2
Alignment explanation
Indices: 245894--245918 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
245884 ACTTCAAACA
245894 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 A
245919 ACGTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:255783 original size:44 final size:44
Alignment explanation
Indices: 255720--255815 Score: 183
Period size: 44 Copynumber: 2.2 Consensus size: 44
255710 CAAGACTAAA
255720 TATCTATTAAAAGCATGAATACTTTACCTCTTAAAAAATGTGGG
1 TATCTATTAAAAGCATGAATACTTTACCTCTTAAAAAATGTGGG
255764 TATCTATTAAAAGCATGAATACTTTACCTCTTAAAAAATGTGGG
1 TATCTATTAAAAGCATGAATACTTTACCTCTTAAAAAATGTGGG
*
255808 TACCTATT
1 TATCTATT
255816 TTAATTGGCT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (44 bp):
TATCTATTAAAAGCATGAATACTTTACCTCTTAAAAAATGTGGG
Found at i:259061 original size:10 final size:9
Alignment explanation
Indices: 259021--259097 Score: 54
Period size: 8 Copynumber: 8.6 Consensus size: 9
259011 ATAAGTATTA
259021 TAAAAATAT
1 TAAAAATAT
*
259030 T-TAAA-AT
1 TAAAAATAT
259037 TAAAAA-AT
1 TAAAAATAT
*
259045 AAAAAATATT
1 TAAAAATA-T
*
259055 TAAAAATGGT
1 TAAAAAT-AT
259065 TAAAAATA-
1 TAAAAATAT
259073 TAAAAATACAT
1 TAAAAAT--AT
*
259084 TTAAAATAT
1 TAAAAATAT
259093 TAAAA
1 TAAAA
259098 TTGAAATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
7 3 0.06
8 20 0.38
9 8 0.15
10 16 0.30
11 6 0.11
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAAAATAT
Found at i:259602 original size:19 final size:19
Alignment explanation
Indices: 259541--259832 Score: 67
Period size: 19 Copynumber: 15.4 Consensus size: 19
259531 TTTTTATGAT
* *
259541 TTTTTTATAAGTTTTATAA
1 TTTTTAATAACTTTTATAA
* * **
259560 GTTTGTATTAACTTCAAT-A
1 -TTTTTAATAACTTTTATAA
*
259579 TTTTTAATGACTTTTATAA
1 TTTTTAATAACTTTTATAA
* * *
259598 TTTTTTATAATTTTTATGA
1 TTTTTAATAACTTTTATAA
*
259617 TTTTT-ATAGAATTTTAATATA
1 TTTTTAATA-ACTTTT-ATA-A
* *
259638 TTTTT-ATAAAATTTT-CAA
1 TTTTTAAT-AACTTTTATAA
*
259656 TGTTTT-ATTACTTTTATAA
1 T-TTTTAATAACTTTTATAA
* * *
259675 CTTTTTTATAATTTATTAGAA
1 -TTTTTAATAACTT-TTATAA
*
259696 TTTATT-AT-ATTTTTATAA
1 TTT-TTAATAACTTTTATAA
* *
259714 TATTT-ATAAATTTTTATATA
1 TTTTTAAT-AACTTTTATA-A
* *
259734 GTTTT-ATAATTTTTATAA
1 TTTTTAATAACTTTTATAA
*
259752 -GTTTATATCAA-TTTTCAT-A
1 TTTTTA-AT-AACTTTT-ATAA
*
259771 TTTTTAAT-A--TTCATTAA
1 TTTTTAATAACTTTTA-TAA
** *
259788 TTTTT-ATATTTTTTATTA
1 TTTTTAATAACTTTTATAA
* *
259806 TTTTTAAATAATTTTTATGA
1 TTTTT-AATAACTTTTATAA
259826 TTTTTAA
1 TTTTTAA
259833 ATTATTTTTA
Statistics
Matches: 210, Mismatches: 36, Indels: 53
0.70 0.12 0.18
Matches are distributed among these distances:
15 1 0.00
16 5 0.02
17 14 0.07
18 37 0.18
19 77 0.37
20 54 0.26
21 21 0.10
22 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTTAATAACTTTTATAA
Found at i:259603 original size:10 final size:10
Alignment explanation
Indices: 259590--259766 Score: 86
Period size: 10 Copynumber: 18.2 Consensus size: 10
259580 TTTTAATGAC
259590 TTTTATAATT
1 TTTTATAATT
259600 TTTTATAA-T
1 TTTTATAATT
*
259609 TTTTATGA-T
1 TTTTATAATT
*
259618 TTTTATAGAAT
1 TTTTATA-ATT
*
259629 TTTAAT-ATAT
1 TTTTATAAT-T
**
259639 TTTTATAAAA
1 TTTTATAATT
* *
259649 TTTT-CAATG
1 TTTTATAATT
* *
259658 TTTTATTA-C
1 TTTTATAATT
259667 TTTTATAACTT
1 TTTTATAA-TT
259678 TTTTATAATT
1 TTTTATAATT
* *
259688 TATTAGAATT
1 TTTTATAATT
*
259698 TATTAT-A-T
1 TTTTATAATT
259706 TTTTATAA-T
1 TTTTATAATT
* *
259715 ATTTATAAAT
1 TTTTATAATT
*
259725 TTTTAT-ATAG
1 TTTTATAAT-T
259735 TTTTATAA-T
1 TTTTATAATT
*
259744 TTTTATAAGT
1 TTTTATAATT
*
259754 TTATATCAATT
1 TTTTAT-AATT
259765 TT
1 TT
259767 CATATTTTTA
Statistics
Matches: 128, Mismatches: 26, Indels: 25
0.72 0.15 0.14
Matches are distributed among these distances:
8 6 0.05
9 48 0.38
10 53 0.41
11 21 0.16
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.61
Consensus pattern (10 bp):
TTTTATAATT
Found at i:259611 original size:9 final size:9
Alignment explanation
Indices: 259590--259835 Score: 153
Period size: 9 Copynumber: 26.1 Consensus size: 9
259580 TTTTAATGAC
259590 TTTTATAATT
1 TTTTATAA-T
259600 TTTTATAAT
1 TTTTATAAT
*
259609 TTTTATGAT
1 TTTTATAAT
259618 TTTTATAGAAT
1 TTTTAT--AAT
*
259629 TTTAATATAT
1 TTTTATA-AT
*
259639 TTTTATAAAA
1 TTTTAT-AAT
*
259649 TTTT-CAAT
1 TTTTATAAT
* *
259657 GTTTTATTAC
1 -TTTTATAAT
259667 TTTTATAACTT
1 TTTTATAA--T
259678 TTTTATAAT
1 TTTTATAAT
*
259687 TTATTAGAAT
1 TT-TTATAAT
259697 TTATTAT-AT
1 TT-TTATAAT
259706 TTTTATAAT
1 TTTTATAAT
*
259715 ATTTATAAAT
1 TTTTAT-AAT
*
259725 TTTTATATAG
1 TTTTATA-AT
259735 TTTTATAAT
1 TTTTATAAT
259744 TTTTATAAGT
1 TTTTATAA-T
*
259754 TTATATCAAT
1 TTTTAT-AAT
*
259764 TTTCAT-A-
1 TTTTATAAT
259771 TTTT-TAAT
1 TTTTATAAT
* *
259779 ATTCATTAAT
1 TTTTA-TAAT
*
259789 TTTTATATT
1 TTTTATAAT
*
259798 TTTTATTAT
1 TTTTATAAT
259807 TTTTAAATAAT
1 TTTT--ATAAT
*
259818 TTTTATGAT
1 TTTTATAAT
259827 TTTTA-AAT
1 TTTTATAAT
259835 T
1 T
259836 ATTTTTATGG
Statistics
Matches: 184, Mismatches: 32, Indels: 42
0.71 0.12 0.16
Matches are distributed among these distances:
6 1 0.01
7 4 0.02
8 12 0.07
9 74 0.40
10 67 0.36
11 26 0.14
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:259621 original size:20 final size:19
Alignment explanation
Indices: 259531--259843 Score: 107
Period size: 20 Copynumber: 15.9 Consensus size: 19
259521 CCAATTTAAG
259531 TTTTTATGATTTTTTTATAA
1 TTTTTAT-ATTTTTTTATAA
* ** *
259551 GTTTTATAAGTTTGTATTAA
1 TTTTTATATTTTTTTA-TAA
* ** * *
259571 CTTCAATA-TTTTTAATGA
1 TTTTTATATTTTTTTATAA
* *
259589 CTTTTATAATTTTTTATAA
1 TTTTTATATTTTTTTATAA
* *
259608 TTTTTATGATTTTTATAGAA
1 TTTTTAT-ATTTTTTTATAA
* *
259628 TTTTAATATATTTTTATAAAA
1 TTTT--TATATTTTTTTATAA
* * *
259649 TTTTCA-A-TGTTTTATTA
1 TTTTTATATTTTTTTATAA
* *
259666 CTTTTATAACTTTTTTATAA
1 TTTTTAT-ATTTTTTTATAA
* * *
259686 TTTATTAGAATTTATTAT-A
1 TTT-TTATATTTTTTTATAA
* *
259705 TTTTTATA-ATATTTATAAA
1 TTTTTATATTTTTTTAT-AA
**
259724 TTTTTATATAGTTTTATAA
1 TTTTTATATTTTTTTATAA
** *
259743 TTTTTATAAGTTTATATCAA
1 TTTTTATATTTTTTTAT-AA
*
259763 TTTTCATATTTTTAATATTCATTAA
1 TTTTTATA-TTTT--T-TT-A-TAA
*
259788 TTTTTATA-TTTTTTATTA
1 TTTTTATATTTTTTTATAA
* * *
259806 TTTTTAAATAATTTTTATGA
1 TTTTTATAT-TTTTTTATAA
*
259826 TTTTTAAATTATTTTTAT
1 TTTTTATATT-TTTTTAT
259844 GGAAAATATA
Statistics
Matches: 218, Mismatches: 53, Indels: 44
0.69 0.17 0.14
Matches are distributed among these distances:
17 15 0.07
18 22 0.10
19 55 0.25
20 86 0.39
21 21 0.10
22 3 0.01
23 4 0.02
24 1 0.00
25 10 0.05
26 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTTATATTTTTTTATAA
Found at i:259631 original size:28 final size:30
Alignment explanation
Indices: 259576--259644 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
259566 ATTAACTTCA
*
259576 ATATTTTTAATGACTTTTATAAT-TTTTTAT
1 ATATTTTT-ATGACTTTTATAATATTTTAAT
*
259606 A-ATTTTTATGATTTTTATAGA-ATTTTAAT
1 ATATTTTTATGACTTTTATA-ATATTTTAAT
259635 ATATTTTTAT
1 ATATTTTTAT
259645 AAAATTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 11 0.32
29 14 0.41
30 9 0.26
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (30 bp):
ATATTTTTATGACTTTTATAATATTTTAAT
Found at i:259690 original size:67 final size:67
Alignment explanation
Indices: 259600--259775 Score: 191
Period size: 67 Copynumber: 2.6 Consensus size: 67
259590 TTTTATAATT
** *
259600 TTTTATAATTTTTATGATTTTTATAGAATTTTAATATATTTTTATAAAATTT-TCAATGTTTTAT
1 TTTTATAATTTTTAT-AAGTTTATAGAATTTTAATATATTTTTATAAAATTTATAAAT-TTTTAT
259664 -TAC
64 ATAC
* *
259667 TTTTATAACTTTTTTATAA-TTTATTAGAA-TTTATTATATTTTTATAATATTTATAAATTTTTA
1 TTTTATAA--TTTTTATAAGTTTA-TAGAATTTTAATATATTTTTATAAAATTTATAAATTTTTA
*
259730 TATAG
63 TATAC
* *
