Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007804.1 Hibiscus syriacus cultivar Beakdansim tig00110122_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: 1697051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:492758 original size:6 final size:6
Alignment explanation
Indices: 492749--492782 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
492739 CTTTTGCAAC
* *
492749 TTTTAT TTTTAT TTTTAT TTTTCT TTTCAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
492783 TAAATTTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:492833 original size:12 final size:12
Alignment explanation
Indices: 492786--492856 Score: 53
Period size: 12 Copynumber: 5.9 Consensus size: 12
492776 CATTTTTTAA
492786 ATTTG-TTATTTT
1 ATTTGTTTA-TTT
492798 ATTCT-TTTATTT
1 ATT-TGTTTATTT
492810 ACTCTTGATTTATTT
1 A-T-TTG-TTTATTT
492825 ATTTGTTTA-TT
1 ATTTGTTTATTT
492836 -TTT-TTTATTT
1 ATTTGTTTATTT
*
492846 TTTTGTTTATT
1 ATTTGTTTATT
492857 GTCGCTATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.08
10 5 0.10
11 5 0.10
12 17 0.34
13 9 0.18
14 2 0.04
15 8 0.16
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75
Consensus pattern (12 bp):
ATTTGTTTATTT
Found at i:492971 original size:20 final size:21
Alignment explanation
Indices: 492946--492987 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
492936 CTCGAATCGG
492946 ATTTTTAAATTTCA-ATTTAA
1 ATTTTTAAATTTCACATTTAA
*
492966 ATTTTTAATTTTCACATTTAA
1 ATTTTTAAATTTCACATTTAA
492987 A
1 A
492988 GACAACCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTTAAATTTCACATTTAA
Found at i:498283 original size:164 final size:164
Alignment explanation
Indices: 498011--498790 Score: 924
Period size: 164 Copynumber: 4.7 Consensus size: 164
498001 TAAAAAAGAT
* * * * * * *
498011 ATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGTGAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGT-AACCAAAGACCTTCGAGTTCGACT
*
498076 ACGCTCAGCT-CAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
65 ACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* *
498140 ACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCAC
129 ACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCAC
* * *
498176 ATCATTTACAGCATAACTCAAGGCTAGAAGGTTTATCTGTAACCGAAGACCTTCGAGTTCGACTA
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
* *
498241 CGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * *
498306 CCTCGAGTTCGATTACAGTCAGCTTCGAGGGCAC
131 CCCCAAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * ** ** *
498340 ATTATTTGTAGCATAACTTAA-ATTGAGAAGGGTTATCTACCAACCAAAGACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTCAAGGCT-AGAAGGGTTATCT-GTAACCAAAGACCTTCGAGTTCGAC
* * * *
498404 TACGCTCAGCTCCAAGGCATATCATTTGTAGCATAGATTAAGTCGAGAAGGGCTATCTTCCAAAG
64 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
*
498469 ACCCCCAAGTTCAATTACACTCAGCTTCGAGGGCAC
129 ACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCAC
** *
498505 ATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTA
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
* * * * * *
498570 CGCTCAGCTCCACGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTACCAAGCAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT-GC---CAA
** * * * *
498635 AGACCTTCAAGTTCGACTACGCTCAGC-TCCAAGGCAC
127 AGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * *
498672 GTCATTTGCGGTATAACTCAAGGCTAGAAGGGCTATC--T-ACCAAAGACCTTCGAGTTTGACTA
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
* * * * ***
498734 CGCTCAGCTCTAGGGCACATCATTTACAGCATAGCCTAAGGAAAGAAGGGCTATCTG
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
498791 TCAATAAAAT
Statistics
Matches: 533, Mismatches: 74, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
163 1 0.00
164 283 0.53
165 184 0.35
166 1 0.00
167 39 0.07
168 25 0.05
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (164 bp):
ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
CCCCAAGTTCGATTACACTCAGCTTCGAGGGCAC
Found at i:498628 original size:248 final size:247
Alignment explanation
Indices: 498022--498793 Score: 835
Period size: 248 Copynumber: 3.1 Consensus size: 247
498012 TCATTTGCAA
* * * *
498022 CATAGCTCAAGGCAAGAAGGGCTATTTGTGAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGCTATCTGT-CACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * * **
498087 AACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT----GCCAAAGACCCCCGA
65 AACGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGA
* * * * * * **
498148 GTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGTTTATC
130 GTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATC
* * *
498213 TGTAACCGAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAG
194 T-T--CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAGGGCACATCATTTATAG
* * * * *
498270 CATAGCTTAAGTCGAGAAGGGCTATC--T-ACCAAAGACCCTCGAGTTCGATTACAG-TCAGCTT
1 CATAGCTCAAGGCAAGAAGGGCTATCTGTCACCAAAGACCTTCGAGTTCGACTAC-GCTCAGC-T
* * * * * * *
498331 CGAGGGCACATTATTTGTAGCATAACTTAAATTGAGAAGGGTTATCTACCAACCAAAGACCTTTG
64 CAACGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCG
* * * * *
498396 AGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAGA-TTAAGTCGAGAAGGGCTAT
129 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA-ACTCAAGGCTAGAAGGGCTAT
** * * * * *
498460 CTTCCAAAGACCCCCAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTATAG
193 CTTCCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAGGGCACATCATTTATAG
* * * *
498516 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
1 CATAGCTCAAGGCAAGAAGGGCTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCA
* * * *
498581 ACGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTACCAAGCAAAGACCTTCAAG
66 ACGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAG
* * * *
498646 TTCGACTACGCTCAGCTCCAAGGCACGTCATTTGCGGTATAACTCAAGGCTAGAAGGGCTATCTA
131 TTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTT
* * *
498711 CCAAAGACCTTCGAGTTTGACTACGCTCAGCTCTAGGGCACATCATTTACAG
196 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAGGGCACATCATTTATAG
*
498763 CATAGC-CTAAGGAAAGAAGGGCTATCTGTCA
1 CATAGCTC-AAGGCAAGAAGGGCTATCTGTCA
498794 ATAAAATTAT
Statistics
Matches: 426, Mismatches: 84, Indels: 29
0.79 0.16 0.05
Matches are distributed among these distances:
244 26 0.06
245 64 0.15
246 41 0.10
247 46 0.11
248 195 0.46
249 54 0.13
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (247 bp):
CATAGCTCAAGGCAAGAAGGGCTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCA
ACGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAG
TTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTT
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAGGGCACATCATTTATAG
Found at i:498839 original size:329 final size:327
Alignment explanation
Indices: 498056--498792 Score: 973
Period size: 329 Copynumber: 2.2 Consensus size: 327
498046 TTTGTGAACA
* *
498056 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
*
498121 GAAGGGCTATCTG-CCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTAC
66 GAAGGGCTATCTGTCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
* *
498185 AGCATAACTCAAGGCTAGAAGGTTTATCTGTAACCGAAGACCTTCGAGTTCGACTACGCTCAGCT
131 AGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
** * *
498250 CCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCGAGTT
196 CCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCAAGTT
* * * * * * * *
498315 CGATTACAGTCAGCTTCGAGGGCACATTATTTGTAGCATAACTTAAATTGAGAAGGGTTATCTAC
261 CGACTACAGTCAGCTTCCAAGGCACATCATTTGCAGCATAACTCAAACTGAGAAGGGCTATCT--
498380 CAACC
324 -AACC
* * * *
498385 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAGATTAAGTCGA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
* * *
498450 GAAGGGCTATCT-TCCAAAGACCCCCAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTAT
66 GAAGGGCTATCTGTCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
*
498514 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
131 AGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
* * * *
498579 CCACGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTACCAAGCAAAGACCTTCA
196 CCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTA-C---CAAAGACCCTCA
* * * *
498644 AGTTCGACTAC-GCTCAGC-TCCAAGGCACGTCATTTGCGGTATAACTCAAGGCT-AGAAGGGCT
257 AGTTCGACTACAG-TCAGCTTCCAAGGCACATCATTTGCAGCATAACTCAA-ACTGAGAAGGGCT
498706 ATCT-ACC
320 ATCTAACC
* * * * * * ***
498713 AAAGACCTTCGAGTTTGACTACGCTCAGCTCTAGGGCACATCATTTACAGCATAGCCTAAGGAAA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
498778 GAAGGGCTATCTGTC
66 GAAGGGCTATCTGTC
498793 AATAAAATTA
Statistics
Matches: 355, Mismatches: 45, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
328 68 0.19
329 224 0.63
330 1 0.00
332 36 0.10
333 26 0.07
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (327 bp):
AAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
GAAGGGCTATCTGTCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
AGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
CCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCAAGTT
CGACTACAGTCAGCTTCCAAGGCACATCATTTGCAGCATAACTCAAACTGAGAAGGGCTATCTAA
CC
Found at i:499342 original size:2 final size:2
Alignment explanation
Indices: 499335--499369 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
499325 TTTTTATTAT
499335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
499370 GTTCACAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:499481 original size:36 final size:37
Alignment explanation
Indices: 499396--499630 Score: 144
Period size: 39 Copynumber: 6.2 Consensus size: 37
499386 TGGAAATACA
* *
499396 TATATAATATATAGTTTTCTTAAAA-ACATTTT-AAAAA
1 TATAT-ATATATAGTTTTTTTAAAACAC-TTTTGAAAAC
*
499433 TGTATAGTATATAGTTTTTTTAAAACACTTTTGAAAAC
1 TATATA-TATATAGTTTTTTTAAAACACTTTTGAAAAC
*
499471 TATATAATATATAG--TTTTTAAAACA-TTTTAGAAAAA
1 TATAT-ATATATAGTTTTTTTAAAACACTTTT-GAAAAC
** * *
499507 TATATA-ATATA-TGGGTTTTAAAGTCATATTTTTTGAAAAC
1 TATATATATATAGT-TTTTTTAAA---ACA-CTTTTGAAAAC
* *
499547 TTATATAATATATAGTTTTTTAAAAACATTTTTGAAAAC
1 -TATAT-ATATATAGTTTTTTTAAAACACTTTTGAAAAC
* * * * *
499586 TAATATATAATATA-TAATTTCTAAAACTCTTTTGGAAAT
1 T-ATATAT-ATATAGT-TTTTTTAAAACACTTTTGAAAAC
499625 TATATA
1 TATATA
499631 GTTTTTTAAA
Statistics
Matches: 159, Mismatches: 19, Indels: 39
0.73 0.09 0.18
Matches are distributed among these distances:
34 5 0.03
35 5 0.03
36 29 0.18
37 25 0.16
38 26 0.16
39 40 0.25
40 7 0.04
41 9 0.06
42 1 0.01
43 11 0.07
44 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (37 bp):
TATATATATATAGTTTTTTTAAAACACTTTTGAAAAC
Found at i:499552 original size:41 final size:36
Alignment explanation
Indices: 499376--499601 Score: 159
Period size: 36 Copynumber: 5.8 Consensus size: 36
499366 TATAGTTCAC
*
