Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000426.1 Hibiscus syriacus cultivar Beakdansim tig00000778_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: 3165331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 15
Found at i:1194200 original size:18 final size:18
Alignment explanation
Indices: 1194176--1194211 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1194166 ATTTAAATTC
1194176 CTTTTTTT-TCATTTTCT
1 CTTTTTTTCTCATTTTCT
*
1194193 CTTTTTTTCTCCTTTTCT
1 CTTTTTTTCTCATTTTCT
1194211 C
1 C
1194212 CCGATTTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTTTTTCTCATTTTCT
Found at i:1194592 original size:32 final size:32
Alignment explanation
Indices: 1194522--1194594 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
1194512 TCAGGTTAGG
*
1194522 TCAATATCAAATCGATTAATTTTCGGGTCATA
1 TCAATATCAAATAGATTAATTTTCGGGTCATA
* * * *
1194554 TTAATATCAAATAGTTTAGTTTTCGGGTTGA-A
1 TCAATATCAAATAGATTAATTTTCGGG-TCATA
1194586 TCAATATCA
1 TCAATATCA
1194595 TATCGGTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (32 bp):
TCAATATCAAATAGATTAATTTTCGGGTCATA
Found at i:1195766 original size:16 final size:16
Alignment explanation
Indices: 1195721--1195759 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1195711 TCGGTTTATA
*
1195721 TTTAGTTCGGGTTACT
1 TTTAGTTCGAGTTACT
*
1195737 TTCAGTTCGAGTTACT
1 TTTAGTTCGAGTTACT
1195753 TTTAGTT
1 TTTAGTT
1195760 TGTGTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (16 bp):
TTTAGTTCGAGTTACT
Found at i:1196866 original size:129 final size:129
Alignment explanation
Indices: 1196700--1196949 Score: 421
Period size: 129 Copynumber: 1.9 Consensus size: 129
1196690 AAACAAAGGG
*
1196700 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGAAAAGTATGAAAAACACAGCTGGAATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGAAAAGTATGAAAAACACAGCGGGAATTGAAATT
* *
1196765 AATTTAGATGCTGAAAGGGAATTCAAT-TTCCTCGTAGGATCTTCTTCTTCCTTAATCCATCGGA
66 AATTTAGAAGCTGAAAGGGAATTCAATATT-CTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
* * * *
1196829 AGAGAGATAGAGAAGCTGCTCGGATGGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGAAAAGTATGAAAAACACAGCGGGAATTGAAATT
1196894 AATTTAGAAGCTGAAAGGGAATTCAATATTCTCATAGGATCTTCTTCTTCCTTAAT
66 AATTTAGAAGCTGAAAGGGAATTCAATATTCTCATAGGATCTTCTTCTTCCTTAAT
1196950 GCATAGGATA
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
129 111 0.98
130 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (129 bp):
AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGAAAAGTATGAAAAACACAGCGGGAATTGAAATT
AATTTAGAAGCTGAAAGGGAATTCAATATTCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
Found at i:1197823 original size:17 final size:17
Alignment explanation
Indices: 1197801--1197836 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1197791 GTCGAGTCTA
1197801 GTCAATTTTCAGGTCGG
1 GTCAATTTTCAGGTCGG
*
1197818 GTCAATTTTCGGGTCGG
1 GTCAATTTTCAGGTCGG
1197835 GT
1 GT
1197837 GATAATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.17, G:0.33, T:0.36
Consensus pattern (17 bp):
GTCAATTTTCAGGTCGG
Found at i:1198821 original size:21 final size:21
Alignment explanation
Indices: 1198806--1198861 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1198796 AAGCAGAGAC
*
1198806 AGAAGCAAAGAGAGCATCGAG
1 AGAAGCAGAGAGAGCATCGAG
1198827 AGAAGCAGAGAGAGCATCGAG
1 AGAAGCAGAGAGAGCATCGAG
1198848 AGAAGCAGAGAGAG
1 AGAAGCAGAGAGAG
1198862 AAGCAACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.46, C:0.12, G:0.38, T:0.04
Consensus pattern (21 bp):
AGAAGCAGAGAGAGCATCGAG
Found at i:1198839 original size:12 final size:11
Alignment explanation
Indices: 1198791--1198867 Score: 63
Period size: 12 Copynumber: 7.0 Consensus size: 11
1198781 AAGCTGAAGC
1198791 GAGAGAAGCAGA
1 GAGAGAAGCA-A
*
1198803 GACAGAAGCAA
1 GAGAGAAGCAA
*
1198814 -AGAG-AGCATC
1 GAGAGAAGCA-A
1198824 GAGAGAAGC-A
1 GAGAGAAGCAA
*
1198834 GAGAG-AGCATC
1 GAGAGAAGCA-A
1198845 GAGAGAAGCAGA
1 GAGAGAAGCA-A
1198857 GAGAGAAGCAA
1 GAGAGAAGCAA
1198868 CATTTTAGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
9 7 0.13
10 8 0.15
11 11 0.21
12 26 0.50
ACGTcount: A:0.48, C:0.13, G:0.36, T:0.03
Consensus pattern (11 bp):
GAGAGAAGCAA
Found at i:1199308 original size:42 final size:41
Alignment explanation
Indices: 1199236--1199352 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 41
1199226 GTTTCCCCCT
* *
1199236 AAAAACGCCGCTAAATGACCAACCTATTGCGGCAG-TTGTGCAC
1 AAAAACGCCGCTAAAT-ACAAACCTGTTGCGG-AGTTTGT-CAC
* * *
1199279 -GAAACGCCGCTAAATATCAAATCTGTTGCGGTGTTTGTCAC
1 AAAAACGCCGCTAAATA-CAAACCTGTTGCGGAGTTTGTCAC
1199320 TAAAAACGCCGCTAAATAGCAAACCTGTTGCGG
1 -AAAAACGCCGCTAAATA-CAAACCTGTTGCGG
1199353 GAAAACACCT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
41 5 0.08
42 29 0.47
43 28 0.45
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (41 bp):
AAAAACGCCGCTAAATACAAACCTGTTGCGGAGTTTGTCAC
Found at i:1200055 original size:16 final size:15
Alignment explanation
Indices: 1200029--1200077 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1200019 TTGGATCGGT
1200029 TTATATTTAGTTCGAG
1 TTAT-TTTAGTTCGAG
*
1200045 TTACTTTTAGTTTGAG
1 TTA-TTTTAGTTCGAG
*
1200061 TTATTTTCGGTTCGAG
1 TTATTTT-AGTTCGAG
1200077 T
1 T
1200078 CAAATTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 4 0.14
16 23 0.82
17 1 0.04
ACGTcount: A:0.18, C:0.08, G:0.20, T:0.53
Consensus pattern (15 bp):
TTATTTTAGTTCGAG
Found at i:1201718 original size:21 final size:21
Alignment explanation
Indices: 1201688--1201735 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1201678 TAATTTTCAA
*
1201688 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1201709 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1201730 ACATTG
1 ACATTG
1201736 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1206362 original size:21 final size:21
Alignment explanation
Indices: 1206332--1206379 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1206322 TAATTTTCAA
*
1206332 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1206353 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1206374 ACATTG
1 ACATTG
1206380 CAATTAGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1206740 original size:32 final size:32
Alignment explanation
Indices: 1206670--1206742 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
1206660 TCAGGTTAGG
1206670 TCAATATCAAATCGATTAATTTTCGGGTCATA
1 TCAATATCAAATCGATTAATTTTCGGGTCATA
* * * *
1206702 TTAATATCAAATCGTTTAGTTTTCGGGTTGA-A
1 TCAATATCAAATCGATTAATTTTCGGG-TCATA
1206734 TCAATATCA
1 TCAATATCA
1206743 TATTGGTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (32 bp):
TCAATATCAAATCGATTAATTTTCGGGTCATA
Found at i:1207914 original size:16 final size:16
Alignment explanation
Indices: 1207869--1207907 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1207859 TCGGTTTATA
*
1207869 TTTAGTTCGGGTTACT
1 TTTAGTTCGAGTTACT
*
1207885 TTCAGTTCGAGTTACT
1 TTTAGTTCGAGTTACT
1207901 TTTAGTT
1 TTTAGTT
1207908 TGTGTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (16 bp):
TTTAGTTCGAGTTACT
Found at i:1209070 original size:129 final size:127
Alignment explanation
Indices: 1208840--1209083 Score: 382
Period size: 129 Copynumber: 1.9 Consensus size: 127
1208830 AAAGGGAGAG
* * *
1208840 AGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCTGGAATTGAAATTAATT
1 AGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGCAAGAAAAACACAGCGGGAATTGAAATTAATT
* *
1208905 TAGATGCTGAAAGGGAATTCAATTTCCTCGTAGGATCTTCTTCTTCCTTAATCCATCGGAAGAT
66 TAGAGGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTC-T-TTCCTTAATCCATCGGAAGAT
* * *
1208969 AGATAGAGAAGCTGCTCGGATGGCATTGGAAAGCAAGAAAAACACAGCGGGGATTGAAATTAATT
1 AGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGCAAGAAAAACACAGCGGGAATTGAAATTAATT
1209034 TAGAGGCTGAAAGGGAATTCAATATT-CTCATAGGATCTTCTTTCCTTAAT
66 TAGAGGCTGAAAGGGAATTCAAT-TTCCTCATAGGATCTTCTTTCCTTAAT
1209084 GCATAGGATA
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
127 9 0.08
128 1 0.01
129 94 0.89
130 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (127 bp):
AGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGCAAGAAAAACACAGCGGGAATTGAAATTAATT
TAGAGGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTTCCTTAATCCATCGGAAGAT
Found at i:1209357 original size:15 final size:15
Alignment explanation
Indices: 1209333--1209366 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1209323 TGATACTATT
* *
1209333 ATCATTATCATTATC
1 ATCATAATCATAATC
1209348 ATCATAATCATAATC
1 ATCATAATCATAATC
1209363 ATCA
1 ATCA
1209367 CAACGGAAAG
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:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (15 bp):
ATCATAATCATAATC
Found at i:1209895 original size:17 final size:17
Alignment explanation
Indices: 1209875--1209908 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1209865 AGAGTCGAGC
1209875 CAATTTTCAGGTCGGGT
1 CAATTTTCAGGTCGGGT
*
1209892 CAATTTTCGGGTCGGGT
1 CAATTTTCAGGTCGGGT
1209909 GATAATTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.32, T:0.35
