Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold370
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: 857924
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:459313 original size:19 final size:19
Alignment explanation
Indices: 459289--459353 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
459279 TAGCCAAACT
459289 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
459308 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
459321 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
459342 TGTATCGATACA
1 TGTATCGATACA
459354 TTAGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:459325 original size:13 final size:13
Alignment explanation
Indices: 459307--459332 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
459297 TACACAAAAT
459307 ATGTATCGATACA
1 ATGTATCGATACA
459320 ATGTATCGATACA
1 ATGTATCGATACA
459333 CAAAAAATAT
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:459330 original size:32 final size:33
Alignment explanation
Indices: 459289--459353 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
459279 TAGCCAAACT
459289 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
459321 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
459354 TTAGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:464629 original size:11 final size:10
Alignment explanation
Indices: 464598--464628 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
464588 CCTAATCTTC
464598 ACAAAAAAAA
1 ACAAAAAAAA
464608 ACAAAAAAAA
1 ACAAAAAAAA
464618 ACAAAAAAAA
1 ACAAAAAAAA
464628 A
1 A
464629 AGGGAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:465587 original size:31 final size:31
Alignment explanation
Indices: 465546--465764 Score: 212
Period size: 31 Copynumber: 6.9 Consensus size: 31
465536 CTTCAAATAC
* *
465546 CTTCTTAAAGTCCATGACTCCGTGGCACCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
*
465577 CTTCTCAAAGTCCACGACTCAGTGGCATCCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCA-CCTT
* *
465609 -TTCTTCAAAGTCCACGACTCAGTGGCA-ATCT
1 CTTC-TCAAAGTCCACGACTCCGTGGCACCT-T
* *
465640 CTGCTCAAAGTCCATGACTCCGTGGCACCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* * *
465671 CCTT-TCAAAGCCCACAACTTCGTGGCACTCGTT
1 -CTTCTCAAAGTCCACGACTCCGTGGCAC-C-TT
*
465704 -TTCCTTCTAAGTCCACGACTCCGTGGCACCTT
1 CTT-C-TCAAAGTCCACGACTCCGTGGCACCTT
* * *
465736 CTTTTCAAAGCCCACAACTCCGTGGCACC
1 CTTCTCAAAGTCCACGACTCCGTGGCACC
465765 ATTAAGCCCA
Statistics
Matches: 155, Mismatches: 21, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
30 1 0.01
31 94 0.61
32 35 0.23
33 5 0.03
34 20 0.13
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28
Consensus pattern (31 bp):
CTTCTCAAAGTCCACGACTCCGTGGCACCTT
Found at i:465818 original size:90 final size:87
Alignment explanation
Indices: 465678--465850 Score: 251
Period size: 90 Copynumber: 2.0 Consensus size: 87
465668 CTTCCTTTCA
* *
465678 AAGCCCACAACTTCGTGGCACTCGTTTTCCTTCTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACTCGTTTTCCTTCTAAGTCCACAACTCCGTGGCACC--CTTTT-A
465743 AAGCCCACAACTCCGTGGCACCATT
63 AAGCCCACAACTCCGTGGCACCATT
*
465768 AAGCCCACAACTCCGTGGCACT-TTTTTCATCTT-TAAGTCCACAACTCCGTGGCACCCTTTTAA
1 AAGCCCACAACTCCGTGGCACTCGTTTTC--CTTCTAAGTCCACAACTCCGTGGCACCCTTTTAA
*
465831 AGCCCACAACTTCGTGGCAC
64 AGCCCACAACTCCGTGGCAC
465851 TCGTTTTCCT
Statistics
Matches: 77, Mismatches: 4, Indels: 7
0.88 0.05 0.08
Matches are distributed among these distances:
87 21 0.27
88 5 0.06
89 5 0.06
90 43 0.56
91 3 0.04
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.27
Consensus pattern (87 bp):
AAGCCCACAACTCCGTGGCACTCGTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAAG
CCCACAACTCCGTGGCACCATT
Found at i:465847 original size:62 final size:60
Alignment explanation
Indices: 465747--465911 Score: 237
Period size: 62 Copynumber: 2.7 Consensus size: 60
465737 TTTTCAAAGC
* * *
465747 CCACAACTCCGTGGCA-CCATTAAGCCCACAACTCCGTGGCACT-TTTTTCATCTT-TAAGT
1 CCACAACTCCGTGGCACCCTTTAAGCCCACAACTTCGTGGCACTCGTTTTC--CTTCTAAGT
465806 CCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTTCGTGGCACTCGTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCACCC-TTT-AAGCCCACAACTTCGTGGCACTCGTTTTCCTTCTAAGT
465868 CCACAACTCCGTGGCACCCGTTTAAGCCCACAACTTCGTGGCAC
1 CCACAACTCCGTGGCACCC-TTTAAGCCCACAACTTCGTGGCAC
465912 CCTTTTAAGT
Statistics
Matches: 97, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
59 16 0.16
60 2 0.02
61 26 0.27
62 48 0.49
63 5 0.05
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.26
Consensus pattern (60 bp):
CCACAACTCCGTGGCACCCTTTAAGCCCACAACTTCGTGGCACTCGTTTTCCTTCTAAGT
Found at i:465855 original size:152 final size:150
Alignment explanation
Indices: 465646--465979 Score: 433
Period size: 152 Copynumber: 2.2 Consensus size: 150
465636 ATCTCTGCTC
** *
465646 AAAGTCCATGACTCCGTGGCACCTTCCTTTCAAAGCCCACAACTTCGTGGCACTCGTTTTCCTTC
1 AAAGTCCACAACTCCGTGGCA-C--CCTTTTAAAGCCCACAACTTCGTGGCACTCGTTTTCCTTC
* *
465711 TAAGTCCACGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCA-CC-ATTAAGCCC
63 TAAGTCCACAACTCCGTGGCACC--CGTTT--AAGCCCACAACTCCGTGGCACCCTATTAAGCCC
465774 ACAACTCCGTGGCA-CTTTTTTCATCTTT
124 ACAACTCCGTGGCACCTTTTTTC--CTTT
465802 -AAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTTCGTGGCACTCGTTTTCCTTCTAA
1 AAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTTCGTGGCACTCGTTTTCCTTCTAA
* * * *
465866 GTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTTCGTGGCACCCTTTTAAGTCCACGACTC
66 GTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACCCTATTAAGCCCACAACTC
465931 CGTGGCACCCTTTTTTCCTTT
131 CGTGGCA-CCTTTTTTCCTTT
* * * *
465952 AAAGCCCACAACTACATGGCACTCTTTT
1 AAAGTCCACAACTCCGTGGCACCCTTTT
465980 CCTTTTAAGT
Statistics
Matches: 160, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
148 19 0.12
149 2 0.01
150 28 0.17
151 23 0.14
152 69 0.43
154 1 0.01
155 18 0.11
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (150 bp):
AAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTTCGTGGCACTCGTTTTCCTTCTAA
GTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACCCTATTAAGCCCACAACTC
CGTGGCACCTTTTTTCCTTT
Found at i:465910 original size:89 final size:89
Alignment explanation
Indices: 465799--465973 Score: 228
Period size: 89 Copynumber: 2.0 Consensus size: 89
465789 TTTTTTCATC
* * *
465799 TTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTTCGTGGCACTC-GTTTTCCTTC
1 TTTAAGCCCACAACTCCGTGGCACCCTTTT-AAGCCCACAACTCCGTGGCACCCTGTTTTCCTT-
* * *
465863 T-AAGTCCACAACTCCGTGGCACCCG
64 TAAAGCCCACAACTACATGGCACCCG
* * * *
465888 TTTAAGCCCACAACTTCGTGGCACCCTTTTAAGTCCACGACTCCGTGGCACCCTTTTTTCCTTTA
1 TTTAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCCTGTTTTCCTTTA
465953 AAGCCCACAACTACATGGCAC
66 AAGCCCACAACTACATGGCAC
465974 TCTTTTCCTT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 20 0.27
89 54 0.73
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.27
Consensus pattern (89 bp):
TTTAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCCTGTTTTCCTTTA
AAGCCCACAACTACATGGCACCCG
Found at i:465941 original size:27 final size:27
Alignment explanation
Indices: 465858--465944 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
465848 CACTCGTTTT
*
465858 CCTTCTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* * *
465885 CCGTTTAAGCCCACAACTTCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
465912 CCTTTTAAGTCCACGACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
465939 CCTTTT
1 CCTTTT
465945 TTCCTTTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.20, C:0.38, G:0.16, T:0.26
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:465994 original size:33 final size:34
Alignment explanation
Indices: 465912--465995 Score: 98
Period size: 35 Copynumber: 2.5 Consensus size: 34
465902 TTCGTGGCAC
* * * *
465912 CCTTTTAAGTCCACGACTCCGTGGCACCCTTTTTT
1 CCTTTTAAGTCCACAACTACATGGCA-CCTCTTTT
* *
465947 CCTTTAAAGCCCACAACTACATGGCA-CTCTTTT
1 CCTTTTAAGTCCACAACTACATGGCACCTCTTTT
465980 CCTTTTAAGTCCACAA
1 CCTTTTAAGTCCACAA
465996 GTCGATGGCA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 20 0.49
35 21 0.51
ACGTcount: A:0.23, C:0.33, G:0.11, T:0.33
Consensus pattern (34 bp):
CCTTTTAAGTCCACAACTACATGGCACCTCTTTT
