Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 137 of 161
Found at i:42650244 original size:153 final size:155
Alignment explanation
Indices: 42649964--42650275 Score: 601
Period size: 153 Copynumber: 2.0 Consensus size: 155
42649954 TTTAAAACAA
42649964 AAAAAATTTATAACTTCATTTTATCAGTGTTTTAAAGAAAAAAAAACTGAACCTATCCTCTCCCT
1 AAAAAATTTATAACTTCATTTTATCAGTGTTTTAAAGAAAAAAAAACTGAACCTATCCTCTCCCT
42650029 TTCAAGGTTCCCAGCAGCCAAACATGGCCCACGCCGGCGAGCGGCGGTTCCAAAGGCCAAAGCTC
66 TTCAAGGTTCCCAGCAGCCAAACATGGCCCACGCCGGCGAGCGGCGGTTCCAAAGGCCAAAGCTC
42650094 CTTCACGAGCGGTGGTCGGAGCGAG
131 CTTCACGAGCGGTGGTCGGAGCGAG
42650119 AAAAAA-TTATAACTTCATTTTATCAGTGTTTTAAAG-AAAAAAAACTGAACCTATCCTCTCCCT
1 AAAAAATTTATAACTTCATTTTATCAGTGTTTTAAAGAAAAAAAAACTGAACCTATCCTCTCCCT
*
42650182 TTCAAGGTTCCCAGTAGCCAAACATGGCCCACGCCGGCGAGCGGCGGTTCCAAAGGCCAAAGCTC
66 TTCAAGGTTCCCAGCAGCCAAACATGGCCCACGCCGGCGAGCGGCGGTTCCAAAGGCCAAAGCTC
42650247 CTTCACGAGCGGTGGTCGGAGCGAG
131 CTTCACGAGCGGTGGTCGGAGCGAG
42650272 AAAA
1 AAAA
42650276 GGAGGGCTTT
Statistics
Matches: 156, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
153 120 0.77
154 30 0.19
155 6 0.04
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (155 bp):
AAAAAATTTATAACTTCATTTTATCAGTGTTTTAAAGAAAAAAAAACTGAACCTATCCTCTCCCT
TTCAAGGTTCCCAGCAGCCAAACATGGCCCACGCCGGCGAGCGGCGGTTCCAAAGGCCAAAGCTC
CTTCACGAGCGGTGGTCGGAGCGAG
Found at i:42650704 original size:160 final size:159
Alignment explanation
Indices: 42650462--42650781 Score: 615
Period size: 160 Copynumber: 2.0 Consensus size: 159
42650452 TTGTTTTTTT
42650462 TAGTTTCAAAGAGTAGTAAAAAAACAGAAAATAGAAGAATATATAAAAAAATTATTAAGAACAGA
1 TAGTTTCAAAGAGTAGTAAAAAAACAGAAAATAGAAGAATATATAAAAAAATTATTAAGAACAGA
42650527 GAAAGAAATTTGGAGTCAACCTTTTCAATTTTTTTGATCTGCTCCC-TTTTTTTTTGAATACAGA
66 GAAAGAAATTTGGAGTCAACCTTTTCAATTTTTTTGATCTGCTCCCTTTTTTTTTTGAATACAGA
42650591 TTTTGGTGGCTTTTATAGCCAAAAGATAA
131 TTTTGGTGGCTTTTATAGCCAAAAGATAA
42650620 TAGTTTCAAAGAGTAGTAAAAAAAACAGAAAATAGAAGAATATATAAAAAAAATTATTAAGAACA
1 TAGTTTCAAAGAGTAGT-AAAAAAACAGAAAATAGAAGAATATAT-AAAAAAATTATTAAGAACA
42650685 GAGAAAGAAATTTGGAGTCAACCTTTTCAATTTTTTTGATCTGCTCCCTTTTTTTTTTGAATACA
64 GAGAAAGAAATTTGGAGTCAACCTTTTCAATTTTTTTGATCTGCTCCCTTTTTTTTTTGAATACA
42650750 GATTTTGGTGGCTTTTATAGCCAAAAGATAA
129 GATTTTGGTGGCTTTTATAGCCAAAAGATAA
42650781 T
1 T
42650782 CCTAAAAATC
Statistics
Matches: 159, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
158 17 0.11
159 27 0.17
160 67 0.42
161 48 0.30
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (159 bp):
TAGTTTCAAAGAGTAGTAAAAAAACAGAAAATAGAAGAATATATAAAAAAATTATTAAGAACAGA
GAAAGAAATTTGGAGTCAACCTTTTCAATTTTTTTGATCTGCTCCCTTTTTTTTTTGAATACAGA
TTTTGGTGGCTTTTATAGCCAAAAGATAA
Found at i:42651983 original size:205 final size:205
Alignment explanation
Indices: 42651626--42651996 Score: 625
Period size: 205 Copynumber: 1.8 Consensus size: 205
42651616 CTTTGTTTTA
* * * * *
42651626 ATCCGCTCCACTGTAACTTTAGGGAGATAGGATAGTGTCTTCGATCTGCTCTGCTGTAATCTCAG
1 ATCCACTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAAACTCAG
* *
42651691 GGAGATAAGATCCCTAGCTTCAATCTGCTCCACTATAACCTCAGGGAGATAAGATCTGAAATTCT
66 GAAGATAAGATCCCTAGCTTCAATCTGCTCCACTATAACCTCAGGGAGATAAGACCTGAAATTCT
*
42651756 TCGGTCTACTCTACCGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCA
131 TCGGTCTACTCCACCGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCA
42651821 GAGAGATAAG
196 GAGAGATAAG
42651831 ATCCACTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAAACTCAG
1 ATCCACTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAAACTCAG
** * *
42651896 GAAGATAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCT
66 GAAGATAAGATCCCTAGCTTCAATCTGCTCCACTATAACCTCAGGGAGATAAGACCTGAAATTCT
*
42651961 TCGGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
131 TCGGTCTACTCCACCGTAACCTCAGGGAGATAAGAC
42651997 TTGTATATTC
Statistics
Matches: 153, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
205 153 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (205 bp):
ATCCACTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAAACTCAG
GAAGATAAGATCCCTAGCTTCAATCTGCTCCACTATAACCTCAGGGAGATAAGACCTGAAATTCT
TCGGTCTACTCCACCGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCA
GAGAGATAAG
Found at i:42651992 original size:90 final size:90
Alignment explanation
Indices: 42651868--42652038 Score: 225
Period size: 90 Copynumber: 1.9 Consensus size: 90
42651858 TAGGATAGTG
* * * * * * *
42651868 TCTTCGATCTGCTCCGCTGTAAACTCAGGAAGATAAGATTTCTGGCTTCAATCTGCTCCACTGTA
1 TCTTCGATCTACTCCACTGTAAACTCAGGAAGATAAGACTTCTAGATTCAACCTGCCCCACTGTA
42651933 ACCTCAGGGAGATAAGACCTGAAAT
66 ACCTCAGGGAGATAAGACCTGAAAT
* * * * *
42651958 TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGTATATTCAACCTGCCCCACTGTA
1 TCTTCGATCTACTCCACTGTAAACTCAGGAAGATAAGACTTCTAGATTCAACCTGCCCCACTGTA
*
42652023 ACTTCAGGGAGATAAG
66 ACCTCAGGGAGATAAG
42652039 GTTTGTGGCT
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
90 68 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (90 bp):
TCTTCGATCTACTCCACTGTAAACTCAGGAAGATAAGACTTCTAGATTCAACCTGCCCCACTGTA
ACCTCAGGGAGATAAGACCTGAAAT
Found at i:42652066 original size:44 final size:44
Alignment explanation
Indices: 42651836--42652124 Score: 216
Period size: 44 Copynumber: 6.6 Consensus size: 44
42651826 ATAAGATCCA
* * *
42651836 CTCCACTGTAACTTCAAGGAGATAGGA-TAGTGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGTGTCTTCGATCTG
* * * * * *
42651879 CTCCGCTGTAAAC-TCAGGAAGATAAGATTTCTGGCTTCAATCTG
1 CTCCACTGT-AACTTCAGGGAGATAAGACTTGTGTCTTCGATCTG
* * * *
42651923 CTCCACTGTAACCTCAGGGAGATAAGACCTGAAAT-TCTTCGGTCTA
1 CTCCACTGTAACTTCAGGGAGATAAGACTTG---TGTCTTCGATCTG
* * * * *
42651969 CTCCACTGTAACCTCAGGGAGATAAGACTTGTATATTCAACCTG
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGTGTCTTCGATCTG
* ** * *
42652013 CCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTCCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGTGTCTTCGATCTG
* * * *
42652057 CTCCTCTGT-AGTCTCAGGGAGATAAGAC-T-TG-ATACGATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGACTTGTGTCTTCGATCTG
*
42652098 CTCCACCGTAA-TCTCAGGGAGATAAGA
1 CTCCACTGTAACT-TCAGGGAGATAAGA
42652125 TCTCTAATAT
Statistics
Matches: 195, Mismatches: 42, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
41 31 0.16
42 3 0.02
43 26 0.13
44 97 0.50
46 37 0.19
47 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGAGATAAGACTTGTGTCTTCGATCTG
Found at i:42652074 original size:134 final size:133
Alignment explanation
Indices: 42651835--42652084 Score: 313
Period size: 134 Copynumber: 1.9 Consensus size: 133
42651825 GATAAGATCC
* * * * * * * *
42651835 ACTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAAACTCAGGAAG
1 ACTCCACTGTAACCTCAAGGAGATAAGATAGTATATTCAACCTGCCCCACTGTAAACTCAGGAAG
*
42651900 ATAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTTCGG
66 ATAAGATTTCTGGCTCCAATCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTTCGG
42651965 TCT
131 TCT
* * *
42651968 ACTCCACTGTAACCTCAGGGAGATAAGACTTGTATATTCAACCTGCCCCACTGT-AACTTCAGGG
1 ACTCCACTGTAACCTCAAGGAGATAAGA-TAGTATATTCAACCTGCCCCACTGTAAAC-TCAGGA
* * * * **
42652032 AGATAAGGTTTGTGGCTCCGATCTGCTCCTCTGTAGTCTCAGGGAGATAAGAC
64 AGATAAGATTTCTGGCTCCAATCTGCTCCACTGTAACCTCAGGGAGATAAGAC
42652085 TTGATACGAT
Statistics
Matches: 97, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
133 28 0.29
134 69 0.71
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (133 bp):
ACTCCACTGTAACCTCAAGGAGATAAGATAGTATATTCAACCTGCCCCACTGTAAACTCAGGAAG
ATAAGATTTCTGGCTCCAATCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTTCGG
TCT
Found at i:42666422 original size:20 final size:19
Alignment explanation
Indices: 42666394--42666468 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
42666384 TTTTAAAATT
*
42666394 AAGTGAAAATGATTTTAACC
1 AAGTCAAAATGATTTTAA-C
* *
42666414 AAGTCAAAATGATTTCCATC
1 AAGTCAAAATGATTT-TAAC
* *
42666434 AAGTTAAAATCATTTTAAC
1 AAGTCAAAATGATTTTAAC
42666453 ACA-TCAAAATGATTTT
1 A-AGTCAAAATGATTTT
42666469 CAAACAAGCC
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
19 14 0.32
20 29 0.66
21 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (19 bp):
AAGTCAAAATGATTTTAAC
Found at i:42669987 original size:16 final size:16
Alignment explanation
Indices: 42669966--42670002 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
42669956 TTTGGTTCGC
42669966 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
42669982 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
42669998 TGTAT
1 TGTAT
42670003 AATAAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:42670179 original size:47 final size:46
Alignment explanation
Indices: 42670128--42670288 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
42670118 GATTTAATAA
42670128 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
42670175 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
42670216 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
42670263 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
42670289 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:42672120 original size:22 final size:22
Alignment explanation
Indices: 42672092--42672147 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
42672082 GATCAATAAA
42672092 AGTAAATGCATTGAATTTCTCC
1 AGTAAATGCATTGAATTTCTCC
42672114 AGTAAATGCATTGAATTTCTCC
1 AGTAAATGCATTGAATTTCTCC
42672136 AGTAAACTGCAT
1 AGTAAA-TGCAT
42672148 CATCATCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (22 bp):
AGTAAATGCATTGAATTTCTCC
Found at i:42697235 original size:355 final size:355
Alignment explanation
Indices: 42696584--42697288 Score: 1169
Period size: 355 Copynumber: 2.0 Consensus size: 355
42696574 GTTCAGCAAA
* *
42696584 TCACAATACAAAAGGGATTCTGGACTACGTTCACAGTGATGTGTGAGGACCTACTAAAGTGGCTT
1 TCACAATACAAAAGGAATTCTGGACTACGTTCAAAGTGATGTGTGAGGACCTACTAAAGTGGCTT
* *
42696649 CTTTGGGAGGTATGCACTGTTTTGTTACTTTTGTTGATGATTATTCAAGAAAAGTATGGATGTAT
66 CTTTGGGAGGTATGCACTATTTTGTTACTTTTGTTGATGATTATTCAAGAAAAATATGGATGTAT
* *
42696714 CTAATGAAAAGAAAAAATGAAGTTTTGGATGCATTTTTGAAATGGAAAAAGATAGTGGAGACCCA
131 CTAATGAAAAGAAAAAATAAAGTTTTGGATGCATTTCTGAAATGGAAAAAGATAGTGGAGACCCA
* * * * * *
42696779 TATTGGTCGAAAGGTTAAACGACTTCGATCAGACAATGGTACTGAGTACCAGAAAGATCCATTTC
196 AACTGGTCAAAAAGTCAAACGACTTCGATCAGACAATGGTACTGAGTACAAGAAAGATCCATTTC
* *
42696844 TACAAGTATGTCAAGATGAGGGCATTGTGTGACACTTCACTGTTCGAGATACACCACAATAAAAT
