Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 35
Found at i:2172358 original size:23 final size:20
Alignment explanation
Indices: 2172299--2172359 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
2172289 TTTTGGTGCA
*
2172299 GAGGGAATCGATCCCCCCAT
1 GAGGGAACCGATCCCCCCAT
* **
2172319 GAGGGAACCAATTCCCCCTTT
1 GAGGGAACCGA-TCCCCCCAT
2172340 GAAGGGGAACCGATCCCCCC
1 G-A-GGGAACCGATCCCCCC
2172360 CCACAGGGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 9 0.28
21 8 0.25
22 7 0.22
23 8 0.25
ACGTcount: A:0.25, C:0.36, G:0.25, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCAT
Found at i:2174023 original size:12 final size:12
Alignment explanation
Indices: 2174008--2174036 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2173998 AGATGAACCT
2174008 GAGCAGCCCGAA
1 GAGCAGCCCGAA
2174020 GAGCAGCCCGAA
1 GAGCAGCCCGAA
2174032 GAGCA
1 GAGCA
2174037 AGCACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAA
Found at i:2176111 original size:14 final size:14
Alignment explanation
Indices: 2176092--2176128 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2176082 TCCCGTGGCA
2176092 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
2176106 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
2176120 TTCTTCTTC
1 TT-TTCTTC
2176129 TTCTTTTTAT
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:2177215 original size:20 final size:20
Alignment explanation
Indices: 2177190--2177280 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
2177180 TTGAAATTTA
*
2177190 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
**
2177210 GCGTTGCGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
* *
2177231 ACGTTGCGATAGTCAGAATT
1 GCGTTGCGATAGTCAGAATC
*
2177251 GCGTTACGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
2177271 GCGTTGCGAT
1 GCGTTGCGAT
2177281 TTACATATTC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.04
20 40 0.70
21 13 0.23
22 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:2177320 original size:21 final size:21
Alignment explanation
Indices: 2177296--2177342 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2177286 TATTCGCATT
*
2177296 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
2177317 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
2177338 GCGAT
1 GCGAT
2177343 AGTCAAAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:2179130 original size:21 final size:21
Alignment explanation
Indices: 2179105--2179144 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2179095 AAGACTCTAT
2179105 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
2179126 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
2179145 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:2193619 original size:22 final size:24
Alignment explanation
Indices: 2193585--2193642 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
2193575 TTAAAATTTT
* *
2193585 TATATAAA-ATTTTAAAAATAAAA
1 TATATAAATTTTTTAAAAAGAAAA
* *
2193608 T-TATATATTTTTTGAAAAGAAAA
1 TATATAAATTTTTTAAAAAGAAAA
2193631 TATATAAATTTT
1 TATATAAATTTT
2193643 GAAATAACCC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 5 0.18
23 14 0.50
24 9 0.32
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (24 bp):
TATATAAATTTTTTAAAAAGAAAA
Found at i:2193643 original size:22 final size:23
Alignment explanation
Indices: 2193584--2193646 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
2193574 TTTAAAATTT
* *
2193584 TTATATAAAATTTTAAAAATAAAA
1 TTATAT-AAATTTTGAAAAGAAAA
**
2193608 TTATATATTTTTTGAAAAGAAAA
1 TTATATAAATTTTGAAAAGAAAA
2193631 -TATATAAATTTTGAAA
1 TTATATAAATTTTGAAA
2193647 TAACCCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 14 0.42
23 13 0.39
24 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
TTATATAAATTTTGAAAAGAAAA
Found at i:2203394 original size:12 final size:12
Alignment explanation
Indices: 2203369--2203438 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
2203359 ACGAAGATAT
* *
2203369 CAGAAATCAAAA
1 CAGAATTCAGAA
2203381 CAGAATTCAGAA
1 CAGAATTCAGAA
2203393 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
2203405 CAGAATCCAGAT
1 CAGAATTCAGAA
*
2203417 CAGAAATCAGAA
1 CAGAATTCAGAA
2203429 CAGAATTCAG
1 CAGAATTCAG
2203439 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:2203438 original size:48 final size:47
Alignment explanation
Indices: 2203367--2203475 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
2203357 AAACGAAGAT
*
2203367 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
2203414 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
2203462 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
2203476 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:2203473 original size:24 final size:25
Alignment explanation
Indices: 2203367--2203475 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
2203357 AAACGAAGAT
*
2203367 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
2203391 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
2203415 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
2203439 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
2203464 -TCGGAAATCAGA
1 ATCAGAAATCAGA
2203476 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:2204637 original size:18 final size:18
Alignment explanation
Indices: 2204616--2204651 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2204606 CTTCCATCCG
*
2204616 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2204634 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2204652 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:2205989 original size:18 final size:18
Alignment explanation
Indices: 2205968--2206020 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
2205958 AACTCCGGTC
2205968 AACGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCGGGTA
*
2205986 AACGGGTCGGGTCGGGTC
1 AACGGGTCGGGTCGGGTA
2206004 AACGGGTCGGGTCGGGT
1 AACGGGTCGGGTCGGGT
2206021 TGTGACCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.13, C:0.19, G:0.51, T:0.17
Consensus pattern (18 bp):
AACGGGTCGGGTCGGGTA
Found at i:2208962 original size:11 final size:11
Alignment explanation
Indices: 2208946--2208972 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2208936 TCGGACATCA
2208946 AATGACAAAGT
1 AATGACAAAGT
2208957 AATGACAAAGT
1 AATGACAAAGT
2208968 AATGA
1 AATGA
2208973 ATTAATGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.19
Consensus pattern (11 bp):
AATGACAAAGT
Found at i:2209978 original size:43 final size:43
Alignment explanation
Indices: 2209930--2210079 Score: 148
Period size: 41 Copynumber: 3.6 Consensus size: 43
2209920 GACAAACGCT
* *
2209930 GCTAAAACGTAATACTTTAATGGCGTTTTAAGCAAAAAATGCC
1 GCTAAAACGTAATACTTTAGTGGCGTTTTAACCAAAAAATGCC
* *
2209973 GCTAAATAC-TCATACTTTAGTGGCGTTTT--CCAAAAAATGTC
1 GCTAAA-ACGTAATACTTTAGTGGCGTTTTAACCAAAAAATGCC
* * ** *
2210014 GTTAAAACGTAGTACTTTAGTGGCGTTTTAA-TTAAAAACGCC
1 GCTAAAACGTAATACTTTAGTGGCGTTTTAACCAAAAAATGCC
* *
2210056 TCTAAAGAC-TCATACTTTAGTGGC
1 GCTAAA-ACGTAATACTTTAGTGGC
2210080 ACTTTTTGAA
Statistics
Matches: 87, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
40 2 0.02
41 33 0.38
42 24 0.28
43 26 0.30
44 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (43 bp):
GCTAAAACGTAATACTTTAGTGGCGTTTTAACCAAAAAATGCC
Found at i:2218747 original size:42 final size:43
Alignment explanation
Indices: 2218682--2218860 Score: 181
Period size: 42 Copynumber: 4.2 Consensus size: 43
2218672 AAGGTAATTA
*
2218682 GCGGCGTTTGTATCCAAAGACGCCGCTATAGATCT-GACTTTTT
1 GCGGCGTTTG-ATCCAAAAACGCCGCTATAGATCTCGACTTTTT
* *
2218725 GCAGCGTTTCATCCAAAAACGCCG-TGATAGATCTCGATCTTTTT
1 GCGGCGTTTGATCCAAAAACGCCGCT-ATAGATCTCGA-CTTTTT
* * *
2218769 --GGCGTTTGTTACAAAAACGCCGCTATAGATCT-GACATTTT
1 GCGGCGTTTGATCCAAAAACGCCGCTATAGATCTCGACTTTTT
* * * **
2218809 GTGGCATTTGTTCCAAAAACGTTGCTATAGATCTCGA-TCTTTT
1 GCGGCGTTTGATCCAAAAACGCCGCTATAGATCTCGACT-TTTT
2218852 GCGGCGTTT
1 GCGGCGTTT
2218861 TCCACTATAA
Statistics
Matches: 113, Mismatches: 15, Indels: 16
0.78 0.10 0.11
Matches are distributed among these distances:
40 5 0.04
41 3 0.03
42 75 0.66
43 24 0.21
44 6 0.05
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (43 bp):
GCGGCGTTTGATCCAAAAACGCCGCTATAGATCTCGACTTTTT
Found at i:2218801 original size:84 final size:86