Found at i:466004 original size:33 final size:35
Alignment explanation
Indices: 465912--466005 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 35
465902 TTCGTGGCAC
* * *
465912 CCTTTTAAGTCCACGACTCCG-TGGCACCCTTTTTT
1 CCTTTTAAGTCCACAACTACGATGGCA-CCTCTTTT
* *
465947 CCTTTAAAGCCCACAACTAC-ATGGCA-CTCTTTT
1 CCTTTTAAGTCCACAACTACGATGGCACCTCTTTT
*
465980 CCTTTTAAGTCCACAAGT-CGATGGCA
1 CCTTTTAAGTCCACAACTACGATGGCA
466006 ACCTTCTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
32 1 0.02
33 27 0.55
35 21 0.43
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (35 bp):
CCTTTTAAGTCCACAACTACGATGGCACCTCTTTT
Found at i:466057 original size:32 final size:33
Alignment explanation
Indices: 465991--466111 Score: 201
Period size: 33 Copynumber: 3.7 Consensus size: 33
465981 CTTTTAAGTC
*
465991 CACAAGTCGATGGCAA-CCTTCTTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTC-TCTAAAGCCCA
466024 CACAAGTCGGTGGCAACCCTTCTC-AAAGCCCA
1 CACAAGTCGGTGGCAACCCTTCTCTAAAGCCCA
*
466056 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTCTCTAAAGCCCA
466089 CACAAGTCGGTGGCAACCCTTCT
1 CACAAGTCGGTGGCAACCCTTCT
466112 AAGCCCAATA
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
32 31 0.37
33 47 0.57
34 5 0.06
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.19
Consensus pattern (33 bp):
CACAAGTCGGTGGCAACCCTTCTCTAAAGCCCA
Found at i:466070 original size:65 final size:63
Alignment explanation
Indices: 465991--466118 Score: 213
Period size: 65 Copynumber: 2.0 Consensus size: 63
465981 CTTTTAAGTC
465991 CACAAGTCGATGGCAACC-TTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCC
1 CACAAGTCGATGGCAACCATTC-TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT--AAGCCC
466055 A
63 A
*
466056 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAGCCCA
1 CACAAGTCGATGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAGCCCA
466119 ATATAGCTGG
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
63 7 0.11
65 51 0.84
66 3 0.05
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (63 bp):
CACAAGTCGATGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAGCCCA
Found at i:466169 original size:49 final size:49
Alignment explanation
Indices: 466111--466292 Score: 241
Period size: 49 Copynumber: 3.8 Consensus size: 49
466101 GCAACCCTTC
* *
466111 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
466160 TAAGTCCAATGTAACTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
466203 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
466252 TAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC
466293 ATTAAGCCCA
Statistics
Matches: 114, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
43 38 0.33
45 1 0.01
47 1 0.01
49 74 0.65
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:466221 original size:43 final size:43
Alignment explanation
Indices: 466157--466339 Score: 186
Period size: 43 Copynumber: 4.1 Consensus size: 43
466147 GCACCTTCAT
* *
466157 CTTTAAGTCCAATGTAACTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
466200 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG--CA--C
* *
466247 ATCTTTAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * * * * * * *
466292 CATTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
466335 CTTTA
1 CTTTA
466340 TCACTTTTCT
Statistics
Matches: 115, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
43 73 0.63
45 3 0.03
47 3 0.03
49 36 0.31
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:466273 original size:92 final size:92
Alignment explanation
Indices: 466106--466333 Score: 366
Period size: 92 Copynumber: 2.5 Consensus size: 92
466096 CGGTGGCAAC
* *
466106 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGTCCAATG
466171 TAACTGGCCTTGAATCAGCACATTGGCA
65 TAACTGGCCTTGAATCAGCACATTGGCA
* *
466199 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGTCTAATGT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGTCCAATGT
*
466264 AGCTGGCCTTGAATCAGCACATTGGCA
66 AACTGGCCTTGAATCAGCACATTGGCA
* * * *
466291 CCATTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCA
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
466334 TCTTTATCAC
Statistics
Matches: 125, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
92 121 0.97
93 4 0.03
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (92 bp):
CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGTCCAATGT
AACTGGCCTTGAATCAGCACATTGGCA
Found at i:467191 original size:33 final size:33
Alignment explanation
Indices: 467154--467220 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
467144 TTCAACGATT
467154 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
467187 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
467220 T
1 T
467221 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:467192 original size:13 final size:13
Alignment explanation
Indices: 467174--467198 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
467164 CATAAAATGT
467174 TGTATCGATACAA
1 TGTATCGATACAA
467187 TGTATCGATACA
1 TGTATCGATACA
467199 TATTTTTTTG
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:467336 original size:52 final size:50
Alignment explanation
Indices: 467276--467420 Score: 182
Period size: 52 Copynumber: 2.8 Consensus size: 50
467266 ATCGATACAT
* *
467276 TGTATCGATATACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* * *
467328 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGTCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
467380 TGTATCGATACACTATTAAATGTATCGATACATGCAAGCAA
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAA
467421 CTTTTCATAT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:471561 original size:19 final size:20
Alignment explanation
Indices: 471518--471568 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
471508 TACAAGCCAA
**
471518 TGTATCGATACATTTTATGG
1 TGTATCGATACATACTATGG
*
471538 TGTATCGATACATACTGT-G
1 TGTATCGATACATACTATGG
471557 TGTATCGATACA
1 TGTATCGATACA
471569 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATACTATGG
Found at i:472141 original size:108 final size:108
Alignment explanation
Indices: 471999--472429 Score: 646
Period size: 108 Copynumber: 4.0 Consensus size: 108
471989 TTTACAAAAG
* * * * * *
471999 AGTTATCTTATATAAAGGGCGTTCGTACGTCGCTTTACGACTCTAAACTATAACCTATTTCGGGG
1 AGTTATCTTATGTAAAAGGCGTTCGTACGTCGCTTTACGACTCTAGACGATGACCTATTTCGAGG
* *
472064 TCAATCTTTTGGTGCCCGAATTTACGTAATTAATGCAAAAATA
66 CCAATCTTTTGGTGCCCGAATTTACATAATTAATGCAAAAATA
* * **
472107 AGTTGTCTTATGTAAAGGGCGTTCGTACACCGCTTTACGACTCTAGACGATGACCTATTTCGAGG
1 AGTTATCTTATGTAAAAGGCGTTCGTACGTCGCTTTACGACTCTAGACGATGACCTATTTCGAGG
* * * *
472172 TCAATCTTTTAGTGCCTGAATTTACGTAATTAATGCAAAAATA
66 CCAATCTTTTGGTGCCCGAATTTACATAATTAATGCAAAAATA
* *
472215 AGTTATCTTATGTAAAAGGTGTTCGTACGTTGCTTTACGACTCTAGACGATGACCTATTTCGAGG
1 AGTTATCTTATGTAAAAGGCGTTCGTACGTCGCTTTACGACTCTAGACGATGACCTATTTCGAGG
*
472280 CCAATCTTTTGGTGCCCGAATTTACATAATTAGTGCAAAAATA
66 CCAATCTTTTGGTGCCCGAATTTACATAATTAATGCAAAAATA
* * *
472323 AGTTGTCTTATGTAAAAGGCGTTCGTACGTCGCTTTACGACTCTAGACAATGACCTATTTCGGGG
1 AGTTATCTTATGTAAAAGGCGTTCGTACGTCGCTTTACGACTCTAGACGATGACCTATTTCGAGG
* *
472388 CCAATCTTTTGATGCTCGAATTTACATAATTAATGCAAAAAT
66 CCAATCTTTTGGTGCCCGAATTTACATAATTAATGCAAAAAT
472430 GAATTCTAAA
Statistics
Matches: 294, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 294 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (108 bp):
AGTTATCTTATGTAAAAGGCGTTCGTACGTCGCTTTACGACTCTAGACGATGACCTATTTCGAGG
CCAATCTTTTGGTGCCCGAATTTACATAATTAATGCAAAAATA
Found at i:473097 original size:11 final size:11
Alignment explanation
Indices: 473067--473108 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
473057 CTTTCCATCT
473067 TCTTTCCTTCTC
1 TCTTT-CTTCTC
*
473079 TC-TTCTTCTT
1 TCTTTCTTCTC
473089 TCTTTCTTCTC
1 TCTTTCTTCTC
*
473100 CCTTTCTTC
1 TCTTTCTTC
473109 CTTGGTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 7 0.27
11 17 0.65
12 2 0.08
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (11 bp):
TCTTTCTTCTC
Found at i:474512 original size:13 final size:13
Alignment explanation
Indices: 474479--474512 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
474469 CTTGCGTTAA
*
474479 AAAAAGTATATTT
1 AAAAAGTGTATTT
