Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000114.1 Hibiscus syriacus cultivar Beakdansim tig00000205_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: 799156
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:215278 original size:15 final size:15
Alignment explanation
Indices: 215260--215317 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
215250 TCACTTAGCG
*
215260 CATTTTCACGTATAA
1 CATTTTCACATATAA
*
215275 CATTTTCATATATAA
1 CATTTTCACATATAA
* *
215290 TATATTCACATATAAA
1 CATTTTCACATAT-AA
215306 CATTTTCACATA
1 CATTTTCACATA
215318 CCCATAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
15 23 0.66
16 12 0.34
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.41
Consensus pattern (15 bp):
CATTTTCACATATAA
Found at i:215743 original size:18 final size:18
Alignment explanation
Indices: 215720--215767 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
215710 TCTCTTCTAT
215720 GGTATCGATACCCACTTC
1 GGTATCGATACCCACTTC
215738 GGTATCGATACCCACTTC
1 GGTATCGATACCCACTTC
215756 GGTATCGATACC
1 GGTATCGATACC
215768 ATTTTGGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (18 bp):
GGTATCGATACCCACTTC
Found at i:220077 original size:38 final size:38
Alignment explanation
Indices: 220016--220094 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
220006 CAATAAATGG
* * * * *
220016 AGATTTCAGAAATCAAAATAGAATTCATATCATATATC
1 AGATATCAGAAATCAAAACAGAATCCATATCAGAAATC
*
220054 AGATATCAGAAATCAGAACAGAATCCATATCAGAAATC
1 AGATATCAGAAATCAAAACAGAATCCATATCAGAAATC
220092 AGA
1 AGA
220095 ACATAATTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.24
Consensus pattern (38 bp):
AGATATCAGAAATCAAAACAGAATCCATATCAGAAATC
Found at i:220114 original size:24 final size:24
Alignment explanation
Indices: 220058--220118 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
220048 TATATCAGAT
*
220058 ATCAGAAATCAGAACAGAATCCAT
1 ATCAGAAATCAGAACAGAATCCAA
* *
220082 ATCAGAAATCAGAACATAATTCAA
1 ATCAGAAATCAGAACAGAATCCAA
220106 ATC-GAAAATCAGA
1 ATCAG-AAATCAGA
220119 TAAAACATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATCCAA
Found at i:224841 original size:24 final size:24
Alignment explanation
Indices: 224814--224876 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
224804 CATATATTAG
224814 ATATCAGAAATCAGAACAAAATCC
1 ATATCAGAAATCAGAACAAAATCC
* * *
224838 ATATAAGAAATCAGAACATAATTC
1 ATATCAGAAATCAGAACAAAATCC
* *
224862 AAATCGGAAATCAGA
1 ATATCAGAAATCAGA
224877 TAAAACATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAAAATCC
Found at i:225694 original size:2 final size:2
Alignment explanation
Indices: 225689--225724 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
225679 CATTCAAGTG
225689 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
225725 GTAGTTCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:239396 original size:22 final size:22
Alignment explanation
Indices: 239371--239416 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
239361 AATTAATTAT
239371 ATTTAATATATTT-TTAAATTTA
1 ATTTAATAT-TTTATTAAATTTA
* *
239393 ATTTTATATTTTATTCAATTTA
1 ATTTAATATTTTATTAAATTTA
239415 AT
1 AT
239417 CCCAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTAATATTTTATTAAATTTA
Found at i:244473 original size:26 final size:25
Alignment explanation
Indices: 244425--244473 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
244415 TATAGGCTAA
* *
244425 AAATAGGATTAAAATCGTCCATAAC
1 AAATAGGATTAAAACCATCCATAAC
*
244450 AAATCAGGATTAAAACCATTCATA
1 AAAT-AGGATTAAAACCATCCATA
244474 GTAACACTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.24
Consensus pattern (25 bp):
AAATAGGATTAAAACCATCCATAAC
Found at i:255733 original size:26 final size:26
Alignment explanation
Indices: 255697--255750 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
255687 ACCGAAGTGC
**
255697 TAATACACATAAGGTTGTGTCCACCA
1 TAATACACATAAGGTCATGTCCACCA
255723 TAATACACATAAGGTCATGTCCACCA
1 TAATACACATAAGGTCATGTCCACCA
255749 TA
1 TA
255751 TGCAGTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (26 bp):
TAATACACATAAGGTCATGTCCACCA
Found at i:261080 original size:59 final size:59
Alignment explanation
Indices: 261017--261283 Score: 313
Period size: 59 Copynumber: 4.5 Consensus size: 59
261007 TAAATCGAGA
* * *
261017 AAAGGAAATGTTGATCCCTCATA-TGAGGTGTTACTGATTCAAAGTGTTATGAATCAAAC
1 AAAGGAAATGTTGATCCCTCA-AGTGAGGCGTTACTGATTCAAAGTGTTGTGAATCAAGC
* * * * *
261076 AAAGGAAATATTGATCCCTCAAGTGAGACGTTGCTGATTCGAAGTGTTGTGAATCGAGC
1 AAAGGAAATGTTGATCCCTCAAGTGAGGCGTTACTGATTCAAAGTGTTGTGAATCAAGC
* * ** **
261135 AAAGGAAATGTTGATCCCTTAAGTAAGGCGTTGA-TGATTTGAAGTGTTGTGAATGGAGC
1 AAAGGAAATGTTGATCCCTCAAGTGAGGCGTT-ACTGATTCAAAGTGTTGTGAATCAAGC
* * **
261194 AAAGGAAATGTTAATCCCTCAAGTGAGGCTTTGTTGATTCAAAGTGTTGTGAATCAAGC
1 AAAGGAAATGTTGATCCCTCAAGTGAGGCGTTACTGATTCAAAGTGTTGTGAATCAAGC
* * *
261253 AAATGAAATATTAATCCCTCAAGTGAGGCGT
1 AAAGGAAATGTTGATCCCTCAAGTGAGGCGT
261284 AGTTTATTTT
Statistics
Matches: 178, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
58 1 0.01
59 177 0.99
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (59 bp):
AAAGGAAATGTTGATCCCTCAAGTGAGGCGTTACTGATTCAAAGTGTTGTGAATCAAGC
Found at i:261173 original size:118 final size:118
Alignment explanation
Indices: 260961--261283 Score: 362
Period size: 118 Copynumber: 2.7 Consensus size: 118
260951 ATTCTCTACT
* * * * ** * *
260961 GGAAATATTGGTCCATCATGTGAGGCATCGCTGATTCGAAGTACTGTAAATCGAGAAAAGGAAAT
1 GGAAATATTGATCCCTCAAGTGAGGCATTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGGAAAT
*
261026 GTTGATCCCTCATA-TGAGGTGTTACTGATTCAAAGTGTTATGAATCAAACAAA
66 GTTGATCCCTCA-AGTGAGGCGTTACTGATTCAAAGTGTTATGAATCAAACAAA
* *
261079 GGAAATATTGATCCCTCAAGTGAGACGTTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGGAAAT
1 GGAAATATTGATCCCTCAAGTGAGGCATTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGGAAAT
* * ** * ** *
261144 GTTGATCCCTTAAGTAAGGCGTTGA-TGATTTGAAGTGTTGTGAATGGAGCAAA
66 GTTGATCCCTCAAGTGAGGCGTT-ACTGATTCAAAGTGTTATGAATCAAACAAA
* * * * * * *
261197 GGAAATGTTAATCCCTCAAGTGAGGCTTTGTTGATTCAAAGTGTTGTGAATCAAGCAAATGAAAT
1 GGAAATATTGATCCCTCAAGTGAGGCATTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGGAAAT
* *
261262 ATTAATCCCTCAAGTGAGGCGT
66 GTTGATCCCTCAAGTGAGGCGT
261284 AGTTTATTTT
Statistics
Matches: 172, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
117 1 0.01
118 170 0.99
119 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (118 bp):
GGAAATATTGATCCCTCAAGTGAGGCATTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGGAAAT
GTTGATCCCTCAAGTGAGGCGTTACTGATTCAAAGTGTTATGAATCAAACAAA
Found at i:261348 original size:38 final size:39
Alignment explanation
Indices: 261299--261854 Score: 464
Period size: 39 Copynumber: 14.7 Consensus size: 39
261289 ATTTTAAGAA
* * * * * *
261299 AAACAATCTCAAGTGAGAT-AAACCTTCTATTTTGAGAG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * * * * **
261337 AAACTACCTCAAACAAGAT-AAACCTTCTATTTCAAGCA
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
261375 AAACTACCTCAAGCGAGATAAAATCTTCTGTTTCTAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
261414 AAACTTTCTCAAGTGAGAT-AAATCTTCTGTTTCGGGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
261452 AAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
261491 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
261530 AAAGTATCTCAAGAGAGATAAAATCTTCTGTTTTGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* ** **
261569 AAACTATCTCAAGCGAGAT-GAATC-T-TGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* ** * * * *
261605 AAACAATCTTGAGTGAAATGAAATGTCTTCTGTTTCGAGTA
1 AAACTATCTCAAGCGAGAT-AAA-ATCTTCTGTTTCGAGTG
* *
261646 AAACTATCTCAAGCAAGATAAAA-C-T-TGTTT----TA
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * *
261678 AAACAATCTCAAGTGAGAT-GAATCTTCTGCTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * *
261716 AAACTATCTCAAACAAGATAAAATCTTTTGTTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* ** **
261755 AAACTATCTCAAGCGAGAT-GAAT-TT-TGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
** ** * *
261791 AAAAAATCTCAAATGAGCT-AAATCTTCTGTTTTGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
261829 AAACTATCTCAAGCGAGATAAAATCT
1 AAACTATCTCAAGCGAGATAAAATCT
261855 AGTTTTAAGA
Statistics
Matches: 414, Mismatches: 86, Indels: 35
0.77 0.16 0.07
Matches are distributed among these distances:
31 2 0.00
32 19 0.05
33 1 0.00
34 4 0.01
36 52 0.13
37 6 0.01
38 127 0.31
39 178 0.43
40 4 0.01
41 21 0.05
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
Found at i:261441 original size:77 final size:77
Alignment explanation
Indices: 261299--261926 Score: 448
Period size: 77 Copynumber: 8.3 Consensus size: 77
261289 ATTTTAAGAA
* * * * * * * * *
261299 AAACAATCTCAAGTGAGAT-AAACCTTCTATTT-TGAGAGAAACTACCTCAAACAAGATAAACCT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCT-AGTGAAACTATCTCAAGCGAGATAAATCT
* * **
261362 TCTATTTCAAGCA
65 TCTGTTTCGAGTG
* * *
261375 AAACTACCTCAAGCGAGATAAAATCTTCTGTTTCTAGTGAAACTTTCTCAAGTGAGATAAATCTT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCTAGTGAAACTATCTCAAGCGAGATAAATCTT
*
261440 CTGTTTCGGGTG
66 CTGTTTCGAGTG
* *
261452 AAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCTAGTGAAACTATCTCAAGCGAGAT-AAATCT
261517 TCTGTTTCGAGTG
65 TCTGTTTCGAGTG
* * *
261530 AAAGTATCTCAAGAGAGATAAAATCTTCTGTTT-TGAGTGAAACTATCTCAAGCGAGATGAATC-
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCT-AGTGAAACTATCTCAAGCGAGATAAATCT
** **
261593 T-TGTTTTAAGAA
65 TCTGTTTCGAGTG
* ** * * * * * * *
261605 AAACAATCTTGAGTGAAATGAAATGTCTTCTGTTTCGAGTAAAACTATCTCAAGCAAGATAAAAC
1 AAACTATCTCAAGCGAGAT-AAA-ATCTTCTGTTTCTAGTGAAACTATCTCAAGCGAGATAAATC
*
261670 -T-TGTTT----TA
64 TTCTGTTTCGAGTG
* * * * * * *
261678 AAACAATCTCAAGTGAGAT-GAATCTTCTGCTTCGAGTGAAACTATCTCAAACAAGATAAAATCT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCTAGTGAAACTATCTCAAGCGAGAT-AAATCT
* *
261742 TTTGTTTCAAGTG
65 TCTGTTTCGAGTG
* ** ** ** *
261755 AAACTATCTCAAGCGAGAT-GAAT-TT-TGTTT-TAAGAAAAAAAATCTCAAATGAGCTAAATCT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCT-AGTGAAACTATCTCAAGCGAGATAAATCT
*
261816 TCTGTTTTGAGTG
65 TCTGTTTCGAGTG
* ** * ** * * *
261829 AAACTATCTCAAGCGAGATAAAATC-T-AGTTT-TAAGAAAAACAATCTTGAGTGAAAATGAATC
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCT-AGTGAAACTATCTCAAGCG-AGATAAATC
*
261891 TTCTGTTTTGAGTG
64 TTCTGTTTCGAGTG
*
261905 AAACTTTCTCAAGCGAGATAAA
1 AAACTATCTCAAGCGAGATAAA
261927 TTTTGTTTGG
Statistics
Matches: 455, Mismatches: 79, Indels: 36
0.80 0.14 0.06
Matches are distributed among these distances:
70 32 0.07
71 5 0.01
72 1 0.00
73 22 0.05
74 35 0.08
75 65 0.14
76 63 0.14
77 160 0.35
78 72 0.16
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (77 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCTAGTGAAACTATCTCAAGCGAGATAAATCTT
CTGTTTCGAGTG
Found at i:261800 original size:36 final size:36
Alignment explanation
Indices: 261290--261934 Score: 130
Period size: 39 Copynumber: 17.1 Consensus size: 36
261280 GCGTAGTTTA
* * *
261290 TTTTAAGAAAAACAATCTCAAGTGAGATAAACCTTCTA
1 TTTTAAGAAAAACAATCTCAAGCGAGATAAA--TTTTG
* * * * * * * *
261328 TTTTGAGAGAAACTACCTCAAACAAGATAAACCTTCTA
1 TTTTAAGAAAAACAATCTCAAGCGAGATAAA--TTTTG
* * * *
261366 TTTCAAGCAAAACTACCTCAAGCGAGATAAAATCTTCTG
1 TTTTAAGAAAAACAATCTCAAGCGAGAT-AAAT-TT-TG
** ** *
261405 TTTCT-AGTGAAACTTTCTCAAGTGAGATAAATCTTCTG
1 TTT-TAAGAAAAACAATCTCAAGCGAGATAAAT-TT-TG
*** ** *
261443 TTTCGGGTGAAACTATCTCAAGCGAGATAAAATCTTATG
1 TTTTAAGAAAAACAATCTCAAGCGAGAT-AAAT-TT-TG
