Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 4 of 128
Found at i:1184114 original size:17 final size:17
Alignment explanation
Indices: 1184089--1184123 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1184079 CGGTTAGGCA
* *
1184089 TATATTTGTACTTGTAG
1 TATACTTGTAATTGTAG
1184106 TATACTTGTAATTGTAG
1 TATACTTGTAATTGTAG
1184123 T
1 T
1184124 TTTGGCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (17 bp):
TATACTTGTAATTGTAG
Found at i:1195354 original size:50 final size:50
Alignment explanation
Indices: 1195286--1195381 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
1195276 GATGCATGAG
*
1195286 GAGGCTTACGGAAGGTAATAAGTATAGCCCTGCTCCCAAACGCATTGGGA
1 GAGGCTTACGGAAGGTAATAAGTATAGCCCTACTCCCAAACGCATTGGGA
* * * * *
1195336 GAGGTTTACGGAATGTAATAAGTATGGCGCTACTTCCAAACGCATT
1 GAGGCTTACGGAAGGTAATAAGTATAGCCCTACTCCCAAACGCATT
1195382 TAATAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (50 bp):
GAGGCTTACGGAAGGTAATAAGTATAGCCCTACTCCCAAACGCATTGGGA
Found at i:1195995 original size:16 final size:17
Alignment explanation
Indices: 1195964--1195996 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1195954 TCGTCATCGA
1195964 CGAATCCTGTATTTGAT
1 CGAATCCTGTATTTGAT
*
1195981 CGAATCTTG-ATTTGAT
1 CGAATCCTGTATTTGAT
1195997 TTGCTCAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (17 bp):
CGAATCCTGTATTTGAT
Found at i:1196405 original size:26 final size:27
Alignment explanation
Indices: 1196376--1196428 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
1196366 ATGCATTTGC
1196376 AAGTCTTCATTGAATTTG-TTTACATA
1 AAGTCTTCATTGAATTTGATTTACATA
* *
1196402 AAGTCTTCATTGATTTTGATTTCCATA
1 AAGTCTTCATTGAATTTGATTTACATA
1196429 TTATGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.47
Consensus pattern (27 bp):
AAGTCTTCATTGAATTTGATTTACATA
Found at i:1198195 original size:108 final size:109
Alignment explanation
Indices: 1198067--1198283 Score: 427
Period size: 108 Copynumber: 2.0 Consensus size: 109
1198057 CACTAAAAAT
1198067 ATTAAAATAAATATTTCTCAACAATTTGAAAATAAATTTTAAAAAATTTTGAAAAGTAAATGAAC
1 ATTAAAATAAATATTTCTCAACAATTTGAAAATAAATTTTAAAAAATTTTGAAAAGTAAATGAAC
1198132 TAAATTCCATATATACGAAGAGCATACGAATTTTGAATTTATTG
66 TAAATTCCATATATACGAAGAGCATACGAATTTTGAATTTATTG
1198176 ATTAAAAT-AATATTTCTCAACAATTTGAAAATAAATTTTAAAAAATTTTGAAAAGTAAATGAAC
1 ATTAAAATAAATATTTCTCAACAATTTGAAAATAAATTTTAAAAAATTTTGAAAAGTAAATGAAC
1198240 TAAATTCCATATATACGAAGAGCATACGAATTTTGAATTTATTG
66 TAAATTCCATATATACGAAGAGCATACGAATTTTGAATTTATTG
1198284 TAACTTTAAT
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 100 0.93
109 8 0.07
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.35
Consensus pattern (109 bp):
ATTAAAATAAATATTTCTCAACAATTTGAAAATAAATTTTAAAAAATTTTGAAAAGTAAATGAAC
TAAATTCCATATATACGAAGAGCATACGAATTTTGAATTTATTG
Found at i:1199282 original size:9 final size:9
Alignment explanation
Indices: 1199265--1199301 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1199255 TGAGTTTTCG
1199265 AATTCGAAT
1 AATTCGAAT
*
1199274 AACTCGAAT
1 AATTCGAAT
1199283 AATTCGAAT
1 AATTCGAAT
1199292 AATTCGAAT
1 AATTCGAAT
1199301 A
1 A
1199302 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1200035 original size:5 final size:5
Alignment explanation
Indices: 1200025--1200050 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1200015 CTCGAAAATT
1200025 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
1200051 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:1202108 original size:40 final size:40
Alignment explanation
Indices: 1202064--1202183 Score: 101
Period size: 40 Copynumber: 3.1 Consensus size: 40
1202054 AGCTACTTCA
1202064 AAGGTTATTTTTTTATATTTTCTTTTCATTATGAAAGTTT
1 AAGGTTATTTTTTTATATTTTCTTTTCATTATGAAAGTTT
* * ** * * * *
1202104 AAGG----TTTGTCATA-TGACATTTCA--ATAAATACTTC
1 AAGGTTATTTTTTTATATTTTCTTTTCATTATGAA-AGTTT
*
1202138 AAAGTTATTTTTTTATATTTTCTTTTCATTATGAAAGTTT
1 AAGGTTATTTTTTTATATTTTCTTTTCATTATGAAAGTTT
1202178 AAGGTT
1 AAGGTT
1202184 TGTCATATGA
Statistics
Matches: 54, Mismatches: 18, Indels: 16
0.61 0.20 0.18
Matches are distributed among these distances:
33 4 0.07
34 6 0.11
35 7 0.13
36 7 0.13
38 7 0.13
39 7 0.13
40 12 0.22
41 4 0.07
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (40 bp):
AAGGTTATTTTTTTATATTTTCTTTTCATTATGAAAGTTT
Found at i:1202150 original size:74 final size:75
Alignment explanation
Indices: 1202057--1202206 Score: 293
Period size: 74 Copynumber: 2.0 Consensus size: 75
1202047 AATTTTAAGC
1202057 TACTTCAAAGGTTATTTTTTTATATTTTCTTTTCATTATGAAAGTTTAAGGTTTGTCATATGACA
1 TACTTCAAAGGTTATTTTTTTATATTTTCTTTTCATTATGAAAGTTTAAGGTTTGTCATATGACA
1202122 TTTCAATAAA
66 TTTCAATAAA
1202132 TACTTCAAA-GTTATTTTTTTATATTTTCTTTTCATTATGAAAGTTTAAGGTTTGTCATATGACA
1 TACTTCAAAGGTTATTTTTTTATATTTTCTTTTCATTATGAAAGTTTAAGGTTTGTCATATGACA
1202196 TTTCAATAAA
66 TTTCAATAAA
1202206 T
1 T
1202207 TGCAATGAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 66 0.88
75 9 0.12
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (75 bp):
TACTTCAAAGGTTATTTTTTTATATTTTCTTTTCATTATGAAAGTTTAAGGTTTGTCATATGACA
TTTCAATAAA
Found at i:1205721 original size:16 final size:16
Alignment explanation
Indices: 1205700--1205733 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1205690 CAAAATGTAC
1205700 AACCCAAAATGACCCT
1 AACCCAAAATGACCCT
* *
1205716 AACCCAAAGTTACCCT
1 AACCCAAAATGACCCT
1205732 AA
1 AA
1205734 ACTTGAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.35, G:0.06, T:0.15
Consensus pattern (16 bp):
AACCCAAAATGACCCT
Found at i:1207156 original size:141 final size:142
Alignment explanation
Indices: 1206991--1207275 Score: 547
Period size: 141 Copynumber: 2.0 Consensus size: 142
1206981 ATGTTTAATT
1206991 AATATATGAATTTAATGCACCATTAGTAAAAAAAATATACCTCATCATCCAATAAAAATAAATAA
1 AATATATGAATTTAATGCACCATTAGTAAAAAAAATATACCTCATCATCCAATAAAAATAAATAA
1207056 ACTTAAAAATAAATATTAACAATTT-AATTTAAATATAATTAAATAATTATAAATAAATATTAAA
66 ACTTAAAAATAAATATTAACAATTTAAATTT-AATATAATTAAATAATTATAAATAAATATTAAA
1207120 ACCCTGAATTCTA
130 ACCCTGAATTCTA
1207133 AATATATGAA-TTAATGCACCATTAGTAAAAAAAATATACCTCATCATCCAATAAAAATAAATAA
1 AATATATGAATTTAATGCACCATTAGTAAAAAAAATATACCTCATCATCCAATAAAAATAAATAA
1207197 ACTTAAAAATAAATATTAACAATTTAAATTTAATATAATTAAATAATTATAAATAAATATTAAAA
66 ACTTAAAAATAAATATTAACAATTTAAATTTAATATAATTAAATAATTATAAATAAATATTAAAA
1207262 CCCTGAATTCTA
131 CCCTGAATTCTA
1207274 AA
1 AA
1207276 ATTTAAACTC
Statistics
Matches: 142, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
141 127 0.89
142 15 0.11
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (142 bp):
AATATATGAATTTAATGCACCATTAGTAAAAAAAATATACCTCATCATCCAATAAAAATAAATAA
ACTTAAAAATAAATATTAACAATTTAAATTTAATATAATTAAATAATTATAAATAAATATTAAAA
CCCTGAATTCTA
Found at i:1220688 original size:30 final size:31
Alignment explanation
Indices: 1220654--1220718 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
1220644 CTTAACTAAA
* *
1220654 AAAAATTATAATTTAA-TCATTAAACTATTC
1 AAAAATTATAATTTAAGTCAATAAACTATCC
* * *
1220684 AAAAATTTTCATTTAAGTCAATCAACTATCC
1 AAAAATTATAATTTAAGTCAATAAACTATCC
1220715 AAAA
1 AAAA
1220719 TTTTTTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.48
31 15 0.52
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (31 bp):
AAAAATTATAATTTAAGTCAATAAACTATCC
Found at i:1223506 original size:31 final size:31
Alignment explanation
Indices: 1223463--1223531 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1223453 ACTTTATCTC
* * * * *
1223463 TAAACTTGACAATTGTTCTTATATTGGAGCA
1 TAAACTTAACAATTATTCTCACATTGAAGCA
*
1223494 TAAACTTAACAATTATTCTCACATTGAAGCC
1 TAAACTTAACAATTATTCTCACATTGAAGCA
1223525 TAAACTT
1 TAAACTT
1223532 TAAAGGTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (31 bp):
TAAACTTAACAATTATTCTCACATTGAAGCA
Found at i:1227320 original size:3 final size:3
Alignment explanation
Indices: 1227312--1227339 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1227302 CTTGAGAGAA
1227312 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1227340 GTGTGGCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1229617 original size:11 final size:11
Alignment explanation
Indices: 1229588--1229617 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1229578 TGCAATTTCA
