Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000228.1 Hibiscus syriacus cultivar Beakdansim tig00000398_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: 62058
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5001 original size:97 final size:98
Alignment explanation
Indices: 4844--5022 Score: 238
Period size: 97 Copynumber: 1.8 Consensus size: 98
4834 AAAAATACAA
* * *
4844 ATATATTAACAGTAAATAAAACTAATTTTGCATGTAACATAATTTAATAATGTCATAAGTTCTAC
1 ATATATTAACAGTAAATAAAACTAATTTTACATGTAACATAATATAATAATATCATAAGTTCTAC
4909 TTCTTGTT-TATTTAGAAATAAATAAATAATAAT
66 TTCTTGTTCT-TTTAGAAATAAATAAATAATAAT
* * **
4942 ATATATTAAGAGTAAATAAAA-TATTTTTACATGTAATTTACA-ATAATAATATCATAAGTTCTA
1 ATATATTAACAGTAAATAAAACTAATTTTACATGTAACATA-ATATAATAATATCATAAGTTCTA
* *
5005 GTTGTTGTTCTTTTAGAA
65 CTTCTTGTTCTTTTAGAA
5023 TTTTTTTTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
97 48 0.69
98 22 0.31
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.41
Consensus pattern (98 bp):
ATATATTAACAGTAAATAAAACTAATTTTACATGTAACATAATATAATAATATCATAAGTTCTAC
TTCTTGTTCTTTTAGAAATAAATAAATAATAAT
Found at i:6253 original size:10 final size:10
Alignment explanation
Indices: 6238--6284 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
6228 GAAATAAGAT
6238 AAAAAAAT-A
1 AAAAAAATAA
6247 AAAAAAATCAA
1 AAAAAAAT-AA
** *
6258 AGGAAAGTAA
1 AAAAAAATAA
6268 AAAAAAATAA
1 AAAAAAATAA
6278 AAAAAAA
1 AAAAAAA
6285 AATTATCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 8 0.27
10 16 0.53
11 6 0.20
ACGTcount: A:0.83, C:0.02, G:0.06, T:0.09
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:8525 original size:84 final size:84
Alignment explanation
Indices: 8299--9164 Score: 925
Period size: 84 Copynumber: 10.5 Consensus size: 84
8289 AACTCGACGA
** *
8299 TTTTGTTGATAGATAACCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTGCCTTCGG-GCTGAG
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTT-GGAGCTGAG
*
8363 TGGAATCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* ** * **
8383 ---T-TTGGTAGATAACCCTTCTCCCCTTGA-CTTATGCTGCAAATGATACGCCTTCGG-GCTGA
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGC-TATGTTGCAAATGATGTGCCTT-GGAGCTGA
*
8442 GTATAATCGAACTCGAAGGTC
64 GTGTAATCGAACTCGAAGGTC
* * *
8463 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGT
* *
8528 GTAGTCGAACTCGAAAGTC
66 GTAATCGAACTCGAAGGTC
* * * * *
8547 ---T-TTGGCAGATAGCCCTTCTTGCCTTAAGTTGTGCTGCAAATGATGTGCCTT-GAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGT
8607 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * * *
8626 ---T-TTGCCAGATAACCCTTATGGCCTTGAGTTATGCTGCAAATGACGTGCCTCT-GAGTTGAG
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT-TGGAGCTGAG
*
8686 TGTAATCGAACTCAAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * *
8706 ---T-TTGGTAGATAACCCTTCTTGTCTTAAGCTATGCTT-CAAATGATGTGCCTT-GAGCTGAT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG-TTGCAAATGATGTGCCTTGGAGCTGAG
*
8765 TTTAATCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * * *
8785 TTTTGTTGGAAAATAAACCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGT
*
8850 GTAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * *
8869 TTTTATTGGAAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAG-
* *
8934 T-TAGTCAAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * * *
8953 TTTTGGTGGCAAATAGCCCTTCTTACCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGT
*
9018 GTAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * ** * ** * *
9037 TTGTGTTGGTAGATAACCATTCCAGCCTTGAGTTATACTACAAATGATGTGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGT
9102 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * *
9121 TTTTGGTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAA
9165 ATAAATAAAA
Statistics
Matches: 663, Mismatches: 102, Indels: 34
0.83 0.13 0.04
Matches are distributed among these distances:
79 94 0.14
80 177 0.27
81 3 0.00
82 3 0.00
83 44 0.07
84 341 0.51
85 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (84 bp):
TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGT
GTAATCGAACTCGAAGGTC
Found at i:8984 original size:168 final size:163
Alignment explanation
Indices: 8311--9164 Score: 1022
Period size: 168 Copynumber: 5.2 Consensus size: 163
8301 TTGTTGATAG
* * * *
8311 ATAACCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTGCCTTCGG-GCTGAGTGGAATCGAACT
1 ATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTCGAACT
** ** *
8375 CGAAGGTCTTTGGTAGATAACCCTTCTCCCCTTGA-CTTATGCTGCAAATGATACGCCTTCGGGC
65 CGAAGGTCTTTGGTAGATAACCCTTCTTGCCTTGAGC-TATGCTGCAAATGATGTGCCTT-GAGC