Alignment explanation
Indices: 2218682--2218860 Score: 229
Period size: 84 Copynumber: 2.1 Consensus size: 86
2218672 AAGGTAATTA
* * * *
2218682 GCGGCGTTTGTATCCAAAGACGCCGCTATAGATCTGACTTTTTGCAGCGTTTCATCCAAAAACGC
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATCTGACATTTTGCAGCATTTCATCCAAAAACGC
2218747 CG-TGATAGATCTCGATCTTTT
66 CGCT-ATAGATCTCGATCTTTT
* ** ** *
2218768 -TGGCGTTTGT-TACAAAAACGCCGCTATAGATCTGACATTTTGTGGCATTTGTTCCAAAAACGT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATCTGACATTTTGCAGCATTTCATCCAAAAACGC
*
2218831 TGCTATAGATCTCGATCTTTT
66 CGCTATAGATCTCGATCTTTT
2218852 GCGGCGTTT
1 GCGGCGTTT
2218861 TCCACTATAA
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
84 62 0.78
85 17 0.22
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (86 bp):
GCGGCGTTTGTATACAAAAACGCCGCTATAGATCTGACATTTTGCAGCATTTCATCCAAAAACGC
CGCTATAGATCTCGATCTTTT
Found at i:2219232 original size:20 final size:20
Alignment explanation
Indices: 2219183--2219233 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2219173 TACCTAGAAC
* *
2219183 CCCTTGTTTATGTAGTTCCT
1 CCCTAGTTTCTGTAGTTCCT
2219203 CCCTAGTTTCTGTAGTTCCT
1 CCCTAGTTTCTGTAGTTCCT
2219223 CCCTAGTTTCT
1 CCCTAGTTTCT
2219234 CTCGAACACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.10, C:0.29, G:0.14, T:0.47
Consensus pattern (20 bp):
CCCTAGTTTCTGTAGTTCCT
Found at i:2220864 original size:65 final size:63
Alignment explanation
Indices: 2220756--2220945 Score: 217
Period size: 65 Copynumber: 3.0 Consensus size: 63
2220746 GTGAACCAAT
* **
2220756 CCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGTATTTCATGCATCGATGCACAT
1 CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGTATTTCATGCATCGATGCACA-
2220819 A
63 A
* *
2220820 CTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGTATTTGATGCATCGATGCACC
1 CCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGTATTTCATGCATCGATGCA-C
*
2220883 AG
62 AA
* *
2220885 CCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTCATGCATCGATGCAC
1 CCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGTATTTCATGCATCGATGCAC
2220946 TCTTAGTGCA
Statistics
Matches: 109, Mismatches: 9, Indels: 17
0.81 0.07 0.13
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 46 0.42
65 53 0.49
66 5 0.05
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
CCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGTATTTCATGCATCGATGCACAA
Found at i:2223070 original size:21 final size:21
Alignment explanation
Indices: 2223045--2223094 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2223035 CAAATGTCAA
2223045 TGATGATCATCAAAAGAAAAT
1 TGATGATCATCAAAAGAAAAT
2223066 TGATGATCATCAAAAGAAAAT
1 TGATGATCATCAAAAGAAAAT
2223087 TGATGATC
1 TGATGATC
2223095 TTAAAGCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (21 bp):
TGATGATCATCAAAAGAAAAT
Found at i:2226826 original size:23 final size:22
Alignment explanation
Indices: 2226756--2226836 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
2226746 TTGTGCTTCA
2226756 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCA-CCC-TTGAATG
* * *
2226780 TGCATCGATACA-CCATGAAGG
1 TGCATCGATGCACCCTTGAATG
*
2226801 TGCACCGATGCACGCCTTGAATG
1 TGCATCGATGCAC-CCTTGAATG
*
2226824 TGCATTGATGCAC
1 TGCATCGATGCAC
2226837 AAGGCCATGC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 18 0.39
24 11 0.24
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACCCTTGAATG
Found at i:2226853 original size:20 final size:20
Alignment explanation
Indices: 2226824--2226875 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2226814 GCCTTGAATG
* *
2226824 TGCATTGATGCACAAGGCCA
1 TGCATCGATGCACAAGACCA
2226844 TGCATCGATGCACAAGACCA
1 TGCATCGATGCACAAGACCA
*
2226864 TGTATCGATGCA
1 TGCATCGATGCA
2226876 TCTATCGGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCACAAGACCA
Found at i:2228444 original size:21 final size:21
Alignment explanation
Indices: 2228402--2228445 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2228392 ACCCCGGGAG
* *
2228402 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
2228423 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
2228444 CT
1 CT
2228446 CCTTCGGCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:2228823 original size:29 final size:28
Alignment explanation
Indices: 2228791--2228845 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
2228781 GGATGTTTAA
2228791 ATTTGATGGTTGT-TGGATGTTTTGAACTT
1 ATTTG-TGGTTGTATGGAT-TTTTGAACTT
* *
2228820 ATTTGTTGTTTTATGGATTTTTGAAC
1 ATTTGTGGTTGTATGGATTTTTGAAC
2228846 ATAATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.18, C:0.04, G:0.24, T:0.55
Consensus pattern (28 bp):
ATTTGTGGTTGTATGGATTTTTGAACTT
Found at i:2229770 original size:21 final size:21
Alignment explanation
Indices: 2229753--2229822 Score: 122
Period size: 21 Copynumber: 3.3 Consensus size: 21
2229743 TTGATGCACC
2229753 GATGCACCTTGGGTATGCATA
1 GATGCACCTTGGGTATGCATA
2229774 GATGCACCTTGGGTATGCATA
1 GATGCACCTTGGGTATGCATA
* *
2229795 TATGCACCTTGGGTATGCATC
1 GATGCACCTTGGGTATGCATA
2229816 GATGCAC
1 GATGCAC
2229823 TAACGCTCCC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (21 bp):
GATGCACCTTGGGTATGCATA
Found at i:2231756 original size:43 final size:42
Alignment explanation
Indices: 2231703--2231858 Score: 177
Period size: 43 Copynumber: 3.6 Consensus size: 42
2231693 AGATCCGAAG
* * * *
2231703 CCCCTGATTTTTTCAATCCCACCTTTAACCTTTATAATTGAGA
1 CCCCTAATTTTTTCAATCTCA-CTTTTATCTTTATAATTGAGA
* *
2231746 CCCCTAATTTTTTCAATCTCACTTTCTATCTTTATAACTGAAA
1 CCCCTAATTTTTTCAATCTCACTTT-TATCTTTATAATTGAGA
* * *
2231789 CCCCTAATTTTTTGAATTTCATATTTTATCTTTATAATTGAGA
1 CCCCTAATTTTTTCAATCTCA-CTTTTATCTTTATAATTGAGA
* *
2231832 CCCCTAATTTTTTTCAGTCACACTTTT
1 CCCCTAA-TTTTTTCAATCTCACTTTT
2231859 TACAAACCCT
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
42 4 0.04
43 77 0.82
44 13 0.14
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.46
Consensus pattern (42 bp):
CCCCTAATTTTTTCAATCTCACTTTTATCTTTATAATTGAGA
Found at i:2233508 original size:17 final size:16
Alignment explanation
Indices: 2233486--2233519 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2233476 TAAAAACAGT
2233486 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
2233503 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
2233519 A
1 A
2233520 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:2242660 original size:7 final size:7
Alignment explanation
Indices: 2242645--2242677 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2242635 TTTTAAATTC
*
2242645 TTTTATA
1 TTTTTTA
2242652 TTTTTTA
1 TTTTTTA
2242659 TTTTTTA
1 TTTTTTA
2242666 -TTTTTA
1 TTTTTTA
2242672 TTTTTT
1 TTTTTT
2242678 TATTGATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:2242671 original size:13 final size:13
Alignment explanation
Indices: 2242653--2242677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2242643 TCTTTTATAT
2242653 TTTTTATTTTTTA
1 TTTTTATTTTTTA
2242666 TTTTTATTTTTT
1 TTTTTATTTTTT
2242678 TATTGATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:2248778 original size:7 final size:7
Alignment explanation
Indices: 2248755--2248796 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
2248745 TTTAGAATTC
2248755 ATGGTTT
1 ATGGTTT
2248762 -TGGATTT
1 ATGG-TTT
2248769 ATGGTTT
1 ATGGTTT
2248776 ATGGTTT
1 ATGGTTT
2248783 ATGGTTT
1 ATGGTTT
2248790 ATAGGTT
1 AT-GGTT
2248797 AGAATACAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.09
7 22 0.69
8 7 0.22
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.55
Consensus pattern (7 bp):
ATGGTTT
Found at i:2253217 original size:29 final size:30
Alignment explanation
Indices: 2253169--2253230 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
2253159 ATGAACGTGG
* *
2253169 ATGGATAGGTCGCCATGGCATCCCAGTGAC
1 ATGGATAGGTCGCCAGGGCATCCCAGCGAC
*
2253199 ATGG-TAGGTCGCCAGGGCATCCGAGCGAC
1 ATGGATAGGTCGCCAGGGCATCCCAGCGAC
2253228 ATG
1 ATG
2253231 CATGCTTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.23, C:0.26, G:0.34, T:0.18
Consensus pattern (30 bp):
ATGGATAGGTCGCCAGGGCATCCCAGCGAC
Found at i:2253363 original size:11 final size:11
Alignment explanation
Indices: 2253349--2253418 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
2253339 CGTGAATTCA
2253349 GCTGCATTATT
1 GCTGCATTATT
2253360 GCTGCATTATT