** ** *
261482 TTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
1 TTTTAAGAAAAACAATCTCAAGCGAGAT-AAAT-TT-TG
** ** ** *
261521 TTTCGAGTGAAAGTATCTCAAGAGAGATAAAATCTTCTG
1 TTTTAAGAAAAACAATCTCAAGCGAGAT-AAAT-TT-TG
* ** * * *
261560 TTTTGAGTGAAACTATCTCAAGCGAGATGAATCTTG
1 TTTTAAGAAAAACAATCTCAAGCGAGATAAATTTTG
** * *
261596 TTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCTTCTG
1 TTTTAAGAAAAACAATCTCAAGCGAGAT-AAA--T-TT-TG
** * * * **
261637 TTTCGAGTAAAACTATCTCAAGCAAGATAAAACTTG
1 TTTTAAGAAAAACAATCTCAAGCGAGATAAATTTTG
* *
261673 TTTT----AAAACAATCTCAAGTGAGATGAATCTTCTG
1 TTTTAAGAAAAACAATCTCAAGCGAGATAAAT-TT-TG
* ** ** * * *
261707 CTTCGAGTGAAACTATCTCAAACAAGATAAAATCTTTTG
1 TTTTAAGAAAAACAATCTCAAGCGAGAT-AAA--TTTTG
* ** * *
261746 TTTCAAGTGAAACTATCTCAAGCGAGATGAATTTTG
1 TTTTAAGAAAAACAATCTCAAGCGAGATAAATTTTG
* ** *
261782 TTTTAAGAAAAAAAATCTCAAATGAGCTAAATCTTCTG
1 TTTTAAGAAAAACAATCTCAAGCGAGATAAAT-TT-TG
* ** * * *
261820 TTTTGAGTGAAACTATCTCAAGCGAGATAAAATCTAG
1 TTTTAAGAAAAACAATCTCAAGCGAGAT-AAATTTTG
** * * *
261857 TTTTAAGAAAAACAATCTTGAGTGAAAATGAATCTTCTG
1 TTTTAAGAAAAACAATCTCAAGCG-AGATAAAT-TT-TG
* ** **
261896 TTTTGAGTGAAACTTTCTCAAGCGAGATAAATTTTG
1 TTTTAAGAAAAACAATCTCAAGCGAGATAAATTTTG
261932 TTT
1 TTT
261935 GGACATATTG
Statistics
Matches: 465, Mismatches: 116, Indels: 54
0.73 0.18 0.09
Matches are distributed among these distances:
32 19 0.04
33 1 0.00
34 4 0.01
36 60 0.13
37 30 0.06
38 140 0.30
39 183 0.39
40 6 0.01
41 22 0.05
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (36 bp):
TTTTAAGAAAAACAATCTCAAGCGAGATAAATTTTG
Found at i:261829 original size:74 final size:75
Alignment explanation
Indices: 261736--261934 Score: 256
Period size: 76 Copynumber: 2.7 Consensus size: 75
261726 AAACAAGATA
* ** *
261736 AAATCTTTTGTTTCAAGTGAAACTATCTCAAGCGAGATGAATTTTGTTTTAAGAAAAAAAATCTC
1 AAATCTTCTGTTTTGAGTGAAACTATCTCAAGCGAGATAAATTTTGTTTTAAGAAAAAAAATCTC
**
261801 AAATG-AGCT
66 AAATGAAAAT
* * *
261810 AAATCTTCTGTTTTGAGTGAAACTATCTCAAGCGAGATAAAATCTAGTTTTAAGAAAAACAATCT
1 AAATCTTCTGTTTTGAGTGAAACTATCTCAAGCGAGAT-AAATTTTGTTTTAAGAAAAAAAATCT
** *
261875 TGAGTGAAAAT
65 CAAATGAAAAT
* *
261886 GAATCTTCTGTTTTGAGTGAAACTTTCTCAAGCGAGATAAATTTTGTTT
1 AAATCTTCTGTTTTGAGTGAAACTATCTCAAGCGAGATAAATTTTGTTT
261935 GGACATATTG
Statistics
Matches: 107, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
74 35 0.33
75 34 0.32
76 38 0.36
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (75 bp):
AAATCTTCTGTTTTGAGTGAAACTATCTCAAGCGAGATAAATTTTGTTTTAAGAAAAAAAATCTC
AAATGAAAAT
Found at i:261933 original size:186 final size:185
Alignment explanation
Indices: 261420--261934 Score: 594
Period size: 186 Copynumber: 2.7 Consensus size: 185
261410 AGTGAAACTT
*
261420 TCTCAAGTGAGATAAATCTTCTGTTTCGGGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTT
1 TCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC-TA-GTTT
* * * * * *
261485 CGAGTGAAACTATCTCAAGCGAGATAA--AATCTTCTGTTTCGAGTGAAAGTATCTCAAGAGAGA
64 -TAG-AAAACAATCTCAAGTGA-A-AATGAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGA
** *
261548 TAAAATCTTCTGTTTTGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAA
125 TAAAAT-TT-TGTTTCAAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAAAA
** * * * *
261611 TCTTGAGTGAAATGAAATGTCTTCTGTTTCGAGTAAAACTATCTCAAGCAAGATAAAA-CTTGTT
1 TCTCAAGTGAGAT-AAA--TCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTAGTT
* * * *
261675 TT--AAAACAATCTCAAGTG-AGATGAATCTTCTGCTTCGAGTGAAACTATCTCAAACAAGATAA
63 TTAGAAAACAATCTCAAGTGAAAATGAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAA
*
261737 AATCTTTTGTTTCAAGTGAAACTATCTCAAGCGAGATGAATTTTGTTTTAAGAAAAAAAA
128 AA--TTTTGTTTCAAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAAAA
* * *
261797 TCTCAAATGAGCTAAATCTTCTGTTTTGAGTGAAACTATCTCAAGCGAGATAAAATCTAGTTTTA
1 TCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTAGTTTT-
** * *
261862 AGAAAAACAATCTTGAGTGAAAATGAATCTTCTGTTTTGAGTGAAACTTTCTCAAGCGAGAT-AA
65 AG-AAAACAATCTCAAGTGAAAATGAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAA
261926 ATTTTGTTT
129 ATTTTGTTT
261935 GGACATATTG
Statistics
Matches: 273, Mismatches: 38, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
183 36 0.13
184 8 0.03
185 4 0.01
186 101 0.37
187 15 0.05
188 18 0.07
189 36 0.13
191 14 0.05
192 4 0.01
193 1 0.00
194 36 0.13
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (185 bp):
TCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTAGTTTTA
GAAAACAATCTCAAGTGAAAATGAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAT
TTTGTTTCAAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAAAA
Found at i:262260 original size:17 final size:17
Alignment explanation
Indices: 262234--262277 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
262224 AGCAATCTTG
262234 GTTC-TCTTCTTGATCT
1 GTTCGTCTTCTTGATCT
262250 GTTCGTCTTCTTGATCT
1 GTTCGTCTTCTTGATCT
262267 GTTCGTCTTCT
1 GTTCGTCTTCT
262278 CTTCTCCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.05, C:0.25, G:0.16, T:0.55
Consensus pattern (17 bp):
GTTCGTCTTCTTGATCT
Found at i:266824 original size:54 final size:54
Alignment explanation
Indices: 266768--267169 Score: 513
Period size: 54 Copynumber: 7.4 Consensus size: 54
266758 TCCTAAATGG
* * *
266768 TTATTCATCAACATATGATGAATTTCGT-ACTTTTCACATTTAGTGCCGAAACGG
1 TTATTCATCAACATATGATGAATTTCGTGA-TTTGCACACTTAGTGCCGAAACGA
* * * ** *
266822 TTATTCATCAACATATGATGAATTCCGTGAATTGTACACTTAGTGTTGAAACGG
1 TTATTCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTGCCGAAACGA
* * * *
266876 TTATTCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTGTCAAAATGG
1 TTATTCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTGCCGAAACGA
* * *
266930 TTATTCATCACCATATGATGAATTCCATGATTTGCACACTTAGTGCCGAAACGA
1 TTATTCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTGCCGAAACGA
* ** *
266984 TTATTCATCAACATATGATGAATTCCGTGATTTG-ACCACTTAGTGTTGAAACAA
1 TTATTCATCAACATATGATGAATTTCGTGATTTGCA-CACTTAGTGCCGAAACGA
* * * *
267038 TTATTCATCAATATATGATGAATTTCATGATTTGCACACTTAGTGCCAAAACAA
1 TTATTCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTGCCGAAACGA
* * *
267092 TTATTCATCAACATATGATGAA-TTCTGTGATTTGCAAACTTAGTGCCGGAACAA
1 TTATTCATCAACATATGATGAATTTC-GTGATTTGCACACTTAGTGCCGAAACGA
267146 TTATTCATCAACATATGATGAATT
1 TTATTCATCAACATATGATGAATT
267170 CTGTACTTTG
Statistics
Matches: 307, Mismatches: 36, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
53 4 0.01
54 300 0.98
55 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (54 bp):
TTATTCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTGCCGAAACGA
Found at i:266897 original size:26 final size:26
Alignment explanation
Indices: 266815--266897 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 26
266805 ATTTAGTGCC
266815 GAAACGGTTATTCATCAACATATGAT
1 GAAACGGTTATTCATCAACATATGAT
* * * * * *
266841 GAATTCCGTGAATT-GT-ACACTTAGTGTT
1 GAA-ACGGT-TATTCATCA-ACATA-TGAT
266869 GAAACGGTTATTCATCAACATATGAT
1 GAAACGGTTATTCATCAACATATGAT
266895 GAA
1 GAA
266898 TTTCGTGATT
Statistics
Matches: 39, Mismatches: 12, Indels: 12
0.62 0.19 0.19
Matches are distributed among these distances:
26 13 0.33
27 16 0.41
28 10 0.26
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (26 bp):
GAAACGGTTATTCATCAACATATGAT
Found at i:267029 original size:162 final size:162
Alignment explanation
Indices: 266744--267170 Score: 615
Period size: 162 Copynumber: 2.6 Consensus size: 162
266734 AATCCTATGG
* * * * * * *
266744 TTTGTACACATAGTTCCTAAATGGTTATTCATCAACATATGATGAATTTCGT-ACTTTTCACATT
1 TTTGCACACTTAGTGCCAAAATGGTTATTCATCAACATATGATGAATTCCGTGA-TTTGCACACT
*
266808 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAATTGTACACTTAGTGTTGAAA
65 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAATTGTACACTTAGTGTTGAAA
** *
266873 CGGTTATTCATCAACATATGATGAATTTCGTGA
130 CAATTATTCATCAACATATGATGAATTTCATGA
* * *
266906 TTTGCACACTTAGTGTCAAAATGGTTATTCATCACCATATGATGAATTCCATGATTTGCACACTT
1 TTTGCACACTTAGTGCCAAAATGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTT
*
266971 AGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGATTTG-ACCACTTAGTGTTGAAA
66 AGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAATTGTA-CACTTAGTGTTGAAA
*
267035 CAATTATTCATCAATATATGATGAATTTCATGA
130 CAATTATTCATCAACATATGATGAATTTCATGA
*** * *
267068 TTTGCACACTTAGTGCCAAAACAATTATTCATCAACATATGATGAATTCTGTGATTTGCAAACTT
1 TTTGCACACTTAGTGCCAAAATGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTT
* *
267133 AGTGCCGGAACAATTATTCATCAACATATGATGAATTC
66 AGTGCCGAAACGATTATTCATCAACATATGATGAATTC
267171 TGTACTTTGC
Statistics
Matches: 237, Mismatches: 26, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
161 1 0.00
162 235 0.99
163 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (162 bp):
TTTGCACACTTAGTGCCAAAATGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTT
AGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAATTGTACACTTAGTGTTGAAAC
AATTATTCATCAACATATGATGAATTTCATGA
Found at i:267170 original size:54 final size:54
Alignment explanation
Indices: 266700--267192 Score: 494
Period size: 54 Copynumber: 9.1 Consensus size: 54
266690 AATGCACCCG
* * * * * * * * * * *
266700 TAGTGCCCATACGATCATTCATAAACATTTTATGAATCCTATGGTTTGTACACA
1 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTGATTTGCACACT
* * * * * *
266754 TAGTTCCTAAATGGTTATTCATCAACATATGATGAATT-TCGT-ACTTTTCACATT
1 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCT-GTGA-TTTGCACACT
* * * *
266808 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAATTGTACACT
1 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTGATTTGCACACT
** *
266862 TAGTGTTGAAACGGTTATTCATCAACATATGATGAATT-TCGTGATTTGCACACT
1 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCT-GTGATTTGCACACT
* * * * * **
266916 TAGTGTCAAAATGGTTATTCATCACCATATGATGAATTCCATGATTTGCACACT
1 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTGATTTGCACACT
*
266970 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGATTTG-ACCACT
1 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTGATTTGCA-CACT
** * * *
267024 TAGTGTTGAAACAATTATTCATCAATATATGATGAATT-TCATGATTTGCACACT
1 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCT-GTGATTTGCACACT
* * *
267078 TAGTGCCAAAACAATTATTCATCAACATATGATGAATTCTGTGATTTGCAAACT
1 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTGATTTGCACACT
* * *
267132 TAGTGCCGGAACAATTATTCATCAACATATGATGAATTCTGT-ACTTTGCACATT
1 TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTGA-TTTGCACACT
*
267186 TAATGCC
1 TAGTGCC
267193 TATTTGGTAA
Statistics
Matches: 370, Mismatches: 58, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
53 3 0.01
54 364 0.98
55 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (54 bp):
TAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTGATTTGCACACT
Found at i:273797 original size:54 final size:54
Alignment explanation
Indices: 273739--274215 Score: 544
Period size: 54 Copynumber: 8.9 Consensus size: 54
273729 TCATACGATC
* * * * * * *
273739 ATTCATAAACATATTATG-ATTCTCATGGTTTGCACACATAGTTCCTAAACAGTT
1 ATTCATCAACATATGATGAATTCTCGTGATTTGCACACTTAGTGCCGAAAC-GTT
* * * *
273793 ATTCATCAACATATGATGAATTC-CGT-ACTTTTCATATTTAGTGCCAAAACGGTT
1 ATTCATCAACATATGATGAATTCTCGTGA-TTTGCACACTTAGTGCCGAAAC-GTT
* * *
273847 ATTCATCAACATATGATGAATTCT-GTGAATTGCACACTTAGTTCCAAAACGATT
1 ATTCATCAACATATGATGAATTCTCGTGATTTGCACACTTAGTGCCGAAACG-TT
* *
273901 ATTCATCAACATATGATGAATT-TCGTGATTTGCACACTTATTGCCGAAATGGTT
1 ATTCATCAACATATGATGAATTCTCGTGATTTGCACACTTAGTGCCGAAA-CGTT
