Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005168.1 Hibiscus syriacus cultivar Beakdansim tig00011662_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: 818383
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:230819 original size:27 final size:26
Alignment explanation
Indices: 230760--230829 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
230750 TTACTATTAT
* * *
230760 ATATATATCTTTTTATTTTTTCCATT
1 ATATATATCTTTTTATTATTACCATC
* *
230786 GTTTATATCTTTATTATTATTACCATC
1 ATATATATCTTT-TTATTATTACCATC
*
230813 ATATATATTATTTTTAT
1 ATATATA-TCTTTTTAT
230830 ATTCTATATT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
26 10 0.29
27 20 0.59
28 4 0.12
ACGTcount: A:0.27, C:0.10, G:0.01, T:0.61
Consensus pattern (26 bp):
ATATATATCTTTTTATTATTACCATC
Found at i:234487 original size:3 final size:3
Alignment explanation
Indices: 234481--234540 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
234471 CAACAACAAC
234481 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
234529 AAT AAT AAT AAT
1 AAT AAT AAT AAT
234541 TGTTAAAATC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:234905 original size:56 final size:56
Alignment explanation
Indices: 234796--234905 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 56
234786 CAGACCACAC
* * * **
234796 GCAGACATTGGGCTTCGCAGACCGTTTGGTTTTTAGAAGACAAAAGCTCTTCTAGT
1 GCAGACATTAGGCTTCGCAGACCGTTTGGTTTATAAAAGACAAAAGCGATTCTAGT
*
234852 GCAGACATTAGGCTTCGTAGACCGTTTGGTTTATAAAAGACAAAAGCGATTCTA
1 GCAGACATTAGGCTTCGCAGACCGTTTGGTTTATAAAAGACAAAAGCGATTCTA
234906 ACGTATGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (56 bp):
GCAGACATTAGGCTTCGCAGACCGTTTGGTTTATAAAAGACAAAAGCGATTCTAGT
Found at i:235143 original size:19 final size:21
Alignment explanation
Indices: 235119--235161 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
235109 GATAAATTTA
*
235119 TTAAT-AATTTTATAA-TATT
1 TTAATAAATTTAATAAGTATT
235138 TTAATAAATTTAATAAGTATT
1 TTAATAAATTTAATAAGTATT
235159 TTA
1 TTA
235162 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAATAAATTTAATAAGTATT
Found at i:235173 original size:28 final size:31
Alignment explanation
Indices: 235086--235172 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
235076 TTCGATAATA
* *
235086 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAATAATTTTATAATATTTTA-ATAAATT
*
235117 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAATAATTTTATAATATTTTAATAAATT
* *
235148 TAATAAGT-ATTTTATATTTTTTTAA
1 TAATAA-TAATTTTATAATATTTTAA
235173 ACTTTATTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 43 0.90
32 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TAATAATAATTTTATAATATTTTAATAAATT
Found at i:235276 original size:21 final size:23
Alignment explanation
Indices: 235234--235294 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 23
235224 ACTTTATTTG
235234 AAAAAATATATATTAAACTTAAT
1 AAAAAATATATATTAAACTTAAT
*
235257 AAAAAATATTATACAATTAAACTTAGT
1 AAAAAATA-TAT---ATTAAACTTAAT
235284 AAAAAATATAT
1 AAAAAATATAT
235295 TATGCGATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 8 0.24
24 3 0.09
26 3 0.09
27 19 0.58
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAATATATATTAAACTTAAT
Found at i:235451 original size:31 final size:30
Alignment explanation
Indices: 235385--235452 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
235375 CATTTTCGCC
235385 AATAAATT-TTAAAAAATTAGAAAATACTT
1 AATAAATTATTAAAAAATTAGAAAATACTT
* * *
235414 ATTAAATATATTAAAAGATTATAAAATTA-TT
1 AATAAAT-TATTAAAAAATTAGAAAA-TACTT
235445 AATAAATT
1 AATAAATT
235453 TATCTAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 6 0.19
30 2 0.06
31 22 0.69
32 2 0.06
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (30 bp):
AATAAATTATTAAAAAATTAGAAAATACTT
Found at i:236113 original size:21 final size:21
Alignment explanation
Indices: 236081--236128 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
236071 CTAAAAATGA
236081 TTTCTTTCCCTCTCTTCCCCC
1 TTTCTTTCCCTCTCTTCCCCC
* *
236102 TTTCTCTT-CCTCT-TTTCCCT
1 TTTCT-TTCCCTCTCTTCCCCC
236122 TTTCTTT
1 TTTCTTT
236129 TCCCATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 10 0.42
22 2 0.08
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTCTTTCCCTCTCTTCCCCC
Found at i:240178 original size:194 final size:192
Alignment explanation
Indices: 239924--240284 Score: 429
Period size: 194 Copynumber: 1.9 Consensus size: 192
239914 TGATGATAAC
* ** * **
239924 TAGTTACGTCACTAAATTATTTAAAATTTCATTATTGATAATTTATATCGTCGTAAATAATACAT
1 TAGTTACATCACTAAATTAAATAAAATTTCATTACTGATAATTTATATCGTCACAAATAATACAT
* * ** * * *
239989 TATAAT-AGACCTATATATGATGAAAGTGATATCATCACATTTTTAGTGACATAATATAAAT-GT
66 CAAAATCA-ACCTATATATGAAAAAAAT-ATATCATCACATTTTTAGTGAAATAATAT--ATCAT
* *
240052 TACCTAAGAATATAATGAATGACGTTTATGCATAATGTCACTTTATAATTTATATTCTATGATAG
127 TACCTAAGAATATAATGAATGACGATTATGCATAACGTCACTTTATAATTTATATTCTATGATAG
240117 T
192 T
* * * * **
240118 TAGTTACATCACTAAATTAAATAAGATTTCGTTACTGGTAATTTATATTGTCACAAATAATGTAT
1 TAGTTACATCACTAAATTAAATAAAATTTCATTACTGATAATTTATATCGTCACAAATAATACAT
* * **
240183 CAAAATCAACTTATATGTGAAAAAAATATATTGTCACATTTTTAGTGAAATAATATATCATTACC
66 CAAAATCAACCTATATATGAAAAAAATATATCATCACATTTTTAGTGAAATAATATATCATTACC
* *
240248 TAATAATATTATGAATGACGATTATGCATAACGTCAC
131 TAAGAATATAATGAATGACGATTATGCATAACGTCAC
240285 CATATATAAT
Statistics
Matches: 138, Mismatches: 27, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
191 2 0.01
192 38 0.28
193 26 0.19
194 71 0.51
195 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (192 bp):
TAGTTACATCACTAAATTAAATAAAATTTCATTACTGATAATTTATATCGTCACAAATAATACAT
CAAAATCAACCTATATATGAAAAAAATATATCATCACATTTTTAGTGAAATAATATATCATTACC
TAAGAATATAATGAATGACGATTATGCATAACGTCACTTTATAATTTATATTCTATGATAGT
Found at i:241189 original size:18 final size:17
Alignment explanation
Indices: 241163--241196 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
241153 GTGCTATATG
241163 ATTTCAAAAATAAAAATT
1 ATTTC-AAAATAAAAATT
*
241181 ATTTTAAAATAAAAAT
1 ATTTCAAAATAAAAAT
241197 AAACTTTATA
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:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTCAAAATAAAAATT
Found at i:241204 original size:18 final size:17
Alignment explanation
Indices: 241169--241211 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
241159 TATGATTTCA
* *
241169 AAAATAAAAATTATTTT
1 AAAATAAAAATAACTTT
241186 AAAATAAAAATAAACTTT
1 AAAATAAAAAT-AACTTT
*
241204 ATAATAAA
1 AAAATAAA
241212 TATCAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAAAAATAACTTT
Found at i:254553 original size:17 final size:17
Alignment explanation
Indices: 254533--254572 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
254523 TAAGTATGTT
254533 CATTTAAGCATGCATTG
1 CATTTAAGCATGCATTG
*
254550 CATTTAAGCATGCATTT
1 CATTTAAGCATGCATTG
254567 CATTTA
1 CATTTA
254573 GGTAAGTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:254635 original size:17 final size:17
Alignment explanation
Indices: 254626--254688 Score: 92
Period size: 17 Copynumber: 3.7 Consensus size: 17
254616 TCATTCATGC
254626 ATTTAGTTCATTAATAA
1 ATTTAGTTCATTAATAA
*
254643 AGTTAGTTCATTAATAA
1 ATTTAGTTCATTAATAA
254660 ATTTAGTTCATTAATCAA
1 ATTTAGTTCATTAAT-AA
*
254678 A-CTAGTTCATT
1 ATTTAGTTCATT
254689 TATTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
17 39 0.93
18 3 0.07
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTTAGTTCATTAATAA
Found at i:254653 original size:34 final size:33
Alignment explanation
Indices: 254579--254688 Score: 114
Period size: 34 Copynumber: 3.3 Consensus size: 33
254569 TTTAGGTAAG
* * *
254579 TAGTTCATTTATGCATCTA-ATCATTTAATAAAC
1 TAGTTCATTAATGCATTTAGTTCA-TTAATAAAC
* * *
254612 TACTTCATTCATGCATTTAGTTCATTAATAAAGT
1 TAGTTCATTAATGCATTTAGTTCATTAATAAA-C
**
254646 TAGTTCATTAATAAATTTAGTTCATTAATCAAAC
1 TAGTTCATTAATGCATTTAGTTCATTAAT-AAAC
254680 TAGTTCATT
1 TAGTTCATT
254689 TATTAAACTA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
33 24 0.38
34 37 0.58
35 3 0.05
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (33 bp):
TAGTTCATTAATGCATTTAGTTCATTAATAAAC
Found at i:254696 original size:17 final size:17
Alignment explanation
Indices: 254629--254715 Score: 88
Period size: 17 Copynumber: 5.1 Consensus size: 17
254619 TTCATGCATT
*
254629 TAGTTCATTAAT-AAAGT
1 TAGTTCATTAATCAAA-C
*
254646 TAGTTCATTAAT-AAATT
1 TAGTTCATTAATCAAA-C
254663 TAGTTCATTAATCAAAC
1 TAGTTCATTAATCAAAC
* *
254680 TAGTTCATTTATTAAAC
1 TAGTTCATTAATCAAAC
* *
254697 TAGTGCATTAACCAAAC
1 TAGTTCATTAATCAAAC
254714 TA
1 TA
254716 ACTCTTAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