1 GCTGCATTATT
* * *
2253371 ACAGCCCTTATT
1 GCTG-CATTATT
*
2253383 GTTGCATTATT
1 GCTGCATTATT
* *
2253394 GCAGCCCTTATT
1 GCTG-CATTATT
*
2253406 GATGCATTATT
1 GCTGCATTATT
2253417 GC
1 GC
2253419 AGTCGTTCAA
Statistics
Matches: 43, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
11 28 0.65
12 15 0.35
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.41
Consensus pattern (11 bp):
GCTGCATTATT
Found at i:2253417 original size:23 final size:23
Alignment explanation
Indices: 2253355--2253420 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
2253345 TTCAGCTGCA
* *
2253355 TTATTGCTGCATTATTACAGCCC
1 TTATTGATGCATTATTGCAGCCC
*
2253378 TTATTGTTGCATTATTGCAGCCC
1 TTATTGATGCATTATTGCAGCCC
2253401 TTATTGATGCATTATTGCAG
1 TTATTGATGCATTATTGCAG
2253421 TCGTTCAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (23 bp):
TTATTGATGCATTATTGCAGCCC
Found at i:2253674 original size:38 final size:38
Alignment explanation
Indices: 2253626--2253731 Score: 105
Period size: 36 Copynumber: 2.8 Consensus size: 38
2253616 TTATTATTTT
** *
2253626 AAATTATTAGTTTGTTAGTTTA-TGGTTTAAGGTAAAACA
1 AAATTATTAGTTAATTAG-TTAGTAGTTTAAGGTAAAA-A
2253665 AAATT-TTAGTTAATTAGTTAGTTAGTTTAAGGT-AAAA
1 AAATTATTAGTTAATTAGTTAG-TAGTTTAAGGTAAAAA
*
2253702 AAA--ATTAGTTAATTAGTTTGTTAGTTTAAG
1 AAATTATTAGTTAATTAGTTAG-TAGTTTAAG
2253732 TTATATTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
36 25 0.42
37 7 0.12
38 13 0.22
39 15 0.25
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.44
Consensus pattern (38 bp):
AAATTATTAGTTAATTAGTTAGTAGTTTAAGGTAAAAA
Found at i:2253717 original size:36 final size:38
Alignment explanation
Indices: 2253650--2253731 Score: 132
Period size: 36 Copynumber: 2.2 Consensus size: 38
2253640 TTAGTTTATG
2253650 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTTA
1 GTTTAAGGTAAAACAAAA-TTTAGTTAATTAGTTAGTTA
*
2253689 GTTTAAGGTAAAA-AAAA-TTAGTTAATTAGTTTGTTA
1 GTTTAAGGTAAAACAAAATTTAGTTAATTAGTTAGTTA
2253725 GTTTAAG
1 GTTTAAG
2253732 TTATATTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
36 25 0.60
38 4 0.10
39 13 0.31
ACGTcount: A:0.40, C:0.01, G:0.17, T:0.41
Consensus pattern (38 bp):
GTTTAAGGTAAAACAAAATTTAGTTAATTAGTTAGTTA
Found at i:2253744 original size:21 final size:21
Alignment explanation
Indices: 2253719--2253758 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2253709 GTTAATTAGT
2253719 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
2253740 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
2253759 GATTCATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:2254072 original size:26 final size:28
Alignment explanation
Indices: 2254012--2254073 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
2254002 ATAAAAGAAT
*
2254012 AATTATTTAAATTAGTTTAATATTATAA
1 AATTAGTTAAATTAGTTTAATATTATAA
*
2254040 ATTATTAGTT-AATTAGTTTATTATTAT-A
1 A--ATTAGTTAAATTAGTTTAATATTATAA
2254068 AATTAG
1 AATTAG
2254074 GGTAAAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 5 0.17
28 3 0.10
29 16 0.53
30 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (28 bp):
AATTAGTTAAATTAGTTTAATATTATAA
Found at i:2254126 original size:21 final size:21
Alignment explanation
Indices: 2254101--2254140 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2254091 GTTAATTAAT
2254101 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
2254122 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
2254141 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:2254262 original size:36 final size:39
Alignment explanation
Indices: 2254192--2254267 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 39
2254182 TTACATATTA
* *
2254192 ATAAAAATAATTTGTTAATTTGTTAGTAGTTAGTTATAT
1 ATAAAAATAATATGTTAATTAGTTAGTAGTTAGTTATAT
*
2254231 ATAAAAA-AATATG-TAATTAGTTTGT-GTTAGTTATAT
1 ATAAAAATAATATGTTAATTAGTTAGTAGTTAGTTATAT
2254267 A
1 A
2254268 GTTAAGTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 12 0.35
37 10 0.29
38 5 0.15
39 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (39 bp):
ATAAAAATAATATGTTAATTAGTTAGTAGTTAGTTATAT
Found at i:2255613 original size:23 final size:23
Alignment explanation
Indices: 2255573--2255616 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2255563 ATTATTTATT
*
2255573 ATTTAAATTAACTATATTATTTG
1 ATTTAAATCAACTATATTATTTG
* *
2255596 ATTTAAATCAATTTTATTATT
1 ATTTAAATCAACTATATTATT
2255617 AATTTAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTAAATCAACTATATTATTTG
Found at i:2257703 original size:26 final size:24
Alignment explanation
Indices: 2257639--2257703 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
2257629 TGATTACTAA
*
2257639 TATTACTAATAATGATTTAATAAT
1 TATTATTAATAATGATTTAATAAT
* *
2257663 TATTATTAATCTAATGATTTGATATT
1 TATTATTAA--TAATGATTTAATAAT
2257689 TAATTATTTAATAAT
1 T-ATTA-TTAATAAT
2257704 AATATGATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 8 0.24
26 18 0.53
27 4 0.12
28 4 0.12
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (24 bp):
TATTATTAATAATGATTTAATAAT
Found at i:2257986 original size:21 final size:21
Alignment explanation
Indices: 2257970--2258008 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2257960 TATAAATTAA
2257970 ACAAAATATTTTTTAAACAAC
1 ACAAAATATTTTTTAAACAAC
*
2257991 ACTAAATA-TTTTTAAACA
1 ACAAAATATTTTTTAAACA
2258009 CAATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (21 bp):
ACAAAATATTTTTTAAACAAC
Found at i:2258019 original size:17 final size:17
Alignment explanation
Indices: 2257966--2258024 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
2257956 ATAATATAAA
*
2257966 TTAAACAAAATA-TTTT
1 TTAAACACAATATTTTT
* *
2257982 TTAAACAACACTAAATATTT
1 TTAAAC-ACA--ATATTTTT
2258002 TTAAACACAATATTTTT
1 TTAAACACAATATTTTT
2258019 TTAAAC
1 TTAAAC
2258025 GGGAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 6 0.18
17 14 0.41
19 5 0.15
20 9 0.26
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:2258557 original size:21 final size:21
Alignment explanation
Indices: 2258524--2258572 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2258514 AATATAATAT
2258524 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
2258545 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2258566 ATTAACT
1 A-TAACT
2258573 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2259721 original size:49 final size:50
Alignment explanation
Indices: 2259668--2259845 Score: 136
Period size: 49 Copynumber: 3.6 Consensus size: 50
2259658 TAGGATTTTT
* *
2259668 TTTAATAATTATATGATTTAGTAATAATTTGATAATAATGATT-T-TAAT-A
1 TTTAATAA-TA-ATCATTTAGTAATGATTTGATAATAATGATTATATAATGA
* * *
2259717 TTTAAT-GTACGGATTATTTAGTAATGATTTGATAATAATCATTATAATAATGA
1 TTTAATAATA---ATCATTTAGTAATGATTTGATAATAATGATTAT-ATAATGA
* *
2259770 TTTAGTAATAATCATTATAATAATGATTTGATAATAATGA-TA-ATAATGA
1 TTTAATAATAATCATT-TAGTAATGATTTGATAATAATGATTATATAATGA
* * * * *
2259819 CTTAGTAATTATTA-TTAATAATGATTT
1 TTTAATAATAATCATTTAGTAATGATTT
2259846 ATTATTAATA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
47 14 0.13
48 1 0.01
49 52 0.48
50 1 0.01
51 7 0.06
52 25 0.23
53 6 0.06
54 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (50 bp):
TTTAATAATAATCATTTAGTAATGATTTGATAATAATGATTATATAATGA
Found at i:2259768 original size:26 final size:26
Alignment explanation
Indices: 2259738--2259816 Score: 124
Period size: 26 Copynumber: 3.0 Consensus size: 26
2259728 GATTATTTAG
2259738 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
2259764 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* *
2259790 TAATGATTTGATAATAATGATAATAA
1 TAATGATTTGATAATAATCATTATAA
2259816 T
1 T
2259817 GACTTAGTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
25 1 0.02
26 47 0.96
27 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.42
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:2259864 original size:17 final size:17
Alignment explanation
Indices: 2259824--2259865 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2259814 AATGACTTAG
2259824 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
2259841 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
2259858 TAATTATT
1 TAATTATT
2259866 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:2260974 original size:23 final size:23
Alignment explanation
Indices: 2260946--2260989 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2260936 CAATTAAATT