273955 ATTCATCAACATATGATGAATTC-CGTGATTTGCACACTTAGTGCCGAAACGATT
1 ATTCATCAACATATGATGAATTCTCGTGATTTGCACACTTAGTGCCGAAACG-TT
* *
274009 ATTCATCAACATATGATGAATT-TCGTCATTTGCACACTTAGTGCCGAAACGACT
1 ATTCATCAACATATGATGAATTCTCGTGATTTGCACACTTAGTGCCGAAACG-TT
* *
274063 ATTCATCAACATATGATGTATTCT-ATGATTTGCACACTTAGTGCCGAAACGGTT
1 ATTCATCAACATATGATGAATTCTCGTGATTTGCACACTTAGTGCCGAAAC-GTT
* * * * *
274117 ATTCATCAATATATGATGAATTAT-GTGATTTGCACACTTAGTGTCAAAATGATT
1 ATTCATCAACATATGATGAATTCTCGTGATTTGCACACTTAGTGCCGAAACG-TT
* *
274171 ATTCATCAACATATGATGAATTC-CAT-ACTTTGCACATTTAGTGCC
1 ATTCATCAACATATGATGAATTCTCGTGA-TTTGCACACTTAGTGCC
274216 TATTTGGTAA
Statistics
Matches: 367, Mismatches: 41, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
53 5 0.01
54 354 0.96
55 8 0.02
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTCTCGTGATTTGCACACTTAGTGCCGAAACGTT
Found at i:274205 original size:162 final size:162
Alignment explanation
Indices: 273739--274215 Score: 622
Period size: 162 Copynumber: 2.9 Consensus size: 162
273729 TCATACGATC
* * * * * * *
273739 ATTCATAAACATATTATGATTCTCATGGTTTGCACACATAGTTCCTAAACAGTTATTCATCAACA
1 ATTCATCAACATATGATGATTCTCATGATTTGCACACTTAGTGCCGAAACGGTTATTCATCAACA
* * * *
273804 TATGATGAATTCCGT-ACTTTTCATATTTAGTGCCAAAACGGTTATTCATCAACATATGATGAAT
66 TATGATGAATTCCGTGA-TTTGCACACTTAGTGCCAAAACGATTATTCATCAACATATGATGAAT
* * * *
273868 TCTGTGA-ATTGCACACTTAGTTCCAAAACGATT
130 TCCGT-ACTTTGCACACTTAGTGCCAAAACGACT
* * *
273901 ATTCATCAACATATGATGAATT-TCGTGATTTGCACACTTATTGCCGAAATGGTTATTCATCAAC
1 ATTCATCAACATATGATG-ATTCTCATGATTTGCACACTTAGTGCCGAAACGGTTATTCATCAAC
*
273965 ATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAAT
65 ATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGATTATTCATCAACATATGATGAAT
* *
274030 TTCGT-CATTTGCACACTTAGTGCCGAAACGACT
130 TCCGTAC-TTTGCACACTTAGTGCCAAAACGACT
*
274063 ATTCATCAACATATGATGTATTCT-ATGATTTGCACACTTAGTGCCGAAACGGTTATTCATCAAT
1 ATTCATCAACATATGATG-ATTCTCATGATTTGCACACTTAGTGCCGAAACGGTTATTCATCAAC
** * *
274127 ATATGATGAATTATGTGATTTGCACACTTAGTGTCAAAATGATTATTCATCAACATATGATGAAT
65 ATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGATTATTCATCAACATATGATGAAT
* *
274192 TCCATACTTTGCACATTTAGTGCC
130 TCCGTACTTTGCACACTTAGTGCC
274216 TATTTGGTAA
Statistics
Matches: 275, Mismatches: 34, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
162 269 0.98
163 6 0.02
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (162 bp):
ATTCATCAACATATGATGATTCTCATGATTTGCACACTTAGTGCCGAAACGGTTATTCATCAACA
TATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGATTATTCATCAACATATGATGAATT
CCGTACTTTGCACACTTAGTGCCAAAACGACT
Found at i:274289 original size:15 final size:15
Alignment explanation
Indices: 274269--274297 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
274259 TGACTAGTAT
274269 AACATATAGTTACAC
1 AACATATAGTTACAC
274284 AACATATAGTTACA
1 AACATATAGTTACA
274298 TAATTAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (15 bp):
AACATATAGTTACAC
Found at i:274694 original size:21 final size:21
Alignment explanation
Indices: 274647--274697 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
274637 TGTGATCAAT
*
274647 GGTATCGATACCATCCTCATA
1 GGTATCGATACCATCCTAATA
*
274668 -GTATCGATACCA-CTTGAATA
1 GGTATCGATACCATCCT-AATA
274688 GGTATCGATA
1 GGTATCGATA
274698 TTACTCAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 15 0.58
21 9 0.35
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (21 bp):
GGTATCGATACCATCCTAATA
Found at i:278511 original size:15 final size:16
Alignment explanation
Indices: 278485--278514 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
278475 TTTAAAAATG
278485 GTTTATAAAATTCAAT
1 GTTTATAAAATTCAAT
278501 GTTTA-AAAATTCAA
1 GTTTATAAAATTCAA
278515 ATTGAGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
GTTTATAAAATTCAAT
Found at i:283244 original size:23 final size:23
Alignment explanation
Indices: 283192--283245 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
283182 GACTGCGTAG
283192 AATTTGTCTCGAATGACCACATA
1 AATTTGTCTCGAATGACCACATA
* *
283215 AAATTGTCTCGAATGACCAGATA
1 AATTTGTCTCGAATGACCACATA
*
283238 GATTTGTC
1 AATTTGTC
283246 CCAAAGGACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (23 bp):
AATTTGTCTCGAATGACCACATA
Found at i:283412 original size:15 final size:15
Alignment explanation
Indices: 283394--283466 Score: 65
Period size: 16 Copynumber: 4.7 Consensus size: 15
283384 CACATAGGTT
* *
283394 ATTTTCACGTATAAC
1 ATTTTCACATAGAAC
* *
283409 ATTTTTCACTTAGCAC
1 A-TTTTCACATAGAAC
283425 ATTTTCACATAGAAC
1 ATTTTCACATAGAAC
* *
283440 ATATTCACATATAAAC
1 ATTTTCACATA-GAAC
*
283456 ATTTTAACATA
1 ATTTTCACATA
283467 CCAATAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
15 23 0.49
16 24 0.51
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (15 bp):
ATTTTCACATAGAAC
Found at i:285598 original size:2 final size:2
Alignment explanation
Indices: 285593--285651 Score: 56
Period size: 2 Copynumber: 31.5 Consensus size: 2
285583 ATTAAAAAAG
* *
285593 TA TA TA TA TA CA TA TA TGA TA TA TA -A TA -A TA TT TA T- TA T-
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
285632 TA TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
285652 GTGTGTTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
1 5 0.11
2 40 0.85
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:285650 original size:15 final size:15
Alignment explanation
Indices: 285593--285650 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
285583 ATTAAAAAAG
285593 TATATATATACATATA
1 TATATATATA-ATATA
*
285609 TGATATATAATAATATT
1 T-ATATAT-ATAATATA
285626 TAT-TATTATAATATA
1 TATATA-TATAATATA
285641 TATATATATA
1 TATATATATA
285651 TGTGTGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 16 0.44
16 6 0.17
17 11 0.31
18 3 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
TATATATATAATATA
Found at i:285730 original size:28 final size:26
Alignment explanation
Indices: 285688--285745 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
285678 TATATTAAAA
285688 AATATATTACTTTTTAAAAAAACTATAT
1 AATATATTACTTTTT--AAAAACTATAT
*
285716 AATATA-TACTATTTTTAAAACTATAT
1 AATATATTACT-TTTTAAAAACTATAT
285742 AATA
1 AATA
285746 CACTATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 14 0.50
27 4 0.14
28 10 0.36
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (26 bp):
AATATATTACTTTTTAAAAACTATAT
Found at i:285752 original size:29 final size:26
Alignment explanation
Indices: 285706--285770 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
285696 ACTTTTTAAA
285706 AAAACTATATAATATATACTATTTTT-
1 AAAACTATATAATATATA-TATTTTTC
285732 AAAACTATATAATACACTATATATTTTTC
1 AAAACTATATAAT--A-TATATATTTTTC
*
285761 AAAACCATAT
1 AAAACTATAT
285771 TTTCAAAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 13 0.38
28 8 0.24
29 13 0.38
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAACTATATAATATATATATTTTTC
Found at i:285772 original size:15 final size:15
Alignment explanation
Indices: 285752--285784 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
285742 AATACACTAT
285752 ATATTTTTCAAAACC
1 ATATTTTTCAAAACC
*
285767 ATA-TTTTCAAAACT
1 ATATTTTTCAAAACC
285781 ATAT
1 ATAT
285785 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.81
15 3 0.19
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATTTTTCAAAACC
Found at i:285802 original size:27 final size:26
Alignment explanation
Indices: 285770--285863 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 26
285760 CAAAACCATA
285770 TTTTCAAAACTATATATATATA-TAT
1 TTTTCAAAACTATATATATATAGTAT
285795 TAGTTTCAAAACTATATA-ATATAGTAT
1 T--TTTCAAAACTATATATATATAGTAT
285822 TTTTCAAAAACTA-ATATACTAT--T-T
1 TTTTC-AAAACTATATATA-TATAGTAT
*
285846 TTTT-AAATCTATATATAT
1 TTTTCAAAACTATATATAT
285864 TATTTTATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 17
0.77 0.01 0.22
Matches are distributed among these distances:
22 7 0.11
23 5 0.08
24 5 0.08
25 9 0.15
26 13 0.21
27 22 0.36
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTTCAAAACTATATATATATAGTAT
Found at i:285806 original size:41 final size:42
Alignment explanation
Indices: 285725--285811 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 42
285715 TAATATATAC
*
285725 TATTTTTAAAACTATATAATACACTATATATTTTTCAAAACCA
1 TATTTTCAAAACTATATAATA-ACTATATATTTTTCAAAACCA
*
285768 TATTTTCAAAACTATAT-AT-A-TATATATTAGTTTCAAAACTA
1 TATTTTCAAAACTATATAATAACTATATATT--TTTCAAAACCA
285809 TAT
1 TAT
285812 AATATAGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
39 8 0.20
40 1 0.03
41 13 0.32
42 2 0.05
43 16 0.40
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.44
Consensus pattern (42 bp):
TATTTTCAAAACTATATAATAACTATATATTTTTCAAAACCA
Found at i:285867 original size:23 final size:22
Alignment explanation
Indices: 285811--285874 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
285801 CAAAACTATA
* **
285811 TAATATAGTATTTTTCAAAAAC
1 TAATATACTATTTTTTTAAAAC
*
285833 TAATATACTATTTTTTTAAATC
1 TAATATACTATTTTTTTAAAAC
*
285855 TATATATATTATTTTATTTA
1 TA-ATATACTATTTT-TTTA
285875 TACTATACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 20 0.57
23 11 0.31
24 4 0.11
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATATACTATTTTTTTAAAAC
Found at i:285880 original size:23 final size:22
Alignment explanation
Indices: 285829--285881 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
285819 TATTTTTCAA
285829 AAACTA-ATATACTATTTTTTT
1 AAACTATATATACTATTTTTTT
*
285850 AAATCTATATATATTATTTTATTT
1 AAA-CTATATATACTATTTT-TTT
*
285874 ATACTATA
1 AAACTATA
285882 CTTATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.11
22 3 0.11
23 16 0.59
24 5 0.19
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.53
Consensus pattern (22 bp):
AAACTATATATACTATTTTTTT
Found at i:286384 original size:94 final size:94
Alignment explanation
Indices: 286272--286462 Score: 382
Period size: 94 Copynumber: 2.0 Consensus size: 94
286262 TTCAACCATT
286272 CTTCCTCGTTTTCAAGCTTGAATAAACATGCTAAAGTATACAACATAATGTTTTTATCATATCTA
1 CTTCCTCGTTTTCAAGCTTGAATAAACATGCTAAAGTATACAACATAATGTTTTTATCATATCTA
286337 ACATAGAAATCAATTTAAAACATCAACCC
66 ACATAGAAATCAATTTAAAACATCAACCC
286366 CTTCCTCGTTTTCAAGCTTGAATAAACATGCTAAAGTATACAACATAATGTTTTTATCATATCTA
1 CTTCCTCGTTTTCAAGCTTGAATAAACATGCTAAAGTATACAACATAATGTTTTTATCATATCTA
286431 ACATAGAAATCAATTTAAAACATCAACCC
66 ACATAGAAATCAATTTAAAACATCAACCC
286460 CTT
1 CTT
286463 TAACTTTTCA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (94 bp):
CTTCCTCGTTTTCAAGCTTGAATAAACATGCTAAAGTATACAACATAATGTTTTTATCATATCTA
ACATAGAAATCAATTTAAAACATCAACCC
Found at i:288750 original size:12 final size:12
Alignment explanation
Indices: 288733--288763 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
288723 TGTGACTATC
288733 TATATATATGTG
1 TATATATATGTG
288745 TATATATATGTG
1 TATATATATGTG
288757 TATATAT
1 TATATAT
288764 TTAATCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (12 bp):
TATATATATGTG
Found at i:290595 original size:13 final size:13
Alignment explanation
Indices: 290576--290606 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
290566 TATTACACAC
290576 ATATAGTTTAAAA
1 ATATAGTTTAAAA
*
290589 TTATAGTTTAAAA
1 ATATAGTTTAAAA
290602 ATATA
1 ATATA
290607 TGTATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (13 bp):
ATATAGTTTAAAA
Found at i:294307 original size:21 final size:20
Alignment explanation
Indices: 294247--294322 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 20
294237 AATATTAAGA
*