261 TACAAGTATGTCAAGATGAGGGCATTGTGCGACACTTCACTGTTCGAGATACACCACAACAAAAT
* *
42696909 GGGGTGGCAAAACGTATGAATCGGAGTAAT
326 AGGGTGGCAAAACATATGAATCGGAGTAAT
*
42696939 TCACAATACAAAAGGAATTCTGGACTACGTTCAAAGTGATGTGTG-GAGACCTATTAAAGTGGCT
1 TCACAATACAAAAGGAATTCTGGACTACGTTCAAAGTGATGTGTGAG-GACCTACTAAAGTGGCT
* *
42697003 TCTTTGGGAGGTATGCACTATTTTGTTACTTTTGTTGATGATTATTCAATAAAAATATGGGTGTA
65 TCTTTGGGAGGTATGCACTATTTTGTTACTTTTGTTGATGATTATTCAAGAAAAATATGGATGTA
* *
42697068 TCTAATGAAAAGAAAAAATAAAGTTTTGGATGCATTTCTGAAATGGAAGAAGATGGTGGAGACCC
130 TCTAATGAAAAGAAAAAATAAAGTTTTGGATGCATTTCTGAAATGGAAAAAGATAGTGGAGACCC
* * *
42697133 AAACTGGTCAAAAAGTCAAGCGACTTCGATCAGACAATGGTATTGAGTACAAGAATGATCCATTT
195 AAACTGGTCAAAAAGTCAAACGACTTCGATCAGACAATGGTACTGAGTACAAGAAAGATCCATTT
42697198 CTACAAGTATGTCAAGATGAGGGCATTGTGCGACACTTCACTGTTCGAGATACACCACAACAAAA
260 CTACAAGTATGTCAAGATGAGGGCATTGTGCGACACTTCACTGTTCGAGATACACCACAACAAAA
*
42697263 TAGGGTGGCAGAACATATGAATCGGA
325 TAGGGTGGCAAAACATATGAATCGGA
42697289 CTATACTGGA
Statistics
Matches: 324, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
354 1 0.00
355 323 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (355 bp):
TCACAATACAAAAGGAATTCTGGACTACGTTCAAAGTGATGTGTGAGGACCTACTAAAGTGGCTT
CTTTGGGAGGTATGCACTATTTTGTTACTTTTGTTGATGATTATTCAAGAAAAATATGGATGTAT
CTAATGAAAAGAAAAAATAAAGTTTTGGATGCATTTCTGAAATGGAAAAAGATAGTGGAGACCCA
AACTGGTCAAAAAGTCAAACGACTTCGATCAGACAATGGTACTGAGTACAAGAAAGATCCATTTC
TACAAGTATGTCAAGATGAGGGCATTGTGCGACACTTCACTGTTCGAGATACACCACAACAAAAT
AGGGTGGCAAAACATATGAATCGGAGTAAT
Found at i:42698547 original size:17 final size:17
Alignment explanation
Indices: 42698525--42698557 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42698515 ATAGAAAGTC
42698525 AAAGATATGGGTATCAT
1 AAAGATATGGGTATCAT
42698542 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
42698558 AAATCTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (17 bp):
AAAGATATGGGTATCAT
Found at i:42716375 original size:22 final size:24
Alignment explanation
Indices: 42716350--42716394 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
42716340 ATATGACAAA
42716350 GAATTAAG-TAGAAAAG-AAGTAT
1 GAATTAAGTTAGAAAAGTAAGTAT
42716372 GAATTAAGTTAGAAAAGTAAGTA
1 GAATTAAGTTAGAAAAGTAAGTA
42716395 AACTTAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 8 0.38
24 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24
Consensus pattern (24 bp):
GAATTAAGTTAGAAAAGTAAGTAT
Found at i:42717633 original size:75 final size:74
Alignment explanation
Indices: 42717505--42717653 Score: 244
Period size: 75 Copynumber: 2.0 Consensus size: 74
42717495 CTCAGTGTAC
* *
42717505 GGTTGTTTCCGTGCGCAGGTCGATAAAAATCAAAGGTTCCGGTTCAGCGTCCAGATCAATCTCGA
1 GGTTGTTTCCGTGCGCAAGTCGATAAAAATCAAAGGTTCCGGTTCAGCATCCAGATCAATCTCGA
*
42717570 CTCTAGCAT
66 CTCCAGCAT
* *
42717579 NGGTTGTTTCCGTGCGCAAGTCGATAGAAATCAAAGGTTCTGGTTCAGCATCCAGATCAATCTCG
1 -GGTTGTTTCCGTGCGCAAGTCGATAAAAATCAAAGGTTCCGGTTCAGCATCCAGATCAATCTCG
42717644 ACTCCAGCAT
65 ACTCCAGCAT
42717654 AAAGATTTTG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (74 bp):
GGTTGTTTCCGTGCGCAAGTCGATAAAAATCAAAGGTTCCGGTTCAGCATCCAGATCAATCTCGA
CTCCAGCAT
Found at i:42725888 original size:15 final size:17
Alignment explanation
Indices: 42725858--42725889 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42725848 CAACAATTAA
42725858 TTAACTTTTTATAATTT
1 TTAACTTTTTATAATTT
42725875 TTAA-TTTTTA-AATTT
1 TTAACTTTTTATAATTT
42725890 AAAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 6 0.40
17 4 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAACTTTTTATAATTT
Found at i:42735825 original size:4 final size:4
Alignment explanation
Indices: 42735816--42735861 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
42735806 CCTACTTTCT
42735816 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
42735862 CTTCAGCTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:42739753 original size:25 final size:24
Alignment explanation
Indices: 42739722--42739794 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 24
42739712 CCACAGCTTG
42739722 TATGAGCTTACCGATTTGCAGCTCA
1 TATGAGCTTACCGATTT-CAGCTCA
* *
42739747 TGA-GAGCTTATCGATTCTCAGCTCG
1 T-ATGAGCTTACCGATT-TCAGCTCA
*
42739772 TATGAGCTTACCGTATTTTAGCT
1 TATGAGCTTACCG-ATTTCAGCT
42739795 TTGAAGAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 1 0.03
25 34 0.85
26 5 0.12
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (24 bp):
TATGAGCTTACCGATTTCAGCTCA
Found at i:42741852 original size:24 final size:24
Alignment explanation
Indices: 42741820--42741874 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
42741810 TCTTCCAGTT
42741820 AAACTCTGTTTATTTATTTCAATC
1 AAACTCTGTTTATTTATTTCAATC
* *
42741844 AAACTCTGTTTATTTGTTTTAATC
1 AAACTCTGTTTATTTATTTCAATC
42741868 AAACTCT
1 AAACTCT
42741875 AATTAGTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTATTTCAATC
Found at i:42763061 original size:3 final size:3
Alignment explanation
Indices: 42763053--42763079 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42763043 TTTCTCTTGG
42763053 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
42763080 TTACAGATTA
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:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:42763898 original size:15 final size:15
Alignment explanation
Indices: 42763878--42763906 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42763868 GTACCAGACA
42763878 TGGATAATGAAAAAT
1 TGGATAATGAAAAAT
42763893 TGGATAATGAAAAA
1 TGGATAATGAAAAA
42763907 CAAGTCACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (15 bp):
TGGATAATGAAAAAT
Found at i:42767001 original size:50 final size:50
Alignment explanation
Indices: 42766938--42767033 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
42766928 CAGCAAATAC
* * *
42766938 ATGGTCCAAAGAGCGAAACTTGGTTTCAAGTTACGGAAATAAGTCTCAAT
1 ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCTCAAT
* * *
42766988 ATGGTCCATAGAGCAAAATTTTGTTTCAAGTTACAGAAAGAAGTCT
1 ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCT
42767034 AAATTAAACA
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:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (50 bp):
ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCTCAAT
Found at i:42772060 original size:19 final size:19
Alignment explanation
Indices: 42772029--42772072 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
42772019 CAAGCTTAAT
42772029 ATTAAATTAATTAAGATTTA
1 ATTAAATTAATTAAG-TTTA
*
42772049 GTTAAA-TAATTAAGTTTA
1 ATTAAATTAATTAAGTTTA
42772067 ATTAAA
1 ATTAAA
42772073 CGTTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 8 0.36
20 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (19 bp):
ATTAAATTAATTAAGTTTA
Found at i:42773385 original size:16 final size:17
Alignment explanation
Indices: 42773342--42773387 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
42773332 GAGTATAGTT
42773342 TAATA-GTATATG-TTA
1 TAATATGTATATGATTA
*
42773357 TAATATG-AAATGATTA
1 TAATATGTATATGATTA
42773373 T-ATATGTATATGATT
1 TAATATGTATATGATT
42773388 TTGGTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (17 bp):
TAATATGTATATGATTA
Found at i:42783061 original size:6 final size:6
Alignment explanation
Indices: 42783015--42783048 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
42783005 AGCAGTGGAG
42783015 AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
42783049 AATAAGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:42787808 original size:17 final size:17
Alignment explanation
Indices: 42787760--42787824 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
42787750 AAATTTTAGG
*
42787760 CTTAAGTGAATTTTTGAA
1 CTTAAGT-AAATTTTGAA
**
42787778 CTTAAGTATGTTTTGAA
1 CTTAAGTAAATTTTGAA
*
42787795 CTTAAGTAAATTTTTAA
1 CTTAAGTAAATTTTGAA
* *
42787812 TTTGAGTAAATTT
1 CTTAAGTAAATTT
42787825 CAAACTGCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 33 0.82
18 7 0.17
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (17 bp):
CTTAAGTAAATTTTGAA
Found at i:42788260 original size:124 final size:126
Alignment explanation
Indices: 42787990--42788277 Score: 321
Period size: 124 Copynumber: 2.3 Consensus size: 126
42787980 TTTAGAGTTG
* * * * **
42787990 TTTTTAGAGGTTGCAATCATAAACCGACAAATCTTTATAACATTAGCTGGGAGCGTAGGTCTGCT
1 TTTTTAGAGGTTGCGATCATAAA-CGAAAAACCTTTATAACATTAGCTGAGAGCGTAGGTCCACT
* * * * ** * *
42788055 AGTTTTGTTGGAGATGCGAGCAAGCTCTTAGAATATCATCTGGGAACATAGGTTTGCTAGTTG
65 AGCTGTGTT-GAGATGCGAGCAAGCTCTTAGAATATCAGCTGAGAACATAGGTCCGCTAGCTA
* *
42788118 TTTTTAGAGGTTGCGATCATAAATCGAAAAACCTTTATTACATTAGTTGAGAGCGTAGGTCCACT
1 TTTTTAGAGGTTGCGATCATAAA-CGAAAAACCTTTATAACATTAGCTGAGAGCGTAGGTCCACT
* * * *
42788183 AGCTGTGTT-AGA-GC-TGCGAGTTCTTAGAATATCAGCTGAGAATATAGGTCCGCTAGCTA
65 AGCTGTGTTGAGATGCGAGCAAGCTCTTAGAATATCAGCTGAGAACATAGGTCCGCTAGCTA
* *
42788242 TTTTTGGAGGTTGTGATCATAAACTGAAAAACCTTT
1 TTTTTAGAGGTTGCGATCATAAAC-GAAAAACCTTT
42788278 GAATAATACT
Statistics
Matches: 136, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
123 1 0.01
124 67 0.49
125 2 0.01
126 3 0.02
128 63 0.46
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (126 bp):
TTTTTAGAGGTTGCGATCATAAACGAAAAACCTTTATAACATTAGCTGAGAGCGTAGGTCCACTA
GCTGTGTTGAGATGCGAGCAAGCTCTTAGAATATCAGCTGAGAACATAGGTCCGCTAGCTA
Found at i:42792215 original size:62 final size:62
Alignment explanation
Indices: 42792118--42792243 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
42792108 ATACAACATA
42792118 TTCCCAAAACATCATTAACTAAGTTCCATAATTCACATATTTAGCCATATTTCATGCATTCT
1 TTCCCAAAACATCATTAACTAAGTTCCATAATTCACATATTTAGCCATATTTCATGCATTCT
42792180 TTCCCAAAACATCATTAACTAAGTTCCATAATTCACATATTTAGCCATATTTCATGCATTCT
1 TTCCCAAAACATCATTAACTAAGTTCCATAATTCACATATTTAGCCATATTTCATGCATTCT
42792242 TT
1 TT
42792244 TACACATTAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (62 bp):
TTCCCAAAACATCATTAACTAAGTTCCATAATTCACATATTTAGCCATATTTCATGCATTCT
Found at i:42792322 original size:10 final size:10
Alignment explanation
Indices: 42792295--42792339 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
42792285 GACACACATC
42792295 AATCACATAT
1 AATCACATAT
*
42792305 AAGCACATAT
1 AATCACATAT
* *
42792315 AATTACATAC
1 AATCACATAT
*
42792325 AATCACATTT
1 AATCACATAT
42792335 AATCA
1 AATCA
42792340 AAGTGTATGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (10 bp):
AATCACATAT
Found at i:42801466 original size:20 final size:22
Alignment explanation
