Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008225.1 Hibiscus syriacus cultivar Beakdansim tig00110858_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1890193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1104511 original size:76 final size:76
Alignment explanation
Indices: 1104406--1105118 Score: 1338
Period size: 76 Copynumber: 9.4 Consensus size: 76
1104396 GAGGTCTTAA
* * * *
1104406 AAACATCATGCATTGCAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1104471 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1104482 AAACATCATGCACGGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1104547 AGGCTTTTTGG
66 AGGCTTTTTGG
1104558 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1104623 AGGCTTTTTGG
66 AGGCTTTTTGG
1104634 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1104699 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1104710 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1104774 AGGCTTTTTGG
66 AGGCTTTTTGG
1104785 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1104850 AGGCTTTTTGG
66 AGGCTTTTTGG
1104861 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1104926 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1104937 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1105002 AGGCTTTTTGG
66 AGGCTTTTTGG
1105013 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1105078 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1105089 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
1105119 TGAGAAATAG
Statistics
Matches: 623, Mismatches: 13, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
75 74 0.12
76 549 0.88
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1105105 original size:379 final size:379
Alignment explanation
Indices: 1104406--1105118 Score: 1354
Period size: 379 Copynumber: 1.9 Consensus size: 379
1104396 GAGGTCTTAA
* *
1104406 AAACATCATGCATTGCAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1104471 AGGCTTTTTGGAAACATCATGCACGGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACGGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
*
1104536 AAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT
131 AAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTT
1104601 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGAC
*
1104666 CCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGC
261 CCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
1104731 TTACAGATGACCCGAAGGATTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGG
326 TTACAGATGACCCGAAGGATTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGG
* *
1104785 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
*
1104850 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACGGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
*
1104915 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTT
131 AAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTT
1104980 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGAC
1105045 CCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
261 CCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
1105110 TTACAGATG
326 TTACAGATG
1105119 TGAGAAATAG
Statistics
Matches: 326, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
379 326 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (379 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACGGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTT
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGAC
CCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
TTACAGATGACCCGAAGGATTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGG
Found at i:1105800 original size:22 final size:22
Alignment explanation
Indices: 1105775--1105829 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1105765 GATAAAGCTT
*
1105775 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
1105797 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1105819 TCATCTTTGAA
1 TCATCTTTGAA
1105830 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1108641 original size:82 final size:82
Alignment explanation
Indices: 1108361--1108801 Score: 683
Period size: 82 Copynumber: 5.4 Consensus size: 82
1108351 CCTACTGAAT
* **
1108361 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCGAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAATTCA
1108425 ATGATTGGTTCTG-CCAAAC
65 ATGATT-GTTCTGTCC-AAC
* *
1108444 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAA
1108509 TGATTGGTTCTG-CCAAAC
66 TGATT-GTTCTGTCC-AAC
* * * **
1108527 CAGATCATATAACTCAAAGAACACTACCAGAAGATGCTA-TGAACACATTCATCTTCCGAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAATTCA
*
1108591 ATGATTGTCCTGTCCAAC
65 ATGATTGTTCTGTCCAAC
* *
1108609 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAA
1108674 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
1108691 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAA
1108756 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
1108773 CAGATCAGATAACTCAAAGAACACTTCCA
1 CAGATCAGATAACTCAAAGAACACTTCCA
1108802 TTGATAAAGA
Statistics
Matches: 331, Mismatches: 23, Indels: 9
0.91 0.06 0.02
Matches are distributed among these distances:
82 190 0.57
83 139 0.42
84 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (82 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAA
TGATTGTTCTGTCCAAC
Found at i:1108772 original size:164 final size:165
Alignment explanation
Indices: 1108361--1108801 Score: 764
Period size: 164 Copynumber: 2.7 Consensus size: 165
1108351 CCTACTGAAT
1108361 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCGAATTCAA
1108426 TGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAA
66 TGATT-GTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAA
1108490 ATTCATCTTCTAAACTCAATGATTGGTTCTGCCAAAC
129 ATTCATCTTCTAAACTCAATGATTGGTTCTGCCAAAC
* *
1108527 CAGATCATATAACTCAAAGAACACTACCAGAAGATGCTATGAACACATTCATCTTCCGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCGAATTCAA
*
1108592 TGATTGTCCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAAT
66 TGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAAT
1108657 TCATCTTCTAAACTCAATGATT-GTTCTGTCC-AAC
131 TCATCTTCTAAACTCAATGATTGGTTCTG-CCAAAC
* **
1108691 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCGAATTCA
1108755 ATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
65 ATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
1108802 TTGATAAAGA
Statistics
Matches: 263, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
164 111 0.42
165 82 0.31
166 70 0.27
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (165 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCGAATTCAA
TGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAAT
TCATCTTCTAAACTCAATGATTGGTTCTGCCAAAC
Found at i:1116829 original size:12 final size:12
Alignment explanation
Indices: 1116812--1116836 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1116802 CACCGTACTC
1116812 CGCCGCCGGCCA
1 CGCCGCCGGCCA
1116824 CGCCGCCGGCCA
1 CGCCGCCGGCCA
1116836 C
1 C
1116837 CGTAACGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.60, G:0.32, T:0.00
Consensus pattern (12 bp):
CGCCGCCGGCCA
Found at i:1117542 original size:3 final size:3
Alignment explanation
Indices: 1117534--1117606 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
1117524 TGTAATATAT
*
1117534 TAA TAA TAA TATA TAA T-A TAAA TAA TAA TAA TAA T-A TTA TAA TAA
1 TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* ** **
1117579 CAA TAA TTT TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1117607 TTAAGTAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
2 4 0.07
3 46 0.84
4 5 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:1119025 original size:20 final size:20
Alignment explanation
Indices: 1119000--1119039 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1118990 TTGATATATA
1119000 TAAGGCACTAAGTAAGGTCT
1 TAAGGCACTAAGTAAGGTCT
1119020 TAAGGCACTAAGTAAGGTCT
1 TAAGGCACTAAGTAAGGTCT
1119040 CAACTTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (20 bp):
TAAGGCACTAAGTAAGGTCT
Found at i:1121622 original size:34 final size:34
Alignment explanation
Indices: 1121582--1121683 Score: 204
Period size: 34 Copynumber: 3.0 Consensus size: 34
1121572 TTGATGTGTC
1121582 CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
1 CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
1121616 CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
1 CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
1121650 CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
1 CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
1121684 TTTTTATAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (34 bp):
CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
Found at i:1124987 original size:23 final size:23
Alignment explanation
Indices: 1124952--1125022 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
1124942 GAGTCGAGGG
* *
1124952 TTCTACGCAGTCCTTCAAGATAA
1 TTCTACGCGGTCCTTCAGGATAA
* * *
1124975 TTCTACGTGGTCCTTCGGGATAT
1 TTCTACGCGGTCCTTCAGGATAA
* *
1124998 TTTTATGCGGTCCTTCAGGATAA
1 TTCTACGCGGTCCTTCAGGATAA
1125021 TT
1 TT
1125023 TTATGTGGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCAGGATAA
Found at i:1125024 original size:23 final size:23
Alignment explanation
Indices: 1124961--1125027 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1124951 GTTCTACGCA
* * * *
1124961 GTCCTTCAAGATAATTCTACGTG
1 GTCCTTCAGGATAATTTTATGCG
* *
1124984 GTCCTTCGGGATATTTTTATGCG
1 GTCCTTCAGGATAATTTTATGCG
1125007 GTCCTTCAGGATAATTTTATG
1 GTCCTTCAGGATAATTTTATG
1125028 TGGTTCTTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (23 bp):
GTCCTTCAGGATAATTTTATGCG
Found at i:1129154 original size:31 final size:31
Alignment explanation
Indices: 1129116--1129203 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 31
1129106 AGAATGACCT
1129116 GAACCCGAATTGACCCGA-AAATATGATACCC
1 GAACCCGAATTGACCCGATAAATATGA-ACCC
* * **
1129147 GAACCCGAACTGCATCCGATTGATATGAACCC
1 GAACCCGAATTG-ACCCGATAAATATGAACCC
*
1129179 GAACCCGAGATTGACCCGGTAAATA
1 GAACCCGA-ATTGACCCGATAAATA
1129204 ACTGGTATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
31 11 0.24
32 25 0.56
33 9 0.20
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.17
Consensus pattern (31 bp):
GAACCCGAATTGACCCGATAAATATGAACCC
Found at i:1129242 original size:16 final size:16
Alignment explanation
Indices: 1129221--1129266 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
1129211 TTACCCGACC