294247 GGTACCGATACCCCTATGAAT
1 GGTACCAATA-CCCTATGAAT
** *
294268 GAGTATTAATATACCTATGAAT
1 G-GTACCAATA-CCCTATGAAT
*
294290 GGATACCGATACCCTATGAAT
1 GG-TACCAATACCCTATGAAT
294311 GGTACCAATACC
1 GGTACCAATACC
294323 ATGCAAGGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
20 9 0.21
21 13 0.30
22 21 0.49
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (20 bp):
GGTACCAATACCCTATGAAT
Found at i:295933 original size:258 final size:247
Alignment explanation
Indices: 295483--295987 Score: 866
Period size: 258 Copynumber: 2.0 Consensus size: 247
295473 TATTAGGATA
*
295483 GAGCTATAATATTTCTTTATTTTGATTGGAGTAAGAATTGATTACCTCAAGGTATGAGGCACGAT
1 GAGCTATAATATTTCTTTATTTTGATAGGAGTAAGAATTGATTACCTCAAGGTATGAGGCACGAT
295548 AGGAAATAATTAAATATTATTAGGTTTTGTTCTAAAATTCATATAGTTTTGTTTTAAGGGATCTT
66 AGGAAATAATTAAATATTATTAGGTTTTGTTCTAAAATTCATATAGTTTTGTTTTAAGGGATCTT
*
295613 TAACTAAATTAAATTTGAACGTGTAAATTTTATTGCAAAGACAATTAATTAATCGGCTAGGTAAC
131 TAACTAAATTAAATTTGAACGTGTAAATTTTATTGCAAAGACAATTAATTAATCGACTAGGTAAC
295678 GATTTAGGGTGTTGTGGGGATGCTAATCCTTTCCCACACATAACCGACTCCC
196 GATTTAGGGTGTTGTGGGGATGCTAATCCTTTCCCACACATAACCGACTCCC
295730 GAGCTATAATATTTCTTTATTTTGATAGGAGTAAGAATTGATTACCTCAAGGTATGAGGGGTCAT
1 GAGCTATAATATTTCTTTATTTTGATAGGAGTAAGAATTGATTACCTCAAGGTATGA--GG-CA-
295795 TTCTTCTCGATAGGAAATAATTAAATATTATTAGGTTTTGTTCTAAAATTCATATAGTTTTGTTT
62 -------CGATAGGAAATAATTAAATATTATTAGGTTTTGTTCTAAAATTCATATAGTTTTGTTT
* *
295860 TAAGGGATCTTTAACTAAATTAAATTTTAACTTGTAAATTTTATTGCAAAGACAATTAATTAATC
120 TAAGGGATCTTTAACTAAATTAAATTTGAACGTGTAAATTTTATTGCAAAGACAATTAATTAATC
*
295925 GACTAGGTAACGATTTAGGGTGTTGTGGGGATGCTAATCCTTTCCCATACATAACCGACTCCC
185 GACTAGGTAACGATTTAGGGTGTTGTGGGGATGCTAATCCTTTCCCACACATAACCGACTCCC
295988 AAACTCATTT
Statistics
Matches: 242, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
247 56 0.23
249 2 0.01
250 2 0.01
258 182 0.75
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (247 bp):
GAGCTATAATATTTCTTTATTTTGATAGGAGTAAGAATTGATTACCTCAAGGTATGAGGCACGAT
AGGAAATAATTAAATATTATTAGGTTTTGTTCTAAAATTCATATAGTTTTGTTTTAAGGGATCTT
TAACTAAATTAAATTTGAACGTGTAAATTTTATTGCAAAGACAATTAATTAATCGACTAGGTAAC
GATTTAGGGTGTTGTGGGGATGCTAATCCTTTCCCACACATAACCGACTCCC
Found at i:307980 original size:135 final size:135
Alignment explanation
Indices: 307589--308187 Score: 828
Period size: 135 Copynumber: 4.4 Consensus size: 135
307579 GTTTGATCTT
*
307589 CGAAGCAAATCACATTCGATTCAATCTTCCCTAAAGAGCAGAGAAGTGGATCAAAGTTTCCTCGA
1 CGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTCCTCGA
* * * * * *
307654 GTCTGACCTCCCCTAAAGAGTAGTGGAGTAAATTCTTTATTCTTTCAGATTTGGTCTTCTTGAAG
66 GTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTCTATTCTTTCAGATTTGATCTTCCTGAAG
307719 AGCAG
131 AGCAG
* * * *
307724 CAAAGCAAATCACATTTGACTCAATATT-CCTGAAGAGCAGAGAAGTGGATCAAAGTTTCCTCGA
1 CGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTCCTCGA
* * *
307788 GTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTTCTTCTTTCAGATTTAATCTTCCTGAAG
66 GTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTCTATTCTTTCAGATTTGATCTTCCTGAAG
307853 AGCAG
131 AGCAG
* * * *
307858 CGAAGAAAATCACATTCGATTCAATATTCCCTAAAGAGCAGAGAAGTGGATCAAAGTTTTTCTCG
1 CGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAG-TTTCCTCG
* * * *
307923 ATTCTGACCTCCCCTAAAGAGTAGCGGAGCATATTCTCT-TTCTTTCATATTTGATCTTCATGAA
65 AGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTCTATTCTTTCAGATTTGATCTTCCTGAA
307987 GAGCAG
130 GAGCAG
* * * * *
307993 CAAAGTAAATCACATTCGATTCAATCTTCCCTGAAGATCAGAGAAGTAGATCAAAGCTTTTCTCG
1 CGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAG-TTTCCTCG
* *
308058 AGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTTTCT-TTCTTTCAGATTTGATCCTCCTGAA
65 AGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTCTATTCTTTCAGATTTGATCTTCCTGAA
308122 GAGCAG
130 GAGCAG
* * * ** *
308128 TGAATCAAATCAAATTCGATTCAATCTTTTCTGAAGAGCA-ACGAAGTGAATCAAAGTTTC
1 CGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGA-GAAGTGGATCAAAGTTTC
308188 ATTGAGGTTG
Statistics
Matches: 413, Mismatches: 48, Indels: 7
0.88 0.10 0.01
Matches are distributed among these distances:
134 126 0.31
135 244 0.59
136 43 0.10
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (135 bp):
CGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTCCTCGA
GTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTCTATTCTTTCAGATTTGATCTTCCTGAAG
AGCAG
Found at i:324056 original size:15 final size:16
Alignment explanation
Indices: 324030--324059 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
324020 CTAAAAAATG
324030 GTTTATAAAATTCAAT
1 GTTTATAAAATTCAAT
324046 GTTTA-AAAATTCAA
1 GTTTATAAAATTCAA
324060 ATTGAGCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
GTTTATAAAATTCAAT
Found at i:324661 original size:30 final size:30
Alignment explanation
Indices: 324627--324752 Score: 139
Period size: 30 Copynumber: 4.2 Consensus size: 30
324617 TCAGCCATTC
*
324627 AAATTTTTATTTTTTCTATTTTAGTCCTTT
1 AAATTTCTATTTTTTCTATTTTAGTCCTTT
* * *
324657 AAATTTCTA-TTTTTCTATTTTACTCCATC
1 AAATTTCTATTTTTTCTATTTTAGTCCTTT
*
324686 AAATTTCTATTTTTTACTATTTTAGTTCTTT
1 AAATTTCTATTTTTT-CTATTTTAGTCCTTT
* * * *
324717 AAGTTTCTATGATTTT-TATTTTGGTCCCTT
1 AAATTTCTAT-TTTTTCTATTTTAGTCCTTT
324747 AAATTT
1 AAATTT
324753 TCGAATATGT
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
29 26 0.33
30 29 0.37
31 20 0.25
32 4 0.05
ACGTcount: A:0.22, C:0.13, G:0.05, T:0.60
Consensus pattern (30 bp):
AAATTTCTATTTTTTCTATTTTAGTCCTTT
Found at i:326631 original size:18 final size:18
Alignment explanation
Indices: 326604--326641 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
326594 ATTGATTATC
*
326604 TTGTTTGTACTAACTCAT
1 TTGTTCGTACTAACTCAT
326622 TTGTTCGTACTAACTCAT
1 TTGTTCGTACTAACTCAT
326640 TT
1 TT
326642 CTTTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50
Consensus pattern (18 bp):
TTGTTCGTACTAACTCAT
Found at i:328486 original size:17 final size:14
Alignment explanation
Indices: 328478--328588 Score: 89
Period size: 14 Copynumber: 8.4 Consensus size: 14
328468 AAGCAGAAAT
328478 AAAAACAAAGAGAA
1 AAAAACAAAGAGAA
*
328492 AAAAACAAAGAAAA
1 AAAAACAAAGAGAA
328506 AACAAAGTCCAAAGAG-A
1 AA-AAA---CAAAGAGAA
*
328523 AGAAA-AAA-AG-A
1 AAAAACAAAGAGAA
328534 AAAAACAAAGAG--
1 AAAAACAAAGAGAA
328546 -AAAACAAAGAG--
1 AAAAACAAAGAGAA
328557 AAAAACAAAGAG-A
1 AAAAACAAAGAGAA
*
328570 AAAAACAAAAAGAA
1 AAAAACAAAGAGAA
328584 AAAAA
1 AAAAA
328589 ATACAAGAAG
Statistics
Matches: 83, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
11 18 0.22
12 17 0.20
13 13 0.16
14 21 0.25
15 3 0.04
16 3 0.04
17 2 0.02
18 6 0.07
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.01
Consensus pattern (14 bp):
AAAAACAAAGAGAA
Found at i:328493 original size:12 final size:12
Alignment explanation
Indices: 328478--328586 Score: 88
Period size: 11 Copynumber: 9.4 Consensus size: 12
328468 AAGCAGAAAT
328478 AAAAACAAAGAG
1 AAAAACAAAGAG
328490 AAAAAAACAAAGA-
1 --AAAAACAAAGAG
*
328503 AAAAACAAAG-T
1 AAAAACAAAGAG
** * *
328514 CCAAAGAGA-AG
1 AAAAACAAAGAG
328525 -AAAA-AAAGA-
1 AAAAACAAAGAG
328534 AAAAACAAAGAG
1 AAAAACAAAGAG
328546 -AAAACAAAGAG
1 AAAAACAAAGAG
328557 AAAAACAAAGAG
1 AAAAACAAAGAG
*
328569 AAAAAACAAAAAG
1 -AAAAACAAAGAG
328582 AAAAA
1 AAAAA
328587 AAATACAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
9 2 0.03
10 8 0.10
11 31 0.39
12 16 0.20
13 11 0.14
14 11 0.14
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.01
Consensus pattern (12 bp):
AAAAACAAAGAG
Found at i:328536 original size:31 final size:32
Alignment explanation
Indices: 328483--328543 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
328473 GAAATAAAAA
328483 CAAAGAGAAAAAAACAAAGAAAAAACAAAGTC
1 CAAAGAGAAAAAAACAAAGAAAAAACAAAGTC
*
328515 CAAAGAGAAGAAAA-AAAGAAAAAACAAAG
1 CAAAGAGAAAAAAACAAAGAAAAAACAAAG
328544 AGAAAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.74, C:0.10, G:0.15, T:0.02
Consensus pattern (32 bp):
CAAAGAGAAAAAAACAAAGAAAAAACAAAGTC
Found at i:328573 original size:42 final size:42
Alignment explanation
Indices: 328491--328580 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
328481 AACAAAGAGA
* * *
328491 AAAAAACAAAGAAAAAACAAAGTCCAAAGAGAAGAAAAAAAG
1 AAAAAACAAAGAAAAAACAAAGTACAAAAAAAAGAAAAAAAG
* * *
328533 AAAAAACAAAGAGAAAACAAAG-AGAAAAACAAAGAGAAAAAAC
1 AAAAAACAAAGAAAAAACAAAGTACAAAAA-AAAGA-AAAAAAG
328576 AAAAA
1 AAAAA
328581 GAAAAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 4 0.10
42 25 0.62
43 11 0.28
ACGTcount: A:0.77, C:0.09, G:0.13, T:0.01
Consensus pattern (42 bp):
AAAAAACAAAGAAAAAACAAAGTACAAAAAAAAGAAAAAAAG
Found at i:328597 original size:14 final size:13
Alignment explanation
Indices: 328478--328587 Score: 77
Period size: 13 Copynumber: 8.4 Consensus size: 13
328468 AAGCAGAAAT
*
328478 AAAAACAAAGAGA
1 AAAAACAAAAAGA
*
328491 AAAAA-ACAAAGA
1 AAAAACAAAAAGA
328503 AAAAACAAAGTCCAAAGA
1 AAAAAC-AA----AAAGA
*
328521 GAAGAA-AAAAAGA
1 -AAAAACAAAAAGA
328534 AAAAAC--AAAGA
1 AAAAACAAAAAGA
* *
328545 GAAAACAAAGAG-
1 AAAAACAAAAAGA
*
328557 AAAAACAAAGAGA
1 AAAAACAAAAAGA
328570 AAAAACAAAAAGA
1 AAAAACAAAAAGA
328583 AAAAA
1 AAAAA
328588 AATACAAGAA
Statistics
Matches: 77, Mismatches: 9, Indels: 22
0.71 0.08 0.20
Matches are distributed among these distances:
11 10 0.13
12 25 0.32
13 30 0.39
14 1 0.01
17 2 0.03
18 5 0.06
19 4 0.05
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.01
Consensus pattern (13 bp):
AAAAACAAAAAGA
Found at i:329855 original size:37 final size:34
Alignment explanation
Indices: 329800--330029 Score: 143
Period size: 30 Copynumber: 7.0 Consensus size: 34
329790 GAAAAAAACT
* *
329800 TTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTC
1 TTGAGACTGTTTCTCTTGAAACAAAG-TTTG--TCTC
*
329837 TTGAGACTGTTTTTCTTGAAACAAAG---GTCT-
1 TTGAGACTGTTTCTCTTGAAACAAAGTTTGTCTC
*
329867 TTGAGTCTGTTTCTCTTGAAACAAAGTTCTGTCTC
1 TTGAGACTGTTTCTCTTGAAACAAAGTT-TGTCTC
* * *
329902 TTGAGACAGTTTTTCTTGAAA-AAA-----TC-A
1 TTGAGACTGTTTCTCTTGAAACAAAGTTTGTCTC
329929 TTGAGTA-TGTTTCTCTTGAAAC-AAGTTTTGTCTCCC
1 TTGAG-ACTGTTTCTCTTGAAACAAAG-TTTGTCT--C
** * *
329965 TTGAGACAATTTATCTTGAAACAAA---AGTCT-
1 TTGAGACTGTTTCTCTTGAAACAAAGTTTGTCTC
* *
329995 TTGAGTCTATTTCTCTTGAAACAAAGTTTTGTCTC
1 TTGAGACTGTTTCTCTTGAAACAAAG-TTTGTCTC
330030 ACTTGACATA
Statistics
Matches: 150, Mismatches: 20, Indels: 48
0.69 0.09 0.22
Matches are distributed among these distances:
27 19 0.13
28 3 0.02
30 46 0.31
31 3 0.02
33 7 0.05
34 11 0.07
35 19 0.13
36 17 0.11
37 25 0.17
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (34 bp):
TTGAGACTGTTTCTCTTGAAACAAAGTTTGTCTC
Found at i:329995 original size:128 final size:128
Alignment explanation
Indices: 329723--330118 Score: 483
Period size: 130 Copynumber: 3.1 Consensus size: 128
329713 TGTCTTTGAA
* * * *
329723 GAAA-AAAA-TCTTTGAGTATGTTTCTCTGGAAACAAAGTTTTATCTCTCTTGAGACAATTTCTT
1 GAAACAAAAGTCTTTGAGTCTGTTTCTCTTGAAACAAAG--TTATGTCTCTTGAGACAGTTT-TT
* * *
329786 -TTGAGAAAAAAACTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACTGTTTT
63 CTT--GAAAAAAACTTTGAGTATGTTTCCCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAGTTTA
329850 TCTT
125 TCTT
* *
329854 GAAACAAAGGTCTTTGAGTCTGTTTCTCTTGAAACAAAGTTCTGTCTCTTGAGACAGTTTTTCTT
1 GAAACAAAAGTCTTTGAGTCTGTTTCTCTTGAAACAAAGTTATGTCTCTTGAGACAGTTTTTCTT
* * * * *
329919 GAAAAAATCATTGAGTATGTTTCTCTTGAAACAAGTTTTGTCTCCCTTGAGACAATTTATCTT
66 GAAAAAAACTTTGAGTATGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTATCTT
* * * *