499376 AAACAGTTTTTGGAAATACATATATAATATATAGTTTTCTTAA
1 AAACA-TTTTT-GAAA-AC-TATATAATATATAG-GTT-TT-A
* * * *
499419 AAACA-TTTT-AAAAATGTATAGTATATAGTTTTTTTA
1 AAACATTTTTGAAAACTATATAATATATAG--GTTTTA
* *
499455 AAACACTTTTGAAAACTATATAATATATAGTTTTTA
1 AAACATTTTTGAAAACTATATAATATATAGGTTTTA
* * *
499491 AAACATTTTAGAAAAATATATAATATATGGGTTTTA
1 AAACATTTTTGAAAACTATATAATATATAGGTTTTA
* *
499527 AAGTCATATTTTTTGAAAACTTATATAATATATAGTTTTTTAA
1 AA---ACA-TTTTTGAAAAC-TATATAATATATAG-GTTTT-A
499570 AAACATTTTTGAAAACTAATATATAATATATA
1 AAACATTTTTGAAAAC---TATATAATATATA
499602 ATTTCTAAAA
Statistics
Matches: 153, Mismatches: 18, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
36 45 0.29
37 18 0.12
38 21 0.14
39 16 0.10
40 11 0.07
41 30 0.20
42 4 0.03
43 8 0.05
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (36 bp):
AAACATTTTTGAAAACTATATAATATATAGGTTTTA
Found at i:499674 original size:32 final size:33
Alignment explanation
Indices: 499615--499695 Score: 137
Period size: 32 Copynumber: 2.5 Consensus size: 33
499605 TCTAAAACTC
*
499615 TTTTGGAAATTATATAGTTTTTTAAAAAAACAT
1 TTTTGAAAATTATATAGTTTTTTAAAAAAACAT
499648 TTTTGAAAATTATATAG-TTTTTAAAAAAACAT
1 TTTTGAAAATTATATAGTTTTTTAAAAAAACAT
499680 TTTTGAAAATTTATAT
1 TTTTGAAAA-TTATAT
499696 TTAATATATA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 24 0.52
33 22 0.48
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.47
Consensus pattern (33 bp):
TTTTGAAAATTATATAGTTTTTTAAAAAAACAT
Found at i:499783 original size:13 final size:13
Alignment explanation
Indices: 499767--499791 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
499757 AAATAAATAT
499767 TTATTTATTATTG
1 TTATTTATTATTG
499780 TTATTTATTATT
1 TTATTTATTATT
499792 ATTTGTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTTATTATTG
Found at i:499797 original size:17 final size:17
Alignment explanation
Indices: 499764--499811 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
499754 ATTAAATAAA
499764 TATTTATTTATTA-TTGT
1 TATTTA-TTATTATTTGT
499781 TATTTATTATTATTTGT
1 TATTTATTATTATTTGT
*
499798 T-TCTATTACTTATT
1 TATTTATTA-TTATT
499812 ATTCATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (17 bp):
TATTTATTATTATTTGT
Found at i:500987 original size:17 final size:19
Alignment explanation
Indices: 500949--500998 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
500939 AAGTTTTATT
*
500949 TTATTTTGTTTTATCGTCA
1 TTATTTTATTTTATCGTCA
*
500968 TTATTTT-TTTTCTCGT-A
1 TTATTTTATTTTATCGTCA
500985 TTATTTTATTTTAT
1 TTATTTTATTTTAT
500999 TGCTTCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.29
18 13 0.46
19 7 0.25
ACGTcount: A:0.16, C:0.08, G:0.06, T:0.70
Consensus pattern (19 bp):
TTATTTTATTTTATCGTCA
Found at i:505325 original size:21 final size:21
Alignment explanation
Indices: 505299--505344 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
505289 ATTCAAATCG
505299 AGATGCAGTGGAGAACTTCAT
1 AGATGCAGTGGAGAACTTCAT
*
505320 AGATGCAGTGGAGAACTTCTT
1 AGATGCAGTGGAGAACTTCAT
505341 AGAT
1 AGAT
505345 ATGAATCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (21 bp):
AGATGCAGTGGAGAACTTCAT
Found at i:507342 original size:14 final size:14
Alignment explanation
Indices: 507316--507353 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
507306 AATTGGAATT
*
507316 AAATAAAAAAACAGA
1 AAATAATAAAACA-A
507331 AAA-AATAAAACAA
1 AAATAATAAAACAA
507344 AAATAATAAA
1 AAATAATAAA
507354 TAAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.19
14 14 0.67
15 3 0.14
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.11
Consensus pattern (14 bp):
AAATAATAAAACAA
Found at i:507364 original size:19 final size:19
Alignment explanation
Indices: 507315--507370 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
507305 AAATTGGAAT
* *
507315 TAAATAAAAAAACAGA-AA
1 TAAATAAAAAAAAAAATAA
*
507333 -AAAT-AAAACAAAAATAA
1 TAAATAAAAAAAAAAATAA
507350 TAAATAAAAAAAAAAATAA
1 TAAATAAAAAAAAAAATAA
507369 TA
1 TA
507371 TATATATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 7 0.23
17 6 0.19
18 4 0.13
19 14 0.45
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (19 bp):
TAAATAAAAAAAAAAATAA
Found at i:507424 original size:14 final size:13
Alignment explanation
Indices: 507403--507461 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
507393 AAAACAAGTG
507403 AAAAAATAATAAT
1 AAAAAATAATAAT
507416 AATAAAATAATAAT
1 AA-AAAATAATAAT
* *
507430 AAACAAATACTAAG
1 AAA-AAATAATAAT
*
507444 AAGAAAAAAATAAT
1 AA-AAAATAATAAT
507458 AAAA
1 AAAA
507462 TAAAGTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 5 0.13
14 32 0.84
15 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:507602 original size:2 final size:2
Alignment explanation
Indices: 507595--507640 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
507585 TATGTAGATA
507595 AT AT AT AT AT AT A- AT A- AT AGT A- AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
507634 AT AT AT A
1 AT AT AT A
507641 ACAACAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.10
2 33 0.85
3 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:507733 original size:49 final size:48
Alignment explanation
Indices: 507622--507777 Score: 125
Period size: 52 Copynumber: 3.1 Consensus size: 48
507612 TAGTAATAAT
* * * * *
507622 ATATATATATATATATATAACAACAATAATATCAATAAAAAAATAAAAAATAA
1 ATATATATATATATATATAATAATAA-AAAAT--AT-AGAAAATAAATAA-AA
*
507675 ATATA-ATATAATATAATGGTAATAAATAAAAAATATAGAAAATAAATAGAAA
1 ATATATATAT-ATAT-AT-ATAAT-AATAAAAAATATAGAAAATAAATA-AAA
* * * *
507727 ATATATATATATATATATAATATTATAAAATATAGTACATAAATAAAA
1 ATATATATATATATATATAATAATAAAAAATATAGAAAATAAATAAAA
507775 ATA
1 ATA
507778 ACCAAATAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
48 6 0.07
49 20 0.23
50 4 0.05
51 2 0.02
52 25 0.29
53 16 0.19
54 2 0.02
55 7 0.08
56 4 0.05
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (48 bp):
ATATATATATATATATATAATAATAAAAAATATAGAAAATAAATAAAA
Found at i:507991 original size:21 final size:22
Alignment explanation
Indices: 507955--508014 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
507945 ATATAGAAAA
*
507955 TAAATAAATAATATATATATATG
1 TAAATAAATAAAATATA-ATATG
*
507978 T-AAT-AATAAAATATAATATT
1 TAAATAAATAAAATATAATATG
507998 TAAATAAATAAAA-ATAA
1 TAAATAAATAAAATATAA
508015 GAAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 5 0.15
21 17 0.52
22 10 0.30
23 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAATAAATAAAATATAATATG
Found at i:508013 original size:28 final size:27
Alignment explanation
Indices: 507921--508014 Score: 66
Period size: 28 Copynumber: 3.3 Consensus size: 27
507911 AAAGAGAAAG
*
507921 TAAAAAT-AAAATAATA-TAAGAATAATA
1 TAAAAATAAAAATAATATTTA-AATAA-A
* * **
507948 TAGAAAATAAATAAATAATATATATATATG
1 TA-AAAAT-AA-AAATAATATTTAAATAAA
*
507978 TAATAATAAAATATAATATTTAAATAAA
1 TAAAAATAAAA-ATAATATTTAAATAAA
508006 TAAAAATAA
1 TAAAAATAA
508015 GAAAAAAAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
27 4 0.08
28 27 0.54
29 4 0.08
30 3 0.06
31 11 0.22
32 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (27 bp):
TAAAAATAAAAATAATATTTAAATAAA
Found at i:510015 original size:80 final size:80
Alignment explanation
Indices: 509701--510483 Score: 926
Period size: 80 Copynumber: 9.7 Consensus size: 80
509691 GATAATTTTG
* * * *
509701 TTGGCATATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTGCCTTTGAGCTGAGTGTA
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTA
* *
509766 ATCGAAAT-AAATGGTCT
64 ATCGAACTCGAA-GGTCT
* * * *
509783 TTGATGACAAATAACCCTTCTCGCCTTGAGTTATGCTGTAAATGATGTGCC-TTGTAGCTGAGTG
1 TTG--G-CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTG-AGCTGAGTG
*
509847 TAATTGAACTCGAAGGTCT
62 TAATCGAACTCGAAGGTCT
* * * * *
509866 TTGGCAGATAACCCTTCTAGCCTTGAG-TTTGCTGCAAATGACGTGCCTCTGAGCTTAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
*
509930 CGAACTTGAAGGTCT
66 CGAACTCGAAGGTCT
* *
509945 TTGGCAGATATCCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
510010 CGAACTCGAAGGTCT
66 CGAACTCGAAGGTCT
* * * * * * *
510025 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCATATAATGTTCCTCTGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
*
510090 CGAACTCGAAAGTCT
66 CGAACTCGAAGGTCT
*
510105 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
* *
510170 CGAAATCGAAAGTCT
66 CGAACTCGAAGGTCT
* * * * * * *
510185 TTGGCAGATAACACTTATAGCCTTAAGTTATGCTACAAATGATGTGCCTCTGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
510250 CGAACTCGAAGGTCT
66 CGAACTCGAAGGTCT
* * * * *
510265 TTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATAATGTGTCTTTGAGTTGAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
* *
510330 TGAACTCGAAGGTAT
66 CGAACTCGAAGGTCT
* ** * * * *
510345 TTGGCAGATAACCCATCTAACCTTGAGTTATGCTGCAAATGATGCGCCTTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
*
510410 CGAACTTGAAGGTCTTTT
66 CGAACTCGAAGGTC---T
* * ** *
510428 GTTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGAAAATGATGTGCC-TTGAGCT
1 -TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCT
510484 ATGCTACAAA
Statistics
Matches: 597, Mismatches: 93, Indels: 21
0.84 0.13 0.03
Matches are distributed among these distances:
79 67 0.11
80 410 0.69
81 1 0.00
82 6 0.01
83 41 0.07
84 41 0.07
85 31 0.05
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (80 bp):
TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
CGAACTCGAAGGTCT
Found at i:510494 original size:26 final size:26
Alignment explanation
Indices: 510447--510510 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
510437 TAGCCCTTCT
*
510447 TGCCTTGAGCTATATTGAAAATGATG
1 TGCCTTGAGCTATACTGAAAATGATG
* *
510473 TGCCTTGAGCTATGCT-ACAAATGTTG
1 TGCCTTGAGCTATACTGA-AAATGATG
510499 TGCCTTTGAGCT
1 TGCC-TTGAGCT
510511 GAGTGTAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.03
26 25 0.76
27 7 0.21
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (26 bp):
TGCCTTGAGCTATACTGAAAATGATG
Found at i:510565 original size:110 final size:110
Alignment explanation
Indices: 510365--510595 Score: 300
Period size: 110 Copynumber: 2.1 Consensus size: 110
510355 ACCCATCTAA
* * * * *
510365 CCTTGAGTTATGCTGCAAATGATGCGCCTTTGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGT
1 CCTTGAGCTATGCTACAAATGATGCGCCTTTGAGCTGAGCGTAATCAAACTCGAAGGTCTTTTGT
* * *
510430 TGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGAAAATGATGTG
66 TGGCAAATAACCCTTCTAGCCTTGAGCTATACTGAAAATGATGTG
* * *
510475 CCTTGAGCTATGCTACAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGCTACAAATGATGCGCCTTTGAGCTGAGCGTAATCAAACTCGAAGGTCTTTTGT
* * * * * *
510540 TGGCAGATAATCCTTCTAGCTTTGAGTTATGCTGCAAATGATGTG
66 TGGCAAATAACCCTTCTAGCCTTGAGCTATACTGAAAATGATGTG
510585 CCTTGGAGCTA
1 CCTT-GAGCTA
510596 AGCGTAGTCG
Statistics
Matches: 103, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
110 97 0.94
111 6 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (110 bp):