Consensus pattern (17 bp):
CAATTTTCAGGTCGGGT
Found at i:1210954 original size:21 final size:21
Alignment explanation
Indices: 1210925--1210973 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1210915 AGCTGAAGCG
1210925 AGAGAAGCAGAGACAGAAGCAA
1 AGAG-AGCAGAGACAGAAGCAA
** * *
1210947 AGAGAGCATCGAGAGAAGCAG
1 AGAGAGCAGAGACAGAAGCAA
1210968 AGAGAG
1 AGAGAG
1210974 AAGCAACATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.49, C:0.12, G:0.37, T:0.02
Consensus pattern (21 bp):
AGAGAGCAGAGACAGAAGCAA
Found at i:1210972 original size:12 final size:12
Alignment explanation
Indices: 1210924--1210978 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
1210914 AAGCTGAAGC
1210924 GAGAGAAGCAGA
1 GAGAGAAGCAGA
*
1210936 GACAGAAGCA-A
1 GAGAGAAGCAGA
**
1210947 -AGAG-AGCATC
1 GAGAGAAGCAGA
1210957 GAGAGAAGCAGA
1 GAGAGAAGCAGA
1210969 GAGAGAAGCA
1 GAGAGAAGCA
1210979 ACATTTTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 4 0.11
10 3 0.09
11 5 0.14
12 23 0.66
ACGTcount: A:0.49, C:0.13, G:0.36, T:0.02
Consensus pattern (12 bp):
GAGAGAAGCAGA
Found at i:1212189 original size:16 final size:16
Alignment explanation
Indices: 1212165--1212212 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
1212155 GTTTATATTT
* *
1212165 AGTTCGAGTTTCTTTC
1 AGTTTGAGTTACTTTC
*
1212181 AGTTTGAGTTACTTTT
1 AGTTTGAGTTACTTTC
* *
1212197 AGTTTGTGTTATTTTC
1 AGTTTGAGTTACTTTC
1212213 GGTTCGAGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.15, C:0.10, G:0.19, T:0.56
Consensus pattern (16 bp):
AGTTTGAGTTACTTTC
Found at i:1213316 original size:129 final size:129
Alignment explanation
Indices: 1213155--1213404 Score: 412
Period size: 129 Copynumber: 1.9 Consensus size: 129
1213145 ATACAACGGG
* * *
1213155 AGAGAGATAGAGAAGCTTCTCGGATGGCATTGGAAAGTATGAAAAACACAGCTGGGATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATAGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
* * *
1213220 AATTTAGATGCTGAAAGGGAATTCAAT-TTCCTCGTAGGGTCTTCTTCTTCCTTAATCCATCGGA
66 AATTTAGAAGCTGAAAGGGAATTCAATATT-CTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
* *
1213284 AGAGAGATAGAGAATCTGCTCGGATATCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATAGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
1213349 AATTTAGAAGCTGAAAGGGAATTCAATATTCTCATAGGATCTTCTTCTTCCTTAAT
66 AATTTAGAAGCTGAAAGGGAATTCAATATTCTCATAGGATCTTCTTCTTCCTTAAT
1213405 GCATAGGATA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
129 110 0.98
130 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (129 bp):
AGAGAGATAGAGAAGCTGCTCGGATAGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
AATTTAGAAGCTGAAAGGGAATTCAATATTCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
Found at i:1216164 original size:1 final size:1
Alignment explanation
Indices: 1216160--1216194 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
1216150 CTTGTACTGA
1216160 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1216195 GCCCCCTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1216934 original size:115 final size:115
Alignment explanation
Indices: 1216724--1217024 Score: 362
Period size: 115 Copynumber: 2.7 Consensus size: 115
1216714 AAGCGTTGGA
1216724 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGTTGGATGAGTTCTTTCATTATGAACTCT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGTTGGATGAGTTCTTTCATTATGAACTCT
*
1216789 TTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATCGAACCAAGG
66 TTCACTGAAAATGTTGACCCACCTCCTTCTGTGATGAAATCGAACCAAGG
1216839 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCT-TTGGATGAGTT-TTTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-T-CT-TGTTGGATGAGTTCTTTCATTATGAAC
* * * * *
1216902 TC-TTCACTGAAAATGTTGACCCATCTCTTTCTGTGATGGATTTG----AA-G
63 TCTTTCACTGAAAATGTTGACCCACCTCCTTCTGTGATGAAATCGAACCAAGG
* * *
1216949 --GAACAAGTTCTTCTCATTATGAACTT-ATC-C-T-TTAGATGAGTTCTTCTCATTATGAGCTC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGTTGGATGAGTTCTT-TCATTATGAACTC
* *
1217008 -TCCATTGAAAATGTTGA
65 TTTCACTGAAAATGTTGA
1217025 TGCGAAGTTG
Statistics
Matches: 170, Mismatches: 11, Indels: 21
0.84 0.05 0.10
Matches are distributed among these distances:
102 11 0.06
103 2 0.01
104 28 0.16
107 2 0.01
108 26 0.15
110 1 0.01
111 2 0.01
115 68 0.40
116 16 0.09
117 13 0.08
118 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (115 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGTTGGATGAGTTCTTTCATTATGAACTCT
TTCACTGAAAATGTTGACCCACCTCCTTCTGTGATGAAATCGAACCAAGG
Found at i:1217280 original size:128 final size:131
Alignment explanation
Indices: 1217034--1217312 Score: 340
Period size: 128 Copynumber: 2.1 Consensus size: 131
1217024 ATGCGAAGTT
* *
1217034 GAACAAGTTC-TCTCATTATGAACTTCTT-CTTCT-TCGTTTGATGAGTTCTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATG-ACTTCTTCCCTCTGTCG---GATGAGTTCTTCTCATTATGAAC
* * ** * *
1217096 TCTTCACTGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTATGAATCGAGTGAT
62 TATCCACTGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTATGAATCGAGTGAT
1217161 AGGTC
127 AGGTC
1217166 G-AC-AGCTCTTCTCATTATGACTTCTTCCCTCTGTCGGATGAG-TCTTCTCATTATG-ACTATC
1 GAACAAGCTCTTCTCATTATGACTTCTTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTATC
* * * *
1217227 CATTGGAAATACTGATCCTTC-AGCAAGGTGTCACTGATTCAAAATGTCGTGAATCTAGTGATAG
66 CACT-GAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGT-ATGAATCGAGTGATAG
1217291 GTC
129 GTC
1217294 GAACAAGCTCTTCTCATTA
1 GAACAAGCTCTTCTCATTA
1217313 CTAGAATAAG
Statistics
Matches: 128, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
127 31 0.24
128 44 0.34
129 8 0.06
130 25 0.20
131 16 0.12
132 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (131 bp):
GAACAAGCTCTTCTCATTATGACTTCTTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTATC
CACTGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTATGAATCGAGTGATAGGT
C
Found at i:1218229 original size:23 final size:21
Alignment explanation
Indices: 1218200--1218253 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 21
1218190 GATTAGTACA
1218200 ATATATTTATAAACATATCATTT
1 ATATATTTATAAA-ATA-CATTT
1218223 ATATATTTA-AAAATACATTT
1 ATATATTTATAAAATACATTT
1218243 A-ATAATTTATA
1 ATAT-ATTTATA
1218254 TCACGTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 2 0.07
20 11 0.38
21 4 0.14
22 3 0.10
23 9 0.31
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATATTTATAAAATACATTT
Found at i:1218233 original size:21 final size:20
Alignment explanation
Indices: 1218200--1218243 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 20
1218190 GATTAGTACA
1218200 ATATATTTATAAACATATCATTT
1 ATATATTTA-AAA-ATA-CATTT
1218223 ATATATTTAAAAATACATTT
1 ATATATTTAAAAATACATTT
1218243 A
1 A
1218244 ATAATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 3 0.14
22 3 0.14
23 9 0.43
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATTTAAAAATACATTT
Found at i:1220686 original size:2 final size:2
Alignment explanation
Indices: 1220679--1220750 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
1220669 ACCATGGGAG
1220679 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1220720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1220751 CCATGTTCAT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1222557 original size:19 final size:19
Alignment explanation
Indices: 1222503--1222558 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
1222493 TGGGATGCAA
1222503 ATGGAATATGATTATACAT
1 ATGGAATATGATTATACAT
* **
1222522 AT-GATTA-GA--GCACAT
1 ATGGAATATGATTATACAT
1222537 ATGGAATATGATTATACAT
1 ATGGAATATGATTATACAT
1222556 ATG
1 ATG
1222559 ATTAAAACAC
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
15 6 0.22
16 4 0.15
17 4 0.15
18 4 0.15
19 9 0.33
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (19 bp):
ATGGAATATGATTATACAT
Found at i:1222570 original size:34 final size:34
Alignment explanation
Indices: 1222503--1222570 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
1222493 TGGGATGCAA
* *
1222503 ATGGAATATGATTATACATATGATTAGAGCACAT
1 ATGGAATATGATTATACATATGATTAAAACACAT
1222537 ATGGAATATGATTATACATATGATTAAAACACAT
1 ATGGAATATGATTATACATATGATTAAAACACAT
1222571 GAGAGATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (34 bp):
ATGGAATATGATTATACATATGATTAAAACACAT
Found at i:1225792 original size:11 final size:11
Alignment explanation
Indices: 1225776--1225800 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1225766 TAGGTACCGA
1225776 TACTCAAAGGG
1 TACTCAAAGGG
1225787 TACTCAAAGGG
1 TACTCAAAGGG
1225798 TAC
1 TAC
1225801 CAATATTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (11 bp):
TACTCAAAGGG
Found at i:1226040 original size:20 final size:20
Alignment explanation
Indices: 1226017--1226060 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1226007 AAACAGCCAC
*
1226017 AAACTCATTCCAACATATAA
1 AAACTCATTCAAACATATAA
1226037 AAACTCATTCAAACATATAA
1 AAACTCATTCAAACATATAA
1226057 AAAC
1 AAAC
1226061 AAGTTGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (20 bp):
AAACTCATTCAAACATATAA