329982 GAAACAAAAGTCTTTGAGTCTATTTCTCTTGAAACAAAGTTTTGTCTCACTTGACATAGTTTTTC
1 GAAACAAAAGTCTTTGAGTCTGTTTCTCTTGAAACAAAGTTATGTCT--CTTGAGACAGTTTTTC
* * * * **
330047 TTGAAAAAACCTTTGAGTATATTTCCCTTGAAATAAGTTTTATCTCTCTTGAGACAGTTTCCCTT
64 TTGAAAAAAACTTTGAGTATGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTATCTT
330112 GAAACAA
1 GAAACAA
330119 GTTTTGTCTC
Statistics
Matches: 231, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
128 71 0.31
129 28 0.12
130 78 0.34
131 24 0.10
132 3 0.01
133 27 0.12
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (128 bp):
GAAACAAAAGTCTTTGAGTCTGTTTCTCTTGAAACAAAGTTATGTCTCTTGAGACAGTTTTTCTT
GAAAAAAACTTTGAGTATGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTATCTT
Found at i:330108 original size:36 final size:36
Alignment explanation
Indices: 330068--330153 Score: 145
Period size: 36 Copynumber: 2.4 Consensus size: 36
330058 TTTGAGTATA
*
330068 TTTCCCTTGAAATAAGTTTTATCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAGTTTTATCTCTCTTGAGACAG
* *
330104 TTTCCCTTGAAACAAGTTTTGTCTCTCTTTAGACAG
1 TTTCCCTTGAAACAAGTTTTATCTCTCTTGAGACAG
330140 TTTCCCTTGAAACA
1 TTTCCCTTGAAACA
330154 CAATCTTTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAGTTTTATCTCTCTTGAGACAG
Found at i:330484 original size:129 final size:130
Alignment explanation
Indices: 330241--330715 Score: 459
Period size: 129 Copynumber: 3.6 Consensus size: 130
330231 TAGCATGTCG
** * * *
330241 TCCTCATCACGTAGGAACCGTGTCATTCCCTAACTAGACCTCCTCATCACGTAGGAGTCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA-TCCCCGACCAAACCTCCTCATCACGTAGGAGTTGTGTCA
* * *
330306 CCCCTAGATAACCAGTCATCCTCATCATGTAGGAACCATGTTATTATCCCTAAAAATGACATGAC
65 CCCCTAGATAACCAGTCATCCTCATCACGTAGGAACCAAGTTATCATCCCTAAAAATGACATGAC
330371 A
130 A
** * **
330372 TCCTCATCACGTAGGAATTGTGTCATCCCCGACCAAACCTCCTTATCATATAGGAGTTGTGTCAC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCGACCAAACCTCCTCATCACGTAGGAGTTGTGTCAC
* * * *
330437 CCC-AGATAACCAGTTATCTTCATCACGTAGGAACCAAGTTATCATCCCTAAAGATGACATGTCA
66 CCCTAGATAACCAGTCATCCTCATCACGTAGGAACCAAGTTATCATCCCTAAAAATGACATGACA
* * * * *
330501 TCCTTATCACGTAAGAACCGTGTCATCCACCGACCATACCTCCTCATCACGTATGA-TTCGTGTA
1 TCCTCATCACGTAGGAACCGTGTCATCC-CCGACCAAACCTCCTCATCACGTAGGAGTT-GTGTC
* * * * * ** ** * * *
330565 ACCCCTAGATAACCAGCCGTCCTTATTACATAGGAGTCGTGCTATCACCCTCCCTAAAGATGGCC
64 ACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACCAAGTTATCA---TCCCTAAAAAT-GAC
* **
330630 AAGATG
125 ATGACA
* *** * *
330636 TCCTCATCACGTAGGAACAGTGTCATCCCCCGACCAGTTCTCCTCATCAAGTAGGAGTCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCAT-CCCCGACCAAACCTCCTCATCACGTAGGAGTTGTGTCA
* *
330701 CCCTTAGATGACCAG
65 CCCCTAGATAACCAG
330716 AACTCTTCAT
Statistics
Matches: 279, Mismatches: 56, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
129 80 0.29
130 66 0.24
131 52 0.19
134 11 0.04
135 67 0.24
136 3 0.01
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (130 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCGACCAAACCTCCTCATCACGTAGGAGTTGTGTCAC
CCCTAGATAACCAGTCATCCTCATCACGTAGGAACCAAGTTATCATCCCTAAAAATGACATGACA
Found at i:332524 original size:29 final size:28
Alignment explanation
Indices: 332461--332558 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 28
332451 ACTGTTCATC
*
332461 TCTTCAAATTTCTATTTTTCTATTTTAG
1 TCTTTAAATTTCTATTTTTCTATTTTAG
*
332489 TCGTTTAAATTTCTATTTTTGCT-TTTTAAT
1 TC-TTTAAATTTCTATTTTT-CTATTTT-AG
* * *
332519 TCTTTAAGTTTCTGTTATTT-TATTTTGG
1 TCTTTAAATTTCTATT-TTTCTATTTTAG
*
332547 TCCCTTAAATTT
1 T-CTTTAAATTT
332559 TCGAATATGT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
28 4 0.07
29 44 0.79
30 8 0.14
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.61
Consensus pattern (28 bp):
TCTTTAAATTTCTATTTTTCTATTTTAG
Found at i:336710 original size:16 final size:18
Alignment explanation
Indices: 336670--336717 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
336660 TGTTTATGAG
336670 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
336688 GGAATTGAAATCTGT-AA
1 GGAATTGGAATCTGTGAA
336705 -GAATTGGAATCTG
1 GGAATTGGAATCTG
336718 AATCTGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 12 0.43
17 2 0.07
18 14 0.50
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:338624 original size:3 final size:3
Alignment explanation
Indices: 338616--338642 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
338606 CGATGAGTTT
338616 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
338643 GGTTAACGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:342704 original size:33 final size:33
Alignment explanation
Indices: 342636--342704 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 33
342626 GGTAATATAT
342636 TTTATTAAAATAAAAATATTATAAGGTATATTATTA
1 TTTATTAAAATAAAAATATTAT-A--TATATTATTA
*
342672 TTTATTAAAATAAGAATATTACT-TATATTATTA
1 TTTATTAAAATAAAAATATTA-TATATATTATTA
342705 AAATAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
33 10 0.32
36 20 0.65
37 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (33 bp):
TTTATTAAAATAAAAATATTATATATATTATTA
Found at i:342707 original size:26 final size:24
Alignment explanation
Indices: 342663--342710 Score: 78
Period size: 26 Copynumber: 1.9 Consensus size: 24
342653 ATTATAAGGT
342663 ATATTATTATTTATTAAAATAAGA
1 ATATTATTATTTATTAAAATAAGA
342687 ATATTACTTATATTATTAAAATAA
1 ATATTA-TTAT-TTATTAAAATAA
342711 AAAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 12 0.55
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATTATTATTTATTAAAATAAGA
Found at i:343861 original size:27 final size:28
Alignment explanation
Indices: 343791--343890 Score: 166
Period size: 28 Copynumber: 3.6 Consensus size: 28
343781 GAGATAGTTT
* *
343791 TCTCACGACCCTCGATTTTGATTTGCGA
1 TCTCACGACGCTCGATTTTGATTCGCGA
343819 TCTCACGACGCTCGATTTTGATTCGCGA
1 TCTCACGACGCTCGATTTTGATTCGCGA
*
343847 TCT-ACGACGCTCGATTCTGATTCGCGA
1 TCTCACGACGCTCGATTTTGATTCGCGA
343874 TCTCACGACGCTCGATT
1 TCTCACGACGCTCGATT
343891 CTAATTCGTA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
27 26 0.38
28 42 0.62
ACGTcount: A:0.18, C:0.30, G:0.20, T:0.32
Consensus pattern (28 bp):
TCTCACGACGCTCGATTTTGATTCGCGA
Found at i:343898 original size:55 final size:55
Alignment explanation
Indices: 343795--343898 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
343785 TAGTTTTCTC
* * * *
343795 ACGACCCTCGATTTTGATTTGCGATCTCACGACGCTCGATTTTGATTCGCGATCT
1 ACGACCCTCGATTCTGATTCGCGATCTCACGACGCTCGATTCTAATTCGCGATCT
*
343850 ACGACGCTCGATTCTGATTCGCGATCTCACGACGCTCGATTCTAATTCG
1 ACGACCCTCGATTCTGATTCGCGATCTCACGACGCTCGATTCTAATTCG
343899 TACTTTTCGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (55 bp):
ACGACCCTCGATTCTGATTCGCGATCTCACGACGCTCGATTCTAATTCGCGATCT
Found at i:345991 original size:15 final size:16
Alignment explanation
Indices: 345965--345994 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
345955 CTAAAAAATG
345965 GTTTATAAAATTCAAT
1 GTTTATAAAATTCAAT
345981 GTTTA-AAAATTCAA
1 GTTTATAAAATTCAA
345995 ATTGAGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
GTTTATAAAATTCAAT
Found at i:346160 original size:33 final size:33
Alignment explanation
Indices: 346118--346184 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
346108 AACAAATGCT
346118 AAATAAACACGTTTGTTAATAGGGATGGACATA
1 AAATAAACACGTTTGTTAATAGGGATGGACATA
346151 AAATAAACACGTTTGTTAATAGGGATGGACATA
1 AAATAAACACGTTTGTTAATAGGGATGGACATA
346184 A
1 A
346185 GATTTTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (33 bp):
AAATAAACACGTTTGTTAATAGGGATGGACATA
Found at i:352549 original size:21 final size:23
Alignment explanation
Indices: 352498--352549 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
352488 GATTCCCCTG
*
352498 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAACCGGTTCCCCTTCA
**
352521 AAGGGGGAACCGGTT-CCC-TCA
1 TGGGGGGAACCGGTTCCCCTTCA
352542 TGGGGGGA
1 TGGGGGGA
352550 TCGATTCCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.17, C:0.23, G:0.40, T:0.19
Consensus pattern (23 bp):
TGGGGGGAACCGGTTCCCCTTCA
Found at i:356418 original size:22 final size:21
Alignment explanation
Indices: 356376--356415 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
356366 GAGATTATTT
*
356376 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
356397 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
356416 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:361139 original size:31 final size:31
Alignment explanation
Indices: 361080--361139 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
361070 TATTTAATGG
* * *
361080 TAGGTGGATTGATTGATAAGATTTAAATAAT
1 TAGGTGGATTGATTGACAAAATTAAAATAAT
361111 TAGGT-GACTTGATTGACAAAATTAAAATA
1 TAGGTGGA-TTGATTGACAAAATTAAAATA
361140 TTTATGGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (31 bp):
TAGGTGGATTGATTGACAAAATTAAAATAAT
Found at i:361255 original size:11 final size:11
Alignment explanation
Indices: 361218--361265 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
361208 TTTTATAAAT
361218 ATTATATTT-TA
1 ATTA-ATTTATA
*
361229 ATTAAATTATA
1 ATTAATTTATA
* *
361240 TTTAATTTTTA
1 ATTAATTTATA
361251 ATTAATTTATA
1 ATTAATTTATA
361262 ATTA
1 ATTA
361266 TACTTTTAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
10 3 0.10
11 27 0.90
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTAATTTATA
Found at i:365297 original size:69 final size:68
Alignment explanation
Indices: 365156--365430 Score: 316
Period size: 69 Copynumber: 4.0 Consensus size: 68
365146 ATGTATTTAG
* * * *
365156 ATCCTTCTGGGCTCCCGTGCGAGTCACCTGAAACAATGTATGATTAGGTGCACCCGTACGAGTCA
1 ATCCTTC-GGGCTCCCATGCGAGTCACCCGAAATAA-GTATGATTAGGTGCTCCCGTACGAGTCA
365221 CTCTA
64 CTCTA
* * * * *
365226 ATCCTTCGAGGCTCCCATGCGAGCCACCTGAAATTAGTATGATTAAGTGCTCCCGTGCGAGTCAC
1 ATCCTTCG-GGCTCCCATGCGAGTCACCCGAAATAAGTATGATTAGGTGCTCCCGTACGAGTCAC
365291 TCTA
65 TCTA
*** * * * *
365295 ATCCTTCAGGGCTCATGTGCAAGTCACCCAAAATAAGTATGATTAGGTGCTCCTGTACAGGGTCA
1 ATCCTTC-GGGCTCCCATGCGAGTCACCCGAAATAAGTATGATTAGGTGCTCCCGTAC-GAGTCA
365360 CTCTA
64 CTCTA
** * * *
365365 ATCCTTCGGGCTCCCATATGAGTCACCCGAAAAAAGTATGATTAGGTGCTCTCGTGCGAGTCACT
1 ATCCTTCGGGCTCCCATGCGAGTCACCCGAAATAAGTATGATTAGGTGCTCCCGTACGAGTCACT
365430 C
66 C
365431 GAAATAAGTA
Statistics
Matches: 171, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
68 8 0.05
69 115 0.67
70 48 0.28
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (68 bp):
ATCCTTCGGGCTCCCATGCGAGTCACCCGAAATAAGTATGATTAGGTGCTCCCGTACGAGTCACT
CTA
Found at i:365421 original size:138 final size:139
Alignment explanation
Indices: 365156--365430 Score: 365
Period size: 138 Copynumber: 2.0 Consensus size: 139
365146 ATGTATTTAG
* * * **
365156 ATCCTTCTGGGCTCCCGTGCGAGTCACCTGAAACAATGTATGATTAGGTGCACCCGTACGAGTCA
1 ATCCTTCAGGGCTCACGTGCAAGTCACCCAAAACAATGTATGATTAGGTGCACCCGTACGAGTCA
* * **
365221 CTCTAATCCTTCGAGGCTCCCATGCGAGCCACCTGAAATTAGTATGATTAAGTGCTCCCGTGCGA
66 CTCTAATCCTTCGAGGCTCCCATACGAGCCACCCGAAAAAAGTATGATTAAGTGCTCCCGTGCGA
365286 GTCACTCTA
131 GTCACTCTA
* * * * *
365295 ATCCTTCAGGGCTCATGTGCAAGTCACCCAAAATAA-GTATGATTAGGTGCTCCTGTACAGGGTC
1 ATCCTTCAGGGCTCACGTGCAAGTCACCCAAAACAATGTATGATTAGGTGCACCCGTAC-GAGTC
* * * *
365359 ACTCTAATCCTTCG-GGCTCCCATATGAGTCACCCGAAAAAAGTATGATTAGGTGCTCTCGTGCG
65 ACTCTAATCCTTCGAGGCTCCCATACGAGCCACCCGAAAAAAGTATGATTAAGTGCTCCCGTGCG
365423 AGTCACTC
130 AGTCACTC
365431 GAAATAAGTA
Statistics
Matches: 117, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
138 70 0.60
139 47 0.40
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (139 bp):