CCTTGAGCTATGCTACAAATGATGCGCCTTTGAGCTGAGCGTAATCAAACTCGAAGGTCTTTTGT
TGGCAAATAACCCTTCTAGCCTTGAGCTATACTGAAAATGATGTG
Found at i:510608 original size:194 final size:190
Alignment explanation
Indices: 510283--510678 Score: 533
Period size: 194 Copynumber: 2.1 Consensus size: 190
510273 TAGCCCTTCT
* * * * **
510283 TGCCTTGAGCTATGTTGCAAATAATGTGTCTTTGAGTTGAGTGTAATTGAACTCGAAGGTATTTG
1 TGCCTTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTATTTG
* *
510348 GCAGATAACCCATCTAACCTTGAGTTATGCTGCAAATGATGCGCCTTTGAGCTGAGCGTAGTCGA
66 GCAGATAACCCATCTAACCTTGAGTTATGCTGCAAATGATGCGCCTTGGAGCTAAGCGTAGTCGA
* * *
510413 ACTTGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGA-GCTATATTGAAAATGATG
131 ACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCATT-ATGCTATATTGAAAATGATG
** *
510473 TGCCTTGAGCTATGCTACAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTT
1 TGCCTTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGG---TAT
* * * * *
510538 GTTGGCAGATAATCCTTCTAGCTTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTAAGCGTAG
63 -TTGGCAGATAACCCATCTAACCTTGAGTTATGCTGCAAATGATGCGCCTTGGAGCTAAGCGTAG
* * *
510603 TCGAACTCGAAGGTCTTTTGTTGGTAAATAACCCTTCTTGCATTATGCTATGTTGCAAATGATG
127 TCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCATTATGCTATATTGAAAATGATG
510667 TGCCTTGGAGCT
1 TGCCTT-GAGCT
510679 GAGCATAGTC
Statistics
Matches: 178, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
190 51 0.29
193 3 0.02
194 119 0.67
195 5 0.03
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (190 bp):
TGCCTTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTATTTG
GCAGATAACCCATCTAACCTTGAGTTATGCTGCAAATGATGCGCCTTGGAGCTAAGCGTAGTCGA
ACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCATTATGCTATATTGAAAATGATG
Found at i:510618 original size:84 final size:84
Alignment explanation
Indices: 510474--510908 Score: 539
Period size: 84 Copynumber: 5.2 Consensus size: 84
510464 AAAATGATGT
* * * * * *
510474 GCCTTGAGCTATGCTACAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTG
1 GCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* *
510539 TTGGCAGATAATCCTTCTA
66 TTGGTAGATAACCCTTCTA
* * *
510558 GCTTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTG
1 GCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* *
510623 TTGGTAAATAACCCTTCTT
66 TTGGTAGATAACCCTTCTA
* * * *
510642 GCATT-ATGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTT
1 GCCTTGA-GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
* *
510706 GTTGGTAGATAACGCTTATA
65 GTTGGTAGATAACCCTTCTA
* ** * *
510726 GCCTTGAGTTATATTTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTA
1 GCCTTGAGCTAT-GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
* * *
510791 GTTGGCAGATAGCCCTTCTT
65 GTTGGTAGATAACCCTTCTA
* * * * *
510811 GCCTTGAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTG
1 GCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* *
510876 TTGGTAGATAGCCCTTCTC
66 TTGGTAGATAACCCTTCTA
510895 GCCTTGAGCTATGC
1 GCCTTGAGCTATGC
510909 CGTAAATAGA
Statistics
Matches: 301, Mismatches: 47, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
83 1 0.00
84 226 0.75
85 74 0.25
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (84 bp):
GCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
TTGGTAGATAACCCTTCTA
Found at i:510809 original size:169 final size:168
Alignment explanation
Indices: 510477--510908 Score: 589
Period size: 169 Copynumber: 2.6 Consensus size: 168
510467 ATGATGTGCC
*
510477 TTGAGCTATGCTACAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTG
1 TTGAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTG
* * *
510542 GCAGATAATCCTTCTAGCTTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGA
66 GTAGATAATCCTTATAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGA
* *
510607 ACTCGAAGGTCTTTTGTTGGTAAATAACCCTTCTTGCA
131 ACTCGAAGGTCTTTAGTTGGCAAATAACCCTTCTTGCA
* * * ** *
510645 TT-ATGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTTGTT
1 TTGA-GCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTT
** * *
510709 GGTAGATAA-CGCTTATAGCCTTGAGTTATATTTGCATATGATGTGCCTTGGAGCTGAGCGTAGT
65 GGTAGATAATC-CTTATAGCCTTGAGTTAT-GCTGCAAATGATGTGCCTTGGAGCTAAGCGTAGT
* * *
510773 CGAACTCGAAGGTCTTTAGTTGGCAGATAGCCCTTCTTGCC
128 CGAACTCGAAGGTCTTTAGTTGGCAAATAACCCTTCTTGCA
**
510814 TTGAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTGTTG
1 TTGAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTG
** * * *
510879 GTAGATAGCCCTTCTCGCCTTGAGCTATGC
66 GTAGATAATCCTTATAGCCTTGAGTTATGC
510909 CGTAAATAGA
Statistics
Matches: 226, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
167 2 0.01
168 79 0.35
169 143 0.63
170 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (168 bp):
TTGAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTG
GTAGATAATCCTTATAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGA
ACTCGAAGGTCTTTAGTTGGCAAATAACCCTTCTTGCA
Found at i:512233 original size:95 final size:94
Alignment explanation
Indices: 512026--512280 Score: 314
Period size: 95 Copynumber: 2.7 Consensus size: 94
512016 GGCTAGTTGG
* * * * *
512026 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAATA-TCATTGTATAGAT
1 ATCCATAAAGACGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGATTTATTG--T--AT
* *
512090 ATTATAATCACCTTTTTAGGCTAGCTGAATATT
62 ATTATAATCACCTTTTCAAGCTAGCTGAATATT
* *
512123 ATCCATAAAGACGAGGTGTTTAACAAATTGCTCTAGAGGGACAACTCAAGATTTATTGTATATTA
1 ATCCATAAAGACGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGATTTATTGTATATTA
*
512188 TAATCACCTTTATCAAGCTAGCTGAATCTT
66 TAATCACCTTT-TCAAGCTAGCTGAATATT
* * * * * *
512218 ATCCATAAAGTCGAGGCGTTTAACCAATTACTTTAGATGGATAACTCAAGCTTTATTGTATAT
1 ATCCATAAAGACGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGATTTATTGTATAT
512281 ATGTAATATT
Statistics
Matches: 138, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
94 17 0.12
95 70 0.51
96 1 0.01
97 45 0.33
98 5 0.04
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (94 bp):
ATCCATAAAGACGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGATTTATTGTATATTA
TAATCACCTTTTCAAGCTAGCTGAATATT
Found at i:514982 original size:17 final size:17
Alignment explanation
Indices: 514960--515023 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 17
514950 AAATAAGTAG
514960 AAATAAAAATAAAAACA
1 AAATAAAAATAAAAACA
*
514977 AAATAAACAA-AATGGTAACA
1 AAATAAA-AATAA---AAACA
514997 TAAATAAAAAT-AAAACA
1 -AAATAAAAATAAAAACA
515014 AGAATAAAAA
1 A-AATAAAAA
515024 ACTAGGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
16 1 0.03
17 21 0.55
18 2 0.05
20 7 0.18
21 7 0.18
ACGTcount: A:0.75, C:0.06, G:0.05, T:0.14
Consensus pattern (17 bp):
AAATAAAAATAAAAACA
Found at i:515075 original size:10 final size:11
Alignment explanation
Indices: 515047--515115 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 11
515037 GGAATTAAAT
515047 AAAAATAGAAAC
1 AAAAATA-AAAC
515059 AAAAATAAAAC
1 AAAAATAAAAC
515070 AAAATAATAATAA-
1 -AAA-AATAA-AAC
* *
515083 ATAAATAAAAG
1 AAAAATAAAAC
515094 AAAAATAATAA-
1 AAAAATAA-AAC
515105 AAATAATAAAA
1 AAA-AATAAAA
515116 AATAATATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
10 2 0.04
11 21 0.43
12 19 0.39
13 5 0.10
14 2 0.04
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAC
Found at i:515090 original size:24 final size:24
Alignment explanation
Indices: 515061--515115 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
515051 ATAGAAACAA
*
515061 AAATAAAA-CAAAATAATAATAAAT
1 AAATAAAAGAAAAATAATAA-AAAT
515085 AAATAAAAGAAAAATAATAAAAAT
1 AAATAAAAGAAAAATAATAAAAAT
515109 -AATAAAA
1 AAATAAAA
515116 AATAATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 7 0.24
24 12 0.41
25 10 0.34
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (24 bp):
AAATAAAAGAAAAATAATAAAAAT
Found at i:515108 original size:34 final size:36
Alignment explanation
Indices: 515049--515120 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 36
515039 AATTAAATAA
*
515049 AAATAGAAACAAAAATAAAACAAAATAATAATAAAT
1 AAATAGAAACAAAAATAAAACAAAATAATAAAAAAT
* *
515085 AAATA-AAAGAAAAATAATA-AAAATAATAAAAAAT
1 AAATAGAAACAAAAATAAAACAAAATAATAAAAAAT
515119 AA
1 AA
515121 TATATACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 16 0.48
35 12 0.36
36 5 0.15
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (36 bp):
AAATAGAAACAAAAATAAAACAAAATAATAAAAAAT
Found at i:515117 original size:83 final size:82
Alignment explanation
Indices: 514960--515118 Score: 182
Period size: 83 Copynumber: 1.9 Consensus size: 82
514950 AAATAAGTAG
** *
514960 AAATAAAAATAAAAACAAAATAAACAAAATGGTAACATAAATAAAAATAAAACAAGAATAAAAAA
1 AAATAAAAATAAAAACAAAATAAACAAAATAATAACATAAATAAAAATAAAAAAAGAATAAAAAA
*
515025 CTAGGAAAAATTGGAATT
66 ATA-GAAAAATTGGAATT
* *
515043 AAATAAAAATAGAAACAAAAATAAAACAAAATAAT-A-ATAAATAAATAA-AAGAAAAATAATAA
1 AAATAAAAATAAAAAC-AAAAT-AAACAAAATAATAACATAAATAAA-AATAA-AAAAAGAATAA
515105 AAATAATA-AAAAAT
62 AAA-AATAGAAAAAT
515119 AATATATACA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
83 32 0.49
84 20 0.31
85 13 0.20
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (82 bp):
AAATAAAAATAAAAACAAAATAAACAAAATAATAACATAAATAAAAATAAAAAAAGAATAAAAAA
ATAGAAAAATTGGAATT
Found at i:515120 original size:38 final size:38
Alignment explanation
Indices: 515042--515116 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
515032 AAATTGGAAT
* *
515042 TAAATAAAAATAGAAACAAAAATAAAACAAAATAATAA
1 TAAATAAAAAAAGAAACAAAAATAAAACAAAATAAAAA
* *
515080 TAAATAAATAAAAGAAA-AATAATAAAA-ATAATAAAAA
1 TAAATAAA-AAAAGAAACAAAAATAAAACAAAATAAAAA
515117 ATAATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.25
38 17 0.53
39 7 0.22
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (38 bp):
TAAATAAAAAAAGAAACAAAAATAAAACAAAATAAAAA
Found at i:515121 original size:19 final size:20
Alignment explanation
Indices: 515042--515122 Score: 67
Period size: 19 Copynumber: 4.0 Consensus size: 20
515032 AAATTGGAAT
* *
515042 TAAATAAAAATAGAAACAAAAA
1 TAAATAAAAA-A-AAATAATAA
* *
515064 TAAA-ACAAAATAATAATAAA
1 TAAATAAAAAAAAATAAT-AA
515084 TAAATAAAAGAAAAATAATAA
1 TAAATAAAA-AAAAATAATAA
*
515105 -AAATAATAAAAAATAATA
1 TAAATAAAAAAAAATAATA
515123 TATACATATA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 14 0.29
20 14 0.29
21 9 0.18
22 12 0.24
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (20 bp):
TAAATAAAAAAAAATAATAA
Found at i:515354 original size:2 final size:2
Alignment explanation
Indices: 515347--515403 Score: 84
Period size: 2 Copynumber: 29.5 Consensus size: 2
515337 TGTGTAGATA
515347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AGT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
515388 A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
515404 ACAATAATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.06
