Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009023.1 Hibiscus syriacus cultivar Beakdansim tig00112416_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: 540103
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 3
Found at i:2035 original size:16 final size:17
Alignment explanation
Indices: 2008--2042 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1998 TATCGCCGAC
2008 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
2025 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
2041 CG
1 CG
2043 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:16740 original size:30 final size:30
Alignment explanation
Indices: 16706--16791 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 30
16696 ATGTTAATAC
*
16706 TATTTTAATCCTTTAAATTTCTGTTTGTAT
1 TATTTTAATCCTTTAAATTTATGTTTGTAT
** * * *
16736 TATTTTGGTACTTTAAATTTATGTTTTTTGT
1 TATTTTAATCCTTTAAATTTATG-TTTGTAT
* *
16767 TA-TTTAATCCCTTAAATTTTTGTTT
1 TATTTTAATCCTTTAAATTTATGTTT
16792 TTCTCTTGCA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
29 3 0.07
30 34 0.77
31 7 0.16
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.62
Consensus pattern (30 bp):
TATTTTAATCCTTTAAATTTATGTTTGTAT
Found at i:20999 original size:32 final size:32
Alignment explanation
Indices: 20925--20999 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
20915 GCATCTTTAA
*
20925 AGATTCAACAGTAAATATTGGGGCATATTTGG
1 AGATTCAACATTAAATATTGGGGCATATTTGG
* *
20957 AGATTCAACATTGAATATTGTGGCATATTTGG
1 AGATTCAACATTAAATATTGGGGCATATTTGG
*
20989 GGATTCAACAT
1 AGATTCAACAT
21000 CCTGATGCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (32 bp):
AGATTCAACATTAAATATTGGGGCATATTTGG
Found at i:21565 original size:120 final size:120
Alignment explanation
Indices: 21401--21621 Score: 313
Period size: 120 Copynumber: 1.8 Consensus size: 120
21391 CTCGAGAGTA
* *
21401 GATTTCAACTTCACGACGAAGGATATCTAACTCGAAGCTAAACTTCACAACGAAGGGGTCATTCA
1 GATTTCAACTTCACGACGAAGGATATCTAACTCGAAGCTAAACTTCACAACGAAGGGGCCATCCA
** *
21466 CGGTTTCAACTTCACGACGAAGGGA-ATCGTGTCCACTCGCAACAGCACAAGCTTG
66 CAATTTCAACTTCACGACGAA-GGATATCGTGCCCACTCGCAACAGCACAAGCTTG
* * *
21521 GATTTCAACTTCATGACGAAGGATAT-TCAAGTC-AAGGCTCAACTTCACAACGAAGGGGCCATC
1 GATTTCAACTTCACGACGAAGGATATCT-AACTCGAA-GCTAAACTTCACAACGAAGGGGCCATC
*
21584 CACAATTTCAACTTCACGACGGAGGATATCGTGCCCAC
64 CACAATTTCAACTTCACGACGAAGGATATCGTGCCCAC
21622 ACATCCACTA
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
119 6 0.07
120 83 0.93
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (120 bp):
GATTTCAACTTCACGACGAAGGATATCTAACTCGAAGCTAAACTTCACAACGAAGGGGCCATCCA
CAATTTCAACTTCACGACGAAGGATATCGTGCCCACTCGCAACAGCACAAGCTTG
Found at i:21628 original size:43 final size:43
Alignment explanation
Indices: 21580--21733 Score: 211
Period size: 43 Copynumber: 3.6 Consensus size: 43
21570 ACGAAGGGGC
* *
21580 CATCCACAATTTCAACTTCACGACGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
* * *
21623 CATCCACTATTTCAACTCCACGACGGAGGATATCGTACCAACGA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCAC-A
*
21667 -ATCCACGATTTCAACTCCACGATGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
* * *
21709 CAACCACGGTTTCAACTTCACGACG
1 CATCCACGATTTCAACTCCACGACG
21734 AAGGGAATCG
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
42 1 0.01
43 95 0.98
44 1 0.01
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
Found at i:21731 original size:86 final size:86
Alignment explanation
Indices: 21581--21746 Score: 244
Period size: 86 Copynumber: 1.9 Consensus size: 86
21571 CGAAGGGGCC
* * *
21581 ATCCACAATTTCAACTTCACGACGGAGGATATCGTGCCCACACATCCACTATTTCAACTCCACGA
1 ATCCACAATTTCAACTCCACGACGGAGGATATCGTGCCCACACAACCACGATTTCAACTCCACGA
*
21646 CGGA-GGATATCGTACCAACGA
66 CGAAGGGA-ATCGTACCAACGA
* * * *
21667 ATCCACGATTTCAACTCCACGATGGAGGATATCGTGCCCACACAACCACGGTTTCAACTTCACGA
1 ATCCACAATTTCAACTCCACGACGGAGGATATCGTGCCCACACAACCACGATTTCAACTCCACGA
21732 CGAAGGGAATCGTAC
66 CGAAGGGAATCGTAC
21747 ACACAAGCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 68 0.96
87 3 0.04
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (86 bp):
ATCCACAATTTCAACTCCACGACGGAGGATATCGTGCCCACACAACCACGATTTCAACTCCACGA
CGAAGGGAATCGTACCAACGA
Found at i:22055 original size:83 final size:83
Alignment explanation
Indices: 21824--22359 Score: 640
Period size: 83 Copynumber: 6.4 Consensus size: 83
21814 GAGTATCTGC
* * * * * * *
21824 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACACCATTTGCAGCATAGCTTAAGTCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
* *
21889 AGAAGGGCTGTCTGTCAA
66 AGAAGGGTTATCTGTCAA
* * * *
21907 CCAAAGACCTTCAAGTTCGATTACACTTAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGG
1 -CAAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACATCATTTACAGCATAACTCAAGG
21972 CTAGAAGGGTTATCTGTCAA
64 CTAGAAGGGTTATCTGTCAA
* *
21992 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTATAGTATAACTCAAGGCT
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
22057 AGAAGGGTTATCTGTCAA
66 AGAAGGGTTATCTGTCAA
* * * * * * * *
22075 AAAACACCTTCGAGTTCGATTTCACTCAGTTCAAAGGCACATCATTTGCAACATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
** *
22140 AGAAGGGTTATCTACCGA
66 AGAAGGGTTATCTGTCAA
* * * * * *
22158 CAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCATATCAATTGCAGTATAACTCAATGC
1 C-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGC
*
22223 TAGAAGGGTTATATGTCAA
65 TAGAAGGGTTATCTGTCAA
* * *
22242 CAAAGACCTTTGAGTTCGATTACACTCAACTCAAAGGCATATCAAATTTACAGCATAACTCAAGG
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAGCATAACTCAAGG
* * *
22307 CGAGAAGGGCTATCTGTCAT
64 CTAGAAGGGTTATCTGTCAA
* * * *
22327 CAAGGACCTTCGAGTTTGATTTCATTCAGCTCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCA
22360 GGGGCATATC
Statistics
Matches: 383, Mismatches: 65, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
83 158 0.41
84 124 0.32
85 101 0.26
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (83 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
AGAAGGGTTATCTGTCAA
Found at i:22195 original size:167 final size:166
Alignment explanation
Indices: 21824--22359 Score: 640
Period size: 167 Copynumber: 3.2 Consensus size: 166
21814 GAGTATCTGC
* * * * * * *
21824 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACACCATTTGCAGCATAGCTTAAGTCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATAACTCAAGGCT
* * * * * *
21889 AGAAGGGCTGTCTGTCAACCAAAGACCTTCAAGTTCGATTACACTTAGCTTCGAGGGCACATCAT
66 AGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTACACTCAG-TTCAAAGGCACATCAT
* **
21954 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA
129 TTACAGCATAACTCAAGGCAAGAAGGGTTATCTACCAA
**
21992 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTATAGTATAACTCAAGGCT
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATAACTCAAGGCT
* * *
22057 AGAAGGGTTATCTGTCAAAAAACACCTTCGAGTTCGATTTCACTCAGTTCAAAGGCACATCATTT
66 AGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGTTCAAAGGCACATCATTT
* * * *
22122 GCAACATAGCTCAAGGCAAGAAGGGTTATCTACCGA
131 ACAGCATAACTCAAGGCAAGAAGGGTTATCTACCAA
* * * *
22158 CAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCATATCAATTGCAGTATAACTCAATGC
1 C-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATAACTCAAGGC
* * ** *
22223 TAGAAGGGTTATATGTCAACAAAGACCTTTGAGTTCGATTACACTCAACTCAAAGGCATATCAAA
65 TAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGTTCAAAGGCACATC--A
* * ** *
22288 TTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAT
128 TTTACAGCATAACTCAAGGCAAGAAGGGTTATCTACCAA
* * * *
22327 CAAGGACCTTCGAGTTTGATTTCATTCAGCTCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCA
22360 GGGGCATATC
Statistics
Matches: 312, Mismatches: 53, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
166 46 0.15
167 135 0.43
168 99 0.32
169 32 0.10
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (166 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATAACTCAAGGCT
AGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGTTCAAAGGCACATCATTT
ACAGCATAACTCAAGGCAAGAAGGGTTATCTACCAA
Found at i:23575 original size:30 final size:30
Alignment explanation
Indices: 23541--23626 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 30
23531 ATGTTAATAC
*
23541 TATTTTAATCCTTTAAATTTCTGTTTGTAT
1 TATTTTAATCCTTTAAATTTATGTTTGTAT
** * * *
23571 TATTTTGGTACTTTAAATTTATGTTTTTTGT
1 TATTTTAATCCTTTAAATTTATG-TTTGTAT
* *
23602 TA-TTTAATCCCTTAAATTTTTGTTT
1 TATTTTAATCCTTTAAATTTATGTTT
23627 TTCTCTTGCA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
29 3 0.07
30 34 0.77
31 7 0.16
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.62
Consensus pattern (30 bp):
TATTTTAATCCTTTAAATTTATGTTTGTAT
Found at i:26183 original size:24 final size:24
Alignment explanation
Indices: 26166--26253 Score: 140
Period size: 24 Copynumber: 3.7 Consensus size: 24
26156 ATCATAACAT
*
26166 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAG
*
26190 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
*
26214 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
*
26238 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
26254 TATAATATCC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAG
Found at i:26201 original size:12 final size:13