*
2260946 AATAATAAAATTGATTTAAATCA
1 AATAATAAAATTAATTTAAATCA
* *
2260969 AATAATATAGTTAATTTAAAT
1 AATAATAAAATTAATTTAAAT
2260990 AATAAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
AATAATAAAATTAATTTAAATCA
Found at i:2262176 original size:4 final size:4
Alignment explanation
Indices: 2262167--2262197 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2262157 TAATGTTAAG
*
2262167 TAAC TAAC TAAC TAAC TAAC TAAC TATC TAA
1 TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAA
2262198 TTTACAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (4 bp):
TAAC
Found at i:2262354 original size:36 final size:38
Alignment explanation
Indices: 2262313--2262383 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 38
2262303 CTTAACTATT
* *
2262313 TAACTAAC-ACAAACTAATTACATATT-TTTTTATATA
1 TAACTAACGACAAACAAATTACAAATTATTTTTATATA
*
2262349 TAACTAACGACTAACAAATTACAAATTATTTTTAT
1 TAACTAACGACAAACAAATTACAAATTATTTTTAT
2262384 TAATATGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 8 0.27
37 15 0.50
38 7 0.23
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.39
Consensus pattern (38 bp):
TAACTAACGACAAACAAATTACAAATTATTTTTATATA
Found at i:2262459 original size:21 final size:21
Alignment explanation
Indices: 2262435--2262474 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2262425 TTTCTATATG
2262435 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
2262456 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
2262475 ATTCATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:2262716 original size:27 final size:29
Alignment explanation
Indices: 2262681--2262745 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 29
2262671 AAAATATAAC
*
2262681 TTAACTATTTA-ACTAACTACA-A-ACTAA
1 TTAAATATTTAGACTAACTA-ATACACTAA
2262708 TTAAATA-TTAGACTAACTAATACACTAA
1 TTAAATATTTAGACTAACTAATACACTAA
*
2262736 TTAATTATTT
1 TTAAATATTT
2262746 TTTAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 4 0.12
27 15 0.47
28 11 0.34
29 2 0.06
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAATACACTAA
Found at i:2262852 original size:21 final size:21
Alignment explanation
Indices: 2262799--2262838 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2262789 TTTATGTATC
2262799 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
2262820 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
2262839 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:2262869 original size:38 final size:39
Alignment explanation
Indices: 2262826--2262909 Score: 143
Period size: 38 Copynumber: 2.2 Consensus size: 39
2262816 AATAATATAA
*
2262826 CTTAAACTAACAAACTAATTAACT-AAATTTTTTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
*
2262864 CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
2262903 CTTAAAC
1 CTTAAAC
2262910 CATAAACTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
38 23 0.53
39 20 0.47
ACGTcount: A:0.42, C:0.17, G:0.01, T:0.40
Consensus pattern (39 bp):
CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
Found at i:2262918 original size:38 final size:37
Alignment explanation
Indices: 2262837--2262933 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 37
2262827 TTAAACTAAC
* *
2262837 AAACTAATTAACT-AAATTTTTTTTTACCTTAAACTA
1 AAACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
2262873 ACTAACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
1 A--AACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
**
2262912 TAAACTAACAAACTAATAATTT
1 -AAACTAATTAACTAA-AATTT
2262934 AAAATAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
36 1 0.02
38 24 0.46
39 26 0.50
40 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.39
Consensus pattern (37 bp):
AAACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
Found at i:2262933 original size:39 final size:38
Alignment explanation
Indices: 2262826--2262933 Score: 103
Period size: 38 Copynumber: 2.8 Consensus size: 38
2262816 AATAATATAA
* ** *
2262826 CTTAAACTAACAAACTAATTAACT-AAATTTTTTTTTAC
1 CTTAAACCAAC-AACTAACAAACTAAAATTTTGTTTTAC
* **
2262864 CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACCAAC-AACTAACAAACTAAAATTTTGTTTTAC
2262903 CTTAAACCATA-AACTAACAAACTAATAATTT
1 CTTAAACCA-ACAACTAACAAACTAA-AATTT
2262934 AAAATAATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
38 35 0.56
39 26 0.42
40 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.38
Consensus pattern (38 bp):
CTTAAACCAACAACTAACAAACTAAAATTTTGTTTTAC
Found at i:2263169 original size:23 final size:23
Alignment explanation
Indices: 2263139--2263196 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
2263129 GCTGAACGAT
2263139 TGCAATAATGCAACAATAAGGGC
1 TGCAATAATGCAACAATAAGGGC
* *
2263162 TGCAATAATGCAACAATAAGTGT
1 TGCAATAATGCAACAATAAGGGC
*
2263185 TGTAATAATGCA
1 TGCAATAATGCA
2263197 GCTGAATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (23 bp):
TGCAATAATGCAACAATAAGGGC
Found at i:2263367 original size:29 final size:29
Alignment explanation
Indices: 2263324--2263407 Score: 123
Period size: 29 Copynumber: 2.9 Consensus size: 29
2263314 ATGCATATCT
* *
2263324 CTGGAATGCCCTGGCTACCTACCATGTCG
1 CTGGGATGCCCTGGCGACCTACCATGTCG
* *
2263353 CTGGGATGCCATGGCGACCTACAATGTCG
1 CTGGGATGCCCTGGCGACCTACCATGTCG
2263382 CTGGGATGCCCTGGCGACCTATCCAT
1 CTGGGATGCCCTGGCGACCTA-CCAT
2263408 CCACGTGCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 45 0.94
30 3 0.06
ACGTcount: A:0.18, C:0.32, G:0.27, T:0.23
Consensus pattern (29 bp):
CTGGGATGCCCTGGCGACCTACCATGTCG
Found at i:2264766 original size:37 final size:37
Alignment explanation
Indices: 2264716--2264809 Score: 179
Period size: 37 Copynumber: 2.5 Consensus size: 37
2264706 GTGGCGTATA
2264716 TGGTGCCTTTGTAATTTATTGACTTCCGGCTTTATGT
1 TGGTGCCTTTGTAATTTATTGACTTCCGGCTTTATGT
2264753 TGGTGCCTTTGTAATTTATTGACTTCCGGCTTTATGT
1 TGGTGCCTTTGTAATTTATTGACTTCCGGCTTTATGT
*
2264790 TGTTGCCTTTGTAATTTATT
1 TGGTGCCTTTGTAATTTATT
2264810 TGTTTATTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.14, C:0.15, G:0.20, T:0.51
Consensus pattern (37 bp):
TGGTGCCTTTGTAATTTATTGACTTCCGGCTTTATGT
Found at i:2274249 original size:24 final size:25
Alignment explanation
Indices: 2274197--2274249 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
2274187 AGACAGTTTG
* * **
2274197 TTAAGAGTCAGATTTTTTGGTAGTG
1 TTAAAAGTCAGATTTTTCGGTAGCA
2274222 TTAAAAGTCAGATTTTTCGGT-GCA
1 TTAAAAGTCAGATTTTTCGGTAGCA
2274246 TTAA
1 TTAA
2274250 TATACCGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.42
Consensus pattern (25 bp):
TTAAAAGTCAGATTTTTCGGTAGCA
Found at i:2278874 original size:25 final size:25
Alignment explanation
Indices: 2278840--2278888 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2278830 AGTGGGAGAT
*
2278840 TGTTAAAAGTTAGATTTTTCGGTGG
1 TGTTAAAAGTCAGATTTTTCGGTGG
2278865 TGTTAAAAGTCAGATTTTTCGGTG
1 TGTTAAAAGTCAGATTTTTCGGTG
2278889 CATTAATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.06, G:0.27, T:0.43
Consensus pattern (25 bp):
TGTTAAAAGTCAGATTTTTCGGTGG
Found at i:2278894 original size:24 final size:25
Alignment explanation
Indices: 2278842--2278894 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
2278832 TGGGAGATTG
* **
2278842 TTAAAAGTTAGATTTTTCGGTGGTG
1 TTAAAAGTCAGATTTTTCGGTGGCA
2278867 TTAAAAGTCAGATTTTTCGGT-GCA
1 TTAAAAGTCAGATTTTTCGGTGGCA
2278891 TTAA
1 TTAA
2278895 TGCATCGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.42
Consensus pattern (25 bp):
TTAAAAGTCAGATTTTTCGGTGGCA
Found at i:2279164 original size:34 final size:34
Alignment explanation
Indices: 2279104--2279171 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
2279094 TTTCTTGAGA
*
2279104 ATTGTTTTCTCCTTTTTATCAAGAGAAAA-TTGTC
1 ATTGTTTTCTCCTTTTGATC-AGAGAAAAGTTGTC
2279138 ATTGTTTTCTCCTTGTTAGATC-GAGAAAAGTTGT
1 ATTGTTTTCTCCTT-TT-GATCAGAGAAAAGTTGT
2279172 AATTCCTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 21 0.70
35 6 0.20
36 3 0.10
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (34 bp):
ATTGTTTTCTCCTTTTGATCAGAGAAAAGTTGTC
Found at i:2279805 original size:23 final size:23
Alignment explanation
Indices: 2279761--2279805 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2279751 TCGTGTTTGG
* *
2279761 TTCATTTAGCGTTTGCGGACATA
1 TTCATTTAACGTTTGCGAACATA
*
