Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 2 of 208
Found at i:454775 original size:101 final size:102
Alignment explanation
Indices: 454590--454776 Score: 270
Period size: 101 Copynumber: 1.8 Consensus size: 102
454580 AGATCCCATG
* * **
454590 TAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCATGTAAGACCAT
1 TAAGACCATGTCTGGGACATGGCATGGGCATCC---A-ATCACGAGACATCCCATGTAAGACCAT
454655 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCCTA
62 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCCTA
454696 TAAGACCATGTCTGGGACATGGCATGGGCA-CC-ATCACGAGAACATCCCATGTAAGACCATGTC
1 TAAGACCATGTCTGGGACATGGCATGGGCATCCAATCACGAG-ACATCCCATGTAAGACCATGTC
*
454759 TGGGACATGGCTTTGGCA
65 TGGGACATGGCATTGGCA
454777 TGTTATTATC
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
100 7 0.09
101 37 0.49
105 2 0.03
106 29 0.39
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.22
Consensus pattern (102 bp):
TAAGACCATGTCTGGGACATGGCATGGGCATCCAATCACGAGACATCCCATGTAAGACCATGTCT
GGGACATGGCATTGGCACCGAGATGAGAGGTCCCCTA
Found at i:458921 original size:46 final size:45
Alignment explanation
Indices: 458854--459215 Score: 359
Period size: 46 Copynumber: 8.6 Consensus size: 45
458844 TTTGAGTACT
* *
458854 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
458900 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * *
458936 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTATACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
458982 TCTGATCAAGTGAAAAAGTGAT-A-----AGC---GCTAAACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
459018 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
459054 TCTGATCAAGTGAGAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
459100 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* * *
459146 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTATACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
459191 TCTGATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
459216 ATCATACGTA
Statistics
Matches: 274, Mismatches: 17, Indels: 53
0.80 0.05 0.15
Matches are distributed among these distances:
36 89 0.32
37 3 0.01
38 3 0.01
39 1 0.00
40 6 0.02
41 1 0.00
42 4 0.01
43 13 0.05
44 3 0.01
45 22 0.08
46 129 0.47
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:458931 original size:36 final size:36
Alignment explanation
Indices: 458890--459080 Score: 238
Period size: 36 Copynumber: 5.0 Consensus size: 36
458880 GGTAGCTTTA
458890 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
458926 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAA---GT
*
458965 AGCTTTAGCTATACTTATCTGATCAAGTGAAAAAGTGATAAGC
1 -GC--TA-C---ACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
459008 GCTAAACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
459044 GCTATACTTATCTGATCAAGTGAGAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
459080 G
1 G
459081 TTAGCCTTAG
Statistics
Matches: 136, Mismatches: 9, Indels: 20
0.82 0.05 0.12
Matches are distributed among these distances:
36 97 0.71
39 2 0.01
40 4 0.03
42 4 0.03
43 2 0.01
46 27 0.20
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:458991 original size:82 final size:82
Alignment explanation
Indices: 458854--459172 Score: 379
Period size: 82 Copynumber: 3.9 Consensus size: 82
458844 TTTGAGTACT
*
458854 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
458919 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
* *
458936 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTATACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
459001 GATAAGCGCTAAACTTA
66 GATAAGTGCTACACTTA
* *
459018 TCTGATCAAGTGAAAAAGTGATAA---GT-GC--TA--T--ACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
459073 GATAAGTGTTAGCCTTAGCTACACTTA
66 GAT-A-----AG---T-GCTACACTTA
* * * *
459100 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
459165 GATAAGTG
66 GATAAGTG
459173 GTAGCCTAGC
Statistics
Matches: 206, Mismatches: 11, Indels: 40
0.80 0.04 0.16
Matches are distributed among these distances:
72 26 0.13
73 1 0.00
74 1 0.00
76 2 0.01
78 4 0.02
79 2 0.01
82 133 0.65
83 1 0.00
85 2 0.01
86 4 0.02
88 2 0.01
90 1 0.00
91 1 0.00
92 26 0.13
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:459103 original size:118 final size:118
Alignment explanation
Indices: 458890--459124 Score: 398
Period size: 118 Copynumber: 2.0 Consensus size: 118
458880 GGTAGCTTTA
*
458890 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
1 GCTAAACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
* *
458955 GATAAGTGGTAGCTTTAGCTATACTTATCTGATCAAGTGAAAAAGTGATAAGC
66 GATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGC
* * *
459008 GCTAAACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGAGAAAGT
1 GCTAAACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
* *
459073 GATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAG
66 GATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
459125 TGGTAGCCTT
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 109 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (118 bp):
GCTAAACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
GATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGC
Found at i:460228 original size:51 final size:51
Alignment explanation
Indices: 460167--460266 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
460157 AATTATTTAA
460167 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * * * **
460218 AAATATGGATTTCAGAGAAATTTGGAAGGAATTTGAGAGTTAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
460267 GGAAATTTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.26, T:0.28
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:460269 original size:22 final size:23
Alignment explanation
Indices: 460247--460301 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
460237 ATTTGGAAGG
**
460247 AATTTGAGAGTTAATTGAGAGGA
1 AATTTGAGAGGAAATTGAGAGGA
460270 AATTT-AGAGGAAATTGAGAGGA
1 AATTTGAGAGGAAATTGAGAGGA
460292 AATTTGAGAG
1 AATTTGAGAG
460302 AAGATTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (23 bp):
AATTTGAGAGGAAATTGAGAGGA
Found at i:460273 original size:11 final size:11
Alignment explanation
Indices: 460244--460301 Score: 71
Period size: 11 Copynumber: 5.2 Consensus size: 11
460234 GAAATTTGGA
*
460244 AGGAATTTGAG
1 AGGAAATTGAG
**
460255 AGTTAATTGAG
1 AGGAAATTGAG
*
460266 AGGAAATTTAG
1 AGGAAATTGAG
460277 AGGAAATTGAG
1 AGGAAATTGAG
460288 AGGAAATTTGAG
1 AGGAAA-TTGAG
460300 AG
1 AG
460302 AAGATTAGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
11 32 0.82
12 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.26
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:474556 original size:19 final size:20
Alignment explanation
Indices: 474517--474562 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
474507 CTATGCTTAC
474517 TTTAAATTAAAATTTACA-T
1 TTTAAATTAAAATTTACATT
*
474536 TTTAAATTAATTATTTA-ATT
1 TTTAAATTAA-AATTTACATT
474556 TTTAAAT
1 TTTAAAT
474563 ACATAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAAATTAAAATTTACATT
Found at i:479016 original size:31 final size:30
Alignment explanation
Indices: 478976--479046 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
478966 CAAATGCTCA
*
478976 AATC-AATTCGGTAATATATATCCATATAC
1 AATCAAATTCGGCAATATATATCCATATAC
* * *
479005 GAATCAAATTCGGCAGTGTATATCTATATAC
1 -AATCAAATTCGGCAATATATATCCATATAC
479036 ACATCAAATTC
1 A-ATCAAATTC
479047 TACAATGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.14
31 30 0.86
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (30 bp):
AATCAAATTCGGCAATATATATCCATATAC
Found at i:479056 original size:31 final size:31
Alignment explanation
Indices: 478992--479067 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
478982 TTCGGTAATA
* *
478992 TATATCCATATACGAATCAAATTCGGCAGTG
1 TATATCCATATACGAATCAAATTCGACAATG
* *
479023 TATATCTATATAC-ACATCAAATTCTACAATG
1 TATATCCATATACGA-ATCAAATTCGACAATG
*
479054 TATAAACCATATAC
1 TAT-ATCCATATAC
479068 ATTTAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 1 0.03
31 28 0.76
32 8 0.22
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.32
Consensus pattern (31 bp):
TATATCCATATACGAATCAAATTCGACAATG
Found at i:481835 original size:18 final size:18
Alignment explanation
Indices: 481808--481846 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
481798 GAACAACATC
* *
481808 TAAAAATTCAATATATTT
1 TAAAAATTCAACATAGTT
*
481826 TAAAATTTCAACATAGTT
1 TAAAAATTCAACATAGTT
481844 TAA
1 TAA
481847 GTAGTATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAAAATTCAACATAGTT
Found at i:481970 original size:15 final size:15