Found at i:1239423 original size:24 final size:23
Alignment explanation
Indices: 1239379--1239424 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1239369 CTAAATAAAA
* *
1239379 ATAATTTATTAATTAAATATTAG
1 ATAAATTATTAAATAAATATTAG
*
1239402 ATAAATTATATAAATAATTATTA
1 ATAAATTAT-TAAATAAATATTA
1239425 ATATTTGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATAAATTATTAAATAAATATTAG
Found at i:1245929 original size:20 final size:20
Alignment explanation
Indices: 1245904--1245961 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1245894 AGTTGAAAAC
*
1245904 CGCGTTGCGATTTTCCATTT
1 CGCGTTGCGATTTTCCAGTT
* **
1245924 CGCGTTGTGATAGTCCAAGTT
1 CGCGTTGCGATTTTCC-AGTT
1245945 -GTCGTTGCGATTTTCCA
1 CG-CGTTGCGATTTTCCA
1245962 AATTCGTTGC
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
CGCGTTGCGATTTTCCAGTT
Found at i:1245961 original size:21 final size:21
Alignment explanation
Indices: 1245904--1245967 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1245894 AGTTGAAAAC
*
1245904 CGCGTTGCGATTTTCC-ATTT
1 CGCGTTGCGATTTTCCAAGTT
* **
1245924 CGCGTTGTGATAGTCCAAGTT
1 CGCGTTGCGATTTTCCAAGTT
*
1245945 -GTCGTTGCGATTTTCCAAATT
1 CG-CGTTGCGATTTTCCAAGTT
1245966 CG
1 CG
1245968 TTGCGAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 14 0.42
21 18 0.55
22 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (21 bp):
CGCGTTGCGATTTTCCAAGTT
Found at i:1247139 original size:22 final size:22
Alignment explanation
Indices: 1247111--1247225 Score: 121
Period size: 22 Copynumber: 5.4 Consensus size: 22
1247101 AATTTGGAAA
1247111 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
** *
1247133 ATCGCAACGA-ATTTGTAAACT
1 ATCGCAACGACAACTGTAGACT
*
1247154 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
1247176 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
1247195 ATCGCAACGACAAATGTAGACT
1 ATCGCAACGACAACTGTAGACT
1247217 ATCGCAACG
1 ATCGCAACG
1247226 CGAAATGGAA
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
19 13 0.18
20 2 0.03
21 19 0.26
22 39 0.53
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1247168 original size:43 final size:41
Alignment explanation
Indices: 1247093--1247245 Score: 227
Period size: 41 Copynumber: 3.7 Consensus size: 41
1247083 CAACGAATTT
1247093 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
* *
1247134 TCGCAACGAATTTGTAAACTATCGCAACAACAACTGTAGACTA
1 TCGCAACGAATTTGGAAA--ATCGCAACGACAACTGTAGACTA
*
1247177 TCGCAACGAATTTGGAAAATCGCAACGACAAATGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
*
1247218 TCGCAACGCGAA-ATGGAAAATCGCAACG
1 TCGCAA--CGAATTTGGAAAATCGCAACG
1247246 CGATTTTCAA
Statistics
Matches: 102, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
41 44 0.43
42 15 0.15
43 43 0.42
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:1247242 original size:20 final size:20
Alignment explanation
Indices: 1247189--1247308 Score: 109
Period size: 20 Copynumber: 5.9 Consensus size: 20
1247179 GCAACGAATT
1247189 TGGAAAATCGCAACGAC-AAA
1 TGGAAAATCGCAACG-CGAAA
**
1247209 TGTAGACTATCGCAACGCGAAA
1 TG--GAAAATCGCAACGCGAAA
**
1247231 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAA
** * *
1247251 TTCAACTATCGCAACACGAAA
1 TGGAA-AATCGCAACGCGAAA
1247272 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
*
1247292 T-GAAAATCGCAAAGCGA
1 TGGAAAATCGCAACGCGA
1247309 TTTTCAACTA
Statistics
Matches: 79, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
19 15 0.19
20 33 0.42
21 15 0.19
22 16 0.20
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.15
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:1247309 original size:60 final size:61
Alignment explanation
Indices: 1247217--1247330 Score: 194
Period size: 60 Copynumber: 1.9 Consensus size: 61
1247207 AATGTAGACT
*
1247217 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACACGAAATGGAAA
1 ATCGCAACGCGAAATGGAAAATCGCAAAGCGATTTTCAACTATCGCAACACGAAATGGAAA
* *
1247278 ATCGCAACGCGAAAT-GAAAATCGCAAAGCGATTTTCAACTATTGCAACGCGAA
1 ATCGCAACGCGAAATGGAAAATCGCAAAGCGATTTTCAACTATCGCAACACGAA
1247331 TTTGCGATAG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
60 35 0.70
61 15 0.30
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (61 bp):
ATCGCAACGCGAAATGGAAAATCGCAAAGCGATTTTCAACTATCGCAACACGAAATGGAAA
Found at i:1250458 original size:20 final size:21
Alignment explanation
Indices: 1250430--1250469 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1250420 AGTTTCGAAG
* *
1250430 TTTCTCAAAA-GTTTTGAAAC
1 TTTCACAAAATGTGTTGAAAC
1250450 TTTCACAAAATGTGTTGAAA
1 TTTCACAAAATGTGTTGAAA
1250470 AGATTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (21 bp):
TTTCACAAAATGTGTTGAAAC
Found at i:1252326 original size:26 final size:25
Alignment explanation
Indices: 1252297--1252354 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
1252287 ATGAACATAA
*
1252297 GATATAGCTATATG-CAATTATTATAT
1 GATATAG-TATATGAC-ATTACTATAT
1252323 GATATGAGTATATGACATTACTATAT
1 GATAT-AGTATATGACATTACTATAT
*
1252349 GGTATA
1 GATATA
1252355 AATAGGACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.04
26 24 0.86
27 3 0.11
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (25 bp):
GATATAGTATATGACATTACTATAT
Found at i:1255826 original size:23 final size:21
Alignment explanation
Indices: 1255799--1255883 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 21
1255789 CAACTCTTTT
1255799 TTTATGACACGTTTTCTTATAC
1 TTTATGACACGTTTTCTTAT-C
*
1255821 ATTTATGATACGTTTTTCTCTATC
1 -TTTATGACACG-TTTTCT-TATC
*
1255845 TTTATGACACATTTTCTTATGTC
1 TTTATGACACGTTTTCTTA--TC
*
1255868 TTTATGACATGTTTTC
1 TTTATGACACGTTTTC
1255884 GATCGTTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
21 2 0.04
22 6 0.11
23 35 0.66
24 7 0.13
25 3 0.06
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTATGACACGTTTTCTTATC
Found at i:1261639 original size:15 final size:14
Alignment explanation
Indices: 1261599--1261641 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
1261589 ATGAATTACA
* *
1261599 TTTTCTGGAAAATA
1 TTTTCCGGAAAATG
1261613 TTTTCCGGAAAATG
1 TTTTCCGGAAAATG
1261627 TTTTCCAGGAAAATG
1 TTTTCC-GGAAAATG
1261642 AATTACATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (14 bp):
TTTTCCGGAAAATG
Found at i:1261809 original size:23 final size:26
Alignment explanation
Indices: 1261755--1261830 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 26
1261745 TAAATACAAT
*
1261755 AAATAATATTA-TTATCATAAA-ACTTA
1 AAATAAT-TTATTTATTATAAATA-TTA
*
1261781 ATATAA-TTATTT-TTA-AAATATTA
1 AAATAATTTATTTATTATAAATATTA
1261804 AAATAATTTATTTATTATTAAATATTA
1 AAATAATTTATTTATTA-TAAATATTA
1261831 TTTTTATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
23 11 0.27
24 12 0.29
25 5 0.12
26 5 0.12
27 8 0.20
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATAATTTATTTATTATAAATATTA
Found at i:1261909 original size:90 final size:86
Alignment explanation
Indices: 1261794--1261963 Score: 191
Period size: 88 Copynumber: 1.9 Consensus size: 86
1261784 TAATTATTTT
* * * * *
1261794 TAAAATATTAAAATAATTTATTTA-TTATTAAA-TATTATTTTTATAATTTTATTAATAAAAATA
1 TAAAATATTAAAATAATTTAATTATTTATTAAAGTAATAGTGTTAT-ATTATATT-ATAAAAATA
*
1261857 TTAATATTGGTATATTTTATTGAAA
64 TT-A-ATTAGTATATTTTATTGAAA
* * *
1261882 TAAAATATTTTAAATTATGTTAATTATTTATTAAAGTAATAGTGTTATATTATATTTTAAAAATA
1 TAAAATA-TTAAAATAAT-TTAATTATTTATTAAAGTAATAGTGTTATATTATATTATAAAAATA
1261947 TTAATTAGTATATTTTA
64 TTAATTAGTATATTTTA
1261964 AATATCTTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
88 20 0.29
89 9 0.13
90 16 0.23
91 15 0.22
92 9 0.13
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (86 bp):
TAAAATATTAAAATAATTTAATTATTTATTAAAGTAATAGTGTTATATTATATTATAAAAATATT
AATTAGTATATTTTATTGAAA
Found at i:1261982 original size:23 final size:23
Alignment explanation
Indices: 1261933--1261983 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1261923 GTGTTATATT
**
1261933 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
1261956 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1261979 ATATT
1 ATATT
1261984 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1262072 original size:27 final size:26
Alignment explanation
Indices: 1261991--1262203 Score: 69
Period size: 27 Copynumber: 8.2 Consensus size: 26
1261981 ATTATTAGAT
1261991 TATTATATTAATATTAAATATAA-AAATAA
1 TATTAT-TT-ATA-TAAAT-TAATAAATAA
* * *
1262020 TATTATTCATTATTAA-TAATTTAATAA
1 TATTATTTA-TATAAATTAA-TAAATAA
1262047 TATTATTTATATGAAATTAATAAATAA
1 TATTATTTATAT-AAATTAATAAATAA
* * ** *
1262074 TATAAATTT-TATTAA-TAATTTATTA
1 TAT-TATTTATATAAATTAATAAATAA
*
1262099 TA-TA-TTAT-TAAAATAA-AAATAA
1 TATTATTTATATAAATTAATAAATAA
* *
1262121 TA-T-CTTATAT-TATT-ATAATATAA
1 TATTATTTATATAAATTAATAA-ATAA
1262144 TTGATTATTTTATTATAATATTAA-AAATAA
1 -T-ATTA-TTTA-TATAA-ATTAATAAATAA
*
1262174 TATTATATTAGA-AATATTAATAAAT-A
1 TATTAT-TTATATAA-ATTAATAAATAA
1262200 TATT
1 TATT
1262204 TTAAATATTT
Statistics
Matches: 140, Mismatches: 21, Indels: 49
0.67 0.10 0.23
Matches are distributed among these distances:
21 1 0.01
22 19 0.14
23 10 0.07
24 1 0.01