2279784 TTCATTTAACGTTTGTGAACAT
1 TTCATTTAACGTTTGCGAACAT
2279806 GTCCGTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (23 bp):
TTCATTTAACGTTTGCGAACATA
Found at i:2280029 original size:24 final size:24
Alignment explanation
Indices: 2279977--2280033 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2279967 GAGAACTGAG
*
2279977 TAAACAAGTCAATAAATGAGCTTA
1 TAAACAAGTCAATAAACGAGCTTA
* *
2280001 TAAACGAGTCAATAAACGAG-TTT
1 TAAACAAGTCAATAAACGAGCTTA
2280024 TCAAACAAGT
1 T-AAACAAGT
2280034 TTTCCCGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (24 bp):
TAAACAAGTCAATAAACGAGCTTA
Found at i:2282297 original size:23 final size:23
Alignment explanation
Indices: 2282271--2282331 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
2282261 TTTTAAAGTT
2282271 TTTTAAATATAATTTATTTTTTA
1 TTTTAAATATAATTTATTTTTTA
2282294 TTTTAAATATAATTTATTTTTTA
1 TTTTAAATATAATTTATTTTTTA
*
2282317 TTTTAAATAAAATTT
1 TTTTAAATATAATTT
2282332 CAAAATTACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAAATATAATTTATTTTTTA
Found at i:2286793 original size:2 final size:2
Alignment explanation
Indices: 2286786--2286813 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2286776 TGGTCAAATA
2286786 AT AT AT 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
2286814 GACTGAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2286939 original size:22 final size:22
Alignment explanation
Indices: 2286914--2286959 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2286904 GAACCAAAAT
* *
2286914 GACCCGAAACTGAAACTAACCC
1 GACCCAAAACTGAAACAAACCC
* *
2286936 GACCCAAAATTGACACAAACCC
1 GACCCAAAACTGAAACAAACCC
2286958 GA
1 GA
2286960 AACCGACCCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.35, G:0.13, T:0.09
Consensus pattern (22 bp):
GACCCAAAACTGAAACAAACCC
Found at i:2295584 original size:35 final size:35
Alignment explanation
Indices: 2295545--2295615 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2295535 TTAGAACCAA
2295545 CACCACGTGTGACCCCTGGTGTAGTATTAGGAGTT
1 CACCACGTGTGACCCCTGGTGTAGTATTAGGAGTT
2295580 CACCACGTGTGACCCCTGGTGTAGTATTAGGAGTT
1 CACCACGTGTGACCCCTGGTGTAGTATTAGGAGTT
2295615 C
1 C
2295616 CAACATTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (35 bp):
CACCACGTGTGACCCCTGGTGTAGTATTAGGAGTT
Found at i:2301485 original size:2 final size:2
Alignment explanation
Indices: 2301473--2301507 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
2301463 AATCTATGTG
2301473 AT AT GAT AT AT AT 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 AT AT
2301508 GACAATAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2302351 original size:22 final size:22
Alignment explanation
Indices: 2302321--2302374 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
2302311 TGTATAAACA
2302321 GTATCGATACCATATG-GAAGGG
1 GTATCGATACCATATGTGAA-GG
* *
2302343 GTATAGATA-CATATGTGGAGG
1 GTATCGATACCATATGTGAAGG
2302364 GTATCGATACC
1 GTATCGATACC
2302375 TGGGGATCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (22 bp):
GTATCGATACCATATGTGAAGG
Found at i:2306865 original size:18 final size:18
Alignment explanation
Indices: 2306842--2306876 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2306832 CCATTATGAA
*
2306842 ATGTCCCGAATGACCACT
1 ATGTCCCGAATAACCACT
2306860 ATGTCCCGAATAACCAC
1 ATGTCCCGAATAACCAC
2306877 GTAGAACCCT
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:0.31, C:0.34, G:0.14, T:0.20
Consensus pattern (18 bp):
ATGTCCCGAATAACCACT
Found at i:2309459 original size:18 final size:18
Alignment explanation
Indices: 2309410--2309462 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
2309400 GTTCTTAAAG
*
2309410 AGTGGTCCTTCGGAACAT
1 AGTGGTCCTTCGGGACAT
* *
2309428 AGTGGTGCTCCGGGACAT
1 AGTGGTCCTTCGGGACAT
2309446 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
2309463 AATTTCATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2316226 original size:14 final size:15
Alignment explanation
Indices: 2316204--2316236 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2316194 TATAGTTCTC
2316204 TTTCCTTA-TTCTTA
1 TTTCCTTATTTCTTA
*
2316218 TTTCGTTATTTCTTA
1 TTTCCTTATTTCTTA
2316233 TTTC
1 TTTC
2316237 ATAACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.12, C:0.18, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTCCTTATTTCTTA
Found at i:2318902 original size:18 final size:18
Alignment explanation
Indices: 2318876--2318917 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2318866 GACCCCAATT
*
2318876 AGAAATGTAAAGAATTTG
1 AGAATTGTAAAGAATTTG
2318894 AGAATTGTAAAGAATTTG
1 AGAATTGTAAAGAATTTG
2318912 AGAATT
1 AGAATT
2318918 TGTGCAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (18 bp):
AGAATTGTAAAGAATTTG
Found at i:2324128 original size:24 final size:24
Alignment explanation
Indices: 2324101--2324171 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
2324091 TCCAATTTGA
* *
2324101 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACATGACCTGG
*
2324125 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* * * *
2324149 ATTATGATCTAATACTTGACCTG
1 ATTCTGATATGATACATGACCTG
2324172 AATTATGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:2324176 original size:24 final size:24
Alignment explanation
Indices: 2324112--2324178 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
2324102 TTCTGTTATG
* * *
2324112 ATACCTGACCTGGATTCTGATCTG
1 ATACATGACCTGGATTATGATCTA
2324136 ATACATGACCTGGATTATGATCTA
1 ATACATGACCTGGATTATGATCTA
* *
2324160 ATACTTGACCTGAATTATG
1 ATACATGACCTGGATTATG
2324179 TTTTAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (24 bp):
ATACATGACCTGGATTATGATCTA
Found at i:2324384 original size:13 final size:13
Alignment explanation
Indices: 2324366--2324390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2324356 GGTTTTTGAA
2324366 TTTTAAAAATATG
1 TTTTAAAAATATG
2324379 TTTTAAAAATAT
1 TTTTAAAAATAT
2324391 CTATGTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTTAAAAATATG
Found at i:2328720 original size:24 final size:24
Alignment explanation
Indices: 2328692--2328738 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2328682 ACATGGATTA
*
2328692 TGATCTGATACATGACCTGAATTC
1 TGATCTAATACATGACCTGAATTC
*
2328716 TGATCTAATACTTGACCTGAATT
1 TGATCTAATACATGACCTGAATT
2328739 ATGTTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (24 bp):
TGATCTAATACATGACCTGAATTC
Found at i:2331438 original size:24 final size:24
Alignment explanation
Indices: 2331392--2331438 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
2331382 GACCAAACCC
**
2331392 ACAAAAACCCACTTCAAATAACAA
1 ACAAAAACCCACAGCAAATAACAA
2331416 ACAAGAAACCCACAGCAAA-AACA
1 ACAA-AAACCCACAGCAAATAACA
2331439 TGAAACCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.60, C:0.30, G:0.04, T:0.06
Consensus pattern (24 bp):
ACAAAAACCCACAGCAAATAACAA
Found at i:2333111 original size:81 final size:82
Alignment explanation
Indices: 2332973--2333135 Score: 274
Period size: 81 Copynumber: 2.0 Consensus size: 82
2332963 GTACCTAAAA
*
2332973 GGCTAAAACGATGTCATTTTAAGCATAAAATAACCGCATCAAAACGATGTCGTTTTGTCATTGTC
1 GGCTAAAACGATGTCATTTTAAGCATAAAATAACCGCACCAAAACGATGTCGTTTTGTCATTGTC
2333038 ATCACACCATTTTATTT
66 ATCACACCATTTTATTT
* * *
2333055 GGCTAAAACGATGTCATTTTAGGCAT-AAATAACCGCACCAAAATGATGTTGTTTTGTCATTGTC
1 GGCTAAAACGATGTCATTTTAAGCATAAAATAACCGCACCAAAACGATGTCGTTTTGTCATTGTC
*
2333119 GTCACACCATTTTATTT
66 ATCACACCATTTTATTT
2333136 TCAATAGTCC
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
81 51 0.67
82 25 0.33
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (82 bp):
GGCTAAAACGATGTCATTTTAAGCATAAAATAACCGCACCAAAACGATGTCGTTTTGTCATTGTC
ATCACACCATTTTATTT
Found at i:2340412 original size:76 final size:76
Alignment explanation
Indices: 2340316--2340460 Score: 272
Period size: 76 Copynumber: 1.9 Consensus size: 76
2340306 GTAAGATGTC
*
2340316 TGGATGACAGAGCGTTTTTAATCAAAATGTAATGTTACAAACTTTTACTCATGCATGTAATTACG
1 TGGATGACAGAGCATTTTTAATCAAAATGTAATGTTACAAACTTTTACTCATGCATGTAATTACG
2340381 AGAAAGACGTA
66 AGAAAGACGTA
*
2340392 TGGATGACAGAGTATTTTTAATCAAAATGTAATGTTACAAACTTTTACTCATGCATGTAATTACG
1 TGGATGACAGAGCATTTTTAATCAAAATGTAATGTTACAAACTTTTACTCATGCATGTAATTACG
2340457 AGAA
66 AGAA
2340461 TGATGTCGTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (76 bp):