259735 TTTTATAATTTTTATAAGTTTATATCAATTTTCATAT-TTTT
1 TTTTATAATTTTTATAAGTTTATA-GAATTTTAATATATTTT
259776 AATATTCATT
Statistics
Matches: 93, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
66 11 0.12
67 49 0.53
68 26 0.28
69 7 0.08
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (67 bp):
TTTTATAATTTTTATAAGTTTATAGAATTTTAATATATTTTTATAAAATTTATAAATTTTTATAT
AC
Found at i:267348 original size:24 final size:25
Alignment explanation
Indices: 267316--267362 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
267306 TGGGAAATAG
*
267316 GGGTTTTTTCGGAAT-TTAACTTTA
1 GGGTATTTTCGGAATGTTAACTTTA
* *
267340 GGGTATTTTGGGGATGTTAACTT
1 GGGTATTTTCGGAATGTTAACTT
267363 AGGTGGCCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.19, C:0.06, G:0.28, T:0.47
Consensus pattern (25 bp):
GGGTATTTTCGGAATGTTAACTTTA
Found at i:270427 original size:14 final size:15
Alignment explanation
Indices: 270408--270436 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
270398 CCCCTTTACG
270408 CACGTG-CCATTTCA
1 CACGTGACCATTTCA
270422 CACGTGACCATTTCA
1 CACGTGACCATTTCA
270437 TCTTGGCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (15 bp):
CACGTGACCATTTCA
Found at i:277776 original size:23 final size:23
Alignment explanation
Indices: 277740--277841 Score: 100
Period size: 23 Copynumber: 4.3 Consensus size: 23
277730 ACACTAGCAC
277740 GCTCTCTGTTATTAGCA-TTGTGTGT
1 GCTCTCTG--ATTAGCACTT-TGTGT
*
277765 GCTCTCTAATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
277788 GCTCTTTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* * *
277811 ACTCTCTGTTTCA-CACTGTGTGT
1 GCTCTCTGATT-AGCACTTTGTGT
277834 GCTCTCTG
1 GCTCTCTG
277842 TTGCCCAGCA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
23 55 0.85
24 3 0.05
25 7 0.11
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:277842 original size:23 final size:23
Alignment explanation
Indices: 277740--277869 Score: 93
Period size: 23 Copynumber: 5.5 Consensus size: 23
277730 ACACTAGCAC
*
277740 GCTCTCTGTTATTAGCATTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
** *
277765 GCTCTCTAATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * * *
277788 GCTCTTTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
277811 ACTCTCTGTTTCA-CACTGTGTGT
1 GCTCTCTGTTT-AGCACTGTGTGT
* *
277834 GCTCTCTGTTGCCCAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
277859 GCTCTCTGTTT
1 GCTCTCTGTTT
277870 GTTCTGTATA
Statistics
Matches: 84, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
23 57 0.68
24 1 0.01
25 22 0.26
26 4 0.05
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:279051 original size:33 final size:32
Alignment explanation
Indices: 278993--279054 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
278983 AAATTTATAT
* *
278993 AATACATATATTATAATATATTTTTATTTCAC
1 AATACATATATTAAAATAAATTTTTATTTCAC
279025 AATATCATAT-TTAAAATAAATGTTTTATTT
1 AATA-CATATATTAAAATAAAT-TTTTATTT
279055 TTTCAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (32 bp):
AATACATATATTAAAATAAATTTTTATTTCAC
Found at i:279125 original size:21 final size:23
Alignment explanation
Indices: 279084--279127 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
279074 TAATAATACT
279084 AAACATTAATTAACGATTCATTTC
1 AAACATTAATTAAC-ATTCATTTC
279108 AAAC-TTAATTAA-ATTCATTT
1 AAACATTAATTAACATTCATTT
279128 GATGGGGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
23 8 0.40
24 4 0.20
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (23 bp):
AAACATTAATTAACATTCATTTC
Found at i:285838 original size:4 final size:4
Alignment explanation
Indices: 285821--285852 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
285811 AAAATCAAAG
*
285821 GAAA GAAG GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
285853 ACTCAAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:287450 original size:21 final size:21
Alignment explanation
Indices: 287411--287450 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
287401 TCTTGCCAAC
* **
287411 TGTGTAGAAAACTTGTCTAGT
1 TGTGCAGAAAACTCATCTAGT
287432 TGTGCAGAAAACTCATCTA
1 TGTGCAGAAAACTCATCTA
287451 ACACACGCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (21 bp):
TGTGCAGAAAACTCATCTAGT
Found at i:300306 original size:15 final size:15
Alignment explanation
Indices: 300286--300318 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
300276 CTTTTACAAA
300286 TTTAAACACT-AAAAT
1 TTTAAAC-CTCAAAAT
300301 TTTAAACCTCAAAAT
1 TTTAAACCTCAAAAT
300316 TTT
1 TTT
300319 CGAAACTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (15 bp):
TTTAAACCTCAAAAT
Found at i:310716 original size:17 final size:17
Alignment explanation
Indices: 310691--310736 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
310681 CCAACAGAAT
310691 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
310708 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAA
310725 TTAAATTTATTT
1 TTAAATTTATTT
310737 AATGTTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:311382 original size:3 final size:3
Alignment explanation
Indices: 311376--311446 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
311366 TTATGGCATC
311376 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
311424 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
311447 CATATATTAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:312664 original size:30 final size:29
Alignment explanation
Indices: 312536--312914 Score: 177
Period size: 29 Copynumber: 12.8 Consensus size: 29
312526 TGGAGGTCCT
* * * * *
312536 TAAACTGTCCAGAAATCATATTTTAACCC
1 TAAACTTTCCAAAAATTACATTTTTACCC
*
312565 -AGAACTTTCCAAAAATTATA-TTTTACCCC
1 TA-AACTTTCCAAAAATTACATTTTTA-CCC
* * * * *
312594 TAAACTTTTTC-GAAATTCCATTTTTTGATCG
1 TAAAC-TTTCCAAAAATTACA-TTTTT-ACCC
* * *
312625 TAAATTTTCCAAAAATTATATTTTTACCT
1 TAAACTTTCCAAAAATTACATTTTTACCC
* * *
312654 TCGAACTTTCC-AAAATTCCATTTTTAACCT
1 T-AAACTTTCCAAAAATTACATTTTT-ACCC
** *
312684 TAATTTTTTCAAAAATTACATTTTTACACC
1 TAAACTTTCCAAAAATTACATTTTTAC-CC
*
312714 TAAACTTTCC-AAAATTCCATTTTTGACCC
1 TAAACTTTCCAAAAATTACATTTTT-ACCC
*
312743 TAAATTTTCCAAAAATTACATTTTTACCC
1 TAAACTTTCCAAAAATTACATTTTTACCC
* * * *
312772 TCGAACTTTTC-GAAATTCCATTTTTGATCCC
1 T-AAACTTTCCAAAAATTACATTTTT-A-CCC
** * *
312803 -AAGTTTTCTAAAAATTACAATTTTACCCC
1 TAAACTTTCCAAAAATTACATTTTTA-CCC
* *
312832 CAAACTTTCC-AAAATTACCA-TTTCACCC
1 TAAACTTTCCAAAAATTA-CATTTTTACCC
* * *
312860 TCGAA-TGTCTAAAAA-TATCATTTTTTACCC
1 T-AAACTTTCCAAAAATTA-CA-TTTTTACCC
* * *
312890 CAAACCTTACAAAAATTACCATTTT
1 TAAACTTTCCAAAAATTA-CATTTT
312915 ACCATCGAAT
Statistics
Matches: 260, Mismatches: 64, Indels: 51
0.69 0.17 0.14
Matches are distributed among these distances:
28 15 0.06
29 117 0.45
30 105 0.40
31 22 0.08
32 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (29 bp):
TAAACTTTCCAAAAATTACATTTTTACCC
Found at i:312707 original size:59 final size:58
Alignment explanation
Indices: 312556--312854 Score: 289
Period size: 59 Copynumber: 5.0 Consensus size: 58
312546 AGAAATCATA
* * * * *
312556 TTTTAACCCAGAACTTTCCAAAAATTATA-TTTTACCC-CTAAACTTTTTCGAAATTCCATT
1 TTTTAACCTA-AATTTTCCAAAAATTACATTTTTACCCTC-AAAC-TTTCCAAAATTCCA-T
* * * * *
312616 TTTTGATCGTAAATTTTCCAAAAATTATATTTTTACCTTCGAACTTTCCAAAATTCCAT
1 TTTT-AACCTAAATTTTCCAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCCAT
* *
312675 TTTTAACCTTAATTTTTTCAAAAATTACATTTTTACACCT-AAACTTTCCAAAATTCCAT
1 TTTTAACC-TAAATTTTCCAAAAATTACATTTTTAC-CCTCAAACTTTCCAAAATTCCAT
* * * *
312734 TTTTGACCCTAAATTTTCCAAAAATTACATTTTTACCCTCGAACTTTTCGAAATTCCAT
1 TTTT-AACCTAAATTTTCCAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCCAT
* * * * * *