474492 AAAAAGTGTATTT
1 AAAAAGTGTATTT
474505 AAAAAGTG
1 AAAAAGTG
474513 GGTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (13 bp):
AAAAAGTGTATTT
Found at i:475219 original size:12 final size:12
Alignment explanation
Indices: 475204--475237 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
475194 TTTTATTTTT
475204 ATTTTTAATATA
1 ATTTTTAATATA
*
475216 ATTTTTAATTTA
1 ATTTTTAATATA
475228 ATTTTTAATA
1 ATTTTTAATA
475238 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTTAATATA
Found at i:475255 original size:24 final size:25
Alignment explanation
Indices: 475198--475255 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
475188 ATATTATTTT
*
475198 ATTTTTATTTTTAATATAATTTTTA
1 ATTTTTATTTTTAATATAATTTATA
*
475223 A-TTTAATTTTT-A-ATAATTTAATA
1 ATTTTTATTTTTAATATAATTT-ATA
475246 ATTTTTATTT
1 ATTTTTATTT
475256 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.25
23 4 0.14
24 16 0.57
25 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
ATTTTTATTTTTAATATAATTTATA
Found at i:475953 original size:26 final size:26
Alignment explanation
Indices: 475924--476003 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 26
475914 TTAATGATAA
*
475924 TTATATTTAA-AATATTATATAAATTT
1 TTATATTTAATAAT-TTATATAAATAT
* *
475950 TTAT-TATTAATAATTTATTTATATAT
1 TTATAT-TTAATAATTTATATAAATAT
475976 TTATATTT-AT-ATTT-T-TAAATA-
1 TTATATTTAATAATTTATATAAATAT
475997 TTATATT
1 TTATATT
476004 ATATTTTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
21 7 0.15
22 5 0.11
23 1 0.02
24 4 0.09
25 3 0.06
26 23 0.49
27 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATATTTAATAATTTATATAAATAT
Found at i:476005 original size:20 final size:20
Alignment explanation
Indices: 475923--476010 Score: 69
Period size: 18 Copynumber: 4.5 Consensus size: 20
475913 TTTAATGATA
*
475923 ATTATA-TTTAAAATATTAT
1 ATTATATTTTTAAATATTAT
* *
475942 A-TAAATTTTT-ATTATTA-
1 ATTATATTTTTAAATATTAT
* *
475959 ATAAT-TTATTTATATATTTAT
1 ATTATATT-TTTAAATA-TTAT
475980 ATTTATATTTTTAAATATTAT
1 A-TTATATTTTTAAATATTAT
476001 ATTATATTTT
1 ATTATATTTT
476011 AATTATTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
17 3 0.06
18 13 0.25
19 6 0.12
20 12 0.23
21 6 0.12
22 10 0.19
23 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATATTTTTAAATATTAT
Found at i:476021 original size:11 final size:12
Alignment explanation
Indices: 475948--476032 Score: 65
Period size: 12 Copynumber: 7.2 Consensus size: 12
475938 TTATATAAAT
475948 TTTTATTATTAATA
1 TTTTA-TATT-ATA
*
475962 ATTTAT-TTATA
1 TTTTATATTATA
475973 TATTTATATTTATA
1 T-TTTATA-TTATA
475987 TTTT-TA--A-A
1 TTTTATATTATA
*
475995 TATTATATTATA
1 TTTTATATTATA
*
476007 TTTTA-ATTATT
1 TTTTATATTATA
476018 TTTTATATTATA
1 TTTTATATTATA
476030 TTT
1 TTT
476033 ATGCTTCACC
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
11 14 0.25
12 22 0.39
13 4 0.07
14 10 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTATATTATA
Found at i:476025 original size:18 final size:19
Alignment explanation
Indices: 475976--476026 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
475966 ATTTATATAT
475976 TTATATTTATATTTTTAAATA
1 TTAT-TTTATA-TTTTAAATA
* *
475997 TTATATTATATTTTAATTA
1 TTATTTTATATTTTAAATA
476016 TT-TTTTATATT
1 TTATTTTATATT
476027 ATATTTATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.30
19 10 0.37
20 5 0.19
21 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTATATTTTAAATA
Found at i:476028 original size:28 final size:31
Alignment explanation
Indices: 475971--476031 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 31
475961 AATTTATTTA
*
475971 TATATTTATATTTATATTTTTAAATATTATAT
1 TATATTTATAATTATATTTTT-AATATTATAT
476003 TATATTT-TAATTAT-TTTTT-ATATTATAT
1 TATATTTATAATTATATTTTTAATATTATAT
476031 T
1 T
476032 TATGCTTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 10 0.36
30 5 0.18
31 6 0.21
32 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TATATTTATAATTATATTTTTAATATTATAT
Found at i:478050 original size:2 final size:2
Alignment explanation
Indices: 478033--478072 Score: 62
Period size: 2 Copynumber: 19.0 Consensus size: 2
478023 ACTAGCTTTT
478033 GA GA TGA GA TGA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA -GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
478073 CCAAAGCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 32 0.89
3 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.47, T:0.05
Consensus pattern (2 bp):
GA
Found at i:478438 original size:27 final size:29
Alignment explanation
Indices: 478374--478438 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
478364 ACTGAATAAG
478374 TTTGAATTAGATTATTTTGTATTTAAATT
1 TTTGAATTAGATTATTTTGTATTTAAATT
* *
478403 TTATTAATTA-ATT-TTTT-TATTTAGATT
1 TT-TGAATTAGATTATTTTGTATTTAAATT
478430 TCTTGAATT
1 T-TTGAATT
478439 TTAAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 15 0.48
28 5 0.16
29 5 0.16
30 6 0.19
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.62
Consensus pattern (29 bp):
TTTGAATTAGATTATTTTGTATTTAAATT
Found at i:479996 original size:14 final size:14
Alignment explanation
Indices: 479974--480008 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
479964 TTGTTGTTAT
479974 ATTTAAAAATTTAA
1 ATTTAAAAATTTAA
*
479988 ATTTTAAAATTTAA
1 ATTTAAAAATTTAA
480002 ATTTAAA
1 ATTTAAA
480009 TTTTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTAAAAATTTAA
Found at i:480274 original size:6 final size:7
Alignment explanation
Indices: 480244--480272 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
480234 ACTAATTTTG
480244 AAATTT-
1 AAATTTA
480250 AAATTTA
1 AAATTTA
480257 AAATTTA
1 AAATTTA
480264 AAATTTA
1 AAATTTA
480271 AA
1 AA
480273 TTACCAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:480883 original size:2 final size:2
Alignment explanation
Indices: 480876--480903 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
480866 ATGCATATGC
480876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
480904 TGAGAAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:481765 original size:16 final size:16
Alignment explanation
Indices: 481744--481793 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
481734 CATTTTAAGG
*
481744 TTCAGATCATTTCGAA
1 TTCAGATAATTTCGAA
**
481760 TTCAGATTGTTTCGAA
1 TTCAGATAATTTCGAA
*
481776 TTCATATAATTTCGAA
1 TTCAGATAATTTCGAA
481792 TT
1 TT
481794 TAAGTCAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (16 bp):
TTCAGATAATTTCGAA
Found at i:484562 original size:11 final size:12
Alignment explanation
Indices: 484543--484615 Score: 58
Period size: 12 Copynumber: 5.9 Consensus size: 12
484533 ATACAATAAA
*
484543 AAAACATATT-T
1 AAAATATATTAT
484554 AAAATATATTAT
1 AAAATATATTAT
*
484566 AAAATATAATAT
1 AAAATATATTAT
* *
484578 AAAAAATAATATT
1 AAAATATATTA-T
* *
484591 AATATATAAATAT
1 AAAATAT-ATTAT
484604 ATAAATATATTA
1 A-AAATATATTA
484616 AAATTTATGT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
11 9 0.18
12 22 0.43
13 11 0.22
14 9 0.18
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (12 bp):
AAAATATATTAT
Found at i:484568 original size:12 final size:12
Alignment explanation
Indices: 484553--484612 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
484543 AAAACATATT
*
484553 TAAAATATATTA
1 TAAAATATAATA
484565 TAAAATATAATA
1 TAAAATATAATA
*
484577 TAAAAAATAATA
1 TAAAATATAATA
*
484589 TTAATATATAAATA
1 -TAAAATAT-AATA
484603 TATAAATATA
1 TA-AAATATA
484613 TTAAAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 22 0.55
13 9 0.22
14 9 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAAATATAATA
Found at i:484580 original size:24 final size:26
Alignment explanation
Indices: 484553--484615 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 26
484543 AAAACATATT
484553 TAAAATATATTA-TAAAATAT-AATA
1 TAAAATATATTATTAAAATATAAATA
* * *
484577 TAAAAAATAATATTAATATATAAATA
1 TAAAATATATTATTAAAATATAAATA
484603 TATAAATATATTA
1 TA-AAATATATTA
484616 AAATTTATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 10 0.32
25 7 0.23
26 6 0.19
27 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TAAAATATATTATTAAAATATAAATA
Found at i:484602 original size:8 final size:8
Alignment explanation
Indices: 484563--484613 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