Alignment explanation
Indices: 26166--26248 Score: 70
Period size: 12 Copynumber: 6.8 Consensus size: 13
26156 ATCATAACAT
26166 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
26179 TAT-CAGATCAA-
1 AATCCAGGTCAAG
26190 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
26203 TATCC-GATC-AG
1 AATCCAGGTCAAG
26214 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
26227 TATCC-GATC-AG
1 AATCCAGGTCAAG
26238 AATCCAGGTCA
1 AATCCAGGTCA
26249 GGTATTATAA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
11 14 0.27
12 26 0.50
13 12 0.23
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:28734 original size:13 final size:13
Alignment explanation
Indices: 28716--28757 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
28706 CTAGTCAACA
28716 GTCAACGGGTCGG
1 GTCAACGGGTCGG
28729 GTCAACGGGTCGG
1 GTCAACGGGTCGG
* *
28742 GTCAATGGGTGGG
1 GTCAACGGGTCGG
28755 GTC
1 GTC
28758 GGGTTGTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.14, C:0.19, G:0.48, T:0.19
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:30031 original size:42 final size:42
Alignment explanation
Indices: 29975--30064 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
29965 ATATATTATT
* *
29975 TTGGG-TCGGATCGGGTTTGAATTTTATCTCAAAAGATCAAG
1 TTGGGTTCGGATCGGGTTCGAATCTTATCTCAAAAGATCAAG
*
30016 TTGGGTTCGGGTCGGGTTCGAATCTTATCTCAAAAGATCAAG
1 TTGGGTTCGGATCGGGTTCGAATCTTATCTCAAAAGATCAAG
*
30058 TCGGGTT
1 TTGGGTT
30065 GGGGCCAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 5 0.11
42 39 0.89
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.33
Consensus pattern (42 bp):
TTGGGTTCGGATCGGGTTCGAATCTTATCTCAAAAGATCAAG
Found at i:30128 original size:27 final size:28
Alignment explanation
Indices: 30066--30129 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
30056 AGTCGGGTTG
*
30066 GGGCCAAGTGGAAGGTATATATATTTTT
1 GGGCCAGGTGGAAGGTATATATATTTTT
* *
30094 GGGTCAGGTGGAAGGTTTATA-ATTTTT
1 GGGCCAGGTGGAAGGTATATATATTTTT
30121 GGGCCAGGT
1 GGGCCAGGT
30130 CTGGTAGACC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 14 0.44
28 18 0.56
ACGTcount: A:0.23, C:0.08, G:0.34, T:0.34
Consensus pattern (28 bp):
GGGCCAGGTGGAAGGTATATATATTTTT
Found at i:30907 original size:20 final size:20
Alignment explanation
Indices: 30884--30994 Score: 80
Period size: 20 Copynumber: 5.3 Consensus size: 20
30874 GTTTCCAGAT
*
30884 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
30904 TCGCATTGCGATTTTCCCGACTA
1 TCGCAATGCGA--TT-CTGACTA
*
30927 TCGCAATGCGATTTTCCGACTA
1 TCGCAATGCGA--TTCTGACTA
* * * *
30949 TCGTAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
30969 TCGCAATGCGATTTTGACTA
1 TCGCAATGCGATTCTGACTA
30989 TCGCAA
1 TCGCAA
30995 CACTGAATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.01
20 32 0.44
21 1 0.01
22 19 0.26
23 20 0.27
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:30948 original size:22 final size:23
Alignment explanation
Indices: 30899--30959 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
30889 ACGCGATTCT
*
30899 GACTATCGCATTGCGATTTTCCC
1 GACTATCGCAATGCGATTTTCCC
30922 GACTATCGCAATGCGATTTT-CC
1 GACTATCGCAATGCGATTTTCCC
*
30944 GACTATCGTAATGCGA
1 GACTATCGCAATGCGA
30960 ATATGTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 17 0.47
23 19 0.53
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (23 bp):
GACTATCGCAATGCGATTTTCCC
Found at i:31847 original size:24 final size:24
Alignment explanation
Indices: 31815--31868 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
31805 GTATTCGAAA
31815 TTTGATCTTGGTCAATAAC-CGGAC
1 TTTGATCTTGGTCAAT-ACTCGGAC
*
31839 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
31863 TTTGAT
1 TTTGAT
31869 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:34152 original size:18 final size:18
Alignment explanation
Indices: 34129--34163 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34119 AGCAAAAGGC
34129 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
*
34147 AATCAAAATCTCAATCA
1 AATCAAAATCGCAATCA
34164 CAACCGGCTT
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:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:34366 original size:20 final size:20
Alignment explanation
Indices: 34341--34582 Score: 222
Period size: 20 Copynumber: 12.7 Consensus size: 20
34331 CACATTCATT
34341 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
34361 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
*
34381 TGAATATCGCAACAG-G---A
1 TGACTATCGCAAC-GCGAATA
* *
34398 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
34415 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
*
34435 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
34452 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
34469 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
34489 TGACTATCGCAACACGAATT
1 TGACTATCGCAACGCGAATA
* * *
34509 TAACTATCGCAAAGCGAATT
1 TGACTATCGCAACGCGAATA
*
34529 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
34549 TGATTATCGCAACGGGAATT
1 TGACTATCGCAACGCGAATA
34569 TGACTATCGCAACG
1 TGACTATCGCAACG
34583 AGAAAATCGC
Statistics
Matches: 184, Mismatches: 24, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
13 1 0.01
14 16 0.09
15 1 0.01
16 2 0.01
17 6 0.03
18 2 0.01
19 1 0.01
20 154 0.84
21 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:34412 original size:54 final size:54
Alignment explanation
Indices: 34346--34561 Score: 279
Period size: 54 Copynumber: 3.9 Consensus size: 54
34336 TCATTTGACT
* * * *
34346 ATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGCAACAGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACAGGATA
*
34400 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACAGGATA
* *
34454 ATCGCAATGCGAAAATGACTATCGCAACGCGAATATGACTATCGCAACACGAATTTAA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACA-GGA--T-A
* ** *
34512 CTATCGCAAAGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAAC
1 --ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAAC
34562 GGGAATTTGA
Statistics
Matches: 143, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
54 96 0.67
55 2 0.01
57 1 0.01
58 1 0.01
60 43 0.30
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACAGGATA
Found at i:34478 original size:74 final size:74
Alignment explanation
Indices: 34341--34520 Score: 213
Period size: 74 Copynumber: 2.4 Consensus size: 74
34331 CACATTCATT
* * * * * *
34341 TGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGCAACAGGATAATCGCA
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGGGAAATCGAATAGCGCAAAAGGATAATCGCA
*
34406 ATGCGAAAA
66 ACGCGAAAA
*
34415 TGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAAT-GCG-AAAATGACT-ATC
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGGGA-AATCG-AATAGCGCAAAAGGA-TAATC
*
34477 GCAACGCGAATA
63 GCAACGCGAAAA
* *
34489 TGACTATCGCAACACGAATTTAACTATCGCAA
1 TGACTATCGCAACGCGAATTTGACTATCGCAA
34521 AGCGAATTTG
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
74 83 0.90
75 6 0.07
76 3 0.03
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (74 bp):
TGACTATCGCAACGCGAATTTGACTATCGCAACGGGAAATCGAATAGCGCAAAAGGATAATCGCA
ACGCGAAAA
Found at i:34764 original size:36 final size:34
Alignment explanation
Indices: 34717--34796 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 34
34707 CCAACTTTTA
*
34717 ATCAATTAAACAAGCACAAATAATAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
34753 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
34783 ATCAATTAAACAAA
1 ATCAATTAAACAAA
34797 TCAACTCTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
30 27 0.69
32 2 0.05
34 3 0.08
36 7 0.18
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.28
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:34768 original size:30 final size:30
Alignment explanation
Indices: 34732--34797 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
34722 TTAAACAAGC
*
34732 ACAAATAATAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
34762 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
34792 ACAAAT
1 ACAAAT
34798 CAACTCTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:36839 original size:20 final size:20
Alignment explanation
Indices: 36814--36881 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
36804 GCGATTCTTT
* **
36814 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCATTTTCG
* *
36834 CGTTGCAATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
36854 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
36874 CGTTGCGA
1 CGTTGCGA
36882 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:37052 original size:18 final size:18
Alignment explanation
Indices: 37029--37078 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
37019 TTTACTAAGC
*
37029 AATCTAAGTAAAATGGTT
1 AATCTAAGTGAAATGGTT
37047 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
37065 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
37079 TACGAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:38858 original size:19 final size:20
Alignment explanation
Indices: 38799--38885 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
38789 TCTGAAACTT
38799 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
38819 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