* *
8439 TGAGTATAATCGAACTCGAAGGTCTTTTGTTGGCAA
128 TGAGTGTAATCGAACTCGAAGGTCTTTTGGTGGCAA
*
8475 ATAACCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * *
8540 GAAAGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTGTGCTGCAAATGATGTGCCTTGAGCTGA
66 GAAGGTCTTTGGTAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGAGCTGA
* *
8605 GTGTAATCGAACTCGAAGGTC--TT--TGCCAG
131 GTGTAATCGAACTCGAAGGTCTTTTGGTGGCAA
* * * * * * * *
8634 ATAACCCTTATGGCCTTGAGTTATGCTGCAAATGACGTGCCTCT-GAGTTGAGTGTAATCGAACT
1 ATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT-TGGAGCTGAGCGTAGTCGAACT
* * * *
8698 CAAAGGTCTTTGGTAGATAACCCTTCTTGTCTTAAGCTATGCTTCAAATGATGTGCCTTGAGCTG
65 CGAAGGTCTTTGGTAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGAGCTG
* * * *
8763 ATTTTAATCGAACTCGAAGGTCTTTTGTTGGAAA
130 AGTGTAATCGAACTCGAAGGTCTTTTGGTGGCAA
* *
8797 ATAAACCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
8862 GAAGGTCTTTTATTGGAAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGA
66 GAAGGTC---T-TTGGTAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTT-GA
* *
8927 GCTGAGCT-TAGTCAAACTCGAAGGTCTTTTGGTGGCAA
126 GCTGAG-TGTAATCGAACTCGAAGGTCTTTTGGTGGCAA
* *
8965 ATAGCCCTTCTTACCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* ** * * *
9030 GAAGGTCTTGTGTTGGTAGATAACCATTCCAGCCTTGAGTTATACTACAAATGATGTGCCTTTGA
66 GAAGGTC---T-TTGGTAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCC-TTGA
* *
9095 GCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGACAG
126 GCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGGCAA
* *
9133 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA
1 ATAACCCTTCTTGCCTTGAGCTATGTTGCAAA
9165 ATAAATAAAA
Statistics
Matches: 594, Mismatches: 80, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
159 134 0.23
160 1 0.00
161 4 0.01
162 1 0.00
163 92 0.15
164 106 0.18
166 1 0.00
167 45 0.08
168 207 0.35
169 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (163 bp):
ATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGGTAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGAGCTGA
GTGTAATCGAACTCGAAGGTCTTTTGGTGGCAA
Found at i:10462 original size:95 final size:95
Alignment explanation
Indices: 10279--10537 Score: 337
Period size: 95 Copynumber: 2.7 Consensus size: 95
10269 GGCTAGCTGA
* * *
10279 ATCCATAAAGCC-GGGCATTT-ACCAATTGCTCTAGAGGGACAACTTAA--TATCATTGGATAGA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCT-TTATT-G-T--A
*
10340 TATTATAATCACCTTTATCAGGCTAGCTGAATATT
61 TATTATAATCACCTTCATCAGGCTAGCTGAATATT
10375 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* *
10440 TAATCATCTTCATCAGGCTAGCTGAATCTT
66 TAATCACCTTCATCAGGCTAGCTGAATATT
* * * **
10470 ATCCATAAAGTCGGGGTGTTTAACCAATTGCTTTAGAGGGACAGTTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
10535 ATA
65 ATA
10538 TATTATAATA
Statistics
Matches: 147, Mismatches: 11, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
95 91 0.62
96 16 0.11
97 8 0.05
98 27 0.18
99 4 0.03
100 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTCATCAGGCTAGCTGAATATT
Found at i:13150 original size:27 final size:26
Alignment explanation
Indices: 13120--13180 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
13110 AAAAGCAATA
13120 AATAAAAAACTAAAA-TAAA-ATAAAAG
1 AATAAAAAA-TAAAATTAAAGA-AAAAG
13146 TAATAAATAAATAAAATTAAAGAAAAAG
1 -AATAAA-AAATAAAATTAAAGAAAAAG
13174 AATAAAA
1 AATAAAA
13181 TAAAACAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
26 1 0.03
27 17 0.55
28 12 0.39
29 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (26 bp):
AATAAAAAATAAAATTAAAGAAAAAG
Found at i:13230 original size:9 final size:9
Alignment explanation
Indices: 13213--13252 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
13203 AATCATAGGA
13213 AAAAATAAT
1 AAAAATAAT
*
13222 AACAATAAT
1 AAAAATAAT
13231 AAAAATAAT
1 AAAAATAAT
*
13240 AATAA-AAT
1 AAAAATAAT
13248 AAAAA
1 AAAAA
13253 ATCAAAGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATAAT
Found at i:13253 original size:18 final size:19
Alignment explanation
Indices: 13212--13254 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
13202 AAATCATAGG
13212 AAAAAATAATAACAATAAT
1 AAAAAATAATAACAATAAT
*
13231 -AAAAATAATAATAA-AAT
1 AAAAAATAATAACAATAAT
13248 AAAAAAT
1 AAAAAAT
13255 CAAAGGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAAATAATAACAATAAT
Found at i:13274 original size:30 final size:29
Alignment explanation
Indices: 13231--13363 Score: 100
Period size: 30 Copynumber: 4.5 Consensus size: 29
13221 TAACAATAAT
13231 AAAAATAATAATAAAATAAAAAATCAAAGGA