Alignment explanation
Indices: 481952--481986 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
481942 TTCTCCTTTC
481952 TTTCTTTCCTTCCTT
1 TTTCTTTCCTTCCTT
* *
481967 TTTCTTTTCTTTCTT
1 TTTCTTTCCTTCCTT
481982 TTTCT
1 TTTCT
481987 CCCTGTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTTCCTTCCTT
Found at i:482006 original size:11 final size:10
Alignment explanation
Indices: 481992--482036 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
481982 TTTCTCCCTG
481992 TTTTGTTTCT
1 TTTTGTTTCT
482002 ATTTTGTTTCGT
1 -TTTTGTTTC-T
* *
482014 TTCTATTTCT
1 TTTTGTTTCT
482024 TTTTGTTTCT
1 TTTTGTTTCT
482034 TTT
1 TTT
482037 ATTTCTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 12 0.41
11 16 0.55
12 1 0.03
ACGTcount: A:0.04, C:0.11, G:0.09, T:0.76
Consensus pattern (10 bp):
TTTTGTTTCT
Found at i:482031 original size:16 final size:16
Alignment explanation
Indices: 481990--482033 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
481980 TTTTTCTCCC
481990 TGTTTTGTTTCTATTT
1 TGTTTTGTTTCTATTT
*
482006 TGTTTCGTTTCTATTT
1 TGTTTTGTTTCTATTT
482022 CT-TTTTGTTTCT
1 -TGTTTTGTTTCT
482034 TTTATTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.05, C:0.11, G:0.11, T:0.73
Consensus pattern (16 bp):
TGTTTTGTTTCTATTT
Found at i:482068 original size:7 final size:7
Alignment explanation
Indices: 482056--482118 Score: 58
Period size: 7 Copynumber: 8.6 Consensus size: 7
482046 ATTTACTTAT
482056 TATAATA
1 TATAATA
482063 TATAATA
1 TATAATA
482070 TA-ATATA
1 TATA-ATA
482077 TACTTAATA
1 TA--TAATA
*
482086 -ACTAAGA
1 TA-TAATA
482093 TATAATA
1 TATAATA
482100 TTATAATA
1 -TATAATA
482108 TATAATA
1 TATAATA
482115 TATA
1 TATA
482119 TTTTCAGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
6 1 0.02
7 33 0.70
8 9 0.19
9 3 0.06
10 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (7 bp):
TATAATA
Found at i:482129 original size:7 final size:7
Alignment explanation
Indices: 482119--482143 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
482109 ATAATATATA
482119 TTTTCAG
1 TTTTCAG
482126 TTTTCAG
1 TTTTCAG
482133 TTTTCAG
1 TTTTCAG
482140 TTTT
1 TTTT
482144 ATAAATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (7 bp):
TTTTCAG
Found at i:482388 original size:27 final size:27
Alignment explanation
Indices: 482358--482411 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
482348 TATCTACGAG
482358 TCTGATTTACGGTTACGGAGTCTCGAA
1 TCTGATTTACGGTTACGGAGTCTCGAA
482385 TCTGATTTACGGTTACGGAGTCTCGAA
1 TCTGATTTACGGTTACGGAGTCTCGAA
482412 AATGCACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (27 bp):
TCTGATTTACGGTTACGGAGTCTCGAA
Found at i:483493 original size:18 final size:16
Alignment explanation
Indices: 483461--483494 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
483451 AAAAAAAGCT
483461 ATTTTTTATATTTTTA
1 ATTTTTTATATTTTTA
483477 ATTTATTTATCATTTTTA
1 ATTT-TTTAT-ATTTTTA
483495 TGTTTCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTATATTTTTA
Found at i:483670 original size:19 final size:19
Alignment explanation
Indices: 483630--483672 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
483620 TGTTTTTTCC
* *
483630 ATTTTGAATAATTTTTATA
1 ATTTTCAATAATTTTTAAA
483649 ATTTTCAAT-ATTTTTAGAA
1 ATTTTCAATAATTTTTA-AA
483668 ATTTT
1 ATTTT
483673 TCGTACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTTCAATAATTTTTAAA
Found at i:500182 original size:12 final size:12
Alignment explanation
Indices: 500165--500192 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
500155 AGTATGGAGG
500165 ATCAATGTTAGA
1 ATCAATGTTAGA
500177 ATCAATGTTAGA
1 ATCAATGTTAGA
500189 ATCA
1 ATCA
500193 CATACCCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (12 bp):
ATCAATGTTAGA
Found at i:501019 original size:8 final size:9
Alignment explanation
Indices: 500993--501026 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
500983 ACTAAAGGGG
500993 AAGAAAATA
1 AAGAAAATA
501002 AAGAAAATA
1 AAGAAAATA
501011 AAG-AAATA
1 AAGAAAATA
*
501019 AAAAAAAT
1 AAGAAAAT
501027 TAAATTGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (9 bp):
AAGAAAATA
Found at i:503016 original size:15 final size:15
Alignment explanation
Indices: 502992--503022 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
502982 ATATACATAC
502992 ATTTTCATTTTTTTT
1 ATTTTCATTTTTTTT
*
503007 ATTTTTATTTTTTTT
1 ATTTTCATTTTTTTT
503022 A
1 A
503023 CTTTATTATA
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:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (15 bp):
ATTTTCATTTTTTTT
Found at i:509376 original size:89 final size:89
Alignment explanation
Indices: 509222--509985 Score: 1174
Period size: 89 Copynumber: 8.6 Consensus size: 89
509212 GTTGAAATAT
* * * *
509222 AACAGATATTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATA
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
** *
509287 CTGGTGGCGAAACAGATCAAAGAA
66 CTGGTGGCGAAGTAGATCGAAGAA
** * * * *
509311 AGTAGATATTGTCTTCACGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATA
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
*
509376 CTGGTGGCGAAGCAGATCGAAGAA
66 CTGGTGGCGAAGTAGATCGAAGAA
509400 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AAGCAGATCTTGTCTTCCCAT
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA-CAGATCTTGTCTTCCCAT
509464 ACTGGTGGCGAAGTAGATCGAAGAA
65 ACTGGTGGCGAAGTAGATCGAAGAA
* **
509489 AACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGTAGATCTTGTCTTCCCATA
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
509554 CTGGTGGCGAAGTAGATCGAAGAA
66 CTGGTGGCGAAGTAGATCGAAGAA
* * *
509578 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGA-AACAAATCTTGTCTCCCCATA
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
* *
509642 CTGGTGGTGGAGTAGATCGAAGAA
66 CTGGTGGCGAAGTAGATCGAAGAA
* *
509666 AATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATA
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
509731 CTGGTGGCGAAGTAGATCGAAGAA
66 CTGGTGGCGAAGTAGATCGAAGAA
* * * *
509755 AACGGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGAAAACAAATCTTGTCTTCCCATA
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
*
509820 CTGGTGGCGAAGCAGATCGAAGAA
66 CTGGTGGCGAAGTAGATCGAAGAA
* *
509844 AACATATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATA
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
509909 CTGGTGGCGAAGTAGATCGAAGAA
66 CTGGTGGCGAAGTAGATCGAAGAA
* * * *
509933 AGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGA-AACCAGATCT
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA-CAGATCT
509986 ATCTCCCTGG
Statistics
Matches: 623, Mismatches: 48, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
88 84 0.13
89 538 0.86
90 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (89 bp):
AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
CTGGTGGCGAAGTAGATCGAAGAA
Found at i:509932 original size:355 final size:355
Alignment explanation
Indices: 509222--509978 Score: 1208
Period size: 355 Copynumber: 2.1 Consensus size: 355
509212 GTTGAAATAT
* * * * *
509222 AACAGATATTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATA
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AACAAATCTTGCCTCCCCATA
* *
509287 CTGGTGGCGAAACAGATCAAAGAAAGTAGATATTGTCTTCACGTACTGGCGTGAAGTAGATCAGA
65 CTGGTGGCGAAACAGATCAAAGAAAATAGATATTGTCTTCACGTACTGGCGTGAAGTAGATCAAA
509352 GATAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCA
130 GATAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCA
* * * *
509417 TGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
195 TGTACTGGCATGAAGTAGATCAAAGAAAACAAATCTTGTCTTCCCATACTGGTGGCGAAGCAGAT
* * **
509482 CGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGTAGATCTTGTCT
260 CGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCT
509547 TCCCATACTGGTGGCGAAGTAGATCGAAGAA
325 TCCCATACTGGTGGCGAAGTAGATCGAAGAA
* *
509578 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGAAACAAATCTTGTCTCCCCATAC
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAACAAATCTTGCCTCCCCATAC
* * ** * * *
509643 TGGTGGTGGAGTAGATCGAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAG
66 TGGTGGCGAAACAGATCAAAGAAAATAGATATTGTCTTCACGTACTGGCGTGAAGTAGATCAAAG
* * * *
509708 ATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACGGATCTTGTCTTCAT
131 ATAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCAT
509773 GTACTGGCATGAAGTAGATCAAAGAAAACAAATCTTGTCTTCCCATACTGGTGGCGAAGCAGATC
196 GTACTGGCATGAAGTAGATCAAAGAAAACAAATCTTGTCTTCCCATACTGGTGGCGAAGCAGATC
*
509838 GAAGAAAACATATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTT
261 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTT
509903 CCCATACTGGTGGCGAAGTAGATCGAAGAA
326 CCCATACTGGTGGCGAAGTAGATCGAAGAA
* * * *
509933 AGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGAAAC
1 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAC
509979 CAGATCTATC
Statistics
Matches: 367, Mismatches: 34, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
355 327 0.89
356 40 0.11
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (355 bp):
AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAACAAATCTTGCCTCCCCATAC
TGGTGGCGAAACAGATCAAAGAAAATAGATATTGTCTTCACGTACTGGCGTGAAGTAGATCAAAG
ATAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCAT
GTACTGGCATGAAGTAGATCAAAGAAAACAAATCTTGTCTTCCCATACTGGTGGCGAAGCAGATC
GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTT
CCCATACTGGTGGCGAAGTAGATCGAAGAA
Found at i:510062 original size:44 final size:44
Alignment explanation
Indices: 509966--510063 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
509956 GGTGTGAAGT
** *
509966 AGATCGAAGA-AACCAGATCTATCTCCCTGGGCAGCAGTGGAAT
1 AGATCGAAGATAACCAGATCTATCTCCCTAAGCAGCAGTGGAAC
* * * * *
510009 AGATTGAAGATTA-CAGATCTTATCTCCTTAAGCAGTAGTGGAGC
1 AGATCGAAGATAACCAGATC-TATCTCCCTAAGCAGCAGTGGAAC
510053 AGATCGAAGAT
1 AGATCGAAGAT
510064 GGTGGATTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
43 15 0.34
44 29 0.66
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (44 bp):
AGATCGAAGATAACCAGATCTATCTCCCTAAGCAGCAGTGGAAC
Found at i:511877 original size:12 final size:13
Alignment explanation
Indices: 511852--511880 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
511842 ATAGTTTATA
511852 TATACTTACATTT
1 TATACTTACATTT
511865 TATACTT-CATTT
1 TATACTTACATTT
511877 TATA
1 TATA
511881 TATACCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (13 bp):
TATACTTACATTT
Found at i:512019 original size:15 final size:15
Alignment explanation
Indices: 511995--512025 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
511985 ATATACATAC
511995 ATTTTCATTTTTTTT
1 ATTTTCATTTTTTTT
*
512010 ATTTTTATTTTTTTT
1 ATTTTCATTTTTTTT
512025 A
1 A
512026 CTTTATTATA
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:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (15 bp):
ATTTTCATTTTTTTT
Found at i:513718 original size:30 final size:30
Alignment explanation
Indices: 513682--513747 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
513672 GACAGCTAAA
513682 GCTATCCTTGCCTAATCACATGTTAGAATT
1 GCTATCCTTGCCTAATCACATGTTAGAATT
* *
513712 GCTATCCTTGCCTGATCGCATGTTAGAATT
1 GCTATCCTTGCCTAATCACATGTTAGAATT
*
513742 GTTATC
1 GCTATC
513748 TTAAAGTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (30 bp):
GCTATCCTTGCCTAATCACATGTTAGAATT
Found at i:518456 original size:15 final size:15
Alignment explanation
Indices: 518436--518479 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
518426 GGTTAATAGG
*
518436 AAAGAAAAAAAGGGA
1 AAAGAAAAAAAGGAA
*
518451 AAAGAAAAGAAAAGAA
1 AAAGAAAA-AAAGGAA
518467 AAAGAAAGAAAAG
1 AAAGAAA-AAAAG
518480 AGACGAGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 8 0.33
16 15 0.62
17 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAGGAA
Found at i:518480 original size:15 final size:15
Alignment explanation
Indices: 518436--518480 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
518426 GGTTAATAGG
*
518436 AAAGAAA-AAAAGGGA
1 AAAGAAAGAAAA-GAA
518451 AAAGAAAAGAAAAGAA
1 AAAG-AAAGAAAAGAA
518467 AAAGAAAGAAAAGA
1 AAAGAAAGAAAAGA
518481 GACGAGACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 14 0.52
16 9 0.33
17 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAGAA
Found at i:520710 original size:45 final size:45
Alignment explanation
Indices: 520641--520740 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
520631 TAACGGTAGT
* *
520641 AGTAATAGTAACAGTATTCAACACACAAAGT-TCTGGATCTGTAAC
1 AGTAATAGTAACAGTATTCAACACACAAAGTATC-GAATCAGTAAC
* * *
520686 AGTAATGGTAACAGTGTTCGACACACAAAGTATCGAATCAGTAAC
1 AGTAATAGTAACAGTATTCAACACACAAAGTATCGAATCAGTAAC
*
520731 AGTAACAGTA
1 AGTAATAGTA
520741 GTCGGCACAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 45 0.96
46 2 0.04
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (45 bp):
AGTAATAGTAACAGTATTCAACACACAAAGTATCGAATCAGTAAC
Found at i:522862 original size:5 final size:5
Alignment explanation
Indices: 522852--522878 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
522842 ATAATTTCAA
522852 TTGCT TTGCT TTGCT TTGCT TTGCT TT
1 TTGCT TTGCT TTGCT TTGCT TTGCT TT
522879 TTGTTTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.19, T:0.63
Consensus pattern (5 bp):
TTGCT
Found at i:541455 original size:18 final size:17
Alignment explanation
Indices: 541412--541455 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
541402 CATGTTAAGC
*
541412 ATATAATATTTTATATT
1 ATATAATTTTTTATATT
* *
541429 ATGTTATTTTTATATATT
1 ATATAATTTTT-TATATT
541447 ATATAATTT
1 ATATAATTT
541456 ATAACACAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATATAATTTTTTATATT
Found at i:542200 original size:13 final size:13
Alignment explanation
Indices: 542182--542212 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
542172 AAAAACAAAA
542182 TTTATACTCAACT
1 TTTATACTCAACT
*
542195 TTTATAGTCAACT
1 TTTATACTCAACT
542208 TTTAT
1 TTTAT
542213 GGGAAAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.03, T:0.52
Consensus pattern (13 bp):
TTTATACTCAACT
Found at i:546392 original size:3 final size:3
Alignment explanation
Indices: 546384--546410 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
546374 AGGGTGAAAT
546384 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
546411 GGAATAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:551645 original size:18 final size:18
Alignment explanation
Indices: 551611--551649 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
551601 AGGATATAAT
*
551611 AAAAATATTTAAGAATTA
1 AAAAAGATTTAAGAATTA
551629 AAAAAGATTATAA-AATTA
1 AAAAAGATT-TAAGAATTA
551647 AAA
1 AAA
551650 TATTCTATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAAGATTTAAGAATTA
Found at i:557111 original size:24 final size:24
Alignment explanation
Indices: 557084--557134 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
557074 AATACAATAT
557084 TACCATAGCAAAAAAACTTACACA
1 TACCATAGCAAAAAAACTTACACA
557108 TACCATAGCAAAAAAACTTACACA
1 TACCATAGCAAAAAAACTTACACA
557132 TAC
1 TAC
557135 TTTTACCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.53, C:0.25, G:0.04, T:0.18
Consensus pattern (24 bp):
TACCATAGCAAAAAAACTTACACA
Found at i:558767 original size:19 final size:20
Alignment explanation
Indices: 558722--558769 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
558712 TAGGTACGAT
558722 AATTTTTATAATTCTTTTAC
1 AATTTTTATAATTCTTTTAC
*
558742 AAATTTTATAATTC-TTTAC
1 AATTTTTATAATTCTTTTAC
*
558761 ATTTTTTAT
1 AATTTTTAT
558770 CATTTTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTTTTATAATTCTTTTAC
Found at i:558880 original size:28 final size:27
Alignment explanation
Indices: 558849--558909 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
558839 TTTCTTTTTA
558849 ATTTTTAATAAAATTAAATATTTCTTAT
1 ATTTTTAATAAAATTAAAT-TTTCTTAT
* * *
558877 ATTTTTATTAAAATTTAATTTTTTTAT
1 ATTTTTAATAAAATTAAATTTTCTTAT
558904 -TTTTTA
1 ATTTTTA
558910 TCATTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 6 0.20
27 7 0.23
28 17 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTTTTAATAAAATTAAATTTTCTTAT
Found at i:559834 original size:54 final size:55
Alignment explanation
Indices: 559752--559901 Score: 203
Period size: 54 Copynumber: 2.7 Consensus size: 55
559742 AGACAGGGCG
*
559752 TTAAGACTATGAACTATCATCAGTTTTGCTCTAAAGCTGAACCA-AAGTAGAGCA
1 TTAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAGAAGTAGAGCA
* *
559806 TTAAGACTACGAACTAACATCAGTTTTGCTCTAAAGCTGAAGCAGAAGTAGAGCA
1 TTAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAGAAGTAGAGCA
** * * * *
559861 AGACGACAATGAACTAACATCAGTTTAGCTCCAAAGACTGA
1 TTAAGACTATGAACTAACATCAGTTTTGCTCTAAAG-CTGA
559902 CAGATTACTT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 41 0.49
55 39 0.46
56 4 0.05
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (55 bp):
TTAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAGAAGTAGAGCA
Found at i:564656 original size:30 final size:30
Alignment explanation
Indices: 564622--564682 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
564612 GATATGTTAT
*
564622 ACAACATTCTTGGGTCTTATATAAACCTAC
1 ACAACATTATTGGGTCTTATATAAACCTAC
564652 ACAACATTATTGGGTCTTATATAAACCTAC
1 ACAACATTATTGGGTCTTATATAAACCTAC
564682 A
1 A
564683 AATGTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (30 bp):
ACAACATTATTGGGTCTTATATAAACCTAC
