Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007825.1 Hibiscus syriacus cultivar Beakdansim tig00110163_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2082551
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1339200 original size:20 final size:21
Alignment explanation
Indices: 1339151--1339204 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
1339141 CGGTTTACAT
*
1339151 ATTCGCGTTGCGAATTTGGAA
1 ATTCGCGTTGCGAAATTGGAA
*
1339172 ATT-GAGTTGCGAAATTGG-A
1 ATTCGCGTTGCGAAATTGGAA
*
1339191 GTTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
1339205 TTTATTGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.31
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTGGAA
Found at i:1344915 original size:21 final size:21
Alignment explanation
Indices: 1344889--1344930 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1344879 TTCTACAGGG
1344889 GTATCGATACCCTGCTACAGT
1 GTATCGATACCCTGCTACAGT
*
1344910 GTATCGATACCTTGCTACAGT
1 GTATCGATACCCTGCTACAGT
1344931 AATTTCGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (21 bp):
GTATCGATACCCTGCTACAGT
Found at i:1345716 original size:30 final size:30
Alignment explanation
Indices: 1345681--1345771 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
1345671 AATGGATTTA
* **
1345681 TTTAGTGACCAAATTATAAA-TTTGGTAAAG
1 TTTAGTGACCAAAGTATAAACTTT-AAAAAG
1345711 TTTAGTGACCAAAGTATAAACTTTAAAAAG
1 TTTAGTGACCAAAGTATAAACTTTAAAAAG
* * * *
1345741 TTTAGGGACCAAAATGT-AATTTTAAAAAG
1 TTTAGTGACCAAAGTATAAACTTTAAAAAG
1345770 TT
1 TT
1345772 ACATATGGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 13 0.25
30 37 0.70
31 3 0.06
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (30 bp):
TTTAGTGACCAAAGTATAAACTTTAAAAAG
Found at i:1346755 original size:31 final size:31
Alignment explanation
Indices: 1346682--1346759 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 31
1346672 TTTTACAATC
* * * **
1346682 TTTGGAAAAA-TTCAGGGACCATTTTGTAAT
1 TTTGGAAAAAGTTGAGGAACCAATTCATAAT
*
1346712 TTTCG-AAAAGTTGAGGAACCAATTCATAAT
1 TTTGGAAAAAGTTGAGGAACCAATTCATAAT
1346742 TTTGGAAAAAGTTG-GGAA
1 TTTGGAAAAAGTTGAGGAA
1346760 TGGTTGTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 4 0.10
30 27 0.69
31 8 0.21
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (31 bp):
TTTGGAAAAAGTTGAGGAACCAATTCATAAT
Found at i:1347000 original size:18 final size:18
Alignment explanation
Indices: 1346954--1347002 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1346944 TGATAATTCC
*
1346954 ATTACTGGAATTTATGGA
1 ATTACTCGAATTTATGGA
*
1346972 ATTTCTCGAATTTAT-GA
1 ATTACTCGAATTTATGGA
*
1346989 AGTTACTTGAATTT
1 A-TTACTCGAATTT
1347003 TTGGTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (18 bp):
ATTACTCGAATTTATGGA
Found at i:1348009 original size:38 final size:38
Alignment explanation
Indices: 1347958--1348080 Score: 174
Period size: 38 Copynumber: 3.2 Consensus size: 38
1347948 GGGTCGAGGG
* *
1347958 TTACATCCTTCGAGATGACAGGTCCTCCGGGACACATA
1 TTACATCCTTCGAGATGACAGGTCCTACGGGACACAGA
* *
1347996 TTACATCCTTCGAGATGACAGGTCCTTCGGAACACAGA
1 TTACATCCTTCGAGATGACAGGTCCTACGGGACACAGA
* * *
1348034 TTACATCCTTCGGGATGATAGGTCCTACGGGACATAGA
1 TTACATCCTTCGAGATGACAGGTCCTACGGGACACAGA
*
1348072 TGACATCCT
1 TTACATCCT
1348081 GCAGGATGAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (38 bp):
TTACATCCTTCGAGATGACAGGTCCTACGGGACACAGA
Found at i:1348088 original size:38 final size:37
Alignment explanation
Indices: 1347958--1348094 Score: 157
Period size: 38 Copynumber: 3.6 Consensus size: 37
1347948 GGGTCGAGGG
* *
1347958 TTACATCCTTCGAGATGACAGGTCCTCCGGGACACATA
1 TTACATCCTTCG-GATGACAGGTCCTACGGGACACAGA
* *
1347996 TTACATCCTTCGAGATGACAGGTCCTTCGGAACACAGA
1 TTACATCCTTCG-GATGACAGGTCCTACGGGACACAGA
* *
1348034 TTACATCCTTCGGGATGATAGGTCCTACGGGACATAGA
1 TTACATCCTTC-GGATGACAGGTCCTACGGGACACAGA
* * *
1348072 TGACATCCTGCAGGATGATAGGT
1 TTACATCCTTC-GGATGACAGGT
1348095 AATTCGGGAC
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 87 0.99
39 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (37 bp):
TTACATCCTTCGGATGACAGGTCCTACGGGACACAGA
Found at i:1348101 original size:76 final size:76
Alignment explanation
Indices: 1347958--1348107 Score: 185
Period size: 76 Copynumber: 2.0 Consensus size: 76
1347948 GGGTCGAGGG
* * * * **
1347958 TTACATCCTTCGAGATGACAGGTCCTCCGGGACACATATTACATCCTTCGAGATGACAGGTCCTT
1 TTACATCCTTCGAGATGACAGGTCCTACGGGACACAGATGACATCCTGCGAGATGACAGGTAATT
1348023 CGGAACACAGA
66 CGGAACACAGA
* * * *
1348034 TTACATCCTTCGGGATGATAGGTCCTACGGGACATAGATGACATCCTGC-AGGATGATAGGTAAT
1 TTACATCCTTCGAGATGACAGGTCCTACGGGACACAGATGACATCCTGCGA-GATGACAGGTAAT
*
1348098 TCGGGACACA
65 TCGGAACACA
1348108 ATTTATACGA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
75 1 0.02
76 61 0.98
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (76 bp):
TTACATCCTTCGAGATGACAGGTCCTACGGGACACAGATGACATCCTGCGAGATGACAGGTAATT
CGGAACACAGA
Found at i:1348103 original size:38 final size:38
Alignment explanation
Indices: 1347985--1348107 Score: 104
Period size: 38 Copynumber: 3.2 Consensus size: 38
1347975 ACAGGTCCTC
* * * * **
1347985 CGGGACACATATTACATCCTTC-GAGATGACAGGTCCTT
1 CGGGACACAGATGACATCCTGCAG-GATGATAGGTAATT
* * * * ** *
1348023 CGGAACACAGATTACATCCTTCGGGATGATAGGTCCTA
1 CGGGACACAGATGACATCCTGCAGGATGATAGGTAATT
*
1348061 CGGGACATAGATGACATCCTGCAGGATGATAGGTAATT
1 CGGGACACAGATGACATCCTGCAGGATGATAGGTAATT
1348099 CGGGACACA
1 CGGGACACA
1348108 ATTTATACGA
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 70 0.99
39 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (38 bp):
CGGGACACAGATGACATCCTGCAGGATGATAGGTAATT
Found at i:1348215 original size:23 final size:24
Alignment explanation
Indices: 1348183--1348246 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
1348173 CTCAGTACTG
* *
1348183 TACATAGGCTAATGCATAG-CTAA
1 TACATGGGCTAATACATAGACTAA
*
1348206 TACATGGGCTAATACATTGACTAA
1 TACATGGGCTAATACATAGACTAA
*
1348230 TACATGGGTTAATACAT
1 TACATGGGCTAATACAT
1348247 GGTCTTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 16 0.44
24 20 0.56
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (24 bp):
TACATGGGCTAATACATAGACTAA
Found at i:1348216 original size:12 final size:12
Alignment explanation
Indices: 1348183--1348248 Score: 71
Period size: 12 Copynumber: 5.6 Consensus size: 12
1348173 CTCAGTACTG
*
1348183 TACATAGGCTAA
1 TACATGGGCTAA
* *
1348195 TGCAT-AGCTAA
1 TACATGGGCTAA
1348206 TACATGGGCTAA
1 TACATGGGCTAA
* *
1348218 TACATTGACTAA
1 TACATGGGCTAA
*
1348230 TACATGGGTTAA
1 TACATGGGCTAA
1348242 TACATGG
1 TACATGG
1348249 TCTTATAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
11 9 0.20
12 35 0.80
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (12 bp):
TACATGGGCTAA
Found at i:1349077 original size:32 final size:32
Alignment explanation
Indices: 1349009--1349418 Score: 585
Period size: 32 Copynumber: 12.9 Consensus size: 32
1348999 GAAGGACCTA
*
1349009 TCCATATGTTCCG-AAGAACATAGGTAA--CTG
1 TCCATATGTCCCGAAAG-ACATAGGTAATTCTG
*
1349039 TCCATATATCCCGAAAGACATAGGTAATTCTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
*
1349071 TCCATATGTCCCGAAAGACATAGGTAATTTTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
*
1349103 TCCATATGTCCCGAAAGACATAGATAATAT-TG
1 TCCATATGTCCCGAAAGACATAGGTAAT-TCTG
* **
1349135 TCTATATGTCCCGAAAGACATAGGTAACACTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
* * **
1349167 TTCATATGTCCCGAAAGACAAAGGTAATAATG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
1349199 TCCATATGTCCCGAAAGACATAGGTAATTCTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
*
1349231 TCCATATGTCCCGAAAGACATAGGTAATACTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
*
1349263 TCCATATGTCCCGAAATACATAGGTAATTCTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
* *
1349295 TCCATATATCCCGAAAGACATAGGTAATACTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
* **
1349327 TCCATATATCCCGAAAGACATAGGTAATAATG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
* *
1349359 TCCATATGTCCCGAAAGATATAGGTAATTTTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
*
1349391 TCCATATGTCCCAAAAGACATAGGTAAT
1 TCCATATGTCCCGAAAGACATAGGTAAT
1349419 ACTTGACTCT
Statistics
Matches: 344, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
30 21 0.06
31 3 0.01
32 319 0.93
33 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (32 bp):
TCCATATGTCCCGAAAGACATAGGTAATTCTG
Found at i:1351805 original size:29 final size:30
Alignment explanation
Indices: 1351748--1351805 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
1351738 AAACTTTCTG
* * *
1351748 ATTTTTGTCTCAAAATTAATTAAGAATTTC
1 ATTTTAGTCCCAAAATTAATCAAGAATTTC
*
1351778 ATTTTAGTCCCAAAATTTATCAA-AATTT
1 ATTTTAGTCCCAAAATTAATCAAGAATTT
1351806 GAATTTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (30 bp):
ATTTTAGTCCCAAAATTAATCAAGAATTTC
Found at i:1353774 original size:13 final size:13
Alignment explanation
Indices: 1353758--1353782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1353748 ATTAAAGGGA
1353758 AAAATAATAAAAT
1 AAAATAATAAAAT
1353771 AAAATAATAAAA
1 AAAATAATAAAA
1353783 ATAATAAACA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:1354698 original size:12 final size:12
Alignment explanation
Indices: 1354681--1354718 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1354671 AAAATAAAAA