17 58 0.95
18 3 0.05
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:254706 original size:34 final size:34
Alignment explanation
Indices: 254603--254715 Score: 97
Period size: 34 Copynumber: 3.4 Consensus size: 34
254593 ATCTAATCAT
* * ** *
254603 TTAAT-AAACTACTTCATTCATGCATTTAGTTCA
1 TTAATCAAACTAGTTCATTAATAAATCTAGTTCA
* *
254636 TTAAT-AAAGTTAGTTCATTAATAAATTTAGTTCA
1 TTAATCAAA-CTAGTTCATTAATAAATCTAGTTCA
* *
254670 TTAATCAAACTAGTTCATTTATTAAA-CTAGTGCA
1 TTAATCAAACTAGTTCA-TTAATAAATCTAGTTCA
*
254704 TTAACCAAACTA
1 TTAATCAAACTA
254716 ACTCTTAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
33 8 0.12
34 49 0.73
35 10 0.15
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (34 bp):
TTAATCAAACTAGTTCATTAATAAATCTAGTTCA
Found at i:255284 original size:21 final size:22
Alignment explanation
Indices: 255259--255302 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
255249 TTAAGGCCAA
* *
255259 ATTCAGCTTCAAATTG-TCTAG
1 ATTCAGCTCCAAAATGATCTAG
*
255280 ATTCATCTCCAAAATGATCTAG
1 ATTCAGCTCCAAAATGATCTAG
255302 A
1 A
255303 ATATTCAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (22 bp):
ATTCAGCTCCAAAATGATCTAG
Found at i:256538 original size:17 final size:17
Alignment explanation
Indices: 256516--256585 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
256506 AATTAATAGT
*
256516 TAGTTTGATTAATGCAC
1 TAGTTTGATTAATGAAC
* *
256533 TAGTTTAATAAATGAAC
1 TAGTTTGATTAATGAAC
*
256550 TAGTTTGATTAATGAGC
1 TAGTTTGATTAATGAAC
*
256567 TAACTTT-ATTAATGAAC
1 T-AGTTTGATTAATGAAC
256584 TA
1 TA
256586 ACTGCATGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
16 1 0.02
17 39 0.89
18 4 0.09
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (17 bp):
TAGTTTGATTAATGAAC
Found at i:256581 original size:34 final size:34
Alignment explanation
Indices: 256516--256585 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
256506 AATTAATAGT
*
256516 TAGTTTGATTAATGCACTAGTTTAATAAATGAAC
1 TAGTTTGATTAATGCACTACTTTAATAAATGAAC
*
256550 TAGTTTGATTAATG-AGCTAACTTT-ATTAATGAAC
1 TAGTTTGATTAATGCA-CT-ACTTTAATAAATGAAC
256584 TA
1 TA
256586 ACTGCATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 1 0.03
34 27 0.84
35 4 0.12
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (34 bp):
TAGTTTGATTAATGCACTACTTTAATAAATGAAC
Found at i:256586 original size:17 final size:16
Alignment explanation
Indices: 256523--256611 Score: 61
Period size: 17 Copynumber: 5.3 Consensus size: 16
256513 AGTTAGTTTG
* *
256523 ATTAATGCACTAGTTT
1 ATTAATGAACTACTTT
* *
256539 AATAAATGAACTAGTTT
1 -ATTAATGAACTACTTT
*
256556 GATTAATGAGCTAACTTT
1 -ATTAATGAACT-ACTTT
**
256574 ATTAATGAACTAACTGC
1 ATTAATGAACT-ACTTT
* *
256591 ATGAATGAAATACTTT
1 ATTAATGAACTACTTT
256607 ATTAA
1 ATTAA
256612 ATGACTAGAT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
16 7 0.12
17 46 0.81
18 4 0.07
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (16 bp):
ATTAATGAACTACTTT
Found at i:256611 original size:33 final size:33
Alignment explanation
Indices: 256569--256632 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
256559 TAATGAGCTA
*
256569 ACTTTATT-AATGAACTA-ACTGCATGAATGAAAT
1 ACTTTATTAAATG-ACTAGA-TGCATAAATGAAAT
256602 ACTTTATTAAATGACTAGATGCATAAATGAA
1 ACTTTATTAAATGACTAGATGCATAAATGAA
256633 CCACTTCCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (33 bp):
ACTTTATTAAATGACTAGATGCATAAATGAAAT
Found at i:257594 original size:21 final size:19
Alignment explanation
Indices: 257568--257616 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
257558 GGATATCGAC
*
257568 AAAAAACATATTTAACAATGA
1 AAAAAACAAATTTAA-AAT-A
* *
257589 AGAAAATAAATTTAAAATA
1 AAAAAACAAATTTAAAATA
257608 AAAAAACAA
1 AAAAAACAA
257617 TTACCTGCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 3 0.13
21 12 0.52
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAAAACAAATTTAAAATA
Found at i:266885 original size:21 final size:20
Alignment explanation
Indices: 266856--266925 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
266846 ATTTACACGA
*
266856 GTATTGATACTCTCACCTTGG
1 GTATCGATACT-TCACCTTGG
266877 GTATCGATACTATTC-CCTTGG
1 GTATCGATAC--TTCACCTTGG
266898 GTATC-ATTACTT-A-CTTGG
1 GTATCGA-TACTTCACCTTGG
266916 GTATCGATAC
1 GTATCGATAC
266926 CAAAATAGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
18 13 0.30
19 3 0.07
20 1 0.02
21 23 0.53
22 2 0.05
23 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (20 bp):
GTATCGATACTTCACCTTGG
Found at i:273456 original size:40 final size:40
Alignment explanation
Indices: 273381--273504 Score: 142
Period size: 40 Copynumber: 3.1 Consensus size: 40
273371 TCGAGTCAAA
* * *
273381 TATATGCACCGTAGTGC-TTACACATAAGGTCGTGGCCAC
1 TATATGCACCGAAATGCATTACACATAAAGTCGTGGCCAC
* *
273420 TATATGCACCGAAATACATTACACATAAAGTTGTGGCCAC
1 TATATGCACCGAAATGCATTACACATAAAGTCGTGGCCAC
* ** * *
273460 CATATGCAGGGAAATGCATTACACATAAGGTCGTGCCCAC
1 TATATGCACCGAAATGCATTACACATAAAGTCGTGGCCAC
*
273500 CATAT
1 TATAT
273505 ACGCTGAAGT
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 14 0.19
40 58 0.81
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (40 bp):
TATATGCACCGAAATGCATTACACATAAAGTCGTGGCCAC
Found at i:282528 original size:19 final size:21
Alignment explanation
Indices: 282491--282533 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
282481 TAACTTTTTC
*
282491 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
282511 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
282531 TTT
1 TTT
282534 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:285842 original size:24 final size:24
Alignment explanation
Indices: 285815--285864 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
285805 TGGTGGTTGA
*
285815 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
285839 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
285863 TT
1 TT
285865 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:288077 original size:107 final size:108
Alignment explanation
Indices: 287887--288085 Score: 264
Period size: 107 Copynumber: 1.9 Consensus size: 108
287877 GTAAACTATT
* *
287887 CATTTATGGATAAAATTTATTTTAAGGAAAATTACCACTTAGGTCCCTAAAATTTTCCCAATTTT
1 CATTTATGGATAAAAATTATTTTAAGGAAAATAACCACTTAGGTCCCTAAAATTTTCCCAATTTT
287952 ATACTTTAGCCAATAAACTTTCAAAATGGTCACTAACCAAATC
66 ATACTTTAGCCAATAAACTTTCAAAATGGTCACTAACCAAATC
* * * *
287995 CATTTATGGAATAAAAATTCTTTT-TGGAAAAATAACCA-TGTAGGT-CCTTAAGTTTT-CCAAT
1 CATTTATGG-ATAAAAATTATTTTAAGG-AAAATAACCACT-TAGGTCCCTAAAATTTTCCCAAT
*
288056 TTTTTACTTTAGCC-ATCAAACTTTCAAAAT
63 TTTATACTTTAGCCAAT-AAACTTTCAAAAT
288086 TTATAGTTTG
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
106 2 0.03
107 31 0.39
108 21 0.26
109 26 0.32
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (108 bp):
CATTTATGGATAAAAATTATTTTAAGGAAAATAACCACTTAGGTCCCTAAAATTTTCCCAATTTT
ATACTTTAGCCAATAAACTTTCAAAATGGTCACTAACCAAATC
Found at i:290372 original size:46 final size:46
Alignment explanation
Indices: 290305--290429 Score: 232
Period size: 46 Copynumber: 2.7 Consensus size: 46
290295 CTTTCATGTC
* *
290305 TTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGTATCCT
1 TTCATGCAGTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCT
290351 TTCATGCAGTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCT
1 TTCATGCAGTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCT
290397 TTCATGCAGTTTATTTATGGCATCCTTTCATGC
1 TTCATGCAGTTTATTTATGGCATCCTTTCATGC
290430 ATTTTATTTA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (46 bp):
TTCATGCAGTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCT
Found at i:290424 original size:72 final size:72
Alignment explanation
Indices: 290346--290501 Score: 267
Period size: 72 Copynumber: 2.2 Consensus size: 72
290336 GCCTTAATGT
* *
290346 ATCCTTTCATGCAGTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCAGTTTAT
1 ATCCTTTCATGCAGTTTATTTATAGCATCCTTTCATACCTTAATGCATCCTTTCATGCAGTTTAT
290411 TTATGGC
66 TTATGGC
* * *
290418 ATCCTTTCATGCATTTTATTTATAGCATCCTTTTATACCTTAATGCATCCTTTCATGCATTTTAT
1 ATCCTTTCATGCAGTTTATTTATAGCATCCTTTCATACCTTAATGCATCCTTTCATGCAGTTTAT
290483 TTATGGC
66 TTATGGC
290490 ATCCTTTCATGC
1 ATCCTTTCATGC
290502 CTTAATGCAT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 79 1.00
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.46
Consensus pattern (72 bp):
ATCCTTTCATGCAGTTTATTTATAGCATCCTTTCATACCTTAATGCATCCTTTCATGCAGTTTAT
TTATGGC
Found at i:290466 original size:46 final size:45
Alignment explanation
Indices: 290416--290677 Score: 354
Period size: 46 Copynumber: 5.8 Consensus size: 45
290406 TTTATTTATG
*
290416 GCATCCTTTCATGCATTTTATTTATAGCATCCTTTTATACCTTAAT