Found at i:564751 original size:15 final size:15
Alignment explanation
Indices: 564733--564764 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
564723 CAACAACCTA
*
564733 AAAATAAAAAAATTT
1 AAAATAAAAAAACTT
564748 AAAATAAAAAAACTT
1 AAAATAAAAAAACTT
564763 AA
1 AA
564765 TTGCACTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAATAAAAAAACTT
Found at i:565716 original size:20 final size:19
Alignment explanation
Indices: 565689--565733 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
565679 TTTTATGATT
565689 TTAA-AAAAATTCTATATTC
1 TTAATAAAAATTCTAT-TTC
*
565708 TTAATAAAATTTCTATTTC
1 TTAATAAAAATTCTATTTC
*
565727 TTTATAA
1 TTAATAA
565734 TTTTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATAAAAATTCTATTTC
Found at i:567054 original size:12 final size:12
Alignment explanation
Indices: 567039--567063 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
567029 CATTAGGCTA
567039 GAATTTAGATAG
1 GAATTTAGATAG
567051 GAATTTAGATAG
1 GAATTTAGATAG
567063 G
1 G
567064 TAGTGCGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (12 bp):
GAATTTAGATAG
Found at i:570777 original size:151 final size:151
Alignment explanation
Indices: 570503--570804 Score: 541
Period size: 151 Copynumber: 2.0 Consensus size: 151
570493 GAATGTAAGT
*
570503 TCGAGTGTCTTAAATCACATTATCTTCTCATTCAATGGCTAGAGAGAGGTTATACCTAATTCTAG
1 TCGAGTGTCTTAAATCACATTATCTTCTCATTCAATGGCTAGAGAGAGGTTATACCTAATTCTAA
*
570568 GTATTGTAATTACAAGTTGTGAATTGACCCAACTTATAAAGACTAAGAGTCTATGAACTTTGGAA
66 GTATTGTAATTACAAATTGTGAATTGACCCAACTTATAAAGACTAAGAGTCTATGAACTTTGGAA
570633 AACACATTGAAACTAAAACAA
131 AACACATTGAAACTAAAACAA
* * * *
570654 TCGAGTGTCTTAAATCGCATTGTCTTCTCATTCAATGGCTAGAGAGGGGTTATACCTAATTTTAA
1 TCGAGTGTCTTAAATCACATTATCTTCTCATTCAATGGCTAGAGAGAGGTTATACCTAATTCTAA
*
570719 GTATTGTAATTATAAATTGTGAATTGACCCAACTTATAAAGACTAAGAGTCTATGAACTTTGGAA
66 GTATTGTAATTACAAATTGTGAATTGACCCAACTTATAAAGACTAAGAGTCTATGAACTTTGGAA
570784 AACACATTGAAACTAAAACAA
131 AACACATTGAAACTAAAACAA
570805 CTAGTCGGAA
Statistics
Matches: 144, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
151 144 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (151 bp):
TCGAGTGTCTTAAATCACATTATCTTCTCATTCAATGGCTAGAGAGAGGTTATACCTAATTCTAA
GTATTGTAATTACAAATTGTGAATTGACCCAACTTATAAAGACTAAGAGTCTATGAACTTTGGAA
AACACATTGAAACTAAAACAA
Found at i:572893 original size:5 final size:5
Alignment explanation
Indices: 572883--572915 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
572873 TAGGTAACCC
572883 AACAA AACAA AACAA AACAA AACAA AACAA AAC
1 AACAA AACAA AACAA AACAA AACAA AACAA AAC
572916 CTCCTGTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:579200 original size:24 final size:24
Alignment explanation
Indices: 579168--579216 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
579158 ATAAGTGATA
579168 GGAATATCATCAACAACGGGAAGG
1 GGAATATCATCAACAACGGGAAGG
579192 GGAATATCATCAACAACGGGAAGG
1 GGAATATCATCAACAACGGGAAGG
579216 G
1 G
579217 CGTAGGCCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.31, T:0.12
Consensus pattern (24 bp):
GGAATATCATCAACAACGGGAAGG
Found at i:579420 original size:21 final size:21
Alignment explanation
Indices: 579394--579434 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
579384 ATCTGCTCAA
* *
579394 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
579415 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
579435 TTGGTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:584732 original size:29 final size:27
Alignment explanation
Indices: 584667--584733 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 27
584657 TTTTTGGGTA
584667 AAATTATTATAAAAGTCATCTAATTATG
1 AAATT-TTATAAAAGTCATCTAATTATG
** *
584695 AAAAGTTATAAAATGATCATCTAATTATT
1 AAATTTTATAAAA-G-TCATCTAATTATG
*
584724 TAATTTTATA
1 AAATTTTATA
584734 TTTTTTGGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 8 0.26
28 4 0.13
29 19 0.61
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (27 bp):
AAATTTTATAAAAGTCATCTAATTATG
Found at i:590864 original size:16 final size:16
Alignment explanation
Indices: 590839--590891 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
590829 TTGGTTCGCT
*
590839 GTAATAGAATAGAGGC
1 GTAATGGAATAGAGGC
*
590855 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
590871 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
590887 GTAAT
1 GTAAT
590892 AGGTAATTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.40, C:0.06, G:0.32, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:590960 original size:44 final size:46
Alignment explanation
Indices: 590871--590961 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
590861 GAATAGATGC
*
590871 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
590917 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
590961 G
1 G
590962 GAACAGAGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 20 0.45
45 3 0.07
46 21 0.48
ACGTcount: A:0.26, C:0.04, G:0.31, T:0.38
Consensus pattern (46 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
Found at i:590962 original size:39 final size:44
Alignment explanation
Indices: 590871--590977 Score: 134
Period size: 46 Copynumber: 2.5 Consensus size: 44
590861 GAATAGATGC
*
590871 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--AT
590917 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
* *
590957 G-AATGGAACAGAGGTGTAATA
1 GTAATGGAATAGAGGCGTAATA
590978 ACATAAGGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
39 17 0.30
40 2 0.04
43 1 0.02
44 13 0.23
45 3 0.05
46 21 0.37
ACGTcount: A:0.29, C:0.05, G:0.31, T:0.36
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
Found at i:591140 original size:15 final size:15
Alignment explanation
Indices: 591120--591158 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
591110 CATAATTGTT
591120 ATAAAATATAATTTA
1 ATAAAATATAATTTA
591135 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
591152 ATAAAAT
1 ATAAAAT
591159 TTTAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:591147 original size:17 final size:17
Alignment explanation
Indices: 591125--591158 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
591115 TTGTTATAAA
591125 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
591142 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
591159 TTTAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:591281 original size:17 final size:17
Alignment explanation
Indices: 591241--591274 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
591231 TTATTATTAA
591241 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
591258 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
591275 TGTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:591328 original size:117 final size:116
Alignment explanation
Indices: 591105--591593 Score: 791
Period size: 117 Copynumber: 4.3 Consensus size: 116
591095 TTAATCATAT
* * *
591105 TTTAACATAATTGTTATAAAATATAATTTAATAAAATATATAATTTAATAAAATTTTAATAAATA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTTTAATAAATA
*
591170 TTCTTATATGAATTTACTAATAAAATCATAATATATGATACTAAAATATAA
66 TTCTTATATGAATTTACTAATAAAATCATAATATATAATACTAAAATATAA
591221 TTTAAAATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTGTTAATAAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATT-TTAATAAAT
591286 ATTCTTATATGAATTTACTAATAAAATCATAATATATAATACTAAAATATAA
65 ATTCTTATATGAATTTACTAATAAAATCATAATATATAATACTAAAATATAA
* * *
591338 TTTAACATAATTGTTATAAAATATAATTTAATAAAATATATAATTTAATAAAATTGTTAATAAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATT-TTAATAAAT
591403 ATTCTTATATGAATTTACTAATAAAATCATAATATATAATACTAAAATATAA
65 ATTCTTATATGAATTTACTAATAAAATCATAATATATAATACTAAAATATAA
*
591455 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAA--TT-CT---T
1 TTTAAAATAATTATTATTAAATATAATTTAATAA-AATATATAATTTAATAAAATTTTAATAAAT
591514 ATTCTTATATGAATTTAC---TAAAATCATAATATATAATACTATAAAATATAA
65 ATTCTTATATGAATTTACTAATAAAATCATAATATATAATAC--TAAAATATAA
591565 TTT-AAATAATTATTATTAAATATAATTTA
1 TTTAAAATAATTATTATTAAATATAATTTA
591594 TAATCTACTT
Statistics
Matches: 358, Mismatches: 11, Indels: 15
0.93 0.03 0.04
Matches are distributed among these distances:
108 21 0.06
109 26 0.07
110 13 0.04
111 19 0.05
114 1 0.00
115 2 0.01
116 52 0.15
117 205 0.57
118 19 0.05
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (116 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTTTAATAAATA
TTCTTATATGAATTTACTAATAAAATCATAATATATAATACTAAAATATAA
Found at i:591373 original size:15 final size:15
Alignment explanation
Indices: 591353--591391 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
591343 CATAATTGTT
