Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold186
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: 1043505
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.30
Warning! 56388 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:458158 original size:156 final size:157
Alignment explanation
Indices: 457874--458168 Score: 366
Period size: 156 Copynumber: 1.9 Consensus size: 157
457864 TAAACTTTCG
* * * *
457874 TGAAAGTATCCCAATAATCCTAAAGGACTTAAAAATAATCATAAATGAGATGAACCTATCCTAAA
1 TGAAAGTATCCCAATAACCCTAAAGGACTTAAAAATAACCATAAATGAGATAAACCTATACTAAA
*** **
457939 TGCACACCTTGGGTATAGAAGCATCCCAGTGACAACCTAAGACTCGATTTTAAGAAAATTATGAA
66 TGCACACCTTCAATATAGAAGCATCCCAGTGACAACCTAAGACTCGATACTAAGAAAATTATGAA
458004 AATG-CCCTTAGGGTATGCCTTCGACA
131 AATGTCCCTTAGGGTATGCCTTCGACA
* * *
458030 TGAAAGTAT-CCAGGTAACCCTAAAGGACTTAAAAATGACCGTAAATG-GAATAAACCTATACTA
1 TGAAAGTATCCCA-ATAACCCTAAAGGACTTAAAAATAACCATAAATGAG-ATAAACCTATACTA
* * * * *
458093 AATGCACACCTTCAATATA-AGAGCATCTCGGTGACAACTTAGGACTCTGA-ACTAAGAGAATTA
64 AATGCACACCTTCAATATAGA-AGCATCCCAGTGACAACCTAAGACTC-GATACTAAGAAAATTA
458156 TGAAAATGTCCCT
127 TGAAAATGTCCCT
458169 GGGCATACCT
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
155 5 0.04
156 106 0.91
157 6 0.05
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (157 bp):
TGAAAGTATCCCAATAACCCTAAAGGACTTAAAAATAACCATAAATGAGATAAACCTATACTAAA
TGCACACCTTCAATATAGAAGCATCCCAGTGACAACCTAAGACTCGATACTAAGAAAATTATGAA
AATGTCCCTTAGGGTATGCCTTCGACA
Found at i:460313 original size:20 final size:20
Alignment explanation
Indices: 460269--460322 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
460259 TTCTATAATT
* * *
460269 TGTATTGATACAATTAGTTAA
1 TGTATTGATAC-ATAAATGAA
460290 TGTATTGATACATAAATGAA
1 TGTATTGATACATAAATGAA
460310 TGTATTGATACAT
1 TGTATTGATACAT
460323 GCTTGAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.41
Consensus pattern (20 bp):
TGTATTGATACATAAATGAA
Found at i:460329 original size:20 final size:21
Alignment explanation
Indices: 460288--460340 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
460278 ACAATTAGTT
460288 AATGTATTGATACATAAATG-
1 AATGTATTGATACATAAATGA
***
460308 AATGTATTGATACATGCTTGA
1 AATGTATTGATACATAAATGA
460329 AATGTATTGATA
1 AATGTATTGATA
460341 TTGGACCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (21 bp):
AATGTATTGATACATAAATGA
Found at i:462060 original size:20 final size:20
Alignment explanation
Indices: 462035--462111 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 20
462025 TTTTACCCAG
*
462035 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
462055 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
** *
462075 CCGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
* *
462095 ATATATTGATACATTTT
1 ATGTATCGATACATTTT
462112 ATCTTTTTAC
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:462091 original size:91 final size:91
Alignment explanation
Indices: 461992--462159 Score: 273
Period size: 91 Copynumber: 1.8 Consensus size: 91
461982 TTATTTTAAA
* * * *
461992 ATACATTCTTCAATGTATTGATACATTCTATCTTTTTACCCAGATGTATTGATACATTTTTCAAT
1 ATACATTCTTCAATATATTGATACATTCTATCTTTTTACCCAGATGTATCGATACATGTATCAAT
462057 GTATCGATACATGTATGACCGTATCG
66 GTATCGATACATGTATGACCGTATCG
* * *
462083 ATACATTCTTCAATATATTGATACATTTTATCTTTTTACCCAGATGTATCGATACATGTATGACT
1 ATACATTCTTCAATATATTGATACATTCTATCTTTTTACCCAGATGTATCGATACATGTATCAAT
462148 GTATCGATACAT
66 GTATCGATACAT
462160 TCTTCAATGT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 70 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (91 bp):
ATACATTCTTCAATATATTGATACATTCTATCTTTTTACCCAGATGTATCGATACATGTATCAAT
GTATCGATACATGTATGACCGTATCG
Found at i:462130 original size:71 final size:73
Alignment explanation
Indices: 462055--462206 Score: 236
Period size: 71 Copynumber: 2.1 Consensus size: 73
462045 ACATTTTTCA
* *
462055 ATGTATCGATACATGTATGACCGTATCGATACATTCTTCAATATATTGATACATTTTAT-C-TTT
1 ATGTATCGATACATGTATGACCGTATCGATACATTCTTCAATATATCGATACATTCTATCCTTTT
462118 TTACCCAG
66 TTACCCAG
* * *
462126 ATGTATCGATACATGTATGACTGTATCGATACATTCTTCAATGTATCGATACATTCTGTCCTTTT
1 ATGTATCGATACATGTATGACCGTATCGATACATTCTTCAATATATCGATACATTCTATCCTTTT
*
462191 TTTCCCAG
66 TTACCCAG
462199 ATGTATCG
1 ATGTATCG
462207 CTATATTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
71 54 0.74
72 1 0.01
73 18 0.25
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (73 bp):
ATGTATCGATACATGTATGACCGTATCGATACATTCTTCAATATATCGATACATTCTATCCTTTT
TTACCCAG
Found at i:462172 original size:91 final size:91
Alignment explanation
Indices: 461992--462182 Score: 267
Period size: 91 Copynumber: 2.1 Consensus size: 91
461982 TTATTTTAAA
* * * *
461992 ATACATTCTTCAATGTATTGATACATTCTATCTTTTTACCCAGATGTATTGATACATTTTTCAAT
1 ATACATTCTTCAATATATTGATACATTCTATCTTTTTACCCAGATGTATCGATACATGTATCAAT
* *
462057 GTATCGATACATGTATGACCGTATCG
66 GTATCGATACATGTATCAACGTATCG
* * *
462083 ATACATTCTTCAATATATTGATACATTTTATCTTTTTACCCAGATGTATCGATACATGTATGACT
1 ATACATTCTTCAATATATTGATACATTCTATCTTTTTACCCAGATGTATCGATACATGTATCAAT
* *
462148 GTATCGATACAT-TCTTCAATGTATCG
66 GTATCGATACATGT-ATCAACGTATCG
462174 ATACATTCT
1 ATACATTCT
462183 GTCCTTTTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
90 1 0.01
91 87 0.99
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (91 bp):
ATACATTCTTCAATATATTGATACATTCTATCTTTTTACCCAGATGTATCGATACATGTATCAAT
GTATCGATACATGTATCAACGTATCG
Found at i:462229 original size:73 final size:71
Alignment explanation
Indices: 462055--462232 Score: 212
Period size: 71 Copynumber: 2.5 Consensus size: 71
462045 ACATTTTTCA
* ** * *
462055 ATGTATCGATACATGTATGACCGTATCGATACATTCTTCAATATATTGATACATTTTATCTTTTT
1 ATGTATCGATACATGTATCAATGTATCGATACATTCTTCAATATATCGATACATTCTATCTTTTT
462120 ACCCAG
66 ACCCAG
* * * *
462126 ATGTATCGATACATGTATGACTGTATCGATACATTCTTCAATGTATCGATACATTCTGTCCTTTT
1 ATGTATCGATACATGTATCAATGTATCGATACATTCTTCAATATATCGATACATTCTAT-C-TTT
*
462191 TTTCCCAG
64 TTACCCAG
* * * *
462199 ATGTATCGCTATATTTTTCAATGTATCGATACAT
1 ATGTATCGATACATGTATCAATGTATCGATACAT
462233 CTAGTTAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
71 54 0.58
72 1 0.01
73 38 0.41
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (71 bp):
ATGTATCGATACATGTATCAATGTATCGATACATTCTTCAATATATCGATACATTCTATCTTTTT
ACCCAG
Found at i:473950 original size:21 final size:20
Alignment explanation
Indices: 473912--473969 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
473902 AAGAAAAAAC
473912 AAAAAAACATAAAAAAACCA
1 AAAAAAACATAAAAAAACCA
473932 AAAATAAACA-AAAATAAACCA
1 AAAA-AAACATAAAA-AAACCA
*
473953 AGAAAAA-ATAACAAAAA
1 AAAAAAACATAA-AAAAA
473970 AATCGAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.03
20 16 0.48
21 16 0.48
ACGTcount: A:0.79, C:0.12, G:0.02, T:0.07
Consensus pattern (20 bp):
AAAAAAACATAAAAAAACCA
Found at i:473959 original size:25 final size:25
Alignment explanation
Indices: 473900--473969 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
473890 TCCTTTATAC
*
473900 CCAAGAAAAAACAAA-AAAACATAAA
1 CCAAGAAAAAATAAACAAAA-ATAAA
** **
473925 AAAACCAAAAATAAACAAAAATAAA
1 CCAAGAAAAAATAAACAAAAATAAA
473950 CCAAGAAAAAAT-AACAAAAA
1 CCAAGAAAAAATAAACAAAAA
473970 AATCGAAAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
24 8 0.23
25 23 0.66
26 4 0.11
ACGTcount: A:0.77, C:0.14, G:0.03, T:0.06
Consensus pattern (25 bp):
CCAAGAAAAAATAAACAAAAATAAA
Found at i:475288 original size:32 final size:32
Alignment explanation
Indices: 475245--475779 Score: 383
Period size: 32 Copynumber: 17.9 Consensus size: 32
475235 GTCAATGGCA
*
475245 TCATTTCAAAGCCCACATAAGTCGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* **
475277 TCATTTGAAAGCCCACACAAGTTAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
475307 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
475339 TCATTTGAAAGCCCACACAAGTTGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
475371 CCATTTCAAAGCCCACACAAGTTGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
475403 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
475435 -CTATTTCAAAG-CC-CTCAAGTTGGTGGC-A-
1 TC-ATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
475463 TCTTTTCAAAG--C-CACAAGTCAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
475491 -CCTTTCAAAG-CC-CACAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * * *
475518 TCCTTTCAAAG-TC-CACTAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
475546 TCTTTTCAAAG-CC-CACAAGTCGATGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
475574 TCTTTTCAAAG-CC-CACAAGTCAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * * *
475603 -CCTTTCAAAG-CC-CATAAGTCAGTGGC-AT
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
475631 TCTTTTCAAAG-CC-CACAAGTCAGTGGC-AT
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
475660 TCTTTTCAAAG-CC-CATAAGTCAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * * * *
475689 TCTTTTCAAAGCCCACACGAGTCGATTGTAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* **
475721 TCTTTTCAAAGCCCACACAAGTTAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * * *
475752 -CCTTTAAAAGCCCACGCAAGTTGGTGGC
1 TCATTTCAAAGCCCACACAAGTCGGTGGC
475780 TACCGTTTTC
Statistics
Matches: 440, Mismatches: 51, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
27 22 0.05
28 123 0.28
29 66 0.15
30 64 0.15
31 15 0.03
32 150 0.34
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (32 bp):
TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
Found at i:475495 original size:28 final size:29
Alignment explanation
Indices: 475193--475766 Score: 472
Period size: 28 Copynumber: 19.4 Consensus size: 29
475183 CATTCATTTC
* *
475193 TTCAAAGCCCACAAGTCAGTAGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
475221 CTCAAAGTCCACAAGTCAATGGCA-TCAT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
475249 TTCAAAGCCCACATAAGTCGGTGGCAACTCAT
1 TTCAAAGCCCAC--AAGTCAGTGGC-ACTCTT
* * *
475281 TTGAAAGCCCACACAAGTTAGTGGCA-TCAT
1 TTCAAAG-CC-CACAAGTCAGTGGCACTCTT
* *
475311 TTCAAAGCCCACACAAGTCGGTGGCAACTCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ACTCTT
* ** * *
475343 TTGAAAGCCCACACAAGTTGGTGGCAACCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ACTCTT
** * *
475375 TTCAAAGCCCACACAAGTTGGTGGCAACCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ACTCTT
*
475407 TTCAAAGCCCACACAAGTCGGTGGCAAC-CTAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ACTCT-T
* **
475439 TTCAAAGCCCTCAAGTTGGTGGCA-TCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
475467 TTCAAAG-CCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
475494 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
475522 TTCAAAGTCCACTAGTCAGTGGCA-TCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
475550 TTCAAAGCCCACAAGTC-GATGGCA-TCTT
1 TTCAAAGCCCACAAGTCAG-TGGCACTCTT
*
475578 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
475606 TTCAAAGCCCATAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
475635 TTCAAAGCCCACAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
475664 TTCAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* **
475693 TTCAAAGCCCACACGAGTCGATTGTAACTCTT
1 TTCAAAGCCCACA--AGTC-AGTGGCACTCTT
* *
475725 TTCAAAGCCCACACAAGTTAGTGGCAC-CCT
1 TTCAAAG-CC-CACAAGTCAGTGGCACTCTT
*
475755 TTAAAAGCCCAC
1 TTCAAAGCCCAC
475767 GCAAGTTGGT
Statistics
Matches: 475, Mismatches: 49, Indels: 44
0.84 0.09 0.08
Matches are distributed among these distances:
27 23 0.05
28 159 0.33
29 75 0.16
30 55 0.12
31 15 0.03
32 137 0.29
33 4 0.01
34 7 0.01
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (29 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCTT
Found at i:475790 original size:62 final size:57
Alignment explanation
Indices: 475193--475792 Score: 435
Period size: 62 Copynumber: 10.1 Consensus size: 57
475183 CATTCATTTC
* * * * * *
475193 TTCAAAGCCCACAAGTCAGTAGCATCC-TCTCAAAGTCCA-CAAGTCAATGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACCAAGTCAGTGGCACCTT
* * * * * *
475249 TTCAAAGCCCACATAAGTCGGTGGCAACTCATTTGAAAGCCCACACAAGTTAGTGGCATCAT
1 TTCAAAGCCCAC--AAGTCAGTGGC-AC-CTTTTCAAAGCCCAC-CAAGTCAGTGGCACCTT
* * * ** *
475311 TTCAAAGCCCACACAAGTCGGTGGCAACTCATTTGAAAGCCCACACAAGTTGGTGGCAACCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CTTTTCAAAGCCCAC-CAAGTCAGTGGC-A-CCTT
** * *
475375 TTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCTAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-CCTTTTCAAAGCCCAC-CAAGTCAGTGGC-ACCT-T
* ** * *
475439 TTCAAAGCCCTCAAGTTGGTGGCATCTTTTCAAAG-CCA-CAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACCAAGTCAGTGGCACCTT
* * *
475494 TTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGTCCA-CTAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACCAAGTCAGTGGCACCTT
* *
475550 TTCAAAGCCCACAAGTC-GATGGCATCTTTTCAAAGCCCA-CAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAG-TGGCACCTTTTCAAAGCCCACCAAGTCAGTGGCACCTT
* * *
475606 TTCAAAGCCCATAAGTCAGTGGCATTCTTTTCAAAGCCCA-CAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACCAAGTCAGTGGCA-CCTT
* * * **
475664 TTCAAAGCCCATAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTCGATTGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCAC-CAAGTC-AGTGGCAC-CTT
* * * **
475725 TTCAAAGCCCACACAAGTTAGTGGCACCCTTTAAAAGCCCACGCAAGTTGGTGGCTACCGTT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCTTTTCAAAGCCCAC-CAAGTCAGTGGC-ACC-TT
475787 TTCAAA
1 TTCAAA
475793 TCACCATTGT
Statistics
Matches: 465, Mismatches: 50, Indels: 52
0.82 0.09 0.09
Matches are distributed among these distances:
55 32 0.07
56 101 0.22
57 40 0.09
58 50 0.11
59 5 0.01
60 23 0.05
61 18 0.04
62 106 0.23
63 21 0.05
64 68 0.15
65 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.23
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACCAAGTCAGTGGCACCTT
Found at i:475896 original size:42 final size:43
Alignment explanation
Indices: 475843--475950 Score: 137
Period size: 49 Copynumber: 2.4 Consensus size: 43
475833 GGCACCTTTA
*
475843 TTAGCCCAATGTCGCTG-ATCAGCACATTGGTCCACTTTTCCC
1 TTAGCCCAATGTCGCTGAATCAGCACAGTGGTCCACTTTTCCC
*
475885 TTAGCCCAATGTCGCCGGCCTTGAATCAGCACAGTGGTCCACTTTTCCT
1 TTAGCCCAATGT---C-G-C-TGAATCAGCACAGTGGTCCACTTTTCCC
475934 TTAGCCCAATGTCGCTG
1 TTAGCCCAATGTCGCTG
475951 GCCTTGAATT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
42 12 0.21
43 2 0.04
44 1 0.02
45 2 0.04
46 2 0.04
47 1 0.02
48 2 0.04
49 35 0.61
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30
Consensus pattern (43 bp):
TTAGCCCAATGTCGCTGAATCAGCACAGTGGTCCACTTTTCCC
Found at i:475917 original size:49 final size:49
Alignment explanation
Indices: 475860--475968 Score: 182
Period size: 49 Copynumber: 2.2 Consensus size: 49
475850 AATGTCGCTG
475860 ATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTCGCCGGCCTTGA
1 ATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTCGCCGGCCTTGA
* * *
475909 ATCAGCACAGTGGTCCACTTTTCCTTTAGCCCAATGTCGCTGGCCTTGA
1 ATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTCGCCGGCCTTGA
*
475958 ATTAGCACATT
1 ATCAGCACATT
475969 AGCACTCCTC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.20, C:0.31, G:0.18, T:0.30
Consensus pattern (49 bp):
ATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTCGCCGGCCTTGA
Found at i:480695 original size:3 final size:3
Alignment explanation
Indices: 480681--480711 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
480671 CATCAAAGTC
*
480681 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
480712 TTGACTCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:487214 original size:32 final size:32
Alignment explanation
Indices: 487178--487241 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
487168 AAAGAGAATG
*
487178 ATTGTATACAAGCTTGAACAAATCGGAAAGAT
1 ATTGTATACAAGCTTGAACAAATCAGAAAGAT
*
487210 ATTGTATATAAGCTTGAACAAATCAGAAAGAT
1 ATTGTATACAAGCTTGAACAAATCAGAAAGAT
487242 CATAAATGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (32 bp):
ATTGTATACAAGCTTGAACAAATCAGAAAGAT
Found at i:487710 original size:20 final size:19
Alignment explanation
Indices: 487663--487719 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
487653 TTGTATTGAT
*
487663 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
*
487682 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
487701 ACATTTGTATCGATACATG
1 ACA-TTGTATCGATACATG
487720 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:488773 original size:152 final size:151
Alignment explanation
Indices: 488515--489000 Score: 557
Period size: 152 Copynumber: 3.2 Consensus size: 151
488505 CCAAAATAAA
* * * * * * * *
488515 AATATTTGATGAATTTTTAAAAATTTTAAACTAAGAAAAATCCAACCAGAGAAATTTACGAAGTA
1 AATATTTGAAGAA-TTTTGAAAATTATAAACTTAGAAAAATCCTACTAGAAAAATTTACGGAGTA
* *** * *
488580 GAAAACTTCGTATCTTGGTTTTAGAAAAATTCTAAAACTCATAAAATAAGTTCATTTTTCAAAAC
65 GAAAACTTCATATCTTGGTAACAGAAAAATTCTAAAACTCATAAAATAAATTAATTTTTCAAAAC
*
488645 TGATTTAATAT-AGGTTAAACAAT
130 TGATTTAATATGA-ATTAAA-AAT
* *
488668 AATATTTAAAGAGTTTTGAAAATTATAAACTTAGAAAAATCCTACTAGAAAAATTTACGGAG-AG
1 AATATTTGAAGAATTTTGAAAATTATAAACTTAGAAAAATCCTACTAGAAAAATTTACGGAGTAG
* * * * *
488732 AAAAGTCCATATCTTGGTAGCAGAAAAACTTTTAAATCTCAT-AAATAAATTGAATTTTTCAAAA
66 AAAACTTCATATCTTGGTAACAGAAAAA-TTCTAAAACTCATAAAATAAATT-AATTTTTCAAAA
* * *
488796 CTGATTTACTCTGAATTAAATAGT
129 CTGATTTAATATGAATTAAA-AAT
* * *
488820 AACATTTGAAGAATTTTGAAAATTATAAACTTAGAAAAATCATA-TCGAAGAAATTTACGGAGTA
1 AATATTTGAAGAATTTTGAAAATTATAAACTTAGAAAAATCCTACTAGAA-AAATTTACGGAGTA
* * *
488884 GAAAACTTCATATCTTGATAACAGAAAAATTCTAAAGCTTATAAAATAAATTAATATTTTCAAAA
65 GAAAACTTCATATCTTGGTAACAGAAAAATTCTAAAACTCATAAAATAAATTAAT-TTTTCAAAA
* *
488949 CTGATTTTATGTGAATTAAAAAT
129 CTGATTTAATATGAATTAAAAAT
* *
488972 CATATTTGAAGAATTTTTAAAATTATAAA
1 AATATTTGAAGAATTTTGAAAATTATAAA
489001 TTTTAAAAAT
Statistics
Matches: 282, Mismatches: 44, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
151 36 0.13
152 174 0.62
153 72 0.26
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (151 bp):
AATATTTGAAGAATTTTGAAAATTATAAACTTAGAAAAATCCTACTAGAAAAATTTACGGAGTAG
AAAACTTCATATCTTGGTAACAGAAAAATTCTAAAACTCATAAAATAAATTAATTTTTCAAAACT
GATTTAATATGAATTAAAAAT
Found at i:495599 original size:13 final size:13
Alignment explanation
Indices: 495581--495606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
495571 AATTTTTTTG
495581 TGTATCGATACAT
1 TGTATCGATACAT
495594 TGTATCGATACAT
1 TGTATCGATACAT
495607 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:497202 original size:13 final size:13
Alignment explanation
Indices: 497186--497222 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
497176 AATCCCCCTA
*
497186 TATCGATACAGTG
1 TATCGATACAATG
497199 TATCGATACAATG
1 TATCGATACAATG
497212 TATCGATACAA
1 TATCGATACAA
497223 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:506722 original size:21 final size:21
Alignment explanation
Indices: 506689--506729 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
506679 CTAAGTAAAA
506689 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
506710 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
506730 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:506795 original size:21 final size:20
Alignment explanation
Indices: 506766--506822 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
506756 AAAACCCTGA
**
506766 AAAGTATCGATACACATTTT
1 AAAGTATCGATACACATTGC
*
506786 AAATGTATCGATACAGATTGC
1 AAA-GTATCGATACACATTGC
*
506807 ATAGTATCGATACACA
1 AAAGTATCGATACACA
506823 AAAATATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACACATTGC
Found at i:506891 original size:53 final size:53
Alignment explanation
Indices: 506810--506946 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
506800 AGATTGCATA
*
506810 GTATCGATACACAAAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACAC-AAAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
* *
506864 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACAAAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
506917 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACAAAATATGTATCGATACA
506947 TTGGTAGTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 67 0.85
54 12 0.15
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (53 bp):
GTATCGATACACAAAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:507037 original size:14 final size:14
Alignment explanation
Indices: 507012--507079 Score: 74
Period size: 14 Copynumber: 5.2 Consensus size: 14
507002 GTATCGATAC
507012 ATCACT-TTCATGT
1 ATCACTATTCATGT
507025 ATCACTATTCATGT
1 ATCACTATTCATGT
507039 ATCACTATTC----
1 ATCACTATTCATGT
* *
507049 ATCACTGTTCACGT
1 ATCACTATTCATGT
*
507063 ATCACTATTCATAT
1 ATCACTATTCATGT
507077 ATC
1 ATC
507080 GTTAAAAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.20
13 6 0.13
14 31 0.67
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.41
Consensus pattern (14 bp):
ATCACTATTCATGT
Found at i:507054 original size:24 final size:24
Alignment explanation
Indices: 507025--507074 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
507015 ACTTTCATGT
*
507025 ATCACTATTCATGTATCACTATTC
1 ATCACTATTCACGTATCACTATTC
*
507049 ATCACTGTTCACGTATCACTATTC
1 ATCACTATTCACGTATCACTATTC
507073 AT
1 AT
507075 ATATCGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (24 bp):
ATCACTATTCACGTATCACTATTC
Found at i:507091 original size:38 final size:38
Alignment explanation
Indices: 507012--507097 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 38
507002 GTATCGATAC
* * ***
507012 ATCACT-TTCATGTATCACTATTCATGTATCACTATTC
1 ATCACTGTTCACGTATCACTATTCATATATCACTAAAA
**
507049 ATCACTGTTCACGTATCACTATTCATATATCGTTAAAA
1 ATCACTGTTCACGTATCACTATTCATATATCACTAAAA
507087 ATCACTGTTCA
1 ATCACTGTTCA
507098 TCACTATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 6 0.15
38 35 0.85
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (38 bp):
ATCACTGTTCACGTATCACTATTCATATATCACTAAAA
Found at i:507126 original size:13 final size:13
Alignment explanation
Indices: 507108--507146 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
507098 TCACTATTTA
507108 TGTATCGATACAT
1 TGTATCGATACAT
* *
507121 TGTATCAATACAC
1 TGTATCGATACAT
507134 TGTATCGATACAT
1 TGTATCGATACAT
507147 CATAAATAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:510101 original size:80 final size:80
Alignment explanation
Indices: 510002--510315 Score: 377
Period size: 80 Copynumber: 4.0 Consensus size: 80
509992 GTTAGGATCC
* * * * * * *
510002 CCTTGGAGATAGTGAGGTTGGAGTATCCCCAAAGATGAAGACTTT-A-GTATTGTGAAAGTAAAA
1 CCTTGGAGATGGTGGGGTTGGAGTATCCCCAGAGATGAAAAATTTGATGT-TT-TGGAATTAAAA
*
510065 ATGGGGTTGGAGTATCC
64 ATGGGGTTGGAGTATCT
** *
510082 CCTCAGAGATGATGGGGTTGGAGTAT-CCCAGAGATGAAAAATTTGATGTTTTGGAATTAAAAAT
1 CCTTGGAGATGGTGGGGTTGGAGTATCCCCAGAGATGAAAAATTTGATGTTTTGGAATTAAAAAT
* *
510146 GGGGTTAGAATATCT
66 GGGGTTGGAGTATCT
* * *
510161 CCTTGGAGATGGTGGAGTTGGAGTATCCCTAGAGATGAAAATTTTGATGTTTTGGAATTAAAAAT
1 CCTTGGAGATGGTGGGGTTGGAGTATCCCCAGAGATGAAAAATTTGATGTTTTGGAATTAAAAAT
510226 GGGGTTGGAGTATCT
66 GGGGTTGGAGTATCT
* * * * *
510241 CCTTGGAAATGGTGGGGTTGGAGTAT--CCAGAGATGAAAAATTTGGTGTTTTAGAAGTAAAAAC
1 CCTTGGAGATGGTGGGGTTGGAGTATCCCCAGAGATGAAAAATTTGATGTTTTGGAATTAAAAAT
*
510304 GGGATTGGAGTA
66 GGGGTTGGAGTA
510316 CCCTTCTTGA
Statistics
Matches: 201, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
78 42 0.21
79 60 0.30
80 97 0.48
81 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.30
Consensus pattern (80 bp):
CCTTGGAGATGGTGGGGTTGGAGTATCCCCAGAGATGAAAAATTTGATGTTTTGGAATTAAAAAT
GGGGTTGGAGTATCT
Found at i:512145 original size:34 final size:35
Alignment explanation
Indices: 512107--512173 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
512097 CCTTACAAGA
512107 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
512141 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
512174 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:512670 original size:13 final size:13
Alignment explanation
Indices: 512652--512677 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
512642 CTATTTATGA
512652 TGTATCGATACAC
1 TGTATCGATACAC
512665 TGTATCGATACAC
1 TGTATCGATACAC
512678 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:512906 original size:20 final size:20
Alignment explanation
Indices: 512843--512913 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
512833 GCCAATGACC
**
512843 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
512863 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
512883 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
512903 TGTATCGATAC
1 TGTATCGATAC
512914 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:512979 original size:21 final size:21
Alignment explanation
Indices: 512953--512993 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
512943 GTCAACCTTG
512953 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
512974 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
512994 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:514646 original size:13 final size:13
Alignment explanation
Indices: 514628--514652 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