2 46 0.90
3 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:515413 original size:15 final size:17
Alignment explanation
Indices: 515344--515436 Score: 57
Period size: 16 Copynumber: 5.5 Consensus size: 17
515334 AAATGTGTAG
* * *
515344 ATAATATATATATATAT
1 ATAATATAAAAATAAAT
* * *
515361 AT-ATATATATATATAT
1 ATAATATAAAAATAAAT
* *
515377 ATAATAGTAATAATATAT
1 ATAATA-TAAAAATAAAT
*
515395 ATATATATAACAAT-AAT
1 ATA-ATATAAAAATAAAT
*
515412 ATCA-ATAAAAATAAAT
1 ATAATATAAAAATAAAT
515428 ATAATATAA
1 ATAATATAA
515437 TGGTAATAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
15 7 0.11
16 23 0.37
17 13 0.21
18 17 0.27
19 3 0.05
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (17 bp):
ATAATATAAAAATAAAT
Found at i:515491 original size:25 final size:25
Alignment explanation
Indices: 515347--515492 Score: 89
Period size: 25 Copynumber: 5.6 Consensus size: 25
515337 TGTGTAGATA
* * *
515347 ATATATAT-ATATATATATATATAT
1 ATATATATAATAAATAAATAAATAT
*
515371 ATATATATAATAGTAAT-AATATATAT
1 ATATATATAATA--AATAAATAAATAT
* * *
515397 ATATATAACAATAATATCAATAAAAATAA
1 ATATAT-ATAATAA-AT-AA-ATAAATAT
* *
515426 ATATAATATAATGGTAATAAATAAAAAT
1 ATAT-ATATAAT--AAATAAATAAATAT
* *
515454 ATATAGAAAATAAATAAATAAATAT
1 ATATATATAATAAATAAATAAATAT
*
515479 ATATATATTATAAA
1 ATATATATAATAAA
515493 ATATAGTACT
Statistics
Matches: 93, Mismatches: 18, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
24 8 0.09
25 27 0.29
26 16 0.17
27 12 0.13
28 10 0.11
29 15 0.16
30 4 0.04
31 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (25 bp):
ATATATATAATAAATAAATAAATAT
Found at i:515576 original size:63 final size:58
Alignment explanation
Indices: 515439--515550 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 58
515429 TAATATAATG
** *
515439 GTAAT-AAATAAAAATATATAGAAAATAAATAAATAAATATATATATATTATAAAATATA
1 GTAATAAAATAAAAA-ATA-ACCAAATAAATAAATAAATATATATATATAATAAAATATA
* * *
515498 GTACTTAAATAAAAAATAACCAAATAAATATAATTAATATATATATATAATAA
1 GTAATAAAATAAAAAATAACCAAATAAATA-AATAAATATATATATATAATAA
515551 TAGGTATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 10 0.22
59 27 0.59
60 9 0.20
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (58 bp):
GTAATAAAATAAAAAATAACCAAATAAATAAATAAATATATATATATAATAAAATATA
Found at i:515621 original size:30 final size:30
Alignment explanation
Indices: 515556--515632 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
515546 AATAATAGGT
* *
515556 ATATAAATAAAATATTAAAAAAATATACACAC
1 ATATATAT-AAATA-TAAAAAAATACACACAC
* *
515588 ATATATATAAATATAACAAAATACACACGC
1 ATATATATAAATATAAAAAAATACACACAC
*
515618 ATATATATATATATA
1 ATATATATAAATATA
515633 TATAACAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 28 0.70
31 5 0.12
32 7 0.17
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.29
Consensus pattern (30 bp):
ATATATATAAATATAAAAAAATACACACAC
Found at i:515664 original size:22 final size:22
Alignment explanation
Indices: 515634--515686 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
515624 ATATATATAT
*
515634 ATAACAAAA-TAAGTAATATAAA-
1 ATAATAAAAGTAA-TAATA-AAAG
515656 ATAATAAAAGTAATAATAAAAG
1 ATAATAAAAGTAATAATAAAAG
*
515678 GTAATAAAA
1 ATAATAAAA
515687 AGAAAGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.11
22 21 0.78
23 3 0.11
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (22 bp):
ATAATAAAAGTAATAATAAAAG
Found at i:515666 original size:19 final size:21
Alignment explanation
Indices: 515644--515686 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
515634 ATAACAAAAT
515644 AAGTAAT-ATAAAA-TAATAA
1 AAGTAATAATAAAAGTAATAA
515663 AAGTAATAATAAAAGGTAATAA
1 AAGTAATAATAAAA-GTAATAA
515685 AA
1 AA
515687 AGAAAGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 6 0.29
22 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (21 bp):
AAGTAATAATAAAAGTAATAA
Found at i:515672 original size:12 final size:13
Alignment explanation
Indices: 515655--515684 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
515645 AGTAATATAA
515655 AATAATAAAA-GT
1 AATAATAAAAGGT
515667 AATAATAAAAGGT
1 AATAATAAAAGGT
515680 AATAA
1 AATAA
515685 AAAGAAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (13 bp):
AATAATAAAAGGT
Found at i:515724 original size:11 final size:10
Alignment explanation
Indices: 515647--515739 Score: 50
Period size: 11 Copynumber: 8.9 Consensus size: 10
515637 ACAAAATAAG
515647 TAATATAAAA
1 TAATATAAAA
*
515657 TAATA-AAAG
1 TAATATAAAA
515666 TAATAATAAAA
1 TAAT-ATAAAA
515677 GGTAATA-AAAA
1 --TAATATAAAA
* *
515688 GAA-AGAGAAA
1 TAATATA-AAA
*
515698 GTAAAAATAAAA
1 -T-AATATAAAA
515710 TAATATAAGAA
1 TAATATAA-AA
515721 TAATATAAAAA
1 TAATAT-AAAA
515732 TAA-ATAAA
1 TAATATAAA
515740 TAAAATATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 23
0.69 0.06 0.24
Matches are distributed among these distances:
8 1 0.02
9 13 0.20
10 17 0.26
11 21 0.32
12 8 0.12
13 6 0.09
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.22
Consensus pattern (10 bp):
TAATATAAAA
Found at i:515746 original size:21 final size:21
Alignment explanation
Indices: 515722--515791 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
515712 ATATAAGAAT
*
515722 AATATAAAAATAAATAAATAA
1 AATATAAATATAAATAAATAA
* *
515743 AATATATATATGTAAT-AATAA
1 AATATAAATAT-AAATAAATAA
*
515764 AATATAATATTTAAATAAATAA
1 AATATAA-ATATAAATAAATAA
515786 AA-ATAA
1 AATATAA
515792 GAAAAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
21 27 0.68
22 13 0.32
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (21 bp):
AATATAAATATAAATAAATAA
Found at i:516665 original size:37 final size:37
Alignment explanation
Indices: 516612--516716 Score: 165
Period size: 37 Copynumber: 2.8 Consensus size: 37
516602 CATTTTCGTC
516612 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * *
516649 TTGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
516686 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
516717 CCACAAGTAC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:517841 original size:19 final size:19
Alignment explanation
Indices: 517817--517853 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
517807 ACCTTACTAA
517817 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
517836 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
517854 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:521324 original size:7 final size:7
Alignment explanation
Indices: 521282--521357 Score: 75
Period size: 7 Copynumber: 10.6 Consensus size: 7
521272 AATCAAGAAC
521282 AAAAAGA
1 AAAAAGA
521289 AAAGAAGCA
1 AAA-AAG-A
521298 AAAAAGTA
1 AAAAAG-A
521306 AAAAA-A
1 AAAAAGA
*
521312 ACAAAGA
1 AAAAAGA
521319 AAAAAGA
1 AAAAAGA
*
521326 GAAAAGA
1 AAAAAGA
*
521333 GAAAAAGC
1 -AAAAAGA
521341 AAAAAG-
1 AAAAAGA
521347 AAAAAGA
1 AAAAAGA
521354 AAAA
1 AAAA
521358 GGGACAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
6 11 0.19
7 26 0.45
8 17 0.29
9 4 0.07
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:521329 original size:39 final size:34
Alignment explanation
Indices: 521276--521357 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 34
521266 AGATCCAATC
*
521276 AAGAACAAAAAGAAAAGAAGCAAAAAAGTAAAAAAAACA
1 AAGAA-AAAAAGAAAAG-AG--AAAAAGCAAAAAAAA-A
*
521315 AAGAAAAAAGAGAAAAGAGAAAAAGCAAAAAGAAA
1 AAGAAAAAA-AGAAAAGAGAAAAAGCAAAAAAAAA
521350 AAGAAAAA
1 AAGAAAAA
521358 GGGACAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
35 9 0.22
36 13 0.32
38 6 0.15
39 12 0.30
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.01
Consensus pattern (34 bp):
AAGAAAAAAAGAAAAGAGAAAAAGCAAAAAAAAA
Found at i:521352 original size:21 final size:20
Alignment explanation
Indices: 521282--521357 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 20
521272 AATCAAGAAC
521282 AAAAAGAAAAGAAGCAAAAAAG
1 AAAAAGAAAA-AAGC-AAAAAG
*
521304 TAAAAA-AAACAAAGAAAAAAG
1 -AAAAAGAAA-AAAGCAAAAAG
521325 AGAAAAGAGAAAAAGCAAAAAG
1 A-AAAAGA-AAAAAGCAAAAAG
521347 AAAAAGAAAAA
1 AAAAAGAAAAA
521358 GGGACAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
20 5 0.11
21 16 0.34
22 18 0.38
23 8 0.17
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAAGCAAAAAG
Found at i:521995 original size:22 final size:22
Alignment explanation
Indices: 521970--522029 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
521960 AACCGTTGAG
521970 CATCAAATGCCAAACCTATGAA
1 CATCAAATGCCAAACCTATGAA
* *
521992 CATCAAATGCCAAACATTTGAA
1 CATCAAATGCCAAACCTATGAA
522014 CATCAAATGCCAAACC
1 CATCAAATGCCAAACC
522030 CTTAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.45, C:0.28, G:0.08, T:0.18
Consensus pattern (22 bp):
CATCAAATGCCAAACCTATGAA
Found at i:523138 original size:106 final size:106
Alignment explanation
Indices: 522837--523686 Score: 1346
Period size: 106 Copynumber: 8.0 Consensus size: 106
522827 ATATCGTGCC
* * * *
522837 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
522902 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
522943 ACTCCAGACAACGCAAGTTCAACTTCACAACGAA-GGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
523007 AATTTCAGAGCCAATATCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
523048 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
523113 AATTTTAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
523154 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT-
* *
523218 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
523260 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
523325 AATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
523366 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
523431 AATTTTAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
523472 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
523537 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
523578 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACTGCTGGTTGTCAATAAACAACTTC-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
** * * *
523642 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
523683 ACTC
1 ACTC
523687 AGAACAATGC
Statistics
Matches: 689, Mismatches: 52, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
105 140 0.20
106 547 0.79
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:524492 original size:36 final size:37
Alignment explanation
Indices: 524402--524504 Score: 154
Period size: 36 Copynumber: 2.8 Consensus size: 37
524392 ATTTTCGTCC
* *
524402 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTTAAACTCCTAAAAATAGGATAGAAGTT
*
524439 TGCTAGGATTTAAACTCCTAAAAATAGGATAG-AGTT
1 TACTAGGATTTAAACTCCTAAAAATAGGATAGAAGTT
* *
524475 TACTATGATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTTAAACTCCTAAAAATAGGAT
524505 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 30 0.50
37 30 0.50
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (37 bp):
TACTAGGATTTAAACTCCTAAAAATAGGATAGAAGTT