25 13 0.09
26 19 0.14
27 37 0.26
28 20 0.14
29 10 0.07
30 4 0.03
31 5 0.04
32 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
TATTATTTATATAAATTAATAAATAA
Found at i:1262073 original size:54 final size:55
Alignment explanation
Indices: 1261991--1262107 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 55
1261981 ATTATTAGAT
* *
1261991 TATTATATTAATATTAAATATAAAAATAATAT-TATTCATTATTAATAATTTAATA-A
1 TATTAT-TTAATATGAAATATAAAAATAATATAAATT--TTATTAATAATTTAATATA
*
1262047 TATTATTT-ATATGAAAT-TAATAAATAATATAAATTTTATTAATAATTTATTATA
1 TATTATTTAATATGAAATATAA-AAATAATATAAATTTTATTAATAATTTAATATA
1262101 TATTATT
1 TATTATT
1262108 AAAATAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
53 19 0.35
54 25 0.45
55 5 0.09
56 6 0.11
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (55 bp):
TATTATTTAATATGAAATATAAAAATAATATAAATTTTATTAATAATTTAATATA
Found at i:1262179 original size:23 final size:23
Alignment explanation
Indices: 1262126--1262212 Score: 65
Period size: 23 Copynumber: 3.7 Consensus size: 23
1262116 AATAATATCT
* *
1262126 TATATTATTATAATA-TAATTGAT
1 TATATTATTATAATATTAA-TAAA
*
1262149 TATTTTATTATAATATTAA-AAA
1 TATATTATTATAATATTAATAAA
*
1262171 TAATATTATATTAGAAATATTAATAAA
1 T-ATA-T-TATTA-TAATATTAATAAA
1262198 TATATT-TTA-AATATT
1 TATATTATTATAATATT
1262213 TTAATAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
21 6 0.11
22 2 0.04
23 19 0.36
24 5 0.09
25 6 0.11
26 11 0.21
27 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATATTATTATAATATTAATAAA
Found at i:1270553 original size:60 final size:60
Alignment explanation
Indices: 1270477--1270589 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
1270467 TCACGTCCTT
* * *
1270477 AAACTATGACTTTTATTTTAAATTAATCTCTAAACTTTTGAATGTTTTAATTTTATTCTC
1 AAACTATGACTTTTATTCTAAATTAATCTCTAAACTTTTGAATATTTCAATTTTATTCTC
* * * *
1270537 AAACTATGA-TTATTATTCTAAATTAGTTTTTAAACTTTTTAATATTTCAATTT
1 AAACTATGACTT-TTATTCTAAATTAATCTCTAAACTTTTGAATATTTCAATTT
1270590 CATCCTTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 2 0.04
60 43 0.96
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.52
Consensus pattern (60 bp):
AAACTATGACTTTTATTCTAAATTAATCTCTAAACTTTTGAATATTTCAATTTTATTCTC
Found at i:1276325 original size:14 final size:14
Alignment explanation
Indices: 1276306--1276333 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1276296 AAGTGAAAGA
1276306 ATAGTTATATAATT
1 ATAGTTATATAATT
1276320 ATAGTTATATAATT
1 ATAGTTATATAATT
1276334 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:1277369 original size:38 final size:35
Alignment explanation
Indices: 1277292--1277372 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 35
1277282 TTTAATTTTG
* * * *
1277292 TAAAAAAATTATATAAATTTTATGAATTTAATTTTT
1 TAAAAAAA-TATATAAATTATATGAATTCAACTTAT
1277328 TAAAGAAAATATATAAATTATAGTAGAATTCAACTTAT
1 TAAA-AAAATATATAAATTATA-T-GAATTCAACTTAT
1277366 TAAAAAA
1 TAAAAAA
1277373 CAAATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
36 16 0.42
37 8 0.21
38 14 0.37
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (35 bp):
TAAAAAAATATATAAATTATATGAATTCAACTTAT
Found at i:1277518 original size:18 final size:18
Alignment explanation
Indices: 1277495--1277540 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1277485 AACATTCCCA
1277495 GTAATCTTATTCCAACCG
1 GTAATCTTATTCCAACCG
*
1277513 GTAATCTTATTCCCACCG
1 GTAATCTTATTCCAACCG
* *
1277531 ATAATTTTAT
1 GTAATCTTAT
1277541 ATTTCGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (18 bp):
GTAATCTTATTCCAACCG
Found at i:1277963 original size:69 final size:71
Alignment explanation
Indices: 1277864--1278000 Score: 192
Period size: 68 Copynumber: 1.9 Consensus size: 71
1277854 TAAAATGGGT
* *
1277864 CCCACTAAATTATATATTTTCGAGT-TTTTAAAT-AAAAAATGATGTTT-AAAT-TTTTTAAATT
1 CCCACTAAATTACATATTTTCGAGTATTTAAAATAAAAAAAT-ATGTTTAAAATATTTTTAAATT
1277925 ATTGAGG
65 ATTGAGG
*
1277932 CCCACTAAATTACCATATTTTCGAGTATTTAAAATAAAAAAAATATGTTTAAAATATTTTTTAAT
1 CCCACTAAATTA-CATATTTTCGAGTATTTAAAAT-AAAAAAATATGTTTAAAATATTTTTAAAT
1277997 TATT
64 TATT
1278001 AAACTTAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
68 12 0.20
69 12 0.20
70 7 0.12
71 6 0.10
72 11 0.18
73 12 0.20
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (71 bp):
CCCACTAAATTACATATTTTCGAGTATTTAAAATAAAAAAATATGTTTAAAATATTTTTAAATTA
TTGAGG
Found at i:1306495 original size:20 final size:20
Alignment explanation
Indices: 1306472--1306646 Score: 154
Period size: 20 Copynumber: 8.7 Consensus size: 20
1306462 GTTTCCAGAT
1306472 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
** *
1306492 TCGCATTGCGATTTTCCGACTA
1 TCGCAACGCGA--TTCTGACTA
* * * *
1306514 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
* * * *
1306534 TTGCAATGCGAGTATGACTA
1 TCGCAACGCGATTCTGACTA
1306554 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
1306574 TCACAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
1306594 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
**
1306614 TCGCAACGCGAAGCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
1306634 TCACAATGCGATT
1 TCGCAACGCGATT
1306647 TTCAAAGCGC
Statistics
Matches: 124, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
19 1 0.01
20 104 0.84
21 1 0.01
22 18 0.15
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1306845 original size:22 final size:22
Alignment explanation
Indices: 1306820--1306862 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1306810 GGCGACATCC
*
1306820 GTCCCCAACTCCGACTAAATCA
1 GTCCCCAACTCCGACGAAATCA
*
1306842 GTCCCCATCTCCGACGAAATC
1 GTCCCCAACTCCGACGAAATC
1306863 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.42, G:0.12, T:0.19
Consensus pattern (22 bp):
GTCCCCAACTCCGACGAAATCA
Found at i:1307353 original size:20 final size:20
Alignment explanation
Indices: 1307249--1307355 Score: 101
Period size: 20 Copynumber: 5.5 Consensus size: 20
1307239 AGAATCGCAA
*
1307249 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
1307268 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
1307287 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** * *
1307307 TGCGATAGTCTTTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
* *
1307327 TACGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
1307347 TGCGATTTT
1 TGCGATTTT
1307356 AAGTTTCAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
19 26 0.35
20 48 0.65
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.47
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1309117 original size:18 final size:18
Alignment explanation
Indices: 1309091--1309140 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
1309081 TTTACTCGTA
1309091 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
1309109 ATTTTACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1309127 ATTTCACTTAGATT
1 ATTTCACTTAGATT
1309141 GCTTAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1309383 original size:20 final size:20
Alignment explanation
Indices: 1309358--1309413 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
1309348 GCAATTCTCT
1309358 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1309378 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1309398 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
1309414 CGTGTTGCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1309420 original size:18 final size:19
Alignment explanation
Indices: 1309358--1309424 Score: 100
Period size: 20 Copynumber: 3.5 Consensus size: 19
1309348 GCAATTCTCT
1309358 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
1309378 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
1309398 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
1309416 TGTTGCGAT
1 CGTTGCGAT
1309425 TTTAAGTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
18 12 0.26
20 34 0.74
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1310005 original size:21 final size:21
Alignment explanation
Indices: 1309914--1310018 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
1309904 GACTCACCTG
*
1309914 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1309936 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1309956 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1309977 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1309998 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1310019 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1310011 original size:42 final size:42
Alignment explanation
Indices: 1309911--1310021 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
1309901 CCCGACTCAC
* * * *
1309911 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
1309953 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
1309995 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1310022 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1311441 original size:14 final size:14
Alignment explanation
Indices: 1311407--1311468 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
1311397 TTGCTTGTTT
*