*
1229588 TTATTATATTG
1 TTATTATTTTG
1229599 TTATTATTTTG
1 TTATTATTTTG
1229610 TTATTATT
1 TTATTATT
1229618 GTTTGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (11 bp):
TTATTATTTTG
Found at i:1230009 original size:73 final size:74
Alignment explanation
Indices: 1229914--1230061 Score: 280
Period size: 73 Copynumber: 2.0 Consensus size: 74
1229904 GATATATTAT
1229914 ATTTTTAAAATTTATTTTTATATAAAAAAAGTAATATAAAAAATTTAATAAAGATGAATCGAGCT
1 ATTTTTAAAATTTATTTTTATATAAAAAAAGTAATATAAAAAATTTAATAAAGATGAATCGAGCT
1229979 CAAATTTTA
66 CAAATTTTA
*
1229988 ATTTTTAAAA-TTATTTTTATATGAAAAAAGTAATATAAAAAATTTAATAAAGATGAATCGAGCT
1 ATTTTTAAAATTTATTTTTATATAAAAAAAGTAATATAAAAAATTTAATAAAGATGAATCGAGCT
1230052 CAAATTTTA
66 CAAATTTTA
1230061 A
1 A
1230062 CATTTTTATC
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
73 63 0.86
74 10 0.14
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (74 bp):
ATTTTTAAAATTTATTTTTATATAAAAAAAGTAATATAAAAAATTTAATAAAGATGAATCGAGCT
CAAATTTTA
Found at i:1234022 original size:17 final size:18
Alignment explanation
Indices: 1234000--1234034 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1233990 ATGTTTTTAT
1234000 AATTGG-TCCAGTAGTTG
1 AATTGGTTCCAGTAGTTG
*
1234017 AATTGGTTCGAGTAGTTG
1 AATTGGTTCCAGTAGTTG
1234035 GTCCAGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.23, C:0.09, G:0.31, T:0.37
Consensus pattern (18 bp):
AATTGGTTCCAGTAGTTG
Found at i:1234062 original size:12 final size:12
Alignment explanation
Indices: 1234045--1234078 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1234035 GTCCAGTTTG
1234045 ATTAAATAAATT
1 ATTAAATAAATT
1234057 ATTAAA-AAATT
1 ATTAAATAAATT
1234068 ATTAAAATAAA
1 ATT-AAATAAA
1234079 AATATTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 9 0.45
13 3 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATTAAATAAATT
Found at i:1234068 original size:11 final size:11
Alignment explanation
Indices: 1234045--1234074 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1234035 GTCCAGTTTG
1234045 ATTAAATAAATT
1 ATTAAA-AAATT
1234057 ATTAAAAAATT
1 ATTAAAAAATT
1234068 ATTAAAA
1 ATTAAAA
1234075 TAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:1234080 original size:16 final size:17
Alignment explanation
Indices: 1234059--1234098 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1234049 AATAAATTAT
1234059 TAAAAAATTATTA-AAA
1 TAAAAAATTATTAGAAA
1234075 T-AAAAA-TATTAGAAA
1 TAAAAAATTATTAGAAA
1234090 TAGAAAAAT
1 TA-AAAAAT
1234099 ATAGTACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 5 0.25
15 9 0.45
16 1 0.05
17 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
TAAAAAATTATTAGAAA
Found at i:1240775 original size:20 final size:20
Alignment explanation
Indices: 1240750--1240789 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1240740 TAACCCACAT
1240750 AACCAGCGGCCGTAGAAGGC
1 AACCAGCGGCCGTAGAAGGC
* *
1240770 AACCAGTGGCTGTAGAAGGC
1 AACCAGCGGCCGTAGAAGGC
1240790 TGGTTTTTAA
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:0.30, C:0.25, G:0.35, T:0.10
Consensus pattern (20 bp):
AACCAGCGGCCGTAGAAGGC
Found at i:1250231 original size:3 final size:3
Alignment explanation
Indices: 1250223--1250249 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1250213 AGGCGAAGAC
1250223 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1250250 AAGGATCAAC
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):
GAT
Found at i:1252693 original size:147 final size:148
Alignment explanation
Indices: 1252419--1252707 Score: 553
Period size: 148 Copynumber: 2.0 Consensus size: 148
1252409 ACTACCTTTT
*
1252419 TTTTTTTTAATGATTGTTTGGGATTTTATTGGAAGACTAAATGATTTAGAATTGGGAAGTTTAAT
1 TTTTTTTTAATGATTGTTTGGGATTTTATTGGAAGACTAAATGATTTAGAATGGGGAAGTTTAAT
1252484 TTTTTGAGAATTTTTTTATTTGGGTTTGACTTGTTTTCAGTAATTTAATCATAATTTGTTGCAGT
66 TTTTTGAGAATTTTTTTATTTGGGTTTGACTTGTTTTCAGTAATTTAATCATAATTTGTTGCAGT
1252549 TCTAGAATTAAACTACCC
131 TCTAGAATTAAACTACCC
1252567 TTTTTTTTAATGATTGTTTGGGATTTTATTGGAAGACTAAATGATTTAGAATGGGGAAGTTTAAT
1 TTTTTTTTAATGATTGTTTGGGATTTTATTGGAAGACTAAATGATTTAGAATGGGGAAGTTTAAT
*
1252632 TTTTTGAGAA-TTTTTTATTTGGGTTTGCCTTGTTTTCAGTAATTTAATCATAATTTGTTGCAGT
66 TTTTTGAGAATTTTTTTATTTGGGTTTGACTTGTTTTCAGTAATTTAATCATAATTTGTTGCAGT
1252696 TCTAGAATTAAA
131 TCTAGAATTAAA
1252708 GAGCTGCTTT
Statistics
Matches: 139, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
147 65 0.47
148 74 0.53
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.49
Consensus pattern (148 bp):
TTTTTTTTAATGATTGTTTGGGATTTTATTGGAAGACTAAATGATTTAGAATGGGGAAGTTTAAT
TTTTTGAGAATTTTTTTATTTGGGTTTGACTTGTTTTCAGTAATTTAATCATAATTTGTTGCAGT
TCTAGAATTAAACTACCC
Found at i:1254825 original size:89 final size:89
Alignment explanation
Indices: 1254686--1254854 Score: 275
Period size: 89 Copynumber: 1.9 Consensus size: 89
1254676 AATTATCAAG
* * *
1254686 TTATATACCTACGTTCGAGTACCATCTATGTAAACCATGATTAATCGTGAGTTGAATTAGTTTTA
1 TTATATACCTACGTTCGAGTACCATCTATGCAAACCATGATTAATAGTGAGTCGAATTAGTTTTA
1254751 CGAATTAATTATTCAATTCAGAGC
66 CGAATTAATTATTCAATTCAGAGC
* * *
1254775 TTATATACCTATGTTCGAGTACCATCTATGCAAACCATGTTTAATAGTGAGTCGAGTTAGTTTTA
1 TTATATACCTACGTTCGAGTACCATCTATGCAAACCATGATTAATAGTGAGTCGAATTAGTTTTA
*
1254840 CGAATTACTTATTCA
66 CGAATTAATTATTCA
1254855 GTTCGGTGCT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (89 bp):
TTATATACCTACGTTCGAGTACCATCTATGCAAACCATGATTAATAGTGAGTCGAATTAGTTTTA
CGAATTAATTATTCAATTCAGAGC
Found at i:1259762 original size:6 final size:7
Alignment explanation
Indices: 1259736--1259761 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1259726 TTTAAAATAC
1259736 TTTTTTA
1 TTTTTTA
1259743 TTTTTTA
1 TTTTTTA
1259750 TTTTTTA
1 TTTTTTA
1259757 TTTTT
1 TTTTT
1259762 AAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:1259783 original size:33 final size:33
Alignment explanation
Indices: 1259722--1259784 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1259712 TATTTTAAAA
** * *
1259722 TATTTTTAAAATACTTTTTTATTTTTTATTTTT
1 TATTTTTAAAATAAATTTTTAGTGTTTATTTTT
*
1259755 TATTTTTAAAATAAATTTTTGGTGTTTATT
1 TATTTTTAAAATAAATTTTTAGTGTTTATT
1259785 CAAAAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (33 bp):
TATTTTTAAAATAAATTTTTAGTGTTTATTTTT
Found at i:1260419 original size:83 final size:83
Alignment explanation
Indices: 1260280--1260443 Score: 267
Period size: 83 Copynumber: 2.0 Consensus size: 83
1260270 ACAAATTAAT
* *
1260280 GGATCTATTTAAAGCCGCAGAATGTTCACATAATCATTTCCAATGAAATTTCAAAATTCATGATA
1 GGATCTATTTAAAGCCCCAGAATGTTCACATAATCATTTCCAATGAAATGTCAAAATTCATGATA
1260345 AAACATAACATACACAGG
66 AAACATAACATACACAGG
* *
1260363 GGATCTATTTAAATCCCCA-AAGTGTTCACATAATCATTTCCAATGGAATGTCAAAATTCATGAT
1 GGATCTATTTAAAGCCCCAGAA-TGTTCACATAATCATTTCCAATGAAATGTCAAAATTCATGAT
*
1260427 AAAACATAGCATACACA
65 AAAACATAACATACACA
1260444 AGAGCGAAGC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
82 2 0.03
83 73 0.97
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (83 bp):
GGATCTATTTAAAGCCCCAGAATGTTCACATAATCATTTCCAATGAAATGTCAAAATTCATGATA
AAACATAACATACACAGG
Found at i:1261932 original size:5 final size:5
Alignment explanation
Indices: 1261922--1261951 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1261912 TCTAAAATTA
1261922 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1261952 AACTAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:1263050 original size:16 final size:16
Alignment explanation
Indices: 1263029--1263061 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1263019 TTTATTATAC
*
1263029 AAAATTAATAAGAAAA
1 AAAATTAAAAAGAAAA
1263045 AAAATTAAAAAGAAAA
1 AAAATTAAAAAGAAAA
1263061 A
1 A
1263062 TATAATTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAATTAAAAAGAAAA
Found at i:1266123 original size:3 final size:3
Alignment explanation
Indices: 1266115--1266143 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1266105 AATCTCACTT
1266115 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1266144 CCCATCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1266848 original size:2 final size:2
Alignment explanation
Indices: 1266843--1266886 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1266833 AAAATAATGG