Found at i:525277 original size:25 final size:26
Alignment explanation
Indices: 525223--525279 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
525213 AAAATAATAA
* *
525223 ATAAATATACATGTATATATATACGT
1 ATAAATAAACATGAATATATATACGT
*
525249 -TAAATAAACATGAATATATATA-TT
1 ATAAATAAACATGAATATATATACGT
525273 ATAAATA
1 ATAAATA
525280 TGTGGTATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (26 bp):
ATAAATAAACATGAATATATATACGT
Found at i:528460 original size:21 final size:21
Alignment explanation
Indices: 528436--528476 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
528426 TTTTCAACAG
*
528436 AAGAAAATATTAATATTCCAA
1 AAGAAAATATTAATAATCCAA
528457 AAGAAAATATTAATAATCCA
1 AAGAAAATATTAATAATCCA
528477 TATCCTATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.27
Consensus pattern (21 bp):
AAGAAAATATTAATAATCCAA
Found at i:533058 original size:35 final size:35
Alignment explanation
Indices: 533012--533131 Score: 161
Period size: 35 Copynumber: 3.4 Consensus size: 35
533002 CCTTTAATCC
533012 ATAAGGAATTACCAACTGATCGGTGCTGAACCTAT
1 ATAAGGAATTACCAACTGATCGGTGCTGAACCTAT
* *
533047 ATAAGGAATTACCAACCGATCGGTGTTGAACC-AGT
1 ATAAGGAATTACCAACTGATCGGTGCTGAACCTA-T
* * *
533082 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTAT
1 ATAAGGAATTACCAAC-TGATCGGTGCTGAACCTAT
*
533118 ATAAAGAATTACCA
1 ATAAGGAATTACCA
533132 GTAGATCAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
34 1 0.01
35 46 0.62
36 26 0.35
37 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (35 bp):
ATAAGGAATTACCAACTGATCGGTGCTGAACCTAT
Found at i:533146 original size:35 final size:35
Alignment explanation
Indices: 533012--533150 Score: 129
Period size: 35 Copynumber: 3.9 Consensus size: 35
533002 CCTTTAATCC
* * *
533012 ATAAGGAATTACCAACT-GATCGGTGCTGAACCTAT
1 ATAAGGAATTACC-AGTAGATCAGAGCTGAACCTAT
*** * * *
533047 ATAAGGAATTACCAACCGATCGGTGTTGAACC-AGT
1 ATAAGGAATTACCAGTAGATCAGAGCTGAACCTA-T
*
533082 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTAT
1 ATAAGGAATTACCAG-TAGATCAGAGCTGAACCTAT
* *
533118 ATAAAGAATTACCAGTAGATCAAAGCTGAACCT
1 ATAAGGAATTACCAGTAGATCAGAGCTGAACCT
533151 GTAGAGACTT
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
34 2 0.02
35 58 0.66
36 27 0.31
37 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (35 bp):
ATAAGGAATTACCAGTAGATCAGAGCTGAACCTAT
Found at i:533148 original size:71 final size:70
Alignment explanation
Indices: 533012--533149 Score: 168
Period size: 71 Copynumber: 2.0 Consensus size: 70
533002 CCTTTAATCC
* * * * *** *
533012 ATAAGGAATTACCAACTGATCGGTGCTGAACCTATATAAGGAATTACCAACCGATCGGTGTTGAA
1 ATAAGGAATTACCAACTGATCAGAGCTGAACCTATATAAAGAATTACCAACAGATCAAAGCTGAA
533077 CCAGT
66 CCAGT
* **
533082 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTATATAAAGAATTACCAGTAGATCAAAGCTGA
1 ATAAGGAATTACCAAC-TGATCAGAGCTGAACCTATATAAAGAATTACCAACAGATCAAAGCTGA
533147 ACC
65 ACC
533150 TGTAGAGACT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
70 15 0.27
71 41 0.73
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (70 bp):
ATAAGGAATTACCAACTGATCAGAGCTGAACCTATATAAAGAATTACCAACAGATCAAAGCTGAA
CCAGT
Found at i:533971 original size:26 final size:26
Alignment explanation
Indices: 533925--533975 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
533915 GGGTATCTTA
*
533925 GGTCATTTACACTCTAGGGGCATTTT
1 GGTCATTTACACTCTAAGGGCATTTT
*
533951 GGTCATTTACAGT-TCAAGGGCATTT
1 GGTCATTTACACTCT-AAGGGCATTT
533976 CAATCATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.37
Consensus pattern (26 bp):
GGTCATTTACACTCTAAGGGCATTTT
Found at i:537414 original size:36 final size:35
Alignment explanation
Indices: 537304--537443 Score: 140
Period size: 36 Copynumber: 4.0 Consensus size: 35
537294 CCTTAGACCC
* *
537304 ATAAGGAATTACCAAC-TGATCGATACTGAACCTAT
1 ATAAGGAATTACCAGCTTGATCGA-GCTGAACCTAT
* * * * * **
537339 ATAAGGAAATACCA-ATCGATCGTGTTGAACCCGT
1 ATAAGGAATTACCAGCTTGATCGAGCTGAACCTAT
*
537373 ATAAGGAATTACCAGCTTGATCAGAGCTAAACCTAT
1 ATAAGGAATTACCAGCTTGATC-GAGCTGAACCTAT
*
537409 ATAAGGAATTACTAGCTTGATCAGAGCTGAACCTA
1 ATAAGGAATTACCAGCTTGATC-GAGCTGAACCTA
537444 CGAAGACTTC
Statistics
Matches: 84, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
34 20 0.24
35 23 0.27
36 41 0.49
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (35 bp):
ATAAGGAATTACCAGCTTGATCGAGCTGAACCTAT
Found at i:541427 original size:40 final size:39
Alignment explanation
Indices: 541365--541541 Score: 212
Period size: 40 Copynumber: 4.5 Consensus size: 39
541355 GCATATCGAT
* *
541365 TAAGCATTTCGGTGCATATGGTGGGCACAACCTTATGTG
1 TAAGCACTTCGGTGCATATGGTGGGCACGACCTTATGTG
* * *
541404 TAATGTACTTCGGTGCATATGGTGGCCACGACCTTATGTT
1 TAA-GCACTTCGGTGCATATGGTGGGCACGACCTTATGTG
* * * *
541444 TAATGCACTTCGATGTATTTGGTAGGCACGACCTTATGTG
1 TAA-GCACTTCGGTGCATATGGTGGGCACGACCTTATGTG
* *
541484 TAAGCACTTCAGTGCATATGGTGGGCACGATCTTATGTG
1 TAAGCACTTCGGTGCATATGGTGGGCACGACCTTATGTG
*
541523 TAAGAACTAT-GGTGCATAT
1 TAAGCACT-TCGGTGCATAT
541542 ATTTGACTCG
Statistics
Matches: 116, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 48 0.41
40 68 0.59
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (39 bp):
TAAGCACTTCGGTGCATATGGTGGGCACGACCTTATGTG
Found at i:542356 original size:16 final size:15
Alignment explanation
Indices: 542335--542372 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
542325 TTTAGACTCC
542335 ACTTGATCGCTCTCAA
1 ACTTGAT-GCTCTCAA
542351 ACTTGAATGCTCTCAA
1 ACTTG-ATGCTCTCAA
542367 ACTTGA
1 ACTTGA
542373 ACCAATGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.86
17 2 0.10
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (15 bp):
ACTTGATGCTCTCAA
Found at i:542373 original size:16 final size:16
Alignment explanation
Indices: 542343--542373 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
542333 CCACTTGATC
542343 GCTCTCAAACTTGAAT
1 GCTCTCAAACTTGAAT
542359 GCTCTCAAACTTGAA
1 GCTCTCAAACTTGAA
542374 CCAATGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (16 bp):
GCTCTCAAACTTGAAT
Found at i:542560 original size:17 final size:17
Alignment explanation
Indices: 542547--542588 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
542537 ACATAAAATA
542547 TGACTTTTCATAAATTT
1 TGACTTTTCATAAATTT
542564 TGACTTTTCATAAATTT
1 TGACTTTTCATAAATTT
542581 TGACTTTT
1 TGACTTTT
542589 TTTGTCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (17 bp):
TGACTTTTCATAAATTT
Found at i:542675 original size:18 final size:19
Alignment explanation
Indices: 542652--542696 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
542642 TCTGCTAAAA
542652 GTCAATGGTT-AGGTTAAG
1 GTCAATGGTTCAGGTTAAG
542670 GTCAATGGTTCAGGTTAAG
1 GTCAATGGTTCAGGTTAAG
542689 GTCAATGG
1 GTCAATGG
542697 GTCATATCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.27, C:0.09, G:0.33, T:0.31
Consensus pattern (19 bp):
GTCAATGGTTCAGGTTAAG
Found at i:545220 original size:12 final size:12
Alignment explanation
Indices: 545203--545238 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
545193 AGAGGCGAGG
545203 GTATCACCTTTT
1 GTATCACCTTTT
*
545215 GTATCACCTTTA
1 GTATCACCTTTT
*
545227 GAATCACCTTTT
1 GTATCACCTTTT
545239 CCACAGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.44
Consensus pattern (12 bp):
GTATCACCTTTT
Found at i:550600 original size:21 final size:21
Alignment explanation
Indices: 550562--550601 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
550552 TGAAATTCAA
*
550562 ATTTTATTTAATTAATTTATT
1 ATTTTATTTAATAAATTTATT
550583 ATTTTA-TTAATAATATTTA
1 ATTTTATTTAATAA-ATTTA
550602 CTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTATTTAATAAATTTATT
Found at i:551515 original size:2 final size:2
Alignment explanation
Indices: 551508--551537 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
551498 ATTTTACTTA
551508 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
551538 TAAATCGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:552018 original size:209 final size:208
Alignment explanation
Indices: 551654--552079 Score: 789
Period size: 209 Copynumber: 2.0 Consensus size: 208
551644 AAATTCTAAA
551654 AGACTCAACGTATAATTATAAATTAGTTAAAAATTTAAAGATAAATTATTTAAAATAAAAATATT
1 AGACTCAACGTATAATTATAAATTAGTTAAAAATTTAAAGATAAATTATTTAAAATAAAAATATT
551719 AATTAAATTATTTTTCATAATTTTTCAACTTTTTTCAATAATTTTTTATTGTTAAAAAATTATGG
66 AATTAAATTATTTTTCATAATTTTTCAACTTTTTTCAATAATTTTTTATTGTTAAAAAATTATGG
551784 AAATAATGTAATTAATATTTATTTTAAATAATTTATCTTTAGAATTTTAACTAATTTAAAATTAT
131 AAATAATGTAATTAATA-TTATTTTAAATAATTTATCTTTAGAATTTTAACTAATTTAAAATTAT
551849 ACATTGAGTATTTT
195 ACATTGAGTATTTT
551863 AGACTCAACGTATAATTATAAATTAGTTAAAAATTTAAAGATAAATTATTTAAAATAAAAATATT
1 AGACTCAACGTATAATTATAAATTAGTTAAAAATTTAAAGATAAATTATTTAAAATAAAAATATT
551928 AATTAAATTATTTTTCATAATTTTTTCAACATTTTTTCAAATAATTTTTTATTGTTAAAAAATTA
66 AATTAAATTATTTTTCATAA-TTTTTCAAC-TTTTTTC-AATAATTTTTTATTGTTAAAAAATTA
551993 TGGAAAATAATGTAATTAATATTTTATTTTAAATAATTTATCTTTAGAATTTTAACTAATTTAAA
128 TGG-AAATAATGTAATTAATA--TTATTTTAAATAATTTATCTTTAGAATTTTAACTAATTTAAA
552058 ATTATACATTGAGTATTTT
190 ATTATACATTGAGTATTTT
552077 AGA
1 AGA
552080 ATTTTGAATA
Statistics
Matches: 212, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
209 85 0.40
210 9 0.04
211 7 0.03
212 29 0.14
213 17 0.08
214 65 0.31
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (208 bp):
AGACTCAACGTATAATTATAAATTAGTTAAAAATTTAAAGATAAATTATTTAAAATAAAAATATT
AATTAAATTATTTTTCATAATTTTTCAACTTTTTTCAATAATTTTTTATTGTTAAAAAATTATGG
AAATAATGTAATTAATATTATTTTAAATAATTTATCTTTAGAATTTTAACTAATTTAAAATTATA
CATTGAGTATTTT
Found at i:554059 original size:21 final size:22
Alignment explanation
Indices: 554033--554079 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
554023 TTATTTTGGA
554033 TAAATTAT-ATAGATCA-AATTT
1 TAAATTATAAT-GATCATAATTT
*
554054 TAAATTATAATTATCATAATTT
1 TAAATTATAATGATCATAATTT
554076 TAAA
1 TAAA
554080 AATAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (22 bp):
TAAATTATAATGATCATAATTT
Found at i:554084 original size:21 final size:21
Alignment explanation
Indices: 554045--554084 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
554035 AATTATATAG
*
554045 ATCAAATTTTAAATTATAATT
1 ATCAAATTTTAAATAATAATT
554066 ATCATAATTTTAAA-AATAA
1 ATCA-AATTTTAAATAATAA
554085 AAATATACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
ATCAAATTTTAAATAATAATT
Found at i:554871 original size:80 final size:79
Alignment explanation
Indices: 554749--554924 Score: 286
Period size: 80 Copynumber: 2.2 Consensus size: 79
554739 CTATATATAT
554749 ATAAATGTTTAATAATAAGTAAATTATATTTTAAAAGATATATGAAAATACTCTAAGCTCATAAT
1 ATAAATGTTTAATAATAAGTAAATTATATTTTAAAAGATATATGAAAATACTCTAAGCTCATAAT
554814 TTTTTATTCGAATA
66 TTTTTATTCGAATA
554828 ATAAATGTTTAATAAATAAGTAAAAATTATATTTT-AAA-ATATATGAAAATACTCTAAGCTCAT
1 ATAAATGTTTAAT-AATAAGT--AAATTATATTTTAAAAGATATATGAAAATACTCTAAGCTCAT