312793 TTTTGATCCCAAGTTTTCTAAAAATTACAATTTTACCCCCAAACTTTCCAAAATTACCAT
1 TTTT-AACCTAAATTTTCCAAAAATTACATTTTTACCCTCAAACTTTCCAAAATT-CCAT
312853 TT
1 TT
312855 CACCCTCGAA
Statistics
Matches: 201, Mismatches: 30, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
58 5 0.02
59 138 0.69
60 44 0.22
61 13 0.06
62 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.41
Consensus pattern (58 bp):
TTTTAACCTAAATTTTCCAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCCAT
Found at i:312766 original size:118 final size:116
Alignment explanation
Indices: 312574--312854 Score: 357
Period size: 118 Copynumber: 2.4 Consensus size: 116
312564 CAGAACTTTC
* * * * *
312574 CAAAAATTATATTTTACCCCTAAACTTTTTCGAAATTCCATTTTTTGATCGTAAATTTTCCAAAA
1 CAAAAATTACATTTTACCCCTAAAC-TTTCCAAAATTCCA-TTTTTGACCCTAAATTTTCCAAAA
* * * *
312639 ATTATATTTTTACCTTCGAACTTTCCAAAATTCCATTTTT-AACCTTAATTTTTT
64 ATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGAACC-CAA-GTTTT
*
312693 CAAAAATTACATTTTTACACCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTCCAAAAA
1 CAAAAATTACA-TTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTCCAAAAA
* * *
312758 TTACATTTTTACCCTCGAACTTTTCGAAATTCCATTTTTGATCCCAAGTTTT
65 TTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGAACCCAAGTTTT
*
312810 CTAAAAATTACAATTTTACCCCCAAACTTTCCAAAATTACCATTT
1 C-AAAAATTAC-ATTTTACCCCTAAACTTTCCAAAATT-CCATTT
312855 CACCCTCGAA
Statistics
Matches: 142, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
117 5 0.04
118 92 0.65
119 32 0.23
120 13 0.09
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (116 bp):
CAAAAATTACATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTCCAAAAAT
TACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGAACCCAAGTTTT
Found at i:312886 original size:59 final size:58
Alignment explanation
Indices: 312823--312971 Score: 183
Period size: 59 Copynumber: 2.5 Consensus size: 58
312813 AAAATTACAA
* * * *
312823 TTTTACCCCCAAACTTTCCAAAATTACCATTTCACCCTCGAATGTCTAAAAATATCATT
1 TTTTACCCCCAAACTTTCAAAAATTACCATTTCACCATCGAATATCTAAAAAT-GCATT
* *
312882 TTTTA-CCCCAAACCTTACAAAAATTACCATTTTACCATCGAATATCTAAAAATGCATT
1 TTTTACCCCCAAA-CTTTCAAAAATTACCATTTCACCATCGAATATCTAAAAATGCATT
* * *
312940 TTTTGACCCCGAACCTTTCAAAAATTATCATT
1 TTTT-ACCCCCAAACTTTCAAAAATTACCATT
312972 CTATCCCCGG
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
58 15 0.19
59 57 0.74
60 5 0.06
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (58 bp):
TTTTACCCCCAAACTTTCAAAAATTACCATTTCACCATCGAATATCTAAAAATGCATT
Found at i:312989 original size:59 final size:59
Alignment explanation
Indices: 312842--313030 Score: 172
Period size: 59 Copynumber: 3.2 Consensus size: 59
312832 CAAACTTTCC
* *
312842 AAAATTACCATT-TCACC-CTCGAATGTCTAAAAATATCATTTTTT-ACCCCAAACCTTACA
1 AAAATTACCATTCT-ACCAC-CGAATGTCTAAAAAT-CCATTTTTTGACCCCGAACCTTACA
* * * * *
312901 AAAATTACCATTTTACCATCGAATATCTAAAAATGCATTTTTTGACCCCGAACCTTTCA
1 AAAATTACCATTCTACCACCGAATGTCTAAAAATCCATTTTTTGACCCCGAACCTTACA
* * * ** * *
312960 AAAATTATCATTCTATCC-CCGGATGTCTAAATATTCCA-TTTTTGACATCGAACCTTCCG
1 AAAATTACCATTCTA-CCACCGAATGTCTAAA-AATCCATTTTTTGACCCCGAACCTTACA
313019 AAAATTACCATT
1 AAAATTACCATT
313031 TTATTCTCGA
Statistics
Matches: 108, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
58 8 0.07
59 93 0.86
60 7 0.06
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (59 bp):
AAAATTACCATTCTACCACCGAATGTCTAAAAATCCATTTTTTGACCCCGAACCTTACA
Found at i:315136 original size:34 final size:33
Alignment explanation
Indices: 315104--315167 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
315094 CAATAAATTA
315104 TTAAAT-TTAAATTATAAGTACTTTTAAAAAAT
1 TTAAATCTTAAATTATAAGTACTTTTAAAAAAT
* ** *
315136 TTGAATCTTTCATTATAAGTATTTTTAAAAAA
1 TTAAATCTTAAATTATAAGTACTTTTAAAAAA
315168 ATGGTTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (33 bp):
TTAAATCTTAAATTATAAGTACTTTTAAAAAAT
Found at i:320125 original size:79 final size:78
Alignment explanation
Indices: 319991--320138 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 78
319981 ACGATCCTAA
* * * * *
319991 CACCCAGTGCCTAGCGGATAAACCGCAAAACTGAGCCCAGCTCTAGTTGGTTTAACCAACAATGT
1 CACCCAATGCCTAGCGAATAAACCACAAAACTGAGCCCAACTCTAGTTGGATTAACCAACAAT-T
320056 TTGTGAAATCTTGG
65 TTGTGAAATCTTGG
* * *
320070 CACCCAATGCCTAGCGAATAAACCACAAAAGTGAGCCCAACTGTAGTTGGATTAACCAACGATTT
1 CACCCAATGCCTAGCGAATAAACCACAAAACTGAGCCCAACTCTAGTTGGATTAACCAACAATTT
320135 TGTG
66 TGTG
320139 CCCAGCGCTA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
78 6 0.10
79 55 0.90
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (78 bp):
CACCCAATGCCTAGCGAATAAACCACAAAACTGAGCCCAACTCTAGTTGGATTAACCAACAATTT
TGTGAAATCTTGG
Found at i:320151 original size:181 final size:185
Alignment explanation
Indices: 319813--320169 Score: 463
Period size: 181 Copynumber: 2.0 Consensus size: 185
319803 TGGCACCCGA
* *
319813 TGCCTAGCAGATAAACCGCAATAAGTGAGCCTAGCTCTAGTTGGATTAACCAACGAAAATTTCGT
1 TGCCTAGCAGATAAACCGCAATAACTGAGCCCAGCTCTAGTTGGATTAACCAACGAAAATTTCGT
* * * * *
319878 CAATTTTTAGCACCCAGTGCCTAGCGAATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGATTA
66 CAAATCTTAGCACCCAATGCCTAGCGAATAAACCACAATAAGTGAGCCCAACTCTAGTTGGATTA
* * * * ** *
319943 ATCAACGGGTTTGCTCACGGTGCTAGTCGGATAAACCGACGATCCTAACACCCAG
131 ACCAACGAGTTTGCTCACAGCGCTAGTCAAATAAACCCACGATCCTAACACCCAG
* * **
319998 TGCCTAGCGGATAAACCGCAA-AACTGAGCCCAGCTCTAGTTGGTTTAACCAAC-AATGTTT-GT
1 TGCCTAGCAGATAAACCGCAATAACTGAGCCCAGCTCTAGTTGGATTAACCAACGAAAATTTCGT
* * *
320060 GAAATCTTGGCACCCAATGCCTAGCGAATAAACCACAA-AAGTGAGCCCAACTGTAGTTGGATTA
66 CAAATCTTAGCACCCAATGCCTAGCGAATAAACCACAATAAGTGAGCCCAACTCTAGTTGGATTA
* *
320124 ACCAACGATTTTG-TGCCCAGCGCTAGTCAAATAAACCCACGATCCT
131 ACCAACGAGTTTGCT-CACAGCGCTAGTCAAATAAACCCACGATCCT
320170 TTAATAATTC
Statistics
Matches: 148, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
180 1 0.01
181 59 0.40
182 34 0.23
183 5 0.03
184 29 0.20
185 20 0.14
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (185 bp):
TGCCTAGCAGATAAACCGCAATAACTGAGCCCAGCTCTAGTTGGATTAACCAACGAAAATTTCGT
CAAATCTTAGCACCCAATGCCTAGCGAATAAACCACAATAAGTGAGCCCAACTCTAGTTGGATTA
ACCAACGAGTTTGCTCACAGCGCTAGTCAAATAAACCCACGATCCTAACACCCAG
Found at i:325419 original size:22 final size:22
Alignment explanation
Indices: 325376--325419 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
325366 TCATGTATAG
* *
325376 TCTCGAGACAAGTAATCTTCGA
1 TCTCGAGACAAATAATCATCGA
325398 TCTCGAGACAAAATAA-CATCGA
1 TCTCGAGAC-AAATAATCATCGA
325420 AGTTAAATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (22 bp):
TCTCGAGACAAATAATCATCGA
Found at i:327524 original size:28 final size:28
Alignment explanation
Indices: 327475--327546 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
327465 AATTGCTATC
* *
327475 AACTGACCAGCTAACTGCTAACTGACTCT
1 AACTAACCAGCTAACTGCTAACAGACT-T
*
327504 AAC-AACCAGCTAACTGTTAACAGACTT
1 AACTAACCAGCTAACTGCTAACAGACTT
*
327531 AACTAACCAACTAACT
1 AACTAACCAGCTAACT
327547 ACTAGTTACT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 4 0.11
28 31 0.82
29 3 0.08
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (28 bp):
AACTAACCAGCTAACTGCTAACAGACTT
Found at i:330889 original size:20 final size:21
Alignment explanation
Indices: 330861--330903 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
330851 AAAAACTTTT
330861 GGGGAGAAAAAT-AGAATAAG
1 GGGGAGAAAAATAAGAATAAG
* *
330881 GGGGGGAAAAATAAGCATAAG
1 GGGGAGAAAAATAAGAATAAG
330902 GG
1 GG
330904 TGGTTGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.40, T:0.09
Consensus pattern (21 bp):
GGGGAGAAAAATAAGAATAAG
Found at i:336390 original size:3 final size:3
Alignment explanation