591353 ATAAAATATAATTTA
1 ATAAAATATAATTTA
591368 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
591385 ATAAAAT
1 ATAAAAT
591392 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:591398 original size:17 final size:17
Alignment explanation
Indices: 591358--591391 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
591348 TTGTTATAAA
591358 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
591375 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
591392 TGTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:591463 original size:20 final size:21
Alignment explanation
Indices: 591424--591463 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
591414 AATTTACTAA
*
591424 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
591445 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
591464 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:591476 original size:26 final size:28
Alignment explanation
Indices: 591431--591510 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
591421 TAATAAAATC
591431 ATAATATATAATACTAAAATATAATTTAA-A
1 ATAATATATAAT--T-AAATATAATTTAATA
*
591461 ATAAT-TATTATTAAATATAATTTAATA
1 ATAATATATAATTAAATATAATTTAATA
* *
591488 ATAATATATAATTTAATAAAATT
1 ATAATATATAATTAAATATAATT
591511 CTTATTCTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 13 0.30
27 7 0.16
28 14 0.32
29 5 0.11
30 5 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
ATAATATATAATTAAATATAATTTAATA
Found at i:591543 original size:44 final size:41
Alignment explanation
Indices: 591208--591543 Score: 137
Period size: 43 Copynumber: 8.3 Consensus size: 41
591198 TAATATATGA
591208 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
1 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
* * *
591249 TAATAAAATATATAATTTAATAA-AATTGTTAATAAATAT--TCT
1 TACT-AAA-ATATAATTTAA-AATAATTATTATTAAATATAAT-T
* * * *
591291 TA-T---AT-GAATTTACTAATAA-AATCA-TAATATATAA--
1 TACTAAAATATAATTTA-AAATAATTATTATTAA-ATATAATT
* * *
591325 TACTAAAATATAATTTAACATAATTGTTATAAAATATAATT
1 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
* * *
591366 TAATAAAATATATAATTTAATAA-AATTGTTAATAAATAT--TCT
1 TACT-AAA-ATATAATTTAA-AATAATTATTATTAAATATAAT-T
* * * *
591408 TA-T---AT-GAATTTACTAATAA-AATCA-TAATATATAA--
1 TACTAAAATATAATTTA-AAATAATTATTATTAA-ATATAATT
591442 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
1 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
* * **
591483 TAATAATAATATATAATTTAATAA-AATTCTTATTCTTATATGAATT
1 TACT-A-AA-ATATAATTTAA-AATAATTATTATT-AAATAT-AATT
591529 TACTAAAATCATAAT
1 TACTAAAAT-ATAAT
591544 ATATAATACT
Statistics
Matches: 219, Mismatches: 33, Indels: 83
0.65 0.10 0.25
Matches are distributed among these distances:
34 10 0.05
35 30 0.14
36 8 0.04
38 13 0.06
39 29 0.13
40 5 0.02
41 13 0.06
42 13 0.06
43 54 0.25
44 30 0.14
45 7 0.03
46 7 0.03
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (41 bp):
TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
Found at i:591589 original size:32 final size:32
Alignment explanation
Indices: 591553--591616 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
591543 TATATAATAC
*
591553 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
** ** *
591585 TATAATTTATAATCTACTTTATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
591617 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATCTAAATAATTATTATTAAA
Found at i:597462 original size:26 final size:25
Alignment explanation
Indices: 597412--597463 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
597402 GCCGTTCGAA
597412 ATATATAAAAATTTAAAAATCTAAAT
1 ATATATAAAAATTTAAAAA-CTAAAT
*
597438 ATATATTAAAACTTTATAAAA-TAAAT
1 ATATA-TAAAAATTTA-AAAACTAAAT
597464 TTTCAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 10 0.43
27 9 0.39
28 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATATAAAAATTTAAAAACTAAAT
Found at i:597734 original size:23 final size:23
Alignment explanation
Indices: 597691--597734 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
597681 GAATTTCAAT
* *
597691 AAATTTTTATTTTTTACTTTTTG
1 AAATTTTTACTTTATACTTTTTG
597714 AAATTTTTAACTTTATA-TTTT
1 AAATTTTT-ACTTTATACTTTT
597735 GTTTATGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (23 bp):
AAATTTTTACTTTATACTTTTTG
Found at i:599731 original size:23 final size:23
Alignment explanation
Indices: 599701--599746 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
599691 TTAAGTACTT
599701 AATTTTCACTTTTACAAATTGCC
1 AATTTTCACTTTTACAAATTGCC
*
599724 AATTTTCACTTTTGCAAATTGCC
1 AATTTTCACTTTTACAAATTGCC
599747 TCCATCGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (23 bp):
AATTTTCACTTTTACAAATTGCC
Found at i:601070 original size:20 final size:20
Alignment explanation
Indices: 601045--601094 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
601035 TGGCTTAAAA
601045 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
601065 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
601082 GTGGTAGTGGATT
1 TTGGTAGTGGATT
601095 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:605709 original size:20 final size:20
Alignment explanation
Indices: 605684--605733 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
605674 TGGCTTAAAA
605684 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
605704 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
605721 GTGGTAGTGGATT
1 TTGGTAGTGGATT
605734 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:625150 original size:15 final size:15
Alignment explanation
Indices: 625132--625174 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
625122 TTTTAAAATT
625132 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
* **
625147 TAAAAATTTTAAAAA
1 TAAAAAATAAAAAAA
625162 TAAAAATATAAAA
1 TAAAAA-ATAAAA
625175 TTAAATTTCA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAAAATAAAAAAA
Found at i:625160 original size:23 final size:23
Alignment explanation
Indices: 625126--625174 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
625116 ATTTAATTTT
625126 AAAATTTAAAAAATAAAAAAATA
1 AAAATTTAAAAAATAAAAAAATA
* *
625149 AAAATTTTAAAAATAAAAATATA
1 AAAATTTAAAAAATAAAAAAATA
625172 AAA
1 AAA
625175 TTAAATTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAATTTAAAAAATAAAAAAATA
Found at i:627599 original size:89 final size:89
Alignment explanation
Indices: 627502--627680 Score: 358
Period size: 89 Copynumber: 2.0 Consensus size: 89
627492 AAATTTTTAA
627502 TATATTTTTTATTTTAACGATTTATTTAATCGATTTAATGGCTTGACTGGTTCGACTATTAATCT
1 TATATTTTTTATTTTAACGATTTATTTAATCGATTTAATGGCTTGACTGGTTCGACTATTAATCT
627567 ATTCAGAAAATCTGGCTAAATATT
66 ATTCAGAAAATCTGGCTAAATATT
627591 TATATTTTTTATTTTAACGATTTATTTAATCGATTTAATGGCTTGACTGGTTCGACTATTAATCT
1 TATATTTTTTATTTTAACGATTTATTTAATCGATTTAATGGCTTGACTGGTTCGACTATTAATCT
627656 ATTCAGAAAATCTGGCTAAATATT
66 ATTCAGAAAATCTGGCTAAATATT
627680 T
1 T
627681 CTCACGCTTC
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.46
Consensus pattern (89 bp):
TATATTTTTTATTTTAACGATTTATTTAATCGATTTAATGGCTTGACTGGTTCGACTATTAATCT
ATTCAGAAAATCTGGCTAAATATT
Found at i:628253 original size:8 final size:9
Alignment explanation
Indices: 628234--628258 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
628224 TCTTTATTGA
628234 TTTAAAATT
1 TTTAAAATT
628243 TTTAAAATT
1 TTTAAAATT
628252 TTTAAAA
1 TTTAAAA
628259 GACCTAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAAAATT
Found at i:635264 original size:3 final size:3
Alignment explanation
Indices: 635256--635337 Score: 55
Period size: 3 Copynumber: 28.3 Consensus size: 3
635246 TGTTATTAAT
* * * **
635256 TTA TTA TTA TAA TTA TAA TTA TAA TTA TTAA TTA TTA TTA TGG TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
* * *
635301 TT- TTA TT- TAA ATA TTA TTA TTA ATA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
635338 GAAATAAAAT
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
2 7 0.12
3 50 0.83
4 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:635287 original size:19 final size:20
Alignment explanation
Indices: 635248--635296 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
635238 TGAGATTTTG
*
635248 TTATTAATTTATTATTA-TAA
1 TTATTAA-TTATAATTATTAA
635268 TTA-TAATTATAATTATTAA
1 TTATTAATTATAATTATTAA
635287 TTATT-ATTAT
1 TTATTAATTAT
635297 GGTTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 8 0.31
19 14 0.54
20 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTAATTATAATTATTAA
Found at i:635469 original size:3 final size:3
Alignment explanation
Indices: 635461--635499 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
635451 ATGAATTAAA
*