*
1354681 AATATTAATATT
1 AATATTAATAAT
1354693 AATATTAATAAT
1 AATATTAATAAT
*
1354705 AATAATAATAAT
1 AATATTAATAAT
1354717 AA
1 AA
1354719 AATATAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:1354706 original size:3 final size:3
Alignment explanation
Indices: 1354668--1354722 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
1354658 AACGGAGCCT
* * * * *
1354668 ATA AAA ATA A-A AAA ATA TTA ATA TTA ATA TTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1354715 ATA A-A ATA
1 ATA ATA ATA
1354723 TAACATAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1355581 original size:124 final size:123
Alignment explanation
Indices: 1355347--1355624 Score: 358
Period size: 124 Copynumber: 2.2 Consensus size: 123
1355337 CTTTGAGTTG
* * * * * * *
1355347 GATATCCTTCACCGTGAACTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGCACGATTCCC
1 GATATCCTTCATCGTGAAGTTGAAATCCAATCAAAAGATGAATGCTGCTGGTGAGCACGATTCCC
* * * ** *
1355412 TTCGTCGTGAAGTTGAAACCGTGGGTGGCCCCTTTGTTGTGAAGTTGAGCCTTGAATT
66 TTCATCGTGAAGTTGAAACCGTGGATGGCCCATTCATTGTAAAGTTGAGCCTTGAATT
* * * *
1355470 AGATATCATTCATCGTGAAGGTGAAATTCAATCAAAAGATGAATGTTGCTGGTGAGCACGATTCC
1 -GATATCCTTCATCGTGAAGTTGAAATCCAATCAAAAGATGAATGCTGCTGGTGAGCACGATTCC
* *
1355535 CTTCATCGTGAAGTTGAAACCGTGGATGGCTCATTCATTGTAAAGTTGAGCCTTGACTT
65 CTTCATCGTGAAGTTGAAACCGTGGATGGCCCATTCATTGTAAAGTTGAGCCTTGAATT
*
1355594 GAATATCCTTCGTCGTGAAGTTGAAATCCAA
1 G-ATATCCTTCATCGTGAAGTTGAAATCCAA
1355625 GCTTGTATTG
Statistics
Matches: 130, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
123 1 0.01
124 129 0.99
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (123 bp):
GATATCCTTCATCGTGAAGTTGAAATCCAATCAAAAGATGAATGCTGCTGGTGAGCACGATTCCC
TTCATCGTGAAGTTGAAACCGTGGATGGCCCATTCATTGTAAAGTTGAGCCTTGAATT
Found at i:1355828 original size:110 final size:110
Alignment explanation
Indices: 1355703--1356107 Score: 648
Period size: 110 Copynumber: 3.7 Consensus size: 110
1355693 CCCCTTCACC
* *
1355703 GTGAAGTTGAAATTGACTTTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTTGCCCCTTCG
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
* **
1355768 CTATGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCTTAACT
66 CTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
* * *
1355813 GTGAAATTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTTGCCCCTTCG
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
* *
1355878 TTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCTTTCGCT
66 CTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
* *
1355923 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTATTGACAGTCAGTCGCCCCTTCA
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
* * *
1355988 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATACTTCGTT
66 CTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
* *
1356033 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAATTAGTCGCCCCTTCG
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
*
1356098 CTGTGAAGTT
66 CTATGAAGTT
1356108 AAAATTGACT
Statistics
Matches: 273, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 273 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (110 bp):
GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
CTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
Found at i:1356134 original size:67 final size:63
Alignment explanation
Indices: 1356026--1356170 Score: 236
Period size: 67 Copynumber: 2.2 Consensus size: 63
1356016 GTCCAATATA
* *
1356026 CTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAATTAGTCGC
1 CTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAC----AGTCGC
1356091 CC
62 CC
1356093 CTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCGCCC
1 CTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCGCCC
1356156 CTTCGCTGTGAAGTT
1 CTTCGCTGTGAAGTT
1356171 GAGCAACCAC
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
63 23 0.30
67 53 0.70
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (63 bp):
CTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCGCCC
Found at i:1358857 original size:17 final size:19
Alignment explanation
Indices: 1358821--1358857 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1358811 TGCGCATGAT
1358821 GAAAACAAAATAAAAGAGA
1 GAAAACAAAATAAAAGAGA
1358840 GAAAA-AAAATAAAA-AGA
1 GAAAACAAAATAAAAGAGA
1358857 G
1 G
1358858 TTAGTGAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (19 bp):
GAAAACAAAATAAAAGAGA
Found at i:1359736 original size:13 final size:13
Alignment explanation
Indices: 1359720--1359744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1359710 ATTAAAGAGA
1359720 AAAATAATAAAAT
1 AAAATAATAAAAT
1359733 AAAATAATAAAA
1 AAAATAATAAAA
1359745 ATAATAAACA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:1362834 original size:21 final size:20
Alignment explanation
Indices: 1362797--1362837 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1362787 GGTATATTTG
**
1362797 TTTTTTTTTCTTTTCTCTGT
1 TTTTTTTTTCTCGTCTCTGT
1362817 TTTTTTTTTCTCCGTCTCTGT
1 TTTTTTTTTCT-CGTCTCTGT
1362838 CTCTAGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (20 bp):
TTTTTTTTTCTCGTCTCTGT
Found at i:1363356 original size:3 final size:3
Alignment explanation
Indices: 1363337--1363464 Score: 204
Period size: 3 Copynumber: 42.7 Consensus size: 3
1363327 ATTTAATATT
*
1363337 TAA T-A TAA TAG TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* *
1363382 TAA TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1363430 TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1363465 TGGATAAAAA
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.02
3 110 0.96
4 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1364055 original size:224 final size:225
Alignment explanation
Indices: 1363785--1364418 Score: 1123
Period size: 224 Copynumber: 2.8 Consensus size: 225
1363775 GAATTATGCC
* * * * *
1363785 AAAA-GTTGAACAAGTTCTTCTTATTATGAACGTATTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
1363849 TATGAACTTC-TCCGGAAAAGATAATCCATCAATTGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAAC-TCAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
1363913 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
1363978 AAAGCTGATCCATTAAATGATGGATTCATAT
195 AAAGCTGATCCATTAAATGATGGATTCATAT
1364009 -AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1364073 TATGAACTCGAACTGG-AAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTC-AACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
1364137 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
1364202 AAAGCTGATCCATTAAATGATGGATTCATAT
195 AAAGCTGATCCATTAAATGATGGATTCATAT
1364233 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1364298 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTC-AACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
1364363 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1364419 CGAAAAGCTG
Statistics
Matches: 395, Mismatches: 10, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
223 5 0.01
224 203 0.51
225 83 0.21
226 104 0.26
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (225 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
AAGCTGATCCATTAAATGATGGATTCATAT
Found at i:1364289 original size:113 final size:113
Alignment explanation
Indices: 1363785--1364418 Score: 1008
Period size: 113 Copynumber: 5.6 Consensus size: 113
1363775 GAATTATGCC
* * * * *
1363785 AAAA-GTTGAACAAGTTCTTCTTATTATGAACGTATTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
1363849 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
1363896 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
1363961 TATGAACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCA--T
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
1364007 ATAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 A-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**** *
1364072 TTATGAACTCGAACTGG-AAAGATGATCCACCAAATGATGGATTCAGGT
65 TTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
1364120 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * **
1364185 TATGAACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
1364233 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** *
1364298 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
1364346 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1364411 TATGAACT
66 TATGAACT
1364419 CGAAAAGCTG
Statistics
Matches: 482, Mismatches: 35, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
111 31 0.06
112 214 0.44
113 237 0.49
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
Found at i:1365191 original size:83 final size:83
Alignment explanation
Indices: 1365090--1365725 Score: 1112
Period size: 83 Copynumber: 7.7 Consensus size: 83
1365080 CTTACCAAAA
* *
1365090 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGTTATTAACAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAA
*
1365155 TGATTGATTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
* *
1365173 CAGATCAGATAACTCAAAGAAAACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAA
1365238 TGATTGGTTCTG-CCAAAC
66 TGATTGGTTCTGTCC-AAC
*
1365256 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAA
1365321 TGATTGGTTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