ATCCTTCAGGGCTCACGTGCAAGTCACCCAAAACAATGTATGATTAGGTGCACCCGTACGAGTCA
CTCTAATCCTTCGAGGCTCCCATACGAGCCACCCGAAAAAAGTATGATTAAGTGCTCCCGTGCGA
GTCACTCTA
Found at i:365464 original size:38 final size:38
Alignment explanation
Indices: 365374--365468 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
365364 AATCCTTCGG
*
365374 GCTCCCATATGAGTCACCCGAAAAAAGTATGATTAGGT
1 GCTCCCATATGAGTCACTCGAAAAAAGTATGATTAGGT
* * ** *
365412 GCTCTCGTGCGAGTCACTCGAAATAAGTATGATTAGGT
1 GCTCCCATATGAGTCACTCGAAAAAAGTATGATTAGGT
365450 GCTCCCATATGAGTCACTC
1 GCTCCCATATGAGTCACTC
365469 TAATCCTTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.26
Consensus pattern (38 bp):
GCTCCCATATGAGTCACTCGAAAAAAGTATGATTAGGT
Found at i:365715 original size:51 final size:51
Alignment explanation
Indices: 365632--366275 Score: 767
Period size: 51 Copynumber: 12.7 Consensus size: 51
365622 ATATTTACAC
* ** * *
365632 CAGTGAAACTTAACATAGACTTACACTAGTTAAATTAACCCTTAATTCTAA
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
* *
365683 AAGTGAAACATTACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
***
365734 CAGTGAAACATAACATAGACTTACACCGACCAAATTAACCCTTAATTCCAG
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
**
365785 CAGTGAAACATAACATAGACTTACATTGGTTAAATTAA-CCTATAATTCCAG
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCT-TAATTCCAG
* * * * * *
365836 CAATGAAACATAACATAGACTTATACTGGTGAAA-TAACACTTAATTCCAA
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
* * * * * *
365886 CAGTGAAACATAACATAGACTTATATCGATCAAATTAGCCCTTAAATCCAG
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
* * * *
365937 AAGTGAAACATAACATATACTTACA-CAGTCAAATTAACCCTTAATTCCAG
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
* * * *
365987 CAGTGGAACATAACATATACTTACACCAGTCAAATTAACCCTTAATTCCAG
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
*
366038 CAGTGAAACATAACATATACTTACACCGGTTAAATTAACCCTTAATTCCAG
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
** * * **** *
366089 TGGTAAAACATAACATAAACTTACATTAATTAAATTAACCCTTAATTCGAG
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
* * * * *
366140 TAGTGAAACATAACATAGACTTACATCGGTGAAA-TAACACTTAATTCCAA
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
* * * *
366190 CAGTGAAACATATCATAGACTTACACCAGTTAAATTAACCTTTACTTCCA-
1 CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
*
366240 CTAGTGAAACATAACATAGACTTACACCGGTGAAAT
1 C-AGTGAAACATAACATAGACTTACACCGGTTAAAT
366276 AACAAATTAT
Statistics
Matches: 513, Mismatches: 74, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
50 130 0.25
51 383 0.75
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (51 bp):
CAGTGAAACATAACATAGACTTACACCGGTTAAATTAACCCTTAATTCCAG
Found at i:365946 original size:152 final size:153
Alignment explanation
Indices: 365633--366265 Score: 801
Period size: 152 Copynumber: 4.2 Consensus size: 153
365623 TATTTACACC
* * * * *
365633 AGTGAAACTTAACATAGACTTACACTAGTTAAATTAACCCTTAATTCTA-AAAGTGAAACATTAC
1 AGTGAAACATAACATAGACTTACATTAGTTAAATTAACCCTTAATTCCAGCAA-TGAAACATAAC
* * *
365697 ATAGACTTACACCGGTTAAATTAACCCTTAATTCCAGCAGTGAAACATAACATAGACTTACACCG
65 ATAGACTTACACCGGTGAAATTAACACTTAATTCCAACAGTGAAACATAACATAGACTTACACCG
* *
365762 ACCAAATTAACCCTTAATTCCAGC
130 ATCAAATTAACCCTTAATTCCAGT
*
365786 AGTGAAACATAACATAGACTTACATTGGTTAAATTAA-CCTATAATTCCAGCAATGAAACATAAC
1 AGTGAAACATAACATAGACTTACATTAGTTAAATTAACCCT-TAATTCCAGCAATGAAACATAAC
* * * *
365850 ATAGACTTATACTGGTGAAA-TAACACTTAATTCCAACAGTGAAACATAACATAGACTTATATCG
65 ATAGACTTACACCGGTGAAATTAACACTTAATTCCAACAGTGAAACATAACATAGACTTACACCG
* * *
365914 ATCAAATTAGCCCTTAAATCCAGA
130 ATCAAATTAACCCTTAATTCCAGT
* * * * *
365938 AGTGAAACATAACATATACTTACA-CAGTCAAATTAACCCTTAATTCCAGCAGTGGAACATAACA
1 AGTGAAACATAACATAGACTTACATTAGTTAAATTAACCCTTAATTCCAGCAATGAAACATAACA
* * * * * * *
366002 TATACTTACACCAGTCAAATTAACCCTTAATTCCAGCAGTGAAACATAACATATACTTACACCGG
66 TAGACTTACACCGGTGAAATTAACACTTAATTCCAACAGTGAAACATAACATAGACTTACACCGA
*
366067 TTAAATTAACCCTTAATTCCAGT
131 TCAAATTAACCCTTAATTCCAGT
* * * * * * *
366090 GGTAAAACATAACATAAACTTACATTAATTAAATTAACCCTTAATTCGAGTAGTGAAACATAACA
1 AGTGAAACATAACATAGACTTACATTAGTTAAATTAACCCTTAATTCCAGCAATGAAACATAACA
* *
366155 TAGACTTACATCGGTGAAA-TAACACTTAATTCCAACAGTGAAACATATCATAGACTTACACC-A
66 TAGACTTACACCGGTGAAATTAACACTTAATTCCAACAGTGAAACATAACATAGACTTACACCGA
* * * *
366218 GTTAAATTAACCTTTACTTCCACT
131 -TCAAATTAACCCTTAATTCCAGT
366242 AGTGAAACATAACATAGACTTACA
1 AGTGAAACATAACATAGACTTACA
366266 CCGGTGAAAT
Statistics
Matches: 412, Mismatches: 62, Indels: 13
0.85 0.13 0.03
Matches are distributed among these distances:
151 45 0.11
152 248 0.60
153 117 0.28
154 2 0.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (153 bp):
AGTGAAACATAACATAGACTTACATTAGTTAAATTAACCCTTAATTCCAGCAATGAAACATAACA
TAGACTTACACCGGTGAAATTAACACTTAATTCCAACAGTGAAACATAACATAGACTTACACCGA
TCAAATTAACCCTTAATTCCAGT
Found at i:366000 original size:26 final size:26
Alignment explanation
Indices: 365924--366051 Score: 77
Period size: 25 Copynumber: 5.0 Consensus size: 26
365914 ATCAAATTAG
* *
365924 CCCTTAAATCCAGAAGTGAAACATAA
1 CCCTTAATTCCAGCAGTGAAACATAA
* * * * *
365950 -CATATACTTACA-CAGTCAAA-TTAA
1 CCCT-TAATTCCAGCAGTGAAACATAA
*
365974 CCCTTAATTCCAGCAGTGGAACATAA
1 CCCTTAATTCCAGCAGTGAAACATAA
* * * * * *
366000 -CATATACTTACACCAGTCAAA-TTAA
1 CCCT-TAATTCCAGCAGTGAAACATAA
366025 CCCTTAATTCCAGCAGTGAAACATAA
1 CCCTTAATTCCAGCAGTGAAACATAA
366051 C
1 C
366052 ATATACTTAC
Statistics
Matches: 69, Mismatches: 26, Indels: 14
0.63 0.24 0.13
Matches are distributed among these distances:
24 9 0.13
25 34 0.49
26 26 0.38
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.24
Consensus pattern (26 bp):
CCCTTAATTCCAGCAGTGAAACATAA
Found at i:366171 original size:26 final size:26
Alignment explanation
Indices: 366141--366274 Score: 98
Period size: 26 Copynumber: 5.3 Consensus size: 26
366131 TAATTCGAGT
*
366141 AGTGAAACATAACATAGACTTACATC
1 AGTGAAACATAACATAGACTTACACC
* * *
366167 GGTG-AA-ATAACACTTA-A-TTCCAAC
1 AGTGAAACATAACA--TAGACTTACACC
*
366191 AGTGAAACATATCATAGACTTACACC
1 AGTGAAACATAACATAGACTTACACC
* * * ** * *
366217 AGTTAAA-TTAACCTTTACTTCCACT
1 AGTGAAACATAACATAGACTTACACC
366242 AGTGAAACATAACATAGACTTACACC
1 AGTGAAACATAACATAGACTTACACC
*
366268 GGTGAAA
1 AGTGAAA
366275 TAACAAATTA
Statistics
Matches: 78, Mismatches: 23, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
24 16 0.21
25 23 0.29
26 39 0.50
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (26 bp):
AGTGAAACATAACATAGACTTACACC
Found at i:366212 original size:304 final size:305
Alignment explanation
Indices: 365633--366266 Score: 898
Period size: 304 Copynumber: 2.1 Consensus size: 305
365623 TATTTACACC
* * * *
365633 AGTGAAACTTAACATAGACTTACACTAGTTAAATTAACCCTTAATTCTAAAAGTGAAACATTACA
1 AGTGAAACATAACATAGACTTACACTAGTCAAATTAACCCTTAATTCCAAAAGTGAAACATAACA
* *
365698 TAGACTTACACCGGTTAAATTAACCCTTAATTCCAGCAGTGAAACATAACATAGACTTACACCGA
66 TAGACTTACACCAGTCAAATTAACCCTTAATTCCAGCAGTGAAACATAACATAGACTTACACCGA
* * **
365763 CCAAATTAACCCTTAATTCCAGCAGTGAAACATAACATAGACTTACATTGGTTAAATTAACCTAT
131 CCAAATTAACCCTTAATTCCAGCAGTAAAACATAACATAAACTTACATTAATTAAATTAACCTAT
*
365828 AATTCCAGCAATGAAACATAACATAGACTTATACTGGTGAAATAACACTTAATTCCAACAGTGAA
196 AATTCCAGCAATGAAACATAACATAGACTTACACTGGTGAAATAACACTTAATTCCAACAGTGAA
* * * *
365893 ACATAACATAGACTTATATC-GATCAAATTAGCCCTTAAATCCAGA
261 ACATAACATAGACTTACACCAG-TCAAATTAACCCTTAAATCCACA
* ** *
365938 AGTGAAACATAACATATACTTACAC-AGTCAAATTAACCCTTAATTCCAGCAGTGGAACATAACA
1 AGTGAAACATAACATAGACTTACACTAGTCAAATTAACCCTTAATTCCAAAAGTGAAACATAACA
* * *
366002 TATACTTACACCAGTCAAATTAACCCTTAATTCCAGCAGTGAAACATAACATATACTTACACCGG
66 TAGACTTACACCAGTCAAATTAACCCTTAATTCCAGCAGTGAAACATAACATAGACTTACACCGA
** **
366067 TTAAATTAACCCTTAATTCCAGTGGTAAAACATAACATAAACTTACATTAATTAAATTAACCCT-
131 CCAAATTAACCCTTAATTCCAGCAGTAAAACATAACATAAACTTACATTAATTAAATTAA-CCTA
* * *
366131 TAATTCGAGTAGTGAAACATAACATAGACTTACA-TCGGTGAAATAACACTTAATTCCAACAGTG
195 TAATTCCAGCAATGAAACATAACATAGACTTACACT-GGTGAAATAACACTTAATTCCAACAGTG
* * * ** *
366195 AAACATATCATAGACTTACACCAGTTAAATTAACCTTTACTTCCACT
259 AAACATAACATAGACTTACACCAGTCAAATTAACCCTTAAATCCACA
366242 AGTGAAACATAACATAGACTTACAC
1 AGTGAAACATAACATAGACTTACAC
366267 CGGTGAAATA
Statistics
Matches: 290, Mismatches: 36, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
303 1 0.00
304 262 0.90
305 27 0.09
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (305 bp):
AGTGAAACATAACATAGACTTACACTAGTCAAATTAACCCTTAATTCCAAAAGTGAAACATAACA
TAGACTTACACCAGTCAAATTAACCCTTAATTCCAGCAGTGAAACATAACATAGACTTACACCGA
CCAAATTAACCCTTAATTCCAGCAGTAAAACATAACATAAACTTACATTAATTAAATTAACCTAT
AATTCCAGCAATGAAACATAACATAGACTTACACTGGTGAAATAACACTTAATTCCAACAGTGAA
ACATAACATAGACTTACACCAGTCAAATTAACCCTTAAATCCACA
Found at i:367560 original size:14 final size:14
Alignment explanation
Indices: 367543--367586 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
367533 GTCCGAGTCA
367543 ACCCGTTGACTTTG
1 ACCCGTTGACTTTG
*
367557 ACCCATTGACTTTG
1 ACCCGTTGACTTTG
367571 A-CCGTTGACTTTG
1 ACCCGTTGACTTTG
367584 ACC
1 ACC
367587 GAAAAGTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (14 bp):
ACCCGTTGACTTTG
Found at i:367580 original size:13 final size:13
Alignment explanation
Indices: 367545--367587 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
367535 CCGAGTCAAC
367545 CCGTTGACTTTGA
1 CCGTTGACTTTGA
*
367558 CCCATTGACTTTGA
1 -CCGTTGACTTTGA
367572 CCGTTGACTTTGA
1 CCGTTGACTTTGA
367585 CCG
1 CCG
367588 AAAAGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.16, C:0.28, G:0.21, T:0.35
Consensus pattern (13 bp):
CCGTTGACTTTGA
Found at i:368218 original size:27 final size:28
Alignment explanation
Indices: 368160--368219 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
368150 CTTCGGTTGG
*
368160 GTAAAATTATGAAAATACCCTTATAGGT
1 GTAAAATTATGAAAATACCCTCATAGGT
*
368188 -TAAAATTATGAAAATACCCTCA-AGTT
1 GTAAAATTATGAAAATACCCTCATAGGT
368214 GTAAAA
1 GTAAAA
368220 ATGGTATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (28 bp):
GTAAAATTATGAAAATACCCTCATAGGT
Found at i:369844 original size:30 final size:31
Alignment explanation
Indices: 369766--369846 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
369756 GCGACCCTTA
* *
369766 GGTAGGCTCTGAGGCCCTAAGAACTTTCTTG
1 GGTAGGCTCTCAGGCCCCAAGAACTTTCTTG
* *
369797 GGTAGG-TCCCAAGGCCCCGAGAACTTTCTTG
1 GGTAGGCTCTC-AGGCCCCAAGAACTTTCTTG
369828 GG-AGGCTCTCAGGCCCCAA
1 GGTAGGCTCTCAGGCCCCAA
369847 TATGCTCCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
30 13 0.31
31 29 0.69
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.22
Consensus pattern (31 bp):
GGTAGGCTCTCAGGCCCCAAGAACTTTCTTG
Found at i:378680 original size:16 final size:17
Alignment explanation
Indices: 378661--378703 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
378651 AATGTTGTTC
378661 GAAAAAA-AAGGAAAAA
1 GAAAAAACAAGGAAAAA
* *
378677 GAAAAAACATGGAAAAC
1 GAAAAAACAAGGAAAAA
*
378694 GAAACAACAA
1 GAAAAAACAA
378704 CAAAAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.72, C:0.09, G:0.16, T:0.02
Consensus pattern (17 bp):
GAAAAAACAAGGAAAAA
Found at i:379439 original size:12 final size:12
Alignment explanation
Indices: 379422--379452 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
379412 AGAGACATGG
379422 GCATGACTCTGA
1 GCATGACTCTGA
*
379434 GCATGACTCTGG
1 GCATGACTCTGA
379446 GCATGAC
1 GCATGAC
379453 GGGGCTGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.23
Consensus pattern (12 bp):
GCATGACTCTGA