1 AAAAAT-A-AATAAAATAAAAAATCAAAGGA
* **
13262 AAAAATGAAATAAGATAAAAAAT-AAATCA
1 AAAAAT-AAATAAAATAAAAAATCAAAGGA
13291 AAGGAAAGTAAAATAAAAT--AAAA-CAAAGGA
1 AA--AAA-T-AAATAAAATAAAAAATCAAAGGA
*
13321 AATAA-AAATAAAA-AAAAATTATCAAAGGA
1 AAAAATAAATAAAATAAAAA--ATCAAAGGA
13350 AAAAATAAA-AAAAT
1 AAAAATAAATAAAAT
13364 GTTAAATTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
25 8 0.10
26 3 0.04
28 3 0.04
29 21 0.26
30 27 0.33
31 10 0.12
32 9 0.11
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (29 bp):
AAAAATAAATAAAATAAAAAATCAAAGGA
Found at i:13304 original size:37 final size:35
Alignment explanation
Indices: 13232--13311 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 35
13222 AACAATAATA
*
13232 AAAATAATAATAAAATAAAAAATCAAAGGAAAAAAT
1 AAAATAA-GATAAAATAAAAAATCAAAGGAAAAAAT
* *
13268 GAAATAAGATAAAA-AATAAATCAAAGGAAAGTAAAAT
1 AAAATAAGATAAAATAAAAAATCAAAGG-AA--AAAAT
13305 AAAATAA
1 AAAATAA
13312 AACAAAGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 12 0.32
35 8 0.22
36 6 0.16
37 11 0.30
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.16
Consensus pattern (35 bp):
AAAATAAGATAAAATAAAAAATCAAAGGAAAAAAT
Found at i:13312 original size:25 final size:25
Alignment explanation
Indices: 13280--13338 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
13270 AATAAGATAA
*
13280 AAAATAAATCAAAGGAAAGT-AAAAT
1 AAAATAAAACAAAGGAAA-TAAAAAT
13305 AAAATAAAACAAAGGAAATAAAAAT
1 AAAATAAAACAAAGGAAATAAAAAT
*
13330 AAAAAAAAA
1 AAAATAAAA
13339 TTATCAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 1 0.03
25 30 0.97
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.12
Consensus pattern (25 bp):
AAAATAAAACAAAGGAAATAAAAAT
Found at i:13318 original size:20 final size:20
Alignment explanation
Indices: 13295--13333 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13285 AAATCAAAGG
13295 AAAGTAAAAT-AAAATAAAAC
1 AAAG-AAAATAAAAATAAAAC
*
13315 AAAGGAAATAAAAATAAAA
1 AAAGAAAATAAAAATAAAA
13334 AAAAATTATC
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:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (20 bp):
AAAGAAAATAAAAATAAAAC
Found at i:14694 original size:6 final size:6
Alignment explanation
Indices: 14683--14717 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
14673 TTAGACATTT
14683 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCTCC
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCTCC
14718 AAGCTATTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.83, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTCCC
Found at i:15995 original size:23 final size:23
Alignment explanation
Indices: 15969--16048 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
15959 GTATAAATAC
*
15969 TTAAATTCATAATAT-TTTATATA
1 TTAAATT-AAAATATATTTATATA
* *
15992 TTAACTTAAAATATATTTTTATA
1 TTAAATTAAAATATATTTATATA
*
16015 TTAACTTATTAAATATATTT-TATTA
1 TTAAATTA--AAATATATTTATA-TA
*
16040 TTAACTTAA
1 TTAAATTAA
16049 TTTTAAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
22 6 0.12
23 22 0.44
24 2 0.04
25 20 0.40
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAATTAAAATATATTTATATA
Found at i:16028 original size:25 final size:23
Alignment explanation
Indices: 15980--16048 Score: 95
Period size: 25 Copynumber: 2.9 Consensus size: 23
15970 TAAATTCATA
15980 ATATTTTATATATTAACTTAAAAT
1 ATATTTT-TATATTAACTTAAAAT
16004 ATATTTTTATATTAACTTATTAAAT
1 ATATTTTTATATTAACTTA--AAAT
16029 ATA-TTTTATTATTAACTTAA
1 ATATTTTTA-TATTAACTTAA
16049 TTTTAAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
23 13 0.31
24 12 0.29
25 17 0.40
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTTTTATATTAACTTAAAAT
Found at i:16256 original size:26 final size:26
Alignment explanation
Indices: 16224--16295 Score: 117
Period size: 26 Copynumber: 2.8 Consensus size: 26
16214 TGACCATATT
16224 TTAATTAAATGAAAATGAAAGTAATC
1 TTAATTAAATGAAAATGAAAGTAATC
* * *
16250 TTAATTAAATAAAAACGAAAGTGATC
1 TTAATTAAATGAAAATGAAAGTAATC
16276 TTAATTAAATGAAAATGAAA
1 TTAATTAAATGAAAATGAAA
16296 ATGACAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (26 bp):
TTAATTAAATGAAAATGAAAGTAATC
Found at i:17385 original size:182 final size:181
Alignment explanation
Indices: 17093--17570 Score: 710
Period size: 182 Copynumber: 2.6 Consensus size: 181
17083 CGATCCAAAT
* * * * * *
17093 AAAAAATGTATCGATCCATATCAATATAACAGGTAAAAA-ATGACAAAACCGGTCA-CGAAAAGA
1 AAAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGACAAAA-CGGT-ATCGAAATGA
* * *
17156 CAATACCGGTAAAGCGCTACC-AGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
64 TAAAACCGGTAAATCGCTACCGA-ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