1 GCATCCTTTCATGCATTTTATTTAT-GCATCCTTTCATACCTTAAT
*
290462 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTATTTAT-GCATCCTTTCATACCTTAAT
* * *
290508 GCATCCTTTCATGGAGTTTATTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTATTTAT-GCATCCTTTCATACCTTAAT
* * * *
290554 GCATCCTTTCTTGC--CTTA---ATGCATCATTTCATTCCTTAAT
1 GCATCCTTTCATGCATTTTATTTATGCATCCTTTCATACCTTAAT
*
290594 GCATCCTTTCATGCATTTTATTTATAGCATCCTTTTATACCTTAAT
1 GCATCCTTTCATGCATTTTATTTAT-GCATCCTTTCATACCTTAAT
290640 GCATCCTTTCATGCATTTTATTTATGACATCCTTTCAT
1 GCATCCTTTCATGCATTTTATTTATG-CATCCTTTCAT
290678 GCCAATAATG
Statistics
Matches: 193, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
40 31 0.16
41 2 0.01
42 3 0.02
44 3 0.02
45 3 0.02
46 151 0.78
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.46
Consensus pattern (45 bp):
GCATCCTTTCATGCATTTTATTTATGCATCCTTTCATACCTTAAT
Found at i:290486 original size:118 final size:118
Alignment explanation
Indices: 290305--290547 Score: 432
Period size: 118 Copynumber: 2.1 Consensus size: 118
290295 CTTTCATGTC
* * *
290305 TTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGTATCCTTTCATGCAGTTTATTTATG
1 TTCATGCATTTTATTTATAGCATCCTTTCATACCTTAATGCATCCTTTCATGCAGTTTATTTATG
290370 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCAGTTTATTTATGGCATCCT
66 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCAGTTTATTTATGGCATCCT
* *
290423 TTCATGCATTTTATTTATAGCATCCTTTTATACCTTAATGCATCCTTTCATGCATTTTATTTATG
1 TTCATGCATTTTATTTATAGCATCCTTTCATACCTTAATGCATCCTTTCATGCAGTTTATTTATG
*
290488 GCATCCTTTCATGCCTTAATGCATCCTTTCATGGAGTTTATTTATGGCATCCT
66 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCAGTTTATTTATGGCATCCT
290541 TTCATGC
1 TTCATGC
290548 CTTAATGCAT
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 119 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (118 bp):
TTCATGCATTTTATTTATAGCATCCTTTCATACCTTAATGCATCCTTTCATGCAGTTTATTTATG
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCAGTTTATTTATGGCATCCT
Found at i:290624 original size:26 final size:25
Alignment explanation
Indices: 290592--290679 Score: 96
Period size: 26 Copynumber: 3.6 Consensus size: 25
290582 TCATTCCTTA
290592 ATGCATCCTTTCATGCATTTTATTT
1 ATGCATCCTTTCATGCATTTTATTT
* **
290617 ATAGCATCCTTTTAT--ACCTTA---
1 AT-GCATCCTTTCATGCATTTTATTT
290638 ATGCATCCTTTCATGCATTTTATTT
1 ATGCATCCTTTCATGCATTTTATTT
290663 ATGACATCCTTTCATGC
1 ATG-CATCCTTTCATGC
290680 CAATAATGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
20 11 0.22
21 2 0.04
22 4 0.08
24 4 0.08
25 5 0.10
26 24 0.48
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.47
Consensus pattern (25 bp):
ATGCATCCTTTCATGCATTTTATTT
Found at i:291273 original size:20 final size:20
Alignment explanation
Indices: 291245--291300 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
291235 ATTTCTGACT
*
291245 CCATAGTATCGATACCACTA
1 CCATGGTATCGATACCACTA
*
291265 CCATGGTATCGATA-CTCTA
1 CCATGGTATCGATACCACTA
*
291284 CTATGGTATCGATACCA
1 CCATGGTATCGATACCA
291301 TTTCTGCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (20 bp):
CCATGGTATCGATACCACTA
Found at i:291371 original size:20 final size:18
Alignment explanation
Indices: 291322--291372 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
291312 TGCTTTTAAA
*
291322 TGGTATCGATACCTTCCCT
1 TGGTATCGATA-CTCCCCT
*
291341 TGGTGTCGATACTACCCCT
1 TGGTATCGATACT-CCCCT
291360 TCGGTATCGATAC
1 T-GGTATCGATAC
291373 CGATTGAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.07
19 15 0.56
20 10 0.37
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.33
Consensus pattern (18 bp):
TGGTATCGATACTCCCCT
Found at i:294491 original size:53 final size:53
Alignment explanation
Indices: 294428--294597 Score: 254
Period size: 53 Copynumber: 3.2 Consensus size: 53
294418 TTGTATCAGT
*
294428 ACTATGTGTGCACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGGC
1 ACTATATGTGCACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGGC
*
294481 ACTATATGTGC-CTCCATGGAATTCATAATGAGTTTGTGAATTAGCATTTCGGC
1 ACTATATGTGCAC-CCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGGC
* * * *
294534 ACTATGTATGCATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTTGGC
1 ACTATATGTGCACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGGC
*
294587 ACT-TAGGTGCA
1 ACTATATGTGCA
294598 ACGCATGTAC
Statistics
Matches: 105, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
52 6 0.06
53 99 0.94
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (53 bp):
ACTATATGTGCACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGGC
Found at i:296125 original size:3 final size:3
Alignment explanation
Indices: 296117--296162 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
296107 TTAAAATTAA
296117 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
296163 TGTATAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:296220 original size:23 final size:23
Alignment explanation
Indices: 296194--296237 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
296184 TTTACATAAT
*
296194 ATATATTATATTTTCAAAAACAA
1 ATATAATATATTTTCAAAAACAA
*
296217 ATATAATATGTTTTCAAAAAC
1 ATATAATATATTTTCAAAAAC
296238 TATTTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATAATATATTTTCAAAAACAA
Found at i:296259 original size:2 final size:2
Alignment explanation
Indices: 296252--296291 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
296242 TTCAAAAACC
296252 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
296292 TATGTTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:296310 original size:20 final size:19
Alignment explanation
Indices: 296284--296329 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
296274 ATATATATAT
*
296284 ATATATATTATGTTTTCAAA
1 ATATATATTA-ATTTTCAAA
*
296304 ATTTATA-TAATTTTCAAA
1 ATATATATTAATTTTCAAA
296322 ATATATAT
1 ATATATAT
296330 ATACATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 14 0.64
19 2 0.09
20 6 0.27
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATATATTAATTTTCAAA
Found at i:296319 original size:18 final size:18
Alignment explanation
Indices: 296296--296330 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
296286 ATATATTATG
*
296296 TTTTCAAAATTTATATAA
1 TTTTCAAAATATATATAA
296314 TTTTCAAAATATATATA
1 TTTTCAAAATATATATA
296331 TACATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTCAAAATATATATAA
Found at i:307029 original size:30 final size:30
Alignment explanation
Indices: 306989--307046 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
306979 AAAGTTATTT
*
306989 GGATCAATTT-GTAATTTTGTGAAAGTTAGG
1 GGATCAATTTGGTAATTTTG-AAAAGTTAGG
*
307019 GGATCTATTTGGTAATTTTGAAAAGTTA
1 GGATCAATTTGGTAATTTTGAAAAGTTA
307047 AGGGCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.41
Consensus pattern (30 bp):
GGATCAATTTGGTAATTTTGAAAAGTTAGG
Found at i:308814 original size:19 final size:19
Alignment explanation
Indices: 308790--308857 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
308780 TGCATTGTGT
*
308790 TATGAATCTGAAATTAAGA
1 TATGAATCTGAAAATAAGA
*
308809 TATGAATCTGAAAATAAGT
1 TATGAATCTGAAAATAAGA
* * * *
308828 TATGAATATGGAAATATGT
1 TATGAATCTGAAAATAAGA
*
308847 TCTGAATCTGA
1 TATGAATCTGA
308858 GAATGAATTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.34
Consensus pattern (19 bp):
TATGAATCTGAAAATAAGA
Found at i:308944 original size:13 final size:13
Alignment explanation
Indices: 308888--308946 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
308878 AAGTACTAGT
308888 TATGAAAAATGAAA
1 TATG-AAAATGAAA
*
308902 TTTGAAAATG-AA
1 TATGAAAATGAAA
*
308914 TATGAAAGT-AATA
1 TATGAAAATGAA-A
*
308927 GATGAAAATGAAA
1 TATGAAAATGAAA
308940 TATGAAA
1 TATGAAA
308947 GTTCTAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
12 10 0.28
13 21 0.58
14 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (13 bp):
TATGAAAATGAAA
Found at i:309887 original size:29 final size:29
Alignment explanation
Indices: 309845--309901 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
309835 AGTGTTGGCC
*
309845 GTAGGTCGCCATGCACTCCGGGTGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
309874 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
309902 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.32, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:309936 original size:12 final size:12
Alignment explanation
Indices: 309919--309943 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
309909 CTCAAACAGA
309919 GAGAATGAACGT
1 GAGAATGAACGT
309931 GAGAATGAACGT
1 GAGAATGAACGT
309943 G
1 G
309944 TTGCATGGCA