TGGATGACAGAGCATTTTTAATCAAAATGTAATGTTACAAACTTTTACTCATGCATGTAATTACG
AGAAAGACGTA
Found at i:2348011 original size:2 final size:2
Alignment explanation
Indices: 2348004--2348034 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2347994 ACTTTTGTCG
2348004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2348035 ATGACCTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2349246 original size:2 final size:2
Alignment explanation
Indices: 2349239--2349307 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
2349229 ATACTAAGGG
2349239 TA TA TA TA TA TA TA TA TA 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
2349281 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 T
2349308 CACCATGGAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2354292 original size:20 final size:20
Alignment explanation
Indices: 2354267--2354305 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2354257 AAAAATATAT
* *
2354267 TTTCATTTGTGTTCGTTTAC
1 TTTCATTTATGTTCATTTAC
2354287 TTTCATTTATGTTCATTTA
1 TTTCATTTATGTTCATTTA
2354306 TTGCGTTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.13, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTCATTTATGTTCATTTAC
Found at i:2354301 original size:10 final size:10
Alignment explanation
Indices: 2354268--2354363 Score: 50
Period size: 10 Copynumber: 8.9 Consensus size: 10
2354258 AAAATATATT
*
2354268 TTCATTTGTG
1 TTCATTTATG
*
2354278 TTCGTTTACT-
1 TTCATTTA-TG
2354288 TTCATTTATG
1 TTCATTTATG
2354298 TTCATTTATTGCG
1 TTCATTTA-T--G
* *
2354311 TTCGTTTACG
1 TTCATTTATG
2354321 TTCATTCATTTATG
1 -T---TCATTTATG
* *
2354335 TTCGTTTACG
1 TTCATTTATG
*
2354345 TTAATTTATG
1 TTCATTTATG
2354355 TTCATTTAT
1 TTCATTTAT
2354364 TGTGTTCGTT
Statistics
Matches: 64, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
9 1 0.02
10 44 0.69
11 3 0.05
13 9 0.14
14 7 0.11
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.57
Consensus pattern (10 bp):
TTCATTTATG
Found at i:2354374 original size:33 final size:34
Alignment explanation
Indices: 2354288--2354409 Score: 97
Period size: 34 Copynumber: 3.5 Consensus size: 34
2354278 TTCGTTTACT
* ** *
2354288 TTCATTTATGTTCATTTATTGCGTTCGTTTACGTTCA
1 TTCATTTATGTTCGTTTA---CGTTAATTTATGTTCA
2354325 TTCATTTATGTTCGTTTACGTTAATTTATGTTCA
1 TTCATTTATGTTCGTTTACGTTAATTTATGTTCA
* * * *
2354359 TTTA-TTGTGTTCGTTTACTTTCATTTAT-TT-A
1 TTCATTTATGTTCGTTTACGTTAATTTATGTTCA
*
2354390 TGTTCATTTACGTTCGTTTA
1 --TTCATTTATGTTCGTTTA
2354410 TTGTGTTTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
31 1 0.01
32 2 0.03
33 24 0.34
34 27 0.38
37 17 0.24
ACGTcount: A:0.17, C:0.13, G:0.12, T:0.57
Consensus pattern (34 bp):
TTCATTTATGTTCGTTTACGTTAATTTATGTTCA
Found at i:2354398 original size:37 final size:35
Alignment explanation
Indices: 2354348--2354444 Score: 101
Period size: 37 Copynumber: 2.7 Consensus size: 35
2354338 GTTTACGTTA
2354348 ATTTATGTTCATTTATTGTGTTCGTTTACTT-TCATTT
1 ATTTATGTTCATTTATT-TGTTCGTTTA-TTGT-ATTT
* *
2354385 ATTTATGTTCATTTA--CGTTCGTTTATTGTGTTT
1 ATTTATGTTCATTTATTTGTTCGTTTATTGTATTT
*
2354418 ATTTATGTTCGTTTATATATGTTCGTT
1 ATTTATGTTCATTTAT-T-TGTTCGTT
2354445 CATTTGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
33 19 0.37
34 10 0.20
37 22 0.43
ACGTcount: A:0.16, C:0.09, G:0.13, T:0.61
Consensus pattern (35 bp):
ATTTATGTTCATTTATTTGTTCGTTTATTGTATTT
Found at i:2354410 original size:57 final size:57
Alignment explanation
Indices: 2354268--2354410 Score: 214
Period size: 57 Copynumber: 2.5 Consensus size: 57
2354258 AAAATATATT
* *
2354268 TTCATTTGTGTTCGTTTACTTTCATTTATGTTCATTTATTGCGTTCGTTTACGTTCA
1 TTCATTTATGTTCGTTTACGTTCATTTATGTTCATTTATTGCGTTCGTTTACGTTCA
* * *
2354325 TTCATTTATGTTCGTTTACGTTAATTTATGTTCATTTATTGTGTTCGTTTACTTTCA
1 TTCATTTATGTTCGTTTACGTTCATTTATGTTCATTTATTGCGTTCGTTTACGTTCA
* * *
2354382 TTTATTTATGTTCATTTACGTTCGTTTAT
1 TTCATTTATGTTCGTTTACGTTCATTTAT
2354411 TGTGTTTATT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 77 1.00
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (57 bp):
TTCATTTATGTTCGTTTACGTTCATTTATGTTCATTTATTGCGTTCGTTTACGTTCA
Found at i:2354421 original size:23 final size:23
Alignment explanation
Indices: 2354348--2354433 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
2354338 GTTTACGTTA
*
2354348 ATTTATGTTCATTTATTGTGTTC
1 ATTTACGTTCATTTATTGTGTTC
* * *
2354371 GTTTACTTTCATTTATTTATGTTC
1 ATTTACGTTCATTTA-TTGTGTTC
* *
2354395 ATTTACGTTCGTTTATTGTGTTT
1 ATTTACGTTCATTTATTGTGTTC
* *
2354418 ATTTATGTTCGTTTAT
1 ATTTACGTTCATTTAT
2354434 ATATGTTCGT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 33 0.63
24 19 0.37
ACGTcount: A:0.16, C:0.09, G:0.13, T:0.62
Consensus pattern (23 bp):
ATTTACGTTCATTTATTGTGTTC
Found at i:2354433 original size:14 final size:14
Alignment explanation
Indices: 2354414--2354461 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2354404 CGTTTATTGT
2354414 GTTTATTTATGTTC
1 GTTTATTTATGTTC
*
2354428 GTTTATATATGTTC
1 GTTTATTTATGTTC
* *
2354442 GTTCATTTGTGTTC
1 GTTTATTTATGTTC
*
2354456 ATTTAT
1 GTTTAT
2354462 CATTTAAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.17, C:0.08, G:0.15, T:0.60
Consensus pattern (14 bp):
GTTTATTTATGTTC
Found at i:2354433 original size:47 final size:47
Alignment explanation
Indices: 2354339--2354441 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 47
2354329 TTTATGTTCG
* * * *
2354339 TTTACGTTAATTTATGTTCATTTATTGTGTTCGTTTACTTTCATTTA
1 TTTATGTTCATTTACGTTCATTTATTGTGTTCATTTACTTTCATTTA
* * *
2354386 TTTATGTTCATTTACGTTCGTTTATTGTGTTTATTTA-TGTTCGTTTA
1 TTTATGTTCATTTACGTTCATTTATTGTGTTCATTTACT-TTCATTTA
*
2354433 TATATGTTC
1 TTTATGTTC
2354442 GTTCATTTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 1 0.02
47 46 0.98
ACGTcount: A:0.17, C:0.10, G:0.13, T:0.60
Consensus pattern (47 bp):
TTTATGTTCATTTACGTTCATTTATTGTGTTCATTTACTTTCATTTA
Found at i:2362643 original size:19 final size:19
Alignment explanation
Indices: 2362594--2362647 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2362584 GCTCTACTTT
*
2362594 TATTAAAATGATATTAAAA
1 TATTAAAATAATATTAAAA
* *
2362613 TATTATATTAATATT-AAA
1 TATTAAAATAATATTAAAA
2362631 TATATAAAATAATATTA
1 TAT-TAAAATAATATTA
2362648 TTTTTGGTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TATTAAAATAATATTAAAA
Found at i:2363161 original size:30 final size:30
Alignment explanation
Indices: 2363123--2363188 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
2363113 ACCTCTTTAA
2363123 ATTG-TAGTATCGATACCCCCTTGAGAGGT
1 ATTGATAGTATCGATACCCCCTTGAGAGGT
2363152 ATTGATAGTATCGATACCCCCTTGAGAGGT
1 ATTGATAGTATCGATACCCCCTTGAGAGGT
2363182 ATTGATA
1 ATTGATA
2363189 CCATCAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.11
30 32 0.89
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (30 bp):
ATTGATAGTATCGATACCCCCTTGAGAGGT
Found at i:2364355 original size:63 final size:64
Alignment explanation
Indices: 2364264--2364449 Score: 240
Period size: 64 Copynumber: 2.9 Consensus size: 64
2364254 TATTTTAAAC
* *
2364264 ATTATATTTTA-ACTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGAT
1 ATTATATTTTATA-TTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAAT
*
2364328 ATTAT-TTTTATATTTGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGAAT
1 ATTATATTTTATATTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAAT
* * *
2364390 ATTATATTATT-T-TTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTATGATTTA
1 ATTATATT-TTATATTT--GTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTA
2364450 AGATGTTTTA
Statistics
Matches: 110, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
62 33 0.30
63 31 0.28
64 46 0.42
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (64 bp):
ATTATATTTTATATTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAAT
Found at i:2364380 original size:19 final size:19
Alignment explanation
Indices: 2364352--2364414 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
2364342 TGTATTTTAG
*
2364352 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
2364371 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
2364390 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
2364411 TTTA
1 TTTA
2364415 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:2364470 original size:21 final size:21
Alignment explanation
Indices: 2364425--2364470 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