17220 TTTGTGAATTTAAAAGAGAAGTAGGTTTAGCACCTATAAAGTGTCGATACTTTA
128 TTTGTGAATTTAAAAGAGAAGTAGGTTTAGCACCTATAAAGTGTCGATACTTTA
* *
17274 TAAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGACAAAACATGTATCGAAATGAT
1 AAAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGACAAAAC-GGTATCGAAATGAT
* *
17339 AAAATCGGTAAATTGCTACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
65 AAAACCGGTAAATCGCTACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* *
17404 TGTGAATTTAAAAGAGAAGTAGTTTTAGCATCTATAAAGTGTCGATACTTTA
130 TGTGAATTTAAAAGAGAAGTAGGTTTAGCACCTATAAAGTGTCGATACTTTA
* *
17456 AAAAAATGTATCGACCTACAACGATATAACAAGTAAAAATATGACAAAATCGGTATCGAAATGAT
1 AAAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGACAAAA-CGGTATCGAAATGAT
* * *
17521 AAAACCGGTAAATCGCTACTGGATATATTGAAAGTGTTGATACTTTAATA
65 AAAACCGGTAAATCGCTACCGAATATATTGAAAGTGTCGATACTTTAATA
17571 AGTACGTGTA
Statistics
Matches: 268, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
181 35 0.13
182 231 0.86
183 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (181 bp):
AAAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGACAAAACGGTATCGAAATGATA
AAACCGGTAAATCGCTACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
GTGAATTTAAAAGAGAAGTAGGTTTAGCACCTATAAAGTGTCGATACTTTA
Found at i:19664 original size:15 final size:15
Alignment explanation
Indices: 19644--19672 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19634 ATTGTATTGG
19644 GGGATGACGGTGAGA
1 GGGATGACGGTGAGA
19659 GGGATGACGGTGAG
1 GGGATGACGGTGAG
19673 GGAAAATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.55, T:0.14
Consensus pattern (15 bp):
GGGATGACGGTGAGA
Found at i:19781 original size:21 final size:21
Alignment explanation
Indices: 19757--19800 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
19747 AAGACAATTA
*
19757 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
*
19778 AGAGTCAAAGAGACACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
19799 AG
1 AG
19801 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.32, T:0.14
Consensus pattern (21 bp):
AGAGTCAAAGAGAAACTTGAG
Found at i:19891 original size:33 final size:33
Alignment explanation
Indices: 19849--19914 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
19839 ATATAGATGG
*
19849 AGTGGTGAAAGAATTAGAGGTGTTGAGGCGTGA
1 AGTGGTGAAAGAATTAGAGGTGTTAAGGCGTGA
* *
19882 AGTGGTGAAAGAATTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAATTAGAGGTGTTAAGGCGTGA
19915 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.02, G:0.42, T:0.26
Consensus pattern (33 bp):
AGTGGTGAAAGAATTAGAGGTGTTAAGGCGTGA
Found at i:20123 original size:18 final size:18
Alignment explanation
Indices: 20100--20138 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
20090 GAAAAAATAT
20100 GAAGAAGAAAAGAGAGAG
1 GAAGAAGAAAAGAGAGAG
*
20118 GAAGAAGAAAAGAGGGAG
1 GAAGAAGAAAAGAGAGAG
20136 GAA
1 GAA
20139 ATGAGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAAAGAGAGAG
Found at i:21782 original size:3 final size:3
Alignment explanation
Indices: 21756--21824 Score: 66
Period size: 3 Copynumber: 23.0 Consensus size: 3
21746 GGTCAATAAA
* * * * * * * *
21756 GAT GAA GAT GAC GAT GAA GAT GAT GAT GAT GAA GAT GAC GAC GAC GAC
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
21804 GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT
21825 CCAAACAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.22
Consensus pattern (3 bp):
GAT
Found at i:21791 original size:27 final size:27
Alignment explanation
Indices: 21756--21820 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
21746 GGTCAATAAA
* *
21756 GATGAAGATGACGATGAAGATGATGAT
1 GATGAAGATGACGACGAAGACGATGAT
*
21783 GATGAAGATGACGACGACGACGATGAT
1 GATGAAGATGACGACGAAGACGATGAT
*
21810 GATGATGATGA
1 GATGAAGATGA
21821 TGATCCAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.38, C:0.08, G:0.34, T:0.20
Consensus pattern (27 bp):
GATGAAGATGACGACGAAGACGATGAT
Found at i:23257 original size:127 final size:128
Alignment explanation
Indices: 23031--23289 Score: 367
Period size: 127 Copynumber: 2.0 Consensus size: 128
23021 CCATAAAGTG
* * *
23031 TCGATACATTTTTAAAAAGTAACGACCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
1 TCGATACATTTTCAAAAAGTAACGACCCCAAAAACATCGAAACCAATAATTATAATGTAAGAGGT
* * *
23096 AAATTTACAATGTAACAGGTATAAATATACTGGTTTTATGA-AAAATATGTCTATAACATGCA
66 AAATTTACAATATAACAGGTATAAATATACTGGTTTTATGAGAAAATAGGTCTACAACATGCA
** *
23158 TCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCAATAATTATAATGTAAGAGGT
1 TCGATACATTTTCAAAAAGTAACGACCCCAAAAACATCGAAACCAATAATTATAATGTAAGAGGT
* ** * * * *
23223 AATTTTGTAATATAGCCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACAACATGTA
66 AAATTTACAATATAACAGGTATAAATATACTGGTTTTATGAGAAAATAGGTCTACAACATGCA
23286 TCGA
1 TCGA
23290 CACTTTTTAA
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
127 94 0.82
128 21 0.18
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.30
Consensus pattern (128 bp):
TCGATACATTTTCAAAAAGTAACGACCCCAAAAACATCGAAACCAATAATTATAATGTAAGAGGT
AAATTTACAATATAACAGGTATAAATATACTGGTTTTATGAGAAAATAGGTCTACAACATGCA
Found at i:23474 original size:179 final size:179
Alignment explanation
Indices: 23173--23896 Score: 854
Period size: 200 Copynumber: 3.8 Consensus size: 179
23163 ACATTTTCAA
* * *
23173 AAAGTGTCGATCCCAAAAACATCGAAACCAATAATTATAATGTAAGAGGTAATTTTGTAATATAG
1 AAAGTGTCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAATTTTGTAATATAA
*
23238 CCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATAT
66 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATAT
23303 TGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACGCAC
131 TGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACGCAC
* *
23352 AAAGTGTCGATCCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAATATTGTAATATAA
1 AAAGTGTCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAATTTTGTAATATAA
* ** * *
23417 CTGGTATAAATATACCCATTTTATGAGAGAATAAGTCTACAACATGTATCAACACTTTTTAATAT
66 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATAT
*
23482 TGTGTCAATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACGCAC
131 TGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACGCAC
* *
23531 AAAGTGTCGATACATTTTCAAAAAGTGTCGATTCCAAAAATATCGTAACCGATAATTATAATGTA
1 AAAGTGTCG--------------A---TC----CCAAAAACATCGAAACCGATAATTATAATGTA
23596 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACA
45 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACA
* * *
23661 TGTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCTAGAATGAATGCCAAAAAGGGTGAA
110 TGTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAA
* *
23726 CGAAT
175 CGCAC
*
23731 AAAGTGTCGATATATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTA
1 AAA--GT-G------------------TCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* * *
23796 ATAGGTAATTTTGTAATATAACCGATATAAATATACCGTTTTTATGAGATAATAGGTCTACAACA
45 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACA
*
23861 TGTATCGATACTTTTTAATATTGTGTCGATACTTTT
110 TGTATCGACACTTTTTAATATTGTGTCGATACTTTT
23897 AAATAACTCA
Statistics
Matches: 471, Mismatches: 32, Indels: 63
0.83 0.06 0.11
Matches are distributed among these distances:
179 176 0.37
193 1 0.00
196 2 0.00
200 283 0.60
202 2 0.00
203 1 0.00
204 2 0.00
207 1 0.00
221 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (179 bp):
AAAGTGTCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAATTTTGTAATATAA
CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATAT
TGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACGCAC
Found at i:23641 original size:200 final size:200
Alignment explanation
Indices: 23352--23896 Score: 901
Period size: 200 Copynumber: 2.7 Consensus size: 200
23342 GTTAACGCAC
*
23352 AAAGTGTCGATCCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAATATTGTAATATAA
1 AAAGTGTCGATCCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAATTTTGTAATATAA
* * * *
23417 CTGGTATAAATATACCCATTTTATGAGAGAATAAGTCTACAACATGTATCAACACTTTTTAATAT
66 CCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATAT
* * * *
23482 TGTGTCAATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACGCACAAAGTGTCGATACATT
131 TGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAAGGGTGAACGAACAAAGTGTCGATACATT
23547 TTCAA
196 TTCAA
* *
23552 AAAGTGTCGATTCCAAAAATATCGTAACCGATAATTATAATGTAATAGGTAATTTTGTAATATAA
1 AAAGTGTCGATCCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAATTTTGTAATATAA
*
23617 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATAT
66 CCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATAT
* * *
23682 TGTGTCGATACTTTTTGTCTAGAATGAATGCCAAAAAGGGTGAACGAATAAAGTGTCGATATATT
131 TGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAAGGGTGAACGAACAAAGTGTCGATACATT
23747 TTCAA
196 TTCAA
* *
23752 AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAA
1 AAAGTGTCGATCCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAATTTTGTAATATAA
* * * *
23817 CCGATATAAATATACCGTTTTTATGAGATAATAGGTCTACAACATGTATCGATACTTTTTAATAT
66 CCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATAT
23882 TGTGTCGATACTTTT
131 TGTGTCGATACTTTT
23897 AAATAACTCA