1266843 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1266885 GA
1 GA
1266887 TTGTTGGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1269321 original size:21 final size:19
Alignment explanation
Indices: 1269296--1269343 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
1269286 GCTACTAGGC
*
1269296 AAGGTATCGATACTTTTGTGA
1 AAGGTATCAATA-TTTTGT-A
* *
1269317 AAGGTACCAATATTTTGTT
1 AAGGTATCAATATTTTGTA
1269336 AAGGTATC
1 AAGGTATC
1269344 CAAGCTGGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.30
20 6 0.26
21 10 0.43
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (19 bp):
AAGGTATCAATATTTTGTA
Found at i:1270090 original size:21 final size:21
Alignment explanation
Indices: 1270064--1270105 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1270054 CCTCATTAGT
1270064 AAGTCAACCTCATGCTTAATC
1 AAGTCAACCTCATGCTTAATC
*
1270085 AAGTCAACGTCATGCTTAATC
1 AAGTCAACCTCATGCTTAATC
1270106 GAGTTTCTAA
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:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (21 bp):
AAGTCAACCTCATGCTTAATC
Found at i:1271021 original size:17 final size:17
Alignment explanation
Indices: 1270999--1271032 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1270989 ATTCCAACAG
1270999 ATTTAATAAAATCAATT
1 ATTTAATAAAATCAATT
*
1271016 ATTTAATTAAATCAATT
1 ATTTAATAAAATCAATT
1271033 TAATCCAAGT
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:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAATAAAATCAATT
Found at i:1271856 original size:19 final size:18
Alignment explanation
Indices: 1271832--1271878 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1271822 CTAAATAGTC
*
1271832 TAAAAAAATATTATATTTA
1 TAAAAAAAT-CTATATTTA
*
1271851 TAAAAATAATCTATGTTTA
1 TAAAAA-AATCTATATTTA
1271870 -AAAAAAATC
1 TAAAAAAATC
1271879 ACCAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 5 0.20
19 13 0.52
20 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAAAAAATCTATATTTA
Found at i:1274050 original size:13 final size:13
Alignment explanation
Indices: 1274032--1274057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1274022 ATCTAACATA
1274032 ATTTAATTTAATT
1 ATTTAATTTAATT
1274045 ATTTAATTTAATT
1 ATTTAATTTAATT
1274058 TTGTACTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTAATTTAATT
Found at i:1274237 original size:2 final size:2
Alignment explanation
Indices: 1274230--1274256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1274220 NNNNNNNNNN
1274230 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 A
1274257 AATCCCTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1286329 original size:14 final size:14
Alignment explanation
Indices: 1286310--1286343 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1286300 TCATTATTTT
1286310 CCTATAACCAAAAC
1 CCTATAACCAAAAC
1286324 CCTATAACCAAAAC
1 CCTATAACCAAAAC
1286338 CC-ATAA
1 CCTATAA
1286344 ACTCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:1290286 original size:241 final size:240
Alignment explanation
Indices: 1289819--1290305 Score: 751
Period size: 241 Copynumber: 2.0 Consensus size: 240
1289809 AGGAATTTGC
* * *
1289819 AAACTAAAGTTTTGTGAGCACTGCGTTTTTGGGAAGTAAAAGAGAGTTTGATTCACTAGAGGAAT
1 AAACTAAAGTTCTGTGAGCACTGCATTTTTGGGAAGCAAAAGAGAGTTTGATTCACTAGAGGAAT
* * * * * *
1289884 TCATAACACGAAGGGAACGTTGGAGTATATTTATTTTGATCTGTGGGGCCATCCAGAGTGCCTTC
66 CCATAACACGAAGAGAACGTTAGAATATATTCATTTTGATCTGTGGGGCCATCCAGAGTGCATTC
1289949 AAGAGGTGGAGCTAATTATATGCTAACTTTTATTGATGATTTTTCCAAAAAAGTTTAGGCGTTCT
131 AAGAGGTGGAGCTAATTATATGCTAACTTTTATTGATGATTTTTCCAAAAAAGTTTAGGCGTTCT
* *
1290014 TCCTAAAGCAGAAAAGCGATGTGTTTTCTGCATTTAAGTCTTGGA
196 TCCTAAAGCAAAAAAGCGATGTGCTTTCTGCATTTAAGTCTTGGA
*
1290059 AAACTAAAGTTCTGTGAGGACTGCATTTTTGGGAAGCAAAAGAGAGTTTGATTCACTAGAGGAAT
1 AAACTAAAGTTCTGTGAGCACTGCATTTTTGGGAAGCAAAAGAGAGTTTGATTCACTAGAGGAAT
1290124 CCATAACACGAAGAGAACGTTAGAATATATTCATTTTGATCTGTGTGGGCCATCCAGAGTGCATT
66 CCATAACACGAAGAGAACGTTAGAATATATTCATTTTGATCTGTG-GGGCCATCCAGAGTGCATT
** * * * * *
1290189 CGGGAGGTGGAGTTAATTATATGTTAACTTTTATTGATGATTTTTCTAGAAAAGTTT-GAGTGTT
130 CAAGAGGTGGAGCTAATTATATGCTAACTTTTATTGATGATTTTTCCAAAAAAGTTTAG-GCGTT
* * *
1290253 CTTCCTGAAGTAAAAAAGTGATGTGCTTTCTGCATTTAAGTCTTGGA
194 CTTCCTAAAGCAAAAAAGCGATGTGCTTTCTGCATTTAAGTCTTGGA
1290300 AAACTA
1 AAACTA
1290306 TGATTAAAAA
Statistics
Matches: 223, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
240 102 0.46
241 121 0.54
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (240 bp):
AAACTAAAGTTCTGTGAGCACTGCATTTTTGGGAAGCAAAAGAGAGTTTGATTCACTAGAGGAAT
CCATAACACGAAGAGAACGTTAGAATATATTCATTTTGATCTGTGGGGCCATCCAGAGTGCATTC
AAGAGGTGGAGCTAATTATATGCTAACTTTTATTGATGATTTTTCCAAAAAAGTTTAGGCGTTCT
TCCTAAAGCAAAAAAGCGATGTGCTTTCTGCATTTAAGTCTTGGA
Found at i:1294722 original size:15 final size:15
Alignment explanation
Indices: 1294702--1294732 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1294692 GAAGTTCCAA
1294702 ACTATACGTGGGCTT
1 ACTATACGTGGGCTT
1294717 ACTATACGTGGGCTT
1 ACTATACGTGGGCTT
1294732 A
1 A
1294733 GATTCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (15 bp):
ACTATACGTGGGCTT
Found at i:1298149 original size:11 final size:11
Alignment explanation
Indices: 1298133--1298157 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1298123 TTAACTAAAA
1298133 AAATTATTTTT
1 AAATTATTTTT
1298144 AAATTATTTTT
1 AAATTATTTTT
1298155 AAA
1 AAA
1298158 GTATAGAGAT
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:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAATTATTTTT
Found at i:1301100 original size:26 final size:27
Alignment explanation
Indices: 1301059--1301120 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
1301049 TTTAAAATAC
* *
1301059 TTTTAAAATAAATTTTTTATTTTTTAT
1 TTTTAAAATAAATTTTTTAATGTTTAT
*
1301086 TTTTAAAAT-ACTTTTTTAATGTTTAT
1 TTTTAAAATAAATTTTTTAATGTTTAT
*
1301112 TTTAAAAAT
1 TTTTAAAAT
1301121 GGGCCGGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTAAAATAAATTTTTTAATGTTTAT
Found at i:1303080 original size:9 final size:9
Alignment explanation
Indices: 1303059--1303107 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
1303049 TTTGGTTAAA
*
1303059 AATTAGCCG
1 AATTAACCG
*
1303068 AATTAACCA
1 AATTAACCG
1303077 AATTAACCG
1 AATTAACCG
*
1303086 AATTACCCG
1 AATTAACCG
*
1303095 AATTAACCT
1 AATTAACCG
1303104 AATT
1 AATT
1303108 GAATCATACA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:1307565 original size:20 final size:20
Alignment explanation
Indices: 1307524--1307566 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1307514 TTAATTAAAT
* *
1307524 AAATTATTTAAAAATCATAA
1 AAATTATTCAAAAATCACAA
1307544 AAATTATTACAAAAAT-ACAA
1 AAATTATT-CAAAAATCACAA
1307564 AAA
1 AAA
1307567 CATGTTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATTATTCAAAAATCACAA
Found at i:1308431 original size:31 final size:31
Alignment explanation
Indices: 1308396--1308456 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1308386 AAAGCTCAAT
* *
1308396 GACTTAAATAAAAACTTTTGAATAGTTTAGC
1 GACTTAAATAAAAACTTGTGAATAATTTAGC
*
1308427 GACTTAAATGAAAACTTGTGAATAATTTAG
1 GACTTAAATAAAAACTTGTGAATAATTTAG
1308457 TAATCATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (31 bp):
GACTTAAATAAAAACTTGTGAATAATTTAGC
Found at i:1315598 original size:2 final size:2
Alignment explanation
Indices: 1315591--1315647 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
1315581 GGGAAGGGGA
1315591 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * *
1315632 TG AG AG AG TG TG TG TG
1 TG TG TG TG TG TG TG TG
1315648 AGAGAGAGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.05, C:0.00, G:0.51, T:0.44
Consensus pattern (2 bp):
TG
Found at i:1315648 original size:14 final size:14
Alignment explanation
Indices: 1315627--1315653 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1315617 TGTGTGTGTG
1315627 GTGTGTGAGAGAGT
1 GTGTGTGAGAGAGT
1315641 GTGTGTGAGAGAG
1 GTGTGTGAGAGAG
1315654 AGAGAGAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.52, T:0.26
Consensus pattern (14 bp):
GTGTGTGAGAGAGT
Found at i:1315652 original size:2 final size:2
Alignment explanation