1311407 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
1311421 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1311435 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1311450 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1311464 TAATT
1 -AATT
1311469 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1311607 original size:20 final size:20
Alignment explanation
Indices: 1311582--1311620 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1311572 ACGCTAAACT
*
1311582 CAAAATCGCAATGCGAAAGA
1 CAAAATCGCAACGCGAAAGA
1311602 CAAAATCGCAACGCGAAAG
1 CAAAATCGCAACGCGAAAG
1311621 TCAATTCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.23, G:0.21, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAACGCGAAAGA
Found at i:1311673 original size:34 final size:34
Alignment explanation
Indices: 1311630--1311879 Score: 139
Period size: 40 Copynumber: 6.8 Consensus size: 34
1311620 GTCAATTCGT
* *
1311630 GTTGCGATAGTCTAATACGCTTTGCGATTTTCTC
1 GTTGCGATAGTCAAATACGCGTTGCGATTTTCTC
* *
1311664 GTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCGC
1 GTTGCGATAGTCAAATACGCGTTGCGAT--T----TTCTC
* **
1311704 GTTGCGATACTCAAATTTGCGTTGCGATTTTCTC
1 GTTGCGATAGTCAAATACGCGTTGCGATTTTCTC
1311738 GTTGCGATAGTCAAATA-GCCGTTGCGATAGTCAAATTCGT-
1 GTTGCGATAGTCAAATACG-CGTTGCGAT--T----TTC-TC
* *
1311778 GTTGCGATAGACAAATTCGCGTTGCGATAGTCATAT-TC
1 GTTGCGATAGTCAAATACGCGTTGCGAT--T--T-TCTC
* *
1311816 GTGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGA
1 --GTTGCGATAGTCAAATACGCGTTGCGATTTTCT-C
* * * *
1311852 GTTACGATAATCAAATTCGTGTTGCGAT
1 GTTGCGATAGTCAAATACGCGTTGCGAT
1311880 AGTCAAATTC
Statistics
Matches: 177, Mismatches: 19, Indels: 40
0.75 0.08 0.17
Matches are distributed among these distances:
33 1 0.01
34 78 0.44
35 2 0.01
36 3 0.02
37 1 0.01
38 4 0.02
39 1 0.01
40 85 0.48
41 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (34 bp):
GTTGCGATAGTCAAATACGCGTTGCGATTTTCTC
Found at i:1311688 original size:20 final size:20
Alignment explanation
Indices: 1311663--1311907 Score: 237
Period size: 20 Copynumber: 12.8 Consensus size: 20
1311653 GCGATTTTCT
* *
1311663 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
1311683 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1311703 CGTTGCGATACTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
1311723 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
1311737 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
1311756 CCGTTGCGATAGTCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
* *
1311777 TGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1311797 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
1311817 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1311837 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* * *
1311851 AGTTACGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1311871 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1311891 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1311908 GAATGTGTAA
Statistics
Matches: 184, Mismatches: 27, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
14 21 0.11
16 2 0.01
18 2 0.01
19 1 0.01
20 156 0.85
21 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1311708 original size:74 final size:74
Alignment explanation
Indices: 1311623--1311805 Score: 285
Period size: 74 Copynumber: 2.5 Consensus size: 74
1311613 CGCGAAAGTC
* * *
1311623 AATTCGTGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1 AATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1311688 CGATAATCA
66 CGATAATCA
* * * *
1311697 AATTCGCGTTGCGATACTCAAATTTGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAGCCGTTG
1 AATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
*
1311762 CGATAGTCA
66 CGATAATCA
*
1311771 AATTCGTGTTGCGATAGACAAATTCGCGTTGCGAT
1 AATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT
1311806 AGTCATATTC
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 97 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (74 bp):
AATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
CGATAATCA
Found at i:1311741 original size:54 final size:54
Alignment explanation
Indices: 1311683--1311899 Score: 231
Period size: 54 Copynumber: 3.9 Consensus size: 54
1311673 GTCAAATACC
* *
1311683 CGTTGCGATAATCAAATTCGCGTTGCGATACTCAAATTTGCGTTGCGATTTTCT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* * * * *
1311737 CGTTGCGATAGTCAAA-TAGCCGTTGCGATAGTCAAATTCGTGTTGCGATAGACAAATTCG
1 CGTTGCGATAATCAAATTCG-CGTTGCGATAGTCAAATTCGCGTTGCGAT------TTTCT
* * *
1311797 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTT-T
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* * *
1311850 GAGTTACGATAATCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT
1 -CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1311900 ATTCAAATGA
Statistics
Matches: 137, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
53 2 0.01
54 88 0.64
60 45 0.33
61 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:1312130 original size:140 final size:140
Alignment explanation
Indices: 1311878--1312147 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
1311868 TCGTGTTGCG
*
1311878 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
1311943 TAGCAATGTTCAAACTCAAGTTACTAATATATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1312008 AATACACATA
131 AATACACATA
1312018 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
1312083 TATCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1312148 TACAACGTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1312230 original size:18 final size:18
Alignment explanation
Indices: 1312207--1312241 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1312197 AAGCCGGTTG
*
1312207 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1312225 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1312242 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1314297 original size:14 final size:14
Alignment explanation
Indices: 1314278--1314314 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1314268 TCCCGTGGCA
1314278 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
1314292 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
1314306 TTCTTCTTC
1 TT-TTCTTC
1314315 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1315404 original size:20 final size:20
Alignment explanation
Indices: 1315379--1315437 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
1315369 GAAATTCAGT
*
1315379 GTTGCGGCAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
*
1315399 GTTGCGATAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
* *
1315419 GTTGCGATAGTCATAATCG
1 GTTGCGACAGTCAGAATCG
1315438 TATTGCGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (20 bp):
GTTGCGACAGTCAGAATCGC
Found at i:1315443 original size:20 final size:20
Alignment explanation
Indices: 1315387--1315505 Score: 107
Period size: 20 Copynumber: 6.0 Consensus size: 20
1315377 GTGTTGCGGC
* *
1315387 AGTCAGAATCGCGTTGCGAT
1 AGTCATAATCGCATTGCGAT
* *
1315407 AGTCAGAATCGCGTTGCGAT
1 AGTCATAATCGCATTGCGAT
*
1315427 AGTCATAATCGTATTGCGAT
1 AGTCATAATCGCATTGCGAT
* *
1315447 -TTACATATTCGCATTGCGAT
1 AGT-CATAATCGCATTGCGAT
* *
1315467 -TTACATATTCGCATTGCGAT
1 AGT-CATAATCGCATTGCGAT
* *
1315487 AGTCAAAATCGCGTTGCGA
1 AGTCATAATCGCATTGCGA
1315506 ATCTGGAAAC
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
19 1 0.01
20 85 0.98
21 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (20 bp):
AGTCATAATCGCATTGCGAT
Found at i:1315973 original size:87 final size:86
Alignment explanation
Indices: 1315804--1316064 Score: 359
Period size: 87 Copynumber: 3.0 Consensus size: 86
1315794 TTGTACTATG
* *
1315804 CAATCATCATAGACTATTTATTTA-TTTTTATTAATTT-G--AAGTATAAGACAATATTTATTCA
1 CAATCATCATAGACTATTTATTTATTTTTTATTAATTTAGATAAGTATAAGACAATATATGTT-A
*
1315865 AAAATAACTATCAACCATTTGA
65 AAAATAACTCTCAACCATTTGA
*
1315887 CAATCATCATAGACTATTTATTTATTTTTTATTAATTTGAGATAAGTATAAGACAATATCTGTTA
1 CAATCATCATAGACTATTTATTTATTTTTTATTAATTT-AGATAAGTATAAGACAATATATGTTA
*
1315952 AAAATAATTCTCAACCATTTGA
65 AAAATAACTCTCAACCATTTGA
* *
1315974 CAATCATCATAGACTATTTATTTATTTATTTTTATTAATTTAAAGTAAGTATAAAACAATATATG
1 CAATCATCATAGACTATTTATTTA--T-TTTTTATTAATTTAGA-TAAGTATAAGACAATATATG
*
1316039 TTTAAAAATAACTCTCAATCATTTGA
62 -TTAAAAATAACTCTCAACCATTTGA
1316065 GATGAACTCT
Statistics
Matches: 159, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
83 24 0.15
84 13 0.08
86 1 0.01
87 45 0.28
88 19 0.12
89 3 0.02
90 31 0.19
91 23 0.14
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.42
Consensus pattern (86 bp):
CAATCATCATAGACTATTTATTTATTTTTTATTAATTTAGATAAGTATAAGACAATATATGTTAA
AAATAACTCTCAACCATTTGA
Found at i:1321611 original size:23 final size:23
Alignment explanation
Indices: 1321578--1321620 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
1321568 AATATATTCA
1321578 AATTTTTAAAAAATAA-AGGACG
1 AATTTTTAAAAAATAATAGGACG
1321600 AATTTTTAAAAAATAATAGGA
1 AATTTTTAAAAAATAATAGGA
1321621 AATTGGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (23 bp):