Indices: 336382--336410 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
336372 TGGAAAACAG
336382 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
336411 GGTGGTGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:337535 original size:3 final size:3
Alignment explanation
Indices: 337527--337561 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
337517 TATAAACGAA
337527 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
337562 AAGAACCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:344132 original size:17 final size:17
Alignment explanation
Indices: 344095--344174 Score: 97
Period size: 17 Copynumber: 4.6 Consensus size: 17
344085 GTTTTTATTT
344095 TAAATTTTAAATTTGAAAA
1 TAAA-TTTAAATTT-AAAA
* *
344114 TAACTTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
344131 TAAATTTAAATTTTAAA
1 TAAATTTAAATTTAAAA
* *
344148 CAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
344165 TAAATTTAAA
1 TAAATTTAAA
344175 GGGAATATGG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
17 40 0.78
18 8 0.16
19 3 0.06
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:348319 original size:15 final size:16
Alignment explanation
Indices: 348287--348319 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
348277 TCCTCTCTTG
*
348287 TTCATTTTTGGTGTTT
1 TTCATTTCTGGTGTTT
348303 TTCATTTCTGG-GTTT
1 TTCATTTCTGGTGTTT
348318 TT
1 TT
348320 TGTTGTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.06, C:0.09, G:0.18, T:0.67
Consensus pattern (16 bp):
TTCATTTCTGGTGTTT
Found at i:354177 original size:57 final size:57
Alignment explanation
Indices: 354116--354227 Score: 215
Period size: 57 Copynumber: 2.0 Consensus size: 57
354106 AGGGAAACTT
*
354116 CCAAATTAAGTTTTCTGACAATTTATTTTAAAGATTAATTCTCAGAAACAAGATTTA
1 CCAAATTAAGTTTTCTGACAATTTATTTTAAAGATTAATTCCCAGAAACAAGATTTA
354173 CCAAATTAAGTTTTCTGACAATTTATTTTAAAGATTAATTCCCAGAAACAAGATT
1 CCAAATTAAGTTTTCTGACAATTTATTTTAAAGATTAATTCCCAGAAACAAGATT
354228 CAGTATTTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (57 bp):
CCAAATTAAGTTTTCTGACAATTTATTTTAAAGATTAATTCCCAGAAACAAGATTTA
Found at i:354209 original size:29 final size:29
Alignment explanation
Indices: 354120--354210 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
354110 AAACTTCCAA
354120 ATTAAGTTTTCTGACAATTTATTTTAAAG
1 ATTAAGTTTTCTGACAATTTATTTTAAAG
* * *
354149 ATTAA-TTCTCAGAAACAA--GA-TTTACCAA-
1 ATTAAGTTTTCTG--ACAATTTATTTTA--AAG
354177 ATTAAGTTTTCTGACAATTTATTTTAAAG
1 ATTAAGTTTTCTGACAATTTATTTTAAAG
354206 ATTAA
1 ATTAA
354211 TTCCCAGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 18
0.66 0.08 0.25
Matches are distributed among these distances:
27 8 0.17
28 13 0.28
29 18 0.38
30 8 0.17
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.42
Consensus pattern (29 bp):
ATTAAGTTTTCTGACAATTTATTTTAAAG
Found at i:356223 original size:29 final size:29
Alignment explanation
Indices: 356134--356320 Score: 109
Period size: 29 Copynumber: 6.4 Consensus size: 29
356124 TTTGGGGTTT
*
356134 AAAATGGAATTTT-AGACATTCGAGGGTAA
1 AAAATGGAATTTTCAAACATTCG-GGGTAA
* * * *
356163 AACAAT--AACTTTTCGAAA-AATCAGGATCA
1 AA-AATGGAA-TTTTC-AAACATTCGGGGTAA
356192 AAAATGGAATTTTCAAACATTCGGGAGTAA
1 AAAATGGAATTTTCAAACATTCGGG-GTAA
* * * *
356222 AACA-GTAATTTTGAAAGATTCGGGGTAA
1 AAAATGGAATTTTCAAACATTCGGGGTAA
** *
356250 AAAATGGAATTTTCGGACATTCAAGGGT--
1 AAAATGGAATTTTCAAACATTC-GGGGTAA
* ** * *
356278 AAAATGGTAATTTTGAAAGTTTCGAGGTCA
1 AAAATGG-AATTTTCAAACATTCGGGGTAA
356308 AAAATGGAATTTT
1 AAAATGGAATTTT
356321 TGGACATTTG
Statistics
Matches: 118, Mismatches: 27, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
28 25 0.21
29 67 0.57
30 24 0.20
31 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (29 bp):
AAAATGGAATTTTCAAACATTCGGGGTAA
Found at i:356314 original size:30 final size:29
Alignment explanation
Indices: 356230--356527 Score: 161
Period size: 29 Copynumber: 10.2 Consensus size: 29
356220 AAAACAGTAA
* *
356230 TTTTGAAAGATTCGGGGTAAAAAATGGAAT
1 TTTTGAAAGTTTCGAGGT-AAAAATGGAAT
* * *
356260 TTTCGGACA--TTCAAGGGT-AAAATGGTAA-
1 TTT-TGAAAGTTTCGA-GGTAAAAATGG-AAT
356288 TTTTGAAAGTTTCGAGGTCAAAAATGGAAT
1 TTTTGAAAGTTTCGAGGT-AAAAATGGAAT
* *
356318 TTTTGGACA-TTTGGAGGT-AAAATGGTAAT
1 TTTT-GAAAGTTTCGAGGTAAAAATGG-AAT
*
356347 TTTTGAAAGTTTCGA-GTCAAAATTGGAAT
1 TTTTGAAAGTTTCGAGGT-AAAAATGGAAT
* * * *
356376 TTTTGAAACTTTAGGGGT-AAAATGTAAT
1 TTTTGAAAGTTTCGAGGTAAAAATGGAAT
** *
356404 TTTCAAAAGTTT-TAGGGTCAAAAATGGAAT
1 TTTTGAAAGTTTCGA-GGT-AAAAATGGAAT
* **
356434 TTTTGAAAG-TTCGGGGGGGTAAAAATTTAAT
1 TTTTGAAAGTTTC---GAGGTAAAAATGGAAT
*
356465 TTTTG-AAGTTTTG-GCGTCAAAAATGGAAT
1 TTTTGAAAGTTTCGAG-GT-AAAAATGGAAT
* * * * *
356494 TTTGGAAAGTTTGGGGGTAAAAATGTATT
1 TTTTGAAAGTTTCGAGGTAAAAATGGAAT
356523 TTTTG
1 TTTTG
356528 GATAGTTTAG
Statistics
Matches: 205, Mismatches: 37, Indels: 53
0.69 0.13 0.18
Matches are distributed among these distances:
27 4 0.02
28 48 0.23
29 66 0.32
30 61 0.30
31 23 0.11
32 3 0.01
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (29 bp):
TTTTGAAAGTTTCGAGGTAAAAATGGAAT
Found at i:356326 original size:58 final size:58
Alignment explanation
Indices: 356095--356438 Score: 260
Period size: 58 Copynumber: 5.9 Consensus size: 58
356085 TTTTGGATTC
* * * ** *
356095 TCAGGGGTAAAATGGTATTTTTGGGAAA-TTTTGGGGTTTAAAATGGAA-TTTTAGACAT
1 TCAGGGGTAAAATGGTAATTTT--GAAAGTTTCGAGGTCAAAAATGGAATTTTTGGACAT
*** ** ***
356153 TC-GAGGGTAAAACAATAACTTTTCGAAA-AATC-AGGATCAAAAATGGAATTTTCAAACAT
1 TCAG-GGGTAAAATGGTAA-TTTT-GAAAGTTTCGAGG-TCAAAAATGGAATTTTTGGACAT
** * * * *
356212 TC-GGGAGTAAAACAGTAATTTTGAAAGATTCGGGGTAAAAAATGGAATTTTCGGACAT
1 TCAGGG-GTAAAATGGTAATTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTGGACAT
*
356270 TCAAGGGTAAAATGGTAATTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTGGACAT
1 TCAGGGGTAAAATGGTAATTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTGGACAT
* * *
356328 T-TGGAGGTAAAATGGTAATTTTTGAAAGTTTCGA-GTCAAAATTGGAATTTTT-GAAACT
1 TCAGG-GGTAAAATGGTAA-TTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTGGACA-T
* * *
356386 TTAGGGGTAAAAT-GTAATTTTCAAAAGTTT-TAGGGTCAAAAATGGAATTTTTG
1 TCAGGGGTAAAATGGTAATTTT-GAAAGTTTCGA-GGTCAAAAATGGAATTTTTG
356439 AAAGTTCGGG
Statistics
Matches: 236, Mismatches: 34, Indels: 31
0.78 0.11 0.10
Matches are distributed among these distances:
56 5 0.02
57 22 0.09
58 162 0.69
59 47 0.20
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (58 bp):
TCAGGGGTAAAATGGTAATTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTGGACAT
Found at i:356439 original size:58 final size:56
Alignment explanation
Indices: 356189--356525 Score: 261
Period size: 58 Copynumber: 5.8 Consensus size: 56
356179 AAAATCAGGA
* * * * *
356189 TCAAAAATGGAA-TTTTCAAACATTCGGGAGTAAAACAGTAATTTTGAAAGATTCGGGG
1 TCAAAAATGGAATTTTTGAAACTTTAGGG-GTAAAA-TGTAATTTTGAAAGTTTC-GGG
* * * * *
356247 TAAAAAATGGAATTTTCG-GACATTCAAGGGTAAAATGGTAATTTTGAAAGTTTCGAGG
1 TCAAAAATGGAATTTTTGAAAC-TTTAGGGGTAAAAT-GTAATTTTGAAAGTTTCG-GG
* *
356305 TCAAAAATGGAATTTTTG-GACATTT-GGAGGTAAAATGGTAATTTTTGAAAGTTTCGAG
1 TCAAAAATGGAATTTTTGAAAC-TTTAGG-GGTAAAAT-GTAA-TTTTGAAAGTTTCGGG
* * *
356363 TCAAAATTGGAATTTTTGAAACTTTAGGGGTAAAATGTAATTTTCAAAAGTTTTAGGG
1 TCAAAAATGGAATTTTTGAAACTTTAGGGGTAAAATGTAATTTT-GAAAG-TTTCGGG
* ** * *
356421 TCAAAAATGGAATTTTTGAAAGTTCGGGGGGGTAAAAATTTAATTTTTG-AAGTTTTGGCG
1 TCAAAAATGGAATTTTTGAAACTT--TAGGGGT-AAAATGTAA-TTTTGAAAGTTTCGG-G
* * * *
356481 TCAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAAATGTATTTTT
1 TCAAAAATGGAATTTTTGAAACTTTAGGGGT-AAAATGTAATTTT
356526 TGGATAGTTT
Statistics
Matches: 233, Mismatches: 31, Indels: 31
0.79 0.11 0.11
Matches are distributed among these distances:
56 4 0.02
57 14 0.06
58 142 0.61
59 29 0.12
60 32 0.14
61 8 0.03
62 4 0.02
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (56 bp):
TCAAAAATGGAATTTTTGAAACTTTAGGGGTAAAATGTAATTTTGAAAGTTTCGGG
Found at i:356494 original size:29 final size:29
Alignment explanation
Indices: 356230--356527 Score: 173
Period size: 30 Copynumber: 10.2 Consensus size: 29
356220 AAAACAGTAA
* *
356230 TTTTGAAAGATTCGGGGTAAAAAATGGAAT
1 TTTTGAAAGTTTTGGGGT-AAAAATGGAAT
* * ***
356260 TTTCGGACA-TTCAAGGGT-AAAATGGTAA-
1 TTT-TGAAAGTTTTGGGGTAAAAATGG-AAT
* *
356288 TTTTGAAAGTTTCGAGGTCAAAAATGGAAT
1 TTTTGAAAGTTTTGGGGT-AAAAATGGAAT
*
356318 TTTTGGACA--TTTGGAGGT-AAAATGGTAAT
1 TTTT-GAAAGTTTTGG-GGTAAAAATGG-AAT
* * *
356347 TTTTGAAAG-TTTCGAGTCAAAATTGGAAT
1 TTTTGAAAGTTTTGGGGT-AAAAATGGAAT
* * *
356376 TTTTGAAACTTTAGGGGT-AAAATGTAAT
1 TTTTGAAAGTTTTGGGGTAAAAATGGAAT
** *
356404 TTTCAAAAGTTTTAGGGTCAAAAATGGAAT
1 TTTTGAAAGTTTTGGGGT-AAAAATGGAAT
** **
356434 TTTTGAAAGTTCGGGGGGGTAAAAATTTAAT
1 TTTTGAAAGTT--TTGGGGTAAAAATGGAAT
*
356465 TTTTG-AAGTTTTGGCGTCAAAAATGGAAT
1 TTTTGAAAGTTTTGGGGT-AAAAATGGAAT
* * * *
356494 TTTGGAAAGTTTGGGGGTAAAAATGTATT
1 TTTTGAAAGTTTTGGGGTAAAAATGGAAT
356523 TTTTG
1 TTTTG
356528 GATAGTTTAG
Statistics
Matches: 200, Mismatches: 49, Indels: 39
0.69 0.17 0.14
Matches are distributed among these distances:
27 3 0.01
28 52 0.26
29 55 0.28
30 66 0.33
31 20 0.10
32 4 0.02
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (29 bp):
TTTTGAAAGTTTTGGGGTAAAAATGGAAT
Found at i:356529 original size:30 final size:30
Alignment explanation
Indices: 356278--356527 Score: 187
Period size: 30 Copynumber: 8.5 Consensus size: 30
356268 ATTCAAGGGT
* *
356278 AAAATGGTAA-TTTTGAAAGTTTCGAGGTCA
1 AAAATGG-AATTTTTGAAAGTTTGGGGGTCA
* *
356308 AAAATGGAATTTTTGGACA-TTTGGAGGT--
1 AAAATGGAATTTTT-GAAAGTTTGGGGGTCA
* *
356336 AAAATGGTAATTTTTGAAAGTTT-CGAGTCA
1 AAAATGG-AATTTTTGAAAGTTTGGGGGTCA
* * *
356366 AAATTGGAATTTTTGAAACTTTAGGGGT--
1 AAAATGGAATTTTTGAAAGTTTGGGGGTCA
* ** **
356394 AAAATGTAATTTTCAAAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGAAAGTTTGGGGGTCA
*
356424 AAAATGGAATTTTTGAAAGTTCGGGGGGGT-A
1 AAAATGGAATTTTTGAAAGTT--TGGGGGTCA
** * *
356455 AAAATTTAATTTTTG-AAGTTTTGGCGTCA
1 AAAATGGAATTTTTGAAAGTTTGGGGGTCA
*
356484 AAAATGGAATTTTGGAAAGTTTGGGGGT-A
1 AAAATGGAATTTTTGAAAGTTTGGGGGTCA
* *
356513 AAAATGTATTTTTTG
1 AAAATGGAATTTTTG
356528 GATAGTTTAG
Statistics
Matches: 171, Mismatches: 36, Indels: 27
0.73 0.15 0.12
Matches are distributed among these distances:
28 37 0.22
29 52 0.30
30 61 0.36
31 17 0.10
32 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGGAATTTTTGAAAGTTTGGGGGTCA
Found at i:358396 original size:17 final size:17
Alignment explanation
Indices: 358376--358426 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
358366 TTATAATAAT
*
358376 TTTAAAATAAATCTAAA
1 TTTAAAATAAATTTAAA
*
358393 TTTAAAATAAATTTAAT
1 TTTAAAATAAATTTAAA
358410 TTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
358427 AGGTACTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:363746 original size:24 final size:23
Alignment explanation
Indices: 363694--363753 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
363684 ACTTATCATT
* *
363694 AATATAAATTATTTGTAAAATTA
1 AATATAAAATATTTGTAAAAATA
*
363717 ATATATAAAATATTTTTAAAAAATA
1 A-ATATAAAATATTTGT-AAAAATA
363742 AATATAATAATA
1 AATATAA-AATA
363754 AATAAGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 1 0.03
24 19 0.61
25 11 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
AATATAAAATATTTGTAAAAATA
Found at i:363777 original size:31 final size:31
Alignment explanation
Indices: 363742--363820 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
363732 TTAAAAAATA
363742 AATATAATAATAAATAAGATTTAAATAATTT
1 AATATAATAATAAATAAGATTTAAATAATTT
* * * *
363773 AATATAATGATCAATGATATTTAAATAATTT
1 AATATAATAATAAATAAGATTTAAATAATTT
* *
363804 AATATAATTATATATAA
1 AATATAATAATAAATAA
363821 AATATAATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (31 bp):
AATATAATAATAAATAAGATTTAAATAATTT
Found at i:363812 original size:10 final size:10
Alignment explanation
Indices: 363760--363850 Score: 61
Period size: 10 Copynumber: 9.4 Consensus size: 10
363750 AATAAATAAG
363760 ATTTAA-ATA
1 ATTTAATATA
363769 ATTTAATATA
1 ATTTAATATA
*
363779 ATGATCAATGAT-
1 AT--TTAAT-ATA
363791 ATTTAA-ATA
1 ATTTAATATA
363800 ATTTAATATA
1 ATTTAATATA
363810 A-TTATATATA
1 ATTTA-ATATA
363820 A---AATATA
1 ATTTAATATA
* *
363827 ATTTTATCTA
1 ATTTAATATA
*
363837 ATTTTATATA
1 ATTTAATATA
363847 ATTT
1 ATTT
363851 TTAAATAGTT
Statistics
Matches: 67, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
7 6 0.09
8 3 0.04
9 15 0.22
10 35 0.52
12 6 0.09
13 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (10 bp):
ATTTAATATA
Found at i:364894 original size:17 final size:17
Alignment explanation
Indices: 364859--364900 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
364849 AGAAAAAGTA
*
364859 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
364877 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
364894 GTTAAAG
1 GTTAAAG
364901 GTCAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:364900 original size:24 final size:24
Alignment explanation
Indices: 364873--364920 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
364863 CAAGAATATG
*
364873 AAAGGTTAAAGA-AGATGGAAGGTT
1 AAAGG-TAAAGAGAGATGAAAGGTT
*
364897 AAAGGTCAAGAGAGATGAAAGGTT
1 AAAGGTAAAGAGAGATGAAAGGTT
364921 GAACATTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.46, C:0.02, G:0.33, T:0.19
Consensus pattern (24 bp):
AAAGGTAAAGAGAGATGAAAGGTT
Found at i:366658 original size:21 final size:22
Alignment explanation
Indices: 366641--366748 Score: 74
Period size: 23 Copynumber: 4.5 Consensus size: 22
366631 CCGAAGTACT
*
366641 AACAGAGAGCACATAAGTGCTGGG
1 AACAGAGAGCACAAAAGTGCT--G
* * *
366665 CAACAAAGAGCACACACAGTGCTA
1 -AACAGAGAGCACA-AAAGTGCTG
366689 AACAGAGAGCACACAAAGTGCT-
1 AACAGAGAGCACA-AAAGTGCTG
* *
366711 AATCAGAGAGCACACACAGTGCTAAT
1 AA-CAGAGAGCACA-AAAGTGCT--G
366737 AACAGAGAGCAC
1 AACAGAGAGCAC
366749 GAGACGTGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
22 2 0.03
23 39 0.55
25 22 0.31
26 8 0.11
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (22 bp):
AACAGAGAGCACAAAAGTGCTG
Found at i:366697 original size:23 final size:23
Alignment explanation
Indices: 366666--366769 Score: 129
Period size: 23 Copynumber: 4.4 Consensus size: 23
366656 AGTGCTGGGC
*
366666 AACAAAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
366689 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
366712 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
366736 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
*
366760 AACAAAGAGC
1 AACAGAGAGC
366770 GCGCTAGTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
23 50 0.70
24 2 0.03
25 16 0.23
26 3 0.04
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.10
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:366758 original size:48 final size:46
Alignment explanation
Indices: 366666--366769 Score: 138
Period size: 48 Copynumber: 2.2 Consensus size: 46
366656 AGTGCTGGGC
366666 AACAAAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGCTA
1 AACAAAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGCTA
* * * *
366712 ATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGCTA
1 AACAAAGAGCACACACAGTGCT-A-AACAGAGAGCAC-ACAAAGTGCTA
366760 AACAAAGAGC
1 AACAAAGAGC
366770 GCGCTAGTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
46 20 0.41
47 1 0.02
48 27 0.55
49 1 0.02
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.10