484553 TAAAATATAT
484563 TATAAA-A
1 TATAAATA
484570 TAT-AATA
1 TATAAATA
*
484577 TAAAAAATAA
1 T-ATAAAT-A
*
484587 TATTAATA
1 TATAAATA
484595 TATAAATA
1 TATAAATA
484603 TATAAATA
1 TATAAATA
484611 TAT
1 TAT
484614 TAAAATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
6 2 0.06
7 5 0.14
8 20 0.56
9 7 0.19
10 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TATAAATA
Found at i:485813 original size:70 final size:70
Alignment explanation
Indices: 485700--485833 Score: 198
Period size: 70 Copynumber: 1.9 Consensus size: 70
485690 ATTTATAGGC
* *
485700 TCATATTCATTAGTTTTTCCTTTGGATCTCTTGAAACTTTGAGAAATGATTCTTCTT-CATTCTT
1 TCATAATCATTAGTTTTTCCTTTGGATCTCTAGAAACTTTGAGAAATGATTCTT-TTGCATTCTT
485764 ATTGGA
65 ATTGGA
* * * *
485770 TCATAATCATTCGTTTTTCTTTTGGATCTGTAGAAGCTTTGAGAAATGATTCTTTTGCATTCTT
1 TCATAATCATTAGTTTTTCCTTTGGATCTCTAGAAACTTTGAGAAATGATTCTTTTGCATTCTT
485834 GATGCAGTGA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 2 0.04
70 55 0.96
ACGTcount: A:0.22, C:0.15, G:0.14, T:0.49
Consensus pattern (70 bp):
TCATAATCATTAGTTTTTCCTTTGGATCTCTAGAAACTTTGAGAAATGATTCTTTTGCATTCTTA
TTGGA
Found at i:491464 original size:97 final size:97
Alignment explanation
Indices: 491213--491453 Score: 374
Period size: 97 Copynumber: 2.5 Consensus size: 97
491203 TTAAAAAAAT
* *
491213 GGGGTTAGAGTATCCCCTCGAAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGCGAG
1 GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGCGAG
491278 AATAAAATTTAAACTTTGATGCGTTTAAAAGC
66 AATAAAATTTAAACTTTGATGCGTTTAAAAGC
* ** *
491310 GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTAGAGTGTTTCCGATGATGACAATTTAAGTGAG
1 GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGCGAG
* *
491375 AATAAGATTTAAACTTTGATGTGTTTAAAAGC
66 AATAAAATTTAAACTTTGATGCGTTTAAAAGC
* * * *
491407 GGGGTTGGAGTATCCCTTCGGAGGAATAGGATTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGAT
491454 AAATAAAATT
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 129 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.28
Consensus pattern (97 bp):
GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGCGAG
AATAAAATTTAAACTTTGATGCGTTTAAAAGC
Found at i:492511 original size:488 final size:487
Alignment explanation
Indices: 491561--492542 Score: 1750
Period size: 488 Copynumber: 2.0 Consensus size: 487
491551 AAAAAAAGGT
* * * *
491561 TTTGAAACTGATTGGGGTTATACGAAGAAATCCTAATGTCTCGGGATGAAACTCGAGAAAATGAT
1 TTTGAAACTGATTGGGGTTATACGAAGAAATCCCAATGTCTCGAGATGAAACCCGAGAAAATGAA
*
491626 CCAATTTAGACGGCGACCAAAAATAAGGGATAGCATCGCGCTGTCCCACTTTTCAAATTTATTTC
66 CCAATTTAGACGGCAACCAAAAATAAGGGATAGCATCGCGCTGTCCCACTTTTCAAATTTATTTC
* *
491691 GGGTTGATTCGGAGGTTCTAGAGAGTGAAATAGGTACCGTTCGAGAGGTAATTTGATGAGAATCG
131 GAGTTGATTCGGAGGTTCTAGAGAGTGAAATAGGTACCGTTCGAGAGGTAACTTGATGAGAATCG
* * *
491756 ATTTAAAAATATTTTCAAAATCCCGAAAAATCTTTTTTCTAGTGGAATAAATTCTCAAAGTTGGG
196 ATTTAAAAATATTTCCAAAATCCCAAAAAATCTTTTTTCTAATGGAATAAATTCTCAAAGTTGGG
*
491821 TGAAATGCGCTGCTGGTAGAGCACATGACGTAAAGGTGTGACAAACTTTGAAAAATCAGCCCGAA
261 TGAAATGCGCTGCTGGTAGAGCACATGACGTAAAGGTGTGACAAACTTTAAAAAATCAGCCCGAA
491886 TTCATTTGGTATCAAAAAATTACAAACTATACCTTTCTGAAAAGATAATTTCATGAAGTTTTTAT
326 TTCATTTGGTATCAAAAAATTACAAACTATACCTTTCTGAAAAGATAATTTCATGAAGTTTTTAT
* *
491951 GAAAAATATTTGGAAAATTTGAAAAAATTATCTAGCAGGCCAAAACGGCCTGACCAGAATGCAAA
391 GAAAAATATTTGGAAAATTTGAAAAAATTATCTAGAAAGCCAAAACGGCCTGACCAGAATGCAAA
492016 TTGTTGATTCTATGGGTTCTGGATAGTTTAGA
456 TTGTTGATTCTATGGGTTCTGGATAGTTTAGA
*
492048 TTTGAAACTGATTGGGGTTATATGAAGAAATCCCAATGTCTCGAGATGAAACCCGAGAAAATGAA
1 TTTGAAACTGATTGGGGTTATACGAAGAAATCCCAATGTCTCGAGATGAAACCCGAGAAAATGAA
* *
492113 CCAATTTAGACGGCAACCAAAAATAGGGGATAGCATTGCGCTGTCCCACTTTTCAAATTTATTTC
66 CCAATTTAGACGGCAACCAAAAATAAGGGATAGCATCGCGCTGTCCCACTTTTCAAATTTATTTC
* *
492178 GAGTTGATTTC-GAGGTTCTAGAGGGTGAAATAGGTACCGTTCGAGAGGTAACTTGATGAGAATT
131 GAGTTGA-TTCGGAGGTTCTAGAGAGTGAAATAGGTACCGTTCGAGAGGTAACTTGATGAGAATC
492242 GATTTAAAAATATTTCCAAAATCCCAAAAAATCTTTTTTCTTAATGGAATAAATTCTCAAAGTTG
195 GATTTAAAAATATTTCCAAAATCCCAAAAAATCTTTTTTC-TAATGGAATAAATTCTCAAAGTTG
492307 GGTGAAATGCGCTGCTGGTAGAGCACATGACGTAAAGGTGTGACAAACTTTAAAAAATCAGCCCG
259 GGTGAAATGCGCTGCTGGTAGAGCACATGACGTAAAGGTGTGACAAACTTTAAAAAATCAGCCCG
* *
492372 AATTCATTTGGTATCAAAAAATTCCAAACTATACCTTTCTGGAAAGATAATTTCATGAAGTTTTT
324 AATTCATTTGGTATCAAAAAATTACAAACTATACCTTTCTGAAAAGATAATTTCATGAAGTTTTT
*
492437 ATGAAAAATATTTGGAAAATTTGAAAAAATTATCTAGAAAGCCAAAACGGCCTGACTAGAATGCA
389 ATGAAAAATATTTGGAAAATTTGAAAAAATTATCTAGAAAGCCAAAACGGCCTGACCAGAATGCA
492502 AATTGTTGATTCTATGGGTTCTGGATAGTTTAGA
454 AATTGTTGATTCTATGGGTTCTGGATAGTTTAGA
492536 TTTGAAA
1 TTTGAAA
492543 AATCATAACT
Statistics
Matches: 472, Mismatches: 21, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
487 216 0.46
488 256 0.54
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (487 bp):
TTTGAAACTGATTGGGGTTATACGAAGAAATCCCAATGTCTCGAGATGAAACCCGAGAAAATGAA
CCAATTTAGACGGCAACCAAAAATAAGGGATAGCATCGCGCTGTCCCACTTTTCAAATTTATTTC
GAGTTGATTCGGAGGTTCTAGAGAGTGAAATAGGTACCGTTCGAGAGGTAACTTGATGAGAATCG
ATTTAAAAATATTTCCAAAATCCCAAAAAATCTTTTTTCTAATGGAATAAATTCTCAAAGTTGGG
TGAAATGCGCTGCTGGTAGAGCACATGACGTAAAGGTGTGACAAACTTTAAAAAATCAGCCCGAA
TTCATTTGGTATCAAAAAATTACAAACTATACCTTTCTGAAAAGATAATTTCATGAAGTTTTTAT
GAAAAATATTTGGAAAATTTGAAAAAATTATCTAGAAAGCCAAAACGGCCTGACCAGAATGCAAA
TTGTTGATTCTATGGGTTCTGGATAGTTTAGA
Found at i:494151 original size:20 final size:20
Alignment explanation
Indices: 494122--494238 Score: 148
Period size: 20 Copynumber: 5.8 Consensus size: 20
494112 GTAAAAAGAC
*
494122 AGAATATATCGATACATTCA
1 AGAATGTATCGATACATTCA
494142 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTCA
494162 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTCA
*
494182 TA-CATGTATCGATACATTCA
1 -AGAATGTATCGATACATTCA
* *
494202 TA-CATGTATCGATACATTAA
1 -AGAATGTATCGATACATTCA
* *
494222 AAAATGTATCAATACAT
1 AGAATGTATCGATACAT
494239 CTGGGTATTT
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
19 1 0.01
20 88 0.98
21 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTCA
Found at i:494198 original size:12 final size:12
Alignment explanation
Indices: 494165--494218 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
494155 ACATTCAAGA
494165 ATGTATCGATAC
1 ATGTATCGATAC
494177 A--T-TC-ATAC
1 ATGTATCGATAC
494185 ATGTATCGATAC
1 ATGTATCGATAC
494197 A--T-TC-ATAC
1 ATGTATCGATAC
494205 ATGTATCGATAC
1 ATGTATCGATAC
494217 AT
1 AT
494219 TAAAAAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
8 10 0.29
9 4 0.12
10 4 0.12
11 4 0.12
12 12 0.35
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:495236 original size:9 final size:9
Alignment explanation
Indices: 495222--495271 Score: 75
Period size: 9 Copynumber: 5.6 Consensus size: 9
495212 TTTCCTTGGT
495222 TTTTTTTTG
1 TTTTTTTTG
495231 TTTTTTTTG
1 TTTTTTTTG
495240 TTTTTTTCT-
1 TTTTTTT-TG
*
495249 ATTTTTTTG
1 TTTTTTTTG
495258 TTTTTTTTG
1 TTTTTTTTG
495267 TTTTT
1 TTTTT
495272 GGGTATGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 1 0.03
9 35 0.95
10 1 0.03
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:506902 original size:97 final size:96
Alignment explanation
Indices: 506763--506968 Score: 349
Period size: 97 Copynumber: 2.1 Consensus size: 96
506753 AAAAAAACAA
* *
506763 GGTTGGAGTATCCCTCGGAGGAATGGGGTTGGAGTGTTCCCGATAATGACAATTTAAGCGAGAAT
1 GGTTGGAGTATCCCTCAGAGGAATGGGGTTGGAGTGTCCCCGATAATGACAATTTAAGCGAGAAT
506828 AAAATTTAAACTTTGATGCGTTTAAAAGCGG
66 AAAATTTAAACTTTGATGCGTTTAAAAGCGG
* *
506859 GGTTGGAGTATCCACTCAGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAGAA
1 GGTTGGAGTATCC-CTCAGAGGAATGGGGTTGGAGTGTCCCCGATAATGACAATTTAAGCGAGAA
*
506924 TAAAATTTAAACTTTGATGTGTTTAAAAGCGG
65 TAAAATTTAAACTTTGATGCGTTTAAAAGCGG
*
506956 GGTTGGGGTATCC
1 GGTTGGAGTATCC
506969 TTTCGAAAGA
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 13 0.13
97 90 0.87
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.29
Consensus pattern (96 bp):
GGTTGGAGTATCCCTCAGAGGAATGGGGTTGGAGTGTCCCCGATAATGACAATTTAAGCGAGAAT
AAAATTTAAACTTTGATGCGTTTAAAAGCGG
Found at i:507011 original size:97 final size:97
Alignment explanation
Indices: 506763--507002 Score: 322
Period size: 97 Copynumber: 2.5 Consensus size: 97