38839 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
* * *
38858 AAAATCACAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
38877 AAAATCGCA
1 AAAATCGCA
38886 TTGCGATTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.41
20 34 0.59
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:39824 original size:64 final size:65
Alignment explanation
Indices: 39756--39912 Score: 169
Period size: 64 Copynumber: 2.4 Consensus size: 65
39746 TTGAAGGTGT
*** *
39756 ATCGATGCACAGGTAGTGCATCGATGCACT-CTTTTAA-AATA-AATACATCGAATGCAATTCGT
1 ATCGATGCACAGGTAGTGCATCGATGCACTCCCAGTAATAA-ACAA-ACATCGAATGCAATTCAT
39818 GC
64 GC
* * * * * *
39820 ATCGATGCATAAGTAGTGCATCGATGCA-TCCCAGTAATAAACAAACATTGAATGTATTTTATGC
1 ATCGATGCACAGGTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAATTCATGC
*
39884 ACCGATGCACAGGTAGTGCATCGATGCAC
1 ATCGATGCACAGGTAGTGCATCGATGCAC
39913 CGATAGGGAA
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
63 1 0.01
64 71 0.93
65 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (65 bp):
ATCGATGCACAGGTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAATTCATGC
Found at i:40900 original size:103 final size:103
Alignment explanation
Indices: 40676--40893 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
40666 GTCGAGGGTC
*
40676 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
40741 CTGATCATTGGCATATGTATATGATTATTAAGGAATGA
66 CTGATCACTAGCATATGTATATGATTATTAAGGAATGA
40779 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * * *
40844 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 CTGATCACTAGCATATGTATATGATTATTAAGGAATGA
40882 TATGTGGTCCTT
1 TATGTGGTCCTT
40894 ATGGACAGTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
CTGATCACTAGCATATGTATATGATTATTAAGGAATGA
Found at i:40976 original size:23 final size:23
Alignment explanation
Indices: 40909--40977 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
40899 CAGTATTATA
* *
40909 TGGCACTACGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTATATG
*
40932 CGGCACTTCGGTGCAATTATATG
1 TGGCACTTCGGTGCAATTATATG
40955 TGGCACTTCGGTGCAATTATATG
1 TGGCACTTCGGTGCAATTATATG
40978 AGCTATGGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATATG
Found at i:42419 original size:20 final size:20
Alignment explanation
Indices: 42387--42462 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
42377 TGGCGCTTTG
*
42387 AAAATCGCATTGCGATAGTC
1 AAAATCGCGTTGCGATAGTC
** * *
42407 AGCATCGGGTTGCGACAGTC
1 AAAATCGCGTTGCGATAGTC
42427 AAAATCGCGTTGCGATAGTC
1 AAAATCGCGTTGCGATAGTC
* * *
42447 ATACTCGCATTGCGAT
1 AAAATCGCGTTGCGAT
42463 TTACATATTC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (20 bp):
AAAATCGCGTTGCGATAGTC
Found at i:45004 original size:23 final size:23
Alignment explanation
Indices: 44978--45048 Score: 133
Period size: 23 Copynumber: 3.1 Consensus size: 23
44968 AACATAAATG
44978 AACGGATGTAAACGAACACAATA
1 AACGGATGTAAACGAACACAATA
45001 AACGGATGTAAACGAACACAATA
1 AACGGATGTAAACGAACACAATA
*
45024 AACGAATGTAAACGAACACAATA
1 AACGGATGTAAACGAACACAATA
45047 AA
1 AA
45049 TGAACATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.55, C:0.17, G:0.15, T:0.13
Consensus pattern (23 bp):
AACGGATGTAAACGAACACAATA
Found at i:45058 original size:23 final size:23
Alignment explanation
Indices: 44947--45064 Score: 101
Period size: 23 Copynumber: 4.9 Consensus size: 23
44937 CATTTAAATG
* * *
44947 ATAAATGAACATAGATGAACAAA
1 ATAAATGAACATAAACGAACACA
44970 CATAAATGAACGGATGTAAACGAACACA
1 -ATAAATGAAC--A--TAAACGAACACA
* * **
44998 ATAAACGGATGTAAACGAACACA
1 ATAAATGAACATAAACGAACACA
* **
45021 ATAAACGAATGTAAACGAACACA
1 ATAAATGAACATAAACGAACACA
45044 ATAAATGAACATAAACGAACA
1 ATAAATGAACATAAACGAACA
45065 TAAATGAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
23 52 0.66
24 10 0.13
26 1 0.01
27 7 0.09
28 9 0.11
ACGTcount: A:0.56, C:0.15, G:0.14, T:0.14
Consensus pattern (23 bp):
ATAAATGAACATAAACGAACACA
Found at i:45270 original size:24 final size:24
Alignment explanation
Indices: 45238--45291 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
45228 GATTGAGCTA
* *
45238 AACATAAATGAACGAATATAAACG
1 AACATAAATGAACAAACATAAACG
45262 AACATAAATGAACAAACATAAACG
1 AACATAAATGAACAAACATAAACG
45286 AACATA
1 AACATA
45292 TTACCGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.61, C:0.15, G:0.09, T:0.15
Consensus pattern (24 bp):
AACATAAATGAACAAACATAAACG
Found at i:46416 original size:3 final size:3
Alignment explanation
Indices: 46408--46433 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46398 TAGATAAGAA
46408 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
46434 ATCAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:46487 original size:18 final size:18
Alignment explanation
Indices: 46465--46508 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
46455 AAATGAAAAG
*
46465 AAAAAAATTTAAAAA-AA
1 AAAAAAATTGAAAAAGAA
*
46482 ATAAAAAGTTGAAAAAGAA
1 A-AAAAAATTGAAAAAGAA
46501 AAAAAAAT
1 AAAAAAAT
46509 ATAGTACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (18 bp):
AAAAAAATTGAAAAAGAA
Found at i:46535 original size:16 final size:16
Alignment explanation
Indices: 46516--46553 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
46506 AATATAGTAC
*
46516 ATAAAAA-AGGAATAAA
1 ATAAAAATACGAAT-AA
46532 ATAAAAATACGAATAA
1 ATAAAAATACGAATAA
46548 ATAAAA
1 ATAAAA
46554 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (16 bp):
ATAAAAATACGAATAA
Found at i:46538 original size:17 final size:17
Alignment explanation
Indices: 46518--46573 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
46508 TATAGTACAT
*
46518 AAAAAAGGAATAAAATA
1 AAAAAAAGAATAAAATA
* *
46535 AAAATACGAAT-AAATA
1 AAAAAAAGAATAAAATA
* *
46551 AAAGAAAAGAAAAAAAGA
1 AAA-AAAAGAATAAAATA
46569 AAAAA
1 AAAAA
46574 TATTTTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 8 0.26
17 16 0.52
18 7 0.23
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.09
Consensus pattern (17 bp):
AAAAAAAGAATAAAATA
Found at i:47923 original size:35 final size:35
Alignment explanation
Indices: 47810--48058 Score: 196
Period size: 35 Copynumber: 6.8 Consensus size: 35
47800 ATAATTTTGA
* * * * ***
47810 AAAATTATATAATATATATTTTAAAAAATATTAAA
1 AAAACTATATATTATATATTTTCAAAAATGTTTTT
*
47845 AAAACTATATATTATATATTTAC-AAAATGTTTTT
1 AAAACTATATATTATATATTTTCAAAAATGTTTTT
* *
47879 TAAATTATATATTATATAGTTTTCAAAAATG-TTTT
1 AAAACTATATATTATATA-TTTTCAAAAATGTTTTT
* * *
47914 AAAACTATATATTATATAAATGTTTTAAAAATGATTTC
1 AAAACTATATATTATAT--AT-TTTCAAAAATGTTTTT
* *
47952 AAAACTATATATTATATATATTCATAAATGTTTTTT
1 AAAACTATATATTATATATTTTCAAAAATG-TTTTT
** *
47988 CAAAAATCTATATATTATATATATATTTTTAAAATGTTTTCA
1 --AAAA-CTATATA-T-TATATAT-TTTCAAAAATGTTTT-T
*
48030 AAAACCATATATTATATATGTTTCAAAAA
1 AAAACTATATATTATATAT-TTTCAAAAA
48059 GCTTTCCAAA
Statistics
Matches: 171, Mismatches: 29, Indels: 26
0.76 0.13 0.12
Matches are distributed among these distances:
34 23 0.13
35 50 0.29
36 12 0.07
37 25 0.15
38 25 0.15
39 13 0.08
40 5 0.03
41 11 0.06
42 7 0.04
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (35 bp):
AAAACTATATATTATATATTTTCAAAAATGTTTTT
Found at i:48040 original size:39 final size:38
Alignment explanation
Indices: 47850--48118 Score: 192
Period size: 37 Copynumber: 7.0 Consensus size: 38
47840 TTAAAAAAAC
** *
47850 TATATATTATATATTTACAAAATGTTTTTTAAATTATATAT
1 TATATA-TATAT-TTTA-AAAATGTTTTCAAAACTATATAT
* *
47891 TATATA-GT-TTTCAAAAATGTTTT-AAAACTATATAT
1 TATATATATATTTTAAAAATGTTTTCAAAACTATATAT
* * *
47926 TATATAAATGTTTTAAAAATGATTTCAAAACTATATAT
1 TATATATATATTTTAAAAATGTTTTCAAAACTATATAT
** ** *
47964 TATATATAT-TCATAAATGTTTTTTCAAAAATCTATATAT
1 TATATATATATTTTAAAAATGTTTTC-AAAA-CTATATAT
* *
48003 TATATATATATTTTTAAAATGTTTTCAAAAACCATATA-
1 TATATATATATTTTAAAAATGTTTTC-AAAACTATATAT
* * * * *
48041 T-TATATATGTTTCAAAAA-GCTTTCCAAACATTATATAA
1 TATATATATATTTTAAAAATG-TTTTCAAA-ACTATATAT
* **
48079 TATATATATATTTCCAAAAACCATTTTCAAAACTATATAT
1 TATATATATATTT-TAAAAA-TGTTTTCAAAACTATATAT
48119 ATTATACGTT
Statistics
Matches: 183, Mismatches: 32, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
35 16 0.09
36 15 0.08
37 50 0.27
38 27 0.15
39 34 0.19
40 28 0.15
41 13 0.07
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (38 bp):
TATATATATATTTTAAAAATGTTTTCAAAACTATATAT
Found at i:53577 original size:6 final size:6
Alignment explanation
Indices: 53561--53593 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
53551 GAGCTTTGGG
*
53561 TTTTG- TTTTGT TTTTGT TTTTGT TTTCGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
53594 TTCTGTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (6 bp):
TTTTGT
Found at i:53586 original size:22 final size:22
Alignment explanation
Indices: 53560--53601 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
53550 TGAGCTTTGG
*
53560 GTTTT-GTTTTGTTTTTGTTTTT
1 GTTTTCGTTTT-TTTCTGTTTTT
53582 GTTTTCGTTTTTTTCTGTTT
1 GTTTTCGTTTTTTTCTGTTT
53602 GATTCCTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.00, C:0.05, G:0.17, T:0.79
Consensus pattern (22 bp):
GTTTTCGTTTTTTTCTGTTTTT
Found at i:56223 original size:6 final size:6
Alignment explanation
Indices: 56212--56240 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
56202 AACCCTCAAT
56212 AAACCG AAACCG AAACCG AAACCG AAACC