635461 TAT TAT TAT T-T TAT TAT TAT T-T TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
635500 ACTAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:635476 original size:8 final size:9
Alignment explanation
Indices: 635461--635499 Score: 55
Period size: 8 Copynumber: 4.6 Consensus size: 9
635451 ATGAATTAAA
635461 TATTATTAT
1 TATTATTAT
635470 T-TTATTAT
1 TATTATTAT
635478 TATT-TTAT
1 TATTATTAT
*
635486 TATTAATAT
1 TATTATTAT
635495 TATTA
1 TATTA
635500 ACTAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
8 16 0.59
9 11 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTATTAT
Found at i:635477 original size:11 final size:11
Alignment explanation
Indices: 635461--635490 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
635451 ATGAATTAAA
635461 TATTATTATTT
1 TATTATTATTT
635472 TATTATTATTT
1 TATTATTATTT
635483 TATTATTA
1 TATTATTA
635491 ATATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTATTT
Found at i:635478 original size:14 final size:15
Alignment explanation
Indices: 635461--635499 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
635451 ATGAATTAAA
635461 TATTATTATT-TTAT
1 TATTATTATTATTAT
635475 TATTATT-TTATTAT
1 TATTATTATTATTAT
*
635489 TAATATTATTA
1 TATTATTATTA
635500 ACTAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTATTATTATTAT
Found at i:635907 original size:17 final size:18
Alignment explanation
Indices: 635885--635918 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
635875 GTAATGAGTT
635885 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
635902 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
635919 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:636335 original size:19 final size:19
Alignment explanation
Indices: 636311--636347 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
636301 ATCGGGCTTC
636311 GTCGGATATAGTTAGCATA
1 GTCGGATATAGTTAGCATA
636330 GTCGGATATAGTTAGCAT
1 GTCGGATATAGTTAGCAT
636348 GCCATAGGAT
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:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (19 bp):
GTCGGATATAGTTAGCATA
Found at i:638288 original size:23 final size:23
Alignment explanation
Indices: 638262--638312 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
638252 TGTTATTGAT
638262 CAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
*
638285 CAGTGGTAGCTTCGGCTACATAT
1 CAGTGGTAGCTTCGGCTACATAA
638308 CAGTG
1 CAGTG
638313 TTGCACTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:640478 original size:18 final size:18
Alignment explanation
Indices: 640379--640478 Score: 71
Period size: 18 Copynumber: 5.3 Consensus size: 18
640369 GATAATGATC
* *
640379 AAATTTAGCTAAAAATA-
1 AAATTTAACAAAAAATAT
640396 ATAATTTAACAAAAAATAT
1 A-AATTTAACAAAAAATAT
*
640415 AAATGTTAA-AAATTAAATTT
1 AAAT-TTAACAAA--AAATAT
640435 AATATTATACCACAAAAAA-AT
1 AA-ATT-TA--ACAAAAAATAT
*
640456 TAATTTAACAAAAAATAT
1 AAATTTAACAAAAAATAT
640474 AAATT
1 AAATT
640479 AAAAATTAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
17 9 0.14
18 26 0.39
19 7 0.11
20 11 0.17
21 6 0.09
22 3 0.05
23 1 0.02
24 3 0.05
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (18 bp):
AAATTTAACAAAAAATAT
Found at i:646942 original size:19 final size:19
Alignment explanation
Indices: 646903--646942 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
646893 TTTTGAGCAT
646903 AAAATAAAATAGTTTTAAA
1 AAAATAAAATAGTTTTAAA
646922 AAAATTAAAATCA-TTTTAAA
1 AAAA-TAAAAT-AGTTTTAAA
646942 A
1 A
646943 CTTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 14 0.74
21 1 0.05
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAATAAAATAGTTTTAAA
Found at i:654838 original size:101 final size:100
Alignment explanation
Indices: 654699--654927 Score: 350
Period size: 101 Copynumber: 2.3 Consensus size: 100
654689 TGAATTGACG
** *
654699 GATAAGACCATAACTGGGTTATGGCATTATGAAAGTAAGATCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACT-GGTTATGGCACGATGAAAGTAAGACCATGGTTGGACCATGGCAGTGTTT
* *
654764 ATATATAAGATCATAGTTGGGCTATGACATTCTAAT
65 ATATATAAGACCATAGCTGGGCTATGACATTCTAAT
*
654800 GATAAGACCATAACTAGGTTATGGCACGATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACT-GGTTATGGCACGATGAAAGTAAGACCATGGTTGGACCATGGCAGTGTTT
* * *
654865 ATATGTAAGACCATAGCTGGGCTATGACATTTTGAT
65 ATATATAAGACCATAGCTGGGCTATGACATTCTAAT
654901 GATAAGACCATAACTGGTTTATGGCAC
1 GATAAGACCATAACTGG-TTATGGCAC
654928 TACGAATGTA
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
100 2 0.02
101 115 0.98
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29
Consensus pattern (100 bp):
GATAAGACCATAACTGGTTATGGCACGATGAAAGTAAGACCATGGTTGGACCATGGCAGTGTTTA
TATATAAGACCATAGCTGGGCTATGACATTCTAAT
Found at i:660920 original size:35 final size:34
Alignment explanation
Indices: 660881--660950 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 34
660871 ATGCTGATAA
660881 GCCACTTAAATAAATCTAAATCCCAATATCTATTT
1 GCCACTTAAATAAATCTAAATCCCAATATCT-TTT
*
660916 GCCACTTAAATAAATTTAAATCCCAATATCTTTT
1 GCCACTTAAATAAATCTAAATCCCAATATCTTTT
660950 G
1 G
660951 AAAAATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 4 0.12
35 30 0.88
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (34 bp):
GCCACTTAAATAAATCTAAATCCCAATATCTTTT
Found at i:663799 original size:17 final size:17
Alignment explanation
Indices: 663777--663810 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
663767 ATCCACTAAT
*
663777 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
663794 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
663811 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:668438 original size:17 final size:17
Alignment explanation
Indices: 668416--668449 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
668406 ATCCACTAAT
*
668416 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
668433 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
668450 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:677868 original size:12 final size:12
Alignment explanation
Indices: 677851--677880 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
677841 GAACCGGACA
677851 CGAACCAAGCTC
1 CGAACCAAGCTC
677863 CGAACCAAGCTC
1 CGAACCAAGCTC
677875 CGAACC
1 CGAACC
677881 GTAGCTCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.43, G:0.17, T:0.07
Consensus pattern (12 bp):
CGAACCAAGCTC
Found at i:680683 original size:29 final size:29
Alignment explanation
Indices: 680621--680679 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
680611 AAGTTAGGGG
680621 TTTA-ATTTTTTTATGATTTTTATAAAAT
1 TTTATATTTTTTTATGATTTTTATAAAAT
* * *
680649 TTTATATTTTTTTTTTATTTTT-TACAAT
1 TTTATATTTTTTTATGATTTTTATAAAAT
680677 TTT
1 TTT
680680 TATAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (29 bp):
TTTATATTTTTTTATGATTTTTATAAAAT
Found at i:680932 original size:88 final size:92
Alignment explanation
Indices: 680824--680990 Score: 202
Period size: 89 Copynumber: 1.8 Consensus size: 92
680814 AAAAAATTTA
* **
680824 AAGGCTTTTTTATGCAATTTGAAAA-TTCAAGCACCCAACTGAGT-AAAAAAAATTAG-GAG-CT
1 AAGGCTTTTTTAT-CAATTTGAAAAGTTAAAGCACCCAACTGAGTGAAAAAAAAAAAGAGAGACT
680885 TAATTACTT-TTTTCTTTAAGAAGTTTG
65 TAATTACTTATTTTCTTTAAGAAGTTTG
** * *
680912 AAGGCATTTTTTAT-ATATTTGAAAAGTTAAAGTGCTCAATTGAGTGAAAAAAAAAAAGAGAGAC
1 AAGGC-TTTTTTATCA-ATTTGAAAAGTTAAAGCACCCAACTGAGTGAAAAAAAAAAAGAGAGAC
680976 TTAATTACTTATTTT
64 TTAATTACTTATTTT
680991 AAAAATATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
87 1 0.02
88 14 0.22
89 22 0.34
90 10 0.15
91 3 0.05
92 11 0.17
93 4 0.06
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (92 bp):
AAGGCTTTTTTATCAATTTGAAAAGTTAAAGCACCCAACTGAGTGAAAAAAAAAAAGAGAGACTT
AATTACTTATTTTCTTTAAGAAGTTTG
Found at i:681011 original size:89 final size:84
Alignment explanation
Indices: 680787--681011 Score: 193
Period size: 89 Copynumber: 2.5 Consensus size: 84
680777 AATTTTTAAT
* *
680787 AAAAGCAGAGGCTTAATTACTTTTTAAAAAAAATTTAAAGGCTTTTTTATGCAATTTGAAAATTC
1 AAAAG-AGA-GCTTAATTACTTTTT-TAAAAAATTTAAAGGCTTTTTTAT-CAATTTGAAAATTA
680852 AAGCACCCAACTGAGTAAAAAAA
62 AAGCACCCAACTGAGTAAAAAAA
** * * *
680875 ATTAG-GAGCTTAATTACTTTTTTCTTTAAGAAGTTTGAAGGCATTTTTTAT-ATATTTGAAAAG
1 AAAAGAGAGCTTAATTAC---TTT-TTTAAAAAATTTAAAGGC-TTTTTTATCA-ATTTGAAAA-
** * *
680938 TTAAAGTGCTCAATTGAGTGAAAAAAA
59 TTAAAGCACCCAACTGAGT-AAAAAAA
*
680965 AAAAGAGAGACTTAATTACTTATTTTAAAAATATTTAAAGACTTTTT
1 AAAAGAGAG-CTTAATTACTT-TTTTAAAAA-ATTTAAAGGCTTTTT
681012 ACACTCTTAA
Statistics
Matches: 108, Mismatches: 17, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
85 10 0.09
86 2 0.02
87 1 0.01
88 27 0.25
89 38 0.35
90 18 0.17
91 3 0.03
92 9 0.08
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (84 bp):