AATTTTTAAAAAATAATAGGACG
Found at i:1323347 original size:22 final size:21
Alignment explanation
Indices: 1323322--1323362 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1323312 TAATATTTGT
1323322 TACTAAAGGCCCAATTTTTTAA
1 TACTAAA-GCCCAATTTTTTAA
**
1323344 TACTTGAGCCCAATTTTTT
1 TACTAAAGCCCAATTTTTT
1323363 CAGTACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (21 bp):
TACTAAAGCCCAATTTTTTAA
Found at i:1323473 original size:29 final size:31
Alignment explanation
Indices: 1323428--1323487 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
1323418 CCTAAAATTT
* *
1323428 ACTTTTCTTTTAATATTTGTTTTTA-GGAAC
1 ACTTTTCTTTCAATATTTGTTATTATGGAAC
1323458 ACTTTT-TTTCAATATTTGTTATTATGGAAC
1 ACTTTTCTTTCAATATTTGTTATTATGGAAC
1323488 TAGCCTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (31 bp):
ACTTTTCTTTCAATATTTGTTATTATGGAAC
Found at i:1336165 original size:32 final size:32
Alignment explanation
Indices: 1336129--1336265 Score: 152
Period size: 32 Copynumber: 4.3 Consensus size: 32
1336119 CCTATGGTGA
* *
1336129 CCTTGGGTAAGCTCTGAGGCCCCAAGGTATTT
1 CCTTGGGTAAGCTCTTAGGCCCCAAGGTACTT
*
1336161 CCTTGGGTAGGCT-TTAAGGCCCCAAGGTACTT
1 CCTTGGGTAAGCTCTT-AGGCCCCAAGGTACTT
* * * * * *
1336193 CATTGGGTAGGTTCTTAGACCCTAATGTACTT
1 CCTTGGGTAAGCTCTTAGGCCCCAAGGTACTT
*
1336225 CCTTGGGTAAGCTCTTAGGCCCTAAGGTAC-T
1 CCTTGGGTAAGCTCTTAGGCCCCAAGGTACTT
1336256 CCTTTGGGTA
1 CC-TTGGGTA
1336266 GATTCTCAAG
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.04
32 83 0.93
33 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.31
Consensus pattern (32 bp):
CCTTGGGTAAGCTCTTAGGCCCCAAGGTACTT
Found at i:1337343 original size:26 final size:26
Alignment explanation
Indices: 1337318--1337376 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
1337308 GATCAAAACT
1337318 TTAAA-ATATAATTTTAGAGGGTAAC
1 TTAAATATATAATTTTAGAGGGTAAC
1337343 TTAAACTTATATAATTTTAGAGGGTAAAC
1 TTAAA--TATATAATTTTAGAGGGT-AAC
1337372 TTAAA
1 TTAAA
1337377 CTTATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.17
28 17 0.57
29 8 0.27
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (26 bp):
TTAAATATATAATTTTAGAGGGTAAC
Found at i:1337359 original size:28 final size:29
Alignment explanation
Indices: 1337323--1337387 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
1337313 AAACTTTAAA
1337323 ATATAATTTTAGAGGGT-AACTTAAACTT
1 ATATAATTTTAGAGGGTAAACTTAAACTT
1337351 ATATAATTTTAGAGGGTAAACTTAAACTT
1 ATATAATTTTAGAGGGTAAACTTAAACTT
*
1337380 ATAAAATT
1 ATATAATT
1337388 CTAATGAGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.38
Consensus pattern (29 bp):
ATATAATTTTAGAGGGTAAACTTAAACTT
Found at i:1340679 original size:21 final size:21
Alignment explanation
Indices: 1340655--1340695 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1340645 CCAATTATCA
1340655 ATAAATTAATTATTTATTTTC
1 ATAAATTAATTATTTATTTTC
* *
1340676 ATAATTTATTTATTTATTTT
1 ATAAATTAATTATTTATTTT
1340696 ACGTGATTGT
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:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
ATAAATTAATTATTTATTTTC
Found at i:1341636 original size:3 final size:3
Alignment explanation
Indices: 1341624--1341663 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1341614 AAAATTTTAG
1341624 ATA A-A ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1341664 GTAAGGTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1341652 original size:20 final size:20
Alignment explanation
Indices: 1341624--1341663 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1341614 AAAATTTTAG
1341624 ATAAAATAATAATAATAATA
1 ATAAAATAATAATAATAATA
*
1341644 ATAATATAATAATAATAATA
1 ATAAAATAATAATAATAATA
1341664 GTAAGGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAATAATAATAATAATA
Found at i:1343618 original size:14 final size:14
Alignment explanation
Indices: 1343599--1343656 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
1343589 AGACCAAGCT
*
1343599 GCTTTGTTTTCATA
1 GCTTTGCTTTCATA
*
1343613 GCTTTGCTTTCTTA
1 GCTTTGCTTTCATA
1343627 GCTTATG-TTT-AT-
1 GCTT-TGCTTTCATA
1343639 G-TTTGCTTTCATA
1 GCTTTGCTTTCATA
1343652 GCTTT
1 GCTTT
1343657 AGTTTATGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 3 0.08
13 2 0.06
14 22 0.61
15 2 0.06
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.57
Consensus pattern (14 bp):
GCTTTGCTTTCATA
Found at i:1343643 original size:25 final size:25
Alignment explanation
Indices: 1343615--1343667 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
1343605 TTTTCATAGC
*
1343615 TTTGCTTTCTTAGC-TTATGTTTATG
1 TTTGCTTTCATAGCTTTA-GTTTATG
1343640 TTTGCTTTCATAGCTTTAGTTTATG
1 TTTGCTTTCATAGCTTTAGTTTATG
1343665 TTT
1 TTT
1343668 TCATAGCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.13, C:0.11, G:0.15, T:0.60
Consensus pattern (25 bp):
TTTGCTTTCATAGCTTTAGTTTATG
Found at i:1355304 original size:51 final size:52
Alignment explanation
Indices: 1355186--1355406 Score: 216
Period size: 52 Copynumber: 4.3 Consensus size: 52
1355176 GCATCACATG
* * * * * *
1355186 TCCCCAAACCATGACTCATTTTAAACTGGTCCTCAAACATTTGAATATTTCA
1 TCCCCAAACTATGACTCATTCTAAATTAGTCCTAAAACATTTCAATATTTCA
* * *
1355238 TCCTCAAATTATGACTCATTCTAAATTAGTCCTTAAAACA-TTCCA-ATTTCA
1 TCCCCAAACTATGACTCATTCTAAATTAGTCC-TAAAACATTTCAATATTTCA
* * * * *
1355289 TCCCCAAACCATGACTCATTTTAAATTGGTCCTCAAACATTTGAATATTTCA
1 TCCCCAAACTATGACTCATTCTAAATTAGTCCTAAAACATTTCAATATTTCA
* * * * * *
1355341 TACTCAAATTATGAATCATTCTAAATTAGTCCTTAAA-ATATTCCA-ATTTCA
1 TCCCCAAACTATGACTCATTCTAAATTAGTCCTAAAACAT-TTCAATATTTCA
1355392 TCCCCAAACTATGAC
1 TCCCCAAACTATGAC
1355407 CCTCGTTCTA
Statistics
Matches: 134, Mismatches: 31, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
50 6 0.04
51 55 0.41
52 67 0.50
53 6 0.04
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (52 bp):
TCCCCAAACTATGACTCATTCTAAATTAGTCCTAAAACATTTCAATATTTCA
Found at i:1355365 original size:103 final size:103
Alignment explanation
Indices: 1355186--1355406 Score: 397
Period size: 103 Copynumber: 2.1 Consensus size: 103
1355176 GCATCACATG
*
1355186 TCCCCAAACCATGACTCATTTTAAACTGGTCCTCAAACATTTGAATATTTCATCCTCAAATTATG
1 TCCCCAAACCATGACTCATTTTAAACTGGTCCTCAAACATTTGAATATTTCATACTCAAATTATG
*
1355251 ACTCATTCTAAATTAGTCCTTAAAACATTCCAATTTCA
66 AATCATTCTAAATTAGTCCTTAAAACATTCCAATTTCA
*
1355289 TCCCCAAACCATGACTCATTTTAAATTGGTCCTCAAACATTTGAATATTTCATACTCAAATTATG
1 TCCCCAAACCATGACTCATTTTAAACTGGTCCTCAAACATTTGAATATTTCATACTCAAATTATG
*
1355354 AATCATTCTAAATTAGTCCTTAAAATATTCCAATTTCA
66 AATCATTCTAAATTAGTCCTTAAAACATTCCAATTTCA
*
1355392 TCCCCAAACTATGAC
1 TCCCCAAACCATGAC
1355407 CCTCGTTCTA
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (103 bp):
TCCCCAAACCATGACTCATTTTAAACTGGTCCTCAAACATTTGAATATTTCATACTCAAATTATG
AATCATTCTAAATTAGTCCTTAAAACATTCCAATTTCA
Found at i:1360597 original size:16 final size:18
Alignment explanation
Indices: 1360565--1360599 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1360555 ATATAAAAAC
1360565 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
1360583 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
1360599 A
1 A
1360600 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:1360780 original size:35 final size:33
Alignment explanation
Indices: 1360727--1360797 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
1360717 ATAAAAATAT
*
1360727 ATATATAATAACACTAATAAAAAAAACATATATAC
1 ATATATAATAAAACTAAT--AAAAAACATATATAC
* **
1360762 ATATATAATAAAATTAATAGGAAACATATATAC
1 ATATATAATAAAACTAATAAAAAACATATATAC
1360795 ATA
1 ATA
1360798 CAAGAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 16 0.50
35 16 0.50
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.28
Consensus pattern (33 bp):
ATATATAATAAAACTAATAAAAAACATATATAC
Found at i:1361225 original size:37 final size:36
Alignment explanation
Indices: 1361173--1361274 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
1361163 AATATATAAC
1361173 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
1361210 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
1361244 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1361275 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1362123 original size:105 final size:105
Alignment explanation
Indices: 1361820--1362753 Score: 1443
Period size: 105 Copynumber: 9.0 Consensus size: 105
1361810 CATTGTTCCA
* * * ** * * *
1361820 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * * *
1361885 CAGCCGTCCCTTCGTTGTGACGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1361926 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1361986 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1362026 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
1362091 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTTTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1362131 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
1362196 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1362236 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1362301 AGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1362341 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