* *
1129221 TGTTTTCAACCTGACT
1 TGTTTTTAACCTGACA
1129237 TGTTTTTAACCTGACA
1 TGTTTTTAACCTGACA
1129253 TGTTTTTAACCTGA
1 TGTTTTTAACCTGA
1129267 TCTGTAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (16 bp):
TGTTTTTAACCTGACA
Found at i:1129466 original size:9 final size:9
Alignment explanation
Indices: 1129447--1129478 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
1129437 AAATAGACCT
1129447 ATTATATAAA
1 ATTA-ATAAA
1129457 ATTAATAAA
1 ATTAATAAA
1129466 ATTAATAAA
1 ATTAATAAA
1129475 ATTA
1 ATTA
1129479 TTTAAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
ATTAATAAA
Found at i:1129550 original size:20 final size:21
Alignment explanation
Indices: 1129525--1129564 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1129515 GGAAAATTAA
1129525 TATAGTTTAA-TTATATAAAT
1 TATAGTTTAATTTATATAAAT
1129545 TATAGTTTAATTTATATAAA
1 TATAGTTTAATTTATATAAA
1129565 GAAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TATAGTTTAATTTATATAAAT
Found at i:1130151 original size:16 final size:16
Alignment explanation
Indices: 1130127--1130157 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1130117 AAGCAGCAGA
*
1130127 CAGCTGGAAACAACAG
1 CAGCAGGAAACAACAG
1130143 CAGCAGGAAACAACA
1 CAGCAGGAAACAACA
1130158 TGCAACAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.26, G:0.23, T:0.03
Consensus pattern (16 bp):
CAGCAGGAAACAACAG
Found at i:1132827 original size:99 final size:99
Alignment explanation
Indices: 1132628--1132953 Score: 451
Period size: 98 Copynumber: 3.3 Consensus size: 99
1132618 AATGAACAAC
*
1132628 CAACAGTAGCAACAAATTAAACAGTTTATTTAAAACTGTAAATAAAGGCAGCTAACAACCTTATA
1 CAACAGTAGCAATAAATTAAACAGTTTATTT-AAACTGTAAATAAAGGCAGCTAACAACCTTATA
* *
1132693 AAAGCAATCCGAATGAACAACAAACA-AAACAAAT
65 AAAGCAATCCGAATGAAAAACCAACACAAACAAAT
* * * *
1132727 CAATAGTAGCAATAAATTGAACAGTTTATTTAAATTGTAAATAAAGGCAGCTAACAACCTTATAG
1 CAACAGTAGCAATAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
*
1132792 AAGTAATCCGAATGAAAAACCAACACAAACAAAT
66 AAGCAATCCGAATGAAAAACCAACACAAACAAAT
* * *
1132826 CAACAGTAGCTATAAATTAAACATTTTATTTAAACTGTAAATAAA-GTAGCTAACAACCTTATAA
1 CAACAGTAGCAATAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
* *
1132890 AAGCAATCTGAATGAACAACCAACAACACAAACAAAT
66 AAGCAATCCGAATGAA-AA--ACCAACACAAACAAAT
* * *
1132927 C-ACAGTAGCTACAAATTAAACAATTTA
1 CAACAGTAGCAATAAATTAAACAGTTTA
1132954 GTTACCTTTT
Statistics
Matches: 203, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
98 85 0.42
99 78 0.38
100 24 0.12
101 16 0.08
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (99 bp):
CAACAGTAGCAATAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
AAGCAATCCGAATGAAAAACCAACACAAACAAAT
Found at i:1134179 original size:20 final size:20
Alignment explanation
Indices: 1134156--1134201 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
1134146 TCATACATCC
1134156 TAAAATT-ATGATTTAAATTT
1 TAAAATTGATGA-TTAAATTT
*
1134176 T-AAATTGATTATTAAATTT
1 TAAAATTGATGATTAAATTT
1134195 TCAAAAT
1 T-AAAAT
1134202 ACTATAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 14 0.64
20 4 0.18
21 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (20 bp):
TAAAATTGATGATTAAATTT
Found at i:1134695 original size:21 final size:21
Alignment explanation
Indices: 1134666--1134706 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1134656 CTCTCTGGTA
*
1134666 TATAGATACATGATACATGTT
1 TATACATACATGATACATGTT
*
1134687 TATACATACATGATGCATGT
1 TATACATACATGATACATGT
1134707 ACTATAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TATACATACATGATACATGTT
Found at i:1134791 original size:7 final size:7
Alignment explanation
Indices: 1134781--1134853 Score: 51
Period size: 7 Copynumber: 10.6 Consensus size: 7
1134771 TATTGTTTAT
1134781 GTTTAGG
1 GTTTAGG
1134788 GTTTAGG
1 GTTTAGG
*
1134795 GTTTATG
1 GTTTAGG
* *
1134802 ATGTAAGG
1 GT-TTAGG
*
1134810 G-TTAAG
1 GTTTAGG
1134816 GTTTAGG
1 GTTTAGG
* **
1134823 ATTTAAA
1 GTTTAGG
*
1134830 GTTTAGA
1 GTTTAGG
1134837 GTTTA-G
1 GTTTAGG
1134843 GTTTAGG
1 GTTTAGG
1134850 GTTT
1 GTTT
1134854 TTATATAATA
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
6 9 0.18
7 37 0.76
8 3 0.06
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:1134974 original size:27 final size:28
Alignment explanation
Indices: 1134936--1135010 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
1134926 TTTATATGAT
* *
1134936 TATATATATATATATATATATATATAA-
1 TATATATATATACATACATATATATAAG
*
1134963 TATATATATATACATACATGTATATAAG
1 TATATATATATACATACATATATATAAG
1134991 T-TATATATAGTTACATACAT
1 TATATATATA--TACATACAT
1135011 GTACATATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 32 0.76
28 1 0.02
29 9 0.21
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (28 bp):
TATATATATATACATACATATATATAAG
Found at i:1134986 original size:29 final size:28
Alignment explanation
Indices: 1134928--1135024 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 28
1134918 TAATTTACTT
* * * *
1134928 TATATGATTATATATATATATATATATA
1 TATATAATTATATATATACATACATGTA
1134956 TATATAATATATATATATACATACATGTA
1 TATATAAT-TATATATATACATACATGTA
*
1134985 TATA-AGTTATATATAGTTACATACATGTA
1 TATATAATTATATATA--TACATACATGTA
*
1135014 CATAT-ATTATA
1 TATATAATTATA
1135025 AGTTACATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
27 8 0.14
28 9 0.16
29 41 0.71
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (28 bp):
TATATAATTATATATATACATACATGTA
Found at i:1134999 original size:2 final size:2
Alignment explanation
Indices: 1134936--1134988 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
1134926 TTTATATGAT
*
1134936 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1134977 TA CA TG TA TA TA
1 TA TA TA TA TA TA
1134989 AGTTATATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1135076 original size:42 final size:38
Alignment explanation
Indices: 1134985--1135078 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 38
1134975 CATACATGTA
* *
1134985 TATAAGTT--ATATATAGTTACATACATGTACATATAT
1 TATAAGTTACATATATAGTTACATACATGTACACATAC
1135021 TATAAGTTACATATATAGTTTACATTACATGTATACACATAC
1 TATAAGTTACATATATAG-TTACA-TACATG--TACACATAC
1135063 TATAAGTTACATATAT
1 TATAAGTTACATATAT
1135079 TAATTGTTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
36 8 0.16
38 8 0.16
39 5 0.10
40 6 0.12
42 23 0.46
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.40
Consensus pattern (38 bp):
TATAAGTTACATATATAGTTACATACATGTACACATAC
Found at i:1135226 original size:14 final size:14
Alignment explanation
Indices: 1135190--1135228 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1135180 TTTATAAAGT
*
1135190 TAGGATTTAGGGTT
1 TAGGATTTAGGGTA
* *
1135204 TATGTTTTAGGGTA
1 TAGGATTTAGGGTA
1135218 TAGGATTTAGG
1 TAGGATTTAGG
1135229 ATTTTTATAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (14 bp):
TAGGATTTAGGGTA
Found at i:1135278 original size:17 final size:16
Alignment explanation
Indices: 1135258--1135335 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 16
1135248 TTTATTACTT
1135258 TTTATAGTTATATATAG
1 TTTATA-TTATATATAG
*
1135275 TTTATAATAATTATATAG
1 TTTAT-ATTA-TATATAG
* *
1135293 TTT-TAATATAAATAG
1 TTTATATTATATATAG
1135308 TTTATA-TATA-AT--
1 TTTATATTATATATAG
1135320 TTTATATATATATATA
1 TTTATAT-TATATATA
1135336 TATATATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
12 6 0.12
14 6 0.12
15 15 0.30
16 4 0.08
17 8 0.16
18 11 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
TTTATATTATATATAG
Found at i:1135322 original size:26 final size:26
Alignment explanation
Indices: 1135286--1135343 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1135276 TTATAATAAT
* *
1135286 TATATAGTTTTA-ATATAAATAGTTTA
1 TATATAATTTTATATATAAATA-TATA
*
1135312 TATATAATTTTATATATATATATATA
1 TATATAATTTTATATATAAATATATA
1135338 TATATA
1 TATATA
1135344 TTATTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
TATATAATTTTATATATAAATATATA
Found at i:1138768 original size:19 final size:19
Alignment explanation
Indices: 1138744--1138780 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1138734 CGGTCAAACC
1138744 GGTCAAACCGATTCAGACT
1 GGTCAAACCGATTCAGACT
*
1138763 GGTCAAACTGATTCAGAC
1 GGTCAAACCGATTCAGAC
1138781 CAGTCAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (19 bp):
GGTCAAACCGATTCAGACT
Found at i:1138786 original size:19 final size:19
Alignment explanation
Indices: 1138745--1138791 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1138735 GGTCAAACCG
* **
1138745 GTCAAACCGATTCAGACTG
1 GTCAAACTGATTCAGACCA
1138764 GTCAAACTGATTCAGACCA
1 GTCAAACTGATTCAGACCA
*
1138783 GTCAGACTG
1 GTCAAACTG
1138792 GTTTGAACTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (19 bp):
GTCAAACTGATTCAGACCA
Found at i:1150450 original size:2 final size:2
Alignment explanation
Indices: 1150438--1150466 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1150428 AGAGACATTA
1150438 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1150467 GTATGTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1153104 original size:67 final size:66
Alignment explanation
Indices: 1152694--1153287 Score: 580
Period size: 66 Copynumber: 9.0 Consensus size: 66
1152684 TCTTTAGGGA
* * * * * *
1152694 TTTATTTCAAGAGAAATTGTCTCAAGAGAGATAAAATTTTGTTTCAAGGGAAACAACCTCAATG-
1 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAAC-ATCTCAAAGA
1152758 TT
65 TT
*** * * * * * * *
1152760 TGGGTTTCAAGGGAAACTATCTTAAGAGAGAAAAAAC-TTATTTCAAG-GAAAAAAGACTCAAAG
1 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAG-AAACA-TCTCAAAG
1152823 ATT
64 ATT
* * * *
1152826 TGTATTTCAAGAGAAATTGTCTCAAGGGAGACAAAAC-TTGTTTCAAGGGAAACAATCTCAAAGA
1 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAAC-ATCTCAAAGA
1152890 TT
65 TT
** * * *
1152892 TTT-TCCCCAATAAAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACACACTCAAAG
1 TTTAT-TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACA-TCTCAAAG
*
1152956 ACT
64 ATT
* *
1152959 TTTGTTTCAAGAGAAA-TGTCTCAAGAGAGACAAAAC-TTGTTTTAAGAGAAACA-CTCAAAGAT
1 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACATCTCAAAGAT
1153021 T
66 T
* * * * *
1153022 TTTATTTCAAAAGAAATTGTCTCAAGAGAGAAAAAACTTTGTTTCAAGAGAAACATGCTTATAGA
1 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAT-CTCAAAGA
1153087 TT
65 TT
* * * * *
1153089 TTTATTTCAAAAGAAACTGTCTCAAGAGAGATAAAGCTTTGTTTTAAGGGAAACATACTCAAAGA
1 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAT-CTCAAAGA
1153154 TTT
65 -TT
* * *
1153157 TTTTTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA-TTCGTTTCAAGAGAAACGATCTCAAAGA