506753 AAAAAAACAA
* * * * *
506763 GGTTGGAGTATCC-CTCGGAGGAATGGGGTTGGAGTGTTCCCGATAATGACAATTTAAGCGAGAA
1 GGTTGGAGTATCCACTCAGAAGAATAGGATTGGAGTGTCCCCGATAATGACAATTTAAGCGAGAA
506827 TAAAATTTAAACTTTGATGCGTTTAAAAGCGG
66 TAAAATTTAAACTTTGATGCGTTTAAAAGCGG
* * * * *
506859 GGTTGGAGTATCCACTCAGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAGAA
1 GGTTGGAGTATCCACTCAGAAGAATAGGATTGGAGTGTCCCCGATAATGACAATTTAAGCGAGAA
*
506924 TAAAATTTAAACTTTGATGTGTTTAAAAGCGG
66 TAAAATTTAAACTTTGATGCGTTTAAAAGCGG
* ** *
506956 GGTTGGGGTATCCTTTC-GAAAGAATAGGATTGGAGTATCCCCGATAA
1 GGTTGGAGTATCCACTCAG-AAGAATAGGATTGGAGTGTCCCCGATAA
507003 ATAAAATTTT
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
96 14 0.11
97 115 0.89
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.28
Consensus pattern (97 bp):
GGTTGGAGTATCCACTCAGAAGAATAGGATTGGAGTGTCCCCGATAATGACAATTTAAGCGAGAA
TAAAATTTAAACTTTGATGCGTTTAAAAGCGG
Found at i:509102 original size:20 final size:19
Alignment explanation
Indices: 509072--509147 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
509062 GTAAAAAGAT
* *
509072 AAATATATCGATACATTGA
1 AAATGTATCGATACATTCA
509091 AGAATGTATCGATACATTCA
1 A-AATGTATCGATACATTCA
* **
509111 TACATGTATCGATACATTTTT
1 -AAATGTATCGATACA-TTCA
*
509132 CAATGTATCGATACAT
1 AAATGTATCGATACAT
509148 CTAGATACTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.04
20 42 0.89
21 3 0.06
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (19 bp):
AAATGTATCGATACATTCA
Found at i:510220 original size:21 final size:21
Alignment explanation
Indices: 510195--510271 Score: 122
Period size: 21 Copynumber: 3.8 Consensus size: 21
510185 CTGCTAATTT
510195 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGTC
510216 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGTC
**
510237 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGTC
510256 CATGTATCGATACAAT
1 CATGTATCGATACAAT
510272 GTATCGATAC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 16 0.31
20 2 0.04
21 34 0.65
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (21 bp):
CATGTATCGATACAATTTGTC
Found at i:510275 original size:13 final size:13
Alignment explanation
Indices: 510257--510283 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
510247 TACATTGAAC
510257 ATGTATCGATACA
1 ATGTATCGATACA
510270 ATGTATCGATACA
1 ATGTATCGATACA
510283 A
1 A
510284 CGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:510841 original size:15 final size:17
Alignment explanation
Indices: 510821--510854 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
510811 GTTTTCGTTT
510821 TTCT-CCCCTTAAA-AA
1 TTCTCCCCCTTAAACAA
510836 TTCTCCCCCTTAAACAA
1 TTCTCCCCCTTAAACAA
510853 TT
1 TT
510855 ATCTTCTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (17 bp):
TTCTCCCCCTTAAACAA
Found at i:512957 original size:8 final size:8
Alignment explanation
Indices: 512939--512975 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
512929 ATTTCAACAT
512939 CAAACATCA
1 CAAA-ATCA
512948 CAAAATCA
1 CAAAATCA
512956 CAAAATCA
1 CAAAATCA
*
512964 CAAAATCT
1 CAAAATCA
512972 CAAA
1 CAAA
512976 GTTTAATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 23 0.85
9 4 0.15
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
CAAAATCA
Found at i:513127 original size:12 final size:14
Alignment explanation
Indices: 513096--513127 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
513086 ATACAAGTAT
513096 GAGAGATATTTTAA
1 GAGAGATATTTTAA
*
513110 GAGAGATATTTTAC
1 GAGAGATATTTTAA
513124 GAGA
1 GAGA
513128 AATAACAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (14 bp):
GAGAGATATTTTAA
Found at i:519067 original size:19 final size:19
Alignment explanation
Indices: 519022--519078 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
519012 CTGCCAATTT
**
519022 CATGTATCGATACAATTTGTC
1 CATGTATCGATAC-A-TTGAA
519043 CATGTATCGATACATTGAA
1 CATGTATCGATACATTGAA
519062 CATGTATCGATACATTG
1 CATGTATCGATACATTG
519079 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 20 0.59
20 1 0.03
21 13 0.38
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
CATGTATCGATACATTGAA
Found at i:519082 original size:13 final size:13
Alignment explanation
Indices: 519064--519088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
519054 ACATTGAACA
519064 TGTATCGATACAT
1 TGTATCGATACAT
519077 TGTATCGATACA
1 TGTATCGATACA
519089 AGGCAGCATG
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:519104 original size:33 final size:32
Alignment explanation
Indices: 519045--519109 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
519035 AATTTGTCCA
**
519045 TGTATCGATACATTGAACATGTATCGATACAT
1 TGTATCGATACAAGGAACATGTATCGATACAT
*
519077 TGTATCGATACAAGGCAGCATGTATCGATACAT
1 TGTATCGATACAAGG-AACATGTATCGATACAT
519110 CTGAGTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAGGAACATGTATCGATACAT
Found at i:519706 original size:2 final size:2
Alignment explanation
Indices: 519699--519734 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
519689 ATATTGAATT
519699 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
519735 TATTCATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:521331 original size:20 final size:21
Alignment explanation
Indices: 521298--521339 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
521288 CCCACCATTA
* *
521298 TTTGTCTTCTCAAATCAAAAT
1 TTTGTCTTCGCAAACCAAAAT
521319 TTTGT-TTCGCAAACCAAAAT
1 TTTGTCTTCGCAAACCAAAAT
521339 T
1 T
521340 ATCCTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTGTCTTCGCAAACCAAAAT
Found at i:528728 original size:23 final size:22
Alignment explanation
Indices: 528683--528726 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
528673 CATCCGAAAA
528683 AAAGAAAATTTTTAGATTTTTT
1 AAAGAAAATTTTTAGATTTTTT
*
528705 AAAGACAATTTTTAGATTTTTT
1 AAAGAAAATTTTTAGATTTTTT
528727 TAGGTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (22 bp):
AAAGAAAATTTTTAGATTTTTT
Found at i:529263 original size:86 final size:86
Alignment explanation
Indices: 529105--529264 Score: 187
Period size: 86 Copynumber: 1.9 Consensus size: 86
529095 GAACAAAAAG
* * * * * * *
529105 AAAATTTAAGTTTTTTTATGAAAAACGGGTTAGAGTATTCCTTCAAAGTAGTAAGGTTGGAGTTT
1 AAAACTTAAGTTTTTTCATGAAAAACGGGTTAGAGTATCCCTTCAAAGAAATAAGGTTAGAGTAT
***
529170 TTTCGAGAAACAATTATGAAA
66 CCCCGAGAAACAATTATGAAA
* * *
529191 AAAACTTAAG-TTTTTCATGAAGAACGGGATTAGAGTATCCCTTCAGAGAAATAGGGTTAGAGTA
1 AAAACTTAAGTTTTTTCATGAAAAACGGG-TTAGAGTATCCCTTCAAAGAAATAAGGTTAGAGTA
529255 TCCCCGAGAA
65 TCCCCGAGAA
529265 TAAAAATTTT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
85 16 0.27
86 44 0.73
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (86 bp):
AAAACTTAAGTTTTTTCATGAAAAACGGGTTAGAGTATCCCTTCAAAGAAATAAGGTTAGAGTAT
CCCCGAGAAACAATTATGAAA
Found at i:529314 original size:22 final size:22
Alignment explanation
Indices: 529262--529305 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
529252 GTATCCCCGA
529262 GAATAAAAATTTTGATTTTTTT
1 GAATAAAAATTTTGATTTTTTT
529284 GAATAAAAATTTTGATTTTTTT
1 GAATAAAAATTTTGATTTTTTT
529306 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (22 bp):
GAATAAAAATTTTGATTTTTTT
Found at i:529314 original size:23 final size:22
Alignment explanation
Indices: 529266--529315 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
529256 CCCCGAGAAT
*
529266 AAAAATTTTGATTTTTTTGAAT
1 AAAAATTTTGATTTTTTTGAAA
*
529288 AAAAATTTTGATTTTTTTTTAAA
1 AAAAATTTTGA-TTTTTTTGAAA
529311 AAAAA
1 AAAAA
529316 GGTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
AAAAATTTTGATTTTTTTGAAA
Found at i:531984 original size:20 final size:20
Alignment explanation
Indices: 531961--532010 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
531951 TTGTTTTCAA
*
531961 TATCGATACTT-TGAAGTATG
1 TATCGATACTTCTGAACT-TG
*
531981 TATCGATATTTCCTGAACTTG
1 TATCGATACTT-CTGAACTTG
532002 TATCGATAC
1 TATCGATAC
532011 AAAAGGTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.40
21 10 0.40
22 5 0.20
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (20 bp):
TATCGATACTTCTGAACTTG
Found at i:549016 original size:13 final size:13
Alignment explanation
Indices: 548998--549022 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
548988 CATTTTACTA
548998 TGTATCGATACAT
1 TGTATCGATACAT