1362406 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1362446 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA---GTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1362508 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1362548 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1362613 ATCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1362653 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
** * *
1362718 CAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1362754 CCTCGAGTAC
Statistics
Matches: 775, Mismatches: 44, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
100 82 0.11
101 1 0.00
102 104 0.13
103 4 0.01
104 3 0.00
105 506 0.65
106 75 0.10
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1363531 original size:67 final size:66
Alignment explanation
Indices: 1363396--1363553 Score: 194
Period size: 68 Copynumber: 2.4 Consensus size: 66
1363386 AAGATATCTG
* * **
1363396 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACCGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
1363461 TT
65 TT
* * *
1363463 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGAA-AAAATT-TGTTTTAGGGGAAATAAATTCAAAG
1 T-TGTTTCAAGAGAAACCGTCTCAAGGGA-AACAAAATTATGTTTTAAGGGAAATAAATTCAAAG
*
1363526 GTT
64 ATT
*
1363529 TTGTTTCAAGGGAAACCGTCTCAAG
1 TTGTTTCAAGAGAAACCGTCTCAAG
1363554 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
65 21 0.27
66 3 0.04
67 23 0.29
68 30 0.38
69 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACCGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:1363580 original size:36 final size:35
Alignment explanation
Indices: 1363529--1363808 Score: 261
Period size: 36 Copynumber: 8.0 Consensus size: 35
1363519 TTCAAAGGTT
* * *
1363529 TTGTTTCAAGGGAAACCGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1363565 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1363600 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
1363638 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
1363667 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
1363702 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1363739 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1363774 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
1363809 CTCTTATAGT
Statistics
Matches: 202, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 132 0.65
37 33 0.16
38 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1363639 original size:138 final size:137
Alignment explanation
Indices: 1363477--1363790 Score: 414
Period size: 138 Copynumber: 2.3 Consensus size: 137
1363467 TTTCAAGAGT
* * * * *
1363477 AACTGTCTCAAGGGAGAAAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
1363542 AACCGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACCGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
1363606 TCCAAAAGA
129 TCCAAAAGA
** * * * *
1363615 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * * *
1363680 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACCGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
1363745 CAAGAGA
131 CAAAAGA
*
1363752 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1363791 TGTCTCAAGA
Statistics
Matches: 150, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
137 49 0.33
138 101 0.67
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.26
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACCGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:1363753 original size:102 final size:102
Alignment explanation
Indices: 1363565--1363753 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 102
1363555 TAGACGAAAA
*
1363565 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
*
1363630 GACGGAATTTGTTTCAAAGAAAACATATTCAAATATT
66 GACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
* * * ** *
1363667 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
1363731 GACGAAATTTGTTTCAAGAGAAA
66 GACGAAATTTGTTTCAA-AGAAA
1363754 CTGTCTCAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 36 0.46
102 42 0.54
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
Found at i:1364314 original size:17 final size:18
Alignment explanation
Indices: 1364288--1364322 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1364278 TGTTGAATCC
*
1364288 CCAAAGATGCCTCAATAT
1 CCAAAGATGCCCCAATAT
1364306 CCAAA-ATGCCCCAATAT
1 CCAAAGATGCCCCAATAT
1364323 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (18 bp):
CCAAAGATGCCCCAATAT
Found at i:1364762 original size:22 final size:22
Alignment explanation
Indices: 1364736--1364784 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1364726 TTGTGTTTGG
* *
1364736 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
1364758 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
1364780 TCAAA
1 TCAAA
1364785 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:1364791 original size:22 final size:22
Alignment explanation
Indices: 1364748--1364791 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1364738 AAAGGTTTGG
* * *
1364748 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
1364770 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
1364792 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:1365454 original size:16 final size:17
Alignment explanation
Indices: 1365435--1365490 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
1365425 TCTTTTTGAT
*
1365435 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
1365451 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* * *
1365468 TTTTTCT-TTGTTTTTT
1 TTTTGCTCTTGTTTCTC
1365484 TTTTGCT
1 TTTTGCT
1365491 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 26 0.81
17 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:1368733 original size:16 final size:18
Alignment explanation
Indices: 1368701--1368735 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1368691 ATATAAAAAC
1368701 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
1368719 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
1368735 A
1 A
1368736 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:1368899 original size:35 final size:33
Alignment explanation
Indices: 1368848--1368933 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
1368838 AAATATATAA
* * *
1368848 ATATATATATATAATAACACTAATAAAAAAAACAT
1 ATATACATATAGAATAAAACTAAT--AAAAAACAT
* **
1368883 ATATACATATAGAATAAAATTAATAGGAAACAT
1 ATATACATATAGAATAAAACTAATAAAAAACAT
*
1368916 ATATACATACAAGAATAA
1 ATATACATA-TAGAATAA
1368934 TAAAGTAGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 16 0.37
34 7 0.16
35 20 0.47
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (33 bp):
ATATACATATAGAATAAAACTAATAAAAAACAT
Found at i:1369346 original size:37 final size:36
Alignment explanation
Indices: 1369303--1369404 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
1369293 ATAGTATAAC
1369303 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
1369340 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
1369374 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1369405 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1384127 original size:13 final size:13
Alignment explanation
Indices: 1384109--1384135 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1384099 TTATAGACGC
1384109 GCATATGAAGACT
1 GCATATGAAGACT
1384122 GCATATGAAGACT
1 GCATATGAAGACT
1384135 G
1 G
1384136 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:1384155 original size:4 final size:4
Alignment explanation
Indices: 1384146--1384184 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
1384136 TTCAACTATG
1384146 TATT TATT TATT TATT TATT TATT TATT TCA-T TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT T-ATT TATT TAT
1384185 ACATACATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 1 0.03
4 31 0.94
5 1 0.03
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:1386840 original size:11 final size:11
Alignment explanation
Indices: 1386824--1386855 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1386814 TGCCCAAATT
1386824 TATAAAATTTA
1 TATAAAATTTA
1386835 TATAAAATTTA
1 TATAAAATTTA
1386846 TATAAAATTT
1 TATAAAATTT
1386856 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATAAAATTTA
Found at i:1387178 original size:20 final size:20
Alignment explanation
Indices: 1387151--1387240 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
1387141 ATGACCAACA
*
1387151 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1387171 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1387191 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1387211 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1387231 AAATCACAAC
1 AAATCGCAAC
1387241 ACTGAAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.02
20 59 0.98
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1387971 original size:24 final size:24
Alignment explanation