Indices: 42801441--42801493 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
42801431 GTGTTATGCA
42801441 GGTATCGATACTGCCTTT-A-T
1 GGTATCGATACTGCCTTTAAGT
* *
42801461 GGTATCGATATTTCCTTTAAGT
1 GGTATCGATACTGCCTTTAAGT
*
42801483 GGTATCTATAC
1 GGTATCGATAC
42801494 CATTTGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.59
21 1 0.04
22 10 0.37
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (22 bp):
GGTATCGATACTGCCTTTAAGT
Found at i:42802278 original size:10 final size:10
Alignment explanation
Indices: 42802251--42802295 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
42802241 GACACACATC
42802251 AATCACATAT
1 AATCACATAT
*
42802261 AAGCACATAT
1 AATCACATAT
* *
42802271 AATTACATAC
1 AATCACATAT
*
42802281 AATCACATTT
1 AATCACATAT
42802291 AATCA
1 AATCA
42802296 AAGTGTATGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (10 bp):
AATCACATAT
Found at i:42802775 original size:8 final size:8
Alignment explanation
Indices: 42802764--42802788 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42802754 TGTTCATGAT
42802764 TTCACAAA
1 TTCACAAA
42802772 TTCACAAA
1 TTCACAAA
42802780 TTCACAAA
1 TTCACAAA
42802788 T
1 T
42802789 AAACTTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (8 bp):
TTCACAAA
Found at i:42807117 original size:15 final size:15
Alignment explanation
Indices: 42807097--42807145 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 15
42807087 TGTATATTAT
42807097 AATATTAATTAATAA
1 AATATTAATTAATAA
*
42807112 AATATTATTACTTATTAA
1 AATATTA--A-TTAATAA
42807130 AATATT-ATTAATAA
1 AATATTAATTAATAA
42807144 AA
1 AA
42807146 ATATCATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 8 0.28
15 8 0.28
17 1 0.03
18 12 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATTAATTAATAA
Found at i:42807130 original size:18 final size:18
Alignment explanation
Indices: 42807099--42807141 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
42807089 TATATTATAA
42807099 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
42807117 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
42807135 TATTAAT
1 TATTAAT
42807142 AAAAATATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:42807717 original size:20 final size:20
Alignment explanation
Indices: 42807681--42807718 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42807671 ATGAAAACAA
*
42807681 TTAGAATTAAATCTTAAGGT
1 TTAGAATTAAATATTAAGGT
42807701 TTAGAAATTAAA-ATTAAG
1 TTAG-AATTAAATATTAAG
42807719 TGCATGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (20 bp):
TTAGAATTAAATATTAAGGT
Found at i:42816670 original size:41 final size:40
Alignment explanation
Indices: 42816625--42816769 Score: 200
Period size: 41 Copynumber: 3.5 Consensus size: 40
42816615 GACTTTAAGT
*
42816625 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
*
42816666 CTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
* * * *
42816707 CTAGCAAGCTACGTGCCGGTGATTTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA-C
*
42816748 CTAGCAGGCTAAGTGTCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
42816770 ATATGTTAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 2 0.02
41 90 0.98
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (40 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAC
Found at i:42817605 original size:39 final size:39
Alignment explanation
Indices: 42817551--42817650 Score: 146
Period size: 39 Copynumber: 2.6 Consensus size: 39
42817541 CATGTTTTTA
* *
42817551 AGTATTGTGATATATGCTTGAATATTATGTGATTATATG
1 AGTATTGTGATATATGCTTAAATATTAAGTGATTATATG
*
42817590 AGTATTGTGATATATGCTTAAATGTTAAGTGATTATATG
1 AGTATTGTGATATATGCTTAAATATTAAGTGATTATATG
* * *
42817629 TGAAATGTGATATATGCTTAAA
1 AGTATTGTGATATATGCTTAAA
42817651 AGTGAATATG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTAAATATTAAGTGATTATATG
Found at i:42817655 original size:17 final size:17
Alignment explanation
Indices: 42817616--42817664 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
42817606 CTTAAATGTT
*
42817616 AAGTGATTATATG-TGAA
1 AAGTGA-TATATGCTTAA
*
42817633 ATGTGATATATGCTTAA
1 AAGTGATATATGCTTAA
42817650 AAGTGA-ATATGCTTA
1 AAGTGATATATGCTTA
42817665 CCTTATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (17 bp):
AAGTGATATATGCTTAA
Found at i:42819914 original size:22 final size:22
Alignment explanation
Indices: 42819873--42819922 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
42819863 CTCATCTTTA
*
42819873 GTGTTATTGTTTCTTTATTTTT
1 GTGTTATTGTTTCTTAATTTTT
*
42819895 GTGTTAGTTGTTT-TTAATTTAT
1 GTGTTA-TTGTTTCTTAATTTTT
42819917 GT-TTAT
1 GTGTTAT
42819923 CAAGTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 3 0.12
22 15 0.60
23 6 0.24
ACGTcount: A:0.14, C:0.02, G:0.16, T:0.68
Consensus pattern (22 bp):
GTGTTATTGTTTCTTAATTTTT
Found at i:42823165 original size:28 final size:28
Alignment explanation
Indices: 42823034--42823198 Score: 181
Period size: 28 Copynumber: 5.9 Consensus size: 28
42823024 CCATGGCATA
* * *
42823034 TTCAAGTAAGAGTCTGCATGGATTATCT
1 TTCAAGTAAGAGTCCGCAAGGACTATCT
* * *
42823062 ATCAAGTAAGAGTCAGCATGGACTATCT
1 TTCAAGTAAGAGTCCGCAAGGACTATCT
* *
42823090 ATCAAGTAAGAGTCCGCATGGACTATCT
1 TTCAAGTAAGAGTCCGCAAGGACTATCT
* *
42823118 TTCAAGAAAGAGTTCGCAAGGACTATCT
1 TTCAAGTAAGAGTCCGCAAGGACTATCT
* * *
42823146 TTCAAGTAAGAGTCCACAAGGATTGT-T
1 TTCAAGTAAGAGTCCGCAAGGACTATCT
42823173 CTTCAAG-AAGGAGTCCGCAAGGACTA
1 -TTCAAGTAA-GAGTCCGCAAGGACTA
42823199 ACTAATGAGT
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
27 3 0.03
28 116 0.97
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (28 bp):
TTCAAGTAAGAGTCCGCAAGGACTATCT
Found at i:42824918 original size:20 final size:20
Alignment explanation
Indices: 42824893--42824962 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 20
42824883 AAAGCCTACT
42824893 GATCATCGTAACTACCATTG
1 GATCATCGTAACTACCATTG
* *
42824913 GATCATTTCCTTAAAT-CCATTG
1 GATCA--T-CGTAACTACCATTG
42824935 ATGATCATCGTAACTACCATTG
1 --GATCATCGTAACTACCATTG
42824957 GATCAT
1 GATCAT
42824963 TTCCTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
20 11 0.28
21 5 0.12
22 14 0.35
23 5 0.12
24 5 0.12
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (20 bp):
GATCATCGTAACTACCATTG
Found at i:42824934 original size:22 final size:23
Alignment explanation
Indices: 42824905--42824969 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 23
42824895 TCATCGTAAC
42824905 TACCATTGGATCATTTCCTTAAA
1 TACCATTGGATCATTTCCTTAAA
* *
42824928 T-CCATTGATGATCA--T-CGTAAC
1 TACCATTG--GATCATTTCCTTAAA
42824949 TACCATTGGATCATTTCCTTA
1 TACCATTGGATCATTTCCTTA
42824970 TTTTCCAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
20 5 0.15
21 5 0.15
22 14 0.42
23 4 0.12
24 5 0.15
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (23 bp):
TACCATTGGATCATTTCCTTAAA
Found at i:42832818 original size:3 final size:3
Alignment explanation
Indices: 42832810--42832836 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42832800 TTAGTTTCCG
42832810 GCA GCA GCA GCA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA
42832837 TATCAAATTA
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:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:42836441 original size:32 final size:32
Alignment explanation
Indices: 42836396--42836464 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
42836386 GGTGAGACGA
42836396 CTTAATTCCATTATATAAAAACCTAGTTAACT
1 CTTAATTCCATTATATAAAAACCTAGTTAACT
*
42836428 CTTAATTCTATTATATAAAAACCTAGTTAACT
1 CTTAATTCCATTATATAAAAACCTAGTTAACT
42836460 CTTAA
1 CTTAA
42836465 AAGCAATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (32 bp):
CTTAATTCCATTATATAAAAACCTAGTTAACT
Found at i:42847727 original size:20 final size:20
Alignment explanation
Indices: 42847704--42847750 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
42847694 GGGTTAAGAC
*
42847704 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
42847724 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
42847744 TGAGCTG
1 TGAGCTG
42847751 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:42848956 original size:51 final size:53
Alignment explanation
Indices: 42848892--42848999 Score: 166
Period size: 51 Copynumber: 2.1 Consensus size: 53
42848882 AGCAATTAAC
42848892 AAATCAACCGACCATTATTTTATCA-TTACATTGTCTAAAGCAATAGGGAA-G
1 AAATCAACCGACCATTATTTTATCATTTACATTGTCTAAAGCAATAGGGAAGG
* * * *
42848943 AAATCAACTGACCATTGTTTTATCATTTATATTGTCTAAAGTAATAGGGAAGG
1 AAATCAACCGACCATTATTTTATCATTTACATTGTCTAAAGCAATAGGGAAGG
42848996 AAAT
1 AAAT
42849000 TAGATTAGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
51 23 0.45
52 23 0.45
53 5 0.10
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (53 bp):
AAATCAACCGACCATTATTTTATCATTTACATTGTCTAAAGCAATAGGGAAGG
Found at i:42850046 original size:37 final size:37
Alignment explanation
Indices: 42849983--42850069 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
42849973 AAAATGAATA
* *
42849983 ATTCCCTGGCAAAAGAAGATAGAGATGAATAGGAGTG
1 ATTCCCTGCCAAAAGAAGATAGAGATGAACAGGAGTG
* * *
42850020 ATTCTCTGCCAAAAGAA-ATCGAAGATGAACATGAGTG
1 ATTCCCTGCCAAAAGAAGATAG-AGATGAACAGGAGTG
42850057 ATTCCCTGCCAAA
1 ATTCCCTGCCAAA
42850070 TGCGGACGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 3 0.07
37 40 0.93
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (37 bp):
ATTCCCTGCCAAAAGAAGATAGAGATGAACAGGAGTG
Found at i:42850309 original size:22 final size:23
Alignment explanation
Indices: 42850278--42850329 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
42850268 CACATCGACC
42850278 AACAAATCAAATTTAA-ATTCAA
1 AACAAATCAAATTTAACATTCAA
* *
42850300 AACAATTCAAATTTAACTTTCAA
1 AACAAATCAAATTTAACATTCAA
*
42850323 AAAAAAT
1 AACAAAT
42850330 AATTTTCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (23 bp):
AACAAATCAAATTTAACATTCAA
Found at i:42850375 original size:37 final size:37
Alignment explanation
Indices: 42850300--42850379 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
42850290 TTAAATTCAA
* *
42850300 AACAATTCAAATTTAACTTTCAAAAAAAATAATTTTC
1 AACAAATCAAATTTAACTTTCAAAAAAAATAATGTTC
* ** **
42850337 AACAAATCAAATTTAATTTTTTAAAAATTTAATGTTC
1 AACAAATCAAATTTAACTTTCAAAAAAAATAATGTTC
42850374 AA-AAAT
1 AACAAAT
42850380 TTTCTTAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 4 0.11
37 32 0.89
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (37 bp):
AACAAATCAAATTTAACTTTCAAAAAAAATAATGTTC
Found at i:42851837 original size:58 final size:58
Alignment explanation