1 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAAC-ATCTCAAAGA
1153221 -T
65 TT
** * * * * *
1153222 GATGTTTCAAGAGAAACTGTTTCAAGAGAGACAAAA-TTTATTTCAAGGGAAACGATATCAAAGA
1 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAAC-ATCTCAAAGA
1153286 TT
65 TT
1153288 ATGTTTCAAG
Statistics
Matches: 441, Mismatches: 71, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
63 23 0.05
64 21 0.05
65 107 0.24
66 131 0.30
67 123 0.28
68 36 0.08
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (66 bp):
TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACATCTCAAAGAT
T
Found at i:1153216 original size:36 final size:34
Alignment explanation
Indices: 1153161--1153275 Score: 91
Period size: 36 Copynumber: 3.4 Consensus size: 34
1153151 AGATTTTTTT
*
1153161 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCG
1 TTTCAAGAGAAA-CGTCTCAAGAGAGACAAAATT-G
1153197 TTTCAAGAGAAACGATCTCAA-AGATG-----A-TG
1 TTTCAAGAGAAACG-TCTCAAGAGA-GACAAAATTG
* *
1153226 TTTCAAGAGAAACTGTTTCAAGAGAGACAAAATTTA
1 TTTCAAGAGAAAC-GTCTCAAGAGAGACAAAA-TTG
*
1153262 TTTCAAGGGAAACG
1 TTTCAAGAGAAACG
1153276 ATATCAAAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 23
0.70 0.04 0.25
Matches are distributed among these distances:
29 20 0.31
30 5 0.08
31 1 0.02
34 1 0.02
35 5 0.08
36 32 0.50
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (34 bp):
TTTCAAGAGAAACGTCTCAAGAGAGACAAAATTG
Found at i:1153551 original size:40 final size:37
Alignment explanation
Indices: 1153435--1153575 Score: 137
Period size: 37 Copynumber: 3.7 Consensus size: 37
1153425 CGAAGGAAAC
* *
1153435 TGTCTCAA-CTGAGACGAA-ATTTATTTTTAAGAGAAAT
1 TGTCTCAAGC-GAGAC-AAGATTTGTTTTTAAGAAAAAT
*
1153472 TGTCTCAAGCGAGACAAGATTTGGTTTT-AGAAAAAAT
1 TGTCTCAAGCGAGACAAGATTTGTTTTTAAG-AAAAAT
1153509 TGTCTCAAGCGAGACATA-ATTTGTTTTTTTTAAGAAAAAT
1 TGTCTCAAGCGAGACA-AGATTTG---TTTTTAAGAAAAAT
* *
1153549 TGTCTCTAGCGAGACAACACTTTGTTT
1 TGTCTCAAGCGAGACAAGA-TTTGTTT
1153576 CGAGAGAAAC
Statistics
Matches: 89, Mismatches: 5, Indels: 19
0.79 0.04 0.17
Matches are distributed among these distances:
36 4 0.04
37 47 0.53
38 5 0.06
39 1 0.01
40 26 0.29
41 6 0.07
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (37 bp):
TGTCTCAAGCGAGACAAGATTTGTTTTTAAGAAAAAT
Found at i:1154808 original size:13 final size:12
Alignment explanation
Indices: 1154762--1154805 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1154752 TATTATTTTC
1154762 TTTTTTTTTTGT
1 TTTTTTTTTTGT
*
1154774 TCTTTTTTGTTGT
1 T-TTTTTTTTTGT
* *
1154787 TGTTTTCTTTGT
1 TTTTTTTTTTGT
1154799 TTTTTTT
1 TTTTTTT
1154806 CTTCATTGCT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTGT
Found at i:1158910 original size:23 final size:23
Alignment explanation
Indices: 1158880--1158947 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1158870 GAGTCGAGGG
*
1158880 TTCTACGTGGTCCTTC-AGGACAA
1 TTCTACGTGGTCATTCGA-GACAA
*
1158903 TTCTACGTGGTCATTCGAGACAT
1 TTCTACGTGGTCATTCGAGACAA
** *
1158926 TTCTACACGGTCATTCGGGACA
1 TTCTACGTGGTCATTCGAGACA
1158948 TATATGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (23 bp):
TTCTACGTGGTCATTCGAGACAA
Found at i:1159542 original size:17 final size:17
Alignment explanation
Indices: 1159522--1159574 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1159512 TTTAGGGAAG
1159522 TAGTTCATTAATTAAAT
1 TAGTTCATTAATTAAAT
* * * *
1159539 TAGTTGATTCATCAAAC
1 TAGTTCATTAATTAAAT
*
1159556 TAGTTCATTTATTAAAT
1 TAGTTCATTAATTAAAT
1159573 TA
1 TA
1159575 ACTCTTAATT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (17 bp):
TAGTTCATTAATTAAAT
Found at i:1167481 original size:55 final size:55
Alignment explanation
Indices: 1167429--1167918 Score: 602
Period size: 55 Copynumber: 9.1 Consensus size: 55
1167419 ATTTTCAAAT
* * * *
1167429 AACGGGTCTGCTCCCTATTCTTTTA-AGGAGTATA-AGACTCGAACAATCTTCA-ACA
1 AACGGGTCCGCTCTCTATTCCTTCAGA-GAGTATAGA-ACTCGAACAATCTTCATA-A
*
1167484 AACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA-AGACTCG----ATCTTCA-ATA
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATA-A
** * * *
1167535 AACGTTTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCGAACAATCTTCA-ACA
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-A
* * * *
1167590 AACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAATAATCTTCATAA
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
* **
1167645 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCG----ATCTTCAGCA
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
*
1167696 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGA
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
**
1167751 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCG----ATCTTCAGCA
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
1167802 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
*
1167857 AACGGGTCCGCTCTCTATTCCTTTAGAGAGTATAGAACTCGAACAATCTTCATAA
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
*
1167912 AATGGGT
1 AACGGGT
1167919 TTGCTTTACT
Statistics
Matches: 390, Mismatches: 30, Indels: 30
0.87 0.07 0.07
Matches are distributed among these distances:
51 142 0.36
55 246 0.63
56 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (55 bp):
AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
Found at i:1167555 original size:106 final size:107
Alignment explanation
Indices: 1167429--1167908 Score: 567
Period size: 106 Copynumber: 4.5 Consensus size: 107
1167419 ATTTTCAAAT
* * *
1167429 AACGGGTCTGCTCCCTATTCTTTTA-AGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCC
1 AACGGGTCCGCTCTCTATTCTTTCAGA-GAGTATAAGACTCGAACAATCTTCAACAAACGGGTCC
1167493 GCTCCCTATTCCTTCAGAGAGTATA-AGACTCG-ATCTTCA-ATA
65 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAATCTTCATA-A
** * *
1167535 AACGTTTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCG
1 AACGGGTCCGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCG
* *
1167600 CTCCCTATTCGTTCAGGGAGTATAGAACTCGAATAATCTTCATAA
66 CTCCCTATTCCTTCAGAGAGTATAGAACTCG---AATCTTCATAA
* * *
1167645 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCG----ATCTTCAGCAAACGGGTCCG
1 AACGGGTCCGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCG
* *
1167706 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGA
66 CTCCCTATTCCTTCAGAGAGTATAGAACTCG---AATCTTCATAA
* *
1167751 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCG----ATCTTCAGCAAACGGGTCC
1 AACGGGTCCGCTCTCTATTCTTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCC
*
1167811 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
65 GCTCCCTATTCCTTCAGAGAGTATAGAACTCG---AATCTTCATAA
1167857 AACGGGTCCGCTCTCTATTCCTTT-AGAGAGTAT-AGAACTCGAACAATCTTCA
1 AACGGGTCCGCTCTCTATT-CTTTCAGAGAGTATAAG-ACTCGAACAATCTTCA
1167909 TAAAATGGGT
Statistics
Matches: 341, Mismatches: 20, Indels: 22
0.89 0.05 0.06
Matches are distributed among these distances:
105 1 0.00
106 282 0.83
107 5 0.01
110 52 0.15
111 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (107 bp):
AACGGGTCCGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCG
CTCCCTATTCCTTCAGAGAGTATAGAACTCGAATCTTCATAA
Found at i:1167708 original size:161 final size:159
Alignment explanation
Indices: 1167429--1167908 Score: 628
Period size: 161 Copynumber: 3.0 Consensus size: 159
1167419 ATTTTCAAAT
* * * *
1167429 AACGGGTCTGCTCCCTATTCTTTTAAGGAGTATA-AGACTCGAACAATCTTCAACAAACGGGTCC
1 AACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAGA-ACTCGAA-AATCTTCAA-AAACGGGTCC
* * * ** *
1167493 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTTTCCGCTCCCTATTCTTT
63 GCTCTCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAAAAAACGGGTCCGCTCTCTATTCTTT
*
1167558 CAGAGAGTATAGGACTCGAACAATCTTCAACA
128 CAGAGAGTATAGAACTCGAACAATCTTCAACA
*
1167590 AACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAATAATCTTCATAAAACGGGTCCG
1 AACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAA-AATCTTCA-AAAACGGGTCCG
** *
1167655 CTCTCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAGCAAACGGGTCCGCTCTCTATTCCTTC
64 CTCTCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAAAAAACGGGTCCGCTCTCTATTCTTTC
**
1167720 AGAGAGTATAGAACTCGAACAATCTTCATGA
129 AGAGAGTATAGAACTCGAACAATCTTCAACA
* * *
1167751 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCG---ATCTTCAGCAAACGGGTCCGC
1 AACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAAAATCTTCA-AAAACGGGTCCGC
* *
1167813 TCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCC
65 TCTCTATTCCTTCAGAGAGTATAGGACTCG----ATCTTCAAAAAACGGGTCCGCTCTCTATT-C
1167878 TTT-AGAGAGTATAGAACTCGAACAATCTTCA
125 TTTCAGAGAGTATAGAACTCGAACAATCTTCA
1167909 TAAAATGGGT
Statistics
Matches: 287, Mismatches: 25, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
157 48 0.17
161 234 0.82
162 5 0.02
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (159 bp):
AACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAAAATCTTCAAAAACGGGTCCGCT
CTCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAAAAAACGGGTCCGCTCTCTATTCTTTCAG
AGAGTATAGAACTCGAACAATCTTCAACA
Found at i:1167972 original size:37 final size:37
Alignment explanation
Indices: 1167918--1168000 Score: 123
Period size: 37 Copynumber: 2.2 Consensus size: 37
1167908 ATAAAATGGG
* *
1167918 TTTGCTTTACTATTCTTCCGTGAAGGCTTATAGA-TGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTA-AGATTGA
1167955 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
*
1167992 TTTGTTTCA
1 TTTGCTTCA
1168001 AAGATCCAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
36 3 0.07
37 39 0.93
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (37 bp):
TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
Found at i:1169144 original size:7 final size:7
Alignment explanation
Indices: 1169128--1169192 Score: 53
Period size: 7 Copynumber: 9.0 Consensus size: 7
1169118 TCTCCTTTTA
1169128 TTTC-TT
1 TTTCTTT
1169134 TTTCTTT
1 TTTCTTT
1169141 TTTCTTCTT
1 TTTC-T-TT
*
1169150 TTTCATT
1 TTTCTTT
*
1169157 TTTATTT
1 TTTCTTT
*
1169164 TCTCTTT
1 TTTCTTT
1169171 TTAT-TTT
1 TT-TCTTT
1169178 TTTCTTTT
1 TTTC-TTT
1169186 TTTCTTT
1 TTTCTTT
1169193 CACCATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
6 5 0.11
7 27 0.57
8 9 0.19
9 6 0.13
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTCTTT
Found at i:1169148 original size:16 final size:16
Alignment explanation
Indices: 1169129--1169192 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 16
1169119 CTCCTTTTAT
1169129 TTCTTTTTCTTTTTTC
1 TTCTTTTTCTTTTTTC
*
1169145 TTCTTTTTCATTTTTATTT
1 TTCTTTTTC--TTTT-TTC
*
1169164 TCTCTTTTTATTTTTTTC