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:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:310016 original size:29 final size:29
Alignment explanation
Indices: 309983--310056 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
309973 AGGTCGTCAT
309983 GCCCTCCGGGCGACCTTGTACGTCGCCAG
1 GCCCTCCGGGCGACCTTGTACGTCGCCAG
* * *
310012 GCCCTCCTGGCGACCTTGTAGGTCGCCAT
1 GCCCTCCGGGCGACCTTGTACGTCGCCAG
* *
310041 GCACTCCGGGTGACCT
1 GCCCTCCGGGCGACCT
310057 ACCCTCGGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.11, C:0.39, G:0.30, T:0.20
Consensus pattern (29 bp):
GCCCTCCGGGCGACCTTGTACGTCGCCAG
Found at i:310105 original size:33 final size:33
Alignment explanation
Indices: 310060--310123 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
310050 GTGACCTACC
*
310060 CTCGGCTTCCCTCGGATTCCCTCGCATAGCTCG
1 CTCGGCTTCCCTCGGATGCCCTCGCATAGCTCG
310093 CTCGG-TTGCCCTCGGATGCCCTCGCATAGCT
1 CTCGGCTT-CCCTCGGATGCCCTCGCATAGCT
310124 AATTCGGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.09, C:0.41, G:0.23, T:0.27
Consensus pattern (33 bp):
CTCGGCTTCCCTCGGATGCCCTCGCATAGCTCG
Found at i:310112 original size:10 final size:10
Alignment explanation
Indices: 310058--310181 Score: 52
Period size: 10 Copynumber: 11.7 Consensus size: 10
310048 GGGTGACCTA
* *
310058 CCCTCGGCTT
1 CCCTCGGATG
*
310068 CCCTCGGATT
1 CCCTCGGATG
*
310078 CCCTCGCATAG
1 CCCTCGGAT-G
*
310089 CTCGCTCGGTTG
1 C-C-CTCGGATG
310101 CCCTCGGATG
1 CCCTCGGATG
*
310111 CCCTCGCATAG
1 CCCTCGGAT-G
**
310122 CTAATTCGGATGG
1 C--CCTCGGAT-G
**
310135 CTTTCGGATG
1 CCCTCGGATG
*
310145 CTCTCGGATAG
1 CCCTCGGAT-G
310156 -CCTCGGATG
1 CCCTCGGATG
*
310165 CTCTCGGATG
1 CCCTCGGATG
*
310175 GCCTCGG
1 CCCTCGG
310182 TCGGATGGCC
Statistics
Matches: 89, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
9 1 0.01
10 61 0.69
11 12 0.13
12 3 0.03
13 12 0.13
ACGTcount: A:0.11, C:0.35, G:0.27, T:0.27
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:310163 original size:20 final size:20
Alignment explanation
Indices: 310138--310181 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
310128 CGGATGGCTT
310138 TCGGATGCTCTCGGATAGCC
1 TCGGATGCTCTCGGATAGCC
*
310158 TCGGATGCTCTCGGATGGCC
1 TCGGATGCTCTCGGATAGCC
310178 TCGG
1 TCGG
310182 TCGGATGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.30, G:0.34, T:0.25
Consensus pattern (20 bp):
TCGGATGCTCTCGGATAGCC
Found at i:310187 original size:14 final size:14
Alignment explanation
Indices: 310168--310194 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
310158 TCGGATGCTC
310168 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
310182 TCGGATGGCCTCG
1 TCGGATGGCCTCG
310195 AACCGGGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.30, G:0.41, T:0.22
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:311139 original size:16 final size:14
Alignment explanation
Indices: 311114--311153 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
311104 TGACAACCCT
311114 CCGCGAGAGAGAGG
1 CCGCGAGAGAGAGG
311128 CCGCGAGAGAGAGG
1 CCGCGAGAGAGAGG
*
311142 CCGCGACAGAGA
1 CCGCGAGAGAGA
311154 AAAGAACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.45, T:0.00
Consensus pattern (14 bp):
CCGCGAGAGAGAGG
Found at i:312116 original size:168 final size:169
Alignment explanation
Indices: 311875--312186 Score: 384
Period size: 168 Copynumber: 1.8 Consensus size: 169
311865 AAAAAACATG
* * *
311875 TAACAATAACTATAACATATAATTACAAAACTTCTCACTATATAACTTTTTCTGGCACAAAAATA
1 TAACAATAAATATAACATATAATTACAAAACTTCACACTATATAACTTTTTCTGACACAAAAATA
* * * * *
311940 TAGAAATATTTTATAGTATAAT-T-TTTTAT-A-ATGATTAAAATATATAACTATAAAAATAATT
66 GAGAAATA-TTTAT-G-ACAATATATTTTATAATATAATTAAAATATATAAATACAAAAATAATT
312001 TATCACAAAAACTTGAATTTTATTATTTGATGTGATTTTTTA
128 TATCACAAAAACTTGAATTTTATTATTTGATGTGATTTTTTA
* * * *
312043 TAACAATAAATATAACTTATAATTGCAAAACTTGACATTATATAAC-TTTT-TGACACCAAAAAT
1 TAACAATAAATATAACATATAATTACAAAACTTCACACTATATAACTTTTTCTGACA-CAAAAAT
* * *
312106 GGAGGAAATATTTATGACAATATATTTTATCAATATAATTAAAATTTATAAATACAAATATAATT
65 AGA-GAAATATTTATGACAATATATTTTAT-AATATAATTAAAATATATAAATACAAAAATAATT
*
312171 TGTCACAAAAACTTGA
128 TATCACAAAAACTTGA
312187 TTATCATCAT
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
165 4 0.03
166 6 0.05
167 23 0.19
168 46 0.38
169 1 0.01
170 41 0.34
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (169 bp):
TAACAATAAATATAACATATAATTACAAAACTTCACACTATATAACTTTTTCTGACACAAAAATA
GAGAAATATTTATGACAATATATTTTATAATATAATTAAAATATATAAATACAAAAATAATTTAT
CACAAAAACTTGAATTTTATTATTTGATGTGATTTTTTA
Found at i:312170 original size:19 final size:19
Alignment explanation
Indices: 312124--312171 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
312114 TATTTATGAC
* * *
312124 AATATATTTTATCAATATA
1 AATATAATTTATAAATACA
* *
312143 ATTAAAATTTATAAATACA
1 AATATAATTTATAAATACA
312162 AATATAATTT
1 AATATAATTT
312172 GTCACAAAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATAATTTATAAATACA
Found at i:318861 original size:28 final size:28
Alignment explanation
Indices: 318802--318861 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
318792 TATTTTCACT
* * **
318802 CCCCTAAAATTTTATAAATTCAAGTTTT
1 CCCCTAAAATTCTATAAATTCAAATTCA
*
318830 CCCCTAAAATTCTATAAGTTCAAATTCA
1 CCCCTAAAATTCTATAAATTCAAATTCA
318858 CCCC
1 CCCC
318862 GGCATAAAAT
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:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
CCCCTAAAATTCTATAAATTCAAATTCA
Found at i:320258 original size:39 final size:39
Alignment explanation
Indices: 320204--320282 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
320194 TTAGATTAAA
320204 TTTTAAATTGATATTTTGTCATTATAAAACTAACATAAG
1 TTTTAAATTGATATTTTGTCATTATAAAACTAACATAAG
320243 TTTTAAATTGATATTTTGTCATTATAAAACTAACATAAG
1 TTTTAAATTGATATTTTGTCATTATAAAACTAACATAAG
320282 T
1 T
320283 GTTAGCGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (39 bp):
TTTTAAATTGATATTTTGTCATTATAAAACTAACATAAG
Found at i:321871 original size:31 final size:30
Alignment explanation
Indices: 321827--321886 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
321817 TTATTTTGAA
* * *
321827 AAAATTGAAAGTTTAGGTATTAAAATAAATC
1 AAAACTGAAAGTTTAAGTACT-AAATAAATC
*
321858 AAAACTGATAGTTTAAGTACTAAATAAAT
1 AAAACTGAAAGTTTAAGTACTAAATAAAT
321887 AATTTACCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.32
Consensus pattern (30 bp):
AAAACTGAAAGTTTAAGTACTAAATAAATC
Found at i:322700 original size:55 final size:55
Alignment explanation
Indices: 322616--322727 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
322606 ACAGAGATCG
322616 TCGGTCTTCCCTTGAAGGGACTGGTAGCGGTTCACTTGTTTGTTAAGCAAAGATA
1 TCGGTCTTCCCTTGAAGGGACTGGTAGCGGTTCACTTGTTTGTTAAGCAAAGATA
*
322671 TCGGTCTTCCTTTGAAGGGACTGGTAGCGGTTCACTTGTTTGTTAAGCAAAGATA
1 TCGGTCTTCCCTTGAAGGGACTGGTAGCGGTTCACTTGTTTGTTAAGCAAAGATA
322726 TC
1 TC
322728 AACATTAGGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (55 bp):
TCGGTCTTCCCTTGAAGGGACTGGTAGCGGTTCACTTGTTTGTTAAGCAAAGATA
Found at i:328216 original size:19 final size:19
Alignment explanation
Indices: 328192--328230 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
328182 TCAAATGCAT
328192 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
328211 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
328230 T
1 T
328231 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:328272 original size:46 final size:47
Alignment explanation
Indices: 328213--328322 Score: 152
Period size: 47 Copynumber: 2.4 Consensus size: 47
328203 ATGCACTCTC
* *
328213 CATGCATCGATGCAC-TCTGAATA-TTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACCAGAATATTTTTC-AAACATCGAATGCATTT
* **
328259 GATGCATCGATGCACACCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACACCAGAATATTTTTCAAACATCGAATGCATTT
328306 CATGCATCGATGCACAC
1 CATGCATCGATGCACAC
328323 TTGGTGCACC
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
46 14 0.25
47 37 0.66
48 5 0.09
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (47 bp):
CATGCATCGATGCACACCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:335800 original size:21 final size:21
Alignment explanation
Indices: 335758--335801 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
335748 ACCCCGGGAG
*
335758 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
335779 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
335800 CT
1 CT
335802 CCTCCTCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:336130 original size:18 final size:19
Alignment explanation
Indices: 336104--336140 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
336094 GGATTAACTT
336104 TTTGATTTGGATGTTTATG
1 TTTGATTTGGATGTTTATG
336123 TTTG-TTTGGATGTTTATG