514618 ACTGAAGCAA
514628 TGTATCGATACAT
1 TGTATCGATACAT
514641 TGTATCGATACA
1 TGTATCGATACA
514653 ATTTGGAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:517803 original size:34 final size:35
Alignment explanation
Indices: 517765--517831 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
517755 CCTTACAAGA
517765 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
517799 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
517832 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:518328 original size:13 final size:13
Alignment explanation
Indices: 518310--518335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
518300 CTATTTATGA
518310 TGTATCGATACAC
1 TGTATCGATACAC
518323 TGTATCGATACAC
1 TGTATCGATACAC
518336 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:518564 original size:20 final size:20
Alignment explanation
Indices: 518501--518571 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
518491 GCCAATGACC
**
518501 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
518521 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
518541 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
518561 TGTATCGATAC
1 TGTATCGATAC
518572 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:518637 original size:21 final size:21
Alignment explanation
Indices: 518611--518651 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
518601 GTCAACCTTG
518611 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
518632 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
518652 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:521277 original size:32 final size:33
Alignment explanation
Indices: 521219--521281 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
521209 CACCCAGATG
*
521219 TATCGATACATGCTGCTTTGTATCGATACATTA
1 TATCGATACATGCTGCATTGTATCGATACATTA
*
521252 TATCGATACATG-TTCATTGTATCGATACAT
1 TATCGATACATGCTGCATTGTATCGATACAT
521282 GGACAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (33 bp):
TATCGATACATGCTGCATTGTATCGATACATTA
Found at i:521358 original size:20 final size:19
Alignment explanation
Indices: 521333--521385 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
521323 TATCACTATT
521333 TGTATCGATACATG-GTACAA
1 TGTATCGATACATGAG-A-AA
521353 TGTATCGATACATGAAGAAA
1 TGTATCGATACATG-AGAAA
521373 TGTATCGATACAT
1 TGTATCGATACAT
521386 AGCTTGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (19 bp):
TGTATCGATACATGAGAAA
Found at i:524398 original size:13 final size:13
Alignment explanation
Indices: 524380--524404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
524370 CATTTTATGG
524380 TGTATCGATACAA
1 TGTATCGATACAA
524393 TGTATCGATACA
1 TGTATCGATACA
524405 TATGGTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:524420 original size:32 final size:33
Alignment explanation
Indices: 524357--524424 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
524347 CGTTACAAGC
* *
524357 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATATGATGGTGTATCGATA
*
524390 CAATGTATCGATACATATGGT-GTGTATCGATA
1 CAATGTATCGATACATATGATGGTGTATCGATA
524422 CAA
1 CAA
524425 ATTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATATGATGGTGTATCGATA
Found at i:524500 original size:20 final size:20
Alignment explanation
Indices: 524456--524507 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
524446 ACCAATGACT
** *
524456 TGTATCGATACATTTTTTTA
1 TGTATCGATACATTTAGTCA
*
524476 AGTATCGATACATTTAGTCA
1 TGTATCGATACATTTAGTCA
524496 TGTATCGATACA
1 TGTATCGATACA
524508 ATGTATCGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTTAGTCA
Found at i:524513 original size:13 final size:13
Alignment explanation
Indices: 524495--524523 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
524485 ACATTTAGTC
524495 ATGTATCGATACA
1 ATGTATCGATACA
524508 ATGTATCGATACA
1 ATGTATCGATACA
524521 ATG
1 ATG
524524 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:524534 original size:20 final size:20
Alignment explanation
Indices: 524509--524559 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
524499 ATCGATACAA
*
524509 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
524529 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
524549 TGTATCGATAC
1 TGTATCGATAC
524560 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:524611 original size:91 final size:91
Alignment explanation
Indices: 524508--524801 Score: 235
Period size: 91 Copynumber: 3.2 Consensus size: 91
524498 TATCGATACA
524508 ATGTATCGATACAATGCAATCTGTATCGATACATTTAAATGTGTATCGATACTTTTCAGGGTTTT
1 ATGTATCGATACAATGCAATCTGTATCGATACATTTAAATGTGTATCGATACTTTTCAGGGTTTT
524573 GACCTTTTTAGCCTAAGTCAACCTTG
66 GACCTTTTTAGCCTAAGTCAACCTTG
* * * * * *
524599 ATGTATCGATACAAATTTAGCTA-CTGCCA-AGCACTACCA-ATGACT-TGTATCGATACATTTT
1 ATGTATCGATAC-AA--T-GCAATCTG-TATCG-A-TA-CATTTAAATGTGTATCGATAC----T
* * * * * * * * * * **
524660 TTTTA-AGTATCGATAC-ATTTAGTC-ATGT-ATCGATACA
54 TTTCAGGGTTTTGA-CCTTTTTAGCCTAAGTCAAC-CT-TG
524697 ATGTATCGATACAATGCAATCTGTATCGATACATTTAAATGTGTATCGATACTTTTCAGGGTTTT
1 ATGTATCGATACAATGCAATCTGTATCGATACATTTAAATGTGTATCGATACTTTTCAGGGTTTT
524762 GACCTTTTTAGCCTAAGTCAACCTTG
66 GACCTTTTTAGCCTAAGTCAACCTTG
524788 ATGTATCGATACAA
1 ATGTATCGATACAA
524802 ATACCTATGT
Statistics
Matches: 144, Mismatches: 36, Indels: 46
0.64 0.16 0.20
Matches are distributed among these distances:
90 6 0.04
91 37 0.26
92 8 0.06
93 7 0.05
94 21 0.15
95 21 0.15
96 7 0.05
97 8 0.06
98 23 0.16
99 6 0.04
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (91 bp):
ATGTATCGATACAATGCAATCTGTATCGATACATTTAAATGTGTATCGATACTTTTCAGGGTTTT
GACCTTTTTAGCCTAAGTCAACCTTG
Found at i:524628 original size:188 final size:189
Alignment explanation
Indices: 524412--524803 Score: 777
Period size: 189 Copynumber: 2.1 Consensus size: 189
524402 ACATATGGTG
524412 TGTATCGATACAAATTTAGCTACTGCCAAGCACTACCAATGACTTGTATCGATACA-TTTTTTTA
1 TGTATCGATACAAATTTAGCTACTGCCAAGCACTACCAATGACTTGTATCGATACATTTTTTTTA
524476 AGTATCGATACATTTAGTCATGTATCGATACAATGTATCGATACAATGCAATCTGTATCGATACA
66 AGTATCGATACATTTAGTCATGTATCGATACAATGTATCGATACAATGCAATCTGTATCGATACA
524541 TTTAAATGTGTATCGATACTTTTCAGGGTTTTGACCTTTTTAGCCTAAGTCAACCTTGA
131 TTTAAATGTGTATCGATACTTTTCAGGGTTTTGACCTTTTTAGCCTAAGTCAACCTTGA
524600 TGTATCGATACAAATTTAGCTACTGCCAAGCACTACCAATGACTTGTATCGATACATTTTTTTTA
1 TGTATCGATACAAATTTAGCTACTGCCAAGCACTACCAATGACTTGTATCGATACATTTTTTTTA
524665 AGTATCGATACATTTAGTCATGTATCGATACAATGTATCGATACAATGCAATCTGTATCGATACA
66 AGTATCGATACATTTAGTCATGTATCGATACAATGTATCGATACAATGCAATCTGTATCGATACA
524730 TTTAAATGTGTATCGATACTTTTCAGGGTTTTGACCTTTTTAGCCTAAGTCAACCTTGA
131 TTTAAATGTGTATCGATACTTTTCAGGGTTTTGACCTTTTTAGCCTAAGTCAACCTTGA
524789 TGTATCGATACAAAT
1 TGTATCGATACAAAT
524804 ACCTATGTAT
Statistics
Matches: 203, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
188 56 0.28
189 147 0.72
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (189 bp):
TGTATCGATACAAATTTAGCTACTGCCAAGCACTACCAATGACTTGTATCGATACATTTTTTTTA
AGTATCGATACATTTAGTCATGTATCGATACAATGTATCGATACAATGCAATCTGTATCGATACA
TTTAAATGTGTATCGATACTTTTCAGGGTTTTGACCTTTTTAGCCTAAGTCAACCTTGA
Found at i:524702 original size:13 final size:13
Alignment explanation
Indices: 524684--524712 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
524674 ACATTTAGTC
524684 ATGTATCGATACA
1 ATGTATCGATACA
524697 ATGTATCGATACA
1 ATGTATCGATACA
524710 ATG
1 ATG
524713 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:524723 original size:20 final size:20
Alignment explanation
Indices: 524698--524748 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
524688 ATCGATACAA
*
524698 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
524718 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
524738 TGTATCGATAC
1 TGTATCGATAC
524749 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:528864 original size:20 final size:20
Alignment explanation
Indices: 528839--528882 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
528829 TTTGGAAATT
528839 TACATAGAGACATGTATCGA
1 TACATAGAGACATGTATCGA
528859 TACATAGAGACATGTATCGA
1 TACATAGAGACATGTATCGA
528879 TACA
1 TACA
528883 ACTGGAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (20 bp):
TACATAGAGACATGTATCGA
Found at i:528936 original size:13 final size:13
Alignment explanation
Indices: 528918--528945 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
528908 CAACATTCCG
528918 TGTATCGATACAT
1 TGTATCGATACAT
528931 TGTATCGATACAT
1 TGTATCGATACAT
528944 TG
1 TG
528946 GGTACTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:531542 original size:33 final size:32
Alignment explanation
Indices: 531500--531563 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 32
531490 TCATTATTTA
531500 TATCGATACATG-GTACAATGTATCGATACATTC
1 TATCGATACATGAG-A-AATGTATCGATACATTC
531533 TATCGATACATGAAGAAATGTATCGATACAT
1 TATCGATACATG-AGAAATGTATCGATACAT
531564 AGCTTGTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (32 bp):
TATCGATACATGAGAAATGTATCGATACATTC
Found at i:533755 original size:21 final size:22
Alignment explanation
Indices: 533729--533776 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
533719 TAAACCAAAA
533729 ATGATTTTGAAAA-TAAAATTG
1 ATGATTTTGAAAATTAAAATTG
*
533750 ATGA-TTTGAAAATTAAAGTTG
1 ATGATTTTGAAAATTAAAATTG
533771 AT-ATTT
1 ATGATTT
533777 GATTGGAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (22 bp):
ATGATTTTGAAAATTAAAATTG
Found at i:533759 original size:20 final size:21
Alignment explanation
Indices: 533729--533778 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
533719 TAAACCAAAA
533729 ATGATTTTGAAAA-TAAAATTG
1 ATGA-TTTGAAAATTAAAATTG
*
533750 ATGATTTGAAAATTAAAGTTG
1 ATGATTTGAAAATTAAAATTG
533771 AT-ATTTGA
1 ATGATTTGA
533779 TTGGAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (21 bp):
ATGATTTGAAAATTAAAATTG
Found at i:536345 original size:20 final size:20
Alignment explanation
Indices: 536320--536367 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
536310 TGGAGGTGCT
**
536320 AAACATGCTGTAAATGCATG
1 AAACATGCTCAAAATGCATG
536340 AAACATAGCTCAAAATGCATG
1 AAACAT-GCTCAAAATGCATG
*
536361 AATCATG
1 AAACATG
536368 GGCTGTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (20 bp):
AAACATGCTCAAAATGCATG
Found at i:537391 original size:13 final size:13
Alignment explanation
Indices: 537373--537427 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
537363 ATAAAACTTA
537373 TGTATCGATACAT
1 TGTATCGATACAT
537386 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
537404 ATGTATCGATACAT
1 -TGTATCGATACAT
537418 TGTATCGATA
1 TGTATCGATA
537428 AAATACTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 19 0.53
14 1 0.03
16 6 0.17
18 1 0.03
19 9 0.25
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:537393 original size:32 final size:31
Alignment explanation
Indices: 537352--537449 Score: 151
Period size: 32 Copynumber: 3.0 Consensus size: 31
537342 AGTAGCTTAA
537352 ATTGTATCGATATAAAACTTATGTATCGATAC
1 ATTGTATCGATA-AAAACTTATGTATCGATAC
*
537384 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATA-AAAACTTATGTATCGATAC
537416 ATTGTATCGATAAAATACTTTATGTATCGATAC
1 ATTGTATCGATAAAA-AC-TTATGTATCGATAC
537449 A
1 A
537450 AATCGTTGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
31 2 0.03
32 44 0.72
33 15 0.25
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (31 bp):
ATTGTATCGATAAAAACTTATGTATCGATAC
Found at i:537410 original size:19 final size:19
Alignment explanation
Indices: 537354--537416 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
537344 TAGCTTAAAT
* *
537354 TGTATCGATATAAAACTTA
1 TGTATCGATACAACACTTA
537373 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
537386 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
537405 TGTATCGATACA
1 TGTATCGATACA
537417 TTGTATCGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 5 0.14
18 1 0.03
19 21 0.57
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:540331 original size:21 final size:20
Alignment explanation
Indices: 540279--540333 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
540269 CGTTAGGCCA
540279 CATGTATTGATACAATTCAT
1 CATGTATTGATACAATTCAT
* *
540299 CATATATTGATACAATTTAGT
1 CATGTATTGATACAATTCA-T
*
540320 CATGTATCGATACA
1 CATGTATTGATACA
540334 GTCGAAGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
CATGTATTGATACAATTCAT
Found at i:542462 original size:156 final size:155
Alignment explanation
Indices: 542158--542550 Score: 404
Period size: 155 Copynumber: 2.5 Consensus size: 155
542148 CTTTGACATA
* * * * * * * *
542158 AAAGTACCCGATGCCCCTAAAAGACTTAAATAAG-ATTATAGATGGGATAAAGCTATCCTAAATA