Found at i:382108 original size:121 final size:121
Alignment explanation
Indices: 381889--382136 Score: 487
Period size: 121 Copynumber: 2.0 Consensus size: 121
381879 CATAATGGGC
381889 TAAACACTCTAACCGTTATTTTCATTCATTCACTCGAAAACTCTTTGCCCTTTATGAAATCCAAA
1 TAAA-ACTCTAACCGTTATTTTCATTCATTCACTCGAAAACTCTTTGCCCTTTATGAAATCCAAA
381954 ATATATGAATATGACGAATCTGAGTTTATTAAGCAACTATGAGAATGGAAAATAGTG
65 ATATATGAATATGACGAATCTGAGTTTATTAAGCAACTATGAGAATGGAAAATAGTG
382011 TAAAACTCTAACCGTTATTTTCATTCATTCACTCGAAAACTCTTTGCCCTTTATGAAATCCAAAA
1 TAAAACTCTAACCGTTATTTTCATTCATTCACTCGAAAACTCTTTGCCCTTTATGAAATCCAAAA
382076 TATATGAATATGACGAATCTGAGTTTATTAAGCAACTATGAGAATGGAAAATAGTG
66 TATATGAATATGACGAATCTGAGTTTATTAAGCAACTATGAGAATGGAAAATAGTG
382132 TAAAA
1 TAAAA
382137 ACCCCCAAAC
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
121 122 0.97
122 4 0.03
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.33
Consensus pattern (121 bp):
TAAAACTCTAACCGTTATTTTCATTCATTCACTCGAAAACTCTTTGCCCTTTATGAAATCCAAAA
TATATGAATATGACGAATCTGAGTTTATTAAGCAACTATGAGAATGGAAAATAGTG
Found at i:385279 original size:31 final size:31
Alignment explanation
Indices: 385222--385280 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
385212 CCCTGATATC
*
385222 TTTCTTGGATAGGCCCTGTAGCCCCGAGATA
1 TTTCTTGGATAGGCCCCGTAGCCCCGAGATA
* *
385253 TTTCTTAGG-TAGGCCCCGTGGTCCCGAG
1 TTTCTT-GGATAGGCCCCGTAGCCCCGAG
385281 TAACTTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.92
32 2 0.08
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (31 bp):
TTTCTTGGATAGGCCCCGTAGCCCCGAGATA
Found at i:387169 original size:42 final size:42
Alignment explanation
Indices: 387122--387215 Score: 179
Period size: 42 Copynumber: 2.2 Consensus size: 42
387112 GGATGAATGA
387122 AGTTGAGTTTAAAGGTAAAGAATGAGGTAAAAGTAGGAGATT
1 AGTTGAGTTTAAAGGTAAAGAATGAGGTAAAAGTAGGAGATT
387164 AGTTGAGTTTAAAGGTAAAGAATGAGGTAAAAGTAGGAGATT
1 AGTTGAGTTTAAAGGTAAAGAATGAGGTAAAAGTAGGAGATT
*
387206 AGTTAAGTTT
1 AGTTGAGTTT
387216 TTGGTTAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.29
Consensus pattern (42 bp):
AGTTGAGTTTAAAGGTAAAGAATGAGGTAAAAGTAGGAGATT
Found at i:387867 original size:20 final size:21
Alignment explanation
Indices: 387830--387868 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
387820 TTATTTAAGT
**
387830 TATGATTGATGATTATGTGTA
1 TATGATTGATGAAAATGTGTA
387851 TATGATT-ATGAAAATGTG
1 TATGATTGATGAAAATGTG
387869 ACATGTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (21 bp):
TATGATTGATGAAAATGTGTA
Found at i:388068 original size:23 final size:23
Alignment explanation
Indices: 388037--388114 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
388027 CCTTCGGGAT
388037 AAAATTATGTGGTCCTTCAG-GAC
1 AAAA-TATGTGGTCCTTCAGAGAC
* * *
388060 AAACCTATGTGGTCATTC-GAGAT
1 AAA-ATATGTGGTCCTTCAGAGAC
388083 AAAATATGTGGTCCTT-AGAGAC
1 AAAATATGTGGTCCTTCAGAGAC
*
388105 -AATTATGTGG
1 AAAATATGTGG
388115 CACTTCGGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
21 9 0.20
22 16 0.36
23 20 0.44
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (23 bp):
AAAATATGTGGTCCTTCAGAGAC
Found at i:388103 original size:22 final size:22
Alignment explanation
Indices: 388025--388103 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
388015 GTTCTATATA
* *
388025 GTCCTTCGGGATAAAATTATGTG
1 GTCCTTAGAGATAAAA-TATGTG
* *
388048 GTCCTTCAG-GACAAACCTATGTG
1 GTCCTT-AGAGATAAA-ATATGTG
* *
388071 GTCATTCGAGATAAAATATGTG
1 GTCCTTAGAGATAAAATATGTG
388093 GTCCTTAGAGA
1 GTCCTTAGAGA
388104 CAATTATGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
22 16 0.36
23 27 0.61
24 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (22 bp):
GTCCTTAGAGATAAAATATGTG
Found at i:389002 original size:16 final size:16
Alignment explanation
Indices: 388981--389016 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
388971 GTGCCCCGAG
388981 CAGGCAGGGTGAAGAA
1 CAGGCAGGGTGAAGAA
*
388997 CAGGCAGGGTGAGGAA
1 CAGGCAGGGTGAAGAA
389013 CAGG
1 CAGG
389017 TACATCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.47, T:0.06
Consensus pattern (16 bp):
CAGGCAGGGTGAAGAA
Found at i:394451 original size:22 final size:22
Alignment explanation
Indices: 394376--394451 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 22
394366 GTTCTATATA
*
394376 GTCATTCGAGACAAAATTATGTG
1 GTCATTCGGGACAAAA-TATGTG
* * * *
394399 GTCCTTTGGGATAAACCTATGTG
1 GTCATTCGGGACAAA-ATATGTG
* *
394422 GTCCTTCGGGACAAAATATTTG
1 GTCATTCGGGACAAAATATGTG
394444 GTCATTCG
1 GTCATTCG
394452 AGATAATTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
22 12 0.29
23 30 0.71
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (22 bp):
GTCATTCGGGACAAAATATGTG
Found at i:398362 original size:18 final size:18
Alignment explanation
Indices: 398339--398379 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
398329 ATTGGTCACA
398339 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
398357 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
398375 ACCCG
1 ACCCG
398380 TTGACCATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.51, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:400907 original size:48 final size:48
Alignment explanation
Indices: 400851--400959 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
400841 ATATTTTATC
* *
400851 TGATTTCTGACT-TGAATTTTGTTCTGATA-CATTACCTGAATTCTGTTA
1 TGATTTCTGA-TATGAATTATGTTCTGATATC-TGACCTGAATTCTGTTA
* * *
400899 TGATTTCTGATATGGATTATGTTCTGATATCTGATCTGAATTCTGTTT
1 TGATTTCTGATATGAATTATGTTCTGATATCTGACCTGAATTCTGTTA
*
400947 TGATTTATGATAT
1 TGATTTCTGATAT
400960 CTCCGTTTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.50
Consensus pattern (48 bp):
TGATTTCTGATATGAATTATGTTCTGATATCTGACCTGAATTCTGTTA
Found at i:400921 original size:24 final size:24
Alignment explanation
Indices: 400887--400959 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
400877 ATACATTACC
*
400887 TGAATTCTGTTATGATTTCTGATA
1 TGAATTATGTTATGATTTCTGATA
* * * *
400911 TGGATTATGTTCTGATATCTGATC
1 TGAATTATGTTATGATTTCTGATA
* * *
400935 TGAATTCTGTTTTGATTTATGATA
1 TGAATTATGTTATGATTTCTGATA
400959 T
1 T
400960 CTCCGTTTAC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTATGTTATGATTTCTGATA
Found at i:402254 original size:10 final size:10
Alignment explanation
Indices: 402235--402310 Score: 68
Period size: 10 Copynumber: 7.8 Consensus size: 10
402225 CGAAGAGAGT
*
402235 ATATAGAATA
1 ATATATAATA
402245 ATATATAAT-
1 ATATATAATA
*
402254 ATATACAAATA
1 ATATA-TAATA
402265 ATATATAATA
1 ATATATAATA
* *
402275 ATAAATACTA
1 ATATATAATA
* *
402285 ATA-AGAGTA
1 ATATATAATA
402294 ATA-ATAATA
1 ATATATAATA
402303 ATATATAA
1 ATATATAA
402311 AGATAATTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
9 19 0.35
10 30 0.56
11 5 0.09
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (10 bp):
ATATATAATA
Found at i:402275 original size:3 final size:3
Alignment explanation
Indices: 402241--402349 Score: 55
Period size: 3 Copynumber: 34.7 Consensus size: 3
402231 GAGTATATAG
*
402241 AAT AAT ATAT AAT ATAT ACA- AAT AAT ATAT AAT AAT AAAT ACT AAT
1 AAT AAT A-AT AAT A-AT A-AT AAT AAT A-AT AAT AAT -AAT AAT AAT
* * ** *
402287 AAG AGT AAT AAT AAT AAT ATAT AA- AGAT AAT TCT AAT -GT AA- AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT
402331 AAAT AGAT AAT AAT AAT AA
1 -AAT A-AT AAT AAT AAT AA
402350 ATATAGTAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
2 5 0.06
3 53 0.65
4 23 0.28
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:402277 original size:13 final size:13
Alignment explanation
Indices: 402242--402310 Score: 72
Period size: 13 Copynumber: 5.3 Consensus size: 13
402232 AGTATATAGA
402242 ATAATATATAATAT
1 ATAATA-ATAATAT
402256 ATACA-AATAATAT
1 ATA-ATAATAATAT
402269 ATAATAATAA-AT
1 ATAATAATAATAT
* *
402281 ACTAATAAGAGTA-
1 A-TAATAATAATAT
402294 ATAATAATAATAT
1 ATAATAATAATAT
402307 ATAA
1 ATAA
402311 AGATAATTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
12 13 0.28
13 27 0.59
14 5 0.11
15 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (13 bp):
ATAATAATAATAT
Found at i:402302 original size:25 final size:24
Alignment explanation
Indices: 402242--402352 Score: 79
Period size: 24 Copynumber: 4.7 Consensus size: 24
402232 AGTATATAGA
* *
402242 ATAATATATAATATATACAAATAAT
1 ATAATA-ATAATAAATACAAATAAG
*
402267 AT-ATAATAATAAATACTAATAAG
1 ATAATAATAATAAATACAAATAAG
* *
402290 AGTAATAATAAT-AATATATA-AAG
1 A-TAATAATAATAAATACAAATAAG
** *
402313 ATAATTCTAATGTAAA-ATAAAT-AG
1 ATAATAATAA--TAAATACAAATAAG
402337 ATAATAATAATAAATA
1 ATAATAATAATAAATA
402353 TAGTAAAACA
Statistics
Matches: 68, Mismatches: 11, Indels: 16
0.72 0.12 0.17
Matches are distributed among these distances:
22 11 0.16
23 21 0.31
24 24 0.35
25 12 0.18
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (24 bp):
ATAATAATAATAAATACAAATAAG
Found at i:402345 original size:58 final size:59
Alignment explanation
Indices: 402269--402420 Score: 161
Period size: 58 Copynumber: 2.6 Consensus size: 59
402259 CAAATAATAT
* * *
402269 ATAAT-AATAAATACTAATAAGAGTAATAATAATAATAT-ATAAAGATAATTCTAATGTA
1 ATAATAAAT-AATAATAATAAAAGTAATAATAATAATATAAAAAAGATAATTCTAATGTA
* * *
402327 A-AATAAATAGATAATAATAATAAAT-ATAGTAA-AACATAAAAAAGATAATTCTAATGTA
1 ATAATAAATA-ATAATAATAA-AAGTAATAATAATAATATAAAAAAGATAATTCTAATGTA
* * *
402385 ATAATAGATAATAATAAAAAAAGTAATAATAGTAAT
1 ATAATAAATAATAATAATAAAAGTAATAATAATAAT
402421 TTGACCAATG
Statistics
Matches: 75, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
57 11 0.15
58 53 0.71
59 11 0.15
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.30
Consensus pattern (59 bp):
ATAATAAATAATAATAATAAAAGTAATAATAATAATATAAAAAAGATAATTCTAATGTA
Found at i:405127 original size:18 final size:18
Alignment explanation
Indices: 405087--405128 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
405077 AGAAGGCATG
*
405087 CAGCTTGACTGGGTCAGT
1 CAGCATGACTGGGTCAGT
* *
405105 AAGCATGACTGGGTCCGT
1 CAGCATGACTGGGTCAGT
405123 CAGCAT
1 CAGCAT
405129 CTACGCAGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (18 bp):
CAGCATGACTGGGTCAGT
Found at i:409885 original size:18 final size:18
Alignment explanation
Indices: 409845--409886 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
409835 AGAAGGCATG
*
409845 CAGCTTGACTGGGTCAGT
1 CAGCATGACTGGGTCAGT
* *
409863 AAGCATGACTGGGTCCGT
1 CAGCATGACTGGGTCAGT
409881 CAGCAT
1 CAGCAT
409887 CTACGCAGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (18 bp):
CAGCATGACTGGGTCAGT
Found at i:422505 original size:77 final size:76
Alignment explanation
Indices: 422346--422507 Score: 281
Period size: 77 Copynumber: 2.1 Consensus size: 76
422336 AGTTATATTT
422346 ATATTTATTAAAGCTTTTCTTTGATGATTTAATCTATCTTAATATGATTTATAAAAGTAACTTGC
1 ATATTTATTAAAGCTTTTCTTTGATGATTTAATCTATCTTAATATGATTTATAAAAGTAACTTGC
*
422411 TCGCACGAACA
66 TCCCACGAACA
*
422422 ATATTTATTAAATCTTTTCATTT-ATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACTT
1 ATATTTATTAAAGCTTTTC-TTTGATGATTTAATCTATCTTAAT-ATGATTTATAAAAGTAACTT
422486 GCTCCCACGAACA
64 GCTCCCACGAACA
422499 ATATTTATT
1 ATATTTATT
422508 TAATATTAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
76 38 0.46
77 44 0.54
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (76 bp):
ATATTTATTAAAGCTTTTCTTTGATGATTTAATCTATCTTAATATGATTTATAAAAGTAACTTGC
TCCCACGAACA
Found at i:426037 original size:24 final size:24
Alignment explanation
Indices: 425919--426030 Score: 156
Period size: 24 Copynumber: 4.7 Consensus size: 24
425909 ATTTGAATTT
425919 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