Indices: 42851774--42851899 Score: 182
Period size: 58 Copynumber: 2.2 Consensus size: 58
42851764 TTTTAATAAG
* *
42851774 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAACATA
* * * *
42851832 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
42851890 ATTATTATTA
1 ATTATTATTA
42851900 TATGAATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 22 0.36
58 39 0.64
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
Found at i:42851920 original size:58 final size:56
Alignment explanation
Indices: 42851761--42851927 Score: 169
Period size: 58 Copynumber: 2.9 Consensus size: 56
42851751 TATTGTTATT
* * * *
42851761 AAATTTTAATA-AGATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACC
1 AAATTTTAACATA-ATTATTATT-AATATAATTTAA-AAAAATAATATATAATTTAACA
* * *
42851819 ATATTTTAACATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATA
1 AAATTTTAACATAATTATTATT-AATATAATTTAAAAAAATAATATATAATTTAACA
*
42851876 AAATTCTTAATATAATTATTATT-ATATGAA-TTAAAAAATCATAATATATAAT
1 AAATT-TTAACATAATTATTATTAATAT-AATTTAAAAAA--ATAATATATAAT
42851928 ACTATAAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
56 11 0.12
57 24 0.26
58 58 0.62
59 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (56 bp):
AAATTTTAACATAATTATTATTAATATAATTTAAAAAAATAATATATAATTTAACA
Found at i:42855887 original size:47 final size:47
Alignment explanation
Indices: 42855836--42855931 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
42855826 TATTGTAATG
* *
42855836 TTAATTACAATTTTTAATCAAACAATATAAGTAATGTAAAACATTGT
1 TTAATTACAATTTTCAATCAAACAATATAAGTAATATAAAACATTGT
*
42855883 TTAATTATAATTTTCAATCAAACAATATAAGTAATATAAAACATTGT
1 TTAATTACAATTTTCAATCAAACAATATAAGTAATATAAAACATTGT
42855930 TT
1 TT
42855932 GAAGATCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (47 bp):
TTAATTACAATTTTCAATCAAACAATATAAGTAATATAAAACATTGT
Found at i:42858062 original size:25 final size:25
Alignment explanation
Indices: 42858033--42858083 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
42858023 TTACATCAAG
42858033 AAAGCTTAAATGCATCCAAAATCTA
1 AAAGCTTAAATGCATCCAAAATCTA
42858058 AAAGCTTAAATGCATCCAAAATCTA
1 AAAGCTTAAATGCATCCAAAATCTA
42858083 A
1 A
42858084 CAATATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.24
Consensus pattern (25 bp):
AAAGCTTAAATGCATCCAAAATCTA
Found at i:42859186 original size:21 final size:21
Alignment explanation
Indices: 42859160--42859203 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
42859150 AAAAAAAAGA
42859160 TTAAAAAATCTTTATTCTAGG
1 TTAAAAAATCTTTATTCTAGG
*
42859181 TTAAAAAATCTTTATTCTGGG
1 TTAAAAAATCTTTATTCTAGG
42859202 TT
1 TT
42859204 TTCGTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (21 bp):
TTAAAAAATCTTTATTCTAGG
Found at i:42861178 original size:16 final size:18
Alignment explanation
Indices: 42861145--42861182 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42861135 ATCCTTATTT
42861145 AAATAAAATATAATAGTA
1 AAATAAAATATAATAGTA
42861163 AAATAAAATA-AA-AGTA
1 AAATAAAATATAATAGTA
42861179 AAAT
1 AAAT
42861183 CCATATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAATATAATAGTA
Found at i:42865488 original size:20 final size:20
Alignment explanation
Indices: 42865465--42865502 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42865455 ACCAAAATTT
42865465 ATGAGAGAA-TACCAAAAAAA
1 ATGAGA-AAGTACCAAAAAAA
42865485 ATGAGAAAGTACCAAAAA
1 ATGAGAAAGTACCAAAAA
42865503 TTATAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.63, C:0.11, G:0.16, T:0.11
Consensus pattern (20 bp):
ATGAGAAAGTACCAAAAAAA
Found at i:42865854 original size:3 final size:3
Alignment explanation
Indices: 42865846--42865875 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42865836 CACCCTTTTT
42865846 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42865876 CTCCATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42872746 original size:17 final size:17
Alignment explanation
Indices: 42872724--42872787 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
42872714 AATCTTAGAG
42872724 TTCTAATTGTACACAGC
1 TTCTAATTGTACACAGC
* *
42872741 TTCTAATTGTGTCTTAGAG-
1 TTCTAATTGT-AC--ACAGC
*
42872760 TTCTAATTGTATACAGC
1 TTCTAATTGTACACAGC
*
42872777 TTTTAATTGTA
1 TTCTAATTGTA
42872788 GCCTTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 3 0.08
17 20 0.54
18 1 0.03
19 10 0.27
20 3 0.08
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (17 bp):
TTCTAATTGTACACAGC
Found at i:42872763 original size:36 final size:36
Alignment explanation
Indices: 42872716--42872786 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
42872706 GATTATGTAA
42872716 TCTTAGAGTTCTAATTGTACACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTACACAGCTTCTAATTGTG
* *
42872752 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTACACAGCTTCTAATTGT
42872787 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.45
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTACACAGCTTCTAATTGTG
Found at i:42872765 original size:19 final size:18
Alignment explanation
Indices: 42872716--42872769 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
42872706 GATTATGTAA
42872716 TCTTAGAGTTCTAATTGT
1 TCTTAGAGTTCTAATTGT
* *
42872734 AC--ACAGCTTCTAATTGT
1 TCTTAGAG-TTCTAATTGT
42872751 GTCTTAGAGTTCTAATTGT
1 -TCTTAGAGTTCTAATTGT
42872770 ATACAGCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
16 3 0.11
17 10 0.36
18 2 0.07
19 10 0.36
20 3 0.11
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTGT
Found at i:42877356 original size:13 final size:13
Alignment explanation
Indices: 42877338--42877362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42877328 AATTTTAATA
42877338 TTATTTTGTGTGT
1 TTATTTTGTGTGT
42877351 TTATTTTGTGTG
1 TTATTTTGTGTG
42877363 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:42878579 original size:115 final size:114
Alignment explanation
Indices: 42878338--42878670 Score: 551
Period size: 114 Copynumber: 2.9 Consensus size: 114
42878328 TTAAATCAGC
* * * * * * **
42878338 ATATATATATTTATTTTATATTTGATGAGCTATAATTAAAAATATATGAATTTTTAATTAGTTAA
1 ATATGTATATCTATTGTATATTTGATGAGCTATAATTGAAAGTATAT-AAATTGAAATTAGTTAA
42878403 GTATGAATGTTATATATAT-CATAAATGAAGTTCGAATATATGTAAATAT
65 GTATGAATGTTATATATATGCATAAATGAAGTTCGAATATATGTAAATAT
*
42878452 ATATGCATATCTATTGTATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGTTAAT
1 ATATGTATATCTATTGTATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGTTAA-
*
42878517 GTGTGAATGTTATATATATGCATAAATGAAGTTCGAATATATGTAAATAT
65 GTATGAATGTTATATATATGCATAAATGAAGTTCGAATATATGTAAATAT
42878567 ATATGTATATCTATTGTATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGTTAAG
1 ATATGTATATCTATTGTATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGTTAAG
42878632 TATGAATGTTATATATATGCATAAATGAAGTTCGAATAT
66 TATGAATGTTATATATATGCATAAATGAAGTTCGAATAT
42878671 GTATATATGA
Statistics
Matches: 205, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
113 14 0.07
114 98 0.48
115 93 0.45
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.42
Consensus pattern (114 bp):
ATATGTATATCTATTGTATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGTTAAG
TATGAATGTTATATATATGCATAAATGAAGTTCGAATATATGTAAATAT
Found at i:42878852 original size:17 final size:15
Alignment explanation
Indices: 42878821--42878851 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42878811 TGCATATGTG
42878821 TGAGGTTCGAATATA
1 TGAGGTTCGAATATA
42878836 TGAGGTTCGAATATA
1 TGAGGTTCGAATATA
42878851 T
1 T
42878852 AGTTATGTGT
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:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (15 bp):
TGAGGTTCGAATATA
Found at i:42879223 original size:41 final size:40
Alignment explanation
Indices: 42879169--42879277 Score: 173
Period size: 41 Copynumber: 2.6 Consensus size: 40
42879159 TTTCGGACTT
*
42879169 TAAGTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
1 TAAG-CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTA
42879210 TAAAGCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTA
1 T-AAGCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTA
*
42879251 TAAGCTTAGCAGGTTAAGTGCCGGTGA
1 TAAGC-TAGCAGGCTAAGTGCCGGTGA
42879278 ATATGTTAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
40 4 0.06
41 57 0.89
42 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (40 bp):
TAAGCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTA
Found at i:42880658 original size:36 final size:36
Alignment explanation
Indices: 42880611--42880681 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
42880601 GATTATGTAA
42880611 TCTTAGAGTTCTAATTGTACACAACTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTACACAACTTCTAATTGTG
* * *
42880647 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTACACAACTTCTAATTGT
42880682 AGCCTTTGAT
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:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTACACAACTTCTAATTGTG
Found at i:42881676 original size:37 final size:37
Alignment explanation
Indices: 42881634--42881704 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
42881624 TTGTACTTTC
*
42881634 AAATTTAACAATATT-TACAATTTAGTCCTTAAAATCT
1 AAATTT-ACAATATTCTACAATTTAATCCTTAAAATCT
* * *
42881671 AAATTTTCACTATTCTATAATTTAATCCTTAAAA
1 AAATTTACAATATTCTACAATTTAATCCTTAAAA
42881705 ACAGAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 6 0.21
37 23 0.79
ACGTcount: A:0.42, C:0.14, G:0.01, T:0.42
Consensus pattern (37 bp):
AAATTTACAATATTCTACAATTTAATCCTTAAAATCT
Found at i:42882180 original size:24 final size:25
Alignment explanation
Indices: 42882138--42882187 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
42882128 TCTTACTTTC
42882138 AATTATTCACATAAAATCATCCACCA
1 AATTATT-ACATAAAATCATCCACCA
* *
42882164 AATTATT-CATAATATCATTCACCA
1 AATTATTACATAAAATCATCCACCA
42882188 TTCACTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
26 7 0.32
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (25 bp):
AATTATTACATAAAATCATCCACCA
Found at i:42884122 original size:16 final size:17
Alignment explanation
Indices: 42884086--42884122 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
42884076 CAATTTTATT
42884086 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
42884103 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
42884118 TAATA
1 TAATA
42884123 TTCATCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:42891510 original size:9 final size:9
Alignment explanation