1 AAACCG AAACCG AAACCG AAACCG AAACC
56241 CCAAAGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.34, G:0.14, T:0.00
Consensus pattern (6 bp):
AAACCG
Found at i:59932 original size:42 final size:40
Alignment explanation
Indices: 59867--59948 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 40
59857 ATAACTTAAA
*
59867 AAGTTAATTTTGAGTTGATTAATCACAAGTAAAAATAATAAT
1 AAGTTAATTTTGAGTTGAATAATCACAAG-AAAAA-AATAAT
* * *
59909 AAGTTCATTTTGAGTTTAATAATCACATGAAAAAAATAAT
1 AAGTTAATTTTGAGTTGAATAATCACAAGAAAAAAATAAT
59949 GAAATGGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 6 0.17
41 5 0.14
42 25 0.69
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (40 bp):
AAGTTAATTTTGAGTTGAATAATCACAAGAAAAAAATAAT
Found at i:61363 original size:21 final size:21
Alignment explanation
Indices: 61312--61364 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
61302 TGCTATAATG
61312 AATGGCCAATTCGAAAATTTA
1 AATGGCCAATTCGAAAATTTA
* *
61333 AAAGGACAATTCG-AAATATTA
1 AATGGCCAATTCGAAAAT-TTA
61354 AATGGCCAATT
1 AATGGCCAATT
61365 TGGGAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.26
Consensus pattern (21 bp):
AATGGCCAATTCGAAAATTTA
Found at i:67594 original size:20 final size:20
Alignment explanation
Indices: 67556--67594 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
67546 TGGAAATTAA
*
67556 TGTTAGAGTGATGAGTTTGG
1 TGTTAGAATGATGAGTTTGG
67576 TGTTAGAATG-TGAGATTTG
1 TGTTAGAATGATGAG-TTTG
67595 AATATTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.23, C:0.00, G:0.36, T:0.41
Consensus pattern (20 bp):
TGTTAGAATGATGAGTTTGG
Found at i:70394 original size:24 final size:24
Alignment explanation
Indices: 70341--70397 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
70331 TGTTATAAGA
* *
70341 TATATGATATGAACATAAGATATGT
1 TATATGA-ATGAACAAAAAATATGT
70366 T-TATGAATGAA-AAAAAATATGTT
1 TATATGAATGAACAAAAAATATG-T
70389 TATATGAAT
1 TATATGAAT
70398 ATGATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 8 0.29
23 7 0.25
24 12 0.43
25 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (24 bp):
TATATGAATGAACAAAAAATATGT
Found at i:70623 original size:18 final size:18
Alignment explanation
Indices: 70600--70634 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
70590 AAGGTTCTAC
*
70600 GTGGTCCTTCGGGACATA
1 GTGGTCATTCGGGACATA
70618 GTGGTCATTCGGGACAT
1 GTGGTCATTCGGGACAT
70635 TTCTATGCGG
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:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
GTGGTCATTCGGGACATA
Found at i:70667 original size:25 final size:23
Alignment explanation
Indices: 70620--70667 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
70610 GGGACATAGT
*
70620 GGTCATTCGGGACATTTCTATGC
1 GGTCATTCGGGACATTTATATGC
*
70643 GGTCATTTGGGACAAATTTATATGC
1 GGTCATTCGGGAC--ATTTATATGC
70668 CCCTAGTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
25 9 0.43
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (23 bp):
GGTCATTCGGGACATTTATATGC
Found at i:75996 original size:19 final size:19
Alignment explanation
Indices: 75974--76026 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
75964 GCTATGAACT
75974 TGAAAATAAGGTATGAATA
1 TGAAAATAAGGTATGAATA
* *
75993 TGAAATTAA-GTAATGAATC
1 TGAAAATAAGGT-ATGAATA
*
76012 TG-AAATAAGTTATGA
1 TGAAAATAAGGTATGA
76027 GTCCGGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.49, C:0.02, G:0.19, T:0.30
Consensus pattern (19 bp):
TGAAAATAAGGTATGAATA
Found at i:76026 original size:37 final size:37
Alignment explanation
Indices: 75977--76063 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 37
75967 ATGAACTTGA
* * *
75977 AAATAAGGTATGAAT-ATGAAATTAAGTAATGAATCTG
1 AAATAAGTTATGAATCAGGAAA-CAAGTAATGAATCTG
* * **
76014 AAATAAGTTATGAGTCCGGAAACAAGTTTTGAATCTG
1 AAATAAGTTATGAATCAGGAAACAAGTAATGAATCTG
76051 AAATAAGTTATGA
1 AAATAAGTTATGA
76064 GTCCAGAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 38 0.90
38 4 0.10
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.30
Consensus pattern (37 bp):
AAATAAGTTATGAATCAGGAAACAAGTAATGAATCTG
Found at i:76035 original size:19 final size:19
Alignment explanation
Indices: 76013--76078 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
76003 TAATGAATCT
*
76013 GAAATAAGTTATGAGTCCG
1 GAAATAAGTTATGAGTCCA
* * * *
76032 GAAACAAGTTTTGAAT-CT
1 GAAATAAGTTATGAGTCCA
76050 GAAATAAGTTATGAGTCCA
1 GAAATAAGTTATGAGTCCA
*
76069 GAAAAAAGTT
1 GAAATAAGTT
76079 TTGAATCTAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
18 14 0.38
19 23 0.62
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.27
Consensus pattern (19 bp):
GAAATAAGTTATGAGTCCA
Found at i:76064 original size:37 final size:37
Alignment explanation
Indices: 76006--76086 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
75996 AATTAAGTAA
* *
76006 TGAATCTGAAATAAGTTATGAGTCCGGAAACAAGTTT
1 TGAATCTGAAATAAGTTATGAGTCCAGAAAAAAGTTT
76043 TGAATCTGAAATAAGTTATGAGTCCAGAAAAAAGTTT
1 TGAATCTGAAATAAGTTATGAGTCCAGAAAAAAGTTT
76080 TGAATCT
1 TGAATCT
76087 AAGAAAGAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.31
Consensus pattern (37 bp):
TGAATCTGAAATAAGTTATGAGTCCAGAAAAAAGTTT
Found at i:76163 original size:13 final size:12
Alignment explanation
Indices: 76134--76178 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
76124 AAAAGAAATG
*
76134 TGAAAGTGAATA
1 TGAAAGTGAAAA
76146 TGAAAGTGAAAGA
1 TGAAAGTGAAA-A
*
76159 TGAAAATGAGAAA
1 TGAAAGTGA-AAA
76172 TGAAAGT
1 TGAAAGT
76179 TTTGTATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.36
13 16 0.57
14 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (12 bp):
TGAAAGTGAAAA
Found at i:76224 original size:14 final size:14
Alignment explanation
Indices: 76205--76242 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
76195 ATGAAAAAAA
76205 TATGATATGACTAG
1 TATGATATGACTAG
76219 TATGATATGACTAG
1 TATGATATGACTAG
*
76233 TATGAGATGA
1 TATGATATGA
76243 AAATGAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (14 bp):
TATGATATGACTAG
Found at i:77856 original size:126 final size:126
Alignment explanation
Indices: 77491--77927 Score: 511
Period size: 127 Copynumber: 3.5 Consensus size: 126
77481 TTCAATTGCA
* * * * * * * ** *
77491 AAGTAGTTGCACAGTATCGATACAGTGAACTTATCGATACTGTTATTTTGTACTGGATTATCACT
1 AAGTAGTTACACCGTATCGATACCGAGCACGTATTGATACCCTTATTTTATACTGGATTATCACT
*
77556 AGAATTATAGGGTATCGATACCCCATGCGTATCAGTACTATATATTGTTTCTTGAATTTTCC
66 AGAATTATAGGGTATCGATACCCCATGCGTATCAGTACTATA-ATTGTTTCTTGAATTTTCT
* * * * * * *
77618 AAGTAGTTGCACTGTATCTATACCAAGCACGTATCGGTACCCTTATTTTATATTGGATTATCACT
1 AAGTAGTTACACCGTATCGATACCGAGCACGTATTGATACCCTTATTTTATACTGGATTATCACT
* * * * * *
77683 AGAATTGTAGGGTATTGATACCCCATGCATATCGGTATTAATGATTGTTTCTTGAATTTTCT
66 AGAATTATAGGGTATCGATACCCCATGCGTATCAGTACT-ATAATTGTTTCTTGAATTTTCT
** * *
77745 AAGTAGTTACACCGTATCGATACCGAGGGCGTATTGATA-CCTCATTTTATACTGGATTCTCACT
1 AAGTAGTTACACCGTATCGATACCGAGCACGTATTGATACCCTTATTTTATACTGGATTATCACT
* * * *
77809 AGAATTATAGGGTATCGATAGCCCATGCGTATAAGTACTGTTAATTGTTTGTTGAA-TTT-T
66 AGAATTATAGGGTATCGATACCCCATGCGTATCAGTACT-ATAATTGTTTCTTGAATTTTCT
* *
77869 AATGTAGTTACACCGTATCGATACAGATCACGTATTGATACCCTTATTTTATACTGGAT
1 AA-GTAGTTACACCGTATCGATACCGAGCACGTATTGATACCCTTATTTTATACTGGAT
77928 ATTTGTGAAA
Statistics
Matches: 261, Mismatches: 46, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
124 3 0.01
125 36 0.14
126 84 0.32
127 136 0.52
128 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (126 bp):
AAGTAGTTACACCGTATCGATACCGAGCACGTATTGATACCCTTATTTTATACTGGATTATCACT
AGAATTATAGGGTATCGATACCCCATGCGTATCAGTACTATAATTGTTTCTTGAATTTTCT
Found at i:83002 original size:15 final size:17
Alignment explanation
Indices: 82971--83005 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
82961 ATGCATATAT
82971 AAATTATATTAAAAATA
1 AAATTATATTAAAAATA
82988 AAATTATA-T-AAAATA
1 AAATTATATTAAAAATA
83003 AAA
1 AAA
83006 ATAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATTATATTAAAAATA
Found at i:83137 original size:17 final size:15
Alignment explanation
Indices: 83115--83151 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
83105 CCCACCAATA
83115 TATTATTTAAATTATTT
1 TATTATTTAAA-TA-TT
83132 TATTATTTAAATATT
1 TATTATTTAAATATT
83147 TATTA
1 TATTA
83152 AACTCATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
16 2 0.10
17 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTTAAATATT
Found at i:83227 original size:17 final size:16
Alignment explanation
Indices: 83180--83229 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
83170 AAAATATTAA
83180 AATTTTA-TTTTATAT
1 AATTTTATTTTTATAT
*
83195 AATTTT-TTTCT-T-T
1 AATTTTATTTTTATAT
83208 AATTTTATTTTTAATAT
1 AATTTTATTTTT-ATAT
83225 AATTT
1 AATTT
83230 AGATATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 7 0.25
14 5 0.18
15 9 0.32
16 1 0.04
17 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTTATTTTTATAT
Found at i:83283 original size:14 final size:14
Alignment explanation
Indices: 83243--83284 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
83233 TATTATTTTT
83243 TAAAAAATAATTATAA
1 TAAAAAAT-ATTA-AA
83259 -AAAAAAT-TTAAA
1 TAAAAAATATTAAA
83271 TAAAAAATATTAAA
1 TAAAAAATATTAAA
83285 ATCATTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 5 0.21