Indices: 1315647--1315690 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1315637 GAGTGTGTGT
1315647 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1315689 GA
1 GA
1315691 AATGGCATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1315652 original size:16 final size:17
Alignment explanation
Indices: 1315622--1315655 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1315612 GTGTGTGTGT
*
1315622 GTGTGGTGTGTGAGAGA
1 GTGTGGTGTGAGAGAGA
1315639 GTGT-GTGTGAGAGAGA
1 GTGTGGTGTGAGAGAGA
1315655 G
1 G
1315656 AGAGAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.21, C:0.00, G:0.53, T:0.26
Consensus pattern (17 bp):
GTGTGGTGTGAGAGAGA
Found at i:1318258 original size:20 final size:21
Alignment explanation
Indices: 1318233--1318311 Score: 88
Period size: 21 Copynumber: 3.6 Consensus size: 21
1318223 TATATTAAAT
*
1318233 ATATATATTTATTTTTAATCAA
1 ATATATA-TTATTTTAAATCAA
1318255 ATATATATTATTTTAAATCAA
1 ATATATATTATTTTAAATCAA
* *
1318276 ATATATATT-TTATATATATTAA
1 ATATATATTATT-T-TAAATCAA
1318298 ATATATATATATTT
1 ATATATAT-TATTT
1318312 AATATGGGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
20 2 0.04
21 23 0.46
22 21 0.42
23 2 0.04
24 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATATATTATTTTAAATCAA
Found at i:1318307 original size:26 final size:27
Alignment explanation
Indices: 1318258--1318316 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
1318248 TAATCAAATA
*
1318258 TATATTATTTTAAATCAAATATATATTT
1 TATA-TATATTAAATCAAATATATATTT
*
1318286 TATATATATTAAAT-ATATATATATTT
1 TATATATATTAAATCAAATATATATTT
*
1318312 AATAT
1 TATAT
1318317 GGGTTGGGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 15 0.54
27 9 0.32
28 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
TATATATATTAAATCAAATATATATTT
Found at i:1328843 original size:19 final size:20
Alignment explanation
Indices: 1328812--1328882 Score: 96
Period size: 19 Copynumber: 3.6 Consensus size: 20
1328802 ATATATATAA
1328812 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AATTTTTATAAATT
1328832 ATTTTGAA-TTTTA-AAATTT
1 ATTTTGAATTTTTATAAA-TT
1328851 ATTTTGAATTTTT-TAAATT
1 ATTTTGAATTTTTATAAATT
1328870 ATTTTGAATTTTT
1 ATTTTGAATTTTT
1328883 TTTGAAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.06
18 5 0.11
19 26 0.55
20 13 0.28
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.61
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:1329733 original size:63 final size:65
Alignment explanation
Indices: 1329664--1329804 Score: 146
Period size: 69 Copynumber: 2.2 Consensus size: 65
1329654 TAATATAACA
** * *
1329664 ATAAATAATTCAT-TATGAAATAAAAA-TTATTTAAAAATTAAACTCGAGACAGAAATCTTAAAT
1 ATAAATAATTCATGTAACAAATAAAAATTTATTTAAAAATCAAACTCGAAACAGAAATCTTAAAT
* *
1329727 ATAAAT-ATTGATAACGGGTAACAAATAAAAATTTATTTAAAAATCGAACTCGAAACAGAAATCT
1 ATAAATAATTCAT-----GTAACAAATAAAAATTTATTTAAAAATCAAACTCGAAACAGAAATCT
1329791 TAAAT
61 TAAAT
*
1329796 ACAAA-AATT
1 ATAAATAATT
1329805 TTGATATTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
62 5 0.08
63 6 0.10
68 11 0.17
69 41 0.65
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (65 bp):
ATAAATAATTCATGTAACAAATAAAAATTTATTTAAAAATCAAACTCGAAACAGAAATCTTAAAT
Found at i:1342289 original size:3 final size:3
Alignment explanation
Indices: 1342281--1342331 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1342271 GTTAATATCA
1342281 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1342329 AAT
1 AAT
1342332 TAGGTCAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1345171 original size:14 final size:15
Alignment explanation
Indices: 1345142--1345174 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1345132 CGGTTCAATT
1345142 AAATAAATTCATAAA
1 AAATAAATTCATAAA
*
1345157 AAATAAATTTA-AAA
1 AAATAAATTCATAAA
1345171 AAAT
1 AAAT
1345175 TTATTTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAATTCATAAA
Found at i:1346963 original size:17 final size:17
Alignment explanation
Indices: 1346941--1346974 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1346931 TGACAGGCAC
1346941 TTAAAAAATTCGATAAG
1 TTAAAAAATTCGATAAG
1346958 TTAAAAAATTCGATAAG
1 TTAAAAAATTCGATAAG
1346975 GGACAACAAT
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:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
TTAAAAAATTCGATAAG
Found at i:1352095 original size:15 final size:15
Alignment explanation
Indices: 1352061--1352102 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1352051 TTAGTATAGG
*
1352061 CTCTTCCTCTTCCTT
1 CTCTTCTTCTTCCTT
1352076 CTCTTCTTCTTCC-T
1 CTCTTCTTCTTCCTT
1352090 CTTCTTCTT-TTCC
1 C-TCTTCTTCTTCC
1352103 CATTACTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (15 bp):
CTCTTCTTCTTCCTT
Found at i:1352454 original size:33 final size:33
Alignment explanation
Indices: 1352412--1352482 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1352402 GTTGTGGTGT
* *
1352412 TGGGTGCATGATATTGGGTTTTTCATGGTAAGG
1 TGGGCGCATGATATTGGGGTTTTCATGGTAAGG
*
1352445 TGGGCGCATGATGTTGGGGTTTTCATGGTAAGG
1 TGGGCGCATGATATTGGGGTTTTCATGGTAAGG
1352478 TGGGC
1 TGGGC
1352483 CTTATGCCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.15, C:0.08, G:0.41, T:0.35
Consensus pattern (33 bp):
TGGGCGCATGATATTGGGGTTTTCATGGTAAGG
Found at i:1353566 original size:22 final size:23
Alignment explanation
Indices: 1353519--1353566 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1353509 TGAGTTTGGG
*
1353519 AAAAAAATGAAGCCCGTTTTGCA
1 AAAAAAATGAAGCCCGTTTAGCA
1353542 AAAAAAATGAAGCCCGTTTAG-A
1 AAAAAAATGAAGCCCGTTTAGCA
1353564 AAA
1 AAA
1353567 CGGGCCGGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (23 bp):
AAAAAAATGAAGCCCGTTTAGCA
Found at i:1366505 original size:9 final size:9
Alignment explanation
Indices: 1366491--1366521 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1366481 TGCCTCTTAC
1366491 AAATAATAA
1 AAATAATAA
1366500 AAATAATAA
1 AAATAATAA
*
1366509 AAATATTAA
1 AAATAATAA
1366518 AAAT
1 AAAT
1366522 GTTTAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AAATAATAA
Found at i:1368004 original size:21 final size:22
Alignment explanation
Indices: 1367964--1368006 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1367954 TATACCATTG
**
1367964 TTTAAAATTTAAATATATATAA
1 TTTAAAAAATAAATATATATAA
1367986 TTTAAAAAATAAA-ATATATAA
1 TTTAAAAAATAAATATATATAA
1368007 AGTTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAAAATAAATATATATAA
Found at i:1374674 original size:31 final size:32
Alignment explanation
Indices: 1374639--1374709 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
1374629 GATACAAAAT
* *
1374639 AGTTATTGAATTATTTGAAAATTTTT-CTTCA
1 AGTTATTGAACTATTTGAAAATTTTTGCTTAA
* * *
1374670 AGTTATTGAACTGTTTGAAATTTTTTGTTTAA
1 AGTTATTGAACTATTTGAAAATTTTTGCTTAA
1374702 AGTTATTG
1 AGTTATTG
1374710 GGTTAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 23 0.68
32 11 0.32
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (32 bp):
AGTTATTGAACTATTTGAAAATTTTTGCTTAA
Found at i:1378656 original size:15 final size:15
Alignment explanation
Indices: 1378636--1378665 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1378626 AATCTCTGTT
1378636 CCATGATGATCATCA
1 CCATGATGATCATCA
*
1378651 CCATGATGATGATCA
1 CCATGATGATCATCA
1378666 TCACCATTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (15 bp):
CCATGATGATCATCA
Found at i:1378685 original size:18 final size:18
Alignment explanation
Indices: 1378638--1378672 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1378628 TCTCTGTTCC
1378638 ATGATGATCATCACCATG
1 ATGATGATCATCACCATG
1378656 ATGATGATCATCACCAT
1 ATGATGATCATCACCAT
1378673 TGTTTTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (18 bp):
ATGATGATCATCACCATG
Found at i:1380051 original size:179 final size:179
Alignment explanation
Indices: 1379751--1380107 Score: 624
Period size: 179 Copynumber: 2.0 Consensus size: 179
1379741 CTACACTGGC
*
1379751 TTTAGTCTCTTCATAATAGGTATAGGTTTGATTTTGAATTTGTGCCGTTCATCCTGCATTTCTAC
1 TTTAGTCTCTTCATAATAGATATAGGTTTGATTTTGAATTTGTGCCGTTCATCCTGCATTTCTAC
1379816 ACCATTACCTAGGGAAGAATCTAATGTTTAATGATGAACCTCTTTTGAAGTTTATGTCCTTGTGC
66 ACCATTACCTAGGGAAGAATCTAATGTTTAATGATGAACCTCTTTTGAAGTTTATGTCCTTGTGC
*
1379881 ATTTAATTCTTCCTTTAGGAAAAAGGTTTTGAAGATGCAAAGCTAATGT