Indices: 42891484--42891871 Score: 344
Period size: 9 Copynumber: 42.3 Consensus size: 9
42891474 ATTTGCACAG
42891484 GTAAGTTAT
1 GTAAGTTAT
* *
42891493 TTAATTTAT
1 GTAAGTTAT
42891502 GTAAGTTAT
1 GTAAGTTAT
42891511 GTAAGTTAT
1 GTAAGTTAT
* *
42891520 TTAATTTAT
1 GTAAGTTAT
*
42891529 GTAGGTTAT
1 GTAAGTTAT
*
42891538 GTAAGTCCAT
1 GTAAGT-TAT
* *
42891548 GAAATTTAT
1 GTAAGTTAT
*
42891557 GTAAGTTGT
1 GTAAGTTAT
42891566 GTAAGTTAT
1 GTAAGTTAT
* *
42891575 TTAATTTAT
1 GTAAGTTAT
42891584 GTAAGTTAT
1 GTAAGTTAT
42891593 GTAAGTTAT
1 GTAAGTTAT
* *
42891602 TTAATTTAT
1 GTAAGTTAT
*
42891611 GTAGGTTAT
1 GTAAGTTAT
*
42891620 GTAAGTCCAT
1 GTAAGT-TAT
* *
42891630 GAAATTTAT
1 GTAAGTTAT
*
42891639 GTAAGTTGT
1 GTAAGTTAT
42891648 GTAAGTTAT
1 GTAAGTTAT
* *
42891657 TTAATTTAT
1 GTAAGTTAT
42891666 GTAAGTTAT
1 GTAAGTTAT
42891675 GTAAGTTAT
1 GTAAGTTAT
* *
42891684 TTAATTTAT
1 GTAAGTTAT
*
42891693 GTAGGTTAT
1 GTAAGTTAT
*
42891702 GTAAGTCCAT
1 GTAAGT-TAT
* *
42891712 GAAATTTAT
1 GTAAGTTAT
*
42891721 GTAAGTTGT
1 GTAAGTTAT
42891730 GTAAGTTAT
1 GTAAGTTAT
* *
42891739 TTAATTTAT
1 GTAAGTTAT
42891748 GTAAGTTAT
1 GTAAGTTAT
42891757 GTAAGTTAT
1 GTAAGTTAT
* *
42891766 TTAATTTAT
1 GTAAGTTAT
*
42891775 GTAGGTTAT
1 GTAAGTTAT
42891784 GTAAGTTAT
1 GTAAGTTAT
*
42891793 GTATGTTAT
1 GTAAGTTAT
* **
42891802 TTATTTTAT
1 GTAAGTTAT
*
42891811 GCAAGTTTAT
1 GTAAG-TTAT
42891821 GTAAGTTAT
1 GTAAGTTAT
* *
42891830 TTAATTTAT
1 GTAAGTTAT
42891839 GTAAGTTAT
1 GTAAGTTAT
*
42891848 GCAAGCTTAT
1 GTAAG-TTAT
*
42891858 ATACAAGTTAT
1 GT--AAGTTAT
42891869 GTA
1 GTA
42891872 TTATAACATA
Statistics
Matches: 292, Mismatches: 80, Indels: 14
0.76 0.21 0.04
Matches are distributed among these distances:
9 254 0.87
10 30 0.10
11 5 0.02
12 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.48
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:42891522 original size:27 final size:27
Alignment explanation
Indices: 42891484--42891847 Score: 451
Period size: 27 Copynumber: 13.3 Consensus size: 27
42891474 ATTTGCACAG
42891484 GTAAGTTATTTAATTTATGTAAGTTAT
1 GTAAGTTATTTAATTTATGTAAGTTAT
*
42891511 GTAAGTTATTTAATTTATGTAGGTTAT
1 GTAAGTTATTTAATTTATGTAAGTTAT
* ** *
42891538 GTAAGTCCATGAAATTTATGTAAGTTGT
1 GTAAGT-TATTTAATTTATGTAAGTTAT
42891566 GTAAGTTATTTAATTTATGTAAGTTAT
1 GTAAGTTATTTAATTTATGTAAGTTAT
*
42891593 GTAAGTTATTTAATTTATGTAGGTTAT
1 GTAAGTTATTTAATTTATGTAAGTTAT
* ** *
42891620 GTAAGTCCATGAAATTTATGTAAGTTGT
1 GTAAGT-TATTTAATTTATGTAAGTTAT
42891648 GTAAGTTATTTAATTTATGTAAGTTAT
1 GTAAGTTATTTAATTTATGTAAGTTAT
*
42891675 GTAAGTTATTTAATTTATGTAGGTTAT
1 GTAAGTTATTTAATTTATGTAAGTTAT
* ** *
42891702 GTAAGTCCATGAAATTTATGTAAGTTGT
1 GTAAGT-TATTTAATTTATGTAAGTTAT
42891730 GTAAGTTATTTAATTTATGTAAGTTAT
1 GTAAGTTATTTAATTTATGTAAGTTAT
*
42891757 GTAAGTTATTTAATTTATGTAGGTTAT
1 GTAAGTTATTTAATTTATGTAAGTTAT
* * **
42891784 GTAAGTTATGT-ATGTTATTTATTTTAT
1 GTAAGTTATTTAAT-TTATGTAAGTTAT
* * * * *
42891811 GCAAGTTTATGTAAGTTATTTAATTTAT
1 GTAAG-TTATTTAATTTATGTAAGTTAT
42891839 GTAAGTTAT
1 GTAAGTTAT
42891848 GCAAGCTTAT
Statistics
Matches: 292, Mismatches: 39, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
26 2 0.01
27 201 0.69
28 88 0.30
29 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (27 bp):
GTAAGTTATTTAATTTATGTAAGTTAT
Found at i:42891847 original size:82 final size:82
Alignment explanation
Indices: 42891484--42891789 Score: 612
Period size: 82 Copynumber: 3.7 Consensus size: 82
42891474 ATTTGCACAG
42891484 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGTCCATG
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGTCCATG
42891549 AAATTTATGTAAGTTGT
66 AAATTTATGTAAGTTGT
42891566 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGTCCATG
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGTCCATG
42891631 AAATTTATGTAAGTTGT
66 AAATTTATGTAAGTTGT
42891648 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGTCCATG
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGTCCATG
42891713 AAATTTATGTAAGTTGT
66 AAATTTATGTAAGTTGT
42891730 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGT
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGT
42891790 TATGTATGTT
Statistics
Matches: 224, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 224 1.00
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (82 bp):
GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGTCCATG
AAATTTATGTAAGTTGT
Found at i:42892101 original size:16 final size:16
Alignment explanation
Indices: 42892076--42892113 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
42892066 GAAAACGAAG
*
42892076 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
42892091 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
42892107 TAAATTT
1 TAAATTT
42892114 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:42892128 original size:13 final size:13
Alignment explanation
Indices: 42892110--42892137 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42892100 ATACAAATAA
42892110 ATTTAGAAAACTT
1 ATTTAGAAAACTT
42892123 ATTTAGAAAACTT
1 ATTTAGAAAACTT
42892136 AT
1 AT
42892138 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:42892145 original size:17 final size:17
Alignment explanation
Indices: 42892106--42892155 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
42892096 TTTAATACAA
42892106 ATAAATTTAGAAAAC-T
1 ATAAATTTAGAAAACTT
42892122 -T--ATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
42892136 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
42892153 ATA
1 ATA
42892156 TAGATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 2 0.07
17 16 0.53
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAAATTTAGAAAACTT
Found at i:42893191 original size:27 final size:29
Alignment explanation
Indices: 42893137--42893191 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
42893127 TAATTATCAC
*
42893137 AACAATAAACTTAATAATAATTGATAAAGT
1 AACAATAAACTTAATAATAAAT-ATAAAGT
*
42893167 AACAATCAACTTAAT-ATAAAT-TAAA
1 AACAATAAACTTAATAATAAATATAAA
42893192 TCAGAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
29 5 0.22
30 14 0.61
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (29 bp):
AACAATAAACTTAATAATAAATATAAAGT
Found at i:42895651 original size:14 final size:15
Alignment explanation
Indices: 42895618--42895666 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
42895608 ATTAACTATA
42895618 AACCCCTAAACCCAT
1 AACCCCTAAACCCAT
42895633 AACCCCT-AACTCC-T
1 AACCCCTAAAC-CCAT
42895647 AA-CCCTAAACCCAT
1 AACCCCTAAACCCAT
42895661 GAACCC
1 -AACCC
42895667 TTAACCCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 6 0.21
14 10 0.34
15 11 0.38
16 2 0.07
ACGTcount: A:0.37, C:0.47, G:0.02, T:0.14
Consensus pattern (15 bp):
AACCCCTAAACCCAT
Found at i:42895667 original size:15 final size:14
Alignment explanation
Indices: 42895621--42895690 Score: 58
Period size: 15 Copynumber: 5.0 Consensus size: 14
42895611 AACTATAAAC
42895621 CCCTAAACCCATAA
1 CCCTAAACCCATAA
42895635 CCCCT-AACTCC-TAA
1 -CCCTAAAC-CCATAA
42895649 CCCTAAACCCATGAA
1 CCCTAAACCCAT-AA
* *
42895664 CCCTTAACCC-CAA
1 CCCTAAACCCATAA
42895677 CCCTTAAA-CCATAA
1 CCC-TAAACCCATAA
42895691 TCCATAAGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
13 13 0.29
14 15 0.33
15 17 0.38
ACGTcount: A:0.37, C:0.44, G:0.01, T:0.17
Consensus pattern (14 bp):
CCCTAAACCCATAA
Found at i:42895684 original size:29 final size:28
Alignment explanation
Indices: 42895621--42895690 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
42895611 AACTATAAAC
*
42895621 CCCTAAACCCATAACCCCTAACTCCTAA
1 CCCTAAACCCATAACCCCTAACTCCCAA
*
42895649 CCCTAAACCCATGAACCCTTAAC-CCCAA
1 CCCTAAACCCAT-AACCCCTAACTCCCAA
42895677 CCCTTAAA-CCATAA
1 CCC-TAAACCCATAA
42895691 TCCATAAGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 2 0.05
28 23 0.61
29 13 0.34
ACGTcount: A:0.37, C:0.44, G:0.01, T:0.17
Consensus pattern (28 bp):
CCCTAAACCCATAACCCCTAACTCCCAA
Found at i:42895871 original size:7 final size:7
Alignment explanation
Indices: 42895851--42895913 Score: 58
Period size: 7 Copynumber: 8.9 Consensus size: 7
42895841 ATTAACTATA
42895851 AACCCCT
1 AACCCCT
42895858 AAACCCCT
1 -AACCCCT
42895866 AACCCC-
1 AACCCCT
*
42895872 AACCCTT
1 AACCCCT
*
42895879 AACCCTT
1 AACCCCT
42895886 AA-CCCT
1 AACCCCT
42895892 AAACCCCT
1 -AACCCCT
*
42895900 AAACCCTT
1 -AACCCCT
42895908 AACCCC
1 AACCCC
42895914 AATCATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
6 8 0.17
7 22 0.46
8 18 0.38
ACGTcount: A:0.33, C:0.51, G:0.00, T:0.16
Consensus pattern (7 bp):
AACCCCT
Found at i:42895891 original size:14 final size:14
Alignment explanation
Indices: 42895854--42895912 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
42895844 AACTATAAAC
*
42895854 CCCTAAACCCCTAA
1 CCCTAAACCCTTAA
*
42895868 CCC-CAACCCTTAA
1 CCCTAAACCCTTAA
* *
42895881 CCCTTAACCCTAAA
1 CCCTAAACCCTTAA
42895895 CCCCTAAACCCTTAA
1 -CCCTAAACCCTTAA
42895910 CCC
1 CCC
42895913 CAATCATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 11 0.30
14 14 0.38
15 12 0.32
ACGTcount: A:0.32, C:0.51, G:0.00, T:0.17
Consensus pattern (14 bp):
CCCTAAACCCTTAA
Found at i:42895895 original size:42 final size:42
Alignment explanation
Indices: 42895830--42895943 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 42
42895820 AAACATATTG
* *
42895830 AACCA-TAAAACATTAACTATAAACCCCTAAACCCCTAACCCC
1 AACCATTAAACCA-TAACCATAAACCCCTAAACCCCTAACCCC
* * * * *
42895872 AACCCTTAACCCTTAACCCTAAACCCCTAAACCCTTAACCCC
1 AACCATTAAACCATAACCATAAACCCCTAAACCCCTAACCCC
* *
42895914 AATCATTAAACCATATCCATAAACCCCTAA
1 AACCATTAAACCATAACCATAAACCCCTAA
42895944 CCCATATCCC
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 54 0.93
43 4 0.07
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.19
Consensus pattern (42 bp):
AACCATTAAACCATAACCATAAACCCCTAAACCCCTAACCCC
Found at i:42896830 original size:114 final size:114
Alignment explanation
Indices: 42896595--42896880 Score: 287
Period size: 114 Copynumber: 2.5 Consensus size: 114
42896585 ATTTTTAGAC
* * * * *
42896595 AAGCGCCACTAAAGTCTATAAAACCTAAATTG-AAAACGACATCATTTTCTTAACAGTTTTGCAG
1 AAGCGCCACTAAAGTCT-CAAAACCTAAACTGAAAAACGACAACGTTTTCTTAACAGTCTTGCAG
* *
42896659 CACTTCTGATAAAGCGCCACTAAAGCTTCGCTACTACGACGTTTTCTGAA
65 CACTTATGATAAAGCGCCACTAAAGCTTCGCTACTACGACGTTTTCTCAA
* * ** *
42896709 AATCGCCACTAACGTCTCGAAAAGATAAA-TGAAAAACGACAACGTTTTCTTAACAGTCTTGCGG
1 AAGCGCCACTAAAGTCTC-AAAACCTAAACTGAAAAACGACAACGTTTTCTTAACAGTCTTGCAG
* * ** * *