425943 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
425967 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* *
425991 TGATCTGTTACTTGACCT-GATTTC
1 TGATCTGATACTTGACATGGA-TTC
*
426015 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
426031 CTGATTTATG
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
23 3 0.04
24 76 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:426053 original size:24 final size:24
Alignment explanation
Indices: 425967--426040 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
425957 ACATGGATTC
* * *
425967 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
425991 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
426015 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
426039 TG
1 TG
426041 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:430723 original size:49 final size:50
Alignment explanation
Indices: 430669--430771 Score: 127
Period size: 50 Copynumber: 2.1 Consensus size: 50
430659 GTAATCCCAG
* * * *
430669 GTAAATTAGAACAC-AAAATTTAGGATGAATAGATAAAACCTAATAATAA
1 GTAAATTAAAACACTAAAATTTAGGATAAACAAATAAAACCTAATAATAA
* * **
430718 GTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAA
1 GTAAATTAAAACACTAAAATTTAGGATAAACAAATAAAACCTAATAATAA
430768 GTAA
1 GTAA
430772 TTTTTTTTGG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 13 0.29
50 32 0.71
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.24
Consensus pattern (50 bp):
GTAAATTAAAACACTAAAATTTAGGATAAACAAATAAAACCTAATAATAA
Found at i:430785 original size:39 final size:39
Alignment explanation
Indices: 430741--430860 Score: 94
Period size: 40 Copynumber: 3.2 Consensus size: 39
430731 CTAGAATTTA
430741 GGATAAACAAATGAAACCTAATCCTAAGTAATTTTTTTT
1 GGATAAACAAATGAAACCTAATCCTAAGTAATTTTTTTT
* ** * *
430780 GGATAATA-ATAA-GTAAGTTAAAACACT-AG-AA----TTTA
1 GGATAA-ACA-AATGAAACCT-AATC-CTAAGTAATTTTTTTT
430815 GGATAAACAAATGAAACCTAATCCTAAGTAATTTTTTTTT
1 GGATAAACAAATGAAACCTAATCCTAAGTAA-TTTTTTTT
430855 GGATAA
1 GGATAA
430861 TAATAAGTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 25
0.62 0.11 0.27
Matches are distributed among these distances:
33 2 0.03
34 8 0.14
35 16 0.28
39 13 0.22
40 17 0.29
41 2 0.03
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.33
Consensus pattern (39 bp):
GGATAAACAAATGAAACCTAATCCTAAGTAATTTTTTTT
Found at i:430848 original size:35 final size:35
Alignment explanation
Indices: 430735--430848 Score: 83
Period size: 35 Copynumber: 3.1 Consensus size: 35
430725 AAAACACTAG
430735 AATTTAGGATAAACAAATGAAACCTAATCCTAAGT
1 AATTTAGGATAAACAAATGAAACCTAATCCTAAGT
* * ** *
430770 AATTTTTTTTGGATAATA-ATAA-GTAAGTTAAAACACT-AG-
1 AA----TTTAGGATAA-ACA-AATGAAACCT-AATC-CTAAGT
430809 AATTTAGGATAAACAAATGAAACCTAATCCTAAGT
1 AATTTAGGATAAACAAATGAAACCTAATCCTAAGT
430844 AATTT
1 AATTT
430849 TTTTTTGGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 24
0.63 0.11 0.26
Matches are distributed among these distances:
33 2 0.04
34 8 0.14
35 21 0.37
39 16 0.28
40 8 0.14
41 2 0.04
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (35 bp):
AATTTAGGATAAACAAATGAAACCTAATCCTAAGT
Found at i:430895 original size:75 final size:74
Alignment explanation
Indices: 430709--430932 Score: 412
Period size: 74 Copynumber: 3.0 Consensus size: 74
430699 AGATAAAACC
430709 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAAGTAATT
430774 TTTTTTGGA
66 TTTTTTGGA
*
430783 TAATAATAAGTAAGTTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAAGTAA-T
430848 TTTTTTTGGA
65 TTTTTTTGGA
*
430858 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAAACTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAAGTAATT
*
430923 CTTTTTGGA
66 TTTTTTGGA
430932 T
1 T
430933 TAAGCTAAGG
Statistics
Matches: 145, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
74 73 0.50
75 72 0.50
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (74 bp):
TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAAGTAATT
TTTTTTGGA
Found at i:433037 original size:128 final size:128
Alignment explanation
Indices: 432901--433221 Score: 457
Period size: 128 Copynumber: 2.5 Consensus size: 128
432891 ATTTATATAG
* * * * *
432901 AAATATCAGAAAAT-GACTTCTAGGTGCTTTAAGACAACTCTTTTCTCAATATTAAAAAATATAT
1 AAATATCAGAAAATGGACATCCAGTTGCTTTAAGACAAC-CATTTCTCAATATTAAAAAATAAAT
* *
432965 AAATATTAATAAAACATTTATCTAAAAATAATTAAAATATATATAATGTAAAATACTTATTTAA
65 AAATATGAATAAAACATTTATCTAAAAATAATTAAAATATATATAATGGAAAATACTTATTTAA
* * ** * *
433029 AATTATCAGAAAATGGACATCCAGTTACTTTAAGACTGCCATTTCTTAATATTGAAAAATAAATA
1 AAATATCAGAAAATGGACATCCAGTTGCTTTAAGACAACCATTTCTCAATATTAAAAAATAAATA
433094 AATATGAATAAAACATTTATCTAAAAATAATTAAAATATATATAATGGAAAATACTTATTTAA
66 AATATGAATAAAACATTTATCTAAAAATAATTAAAATATATATAATGGAAAATACTTATTTAA
** * *
433157 AAATATCAGAAAATGGACATCCAGTTGCTTTAAGACTGTCC-TTTCTTAATGTTAAAAAATAAAT
1 AAATATCAGAAAATGGACATCCAGTTGCTTTAAGAC-AACCATTTCTCAATATTAAAAAATAAAT
433221 A
65 A
433222 TTAAAATATG
Statistics
Matches: 172, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
128 152 0.88
129 20 0.12
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (128 bp):
AAATATCAGAAAATGGACATCCAGTTGCTTTAAGACAACCATTTCTCAATATTAAAAAATAAATA
AATATGAATAAAACATTTATCTAAAAATAATTAAAATATATATAATGGAAAATACTTATTTAA
Found at i:433342 original size:3 final size:3
Alignment explanation
Indices: 433334--433360 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
433324 TACATGACTA
433334 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
433361 TAAATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:434829 original size:16 final size:16
Alignment explanation
Indices: 434808--434848 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
434798 TGTTTTGTAA
* *
434808 TAATAATATTTATTAT
1 TAATAATAATAATTAT
434824 TAATAATAATAATTAT
1 TAATAATAATAATTAT
434840 T-ATAATAAT
1 TAATAATAAT
434849 TCTTGTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATAATAATAATTAT
Found at i:434829 original size:19 final size:18
Alignment explanation
Indices: 434805--434848 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
434795 GCATGTTTTG
*
434805 TAATAATAATATTTATTA
1 TAATAATAATAATTATTA
434823 TTAATAATAATAATTATTA
1 -TAATAATAATAATTATTA
434842 TAATAAT
1 TAATAAT
434849 TCTTGTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATAATAATAATTATTA
Found at i:435890 original size:18 final size:18
Alignment explanation
Indices: 435853--435890 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
435843 TATGTGAAAG
*
435853 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCAAA
435871 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
435889 AA
1 AA
435891 GATAATCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:436284 original size:11 final size:11
Alignment explanation
Indices: 436268--436305 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
436258 CTTTTTATTA
436268 TTTCTTTTTTC
1 TTTCTTTTTTC
436279 TTTCTTTTTTC
1 TTTCTTTTTTC
436290 TTTCTTTTTT-
1 TTTCTTTTTTC
436300 TTTCTT
1 TTTCTT
436306 CTTCAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.22
11 21 0.78
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:443458 original size:14 final size:16
Alignment explanation
Indices: 443441--443472 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
443431 ATTATTTTTT
443441 TGAAT-TTTAT-TTAA
1 TGAATGTTTATCTTAA
443455 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
443471 TG
1 TG
443473 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:449239 original size:3 final size:3
Alignment explanation
Indices: 449231--449320 Score: 92
Period size: 3 Copynumber: 30.0 Consensus size: 3
449221 GCCTGTTTTG
* *
449231 TAA TAA TAA TATT TAT TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
449276 TTA TTA TAA TAA TTA TAA TAA TTA TAT TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
449321 ACGGGTAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
2 2 0.03
3 69 0.95
4 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:449817 original size:18 final size:17
Alignment explanation
Indices: 449794--449840 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
449784 TGTTTCTGAG
449794 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
449812 GGAATTAGAATCTGTTA
1 GGAATTGGAATCTGTAA
449829 GGAATTGGAATC
1 GGAATTGGAATC
449841 CAATTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:450512 original size:235 final size:235
Alignment explanation
Indices: 450201--450646 Score: 719
Period size: 235 Copynumber: 1.9 Consensus size: 235
450191 GAACCTCTAT
*
450201 CCGAGACCCGATCCGACCAAAATAAAGTTTCACCCGACCCCACCTGACCCGAATATATGAATTAG
1 CCGAGACCCGACCCGACCAAAATAAAGTTTCACCCGA--CCACCTGACCCGAATATATGAATTAG
450266 AAACCCGACCCGACCCGAAATAATAAAAAAA-TATTTTTATTCAATAAAAAC-GATGACTTAATT
64 AAACCCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAG-TGACTTAATT
450329 GGAAAACAAA-TATACATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTAT
128 -GAAAA-AAATTATACATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTAT
*
450393 ATAT-TTTTTGGGTCGGGTCGGGTCGGGTATTTTTCTCCCTAAAC
191 ATATATTTTCGGGTCGGGTCGGGTCGGGTATTTTTCTCCCTAAAC
450437 CCGA-ACCCGACCCGACCAAAATAAAGTTTCACCCGA-C-CC-GACCCGAATATATGAATTAGAA
1 CCGAGACCCGACCCGACCAAAATAAAGTTTCACCCGACCACCTGACCCGAATATATGAATTAGAA
450498 ATCCGACTCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAA
66 A--C--C-CGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAA
*
450563 TTGAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTAT
126 TTGAAAAAAATTATACATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTAT
450628 ATATATTTTCGGGTCGGGT
191 ATATATTTTCGGGTCGGGT
450647 ATTTTTCACC
Statistics
Matches: 198, Mismatches: 3, Indels: 18
0.90 0.01 0.08
Matches are distributed among these distances:
230 23 0.12
231 2 0.01
232 2 0.01
234 4 0.02
235 119 0.60
236 47 0.24
237 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (235 bp):
CCGAGACCCGACCCGACCAAAATAAAGTTTCACCCGACCACCTGACCCGAATATATGAATTAGAA
ACCCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAA
AAAAATTATACATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATA
TTTTCGGGTCGGGTCGGGTCGGGTATTTTTCTCCCTAAAC
Found at i:457149 original size:20 final size:20
Alignment explanation
Indices: 457126--457163 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
457116 AGGCAAAATT
*
457126 GAACCGGGTTGACCTGACTC
1 GAACCAGGTTGACCTGACTC
*
457146 GAACTAGGTTGACCTGAC
1 GAACCAGGTTGACCTGAC
457164 CTGAATCGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (20 bp):
GAACCAGGTTGACCTGACTC
Found at i:459318 original size:12 final size:12
Alignment explanation
Indices: 459286--459323 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
459276 GGAAGTCAAC
459286 GGTCAACGGTCG
1 GGTCAACGGTCG
459298 GGTC-A-GGTCG
1 GGTCAACGGTCG
459308 GGTCAACGGTCG
1 GGTCAACGGTCG
459320 GGTC
1 GGTC
459324 GGGCCGGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.38
11 2 0.08
12 13 0.54
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:459323 original size:5 final size:5
Alignment explanation
Indices: 459293--459362 Score: 79
Period size: 5 Copynumber: 13.8 Consensus size: 5
459283 AACGGTCAAC
* * * *
459293 GGTCG GGTCA GGTCG GGTCAAC GGTCG GGTCG GG-CC GGTAG GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
459344 GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC
459363 AGACCGGTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
4 3 0.06
5 47 0.87
7 4 0.07
ACGTcount: A:0.06, C:0.21, G:0.54, T:0.19
Consensus pattern (5 bp):
GGTCG
Done.