1 T-TCTTTTT-CTTTTTTC
1169182 TT-TTTTTCTTT
1 TTCTTTTTCTTT
1169193 CACCATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
15 3 0.08
16 14 0.36
17 1 0.03
18 7 0.18
19 7 0.18
20 7 0.18
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (16 bp):
TTCTTTTTCTTTTTTC
Found at i:1169179 original size:20 final size:21
Alignment explanation
Indices: 1169140--1169178 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1169130 TCTTTTTCTT
1169140 TTTTCTTCTTTTTCATTTTTA
1 TTTTCTTCTTTTTCATTTTTA
1169161 TTTTC-TCTTTTT-ATTTTT
1 TTTTCTTCTTTTTCATTTTT
1169179 TTCTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTCTTCTTTTTCATTTTTA
Found at i:1169183 original size:34 final size:33
Alignment explanation
Indices: 1169123--1169186 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
1169113 TGAACTCTCC
1169123 TTTTATTTCTTTTTCTTTTTTCTTCTTTTTCAT
1 TTTTATTTCTTTTTCTTTTTTCTTCTTTTTCAT
1169156 TTTTATTTTCTCTTTT-TATTTTT-TTCTTTTT
1 TTTTA-TTTCT-TTTTCT-TTTTTCTTCTTTTT
1169187 TTCTTTCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
33 5 0.18
34 14 0.50
35 9 0.32
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (33 bp):
TTTTATTTCTTTTTCTTTTTTCTTCTTTTTCAT
Found at i:1169193 original size:28 final size:30
Alignment explanation
Indices: 1169122--1169193 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 30
1169112 TTGAACTCTC
* *
1169122 CTTTTATTTCTTTTTCTTTTTTCTTCTTTTT
1 CTTTT-TTTCTTTCTCTTTTTTATTCTTTTT
*
1169153 CATTTTTAT-TTTCTC-TTTTTATT-TTTTT
1 C-TTTTTTTCTTTCTCTTTTTTATTCTTTTT
1169181 CTTTTTTTCTTTC
1 CTTTTTTTCTTTC
1169194 ACCATTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
27 6 0.17
28 10 0.29
29 7 0.20
30 5 0.14
31 3 0.09
32 4 0.11
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (30 bp):
CTTTTTTTCTTTCTCTTTTTTATTCTTTTT
Found at i:1169228 original size:27 final size:27
Alignment explanation
Indices: 1169196--1169249 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
1169186 TTTCTTTCAC
1169196 CATTTTTCTAAT-TTTTTT-CATTTTTT
1 CATTTTTC-AATCTTTTTTCCATTTTTT
*
1169222 CATTTTTCATTCTTTTTTCCATTTTTT
1 CATTTTTCAATCTTTTTTCCATTTTTT
1169249 C
1 C
1169250 TTCAAGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 14 0.56
27 9 0.36
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (27 bp):
CATTTTTCAATCTTTTTTCCATTTTTT
Found at i:1183263 original size:23 final size:23
Alignment explanation
Indices: 1183222--1183295 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
1183212 TCCAGACCCT
* * *
1183222 GTGGGGGTATCGATT-CCCTCTA
1 GTGGGGGAATCGGTTCCCCTCAA
1183244 GTGGGGGAATCGGTTCCCCTTCAA
1 GTGGGGGAATCGGTTCCCC-TCAA
* *
1183268 AT-GGGGAATCAGTTCCCCTTCAA
1 GTGGGGGAATCGGTTCCCC-TCAA
1183291 G-GGGG
1 GTGGGG
1183296 TATCGATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 13 0.30
23 26 0.60
24 4 0.09
ACGTcount: A:0.18, C:0.23, G:0.34, T:0.26
Consensus pattern (23 bp):
GTGGGGGAATCGGTTCCCCTCAA
Found at i:1183305 original size:22 final size:23
Alignment explanation
Indices: 1183246--1183305 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1183236 TCCCTCTAGT
*
1183246 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTCAAA
*
1183269 TGGGGAATC-AGTTCCCCTTC-AA
1 GGGGGAATCGA-TTCCCCTTCAAA
*
1183291 GGGGGTATCGATTCC
1 GGGGGAATCGATTCC
1183306 TCCTGCACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (23 bp):
GGGGGAATCGATTCCCCTTCAAA
Found at i:1189439 original size:55 final size:55
Alignment explanation
Indices: 1189325--1189591 Score: 344
Period size: 55 Copynumber: 4.9 Consensus size: 55
1189315 TTATACGGAA
* * * *
1189325 ATTCATCAACTCATGATGAATT-TCGTGG-TTT--ACACACAGTGCTTGTACGGTG
1 ATTCATCAACCCATGATGAATTCT-GTGGATTTGCACACAAAGTACCTGTACGGTG
* *
1189377 ATTCATCAACTCATGATGAATTCTGTGGATTTGCACACAAAGTTCCTGTACGGTG
1 ATTCATCAACCCATGATGAATTCTGTGGATTTGCACACAAAGTACCTGTACGGTG
* ** * *
1189432 ATTCATCAACCTATGATGAATTCCATGGATTTGCACACAAAGTTCTTGTACGGTG
1 ATTCATCAACCCATGATGAATTCTGTGGATTTGCACACAAAGTACCTGTACGGTG
* * * *
1189487 ATTCATCAACCCATGTTGAATTCTGTGGATTTTCACACGAAGTACCTGTATGGTG
1 ATTCATCAACCCATGATGAATTCTGTGGATTTGCACACAAAGTACCTGTACGGTG
* *
1189542 ATTCATCAACCCATGATGAATTCCGTGGATATGCACACAAAGTACCTGTA
1 ATTCATCAACCCATGATGAATTCTGTGGATTTGCACACAAAGTACCTGTA
1189592 GTACACATAG
Statistics
Matches: 189, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
52 26 0.14
53 4 0.02
55 159 0.84
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (55 bp):
ATTCATCAACCCATGATGAATTCTGTGGATTTGCACACAAAGTACCTGTACGGTG
Found at i:1190035 original size:20 final size:20
Alignment explanation
Indices: 1190010--1190065 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
1190000 TGATGTTGAC
*
1190010 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCATACCA
*
1190030 TGGTATCGATACTACCATACTA
1 TGGTATCGATAC--CCATACCA
*
1190052 TGGTACCGATACCC
1 TGGTATCGATACCC
1190066 CCTTCCAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
TGGTATCGATACCCATACCA
Found at i:1190100 original size:95 final size:95
Alignment explanation
Indices: 1189937--1190140 Score: 302
Period size: 95 Copynumber: 2.1 Consensus size: 95
1189927 CTACTACCCT
* * * * ** * *
1189937 GTATCAATACTTCTATATTATGGTACCGATACCCCCTTCTGGTATCGATACCAAAATTAGGTTTG
1 GTATCGATACTACCATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTAGATTCG
1190002 ATGTTGAC-TGGTATCGATACCCTTACCATG
66 ATGTTG-CTTGGTATCGATACCCTTACCATG
1190032 GTATCGATACTACCATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTAGATTCG
1 GTATCGATACTACCATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTAGATTCG
*
1190097 ATGTTGCTTGGTATCGATACCCTTATCATG
66 ATGTTGCTTGGTATCGATACCCTTACCATG
*
1190127 GTATCGATAGTACC
1 GTATCGATACTACC
1190141 TCATCGGTAT
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 1 0.01
95 97 0.99
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (95 bp):
GTATCGATACTACCATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTAGATTCG
ATGTTGCTTGGTATCGATACCCTTACCATG
Found at i:1193317 original size:11 final size:10
Alignment explanation
Indices: 1193301--1193333 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
1193291 CACAACTTCA
1193301 TTTTTTCAATT
1 TTTTTTC-ATT
1193312 TTTTTTCA-T
1 TTTTTTCATT
1193321 TTTTTTCATT
1 TTTTTTCATT
1193331 TTT
1 TTT
1193334 AGTGGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 5 0.24
11 7 0.33
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:1199118 original size:17 final size:17
Alignment explanation
Indices: 1199098--1199137 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1199088 TTTAGGGAAG
*
1199098 TAGTTCATTAATTAAAC
1 TAGTTCATTAATCAAAC
*
1199115 TAGTTCATTCATCAAAC
1 TAGTTCATTAATCAAAC
1199132 TAGTTC
1 TAGTTC
1199138 GTTTACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:1208659 original size:34 final size:34
Alignment explanation
Indices: 1208621--1208688 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1208611 TTGATGTGTC
1208621 CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
1 CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
1208655 CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
1 CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
1208689 TTTTTATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (34 bp):
CTTGAACTGAAGGCATGATGTTGATGCTGCCATA
Found at i:1222006 original size:30 final size:30
Alignment explanation
Indices: 1221971--1222059 Score: 133
Period size: 30 Copynumber: 3.0 Consensus size: 30
1221961 CACAGTCCAG
*
1221971 GACTTAGTTCAATCACCACCAATCAAATTA
1 GACTTAGTTCCATCACCACCAATCAAATTA
*
1222001 GACTTAGTTCCATCACCACCAATCAAAGTA
1 GACTTAGTTCCATCACCACCAATCAAATTA
* * *
1222031 GAGTTAGATCCATCACCGCCAATCAAATT
1 GACTTAGTTCCATCACCACCAATCAAATT
1222060 GGATTCTCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.37, C:0.28, G:0.10, T:0.25
Consensus pattern (30 bp):
GACTTAGTTCCATCACCACCAATCAAATTA
Found at i:1231285 original size:23 final size:23
Alignment explanation
Indices: 1231255--1231303 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1231245 TGGTGGTTGG
*
1231255 TTTAATGA-ATGTTTAGACTTTAT
1 TTTAATGATATATTT-GACTTTAT
*
1231278 TTTAATGATATATTTGAGTTTAT
1 TTTAATGATATATTTGACTTTAT
1231301 TTT
1 TTT
1231304 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGATATATTTGACTTTAT
Found at i:1237738 original size:12 final size:12
Alignment explanation
Indices: 1237721--1237756 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1237711 TATCATGTTC
1237721 TCATATCACATG
1 TCATATCACATG
*
1237733 TCATATCACATA
1 TCATATCACATG
1237745 TCATATCACATG
1 TCATATCACATG
1237757 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:1238759 original size:3 final size:3
Alignment explanation
Indices: 1238746--1238793 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
1238736 CACGCACAAG
1238746 GAA GAAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1238792 GA
1 GA
1238794 GAGCTCTGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1239475 original size:35 final size:35
Alignment explanation
Indices: 1239425--1239494 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
1239415 ATTTTCCTTT
*
1239425 ACGTCCAAACCTCAATACTTTCTTACACGGAGACA
1 ACGTCCAAACATCAATACTTTCTTACACGGAGACA
1239460 ACGTCCAAACATCAATACTTTCTTACACGGAGACA
1 ACGTCCAAACATCAATACTTTCTTACACGGAGACA
1239495 CTTTCAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (35 bp):
ACGTCCAAACATCAATACTTTCTTACACGGAGACA
Found at i:1244119 original size:15 final size:15
Alignment explanation
Indices: 1244096--1244129 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1244086 CCGTAGGACC
*
1244096 ACTATATCCCGAAGG
1 ACTACATCCCGAAGG
*
1244111 ACTACATCCCGAATG
1 ACTACATCCCGAAGG
1244126 ACTA
1 ACTA
1244130 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1244278 original size:23 final size:26
Alignment explanation
Indices: 1244241--1244309 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
1244231 TTCTCTTGTG
1244241 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
1244265 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
1244290 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
1244310 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:1244291 original size:12 final size:12
Alignment explanation
Indices: 1244274--1244309 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1244264 TATCATGTTC
1244274 TCATATCACATG
1 TCATATCACATG
*
1244286 TCATATCACATA
1 TCATATCACATG
1244298 TCATATCACATG
1 TCATATCACATG
1244310 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:1251537 original size:12 final size:12
Alignment explanation