15 7 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAAAATATTAAA
Found at i:84430 original size:120 final size:121
Alignment explanation
Indices: 84261--84502 Score: 477
Period size: 121 Copynumber: 2.0 Consensus size: 121
84251 AAGAAACACC
84261 TACACTTCGCTTTTGATTAAGTAATCGAGCTGTTTCCAAGCTGTCAACTTCCAAAA-AACTCTCC
1 TACACTTCGCTTTTGATTAAGTAATCGAGCTGTTTCCAAGCTGTCAACTTCCAAAATAACTCTCC
84325 GGTCACCATAATTCCAAGCACGGATCAAACCCTTATGGACACCCCAAAGTTTCGCT
66 GGTCACCATAATTCCAAGCACGGATCAAACCCTTATGGACACCCCAAAGTTTCGCT
84381 TACACTTCGCTTTTGATTAAGTAATCGAGCTGTTTCCAAGCTGTCAACTTCCAAAATAACTCTCC
1 TACACTTCGCTTTTGATTAAGTAATCGAGCTGTTTCCAAGCTGTCAACTTCCAAAATAACTCTCC
84446 GGTCACCATAATTCCAAGCACGGATCAAACCCTTATGGACACCCCAAAGTTTCGCT
66 GGTCACCATAATTCCAAGCACGGATCAAACCCTTATGGACACCCCAAAGTTTCGCT
84502 T
1 T
84503 CCAAGACCGA
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
120 56 0.46
121 65 0.54
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (121 bp):
TACACTTCGCTTTTGATTAAGTAATCGAGCTGTTTCCAAGCTGTCAACTTCCAAAATAACTCTCC
GGTCACCATAATTCCAAGCACGGATCAAACCCTTATGGACACCCCAAAGTTTCGCT
Found at i:89196 original size:118 final size:115
Alignment explanation
Indices: 88964--89197 Score: 425
Period size: 118 Copynumber: 2.0 Consensus size: 115
88954 AAGTGATAAT
88964 AATATATTAACCATAAATACAAATCACTGCACATATAAAGTTTTTAATTCCAAATTTATAATAAG
1 AATATATTAACCATAAATACAAATCACTGCACATATAAAGTTTTTAATTCCAAATTTATAATAAG
89029 AAATAATAAAAAACACAAATTTAAAACAAAATAGAGATTGTTGTGGTGTG
66 AAATAATAAAAAACACAAATTTAAAACAAAATAGAGATTGTTGTGGTGTG
89079 AATATTATTAACCATAAATACAATAATCACTGCACATATAAAGTTTTTAATTCCAAATTTATAAT
1 AATA-TATTAACCATAAATAC-A-AATCACTGCACATATAAAGTTTTTAATTCCAAATTTATAAT
89144 AAGAAATAAT-AAAAACACAAATTTAAAACAAAATAGAGATTGTTGTGTGTGTG
63 AAGAAATAATAAAAAACACAAATTTAAAACAAAATAGAGATTGTTGTG-GTGTG
89197 A
1 A
89198 GAGAGAAGAA
Statistics
Matches: 115, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
115 4 0.03
116 16 0.14
117 38 0.33
118 57 0.50
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.31
Consensus pattern (115 bp):
AATATATTAACCATAAATACAAATCACTGCACATATAAAGTTTTTAATTCCAAATTTATAATAAG
AAATAATAAAAAACACAAATTTAAAACAAAATAGAGATTGTTGTGGTGTG
Found at i:90033 original size:2 final size:2
Alignment explanation
Indices: 90026--90059 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
90016 AAGTTGCATG
90026 AT AT AT 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
90060 TATTTTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94136 original size:25 final size:25
Alignment explanation
Indices: 94089--94136 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
94079 GTACTTTGAA
*
94089 AAAAATAATAATATATTATATTTTT
1 AAAAATAATAATATATTAAATTTTT
*
94114 AAAAATAAT-ATATCTTTAAATTT
1 AAAAATAATAATAT-ATTAAATTT
94137 ATATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAAATAATAATATATTAAATTTTT
Found at i:94215 original size:2 final size:2
Alignment explanation
Indices: 94208--94245 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
94198 TTCAACTAAA
*
94208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
94246 AAAGCACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:98799 original size:23 final size:23
Alignment explanation
Indices: 98750--98803 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
98740 ATGTGGCATC
* *
98750 CAGTCAACAGCTTCTAAAAGGCC
1 CAGTCAACAGCTTCTAAAAGACA
* * *
98773 CAGTCAGCAGCTTCTAGAAGATA
1 CAGTCAACAGCTTCTAAAAGACA
98796 CAGTCAAC
1 CAGTCAAC
98804 CAATTTTTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (23 bp):
CAGTCAACAGCTTCTAAAAGACA
Found at i:104301 original size:20 final size:20
Alignment explanation
Indices: 104276--104316 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
104266 CCGTTAGACA
104276 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
*
104296 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
104316 G
1 G
104317 ACATTCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.29, G:0.39, T:0.17
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:106351 original size:15 final size:15
Alignment explanation
Indices: 106321--106360 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
106311 AAGGCAACTC
106321 ATTTCATTTTCGTTTA
1 ATTT-ATTTTCGTTTA
* *
106337 ATTTGTTTTCTTTTA
1 ATTTATTTTCGTTTA
106352 ATTTATTTT
1 ATTTATTTT
106361 AAATTTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.70
Consensus pattern (15 bp):
ATTTATTTTCGTTTA
Found at i:111726 original size:35 final size:35
Alignment explanation
Indices: 111683--111750 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
111673 TTATTATATT
* *
111683 TTAATAAACTAAATTAAAAATATGGCCCATAAATA
1 TTAATAAACTAAATTAAAAACATGACCCATAAATA
111718 TTAATAAACTAAATTAAAAACATGACCCATAAA
1 TTAATAAACTAAATTAAAAACATGACCCATAAA
111751 CTTATTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.26
Consensus pattern (35 bp):
TTAATAAACTAAATTAAAAACATGACCCATAAATA
Found at i:111845 original size:35 final size:35
Alignment explanation
Indices: 111797--111866 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
111787 TTAAAAACTG
*
111797 TATTAATATACTAAATTAAAAGCAGGACCCATAAA
1 TATTAATAAACTAAATTAAAAGCAGGACCCATAAA
111832 TATTAATAAACTAAATTAAAAGCAGGACCCATAAA
1 TATTAATAAACTAAATTAAAAGCAGGACCCATAAA
111867 CTTATTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.24
Consensus pattern (35 bp):
TATTAATAAACTAAATTAAAAGCAGGACCCATAAA
Found at i:111887 original size:116 final size:116
Alignment explanation
Indices: 111683--111911 Score: 397
Period size: 116 Copynumber: 2.0 Consensus size: 116
111673 TTATTATATT
* *
111683 TTAATAAACTAAATTAAAAATATGGCCCATAAATATTAATAAACTAAATTAAAAACATGACCCAT
1 TTAATAAACTAAATTAAAAACATGGCCCATAAATATTAATAAACTAAATTAAAAACAGGACCCAT
111748 AAACTTATTTCTTATTGACTTATTGTTCTCATCATAACGTTAAAAACTGTA
66 AAACTTATTTCTTATTGACTTATTGTTCTCATCATAACGTTAAAAACTGTA
* * *
111799 TTAATATACTAAATTAAAAGCA-GGACCCATAAATATTAATAAACTAAATTAAAAGCAGGACCCA
1 TTAATAAACTAAATTAAAAACATGG-CCCATAAATATTAATAAACTAAATTAAAAACAGGACCCA
111863 TAAACTTATTTCTTATTGACTTATTGTTCTCATCATAACGTTAAAAACT
65 TAAACTTATTTCTTATTGACTTATTGTTCTCATCATAACGTTAAAAACT
111912 AAATTAATCA
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
115 2 0.02
116 105 0.98
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (116 bp):
TTAATAAACTAAATTAAAAACATGGCCCATAAATATTAATAAACTAAATTAAAAACAGGACCCAT
AAACTTATTTCTTATTGACTTATTGTTCTCATCATAACGTTAAAAACTGTA
Found at i:118700 original size:20 final size:21
Alignment explanation
Indices: 118656--118704 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
118646 TATATATTCA
118656 CGTTGCGAAATTGGAAACTAG
1 CGTTGCGAAATTGGAAACTAG
* *
118677 -GTTGCGAAATTGG-AATTTG
1 CGTTGCGAAATTGGAAACTAG
118696 CGTTGCGAA
1 CGTTGCGAA
118705 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.29
Consensus pattern (21 bp):
CGTTGCGAAATTGGAAACTAG
Found at i:118927 original size:14 final size:14
Alignment explanation
Indices: 118893--118933 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
118883 AACACAAGCA
*
118893 TTTTA-TAAAATTT
1 TTTTATTAAATTTT
*
118906 TATT-TTAAATTTT
1 TTTTATTAAATTTT
118919 TTTTATTAAATTTT
1 TTTTATTAAATTTT
118933 T
1 T
118934 AATCTCTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTATTAAATTTT
Found at i:118981 original size:25 final size:25
Alignment explanation
Indices: 118924--118981 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
118914 ATTTTTTTTA
118924 TTAAATTTTTAATCTCTAATTAAAT
1 TTAAATTTTTAATCTCTAATTAAAT
* * * * *
118949 TCATATTTTTAATTTTTAATTAATT
1 TTAAATTTTTAATCTCTAATTAAAT
118974 TTAAATTT
1 TTAAATTT
118982 ATAAACTTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAAATTTTTAATCTCTAATTAAAT
Found at i:120793 original size:31 final size:31
Alignment explanation
Indices: 120757--120815 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
120747 AACTTAAAAG
* *
120757 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
120788 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
120816 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:120866 original size:22 final size:22
Alignment explanation
Indices: 120840--120882 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
120830 TAATAAATTA
120840 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
120862 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
120883 ATAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:120891 original size:22 final size:22
Alignment explanation
Indices: 120842--120890 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
120832 ATAAATTATT
**
120842 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
120864 TAAAATAAATCAATCCATAATAA
1 TAAAATAAATCAATCCAT-ATAA
120887 TAAA
1 TAAA
120891 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:120892 original size:54 final size:54
Alignment explanation
Indices: 120828--121327 Score: 227
Period size: 54 Copynumber: 9.4 Consensus size: 54
120818 ATACAACTAC
120828 AATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
1 AATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
*** * *
120882 AATAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAAT-CA-
1 AATAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCAT
* * * * ** *
120934 ATTCAT--A-T-TTTAAAATAAATCAATCCATA----CAAATAAAT-TATTTAA