* *
1365339 TAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAA
1365404 TGATTGGTTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
* *
1365422 TAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAA
1365487 TGATTGGTTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
*
1365505 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAA
*
1365570 TGATTGATTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
*
1365588 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAA
*
1365653 TGATTGATTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
* *
1365671 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
1365726 TCAGTTAATG
Statistics
Matches: 534, Mismatches: 17, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
82 2 0.00
83 530 0.99
84 2 0.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAA
TGATTGGTTCTGTCCAAC
Found at i:1366788 original size:10 final size:10
Alignment explanation
Indices: 1366775--1366811 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
1366765 ACCTTTTTTC
1366775 TTTTTTCTTT
1 TTTTTTCTTT
1366785 TTTTTTCCTTT
1 TTTTTT-CTTT
1366796 TTTTTTCTTT
1 TTTTTTCTTT
1366806 TTTTTT
1 TTTTTT
1366812 TCTTCAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1366814 original size:11 final size:11
Alignment explanation
Indices: 1366770--1366815 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
1366760 GACCCACCTT
1366770 TTTTCTTTTTTC
1 TTTT-TTTTTTC
1366782 -TTTTTTTTTC
1 TTTTTTTTTTC
*
1366792 CTTTTTTTTTC
1 TTTTTTTTTTC
1366803 TTTTTTTTTTC
1 TTTTTTTTTTC
1366814 TT
1 TT
1366816 CAAGCATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 7 0.22
11 25 0.78
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:1376074 original size:144 final size:146
Alignment explanation
Indices: 1375812--1376103 Score: 561
Period size: 144 Copynumber: 2.0 Consensus size: 146
1375802 AACATATCCC
1375812 AATACTTTTGGGAAGATGACCATACCATATATACCCAGAGCAAATAGATCAAATCGTACTTTAAT
1 AATACTTTTGGGAAGATGACCATACCA-ATATACCCAGAGCAAATAGATCAAATCGTACTTTAAT
1375877 ATCTGGATGGCTTTGAATAAGTTCTCTGATGTTGGTCCAAGCTATGCCTTCGCTTTCGCCTTTTT
65 ATCTGGATGGCTTTGAATAAGTTCTCTGATGTTGGTCCAAGCTATGCCTTCGCTTTCGCCTTTTT
1375942 G-TTTGTACGGGATACT
130 GTTTTGTACGGGATACT
1375958 AATACTTTTGGGAAGATGACCATACC-ATATACCCAGAGCAAATAGATCAAATCGTACTTTAATA
1 AATACTTTTGGGAAGATGACCATACCAATATACCCAGAGCAAATAGATCAAATCGTACTTTAATA
1376022 TCTGGATGGCTTTGAATAAGTTCTCTGATGTTGGTCCAAGCTATGCCTTCGCTTTCGCCTTTTTG
66 TCTGGATGGCTTTGAATAAGTTCTCTGATGTTGGTCCAAGCTATGCCTTCGCTTTCGCCTTTTTG
1376087 TTTTGTACGGGATACT
131 TTTTGTACGGGATACT
1376103 A
1 A
1376104 CCCATTCTTC
Statistics
Matches: 145, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
144 103 0.71
145 16 0.11
146 26 0.18
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (146 bp):
AATACTTTTGGGAAGATGACCATACCAATATACCCAGAGCAAATAGATCAAATCGTACTTTAATA
TCTGGATGGCTTTGAATAAGTTCTCTGATGTTGGTCCAAGCTATGCCTTCGCTTTCGCCTTTTTG
TTTTGTACGGGATACT
Found at i:1377736 original size:15 final size:15
Alignment explanation
Indices: 1377681--1377737 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
1377671 AAATTTAAAA
1377681 ATTTAAAATATATTT
1 ATTTAAAATATATTT
** *
1377696 AATTTTTAATCT-TTT
1 -ATTTAAAATATATTT
1377711 ATTTCAAAATATATTT
1 ATTT-AAAATATATTT
1377727 ATTTAAAATAT
1 ATTTAAAATAT
1377738 CAGAAAAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
14 4 0.12
15 14 0.42
16 15 0.45
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTAAAATATATTT
Found at i:1378002 original size:19 final size:19
Alignment explanation
Indices: 1377978--1378014 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1377968 AAAACATTTT
1377978 TTAAAA-ATAATAAAATAAA
1 TTAAAACAT-ATAAAATAAA
1377997 TTAAAACATATAAAATAA
1 TTAAAACATATAAAATAA
1378015 TGACTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAAAACATATAAAATAAA
Found at i:1378866 original size:21 final size:20
Alignment explanation
Indices: 1378829--1378869 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1378819 GGTATATTTG
**
1378829 TTTTTTTTTCCTTTCTCTGT
1 TTTTTTTTTCCCGTCTCTGT
1378849 TTTTTTTTTCTCCGTCTCTGT
1 TTTTTTTTTC-CCGTCTCTGT
1378870 CTCTAGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.00, C:0.22, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTTTTTTTCCCGTCTCTGT
Found at i:1379348 original size:20 final size:19
Alignment explanation
Indices: 1379325--1379369 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1379315 TTTTTTTTAT
* *
1379325 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
1379345 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
1379364 TATTTA
1 TATTTA
1379370 ATAATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:1379359 original size:26 final size:30
Alignment explanation
Indices: 1379320--1379375 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1379310 TTATATTTTT
*
1379320 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1379347 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1379376 ATAATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:1379376 original size:3 final size:3
Alignment explanation
Indices: 1379368--1379486 Score: 184
Period size: 3 Copynumber: 39.7 Consensus size: 3
1379358 TTAATATATT
* *
1379368 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1379416 TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1379464 TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
1379487 TGGATAAAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1386474 original size:23 final size:24
Alignment explanation
Indices: 1386446--1386493 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
1386436 TGTATATATA
1386446 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTTATTTCATT
*
1386469 TATTTATTATAATTTTTTTTCATT
1 TATTTATTATAATTTTATTTCATT
1386493 T
1 T
1386494 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTATTATAATTTTATTTCATT
Found at i:1386756 original size:22 final size:21
Alignment explanation
Indices: 1386721--1386775 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1386711 CTATTTAGTA
1386721 TTTTATTATATTATACATACATT
1 TTTTATT-T-TTATACATACATT
* *
1386744 TTTATATTTTTATATATATATT
1 TTT-TATTTTTATACATACATT
1386766 TTTTATTTTT
1 TTTTATTTTT
1386776 TTATTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 7 0.24
22 14 0.48
23 4 0.14
24 4 0.14
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTTTTATACATACATT
Found at i:1386776 original size:30 final size:30
Alignment explanation
Indices: 1386741--1386804 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1386731 TTATACATAC
*
1386741 ATTTTTATATTTT-TATATA-TATATTTTTT
1 ATTTTTTTATTTTATATATACTAT-TTTTTT
*
1386770 ATTTTTTTATTTTATTTATACTATTTTTTT
1 ATTTTTTTATTTTATATATACTATTTTTTT
1386800 ATTTT
1 ATTTT
1386805 CATTATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 12 0.39
30 16 0.52
31 3 0.10
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (30 bp):
ATTTTTTTATTTTATATATACTATTTTTTT
Found at i:1388125 original size:19 final size:19
Alignment explanation
Indices: 1388101--1388137 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1388091 ACCTTACTAA
1388101 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
1388120 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
1388138 ATCATCTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:1391770 original size:16 final size:16
Alignment explanation
Indices: 1391744--1391777 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1391734 ATATCCAATC
1391744 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
1391759 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
1391776 AA
1 AA
1391778 AAAAACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:1391825 original size:6 final size:7
Alignment explanation
Indices: 1391750--1391824 Score: 55
Period size: 8 Copynumber: 9.7 Consensus size: 7
1391740 AATCAAGAAC
1391750 AAAAAAG
1 AAAAAAG
1391757 AAAAGAAG
1 AAAA-AAG
1391765 CAAAAAAG
1 -AAAAAAG
1391773 CAAAAAA-
1 -AAAAAAG
1391780 AAACAAAG
1 AAA-AAAG
1391788 AAAAAATAG
1 -AAAAA-AG
1391797 AAACAATA-
1 AAA-AA-AG
1391805 ACAAAAAG
1 A-AAAAAG
1391813 AAAAAAG
1 AAAAAAG
1391820 AAAAA
1 AAAAA
1391825 GGGACAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 18
0.77 0.00 0.23
Matches are distributed among these distances:
6 3 0.05
7 19 0.32
8 22 0.37
9 15 0.25
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:1392631 original size:22 final size:22
Alignment explanation
Indices: 1392598--1392695 Score: 169
Period size: 22 Copynumber: 4.5 Consensus size: 22
1392588 GCTACCCCAT
*
1392598 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
1392620 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
1392642 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
1392664 TAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
1392686 CAAACCTTTG
1 CAAACCTTTG
1392696 GCCAAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:1393595 original size:106 final size:106
Alignment explanation
Indices: 1393470--1395063 Score: 2477
Period size: 106 Copynumber: 15.0 Consensus size: 106
1393460 ATATCGTGCC
* * * * *