Indices: 1251520--1251544 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1251510 TATCATGTTC
1251520 TCATATCACATA
1 TCATATCACATA
1251532 TCATATCACATA
1 TCATATCACATA
1251544 T
1 T
1251545 ATCACATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1260517 original size:26 final size:26
Alignment explanation
Indices: 1260483--1260534 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1260473 ACATGGTGAA
1260483 GAAGGTTAGGATTCGTATGTTTGAGT
1 GAAGGTTAGGATTCGTATGTTTGAGT
1260509 GAAGGTTAGGATTCGTATGTTTGAGT
1 GAAGGTTAGGATTCGTATGTTTGAGT
1260535 AAAGCTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.04, G:0.35, T:0.38
Consensus pattern (26 bp):
GAAGGTTAGGATTCGTATGTTTGAGT
Found at i:1260545 original size:26 final size:26
Alignment explanation
Indices: 1260490--1260547 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
1260480 GAAGAAGGTT
* * *
1260490 AGGATTCGTATGTTTGAGTGAAGGTT
1 AGGATTCGTATGTTTGAGTAAAGCTA
1260516 AGGATTCGTATGTTTGAGTAAAGCTA
1 AGGATTCGTATGTTTGAGTAAAGCTA
1260542 AGGATT
1 AGGATT
1260548 GATAAAAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.36
Consensus pattern (26 bp):
AGGATTCGTATGTTTGAGTAAAGCTA
Found at i:1261650 original size:201 final size:201
Alignment explanation
Indices: 1261305--1261702 Score: 778
Period size: 201 Copynumber: 2.0 Consensus size: 201
1261295 ATATGTGAAC
*
1261305 ATTAAAGAAAAGATATGATATGTGTATAAGAAGATTTTGATTTTGAAGGAATGAAAAAAATAAAG
1 ATTAAAGAAAAGATATGATATGTGTATAAAAAGATTTTGATTTTGAAGGAATGAAAAAAATAAAG
1261370 GGATAGGAAAAGTCAAAGATGGAGTTTAAAAGATCAAGTATGACAAGAGGTATATTGAGATATAA
66 GGATAGGAAAAGTCAAAGATGGAGTTTAAAAGATCAAGTATGACAAGAGGTATATTGAGATATAA
*
1261435 GTTATAAGTTTGATATTGAAATGATACAATTTTCAATTATTAAAAGAACGAGAATGAATGATTAT
131 GTTATAAGTTTGATAATGAAATGATACAATTTTCAATTATTAAAAGAACGAGAATGAATGATTAT
1261500 TCAATT
196 TCAATT
1261506 ATTAAAGAAAAGATATGATATGTGTATAAAAAGATTTTGATTTTGAAGGAATGAAAAAAATAAAG
1 ATTAAAGAAAAGATATGATATGTGTATAAAAAGATTTTGATTTTGAAGGAATGAAAAAAATAAAG
1261571 GGATAGGAAAAGTCAAAGATGGAGTTTAAAAGATCAAGTATGACAAGAGGTATATTGAGATATAA
66 GGATAGGAAAAGTCAAAGATGGAGTTTAAAAGATCAAGTATGACAAGAGGTATATTGAGATATAA
1261636 GTTATAAGTTTGATAATGAAATGATACAATTTTCAATTATTAAAAGAACGAGAATGAATGATTAT
131 GTTATAAGTTTGATAATGAAATGATACAATTTTCAATTATTAAAAGAACGAGAATGAATGATTAT
1261701 TC
196 TC
1261703 TTTGAACAAA
Statistics
Matches: 195, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
201 195 1.00
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.30
Consensus pattern (201 bp):
ATTAAAGAAAAGATATGATATGTGTATAAAAAGATTTTGATTTTGAAGGAATGAAAAAAATAAAG
GGATAGGAAAAGTCAAAGATGGAGTTTAAAAGATCAAGTATGACAAGAGGTATATTGAGATATAA
GTTATAAGTTTGATAATGAAATGATACAATTTTCAATTATTAAAAGAACGAGAATGAATGATTAT
TCAATT
Found at i:1262919 original size:19 final size:19
Alignment explanation
Indices: 1262895--1262963 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
1262885 ATTTGTGTAC
*
1262895 CGATGCACAGGTAGTGCAT
1 CGATGCACAGATAGTGCAT
*
1262914 CGATGCACACGTTAAGGATGCAT
1 CGATGCACA-GAT-A-G-TGCAT
* *
1262937 CGATACACTGTATAGTGCAT
1 CGATGCACAG-ATAGTGCAT
1262957 CGATGCA
1 CGATGCA
1262964 TACATTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 9 0.22
20 13 0.32
21 2 0.05
22 3 0.08
23 13 0.32
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (19 bp):
CGATGCACAGATAGTGCAT
Found at i:1263257 original size:19 final size:19
Alignment explanation
Indices: 1263244--1263293 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
1263234 ATGTGGTTGT
1263244 TATGATTATATGTGTTATA
1 TATGATTATATGTGTTATA
* * *
1263263 TGTGATTATATGTATTACA
1 TATGATTATATGTGTTATA
*
1263282 T-TAATTATATGT
1 TATGATTATATGT
1263294 ATGCATGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (19 bp):
TATGATTATATGTGTTATA
Found at i:1263263 original size:9 final size:10
Alignment explanation
Indices: 1263246--1263293 Score: 57
Period size: 9 Copynumber: 5.1 Consensus size: 10
1263236 GTGGTTGTTA
1263246 TGATTATATG
1 TGATTATATG
1263256 TG-TTATATG
1 TGATTATATG
1263265 TGATTATATG
1 TGATTATATG
*
1263275 T-ATTACAT-
1 TGATTATATG
*
1263283 TAATTATATG
1 TGATTATATG
1263293 T
1 T
1263294 ATGCATGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 1 0.03
9 21 0.64
10 11 0.33
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (10 bp):
TGATTATATG
Found at i:1264647 original size:23 final size:23
Alignment explanation
Indices: 1264615--1264680 Score: 98
Period size: 22 Copynumber: 2.9 Consensus size: 23
1264605 ACCTTATATA
1264615 GCACTTCGGTGCATTTCTACGTG
1 GCACTTCGGTGCATTTCTACGTG
* *
1264638 GCACTACGGTGCAATTCTAC-TG
1 GCACTTCGGTGCATTTCTACGTG
*
1264660 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTTCTACG
1264681 CTGTGGTGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGTG
Found at i:1264664 original size:22 final size:23
Alignment explanation
Indices: 1264615--1264672 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
1264605 ACCTTATATA
*
1264615 GCACTTCGGTGCATTTCTACGTG
1 GCACTTCGGTGCAATTCTACGTG
*
1264638 GCACTACGGTGCAATTCTAC-TG
1 GCACTTCGGTGCAATTCTACGTG
1264660 GCACTTCGGTGCA
1 GCACTTCGGTGCA
1264673 TTTATACGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGTG
Found at i:1272259 original size:25 final size:25
Alignment explanation
Indices: 1272229--1272276 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
1272219 AGTTCAAAAC
1272229 ATAGCGATTTTGGTCCTTATATAAA
1 ATAGCGATTTTGGTCCTTATATAAA
1272254 ATAGCGATTTTGGTCCTTATATA
1 ATAGCGATTTTGGTCCTTATATA
1272277 TCGGTCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (25 bp):
ATAGCGATTTTGGTCCTTATATAAA
Found at i:1285880 original size:24 final size:23
Alignment explanation
Indices: 1285848--1285894 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
1285838 AGAATTTTCC
1285848 AAAAAAAAT-TTAAATTTTCGAAAT
1 AAAAAAAATGTT-AATTTTC-AAAT
1285872 AAAAAAAATGTTAATTTTCAAAT
1 AAAAAAAATGTTAATTTTCAAAT
1285895 TATTGTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
24 16 0.73
25 2 0.09
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (23 bp):
AAAAAAAATGTTAATTTTCAAAT
Found at i:1288925 original size:10 final size:10
Alignment explanation
Indices: 1288910--1288973 Score: 74
Period size: 10 Copynumber: 6.1 Consensus size: 10
1288900 CATTTAAATG
1288910 ATAAACGAAC
1 ATAAACGAAC
1288920 ATAAACGAAC
1 ATAAACGAAC
*
1288930 CTAAACGAAC
1 ATAAACGAAC
*
1288940 GTAAACGAAC
1 ATAAACGAAC
*
1288950 ATAATAAATGAAC
1 ---ATAAACGAAC
1288963 ATAAACGAAC
1 ATAAACGAAC
1288973 A
1 A
1288974 ACAAAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
10 38 0.83
13 8 0.17
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1289233 original size:10 final size:10
Alignment explanation
Indices: 1289218--1289276 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 10
1289208 TGCCATCTGT
1289218 TGAACATAAA
1 TGAACATAAA
*
1289228 TGAACAACAAA
1 TGAAC-ATAAA
1289239 TGAA-ATAAA
1 TGAACATAAA
1289248 TGAACGAACATAAA
1 T----GAACATAAA
1289262 TGAACATAAA
1 TGAACATAAA
1289272 TGAAC
1 TGAAC
1289277 GATGAACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
9 5 0.12
10 19 0.46
11 8 0.20
13 3 0.07
14 6 0.15
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17
Consensus pattern (10 bp):
TGAACATAAA
Found at i:1289256 original size:24 final size:24
Alignment explanation
Indices: 1289218--1289278 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
1289208 TGCCATCTGT
1289218 TGAACATAAATGAAC--A-ACAAA
1 TGAACATAAATGAACGAACACAAA
*
1289239 TGAA-ATAAATGAACGAACATAAA
1 TGAACATAAATGAACGAACACAAA
1289262 TGAACATAAATGAACGA
1 TGAACATAAATGAACGA
1289279 TGAACATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
20 10 0.29
21 4 0.11
22 1 0.03
23 8 0.23
24 12 0.34
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.16
Consensus pattern (24 bp):
TGAACATAAATGAACGAACACAAA
Found at i:1289283 original size:17 final size:18
Alignment explanation
Indices: 1289261--1289295 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1289251 ACGAACATAA
1289261 ATGAACATAAAT-GAACG
1 ATGAACATAAATCGAACG
1289278 ATGAACATAAATCGAACG
1 ATGAACATAAATCGAACG
1289296 TTCACGAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.17
Consensus pattern (18 bp):
ATGAACATAAATCGAACG
Found at i:1291889 original size:32 final size:31
Alignment explanation
Indices: 1291843--1291935 Score: 116
Period size: 32 Copynumber: 3.0 Consensus size: 31
1291833 GCTTAAGAGT
* * * *
1291843 TGATGTGTACATGTCATGTCGTCACCTTGGG
1 TGATGTGCACATGTCACGTCATCATCTTGGG
*
1291874 TGATGTGGCACATGTCACGTCATCATTTTGGG
1 TGATGT-GCACATGTCACGTCATCATCTTGGG
1291906 TGATGTAGCA-ATGTCACGTCATCATCTTGG
1 TGATGT-GCACATGTCACGTCATCATCTTGG
1291936 AGGTCAAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 25 0.46
32 29 0.54
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (31 bp):
TGATGTGCACATGTCACGTCATCATCTTGGG
Found at i:1292048 original size:32 final size:32
Alignment explanation
Indices: 1292012--1292124 Score: 147
Period size: 32 Copynumber: 3.6 Consensus size: 32
1292002 GCTTAAGAGT
* * * *
1292012 TGATGTGTCACATGTCATGTCGTCACCTTGGG
1 TGATGTGGCACATGTCACGTCATCATCTTGGG
*
1292044 TGATGTGGCACATGTCACGTCATCATTTTGGG
1 TGATGTGGCACATGTCACGTCATCATCTTGGG
*
1292076 TGATGTAGCACATGTCACGTCATCATCTT-GG
1 TGATGTGGCACATGTCACGTCATCATCTTGGG
**
1292107 TGACATGGCACATGTCAC
1 TGATGTGGCACATGTCAC
1292125 TTTATTACAT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
31 17 0.24
32 54 0.76
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (32 bp):
TGATGTGGCACATGTCACGTCATCATCTTGGG
Found at i:1292138 original size:63 final size:64
Alignment explanation
Indices: 1292012--1292190 Score: 159
Period size: 63 Copynumber: 2.8 Consensus size: 64
1292002 GCTTAAGAGT
* * ** **
1292012 TGATGTGTCACATGTCATGTCGTCACCTTGGGTGATGTGGCACATGTCACGTCATCATTTTGGG
1 TGATGTGTCACATGTCACGTCATCACCTTGGGTGACATGGCACATGTCACGTCATCACATTGGG
* * * *
1292076 TGATGTAG-CACATGTCACGTCATCATCTT-GGTGACATGGCACATGTCACTTTATTACATTGGG
1 TGATGT-GTCACATGTCACGTCATCACCTTGGGTGACATGGCACATGTCACGTCATCACATTGGG
* ** * * * * *
1292139 TGACGTG--ATGTGACACATTATCACCTTGGGTGACATGGCACAAGTCATGTCA
1 TGATGTGTCACATGTCACGTCATCACCTTGGGTGACATGGCACATGTCACGTCA
1292191 GTAACATATG
Statistics
Matches: 92, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
61 14 0.15
62 21 0.23
63 32 0.35
64 24 0.26
65 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (64 bp):
TGATGTGTCACATGTCACGTCATCACCTTGGGTGACATGGCACATGTCACGTCATCACATTGGG
Found at i:1295645 original size:23 final size:23
Alignment explanation
Indices: 1295619--1295663 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1295609 CATTGAAATA
1295619 TTTT-AATTTCTTTTTTTGGATTT
1 TTTTGAATTTC-TTTTTTGGATTT