131 ATTTAAATCTTCCTTTAGGAAAAAGGTTTTGAAGATGCAAAGCTAATGT
* * *
1379930 TTTAGTCTCTTCATAATAGATATAGGTTTGATTTTGAATTTGTTCCGTTCATTCTGTATTTCTAC
1 TTTAGTCTCTTCATAATAGATATAGGTTTGATTTTGAATTTGTGCCGTTCATCCTGCATTTCTAC
* * * *
1379995 ACCATTATCTAGGGAAGCATTTAATGTTTAATGATGAATCTCTTTTGAAGTTTATGTCCTTGTGC
66 ACCATTACCTAGGGAAGAATCTAATGTTTAATGATGAACCTCTTTTGAAGTTTATGTCCTTGTGC
*
1380060 ATTTAAATCTTCCTTTAGGTAAAAGGTTTTGAAGATGCAAAGCTAATG
131 ATTTAAATCTTCCTTTAGGAAAAAGGTTTTGAAGATGCAAAGCTAATG
1380108 ATTGATGCTT
Statistics
Matches: 168, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
179 168 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (179 bp):
TTTAGTCTCTTCATAATAGATATAGGTTTGATTTTGAATTTGTGCCGTTCATCCTGCATTTCTAC
ACCATTACCTAGGGAAGAATCTAATGTTTAATGATGAACCTCTTTTGAAGTTTATGTCCTTGTGC
ATTTAAATCTTCCTTTAGGAAAAAGGTTTTGAAGATGCAAAGCTAATGT
Found at i:1387073 original size:10 final size:10
Alignment explanation
Indices: 1387060--1387122 Score: 60
Period size: 10 Copynumber: 6.6 Consensus size: 10
1387050 TTTTATCTTT
1387060 TTTATAATTA
1 TTTATAATTA
*
1387070 TTTACAATTA
1 TTTATAATTA
*
1387080 TTTATCATT-
1 TTTATAATTA
* *
1387089 TTTA-ATTTC
1 TTTATAATTA
1387098 TTTATAATTA
1 TTTATAATTA
*
1387108 TTTACAATT-
1 TTTATAATTA
1387117 TTTATA
1 TTTATA
1387123 CTTTTCTGGT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
8 2 0.05
9 13 0.31
10 27 0.64
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTATAATTA
Found at i:1391529 original size:8 final size:7
Alignment explanation
Indices: 1391487--1391558 Score: 60
Period size: 7 Copynumber: 10.4 Consensus size: 7
1391477 CAATACTAAT
1391487 AATT-AA
1 AATTAAA
1391493 AATT-AA
1 AATTAAA
*
1391499 AATTTAA
1 AATTAAA
**
1391506 AATTTGA
1 AATTAAA
1391513 AATATAAA
1 AAT-TAAA
1391521 AATTAAA
1 AATTAAA
1391528 AATTAAA
1 AATTAAA
*
1391535 AATTTTAA
1 AA-TTAAA
1391543 AA-TAAA
1 AATTAAA
*
1391549 AATAAAA
1 AATTAAA
1391556 AAT
1 AAT
1391559 ATTTTCAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
6 15 0.27
7 30 0.54
8 11 0.20
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:1391533 original size:28 final size:28
Alignment explanation
Indices: 1391491--1391558 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
1391481 ACTAATAATT
*
1391491 AAAATT-AAAATTTAAAATTTGAAATATA
1 AAAATTAAAAATTAAAAATTTGAAA-ATA
*
1391519 AAAATTAAAAATTAAAAATTTTAAAATA
1 AAAATTAAAAATTAAAAATTTGAAAATA
*
1391547 AAAATAAAAAAT
1 AAAATTAAAAAT
1391559 ATTTTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 20 0.56
29 16 0.44
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (28 bp):
AAAATTAAAAATTAAAAATTTGAAAATA
Found at i:1391534 original size:14 final size:14
Alignment explanation
Indices: 1391487--1391558 Score: 60
Period size: 15 Copynumber: 5.2 Consensus size: 14
1391477 CAATACTAAT
1391487 AATT-AAAATT-AA
1 AATTAAAAATTAAA
* **
1391499 AATTTAAAATTTGA
1 AATTAAAAATTAAA
1391513 AATATAAAAATTAAA
1 AAT-TAAAAATTAAA
*
1391528 AATTAAAAATTTTAA
1 AATTAAAAA-TTAAA
*
1391543 AA-TAAAAATAAAA
1 AATTAAAAATTAAA
1391556 AAT
1 AAT
1391559 ATTTTCAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
12 4 0.08
13 11 0.23
14 16 0.33
15 17 0.35
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (14 bp):
AATTAAAAATTAAA
Found at i:1391680 original size:21 final size:21
Alignment explanation
Indices: 1391652--1391709 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
1391642 CTAATAATTA
*
1391652 AAAT-TAAAATTTAAAATTTG
1 AAATATAAAATTAAAAATTTG
*
1391672 AAATATAAAAATTAAAAATTTT
1 AAATAT-AAAATTAAAAATTTG
*
1391694 AAA-ATAAAAATAAAAA
1 AAATATAAAATTAAAAA
1391710 ATAAATTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.42
21 3 0.09
22 16 0.48
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATATAAAATTAAAAATTTG
Found at i:1391710 original size:21 final size:21
Alignment explanation
Indices: 1391649--1391711 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
1391639 ATACTAATAA
* *
1391649 TTAAAATTAAAATTTAAAATT
1 TTAAAATAAAAATTAAAAATT
*
1391670 TGAAATATAAAAATTAAAAATT
1 TTAAA-ATAAAAATTAAAAATT
*
1391692 TTAAAATAAAAATAAAAAAT
1 TTAAAATAAAAATTAAAAAT
1391712 AAATTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAATAAAAATTAAAAATT
Found at i:1391712 original size:160 final size:158
Alignment explanation
Indices: 1391410--1391714 Score: 522
Period size: 160 Copynumber: 1.9 Consensus size: 158
1391400 ATAAAGAGTT
*
1391410 AAAAAAATTTCTATTTTTATTTTAGAGTGGAACCCTTGCCCATGAAATATCATATCAACAAATTT
1 AAAAAAATTTCTATTTTTATTTTAGAGTAGAACCCTTGCCCATGAAATATCATATCAACAAATTT
1391475 AACAATACTAATAATTAAAATTAAAATTTAAAATTTGAAATATAAAAATTAAAAATTAAAAATTT
66 AACAATACTAATAATTAAAATTAAAATTTAAAATTTGAAATATAAAAATTAAAAATTAAAAA-TT
*
1391540 TAAAATAAAAATAAAAAATATTTTCAAAA
130 AAAAATAAAAATAAAAAATATTTTCAAAA
* *
1391569 AAAAAGAATTTTTATTTTTATTTTAGAGTAGAACCCTTGCCCATGAAATATCGTATCAACAAATT
1 AAAAA-AATTTCTATTTTTATTTTAGAGTAGAACCCTTGCCCATGAAATATCATATCAACAAATT
*
1391634 TAACAATACTAATAATTAAAATTAAAATTTAAAATTTGAAATATAAAAATTAAAAATTTTAAAA-
65 TAACAATACTAATAATTAAAATTAAAATTTAAAATTTGAAATATAAAAATTAAAAA-TTAAAAAT
1391698 TAAAAATAAAAAATAAA
129 TAAAAAT-AAAAATAAA
1391715 TTTCAAAATT
Statistics
Matches: 138, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
159 11 0.08
160 121 0.88
161 6 0.04
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (158 bp):
AAAAAAATTTCTATTTTTATTTTAGAGTAGAACCCTTGCCCATGAAATATCATATCAACAAATTT
AACAATACTAATAATTAAAATTAAAATTTAAAATTTGAAATATAAAAATTAAAAATTAAAAATTA
AAAATAAAAATAAAAAATATTTTCAAAA
Found at i:1393576 original size:16 final size:15
Alignment explanation
Indices: 1393555--1393584 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1393545 AGTTGTAAAT
1393555 ATATATATAAAGAAAA
1 ATATATA-AAAGAAAA
1393571 ATATATAAAAGAAA
1 ATATATAAAAGAAA
1393585 TTAGTTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (15 bp):
ATATATAAAAGAAAA
Found at i:1394111 original size:29 final size:26
Alignment explanation
Indices: 1394063--1394155 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 26
1394053 TTGCCATGTC
*
1394063 AAAAATA-AATAAATTTTTAAAAATT
1 AAAAATATAAAAAATTTTTAAAAATT
*
1394088 CAAAAACTATATAAAAATTATTAAAATATT
1 -AAAAA-TATA-AAAAATTTTTAAAA-ATT
*
1394118 ATAAAATATAAAAATATTTTTAAATATT
1 A-AAAATATAAAAA-ATTTTTAAAAATT
*
1394146 AAAAAAATAA
1 AAAAATATAA
1394156 TTGCTAACGT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
26 5 0.09
27 10 0.18
28 9 0.16
29 25 0.45
30 7 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAATATAAAAAATTTTTAAAAATT
Found at i:1394126 original size:27 final size:27
Alignment explanation
Indices: 1394096--1394155 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
1394086 TTCAAAAACT
1394096 ATATAAAAAT-TATTAAAATATTATAAA
1 ATATAAAAATATATTAAAATATTA-AAA
* *
1394123 ATATAAAAATATTTTTAAATATTAAAA
1 ATATAAAAATATATTAAAATATTAAAA
*
1394150 AAATAA
1 ATATAA
1394156 TTGCTAACGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATAAAAATATATTAAAATATTAAAA
Found at i:1394133 original size:18 final size:19
Alignment explanation
Indices: 1394080--1394150 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
1394070 AATAAATTTT
1394080 TAAAA-ATTCAAAAACTA-TA
1 TAAAATATT-AAAAA-TATTA
1394099 TAAAA-ATTATTAAAATATTA
1 TAAAATATTA--AAAATATTA
*
1394119 TAAAATA-TAAAAATATTT
1 TAAAATATTAAAAATATTA
*
1394137 TTAAATATTAAAAA
1 TAAAATATTAAAAA
1394151 AATAATTGCT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
18 15 0.33
19 16 0.36
20 13 0.29
21 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAATATTAAAAATATTA
Found at i:1400568 original size:51 final size:51
Alignment explanation
Indices: 1400485--1400586 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
1400475 AATAACAAAT
* * * *
1400485 TTAACCCTCAACATTTATATATAATATCAATTTAATCCTAATTTTAAAAAA
1 TTAACCCTCAAAATTTACAAATAATATCAATTTAATCCTAATTCTAAAAAA
* * * *
1400536 TTAACCCTCAAAATTTACAAATATTCTTAATTTGATCCTAATTCTAAAAAA
1 TTAACCCTCAAAATTTACAAATAATATCAATTTAATCCTAATTCTAAAAAA
1400587 ATAAAAAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.38
Consensus pattern (51 bp):
TTAACCCTCAAAATTTACAAATAATATCAATTTAATCCTAATTCTAAAAAA
Found at i:1403066 original size:28 final size:27
Alignment explanation
Indices: 1403029--1403094 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 27