1 TTTGATTTGGATGTTTATG
336141 ATATTTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (19 bp):
TTTGATTTGGATGTTTATG
Found at i:336149 original size:17 final size:18
Alignment explanation
Indices: 336108--336151 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
336098 TAACTTTTTG
*
336108 ATTTGGATGTTTATGTTT
1 ATTTGGATGTTTATGTAT
*
336126 GTTTGGATGTTTATG-AT
1 ATTTGGATGTTTATGTAT
336143 ATTTGGATG
1 ATTTGGATG
336152 CTTGACTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (18 bp):
ATTTGGATGTTTATGTAT
Found at i:336849 original size:19 final size:19
Alignment explanation
Indices: 336825--336863 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
336815 TCGAATGCAT
336825 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
336844 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
336863 T
1 T
336864 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:336880 original size:65 final size:64
Alignment explanation
Indices: 336762--336970 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
336752 TATTCAAAGG
* *
336762 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
336823 ATTC
61 ATTT
336827 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
336892 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
336956 CATGCATCGATGCAC
1 CATGCACCGATGCAC
336971 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.41
65 65 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:336988 original size:64 final size:65
Alignment explanation
Indices: 336811--336973 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
336801 GAATTAATTG
* * * *
336811 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
336876 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
336939 A
65 A
336940 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
336974 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:338366 original size:23 final size:23
Alignment explanation
Indices: 338336--338425 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 23
338326 GTTGAGGGTT
*
338336 CTATGTGGTCCTTCAGGACAATC
1 CTATGTGGTCCTTCGGGACAATC
*
338359 CTATGTGGTCCTTCGGGATAATC
1 CTATGTGGTCCTTCGGGACAATC
* * * **
338382 TTATGTGGTCATTCGAGACAAAA
1 CTATGTGGTCCTTCGGGACAATC
*
338405 CTATGTTGTCCTTCGGGACAA
1 CTATGTGGTCCTTCGGGACAA
338426 ATATATGGCA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAATC
Found at i:338906 original size:25 final size:25
Alignment explanation
Indices: 338854--338908 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
338844 TGCTCTGATC
*
338854 TATTT-TGTAAACTTATAGTTTTTG
1 TATTTATGTAAACTTATAGTATTTG
338878 TATTTATGTAAA-TTATTAAGTATTT-
1 TATTTATGTAAACTTA-T-AGTATTTG
338903 TATTTA
1 TATTTA
338909 AATGTGAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 8 0.30
25 13 0.48
26 6 0.22
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.58
Consensus pattern (25 bp):
TATTTATGTAAACTTATAGTATTTG
Found at i:348099 original size:22 final size:22
Alignment explanation
Indices: 348074--348115 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
348064 CAATTCATTT
348074 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
348096 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
348116 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:348451 original size:9 final size:9
Alignment explanation
Indices: 348437--348479 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
348427 TTTTTTACAA
348437 AAAAAAAAC
1 AAAAAAAAC
**
348446 AAAAAAGGC
1 AAAAAAAAC
348455 AAAAAAAAC
1 AAAAAAAAC
348464 ACAAAAAAAC
1 A-AAAAAAAC
348474 AAAAAA
1 AAAAAA
348480 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:348478 original size:20 final size:20
Alignment explanation
Indices: 348433--348479 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
348423 CTATTTTTTT
348433 ACAAAAAAAAAACAAAAAAG
1 ACAAAAAAAAAACAAAAAAG
* *
348453 GCAAAAAAAACACAAAAAA-
1 ACAAAAAAAAAACAAAAAAG
348472 ACAAAAAA
1 ACAAAAAA
348480 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (20 bp):
ACAAAAAAAAAACAAAAAAG
Found at i:352802 original size:22 final size:22
Alignment explanation
Indices: 352777--352818 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
352767 CAATTCATTT
352777 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
352799 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
352819 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:353353 original size:21 final size:22
Alignment explanation
Indices: 353280--353375 Score: 90
Period size: 23 Copynumber: 4.3 Consensus size: 22
353270 GTTGAGGGTT
* *
353280 CTATATGGTCCTTCGGGACAATC
1 CTATGTGGTCCTTCGGGACAA-A
* *
353303 CTATGTAGTCCTTTGGGACAAAA
1 CTATGTGGTCCTTCGGGAC-AAA
353326 CTATGTGGTCCTTCGGGACAAA
1 CTATGTGGTCCTTCGGGACAAA
353348 -TATGTGG-CACTTCGGTG-CAAA
1 CTATGTGGTC-CTTCGG-GACAAA
*
353369 TTATGTG
1 CTATGTG
353376 AGTTGTGGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
20 1 0.02
21 17 0.27
22 10 0.16
23 33 0.52
24 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGGACAAA
Found at i:361820 original size:43 final size:43
Alignment explanation
Indices: 361751--361863 Score: 138
Period size: 43 Copynumber: 2.7 Consensus size: 43
361741 GTTTTCTACT
* * * * *
361751 AAAAC-CCGCTATAGATCATGATCTTTTGCGGCATTTTTATTA
1 AAAACGCCGCTATTGAGCTTGACCTTTTACGGCATTTTTATTA
* **
361793 AAAATGTTGCTATTGAGCTTGACCTTTTACGGCATTTTTATTA
1 AAAACGCCGCTATTGAGCTTGACCTTTTACGGCATTTTTATTA
*
361836 AAAACGCCGCTATTGAGCTTGACATTTT
1 AAAACGCCGCTATTGAGCTTGACCTTTT
361864 TAAGAAAAAC
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 4 0.07
43 54 0.93
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (43 bp):
AAAACGCCGCTATTGAGCTTGACCTTTTACGGCATTTTTATTA
Found at i:361872 original size:33 final size:33
Alignment explanation
Indices: 361825--361896 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
361815 CCTTTTACGG
** * * *
361825 CATTTTTATTAAAAACGCCGCTATTGAGCTTGA
1 CATTTTTAAGAAAAACACCGCTATAGAGCTAGA
*
361858 CATTTTTAAGAAAAACACGGCTATAGAGCTAGA
1 CATTTTTAAGAAAAACACCGCTATAGAGCTAGA
361891 -ATTTTT
1 CATTTTT
361897 GCGGCGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 6 0.18
33 27 0.82
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (33 bp):
CATTTTTAAGAAAAACACCGCTATAGAGCTAGA
Found at i:362603 original size:2 final size:2
Alignment explanation
Indices: 362596--362675 Score: 137
Period size: 2 Copynumber: 41.0 Consensus size: 2
362586 AATTTTAGAT
*
362596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
362637 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
362676 AGATTAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 72 0.97
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:365406 original size:105 final size:105
Alignment explanation
Indices: 365124--366177 Score: 1894
Period size: 105 Copynumber: 10.0 Consensus size: 105
365114 GTTGTGAAGT
* * *
365124 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
365189 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
365230 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
365295 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
365336 TGAAATTGAGAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
365401 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
365441 TGAAATTGAGAAATGTTTGTTGACAACCTGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
365506 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTT
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
365546 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
365611 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
365651 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTCCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
365716 TGGAGTACAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
365756 TGAAATTGAGAAATGTTTGTTGACAACCTA-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAATGTTTGTTGACAACC-AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
365820 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
365861 TGAATTTGAGAAATGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
365926 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
365966 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
366031 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
366071 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
366136 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
366176 TG
1 TG
366178 GGTAAAACCT
Statistics
Matches: 918, Mismatches: 27, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
104 1 0.00
105 805 0.88
106 112 0.12