549011 TGTATCGATACA
1 TGTATCGATACA
549023 ATAGTCCATG
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:554904 original size:240 final size:240
Alignment explanation
Indices: 554481--554962 Score: 874
Period size: 240 Copynumber: 2.0 Consensus size: 240
554471 GACAAAATAA
**
554481 GTCGATGTGAACTAGTTGCAAAACTTTAGAGGTTGTGACAATGTTTACGGGTTTAAAAGAATTTC
1 GTCGATGTGAACTAGTTGCAAAACTTTAGAGGTCATGACAATGTTTACGGGTTTAAAAGAATTTC
554546 TTCTATACTTACCCTTAATACATGCATCACATACTTTATCACAATCAAATTTAACCTTAGGTAAT
66 TTCTATACTTACCCTTAATACATGCATCACATACTTTATCACAATCAAATTTAACCTTAGGTAAT
* * **
554611 TCAATAACAAGGTCTTTCCTAGATAACTTTGAAAGTACACTCATACTTGCGTGTCCTAATTTACG
131 CCAATAACAAGGTCTTGCCTAGATAACTTCAAAAGTACACTCATACTTGCGTGTCCTAATTTACG
554676 GTGCCATAGCCAAGGTATGTCATTATTGTCCACAACAAAACATAT
196 GTGCCATAGCCAAGGTATGTCATTATTGTCCACAACAAAACATAT
*
554721 GTCGATGTGAACTAGTTGCAAAACTTTAGAGGTCATGACAATGTTTATGGGTTTAAAAGAATTTC
1 GTCGATGTGAACTAGTTGCAAAACTTTAGAGGTCATGACAATGTTTACGGGTTTAAAAGAATTTC
* *
554786 TTCTATGCTTACCCTTAATACATGCATCACATACTTTATCACAATCAAGTTTAACCTTAGGTAAT
66 TTCTATACTTACCCTTAATACATGCATCACATACTTTATCACAATCAAATTTAACCTTAGGTAAT
*
554851 CCAATAACAAGGTCTTGCCTAGATAACTTCAAAAGTACACTCATACTTGCGTGTTCTAATTTACG
131 CCAATAACAAGGTCTTGCCTAGATAACTTCAAAAGTACACTCATACTTGCGTGTCCTAATTTACG
554916 GTGCCATAGCCAAGGTATGTCATTATTGTCCACAACAAAACATAT
196 GTGCCATAGCCAAGGTATGTCATTATTGTCCACAACAAAACATAT
554961 GT
1 GT
554963 TTTGGGAACT
Statistics
Matches: 232, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
240 232 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (240 bp):
GTCGATGTGAACTAGTTGCAAAACTTTAGAGGTCATGACAATGTTTACGGGTTTAAAAGAATTTC
TTCTATACTTACCCTTAATACATGCATCACATACTTTATCACAATCAAATTTAACCTTAGGTAAT
CCAATAACAAGGTCTTGCCTAGATAACTTCAAAAGTACACTCATACTTGCGTGTCCTAATTTACG
GTGCCATAGCCAAGGTATGTCATTATTGTCCACAACAAAACATAT
Found at i:555604 original size:35 final size:35
Alignment explanation
Indices: 555565--555632 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
555555 AAATGTGTGA
555565 GGCATAATGAACACATGTATAAGGCATCATATTAT
1 GGCATAATGAACACATGTATAAGGCATCATATTAT
*
555600 GGCATAATGAACACATGTATGAGGCATCATATT
1 GGCATAATGAACACATGTATAAGGCATCATATT
555633 GTGGATTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (35 bp):
GGCATAATGAACACATGTATAAGGCATCATATTAT
Found at i:558059 original size:20 final size:20
Alignment explanation
Indices: 558034--558071 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
558024 GTCGTTGGGC
558034 ACAATGTATCGATACATTTT
1 ACAATGTATCGATACATTTT
*
558054 ACAATGTATCGATCCATT
1 ACAATGTATCGATACATT
558072 GTATCAATAC
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:0.18, G:0.11, T:0.37
Consensus pattern (20 bp):
ACAATGTATCGATACATTTT
Found at i:558135 original size:20 final size:20
Alignment explanation
Indices: 558110--558147 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
558100 TACTGCCAGT
*
558110 TTCATGTATTAATATAATTC
1 TTCATGTATCAATATAATTC
558130 TTCATGTATCAATATAAT
1 TTCATGTATCAATATAAT
558148 GAACATGTAT
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:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATGTATCAATATAATTC
Found at i:563448 original size:20 final size:20
Alignment explanation
Indices: 563408--563461 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
563398 TTCTATAATT
*
563408 TGTATCGATACAATTAGTGAA
1 TGTATCGATAC-ATAAGTGAA
563429 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
563449 TGTATCGATACAT
1 TGTATCGATACAT
563462 GTCTCAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:567400 original size:12 final size:12
Alignment explanation
Indices: 567383--567408 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
567373 TGCCTCAACG
567383 ATCGAGCCTGCA
1 ATCGAGCCTGCA
567395 ATCGAGCCTGCA
1 ATCGAGCCTGCA
567407 AT
1 AT
567409 GTATGCAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (12 bp):
ATCGAGCCTGCA
Found at i:575024 original size:22 final size:22
Alignment explanation
Indices: 574999--575044 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
574989 TAATAATTTA
*
574999 AATATG-ATCATAACATAAAAAT
1 AATATGAAT-ATAAAATAAAAAT
*
575021 AATATGAATATAAAATAAATAT
1 AATATGAATATAAAATAAAAAT
575043 AA
1 AA
575045 AAAATCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (22 bp):
AATATGAATATAAAATAAAAAT
Found at i:576503 original size:2 final size:2
Alignment explanation
Indices: 576493--576532 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
576483 ATTCTTTTTT
*
576493 TA TA T- TA TA TA -A TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
576533 GTTTCAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:576608 original size:33 final size:33
Alignment explanation
Indices: 576556--576619 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
576546 ACTCTATATA
* *
576556 TATATATATATATACACACGTCAGCCTTGCAAG
1 TATATATATACACACACACGTCAGCCTTGCAAG
* * *
576589 TATATATATACACATACACGTCGGCGTTGCA
1 TATATATATACACACACACGTCAGCCTTGCA
576620 CGTGTTTGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (33 bp):
TATATATATACACACACACGTCAGCCTTGCAAG
Found at i:579765 original size:1 final size:1
Alignment explanation
Indices: 579759--579786 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
579749 CATAAACTGC
579759 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
579787 GAATTACACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:580371 original size:23 final size:24
Alignment explanation
Indices: 580328--580375 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
580318 AAGTAAATAT
* *
580328 AAAAACATCAATGCTGACATGAAA
1 AAAAAAATCAACGCTGACATGAAA
580352 AAAAAAATCAACGCTG-CATGAAA
1 AAAAAAATCAACGCTGACATGAAA
580375 A
1 A
580376 TTGTGGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.56, C:0.17, G:0.12, T:0.15
Consensus pattern (24 bp):
AAAAAAATCAACGCTGACATGAAA
Found at i:582326 original size:21 final size:21
Alignment explanation
Indices: 582300--582342 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
582290 ATAAATAAAC
*
582300 ATATATTTTTTTATAAAAATA
1 ATATATTTTTTGATAAAAATA
582321 ATATATTTTTTGATAAAAATA
1 ATATATTTTTTGATAAAAATA
582342 A
1 A
582343 CTAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATATTTTTTGATAAAAATA
Found at i:582341 original size:18 final size:18
Alignment explanation
Indices: 582294--582341 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
582284 ACATAAATAA
* *
582294 ATAAACATATATTTTTTT
1 ATAAAAATATATTTTTTG
582312 ATAAAAATAATATATTTTTTG
1 AT--AAA-AATATATTTTTTG
582333 ATAAAAATA
1 ATAAAAATA
582342 ACTAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.24
19 3 0.12
20 3 0.12
21 13 0.52
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAAAAATATATTTTTTG
Found at i:582370 original size:21 final size:21
Alignment explanation
Indices: 582346--582385 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
582336 AAAATAACTA
*
582346 AATAT-ATATTTTAATATTTAT
1 AATATAATATTAT-ATATTTAT
582367 AATATAATATTATATATTT
1 AATATAATATTATATATTT
582386 TTATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATATAATATTATATATTTAT
Found at i:582370 original size:29 final size:28
Alignment explanation
Indices: 582338--582411 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
582328 TTTTGATAAA
582338 AATAACTAA-ATATATATTTTAATATTTAT
1 AATAA-TAATATATATATTTTAAT-TTTAT
*
582367 AAT-ATAATATTATATATTTTTATTTTAT
1 AATAATAATA-TATATATTTTAATTTTAT
582395 AATATATAATATATATA
1 AATA-ATAATATATATA
582412 AATATAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.08
28 10 0.25
29 21 0.52
30 6 0.15
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
AATAATAATATATATATTTTAATTTTAT
Found at i:582593 original size:16 final size:17
Alignment explanation
Indices: 582572--582605 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
582562 ATATTAAATA
*
582572 AATTTTTAGAT-AATTT
1 AATTTTTAAATAAATTT
582588 AATTTTTAAATAAATTT
1 AATTTTTAAATAAATTT
582605 A
1 A
582606 TTTAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTTTAAATAAATTT
Found at i:583294 original size:20 final size:19
Alignment explanation
Indices: 583266--583303 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
583256 TTAATTAATT
583266 GTGTCTTATACGTGTTATGC
1 GTGTCTTATACGT-TTATGC
*
583286 GTGTTTTATACGTTTATG
1 GTGTCTTATACGTTTATG