1403019 ACTAATAATT
**
1403029 AAAATTAAAATTTGAAATTTGAAATATA
1 AAAATTAAAATTAAAAATTTGAAA-ATA
*
1403057 AAAATTAAAAATTAAAAATTTTAAAATA
1 AAAATT-AAAATTAAAAATTTGAAAATA
*
1403085 AAAATAAAAA
1 AAAATTAAAA
1403095 AGGCTTAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 4 0.12
28 14 0.42
29 15 0.45
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (27 bp):
AAAATTAAAATTAAAAATTTGAAAATA
Found at i:1403975 original size:27 final size:27
Alignment explanation
Indices: 1403945--1404004 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
1403935 TTCAAAAACT
1403945 ATATAAAAAT-TATTGAAATATTATAAA
1 ATATAAAAATATATTGAAATATTA-AAA
* *
1403972 ATATAAAAATATTTTTAAATATTAAAA
1 ATATAAAAATATATTGAAATATTAAAA
*
1403999 AAATAA
1 ATATAA
1404005 TTGCTAACGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
ATATAAAAATATATTGAAATATTAAAA
Found at i:1403983 original size:18 final size:19
Alignment explanation
Indices: 1403960--1403999 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1403950 AAAATTATTG
1403960 AAATATTATAAAATA-TAA
1 AAATATTATAAAATATTAA
* *
1403978 AAATATTTTTAAATATTAA
1 AAATATTATAAAATATTAA
1403997 AAA
1 AAA
1404000 AATAATTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATATTATAAAATATTAA
Found at i:1408583 original size:18 final size:19
Alignment explanation
Indices: 1408560--1408597 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1408550 GGAAGCAGGC
*
1408560 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
1408578 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
1408597 A
1 A
1408598 CCTAGAGTCT
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:1420041 original size:20 final size:20
Alignment explanation
Indices: 1420016--1420055 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1420006 AATATTTTCC
*
1420016 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
1420036 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
1420056 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:1420061 original size:34 final size:35
Alignment explanation
Indices: 1420004--1420070 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1419994 CAAACACCGG
*
1420004 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1420039 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1420071 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1425825 original size:3 final size:3
Alignment explanation
Indices: 1425817--1425884 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
1425807 TAACATTAAC
1425817 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1425865 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1425885 GGACTATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1426704 original size:15 final size:16
Alignment explanation
Indices: 1426676--1426705 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1426666 TCTGCCACTG
1426676 TTTCTTCACATTTTTC
1 TTTCTTCACATTTTTC
1426692 TTTCTTC-CATTTTT
1 TTTCTTCACATTTTT
1426706 GTCTCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTCTTCACATTTTTC
Found at i:1432608 original size:51 final size:51
Alignment explanation
Indices: 1432553--1432649 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
1432543 AAATTTAGCT
* * * *
1432553 CTCAACATTTATATATAATATCAATTTAGTCCTAATTTTAAAAAATTAACC
1 CTCAAAATTTACAAATAATATCAATTTAGTCCTAATTCTAAAAAATTAACC
* * *
1432604 CTCAAAATTTACAAATATTCTCAATTTGGTCCTAATTCTAAAAAAT
1 CTCAAAATTTACAAATAATATCAATTTAGTCCTAATTCTAAAAAAT
1432650 AAAAAAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.38
Consensus pattern (51 bp):
CTCAAAATTTACAAATAATATCAATTTAGTCCTAATTCTAAAAAATTAACC
Found at i:1437070 original size:11 final size:11
Alignment explanation
Indices: 1437056--1437082 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1437046 TATTTTTTAA
1437056 TTTTAAAATAT
1 TTTTAAAATAT
1437067 TTTTAAAATAT
1 TTTTAAAATAT
1437078 TTTTA
1 TTTTA
1437083 TTTTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1437119 original size:36 final size:35
Alignment explanation
Indices: 1437024--1437120 Score: 92
Period size: 37 Copynumber: 2.7 Consensus size: 35
1437014 CCGAATATAA
1437024 TAAATATATATTTTTTT-ATTTTTA-TTTTTTAATTT
1 TAAA-ATA-ATTTTTTTAATTTTTATTTTTTTAATTT
** *
1437059 TAAAAT-ATTTTTAAAATATTTTTATTTTTATTATTTT
1 TAAAATAATTTTT-TTA-ATTTTTATTTTT-TTAATTT
*
1437096 TAAAATAATTTTTTTAATGTTTATT
1 TAAAATAATTTTTTTAATTTTTATT
1437121 AAAAATGGGC
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
32 6 0.12
34 2 0.04
35 11 0.22
36 12 0.24
37 13 0.26
38 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (35 bp):
TAAAATAATTTTTTTAATTTTTATTTTTTTAATTT
Found at i:1438588 original size:28 final size:28
Alignment explanation
Indices: 1438554--1438652 Score: 82
Period size: 26 Copynumber: 3.7 Consensus size: 28
1438544 AAAATATAAC
*
1438554 AAATATATATATGTATATATAAATTATA
1 AAATATATATAAGTATATATAAATTATA
* *
1438582 AAATATATGTACA-TATATGT--ATTATA
1 AAATATATATA-AGTATATATAAATTATA
* ** * *
1438608 AAATGTATATAAGTATACGTATATTTTA
1 AAATATATATAAGTATATATAAATTATA
1438636 AAAT-TATA-AAGTATATA
1 AAATATATATAAGTATATA
1438653 CAAAAAAAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
25 1 0.02
26 28 0.48
27 4 0.07
28 25 0.43
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (28 bp):
AAATATATATAAGTATATATAAATTATA
Found at i:1438624 original size:26 final size:25
Alignment explanation
Indices: 1438554--1438652 Score: 76
Period size: 28 Copynumber: 3.7 Consensus size: 25
1438544 AAAATATAAC
*
1438554 AAATATATATATGTATATATAAATTATA
1 AAAT-TATATAAGTATATAT--ATTATA
* *
1438582 AAATATATGTACA-TATATGTATTATA
1 AAAT-TATATA-AGTATATATATTATA
*
1438608 AAATGTATATAAGTATACGTATATTTTA
1 AAAT-TATATAAGTATA--TATATTATA
1438636 AAATTATA-AAGTATATA
1 AAATTATATAAGTATATA
1438653 CAAAAAAAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
24 2 0.03
25 1 0.02
26 26 0.43
27 4 0.07
28 27 0.45
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (25 bp):
AAATTATATAAGTATATATATTATA
Found at i:1438756 original size:4 final size:4
Alignment explanation
Indices: 1438738--1438785 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
1438728 AAGAAAGTTT
* * * * *
1438738 TAAA TAAA GATA TAAA TAAA CAAA CAAA TAAA TAAA TGAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1438786 GGATTAAGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (4 bp):
TAAA
Found at i:1443736 original size:6 final size:7
Alignment explanation
Indices: 1443720--1443744 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1443710 CATTAAAGTA
1443720 TTTTAAT
1 TTTTAAT
1443727 TTTTAAT
1 TTTTAAT
1443734 TTTTAAT
1 TTTTAAT
1443741 TTTT
1 TTTT
1443745 TTTGTTGAAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:1457820 original size:29 final size:30
Alignment explanation
Indices: 1457761--1457818 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1457751 TCCGAGCCTT
**
1457761 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATAAAAAAGTTTA
* *
1457791 GGGGCAAAATTGTAATTTTAAAAAAGTT
1 GGGGCAAAAATGTAATTATAAAAAAGTT
1457819 AGAGTCAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATAAAAAAGTTTA
Found at i:1462511 original size:66 final size:66
Alignment explanation
Indices: 1462412--1462542 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
1462402 TATTCCGCTG
*
1462412 CCACCACCACCTAGACCTCCAGCTCCACCGCCTACACCACCTGTATCTGGACAACCACCACCACC
1 CCACCACCACCTAGACCTCCAGCTCCACCGCCTACACCACCTGTACCTGGACAACCACCACCACC
1462477 A
66 A
* *
1462478 CCACCACCACCTAGACCTCCAGCTCCGCTGCCTACACCACCTGTACCTGGACAACCACCACCACC
1 CCACCACCACCTAGACCTCCAGCTCCACCGCCTACACCACCTGTACCTGGACAACCACCACCACC
1462543 TAGACCTCCA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.26, C:0.52, G:0.10, T:0.12
Consensus pattern (66 bp):
CCACCACCACCTAGACCTCCAGCTCCACCGCCTACACCACCTGTACCTGGACAACCACCACCACC
A
Found at i:1462577 original size:66 final size:66
Alignment explanation
Indices: 1462412--1462577 Score: 183
Period size: 66 Copynumber: 2.5 Consensus size: 66
1462402 TATTCCGCTG
* * * *
1462412 CCACCACCACCTAGACCTCCAGCTCCACCGCCTACACCACCTGTATCTGGACAACCACCACCACC
1 CCACCACCAACTACACCCCCAGCTCCACCGCCTACACCACCTGTACCTGGACAACCACCACCACC
1462477 A
66 A
* * * * *