1393470 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1393535 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1393576 ACTCCAGACAACGCAAGTTCAATTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1393641 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1393682 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1393747 AATTTCAGAGCCACTTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1393788 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1393853 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1393894 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * *
1393959 AATTTAAGAGTCAATTTTAACTTCACAGCGAAGTATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
1394000 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1394065 AATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1394106 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1394171 AATTTCAGAGCCAATTTCAACTTCACATCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1394212 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1394277 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1394318 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1394383 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1394424 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGATCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1394489 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1394530 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1394595 AATTTCAGAGCCAATTTCAAATTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** *
1394636 ACTCCAGACAATTCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
1394701 AATTTTAGAGCTAATTTCAATTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1394742 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1394807 AATTTCAGAGTCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1394848 ACTCAAGACAACGCAAGTTCAATTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1394913 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * ** *
1394954 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * *
1395019 GATTCCAGAGCCAATTTTAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1395060 ACTC
1 ACTC
1395064 GGAACAATGC
Statistics
Matches: 1365, Mismatches: 123, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 1365 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1395903 original size:37 final size:37
Alignment explanation
Indices: 1395813--1395909 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
1395803 CCTTTTCGTC
1395813 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1395850 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** *
1395887 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
1395910 GATAAGATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1396345 original size:23 final size:23
Alignment explanation
Indices: 1396317--1396363 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
1396307 TGTATATATA
1396317 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTT-TTTCATT
1396340 TATTTATTATAATTTTTTTCATT
1 TATTTATTATAATTTTTTTCATT
1396363 T
1 T
1396364 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTATTATAATTTTTTTCATT
Found at i:1396455 original size:13 final size:13
Alignment explanation
Indices: 1396437--1396462 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1396427 TGTTTACTTA
1396437 TTTACTATATTTT
1 TTTACTATATTTT
1396450 TTTACTATATTTT
1 TTTACTATATTTT
1396463 CCTAACGTTA
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:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:1396676 original size:30 final size:30
Alignment explanation
Indices: 1396576--1396678 Score: 90
Period size: 30 Copynumber: 3.6 Consensus size: 30
1396566 TTATTATTGT
* * * *
1396576 TACTATTTA-GTATTTTATTATATTATACA
1 TACTATTTATTTATTTTTTTATTTTATATA
* *
1396605 TAC-A-TT-TTTATATTTTTATATATATATA
1 TACTATTTATTTATTTTTTTAT-TTTATATA
* *
1396633 TA-TATATATTTATTTTTTTATTTTATTTA
1 TACTATTTATTTATTTTTTTATTTTATATA
1396662 TACTATTTATTTATTTT
1 TACTATTTATTTATTTT
1396679 CATTATGTTT
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
27 11 0.19
28 9 0.16
29 12 0.21
30 25 0.44
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (30 bp):
TACTATTTATTTATTTTTTTATTTTATATA
Found at i:1401122 original size:55 final size:55
Alignment explanation
Indices: 1401038--1401204 Score: 298
Period size: 55 Copynumber: 3.0 Consensus size: 55
1401028 CCACAGGACG
*
1401038 TACACATATAGTGCCCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTT
1 TACACATATAGTGCTCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTT
*
1401093 TACACATATAGTGCTCATATGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
1 TACACATATAGTGCTCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAG-TT
*
1401149 TACACATATAGTGCTCATACGGAAATTCATCAACTTAGTATGAATTTCTTAAGTT
1 TACACATATAGTGCTCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTT
1401204 T
1 T
1401205 TTACACACTT
Statistics
Matches: 107, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
55 54 0.50
56 53 0.50
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (55 bp):
TACACATATAGTGCTCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTT
Found at i:1401177 original size:56 final size:56
Alignment explanation
Indices: 1401038--1401219 Score: 305
Period size: 56 Copynumber: 3.2 Consensus size: 56
1401028 CCACAGGACG
*
1401038 TACACATATAGTGCCCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAG-TT
1 TACACATATAGTGCTCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
*
1401093 TACACATATAGTGCTCATATGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
1 TACACATATAGTGCTCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
*
1401149 TACACATATAGTGCTCATACGGAAATTCATCAACTTAGTATGAATTTCTTAAGTTTT
1 TACACATATAGTGCTCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAG-TTT
1401206 TACACACT-TAGTGC
1 TACACA-TATAGTGC
1401220 CATTTGCTAA
Statistics
Matches: 120, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
55 51 0.43
56 53 0.44
57 15 0.12
58 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (56 bp):
TACACATATAGTGCTCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
Found at i:1401585 original size:22 final size:22
Alignment explanation
Indices: 1401554--1401596 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1401544 TATCGATACT
*
1401554 CATACCATGGTATTGATACTAC
1 CATACCATGGTACTGATACTAC
*
1401576 CATACTATGGTACTGATACTA
1 CATACCATGGTACTGATACTA
1401597 TGTTATGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (22 bp):
CATACCATGGTACTGATACTAC
Found at i:1408539 original size:22 final size:24
Alignment explanation
Indices: 1408482--1408536 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 24
1408472 AGTTGTTTAA
1408482 AATACTTAATTGGTCGCTTGATTTC
1 AATA-TTAATTGGTCGCTTGATTTC
1408507 AATTTTATTAATTGGTCGCTTGATTTC
1 AA---TATTAATTGGTCGCTTGATTTC
1408534 AAT
1 AAT
1408537 TAAATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
24 1 0.04
25 2 0.07
27 22 0.81
28 2 0.07
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (24 bp):
AATATTAATTGGTCGCTTGATTTC
Found at i:1414028 original size:21 final size:20
Alignment explanation
Indices: 1413989--1414053 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
1413979 GTTCGAGTTT
1413989 ATATTTAAATTTAATTATAA
1 ATATTTAAATTTAATTATAA
1414009 ATATTTATAATATT-ATTAT-A
1 ATATTTA-AAT-TTAATTATAA
* *
1414029 CTATTT-GATTCTAATT-TAA
1 ATATTTAAATT-TAATTATAA
1414048 ATATTT
1 ATATTT
1414054 TTTATAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
17 1 0.03
18 4 0.11
19 9 0.24
20 13 0.35
21 8 0.22
22 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (20 bp):
ATATTTAAATTTAATTATAA
Found at i:1418604 original size:18 final size:20
Alignment explanation
Indices: 1418569--1418605 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1418559 CACGGAATGT
1418569 AAGATTATCAATGGGAATAA
1 AAGATTATCAATGGGAATAA
1418589 AAGATTA-CAA-GGGAATA
1 AAGATTATCAATGGGAATA
1418606 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 3 0.18
20 7 0.41
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (20 bp):
AAGATTATCAATGGGAATAA
Found at i:1427737 original size:22 final size:23
Alignment explanation
Indices: 1427712--1427779 Score: 88
Period size: 22 Copynumber: 3.1 Consensus size: 23
1427702 GCGACTTCCG
*
1427712 TCCCCATCTCCGATGAAATTC-A
1 TCCCCATCTCCGACGAAATTCTA
* *
1427734 TCCCCATCTCCGGCGAAA-TCTG
1 TCCCCATCTCCGACGAAATTCTA
1427756 TCCCCATCTCCGACGAAA-TCTA
1 TCCCCATCTCCGACGAAATTCTA
1427778 TC
1 TC
1427780 TATCTCCATC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 2 0.05
22 38 0.95
ACGTcount: A:0.24, C:0.40, G:0.12, T:0.25
Consensus pattern (23 bp):
TCCCCATCTCCGACGAAATTCTA
Found at i:1427825 original size:14 final size:14
Alignment explanation
Indices: 1427806--1427833 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1427796 AGCCACCCTC
1427806 ACAACCATTCACGG
1 ACAACCATTCACGG
1427820 ACAACCATTCACGG
1 ACAACCATTCACGG
1427834 CCACAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (14 bp):
ACAACCATTCACGG
Found at i:1428155 original size:20 final size:20
Alignment explanation
Indices: 1428132--1428190 Score: 118
Period size: 20 Copynumber: 3.0 Consensus size: 20
1428122 TTTGAAACTT
1428132 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
1428152 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
1428172 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
1428191 CGCAATGGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.15