1 AATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
* *
120979 AATAAATCAATCCATACTAATTAAAATAAATCAATCCATACTAATTAAAATAAATCAATCCAT
1 AAT-AAT-AA---AT--TATTTAAAATAAATCAATCCATA-T-TTTAAAATAAATCAATCCAT
** * ** * * **
121042 -ATTTTAAAATAAAT-CAATACATACTAATAAAT-TATTTAAAATAAATCAATCCAT
1 AATAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCAT
** * ** * ** ** *
121096 -ATTTTAAAATAAAT-GAATCCATACTAATAAAT-TATTTAAAATAAATCAATTCAT
1 AATAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCAT
* * *
121150 ACA-ACTACA--A--T--AATAAATCAAACCATATTTTAAAATAAATCAATCCAT
1 A-ATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
*
121198 ACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
1 AATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
*
121252 ACTAATAAATTATTTAAAAT--A--AAT---TATTTTAAAATAAATCAATCCAT
1 AATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
121299 ATTTTATAATAAATTATTTTAAAATAAAT
1 A----ATAATAAATTA-TTTAAAATAAAT
121328 TATTTTATAA
Statistics
Matches: 359, Mismatches: 45, Indels: 83
0.74 0.09 0.17
Matches are distributed among these distances:
43 5 0.01
44 4 0.01
45 2 0.01
46 2 0.01
47 24 0.07
48 49 0.14
49 3 0.01
50 10 0.03
51 11 0.03
52 15 0.04
53 3 0.01
54 174 0.48
55 14 0.04
56 26 0.07
57 1 0.00
60 2 0.01
61 1 0.00
62 10 0.03
63 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (54 bp):
AATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
Found at i:120935 original size:80 final size:80
Alignment explanation
Indices: 120845--121230 Score: 478
Period size: 80 Copynumber: 4.9 Consensus size: 80
120835 AATTATTTAA
120845 AATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAATCAAT
120910 CCATAC-AACTACAAT
66 CCATACTAA-TACAAT
*
120925 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACA-AATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATA-ATAATAAATTATTTAAAATAAATCAA
*
120989 TCCATACTAAT-TAA-
65 TCCATACTAATACAAT
*
121003 AATAAATCAATCCATACTAATTAAAATAAATCAATCC------AT--A-T-TTTAAAATAAATCA
1 AATAAATCAATCCATA-T-TTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAATCA
* *
121058 ATACATACTAATAAATTATTT
64 ATCCATACTAATACA--A--T
* *
121079 AAAATAAATCAATCCATATTTTAAAATAAATGAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAATCA
*
121144 ATTCATAC-AACTACAAT
64 ATCCATACTAA-TACAAT
* *
121161 AATAAATCAAACCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAATCAAT
121226 CCATA
66 CCATA
121231 TTTTAAAATA
Statistics
Matches: 270, Mismatches: 13, Indels: 46
0.82 0.04 0.14
Matches are distributed among these distances:
70 25 0.09
71 2 0.01
72 1 0.00
73 1 0.00
74 2 0.01
76 16 0.06
77 1 0.00
78 31 0.11
79 3 0.01
80 153 0.57
81 3 0.01
82 3 0.01
84 2 0.01
85 3 0.01
86 24 0.09
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAATCAAT
CCATACTAATACAAT
Found at i:120967 original size:18 final size:18
Alignment explanation
Indices: 120946--120995 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 18
120936 TCATATTTTA
120946 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
* *
120964 AAATAAAT-TAT--TTA-
1 AAATAAATCAATCCATAC
120978 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
120996 TAATTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 8
0.67 0.11 0.22
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
17 4 0.17
18 8 0.33
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAAATCAATCCATAC
Found at i:120981 original size:32 final size:27
Alignment explanation
Indices: 120838--121253 Score: 214
Period size: 32 Copynumber: 15.9 Consensus size: 27
120828 AATAATAAAT
120838 TATTTAAAATAAATCAAT-C---CATA
1 TATTTAAAATAAATCAATCCATACATA
*
120861 T-TTTAAAATAAATCAATCCATAATAATAAA
1 TATTTAAAATAAATCAATCCAT-A-CAT--A
120891 TTATTTAAAATAAATCAATCCATACA-A
1 -TATTTAAAATAAATCAATCCATACATA
*
120918 CTA--CAATAATAAATCAAT---T-CATA
1 -TATTTAA-AATAAATCAATCCATACATA
120941 T-TTTAAAATAAATCAATCCATACAAATAAA
1 TATTTAAAATAAATCAATCCATAC--AT--A
120971 TTATTTAAAATAAATCAATCCATAC-TA
1 -TATTTAAAATAAATCAATCCATACATA
120998 -A-TTAAAATAAATCAATCCATAC-TA
1 TATTTAAAATAAATCAATCCATACATA
121022 -A-TTAAAATAAATCAAT-C---CATA
1 TATTTAAAATAAATCAATCCATACATA
*
121043 T-TTTAAAATAAATCAATACATACTAATAAA
1 TATTTAAAATAAATCAATCCATAC--AT--A
121073 TTATTTAAAATAAATCAAT-C---CATA
1 -TATTTAAAATAAATCAATCCATACATA
*
121097 T-TTTAAAATAAATGAATCCATACTAATAAA
1 TATTTAAAATAAATCAATCCATAC--AT--A
*
121127 TTATTTAAAATAAATCAATTCATACA-A
1 -TATTTAAAATAAATCAATCCATACATA
* *
121154 CTA--CAATAATAAATCAA---A-CCATA
1 -TATTTAA-AATAAATCAATCCATACATA
121177 T-TTTAAAATAAATCAATCCATACTAATAAA
1 TATTTAAAATAAATCAATCCATAC--AT--A
121207 TTATTTAAAATAAATCAAT-C---CATA
1 -TATTTAAAATAAATCAATCCATACATA
121231 T-TTTAAAATAAATCAATCCATAC
1 TATTTAAAATAAATCAATCCATAC
121254 TAATAAATTA
Statistics
Matches: 315, Mismatches: 13, Indels: 127
0.69 0.03 0.28
Matches are distributed among these distances:
20 1 0.00
21 2 0.01
22 89 0.28
23 16 0.05
24 41 0.13
25 7 0.02
26 30 0.10
27 7 0.02
28 12 0.04
29 1 0.00
30 7 0.02
31 8 0.03
32 94 0.30
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (27 bp):
TATTTAAAATAAATCAATCCATACATA
Found at i:121010 original size:20 final size:20
Alignment explanation
Indices: 120982--121034 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 20
120972 TATTTAAAAT
*
120982 AAATCAATCCATACTAATTA
1 AAATAAATCCATACTAATTA
121002 AAATAAATCAATCCATACTAATTA
1 AAAT--A--AATCCATACTAATTA
121026 AAATAAATC
1 AAATAAATC
121035 AATCCATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
20 8 0.29
22 1 0.04
24 19 0.68
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAAATCCATACTAATTA
Found at i:121080 original size:134 final size:133
Alignment explanation
Indices: 120942--121275 Score: 374
Period size: 134 Copynumber: 2.5 Consensus size: 133
120932 CAATTCATAT
*
120942 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT-C-CAT-ACTAATTAAA
1 TTTAAAATAAATCAATCCATA-AAATAAA--A--T-AAATAAATCAATACTAATAACTAATTAAA
* *
121004 ATAAATCAATCCATACTAA-T-TAA-AATAAATCAATCCATATTTTAAAATAAATCAATACATAC
60 ATAAATCAATCCATAC-AACTACAATAATAAATCAAACCATATTTTAAAATAAATCAATACATAC
121066 TAATAAATTA
124 TAATAAATTA
*** * * * *
121076 TTTAAAATAAATCAATCCATATTTTAAAATAAATGAATCCATACTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCATAAAATAAAATAAATAAATCAATACTAAT-AACTAATTAAAATAAA
* *
121141 TCAATTCATACAACTACAATAATAAATCAAACCATATTTTAAAATAAATCAATCCATACTAATAA
65 TCAATCCATACAACTACAATAATAAATCAAACCATATTTTAAAATAAATCAATACATACTAATAA
121206 ATTA
130 ATTA
*** * * * *
121210 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCATAAAATAAAATAAATAAATCAATACTAAT-AACTAATTAAAATAAA
121275 T
65 T
121276 TATTTTAAAA
Statistics
Matches: 180, Mismatches: 13, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
128 10 0.06
129 2 0.01
130 2 0.01
131 3 0.02
132 24 0.13
133 6 0.03
134 133 0.74
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (133 bp):
TTTAAAATAAATCAATCCATAAAATAAAATAAATAAATCAATACTAATAACTAATTAAAATAAAT
CAATCCATACAACTACAATAATAAATCAAACCATATTTTAAAATAAATCAATACATACTAATAAA
TTA
Found at i:121102 original size:22 final size:22
Alignment explanation
Indices: 121076--121118 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
121066 TAATAAATTA
121076 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
121098 TTTAAAATAAATGAATCCATA
1 TTTAAAATAAATCAATCCATA
121119 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:121127 original size:22 final size:22
Alignment explanation
Indices: 121078--121126 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
121068 ATAAATTATT
**
121078 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
121100 TAAAATAAATGAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
121123 TAAA
1 TAAA
121127 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:121141 original size:236 final size:234
Alignment explanation
Indices: 120830--121257 Score: 775
Period size: 236 Copynumber: 1.8 Consensus size: 234
120820 ACAACTACAA
120830 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTAT
**
120895 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAAACCATATTTTAAAATAAATCAATCC
120960 ATACAAATAAATTATTTAAAATAAATCAATCCATACTAATTAAAATAAATCAATCCATACTAATT
131 ATACAAATAAATTATTTAAAATAAATCAATCCATA-T-ATTAAAATAAATCAATCCATACTAATT
121025 AAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
194 AAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
* *
121066 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATGAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTAT
*
121131 TTAAAATAAATCAATTCATACAACTACAATAATAAATCAAACCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAAACCATATTTTAAAATAAATCAATCC
* *
121196 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
131 ATACAAATAAATTATTTAAAATAAATCAATCCATATATTAAAATAAATCAATCCATACTAAT
121258 AAATTATTTA
Statistics
Matches: 185, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
234 25 0.14
235 1 0.01
236 159 0.86
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (234 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAAACCATATTTTAAAATAAATCAATCC
ATACAAATAAATTATTTAAAATAAATCAATCCATATATTAAAATAAATCAATCCATACTAATTAA
AATAAATCAATCCATATTTTAAAATAAATCAATACATAC
Found at i:121236 original size:22 final size:22
Alignment explanation
Indices: 121210--121312 Score: 98
Period size: 22 Copynumber: 4.5 Consensus size: 22