1462478 CCACCACCACCTAGACCTCCAGCTCCGCTGCCTACACCACCTGTACCTGGACAACCACCACCACC
1 CCACCACCAACTACACCCCCAGCTCCACCGCCTACACCACCTGTACCTGGACAACCACCACCACC
1462543 TA
66 -A
* * * *
1462545 -GACCTCCAACTCCACCCCC-GGTCCCACCGCCTA
1 CCACCACCAACTACACCCCCAGCT-CCACCGCCTA
1462578 GACCTCCAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 2 0.02
66 83 0.97
67 1 0.01
ACGTcount: A:0.25, C:0.52, G:0.10, T:0.13
Consensus pattern (66 bp):
CCACCACCAACTACACCCCCAGCTCCACCGCCTACACCACCTGTACCTGGACAACCACCACCACC
A
Found at i:1462578 original size:33 final size:33
Alignment explanation
Indices: 1462535--1462610 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
1462525 TGGACAACCA
*
1462535 CCACCACCTAGACCTCCAACTCCACCCCCGGTC
1 CCACCACCTAGACCTCCAACTCCACCACCGGTC
* * *
1462568 CCACCGCCTAGACCTCCAACTCCGCCACCGGTT
1 CCACCACCTAGACCTCCAACTCCACCACCGGTC
*
1462601 CCACCCCCTA
1 CCACCACCTA
1462611 AACCACCTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.20, C:0.57, G:0.11, T:0.13
Consensus pattern (33 bp):
CCACCACCTAGACCTCCAACTCCACCACCGGTC
Found at i:1462633 original size:42 final size:42
Alignment explanation
Indices: 1462574--1462670 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
1462564 GGTCCCACCG
*
1462574 CCTAGACCTCCAACTCCGCCACCGGTTCCACCCCCTAAACCA
1 CCTAGACCTCCAACTCCGCCACCAGTTCCACCCCCTAAACCA
* *
1462616 CCTAGACCTCCACCTCCGCCACCAGTTCCACCCCCTAACCCA
1 CCTAGACCTCCAACTCCGCCACCAGTTCCACCCCCTAAACCA
1462658 CCTAGACCTCCAA
1 CCTAGACCTCCAA
1462671 TTCCACCGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.24, C:0.54, G:0.08, T:0.14
Consensus pattern (42 bp):
CCTAGACCTCCAACTCCGCCACCAGTTCCACCCCCTAAACCA
Found at i:1462675 original size:30 final size:30
Alignment explanation
Indices: 1462634--1462701 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
1462624 TCCACCTCCG
* *
1462634 CCACCAGTTCCACCCCCT-AACCCACCTAGA
1 CCACCAATTCCACCCCCTAAACCC-CCTACA
* *
1462664 CCTCCAATTCCACCGCCTAAACCCCCTACA
1 CCACCAATTCCACCCCCTAAACCCCCTACA
1462694 CCACCAAT
1 CCACCAAT
1462702 GCCTTTGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.28, C:0.53, G:0.04, T:0.15
Consensus pattern (30 bp):
CCACCAATTCCACCCCCTAAACCCCCTACA
Found at i:1468673 original size:131 final size:127
Alignment explanation
Indices: 1468507--1468978 Score: 390
Period size: 131 Copynumber: 3.7 Consensus size: 127
1468497 ATATGCAACA
* * * * * * *
1468507 ATAAAATAAATTGTCGTTAAATATTATAATGTTAGCAATGACTTTAAAATGTCGTTATGTCATTT
1 ATAAAATAAATTGTTGTTAAACATTAAAATATTAGCAA-CACTTTAAAATGTCGTTACGTAATTT
* *
1468572 AATTTTCTTCTTATTAATTACAGCAGCATGATTTGTCATTGTGAATTCTTAATAAAATGTGTAAC
65 AATTTTCTTCTTACTAATTACA-CAACATGATTTGTC-TTGTGAATTCTTAATAAAAT-TGTAAC
1468637 G
127 G
* * * * *
1468638 ATAAAATAAGTTGTTGTTAAACGTTAAAATATTAGCAACAATCTTAAATTGTCTTTACGTAATTT
1 ATAAAATAAATTGTTGTTAAACATTAAAATATTAGCAACACT-TTAAAATGTCGTTACGTAATTT
* * * ** * *
1468703 AACTTTCTGCTTAGT-ATTCACAACAACGCGACTTGTCGTTGTGAATTCCTAATAAAATTTGTAA
65 AATTTTCTTCTTACTAATT-AC-ACAACATGATTTGTC-TTGTGAATTCTTAATAAAA-TTGTAA
1468767 CG
126 CG
** ** *
1468769 A-AAAA-AAA---AAGTTAAATGTGAAAATATTAGCAACATCTTTAAAATGTCGTTACGTAATTT
1 ATAAAATAAATTGTTGTTAAACATTAAAATATTAGCAACA-CTTTAAAATGTCGTTACGTAATTT
* * ** *
1468829 GATTTTCTAT-TTACGAA-T-CACAACATCTTTTGT-TGGTGCATATTCTTAATAAAATT-TACA
65 AATTTTCT-TCTTACTAATTACACAACATGATTTGTCTTGTG-A-ATTCTTAATAAAATTGTA-A
1468889 CGG
126 C-G
* * * * *
1468892 ACAAAATAAATTGTTGTTAAACATTAAAATATTAGCAATAACCTTAAAATATCGTTACATAATTT
1 ATAAAATAAATTGTTGTTAAACATTAAAATATTAGCAA-CACTTTAAAATGTCGTTACGTAATTT
*
1468957 AATTTTCTTATTACTAATTACA
65 AATTTTCTTCTTACTAATTACA
1468979 ACAAAACAAT
Statistics
Matches: 269, Mismatches: 52, Indels: 41
0.74 0.14 0.11
Matches are distributed among these distances:
121 6 0.02
122 5 0.02
123 23 0.09
124 5 0.02
125 3 0.01
126 53 0.20
127 3 0.01
128 54 0.20
129 4 0.01
130 11 0.04
131 100 0.37
132 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (127 bp):
ATAAAATAAATTGTTGTTAAACATTAAAATATTAGCAACACTTTAAAATGTCGTTACGTAATTTA
ATTTTCTTCTTACTAATTACACAACATGATTTGTCTTGTGAATTCTTAATAAAATTGTAACG
Found at i:1478865 original size:18 final size:19
Alignment explanation
Indices: 1478842--1478878 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1478832 TTTTAAAACA
1478842 TATAAA-ATTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
1478860 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
1478879 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:1478879 original size:18 final size:19
Alignment explanation
Indices: 1478842--1478901 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
1478832 TTTTAAAACA
* *
1478842 TATAAA-ATTTGGAATTTT
1 TATAAATATTTTGAACTTT
1478860 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAACTTT
*
1478878 TAAAAATTATTTTGTAACTTT
1 TATAAA-TATTTTG-AACTTT
1478899 TAT
1 TAT
1478902 TGAGAGAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 14 0.40
19 14 0.40
20 2 0.06
21 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (19 bp):
TATAAATATTTTGAACTTT
Found at i:1484861 original size:31 final size:31
Alignment explanation
Indices: 1484822--1484890 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
1484812 AAAAAATTAG
1484822 AGTGACC-AAATTAAAAATAACGCTATTTTAA
1 AGTGACCAAAATT-AAAATAACGCTATTTTAA
*
1484853 ATTGACCAAAATTAAAATAACGCTATTTTAA
1 AGTGACCAAAATTAAAATAACGCTATTTTAA
1484884 AGTGACC
1 AGTGACC
1484891 TTCTGGGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 30 0.86
32 5 0.14
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.29
Consensus pattern (31 bp):
AGTGACCAAAATTAAAATAACGCTATTTTAA
Found at i:1498116 original size:20 final size:20
Alignment explanation
Indices: 1498093--1498130 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1498083 TTAATGTTCG
1498093 GGTTTAAGTTTTGAGTTTGT
1 GGTTTAAGTTTTGAGTTTGT
*
1498113 GGTTTAAGTTTTGGGTTT
1 GGTTTAAGTTTTGAGTTT
1498131 ACAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.32, T:0.55
Consensus pattern (20 bp):
GGTTTAAGTTTTGAGTTTGT
Found at i:1505894 original size:20 final size:19
Alignment explanation
Indices: 1505869--1505907 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1505859 TTCTCTATAA
1505869 TATTTCCCATCACTTTCACT
1 TATTTCCCATCAC-TTCACT
* *
1505889 TATTTCTCTTCACTTCACT
1 TATTTCCCATCACTTCACT
1505908 AATATATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTTCCCATCACTTCACT
Found at i:1516198 original size:38 final size:37
Alignment explanation
Indices: 1516151--1516223 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
1516141 ATGTGTGGAA
* *
1516151 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
1516189 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1516224 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:1519531 original size:2 final size:2
Alignment explanation
Indices: 1519524--1519548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1519514 ATAATTCATT
1519524 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1519549 TTCTAGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1521992 original size:29 final size:29
Alignment explanation
Indices: 1521923--1521989 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
1521913 TCATATATTT
* *
1521923 AGAATTTAGT-TCATCTACTTTTATTTTCA
1 AGAATTTAATATC-TCTACTTTTATTATCA
1521952 AGAATTTAATATCTCTACTTTTTATATATCA
1 AGAATTTAATATCTCTAC-TTTTAT-TATCA
1521983 A-AATTTA
1 AGAATTTA
1521990 TATTTAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 14 0.42
30 14 0.42
31 5 0.15
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.49
Consensus pattern (29 bp):
AGAATTTAATATCTCTACTTTTATTATCA
Found at i:1522316 original size:91 final size:91
Alignment explanation
Indices: 1522205--1522385 Score: 258
Period size: 91 Copynumber: 2.0 Consensus size: 91
1522195 AAAAATTCTC
* *
1522205 ACATTGGGGTTTAAAC-TTTTTTTTGTCCAAATTTAATCCATAAACTTGGGAATTGTTCACATGT
1 ACATTGGGGTATAAACTTTTTTTTTGTCC-AAGTTAATCCATAAACTTGGGAATTGTTCACATGT
1522269 TAAG-GCTTGAACTAGGTAATTGTTCCT
65 T-AGTGCTTGAACTAGGTAATTGTTCCT
** * * * *
1522296 ACATTGGGGTATGGACTTTTTTTTTGTTCAAGTTAATCCTTAAACTTGGTAATTGTTCTCATGTT
1 ACATTGGGGTATAAACTTTTTTTTTGTCCAAGTTAATCCATAAACTTGGGAATTGTTCACATGTT
1522361 AGTGCTTGAACTAGGTAATTGTTCC
66 AGTGCTTGAACTAGGTAATTGTTCC
1522386 CACGTAAGAG