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:1428250 original size:20 final size:20
Alignment explanation
Indices: 1428200--1428250 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1428190 TCGCAATGGG
* *
1428200 ATTTTAGTTTCGCGTTGCGA
1 ATTTAAGTTTCGCGTTACGA
* * *
1428220 TTTTCATTTTCGCGTTACGA
1 ATTTAAGTTTCGCGTTACGA
1428240 ATTTAAGTTTC
1 ATTTAAGTTTC
1428251 AGAAAATACT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.49
Consensus pattern (20 bp):
ATTTAAGTTTCGCGTTACGA
Found at i:1429665 original size:42 final size:42
Alignment explanation
Indices: 1429570--1429668 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
1429560 CCCCCCACTT
* ** * *
1429570 CGAGAGCCATCACCTGATCGAGTCGATTCTACAGTTCGACAC
1 CGAGAGCCATCACCTGATCGAGTCGATTATACACCTCCACAA
* * *
1429612 CCAAAGTCATCACCTGATCGAG-CTGATTATACACCTCCACAA
1 CGAGAGCCATCACCTGATCGAGTC-GATTATACACCTCCACAA
1429654 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
1429669 ATTCCATCAC
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 1 0.02
42 44 0.98
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.20
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGTCGATTATACACCTCCACAA
Found at i:1429810 original size:21 final size:21
Alignment explanation
Indices: 1429786--1429826 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1429776 AGGGGTGTTA
*
1429786 CGTGATGAGATCAGTGCTTTG
1 CGTGATGAGATCAGTACTTTG
*
1429807 CGTGATGAGGTCAGTACTTT
1 CGTGATGAGATCAGTACTTT
1429827 ACGTCACGAT
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:0.15, G:0.32, T:0.34
Consensus pattern (21 bp):
CGTGATGAGATCAGTACTTTG
Found at i:1430072 original size:12 final size:12
Alignment explanation
Indices: 1430055--1430096 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1430045 TTTTTCAGTA
1430055 TTATTTAATT-AT
1 TTATTT-ATTAAT
*
1430067 TTATTTATTGAT
1 TTATTTATTAAT
*
1430079 TTATGTATTAAT
1 TTATTTATTAAT
1430091 TTATTT
1 TTATTT
1430097 TTAGTGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (12 bp):
TTATTTATTAAT
Found at i:1430266 original size:21 final size:21
Alignment explanation
Indices: 1430240--1430337 Score: 124
Period size: 21 Copynumber: 4.7 Consensus size: 21
1430230 GATTCACCTG
1430240 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
1430261 TCATCGTTCAAGAGGCCACTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
1430282 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
*
1430303 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
1430324 CCACCATTCAAGAG
1 TCATCGTTCAAGAG
1430338 CCCGATTCAT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1430291 original size:42 final size:42
Alignment explanation
Indices: 1430244--1430337 Score: 154
Period size: 42 Copynumber: 2.2 Consensus size: 42
1430234 CACCTGTCAT
1430244 CGTTCAAGAGGCCCCTCTCATCGTTCAAGAGG-CCACTCCCAC
1 CGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGTCC-CTCCCAC
*
1430286 CGTTCAAGAGGCCCCTGTCATCGTTCAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGTCCCTCCCAC
*
1430328 CATTCAAGAG
1 CGTTCAAGAG
1430338 CCCGATTCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 47 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGTCCCTCCCAC
Found at i:1431886 original size:29 final size:29
Alignment explanation
Indices: 1431844--1431908 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
1431834 TTGAAGGTAC
1431844 ACTTTCGCAACAATCGCAACACGAATTTG
1 ACTTTCGCAACAATCGCAACACGAATTTG
**
1431873 ACTTTCGCAACAATCGCAACGTGAATTTG
1 ACTTTCGCAACAATCGCAACACGAATTTG
1431902 ACTTTCG
1 ACTTTCG
1431909 TAATGCGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (29 bp):
ACTTTCGCAACAATCGCAACACGAATTTG
Found at i:1434420 original size:24 final size:24
Alignment explanation
Indices: 1434393--1434439 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1434383 CAAAATCTGA
1434393 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
* *
1434417 GTATTGGCCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1434440 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1435415 original size:20 final size:19
Alignment explanation
Indices: 1435392--1435461 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
1435382 TAAAATTCAG
1435392 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTC-AAAATCGA
* ** *
1435412 GTTGTGAAAACAAAATTCGC
1 GTTGCGAATTCAAAA-TCGA
*
1435432 GTTGTGAATTCAGAAATCGA
1 GTTGCGAATTCA-AAATCGA
*
1435452 GATGCGAATT
1 GTTGCGAATT
1435462 TGAAATTCAG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 4 0.10
20 32 0.82
21 3 0.08
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (19 bp):
GTTGCGAATTCAAAATCGA
Found at i:1435519 original size:20 final size:20
Alignment explanation
Indices: 1435494--1435545 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1435484 GGAAAATCAC
1435494 GTTGCGAATTTGGAAACT-GT
1 GTTGCGAATTTGG-AACTCGT
* **
1435514 GTTGCGAAATTGGAGTTCGT
1 GTTGCGAATTTGGAACTCGT
1435534 GTTGCGAATTTG
1 GTTGCGAATTTG
1435546 TTGGTCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.21, C:0.10, G:0.33, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTGGAACTCGT
Found at i:1439154 original size:14 final size:13
Alignment explanation
Indices: 1439118--1439181 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 13
1439108 GAGAGAAAAA
1439118 AATAAAAAATATAT
1 AATAAAAAATA-AT
1439132 ATATAAAAAAATAAT
1 A-AT-AAAAAATAAT
*
1439147 AAT-GAAAATAAAT
1 AATAAAAAAT-AAT
1439160 CAA-AAAAAATAAT
1 -AATAAAAAATAAT
1439173 AAATAAAAA
1 -AATAAAAA
1439182 TTAAATAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
12 5 0.12
13 8 0.20
14 15 0.37
15 5 0.12
16 8 0.20
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (13 bp):
AATAAAAAATAAT
Found at i:1439164 original size:23 final size:21
Alignment explanation
Indices: 1439137--1439179 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 21
1439127 TATATATATA
1439137 AAAAAATAATAATGAAAATAAATC
1 AAAAAA-AATAAT--AAATAAATC
1439161 AAAAAAAATAATAAATAAA
1 AAAAAAAATAATAAATAAA
1439180 AATTAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (21 bp):
AAAAAAAATAATAAATAAATC
Found at i:1439182 original size:23 final size:23
Alignment explanation
Indices: 1439113--1439182 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
1439103 ATCAAGAGAG
* *
1439113 AAAAAAATAAAAAATATATATATAA
1 AAAAAAATAATAAATA-A-AAATAA
* *
1439138 AAAAATAATAATGAAA-ATAAATCA
1 AAAAA-AATAAT-AAATAAAAATAA
1439162 AAAAAAATAATAAATAAAAAT
1 AAAAAAATAATAAATAAAAAT
1439183 TAAATAAAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
22 3 0.08
23 11 0.30
24 9 0.24
25 5 0.14
26 6 0.16
27 3 0.08
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (23 bp):
AAAAAAATAATAAATAAAAATAA
Found at i:1439260 original size:32 final size:31
Alignment explanation
Indices: 1439137--1439287 Score: 85
Period size: 32 Copynumber: 4.7 Consensus size: 31
1439127 TATATATATA
* * *
1439137 AAAAAATAATAATGAAAATAAATCAAAAAAAAT
1 AAAAAATAA-AA-GAAAAAAAATCAAAGAAAAG
* * * *
1439170 AATAAATAAAA-ATTAAATAAAGCAAAAAACAAG
1 AAAAAATAAAAGA--AAAAAAATCAAAGAA-AAG
* * * *
1439203 -AAAAGTGAGAGAAAGAAAAAGTCAAAGGAAAAT
1 AAAAAATAAAAGAAA-AAAAA-TCAAA-GAAAAG
1439236 AATAAAA-AAAAGAAAAAAAATCAAAGAAAAG
1 AA-AAAATAAAAGAAAAAAAATCAAAGAAAAG
1439267 AAAAAATAAAA-AATAAAAAAT
1 AAAAAATAAAAGAA-AAAAAAT
1439288 ATTAAAAAAT
Statistics
Matches: 92, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
30 7 0.08
31 20 0.22
32 31 0.34
33 22 0.24
34 9 0.10
35 3 0.03
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.13
Consensus pattern (31 bp):
AAAAAATAAAAGAAAAAAAATCAAAGAAAAG
Found at i:1439265 original size:31 final size:32
Alignment explanation
Indices: 1439212--1439287 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 32
1439202 GAAAAGTGAG
*
1439212 AGAAAGAAAAAGTCAAAGGAAAATAATAAAA-AAA
1 AGAAA-AAAAA-TCAAAGGAAAAGAA-AAAATAAA
1439246 AGAAAAAAAATCAAA-GAAAAGAAAAAATAAA
1 AGAAAAAAAATCAAAGGAAAAGAAAAAATAAA
1439277 A-AATAAAAAAT
1 AGAA-AAAAAAT
1439288 ATTAAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 6 0.15
31 18 0.46
32 5 0.13
33 5 0.13
34 5 0.13
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.09
Consensus pattern (32 bp):
AGAAAAAAAATCAAAGGAAAAGAAAAAATAAA
Found at i:1439284 original size:19 final size:19
Alignment explanation
Indices: 1439231--1439284 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
1439221 AAGTCAAAGG
1439231 AAAATAATAAAAAAAAGAA
1 AAAATAATAAAAAAAAGAA
*
1439250 AAAA-AATCAAAGAAAAGAA
1 AAAATAAT-AAAAAAAAGAA
1439269 AAAATAA-AAAATAAAA
1 AAAATAATAAAA-AAAA
1439285 AATATTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.20
19 22 0.73
20 2 0.07
ACGTcount: A:0.83, C:0.02, G:0.06, T:0.09
Consensus pattern (19 bp):
AAAATAATAAAAAAAAGAA
Found at i:1439295 original size:10 final size:10
Alignment explanation
Indices: 1439280--1439307 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1439270 AAATAAAAAA
1439280 TAAAAAATAT
1 TAAAAAATAT
1439290 TAAAAAATAT
1 TAAAAAATAT
1439300 TAAAAAAT
1 TAAAAAAT
1439308 GTTATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:1440446 original size:3 final size:3
Alignment explanation
Indices: 1440438--1440476 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1440428 AAAGGAAATA
1440438 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1440477 TATATATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1440524 original size:33 final size:31