1 AAAGTACCTGATACCACTAAAGGACTTAAA-AAGAATTACAAATGGGATGAACCTATCCTAAATA
* ** ** * * * * * *
542222 CCCACATTCAACATAAAAGTGGACCCGGTGA-CAGCTTAAGACTT-ATTCTAGAAAATTATCAAA
65 CCCACCTTCGGCATAAAAGCAGACCCGATGATGA-CGTAGGAGTTAATTCTAAAAAATTATCAAA
** *
542285 ATGCCTTTAGGGGATATCTTCGACGTAG
129 ATGCCTACAGGGGATACCTTCGACGT-G
* * *
542313 AAA-TGGCC-GATATCC-CTAAAGGATTTAAAAAGGATTACAAACTGGGATGAACCTATCCTAAA
1 AAAGT-ACCTGATA-CCACTAAAGGACTTAAAAAGAATTACAAA-TGGGATGAACCTATCCTAAA
* *
542375 TACCTACCTTCGGCATAAAAGCAGACCCGATGATGACGTAGGAGTTAATTCTAAAAAATTATGAA
63 TACCCACCTTCGGCATAAAAGCAGACCCGATGATGACGTAGGAGTTAATTCTAAAAAATTATCAA
542440 AATGCGC-ACAGGGGATACCTTCGACGTG
128 AATGC-CTACAGGGGATACCTTCGACGTG
* * *
542468 AAAGTACCTGATACCACTAAAGGACTTAAAACGAATTATAAATGGGATGAACCTATCCTCAATAC
1 AAAGTACCTGATACCACTAAAGGACTTAAAAAGAATTACAAATGGGATGAACCTATCCTAAATAC
542533 CCACCTTCGGCATAAAAG
66 CCACCTTCGGCATAAAAG
542551 AGAAATCGGT
Statistics
Matches: 197, Mismatches: 31, Indels: 20
0.79 0.12 0.08
Matches are distributed among these distances:
153 3 0.02
154 22 0.11
155 105 0.53
156 66 0.34
157 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (155 bp):
AAAGTACCTGATACCACTAAAGGACTTAAAAAGAATTACAAATGGGATGAACCTATCCTAAATAC
CCACCTTCGGCATAAAAGCAGACCCGATGATGACGTAGGAGTTAATTCTAAAAAATTATCAAAAT
GCCTACAGGGGATACCTTCGACGTG
Found at i:542589 original size:155 final size:156
Alignment explanation
Indices: 542266--542598 Score: 383
Period size: 155 Copynumber: 2.1 Consensus size: 156
542256 CTTAAGACTT
* ** * *
542266 ATTCTAGAAAATTATCAAAATGC-CTTTAGGGGATATCTTCGACGTAGAAATGGCCGATATCCCT
1 ATTCTAAAAAATTATCAAAATGCGC-ACAGGGGATACCTTCGACGTAGAAATGACCGATATCCCT
* * *
542330 AAAGGATTTAAAAAGGATTACAAACTGGGATGAACCTATCCTAAATACCTACCTTCGGCATAAAA
65 AAAGGACTTAAAAAGAATTACAAACTGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAA
* * *
542395 GCAGACCCGATGATGACGTAGGAGTTA
130 GCAGAACCGATGATGACCTAGGAATTA
*
542422 ATTCTAAAAAATTATGAAAATGCGCACAGGGGATACCTTCGACGT-GAAA-GTACCTGATA-CCA
1 ATTCTAAAAAATTATCAAAATGCGCACAGGGGATACCTTCGACGTAGAAATG-ACC-GATATCC-
* * *
542484 CTAAAGGACTTAAAACGAATTATAAA-TGGGATGAACCTATCCTCAATACCCACCTTCGGCATAA
63 CTAAAGGACTTAAAAAGAATTACAAACTGGGATGAACCTATCCTAAATACCCACCTTCGGCATAA
* * *
542548 AAG-AGAAATCGGTGATGACCTAGGAATTGG
128 AAGCAG-AACCGATGATGACCTAGGAATT-A
**
542578 A-TCTAGGAAATTATCAAAATG
1 ATTCTAAAAAATTATCAAAATG
542599 TCTGAAAGCT
Statistics
Matches: 150, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
154 3 0.02
155 81 0.54
156 65 0.43
157 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (156 bp):
ATTCTAAAAAATTATCAAAATGCGCACAGGGGATACCTTCGACGTAGAAATGACCGATATCCCTA
AAGGACTTAAAAAGAATTACAAACTGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAG
CAGAACCGATGATGACCTAGGAATTA
Found at i:543061 original size:32 final size:30
Alignment explanation
Indices: 543025--543083 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
543015 GAAATCAAAT
543025 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
543057 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
543084 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:543362 original size:13 final size:13
Alignment explanation
Indices: 543344--543369 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
543334 ATATTTTTTG
543344 TGTATCGATACAT
1 TGTATCGATACAT
543357 TGTATCGATACAT
1 TGTATCGATACAT
543370 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:543380 original size:32 final size:33
Alignment explanation
Indices: 543323--543387 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
543313 TACAAGCCAA
*
543323 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCAATACAT
543357 TGTATCGATACATA-TTTTGTGTATCAATACA
1 TGTATCGATACATATTTTTGTGTATCAATACA
543388 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 16 0.53
34 14 0.47
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCAATACAT
Found at i:543381 original size:19 final size:19
Alignment explanation
Indices: 543323--543387 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
543313 TACAAGCCAA
543323 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
543344 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
543357 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
*
543376 TGTATCAATACA
1 TGTATCGATACA
543388 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
21 11 0.30
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:545942 original size:13 final size:13
Alignment explanation
Indices: 545924--545958 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
545914 ATCCCCCTGC
545924 ATCGATACAGTGT
1 ATCGATACAGTGT
*
545937 ATCGATACATTGT
1 ATCGATACAGTGT
545950 ATCGATACA
1 ATCGATACA
545959 AAGAAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (13 bp):
ATCGATACAGTGT
Found at i:548058 original size:15 final size:15
Alignment explanation
Indices: 548038--548068 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
548028 ATTTCGTTTG
*
548038 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
548053 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
548068 G
1 G
548069 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:551833 original size:32 final size:30
Alignment explanation
Indices: 551797--551855 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
551787 GAAATCAAAT
551797 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
551829 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
551856 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:552068 original size:20 final size:20
Alignment explanation
Indices: 552043--552080 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
552033 TCCTGTGTGA
552043 ATGTATCGATACAAATTTTG
1 ATGTATCGATACAAATTTTG
*
552063 ATGTATCGATACATATTT
1 ATGTATCGATACAAATTT
552081 GAAAATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACAAATTTTG
Found at i:552154 original size:13 final size:13
Alignment explanation
Indices: 552136--552161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
552126 ATATTTTTTG
552136 TGTATCGATACAT
1 TGTATCGATACAT
552149 TGTATCGATACAT
1 TGTATCGATACAT
552162 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:552172 original size:32 final size:33
Alignment explanation
Indices: 552115--552179 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
552105 TACAAGCCAA
*
552115 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCAATACAT
552149 TGTATCGATACATA-TTTTGTGTATCAATACA
1 TGTATCGATACATATTTTTGTGTATCAATACA
552180 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 16 0.53
34 14 0.47
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCAATACAT
Found at i:552173 original size:19 final size:19
Alignment explanation
Indices: 552115--552179 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
552105 TACAAGCCAA
552115 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
552136 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
552149 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
*
552168 TGTATCAATACA
1 TGTATCGATACA
552180 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
21 11 0.30
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:552924 original size:154 final size:152
Alignment explanation
Indices: 552632--553236 Score: 486
Period size: 154 Copynumber: 3.9 Consensus size: 152
552622 AATTATAGGA
* * * * * * *
552632 GGGACAAACCTATCCTAAATTCCCACCTTCGGCATAAAAATGGACCTGGTGACAACCTAGGACTC
1 GGGATAAACCTATCCT-AACTGCTACCTTCGGCATAAAAGTAGACCTAGTGACAACCTAGGACTC
* * ** *
552697 GATTCTAAAAAATTATGAAAATGCCCCTACAGAATACCTTCGATGTACAAGTACCCGATACCCAT
65 GATTCTAAAAAATTACGAAAATG-CCATAGGGAATACCTTCGACGTACAAGTACCCGATACCCAT
552762 AAAGGACTTAAAAAGGTTTGAAAT
129 AAAGGACTTAAAAAGGTTTGAAAT
* * * * *
552786 GGGATAAACTTATCCTAACTGCATACCTTTGGCATAAAAGTAGACCTAGTGACAACCTAGTAATT
1 GGGATAAACCTATCCTAACTGC-TACCTTCGGCATAAAAGTAGACCTAGTGACAACCTAGGACTC
* * * * * *
552851 GTTTCTAAAAAATTACGAAAATGCCTTTAGGGAATACCTTGGACATAAAAGT-CCTCGATA-CCT
65 GATTCTAAAAAATTACGAAAATGCC-ATAGGGAATACCTTCGACGTACAAGTACC-CGATACCCA
* *
552914 TTATGTGACTTAAAAAGGATAATTG--AT
128 TAAAG-GACTTAAAAAGG-T--TTGAAAT
* * * * * ** ** *
552941 GAGATGAACCTATCGTAAATATCTACCTTCGATATAAAA-TCAGACCCGGTGACAACCTAGGACC
1 GGGATAAACCTATCCTAACT-GCTACCTTCGGCATAAAAGT-AGACCTAGTGACAACCTAGGACT
* * * * * *
553005 CGATTATGAAAAATTACGAAAATGCACATAGGGGATACCTTCAACGTACAAGTACCCGGTACCCC
64 CGATTCTAAAAAATTACGAAAATGC-CATAGGGAATACCTTCGACGTACAAGTACCCGATACCCA
553070 TAAAGGACTTAAAAAGGTTTGAAAT
128 TAAAGGACTTAAAAAGGTTTGAAAT
** * ** * *
553095 GGGATAAACCTATCCTAACTGCCCGCCTTTGGCATAAAAGCGGA-CTAGGTGACAACCTTGGAGT
1 GGGATAAACCTATCCTAACTG-CTACCTTCGGCATAAAAGTAGACCTA-GTGACAACCTAGGACT
* * * * * * * * * * *
553159 TGATTCTAAAATATTACGAAAATACCCCTAGGGGATACTTTTGACGTAAAAGTGCCCGATGCCTA
64 CGATTCTAAAAAATTACGAAAAT-GCCATAGGGAATACCTTCGACGTACAAGTACCCGATACCCA
*
553224 -AAAAGACTTAAAA
128 TAAAGGACTTAAAA
553237 TGACAAGTAA
Statistics
Matches: 348, Mismatches: 85, Indels: 37
0.74 0.18 0.08
Matches are distributed among these distances:
152 3 0.01
153 26 0.07
154 200 0.57
155 107 0.31
156 9 0.03
157 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (152 bp):
GGGATAAACCTATCCTAACTGCTACCTTCGGCATAAAAGTAGACCTAGTGACAACCTAGGACTCG
ATTCTAAAAAATTACGAAAATGCCATAGGGAATACCTTCGACGTACAAGTACCCGATACCCATAA
AGGACTTAAAAAGGTTTGAAAT
Found at i:554834 original size:13 final size:13
Alignment explanation
Indices: 554818--554860 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
554808 TTGAATTTTC
554818 TTTTTTT-TC-TT
1 TTTTTTTCTCTTT
**
554829 TTTTTTTCTCACT
1 TTTTTTTCTCTTT
554842 TTTTTTTCTCTTT
1 TTTTTTTCTCTTT
554855 TTTTTT
1 TTTTTT
554861 CTCCTTTCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 7 0.26
12 2 0.07
13 18 0.67
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTCTCTTT
Found at i:554853 original size:25 final size:23
Alignment explanation
Indices: 554818--554867 Score: 82
Period size: 25 Copynumber: 2.1 Consensus size: 23
554808 TTGAATTTTC
554818 TTTTTTTTCTTTTTTTTTCTCACT
1 TTTTTTTTCTTTTTTTTTCTC-CT
554842 TTTTTTTCTCTTTTTTTTTCTCCT
1 TTTTTTT-TCTTTTTTTTTCTCCT
554866 TT
1 TT
554868 CTGCCAGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTTTCTTTTTTTTTCTCCT
Found at i:554867 original size:13 final size:12
Alignment explanation
Indices: 554818--554863 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
554808 TTGAATTTTC
554818 TTTTTTT-TCTT
1 TTTTTTTCTCTT
*
554829 TTTTTTTCTCACT
1 TTTTTTTCTC-TT
554842 TTTTTTTCTCTT
1 TTTTTTTCTCTT
554854 TTTTTTTCTC
1 TTTTTTTCTC
554864 CTTTCTGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 7 0.23
12 13 0.42
13 11 0.35
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTCTCTT
Found at i:555867 original size:165 final size:165
Alignment explanation
Indices: 555496--556311 Score: 834
Period size: 166 Copynumber: 4.9 Consensus size: 165
555486 GTTTTTTGGG
* * * * * *
555496 AAAATAGAGATTTCAACG-AAAAATCCAAAA-ATCATGAAAATGAATTAATTTTTGAAAAAT-AA
1 AAAAGAGAAATTTCAAGGAAAAAAT-CAAAATCTCATGAAAATGAATGAATTTTTGAAAACTGAA
* ** * * ***
555558 TTTAATATAAAATAAATAATAATATTTTTTAAATTTTAAAAA-T-AAAAA-AATAAAAATCAAAT
65 -TTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAAACAAGAAAAATC-CCC
* *
555620 CGAAAAAATTTACGAAGTAGAAAACTAT-GTATTTCAAA
128 CGAAAAAATTTACGAAGTAGAAAA-TATCATATTTCGAA
* *
555658 AAAAG-GAAAATTTCAAGGAAAAAATTCAAAAT-TTATGGAAATGAATGAATTTTTGAAAACTGA
1 AAAAGAG-AAATTTCAAGGAAAAAA-TCAAAATCTCATGAAAATGAATGAATTTTTGAAAACTGA
* * * *
555721 ATTACTATGAAATAAATAATAACATTTGATGAATTTTAAAAATAAAAAAAGAAGAAAAATCTCCC
64 ATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAAACAAGAAAAATC-CCC
* *
555786 CG-AAAAATTTACGGAGTAGAAGAAT-TCATTTTTCGAA
128 CGAAAAAATTTACGAAGTAGAA-AATATCATATTTCGAA
* * * *
555823 AAAAGAGAAATTTCAAGGAAAAAATTTAAAATTTC-TGAAAATGAAAGAATTTTTGAAAAATGAA
1 AAAAGAGAAATTTCAAGGAAAAAA-TCAAAATCTCATGAAAATGAATGAATTTTTGAAAACTGAA
* *
555887 TTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAGAACCAAGAAAAATCCCCTC
65 TTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAAACAAGAAAAATCCCC-C
** * *
555952 GAAAAAATTTACGAAAAAGAAAATACCGTATTTC-AGA
129 GAAAAAATTTACGAAGTAGAAAATATCATATTTCGA-A
* * * * *
555989 AAAAGAGAAATTTCAAGGAAAAAATAAAAAACTCTTGAAAATGAATGAATTTTTAAAAACTAAAT
1 AAAAGAGAAATTTCAAGGAAAAAATCAAAATCTCATGAAAATGAATGAATTTTTGAAAACTGAAT
* * * * *
556054 TAATATGAAATAAATCATAATGTTTGATGAATTTTAAAAATTGAAAATCAAGAAAAATCCCCCAA
66 TAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAAACAAGAAAAATCCCCCGA
* * *
556119 GAAAAATTTACGGAGTAGAAAATATCGTATTTCG-G
131 -AAAAATTTACGAAGTAGAAAATATCATATTTCGAA
* * * *
556154 AAAAGAGAGAATTTCAAAGAAAAAATCAAGAGCTCATGAAAATGAATGAATATTTG-AAACTGAA