Consensus pattern (46 bp):
AACAAAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGCTA
Found at i:371328 original size:23 final size:23
Alignment explanation
Indices: 371301--371346 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
371291 TTGATTTTTC
371301 ATAATTGTTATGTGTTGTAACAT
1 ATAATTGTTATGTGTTGTAACAT
*
371324 ATAATTGTTATTTGTTGTAACAT
1 ATAATTGTTATGTGTTGTAACAT
371347 TCACTTCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.50
Consensus pattern (23 bp):
ATAATTGTTATGTGTTGTAACAT
Found at i:372720 original size:2 final size:2
Alignment explanation
Indices: 372713--372760 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
372703 TTTTATTGAA
372713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
372755 AT AT AT
1 AT AT AT
372761 GGATTTTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:373624 original size:158 final size:155
Alignment explanation
Indices: 373460--374009 Score: 668
Period size: 158 Copynumber: 3.5 Consensus size: 155
373450 AATTTAAAAA
* *
373460 TGCTGGCTGTGAGGTTCGAACTCACGCGCACTCAAGTGCAGCAGATCTTAAGTCTGCCCCCTTAA
1 TGCTGGCTGTGAGGTTCGAACTCACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAA
* * * * *
373525 CCACTCGGGCAAGCCAGCCAATTGATATGTAAGCTTCACAATATAAATTTTATTAATTTAAATAA
66 CCTCTCGGGCAAACCAGCCAATTGCTATGTAAGTTTCACAATAT--ATTTTATTAATCTAAATAA
373590 CAAGAAAGTAAAATAAAATTAAAATTTT
129 CAAGAAAGTAAAATAAAATTAAAA-TTT
373618 TGCTGGCTGTGAGGTTCGAACTCACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAA
1 TGCTGGCTGTGAGGTTCGAACTCACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAA
* * ** * *
373683 CCTCTCGGGCAAACCAGCCAATTGCTATGT-TGATTTCACAATATCTACT-TTAA-CTATATAGC
66 CCTCTCGGGCAAACCAGCCAATTGCTATGTAAG-TTTCACAATATATTTTATTAATCTAAATAAC
*
373745 AAGAAAGTAATAAAATAAAACTAAAATTT
130 AAGAAAG---TAAAATAAAATTAAAATTT
* * * * * *
373774 T-CTGGCTTTGAGGTTCGAGCTCACTCGCACTTATGTACAGCAGATCTTAAGTCTGCCCCATCAA
1 TGCTGGCTGTGAGGTTCGAACTCACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAA
* * * * *
373838 ACTCTCGGGCAAACCAGCGAATTGCTATGATAA-TTTCACAATGTTTATTTATT--TGTAAATAT
66 CCTCTCGGGCAAACCAGCCAATTGCTATG-TAAGTTTCACAATATAT-TTTATTAATCTAAATA-
* * * *
373900 ATAACTAAA-TAAAATAAAATTATAA-CT
128 ACAA-GAAAGTAAAATAAAATTAAAATTT
373927 TGCTGGCTGTGAGGTTCGAACTCACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAA
1 TGCTGGCTGTGAGGTTCGAACTCACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAA
*
373992 CCTCTCGGGCAAGCCAGC
66 CCTCTCGGGCAAACCAGC
374010 TCAGTGACAG
Statistics
Matches: 337, Mismatches: 43, Indels: 28
0.83 0.11 0.07
Matches are distributed among these distances:
153 2 0.01
154 100 0.30
155 99 0.29
156 13 0.04
157 20 0.06
158 103 0.31
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (155 bp):
TGCTGGCTGTGAGGTTCGAACTCACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAA
CCTCTCGGGCAAACCAGCCAATTGCTATGTAAGTTTCACAATATATTTTATTAATCTAAATAACA
AGAAAGTAAAATAAAATTAAAATTT
Found at i:373843 original size:155 final size:151
Alignment explanation
Indices: 373580--374009 Score: 530
Period size: 154 Copynumber: 2.8 Consensus size: 151
373570 AATTTTATTA
373580 ATTTAA-ATA-ACAAGAAAG---TAAAATAAAATTAAAATTTTTGCTGGCTGTGAGGTTCGAACT
1 ATTTAATATATACAAGAAAGTAATAAAATAAAATTAAAA-TTTT-CTGGCTGTGAGGTTCGAACT
373640 CACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCCAAT
64 CACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCCAAT
* *
373705 TGCTATGTTGATTTCACAATATCT
129 TGCTATG-TAATTTCACAATATAT
* * *
373729 ACTTTAACTATATAGCAAGAAAGTAATAAAATAAAACTAAAATTTTCTGGCTTTGAGGTTCGAGC
1 A-TTTAA-TATATA-CAAGAAAGTAATAAAATAAAATTAAAATTTTCTGGCTGTGAGGTTCGAAC
* * * * * *
373794 TCACTCGCACTTATGTACAGCAGATCTTAAGTCTGCCCCATCAAACTCTCGGGCAAACCAGCGAA
63 TCACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCCAA
* *
373859 TTGCTATGATAATTTCACAATGTTT
128 TTGCTATG-TAATTTCACAATATAT
* * * * * * * *
373884 ATTT-ATTTGTAAATATATAACTAAATAAAATAAAATTATAACTTGCTGGCTGTGAGGTTCGAAC
1 ATTTAATATATACA-AGA-AAGT-AATAAAATAAAATTAAAATTTTCTGGCTGTGAGGTTCGAAC
*
373948 TCACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAGCCAGC
63 TCACGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGC
374010 TCAGTGACAG
Statistics
Matches: 240, Mismatches: 30, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
149 1 0.00
150 5 0.02
151 1 0.00
152 9 0.04
153 5 0.02
154 102 0.43
155 98 0.41
156 4 0.02
157 15 0.06
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (151 bp):
ATTTAATATATACAAGAAAGTAATAAAATAAAATTAAAATTTTCTGGCTGTGAGGTTCGAACTCA
CGCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCCAATTG
CTATGTAATTTCACAATATAT
Found at i:375813 original size:18 final size:17
Alignment explanation
Indices: 375759--375819 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
375749 ACCTCTTCGT
375759 CTTCATCCTCGGAATCA
1 CTTCATCCTCGGAATCA
* * *
375776 TCTTCATCATCAGAACCA
1 -CTTCATCCTCGGAATCA
375794 CTTCCATCCTCGGAATCA
1 CTT-CATCCTCGGAATCA
375812 CTATCATC
1 CT-TCATC
375820 ATCCTCCTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 3 0.09
18 31 0.89
19 1 0.03
ACGTcount: A:0.26, C:0.36, G:0.08, T:0.30
Consensus pattern (17 bp):
CTTCATCCTCGGAATCA
Found at i:380119 original size:29 final size:29
Alignment explanation
Indices: 380082--380166 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
380072 AGAAGTAGTA
*
380082 TAAACATATTGGGTCATTTATGTAAAAAG
1 TAAAAATATTGGGTCATTTATGTAAAAAG
*
380111 TAAAAATATTGGG-CTATTT-TCGTAGAAAG
1 TAAAAATATTGGGTC-ATTTAT-GTAAAAAG
*
380140 TAAAAATATTGAGTCATTTAT-TAAAAA
1 TAAAAATATTGGGTCATTTATGTAAAAA
380167 TGGAAAAGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
28 7 0.15
29 39 0.81
30 2 0.04
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (29 bp):
TAAAAATATTGGGTCATTTATGTAAAAAG
Found at i:380690 original size:29 final size:30
Alignment explanation
Indices: 380654--380719 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
380644 AAGTTTTGAA
380654 TTTAGTTTTTATA-TTTT-AATTTGATCAAT
1 TTTAGTTTTTATACTTTTCAATTTG-TCAAT
* *
380683 TTTAGTTTTTGTACTTTTCGAGTTTGTCAAT
1 TTTAGTTTTTATACTTTTC-AATTTGTCAAT
380714 TTTAGT
1 TTTAGT
380720 CCTAACCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 12 0.38
30 4 0.12
31 11 0.34
32 5 0.16
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.61
Consensus pattern (30 bp):
TTTAGTTTTTATACTTTTCAATTTGTCAAT
Found at i:383860 original size:55 final size:55
Alignment explanation
Indices: 383799--383902 Score: 199
Period size: 55 Copynumber: 1.9 Consensus size: 55
383789 CTGTCGGAGT
383799 AAAAAACCAAAACATATATGTTTGGAAGATACATTAATTAAAGTTTAAATTCGAC
1 AAAAAACCAAAACATATATGTTTGGAAGATACATTAATTAAAGTTTAAATTCGAC
*
383854 AAAAAACCAAAACATATATGTTTGGAAGATACATTAGTTAAAGTTTAAA
1 AAAAAACCAAAACATATATGTTTGGAAGATACATTAATTAAAGTTTAAA
383903 GTTGGTAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (55 bp):
AAAAAACCAAAACATATATGTTTGGAAGATACATTAATTAAAGTTTAAATTCGAC
Found at i:385556 original size:7 final size:7
Alignment explanation
Indices: 385544--385572 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
385534 CCCATGTTTA
385544 TGAAAGG
1 TGAAAGG
385551 TGAAAGG
1 TGAAAGG
385558 TGAAAGG
1 TGAAAGG
385565 TGAAAGG
1 TGAAAGG
385572 T
1 T
385573 CAAATTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.17
Consensus pattern (7 bp):
TGAAAGG
Found at i:386716 original size:153 final size:153
Alignment explanation
Indices: 386438--386742 Score: 583
Period size: 153 Copynumber: 2.0 Consensus size: 153
386428 AATCAAATCG
386438 CATTGTTTGAATTATTCGAGTCAACTCGAATAAGAAATTTCGAATTTTAAGTTCGAGTCGAGTTG
1 CATTGTTTGAATTATTCGAGTCAACTCGAATAAGAAATTTCGAATTTTAAGTTCGAGTCGAGTTG
386503 AATTTTTACAATTCGAATAACTCGAATAAAAGATTAGTGTAATTACCCTTTTGGTCCCTGTTAAT