AAAAGAGAGCTTAATTACTTTTTTAAAAAATTTAAAGGCTTTTTTATCAATTTGAAAATTAAAGC
ACCCAACTGAGTAAAAAAA
Found at i:681122 original size:23 final size:24
Alignment explanation
Indices: 681080--681128 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
681070 TACTATTTGT
* *
681080 AAACAAAATTACAGTTAAATCATA
1 AAACAAAATTACACTGAAATCATA
*
681104 AAAC-AAATTACACTGAAATCGTA
1 AAACAAAATTACACTGAAATCATA
681127 AA
1 AA
681129 TCAGAAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.57, C:0.14, G:0.06, T:0.22
Consensus pattern (24 bp):
AAACAAAATTACACTGAAATCATA
Found at i:683176 original size:21 final size:21
Alignment explanation
Indices: 683152--683196 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
683142 TTAAGCATTC
683152 AAAATAAAAAGTTTTCAATTT
1 AAAATAAAAAGTTTTCAATTT
*
683173 AAAATAAAAAGTTTTTAATTT
1 AAAATAAAAAGTTTTCAATTT
683194 AAA
1 AAA
683197 CACCTACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (21 bp):
AAAATAAAAAGTTTTCAATTT
Found at i:688897 original size:18 final size:17
Alignment explanation
Indices: 688869--688903 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
688859 ATTATTAAGA
*
688869 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
688886 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
688904 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:688924 original size:120 final size:120
Alignment explanation
Indices: 688778--689160 Score: 757
Period size: 120 Copynumber: 3.2 Consensus size: 120
688768 TTTTCAAGTT
*
688778 ATATATTTAATAATTATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
688843 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
688898 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
688963 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
689018 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
689083 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
689138 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
689161 TAAATATGAT
Statistics
Matches: 262, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 262 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
Found at i:689017 original size:18 final size:17
Alignment explanation
Indices: 688989--689023 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
688979 ATTATTAAGA
*
688989 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
689006 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
689024 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:689137 original size:18 final size:17
Alignment explanation
Indices: 689109--689143 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
689099 ATTATTAAGA
*
689109 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
689126 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
689144 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:689400 original size:16 final size:16
Alignment explanation
Indices: 689379--689446 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
689369 GATTTGCTAT
689379 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
689395 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
689411 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
689427 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
689443 TACA
1 TACA
689447 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:716927 original size:19 final size:17
Alignment explanation
Indices: 716886--716928 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
716876 AGATTTTTAA
*
716886 AAAATATATTTAAATTT
1 AAAATATATTCAAATTT
*
716903 AAAATATATTCATATATT
1 AAAATATATTCAAAT-TT
716921 AATAATAT
1 AA-AATAT
716929 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 4 0.18
19 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATATATTCAAATTT
Found at i:728265 original size:6 final size:6
Alignment explanation
Indices: 728254--728287 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
728244 TATGATTTCA
728254 ATATCC ATATCC ATATCC ATATCC ATATCC ATAT
1 ATATCC ATATCC ATATCC ATATCC ATATCC ATAT
728288 TAATTATACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATCC
Found at i:734031 original size:18 final size:19
Alignment explanation
Indices: 734008--734045 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
733998 GGAAGCAAGC
*
734008 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
734026 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
734045 A
1 A
734046 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:743770 original size:112 final size:112
Alignment explanation
Indices: 743515--743789 Score: 270
Period size: 112 Copynumber: 2.4 Consensus size: 112
743505 AAATCTCAAG
** * * * * * *
743515 ACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGAC-TATGATAAA-ACGCC
1 ACCAAAACGCAGAG-TTTGGTCTAGAGGTATATTAGAATTAGTGGCG-CTTACGA-AAACCCACC
*
743578 GCTAAAGCAAGTATTAGCGGCGCATTGTCGAAAGCACCGCAAAAATCTTA
63 GCTAAAGCAAGTATTAGCGGCGCATTGACGAAAGCACCGCAAAAATCTTA
* * ** * * ** * *
743628 ACGAGAACGCATTGTTTTGTCTCGCTGTATATTAGCATTAGTGGTGCTTACGAAAACCCACCGCT
1 ACCAAAACGCAGAGTTTGGTCTAGAGGTATATTAGAATTAGTGGCGCTTACGAAAACCCACCGCT
* * *
743693 AAAGCAAGTATTAGCGGCGC-TT-ACGAAAAGCGCCGCAATATATGTTA
66 AAAGCAAGTATTAGCGGCGCATTGACG-AAAGCACCGCAA-AAATCTTA
*
743740 ACCAAAACGCAGAGTTTGGTCTAGAGGTATATTAGAATTTGTGGCGCTTA
1 ACCAAAACGCAGAGTTTGGTCTAGAGGTATATTAGAATTAGTGGCGCTTA
743790 TGGGAAAACG
Statistics
Matches: 131, Mismatches: 27, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
110 2 0.02
111 17 0.13
112 101 0.77
113 11 0.08
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (112 bp):
ACCAAAACGCAGAGTTTGGTCTAGAGGTATATTAGAATTAGTGGCGCTTACGAAAACCCACCGCT
AAAGCAAGTATTAGCGGCGCATTGACGAAAGCACCGCAAAAATCTTA
Found at i:744006 original size:113 final size:114
Alignment explanation
Indices: 743798--744114 Score: 336
Period size: 114 Copynumber: 2.8 Consensus size: 114
743788 TATGGGAAAA
* * ** *** * *
743798 CGCCGCAAAA-ATCCTAACCAAAGCGCACCGTTTTGGTCTTG-GTGTATGTTACAGTTAGTGGCG
1 CGCCGCAAAATATCTTAACCAAAACGCAAAGTTTTGGTCTTGAG-GTATACAAGAATTAGTGGCG
* * * *
743861 CTTAAGGGAAAACGCCGCTAAAGCATAATATTAGCGGCA-TTTTGTGAGAAG
65 C-AAAGGGAAAACGCCGCTAAAGCATAATATTAGCGACACGTCTG-GAGAAG
* *
743912 CGCCGCAAAATATCTTAACCAAAACGCAAAG-TTTGGTTTTGAGGTATACTAGAATTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAAAGTTTTGGTCTTGAGGTATACAAGAATTAGTGGCGC
* * * *
743976 AAAGGGAACATGCCGCTAAGGCATACTATTAGCGACACGTCTGGAGAAG
66 AAAGGGAAAACGCCGCTAAAGCATAATATTAGCGACACGTCTGGAGAAG
* * * * *
744025 CGCCGCAAAATTTCTTAACCAAAACGCAACGTTTTTGTCTTGATGTATACAATAATTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAAAGTTTTGGTCTTGAGGTATACAAGAATTAGTGGCGC
**
744090 ATACTGGAAAACGCCGCTAAAGCAT
66 A-AAGGGAAAACGCCGCTAAAGCAT
744115 GCTCACCAAA
Statistics
Matches: 169, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
113 66 0.39
114 68 0.40
115 35 0.21
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (114 bp):
CGCCGCAAAATATCTTAACCAAAACGCAAAGTTTTGGTCTTGAGGTATACAAGAATTAGTGGCGC
AAAGGGAAAACGCCGCTAAAGCATAATATTAGCGACACGTCTGGAGAAG
Found at i:744136 original size:77 final size:76
Alignment explanation
Indices: 744042--744190 Score: 192
Period size: 76 Copynumber: 1.9 Consensus size: 76
744032 AAATTTCTTA
* * * *
744042 ACCAAAACGCAACGTTTTTGTCTTGATGTATACAATAATTAGTGGCGCATACTGGAAAACGCCGC
1 ACCAAAACGCAACG-TTTTGTCTTAAGGTATACAAGAATTAGTGGCGCATACGGGAAAACGCCGC
744107 TAAAGCATGCTC
65 TAAAGCATGCTC
* ** * *
744119 ACCAAAACGTAGA-GTTTTGTCTTAAGGTATATTAGAATTAGTGGCGCTTACGGGAGAACGCCGC
1 ACCAAAACGCA-ACGTTTTGTCTTAAGGTATACAAGAATTAGTGGCGCATACGGGAAAACGCCGC
744183 TAAAGCAT
65 TAAAGCAT
744191 ACTATTAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
76 50 0.81
77 11 0.18
78 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (76 bp):
ACCAAAACGCAACGTTTTGTCTTAAGGTATACAAGAATTAGTGGCGCATACGGGAAAACGCCGCT
AAAGCATGCTC
Found at i:744258 original size:191 final size:190
Alignment explanation
Indices: 743929--744305 Score: 463
Period size: 191 Copynumber: 2.0 Consensus size: 190
743919 AAATATCTTA
* * *
743929 ACCAAAACGCAAAGTTTGGTTTTGAGGTATACTAGAATTAGTGGCGCAAAGGGAACATGCCGCTA
1 ACCAAAACGCAAAGTTTGGTCTTAAGGTATACTAGAATTAGTGGCGCAAAGGGAACACGCCGCTA
* * * *
743994 AGGCATACTATTAGCGACACGTCTGGAGAAGCGCCGCAAAATTTCTTAACCAAAACGCAACGTTT
66 AAGCATACTATTAGCGACACGTCTGGAGAAGCACCGCAAAATATATTAACCAAAACGCAACGTTT
** * *
744059 TTGTCTTGATGTATACAATAATTAGTGGCG-CATACTG-GAAAACGCCGCTAAAGCATGCTC
131 AAGTCTTGATGTATACAAGAATTAGTGGCGTC-CAC-GAGAAAACGCCGCTAAAGCATGCTC
* * * * * *
744119 ACCAAAACGTAGAGTTTTGTCTTAAGGTATATTAGAATTAGTGGCGCTTACGGGAGA-ACGCCGC
1 ACCAAAACGCAAAGTTTGGTCTTAAGGTATACTAGAATTAGTGGCGC-AAAGGGA-ACACGCCGC
* * * * * *
744183 TAAAGCATACTATTAGCGGCGCGTTTTGAGAAGTACCGCAAAATATATTAACCAAAACGCAGCGT