554891 AATTTTTTATTCGAATA
63 AATTTTTTATTCGAATA
554908 AT-AATGTATTGAATAAT
1 ATAAATGT-TT-AATAAT
554925 TATCATGTTT
Statistics
Matches: 92, Mismatches: 0, Indels: 9
0.91 0.00 0.09
Matches are distributed among these distances:
79 18 0.20
80 56 0.61
81 6 0.07
82 12 0.13
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (79 bp):
ATAAATGTTTAATAATAAGTAAATTATATTTTAAAAGATATATGAAAATACTCTAAGCTCATAAT
TTTTTATTCGAATA
Found at i:555662 original size:20 final size:20
Alignment explanation
Indices: 555615--555655 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
555605 GTTAATGTTG
*
555615 ATATTATTTATTTTTATAATT
1 ATATT-TTTATTTTTAAAATT
555636 ATATTTTTATTTTTAAAATT
1 ATATTTTTATTTTTAAAATT
555656 CAATTTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATATTTTTATTTTTAAAATT
Found at i:561781 original size:29 final size:29
Alignment explanation
Indices: 561739--561800 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
561729 TTCCTTCCTA
561739 ACAATACCTTTGTAGTGGCGCACGCACAT
1 ACAATACCTTTGTAGTGGCGCACGCACAT
561768 ACAATACCTTTGTAGTGGCGCACGCACAT
1 ACAATACCTTTGTAGTGGCGCACGCACAT
561797 ACAA
1 ACAA
561801 ATTAGAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (29 bp):
ACAATACCTTTGTAGTGGCGCACGCACAT
Found at i:571746 original size:30 final size:29
Alignment explanation
Indices: 571696--571786 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 29
571686 AAATGTCATA
*
571696 AAAACTTAAGATACTTAAATAATAAAAATAG
1 AAAA-TTAAGA-ACTAAAATAATAAAAATAG
**
571727 ATAGTTTAA-AGACTAAAATAATAAAAAGTAG
1 A-AAATTAAGA-ACTAAAATAATAAAAA-TAG
571758 AAAATTAAGTAACTAAAATAATAAAAATA
1 AAAATTAAG-AACTAAAATAATAAAAATA
571787 TATAATAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
30 23 0.46
31 25 0.50
32 2 0.04
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.25
Consensus pattern (29 bp):
AAAATTAAGAACTAAAATAATAAAAATAG
Found at i:573455 original size:12 final size:12
Alignment explanation
Indices: 573437--573476 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
573427 TATGTAACAT
573437 ATATTAATAATA
1 ATATTAATAATA
*
573449 TTATTAATAATA
1 ATATTAATAATA
*
573461 ATAGTAATAATA
1 ATATTAATAATA
573473 ATAT
1 ATAT
573477 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
ATATTAATAATA
Found at i:573480 original size:2 final size:2
Alignment explanation
Indices: 573473--573537 Score: 100
Period size: 2 Copynumber: 34.0 Consensus size: 2
573463 AGTAATAATA
*
573473 AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT A- AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
573512 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
573538 TAATACTAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 55 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:573883 original size:135 final size:135
Alignment explanation
Indices: 573739--573992 Score: 483
Period size: 135 Copynumber: 1.9 Consensus size: 135
573729 CATTGAAAGA
573739 CGTCACTGATTCGAAATG-TCGTGAACCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACT
1 CGTCACTGATTCGAAATGCT-GTGAACCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACT
573803 TCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGATCCCTCAA
65 TCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGATCCCTCAA
573868 GCGAGG
130 GCGAGG
*
573874 CGTCACTGATTCGAAATGCTGTGAATCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTT
1 CGTCACTGATTCGAAATGCTGTGAACCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTT
573939 CTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTT
66 CTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTT
573993 AAGTCACCTC
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
135 116 0.99
136 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (135 bp):
CGTCACTGATTCGAAATGCTGTGAACCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTT
CTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGATCCCTCAAG
CGAGG
Found at i:574155 original size:247 final size:247
Alignment explanation
Indices: 573662--574236 Score: 763
Period size: 247 Copynumber: 2.3 Consensus size: 247
573652 TTGTTGGATT
* * *
573662 GAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * *
573727 TCCATTG-AAAGACGTCACTGATTCGAAATGTCGTGAACCAAGTGATAGGTCGAACAAGCTCTTC
66 TCCATTGAAAAGAAGTCACTCATTC---ATGTCGTGAACC-AGTGATAAG-CGAACAAGCTCTTC
* *
573791 TCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATG
126 TCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTATGAACTCTCCATTGAAAATG
** * *
573856 TTGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGCTGTGAATCAAGTGATAGGTC
191 TCAATCCCTCAAGAGAGGCATCACTGATTCGAAATGCTGTGAATCAAGTGATAGGTC
573913 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * * * *
573978 TCCATTGAAAATGTTAAGTCACCTCTTTC-TGTGGTGGA-C-TTGA-AAG-GAACAAGTTCTTCT
66 TCCATTGAAAA-G--AAGTCA-CTCATTCATGTCGTGAACCAGTGATAAGCGAACAAGCTCTTCT
*
574038 CATTATGAACTTCTTCTCCCTC-TATCGGATGAGTTATTCTCATTATGAACTCTCCATTGGAAAT
127 CATTATGAACTTCTTCTCCCTCGT-T-GGATGAGTTATTCTCATTATGAACTCTCCATTGAAAAT
*
574102 GTCAATCCCTCAAGAGAGGCATCACTGATTCGAAATG-TCGTGAATCGAGTGATAGGTC
190 GTCAATCCCTCAAGAGAGGCATCACTGATTCGAAATGCT-GTGAATCAAGTGATAGGTC
*
574160 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-TATCGGATGAGTTCTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGT-T-GGATGAGTTCTTCTCATTATGAAC
*
574224 TCTCTATTTGAAA
64 TCTCCA-TTGAAA
574237 TACTGATGCG
Statistics
Matches: 292, Mismatches: 21, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
245 1 0.00
246 37 0.13
247 123 0.42
248 31 0.11
249 9 0.03
251 70 0.24
252 10 0.03
253 1 0.00
255 5 0.02
256 5 0.02
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (247 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAAGAAGTCACTCATTCATGTCGTGAACCAGTGATAAGCGAACAAGCTCTTCTCATT
ATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTATGAACTCTCCATTGAAAATGTCAAT
CCCTCAAGAGAGGCATCACTGATTCGAAATGCTGTGAATCAAGTGATAGGTC
Found at i:574268 original size:92 final size:90
Alignment explanation
Indices: 574155--574326 Score: 245
Period size: 92 Copynumber: 1.9 Consensus size: 90
574145 ATCGAGTGAT
* * *
574155 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
1 AGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT-TATCGGACGAATTCTTCTCATTAT
*
574220 GAACTCTCTATTTGAAATACTGATGCG
65 GAACTCTCCA-TTGAAATACTGATGCG
* * * * *
574247 AGGTCAAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTGTTGGACGAATTCTTCTCATTATG
1 AGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTATCGGACGAATTCTTCTCATTATG
574312 AACTCTCCATTGAAA
66 AACTCTCCATTGAAA
574327 ATGTTGATCC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
90 6 0.08
91 29 0.41
92 36 0.51
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (90 bp):
AGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTATCGGACGAATTCTTCTCATTATG
AACTCTCCATTGAAATACTGATGCG
Found at i:574426 original size:16 final size:16
Alignment explanation
Indices: 574371--574427 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
574361 AGGAACAAGT
574371 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
574387 T-TTCTCCTTTAAGACGAGC
1 TCTTCT-CATTATGA--A-C
574406 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
574422 TCTTCT
1 TCTTCT
574428 AGTAATGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 4 0.12
16 14 0.44
17 1 0.03
18 1 0.03
19 8 0.25
20 4 0.12
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:575325 original size:17 final size:17
Alignment explanation
Indices: 575305--575370 Score: 73
Period size: 16 Copynumber: 3.9 Consensus size: 17
575295 AACCCTTCTT
*
575305 TTTCTCTTCATTTTTTA
1 TTTCTTTTCATTTTTTA
*
575322 TTTC-TTTCTTTTTTTA
1 TTTCTTTTCATTTTTTA
*
575338 TTT-TTTTCTTCTTTTTA
1 TTTCTTTTCAT-TTTTTA
*
575355 TTTTTTTTCATTTTTT
1 TTTCTTTTCATTTTTT
575371 TCTTCAAGCA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
16 19 0.44
17 18 0.42
18 6 0.14
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTTTTCATTTTTTA
Found at i:575342 original size:35 final size:35
Alignment explanation
Indices: 575303--575371 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
575293 CGAACCCTTC
575303 TTTTTCTCTTCATTTTT-TATTTCTTTC-TTTTTTTA
1 TTTTTCTCTTC-TTTTTAT-TTTCTTTCATTTTTTTA
* *
575338 TTTTTTTCTTCTTTTTATTTTTTTTCATTTTTTT
1 TTTTTCTCTTCTTTTTATTTTCTTTCATTTTTTT
575372 CTTCAAGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (35 bp):
TTTTTCTCTTCTTTTTATTTTCTTTCATTTTTTTA
Found at i:575344 original size:9 final size:9
Alignment explanation
Indices: 575330--575371 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
575320 TATTTCTTTC
575330 TTTTTTTA-
1 TTTTTTTAT
*
575338 TTTTTTTCT
1 TTTTTTTAT
*
575347 TCTTTTTAT
1 TTTTTTTAT
575356 TTTTTTTCAT
1 TTTTTTT-AT
575366 TTTTTT
1 TTTTTT
575372 CTTCAAGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 7 0.25
9 13 0.46
10 8 0.29
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:575358 original size:23 final size:23
Alignment explanation
Indices: 575299--575359 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
575289 ATCTCGAACC
* *
575299 CTTCTTTTTCTCTTCATTTTTTAT
1 CTTCTTTTT-TTTTTATTTTTTAT
575323 -TTCTTTCTTTTTTTATTTTTT-T
1 CTTCTTT-TTTTTTTATTTTTTAT
575345 CTTCTTTTTATTTTT
1 CTTCTTTTT-TTTTT
575360 TTTCATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 3 0.09
23 27 0.84
24 2 0.06
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.79
Consensus pattern (23 bp):
CTTCTTTTTTTTTTATTTTTTAT
Found at i:578962 original size:16 final size:16
Alignment explanation
Indices: 578941--578973 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
578931 TAATAAATAG
578941 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
578957 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
578973 A
1 A
578974 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:579054 original size:10 final size:10
Alignment explanation
Indices: 579039--579113 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
579029 CATTTAATAA
579039 ATAAACGAAC
1 ATAAACGAAC
579049 ATAAACGAAC
1 ATAAACGAAC
579059 ----ACGAAC
1 ATAAACGAAC
579065 ATAAACGAAC
1 ATAAACGAAC
** *
579075 ACGAAC-ATAA
1 ATAAACGA-AC
579085 ATGAACACGAAC
1 AT-AA-ACGAAC
579097 ATAAACGAAC
1 ATAAACGAAC
579107 ATAAACG
1 ATAAACG
579114 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:579064 original size:16 final size:16
Alignment explanation
Indices: 579043--579107 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
579033 TAATAAATAA
579043 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
579059 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
579075 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
579091 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
579107 A
1 A
579108 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:579878 original size:14 final size:14
Alignment explanation