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:367672 original size:2 final size:2
Alignment explanation
Indices: 367632--367656 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
367622 AACAAACATG
367632 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
367657 GAAATAAAGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:369909 original size:104 final size:105
Alignment explanation
Indices: 369615--370659 Score: 1829
Period size: 104 Copynumber: 10.0 Consensus size: 105
369605 GTTGTGAAGT
* * *
369615 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
369680 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
369721 TGAAATGGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
369786 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
369827 TGAAATTGAGAGATGTTTGTTGACAACCAGC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
369891 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
369931 TGAAATTGAG-AATGTGTGTTGACAACCTGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
369995 TGGAGTCCAATATCCTTCGTTGTGAAGTTG-AATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
370034 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
370099 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
370139 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
370204 TGGAGACCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
370244 TGAAATTGAG-AATGTTTGTTGACAACCTGC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
370307 TGGAGTCCAATATCCTTCGTTGTGAAGTTG-AATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
370346 TGAATTTGAGAAATGTTTGTTGACAACCAGTGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
370411 TGGAGTCCAATATCCTTCGTTGTGAAGTTG-AATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
370450 TGAATTTGAG-AATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
370514 TGGAGTCCAATATCCTTCGTT-TGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* **
370553 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTTATCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
370618 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
370658 TG
1 TG
370660 GGTAAAACCT
Statistics
Matches: 902, Mismatches: 28, Indels: 19
0.95 0.03 0.02
Matches are distributed among these distances:
102 26 0.03
103 207 0.23
104 400 0.44
105 159 0.18
106 110 0.12
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:370423 original size:207 final size:209
Alignment explanation
Indices: 369615--370659 Score: 1834
Period size: 207 Copynumber: 5.0 Consensus size: 209
369605 GTTGTGAAGT
* * *
369615 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGAG-AA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
369680 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAGTTGTTTGTTGA
64 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-ATGTTTGTTGA
369745 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
128 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
369810 GAAGTTGAAATTGGCTC
193 GAAGTTGAAATTGGCTC
369827 TGAAATTGAGAGATGTTTGTTGACAACCAGC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
369891 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AATGTGTGTTGACA
65 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACA
*
369955 ACCTGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
130 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
370020 AGTTG-AATTGGCTC
195 AGTTGAAATTGGCTC
* *
370034 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTC
1 TGAAATTGAG-AATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
370099 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACA
65 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACA
*
370164 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGACCAATATCCTTCGTTGTGA
130 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
370229 AGTTGAAATTGGCTC
195 AGTTGAAATTGGCTC
*
370244 TGAAATTGAGAATGTTTGTTGACAACCTGC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 TGAAATTGAGAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
370308 GGAGTCCAATATCCTTCGTTGTGAAGTTG-AATTGGCTCTGAATTTGAGAAATGTTTGTTGACAA
66 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAA
* *
370372 CCAGTGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
131 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
370437 GTTG-AATTGGCTC
196 GTTGAAATTGGCTC
*
370450 TGAATTTGAGAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 TGAAATTGAGAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
370515 GGAGTCCAATATCCTTCGTT-TGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAA
66 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAA
**
370579 CCAGCGGTCCCTTTATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
131 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
370644 GTTGAAATTGGCTC
196 GTTGAAATTGGCTC
370658 TG
1 TG
370660 GGTAAAACCT
Statistics
Matches: 800, Mismatches: 25, Indels: 20
0.95 0.03 0.02
Matches are distributed among these distances:
206 45 0.06
207 292 0.37
208 235 0.29
209 101 0.13
210 99 0.12
211 18 0.02
212 10 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (209 bp):
TGAAATTGAGAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTC
Found at i:381620 original size:2 final size:2
Alignment explanation
Indices: 381615--381640 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
381605 AATATATACC
381615 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
381641 ATAAAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:383651 original size:24 final size:24
Alignment explanation
Indices: 383619--383674 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
383609 CTATTCTTTC
383619 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
383643 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
383667 GCTTCAAT
1 GCTTCAAT
383675 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:385136 original size:31 final size:31
Alignment explanation
Indices: 385051--385146 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
385041 TTAAAAAACA
* *
385051 TAAGATATTGTCACTTTT-ATTTTTATGTAAT
1 TAAGATATGGTCA-TTTTCATTTTTATTTAAT
* *
385082 TAATATATGGTCACTTTCATTTTTATTTAAT
1 TAAGATATGGTCATTTTCATTTTTATTTAAT
* *
385113 TAAGATATGGTCATTTTCTTTTTTGTTTAAT
1 TAAGATATGGTCATTTTCATTTTTATTTAAT
385144 TAA
1 TAA
385147 AATGTGTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 3 0.05
31 53 0.95
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.55
Consensus pattern (31 bp):
TAAGATATGGTCATTTTCATTTTTATTTAAT
Found at i:387427 original size:18 final size:18
Alignment explanation
Indices: 387404--387449 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
387394 CTTCCTCTTG
387404 GTATCGATACCCACTTAA
1 GTATCGATACCCACTTAA
*
387422 GTATCGATACCCATTTAA
1 GTATCGATACCCACTTAA
387440 GTATCGATAC
1 GTATCGATAC
387450 TACTTGCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (18 bp):
GTATCGATACCCACTTAA
Found at i:393560 original size:21 final size:21
Alignment explanation
Indices: 393516--393561 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
393506 GATCAAAAAT
* *
393516 TTTTATTTATTTTCTGTAATA
1 TTTTATTTATTTTATATAATA
393537 TTTTATTATATTTTATATAA-A
1 TTTTATT-TATTTTATATAATA
393558 TTTT
1 TTTT
393562 TTTTCAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATTTATTTTATATAATA
Found at i:393562 original size:22 final size:21
Alignment explanation
Indices: 393512--393562 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
393502 TTTTGATCAA
* *
393512 AAATTTTTATTTATTTTCTGT
1 AAATTTTTATTTATTTTATAT
393533 -AATATTTTATTATATTTTATAT
1 AAAT-TTTTATT-TATTTTATAT
393555 AAATTTTT
1 AAATTTTT
393563 TTTCAAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 3 0.12
21 7 0.28
22 12 0.48
23 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
AAATTTTTATTTATTTTATAT
Found at i:393817 original size:23 final size:23
Alignment explanation
Indices: 393791--393850 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
393781 AGTCGAGGGT
* *
393791 TCTATGCGGTCTTTCGGGACAAA
1 TCTATGCGGTCCTTCGAGACAAA
* *
393814 TCTATGTGGTCCTTCGAGACAAT
1 TCTATGCGGTCCTTCGAGACAAA
* *
393837 TCAATGGGGTCCTT
1 TCTATGCGGTCCTT
393851 TGGGAGAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (23 bp):
TCTATGCGGTCCTTCGAGACAAA
Found at i:400164 original size:18 final size:17
Alignment explanation
Indices: 400132--400167 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
400122 TTTCATAATG
400132 CTAAAATGGTATCGATA
1 CTAAAATGGTATCGATA
*
400149 CTAAAGTGGATATCGATA
1 CTAAAATGG-TATCGATA
400167 C
1 C
400168 CATAGAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (17 bp):