64 TAAAGCATACTATTAGCGACACGTCTGGAGAAGCACCGCAAAATATATTAACCAAAACGCAACGT
** *
744248 TTAAGTCTTGATGTATACTGGAATTAGTGGCGTCCACGAGAAATCGCCGCTAAAGCAT
129 TTAAGTCTTGATGTATACAAGAATTAGTGGCGTCCACGAGAAAACGCCGCTAAAGCAT
744306 AGTATTAGCG
Statistics
Matches: 157, Mismatches: 26, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
190 42 0.27
191 113 0.72
192 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (190 bp):
ACCAAAACGCAAAGTTTGGTCTTAAGGTATACTAGAATTAGTGGCGCAAAGGGAACACGCCGCTA
AAGCATACTATTAGCGACACGTCTGGAGAAGCACCGCAAAATATATTAACCAAAACGCAACGTTT
AAGTCTTGATGTATACAAGAATTAGTGGCGTCCACGAGAAAACGCCGCTAAAGCATGCTC
Found at i:744371 original size:115 final size:114
Alignment explanation
Indices: 744119--744373 Score: 325
Period size: 115 Copynumber: 2.2 Consensus size: 114
744109 AAGCATGCTC
* * * *
744119 ACCAAAACGTAGAGTTTTGTCTTAAGGTATATTAGAATTAGTGGCGCTTACGGGAGAACGCCGCT
1 ACCAAAACGCAGAGTTTTGTCTTAAGGTATACTAGAATTAGTGGCGCTCACGAGAGAACGCCGCT
*
744184 AAAGCATACTATTAGCGGCGCGTTTTGAGAAGTACCGCAAAATATATTA
66 AAAGCATACTATTAGCGGCGCGTTTTGAGAAGCACCGCAAAATATATTA
* * * * *
744233 ACCAAAACGCAGCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCG-TCCACGAGA-AATCGCC
1 ACCAAAACGCAGAGTTT-TGTCTTAAGGTATACTAGAATTAGTGGCGCT-CACGAGAGAA-CGCC
* * * * *
744296 GCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAGCGCCGGAAAATATCTTA
63 GCTAAAGCATACTATTAGCGGCGCGTTTTGAGAAGCACCGCAAAATATATTA
744348 ACCAAAACGCAGAGTTTTGGTCTTAA
1 ACCAAAACGCAGAGTTTT-GTCTTAA
744374 CCATGCACTA
Statistics
Matches: 119, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
114 18 0.15
115 101 0.85
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (114 bp):
ACCAAAACGCAGAGTTTTGTCTTAAGGTATACTAGAATTAGTGGCGCTCACGAGAGAACGCCGCT
AAAGCATACTATTAGCGGCGCGTTTTGAGAAGCACCGCAAAATATATTA
Found at i:745282 original size:14 final size:15
Alignment explanation
Indices: 745263--745303 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
745253 ACACTTGTAT
745263 GGATTTAGGGTTT-G
1 GGATTTAGGGTTTAG
*
745277 GGATTTAAGGTTTAG
1 GGATTTAGGGTTTAG
745292 GGATTTTAGGGT
1 GGA-TTTAGGGT
745304 CAGATCAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 4 0.17
16 7 0.30
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (15 bp):
GGATTTAGGGTTTAG
Found at i:747647 original size:21 final size:21
Alignment explanation
Indices: 747621--747669 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
747611 CTACAACTTA
*
747621 AAGCAGAGGC-GACAGCGAGGG
1 AAGCAGAGGCTG-CAGCGAGAG
747642 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
747663 AAGCAGA
1 AAGCAGA
747670 AGTTCAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.18, G:0.43, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:748127 original size:43 final size:43
Alignment explanation
Indices: 748040--748219 Score: 157
Period size: 42 Copynumber: 4.2 Consensus size: 43
748030 CAAAAATAGT
* * * * * *
748040 GGCGTTTTTGTACAAAAGCGCCGCGAAAGATTATGATCTCTAGC
1 GGCGTTTTTATA-AAAAACGCCGCTAAAGATCATGTTCTTTAGC
* * * * *
748084 GGTGTTTTTATACAAAGCGCCGTTAAAGAGCATGTTCTTTAGC
1 GGCGTTTTTATAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
* * * *
748127 GGCG-CTTAATAAAAAATGCCACTAAAGATCATGTTCTTTAGC
1 GGCGTTTTTATAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
* * * *
748169 GGCGCTTATA-AAAAAACGCCGCTAAAGAACATGGTCTTTAGC
1 GGCGTTTTTATAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
*
748211 GGCATTTTT
1 GGCGTTTTT
748220 GTTTGTAAAC
Statistics
Matches: 107, Mismatches: 28, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
42 68 0.64
43 29 0.27
44 10 0.09
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
GGCGTTTTTATAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
Found at i:749692 original size:8 final size:8
Alignment explanation
Indices: 749679--749753 Score: 57
Period size: 8 Copynumber: 9.2 Consensus size: 8
749669 GTTAAAACAT
749679 ATATTATA
1 ATATTATA
749687 ATATTATA
1 ATATTATA
749695 ATATTAT-
1 ATATTATA
*
749702 ATCTTA-A
1 ATATTATA
*
749709 TTATTATA
1 ATATTATA
749717 TTATATTATA
1 --ATATTATA
749727 TTATATTATA
1 --ATATTATA
* *
749737 TTA-TATT
1 ATATTATA
749744 ATATTATA
1 ATATTATA
749752 AT
1 AT
749754 GATAAAAGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
7 14 0.26
8 23 0.43
10 17 0.31
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (8 bp):
ATATTATA
Found at i:749703 original size:5 final size:5
Alignment explanation
Indices: 749678--749751 Score: 89
Period size: 5 Copynumber: 14.8 Consensus size: 5
749668 AGTTAAAACA
* * *
749678 TATAT TATAA TATTAT AATAT TATAT CT-TAA T-TAT TATAT TATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT
749728 TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATA
749752 ATGATAAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
4 4 0.07
5 52 0.87
6 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:749789 original size:24 final size:24
Alignment explanation
Indices: 749757--749802 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
749747 TTATAATGAT
749757 AAAAGAAAGAAA-GAAAGAAAAGA
1 AAAAGAAAGAAAGGAAAGAAAAGA
*
749780 AAAAGGAAAGAAAGGAAGGAAAA
1 AAAA-GAAAGAAAGGAAAGAAAA
749803 AGCCACGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 8 0.40
25 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (24 bp):
AAAAGAAAGAAAGGAAAGAAAAGA
Found at i:749790 original size:20 final size:20
Alignment explanation
Indices: 749765--749804 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
749755 ATAAAAGAAA
749765 GAAAGAAAGAAAAGAAAAAG
1 GAAAGAAAGAAAAGAAAAAG
* *
749785 GAAAGAAAGGAAGGAAAAAG
1 GAAAGAAAGAAAAGAAAAAG
749805 CCACGGCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAAAAGAAAAAG
Found at i:750128 original size:18 final size:19
Alignment explanation
Indices: 750099--750134 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
750089 GTGAAAATTT
*
750099 TAAAATTTAGAGATTTAAG
1 TAAAATTTAGAGAGTTAAG
750118 TAAAA-TTAGAGAGTTAA
1 TAAAATTTAGAGAGTTAA
750135 ATCTAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (19 bp):
TAAAATTTAGAGAGTTAAG
Found at i:758650 original size:21 final size:21
Alignment explanation
Indices: 758626--758697 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
758616 GACACCGTCC
*
758626 GTGACGGCGATAACTCACCTT
1 GTGACGGCGATGACTCACCTT
*
758647 GTGACGTCGATGACTCACCTT
1 GTGACGGCGATGACTCACCTT
* *
758668 GTGACGTCGATGACTAACCTT
1 GTGACGGCGATGACTCACCTT
**
758689 CCGACGGCG
1 GTGACGGCG
758698 GAGAATCCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (21 bp):
GTGACGGCGATGACTCACCTT
Found at i:760665 original size:25 final size:26
Alignment explanation
Indices: 760614--760675 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
760604 AGTTTTTTAC
* *
760614 ATAT-TAAAACTATGCAATTAAGAATA
1 ATATATAAAA-TATGCAAATAAAAATA
760640 ATATATAAAATAT-CAAATAAAAATA
1 ATATATAAAATATGCAAATAAAAATA
*
760665 ATAAATAAAAT
1 ATATATAAAAT
760676 CATAAGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.62
26 7 0.22
27 5 0.16
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (26 bp):
ATATATAAAATATGCAAATAAAAATA
Found at i:761038 original size:20 final size:21
Alignment explanation
Indices: 761003--761041 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
760993 CTAAAATATT
761003 TTTAATATTAACATTAATTAA
1 TTTAATATTAACATTAATTAA
*
761024 TTTAAT-TTAATATTAATT
1 TTTAATATTAACATTAATT
761042 CGATAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAATATTAACATTAATTAA
Found at i:765353 original size:11 final size:11
Alignment explanation
Indices: 765337--765362 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
765327 ATTTTTTAAA
765337 TTTTAAAATAC
1 TTTTAAAATAC
765348 TTTTAAAATAC
1 TTTTAAAATAC
765359 TTTT
1 TTTT
765363 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:765373 original size:11 final size:11
Alignment explanation
Indices: 765359--765413 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
765349 TTTAAAATAC
765359 TTTTTTTAAA-
1 TTTTTTTAAAT
765369 -TTTTTTAAA-
1 TTTTTTTAAAT
765378 --TTT-TAAAT
1 TTTTTTTAAAT
765386 TTTTTTTAAAT
1 TTTTTTTAAAT
765397 TTTTTTTAAAT
1 TTTTTTTAAAT
765408 TTTTTT
1 TTTTTT
765414 AATTTTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
7 4 0.10
8 3 0.07
9 9 0.22
10 3 0.07
11 22 0.54
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:778887 original size:10 final size:10
Alignment explanation
Indices: 778872--778907 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
778862 ATTAATATTG
*
778872 ATTTTTTTTT
1 ATTTTTTTTA
778882 ATTTTTTTTAA
1 ATTTTTTTT-A
778893 ATTTTTTTTA
1 ATTTTTTTTA
778903 ATTTT
1 ATTTT
778908 ACATATACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
ATTTTTTTTA
Done.