Alignment explanation
Indices: 1440474--1440547 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1440464 TAATAATATA
**
1440474 ATATA-TATATTTCAAAAATATATTTTTAAACT
1 ATATATTATATTTCAAAAA-AT-TTTCAAAACT
* *
1440506 ATATATTATATTTTAAAAAGTTTTCAAAACT
1 ATATATTATATTTCAAAAAATTTTCAAAACT
1440537 ATATATTATAT
1 ATATATTATAT
1440548 AGTTTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 19 0.51
32 6 0.16
33 12 0.32
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (31 bp):
ATATATTATATTTCAAAAAATTTTCAAAACT
Found at i:1440615 original size:75 final size:71
Alignment explanation
Indices: 1440536--1440922 Score: 271
Period size: 75 Copynumber: 5.2 Consensus size: 71
1440526 TTTTCAAAAC
* *
1440536 TATATAT-TATATAGTTTTCAAAATGTTTT-AAAA-ATATTATAGAAGTTTTCAAAAAATGTTTT
1 TATATATATATATATTTTTCAAAATGTTTTAAAAATATATTATATAAGTTTTC-AAAAAT-TTTT
1440598 TAAAATTA
64 TAAAATTA
*
1440606 TATAT-TATATA-ATTTTTCAAAAATGTTTTTAAAATTATATATTATATAATTTTTCAAAAATAT
1 TATATATATATATATTTTTC-AAAATG-TTTTAAAA--ATATATTATATAAGTTTTCAAAAAT-T
*
1440669 TTTTAAAACTA
61 TTTTAAAATTA
* * *
1440680 TACAT-TATATA-ATTTTTTAAAAATGTTTTAAAAAACTATATACTATATAAGTTTTC-AAAATA
1 TATATATATATATA-TTTTTCAAAATGTTTT-AAAAA-TATAT--TATATAAGTTTTCAAAAATT
1440742 TTTTAAAACTTA
61 TTTTAAAA-TTA
*
1440754 TATA-ATATATAAATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATA-TTTT-AAAAAT
1 TATATATATATATAT-TTTTCAAAATGTTTT--AAAA--ATATATTATATA-AGTTTTCAAAAAT
*
1440816 GTTTTCAAAAATTA
60 -TTTT-TAAAATTA
* * * *
1440830 TATA-ATATATAAATTTTTAAAAATCATTTTCTAAAAAT-TA-TATATTATATTTTATCAAAAAT
1 TATATATATATATATTTTTCAAAAT--GTTT-TAAAAATATATTATA-TA-AGTTT-TCAAAAAT
*
1440892 ATTTTCACAAATTA
60 -TTTTTA-AAATTA
1440906 TATTATTATATATATAT
1 TA-TA-TATATATATAT
1440923 ATATATAAAA
Statistics
Matches: 264, Mismatches: 19, Indels: 59
0.77 0.06 0.17
Matches are distributed among these distances:
69 7 0.03
70 15 0.06
71 4 0.02
72 8 0.03
73 23 0.09
74 61 0.23
75 73 0.28
76 48 0.18
77 14 0.05
78 2 0.01
79 9 0.03
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (71 bp):
TATATATATATATATTTTTCAAAATGTTTTAAAAATATATTATATAAGTTTTCAAAAATTTTTTA
AAATTA
Found at i:1440637 original size:37 final size:37
Alignment explanation
Indices: 1440469--1440917 Score: 357
Period size: 37 Copynumber: 12.3 Consensus size: 37
1440459 AATAATAATA
* * * * *
1440469 ATATAATATAT-ATATTTCAAAAATATATTTTTAAACT
1 ATATATTATATAATTTTTCAAAAATGT-TTTTAAAATT
* *
1440506 ATATA-T-TAT-A-TTTT-AAAAA-GTTTTCAAAACT
1 ATATATTATATAATTTTTCAAAAATGTTTTTAAAATT
*
1440537 ATATATTATAT-AGTTTTC-AAAATG-TTTT-AAA--
1 ATATATTATATAATTTTTCAAAAATGTTTTTAAAATT
* *
1440568 A-ATATTATAGAAGTTTTCAAAAAATGTTTTTAAAATT
1 ATATATTATATAATTTTTC-AAAAATGTTTTTAAAATT
1440605 ATATATTATATAATTTTTCAAAAATGTTTTTAAAATT
1 ATATATTATATAATTTTTCAAAAATGTTTTTAAAATT
* *
1440642 ATATATTATATAATTTTTCAAAAATATTTTTAAAACT
1 ATATATTATATAATTTTTCAAAAATGTTTTTAAAATT
* * * *
1440679 ATACATTATATAATTTTTTAAAAATGTTTTAAAAAACT
1 ATATATTATATAATTTTTCAAAAATGTTTT-TAAAATT
* * *
1440717 ATATACTATATAAGTTTTC-AAAAT-ATTTTAAAACTT
1 ATATATTATATAATTTTTCAAAAATGTTTTTAAAA-TT
* * *
1440753 ATATAATATATAAATGTTTTC-AAAATGTTTTCAAAAACT
1 ATATATTATAT-AAT-TTTTCAAAAATGTTTT-TAAAATT
*
1440792 ATATATTATAT-ATATTTT-AAAAATGTTTTCAAAAATT
1 ATATATTATATAAT-TTTTCAAAAATGTTTT-TAAAATT
* *
1440829 ATATAATATATAAATTTTT-AAAAATCATTTTCTAAAAATT
1 ATATATTATAT-AATTTTTCAAAAAT-GTTTT-T-AAAATT
* * *
1440869 ATATATTATAT--TTTATCAAAAATATTTTCACAAATT
1 ATATATTATATAATTTTTCAAAAATGTTTTTA-AAATT
1440905 ATATTATTATATA
1 ATA-TATTATATA
1440918 TATATATATA
Statistics
Matches: 349, Mismatches: 35, Indels: 55
0.79 0.08 0.13
Matches are distributed among these distances:
30 8 0.02
31 21 0.06
32 2 0.01
33 18 0.05
34 18 0.05
35 13 0.04
36 23 0.07
37 143 0.41
38 62 0.18
39 21 0.06
40 20 0.06
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (37 bp):
ATATATTATATAATTTTTCAAAAATGTTTTTAAAATT
Found at i:1440780 original size:11 final size:11
Alignment explanation
Indices: 1440764--1440788 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1440754 TATAATATAT
1440764 AAATGTTTTCA
1 AAATGTTTTCA
1440775 AAATGTTTTCA
1 AAATGTTTTCA
1440786 AAA
1 AAA
1440789 ACTATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:1442131 original size:6 final size:6
Alignment explanation
Indices: 1442120--1442150 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1442110 ATCGTCGTGG
*
1442120 ATTAGC ATTAGC ATTAGC ATTAGC ATCAGC A
1 ATTAGC ATTAGC ATTAGC ATTAGC ATTAGC A
1442151 AAGTCTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (6 bp):
ATTAGC
Found at i:1442674 original size:23 final size:22
Alignment explanation
Indices: 1442658--1442718 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 22
1442648 ATTTGCATTT
1442658 AATATTTTAATTAATTTGAATCA
1 AATA-TTTAATTAATTTGAATCA
*
1442681 AATATTTAATTAATTTAAAT--
1 AATATTTAATTAATTTGAATCA
* *
1442701 AATATCTAATTATTTTGA
1 AATATTTAATTAATTTGA
1442719 TTTGAATCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 15 0.44
22 15 0.44
23 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (22 bp):
AATATTTAATTAATTTGAATCA
Found at i:1444599 original size:34 final size:34
Alignment explanation
Indices: 1444547--1444630 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 34
1444537 ATTCAAACTT
* *
1444547 AAATATGT-ATTAT-TTTAAT-TTCAAATATACAA
1 AAATATATAATTATCTTTAATATTCAAAT-TAAAA
1444579 AAATATATAATTATCTTTAATATTCAAATTAAAA
1 AAATATATAATTATCTTTAATATTCAAATTAAAA
*
1444613 AAAGTA-ATAAATATCTTT
1 AAA-TATATAATTATCTTT
1444631 TTAAATTGAC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.16
33 5 0.11
34 24 0.53
35 9 0.20
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (34 bp):
AAATATATAATTATCTTTAATATTCAAATTAAAA
Found at i:1444824 original size:190 final size:190
Alignment explanation
Indices: 1444513--1444870 Score: 494
Period size: 190 Copynumber: 1.9 Consensus size: 190
1444503 TTTAAAATAT
*
1444513 TCAAAAGATAAAACTTCTTTTACCATTCAAACTTAAATATGTATTATTTTAATTTCAAATATACA
1 TCAAAAGATAAAACTTCTTTTACCATTCAAACTTAAATAAGTATTATTTTAATTTCAAATATACA
* * *
1444578 AAAATATATAATTATCTTTAATATTCAAATTAAAAAAAGTAATAAATATCTTTTTAAATTGACAT
66 AAAATACATAATTATCTTTAATATTCAAATTAAAAAAAGTAAGAAATATCTTTTTAAATTAACAT
*
1444643 ATTCAAAGAATAATTATCTTACTAATATTCAAATTAAATAATATATTTAATTTACGATGG
131 ATTAAAAGAATAATTATCTTACTAATATTCAAATTAAATAATATATTTAATTTACGATGG
* * * *
1444703 TCAAAAGGT-AAA-TTCTTGTTACTATTCAAGCTT-AATAAGATATTATTTTAATTTGAAATATA
1 TCAAAAGATAAAACTTCTT-TTACCATTCAAACTTAAATAAG-TATTATTTTAATTTCAAATATA
* *
1444765 CAAAAGTACATAACTATAT-TTTAATATTCAAAATTAAAAAGA-TAAGAAATA-CTTTTTTAAAT
64 CAAAAATACATAA-T-TATCTTTAATATTC-AAATTAAAAAAAGTAAGAAATATC-TTTTTAAAT
* * *
1444827 TAACTTATTAAAAGAGTAATTATCTTACTAATATTTAAATTAAA
125 TAACATATTAAAAGAATAATTATCTTACTAATATTCAAATTAAA
1444871 AATTATCTTT
Statistics
Matches: 148, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
188 10 0.07
189 49 0.33
190 75 0.51
191 14 0.09
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (190 bp):
TCAAAAGATAAAACTTCTTTTACCATTCAAACTTAAATAAGTATTATTTTAATTTCAAATATACA
AAAATACATAATTATCTTTAATATTCAAATTAAAAAAAGTAAGAAATATCTTTTTAAATTAACAT
ATTAAAAGAATAATTATCTTACTAATATTCAAATTAAATAATATATTTAATTTACGATGG
Found at i:1453765 original size:15 final size:14
Alignment explanation
Indices: 1453739--1453776 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
1453729 TCAAAATTTT
*
1453739 AAATTAAAAATATA
1 AAATTTAAAATATA
1453753 AAGATTTAAAATATA
1 AA-ATTTAAAATATA
1453768 AAATTTAAA
1 AAATTTAAA
1453777 TTTATGGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AAATTTAAAATATA
Found at i:1453771 original size:22 final size:21
Alignment explanation
Indices: 1453736--1453776 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1453726 AAATCAAAAT
*
1453736 TTTAAATTAAAAATATAAAGA
1 TTTAAAATAAAAATATAAAGA
*
1453757 TTTAAAATATAAAATTTAAA
1 TTTAAAATA-AAAATATAAA
1453777 TTTATGGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TTTAAAATAAAAATATAAAGA
Found at i:1454118 original size:14 final size:15
Alignment explanation
Indices: 1454087--1454121 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1454077 TGAAAAAATG
*
1454087 ACTCGACTCGAGATA
1 ACTCAACTCGAGATA
1454102 ACTCAACTCGA-ATA
1 ACTCAACTCGAGATA
1454116 ACTCAA
1 ACTCAA
1454122 ATTTTTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.20
Consensus pattern (15 bp):
ACTCAACTCGAGATA
Found at i:1455039 original size:16 final size:16
Alignment explanation
Indices: 1454995--1455045 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
1454985 TTTAAAATAT
1454995 TAAAATTAAAG-TTTA
1 TAAAATTAAAGTTTTA
1455010 TAAAATATATAAGTTTTA
1 TAAAAT-TA-AAGTTTTA
*
1455028 -AAAATTACAAGTATTA
1 TAAAATTA-AAGTTTTA
1455044 TA
1 TA
1455046 TTAAATTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 6 0.20
16 11 0.37
17 9 0.30
18 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (16 bp):
TAAAATTAAAGTTTTA
Found at i:1458629 original size:27 final size:27
Alignment explanation
Indices: 1458591--1458650 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
1458581 ATGATCAATG
1458591 CATCTACTCTCCACATGTACATGCATA
1 CATCTACTCTCCACATGTACATGCATA
1458618 CATCTACTCTCCACATGTACATGCATA
1 CATCTACTCTCCACATGTACATGCATA
1458645 CATCTA
1 CATCTA
1458651 AGCAGCAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (27 bp):