CTAAAATGGTATCGATA
Found at i:407127 original size:30 final size:31
Alignment explanation
Indices: 407083--407142 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
407073 ATATTTAAAA
* *
407083 TATATTTATTAATATTCTAATAATATAATAG
1 TATATTTATTAATATTATAATAAAATAATAG
407114 TATATTT-TTAATATTATAATAAAATAATA
1 TATATTTATTAATATTATAATAAAATAATA
407143 AATTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (31 bp):
TATATTTATTAATATTATAATAAAATAATAG
Found at i:407149 original size:18 final size:18
Alignment explanation
Indices: 407126--407160 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
407116 TATTTTTAAT
407126 ATTATAATAAAATAATAA
1 ATTATAATAAAATAATAA
* *
407144 ATTATATTATAATAATA
1 ATTATAATAAAATAATA
407161 TAATATAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTATAATAAAATAATAA
Found at i:407173 original size:23 final size:23
Alignment explanation
Indices: 407124--407177 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
407114 TATATTTTTA
*
407124 ATATTATAATAAAATAATAAATT
1 ATATTATAATAAAATAATAAATG
*
407147 ATATTATAATAATATAATATAA-G
1 ATATTATAATAAAATAATA-AATG
407170 ATATTATA
1 ATATTATA
407178 TTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATAAATG
Found at i:407207 original size:31 final size:31
Alignment explanation
Indices: 407078--407207 Score: 110
Period size: 31 Copynumber: 4.3 Consensus size: 31
407068 TTAAAATATT
* *
407078 TAAAATATATTTATTAATATTCTAATA-AT-A
1 TAAATTATATTT-TTAATATTATAATATATAA
* *
407108 TAATAGTATATTTTTAATATTATAATAAAATAA
1 TAA-ATTATATTTTTAATATTATAAT-ATATAA
* *
407141 TAAATTATA-TTATAATAATATAATATA-AGA
1 TAAATTATATTTTTAATATTATAATATATA-A
* *
407171 T--ATTATATTTTTATTTTTATAATATATAA
1 TAAATTATATTTTTAATATTATAATATATAA
407200 TAAATTAT
1 TAAATTAT
407208 TAATAAAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
28 6 0.07
29 17 0.21
30 20 0.25
31 27 0.33
32 7 0.09
33 4 0.05
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (31 bp):
TAAATTATATTTTTAATATTATAATATATAA
Found at i:407280 original size:19 final size:18
Alignment explanation
Indices: 407256--407324 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
407246 ATATTATTAA
407256 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
407275 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
407293 ATTAATGTAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
407315 ATT-TTAATAA
1 ATTATTAATAA
407325 ATATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:407338 original size:23 final size:22
Alignment explanation
Indices: 407312--407362 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
407302 ATAATCTAAT
* *
407312 AATATTTTAATAAATATATTTAA
1 AATATATTAATAAATAT-TTAAA
*
407335 AATATATTAATTAATATTTAAA
1 AATATATTAATAAATATTTAAA
407357 AATATA
1 AATATA
407363 ATATAACACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATATTAATAAATATTTAAA
Found at i:416996 original size:34 final size:30
Alignment explanation
Indices: 416958--417026 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
416948 TTGATATAAC
416958 AATTTAAGGAAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--AAAAAT-GTTTTTGGACTT-AATTG
*
416992 AATTT-ATAAAATGTTTTTGGACTTAATTG
1 AATTTAAAAAAATGTTTTTGGACTTAATTG
417021 AATTTA
1 AATTTA
417027 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 12 0.36
31 5 0.15
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.43
Consensus pattern (30 bp):
AATTTAAAAAAATGTTTTTGGACTTAATTG
Found at i:417037 original size:29 final size:30
Alignment explanation
Indices: 416968--417027 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
416958 AATTTAAGGA
416968 AAAATGGTTTTTGGACTTGAATTGAATTTAT
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAT
416999 AAAATGTTTTTGGACTT-AATTGAATTTAT
1 AAAATGTTTTTGGACTTGAATTGAATTTAT
417028 TCAAAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 12 0.41
30 12 0.41
31 5 0.17
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAT
Found at i:417132 original size:21 final size:20
Alignment explanation
Indices: 417106--417204 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
417096 AGGGTGTCAA
417106 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
417127 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCA-CCCTGC
417148 AGTGCATCCATGCA-CCTGC
1 AGTGCATCCATGCACCCTGC
* *
417167 ATTAGTGCATCAATGCACCATGC
1 ---AGTGCATCCATGCACCCTGC
417190 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
417205 TCAAACACCG
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.21
21 33 0.49
22 13 0.19
23 4 0.06
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:418437 original size:28 final size:30
Alignment explanation
Indices: 418368--418426 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
418358 CAATTTAAGG
418368 CAAAATGGTTTTTGGACATGAATTGAATTTA
1 CAAAAT-GTTTTTGGACATGAATTGAATTTA
*
418399 CAAAATGTTTTTGGAC-TTAATT-AATTTA
1 CAAAATGTTTTTGGACATGAATTGAATTTA
418427 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 6 0.22
29 5 0.19
30 10 0.37
31 6 0.22
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACATGAATTGAATTTA
Found at i:418532 original size:21 final size:21
Alignment explanation
Indices: 418506--418617 Score: 172
Period size: 21 Copynumber: 5.4 Consensus size: 21
418496 AGGGTGTCAA
418506 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
418527 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
418548 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCCCTGC
*
418569 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
* * *
418590 AGTGAATCGATGCA-CCATGC
1 AGTGCATCCATGCACCCCTGC
418610 AGTGCATC
1 AGTGCATC
418618 TCAAACAGCG
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
20 12 0.14
21 72 0.86
ACGTcount: A:0.21, C:0.37, G:0.21, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:418663 original size:20 final size:20
Alignment explanation
Indices: 418638--418710 Score: 146
Period size: 20 Copynumber: 3.6 Consensus size: 20
418628 AATGGAATTA
418638 GTGCATCGATGCATCCTTAT
1 GTGCATCGATGCATCCTTAT
418658 GTGCATCGATGCATCCTTAT
1 GTGCATCGATGCATCCTTAT
418678 GTGCATCGATGCATCCTTAT
1 GTGCATCGATGCATCCTTAT
418698 GTGCATCGATGCA
1 GTGCATCGATGCA
418711 CGAAGGTTGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.33
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTAT
Found at i:418861 original size:20 final size:22
Alignment explanation
Indices: 418823--418862 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
418813 TATTAGTAGA
418823 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
418845 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
418863 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:419716 original size:21 final size:21
Alignment explanation
Indices: 419674--419716 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
419664 AGGGTGTCAA
*
419674 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCATGC
*
419695 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCACCCATGC
419716 A
1 A
419717 CCTTCACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATGC
Found at i:419805 original size:20 final size:20
Alignment explanation
Indices: 419780--419853 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
419770 AATGTAATTA
419780 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
**
419800 GTGCATCGATGCATCAAGGT-T
1 GTGCATCGATGCATC--CTTCT
* *
419821 GTGCATCAATGCATCCTGCT
1 GTGCATCGATGCATCCTTCT
*
419841 GTGCATCCATGCA
1 GTGCATCGATGCA
419854 CGAAGGCTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 28 0.64
21 15 0.34
22 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:421540 original size:2 final size:2
Alignment explanation
Indices: 421533--421593 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
421523 ATTTGCGTAT
421533 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
421575 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
421594 CTTATTAGTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:422788 original size:16 final size:15
Alignment explanation
Indices: 422769--422825 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
422759 TTTATGTTAG
422769 TATTTTTTTAAATAGT
1 TATTTTTTTAAATA-T
* * *
422785 TATTATTTTATATTAA
1 TATTTTTTTA-AATAT
* *
422801 TATTTATGTAAATAT
1 TATTTTTTTAAATAT
422816 TATTTTTTTA
1 TATTTTTTTA
422826 TTAAAATAAT
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
15 11 0.37
16 16 0.53
17 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
TATTTTTTTAAATAT
Found at i:422805 original size:32 final size:30
Alignment explanation
Indices: 422750--422829 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 30
422740 TAGTGGTAAG
* * * *