Statistics
Matches: 322, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
200 322 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (200 bp):
AAAGTGTCGATCCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAATTTTGTAATATAA
CCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATAT
TGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAAGGGTGAACGAACAAAGTGTCGATACATT
TTCAA
Found at i:24694 original size:15 final size:15
Alignment explanation
Indices: 24676--24705 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24666 TGGCACTTAA
24676 AGATTTACCAAGAGC
1 AGATTTACCAAGAGC
24691 AGATTTACCAAGAGC
1 AGATTTACCAAGAGC
24706 GGTAGCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (15 bp):
AGATTTACCAAGAGC
Found at i:25420 original size:211 final size:211
Alignment explanation
Indices: 25056--25472 Score: 807
Period size: 211 Copynumber: 2.0 Consensus size: 211
25046 CTCTGCCTCA
25056 AGGATATAGGCTATTGCACGCATCTAACTACTTGGTCCCGAAATATGAACGTATATCACAACAAC
1 AGGATATAGGCTATTGCACGCATCTAACTACTTGGTCCCGAAATATGAACGTATATCACAACAAC
25121 TATCCTTATATAAAATTAAAAACAATTCTTCAACAACTGAATACAACTATTATACGTAATGTTCA
66 TATCCTTATATAAAATTAAAAACAATTCTTCAACAACTGAATACAACTATTATACGTAATGTTCA
25186 ATCATGCACTCCTTACGTTGGAGGGCTCTAAACCCTAAACCCTCAAAAGAAACTTGCCTTACCAA
131 ATCATGCACTCCTTACGTTGGAGGGCTCTAAACCCTAAACCCTCAAAAGAAACTTGCCTTACCAA
25251 TTCCTAGCTTAACTCG
196 TTCCTAGCTTAACTCG
* *
25267 AGGATATAGGCTATTGCACGCATCTAACTACTTGGTCCTGAAATGTGAACGTATATCACAACAAC
1 AGGATATAGGCTATTGCACGCATCTAACTACTTGGTCCCGAAATATGAACGTATATCACAACAAC
25332 TATCCTTATATAAAATTAAAAACAATTCTTCAACAACTGAATACAACTATTATACGTAATGTTCA
66 TATCCTTATATAAAATTAAAAACAATTCTTCAACAACTGAATACAACTATTATACGTAATGTTCA
*
25397 ATCATGCACTCCTTACGTTGGAGGGCTCTAAGCCCTAAACCCTCAAAAGAAACTTGCCTTACCAA
131 ATCATGCACTCCTTACGTTGGAGGGCTCTAAACCCTAAACCCTCAAAAGAAACTTGCCTTACCAA
25462 TTCCTAGCTTA
196 TTCCTAGCTTA
25473 CCATTTAGAC
Statistics
Matches: 203, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
211 203 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (211 bp):
AGGATATAGGCTATTGCACGCATCTAACTACTTGGTCCCGAAATATGAACGTATATCACAACAAC
TATCCTTATATAAAATTAAAAACAATTCTTCAACAACTGAATACAACTATTATACGTAATGTTCA
ATCATGCACTCCTTACGTTGGAGGGCTCTAAACCCTAAACCCTCAAAAGAAACTTGCCTTACCAA
TTCCTAGCTTAACTCG
Found at i:28527 original size:200 final size:198
Alignment explanation
Indices: 28161--28863 Score: 805
Period size: 198 Copynumber: 3.5 Consensus size: 198
28151 ATTTTCTACA
* * * *
28161 AGTATCGA-CCAAAAAACATCAAAACCAATAATTATAATGTAATAGGTAAATTAACAATGTATCC
1 AGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACCC
* * * * * * * *
28225 GGTATAAATATA-CTGATTAATTAGAAAACATGTCAACATAATGTATCAACACTTGTGAAATTTG
66 GGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATAATGTATCGACACTTGTTAAATTTG
* * * *
28289 TGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACGGATAAAGTGTCGATACATTT
130 TGTCGATACTTTTTGTCCATAATGAATGCCC-AACGAGGTGCAAGAATAAAGTGTCGATACATTT
28354 ATTAAA-
194 A--AAAT
* * *
28360 AGTATCGATCCTAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACT
1 AGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACCC
* * *
28425 GATATAAATATACCGGTTTTATGAGAAAATAGGTCAGCATAAAGTATCGACACTTGTTAAATTTA
66 GGTATAAATATACCGGTTTTATGAGAAAATAGGTCA-CATAATGTATCGACACTTGTTAAATTTG
* *
28490 TGTCGATA-TATTTTGTCCATAATGAATGCCCAACGAGGTGCAAGAATAAAATGTCAATACATTT
130 TGTCGATACT-TTTTGTCCATAATGAATGCCCAACGAGGTGCAAGAATAAAGTGTCGATACATTT
28554 AAAAT
194 AAAAT
* * * * *
28559 TGTATCGATCCCAAAAACATCGAAA-CGAAAATTACAATGTGATAGGTAAATTTACAATGTACCC
1 AGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACCC
* * * * *
28623 GGTATAAATATACCGGTTTTATGAGAAAATATGTCTAAATAATGTAGCGACACGTT-TTTAGTTT
66 GGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATAATGTATCGACAC-TTGTTAAATTT
* *
28687 GTGTCGATACTTTTT-TCCAGAATGAAATATGAATGTCCAACGAGGTGCAAGCATAAAGTGTCGA
129 GTGTCGATACTTTTTGTCC---AT---A-ATGAATGCCCAACGAGGTGCAAGAATAAAGTGTCGA
*
28751 TACAGTTAAAATT
187 TACATTTAAAA-T
*
28764 A-TATCGATCCAAAAAACATCGAAACCGATAATTATAATGCAATAGGTAAATTTACAATGTTA-C
1 AGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG-TACC
* **
28827 CTGTATAAATATACCGG-TTTACTTCGAAAATAGGTCA
65 CGGTATAAATATACCGGTTTTA-TGAGAAAATAGGTCA
28864 ATATAAGCGA
Statistics
Matches: 432, Mismatches: 53, Indels: 33
0.83 0.10 0.06
Matches are distributed among these distances:
197 3 0.01
198 101 0.23
199 35 0.08
200 95 0.22
201 67 0.16
203 1 0.00
204 69 0.16
205 59 0.14
206 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (198 bp):
AGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACCC
GGTATAAATATACCGGTTTTATGAGAAAATAGGTCACATAATGTATCGACACTTGTTAAATTTGT
GTCGATACTTTTTGTCCATAATGAATGCCCAACGAGGTGCAAGAATAAAGTGTCGATACATTTAA
AAT
Found at i:28959 original size:87 final size:87
Alignment explanation
Indices: 28864--29025 Score: 243
Period size: 87 Copynumber: 1.9 Consensus size: 87
28854 AAATAGGTCA
*
28864 ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACGTAATAATATTT
1 ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTATACGTAATAATATTT
*
28929 CCGGTTAAATGCCTATTTTATT
66 CCGATTAAATGCCTATTTTATT
* * * * * *
28951 ATATAAGCGCTACTTATTACATTATATAAGCGTTACCTAATATGTTATTATACTTTATAATATTT
1 ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTATACGTAATAATATTT
*
29016 CTGATTAAAT
66 CCGATTAAAT
29026 AATATGACAT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 66 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTATACGTAATAATATTT
CCGATTAAATGCCTATTTTATT
Found at i:28998 original size:23 final size:23
Alignment explanation
Indices: 28948--28992 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28938 TGCCTATTTT
* *
28948 ATTATATAAGCGCTACTTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
28971 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
28993 TGTTATTATA
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:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:29094 original size:11 final size:11
Alignment explanation
Indices: 29078--29113 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
29068 AACCGATCAC
29078 ATCATTTTTTA
1 ATCATTTTTTA
29089 ATCATTTTTTA
1 ATCATTTTTTA
29100 ATCATTTTTTA
1 ATCATTTTTTA
29111 ATC
1 ATC
29114 GTCGCACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (11 bp):
ATCATTTTTTA
Found at i:30513 original size:29 final size:31
Alignment explanation
Indices: 30472--30533 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
30462 AACCCGTGAC
* *
30472 GACCACATTTTAATTAAA-CAAAACG-AAGT
1 GACCACATCTTAATTAAATAAAAACGAAAGT
30501 GACCACATCTTAATTAAATAAAAACGAAAGT
1 GACCACATCTTAATTAAATAAAAACGAAAGT
30532 GA
1 GA
30534 TCTTATCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.59
30 6 0.21
31 6 0.21
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (31 bp):
GACCACATCTTAATTAAATAAAAACGAAAGT
Found at i:30764 original size:23 final size:24
Alignment explanation
Indices: 30734--30783 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
30724 TATGTCCTCT
30734 CAAAAGATGCATGG-AAAACACGA
1 CAAAAGATGCATGGAAAAACACGA
30757 CAAAAGATGCATGGAAAAACACGA
1 CAAAAGATGCATGGAAAAACACGA
30781 CAA
1 CAA
30784 CTTCTCGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.54, C:0.18, G:0.20, T:0.08
Consensus pattern (24 bp):
CAAAAGATGCATGGAAAAACACGA
Found at i:31175 original size:15 final size:15
Alignment explanation
Indices: 31157--31212 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
31147 TAACCGGTTT
31157 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
31172 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
31189 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
31204 CGATTTTAA
1 CGGTTTTAA
31213 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:31185 original size:17 final size:17
Alignment explanation
Indices: 31160--31210 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
31150 CCGGTTTCGG
31160 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
31177 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
31192 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
31209 TT
1 TT
31211 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:31628 original size:13 final size:13
Alignment explanation
Indices: 31607--31661 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
31597 AAGTTCGATA
*
31607 AATTCAAATACTT
1 AATTGAAATACTT
31620 AATTGAAATACTT
1 AATTGAAATACTT
* *
31633 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
31647 AATTGAAATACTT
1 AATTGAAATACTT
31660 AA
1 AA
31662 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:31692 original size:33 final size:34
Alignment explanation
Indices: 31647--31739 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 34
31637 AACTCAACAT
* * * *
31647 AATTGAAATACTTAAATACTTCCAAGTTTGAATT
1 AATTCAAATACTTAAAAACTTCCAAGTTTCAATA
*
31681 TA-TCAAATACTTAAAAACTTCCAAG-TTCAATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTCAATA
31713 AATTCAAATACTTAAAAACTT-CAAGTT
1 AATTCAAATACTTAAAAACTTCCAAGTT
31740 CGATAATTGA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
32 10 0.20
33 40 0.78
34 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.34
Consensus pattern (34 bp):
AATTCAAATACTTAAAAACTTCCAAGTTTCAATA