CATCTACTCTCCACATGTACATGCATA
Found at i:1466109 original size:2 final size:2
Alignment explanation
Indices: 1466102--1466144 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1466092 TTCCCCAACC
1466102 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1466144 A
1 A
1466145 CGTTTATTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1467701 original size:17 final size:17
Alignment explanation
Indices: 1467679--1467725 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
1467669 CATTAAAAGC
*
1467679 CTTGTTGCTTAACTCGA
1 CTTGTTGCTCAACTCGA
1467696 CTTGTTGCTCAACTCGA
1 CTTGTTGCTCAACTCGA
1467713 CTTGTTGCTCAAC
1 CTTGTTGCTCAAC
1467726 ATGAATCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (17 bp):
CTTGTTGCTCAACTCGA
Found at i:1469003 original size:37 final size:36
Alignment explanation
Indices: 1468948--1469034 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 36
1468938 TGGTAACCAA
1468948 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTT-AAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
1468985 CTTTAAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTAAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
* *
1469022 -GTTGAAAAATGAT
1 CTTTAAAAAATGAT
1469035 AATGGGATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
35 2 0.05
36 15 0.34
37 27 0.61
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.43
Consensus pattern (36 bp):
CTTTAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:1469432 original size:12 final size:12
Alignment explanation
Indices: 1469415--1469439 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1469405 ATTTTTTGCG
1469415 AGGTTACTATTC
1 AGGTTACTATTC
1469427 AGGTTACTATTC
1 AGGTTACTATTC
1469439 A
1 A
1469440 CGTGAATAGT
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGGTTACTATTC
Found at i:1469461 original size:16 final size:16
Alignment explanation
Indices: 1469440--1469473 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1469430 TTACTATTCA
*
1469440 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1469456 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1469472 CG
1 CG
1469474 GTCGGTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1471837 original size:134 final size:134
Alignment explanation
Indices: 1471580--1471847 Score: 520
Period size: 133 Copynumber: 2.0 Consensus size: 134
1471570 GGTGATGAGT
1471580 TTGGTTATCGGTTTTGGGACTACAAAAATCGGAAGATCATTAGAAGCAGAGACGTCATTTTCAAT
1 TTGGTTATCGGTTTTGGGACTACAAAAATCGGAAGATCATTAGAAGCAGAGACGTCATTTTCAAT
1471645 GAAAATGTGATGTACAAAGAAGGTCAACCGCAGAATCAAGTAATACCGAAGCTGAAACAAAGGAA
66 GAAAATGTGATGTACAAAGAAGGTCAACCGCAGAATCAAGTAATACCGAAGCTGAAACAAAGGAA
1471710 TTTG
131 TTTG
1471714 TTGGTTATCGGTTTT-GGACTACAAAAATCGGAAGATCATTAGAAGCAGAGACGTCATTTTCAAT
1 TTGGTTATCGGTTTTGGGACTACAAAAATCGGAAGATCATTAGAAGCAGAGACGTCATTTTCAAT
1471778 GAAAATGTGATGTACAAAGACAGGTCAACCGCAGAATCAAGTAATACCGAAGCTGAAACAAAGGA
66 GAAAATGTGATGTACAAAGA-AGGTCAACCGCAGAATCAAGTAATACCGAAGCTGAAACAAAGGA
1471843 ATTTG
130 ATTTG
1471848 CTGAGTTCGA
Statistics
Matches: 133, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
133 69 0.52
134 64 0.48
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (134 bp):
TTGGTTATCGGTTTTGGGACTACAAAAATCGGAAGATCATTAGAAGCAGAGACGTCATTTTCAAT
GAAAATGTGATGTACAAAGAAGGTCAACCGCAGAATCAAGTAATACCGAAGCTGAAACAAAGGAA
TTTG
Found at i:1473715 original size:37 final size:38
Alignment explanation
Indices: 1473660--1473743 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
1473650 TGGTAACCAA
1473660 CTTTGAAAAA-ATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGATTTTCAAAGTTTGGTAAATGTTT
* *
1473697 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGATTTTCAAAGTTTGGTAAATGTTT
*
1473734 -GTTGAAAAAT
1 CTTTGAAAAAT
1473744 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:1488146 original size:14 final size:15
Alignment explanation
Indices: 1488103--1488146 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
1488093 AATTTAGTCC
1488103 TAATTTAAATTTA-T
1 TAATTTAAATTTATT
*
1488117 TAATTTAAATTCATT
1 TAATTTAAATTTATT
1488132 TAA-TTAAATTTATT
1 TAATTTAAATTTATT
1488146 T
1 T
1488147 TATATCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATTTAAATTTATT
Found at i:1488519 original size:22 final size:22
Alignment explanation
Indices: 1488492--1488535 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1488482 TAATATAAAA
*
1488492 TAAAAAT-ATTTTTATAAATTTT
1 TAAAAATAAATTTTAT-AATTTT
1488514 TAAAAATAAATTTTATAATTTT
1 TAAAAATAAATTTTATAATTTT
1488536 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAAATAAATTTTATAATTTT
Found at i:1488771 original size:22 final size:22
Alignment explanation
Indices: 1488744--1488787 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1488734 AATATAAAAT
*
1488744 AAAAAT-ATTTTTATAAATTTTA
1 AAAAATAAATTTTAT-AATTTTA
1488766 AAAAATAAATTTTATAATTTTA
1 AAAAATAAATTTTATAATTTTA
1488788 TATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAAATAAATTTTATAATTTTA
Found at i:1488783 original size:251 final size:248
Alignment explanation
Indices: 1488320--1488822 Score: 891
Period size: 251 Copynumber: 2.0 Consensus size: 248
1488310 TCTCATAATA
*
1488320 TTATTAGTAATATAAAAATAAAGAAATTAAAATATTCAAATTATATTTAACTTTTAATATTTTTA
1 TTATTAGTAATATAAAAATAAAGAAATTAAAATATTCAAATGATATTTAACTTTTAATATTTTTA
*
1488385 TATTTTTAAAATAAATAAAAATAAATTAATATTTTATTTTTAAAATCAAATTTAATATTTTTTAT
66 TATTTTTAAAATAAATAAAAATAAATTAATATTTTATTTTTAAAATCAAATATAATATTTTTTAT
* * *
1488450 ATTTCTAGACAAAATCTATGGAATAAATCATATAATATAAAATAAAAATATTTTTATAAATTTTT
131 AATTCTAGACAAAATATATGGAATAAATCATATAATATAAAATAAAAATATTTTTATAAATTTTA
*
1488515 AAAAATAAATTTTATAATTTTATATTTTAAAATAATTGAATTTAATGTAAAAT
196 AAAAATAAATTTTATAATTTTATATTTAAAAATAATTGAATTTAATGTAAAAT
*
1488568 TTATTAGTAATATAAAAATAAATAAATTAAAATATTCAAATGATATTTAACTTTTAATATTTTTA
1 TTATTAGTAATATAAAAATAAAGAAATTAAAATATTCAAATGATATTTAACTTTTAATATTTTTA
1488633 TATTTTTAACATAAATAAATAAAAATAAATTAATATTTTATTTTTAAAATCAAATATAATA-TTT
66 TATTTTT---A-AAATAAATAAAAATAAATTAATATTTTATTTTTAAAATCAAATATAATATTTT
*
1488697 TTATAATTCTAGACAAAATATATGGGATAAATCATATAATATAAAATAAAAATATTTTTATAAAT
127 TTATAATTCTAGACAAAATATATGGAATAAATCATATAATATAAAATAAAAATATTTTTATAAAT
1488762 TTTAAAAAATAAATTTTATAATTTTATATTTAAAAATAATTGAATTTAATGTAAAAT
192 TTTAAAAAATAAATTTTATAATTTTATATTTAAAAATAATTGAATTTAATGTAAAAT
1488819 TTAT
1 TTAT
1488823 AATTACAATT
Statistics
Matches: 243, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
248 70 0.29
251 125 0.51
252 48 0.20
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (248 bp):
TTATTAGTAATATAAAAATAAAGAAATTAAAATATTCAAATGATATTTAACTTTTAATATTTTTA
TATTTTTAAAATAAATAAAAATAAATTAATATTTTATTTTTAAAATCAAATATAATATTTTTTAT
AATTCTAGACAAAATATATGGAATAAATCATATAATATAAAATAAAAATATTTTTATAAATTTTA
AAAAATAAATTTTATAATTTTATATTTAAAAATAATTGAATTTAATGTAAAAT
Found at i:1489192 original size:25 final size:25
Alignment explanation
Indices: 1489145--1489192 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1489135 TTAAAAATAT
* *
1489145 AAATAAATATTGAATTTGGTTTTAA
1 AAATAAATATTGAACTTGATTTTAA
1489170 AAATAAAATATTGAACTT-ATTTT
1 AAAT-AAATATTGAACTTGATTTT
1489193 GATTTGTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (25 bp):
AAATAAATATTGAACTTGATTTTAA
Found at i:1490307 original size:24 final size:23
Alignment explanation
Indices: 1490280--1490335 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
1490270 ATTAAACAAC
1490280 TATTATATAATTTTATAAAATTAA
1 TATTATATAATTTTA-AAAATTAA
* * *
1490304 TATTAAATTATTTTAAATATTAA
1 TATTATATAATTTTAAAAATTAA
1490327 -ATT-TATAAT
1 TATTATATAAT
1490336 AAAATATACA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 4 0.15
22 3 0.11
23 7 0.26
24 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATATAATTTTAAAAATTAA
Found at i:1493853 original size:59 final size:59
Alignment explanation
Indices: 1493782--1493903 Score: 199
Period size: 59 Copynumber: 2.1 Consensus size: 59
1493772 ACTTGTTGGT
* * *
1493782 ACATCAAACGCGTTTATAGCTTTGCGTATGTATGTTTGTCTTGATGACTTTACTCTTTC
1 ACATCAAACGCGTATATAGCTTTGCATATGTATGTTTGTCTCGATGACTTTACTCTTTC
* *
1493841 ACATCAATCGCGTATATAGCTTTGCATATGTGTGTTTGTCTCGATGACTTTACTCTTTC
1 ACATCAAACGCGTATATAGCTTTGCATATGTATGTTTGTCTCGATGACTTTACTCTTTC
1493900 ACAT
1 ACAT
1493904 TTTCATTGCA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (59 bp):
ACATCAAACGCGTATATAGCTTTGCATATGTATGTTTGTCTCGATGACTTTACTCTTTC
Found at i:1496526 original size:2 final size:2
Alignment explanation
Indices: 1496519--1496547 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1496509 AACTTTTAAA
1496519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1496548 AAGTAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1498817 original size:36 final size:36
Alignment explanation
Indices: 1498765--1498835 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
1498755 ACAGGCGGCA
*
1498765 TTAAAACGATGTAGTTTTGAAAAAGTTTAATTTATG
1 TTAAAACGATGCAGTTTTGAAAAAGTTTAATTTATG
* *
1498801 TTAAAACTATGCAGTTTTGAAAGAGTTTAATTTAT
1 TTAAAACGATGCAGTTTTGAAAAAGTTTAATTTAT
1498836 ATTAGAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.42
Consensus pattern (36 bp):
TTAAAACGATGCAGTTTTGAAAAAGTTTAATTTATG
Found at i:1510061 original size:31 final size:31
Alignment explanation