422750 AAAT-TTA-TTTTTATGTTAGTATTTTTTT
1 AAATATTATTTTTTATATTAATATTTATGT
422778 AAATAGTTATTATTTTATATTAATATTTATGT
1 AAATA-TTATT-TTTTATATTAATATTTATGT
422810 AAATATTATTTTTT-TATTAA
1 AAATATTATTTTTTATATTAA
422830 AATAATATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.09
29 6 0.14
30 7 0.16
31 6 0.14
32 21 0.48
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (30 bp):
AAATATTATTTTTTATATTAATATTTATGT
Found at i:422825 original size:31 final size:31
Alignment explanation
Indices: 422757--422859 Score: 89
Period size: 34 Copynumber: 3.2 Consensus size: 31
422747 AAGAAATTTA
* * * *
422757 TTTTTATGTTAGTATTTTTTTAAATAGTTATT
1 TTTTTATATTAATATTTATATAAATA-TTATT
* *
422789 ATTTTATATTAATATTTATGTAAATATTATT
1 TTTTTATATTAATATTTATATAAATATTATT
* *
422820 TTTTTATTAAAATAATATTTATATAATTATTATT
1 TTTTTA-T--ATTAATATTTATATAAATATTATT
*
422854 TATTTA
1 TTTTTA
422860 GAATTATTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
31 10 0.17
32 22 0.38
34 26 0.45
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (31 bp):
TTTTTATATTAATATTTATATAAATATTATT
Found at i:423035 original size:17 final size:17
Alignment explanation
Indices: 422997--423035 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
422987 TAATGTTAAT
* *
422997 ATTTAAATTTATTTTTA
1 ATTTAAATTTATTATGA
*
423014 TTTTAAATTTATTATGA
1 ATTTAAATTTATTATGA
423031 ATTTA
1 ATTTA
423036 TATTAATTGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTAAATTTATTATGA
Found at i:424610 original size:21 final size:21
Alignment explanation
Indices: 424580--424627 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
424570 GCAGGGGTAC
* *
424580 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
424601 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
424622 ATGCCA
1 ATGCCA
424628 TCTCCGTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:424661 original size:21 final size:22
Alignment explanation
Indices: 424635--424724 Score: 125
Period size: 21 Copynumber: 4.3 Consensus size: 22
424625 CCATCTCCGT
* *
424635 AGGGTTACATTCCGAGCCCG-C
1 AGGGTTACATGCCTAGCCCGCC
*
424656 AGGGTTACATTCCTAGCCCGCC
1 AGGGTTACATGCCTAGCCCGCC
424678 A-GGTTACATGCCTAGCCCGCC
1 AGGGTTACATGCCTAGCCCGCC
424699 A-GGTTACATGCCTAGCCCG-C
1 AGGGTTACATGCCTAGCCCGCC
424719 AGGGTT
1 AGGGTT
424725 TTATACCATA
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
20 2 0.03
21 61 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.21
Consensus pattern (22 bp):
AGGGTTACATGCCTAGCCCGCC
Found at i:425290 original size:39 final size:39
Alignment explanation
Indices: 425238--425315 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
425228 AAATGTTTTT
425238 AAAATACAAATTATATT-ATTCGAAATTTAAAATAAAAATA
1 AAAATACAAATTAT-TTAATT-GAAATTTAAAATAAAAATA
* * *
425278 AAAATA-ATATTATTTAAATTTAAATTTAAAATATAAAT
1 AAAATACAAATTATTT-AATTGAAATTTAAAATAAAAAT
425316 TATAGTATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
38 2 0.06
39 22 0.67
40 9 0.27
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (39 bp):
AAAATACAAATTATTTAATTGAAATTTAAAATAAAAATA
Found at i:425297 original size:33 final size:34
Alignment explanation
Indices: 425238--425334 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
425228 AAATGTTTTT
*
425238 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * * *
425272 AAAATAAAAATAATATTATT-TAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
425305 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
425335 CATTAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 27 0.51
34 26 0.49
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:425341 original size:34 final size:33
Alignment explanation
Indices: 425236--425341 Score: 124
Period size: 34 Copynumber: 3.2 Consensus size: 33
425226 ATAAATGTTT
*
425236 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* * *
425270 TAAAAATAAAAATAATATTATT-TAAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
425302 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
425337 TTAAA
1 TTAAA
425342 TTTCAACTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.05
33 24 0.40
34 32 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:425714 original size:128 final size:129
Alignment explanation
Indices: 425486--425921 Score: 743
Period size: 128 Copynumber: 3.4 Consensus size: 129
425476 AAAATCAACT
**
425486 TATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTA-AGAAAT
1 TATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAATAGAGAAAT
425550 AATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA
66 AATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA
* * * * *
425614 TATTCTATGACGAAATAATGTAAGGCGCGCCCCCGGGAACGTGCCTTCATGT-GAATAGTGAAAT
1 TATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAATAGAGAAAT
* *
425678 AATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAGGGACATAATAGGGCAATGATAATA
66 AATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA
**
425742 TATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAAT
1 TATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAATAGAGAAAT
425806 AATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA
66 AATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA
*
425870 TATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGTGCCTTCATGT
1 TATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT
425922 GAATAGTATT
Statistics
Matches: 287, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
127 2 0.01
128 284 0.99
129 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.23
Consensus pattern (129 bp):
TATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAATAGAGAAAT
AATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA
Found at i:426012 original size:8 final size:8
Alignment explanation
Indices: 425999--426039 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
425989 TCACAATCTT
425999 TCAAATTC
1 TCAAATTC
426007 TCAAATTC
1 TCAAATTC
* *
426015 CCAAACTC
1 TCAAATTC
426023 T-AAATTC
1 TCAAATTC
426030 TCAAATTC
1 TCAAATTC
426038 TC
1 TC
426040 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:431295 original size:8 final size:8
Alignment explanation
Indices: 431282--431306 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
431272 TTTGTTTTTG
431282 CATGTTTA
1 CATGTTTA
431290 CATGTTTA
1 CATGTTTA
431298 CATGTTTA
1 CATGTTTA
431306 C
1 C
431307 GTACGTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (8 bp):
CATGTTTA
Found at i:444281 original size:25 final size:25
Alignment explanation
Indices: 444244--444299 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
444234 CACAATGCTA
*
444244 ATGTGGCAGTCCACAATGGATGATG
1 ATGTGGCAATCCACAATGGATGATG
** **
444269 ATGTGGCAATCCATGATGTTTGATG
1 ATGTGGCAATCCACAATGGATGATG
444294 ATGTGG
1 ATGTGG
444300 TAGATAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.30
Consensus pattern (25 bp):
ATGTGGCAATCCACAATGGATGATG
Found at i:448589 original size:22 final size:22
Alignment explanation
Indices: 448546--448589 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
448536 TTTCAGGTTA
* *
448546 AGAAATGTTAATTTCAAGGATT
1 AGAAAGGTTAATTTCAAAGATT
* *
448568 AGAAAGGTTATTTTGAAAGATT
1 AGAAAGGTTAATTTCAAAGATT
448590 GAGTTAGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.36
Consensus pattern (22 bp):
AGAAAGGTTAATTTCAAAGATT
Found at i:449226 original size:26 final size:26
Alignment explanation
Indices: 449204--449256 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
449194 GTACAAATTT
449204 TACGAGGCACTTTCT-AGTGCAAATAC
1 TACGAGGCACTTT-TGAGTGCAAATAC
*
449230 TACTAGGCACTTTTGAGTGC-AATAC
1 TACGAGGCACTTTTGAGTGCAAATAC
449255 TA
1 TA
449257 TATCTACGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (26 bp):
TACGAGGCACTTTTGAGTGCAAATAC
Found at i:456092 original size:18 final size:18
Alignment explanation
Indices: 456066--456101 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
456056 TTTATTTGAT
456066 TGGTAATGATGCTCGAAA
1 TGGTAATGATGCTCGAAA
* *
456084 TGGTGATGATGCTTGAAA
1 TGGTAATGATGCTCGAAA
456102 AACTAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (18 bp):
TGGTAATGATGCTCGAAA
Found at i:456381 original size:32 final size:31
Alignment explanation
Indices: 456336--456398 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
456326 CAAGAAATAA
456336 ATATTAATCACACAACAG-ATGTTCAAAATCT
1 ATATTAATCACACAAC-GCATGTTCAAAATCT
456367 ATATATAATCACACAACGCATGTTCAAAATCT
1 ATAT-TAATCACACAACGCATGTTCAAAATCT
456399 CCAATCCCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 5 0.17
32 25 0.83
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (31 bp):
ATATTAATCACACAACGCATGTTCAAAATCT
Done.