121200 TAATAAATTA
121210 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
121232 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
121255 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
121279 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
121301 TTTATAATAAAT
1 TTTAAAATAAAT
121313 TATTTTAAAA
Statistics
Matches: 61, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
22 35 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:121284 original size:15 final size:15
Alignment explanation
Indices: 121255--121357 Score: 118
Period size: 15 Copynumber: 6.5 Consensus size: 15
121245 AATCCATACT
121255 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
121269 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
121284 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
121306 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
121321 AATAAATTATTTTAT
1 AATAAATTATTTTAA
121336 AATAAATTATTTTAA
1 AATAAATTATTTTAA
121351 AATAAAT
1 AATAAAT
121358 AACCTTATTA
Statistics
Matches: 77, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
14 9 0.12
15 50 0.65
17 1 0.01
18 3 0.04
19 3 0.04
20 1 0.01
22 10 0.13
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:121297 original size:69 final size:67
Alignment explanation
Indices: 121201--121357 Score: 219
Period size: 69 Copynumber: 2.3 Consensus size: 67
121191 AATCCATACT
*
121201 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAAT-AAT-CATA-AAATAAATTAT
121264 TTTAA
63 TTTAA
* * **
121269 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATCATAAAATAAATTATTTT
*
121334 AT
66 AA
121336 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
121358 AACCTTATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
66 9 0.11
67 28 0.35
68 11 0.14
69 33 0.41
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATCATAAAATAAATTATTTT
AA
Found at i:123025 original size:21 final size:19
Alignment explanation
Indices: 122989--123027 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
122979 AATTAATTAA
*
122989 AATAAAAAATTTAATTTAG
1 AATAAAAAATTAAATTTAG
123008 AATATAAAAATATAAATTTA
1 AATA-AAAAAT-TAAATTTA
123028 ATTTTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 6 0.35
21 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AATAAAAAATTAAATTTAG
Found at i:142106 original size:14 final size:14
Alignment explanation
Indices: 142087--142120 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
142077 AAAAGAACAT
142087 GAAAGATGGTCCAA
1 GAAAGATGGTCCAA
142101 GAAAGATGGTCCAA
1 GAAAGATGGTCCAA
142115 GAAAGA
1 GAAAGA
142121 GGACGCCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.29, T:0.12
Consensus pattern (14 bp):
GAAAGATGGTCCAA
Found at i:144401 original size:60 final size:58
Alignment explanation
Indices: 144246--144402 Score: 156
Period size: 60 Copynumber: 2.6 Consensus size: 58
144236 GAATTTGGGT
* *
144246 ATAAAATTGGAATATTCAAAAGTTTAGGGACCAATTTAGAAAGAGGTCATAGTTTAGGG
1 ATAAAATTAGAATATTCAAAAGTTTAAGGA-CAATTTAGAAAGAGGTCATAGTTTAGGG
* * * * * * *
144305 CTGAAATTCGATTGTTCAAAAGCTTAAGTACTAATTTAGAATA-AGAGTCATAGTTT-GTGG
1 ATAAAATTAGAATATTCAAAAGTTTAAGGAC-AATTTAGAA-AGAG-GTCATAGTTTAG-GG
*
144365 ATAAAATTAAAATATTCAAAAGTTTAAGGATCAATTTA
1 ATAAAATTAGAATATTCAAAAGTTTAAGGA-CAATTTA
144403 AATGAGGATT
Statistics
Matches: 77, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
58 1 0.01
59 34 0.44
60 41 0.53
61 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.32
Consensus pattern (58 bp):
ATAAAATTAGAATATTCAAAAGTTTAAGGACAATTTAGAAAGAGGTCATAGTTTAGGG
Found at i:150766 original size:59 final size:58
Alignment explanation
Indices: 150611--150784 Score: 156
Period size: 59 Copynumber: 2.9 Consensus size: 58
150601 GAATTTGGGT
* *
150611 ATAAAATTGGAATATTCAAAAGTTTAGGGACCAATTTAGAAAGAGGGTCATAGTTTAGGG
1 ATAAAATTAGAATATTCAAAAGTTTAAGGA-CAATTTAGAAAGA-GGTCATAGTTTAGGG
* * * * * * *
150671 CTGAAATTCGATTGTTCAAAAGCTTAAGTACTAATTTAGATAAGA-GTCATAGTTT-GTGG
1 ATAAAATTAGAATATTCAAAAGTTTAAGGAC-AATTTAGA-AAGAGGTCATAGTTTAG-GG
* * *
150730 ATAAAATTAAAATATTCAAAAGTTTAAGGATCAATTTA-AATGAGGATTATAGTTT
1 ATAAAATTAGAATATTCAAAAGTTTAAGGA-CAATTTAGAAAGAGG-TCATAGTTT
150785 GGAGACATAT
Statistics
Matches: 90, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
57 3 0.03
58 3 0.03
59 49 0.54
60 31 0.34
61 4 0.04
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (58 bp):
ATAAAATTAGAATATTCAAAAGTTTAAGGACAATTTAGAAAGAGGTCATAGTTTAGGG
Found at i:156947 original size:29 final size:28
Alignment explanation
Indices: 156875--156948 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
156865 ATTAAAAAAA
156875 AAATTCGCCCTTAAAA-TTTTATAAGTTT
1 AAATTCGCCC-TAAAATTTTTATAAGTTT
* *
156903 AAGTTTGTCCCTAAAATTTTTA-AAGTTT
1 AAATTCG-CCCTAAAATTTTTATAAGTTT
156931 AAATTCGCCACTCAAAAT
1 AAATTCGCC-CT-AAAAT
156949 AAAATATTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 2 0.05
28 23 0.61
29 13 0.34
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (28 bp):
AAATTCGCCCTAAAATTTTTATAAGTTT
Found at i:158848 original size:2 final size:2
Alignment explanation
Indices: 158841--158900 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
158831 AATCTGTTCC
158841 AT AT AT AT AT AT AT 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 AT AT AT AT
158883 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
158901 GTACATATCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:162434 original size:85 final size:85
Alignment explanation
Indices: 162271--162439 Score: 295
Period size: 86 Copynumber: 2.0 Consensus size: 85
162261 TACTTTAAAC
* *
162271 TTTTTTATTTTATTAAAAGAGAAAAATATATTTTCCTTTTTCTGAAAGTTATTTATTTGATTTTA
1 TTTTTAATTTTATTAAAAGAGAAAAATACATTTTCCTTTTTCTGAAAGTTATTTATTTGATTTTA
162336 ATCTTTTGAAAAACATTTTA
66 ATCTTTTGAAAAACATTTTA
*
162356 TTTTTAATTTTATTGAAAGAGAAAAATACATTTTTCCTTTTTCTGAAAGTTATTTATTTGATTTT
1 TTTTTAATTTTATTAAAAGAGAAAAATACA-TTTTCCTTTTTCTGAAAGTTATTTATTTGATTTT
162421 AATCTTTTG-AAAACATTTT
65 AATCTTTTGAAAAACATTTT
162440 TTAAACTGTG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 37 0.46
86 43 0.54
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.53
Consensus pattern (85 bp):
TTTTTAATTTTATTAAAAGAGAAAAATACATTTTCCTTTTTCTGAAAGTTATTTATTTGATTTTA
ATCTTTTGAAAAACATTTTA
Found at i:163067 original size:60 final size:60
Alignment explanation
Indices: 162955--163068 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
162945 TAGTCGAGTT
*
162955 ATCATTTTGTAACTTTTAATAGCTGACAGACTTAATAAAGCAACATTATATAGTTGGAGG
1 ATCATTTTGTAACTTTTAATAGCTGACAGACTTAATAAAGCAACACTATATAGTTGGAGG
* ** * * *
163015 ATCATTTTGTAACTTTTATTAG-TCGAGTGACTTAATAAAGTAATACTCTATAGT
1 ATCATTTTGTAACTTTTAATAGCT-GACAGACTTAATAAAGCAACACTATATAGT
163069 CTGTGACCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 1 0.02
60 45 0.98
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (60 bp):
ATCATTTTGTAACTTTTAATAGCTGACAGACTTAATAAAGCAACACTATATAGTTGGAGG
Found at i:163272 original size:30 final size:30
Alignment explanation
Indices: 163236--163326 Score: 173
Period size: 30 Copynumber: 3.0 Consensus size: 30
163226 TAGCTACATT
163236 TGAACTAATGGTCATAGTACCACATATATA
1 TGAACTAATGGTCATAGTACCACATATATA
163266 TGAACTAATGGTCATAGTACCACATATATA
1 TGAACTAATGGTCATAGTACCACATATATA
*
163296 TGAACTAATGGTCATAGTACCACACATATA
1 TGAACTAATGGTCATAGTACCACATATATA
163326 T
1 T
163327 ATATATATTA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.30
Consensus pattern (30 bp):
TGAACTAATGGTCATAGTACCACATATATA
Found at i:163326 original size:2 final size:2
Alignment explanation
Indices: 163321--163372 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
163311 AGTACCACAC
163321 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
163361 AT AT AT AT AT AT
1 AT AT AT AT AT AT
163373 TACATTCAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:163343 original size:17 final size:17
Alignment explanation
Indices: 163321--163372 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
163311 AGTACCACAC
163321 ATATATATATATATTAT
1 ATATATATATATATTAT
163338 ATATATATATATATTAT
1 ATATATATATATATTAT
163355 ATATATATATATA-TAT
1 ATATATATATATATTAT
163371 AT
1 AT
163373 TACATTCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.14
17 30 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATATATATTAT
Found at i:163600 original size:4 final size:4
Alignment explanation
Indices: 163591--163617 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
163581 TTCAACTATG
163591 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
163618 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:165682 original size:29 final size:29
Alignment explanation
Indices: 165636--165735 Score: 155
Period size: 29 Copynumber: 3.4 Consensus size: 29
165626 ACTTTCTACT
* *
165636 ATTTTACTCACTGCACTTTAATTTTTTTCA
1 ATTTT-CTCACTGTACTTTAAATTTTTTCA
*
165666 ATTTTCTCACTATACTTTAAATTTTTTCA
1 ATTTTCTCACTGTACTTTAAATTTTTTCA
165695 ATTTTCTCACTGTACTTTAAATTTTTTCA
1 ATTTTCTCACTGTACTTTAAATTTTTTCA
*
165724 ATTTTCTTACTG
1 ATTTTCTCACTG
165736 AGCTTAATAC
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 60 0.92
30 5 0.08
ACGTcount: A:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTCTCACTGTACTTTAAATTTTTTCA
Found at i:166191 original size:23 final size:22