1 AAAAGAGA-AATTTCAAGGAAAAAATCAAAATCTCATGAAAATGAATGAATTTTTGAAAACTGAA
* * **
556218 TCAATATGAAATAAATAAATAAAAATATTTTATGAATTTTAAAAATTAAAAATTAAGAAAAATCC
65 TTAATATGAAATAAAT-AAT---AATATTTGATGAATTTTAAAAATTAAAAAACAAGAAAAATCC
* * *
556283 TCTCGAAAAAAATTTACGAGGAAGAAAAT
126 -CCCG-AAAAAATTTACGAAGTAGAAAAT
556312 CCTGTTATTT
Statistics
Matches: 551, Mismatches: 77, Indels: 44
0.82 0.11 0.07
Matches are distributed among these distances:
161 1 0.00
162 13 0.02
163 70 0.13
164 7 0.01
165 185 0.34
166 215 0.39
169 38 0.07
170 21 0.04
171 1 0.00
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (165 bp):
AAAAGAGAAATTTCAAGGAAAAAATCAAAATCTCATGAAAATGAATGAATTTTTGAAAACTGAAT
TAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAAACAAGAAAAATCCCCCGA
AAAAATTTACGAAGTAGAAAATATCATATTTCGAA
Found at i:556063 original size:331 final size:328
Alignment explanation
Indices: 555496--556311 Score: 963
Period size: 331 Copynumber: 2.5 Consensus size: 328
555486 GTTTTTTGGG
* * * *
555496 AAAATAGAG-ATTTCAACG-AAAAATCCAAAA-ATCATGAAAATGAATTAATTTTTGAAAAAT-A
1 AAAAGAGAGAATTTCAAAGAAAAAAT-CAAAAGCTCATGAAAATGAATGAATTTTTGAAAAATGA
* * * * * *
555557 ATTTAATATAAAATAAATAATAATATTTTTTAAATTTTAAAAA-TAAAAAAATAAAAATCAAATC
65 A-TTAATATGAAATAAATAATAATATTTTATGAATTTTAAAAATTAAAAAAAGAAAAATCCACTC
* * **
555621 GAAAAAATTTACGAAGTAGAAAACTATGTATTTCAAAAAAAGGAAAATTTCAAGGAAAAAATTCA
129 GAAAAAATTTACGAAGAAGAAAA-TACGTATTTCAAAAAAAGGAAAATTTCAAGGAAAAAATAAA
* * * * *
555686 AAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTACTATGAAATAAATAATAACATTTGAT
193 AAATCTATGAAAATGAATGAATTTTTAAAAACTAAATTAATATGAAATAAATAATAACATTTGAT
*
555751 GAATTTTAAAAATAAAAAAAGAAGAAAAATCTCCCC-GAAAAATTTACGGAGTAGAAGAAT-TCA
258 GAATTTTAAAAATAAAAAAACAAGAAAAATC-CCCCAGAAAAATTTACGGAGTAGAA-AATATCA
*
555814 TTTTTCGA
321 TATTTCGA
* * ** *
555822 AAAA-AGAGAAATTTCAAGGAAAAAATTTAAAATTTC-TGAAAATGAAAGAATTTTTGAAAAATG
1 AAAAGAGAG-AATTTCAAAGAAAAAA-TCAAAAGCTCATGAAAATGAATGAATTTTTGAAAAATG
* * *
555885 AATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAGAACCAAGAAAAATCCCC
64 AATTAATATGAAATAAATAATAATATTTTATGAATTTTAAAAATTAA-AA-AAAGAAAAATCCAC
* *
555950 TCGAAAAAATTTACGAAAAAGAAAATACCGTATTTCAGAAAAA-GAGAAATTTCAAGGAAAAAAT
127 TCGAAAAAATTTACGAAGAAGAAAATA-CGTATTTCAAAAAAAGGA-AAATTTCAAGGAAAAAAT
* **
556014 AAAAAACTCT-TGAAAATGAATGAATTTTTAAAAACTAAATTAATATGAAATAAATCATAATGTT
190 AAAAAA-TCTATGAAAATGAATGAATTTTTAAAAACTAAATTAATATGAAATAAATAATAACATT
** *
556078 TGATGAATTTTAAAAATTGAAAATCAAGAAAAATCCCCCAAGAAAAATTTACGGAGTAGAAAATA
254 TGATGAATTTTAAAAATAAAAAAACAAGAAAAATCCCCC-AGAAAAATTTACGGAGTAGAAAATA
* *
556143 TCGTATTTCGG
318 TCATATTTCGA
* * *
556154 AAAAGAGAGAATTTCAAAGAAAAAATCAAGAGCTCATGAAAATGAATGAATATTTG-AAACTGAA
1 AAAAGAGAGAATTTCAAAGAAAAAATCAAAAGCTCATGAAAATGAATGAATTTTTGAAAAATGAA
*
556218 TCAATATGAAATAAATAAATAAAAATATTTTATGAATTTTAAAAATTAAAAATTAAGAAAAATCC
66 TTAATATGAAATAAAT-AAT---AATATTTTATGAATTTTAAAAATTAAAAA--AAGAAAAATCC
* *
556283 TCTCGAAAAAAATTTACGAGGAAGAAAAT
125 ACTCG-AAAAAATTTACGAAGAAGAAAAT
556312 CCTGTTATTT
Statistics
Matches: 417, Mismatches: 49, Indels: 38
0.83 0.10 0.08
Matches are distributed among these distances:
325 4 0.01
326 4 0.01
327 8 0.02
328 70 0.17
329 8 0.02
330 10 0.02
331 176 0.42
332 70 0.17
333 4 0.01
334 2 0.00
335 40 0.10
336 21 0.05
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (328 bp):
AAAAGAGAGAATTTCAAAGAAAAAATCAAAAGCTCATGAAAATGAATGAATTTTTGAAAAATGAA
TTAATATGAAATAAATAATAATATTTTATGAATTTTAAAAATTAAAAAAAGAAAAATCCACTCGA
AAAAATTTACGAAGAAGAAAATACGTATTTCAAAAAAAGGAAAATTTCAAGGAAAAAATAAAAAA
TCTATGAAAATGAATGAATTTTTAAAAACTAAATTAATATGAAATAAATAATAACATTTGATGAA
TTTTAAAAATAAAAAAACAAGAAAAATCCCCCAGAAAAATTTACGGAGTAGAAAATATCATATTT
CGA
Found at i:556211 original size:18 final size:18
Alignment explanation
Indices: 556190--556224 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
556180 CAAGAGCTCA
*
556190 TGAAAATGAATGAATATT
1 TGAAAATGAATCAATATT
*
556208 TGAAACTGAATCAATAT
1 TGAAAATGAATCAATAT
556225 GAAATAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (18 bp):
TGAAAATGAATCAATATT
Found at i:557639 original size:82 final size:82
Alignment explanation
Indices: 557392--557639 Score: 191
Period size: 82 Copynumber: 3.0 Consensus size: 82
557382 ACGGGTAGGT
* ** * * *
557392 AAAAGATAAAAAGGTTGACTTGGG-TTGAACTGACAAGACAATAGAGGATAAAAAGATTTA-CCT
1 AAAAGAT-AAAAGATTGAC-TGGGACCGAACCGACAAGTCAA-AGAGGAT-AAAAGATTTACCCG
557455 AGGACTAAGCCGACAGGTAAAC
62 A-GACTAAGCCGACAGGTAAAC
** ** ** * * **
557477 AAGGGATAAAAGATTGACTGGGATTGAACCGATGA-TCAAAAATGGATAAGAGATTTACTTGAGA
1 AAAAGATAAAAGATTGACTGGGACCGAACCGACAAGTCAAAGA-GGATAAAAGATTTACCCGAGA
* ** *
557541 CTAAACTAACAAGTAAAC
65 CTAAGCCGACAGGTAAAC
*
557559 AAAAGA-AGAAAG-TTGATTGGGACCGAACCGACAAGTCAACAGAGGATAAAAGATTTACCCGAG
1 AAAAGATA-AAAGATTGACTGGGACCGAACCGACAAGTCAA-AGAGGATAAAAGATTTACCCGAG
*
557622 ACTAAGCCGATAGGTAAA
64 ACTAAGCCGACAGGTAAA
557640 TGATGGAATG
Statistics
Matches: 125, Mismatches: 32, Indels: 15
0.73 0.19 0.09
Matches are distributed among these distances:
81 18 0.14
82 69 0.55
83 14 0.11
84 19 0.15
85 5 0.04
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (82 bp):
AAAAGATAAAAGATTGACTGGGACCGAACCGACAAGTCAAAGAGGATAAAAGATTTACCCGAGAC
TAAGCCGACAGGTAAAC
Found at i:557772 original size:43 final size:43
Alignment explanation
Indices: 557725--557967 Score: 209
Period size: 43 Copynumber: 5.7 Consensus size: 43
557715 CGGGCAGATG
*
557725 ATTGATAAAGGAAGTCTCCCGGGACTAAGCCGACGGGTAGACA
1 ATTGATAAAGGAAGTCTCCCGGGACTAAGCCGATGGGTAGACA
* * *** * * *
557768 ATTGACAAAGGAAATCTCTTAGGACTGAGCCGATGGGCA-AGCG
1 ATTGATAAAGGAAGTCTCCCGGGACTAAGCCGATGGGTAGA-CA
* * * *
557811 ATTGATAAAAGAAGTCTCCCGGGACTGAGCCAATGGGTAAACA
1 ATTGATAAAGGAAGTCTCCCGGGACTAAGCCGATGGGTAGACA
* * * ** *
557854 ATTGATAAAGGAAGTCTTCCAGGACTAAGTCGATAAGCAGACA
1 ATTGATAAAGGAAGTCTCCCGGGACTAAGCCGATGGGTAGACA
* * * * * * *
557897 ATTAATAAAGGAAATCTCCCGAGTCTGAGCTGATAGGTAGACA
1 ATTGATAAAGGAAGTCTCCCGGGACTAAGCCGATGGGTAGACA
* * *
557940 ATTGATAAAAGAAGTGTCTCGGGACTAA
1 ATTGATAAAGGAAGTCTCCCGGGACTAA
557968 ACCAACGAGT
Statistics
Matches: 151, Mismatches: 47, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
42 1 0.01
43 149 0.99
44 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.20
Consensus pattern (43 bp):
ATTGATAAAGGAAGTCTCCCGGGACTAAGCCGATGGGTAGACA
Found at i:557905 original size:86 final size:86
Alignment explanation
Indices: 557729--557967 Score: 248
Period size: 86 Copynumber: 2.8 Consensus size: 86
557719 CAGATGATTG
* * * * *
557729 ATAAAGGAAGTCTCCCGGGACTAAGCCGACGGGTAGACAATTGACAAAGGAAATCTCTTAGGACT
1 ATAAAGGAAGTCTCCCGGGACTGAGCCGATGGGTAGACAATTGATAAAGGAAGTCTCTCAGGACT
* ** * *
557794 GAGCCGATGGGCAAGCGATTG
66 AAGCCGATAAGCAAGCAATTA
* * *
557815 ATAAAAGAAGTCTCCCGGGACTGAGCCAATGGGTAAACAATTGATAAAGGAAGTCT-TCCAGGAC
1 ATAAAGGAAGTCTCCCGGGACTGAGCCGATGGGTAGACAATTGATAAAGGAAGTCTCT-CAGGAC
*
557879 TAAGTCGATAAGC-AGACAATTA
65 TAAGCCGATAAGCAAG-CAATTA
* * * * * * * *
557901 ATAAAGGAAATCTCCCGAGTCTGAGCTGATAGGTAGACAATTGATAAAAGAAGTGTCTCGGGACT
1 ATAAAGGAAGTCTCCCGGGACTGAGCCGATGGGTAGACAATTGATAAAGGAAGTCTCTCAGGACT
557966 AA
66 AA
557968 ACCAACGAGT
Statistics
Matches: 125, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
85 3 0.02
86 121 0.97
87 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (86 bp):
ATAAAGGAAGTCTCCCGGGACTGAGCCGATGGGTAGACAATTGATAAAGGAAGTCTCTCAGGACT
AAGCCGATAAGCAAGCAATTA
Found at i:558305 original size:126 final size:126
Alignment explanation
Indices: 557994--558308 Score: 339
Period size: 126 Copynumber: 2.5 Consensus size: 126
557984 AGGTTAAAGT
* * * *
557994 AGTCTCTCAGGTGAAAGCCGATGGGAAGACAAAGGGTGAAGGAATCTCCCAGGTCAAAGCCGATC
1 AGTCTCTCAGGTCAAAGCCGATGGGAAGACAAAGGGTGAAAGAATCTCCCGGGTCAAAGTCGATC
* * * * ** *
558059 AATAGACAAAGGGTGAAGTAGTCTTCCGGGTCAAAACCGACAGGTAGACAAAGGGTAAAAA
66 AACAAACAAAAGGTAAAAAAGTCTTCCGGGTCAAAACCAACAGGTAGACAAAGGGTAAAAA
* * *
558120 AGTCTCTCAGGTCAAAGCCGACGGGCAA-ACAAAGGATGAAAAAATCTCCCGGGTCAAAGTCGAT
1 AGTCTCTCAGGTCAAAGCCGATGGG-AAGACAAAGGGTGAAAGAATCTCCCGGGTCAAAGTCGAT
* ** * * * **
558184 CGACAAACAAAAGGTAAAAAAGTCTTTTGGGTTAAAGCCAAC-GAGTATACAAAGGGTGAAGGA
65 CAACAAACAAAAGGTAAAAAAGTCTTCCGGGTCAAAACCAACAG-GTAGACAAAGGGT-AAAAA
** * * *
558247 A-TCTCTCAGGTTTAAGCCGATGGGTAGACAAAGGGTGAAAGAGTCTCTCGGGTCAAAGTCGA
1 AGTCTCTCAGGTCAAAGCCGATGGGAAGACAAAGGGTGAAAGAATCTCCCGGGTCAAAGTCGA
558309 CGGGCAAAAA
Statistics
Matches: 155, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
125 2 0.01
126 147 0.95
127 6 0.04
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17
Consensus pattern (126 bp):
AGTCTCTCAGGTCAAAGCCGATGGGAAGACAAAGGGTGAAAGAATCTCCCGGGTCAAAGTCGATC
AACAAACAAAAGGTAAAAAAGTCTTCCGGGTCAAAACCAACAGGTAGACAAAGGGTAAAAA
Found at i:558334 original size:126 final size:124
Alignment explanation
Indices: 558122--558440 Score: 306
Period size: 126 Copynumber: 2.5 Consensus size: 124
558112 GGTAAAAAAG
* * * *
558122 TCTCTCAGGTCAAAGCCGACGGGCAAACAAAGGATGAAAAAATCTCCCGGGTCAAAGTCGATC-G
1 TCTCTCAGGTCAAAGCCGACGGGTAGACAAAGGGTG-AAAAGTCT-CCGGGTCAAAGTCGA-CGG
* *** * * *
558186 ACAAACAAAAGGTAAAAAAGTCTTTTGGGTTAAAGCCAAC-GAGTATACAAAGGGTGAAGGAA
63 GCAAACAAAAGGTAAAAAAGTCTCCCGGGTTAAAGCCAACGGA-CAGACAAAAGGTGAAGGAA
** *
558248 TCTCTCAGGTTTAAGCCGATGGGTAGACAAAGGGTGAAAGAGTCTCTCGGGTCAAAGTCGACGGG
1 TCTCTCAGGTCAAAGCCGACGGGTAGACAAAGGGTGAAA-AGTCTC-CGGGTCAAAGTCGACGGG
* * * * * *
558313 CAAA-AAATGGGTGAAAGAGTCTCCCGGGTTAAAGCCGACGGACAGACAAAAGGTGAAGTAG
64 CAAACAAA-AGGTAAAAAAGTCTCCCGGGTTAAAGCCAACGGACAGACAAAAGGTGAAGGAA
* *
558374 TCTCTTC-GGTCAAAGTCGACGGGTAGACAAAGGGTGTAAAAGTCTCCTGGGTGAAAG-CTGACG
1 TCTC-TCAGGTCAAAGCCGACGGGTAGACAAAGGGTG-AAAAGTCTCC-GGGTCAAAGTC-GACG
558437 GGCA
62 GGCA
558441 TAGAAAGGAT
Statistics
Matches: 159, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
125 10 0.06
126 142 0.89
127 7 0.04
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.18
Consensus pattern (124 bp):
TCTCTCAGGTCAAAGCCGACGGGTAGACAAAGGGTGAAAAGTCTCCGGGTCAAAGTCGACGGGCA
AACAAAAGGTAAAAAAGTCTCCCGGGTTAAAGCCAACGGACAGACAAAAGGTGAAGGAA
Found at i:558418 original size:42 final size:41
Alignment explanation
Indices: 557994--558438 Score: 258
Period size: 42 Copynumber: 10.6 Consensus size: 41
557984 AGGTTAAAGT
* * * *
557994 AGTCTCTCAGGTGAAAGCCGATGGGAAGACAAAGGGTGAAGGA
1 AGTCTCTCGGGTCAAAGCCGACGGGTAGACAAAGGGTGAA--A
* * ** *
558037 A-TCTCCCAGGTCAAAGCCGATC-AATAGACAAAGGGTGAAGT
1 AGTCTCTCGGGTCAAAGCCGA-CGGGTAGACAAAGGGTGAA-A
* * *
558078 AGTCT-TCCGGGTCAAAACCGACAGGTAGACAAAGGGTAAAAA
1 AGTCTCT-CGGGTCAAAGCCGACGGGTAGACAAAGGGT-GAAA
* * * *
558120 AGTCTCTCAGGTCAAAGCCGACGGGCAAACAAAGGATGAAAA
1 AGTCTCTCGGGTCAAAGCCGACGGGTAGACAAAGGGTG-AAA
* * * ** * * *
558162 AATCTCCCGGGTCAAAGTCGATC-GACAAACAAAAGGTAAAAA
1 AGTCTCTCGGGTCAAAGCCGA-CGGGTAGACAAAGGGT-GAAA
* * * * * *
558204 AGTCTTTTGGGTTAAAGCCAACGAGTATACAAAGGGTGAAGGA
1 AGTCTCTCGGGTCAAAGCCGACGGGTAGACAAAGGGTGAA--A
* ** *
558247 A-TCTCTCAGGTTTAAGCCGATGGGTAGACAAAGGGTGAAA
1 AGTCTCTCGGGTCAAAGCCGACGGGTAGACAAAGGGTGAAA
* * *
558287 GAGTCTCTCGGGTCAAAGTCGACGGGCA-AAAAATGGGTGAAA
1 -AGTCTCTCGGGTCAAAGCCGACGGGTAGACAAA-GGGTGAAA
* * ** * *
558329 GAGTCTCCCGGGTTAAAGCCGACGGACAGACAAAAGGTGAAGT
1 -AGTCTCTCGGGTCAAAGCCGACGGGTAGACAAAGGGTGAA-A
*
558372 AGTCTCTTC-GGTCAAAGTCGACGGGTAGACAAAGGGTGTAAA
1 AGTCTC-TCGGGTCAAAGCCGACGGGTAGACAAAGGGTG-AAA
* *
558414 AGTCTC-CTGGGTGAAAGCTGACGGG
1 AGTCTCTC-GGGTCAAAGCCGACGGG
558439 CATAGAAAGG
Statistics
Matches: 307, Mismatches: 74, Indels: 43
0.72 0.17 0.10
Matches are distributed among these distances:
40 2 0.01
41 11 0.04
42 280 0.91
43 14 0.05
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.17
Consensus pattern (41 bp):
AGTCTCTCGGGTCAAAGCCGACGGGTAGACAAAGGGTGAAA
Found at i:558575 original size:44 final size:43
Alignment explanation
Indices: 558526--558853 Score: 204
Period size: 44 Copynumber: 7.6 Consensus size: 43
558516 AATGCAAATC
* * *
558526 ATTTAACTAGGGTGGTAACTATACGTCAAACATGAAGGAGGCAG
1 ATTTAACTAGGGTGGTAACCATACGTCAAACA-GAAAGAGGAAG
* * *
558570 ATTTAACTAGGGTGGTAACCATACATCAAACTGGAATAAAAGG-A-
1 ATTTAACTAGGGTGGTAACCATACGTCAAAC-AG-A-AAGAGGAAG
* * * * *
558614 ACTTGACCAGGGTGGTAACCATACGTCAAATCAGAATGA--AAA
1 ATTTAACTAGGGTGGTAACCATACGTCAAA-CAGAAAGAGGAAG
* * * * * * *
558656 AATCAGACTAGGGTGGTAACCACACATCAGAC--AAGGAGGTAG
1 ATTTA-ACTAGGGTGGTAACCATACGTCAAACAGAAAGAGGAAG
* * * *
558698 ATTTGACCAGGGTGGTAACCATACGTCAAATCAGAATGA-AAAG
1 ATTTAACTAGGGTGGTAACCATACGTCAAA-CAGAAAGAGGAAG
* ** * * *
558741 AATCTAACTAGGGTGGTAACCATACGTCTGATAGGAAAAAGGTAG
1 -ATTTAACTAGGGTGGTAACCATACGTCAAACA-GAAAGAGGAAG
* * *