2364415 GTTTAAATAG
*
2364425 TTTTAAGTGTTTTAATTATGA
1 TTTTAAGTGTTTTAACTATGA
*
2364446 -TTTAAGATGTTTTAGCT-TGA
1 TTTTAAG-TGTTTTAACTATGA
2364466 TTTTA
1 TTTTA
2364471 GGATTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (21 bp):
TTTTAAGTGTTTTAACTATGA
Found at i:2365111 original size:5 final size:5
Alignment explanation
Indices: 2365087--2365123 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
2365077 AAAAAAACCC
2365087 TTTTA TATTTA TTATTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA T-TTTA TT-TTA TTTTA TTTTA TTTTA TTTTA
2365124 ATATATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 20 0.67
6 10 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:2370724 original size:11 final size:11
Alignment explanation
Indices: 2370684--2370729 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
2370674 AGGCAACCCA
*
2370684 TTTCGTTATAT
1 TTTCGTTTTAT
*
2370695 TTTTGTTTTTAT
1 TTTCG-TTTTAT
2370707 TTT--TTTTAT
1 TTTCGTTTTAT
2370716 TTTCGTTTTAT
1 TTTCGTTTTAT
2370727 TTT
1 TTT
2370730 TTTAGCGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 9 0.30
11 13 0.43
12 8 0.27
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTCGTTTTAT
Found at i:2372693 original size:70 final size:67
Alignment explanation
Indices: 2372602--2372795 Score: 257
Period size: 65 Copynumber: 2.9 Consensus size: 67
2372592 TATTTTAAAC
* *
2372602 ATTATATTTTATTTTTGTATTTTAGTTTAAATATGTTTTTAGTATTTTAATTAAGTTTTAGGATA
1 ATTATATTTTA-TTTTGTATTTTAGTTTAAATA-GTTTTTAGTATTTTAATTAAGATTTAGAATA
2372667 TTATT
64 TTA-T
* * *
2372672 TTTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATAT
1 ATTATATTTTAT-TTTGTATTTTAGTTTAAATAGTTTTTAGTATTTTAATTAAGATTTAGAATAT
2372737 TAT
65 TAT
** * *
2372740 ATTAT-TTTT-TTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAAGATTTA
1 ATTATATTTTATTTTGTATTTTAGTTTAAATAGTTTTTAGTATTTTAATTAAGATTTA
2372796 AGATGTTTTA
Statistics
Matches: 111, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
65 40 0.36
66 1 0.01
67 4 0.04
68 5 0.05
69 31 0.28
70 30 0.27
ACGTcount: A:0.29, C:0.01, G:0.11, T:0.59
Consensus pattern (67 bp):
ATTATATTTTATTTTGTATTTTAGTTTAAATAGTTTTTAGTATTTTAATTAAGATTTAGAATATT
AT
Found at i:2373413 original size:20 final size:21
Alignment explanation
Indices: 2373388--2373426 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2373378 CTTTAATTTG
2373388 TTTATTTAATTATT-TTTTCT
1 TTTATTTAATTATTATTTTCT
2373408 TTTATTTAATTATTATTTT
1 TTTATTTAATTATTATTTT
2373427 TAAACCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTATTTAATTATTATTTTCT
Found at i:2378846 original size:16 final size:18
Alignment explanation
Indices: 2378814--2378846 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2378804 ATATATGTGA
2378814 GTTAAGAGTATTAAAGGG
1 GTTAAGAGTATTAAAGGG
2378832 GTTAAGA-TA-TAAAGG
1 GTTAAGAGTATTAAAGG
2378847 ATTTAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (18 bp):
GTTAAGAGTATTAAAGGG
Found at i:2380587 original size:22 final size:22
Alignment explanation
Indices: 2380557--2380598 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2380547 AGTCGAGGGT
*
2380557 TTCATAGGTCATTCGGGACATA
1 TTCACAGGTCATTCGGGACATA
*
2380579 TTCACAGGTCCTTCGGGACA
1 TTCACAGGTCATTCGGGACA
2380599 AATTTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (22 bp):
TTCACAGGTCATTCGGGACATA
Found at i:2385691 original size:32 final size:32
Alignment explanation
Indices: 2385650--2385720 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
2385640 AATTTATGTA
*
2385650 TTTGAATATTTGGATGTTTTGGATT-TGTGTGT
1 TTTGGATATTTGGATG-TTTGGATTGTGTGTGT
* *
2385682 TTTGGATATTTGTATGTTTGGATTGTTTGTGT
1 TTTGGATATTTGGATGTTTGGATTGTGTGTGT
2385714 TTTGGAT
1 TTTGGAT
2385721 GTTTAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 8 0.23
32 27 0.77
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.58
Consensus pattern (32 bp):
TTTGGATATTTGGATGTTTGGATTGTGTGTGT
Found at i:2385723 original size:15 final size:15
Alignment explanation
Indices: 2385664--2385724 Score: 70
Period size: 15 Copynumber: 3.9 Consensus size: 15
2385654 AATATTTGGA
2385664 TGTTTTGGAT-TTGTG
1 TGTTTTGGATGTT-TG
*
2385679 TGTTTTGGATATTTG
1 TGTTTTGGATGTTTG
*
2385694 TATGTTTGGATTGTTTG
1 TGT-TTTGGA-TGTTTG
2385711 TGTTTTGGATGTTT
1 TGTTTTGGATGTTT
2385725 AATTTTGAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 19 0.47
16 14 0.35
17 7 0.17
ACGTcount: A:0.10, C:0.00, G:0.30, T:0.61
Consensus pattern (15 bp):
TGTTTTGGATGTTTG
Found at i:2386137 original size:18 final size:18
Alignment explanation
Indices: 2386114--2386151 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2386104 TTTTAAGATT
2386114 TTATATTCGATTTAAATA
1 TTATATTCGATTTAAATA
*
2386132 TTATATTCGATTTAATTA
1 TTATATTCGATTTAAATA
2386150 TT
1 TT
2386152 CGAATATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (18 bp):
TTATATTCGATTTAAATA
Found at i:2389190 original size:20 final size:20
Alignment explanation
Indices: 2389146--2389573 Score: 445
Period size: 20 Copynumber: 21.2 Consensus size: 20
2389136 AATGACCAAC
*
2389146 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
2389165 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
2389185 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
2389205 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
2389225 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
2389246 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
2389267 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
2389288 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
2389309 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
2389331 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
2389349 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2389369 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
2389391 --AATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2389409 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2389431 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2389449 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2389471 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2389491 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2389509 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2389529 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
2389549 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
2389569 AAAAT
1 AAAAT
2389574 GAGTAAATTC
Statistics
Matches: 355, Mismatches: 27, Indels: 53
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.03
19 15 0.04
20 274 0.77
21 14 0.04
22 40 0.11
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:2389680 original size:6 final size:6
Alignment explanation
Indices: 2389669--2389747 Score: 158
Period size: 6 Copynumber: 13.2 Consensus size: 6
2389659 GACACGTATT
2389669 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2389717 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
2389748 GACGAGACGG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2390245 original size:6 final size:6
Alignment explanation
Indices: 2390234--2390332 Score: 198
Period size: 6 Copynumber: 16.5 Consensus size: 6
2390224 TCTCGTCTCG
2390234 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2390282 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2390330 GGT
1 GGT
2390333 AATACGTGTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2390460 original size:20 final size:20
Alignment explanation
Indices: 2390435--2390698 Score: 202
Period size: 20 Copynumber: 12.8 Consensus size: 20
2390425 CTCATTTTCT
2390435 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2390455 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
2390475 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
2390495 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
2390515 GAAGATCACGTTGCGATTCTCT-
1 G-A-ATCGCGTTGCGATTCT-TG
* *
2390537 TAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
2390557 GAATATCGCGTTGCGATTTTCTTTT
1 G-A-ATCGCGTTGCGA--TTC-TTG
*
2390582 G-A-C-CGTTGCGATT-TTC
1 GAATCGCGTTGCGATTCTTG
*** * *
2390598 TTTTCAACGTTGCGATT-TTCT
1 GAATC-GCGTTGCGATTCTT-G
2390619 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
2390639 GAAGATCACGTTGCGATTCTCT-
1 G-A-ATCGCGTTGCGATTCT-TG
* *