Alignment explanation
Indices: 166144--166185 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
166134 AGCAAAGTAC
*
166144 AAAAATTATTAACTTTTCAATGA
1 AAAAATTATTAAC-TGTCAATGA
166167 AAAAATTATTAA-TGTCAAT
1 AAAAATTATTAACTGTCAAT
166186 TAGAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
23 12 0.67
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (22 bp):
AAAAATTATTAACTGTCAATGA
Found at i:168092 original size:15 final size:15
Alignment explanation
Indices: 168072--168101 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
168062 AATAAGATCT
168072 ATAAATAAATTATTA
1 ATAAATAAATTATTA
*
168087 ATAAATAGATTATTA
1 ATAAATAAATTATTA
168102 TTTGATGCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
ATAAATAAATTATTA
Found at i:168922 original size:21 final size:21
Alignment explanation
Indices: 168898--168966 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
168888 AAACTAATAG
168898 GTTAGGTACTAAACACATTAA
1 GTTAGGTACTAAACACATTAA
* * * *
168919 GTTAAAACGTACCAAA-ACTAATAG
1 GTT---AGGTACTAAACAC-ATTAA
168943 GTTAGGTACTAAACACATTAA
1 GTTAGGTACTAAACACATTAA
168964 GTT
1 GTT
168967 TTTAATGGCA
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
21 17 0.49
22 2 0.06
23 2 0.06
24 14 0.40
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
GTTAGGTACTAAACACATTAA
Found at i:168939 original size:45 final size:45
Alignment explanation
Indices: 168875--168966 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
168865 AGTTTAGGTA
168875 TTAAAACGTACCAAAACTAATAGGTTAGGTACTAAACACATTAAG
1 TTAAAACGTACCAAAACTAATAGGTTAGGTACTAAACACATTAAG
168920 TTAAAACGTACCAAAACTAATAGGTTAGGTACTAAACACATTAAG
1 TTAAAACGTACCAAAACTAATAGGTTAGGTACTAAACACATTAAG
168965 TT
1 TT
168967 TTTAATGGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (45 bp):
TTAAAACGTACCAAAACTAATAGGTTAGGTACTAAACACATTAAG
Found at i:168946 original size:24 final size:24
Alignment explanation
Indices: 168875--168946 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
168865 AGTTTAGGTA
168875 TTAAAACGTACCAAAACTAATAGG
1 TTAAAACGTACCAAAACTAATAGG
* * * *
168899 TT---AGGTACTAAACAC-ATTAAG
1 TTAAAACGTACCAAA-ACTAATAGG
168920 TTAAAACGTACCAAAACTAATAGG
1 TTAAAACGTACCAAAACTAATAGG
168944 TTA
1 TTA
168947 GGTACTAAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
21 14 0.40
22 2 0.06
23 2 0.06
24 17 0.49
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (24 bp):
TTAAAACGTACCAAAACTAATAGG
Found at i:170168 original size:16 final size:16
Alignment explanation
Indices: 170120--170168 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
170110 ATCTGACCCA
** *
170120 AACTGAAAGTAACTCG
1 AACTGAAAACAACTTG
170136 AACTGAAAACAACTTG
1 AACTGAAAACAACTTG
*
170152 AACTGAAAACAATTTG
1 AACTGAAAACAACTTG
170168 A
1 A
170169 CCCAAACTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.20
Consensus pattern (16 bp):
AACTGAAAACAACTTG
Found at i:171654 original size:128 final size:129
Alignment explanation
Indices: 171441--171698 Score: 509
Period size: 128 Copynumber: 2.0 Consensus size: 129
171431 TCACAAAACA
171441 TATACATCACATACAGTGCATTTATTATTATTTCTTTATTGGCCCATGTACACATCTGATAACTA
1 TATACATCACATACAGTGCATTTATTATTATTTCTTTATTGGCCCATGTACACATCTGATAACTA
171506 AAGATATGTGAGTACATAGAGGTTGTGTACATATGATGTCACCACAGCTCATAT-AAGTCCCAC
66 AAGATATGTGAGTACATAGAGGTTGTGTACATATGATGTCACCACAGCTCATATAAAGTCCCAC
171569 TATACATCACATACAGTGCATTTATTATTATTTCTTTATTGGCCCATGTACACATCTGATAACTA
1 TATACATCACATACAGTGCATTTATTATTATTTCTTTATTGGCCCATGTACACATCTGATAACTA
171634 AAGATATGTGAGTACATAGAGGTTGTGTACATATGATGTCACCACAGCTCATATAAAGTCCCAC
66 AAGATATGTGAGTACATAGAGGTTGTGTACATATGATGTCACCACAGCTCATATAAAGTCCCAC
171698 T
1 T
171699 TAGTGGCATA
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 119 0.92
129 10 0.08
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (129 bp):
TATACATCACATACAGTGCATTTATTATTATTTCTTTATTGGCCCATGTACACATCTGATAACTA
AAGATATGTGAGTACATAGAGGTTGTGTACATATGATGTCACCACAGCTCATATAAAGTCCCAC
Found at i:171763 original size:22 final size:20
Alignment explanation
Indices: 171718--171779 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 20
171708 ATGAAAGTTA
171718 TCCCGAAGGACCTCATGTATG
1 TCCCGAAGGACCT-ATGTATG
171739 TCCCGAAGGACCTATGAATATG
1 TCCCGAAGGACCTATG--TATG
* *
171761 TCCAGAATGACCTATGTAT
1 TCCCGAAGGACCTATGTAT
171780 CCCTCGACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
20 6 0.16
21 13 0.35
22 18 0.49
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (20 bp):
TCCCGAAGGACCTATGTATG
Found at i:180565 original size:25 final size:25
Alignment explanation
Indices: 180537--180585 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
180527 CTTTAGCCCC
*
180537 TTTCGTTGCTTGTCCTCTTATGCTG
1 TTTCATTGCTTGTCCTCTTATGCTG
180562 TTTCATTGCTTGTCCTCTTATGCT
1 TTTCATTGCTTGTCCTCTTATGCT
180586 TTTGTGTTTT
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:0.06, C:0.24, G:0.16, T:0.53
Consensus pattern (25 bp):
TTTCATTGCTTGTCCTCTTATGCTG
Found at i:186135 original size:15 final size:15
Alignment explanation
Indices: 186115--186159 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
186105 GCCCATAGCT
186115 CATTTAACAATGCTA
1 CATTTAACAATGCTA
186130 CATTTAACAATGCTA
1 CATTTAACAATGCTA
186145 CATTTAACAATGCTA
1 CATTTAACAATGCTA
186160 TAATGACGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (15 bp):
CATTTAACAATGCTA
Found at i:209664 original size:115 final size:115
Alignment explanation
Indices: 209496--209724 Score: 449
Period size: 115 Copynumber: 2.0 Consensus size: 115
209486 GATATGAACA
209496 TAAAAGGTTATATTATAAATCCAAAAGTTTAGAAAATGAAATTATACAAGGATTTGAAATTTTAT
1 TAAAAGGTTATATTATAAATCCAAAAGTTTAGAAAATGAAATTATACAAGGATTTGAAATTTTAT
209561 AAGATGCTACCACATCCCTACCACCTTCCTCTATCTATCTCTGAACATGG
66 AAGATGCTACCACATCCCTACCACCTTCCTCTATCTATCTCTGAACATGG
209611 TAAAAGGTTATATTATAAATCCAAAAGTTTAGAAAATGAAATTATACAAGGATTTGAAATTTTAT
1 TAAAAGGTTATATTATAAATCCAAAAGTTTAGAAAATGAAATTATACAAGGATTTGAAATTTTAT
*
209676 AAGATGCTACCACATCCCTACCACCTTCCTCTATCTATTTCTGAACATG
66 AAGATGCTACCACATCCCTACCACCTTCCTCTATCTATCTCTGAACATG
209725 ATAGCAAGAC
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 113 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (115 bp):
TAAAAGGTTATATTATAAATCCAAAAGTTTAGAAAATGAAATTATACAAGGATTTGAAATTTTAT
AAGATGCTACCACATCCCTACCACCTTCCTCTATCTATCTCTGAACATGG
Found at i:209882 original size:2 final size:2
Alignment explanation
Indices: 209870--209898 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
209860 TAATATTAAG
209870 AT AT A- 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
209899 TTAAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:222495 original size:2 final size:2
Alignment explanation
Indices: 222488--222523 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
222478 GAGTATGCAT
222488 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
222524 AGAACATTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:235193 original size:5 final size:5
Alignment explanation
Indices: 235179--235221 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
235169 TTTAAATATT
* *
235179 TTAAA CTAAA TTAAA TTAATA TTAAA TTAAAA TTATA TTAAA T
1 TTAAA TTAAA TTAAA TTAA-A TTAAA TT-AAA TTAAA TTAAA T
235222 ATATAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 22 0.69
6 10 0.31
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:235204 original size:11 final size:11
Alignment explanation
Indices: 235179--235230 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
235169 TTTAAATATT
*
235179 TTAAACTAA-A
1 TTAAATTAATA
235189 TTAAATTAATA
1 TTAAATTAATA
*
235200 TTAAATTAAAA
1 TTAAATTAATA
*
235211 TTATATTAAATA
1 TTAAATT-AATA
235223 TATAAATT
1 T-TAAATT
235231 TTAACAGGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 8 0.24
11 17 0.50
12 4 0.12
13 5 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAAATTAATA
Found at i:235206 original size:16 final size:16
Alignment explanation
Indices: 235185--235221 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
235175 TATTTTAAAC
235185 TAAATT-AAATTAATAT
1 TAAATTAAAATT-ATAT
235201 TAAATTAAAATTATAT
1 TAAATTAAAATTATAT
235217 TAAAT
1 TAAAT
235222 ATATAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTAAAATTATAT
Found at i:235672 original size:12 final size:12
Alignment explanation
Indices: 235655--235681 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
235645 ATCTTTCCTT
235655 AGTTATATATTA
1 AGTTATATATTA
235667 AGTTATATATTA
1 AGTTATATATTA
235679 AGT
1 AGT
235682 GAAACTTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (12 bp):
AGTTATATATTA
Found at i:236191 original size:21 final size:21
Alignment explanation
Indices: 236151--236192 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
236141 TGGACACGAG
*
236151 TTTTATTAAATTTTTAGATAA
1 TTTTATTAAATTTTCAGATAA
* *
236172 TTTTATTTAATTTTCGGATAA
1 TTTTATTAAATTTTCAGATAA
236193 ATAGTACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTATTAAATTTTCAGATAA
Found at i:240359 original size:2 final size:2
Alignment explanation
Indices: 240352--240377 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
240342 CTAAACATGC
240352 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
240378 CAATTATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.