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
90 2 0.03
91 67 0.84
92 11 0.14
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.43
Consensus pattern (91 bp):
ACATTGGGGTATAAACTTTTTTTTTGTCCAAGTTAATCCATAAACTTGGGAATTGTTCACATGTT
AGTGCTTGAACTAGGTAATTGTTCCT
Found at i:1528910 original size:21 final size:19
Alignment explanation
Indices: 1528858--1528905 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1528848 ATATCCAAAC
*
1528858 AATAACAACATAATAGTGA
1 AATAACAACAAAATAGTGA
1528877 AATAACAACAAAATAGTGA
1 AATAACAACAAAATAGTGA
1528896 AA-AACAACAA
1 AATAACAACAA
1528906 GAAAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.15
Consensus pattern (19 bp):
AATAACAACAAAATAGTGA
Found at i:1533427 original size:66 final size:66
Alignment explanation
Indices: 1533344--1533473 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
1533334 AGACATAAAA
*
1533344 TAAAGAGTAGTTCAAATTGATAATCCGGAAG-TGGTCAAAGCCCTACAAAAGAGTGGGGGGACGA
1 TAAAGAATAGTTCAAATTGATAATCCGG-AGTTGGTCAAAGCCCTACAAAAGAGTGGGGGGACGA
1533408 AG
65 AG
*
1533410 TAAAGAATAGTTCAAATTGATAATCCGGAGTTGGTCAAAGCCCTACAAGAGAGTGGGGGGACGA
1 TAAAGAATAGTTCAAATTGATAATCCGGAGTTGGTCAAAGCCCTACAAAAGAGTGGGGGGACGA
1533474 CTCAAGAGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 2 0.03
66 59 0.97
ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19
Consensus pattern (66 bp):
TAAAGAATAGTTCAAATTGATAATCCGGAGTTGGTCAAAGCCCTACAAAAGAGTGGGGGGACGAA
G
Found at i:1538503 original size:84 final size:84
Alignment explanation
Indices: 1538406--1538589 Score: 343
Period size: 84 Copynumber: 2.2 Consensus size: 84
1538396 TCTTTTAATT
*
1538406 AATTAAATTAACTAA-ATTATTTTCTCAACTTAATTCTAATTTCGTTAAACTCACGACAACTTTA
1 AATTAATTTAACTAACATTATTTTCT-AACTTAATTCTAATTTCGTTAAACTCACGACAACTTTA
1538470 CCGATAAAAATCTATGAACA
65 CCGATAAAAATCTATGAACA
1538490 AATTAATTTAACTAACATTATTTTCTAACTTAATTCTAATTTCGTTAAACTCACGACAACTTTAC
1 AATTAATTTAACTAACATTATTTTCTAACTTAATTCTAATTTCGTTAAACTCACGACAACTTTAC
1538555 CGATAAAAATCTATGAACA
66 CGATAAAAATCTATGAACA
1538574 AATTAATTTAACTAAC
1 AATTAATTTAACTAAC
1538590 TTGTCCTTAT
Statistics
Matches: 98, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
84 88 0.90
85 10 0.10
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.36
Consensus pattern (84 bp):
AATTAATTTAACTAACATTATTTTCTAACTTAATTCTAATTTCGTTAAACTCACGACAACTTTAC
CGATAAAAATCTATGAACA
Found at i:1540313 original size:55 final size:55
Alignment explanation
Indices: 1540246--1540389 Score: 148
Period size: 55 Copynumber: 2.6 Consensus size: 55
1540236 CCATTTTAGA
* * *
1540246 CAAATATCAGACATAATAAGTTATGAAAACAAGTTCATTTTGGACAACCATTTCTT
1 CAAATGTCAGACATAATAAGTTATGAAAACAAG-CCATTTTAGACAACCATTTCTT
* * * *
1540302 -AAATGTCAGACATGATAAGTTCTGGAAACAGCAGCCATTTTAGACAATCATTTCTT
1 CAAATGTCAGACATAATAAGTTATGAAAACA--AGCCATTTTAGACAACCATTTCTT
* * *
1540358 CACATGTCAGATAAAATATA-TTATGAAAACAA
1 CAAATGTCAGACATAATA-AGTTATGAAAACAA
1540390 CAGTCATTTT
Statistics
Matches: 71, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
55 27 0.38
56 19 0.27
57 24 0.34
58 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (55 bp):
CAAATGTCAGACATAATAAGTTATGAAAACAAGCCATTTTAGACAACCATTTCTT
Found at i:1540398 original size:57 final size:56
Alignment explanation
Indices: 1540247--1540399 Score: 150
Period size: 57 Copynumber: 2.7 Consensus size: 56
1540237 CATTTTAGAC
* * *
1540247 AAATATCAGACATAATAAGTTATGAAAAC-A-AGTTCATTTTGGACAACCATTTCTT
1 AAATGTCAGACAAAATAAGTTATGAAAACAACAG-TCATTTTAGACAACCATTTCTT
** * * * * *
1540302 AAATGTCAGACATGATAAGTTCTGGAAACAGCAGCCATTTTAGACAATCATTTCTT
1 AAATGTCAGACAAAATAAGTTATGAAAACAACAGTCATTTTAGACAACCATTTCTT
* *
1540358 CACATGTCAGATAAAATATA-TTATGAAAACAACAGTCATTTT
1 -AAATGTCAGACAAAATA-AGTTATGAAAACAACAGTCATTTT
1540400 CTGCTAGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
55 25 0.32
56 19 0.24
57 33 0.42
58 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (56 bp):
AAATGTCAGACAAAATAAGTTATGAAAACAACAGTCATTTTAGACAACCATTTCTT
Found at i:1540759 original size:30 final size:31
Alignment explanation
Indices: 1540720--1540839 Score: 108
Period size: 30 Copynumber: 4.0 Consensus size: 31
1540710 ACCCCTATAC
1540720 TTCTCAAAATTTACAATTTGACCCC-AAACT
1 TTCTCAAAATTTACAATTTGACCCCAAAACT
* *
1540750 TT-TCTAAAATTTACATTTTAACCCCAAAACT
1 TTCTC-AAAATTTACAATTTGACCCCAAAACT
* ** *
1540781 TTAT-AAAA-TTAC-ATTTCGACCCTTATACT
1 TTCTCAAAATTTACAATTT-GACCCCAAAACT
* *
1540810 TTCTCAAAATTT-CACTTTGACCCCTAAACT
1 TTCTCAAAATTTACAATTTGACCCCAAAACT
1540840 CTCAATAAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
28 3 0.04
29 17 0.24
30 39 0.54
31 12 0.17
32 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.38
Consensus pattern (31 bp):
TTCTCAAAATTTACAATTTGACCCCAAAACT
Found at i:1540793 original size:29 final size:28
Alignment explanation
Indices: 1540703--1540796 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 28
1540693 TACTTTTTTG
* *
1540703 CATTTTAACCCCTATACTTCTCA-AAATTTA
1 CATTTTAACCCC-AAACTT-T-ATAAAATTA
* * *
1540733 CAATTTGACCCCAAACTTTTCTAAAATTTA
1 CATTTTAACCCCAAAC-TTTATAAAA-TTA
1540763 CATTTTAACCCCAAAACTTTATAAAATTA
1 CATTTTAACCCC-AAACTTTATAAAATTA
1540792 CATTT
1 CATTT
1540797 CGACCCTTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
29 15 0.29
30 33 0.63
31 4 0.08
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.38
Consensus pattern (28 bp):
CATTTTAACCCCAAACTTTATAAAATTA
Found at i:1542098 original size:21 final size:21
Alignment explanation
Indices: 1542054--1542094 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1542044 AGAAATAAAA
1542054 AAAATAAAAATCTTGTGTTTT
1 AAAATAAAAATCTTGTGTTTT
1542075 AAAA-AAAAAT-TTCGTGTTTT
1 AAAATAAAAATCTT-GTGTTTT
1542095 TAAAGTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 13 0.68
21 4 0.21
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (21 bp):
AAAATAAAAATCTTGTGTTTT
Found at i:1542111 original size:17 final size:17
Alignment explanation
Indices: 1542080--1542132 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
1542070 GTTTTAAAAA
*
1542080 AAAATTT-CGTGTTTTT
1 AAAATTTCCATGTTTTT
*
1542096 AAAGTTTCCATG-TTTT
1 AAAATTTCCATGTTTTT
*
1542112 AAAATTTCCGTGTTTTT
1 AAAATTTCCATGTTTTT
1542129 AAAA
1 AAAA
1542133 AAAAATTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.49
Consensus pattern (17 bp):
AAAATTTCCATGTTTTT
Found at i:1542137 original size:22 final size:21
Alignment explanation
Indices: 1542112--1542154 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1542102 TCCATGTTTT
*
1542112 AAAATTTCCGTGTTTTTAAAAA
1 AAAATTT-CGTGTTTTCAAAAA
*
1542134 AAAATTTCTTGTTTTCAAAAA
1 AAAATTTCGTGTTTTCAAAAA
1542155 TTCCCGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAATTTCGTGTTTTCAAAAA
Found at i:1542213 original size:62 final size:62
Alignment explanation
Indices: 1542131--1542272 Score: 157
Period size: 62 Copynumber: 2.3 Consensus size: 62
1542121 GTGTTTTTAA
* * *
1542131 AAAAAAATT-TCTTGTTTTCAAAAATTCCCGTG-TTT-AAATTTTTTTTCGTGTTTTCGTGTTTT
1 AAAAAAATTCTCATG-TTTCAAAAATTCCCGTGTTTTCAAA---ATTTTCATGTTTTCGTGTTTT
1542193 C
62 C
***
1542194 -AAAAAATTCTCATGTTTCAAAAATTTTTGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTC
1 AAAAAAATTCTCATGTTTCAAAAATTCCCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTC
*
1542255 AAAAAAATTCTCGTGTTT
1 AAAAAAATTCTCATGTTT
1542273 TTAAAAAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
61 20 0.29
62 38 0.56
63 7 0.10
64 3 0.04
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (62 bp):
AAAAAAATTCTCATGTTTCAAAAATTCCCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTC
Found at i:1542226 original size:44 final size:44
Alignment explanation
Indices: 1542138--1542229 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
1542128 TAAAAAAAAA
* * **
1542138 TTTCTTGTTTTCAAAAATTCCCGTGTTTAAATTTTTTTTCGTGT
1 TTTCGTGTTTTCAAAAATTCCCATGTTTAAATAATTTTTCGTGT
*
1542182 TTTCGTGTTTTCAAAAAATTCTCATGTTTCAAA-AATTTTT-GTGT
1 TTTCGTGTTTTC-AAAAATTCCCATGTTT-AAATAATTTTTCGTGT
1542226 TTTC
1 TTTC
1542230 AAAATTTTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 19 0.46
45 19 0.46
46 3 0.07
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.54
Consensus pattern (44 bp):
TTTCGTGTTTTCAAAAATTCCCATGTTTAAATAATTTTTCGTGT
Done.