558786 ATTTAACTAGGGTGGTAACCATACGTCAAATCGGAATGA-AAAG
1 ATTTAACTAGGGTGGTAACCATACGTCAAA-CAGAAAGAGGAAG
* *
558829 AATCTAACCAGGGTGGTAACCATAC
1 -ATTTAACTAGGGTGGTAACCATAC
558854 ATTAGATAGG
Statistics
Matches: 214, Mismatches: 53, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
40 4 0.02
41 22 0.10
42 9 0.04
43 27 0.13
44 143 0.67
45 5 0.02
46 4 0.02
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (43 bp):
ATTTAACTAGGGTGGTAACCATACGTCAAACAGAAAGAGGAAG
Found at i:558823 original size:88 final size:89
Alignment explanation
Indices: 558526--558884 Score: 386
Period size: 88 Copynumber: 4.1 Consensus size: 89
558516 AATGCAAATC
* * * ** *
558526 ATTTAACTAGGGTGGTAACTATACGTCAAA-CATGAAGGAGGCAG-ATTTAACTAGGGTGGTAAC
1 ATTTAACCAGGGTGGTAACCATACGTCAAATCA-GAATGA-AAAGAATCTAACTAGGGTGGTAAC
*
558589 CATACATCAAACT-GGAATAAAAGG-A-
64 CATACATCAGACTAGG-A-AAAAGGTAG
* *
558614 ACTTGACCAGGGTGGTAACCATACGTCAAATCAGAATGAAAA-AATC-AGACTAGGGTGGTAACC
1 ATTTAACCAGGGTGGTAACCATACGTCAAATCAGAATGAAAAGAATCTA-ACTAGGGTGGTAACC
* *
558677 ACACATCAGACAAGG----AGGTAG
65 ATACATCAGACTAGGAAAAAGGTAG
*
558698 ATTTGACCAGGGTGGTAACCATACGTCAAATCAGAATGAAAAGAATCTAACTAGGGTGGTAACCA
1 ATTTAACCAGGGTGGTAACCATACGTCAAATCAGAATGAAAAGAATCTAACTAGGGTGGTAACCA
* *
558763 TACGTCTGA-TAGGAAAAAGGTAG
66 TACATCAGACTAGGAAAAAGGTAG
* * *
558786 ATTTAACTAGGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATCTAACCAGGGTGGTAACCA
1 ATTTAACCAGGGTGGTAACCATACGTCAAATCAGAATGAAAAGAATCTAACTAGGGTGGTAACCA
* *
558851 TACATTAGA-TAGGAAAGAGG-AG
66 TACATCAGACTAGGAAAAAGGTAG
*
558873 AGTTTGACCAGG
1 A-TTTAACCAGG
558885 CCCTAACACC
Statistics
Matches: 232, Mismatches: 26, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
82 3 0.01
83 1 0.00
84 44 0.19
85 26 0.11
86 2 0.01
87 30 0.13
88 124 0.53
89 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (89 bp):
ATTTAACCAGGGTGGTAACCATACGTCAAATCAGAATGAAAAGAATCTAACTAGGGTGGTAACCA
TACATCAGACTAGGAAAAAGGTAG
Found at i:558883 original size:44 final size:43
Alignment explanation
Indices: 558691--558884 Score: 140
Period size: 44 Copynumber: 4.4 Consensus size: 43
558681 ATCAGACAAG
* * * *
558691 GAGGTAGATTTGACCAGGGTGGTAACCATACGTCAAATCA-GAAT
1 GAGG-AGATTTAACCAGGGTGGTAACCATACGTTAGAT-AGGAAA
** * *
558735 GAAAAGAATCTAACTAGGGTGGTAACCATACGTCT-GATAGGAAA
1 GAGGAG-ATTTAACCAGGGTGGTAACCATACGT-TAGATAGGAAA
* * * * * *
558779 AAGGTAGATTTAACTAGGGTGGTAACCATACGTCAAATCGGAAT
1 GAGG-AGATTTAACCAGGGTGGTAACCATACGTTAGATAGGAAA
** * *
558823 GAAAAGAATCTAACCAGGGTGGTAACCATACATTAGATAGGAAA
1 GAGGAG-ATTTAACCAGGGTGGTAACCATACGTTAGATAGGAAA
*
558867 GAGGAGAGTTTGACCAGG
1 GAGGAGA-TTTAACCAGG
558885 CCCTAACACC
Statistics
Matches: 113, Mismatches: 30, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
43 6 0.05
44 105 0.93
45 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (43 bp):
GAGGAGATTTAACCAGGGTGGTAACCATACGTTAGATAGGAAA
Found at i:558924 original size:48 final size:49
Alignment explanation
Indices: 558871--558979 Score: 177
Period size: 48 Copynumber: 2.3 Consensus size: 49
558861 AGGAAAGAGG
* *
558871 AGAGTTTGACCAGGCCCTAACACCAATACAATCAAATGAGGGATGAA-A
1 AGAGTTTGACCAGGCCCTAACACCAATACAATCAAATAAGAGATGAACA
*
558919 AGAGTTTGACCAGGCCCTAACACCAATACAGTCAAATAAGAGATGAACA
1 AGAGTTTGACCAGGCCCTAACACCAATACAATCAAATAAGAGATGAACA
558968 A-AGTTTGACCAG
1 AGAGTTTGACCAG
558980 ATATAGCCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 55 0.96
49 2 0.04
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.17
Consensus pattern (49 bp):
AGAGTTTGACCAGGCCCTAACACCAATACAATCAAATAAGAGATGAACA
Found at i:558991 original size:36 final size:36
Alignment explanation
Indices: 558951--559026 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
558941 CCAATACAGT
558951 CAAATAAGAGATGAACAA-AGTTTGACCAGATATAGC
1 CAAATAAGAGATGAA-AAGAGTTTGACCAGATATAGC
* * * *
558987 CAAATGAGGGATGAAAAGAGTTTGATCAGATATAGT
1 CAAATAAGAGATGAAAAGAGTTTGACCAGATATAGC
559023 CAAA
1 CAAA
559027 CAATGATGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 2 0.06
36 33 0.94
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21
Consensus pattern (36 bp):
CAAATAAGAGATGAAAAGAGTTTGACCAGATATAGC
Found at i:559335 original size:91 final size:89
Alignment explanation
Indices: 559230--559428 Score: 224
Period size: 89 Copynumber: 2.2 Consensus size: 89
559220 TCTAGAAGAG
* * * *
559230 AGGGG-TATGATTGGGAATGAATGGTCAGGATATCCTTGTCCT-AGTAAAATCAACCTTTGTGAT
1 AGGGGATATGATTGGGAATGAATGGGC--CATA-CCTTGCCCTAAG-AAAATCAACCTTAGTGAT
* *
559293 GCATCAATACCATCTAGTTGTTAGATAA
62 GCATCAAAACCATCTAGTGGTTAGATAA
** * **
559321 AGGGGATA-GATTGGGAATGTGTGGGCCATACCTTGCCCTAAAGGAAATCAGGCTTAGTGATGCA
1 AGGGGATATGATTGGGAATGAATGGGCCATACCTTGCCCT-AAGAAAATCAACCTTAGTGATGCA
*
559385 TCAAAACCATCTAGTGGTTAGATGA
65 TCAAAACCATCTAGTGGTTAGATAA
559410 AGGGGATATGATTGGGAAT
1 AGGGGATATGATTGGGAAT
559429 ATGTCTCAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
88 8 0.09
89 50 0.54
90 12 0.13
91 20 0.22
92 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (89 bp):
AGGGGATATGATTGGGAATGAATGGGCCATACCTTGCCCTAAGAAAATCAACCTTAGTGATGCAT
CAAAACCATCTAGTGGTTAGATAA
Found at i:561471 original size:14 final size:14
Alignment explanation
Indices: 561452--561480 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
561442 TTTGCAAGCA
561452 TGTTCCACTTTCAG
1 TGTTCCACTTTCAG
561466 TGTTCCACTTTCAG
1 TGTTCCACTTTCAG
561480 T
1 T
561481 TTCATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (14 bp):
TGTTCCACTTTCAG
Found at i:564144 original size:19 final size:19
Alignment explanation
Indices: 564120--564175 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
564110 TGTATTGATA
*
564120 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
* *
564139 CATTGTATCAATACATACT
1 CATTGTATCGATACATGCT
564158 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
564176 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:575896 original size:20 final size:22
Alignment explanation
Indices: 575861--575901 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
575851 AACGGTTAAA
575861 ATCCTAGAATGTATCGATACAC
1 ATCCTAGAATGTATCGATACAC
575883 ATCC-AGAA-GTATCGATACA
1 ATCCTAGAATGTATCGATACA
575902 TTATAGCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (22 bp):
ATCCTAGAATGTATCGATACAC
Found at i:575930 original size:19 final size:20
Alignment explanation
Indices: 575908--575955 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
575898 TACATTATAG
* *
575908 CGATACATGTTC-ATTGTTT
1 CGATACATGCTCAATTGTGT
*
575927 CGATACATACTCAATTGTGT
1 CGATACATGCTCAATTGTGT
575947 CGATACATG
1 CGATACATG
575956 AAACTGGCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (20 bp):
CGATACATGCTCAATTGTGT
Found at i:577982 original size:155 final size:153
Alignment explanation
Indices: 577546--578648 Score: 808
Period size: 155 Copynumber: 7.2 Consensus size: 153
577536 AATGCAAAAT
* * * *
577546 TACCTGATACCCCTAAAGGACTTAAAAAAGAATATAGATGGGACGAACCAATCCTAAATACCCAC
1 TACCCGATACCCCTAAAGGACTT-AAAAAGATTATAGATGGGATGAACCTATCCTAAATACCCAC
* * * *
577611 CTTTGACATAAAACCAGACTCGGTGACAACCTAAGACTTGATTCT-AGAAAATTACCAAAATGAC
65 CTTCGACATAAAAGCAGACTCGGTGACAACCTAAGACTTGGTTCTAAG-AAATTA-CAAAATGTC
*
577675 CTTAAGGGATATCTTCAACGTAGAAG
128 CTTAAGGGATACCTTCAACGTAGAAG
* * * * * * **
577701 TGCCCGATATCCCTAAAAGATTTAAAAAGGATTACAAACTATGATGAACCTATCCTAAATACCCA
1 TACCCGATACCCCTAAAGGACTTAAAAA-GATTATAGA-TGGGATGAACCTATCCTAAATACCCA
* * * * ** **
577766 CCTTCAACATAAAAGCAAAC-CTGGTGATAACCTAAGAGTTCATT-TTGGAAAATTACGAAAATG
64 CCTTCGACATAAAAGCAGACTC-GGTGACAACCTAAGACTTGGTTCTAAG-AAATTAC-AAAATG
* *
577829 TCCTGAAGGGATACCTTCAACGTGGAAG
126 TCCTTAAGGGATACCTTCAACGTAGAAG
* * * * * *
577857 TACTCAATACCCCTAAAGGACTTAAAACAAATTATTGATGGGATGACCCTATCCTGAATACCCAC
1 TACCCGATACCCCTAAAGGACTTAAAA-AGATTATAGATGGGATGAACCTATCCTAAATACCCAC
* * * * * *
577922 CTTCGACATAAAAGCGGACCCGATGACAACCTAGGAATTGGTTCTAAGAAATTATCAAAAT-ACC
65 CTTCGACATAAAAGCAGACTCGGTGACAACCTAAGACTTGGTTCTAAGAAATTA-CAAAATGTCC
* * *
577986 TCTATGGGTACACCTTCAACAT-GAA-
129 T-TAAGGG-ATACCTTCAACGTAGAAG
* * *
578011 -A---G-TATCCCTAAAGGACTTAAAAAGGATTATAGAAGGGATGAACCTATCCTTAATACCCAC
1 TACCCGATACCCCTAAAGGACTTAAAAA-GATTATAGATGGGATGAACCTATCCTAAATACCCAC
* ** * * * **
578071 CTT-TAGCATAAAAGTGGACTCGGTGACAACCTAAGACTCGATTCTAAAAAATTACAAAAATACC
65 CTTCGA-CATAAAAGCAGACTCGGTGACAACCTAAGACTTGGTTCTAAGAAATTAC-AAAATGTC
* * * * * *
578135 CCTAGGGGATATCTTCGACATACAAG
128 CTTAAGGGATACCTTCAACGTAGAAG
* ** * * * * *
578161 TACCCGGTACCTGTAAAGGACTTAAAAAGGTT-TGAAATGGGATAAACCTATCCTAACTGCCCAC
1 TACCCGATACCCCTAAAGGACTTAAAAAGATTAT-AGATGGGATGAACCTATCCTAAATACCCAC
* *
578225 CTT-TAGCATAAAAGCAGAC-CTGGTGACAACCTAAGAATTGGTTCTCAA-AAATTACCAAAATG
65 CTTCGA-CATAAAAGCAGACTC-GGTGACAACCTAAGACTTGGTTCT-AAGAAATTA-CAAAATG
* * *
578287 TTCC-TATGGGTACACCTTCGACGT-GAAAG
126 -TCCTTAAGGG-ATACCTTCAACGTAG-AAG
* * * ** * * * *
578316 TATCCTGGTATCCCTAAAGGACTTCAAAGGGATTATAGAAGGGACGAACTTATCCAAAATACCCA
1 TA-CCCGATACCCCTAAAGGACTT-AAAAAGATTATAGATGGGATGAACCTATCCTAAATACCCA
* ** * * * * *
578381 CATTC-AGCATAAAAGTGGACTCGGTGATAACCTAGGAGTTGGTTCTAAAAAATTATGAAAATGT
64 CCTTCGA-CATAAAAGCAGACTCGGTGACAACCTAAGACTTGGTTCTAAGAAATTA-CAAAATGT
* * *
578445 -CTCAAGAGGAAACCTTCAACGTAAAAG
127 CCTTAAG-GGATACCTTCAACGTAGAAG
* ** * * * * *
578472 TACACGATACCCCTATGGGACTTAAAATGGATAATAGATGAGATGAACCTATCCTAAATATCTAC
1 TACCCGATACCCCTAAAGGACTTAAAA-AGATTATAGATGGGATGAACCTATCCTAAATACCCAC
* * * **
578537 CTTCGGCATAAAAGCAGACTTGGTGACAACCTAAGACTTGGTTCTAA-AAATTAAGAAAATACCC
65 CTTCGACATAAAAGCAGACTCGGTGACAACCTAAGACTTGGTTCTAAGAAATT-ACAAAATGTCC
* * *
578601 TTAAAGGATACCTTCGACGTATAAG
129 TTAAGGGATACCTTCAACGTAGAAG
*
578626 TACCCGATATCCCTAAAGGACTT
1 TACCCGATACCCCTAAAGGACTT
578649 GAAATGACAA
Statistics
Matches: 745, Mismatches: 161, Indels: 85
0.75 0.16 0.09
Matches are distributed among these distances:
148 13 0.02
149 105 0.14
150 2 0.00
151 1 0.00
153 3 0.00
154 140 0.19
155 226 0.30
156 174 0.23
157 79 0.11
158 2 0.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (153 bp):
TACCCGATACCCCTAAAGGACTTAAAAAGATTATAGATGGGATGAACCTATCCTAAATACCCACC
TTCGACATAAAAGCAGACTCGGTGACAACCTAAGACTTGGTTCTAAGAAATTACAAAATGTCCTT
AAGGGATACCTTCAACGTAGAAG
Found at i:578416 original size:460 final size:460
Alignment explanation
Indices: 577556--578648 Score: 1175
Period size: 460 Copynumber: 2.4 Consensus size: 460
577546 TACCTGATAC
* * * *
577556 CCCTAAAGGACTTAAAAAAGAATATAGATGGGACGAACCAATCCTAAATACCCACCTTTGACATA
1 CCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTTG-CATA
* * *
577621 AAACCAGACTCGGTGACAACCTAAGACTTGATTCTAGAAAATTACCAAAATGA-CCTTAAGGGAT
65 AAAGCAGACTCGGTGACAACCTAAGACTTGATTCTAAAAAATTACAAAAAT-ACCCTTAAGGGAT
* * * * * * *
577685 ATCTTCAACGTAGAAGTGCCCGATATCCCTAAAAGATTTAAAAAGGATTACAAACTATGATGAAC
129 ATCTTCGACGTACAAGTACCCGATATCCCTAAAGGACTTAAAAAGGATTACAAACTAGGATAAAC
* * * **
577750 CTATCCTAAATACCCACCTTCAACATAAAAGCAAACCTGGTGATAACCTAAGAGTTCATTTTGGA
194 CTATCCTAAATACCCACCTTCAACATAAAAGCAAACCTGGTGACAACCTAAGAATTCATTCTCAA
* * *
577815 AAATTACGAAAATGTCCTGAAGGGATACCTTCAACGTGGAAGTACTCAATACCCCTAAAGGACTT
259 AAATTACCAAAATGTCCTGAAGGGACACCTTCAACGTGAAAGTACTCAATACCCCTAAAGGACTT
* * * * ** *
577880 AAAACAAATTATTGATGGGATGACCCTATCCTGAATACCCACCTTCGACATAAAAGCGGACCCGA
324 AAAACAAATTATAGAAGGGACGAACCTATCCAAAATACCCACATTCGACATAAAAGCGGACCCGA
* * * *
577945 TGACAACCTAGGAATTGGTTCTAAGAAATTATCAAAATACCTCTATG-GGTACACCTTCAACATG
389 TGACAACCTAGGAATTGGTTCTAAAAAATTATCAAAATACCTC-AAGAGG-AAACCTTCAACATA
578009 AAAGT-AT-
452 AAAGTAATA
* *
578016 CCCTAAAGGACTTAAAAAGGATTATAGAAGGGATGAACCTATCCTTAATACCCACCTTTAGCATA
1 CCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTT-GCATA
** * * *
578081 AAAGTGGACTCGGTGACAACCTAAGACTCGATTCTAAAAAATTACAAAAATACCCCTAGGGGATA
65 AAAGCAGACTCGGTGACAACCTAAGACTTGATTCTAAAAAATTACAAAAATACCCTTAAGGGATA
* * * ** *
578146 TCTTCGACATACAAGTACCCGGTA-CCTGTAAAGGACTTAAAAAGG-TTTGAAA-TGGGATAAAC
130 TCTTCGACGTACAAGTACCCGATATCC-CTAAAGGACTTAAAAAGGATTACAAACTAGGATAAAC
* * * * * **
578208 CTATCCTAACTGCCCACCTTTAGCATAAAAGCAGACCTGGTGACAACCTAAGAATTGGTTCTCAA
194 CTATCCTAAATACCCACCTTCAACATAAAAGCAAACCTGGTGACAACCTAAGAATTCATTCTCAA
* * ** *
578273 AAATTACCAAAATGTTCCT-ATGGGTACACCTTCGACGTGAAAGTA-TCCTGGTATCCCTAAAGG
259 AAATTACCAAAATG-TCCTGAAGGG-ACACCTTCAACGTGAAAGTACT-C-AATACCCCTAAAGG
* *** * *
578336 ACTTCAAAGGGATTATAGAAGGGACGAACTTATCCAAAATACCCACATTC-AGCATAAAAGTGGA
320 ACTTAAAACAAATTATAGAAGGGACGAACCTATCCAAAATACCCACATTCGA-CATAAAAGCGGA
* * * * * **
578400 CTCGGTGATAACCTAGGAGTTGGTTCTAAAAAATTATGAAAATGTCTCAAGAGGAAACCTTCAAC
384 CCCGATGACAACCTAGGAATTGGTTCTAAAAAATTATCAAAATACCTCAAGAGGAAACCTTCAAC
*
578465 GTAAAAGTACACGATA