42896773 CGCTTATGATAAAGCGCCGCTAATTCTT-GACTA-TAGCGGCGTTTT-TCATT
65 CACTTATGATAAAGCGCCACTAAAGCTTCG-CTACTA-CGACGTTTTCTCA-A
* *
42896823 AAGCGCCACTAAAGTCCTCAAAACCTAAACT-AAAAACGGCAGCGTTTTTCTTAACAGT
1 AAGCGCCACTAAAGT-CTCAAAACCTAAACTGAAAAACGACAACG-TTTTCTTAACAGT
42896881 TTTTCCGACG
Statistics
Matches: 141, Mismatches: 23, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
113 7 0.05
114 117 0.83
115 17 0.12
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (114 bp):
AAGCGCCACTAAAGTCTCAAAACCTAAACTGAAAAACGACAACGTTTTCTTAACAGTCTTGCAGC
ACTTATGATAAAGCGCCACTAAAGCTTCGCTACTACGACGTTTTCTCAA
Found at i:42897911 original size:87 final size:87
Alignment explanation
Indices: 42897765--42898120 Score: 694
Period size: 87 Copynumber: 4.1 Consensus size: 87
42897755 ATAGGTTCAA
42897765 GTTCTATTGGACGCAATTTAGTATTGATTTCTCTATATTCCATCAAGTTAGAATTTTTTATTTAT
1 GTTCTATTGGACGCAATTTAGTATTGATTTCTCTATATTCCATCAAGTTAGAATTTTTTATTTAT
42897830 AATTGTTCTTGAAGTTGAAAAT
66 AATTGTTCTTGAAGTTGAAAAT
42897852 GTTCTATTGGACGCAATTTAGTATTGATTTCTCTATATTCCATCAAGTTAGAATTTTTTATTTAT
1 GTTCTATTGGACGCAATTTAGTATTGATTTCTCTATATTCCATCAAGTTAGAATTTTTTATTTAT
42897917 AATTGTTCTTGAAGTTGAAAAT
66 AATTGTTCTTGAAGTTGAAAAT
42897939 GTTCTATTGGACGCAATTTAGTATTGATTTCTCTATATTCCATCAAGTTAGAATTTTTTATTTAT
1 GTTCTATTGGACGCAATTTAGTATTGATTTCTCTATATTCCATCAAGTTAGAATTTTTTATTTAT
42898004 AATTGTTCTTGAAGTTGAAAAT
66 AATTGTTCTTGAAGTTGAAAAT
*
42898026 GTTCTATTGGACGCAATTTAGTATTGATTTCTCTATATTCCATCAAGTTAGAATTTTCTATTTAT
1 GTTCTATTGGACGCAATTTAGTATTGATTTCTCTATATTCCATCAAGTTAGAATTTTTTATTTAT
*
42898091 AATTGTTCTTGAAGTTGAAGAT
66 AATTGTTCTTGAAGTTGAAAAT
42898113 GTTCTATT
1 GTTCTATT
42898121 TAGTCTTCAA
Statistics
Matches: 267, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 267 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (87 bp):
GTTCTATTGGACGCAATTTAGTATTGATTTCTCTATATTCCATCAAGTTAGAATTTTTTATTTAT
AATTGTTCTTGAAGTTGAAAAT
Found at i:42900750 original size:16 final size:16
Alignment explanation
Indices: 42900716--42900755 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
42900706 GTTTTAACCG
* *
42900716 AAAGAAAAGAAGAACA
1 AAAGAAAAGAAAAAAA
*
42900732 AAATAAAAGAAAAAAA
1 AAAGAAAAGAAAAAAA
42900748 AAAGAAAA
1 AAAGAAAA
42900756 TCCCCCCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAGAAAAGAAAAAAA
Found at i:42900755 original size:21 final size:21
Alignment explanation
Indices: 42900716--42900756 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42900706 GTTTTAACCG
* *
42900716 AAAGAAAAGAAGAACAAAATA
1 AAAGAAAAAAAAAACAAAATA
*
42900737 AAAGAAAAAAAAAAGAAAAT
1 AAAGAAAAAAAAAACAAAAT
42900757 CCCCCCTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.05
Consensus pattern (21 bp):
AAAGAAAAAAAAAACAAAATA
Found at i:42901691 original size:3 final size:3
Alignment explanation
Indices: 42901685--42901727 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
42901675 GTATTCTTTG
* *
42901685 TTA TTA TTA TTA TAA TTA TTA TAA TTA -TA TTA TATA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T
42901728 ACCTACATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:42901705 original size:15 final size:15
Alignment explanation
Indices: 42901685--42901728 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
42901675 GTATTCTTTG
42901685 TTATTATTATTATAA
1 TTATTATTATTATAA
*
42901700 TTATTATAATTAT-A
1 TTATTATTATTATAA
42901714 TTATATATTATTATA
1 TTAT-TATTATTATA
42901729 CCTACATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATTATTATAA
Found at i:42901901 original size:26 final size:28
Alignment explanation
Indices: 42901872--42901944 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 28
42901862 ATATACATTT
*
42901872 ATATTTTATAATATTTATACGTTT-T-C
1 ATATTTTATAATATATATACGTTTATAC
* * *
42901898 ATATGTTATAATGTATATATGTTTATAC
1 ATATTTTATAATATATATACGTTTATAC
*
42901926 ATTTTTTATAATATATATA
1 ATATTTTATAATATATATA
42901945 TACATACACT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 20 0.53
27 1 0.03
28 17 0.45
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (28 bp):
ATATTTTATAATATATATACGTTTATAC
Found at i:42903508 original size:29 final size:29
Alignment explanation
Indices: 42903472--42904178 Score: 909
Period size: 29 Copynumber: 23.9 Consensus size: 29
42903462 TCAAAATGGG
* *
42903472 TTAGGGTTAGGGTTTTTACTTAAATTAAG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
*
42903501 TTAAGGTTTAGGG-TTTTAATTAAATTAAA
1 TT-AGGGTTAGGGTTTTTAATTAAATTAAA
*
42903530 CTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
* **
42903559 CTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
42903588 TTAGGGTTTAGGGTTTTTAATTAAATTAAA
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAA
**
42903618 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
42903647 TTAGGGTTTAGGGTTTTTAATTAAATTAAA
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAA
42903677 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
* * * **
42903706 CTCGGGTTAGGGTTTTTAATTAAAATGGA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
42903735 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
*
42903764 TTAGGGTTAAGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
* *
42903793 TTAAACTAGGGTTAGGGTTTTTATTTAAATTAAG
1 -T----TAGGGTTAGGGTTTTTAATTAAATTAAA
*
42903827 TTAGGGTTTAAGG-TTTTAATTAAATTAAA
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAA
42903856 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
* * ***
42903885 CTAGGGTTAGGGTTTTTAATTAAAATGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
42903914 TTAGGGTTAGGGTTTTTAATTAAATTAAATTAAA
1 TTAGGGTTAGGG--TTT--TT-AATTAAATTAAA
* * *
42903948 TTAAATTAGGGTTAGGATTTTTAATTAAATTAAA
1 TT--A--GGGTT-AGGGTTTTTAATTAAATTAAA
42903982 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
* **
42904011 TTAGGGTTAGGGTTTTTAATTAAAATGGA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
42904040 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
*
42904069 TTAGGGTTAGGGTTTTTAATTAAATTAAG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
42904098 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
* *
42904127 TTA-AGTTTGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
* *
42904155 TTA-GGTTAGAGTTTTTAATCAAAT
1 TTAGGGTTAGGGTTTTTAATTAAAT
42904179 AATATCAAAA
Statistics
Matches: 595, Mismatches: 62, Indels: 43
0.85 0.09 0.06
Matches are distributed among these distances:
28 57 0.10
29 398 0.67
30 72 0.12
31 3 0.01
32 1 0.00
33 3 0.01
34 49 0.08
35 2 0.00
36 1 0.00
37 3 0.01
38 3 0.01
39 3 0.01
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.44
Consensus pattern (29 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAAA
Found at i:42903941 original size:5 final size:5
Alignment explanation
Indices: 42903931--42903955 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42903921 TAGGGTTTTT
42903931 AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA
42903956 GGGTTAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:42905351 original size:7 final size:7
Alignment explanation
Indices: 42905341--42905379 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
42905331 TTATATACAT
42905341 AATACTA
1 AATACTA
42905348 AATACTA
1 AATACTA
42905355 AATACTA
1 AATACTA
42905362 AATACTA
1 AATACTA
42905369 AATACTA
1 AATACTA
42905376 AATA
1 AATA
42905380 TCAATCCACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:42906354 original size:14 final size:15
Alignment explanation
Indices: 42906337--42906369 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42906327 AATAATTATC
42906337 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
42906351 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
42906366 TAAA
1 TAAA
42906370 TTTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:42906501 original size:28 final size:29
Alignment explanation
Indices: 42906468--42906523 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
42906458 TTGAAAATAT
42906468 TAAAAAT-TTTAAAATTATT-TTAAAAAAA
1 TAAAAATATTTAAAATT-TTCTTAAAAAAA
42906496 TAAAAATATTTAAAATTTTCTTAAAAAA
1 TAAAAATATTTAAAATTTTCTTAAAAAA
42906524 TGAAATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAAAATATTTAAAATTTTCTTAAAAAAA
Found at i:42906584 original size:22 final size:21
Alignment explanation
Indices: 42906556--42906608 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
42906546 TTAAATATGG
*
42906556 ATTTGAGAGATTTTTTGAAGGA
1 ATTTGAGAGA-TTTTGGAAGGA
42906578 ATTTGAGAGGATTTTGGAAGGA
1 ATTTGAGA-GATTTTGGAAGGA
42906600 ATTTGAGAG
1 ATTTGAGAG
42906609 TTTAAGAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 1 0.03
22 26 0.90
23 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (21 bp):
ATTTGAGAGATTTTGGAAGGA
Found at i:42906628 original size:52 final size:52
Alignment explanation
Indices: 42906561--42906660 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
42906551 TATGGATTTG
* * * * *
42906561 AGAGATTTTTTGAAGGAATTTGAGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTTA
42906613 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
42906661 AATATTTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.31
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTTA
Found at i:42906677 original size:24 final size:22
Alignment explanation
Indices: 42906613--42906668 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
42906603 TGAGAGTTTA
42906613 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
42906635 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
42906657 AGAGAATATTTG
1 AGAGAAT-TTTG
42906669 TTTGTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.29
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:42910559 original size:17 final size:17
Alignment explanation
Indices: 42910537--42910589 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
42910527 ATTTCAAAAA
42910537 AATAATATAATAATTTT
1 AATAATATAATAATTTT
* * *
42910554 AATAATTTTAT-ATTTC
1 AATAATATAATAATTTT
*
42910570 AA-AAAATAATAATTTT
1 AATAATATAATAATTTT
42910586 AATA
1 AATA
42910590 GTTTTAAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
15 5 0.19
16 12 0.44
17 10 0.37
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAATATAATAATTTT
Found at i:42910583 original size:32 final size:35
Alignment explanation
Indices: 42910513--42910595 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 35
42910503 ATCATATGCA
42910513 TTTAATAATTTTATATTTCAAAAAAATAATATAATAAT
1 TTTAATAATTTTATATTTC---AAAATAATATAATAAT