**
1295642 TTTTGGGTTTCTTTTTTGGATT
1 TTTTGAATTTCTTTTTTGGATT
1295664 CAACTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.09, C:0.04, G:0.16, T:0.71
Consensus pattern (23 bp):
TTTTGAATTTCTTTTTTGGATTT
Found at i:1310189 original size:20 final size:20
Alignment explanation
Indices: 1310160--1310215 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1310150 ATTTGCGTTG
*
1310160 CATTTTGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTT
*
1310180 CATTTCGCGTTACGATTTTT
1 CATTTCGCGTTGCGATTTTT
* *
1310200 CAGTTCGTGTTGCGAT
1 CATTTCGCGTTGCGAT
1310216 AGTTTAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.48
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTT
Found at i:1310869 original size:6 final size:6
Alignment explanation
Indices: 1310860--1310886 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1310850 GTCCGTCTCA
1310860 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1310887 AGTATGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1311064 original size:41 final size:41
Alignment explanation
Indices: 1311019--1311112 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
1311009 ACAACTGTAG
*
1311019 ACTATCGCAACGCGAAATGGAAAATCACGGTGCGATTTTTA
1 ACTATCGCAACGCGAAATGGAAAATCACGGTGCGATTTTCA
* *
1311060 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCACGGTGCGATTTTCA
1311101 ACTATCGCAACG
1 ACTATCGCAACG
1311113 TGAATTTGCG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.23
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCACGGTGCGATTTTCA
Found at i:1315661 original size:2 final size:2
Alignment explanation
Indices: 1315654--1315698 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1315644 ACTTATATGT
*
1315654 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1315695 TA TA
1 TA TA
1315699 CATTTTGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1315765 original size:25 final size:25
Alignment explanation
Indices: 1315708--1315769 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
1315698 ACATTTTGTA
* *
1315708 TTTTA-TCTTATTATTTTCTTTACT
1 TTTTATTCTTATTATTATCTTCACT
*
1315732 TTTTTTTCTTATTATTATCTTCA-T
1 TTTTATTCTTATTATTATCTTCACT
1315756 TATTTATTC-TATTA
1 T-TTTATTCTTATTA
1315770 CTATTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 11 0.34
25 21 0.66
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATTCTTATTATTATCTTCACT
Found at i:1315855 original size:133 final size:126
Alignment explanation
Indices: 1315741--1316002 Score: 348
Period size: 126 Copynumber: 2.0 Consensus size: 126
1315731 TTTTTTTTCT
* *
1315741 TATTA-TTATCTTCATT-ATTTATTCTATTACTATTATATAGATTTTTTCCTCCCTCTCATATTT
1 TATTATTTATATTCATTAATTT-TTCCATTACTATTATAT--ATTTTTTCCTCCCTCTCATA-TT
* *
1315804 AGTTATTATATATATGGTATTAATATTATTATATGTTTTTATTAACTTTATTTATTTTACTTTAT
62 AGCTATCAT-TATATGGT-TTAATATTA-TATATG-TTTTATTAACTTTATTTATTTTACTTTAT
1315869 ACGC
123 ACGC
** *
1315873 TATTATTTATATTTTTTAATTTTTCCATTATTATTATATATTTTTTCCTCCCTCTCATATTAGCT
1 TATTATTTATATTCATTAATTTTTCCATTACTATTATATATTTTTTCCTCCCTCTCATATTAGCT
* * *
1315938 ATCATTATATGGTTTGATATTATATATGTTTTATTAATTTTATTTATTCTACTTTATACGC
66 ATCATTATATGGTTTAATATTATATATGTTTTATTAACTTTATTTATTTTACTTTATACGC
1315999 TATT
1 TATT
1316003 TTACATTTTT
Statistics
Matches: 118, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
126 35 0.30
127 6 0.05
128 8 0.07
129 8 0.07
130 9 0.08
131 20 0.17
132 5 0.04
133 23 0.19
134 4 0.03
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (126 bp):
TATTATTTATATTCATTAATTTTTCCATTACTATTATATATTTTTTCCTCCCTCTCATATTAGCT
ATCATTATATGGTTTAATATTATATATGTTTTATTAACTTTATTTATTTTACTTTATACGC
Found at i:1315991 original size:126 final size:130
Alignment explanation
Indices: 1315771--1316002 Score: 366
Period size: 126 Copynumber: 1.8 Consensus size: 130
1315761 ATTCTATTAC
* *
1315771 TATTATATAGATTTTTTCCTCCCTCTCATATTTAGTTATTATATATATGGTATTAATATTATTAT
1 TATTATATAGATTTTTTCCTCCCTCTCATATTTAGCTATCATATATATGGTATTAATATTATTAT
*
1315836 ATGTTTTTATTAACTTTATTTATTTTACTTTATACGCTATTATTTATATTTTTTAATTTTTCCAT
66 ATGTTTTTATTAACTTTATTTATTCTACTTTATACGCTATTATTTATATTTTTTAATTTTTCCAT
* *
1315901 TATTATTATATATTTTTTCCTCCCTCTCATA-TTAGCTATCAT-TATATGGT-TTGATATTA-TA
1 TATTA-TATAGATTTTTTCCTCCCTCTCATATTTAGCTATCATATATATGGTATTAATATTATTA
*
1315962 TATG-TTTTATTAATTTTATTTATTCTACTTTATACGCTATT
65 TATGTTTTTATTAACTTTATTTATTCTACTTTATACGCTATT
1316003 TTACATTTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
126 35 0.37
127 6 0.06
128 8 0.08
129 8 0.08
130 14 0.15
131 24 0.25
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.57
Consensus pattern (130 bp):
TATTATATAGATTTTTTCCTCCCTCTCATATTTAGCTATCATATATATGGTATTAATATTATTAT
ATGTTTTTATTAACTTTATTTATTCTACTTTATACGCTATTATTTATATTTTTTAATTTTTCCAT
Found at i:1326544 original size:1 final size:1
Alignment explanation
Indices: 1326538--1326599 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
1326528 CCTAAGTTGG
* * * * * * *
1326538 AAAAAAAAAAAAAAAACAAAAACAAAAAGAAACAAAAAAAAAACAAAAAACAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1326600 GAGAAGAACG
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.89, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1326586 original size:35 final size:35
Alignment explanation
Indices: 1326538--1326604 Score: 111
Period size: 33 Copynumber: 1.9 Consensus size: 35
1326528 CCTAAGTTGG
1326538 AAAAAAAAAAAAAAAAC-AAAAACAAAA-AGAAAC
1 AAAAAAAAAAAAAAAACAAAAAACAAAAGAGAAAC
1326571 AAAAAAAAAACAAAAAACAAAAAACAAAAGAGAA
1 AAAAAAAAAA-AAAAAACAAAAAACAAAAGAGAA
1326605 GAACGTTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 10 0.32
34 7 0.23
35 10 0.32
36 4 0.13
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (35 bp):
AAAAAAAAAAAAAAAACAAAAAACAAAAGAGAAAC
Found at i:1326683 original size:11 final size:12
Alignment explanation
Indices: 1326645--1326685 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1326635 CCCTAAATTG
*
1326645 AGAAAAGAAAAA
1 AGAAAAGAGAAA
1326657 AGAAAAGAGAAA
1 AGAAAAGAGAAA
*
1326669 AGAAAA-AGAAG
1 AGAAAAGAGAAA
1326680 AGAAAA
1 AGAAAA
1326686 TAAGGTGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AGAAAAGAGAAA
Found at i:1327736 original size:105 final size:105
Alignment explanation
Indices: 1327418--1328893 Score: 2384
Period size: 105 Copynumber: 14.4 Consensus size: 105
1327408 AGGTTTTACC
*
1327418 CAGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1327483 ACGAAGGGACCGCTGG-T-TCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1327521 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1327586 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1327626 CAGAGCCAATTTCAACTTCACAACGAA-G-TATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1327689 ATGAAGGGACCGCTGGTTGTC-ACAAACATTTCTCAAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAA-TT
1327729 CAGAGAGCCAATTTC-ACTTCACAACGAA-GATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 C--AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
1327792 CGACGAAGGGACCGCTGGTTGTCAACAAATA-TTCTCAAATT
64 CGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1327833 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC-ACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1327897 ACGAAGGGACCG-TGGTTGTCAACAAACATTTCTCAAAAT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1327936 CAGAGCCAATTTCAACTT--CAA--AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1327997 ACGAAGGGACCGCTGGTTGTCAACAAACA-TTCTC-AATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1328035 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC-CG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1328099 ATGAAGGGACCGCTGGTTGT---C--A-A-----C-AA-T
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
1328126 CAGAGCCAATTTCAACTTCATAA-GAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1328190 ATGAAGGGACCGCTGGTTGTCAAC-AATATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1328229 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1328294 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1328334 CAGAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1328398 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAA--
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1328436 CAGAGCCAATTTCAACTTCACAACG-AGG--ATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1328498 ACGAAGGGACCGCTGGTTGTCAACAAACA-TTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1328537 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1328602 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATCC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT-T
*
1328642 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1328707 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* ****
1328747 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTATAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** ** * *
1328812 ACGAAGGGACCGCTGACTGTCAACCGACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* *
1328853 CAGAGCCAATTTCAACTTCACAATGAATGATATTGGACTCC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1328894 GAAACAATAC
Statistics
Matches: 1296, Mismatches: 36, Indels: 79
0.92 0.03 0.06
Matches are distributed among these distances:
90 37 0.03
91 45 0.03
92 3 0.00
94 1 0.00
95 1 0.00
96 2 0.00
97 1 0.00
99 50 0.04
100 97 0.07
101 51 0.04
102 94 0.07
103 269 0.21
104 233 0.18
105 355 0.27
106 57 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:1328541 original size:308 final size:310
Alignment explanation
Indices: 1327418--1328893 Score: 2316
Period size: 308 Copynumber: 4.8 Consensus size: 310
1327408 AGGTTTTACC
*
1327418 CAGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1327483 ACGAAGGGACCGCTGG-T-TCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAA--CAGAGCCAATTTCAACTTCACAACG
1327546 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
129 AAGGA-ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
1327611 AACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAA-G-TATTGGACTCCAGACAACGC
193 AACA-TTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
*
1327674 AAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTC-ACAAACATTTCTCAAATTT
257 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AA-TT
1327729 CAGAGAGCCAATTTC-ACTTCACAACGAA-GATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 C--AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
1327792 CGACGAAGGGACCGCTGGTTGTCAACAAATA-TTCTCAAATTCAGAGCCAATTTCAACTTCACAA
64 CGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAA--CAGAGCCAATTTCAACTTCACAA