583304 ATATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.16, C:0.11, G:0.24, T:0.50
Consensus pattern (19 bp):
GTGTCTTATACGTTTATGC
Found at i:587703 original size:72 final size:72
Alignment explanation
Indices: 587586--587734 Score: 262
Period size: 72 Copynumber: 2.1 Consensus size: 72
587576 TTGAGACTTA
*
587586 ATGGAATGTTAGCATGATTTCTACAATATCTTTGCGCTTTCTTTTTTAAGATTCCATTATGCTCT
1 ATGGAATGTTAGCATGATTTCTACAATATCTCTGCGCTTTCTTTTTTAAGATTCCATTATGCTCT
*
587651 GTTGCAT
66 GGTGCAT
* *
587658 ATGGAATGTTAGCATGGTTTCTACAATATCTCTGCGCTTTCTTTTTTGAGATTCCATTATGCTCT
1 ATGGAATGTTAGCATGATTTCTACAATATCTCTGCGCTTTCTTTTTTAAGATTCCATTATGCTCT
587723 GGTGCAT
66 GGTGCAT
587730 ATGGA
1 ATGGA
587735 GGTGTTTTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.44
Consensus pattern (72 bp):
ATGGAATGTTAGCATGATTTCTACAATATCTCTGCGCTTTCTTTTTTAAGATTCCATTATGCTCT
GGTGCAT
Found at i:590818 original size:42 final size:42
Alignment explanation
Indices: 590736--590818 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
590726 CTTTCATCTT
* *
590736 TTTTATTTTTATTATAATTTTTATGATAGTAAAATTTTTTTA
1 TTTTATGTTTATTATAATTTTTATGATACTAAAATTTTTTTA
* *
590778 TTTTATGTTT-TTATTATTTATTATGA-ACTAAATTTATTTTT
1 TTTTATGTTTATTATAATTT-TTATGATACTAAAATT-TTTTT
590819 TAAGGGTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 15 0.43
42 20 0.57
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (42 bp):
TTTTATGTTTATTATAATTTTTATGATACTAAAATTTTTTTA
Found at i:597154 original size:20 final size:19
Alignment explanation
Indices: 597131--597169 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
597121 TTGTGCATTA
597131 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTT-AAGG
597151 TGTATCGATACATTTAAGG
1 TGTATCGATACATTTAAGG
597170 GTTTTGACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATTTAAGG
Found at i:602657 original size:13 final size:13
Alignment explanation
Indices: 602639--602664 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
602629 TACACAAAGT
602639 ATGTATCGATACA
1 ATGTATCGATACA
602652 ATGTATCGATACA
1 ATGTATCGATACA
602665 CAAAAAATTA
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:606898 original size:13 final size:13
Alignment explanation
Indices: 606880--606905 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
606870 CAATTTGGGA
606880 TGTATCGATACAT
1 TGTATCGATACAT
606893 TGTATCGATACAT
1 TGTATCGATACAT
606906 CTTGTGTGTA
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:607062 original size:20 final size:19
Alignment explanation
Indices: 607039--607077 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
607029 TTGTGCATTA
607039 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTT-AAGG
607059 TGTATCGATACATTTAAGG
1 TGTATCGATACATTTAAGG
607078 GTTTTGACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATTTAAGG
Found at i:607867 original size:202 final size:201
Alignment explanation
Indices: 607515--607923 Score: 764
Period size: 202 Copynumber: 2.0 Consensus size: 201
607505 GAGAGAACGA
*
607515 AAAATAGATTTAGTTTTTTGGTTGAAAAACAGGGTTGGAGTATCCCCTCGGAAGAATAGGGTTGG
1 AAAATTGATTTAGTTTTTTGGTTGAAAAACAGGGTTGGAGTATCCCCTCGGAAGAATAGGGTTGG
*
607580 AGTGTCCCCAACAAAAATGATTTAGGTAAAAGTATAAATGATCTTGACACATTTAAAAACTGGTT
66 AGTGTCCCCAACAAAAATGATTTAGGTAAAAGTATAAATGATCTTGACACATTTAAAAACGGGTT
*
607645 TGGAATATCCTCTTGGAATAATGGGGTTAGACTATCCTCGATAAATAAAATTTGGTATAATTTTT
131 TGGAATATCCTCTTGGAATAATGGGGTTAGACTATCCTCGATAAATAAAATTTGGCAT-ATTTTT
607710 TGTGAAG
195 TGTGAAG
*
607717 AAAATTGATTTAGTTTTTTGGTTGAAAAACAGGGTTGGAGTATCCTCTCGGAAGAATAGGGTTGG
1 AAAATTGATTTAGTTTTTTGGTTGAAAAACAGGGTTGGAGTATCCCCTCGGAAGAATAGGGTTGG
*
607782 AGTGTCCCCAACAAAAATGATTTAGGTAAAAGTATAAATGATCTTGGCACATTTAAAAACGGGTT
66 AGTGTCCCCAACAAAAATGATTTAGGTAAAAGTATAAATGATCTTGACACATTTAAAAACGGGTT
607847 TGGAATATCCTCTTGGAATAATGGGGTTAGACTATCCTCGATAAATAAAATTTGGCATATTTTTT
131 TGGAATATCCTCTTGGAATAATGGGGTTAGACTATCCTCGATAAATAAAATTTGGCATATTTTTT
607912 GTGAAG
196 GTGAAG
607918 AAAATT
1 AAAATT
607924 AACGTGAATG
Statistics
Matches: 202, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
201 19 0.09
202 183 0.91
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (201 bp):
AAAATTGATTTAGTTTTTTGGTTGAAAAACAGGGTTGGAGTATCCCCTCGGAAGAATAGGGTTGG
AGTGTCCCCAACAAAAATGATTTAGGTAAAAGTATAAATGATCTTGACACATTTAAAAACGGGTT
TGGAATATCCTCTTGGAATAATGGGGTTAGACTATCCTCGATAAATAAAATTTGGCATATTTTTT
GTGAAG
Found at i:609165 original size:21 final size:20
Alignment explanation
Indices: 609132--609172 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
609122 GAGATGTTAG
*
609132 ACATACTAAAAATGCTTGAA
1 ACATACTAAAAATGCATGAA
*
609152 ACATAGCTCAAAATGCATGAA
1 ACATA-CTAAAAATGCATGAA
609173 CTTGGGCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (20 bp):
ACATACTAAAAATGCATGAA
Found at i:610139 original size:20 final size:20
Alignment explanation
Indices: 610099--610140 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
610089 CAAAACCTAG
**
610099 AATGTATCGATACAATGAAT
1 AATGTATCGATACAAACAAT
610119 AATGTATCGATACAAACAAT
1 AATGTATCGATACAAACAAT
610139 AA
1 AA
610141 ATATATTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAAACAAT
Found at i:611694 original size:32 final size:32
Alignment explanation
Indices: 611631--611691 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
611621 TACGAAGATA
*
611631 TTAAAATTTATATAAAATAAATTATTAAAATT
1 TTAAAATTTATATAAAATAAATTATAAAAATT
* *
611663 TTAAAATTTATAT-AAATATATAATAAAAA
1 TTAAAATTTATATAAAATAAATTATAAAAA
611692 ATTGATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TTAAAATTTATATAAAATAAATTATAAAAATT
Found at i:615682 original size:18 final size:18
Alignment explanation
Indices: 615659--615695 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
615649 AAATTAAAAA
615659 TTATTTTAT-ATTAATATT
1 TTATTTTATAATTAA-ATT
615677 TTATTTTATAATTAAATT
1 TTATTTTATAATTAAATT
615695 T
1 T
615696 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTTATAATTAAATT
Found at i:617220 original size:28 final size:29
Alignment explanation
Indices: 617180--617234 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
617170 AAAATCTAAT
*
617180 TATACAAAAATAATTAT-TATAAAAATTA
1 TATACAAAAATAATTATAGATAAAAATTA
* *
617208 TATACATATATAATTATAGATAAAAAT
1 TATACAAAAATAATTATAGATAAAAAT
617235 GTATTATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (29 bp):
TATACAAAAATAATTATAGATAAAAATTA
Found at i:617316 original size:11 final size:11
Alignment explanation
Indices: 617300--617354 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
617290 TTTAAAAAGT
617300 TTATATTTATA
1 TTATATTTATA
617311 TTATATTTATA
1 TTATATTTATA
617322 -TAT-TTTAT-
1 TTATATTTATA
617330 TATATATTTATA
1 T-TATATTTATA
* *
617342 TCATAATTATA
1 TTATATTTATA
617353 TT
1 TT
617355 TAAAAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 5 0.14
10 6 0.16
11 25 0.68
12 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATATTTATA
Found at i:617325 original size:13 final size:13
Alignment explanation
Indices: 617307--617356 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
617297 AGTTTATATT
617307 TATATTATATTTA
1 TATATTATATTTA
*
617320 TATATTTTA-TTA
1 TATATTATATTTA
*
617332 TATATT-TATATCA
1 TATATTATAT-TTA
617345 TA-ATTATATTTA
1 TATATTATATTTA
617357 AAAATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 2 0.06
12 14 0.45
13 15 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTATATTTA
Found at i:617482 original size:15 final size:15
Alignment explanation
Indices: 617445--617499 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
617435 ATTATTTTTA
* *
617445 ATATTTTATATATGTT
1 ATATTTAATATA-ATT
617461 ATA-TTAATATAATT
1 ATATTTAATATAATT
*
617475 ATATTTAATATTATT
1 ATATTTAATATAATT
*
617490 AAATTTAATA
1 ATATTTAATA
617500 AAAAATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.15
15 26 0.76
16 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
ATATTTAATATAATT
Found at i:618820 original size:2 final size:2
Alignment explanation
Indices: 618813--618853 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
618803 TTCTTGCATT
*
618813 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
618854 TTTCCCCGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:622087 original size:2 final size:2
Alignment explanation