Indices: 1387932--1387978 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1387922 AAATTTGGTC
1387932 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1387956 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1387979 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1388170 original size:12 final size:12
Alignment explanation
Indices: 1388153--1388177 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1388143 ATATAATCCT
1388153 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1388165 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1388177 G
1 G
1388178 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1390539 original size:53 final size:53
Alignment explanation
Indices: 1390476--1390765 Score: 537
Period size: 53 Copynumber: 5.5 Consensus size: 53
1390466 GCAACGAGAG
* * *
1390476 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
1390529 AATCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1390582 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1390634 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1390687 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1390740 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
1390766 TTGCGATTCT
Statistics
Matches: 231, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
52 52 0.23
53 179 0.77
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:1390619 original size:86 final size:84
Alignment explanation
Indices: 1390462--1390641 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 84
1390452 CGGAAATTAC
1390462 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAA-GCGG-AATG
1390527 AAAATCGCAATGCAAAATGAA
64 AAAATCGCAATGCAAAATGAA
*
1390548 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAAAATCGCAAGCGG
* *
1390611 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCAAAATGAA
1390634 AATCGCAA
1 AATCGCAA
1390642 TGCGAAATGA
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
86 53 0.62
87 16 0.19
89 2 0.02
90 1 0.01
91 2 0.02
92 11 0.13
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAAGCGGAATGAA
AATCGCAATGCAAAATGAA
Found at i:1390662 original size:105 final size:106
Alignment explanation
Indices: 1390476--1390765 Score: 537
Period size: 105 Copynumber: 2.7 Consensus size: 106
1390466 GCAACGAGAG
* * * *
1390476 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1390541 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1390582 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1390646 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1390687 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1390752 AAATGAAAATCGCA
66 AAATGAAAATCGCA
1390766 TTGCGATTCT
Statistics
Matches: 179, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
105 104 0.58
106 75 0.42
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (106 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:1390785 original size:158 final size:158
Alignment explanation
Indices: 1390476--1390765 Score: 544
Period size: 158 Copynumber: 1.8 Consensus size: 158
1390466 GCAACGAGAG
1390476 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCA
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCA
1390541 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCG
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCG
1390606 CAACGAGAGAATCGCAATGCGAAATGAA
131 CAACGAGAGAATCGCAATGCGAAATGAA
* * * *
1390634 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCA
1390699 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCG
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCG
1390764 CA
131 CA
1390766 TTGCGATTCT
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 128 1.00
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (158 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCA
AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCG
CAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1390805 original size:53 final size:52
Alignment explanation
Indices: 1390742--1390857 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
1390732 GAAATGAAAA
*
1390742 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
1390794 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1390847 TCGCATTGCGA
1 TCGCATTGCGA
1390858 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1390820 original size:19 final size:19
Alignment explanation
Indices: 1390780--1390867 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
1390770 GATTCTCTCG
1390780 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1390800 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1390819 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1390833 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1390852 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1390868 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1390977 original size:14 final size:14
Alignment explanation
Indices: 1390958--1390994 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1390948 CATCAATTAC
1390958 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1390972 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1390986 ACAAATCAA
1 ACAAATCAA
1390995 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1392959 original size:19 final size:19
Alignment explanation
Indices: 1392917--1393089 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
1392907 TAGTTTACTT
* *
1392917 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
1392937 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
1392956 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
1392975 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1392994 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1393013 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1393027 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1393046 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
1393060 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1393079 TCGCAATGCGA
1 TCGCAACGCGA
1393090 TTTTGGTTTC
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.05
17 7 0.05
18 1 0.01
19 82 0.64
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1393030 original size:14 final size:14
Alignment explanation
Indices: 1393011--1393067 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1393001 GCGAAATGAA
*
1393011 AATCGCAACGACAG
1 AATCGCAACGAAAG
1393025 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
1393042 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
1393058 AATCGCAACG
1 AATCGCAACG
1393068 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1393038 original size:33 final size:33
Alignment explanation
Indices: 1392992--1393084 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1392982 GCGAAACCAA
1392992 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
1393025 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1393058 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1393085 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:1393081 original size:52 final size:52
Alignment explanation
Indices: 1392951--1393089 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
1392941 AACGCGAAAT
* * * *
1392951 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
1393003 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
1393055 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
1393090 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:1393121 original size:19 final size:19
Alignment explanation
Indices: 1393085--1393129 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1393075 AAAATCGCAA
1393085 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1393104 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1393123 TGCGATT
1 TGCGATT
1393130 CTGTCGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.07, C:0.16, G:0.31, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1393139 original size:14 final size:14
Alignment explanation
Indices: 1393120--1393176 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1393110 TTTGGTTTCG
*
1393120 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
1393134 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
1393151 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
1393167 CGTTGCGATT
1 CGTTGCGATT
1393177 TTAAGTTTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1393143 original size:33 final size:33
Alignment explanation
Indices: 1393101--1393194 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
1393091 TTTGGTTTCG
* *
1393101 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGT
1 CGTTGCGATTTTAGTTTCGCGTTGCGATTCTCT
*
1393134 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTT-AGTTTCGCGTTGCGATTCTCT
*
1393167 CGTTGCGATTTTAAGTTTCGTGTTGCGA
1 CGTTGCGATTTT-AGTTTCGCGTTGCGA
1393195 AAGTAAACTA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
33 42 0.79
34 11 0.21
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTAGTTTCGCGTTGCGATTCTCT
Done.