Indices: 1510026--1510084 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1510016 GTTAACACTG
* *
1510026 AGACACCCAAAGTGGTAACGTTTGTAACGTC
1 AGACACCCAAAGTGATAACGTTTATAACGTC
* *
1510057 AGACACTCAAAGTGATAATGTTTATAAC
1 AGACACCCAAAGTGATAACGTTTATAAC
1510085 TTTAGGCACC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (31 bp):
AGACACCCAAAGTGATAACGTTTATAACGTC
Found at i:1520941 original size:24 final size:22
Alignment explanation
Indices: 1520898--1520945 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
1520888 CTTCACCCCT
1520898 TATATTTATTAAAAAGTTGACAA
1 TATATTTATTAAAAAGTTGA-AA
*
1520921 TATATTCTTTTAATAAA-TTGAAA
1 TATATT-TATTAA-AAAGTTGAAA
1520944 TA
1 TA
1520946 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 10 0.45
24 9 0.41
25 3 0.14
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (22 bp):
TATATTTATTAAAAAGTTGAAA
Found at i:1521025 original size:29 final size:30
Alignment explanation
Indices: 1520979--1521047 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
1520969 TTAGTTATGT
* *
1520979 TATTTTTTATAAAATATT-TTTTTTAAAATTA
1 TATTTTTT-TAAAATATTATTGTAT-AAATTA
* *
1521010 TATTTTTTT-AATTATTATTGTATAATTTA
1 TATTTTTTTAAAATATTATTGTATAAATTA
1521039 TATTTTTTT
1 TATTTTTTT
1521048 TGGATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 20 0.61
30 5 0.15
31 8 0.24
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (30 bp):
TATTTTTTTAAAATATTATTGTATAAATTA
Found at i:1521027 original size:17 final size:16
Alignment explanation
Indices: 1520979--1521020 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
1520969 TTAGTTATGT
1520979 TATTTTTTATAAAA-TA
1 TATTTTTT-TAAAATTA
1520995 T-TTTTTTTAAAATTA
1 TATTTTTTTAAAATTA
1521010 TATTTTTTTAA
1 TATTTTTTTAA
1521021 TTATTATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.21
15 9 0.38
16 10 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTTTTTAAAATTA
Found at i:1521028 original size:15 final size:16
Alignment explanation
Indices: 1520978--1521028 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
1520968 ATTAGTTATG
*
1520978 TTATTTTTTATAAAATA
1 TTATTTTTTAT-AATTA
*
1520995 TT-TTTTTTAAAATTA
1 TTATTTTTTATAATTA
1521010 -TATTTTTT-TAATTA
1 TTATTTTTTATAATTA
1521024 TTATT
1 TTATT
1521029 GTATAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 6 0.21
15 14 0.48
16 7 0.24
17 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTTTTATAATTA
Found at i:1521181 original size:14 final size:13
Alignment explanation
Indices: 1521153--1521179 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1521143 TAATCTCAGC
1521153 ATGGGGGTGTTAA
1 ATGGGGGTGTTAA
1521166 ATGGGGGTGTTAA
1 ATGGGGGTGTTAA
1521179 A
1 A
1521180 ATATTCGAGC
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:0.26, C:0.00, G:0.44, T:0.30
Consensus pattern (13 bp):
ATGGGGGTGTTAA
Found at i:1529193 original size:16 final size:16
Alignment explanation
Indices: 1529172--1529214 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
1529162 ATCTTAGCCC
1529172 TGAACAATTGAGAAGA
1 TGAACAATTGAGAAGA
1529188 TGAACAATTGAGAAGA
1 TGAACAATTGAGAAGA
1529204 TGAACAATTGA
1 TGAACAATTGA
1529215 ATCGAAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21
Consensus pattern (16 bp):
TGAACAATTGAGAAGA
Found at i:1529258 original size:36 final size:36
Alignment explanation
Indices: 1529211--1529290 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
1529201 AGATGAACAA
1529211 TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCACT
1 TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCACT
* *
1529247 TTGAATCGAAAGTGTCGATGCTTCGTTTCGTTCACT
1 TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCACT
1529283 TTGAATCG
1 TTGAATCG
1529291 GAAGACAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (36 bp):
TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCACT
Found at i:1530708 original size:36 final size:36
Alignment explanation
Indices: 1530660--1530799 Score: 185
Period size: 36 Copynumber: 3.9 Consensus size: 36
1530650 ATTCAAGAAA
* *
1530660 AACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTG
1 AACGGAAGGAAGCATCGACACTTTCGATTCAAAGTG
* * *
1530696 AACGGAATGAAGCATTGACACTTTCGATTC-AAGAAG
1 AACGGAAGGAAGCATCGACACTTTCGATTCAAAG-TG
* *
1530732 AACGAAAGGAAGCATC-AGCACTTTCGATTCAAAGTA
1 AACGGAAGGAAGCATCGA-CACTTTCGATTCAAAGTG
1530768 AACGGAAGGAAGCATCGACACTTTCGATTCAA
1 AACGGAAGGAAGCATCGACACTTTCGATTCAA
1530800 TTGTTCATCT
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
35 4 0.04
36 81 0.91
37 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (36 bp):
AACGGAAGGAAGCATCGACACTTTCGATTCAAAGTG
Found at i:1530736 original size:72 final size:72
Alignment explanation
Indices: 1530649--1530799 Score: 257
Period size: 72 Copynumber: 2.1 Consensus size: 72
1530639 AAATGAAGGT
* * * *
1530649 GATTCAAGAAAAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAATGAAGCATTGA
1 GATTCAAGAAAAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTAAACGGAAGGAAGCATCGA
1530714 CACTTTC
66 CACTTTC
*
1530721 GATTCAAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTAAACGGAAGGAAGCATCGA
1 GATTCAAGAAAAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTAAACGGAAGGAAGCATCGA
1530786 CACTTTC
66 CACTTTC
1530793 GATTCAA
1 GATTCAA
1530800 TTGTTCATCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.20
Consensus pattern (72 bp):
GATTCAAGAAAAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTAAACGGAAGGAAGCATCGA
CACTTTC
Found at i:1531026 original size:20 final size:20
Alignment explanation
Indices: 1530998--1531061 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
1530988 GTTTGCTAGC
*
1530998 AGTTAAGGCTGTTAATGTTT
1 AGTTGAGGCTGTTAATGTTT
1531018 AGTTGAGGCTGTTAATGTTT
1 AGTTGAGGCTGTTAATGTTT
* *
1531038 AGTTGAGGTTGTTAATGTGT
1 AGTTGAGGCTGTTAATGTTT
1531058 AGTT
1 AGTT
1531062 ACAAAGTCTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.22, C:0.03, G:0.30, T:0.45
Consensus pattern (20 bp):
AGTTGAGGCTGTTAATGTTT
Found at i:1531383 original size:39 final size:39
Alignment explanation
Indices: 1531329--1531405 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
1531319 CCTCATTTGG
1531329 AGGATTTGGAAGAACATGAACGATTTCATCTTTAAAGGA
1 AGGATTTGGAAGAACATGAACGATTTCATCTTTAAAGGA
1531368 AGGATTTGGAAGAACATGAACGATTTCATCTTTAAAGG
1 AGGATTTGGAAGAACATGAACGATTTCATCTTTAAAGG
1531406 TCCCAACTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (39 bp):
AGGATTTGGAAGAACATGAACGATTTCATCTTTAAAGGA
Found at i:1531958 original size:19 final size:19
Alignment explanation
Indices: 1531927--1531963 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1531917 AAAACTAAGG
1531927 AGGAAAAAGAATATTTTTA
1 AGGAAAAAGAATATTTTTA
1531946 AGGAGAAAA-AATATTTTT
1 AGGA-AAAAGAATATTTTT
1531964 CAAGAGCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.32
Consensus pattern (19 bp):
AGGAAAAAGAATATTTTTA
Found at i:1534320 original size:2 final size:2
Alignment explanation
Indices: 1534313--1534341 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1534303 CTCATAGCTC
1534313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1534342 ATAATGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1534491 original size:191 final size:191
Alignment explanation
Indices: 1534167--1534536 Score: 740
Period size: 191 Copynumber: 1.9 Consensus size: 191
1534157 ATACACATCG
1534167 AAAATCAACATGATACTAAATCCAAACTCAAAACCATATAAAACCATTAAGCAAATTAAGATAAA
1 AAAATCAACATGATACTAAATCCAAACTCAAAACCATATAAAACCATTAAGCAAATTAAGATAAA
1534232 AAACATTGCATAAAATAGCGTAAAAATTGTTTCCATTAGGAAATCTCGAGGTTGGCTCATCGCAA
66 AAACATTGCATAAAATAGCGTAAAAATTGTTTCCATTAGGAAATCTCGAGGTTGGCTCATCGCAA
1534297 GCCGTCCTCATAGCTCATATATATATATATATATATATATATATAATAATGAATAGTTGCA
131 GCCGTCCTCATAGCTCATATATATATATATATATATATATATATAATAATGAATAGTTGCA
1534358 AAAATCAACATGATACTAAATCCAAACTCAAAACCATATAAAACCATTAAGCAAATTAAGATAAA
1 AAAATCAACATGATACTAAATCCAAACTCAAAACCATATAAAACCATTAAGCAAATTAAGATAAA
1534423 AAACATTGCATAAAATAGCGTAAAAATTGTTTCCATTAGGAAATCTCGAGGTTGGCTCATCGCAA
66 AAACATTGCATAAAATAGCGTAAAAATTGTTTCCATTAGGAAATCTCGAGGTTGGCTCATCGCAA
1534488 GCCGTCCTCATAGCTCATATATATATATATATATATATATATATAATAA
131 GCCGTCCTCATAGCTCATATATATATATATATATATATATATATAATAA
1534537 GTTGCACTCA
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
191 179 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (191 bp):
AAAATCAACATGATACTAAATCCAAACTCAAAACCATATAAAACCATTAAGCAAATTAAGATAAA
AAACATTGCATAAAATAGCGTAAAAATTGTTTCCATTAGGAAATCTCGAGGTTGGCTCATCGCAA
GCCGTCCTCATAGCTCATATATATATATATATATATATATATATAATAATGAATAGTTGCA
Found at i:1534511 original size:2 final size:2
Alignment explanation
Indices: 1534504--1534532 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1534494 CTCATAGCTC
1534504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1534533 ATAAGTTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1535998 original size:35 final size:35
Alignment explanation
Indices: 1535952--1536019 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
1535942 AACACAATCC
*
1535952 TCAATTTCATTTTAAA-CCTCAAATTCCAAAATAAT
1 TCAATTACATTTTAAATCC-CAAATTCCAAAATAAT
*
1535987 TCAATTACATTTTAAATCCCAAATTCTAAAATA
1 TCAATTACATTTTAAATCCCAAATTCCAAAATA
1536020 CTTTAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 28 0.93
36 2 0.07
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (35 bp):
TCAATTACATTTTAAATCCCAAATTCCAAAATAAT
Done.