Indices: 622080--622107 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
622070 TCATTTTCTA
622080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
622108 TTGCAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:622903 original size:12 final size:12
Alignment explanation
Indices: 622886--622914 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
622876 TTAAAAATTG
622886 CATTTTTGATAA
1 CATTTTTGATAA
622898 CATTTTTGATAA
1 CATTTTTGATAA
622910 CATTT
1 CATTT
622915 ATCTGGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (12 bp):
CATTTTTGATAA
Found at i:624433 original size:13 final size:13
Alignment explanation
Indices: 624415--624443 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
624405 ATACAGACTG
624415 CATTGTATCGATA
1 CATTGTATCGATA
624428 CATTGTATCGATA
1 CATTGTATCGATA
624441 CAT
1 CAT
624444 GACCAAATGC
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:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:624478 original size:21 final size:20
Alignment explanation
Indices: 624431--624483 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
624421 ATCGATACAT
**
624431 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
624451 TGCATCGATACATGAAAAGAA
1 TGTATCGATACATGAAAA-AA
624472 TGTATCGATACA
1 TGTATCGATACA
624484 AGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:626028 original size:33 final size:32
Alignment explanation
Indices: 625986--626048 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
625976 CACCCAAATG
* * *
625986 TATCGATACATTATGCTTTGTATTGATACATTA
1 TATCGATACATGAT-CATTGTATCGATACATTA
626019 TATCGATACATGATCATTGTATCGATACAT
1 TATCGATACATGATCATTGTATCGATACAT
626049 GGATAATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (32 bp):
TATCGATACATGATCATTGTATCGATACATTA
Found at i:626032 original size:20 final size:20
Alignment explanation
Indices: 626009--626070 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
625999 TGCTTTGTAT
*
626009 TGATACATTATATCGATACA
1 TGATACATTGTATCGATACA
626029 TGAT-CATTGTATCGATACA
1 TGATACATTGTATCGATACA
*
626048 TGGATA-ATTGTATCAATACA
1 T-GATACATTGTATCGATACA
626068 TGA
1 TGA
626071 AACTGGCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
TGATACATTGTATCGATACA
Found at i:626136 original size:20 final size:20
Alignment explanation
Indices: 626098--626136 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
626088 TTACCACTAT
**
626098 TTGTATCGATACATGGTATA
1 TTGTATCGATACAACGTATA
626118 TTGTATCGATACAACGTAT
1 TTGTATCGATACAACGTAT
626137 CGATACATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (20 bp):
TTGTATCGATACAACGTATA
Found at i:626142 original size:33 final size:33
Alignment explanation
Indices: 626100--626163 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
626090 ACCACTATTT
*
626100 GTATCGATACATGGT-ATATTGTATCGATACAAC
1 GTATCGATACATGATGA-ATTGTATCGATACAAC
626133 GTATCGATACATGATGAATTGTATCGATACA
1 GTATCGATACATGATGAATTGTATCGATACA
626164 TTGCTTCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (33 bp):
GTATCGATACATGATGAATTGTATCGATACAAC
Found at i:634704 original size:13 final size:13
Alignment explanation
Indices: 634686--634712 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
634676 ACATTATGCT
634686 TTGTATCGATACA
1 TTGTATCGATACA
634699 TTGTATCGATACA
1 TTGTATCGATACA
634712 T
1 T
634713 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:634708 original size:33 final size:32
Alignment explanation
Indices: 634666--634731 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
634656 ACACACCTAG
* *
634666 TTGTATCGATACATTATGCTTTGTATCGATACA
1 TTGTATCGATACATGAT-CATTGTATCGATACA
634699 TTGTATCGATACATGATCATTGTATCGATACA
1 TTGTATCGATACATGATCATTGTATCGATACA
634731 T
1 T
634732 GAAACTGGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (32 bp):
TTGTATCGATACATGATCATTGTATCGATACA
Found at i:634721 original size:19 final size:19
Alignment explanation
Indices: 634697--634733 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
634687 TGTATCGATA
634697 CATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
634716 CATTGTATCGATACATGA
1 CATTGTATCGATACATGA
634734 AACTGGCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:634785 original size:19 final size:19
Alignment explanation
Indices: 634761--634825 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
634751 TTACCATTGT
634761 TTGTATCGATACATGGACA
1 TTGTATCGATACATGGACA
634780 TTGTATCG----AT-G-CA
1 TTGTATCGATACATGGACA
634793 TTGTATCGATACATGGACA
1 TTGTATCGATACATGGACA
*
634812 TTGTATCAATACAT
1 TTGTATCGATACAT
634826 TGTACCGATA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:634796 original size:13 final size:13
Alignment explanation
Indices: 634778--634802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
634768 GATACATGGA
634778 CATTGTATCGATG
1 CATTGTATCGATG
634791 CATTGTATCGAT
1 CATTGTATCGAT
634803 ACATGGACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATG
Found at i:634800 original size:32 final size:32
Alignment explanation
Indices: 634761--634860 Score: 148
Period size: 32 Copynumber: 3.1 Consensus size: 32
634751 TTACCATTGT
*
634761 TTGTATCGATACATGGACATTGTATCGATGCA
1 TTGTATCGATACATGGACATTGTATCGATACA
*
634793 TTGTATCGATACATGGACATTGTATCAATACA
1 TTGTATCGATACATGGACATTGTATCGATACA
*
634825 TTGTACCGATACATGAGGA-ATTGTATCGATACA
1 TTGTATCGATACAT--GGACATTGTATCGATACA
634858 TTG
1 TTG
634861 CTTCTAACGA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 43 0.69
33 16 0.26
34 3 0.05
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACATGGACATTGTATCGATACA
Found at i:635138 original size:19 final size:19
Alignment explanation
Indices: 635114--635151 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
635104 GATAAAGTGT
635114 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
635133 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
635152 ATTTAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (19 bp):
TTGAAAAAAAAAAAAAAAA
Found at i:635142 original size:20 final size:20
Alignment explanation
Indices: 635117--635154 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
635107 AAAGTGTTTG
635117 AAAAAAAAAAAAAAAATTGA
1 AAAAAAAAAAAAAAAATTGA
635137 AAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAATT
635155 TAAATGTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.11
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAATTGA
Found at i:635181 original size:21 final size:21
Alignment explanation
Indices: 635157--635213 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
635147 AAAAAATTTA
635157 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
635178 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
635199 AATGTATCGATACAT
1 AATGTATCGATACAT
635214 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:635293 original size:19 final size:19
Alignment explanation
Indices: 635269--635336 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
635259 AATTCAACAA
635269 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
635288 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
635303 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
635320 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
635337 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:635308 original size:13 final size:13
Alignment explanation
Indices: 635290--635314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
635280 ACATAAGTTT
635290 TGTATCGATACAA
1 TGTATCGATACAA
635303 TGTATCGATACA
1 TGTATCGATACA
635315 TAAGTATTGT
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:635312 original size:32 final size:32
Alignment explanation
Indices: 635271--635333 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
635261 TTCAACAATT
*
635271 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
635303 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
635334 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:635394 original size:13 final size:13
Alignment explanation
Indices: 635376--635401 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
635366 CATTTTTCTG
635376 TGTATCGATACAT
1 TGTATCGATACAT
635389 TGTATCGATACAT
1 TGTATCGATACAT
635402 GGATCTTTGT
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
Done.