1327856 CGAAGGATATTGGACTCCAGAC-ACGCAAGTTCAACTTCACGACGAAGGGACCG-TGGTTGTCAA
127 CGAAGGA-ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
1327919 CAAACATTTCTCAAAATCAGAGCCAATTTCAACTT--CAA--AAGGATATTGGACTCCAGACAAC
191 CAAACA-TTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1327980 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA-TTCTCAATT
255 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
1328035 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC-CG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1328099 ATGAAGGGACCGCTGGTTGTCAAC--A-A----T----CAGAGCCAATTTCAACTTCATAA-GAA
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAACAGAGCCAATTTCAACTTCACAACGAA
*
1328152 GGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAT
131 GGA-ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA-
*
1328217 A-TTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
194 ACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
1328281 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
259 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATT
1328334 CAGAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1328398 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAACAGAGCCAATTTCAACTTCACAACG-A
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAACAGAGCCAATTTCAACTTCACAACGAA
1328462 GG-ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
131 GGAATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
*
1328526 ATTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
196 ATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
* *
1328591 TCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATCC
261 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAT-T
*
1328642 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1328707 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAA--ACAGAGCCAATTTCAACTTCACAACG
* **** **
1328772 AAGGATATTGGACTCAAGACAGTATAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAACC
129 AAGGA-ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-C
* * *
1328837 GACAAC-TTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAATGATATTGGACTCC
192 -A-AACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1328894 GAAACAATAC
Statistics
Matches: 1095, Mismatches: 28, Indels: 79
0.91 0.02 0.07
Matches are distributed among these distances:
292 20 0.02
293 79 0.07
294 13 0.01
295 4 0.00
297 69 0.06
298 34 0.03
299 62 0.06
301 1 0.00
302 2 0.00
303 1 0.00
304 12 0.01
305 38 0.03
306 40 0.04
307 7 0.01
308 261 0.24
309 76 0.07
310 69 0.06
311 110 0.10
312 72 0.07
313 21 0.02
314 50 0.05
315 1 0.00
316 50 0.05
317 3 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (310 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAACAGAGCCAATTTCAACTTCACAACGAA
GGAATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
ATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:1330466 original size:12 final size:13
Alignment explanation
Indices: 1330425--1330487 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
1330415 TTTACTCGTA
1330425 TATATGTAT-TAT
1 TATATGTATATAT
*
1330437 TAGTATAT-TATTACT
1 TA-TATGTATA-TA-T
1330452 TATATGT-TATAT
1 TATATGTATATAT
*
1330464 TATATATATATAT
1 TATATGTATATAT
1330477 ATATATGTATA
1 -TATATGTATA
1330488 CATTTGTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 10 0.24
13 11 0.27
14 17 0.41
15 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (13 bp):
TATATGTATATAT
Found at i:1330689 original size:126 final size:127
Alignment explanation
Indices: 1330530--1330789 Score: 350
Period size: 127 Copynumber: 2.0 Consensus size: 127
1330520 TTTCTATTAT
* * *
1330530 TTATTCTTATTATTTAGTTTTTCTATTACTATTATATAGATTTTTCCTCCTCT-ATATTTAGTTT
1 TTATT-TTATTATTTAATTTTTCCATTACTATTATAT---TTTTTCCTCCTCTCATATTTAG-CT
* * *
1330594 ATTATATATATGGTA-TAATA-TATTATGTG-TTTTA-TAACTTTATTTATTTTACTTTATACGC
61 ATCATATATATGGTATTAATATTATTATATGTTTTTATTAACTTTATTTATTCTACTTTATACGC
1330655 TA
126 TA
* *
1330657 TTATTTTATTTTTTAATTTTTCCATTATTATTATATTTTTTCCTCCTCTCATATTTAGCTATCAT
1 TTATTTTATTATTTAATTTTTCCATTACTATTATATTTTTTCCTCCTCTCATATTTAGCTATCAT
* *
1330722 ATATATGGTATTGATATTATTATATGTTTTTATTAATTTTATTTATTCTACTTTATACGCTA
66 ATATATGGTATTAATATTATTATATGTTTTTATTAACTTTATTTATTCTACTTTATACGCTA
1330784 TTATTT
1 TTATTT
1330790 ACATTTTTGT
Statistics
Matches: 118, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
123 28 0.24
124 12 0.10
125 8 0.07
126 32 0.27
127 38 0.32
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.59
Consensus pattern (127 bp):
TTATTTTATTATTTAATTTTTCCATTACTATTATATTTTTTCCTCCTCTCATATTTAGCTATCAT
ATATATGGTATTAATATTATTATATGTTTTTATTAACTTTATTTATTCTACTTTATACGCTA
Found at i:1334602 original size:75 final size:75
Alignment explanation
Indices: 1334479--1334790 Score: 363
Period size: 75 Copynumber: 4.2 Consensus size: 75
1334469 GTTAACTGGT
* * * * * * ** *
1334479 TAAAATAAAATAAGTGTTACCTATTATGTTAAACTACTTACCGGTTTGTTTGAATATTATTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAAATACTTACCGGTTTGTTTAAAGGTTACTAATA
1334544 ATGTAAACGG
66 ATGTAAACGG
* * **
1334554 TAAAATAAAATAGGCGCTACATATTACGTTAAAATATTTACCGGTTTGTTTAAACTTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAAATACTTACCGGTTTGTTTAAAGGTTACTAATA
**
1334619 ATGTAAACAA
66 ATGTAAACGG
* * * * ** *
1334629 TAAAATAAAATATGTGCTACCTATTACGTTAAAATGCATATAGGTTTGTTTAAAGGTTACTAACA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAAATACTTACCGGTTTGTTTAAAGGTTACTAATA
1334694 ATGTAAACGG
66 ATGTAAACGG
* * * ** * *
1334704 TAAAATAAAATAGGCGTTATCTATTACCTTAAAATACCAACTGGTTTATTTAAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAAATACTTACCGGTTTGTTTAAAGGTTACTAATA
1334769 ATGTAAACGG
66 ATGTAAACGG
1334779 TAAAATAAAATA
1 TAAAATAAAATA
1334791 TTATCTATTG
Statistics
Matches: 199, Mismatches: 38, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 199 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (75 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAAATACTTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGG
Found at i:1334917 original size:23 final size:23
Alignment explanation
Indices: 1334891--1334965 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
1334881 ATATGCACTG
* * *
1334891 CCTATTATATTAAATAGGCGCTA
1 CCTATTACATTCAATAAGCGCTA
1334914 CCTATTACATTCAATAAGCGCTA
1 CCTATTACATTCAATAAGCGCTA
1334937 CC--TTACATTCAATAAGCGCTA
1 CCTATTACATTCAATAAGCGCTA
1334958 CCTATTAC
1 CCTATTAC
1334966 GTTAAACTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
21 21 0.45
23 26 0.55
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.32
Consensus pattern (23 bp):
CCTATTACATTCAATAAGCGCTA
Found at i:1334944 original size:21 final size:21
Alignment explanation
Indices: 1334903--1334960 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
1334893 TATTATATTA
*
1334903 AATAGGCGCTACCTATTACATTC
1 AATAAGCGCTACC--TTACATTC
1334926 AATAAGCGCTACCTTACATTC
1 AATAAGCGCTACCTTACATTC
1334947 AATAAGCGCTACCT
1 AATAAGCGCTACCT
1334961 ATTACGTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 22 0.65
23 12 0.35
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (21 bp):
AATAAGCGCTACCTTACATTC
Found at i:1336435 original size:17 final size:17
Alignment explanation
Indices: 1336413--1336445 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1336403 AGTCCGCTTA
1336413 GCACCAGAACCTCCCTG
1 GCACCAGAACCTCCCTG
1336430 GCACCAGAACCTCCCT
1 GCACCAGAACCTCCCT
1336446 TCCCAATTTC
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:0.24, C:0.48, G:0.15, T:0.12
Consensus pattern (17 bp):
GCACCAGAACCTCCCTG
Found at i:1338149 original size:21 final size:21
Alignment explanation
Indices: 1338108--1338150 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1338098 GAATGGAAAG
* *
1338108 ATAGAGGAATAGGAGAGTGGA
1 ATAGAGAAATAGGAGAATGGA
1338129 ATAGAGAAACTAGG-GAATGGA
1 ATAGAGAAA-TAGGAGAATGGA
1338150 A
1 A
1338151 ATCTTTACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.47, C:0.02, G:0.37, T:0.14
Consensus pattern (21 bp):
ATAGAGAAATAGGAGAATGGA
Found at i:1346370 original size:55 final size:54
Alignment explanation
Indices: 1346286--1346395 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 54
1346276 TGCATACTAG
1346286 TGACATGTAGTGTTTAATGGAAAAAGACTTGCGATGAGTCTATTTCCTAAAGCAA
1 TGACATGTAGTGTTTAATGGAAAAAGACTTGCGATGAGTCTATTT-CTAAAGCAA
*
1346341 TGACATGTAGTGTTTAATGGAAATAGACTTGCGATGAGTCTATTTCTAAAGCAA
1 TGACATGTAGTGTTTAATGGAAAAAGACTTGCGATGAGTCTATTTCTAAAGCAA
1346395 T
1 T
1346396 ATGTATGAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 10 0.19
55 44 0.81
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.33
Consensus pattern (54 bp):
TGACATGTAGTGTTTAATGGAAAAAGACTTGCGATGAGTCTATTTCTAAAGCAA
Found at i:1347719 original size:23 final size:23
Alignment explanation
Indices: 1347687--1347753 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
1347677 ACCTTATATA
1347687 GCACTTCGGTGCATTTCTACGCG
1 GCACTTCGGTGCATTTCTACGCG
* * *
1347710 GCACTACGGTGCAATTCTACGGG
1 GCACTTCGGTGCATTTCTACGCG
* *
1347733 GCACTTCGGTACATTTATACG
1 GCACTTCGGTGCATTTCTACG
1347754 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.28
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCG
Found at i:1352255 original size:31 final size:32
Alignment explanation
Indices: 1352207--1352270 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
1352197 TTAAAAATAT
*
1352207 TTAATATGATACTTGAATTATCATTTTATGTA
1 TTAATATGAGACTTGAATTATCATTTTATGTA
1352239 TTAATATG-GACTTGAATTATCATTTTATGTA
1 TTAATATGAGACTTGAATTATCATTTTATGTA
1352270 T
1 T
1352271 CAGACTATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (32 bp):
TTAATATGAGACTTGAATTATCATTTTATGTA
Found at i:1354650 original size:37 final size:37
Alignment explanation
Indices: 1354606--1354710 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
1354596 CCTTTTCGTC
1354606 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
* * *
1354643 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
** * *
1354680 CTACTATTATTTAAACTCCTAAAGATATGAT
1 CTACTAGGATTCAAACTCCTAAAAATATGAT
1354711 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
Found at i:1355151 original size:18 final size:18
Alignment explanation
Indices: 1355104--1355164 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 18
1355094 AATTTAACCC
1355104 TTATTATTTATATGTATATAT
1 TTATTATTTA-AT-TATAT-T
*
1355125 GTATATATTTAATTATATT
1 TTAT-TATTTAATTATATT
*
1355144 TTATTATTTTATTATAATT
1 TTATTATTTAATTAT-ATT
1355163 TT
1 TT