449 ATAAAAGT--A--ATA
** * * * * * *
578481 CCCCTATGGGACTTAAAATGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCAT
1 -CCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACCTT-TGCAT
* * *
578546 AAAAGCAGACTTGGTGACAACCTAAGACTTGGTTCT-AAAAATTA-AGAAAATACCCTTAAAGGA
64 AAAAGCAGACTCGGTGACAACCTAAGACTTGATTCTAAAAAATTACA-AAAATACCCTTAAGGGA
* *
578609 TACCTTCGACGTATAAGTACCCGATATCCCTAAAGGACTT
128 TATCTTCGACGTACAAGTACCCGATATCCCTAAAGGACTT
578649 GAAATGACAA
Statistics
Matches: 519, Mismatches: 95, Indels: 33
0.80 0.15 0.05
Matches are distributed among these distances:
458 78 0.15
459 49 0.09
460 248 0.48
461 1 0.00
464 3 0.01
465 54 0.10
466 86 0.17
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (460 bp):
CCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGCATAA
AAGCAGACTCGGTGACAACCTAAGACTTGATTCTAAAAAATTACAAAAATACCCTTAAGGGATAT
CTTCGACGTACAAGTACCCGATATCCCTAAAGGACTTAAAAAGGATTACAAACTAGGATAAACCT
ATCCTAAATACCCACCTTCAACATAAAAGCAAACCTGGTGACAACCTAAGAATTCATTCTCAAAA
ATTACCAAAATGTCCTGAAGGGACACCTTCAACGTGAAAGTACTCAATACCCCTAAAGGACTTAA
AACAAATTATAGAAGGGACGAACCTATCCAAAATACCCACATTCGACATAAAAGCGGACCCGATG
ACAACCTAGGAATTGGTTCTAAAAAATTATCAAAATACCTCAAGAGGAAACCTTCAACATAAAAG
TAATA
Found at i:578495 original size:311 final size:300
Alignment explanation
Indices: 577525--578599 Score: 871
Period size: 311 Copynumber: 3.5 Consensus size: 300
577515 ATGCCCCTTG
* * * * * *
577525 GGGATAACTTCAATGCAAAATTAC-CTGATACCCCTAAAGGACTTAAAAAAGAATAT-AGATGGG
1 GGGATACCTTCAACGTAAAAGTACAC-GATACCCCTAAAGGACTTAAAAAGGTAT-TGA-ATGGG
* * * *
577588 ACGAACCAATCCTAAATACCCACCTTT-GACATAAAACCAGA-CTCGGTGACAACCTAAGACTTG
63 ATGAACCTATCCT-AATACCCACCTTTAG-CATAAAAGCAGACCT-GGTGACAACCTAAGAATTG
* * * * * *
577651 ATTCTAGAAAATTACCAAAATGACCT-TAAGGG-ATATCTTCAACGTAGAAGTGCCCGATATCCC
125 GTTCTA-AAAATTACCAAAAT-ACCTCTATGGGTACACCTTCAACAT-GAA-----AG-TATCCC
* * * ** * *
577714 TAAAAGATTTAAAAAGGATTACA-AACTATGATGAACCTATCCTAAATACCCACCTTCAACATAA
181 TAAAGGACTTAAAAAGGATTATAGAA--GGGACGAACCTATCCTAAATACCCACCTTCAGCATAA
*** * * ** *
577778 AAGCAAAC-CTGGTGATAACCTAAGAGTTCATTTTGGAAAATTACGAAAATGTCCTGAA
244 AAGTGGACTC-GGTGATAACCTAAGAGTTGATTCTAAAAAATTACGAAAATGT-CTCAA
** * * **
577836 GGGATACCTTCAACGTGGAAGTACTCAATACCCCTAAAGGACTTAAAACAAATTATTG-ATGGGA
1 GGGATACCTTCAACGTAAAAGTACACGATACCCCTAAAGGACTT-AAA-AAGGTATTGAATGGGA
* * * * * *
577900 TGACCCTATCCTGAATACCCACC-TTCGACATAAAAGCGGACCCGATGACAACCTAGGAATTGGT
64 TGAACCTATCCT-AATACCCACCTTTAG-CATAAAAGCAGACCTGGTGACAACCTAAGAATTGGT
*
577964 TCTAAGAAATTATCAAAATACCTCTATGGGTACACCTTCAACATGAAAGTATCCCTAAAGGACTT
127 TCTAA-AAATTACCAAAATACCTCTATGGGTACACCTTCAACATGAAAGTATCCCTAAAGGACTT
* * *
578029 AAAAAGGATTATAGAAGGGATGAACCTATCCTTAATACCCACCTTTAGCATAAAAGTGGACTCGG
191 AAAAAGGATTATAGAAGGGACGAACCTATCCTAAATACCCACCTTCAGCATAAAAGTGGACTCGG
* * * * ** * *
578094 TGACAACCTAAGACTCGATTCTAAAAAATTACAAAAATACCCCTAG
256 TGATAACCTAAGAGTTGATTCTAAAAAATTACGAAAATGTCTC-AA
* * * * * * **
578140 GGGATATCTTCGACATACAAGTACCCGGTACCTGTAAAGGACTTAAAAAGGT-TTGAAATGGGAT
1 GGGATACCTTCAACGTAAAAGTACACGATACCCCTAAAGGACTTAAAAAGGTATTG-AATGGGAT
* *
578204 AAACCTATCCTAACTGCCCACCTTTAGCATAAAAGCAGACCTGGTGACAACCTAAGAATTGGTTC
65 GAACCTATCCTAA-TACCCACCTTTAGCATAAAAGCAGACCTGGTGACAACCTAAGAATTGGTTC
** * *
578269 TCAAAAATTACCAAAAT-GTTCCTATGGGTACACCTTCGACGTGAAAGTATCCTGGTATCCCTAA
129 T-AAAAATTACCAAAATACCT-CTATGGGTACACCTTCAACATG-AA--A-----GTATCCCTAA
* * * * *
578333 AGGACTTCAAAGGGATTATAGAAGGGACGAACTTATCCAAAATACCCACATTCAGCATAAAAGTG
184 AGGACTTAAAAAGGATTATAGAAGGGACGAACCTATCCTAAATACCCACCTTCAGCATAAAAGTG
* * *
578398 GACTCGGTGATAACCTAGGAGTTGGTTCTAAAAAATTATGAAAATGTCTCAA
249 GACTCGGTGATAACCTAAGAGTTGATTCTAAAAAATTACGAAAATGTCTCAA
* ** * * *
578450 GAGGAAACCTTCAACGTAAAAGTACACGATACCCCTATGGGACTTAAAATGGATAAT-AGATGAG
1 G-GGATACCTTCAACGTAAAAGTACACGATACCCCTAAAGGACTTAAAAAGG-TATTGA-ATGGG
* * ** * *
578514 ATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGCAGACTTGGTGACAACCTAAGACTTGGT
63 ATGAACCTATCCT-AATACCCACCTTTAGCATAAAAGCAGACCTGGTGACAACCTAAGAATTGGT
**
578579 TCTAAAAATTAAGAAAATACC
127 TCTAAAAATTACCAAAATACC
578600 CTTAAAGGAT
Statistics
Matches: 612, Mismatches: 120, Indels: 63
0.77 0.15 0.08
Matches are distributed among these distances:
301 3 0.00
302 6 0.01
303 94 0.15
304 111 0.18
305 27 0.04
306 4 0.01
310 9 0.01
311 272 0.44
312 78 0.13
313 8 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (300 bp):
GGGATACCTTCAACGTAAAAGTACACGATACCCCTAAAGGACTTAAAAAGGTATTGAATGGGATG
AACCTATCCTAATACCCACCTTTAGCATAAAAGCAGACCTGGTGACAACCTAAGAATTGGTTCTA
AAAATTACCAAAATACCTCTATGGGTACACCTTCAACATGAAAGTATCCCTAAAGGACTTAAAAA
GGATTATAGAAGGGACGAACCTATCCTAAATACCCACCTTCAGCATAAAAGTGGACTCGGTGATA
ACCTAAGAGTTGATTCTAAAAAATTACGAAAATGTCTCAA
Found at i:580271 original size:12 final size:10
Alignment explanation
Indices: 580228--580266 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
580218 TCTCCTTGAA
580228 TTTTTTTCTC
1 TTTTTTTCTC
580238 TTTTTTTCTC
1 TTTTTTTCTC
*
580248 AAATTTTTTCTC
1 --TTTTTTTCTC
580260 TTTTTTT
1 TTTTTTT
580267 TTCTCCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 16 0.64
12 9 0.36
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:581278 original size:18 final size:19
Alignment explanation
Indices: 581257--581292 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
581247 AAAAAGTCAA
581257 AATTTAT-AAAAATGAATG
1 AATTTATGAAAAATGAATG
*
581275 AATTTTTGAAAAATGAAT
1 AATTTATGAAAAATGAAT
581293 TCATATGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
AATTTATGAAAAATGAATG
Found at i:581541 original size:167 final size:163
Alignment explanation
Indices: 580910--581712 Score: 680
Period size: 162 Copynumber: 4.9 Consensus size: 163
580900 GGAAAAGGGG
* * * * *
580910 ATTTCAAAG-AAAAATCCAAAACTCATGAAAATGAATGAATTTTTAAAAAACTAATTTAATATGA
1 ATTTCAAGGAAAAAATCAAAAACTCGTGAAAATGAATGAATTTTT-GAAAACTAAATT-ATATGA
** * * * *
580974 AATAAATAATAATATTTTCTGAATTTAAAAAATTAAAAAATAATAAAATATACT-T--AAAAAAT
64 AATAAATAATAATATTTGATAAATTTTAAAAA-TAAAAAACAA-AAAA-ATCCTCTCAAAAAAAT
* ** * * * *
581036 TTTCGGAGTTGCAAACT-CCCTATTTCGGAAAAAA-GAGA
126 TTACGGAGAAG-AAAATACCGTATTTC-AAAAAAAGGAAA
* ** * ** * *
581074 ATTTTAAGGGAAAAGTTC-AAAATTTATAGGAAGTGAATGAATTTTTGAAAACTAAATTACTATG
1 ATTTCAA-GGAAAAAATCAAAAACTCGT-GAAAATGAATGAATTTTTGAAAACTAAATTA-TATG
* * *
581138 AAATAAATAATAATATTTTATAAATTTTAAAAATCAAAAAACAAAAAAAACC-CT-GAAAAAATT
63 AAATAAATAATAATATTTGATAAATTTTAAAAAT-AAAAAACAAAAAAATCCTCTCAAAAAAATT
* * * *
581201 TATGGAGAAGAAACT-CCGTATTTCAGAAAAAGGGAA
127 TACGGAGAAGAAAATACCGTATTTCAAAAAAAGGAAA
* ** * * *
581237 ATTTCAAGGAAAAAAGTC-AAAATTTATAAAAATGAATGAATTTTTGAAAAATGAATTCATATGA
1 ATTTCAAGGAAAAAA-TCAAAAACTCGTGAAAATGAATGAATTTTTGAAAACTAAATT-ATATGA
* * * *
581301 AATAAATAATAATATTTGATGAACTTT-AAAA-AATAAA-AAAAAAATCCCCTCAAAAAAATTTA
64 AATAAATAATAATATTTGATAAATTTTAAAAATAAAAAACAAAAAAATCCTCTCAAAAAAATTTA
** *
581363 CGGATTAGAAAATACCGTATTTCAAAAAAAGAAAA
129 CGGAGAAGAAAATACCGTATTTCAAAAAAAGGAAA
* * *
581398 ATTTCAAGGAAAAAACCAAAAAACTCGTGAAAATGAATGAATTTTTGAAATCTGAATTAGTATGA
1 ATTTCAAGGAAAAAATC-AAAAACTCGTGAAAATGAATGAATTTTTGAAAACTAAATTA-TATGA
* * * * * **
581463 TATAAATCATAATGTTTGATGAATTTTAAAACTTGAAAACTAAGAAAAATCCTCTCAAAAAAATT
64 AATAAATAATAATATTTGATAAATTTTAAAAATAAAAAAC-AA-AAAAATCCTCTCAAAAAAATT
* * * **
581528 TACGGAGTAGAAAACACCATATTTTGAAAAAAGGAAA
127 TACGGAGAAGAAAATACCGTATTTCAAAAAAAGGAAA
* * *
581565 ATTTCAAAGGAAAAAATCAAAAGCTCGTGAAAATGAATGAATTTTGGAAAACTAAATTAATATAA
1 ATTTC-AAGGAAAAAATCAAAAACTCGTGAAAATGAATGAATTTTTGAAAACTAAATT-ATATGA
* * *
581630 AATAAATAAATAAAAATATTTAATAAATTTTAAAAATAAAAAATTAAGAAAAATCCTCTCGAAAA
64 AATAAAT-AAT---AATATTTGATAAATTTTAAAAATAAAAAA-CAA-AAAAATCCTCTCAAAAA
581695 AATTTACGGAGAAGAAAA
123 AATTTACGGAGAAGAAAA
581713 CCTAGTAATT
Statistics
Matches: 526, Mismatches: 85, Indels: 49
0.80 0.13 0.07
Matches are distributed among these distances:
158 9 0.02
159 7 0.01
160 20 0.04
161 38 0.07
162 126 0.24
163 39 0.07
164 29 0.06
165 60 0.11
166 23 0.04
167 102 0.19
168 14 0.03
171 59 0.11
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (163 bp):
ATTTCAAGGAAAAAATCAAAAACTCGTGAAAATGAATGAATTTTTGAAAACTAAATTATATGAAA
TAAATAATAATATTTGATAAATTTTAAAAATAAAAAACAAAAAAATCCTCTCAAAAAAATTTACG
GAGAAGAAAATACCGTATTTCAAAAAAAGGAAA
Found at i:582210 original size:21 final size:21
Alignment explanation
Indices: 582184--582223 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
582174 CGTTCAATTT
* *
582184 CTCAAATATTTTCAAAAAAAC
1 CTCAAAAAATTTCAAAAAAAC
582205 CTCAAAAAATTTCAAAAAA
1 CTCAAAAAATTTCAAAAAA
582224 TAGAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.25
Consensus pattern (21 bp):
CTCAAAAAATTTCAAAAAAAC
Found at i:583100 original size:31 final size:31
Alignment explanation
Indices: 583040--583100 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
583030 AGACTTTCCA
* *
583040 TGCAATTTTAACATGTTTAGGTGCTTTTTGG
1 TGCAATTTTAACATGTTTAGGGGCATTTTGG
*
583071 TGCATTTTTAACAT-TTTAGGGGTCATTTTG
1 TGCAATTTTAACATGTTTAGGGG-CATTTTG
583101 TAATTTTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.20, C:0.10, G:0.21, T:0.49
Consensus pattern (31 bp):
TGCAATTTTAACATGTTTAGGGGCATTTTGG
Found at i:588098 original size:14 final size:14
Alignment explanation
Indices: 588079--588112 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
588069 TTATCATTTA
*
588079 AAAAAAAAGTTGGC
1 AAAAAAAAGTTAGC
588093 AAAAAAAAGTTAGC
1 AAAAAAAAGTTAGC
588107 AAAAAA
1 AAAAAA
588113 GAAATGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAAAAAAGTTAGC
Found at i:590411 original size:79 final size:78
Alignment explanation
Indices: 590320--590914 Score: 608
Period size: 79 Copynumber: 7.6 Consensus size: 78
590310 AGTTTAATAC
* * * * *
590320 TTTGGAGATAAAACTGGGGTTGAAGTATCCTCTCGAAAATAATAGGGTCAGAGAATCCCCGATTG
1 TTTGGAAATAAAACTGGGGTTGGAGTATCC-CTCGAAAATAACAGGGTTAGAGTATCCCCGATTG
*
590385 TGAAAAATTGGTGT
65 TGAAAAATCGGTGT
** * *
590399 TTTGGAAATAAAACCAGGGTTTGAGTATCCTCTCGAAAATAACAGGGTCAGAGTATCCCCGATTG
1 TTTGGAAATAAAACTGGGGTTGGAGTATCC-CTCGAAAATAACAGGGTTAGAGTATCCCCGATTG
*
590464 TGAAAAATCGATGT
65 TGAAAAATCGGTGT
* * * * *
590478 TTTGAAAATAAAA-TCGGGGTTAGAGTATCCCCTCAAAAATAACAGGGTTAAAGTGTCCCCGATT
1 TTTGGAAATAAAACT-GGGGTTGGAGTAT-CCCTCGAAAATAACAGGGTTAGAGTATCCCCGATT
* * * **
590542 AT-AGAAAATAGATAC
64 GTGA-AAAATCGGTGT
** * * * *
590557 TTTGGAAATAAAA-TCGGGGTTGGAGTATCCCTTAAAAATAATAGGGTTCGAGAATCCCTGATTG
1 TTTGGAAATAAAACT-GGGGTTGGAGTATCCCTCGAAAATAACAGGGTTAGAGTATCCCCGATTG
*
590621 TTTGGAAAATCGGTGT
65 --TGAAAAATCGGTGT
** * * *
590637 TTTAAAAATAAAACTAGGGTTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGT
1 TTTGGAAATAAAACTGGGGTTGGAGTATCCCTCGAAAATAACAGGGTTAGAGTATCCCCGATTGT
*
590702 GAAAAATCTGTGT
66 GAAAAATCGGTGT
* * *
590715 TTTGAAAATACAACTGGGGTTGGAGTATTCCCTCGAAAATAAC-GAGGTTGGAGTAT-CCCGATT
1 TTTGGAAATAAAACTGGGGTTGGAGTA-TCCCTCGAAAATAACAG-GGTTAGAGTATCCCCGATT
* *
590778 ATGAAAAATTGGTGT
64 GTGAAAAATCGGTGT
* * ** * * *
590793 TTTGGAAATAAAGCCGAAGTTGGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATTCCCGAATG
1 TTTGGAAATAAAACTGGGGTTGGAGTAT-CCCTCGAAAATAACAGGGTTAGAGTATCCCCGATTG
590858 TGAAAAATCGGTGT
65 TGAAAAATCGGTGT
* *
590872 TTTGGAAATAAAA-TCGGGGTTGGAGTATCCCCCGAAAAAAACA
1 TTTGGAAATAAAACT-GGGGTTGGAGTATCCCTCGAAAATAACA
590915 TGAATGAAAT
Statistics
Matches: 431, Mismatches: 72, Indels: 27
0.81 0.14 0.05
Matches are distributed among these distances:
77 1 0.00
78 141 0.33
79 226 0.52
80 62 0.14
81 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (78 bp):
TTTGGAAATAAAACTGGGGTTGGAGTATCCCTCGAAAATAACAGGGTTAGAGTATCCCCGATTGT
GAAAAATCGGTGT
Found at i:590673 original size:237 final size:232
Alignment explanation
Indices: 590316--590914 Score: 688
Period size: 237 Copynumber: 2.5 Consensus size: 232
590306 AAAAAGTTTA
* * *
590316 ATACTTTGGAGATAAAACTGGGGTTGAAGTATCCTCTCGAAAATAATAGGG-TCAGAGAATCCCC
1 ATACTTTGGAAATAAAAC-GGGGTTGGAGTATCC-CTCAAAAATAATAGGGTTC-GAGAAT-CCC
* * *
590380 GATTGTGAAAAATTGGTGTTTTGGAAATAAAACCAGGGTTTGAGTATCCTCTCGAAAATAACAGG
62 GATTGTGAAAAATCGGTGTTTTGGAAATAAAACTAGGGTTGGAGTATCC-CTCGAAAATAACAGG
590445 GTCAGAGTATCCCCGATTGTGAAAAATC-GATGTTTTGAAAATAAAA-TCGGGGTTAGAGTATCC
126 GTCAGAGTATCCCCGATTGTGAAAAATCTG-TGTTTTGAAAATAAAACT-GGGGTTAGAGTATCC
*
590508 CCTCAAAAATAAC-AGGGTTAAAGTGTCCCCGATTAT-AGAAAATAG
189 CCTCAAAAATAACGA-GGTTAAAGTAT-CCCGATTATGA-AAAATAG
*
590553 ATACTTTGGAAATAAAATCGGGGTTGGAGTATCCCTTAAAAATAATAGGGTTCGAGAATCCCTGA
1 ATACTTTGGAAATAAAA-CGGGGTTGGAGTATCCCTCAAAAATAATAGGGTTCGAGAATCCC-GA
* ** *
590618 TTGTTTGGAAAATCGGTGTTTTAAAAATAAAACTAGGGTTGGAGTATCCCTCGAAAATAACGGGG
64 TTG--TGAAAAATCGGTGTTTTGGAAATAAAACTAGGGTTGGAGTATCCCTCGAAAATAACAGGG