42910551 TTTAATAATTTTATATTTC-AAA-AA-ATAATAAT
1 TTTAATAATTTTATATTTCAAAATAATATAATAAT
*
42910583 TTTAATAGTTTTA
1 TTTAATAATTTTA
42910596 AAATCATTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 20 0.45
33 2 0.05
34 3 0.07
38 19 0.43
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (35 bp):
TTTAATAATTTTATATTTCAAAATAATATAATAAT
Found at i:42914237 original size:41 final size:40
Alignment explanation
Indices: 42914190--42914313 Score: 169
Period size: 41 Copynumber: 3.0 Consensus size: 40
42914180 GTGAAATTAT
*
42914190 TCGGACTATTCGTCTAGCAGGCTAAGTGTCGGTGAACTGAA
1 TCGGACTATT-GTCTAGCAGGCTAAGTGCCGGTGAACTGAA
42914231 TCGGACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCGGACTAT-TGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * *
42914272 TCAGG-CTATAGGCCTAGCAGGCTAAGTGCCGGTGAACGGAA
1 TC-GGACTAT-TGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
42914313 T
1 T
42914314 TAGACTATAA
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
41 74 0.96
42 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (40 bp):
TCGGACTATTGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
Found at i:42914322 original size:41 final size:41
Alignment explanation
Indices: 42914203--42914328 Score: 180
Period size: 41 Copynumber: 3.1 Consensus size: 41
42914193 GACTATTCGT
* * * *
42914203 CTAGCAGGCTAAGTGTCGGTGAACTGAATCGGACTATATGT
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGACTATAAGC
* *
42914244 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAGGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGACTATAAGC
* *
42914285 CTAGCAGGCTAAGTGCCGGTGAACGGAATTAGACTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGACTATAAGC
42914326 CTA
1 CTA
42914329 TCAAGTGAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGACTATAAGC
Found at i:42927067 original size:35 final size:35
Alignment explanation
Indices: 42927021--42927092 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
42927011 ACAGTCAAAA
42927021 CATAATTTGTAACTAGAGGTGCTCATCGGTCGAGC
1 CATAATTTGTAACTAGAGGTGCTCATCGGTCGAGC
42927056 CATAATTTGTAACTAGAGGTGCTCATCGGTCGAGC
1 CATAATTTGTAACTAGAGGTGCTCATCGGTCGAGC
42927091 CA
1 CA
42927093 GGCCCAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (35 bp):
CATAATTTGTAACTAGAGGTGCTCATCGGTCGAGC
Found at i:42927486 original size:21 final size:22
Alignment explanation
Indices: 42927449--42927489 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
42927439 AAATAGGGAG
*
42927449 AAAACAACATGAAAATAGCATT
1 AAAACAACATAAAAATAGCATT
42927471 AAAACAACA-AAAAATAGCA
1 AAAACAACATAAAAATAGCA
42927490 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.66, C:0.15, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAACAACATAAAAATAGCATT
Found at i:42928364 original size:58 final size:58
Alignment explanation
Indices: 42928274--42928389 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
42928264 AAATAGAGAA
42928274 TATTTTCATCAGTTCAAATTCGTACTTTTTTATATATAACAAATATTTTTAAAATTGT
1 TATTTTCATCAGTTCAAATTCGTACTTTTTTATATATAACAAATATTTTTAAAATTGT
*
42928332 TATTTTCATCAGTTCAAATTCGTGCTTTTTTATATATAACAAATATTTTTAAAATTGT
1 TATTTTCATCAGTTCAAATTCGTACTTTTTTATATATAACAAATATTTTTAAAATTGT
42928390 AATTATTTAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (58 bp):
TATTTTCATCAGTTCAAATTCGTACTTTTTTATATATAACAAATATTTTTAAAATTGT
Found at i:42936416 original size:7 final size:7
Alignment explanation
Indices: 42936404--42936437 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
42936394 AAGGGATATT
42936404 AAAGGTG
1 AAAGGTG
42936411 AAAGGTG
1 AAAGGTG
42936418 AAAGGTG
1 AAAGGTG
42936425 AAAGGTG
1 AAAGGTG
42936432 AAAGGT
1 AAAGGT
42936438 TGAACATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (7 bp):
AAAGGTG
Found at i:42939453 original size:15 final size:15
Alignment explanation
Indices: 42939429--42939458 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42939419 GGGTTAACTT
42939429 CCTTTCTATAAACCA
1 CCTTTCTATAAACCA
*
42939444 CCTTTGTATAAACCA
1 CCTTTCTATAAACCA
42939459 AACACAATGA
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:0.30, G:0.03, T:0.33
Consensus pattern (15 bp):
CCTTTCTATAAACCA
Found at i:42940926 original size:49 final size:49
Alignment explanation
Indices: 42940869--42940973 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 49
42940859 TCATGTGTTA
* * *
42940869 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTGACCTTTTAATTCATGATATTAAACTTAATTT
*
42940918 TAATTTTATAAAGTGTTTACCTTTTAATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTGACCTTTTAATTCATGATATTAAACTTAATTT
42940967 TAATTTT
1 TAATTTT
42940974 TTTTCTTAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTGACCTTTTAATTCATGATATTAAACTTAATTT
Found at i:42946602 original size:24 final size:24
Alignment explanation
Indices: 42946554--42946621 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
42946544 AAGGGGTTAC
* *
42946554 AAGAAGATGAAAGGTTAAAGGTTA
1 AAGAAGATGAAAGGTGAAAGATTA
* *
42946578 AAGAAGATGAAATGTGGAAGATTA
1 AAGAAGATGAAAGGTGAAAGATTA
* * *
42946602 AGGGAGATGAAAAGTGAAAG
1 AAGAAGATGAAAGGTGAAAG
42946622 GTTGAACATC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (24 bp):
AAGAAGATGAAAGGTGAAAGATTA
Found at i:42946850 original size:39 final size:40
Alignment explanation
Indices: 42946806--42946887 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 40
42946796 AAAGCAAATA
*
42946806 TGATCAGAACCTATAATGAGATTGTTAAAAAAA-AGGAAG
1 TGATCAGAACCTATAATGAGATTGCTAAAAAAAGAGGAAG
*
42946845 TGATCAGAACCTATAATGAGATTGCTAAAAAAAGAGTAAG
1 TGATCAGAACCTATAATGAGATTGCTAAAAAAAGAGGAAG
42946885 TGA
1 TGA
42946888 ATCATATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 32 0.80
40 8 0.20
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.23
Consensus pattern (40 bp):
TGATCAGAACCTATAATGAGATTGCTAAAAAAAGAGGAAG
Found at i:42958773 original size:20 final size:19
Alignment explanation
Indices: 42958748--42958787 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
42958738 TTCAAATAAT
*
42958748 TTAATTTGATATAATAAAAA
1 TTAATTTGAAAT-ATAAAAA
*
42958768 TTAATTTTAAATATAAAAA
1 TTAATTTGAAATATAAAAA
42958787 T
1 T
42958788 CTTGTACGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAATTTGAAATATAAAAA
Found at i:42960232 original size:15 final size:15
Alignment explanation
Indices: 42960212--42960241 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42960202 GATAGGAGTA
42960212 AATAATAATAATACT
1 AATAATAATAATACT
42960227 AATAATAATAATACT
1 AATAATAATAATACT
42960242 TTTAAGGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAATAATAATACT
Found at i:42960419 original size:17 final size:14
Alignment explanation
Indices: 42960383--42960418 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
42960373 AAGAAAGAAA
42960383 AATAATAAAACAAT
1 AATAATAAAACAAT
42960397 AATAATAAAACAAT
1 AATAATAAAACAAT
42960411 AATAATAA
1 AATAATAA
42960419 TGAAAATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAATAAAACAAT
Found at i:42961538 original size:44 final size:44
Alignment explanation
Indices: 42961488--42962725 Score: 315
Period size: 44 Copynumber: 28.2 Consensus size: 44
42961478 CTTTAGAGAA
*
42961488 ATAAGATTCGCTATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 ATAAGATTCGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * * *
42961532 ATAAGA-TCTACAATCGTCAACCTACTCCACTGCTGCTTAGGGAG
1 ATAAGATTC-GCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * * *
42961576 ATAAGGA-T-GGTGTC-TAAATCTGCTTCC-CTACTACCTTCGGGAA
1 ATAA-GATTCGCTATCTTCAATCTGC-TCCACTACT-GCTTAGGGAG
** * ** *
42961619 ATAAGATTCGCCGTTTTTGATTTGCTCCACTACTGCTTAGGGAG
1 ATAAGATTCGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * * * * *
42961663 ATAA-AATCTACAATCTTCGACCTACTCCACTGCTACTTAGGGAG
1 ATAAGATTC-GCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * ** * * *
42961707 ATAGGACT-GGTGGCTTAAATCTGCTTCC-CTACTACCTTGGGGAAG
1 ATAAGATTCGCTATCTTCAATCTGC-TCCACTACT-GCTTAGGG-AG
* ** * *
42961752 ATAAGATTCACCGTCTTCGATCTGCTCCACTACTGTTTAGGGAG
1 ATAAGATTCGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * * * *
42961796 ATAAGA-TCTACAATTTTCAACCTACTCCACTGCTGCTCAGGGAG
1 ATAAGATTC-GCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
** * ** * * *
42961840 ATAAGGCTAG-TGGCTTAAATCTGCTTCC-CTTACTACCTT-GGAAAG
1 ATAAGATTCGCTATCTTCAATCTGC-TCCAC-TACT-GCTTAGG-GAG
* * *
42961885 ATAAGATTCGCCGTAT-TT-GATCTACTCCACTGCTGCTTAGGGAG
1 ATAAGATTCG-C-TATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * * * * *
42961929 ATAATA-TCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAA
1 ATAAGATTC-GCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
** * * * * *
42961973 ATAAGGCTAG-TAGCTTAAATCTGCTTCACTACTACCTTAGGGAAG
1 ATAAGATTCGCTATCTTCAATCTGCTCCACTACT-GCTTAGGG-AG
* ** * *
42962018 ATAAGATTCACCGTCTTCGATCTGTTCCACTACTGCTTAGGGAG
1 ATAAGATTCGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * * * * * * * *
42962062 ACAGGA-TCTACAATCTACAACCTACTTCACTGCTACTCAGGGAG
1 ATAAGATTC-GCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * ** * *
42962106 ATAGGATT-GGTGGCTTAAATCTGCTCCACTACTGCTTATGGAG
1 ATAAGATTCGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * * * * *
42962149 ATAAGA-TCTACAATCTTCGACCTACTCCACTACTACTCAAGGAG
1 ATAAGATTC-GCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * ** * * *
42962193 AGAGGACTGGC-GGCTTAAATCTGTTTCC-CTACTACCTT-GGGAAG
1 ATAAGATTCGCTATCTTCAATCTG-CTCCACTACT-GCTTAGGG-AG
* ** * * *
42962237 ATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAGTGAG
1 ATAAGATTCGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * *
42962281 ATAAGATATAC-C-ATCTTCAACCTACTCCACTGCTGCTCAGGGAG
1 ATAAGAT-T-CGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * ** * * *
42962325 ATAGGACT-GGTGGCTTAAATCTGCTTCCTACTA-T-C-TCGAGAAG
1 ATAAGATTCGCTATCTTCAATCTGC-TCC-ACTACTGCTTAG-GGAG
* * *
42962368 ATAAGATTCGCCATCTTCAATATGCTCCACCACTGCTTAGGGAG
1 ATAAGATTCGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * *
42962412 ATAAGA-TCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAG
1 ATAAGATTC-GCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * ** *
42962456 ATAGGATT---TATGGCTTAAATCTGCTTC-CTACTATTTCGGGAAG
1 ATAAGATTCGCTAT--CTTCAATCTGCTCCACTACTGCTTAGGG-AG
** *
42962499 ATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 ATAAGATTCGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * *
42962543 ATAAGA-TCTACAATCTTCAACCTACTCCACTGCTGCTTAGGGAG
1 ATAAGATTC-GCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * * *
42962587 ATAAGACT-GGTGA-CTTAAATCTACTTCCTACTA-T-C-TCGGAAAG
1 ATAAGATTCGCT-ATCTTCAATCTGC-TCC-ACTACTGCTTAGG-GAG
** ** * *
42962630 ATAAGATTTACCGTCTTCGATCTGCTCCACTACTGCCTAGGGAG
1 ATAAGATTCGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * ** *
42962674 ACAAGA-TCTGCAATCTTCAATCTACTCCACTGTTGCTCAGGGAG
1 ATAAGATTC-GCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
*
42962718 ATAGGATT
1 ATAAGATT
42962726 TGATATGATG
Statistics
Matches: 825, Mismatches: 292, Indels: 153
0.65 0.23 0.12
Matches are distributed among these distances:
41 2 0.00
42 34 0.04
43 175 0.21
44 462 0.56
45 110 0.13
46 39 0.05
47 2 0.00
48 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
ATAAGATTCGCTATCTTCAATCTGCTCCACTACTGCTTAGGGAG
Found at i:42961808 original size:133 final size:133
Alignment explanation
Indices: 42961501--42962138 Score: 887
Period size: 133 Copynumber: 4.8 Consensus size: 133
42961491 AGATTCGCTA
*
42961501 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCGTCAACCTACTCCACTGCT
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCT
* *
42961566 GCTTAGGGAGATAAGGA-TGGTGTC-TAAATCTGCTTCCCTACTACCTTCGGGAA-ATAAGATTC
66 GCTCAGGGAGATAAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTT-GGGAAGATAAGATTC
*
42961628 GCCG
130 ACCG
* * * * *
42961632 TTTTTGATTTGCTCCACTACTGCTTAGGGAGATAAAATCTACAATCTTCGACCTACTCCACTGCT
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCT
* *
42961697 ACTTAGGGAGAT-AGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGGAAGATAAGATTC
66 GCTCAGGGAGATAAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTT-GGGAAGATAAGATTC
42961761 ACCG
130 ACCG
* *
42961765 TCTTCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCACTGCT
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCT
* *
42961830 GCTCAGGGAGATAAGG-CTAGTGGCTTAAATCTGCTTCCCTTACTACCTTGGAAAGATAAGATTC
66 GCTCAGGGAGATAAGGACTGGTGGCTTAAATCTGCTTCCC-TACTACCTTGGGAAGATAAGATTC
*
42961894 GCCG
130 ACCG
* * * * *
42961898 TATTTGATCTACTCCACTGCTGCTTAGGGAGATAATATCTACAATCTTCAACCTACTCCACTGCT
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCT
* * * *
42961963 GCTCAGGGAAATAAGG-CTAGTAGCTTAAATCTGCTTCACTACTACCTTAGGGAAGATAAGATTC
66 GCTCAGGGAGATAAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTT-GGGAAGATAAGATTC
42962027 ACCG
130 ACCG
* * * * *
42962031 TCTTCGATCTGTTCCACTACTGCTTAGGGAGACAGGATCTACAATCTACAACCTACTTCACTGCT
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCT
* *
42962096 ACTCAGGGAGAT-AGGATTGGTGGCTTAAATCTGC-TCCACTACT
66 GCTCAGGGAGATAAGGACTGGTGGCTTAAATCTGCTTCC-CTACT
42962139 GCTTATGGAG
Statistics
Matches: 449, Mismatches: 50, Indels: 14
0.88 0.10 0.03
Matches are distributed among these distances:
130 4 0.01
131 76 0.17
132 42 0.09
133 315 0.70
134 12 0.03
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (133 bp):
TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCT
GCTCAGGGAGATAAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCA
CCG
Found at i:42962225 original size:87 final size:87
Alignment explanation
Indices: 42962037--42962225 Score: 254
Period size: 87 Copynumber: 2.2 Consensus size: 87
42962027 ACCGTCTTCG
* * * *
42962037 ATCTGTTCCACTACTGCTTAGGGAGACAGGATCTACAATCTACAACCTACTTCACTGCTACTCAG
1 ATCTGTTCCACTACTGCTTAGGGAGACAAGATCTACAATCTACAACCTACTCCACTACTACTCAA
* * *
42962102 GGAGATAGGATTGGTGGCTTAA
66 GGAGAGAGGACTGGCGGCTTAA
* * * * *
42962124 ATCTGCTCCACTACTGCTTATGGAGATAAGATCTACAATCTTCGACCTACTCCACTACTACTCAA
1 ATCTGTTCCACTACTGCTTAGGGAGACAAGATCTACAATCTACAACCTACTCCACTACTACTCAA
42962189 GGAGAGAGGACTGGCGGCTTAA
66 GGAGAGAGGACTGGCGGCTTAA
42962211 ATCTGTTTCC-CTACT
1 ATCTG-TTCCACTACT
42962226 ACCTTGGGAA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
87 85 0.97
88 3 0.03
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (87 bp):
ATCTGTTCCACTACTGCTTAGGGAGACAAGATCTACAATCTACAACCTACTCCACTACTACTCAA
GGAGAGAGGACTGGCGGCTTAA
Found at i:42962239 original size:131 final size:131
Alignment explanation
Indices: 42962124--42962723 Score: 858
Period size: 131 Copynumber: 4.6 Consensus size: 131
42962114 GGTGGCTTAA
* * * * *
42962124 ATCTGCTCCACTACTGCTTATGGAGATAAGATCTACAATCTTCGACCTACTCCACTACTACTCAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
* * * * * *
42962189 GGAGAGAGGACTGGCGGCTTAAATCTGTTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTT
66 GGAGATAGGACTGGTGGCTTAAATCTGCTT-CCTACTATCTCGGGAAGATAAGATTCGCCGTCTT
42962254 CG
130 CG
* * * *
42962256 ATCTGCTCCACTATTGCTTAGTGAGATAAGATATACCATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
* *
42962321 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTATCTCGAGAAGATAAGATTCGCCATCTTC
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTATCTCGGGAAGATAAGATTCGCCGTCTTC
*
42962386 A
131 G
* * *
42962387 ATATGCTCCACCACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
* ** *
42962452 GGAGATAGGATTTATGGCTTAAATCTGCTTCCTACTATTTCGGGAAGATAAGATTCGCCGTCTTC
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTATCTCGGGAAGATAAGATTCGCCGTCTTC
42962517 G
131 G
*
42962518 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
* * * * **
42962583 GGAGATAAGACTGGTGACTTAAATCTACTTCCTACTATCTCGGAAAGATAAGATTTACCGTCTTC
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTATCTCGGGAAGATAAGATTCGCCGTCTTC
42962648 G
131 G
* * * * *
42962649 ATCTGCTCCACTACTGCCTAGGGAGACAAGATCTGCAATCTTCAATCTACTCCACTGTTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
42962714 GGAGATAGGA
66 GGAGATAGGA
42962724 TTTGATATGA
Statistics
Matches: 415, Mismatches: 53, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
131 332 0.80
132 83 0.20
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (131 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
GGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTATCTCGGGAAGATAAGATTCGCCGTCTTC
G
Found at i:42962323 original size:219 final size:220
Alignment explanation
Indices: 42961904--42962349 Score: 635
Period size: 219 Copynumber: 2.0 Consensus size: 220
42961894 GCCGTATTTG
* * * * * *
42961904 ATCTACTCCACTGCTGCTTAGGGAGATAATATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAA
*
42961969 GGAAATAAGGCTAGTAGCTTAAATCTGCTTCACTACTACCTTAGGGAAGATAAGATTCACCGTCT
66 GGAAATAAGGCTAGCAGCTTAAATCTGCTTCACTACTACCTTAGGGAAGATAAGATTCACCGTCT
* * * *
42962034 TCGATCTGTTCCACTACTGCTTAGGGAGACAGGATCTACAATCTACAACCTACTTCACTGCTACT
131 TCGATCTGCTCCACTACTGCTTAGGGAGACAAGATATACAATCTACAACCTACTCCACTGCTACT
*
42962099 CAGGGAGATAGGATTGGTGGCTTAA
196 CAGGGAGATAGGACTGGTGGCTTAA
* *
42962124 ATCTGCTCCACTACTGCTTATGGAGATAAGATCTACAATCTTCGACCTACTCCACTACTACTCAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAA
* * * * * *
42962189 GGAGA-GAGGACTGGCGGCTTAAATCTGTTTCCCTACTACCTT-GGGAAGATAAGATTCACCGTC
66 GGAAATAAGG-CTAGCAGCTTAAATCTGCTTCACTACTACCTTAGGGAAGATAAGATTCACCGTC
* * * * * *
42962252 TTCGATCTGCTCCACTATTGCTTAGTGAGATAAGATATACCATCTTCAACCTACTCCACTGCTGC
130 TTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATATACAATCTACAACCTACTCCACTGCTAC
42962317 TCAGGGAGATAGGACTGGTGGCTTAA
195 TCAGGGAGATAGGACTGGTGGCTTAA
42962343 ATCTGCT
1 ATCTGCT
42962350 TCCTACTATC
Statistics
Matches: 199, Mismatches: 26, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
219 111 0.56
220 88 0.44
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (220 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAA
GGAAATAAGGCTAGCAGCTTAAATCTGCTTCACTACTACCTTAGGGAAGATAAGATTCACCGTCT
TCGATCTGCTCCACTACTGCTTAGGGAGACAAGATATACAATCTACAACCTACTCCACTGCTACT
CAGGGAGATAGGACTGGTGGCTTAA
Found at i:42963411 original size:108 final size:108
Alignment explanation
Indices: 42963213--42963426 Score: 302
Period size: 108 Copynumber: 2.0 Consensus size: 108
42963203 GAAAAACGCT
* * * *
42963213 TGAAAAAGATTATCAAAATGGACAAGATGAAATTTTGTTGAGAACAAAGCTCTAAATAAATGAAT
1 TGAAAAAGATTATCAAAATGGACAACATGAAATTTTATTGAGAACAAAGCTCGAAATAAATAAAT
* * *
42963278 CAATCAAGATAACAAACTTTGCTAAGATACGAACTGAATAAAA
66 CAATCAAGATAACAAACTTTACTAAGATAAGAAATGAATAAAA
* * * * *
42963321 TGAAACAGATTATCACAATGGATAACATGAAATTTTATTGAGAGCAAAGCTCGAAATGAATAAAT
1 TGAAAAAGATTATCAAAATGGACAACATGAAATTTTATTGAGAACAAAGCTCGAAATAAATAAAT
* *
42963386 TAATCAAGATAACAAATTTTACTAAGATAAGAAATGAATAA
66 CAATCAAGATAACAAACTTTACTAAGATAAGAAATGAATAA
42963427 GATAAAGATA
Statistics
Matches: 92, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
108 92 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.25
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATGGACAACATGAAATTTTATTGAGAACAAAGCTCGAAATAAATAAAT
CAATCAAGATAACAAACTTTACTAAGATAAGAAATGAATAAAA
Found at i:42968032 original size:31 final size:31
Alignment explanation
Indices: 42967994--42968055 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
42967984 ACTGCTCATG
*
42967994 CTGAATGAATCCAGGGCCTTCCTAACAAGCA
1 CTGAATGAATCCAAGGCCTTCCTAACAAGCA
*
42968025 CTGAATGAATCCAAGGCCTTCCTAATAAGCA
1 CTGAATGAATCCAAGGCCTTCCTAACAAGCA
42968056 ATTGTAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (31 bp):
CTGAATGAATCCAAGGCCTTCCTAACAAGCA
Found at i:42973471 original size:1 final size:1
Alignment explanation
Indices: 42973461--42973514 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
42973451 TGGCCTCTCA
* * * * * *
42973461 TTTTTCTTTTTATTTTTTTTTTCTTTTTTTTTTCTTTTTTTTGTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42973515 AACATTCTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.02, C:0.06, G:0.04, T:0.89
Consensus pattern (1 bp):
T
Found at i:42973481 original size:11 final size:11
Alignment explanation
Indices: 42973460--42973515 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
42973450 TTGGCCTCTC
42973460 ATTTTTCTTTTT
1 ATTTTT-TTTTT
42973472 ATTTTTTTTTT
1 ATTTTTTTTTT
*
42973483 CTTTTTTTTTT
1 ATTTTTTTTTT
* *
42973494 CTTTTTTTTGT
1 ATTTTTTTTTT
*
42973505 -TTGTTTTTTT
1 ATTTTTTTTTT
42973515 A
1 A
42973516 ACATTCTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
10 8 0.21
11 25 0.64
12 6 0.15
ACGTcount: A:0.05, C:0.05, G:0.04, T:0.86
Consensus pattern (11 bp):
ATTTTTTTTTT
Found at i:42978509 original size:15 final size:15
Alignment explanation
Indices: 42978489--42978518 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42978479 GATAGGAGTA
42978489 AATAATAATAATACT
1 AATAATAATAATACT
*
42978504 AATAATAATAGTACT
1 AATAATAATAATACT
42978519 TTTAAGGTAA
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:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (15 bp):
AATAATAATAATACT
Done.