1355165 TTTTCATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 10 0.29
19 9 0.26
20 5 0.14
21 5 0.14
22 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTATTATTTAATTATATT
Found at i:1355353 original size:22 final size:23
Alignment explanation
Indices: 1355319--1355380 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
1355309 TTTTAGTTAA
*
1355319 TATTA-TATGTATTTATTTC-ATT
1 TATTATTAT-TATTTATTACTATT
1355341 TATTATTATTA-TTATTACTATT
1 TATTATTATTATTTATTACTATT
*
1355363 TAGTATT-TTATTATATTA
1 TATTATTATTATT-TATTA
1355381 TACATACATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 9 0.26
22 17 0.50
23 8 0.24
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (23 bp):
TATTATTATTATTTATTACTATT
Found at i:1355411 original size:14 final size:13
Alignment explanation
Indices: 1355392--1355425 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1355382 ACATACATTT
1355392 TATATTTTTATATA
1 TATATTTTTAT-TA
1355406 TATATTTTTATTA
1 TATATTTTTATTA
*
1355419 TTTATTT
1 TATATTT
1355426 ATACTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATATTTTTATTA
Found at i:1355428 original size:21 final size:21
Alignment explanation
Indices: 1355331--1355442 Score: 72
Period size: 21 Copynumber: 5.3 Consensus size: 21
1355321 TTATATGTAT
*
1355331 TTATTTCATTTAT-TATTATTA
1 TTATTT-ATTTATATATTTTTA
*
1355352 TTATTACTATTTA-GTA-TTTTA
1 TTATT--TATTTATATATTTTTA
** *
1355373 TTATATTATACATACATTTTATA
1 TTAT-TTATTTATATATTTT-TA
*
1355396 TT-TTTATATATATATTTTTA
1 TTATTTATTTATATATTTTTA
*
1355416 TTATTTATTTATACTATTTAT-
1 TTATTTATTTATA-TATTTTTA
1355437 TTATTT
1 TTATTT
1355443 TCATTATTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
20 8 0.11
21 42 0.58
22 18 0.25
23 5 0.07
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (21 bp):
TTATTTATTTATATATTTTTA
Found at i:1355439 original size:13 final size:12
Alignment explanation
Indices: 1355390--1355440 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 12
1355380 ATACATACAT
*
1355390 TTTATATTTTTA
1 TTTATATATTTA
*
1355402 TATATATA-TT-
1 TTTATATATTTA
1355412 TTTAT-TATTTA
1 TTTATATATTTA
1355423 TTTATACTATTTA
1 TTTATA-TATTTA
1355436 TTTAT
1 TTTAT
1355441 TTTCATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 7 0.22
12 6 0.19
13 11 0.34
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATATATTTA
Found at i:1358259 original size:18 final size:18
Alignment explanation
Indices: 1358236--1358273 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1358226 CTTGAGAAAC
1358236 AACATGAGAAAGATGGTA
1 AACATGAGAAAGATGGTA
1358254 AACATGAGAAAGATGGTA
1 AACATGAGAAAGATGGTA
1358272 AA
1 AA
1358274 GCAATAGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.26, T:0.16
Consensus pattern (18 bp):
AACATGAGAAAGATGGTA
Found at i:1359914 original size:21 final size:22
Alignment explanation
Indices: 1359879--1359921 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1359869 ACAAAAAGGG
*
1359879 CAAAAAATAAAAAAGAATAAAA
1 CAAAAAATAAAAAAGAACAAAA
*
1359901 CAAAAAA-AAGAAAGAACAAAA
1 CAAAAAATAAAAAAGAACAAAA
1359922 ATCAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.81, C:0.07, G:0.07, T:0.05
Consensus pattern (22 bp):
CAAAAAATAAAAAAGAACAAAA
Found at i:1359918 original size:16 final size:17
Alignment explanation
Indices: 1359887--1359922 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1359877 GGCAAAAAAT
1359887 AAAAAAGAATAAAACAA
1 AAAAAAGAATAAAACAA
*
1359904 AAAAAAGAA-AGAACAA
1 AAAAAAGAATAAAACAA
1359920 AAA
1 AAA
1359923 TCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.83, C:0.06, G:0.08, T:0.03
Consensus pattern (17 bp):
AAAAAAGAATAAAACAA
Found at i:1360777 original size:22 final size:21
Alignment explanation
Indices: 1360752--1360812 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
1360742 TGAAAGAGAC
1360752 ATATTTTCAAAACTTTTGATTA
1 ATATTTTCAAAACTTTT-ATTA
* *
1360774 ATATTTTTCGAAACTCTTTATTG
1 ATA-TTTTCAAAACT-TTTATTA
*
1360797 ATATTTTCAGAACTTT
1 ATATTTTCAAAACTTT
1360813 GAAAATGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 2 0.06
22 12 0.36
23 16 0.48
24 3 0.09
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (21 bp):
ATATTTTCAAAACTTTTATTA
Found at i:1361576 original size:106 final size:106
Alignment explanation
Indices: 1361448--1361642 Score: 327
Period size: 106 Copynumber: 1.8 Consensus size: 106
1361438 ATATCATGCC
* * *
1361448 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1361513 AAATTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGG
66 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1361554 ACTCCAGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1361619 AATTTCAGAGCCAATTTCAACTTC
66 AAATTCAGAGCCAATTTCAACTTC
1361643 TCAATTTCAG
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 82 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1361646 original size:26 final size:26
Alignment explanation
Indices: 1361610--1361668 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
1361600 TGTCAACAAA
1361610 CAACTTCTCAATTTCAGAGCCAATTT
1 CAACTTCTCAATTTCAGAGCCAATTT
*
1361636 CAACTTCTCAATTTCAGAGGCAATTT
1 CAACTTCTCAATTTCAGAGCCAATTT
1361662 CAACTTC
1 CAACTTC
1361669 ACAACGAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (26 bp):
CAACTTCTCAATTTCAGAGCCAATTT
Found at i:1361743 original size:132 final size:132
Alignment explanation
Indices: 1361504--1361774 Score: 436
Period size: 132 Copynumber: 2.1 Consensus size: 132
1361494 TGTCAACAAA
*
1361504 CAACTTCCCAAATTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACA
1 CAACTTCCCAAATTCAGAGCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACA
* *
1361569 AGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
66 AGTTCAACTTAACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
1361634 TT
131 TT
* * * *
1361636 CAACTTCTCAATTTCAGAGGC-AATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGC
1 CAACTTCCCAAATTCAGA-GCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACAC
* * *
1361700 AAGTTCAACTTAACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAA
65 AAGTTCAACTTAACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAA
1361765 TTT
130 TTT
1361768 CAACTTC
1 CAACTTC
1361775 ACAGCGAAGG
Statistics
Matches: 128, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
132 126 0.98
133 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (132 bp):
CAACTTCCCAAATTCAGAGCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACA
AGTTCAACTTAACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
TT
Found at i:1361760 original size:238 final size:238
Alignment explanation
Indices: 1361448--1361880 Score: 713
Period size: 238 Copynumber: 1.8 Consensus size: 238
1361438 ATATCATGCC
* * *
1361448 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTAACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1361513 AAATTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
66 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGTTCAACT
*
1361578 TCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
1361643 TCAATTTCAGAGGCAATTTCAACTTCACAACGAATGATATTGG
196 TCAATTTCAGAGGCAATTTCAACTTCACAACGAATGATATTGG
* * * *
1361686 ACTCCAGACAACGCAAGTTCAACTTAACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTAACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* **
1361751 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAATGCAAGTTCAACT
66 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGTTCAACT
* * *
1361816 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTC
131 TCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
1361881 ACAGCGAAAG
Statistics
Matches: 178, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
238 178 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (238 bp):
ACTCCAGACAACACAAGTTCAACTTAACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGTTCAACT
TCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
TCAATTTCAGAGGCAATTTCAACTTCACAACGAATGATATTGG
Found at i:1361829 original size:106 final size:106
Alignment explanation
Indices: 1361644--1362430 Score: 1227
Period size: 106 Copynumber: 7.4 Consensus size: 106
1361634 TTCAACTTCT
* * *
1361644 CAATTTCAGAGGCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* *
1361709 TTAACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
* * *
1361750 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAATGCAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1361815 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
* * * *
1361856 CAATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTAGACTCCAGACAACGCAAATTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1361921 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
* *
1361962 CAATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* * * * *
1362027 TTCACGACGAATGGACCGTTGGTTGTCAATAAACAACTTCT
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
*
1362068 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* *
1362133 TTCAAGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
* * * *
1362174 CAATTTCATAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1362239 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
* * * * *
1362280 CAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
*
1362345 TTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
66 TTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCC
* * *
1362386 CGATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACT
1 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACT
1362431 TGGAACAATG
Statistics
Matches: 630, Mismatches: 49, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
105 2 0.00
106 628 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
Found at i:1363231 original size:37 final size:37
Alignment explanation
Indices: 1363180--1363276 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
1363170 CCTTTTCGTC
1363180 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
* *
1363217 TTACTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
** *
1363254 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
1363277 TATAGGATCC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
Found at i:1363589 original size:13 final size:13
Alignment explanation
Indices: 1363556--1363595 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1363546 TTCTTTGCGT
*
1363556 TATATATATTATT
1 TATATATATTATA
* *
1363569 TTTCTATATTATA
1 TATATATATTATA
1363582 TATATATATTATA
1 TATATATATTATA
1363595 T
1 T
1363596 TATTTTTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATATATTATA
Done.