66 AATTTTTACAATTCGAATAACTCGAATAAAAGATTAGTGTAATTACCCTTTTGGTCCCTGTTAAT
*
386568 TTTGAAAATGAGTCAATTGGTCA
131 TTTGAAAATGAGCCAATTGGTCA
*
386591 CATTGTTTGAATTATTCGAGTCAACTCGAATAAGAAATTTCGAATTTTAAGTTCGAGTCTAGTTG
1 CATTGTTTGAATTATTCGAGTCAACTCGAATAAGAAATTTCGAATTTTAAGTTCGAGTCGAGTTG
*
386656 AATTTTTACAATTCGAATAATTCGAATAAAAGATTAGTGTAATTACCCTTTTGGTCCCTGTTAAT
66 AATTTTTACAATTCGAATAACTCGAATAAAAGATTAGTGTAATTACCCTTTTGGTCCCTGTTAAT
386721 TTTGAAAATGAGCCAATTGGTC
131 TTTGAAAATGAGCCAATTGGTC
386743 TCTCTTTTAA
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 149 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (153 bp):
CATTGTTTGAATTATTCGAGTCAACTCGAATAAGAAATTTCGAATTTTAAGTTCGAGTCGAGTTG
AATTTTTACAATTCGAATAACTCGAATAAAAGATTAGTGTAATTACCCTTTTGGTCCCTGTTAAT
TTTGAAAATGAGCCAATTGGTCA
Found at i:386806 original size:20 final size:20
Alignment explanation
Indices: 386753--386807 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
386743 TCTCTTTTAA
386753 CAAAAATTACAAAATAATTTT
1 CAAAAATTA-AAAATAATTTT
*
386774 CAAAAATT-GAAATCAATTTT
1 CAAAAATTAAAAAT-AATTTT
*
386794 -TAAAATTAAAAATA
1 CAAAAATTAAAAATA
386808 TTTATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 11 0.38
20 10 0.34
21 8 0.28
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (20 bp):
CAAAAATTAAAAATAATTTT
Found at i:388846 original size:15 final size:15
Alignment explanation
Indices: 388826--388871 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
388816 ATAAAATAAT
388826 AACATAAGTGATTAA
1 AACATAAGTGATTAA
*
388841 AACATAA-T-ATTTCA
1 AACATAAGTGA-TTAA
388855 AACATAAGTGATTAA
1 AACATAAGTGATTAA
388870 AA
1 AA
388872 TGTAATCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
15 13 0.50
16 1 0.04
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (15 bp):
AACATAAGTGATTAA
Found at i:397582 original size:21 final size:20
Alignment explanation
Indices: 397534--397586 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
397524 TTATAAATAT
*
397534 TTTTGAA-TTTTAAAAATTA
1 TTTTGAATTTTTGAAAATTA
**
397553 TTTCCAATTTTTGAAAATTA
1 TTTTGAATTTTTGAAAATTA
397573 TTTTGTAATTTTTG
1 TTTTG-AATTTTTG
397587 TTAAGAGAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 5 0.19
20 14 0.52
21 8 0.30
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.57
Consensus pattern (20 bp):
TTTTGAATTTTTGAAAATTA
Found at i:400578 original size:19 final size:20
Alignment explanation
Indices: 400541--400585 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
400531 TTAATACTTA
400541 AATTAAAAATTTAGTTAATT
1 AATTAAAAATTTAGTTAATT
400561 AATTAAAAGA-TTAG-TAATT
1 AATTAAAA-ATTTAGTTAATT
400580 -ATTAAA
1 AATTAAA
400586 CGAACTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.25
19 5 0.21
20 12 0.50
21 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATTAAAAATTTAGTTAATT
Found at i:400893 original size:21 final size:22
Alignment explanation
Indices: 400869--400910 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
400859 TAAGTTTAGA
400869 TATAAT-AAAAAGGTTAATTTG
1 TATAATGAAAAAGGTTAATTTG
* *
400890 TATAGTGAAAATGGTTAATTT
1 TATAATGAAAAAGGTTAATTT
400911 TGAATGTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (22 bp):
TATAATGAAAAAGGTTAATTTG
Found at i:406566 original size:21 final size:21
Alignment explanation
Indices: 406519--406594 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
406509 AATAGTGCAG
**
406519 ACTTTTATTGATAGAAGTGAT
1 ACTTTTACCGATAGAAGTGAT
*
406540 AGTTTTACCGATAGAAGTGACT
1 ACTTTTACCGATAGAAGTGA-T
* * **
406562 -CTTTTACCGAAACAAGTCTT
1 ACTTTTACCGATAGAAGTGAT
*
406582 ACTTCTACCGATA
1 ACTTTTACCGATA
406595 CCAAAAAATC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (21 bp):
ACTTTTACCGATAGAAGTGAT
Found at i:409309 original size:31 final size:31
Alignment explanation
Indices: 409274--409335 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
409264 CTACTTGTTT
*
409274 TATAAATTATATATTA-GTCAAA-TTAATTATA
1 TATAAAATATAT-TTATGT-AAATTTAATTATA
409305 TATAAAATATATTTATGTAAATTTAATTATA
1 TATAAAATATATTTATGTAAATTTAATTATA
409336 AATTATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (31 bp):
TATAAAATATATTTATGTAAATTTAATTATA
Found at i:410749 original size:168 final size:169
Alignment explanation
Indices: 410470--410798 Score: 486
Period size: 168 Copynumber: 1.9 Consensus size: 169
410460 ACCAAATCAA
* *
410470 TGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
1 TGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTAAGAAGTAGACCAAATCAATAAAACCA
* * * *
410535 GACAAACTGAGCAAATCTTCGAACCCCTGCTTCCTGATGAGATACTGAGAAGTAGGTTGAAGCAA
66 GACAAACTGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAA
*
410600 TAAATTC-G-T-CTTCCTGATGAGATACAGAGAAGCGGAT
131 TAAA-GCGGTTACTTCCTGATGAGATACAGAGAAGCGGAT
* *
410637 TGAAACAAGTGATGCGGTCATCTTTCTGATGAGATAC-AAGAAGTAGACCAAATCAATAAAACCA
1 TGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTAAGAAGTAGACCAAATCAATAAAACCA
* * *
410701 GGCTCAAAGTGAGTAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGC
66 -G-ACAAACTGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGC
410766 AATAAAGCGGTTACCTTCCTGATGAGATACAGA
129 AATAAAGCGGTTA-CTTCCTGATGAGATACAGA
410799 AAAGTGAACC
Statistics
Matches: 144, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
166 25 0.17
167 37 0.26
168 62 0.43
169 1 0.01
171 19 0.13
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (169 bp):
TGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTAAGAAGTAGACCAAATCAATAAAACCA
GACAAACTGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAA
TAAAGCGGTTACTTCCTGATGAGATACAGAGAAGCGGAT
Found at i:411055 original size:167 final size:169
Alignment explanation
Indices: 410811--411325 Score: 590
Period size: 167 Copynumber: 3.0 Consensus size: 169
410801 AGTGAACCAT
* * * * * *
410811 ATTCGTCTTCTTGATGAGATATAGAGAAGCGAATTGAAACAAGTGATGCGGTCATCTTCCTAATG
1 ATTCATCTTCCTGATGAGATAGAGAGAAGCGAATTGAAATAAGTGATGCGGTCATCTTTCTGATG
* * * * *
410876 AGATATTGAGAAGTAGACCAAATCAATAAAACCA-G-ACAAAGTAAGCAAATCTTTGAACCCCAG
66 AGATACTGAGAAGTAGACCAAATCAATAAAACCAGGCTCAAAGTGAGCAAATCTTCGAATCCCAG
* * *
410939 CTTCCTGATGAGACACTGAGAAGTAGGTCGAAGTAATAA
131 CTTCCTGATGAGAAACTGAGAAGCAGGTCGAAGCAATAA
*
410978 ATTCATCTTCCTGATGAGATAGAGAGAAGCGGATTGAAATAAGTGATGCGGTCATCTTTCTGATG
1 ATTCATCTTCCTGATGAGATAGAGAGAAGCGAATTGAAATAAGTGATGCGGTCATCTTTCTGATG
* * *
411043 AGATACTGAGAAGTAGACCAAATCAATGAAACTAGGCTCAAAGTGAGCAAATC-TCGAATCCAAG
66 AGATACTGAGAAGTAGACCAAATCAATAAAACCAGGCTCAAAGTGAGCAAATCTTCGAATCCCAG
*
411107 CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
131 CTTCCTGATGAGAAACTGAGAAGCAGGTCGAAGCAATAA
* * * * * ** **
411146 AGTGGTTACCTTCCTGATGAGATACAGATAAGTGAACCACATCT-ATCTTCCTGTGATGCGGTCA
1 A-T--TCATCTTCCTGATGAGATAGAGAGAA--G--CGA-AT-TGA-AAT-AAGTGATGCGGTCA
* * *
411210 TC-TTCTTGATGAGATACTTAGAAGTAGACCAAATCAATAAACCCAGGCTCAAAGTGAGTAAATC
55 TCTTTC-TGATGAGATACTGAGAAGTAGACCAAATCAATAAAACCAGGCTCAAAGTGAGCAAATC
* *
411274 TTCGAATCCCAGCTTCTTGATGAGAAACTGAGAAGCAGGCCGAAGCAATAA
119 TTCGAATCCCAGCTTCCTGATGAGAAACTGAGAAGCAGGTCGAAGCAATAA
411325 A
1 A
411326 GCAGTAACCT
Statistics
Matches: 296, Mismatches: 37, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
167 89 0.30
168 46 0.16
169 15 0.05
171 22 0.07
173 1 0.00
175 1 0.00
176 3 0.01
177 5 0.02
178 67 0.23
179 47 0.16
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (169 bp):
ATTCATCTTCCTGATGAGATAGAGAGAAGCGAATTGAAATAAGTGATGCGGTCATCTTTCTGATG
AGATACTGAGAAGTAGACCAAATCAATAAAACCAGGCTCAAAGTGAGCAAATCTTCGAATCCCAG
CTTCCTGATGAGAAACTGAGAAGCAGGTCGAAGCAATAA
Found at i:411160 original size:375 final size:375
Alignment explanation
Indices: 410470--411184 Score: 1225