Indices: 579861--579916 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
579851 AATGAACATA
*
579861 AACGAACATAATCG
1 AACGAACATAACCG
579875 AACGAACAT-A---
1 AACGAACATAACCG
579885 AACGAACATAACCG
1 AACGAACATAACCG
579899 AACGAACATAACCG
1 AACGAACATAACCG
579913 AACG
1 AACG
579917 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:579881 original size:24 final size:24
Alignment explanation
Indices: 579841--579915 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
579831 GATTGGGTTA
*
579841 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
579865 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
579889 AACATAACCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
579913 AAC
1 AAC
579916 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:579915 original size:10 final size:10
Alignment explanation
Indices: 579854--579901 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
579844 ATAAATGAAT
579854 GAACATAAAC
1 GAACATAAAC
579864 GAACATAATCGAAC
1 GAACAT-A---AAC
579878 GAACATAAAC
1 GAACATAAAC
*
579888 GAACATAACC
1 GAACATAAAC
579898 GAAC
1 GAAC
579902 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:579976 original size:39 final size:40
Alignment explanation
Indices: 579933--580009 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
579923 AACGTAAATG
* *
579933 AACGAACAAGACAT-ATGTTCATGTTCGTTCATTTAATTA
1 AACGAACAAAAAATCATGTTCATGTTCGTTCATTTAATTA
*
579972 AACGAACAAAAAATCTTGTTCATGTTCGTTCATTTAAT
1 AACGAACAAAAAATCATGTTCATGTTCGTTCATTTAAT
580010 AAATAAACGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 12 0.35
40 22 0.65
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (40 bp):
AACGAACAAAAAATCATGTTCATGTTCGTTCATTTAATTA
Found at i:586314 original size:22 final size:22
Alignment explanation
Indices: 586289--586347 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
586279 AGAATTAAGT
586289 AACTAAAATAAAAAATAATAAA
1 AACTAAAATAAAAAATAATAAA
** ** *
586311 AACTTTAATTTACAATAATAAA
1 AACTAAAATAAAAAATAATAAA
*
586333 AACTAACATAAAAAA
1 AACTAAAATAAAAAA
586348 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (22 bp):
AACTAAAATAAAAAATAATAAA
Found at i:586452 original size:30 final size:28
Alignment explanation
Indices: 586416--586484 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 28
586406 TAATATAAGT
*
586416 ATAATAAAAATAGATAGTTTAA-AGACTAAA
1 ATAATAAAAATAGA-A-ATTAAGA-ACTAAA
586446 ATAATAAAAAATAGAAATTAAGTAACTAAA
1 ATAAT-AAAAATAGAAATTAAG-AACTAAA
586476 ATAATAAAA
1 ATAATAAAA
586485 TATATAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
29 8 0.23
30 17 0.49
31 10 0.29
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (28 bp):
ATAATAAAAATAGAAATTAAGAACTAAA
Found at i:586595 original size:182 final size:174
Alignment explanation
Indices: 586244--586599 Score: 583
Period size: 182 Copynumber: 2.0 Consensus size: 174
586234 AAGGTACTTA
586244 AATAAAAATAGATAGTTTAAAGACTAAAAAAAAATAGAATTAAGTAACTAAAATAAAAAATAATA
1 AATAAAAATAGATAGTTTAAAGACTAAAAAAAAATAGAATTAAGTAACTAAAATAAAAAATAATA
586309 AAAACTTTAATTTACAATAATAAAAACTAACATAAAAAAATTAAAATTTTAAATTTTAAATAAAG
66 AAAACTTTAATTTACAATAATAAAAACTAACATAAAAAAATTAAAATTTTAAATTTTAAATAAAG
586374 ATAAATGAATTTCTCAAATTGAAAATATTAAATAATATAAGTAT
131 ATAAATGAATTTCTCAAATTGAAAATATTAAATAATATAAGTAT
586418 AATAAAAATAGATAGTTTAAAGACTAAAATAATAAAAAATAGAAATTAAGTAACTAAAATAATAA
1 AATAAAAATAGATAGTTTAAAGACT---A-AA-AAAAAATAG-AATTAAGTAACT--AA-AATAA
*
586483 AATATATAATAAAAACTTTAATTTACAATAATAAAAACTAA-TTAAAAAAATTAAAATTTTAAAT
57 AA-A-ATAATAAAAACTTTAATTTACAATAATAAAAACTAACATAAAAAAATTAAAATTTTAAAT
586547 TTTAAATAAAGAT-AATGAA-TTCTCAAATTGAAAATATTAAATAATATAAGTAT
120 TTTAAATAAAGATAAATGAATTTCTCAAATTGAAAATATTAAATAATATAAGTAT
586600 TAAAATAAAA
Statistics
Matches: 170, Mismatches: 1, Indels: 14
0.92 0.01 0.08
Matches are distributed among these distances:
174 25 0.15
177 1 0.01
178 2 0.01
179 9 0.05
180 12 0.07
182 36 0.21
183 13 0.08
184 36 0.21
185 36 0.21
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (174 bp):
AATAAAAATAGATAGTTTAAAGACTAAAAAAAAATAGAATTAAGTAACTAAAATAAAAAATAATA
AAAACTTTAATTTACAATAATAAAAACTAACATAAAAAAATTAAAATTTTAAATTTTAAATAAAG
ATAAATGAATTTCTCAAATTGAAAATATTAAATAATATAAGTAT
Found at i:586609 original size:185 final size:175
Alignment explanation
Indices: 586242--586612 Score: 588
Period size: 185 Copynumber: 2.1 Consensus size: 175
586232 TTAAGGTACT
586242 TAAATAAAAATAGATAGTTTAAAGACTAAAAAAAAATAGAATTAAGTAACTAAAATAAAAAATAA
1 TAAATAAAAATAGATAGTTTAAAGACTAAAAAAAAATAGAATTAAGTAACTAAAATAAAAAATAA
586307 TAAAAACTTTAATTTACAATAATAAAAACTAACATAAAAAAATTAAAATTTTAAATTTTAAATAA
66 TAAAAACTTTAATTTACAATAATAAAAACTAACATAAAAAAATTAAAATTTTAAATTTTAAATAA
586372 AGATAAATGAATTTCTCAAATTGAAAATATTAAATAATATAAGTA
131 AGATAAATGAATTTCTCAAATTGAAAATATTAAATAATATAAGTA
586417 T-AATAAAAATAGATAGTTTAAAGACTAAAATAATAAAAAATAGAAATTAAGTAACTAAAATAAT
1 TAAATAAAAATAGATAGTTTAAAGACT---A-AA-AAAAAATAG-AATTAAGTAACT--AA-AAT
*
586481 AAAATATATAATAAAAACTTTAATTTACAATAATAAAAACTAA-TTAAAAAAATTAAAATTTTAA
57 AAAA-A-ATAATAAAAACTTTAATTTACAATAATAAAAACTAACATAAAAAAATTAAAATTTTAA
586545 ATTTTAAATAAAGAT-AATGAA-TTCTCAAATTGAAAATATTAAATAATATAAGTA
120 ATTTTAAATAAAGATAAATGAATTTCTCAAATTGAAAATATTAAATAATATAAGTA
586599 TTAAAATAAAAATA
1 -T-AAATAAAAATA
586613 ACCTCAAAAT
Statistics
Matches: 181, Mismatches: 1, Indels: 18
0.90 0.00 0.09
Matches are distributed among these distances:
174 25 0.14
175 1 0.01
177 1 0.01
178 2 0.01
179 9 0.05
180 12 0.07
182 35 0.19
183 14 0.08
184 36 0.20
185 46 0.25
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (175 bp):
TAAATAAAAATAGATAGTTTAAAGACTAAAAAAAAATAGAATTAAGTAACTAAAATAAAAAATAA
TAAAAACTTTAATTTACAATAATAAAAACTAACATAAAAAAATTAAAATTTTAAATTTTAAATAA
AGATAAATGAATTTCTCAAATTGAAAATATTAAATAATATAAGTA
Found at i:588119 original size:19 final size:18
Alignment explanation
Indices: 588090--588125 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
588080 ATCTAACATA
588090 TATTAATAATAATAATAT
1 TATTAATAATAATAATAT
*
588108 TATTATATAATAGTAATA
1 TATTA-ATAATAATAATA
588126 AATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TATTAATAATAATAATAT
Found at i:588124 original size:25 final size:27
Alignment explanation
Indices: 588088--588160 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
588078 ATATCTAACA
*
588088 TATATTAATAAT-AATA-ATAT-TATTA
1 TATAATAATAATAAATATATATATA-TA
*
588113 TATAATAGTAATAAATATATATATATA
1 TATAATAATAATAAATATATATATATA
*
588140 TATAATAA-ACATATATATATA
1 TATAATAATA-ATAAATATATA
588161 ATACTAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 10 0.25
26 5 0.12
27 23 0.57
28 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (27 bp):
TATAATAATAATAAATATATATATATA
Found at i:588146 original size:17 final size:17
Alignment explanation
Indices: 588087--588163 Score: 62
Period size: 17 Copynumber: 4.9 Consensus size: 17
588077 AATATCTAAC
588087 ATATAT-TA-ATAATA-
1 ATATATATATATAATAT
*
588101 ATA-ATAT-TATTATAT
1 ATATATATATATAATAT
588116 A-ATAGTA-ATA-AATAT
1 ATATA-TATATATAATAT
*
588131 ATATATATATATAATAA
1 ATATATATATATAATAT
*
588148 ACATATATATATAATA
1 ATATATATATATAATA
588164 CTAATAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
13 2 0.04
14 10 0.20
15 9 0.18
16 10 0.20
17 19 0.38
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
ATATATATATATAATAT
Found at i:588153 original size:23 final size:22
Alignment explanation
Indices: 588083--588170 Score: 73
Period size: 22 Copynumber: 4.1 Consensus size: 22
588073 AAAAAATATC
588083 TAACATATATTA-ATA-A-TAA
1 TAACATATATTATATATACTAA
* *
588102 TAATAT-TATTATATAATAGTAA
1 TAACATATATTATAT-ATACTAA
588124 TAA-ATATATATATATATA-TAA
1 TAACATATAT-TATATATACTAA
588145 TAAACATATA-TATATAATACTAA
1 T-AACATATATTATAT-ATACTAA
588168 TAA
1 TAA
588171 AAAGGATGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 17
0.76 0.01 0.22
Matches are distributed among these distances:
18 5 0.09
19 7 0.12
20 1 0.02
21 12 0.21
22 19 0.33
23 14 0.24
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (22 bp):
TAACATATATTATATATACTAA
Found at i:588160 original size:44 final size:44
Alignment explanation
Indices: 588087--588171 Score: 113
Period size: 44 Copynumber: 1.9 Consensus size: 44
588077 AATATCTAAC
*
588087 ATATATTAATAATAATAATATTATTATATAATAGTAATAAATAT
1 ATATATTAATAATAATAATATTATTATATAATACTAATAAATAT
588131 ATATATATATATAATAA-ACATA-TA-TATATAATACTAATAAA
1 ATATAT-TA-ATAATAATA-ATATTATTATATAATACTAATAAA
588172 AAGGATGTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
44 22 0.59
45 5 0.14
46 10 0.27
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (44 bp):
ATATATTAATAATAATAATATTATTATATAATACTAATAAATAT
Found at i:588171 original size:23 final size:22
Alignment explanation
Indices: 588087--588171 Score: 97
Period size: 21 Copynumber: 3.9 Consensus size: 22
588077 AATATCTAAC
588087 ATATAT-TAATAATAAT-AATAT
1 ATATATATAAT-ATAATAAATAT
588108 -TATTATATAATAGTAATAAATAT
1 ATA-TATATAATA-TAATAAATAT
*
588131 ATATATAT-ATATAATAAACAT
1 ATATATATAATATAATAAATAT
588152 ATATATATAATACTAATAAA
1 ATATATATAATA-TAATAAA
588172 AAGGATGTCA
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
20 2 0.04
21 21 0.38
22 14 0.25
23 17 0.30
24 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (22 bp):
ATATATATAATATAATAAATAT
Found at i:589558 original size:23 final size:24
Alignment explanation
Indices: 589522--589569 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
589512 ATCCATTTTA
589522 GTATCAGTACCAATGGTAGGTATC
1 GTATCAGTACCAATGGTAGGTATC
589546 GTATC-GTACCAATGGTAGGTATC
1 GTATCAGTACCAATGGTAGGTATC
589569 G
1 G
589570 ATACTCAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (24 bp):
GTATCAGTACCAATGGTAGGTATC
Found at i:592868 original size:21 final size:20
Alignment explanation
Indices: 592782--592939 Score: 68
Period size: 21 Copynumber: 7.8 Consensus size: 20
592772 AAATGACCAA
**
592782 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
592801 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
592821 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
592841 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
592862 GAAAATCACAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
592883 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
592903 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
592924 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
592940 ACACATAAAT
Statistics
Matches: 100, Mismatches: 33, Indels: 11
0.69 0.23 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.40
21 44 0.44
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:592968 original size:20 final size:20
Alignment explanation
Indices: 592907--593135 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
592897 GATTTTCCAG
* ** *
592907 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
592927 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