2390661 TAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2390681 GAATATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
2390699 TTCTTTTGAC
Statistics
Matches: 197, Mismatches: 24, Indels: 44
0.74 0.09 0.17
Matches are distributed among these distances:
16 2 0.01
18 3 0.02
19 4 0.02
20 112 0.57
21 13 0.07
22 55 0.28
23 2 0.01
24 3 0.02
25 3 0.02
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:2390542 original size:42 final size:42
Alignment explanation
Indices: 2390456--2390758 Score: 288
Period size: 42 Copynumber: 7.4 Consensus size: 42
2390446 CGATTCTTGG
* *
2390456 AATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTG
1 AATCGCGTTGCGATTCTTGGAATATCACGTTGCGATTTTCTT
* *
2390496 AATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTCTCTT
1 AATCGCGTTGCGATTCTTGGAATATCACGTTGCGATTTTCTT
* *
2390538 AATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTTCTT
1 AATCGCGTTGCGATTCTTGGAATATCACGTTGCGATTTTCTT
* ** * *
2390580 --TTGACCGTTGCGATT-TT--CTTTTCAACGTTGCGATTTTCTG
1 AATCG--CGTTGCGATTCTTGGAATATC-ACGTTGCGATTTTCTT
* *
2390620 AATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTCTCTT
1 AATCGCGTTGCGATTCTTGGAATATCACGTTGCGATTTTCTT
* *
2390662 AATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTTCTT
1 AATCGCGTTGCGATTCTTGGAATATCACGTTGCGATTTTCTT
* ** * *
2390704 --TTGACCGTTGCGATT-TT--CTTTTCAACGTTGCGATTTTCTA
1 AATCG--CGTTGCGATTCTTGGAATATC-ACGTTGCGATTTTCTT
2390744 AATCGCGTTGCGATT
1 AATCGCGTTGCGATT
2390759 TTTATTTCGC
Statistics
Matches: 215, Mismatches: 33, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
39 6 0.03
40 72 0.33
41 7 0.03
42 128 0.60
43 2 0.01
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.40
Consensus pattern (42 bp):
AATCGCGTTGCGATTCTTGGAATATCACGTTGCGATTTTCTT
Found at i:2390653 original size:22 final size:21
Alignment explanation
Indices: 2390620--2390698 Score: 90
Period size: 22 Copynumber: 3.7 Consensus size: 21
2390610 CGATTTTCTG
2390620 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATTCTTGGA
* *
2390641 AGATCACGTTGCGATTCTCT--T
1 A-ATCGCGTTGCGATTCT-TGGA
*
2390662 AATCGCATTGCGATTCTTGGA
1 AATCGCGTTGCGATTCTTGGA
2390683 ATATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
2390699 TTCTTTTGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 14 0.30
21 3 0.06
22 28 0.60
23 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
AATCGCGTTGCGATTCTTGGA
Found at i:2390657 original size:124 final size:124
Alignment explanation
Indices: 2390481--2390758 Score: 547
Period size: 124 Copynumber: 2.2 Consensus size: 124
2390471 CTTGGAATCG
2390481 CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTCTCTTAATCGCAT
1 CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTCTCTTAATCGCAT
2390546 TGCGATTCTTGGAATATCGCGTTGCGATTTTCTTTTGACCGTTGCGATTTTCTTTTCAA
66 TGCGATTCTTGGAATATCGCGTTGCGATTTTCTTTTGACCGTTGCGATTTTCTTTTCAA
2390605 CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTCTCTTAATCGCAT
1 CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTCTCTTAATCGCAT
2390670 TGCGATTCTTGGAATATCGCGTTGCGATTTTCTTTTGACCGTTGCGATTTTCTTTTCAA
66 TGCGATTCTTGGAATATCGCGTTGCGATTTTCTTTTGACCGTTGCGATTTTCTTTTCAA
*
2390729 CGTTGCGATTTTCTAAATCGCGTTGCGATT
1 CGTTGCGATTTTCTGAATCGCGTTGCGATT
2390759 TTTATTTCGC
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 153 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (124 bp):
CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTCTCTTAATCGCAT
TGCGATTCTTGGAATATCGCGTTGCGATTTTCTTTTGACCGTTGCGATTTTCTTTTCAA
Found at i:2390673 original size:82 final size:82
Alignment explanation
Indices: 2390441--2390702 Score: 275
Period size: 82 Copynumber: 3.2 Consensus size: 82
2390431 TTCTGAATCG
* *
2390441 CGTTGCGATTCTT-GGAATCGCGTTGCGATTCTTGG-AATCGCGTTGCGATTTTCTGAATCGCGT
1 CGTTGCGATT-TTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGATTTTCTTAATCGCGT
2390504 TGCGATTCTTGGAAGATCA
65 TGCGATTCTT-GAAGATCA
* * * *
2390523 CGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTTCTT--TTGACC
1 CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGATTTTCTTAATCG--C
****
2390586 GTTGCGATT-TT-CTTTTCAA
63 GTTGCGATTCTTGAAGATC-A
* * *
2390605 CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTCTCTTAATCGCAT
1 CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGATTTTCTTAATCGCGT
* *
2390670 TGCGATTCTTGGAATATCG
65 TGCGATTCTT-GAAGATCA
2390689 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
2390703 TTTGACCGTT
Statistics
Matches: 147, Mismatches: 22, Indels: 20
0.78 0.12 0.11
Matches are distributed among these distances:
81 3 0.02
82 92 0.63
83 5 0.03
84 44 0.30
85 3 0.02
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (82 bp):
CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGATTTTCTTAATCGCGTT
GCGATTCTTGAAGATCA
Found at i:2390752 original size:20 final size:20
Alignment explanation
Indices: 2390428--2390779 Score: 182
Period size: 20 Copynumber: 17.2 Consensus size: 20
2390418 GAATTTACTC
*
2390428 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
2390448 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
**
2390468 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
2390488 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
** *
2390508 ATTCTTGGAAGATCACGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
2390530 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
2390550 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
2390572 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
2390592 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
2390612 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
** *
2390632 ATTCTTGGAAGATCACGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
2390654 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
2390674 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
2390696 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
2390716 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
2390736 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
2390756 ATTTT-TATTTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
2390775 ATTTT
1 ATTTT
2390780 GTTGGTCATT
Statistics
Matches: 260, Mismatches: 52, Indels: 41
0.74 0.15 0.12
Matches are distributed among these distances:
18 4 0.02
19 19 0.07
20 157 0.60
21 28 0.11
22 52 0.20
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:2399707 original size:15 final size:15
Alignment explanation
Indices: 2399687--2399725 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
2399677 AGATATAGAG
*
2399687 TGGCGAAGTGGTTTT
1 TGGCGAAATGGTTTT
2399702 TGGCGAAATGGTTTT
1 TGGCGAAATGGTTTT
2399717 TGGCGAAAT
1 TGGCGAAAT
2399726 ATCCTAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.08, G:0.36, T:0.36
Consensus pattern (15 bp):
TGGCGAAATGGTTTT
Found at i:2405788 original size:15 final size:15
Alignment explanation
Indices: 2405768--2405802 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2405758 TAGCCTATCT
2405768 GTTATTCCTTTAGAA
1 GTTATTCCTTTAGAA
2405783 GTTATTCCTTTAGAA
1 GTTATTCCTTTAGAA
*
2405798 ATTAT
1 GTTAT
2405803 CCCTCTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (15 bp):
GTTATTCCTTTAGAA
Found at i:2409239 original size:11 final size:11
Alignment explanation
Indices: 2409223--2409257 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2409213 AAAAAAGAGT
2409223 AAAAATAATAA
1 AAAAATAATAA
*
2409234 AGAAATAATAAA
1 AAAAATAAT-AA
2409246 AAAAATAATAA
1 AAAAATAATAA
2409257 A
1 A
2409258 TCTAAGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:2409253 original size:12 final size:12
Alignment explanation
Indices: 2409223--2409257 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2409213 AAAAAAGAGT
2409223 AAAAATAAT-AA
1 AAAAATAATAAA
*
2409234 AGAAATAATAAA
1 AAAAATAATAAA
2409246 AAAAATAATAAA
1 AAAAATAATAAA
2409258 TCTAAGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (12 bp):
AAAAATAATAAA
Found at i:2409287 original size:13 final size:13
Alignment explanation
Indices: 2409269--2409296 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2409259 CTAAGGAAAG
2409269 AATTAAATCACAA
1 AATTAAATCACAA
2409282 AATTAAATCACAA
1 AATTAAATCACAA
2409295 AA
1 AA
2409297 AAATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (13 bp):
AATTAAATCACAA
Done.