Period size: 375 Copynumber: 1.9 Consensus size: 375
410460 ACCAAATCAA
*
410470 TGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
1 TGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATAAAACCA
* * * *
410535 GACAAACTGAGCAAATCTTCGAACCCCTGCTTCCTGATGAGATACTGAGAAGTAGGTTGAAGCAA
66 GACAAACTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGCAA
*
410600 TAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTTCTG
131 TAAATTCATCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTTCTG
* *
410665 ATGAGATACAAGAAGTAGACCAAATCAATAAAACCAGGCTCAAAGTGAGTAAATCTTCGAACCCC
196 ATGAGATACAAGAAGTAGACCAAATCAATAAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCCA
410730 AGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATA
261 AGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATA
410795 CAGAAAAGTGAACCATATTCGTCTTCTTGATGAGATATAGAGAAGCGAAT
326 CAGAAAAGTGAACCATATTCGTCTTCTTGATGAGATATAGAGAAGCGAAT
*
410845 TGAAACAAGTGATGCGGTCATCTTCCTAATGAGATATTGAGAAGTAGACCAAATCAATAAAACCA
1 TGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATAAAACCA
* * *
410910 GACAAAGTAAGCAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGTAA
66 GACAAACTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGCAA
* *
410975 TAAATTCATCTTCCTGATGAGATAGAGAGAAGCGGATTGAAATAAGTGATGCGGTCATCTTTCTG
131 TAAATTCATCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTTCTG
* * * *
411040 ATGAGATACTGAGAAGTAGACCAAATCAATGAAACTAGGCTCAAAGTGAGCAAATC-TCGAATCC
196 ATGAGATAC-AAGAAGTAGACCAAATCAATAAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCC
* *
411104 AAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTACCTTCCTGATGAGAT
260 AAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTGATGAGAT
*
411169 ACAGATAAGTGAACCA
325 ACAGAAAAGTGAACCA
411185 CATCTATCTT
Statistics
Matches: 318, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
375 276 0.87
376 42 0.13
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (375 bp):
TGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATAAAACCA
GACAAACTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGCAA
TAAATTCATCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTTCTG
ATGAGATACAAGAAGTAGACCAAATCAATAAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCCA
AGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATA
CAGAAAAGTGAACCATATTCGTCTTCTTGATGAGATATAGAGAAGCGAAT
Found at i:411224 original size:178 final size:176
Alignment explanation
Indices: 410853--411377 Score: 590
Period size: 179 Copynumber: 3.0 Consensus size: 176
410843 ATTGAAACAA
* * * *
410853 GTGATGCGGTCATCTTCCTAATGAGATATTGAGAAGTAGACCAAATCAATAAAACCA-G-ACAAA
1 GTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAAT-AAACCAGGCTCAAA
* * * * * *
410916 GTAAGCAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGTAATAAA-T
65 GTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGAAACTGAGAAGCAGGTCGAAGCAATAAAGT
* * * * * ** **
410980 -TCATCTTCCTGATGAGAT--AG--AGAGAAGCGGAT-TGA-AAT-AA
130 GTAACCTTCCTGATGAGATACAGAAAGTGAACCAGATCT-ATCTTCCT
*
411020 GTGATGCGGTCATCTT-TCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACTAGGCTCAA
1 GTGATGCGGTCATCTTCT-TGATGAGATACTGAGAAGTAGACCAAATCAAT-AAACCAGGCTCAA
* *
411084 AGTGAGCAAATC-TCGAATCCAAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAG
64 AGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGAAACTGAGAAGCAGGTCGAAGCAATAAAG
* *
411148 TGGTTACCTTCCTGATGAGATACAGATAAGTGAACCACATCTATCTTCCT
129 T-GTAACCTTCCTGATGAGATACAGA-AAGTGAACCAGATCTATCTTCCT
*
411198 GTGATGCGGTCATCTTCTTGATGAGATACTTAGAAGTAGACCAAATCAATAAACCCAGGCTCAAA
1 GTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATAAA-CCAGGCTCAAA
* * *
411263 GTGAGTAAATCTTCGAATCCCAGCTTCTTGATGAGAAACTGAGAAGCAGGCCGAAGCAATAAAGC
65 GTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGAAACTGAGAAGCAGGTCGAAGCAATAAAG-
* * **
411328 AGTAACCTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCCT
129 TGTAACCTTCCTGATGAGATACAGA-AAGTGAACCAGATCTATCTTCCT
411377 G
1 G
411378 ATGAGACACA
Statistics
Matches: 303, Mismatches: 37, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
167 51 0.17
168 46 0.15
169 15 0.05
171 16 0.05
173 2 0.01
176 9 0.03
177 5 0.02
178 67 0.22
179 92 0.30
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (176 bp):
GTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATAAACCAGGCTCAAAG
TGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGAAACTGAGAAGCAGGTCGAAGCAATAAAGTG
TAACCTTCCTGATGAGATACAGAAAGTGAACCAGATCTATCTTCCT
Found at i:412004 original size:6 final size:6
Alignment explanation
Indices: 411995--412085 Score: 66
Period size: 6 Copynumber: 15.7 Consensus size: 6
411985 TGAATTTGTT
* * * *
411995 TTTAAA TTTAAA TTT-AT TTTAAG TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
412041 CTTAAA TTT-AA TATAAG TTTAAA TTT--A TTATCAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-T-AAA TTTAAA TTTA
412086 TCCTAAATAT
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
4 3 0.04
5 13 0.19
6 47 0.70
7 1 0.01
8 3 0.04
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:412016 original size:17 final size:17
Alignment explanation
Indices: 411966--412100 Score: 81
Period size: 17 Copynumber: 7.5 Consensus size: 17
411956 CCTATTTTGC
* * *
411966 TTTAGATTTATCTTAAG
1 TTTAAATTTATTTTAAA
* *
411983 TTTGAATTTGTTTTTAAA
1 TTTAAATTT-ATTTTAAA
412001 TTTAAATTTATTTTAAGTTTAA
1 TTTAAATTTATTTT-A----AA
412023 GTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
* * * *
412041 CTTAAATTTAATATAAG
1 TTTAAATTTATTTTAAA
*
412058 TTTAAATTTATTATCAAA
1 TTTAAATTTATT-TTAAA
**
412076 TTTAAATTTATCCTAAA
1 TTTAAATTTATTTTAAA
*
412093 TATAAATT
1 TTTAAATT
412101 AATAAAGTCC
Statistics
Matches: 90, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
17 44 0.49
18 29 0.32
22 3 0.03
23 14 0.16
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:412021 original size:23 final size:23
Alignment explanation
Indices: 411995--412051 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
411985 TGAATTTGTT
*
411995 TTTAAATTTAAATTTATTTTAAG
1 TTTAAATTTAAATTTATTTTAAA
*
412018 TTTAAGTTTAAATTTATTTTAAA
1 TTTAAATTTAAATTTATTTTAAA
*
412041 CTTAAATTTAA
1 TTTAAATTTAA
412052 TATAAGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTAAATTTAAATTTATTTTAAA
Found at i:412040 original size:11 final size:11
Alignment explanation
Indices: 412001--412040 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
411991 TGTTTTTAAA
412001 TTTAAATTTAT
1 TTTAAATTTAT
* *
412012 TTTAAGTTTAAG
1 TTTAAATTT-AT
412024 TTTAAATTTAT
1 TTTAAATTTAT
412035 TTTAAA
1 TTTAAA
412041 CTTAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:412058 original size:34 final size:35
Alignment explanation
Indices: 412020--412085 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
412010 ATTTTAAGTT
*
412020 TAAGTTTAAATTTATT-TTAAACTTAAATTTAATA
1 TAAGTTTAAATTTATTATCAAACTTAAATTTAATA
*
412054 TAAGTTTAAATTTATTATCAAATTTAAATTTA
1 TAAGTTTAAATTTATTATCAAACTTAAATTTA
412086 TCCTAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (35 bp):
TAAGTTTAAATTTATTATCAAACTTAAATTTAATA
Found at i:412099 original size:35 final size:34
Alignment explanation
Indices: 412026--412100 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 34
412016 AGTTTAAGTT
* * *
412026 TAAATTTATTTTAAACTTAAATTTAATATAAGTT
1 TAAATTTATTTCAAACTTAAATTTAATATAAATA
* *
412060 TAAATTTATTATCAAATTTAAATTT-ATCCTAAATA
1 TAAATTTATT-TCAAACTTAAATTTAAT-ATAAATA
412095 TAAATT
1 TAAATT
412101 AATAAAGTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 12 0.35
35 22 0.65
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (34 bp):
TAAATTTATTTCAAACTTAAATTTAATATAAATA
Done.