** * * *
590683 TTGGAGTATCCCCGATTGTGAAAAATCTGTGTTTTGAAAATACAACTGGGGTTGGAGTATTCCCT
127 TCAGAGTATCCCCGATTGTGAAAAATCTGTGTTTTGAAAATAAAACTGGGGTTAGAGTATCCCCT
* ** *
590748 CGAAAATAACGAGGTTGGAGTATCCCGATTATGAAAAATTG
192 CAAAAATAACGAGGTTAAAGTATCCCGATTATGAAAAATAG
* ** * ** * * *
590789 GTGTTTTGGAAATAAAGCCGAAGTTGGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATTCCCG
1 ATACTTTGGAAATAAA-ACGGGGTTGGAGTAT-CCCTCAAAAATAATAGGGTTCGAG-AATCCCG
* * * *
590854 AATGTGAAAAATCGGTGTTTTGGAAATAAAA-TCGGGGTTGGAGTATCCCCCGAAAAAAACA
63 ATTGTGAAAAATCGGTGTTTTGGAAATAAAACT-AGGGTTGGAGTATCCCTCGAAAATAACA
590915 TGAATGAAAT
Statistics
Matches: 310, Mismatches: 39, Indels: 28
0.82 0.10 0.07
Matches are distributed among these distances:
234 1 0.00
235 51 0.16
236 65 0.21
237 146 0.47
238 47 0.15
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (232 bp):
ATACTTTGGAAATAAAACGGGGTTGGAGTATCCCTCAAAAATAATAGGGTTCGAGAATCCCGATT
GTGAAAAATCGGTGTTTTGGAAATAAAACTAGGGTTGGAGTATCCCTCGAAAATAACAGGGTCAG
AGTATCCCCGATTGTGAAAAATCTGTGTTTTGAAAATAAAACTGGGGTTAGAGTATCCCCTCAAA
AATAACGAGGTTAAAGTATCCCGATTATGAAAAATAG
Found at i:592110 original size:28 final size:28
Alignment explanation
Indices: 592078--592141 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
592068 GCCGGGGTTA
* *
592078 GAGTATCCCCTCA-GAAGTAACGGGGATG
1 GAGTATCCCC-CATGAAATAACGAGGATG
* *
592106 GAGTATCCCCGATGAAATAACGAGGTTG
1 GAGTATCCCCCATGAAATAACGAGGATG
592134 GAGTATCC
1 GAGTATCC
592142 TCGATTGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (28 bp):
GAGTATCCCCCATGAAATAACGAGGATG
Found at i:592189 original size:52 final size:51
Alignment explanation
Indices: 592129--592299 Score: 198
Period size: 52 Copynumber: 3.3 Consensus size: 51
592119 GAAATAACGA
* * *
592129 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGGAAATAAAACCAG
* ** * * *
592181 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAACCAG
* * * *
592233 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGGAAATAAAACCAG
592285 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
592300 TCGAAAATAA
Statistics
Matches: 98, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
52 89 0.91
53 9 0.09
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCAG
Found at i:592345 original size:27 final size:27
Alignment explanation
Indices: 592282--592357 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
592272 GCAATAAAAC
592282 CGGGGTTGGAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTAT-CCC-CGATAAATAA
* * *
592310 CAGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATAAATAA
592337 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
592358 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 3 0.07
27 27 0.63
28 13 0.30
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATAAATAA
Found at i:592432 original size:212 final size:210
Alignment explanation
Indices: 592021--592468 Score: 589
Period size: 212 Copynumber: 2.1 Consensus size: 210
592011 GAAAATAACG
* * * * *
592021 GGGTTGGAGTATCCCCAATTAT-GAGAAATCAATATTTTGGGAATAAAGCCGGGGTTAGAGTATC
1 GGGTTGGAGTATCCCCAATTGTGGAAAAATCAATATTTTAGCAATAAAACCGGGGTTAGAGTATC
* * *
592085 CCCTCAGAAGTAACGGGGATGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
66 CCCTCAGAAATAACAGGGATGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGT
* * *
592150 GAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGCG
131 GAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTAGAGCATCCCCGATTAAA-GAAAATTAGCG
592215 TTTTGAAAATAAAACC
195 TTTTGAAAATAAAACC
* * * * *
592231 AGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTAT
1 -GGGTTGGAGTATCCCCAATTGTGGAAAAATCAATATTTTAGCAATAAAACCGGGGTTAGAGTAT
* * *
592296 CCCCTC-GAAAATAACAGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATT
65 CCCCTCAG-AAATAACAGGGATGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATT
* *
592359 GTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGCATCCCCGATTATAA-AAAATT
129 GTGAA-AAATTGGT-ATTTTTGGAAATAAAATCAGAGTTAGAGCATCCCCGATTA-AAGAAAATT
* *
592423 AGTGTTTTGAAAATAAAATC
191 AGCGTTTTGAAAATAAAACC
*
592443 GGAGTTGGAATATCCCCAATTGTGGA
1 GG-GTTGGAGTATCCCCAATTGTGGA
592469 GAATTGAGAA
Statistics
Matches: 206, Mismatches: 25, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
211 52 0.25
212 116 0.56
213 36 0.17
214 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (210 bp):
GGGTTGGAGTATCCCCAATTGTGGAAAAATCAATATTTTAGCAATAAAACCGGGGTTAGAGTATC
CCCTCAGAAATAACAGGGATGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGT
GAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTAGAGCATCCCCGATTAAAGAAAATTAGCGT
TTTGAAAATAAAACC
Found at i:592439 original size:51 final size:53
Alignment explanation
Indices: 592349--592448 Score: 141
Period size: 51 Copynumber: 1.9 Consensus size: 53
592339 GGGTTGGAGT
* * * *
592349 ATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGC
1 ATCCCCGATTATGAAAAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTAGAGC
592403 ATCCCCGATTAT-AAAAAATTAGTG-TTTTGAAAATAAAATCGGAGTT
1 ATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCGGAGTT
592449 GGAATATCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 21 0.50
53 10 0.24
54 11 0.26
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (53 bp):
ATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCGGAGTTAGAGC
Found at i:592458 original size:51 final size:53
Alignment explanation
Indices: 592130--592459 Score: 178
Period size: 52 Copynumber: 6.3 Consensus size: 53
592120 AAATAACGAG
* * * * * *
592130 GTTGGAGTATCCTCGATTGTG-AAAAATTGGTATTTTTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCGGA
* * *
592182 GTTGGAGTATCCCCGATTA--AAGGAAAATTGGCG-TTTTGAAAATAAAACCAGG-
1 GTTGGAGTATCCCCGATTATGAA--AAAATTAGTGTTTTTGAAAATAAAATC-GGA
* * * * * *
592234 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG-CAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCGGA
** *** * **** ** * *
592286 GTTGGAGTATCCCCTCGAAAAT-AACAGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTAT-CCC-CGATTATGAA-AAAATT--AGTGTTTTTGAAAATAAAATCGGA
* * * *
592341 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAAATTAGTG-TTTTTGAAAATAAAATCGGA
* *
592395 GTTAGAGCATCCCCGATTAT-AAAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCGGA
*
592446 GTTGGAATATCCCC
1 GTTGGAGTATCCCC
592460 AATTGTGGAG
Statistics
Matches: 205, Mismatches: 55, Indels: 37
0.69 0.19 0.12
Matches are distributed among these distances:
51 34 0.17
52 80 0.39
53 35 0.17
54 33 0.16
55 14 0.07
56 7 0.03
57 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:594849 original size:13 final size:13
Alignment explanation
Indices: 594831--594856 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
594821 ACAAAGATCC
594831 ATGTATCGATACA
1 ATGTATCGATACA
594844 ATGTATCGATACA
1 ATGTATCGATACA
594857 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:594852 original size:33 final size:33
Alignment explanation
Indices: 594810--594875 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
594800 AAAATTTCCA
***
594810 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
594843 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
594876 CTTTCCTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:594920 original size:19 final size:18
Alignment explanation
Indices: 594896--594948 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
594886 CAGTAGCTAA
594896 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
*
594915 TTATGTATCTATAC-AAC
1 TTATGTATCGATACAAAC
* *
594932 ATATGTATCGTTACAAA
1 TTATGTATCGATACAAA
594949 TTGTTGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 13 0.45
18 3 0.10
19 13 0.45
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:595010 original size:21 final size:22
Alignment explanation
Indices: 594984--595041 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
594974 GTTGGGACCC
* *
594984 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
*
595005 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTGCACAAA
595026 TGTATCGATACATTTG
1 TGTATCGATACATTTG
595042 GATAATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:596358 original size:14 final size:14
Alignment explanation
Indices: 596341--596379 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
596331 GCATCTTGGC
* *
596341 ACAAACACCATGCA
1 ACAAACACAACGCA
596355 ACAAACACAACGCA
1 ACAAACACAACGCA
596369 ACAAACACAAC
1 ACAAACACAAC
596380 ATATGTCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.56, C:0.36, G:0.05, T:0.03
Consensus pattern (14 bp):
ACAAACACAACGCA
Found at i:597628 original size:50 final size:51
Alignment explanation
Indices: 597513--597651 Score: 178
Period size: 50 Copynumber: 2.8 Consensus size: 51
597503 GTCAAAATTG
* *
597513 CCTA-AATGTATCGATACATTGAGAA-ATGTATCGATACATCTAGGATAAAA
1 CCTAGAATGTATCGATACAATGA-AAGATGTATCAATACATCTAGGATAAAA
* *
597563 CCTAGAATGTATCGATACAATGAAAGATGTATCAATATATCT-GGGTAAAA
1 CCTAGAATGTATCGATACAATGAAAGATGTATCAATACATCTAGGATAAAA
* *
597613 CCTAGAATGTATCGATATAATG-AAGCATGTATCGATACA
1 CCTAGAATGTATCGATACAATGAAAG-ATGTATCAATACA
597652 AATTATGAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
49 3 0.04
50 45 0.57
51 31 0.39
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (51 bp):
CCTAGAATGTATCGATACAATGAAAGATGTATCAATACATCTAGGATAAAA
Found at i:598534 original size:61 final size:61
Alignment explanation
Indices: 598379--598902 Score: 630
Period size: 61 Copynumber: 8.5 Consensus size: 61
598369 ATAAAATGCG
*
598379 TCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAA-GCA
1 TCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
* **
598438 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
* * **
598499 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
* * * *
598560 GCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGGAAA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAGG-CA
* * * * * *
598623 GTGTCCTGC-CTTTTAGGGACTAAAAGGTACTACCAACTTGTATGGGCTTTAAAAGGAAAAGGCA
1 ---TCCTGCTCTTTGA-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
* *
598687 TCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
** * * *
598748 TCCCACTCTTTGATGACTGGAAA-GTGCCACCAACTTGTGTCGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
** * *
598809 TCCCACTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTCGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
* *
598870 TCCTACTTTTTGAGGACTGGAAA-GTGCCACCAA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAA
598903 AGAAGGAAAT
Statistics
Matches: 420, Mismatches: 34, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
59 45 0.11
60 8 0.02
61 301 0.72
62 14 0.03
64 1 0.00
65 11 0.03
66 40 0.10
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
Found at i:598820 original size:249 final size:247
Alignment explanation
Indices: 598378--598865 Score: 712
Period size: 249 Copynumber: 2.0 Consensus size: 247
598368 AATAAAATGC
* * *
598378 GTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGCATCCTG
1 GTCCTGCTCTTTGAGGACTAAAAGGTACCACCAACTTGTATGGGCTTTAAAAGGAAAGCATCCTG
* ** *
598443 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGTGTCCTACTCT
66 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCCCACTCT
* * ** ***
598508 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGTGGCTTGCTCTTTGA
131 TTGAGGACTGAAAGGTGCCACCAACTTGTGTCGGCTTTAAAAAGAAAAGGCAGCCCACTCTTTGA
*
598573 GGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGGAAAGT
196 GGACTGGAAA-GTGCCACCAACTTGTGTCGGCTTTAAAAGGAAAAAGGAAAGT
* *
598625 GTCCTGC-CTTTTAGGGACTAAAAGGTACTACCAACTTGTATGGGCTTTAAAAGGAAAAGGCATC
1 GTCCTGCTCTTTGA-GGACTAAAAGGTACCACCAACTTGTATGGGCTTTAAAAGG-AAA-GCATC
* *
598689 TTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCCAC
63 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCCCAC
* * *
598754 TCTTTGATGACTGGAAA-GTGCCACCAACTTGTGTCGGCTTTAAAAGGAAAAGGCATCCCACTCT
128 TCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTCGGCTTTAAAAAGAAAAGGCAGCCCACTCT
598818 TTGAGGACTGGAAAGTGCCACCAACTTGTGTCGGCTTTAAAAGGAAAA
192 TTGAGGACTGGAAAGTGCCACCAACTTGTGTCGGCTTTAAAAGGAAAA
598866 GGCATCCTAC
Statistics
Matches: 214, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
246 5 0.02
247 43 0.20
248 3 0.01
249 155 0.72
250 8 0.04
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (247 bp):
GTCCTGCTCTTTGAGGACTAAAAGGTACCACCAACTTGTATGGGCTTTAAAAGGAAAGCATCCTG
CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCCCACTCT
TTGAGGACTGAAAGGTGCCACCAACTTGTGTCGGCTTTAAAAAGAAAAGGCAGCCCACTCTTTGA
GGACTGGAAAGTGCCACCAACTTGTGTCGGCTTTAAAAGGAAAAAGGAAAGT
Done.