592947 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
592967 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
592987 AATAGCAACGCATATCCGTA
1 AATCGCAACGCGTATCCGTA
*
593007 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
593027 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
593047 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
593067 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
593087 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
593107 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
593127 AATCACAAC
1 AATCGCAAC
593136 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:594263 original size:33 final size:34
Alignment explanation
Indices: 594188--594352 Score: 169
Period size: 33 Copynumber: 4.8 Consensus size: 34
594178 GCATTTGACT
** * * *
594188 ATCGCAACACGGAAATTACAATCGCAACGA-GAGA
1 ATCGCAATGCGGAAATGAAAATCGCAAC-ATGAAA
*
594222 ATCGCAATGC-GAAATGAAAATCCCAACATGAAA
1 ATCGCAATGCGGAAATGAAAATCGCAACATGAAA
*
594255 ATCACAATGCGGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--C---ATGAAA
594294 ATCGCAATGC-GAAATGAAAATCGCAAC--GAGAA
1 ATCGCAATGCGGAAATGAAAATCGCAACATGA-AA
594326 ATCGCAATGCGGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA
594353 TGCGAAATGA
Statistics
Matches: 113, Mismatches: 9, Indels: 19
0.80 0.06 0.13
Matches are distributed among these distances:
31 2 0.02
32 13 0.12
33 42 0.37
34 23 0.20
36 2 0.02
38 16 0.14
39 15 0.13
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACATGAAA
Found at i:594290 original size:19 final size:19
Alignment explanation
Indices: 594221--594428 Score: 234
Period size: 19 Copynumber: 11.7 Consensus size: 19
594211 GCAACGAGAG
594221 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
594240 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
594254 AATCACAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
594274 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
594293 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
594312 AATCGCAA--CG--A-G-A
1 AATCGCAATGCGAAATGAA
594325 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
594345 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
594363 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
594377 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
594397 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
594416 AATCGCATTGCGA
1 AATCGCAATGCGA
594429 TTCTCTCGTT
Statistics
Matches: 163, Mismatches: 6, Indels: 40
0.78 0.03 0.19
Matches are distributed among these distances:
13 10 0.06
14 22 0.13
15 2 0.01
16 5 0.03
17 4 0.02
18 10 0.06
19 70 0.43
20 40 0.25
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:594347 original size:71 final size:70
Alignment explanation
Indices: 594221--594428 Score: 253
Period size: 71 Copynumber: 2.9 Consensus size: 70
594211 GCAACGAGAG
* *
594221 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCACAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAACGA-G-AAATCGCAATGCGGAAATGAAAATCGCAATGC
594285 GAAATGAA
64 GAAATG-A
594293 AATCGCAATGCGAAATGAAAATCGCAACGAGAAATCGCAATGCGGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAATCGCAATGCGGAAATGAAAATCGCAATGCGA
594358 AATGA
66 AATGA
* * * * * *
594363 AATCGCAACGAGAGAATCG-CAATGCGGAAATGA-AAATCGCAATGC-GAAATGAAAATCGCATT
1 AATCGCAATGCGA-AAT-GAAAAT-C-GCAACGAGAAATCGCAATGCGGAAATGAAAATCGCAAT
594425 GCGA
62 GCGA
594429 TTCTCTCGTT
Statistics
Matches: 123, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
70 12 0.10
71 63 0.51
72 42 0.34
73 6 0.05
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (70 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAATCGCAATGCGGAAATGAAAATCGCAATGCGA
AATGA
Found at i:594349 original size:52 final size:52
Alignment explanation
Indices: 594207--594422 Score: 289
Period size: 52 Copynumber: 4.1 Consensus size: 52
594197 CGGAAATTAC
* * * *
594207 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATG-AAAATCAC
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC-A-ATGCGAAATGAA
* *
594260 AATGCGGAA--ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACGA-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
594312 AATCGCAACGAGA-AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATG-A
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
594363 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
594416 AATCGCA
1 AATCGCA
594423 TTGCGATTCT
Statistics
Matches: 148, Mismatches: 7, Indels: 16
0.87 0.04 0.09
Matches are distributed among these distances:
51 32 0.22
52 74 0.50
53 38 0.26
54 4 0.03
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:594485 original size:53 final size:52
Alignment explanation
Indices: 594418--594535 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 52
594408 GAAATGAAAA
594418 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
594471 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
594523 TCCGCATTGCGAT
1 T-CGCATTGCGAT
594536 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 19 0.30
53 45 0.70
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:594543 original size:20 final size:19
Alignment explanation
Indices: 594437--594535 Score: 136
Period size: 20 Copynumber: 5.4 Consensus size: 19
594427 GATTCTCTCG
594437 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
594457 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
594476 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
594490 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
594509 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
594529 TTGCGAT
1 TTGCGAT
594536 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 25 0.35
20 26 0.37
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:594658 original size:14 final size:14
Alignment explanation
Indices: 594639--594675 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
594629 GCATCAATAC
594639 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
594653 ACAAATCATCTTTT
1 ACAAATCAACTTTT
594667 ACAAATCAA
1 ACAAATCAA
594676 TTAAACATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:596615 original size:19 final size:19
Alignment explanation
Indices: 596573--596745 Score: 141
Period size: 19 Copynumber: 9.6 Consensus size: 19
596563 TAGTTTACTT
* *
596573 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TCAAAA
* *
596593 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATCAAAA
* *
596612 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
596631 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
596650 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
596669 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
* *
596683 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
596702 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
*
596716 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
596735 TCGCAATGCGA
1 TCGCAACGCGA
596746 TTTTTGGTTT
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
14 18 0.15
15 2 0.02
16 4 0.03
17 4 0.03
18 2 0.02
19 82 0.66
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:596686 original size:14 final size:14
Alignment explanation
Indices: 596667--596723 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
596657 GCGAAATGAA
596667 AATCGCAACGACAG
1 AATCGCAACGACAG
*
596681 AATCGCAATGCGAAATG
1 AATCGCAA--CGACA-G
596698 AAAATCGCAACGACAG
1 --AATCGCAACGACAG
596714 AATCGCAACG
1 AATCGCAACG
596724 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.25, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:596694 original size:33 final size:33
Alignment explanation
Indices: 596648--596740 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
596638 GCGAAACCAA
596648 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
596681 AATCGCAATGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
596714 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
596741 TGCGATTTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:596777 original size:14 final size:14
Alignment explanation
Indices: 596758--596816 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
596748 TTTGGTTTCG
596758 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
596772 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
596789 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
596805 CGTTGCGATTTT
1 CGTTGCGATTTT
596817 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:596788 original size:33 final size:33
Alignment explanation
Indices: 596741--596865 Score: 178
Period size: 33 Copynumber: 3.7 Consensus size: 33
596731 AAAATCGCAA
*
596741 TGCGATTTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGA-TTTTGGTTTCGCGTTGCGATTCTGTCGT
596775 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
596808 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
596841 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
596866 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
33 66 0.80
34 17 0.20
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:596796 original size:19 final size:18
Alignment explanation
Indices: 596741--596833 Score: 76
Period size: 19 Copynumber: 5.4 Consensus size: 18
596731 AAAATCGCAA
596741 TGCGATTTTTGGTTTCGCGT
1 TGCGA-TTTT-GTTTCGCGT
596761 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
596775 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
596794 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
596808 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
596827 TGCGATT
1 TGCGATT
596834 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 21
0.71 0.04 0.25
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 25 0.42
20 5 0.08
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:596843 original size:14 final size:14
Alignment explanation
Indices: 596791--596847 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
596781 TTTGGTTTCG
*
596791 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
596805 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
596824 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
596838 CGTTGCGATT
1 CGTTGCGATT
596848 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:598776 original size:20 final size:20
Alignment explanation
Indices: 598745--598827 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
598735 CTTTGGTTGA
598745 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
598765 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
598785 AAATGAAAATCGCAACGCGA-
1 -AATGAAAATCGCAACGAGAG
598805 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
598825 AAT
1 AAT
598828 TGCAACGCGA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 18 0.34
20 20 0.38
21 15 0.28
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Done.