Found at i:31764 original size:21 final size:21
Alignment explanation
Indices: 31740--31779 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31730 ACTTCAAGTT
31740 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
31761 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
31780 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:36867 original size:191 final size:194
Alignment explanation
Indices: 36530--36877 Score: 492
Period size: 191 Copynumber: 1.8 Consensus size: 194
36520 TTTGATATAA
* * * *
36530 AAAATGGTTGTCCCTTGTTCCCATATGTAATGGGGTAAGGGGGAGGTAAGATAGTAGGCTGCTGC
1 AAAATAGTCGTCCCTTGTTCCCATATGTAATGGGGTAAGGGGGAGGCAAGATAGTAGGC-GCTGA
* * * *
36595 CCCCAACATCAGGTTAAGAGCAGCTTCCGTAGAAGACCTCCGAATTATGAAATGCCCTCCGTGGG
65 CCCCAACATCAGGTTAAGAGCAACTTCCGTAGAAGACCTCCAAATTATGAAATGCCCTCCATAGG
* *
36660 ACTCGATCCCACGACCTCAAGGTTAAAAATCTTGTGCTCTACCAACTGAGCTGGATAGTCATCTC
130 AATCGATCCCACGACCTCAAAGTTAAAAATCTTGTGCTCTACCAACTGAGCTGGATAGTCATCTC
36725 AAAATAGTCGTCCCTTGTTCCCATATGTAATGAGGG-AA-GGGGAGGCAAGATAGTA-G-GCTGA
1 AAAATAGTCGTCCCTTGTTCCCATATGTAATG-GGGTAAGGGGGAGGCAAGATAGTAGGCGCTGA
* * * *
36786 CCTCAACA-CTAGGTTGAGAGCAACTTCCGTA-AGAGGCCTCTAAATTATGAAATGCCCTCCATA
65 CCCCAACATC-AGGTTAAGAGCAACTTCCGTAGA-AGACCTCCAAATTATGAAATGCCCTCCATA
36849 GGAATCGATCCCACGACCTCAAAGTTAAA
128 GGAATCGATCCCACGACCTCAAAGTTAAA
36878 GTTAAGAACC
Statistics
Matches: 136, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
190 2 0.01
191 82 0.60
193 1 0.01
194 16 0.12
195 32 0.24
196 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (194 bp):
AAAATAGTCGTCCCTTGTTCCCATATGTAATGGGGTAAGGGGGAGGCAAGATAGTAGGCGCTGAC
CCCAACATCAGGTTAAGAGCAACTTCCGTAGAAGACCTCCAAATTATGAAATGCCCTCCATAGGA
ATCGATCCCACGACCTCAAAGTTAAAAATCTTGTGCTCTACCAACTGAGCTGGATAGTCATCTC
Found at i:38018 original size:361 final size:353
Alignment explanation
Indices: 37353--38062 Score: 1073
Period size: 361 Copynumber: 2.0 Consensus size: 353
37343 AGAAAGACTT
37353 CTCAACTTTCTTTTGTGTTGACTGGGGATTACATTGCTTGAATAGGGGCCAATTAAGGTCGGCGA
1 CTCAACTTTCTTTTGTGTTGACTGGGGATTACATTGCTTGAATAGGGGCCAATTAAGGTCGGCGA
* * * * * * *
37418 AGTGCGGCTTTCTACCAAGGTAATCAATTCTTTGTGCTCCTTTTGTTCTATAGAGGAGATTTGTA
66 AGAGCAGCTTTCAACCAAGGTAATCAATTCCTTGTGCTCCTTTTGTTCTATAGAAGAAATTCGTA
*
37483 ATGTTAATGTAAAATCCAACATCAAAATAAGTGATCAATCAAGTTAGAGGTTATTGCCTTACCTA
131 ATGTTAATGTAAAATACAACATCAAAATAAGTGATCAATCAAGTTAGAGGTTATTGCCTTACCTA
* * * *
37548 ACTTCCTTTCAGTCCCTCTATCTTTAATTTCAACTACCTCCATATCAATAGAACTTATGTCGGAT
196 ACTTCCTTTCAGTCCCTCTATCTATAACTTCAACAACCTCCATATCAATAGAACTTATATCGGAT
** *
37613 TCCTCTGCTTTTACTTTCACTGCCCTATTAGAGGCAGCAGTTTCTTCGAGAGCAATGGTGGTTTT
261 TCCTCAACTTTTACTTTCACTGCCCTATTAGAGGCAGCAGTTTCTTCGAGAGCAATGGTGGATTT
37678 TGCAACTAACCCTTCTGGTTTTATACTG
326 TGCAACTAACCCTTCTGGTTTTATACTG
*
37706 CTCAACTTTCTTTTGTGTTGACTGGGGATTATATTGCTTGAATTGGGATAGGGGCCAATTAAGGT
1 CTCAACTTTCTTTTGTGTTGACTGGGGATTACATTGCTTG-A-----ATAGGGGCCAATTAAGGT
* * *
37771 CGGCGATGAGCAGCTTTCAACCAAGGTTATCAATTCCTTGTGTTCCTTTTGTTCTATATAGAAGA
60 CGGCGAAGAGCAGCTTTCAACCAAGGTAATCAATTCCTTGTGCTCCTTTTGTTC--TATAGAAGA
*
37836 AATTCGTAATGTTAATGTAAAATACAACATCAAAATAAGTGA-CGAATCAAGTTAGAGGTTATTT
123 AATTCGTAATGTTAATGTAAAATACAACATCAAAATAAGTGATC-AATCAAGTTAGAGGTTATTG
* * *
37900 CCTTACCTAACTTCCTTTTAGTCCCTCTATCTATAACTTCAACAACCTCCATATCAGTAGAGCTT
187 CCTTACCTAACTTCCTTTCAGTCCCTCTATCTATAACTTCAACAACCTCCATATCAATAGAACTT
* * * *
37965 CTATCGGATTCCTCAACTTTTACTTTCACTGCTCTATTAGAGGC-GTTAGTTTCTTCGAGTGCAA
252 ATATCGGATTCCTCAACTTTTACTTTCACTGCCCTATTAGAGGCAG-CAGTTTCTTCGAGAGCAA
38029 TGGTGGATTTTGCAACTAACCCTTCTGGTTTTAT
316 TGGTGGATTTTGCAACTAACCCTTCTGGTTTTAT
38063 TGGTTGTGAA
Statistics
Matches: 320, Mismatches: 27, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
353 39 0.12
354 1 0.00
359 65 0.20
360 2 0.01
361 213 0.67
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (353 bp):
CTCAACTTTCTTTTGTGTTGACTGGGGATTACATTGCTTGAATAGGGGCCAATTAAGGTCGGCGA
AGAGCAGCTTTCAACCAAGGTAATCAATTCCTTGTGCTCCTTTTGTTCTATAGAAGAAATTCGTA
ATGTTAATGTAAAATACAACATCAAAATAAGTGATCAATCAAGTTAGAGGTTATTGCCTTACCTA
ACTTCCTTTCAGTCCCTCTATCTATAACTTCAACAACCTCCATATCAATAGAACTTATATCGGAT
TCCTCAACTTTTACTTTCACTGCCCTATTAGAGGCAGCAGTTTCTTCGAGAGCAATGGTGGATTT
TGCAACTAACCCTTCTGGTTTTATACTG
Found at i:39920 original size:21 final size:21
Alignment explanation
Indices: 39894--40028 Score: 125
Period size: 21 Copynumber: 6.5 Consensus size: 21
39884 GTTTCCAGAT
*
39894 TCGCAACGCGAAATTGGACTA
1 TCGCAATGCGAAATTGGACTA
*
39915 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAAATTGGACTA
* * * *
39936 TTGCAATGCGATAGTCGACTA
1 TCGCAATGCGAAATTGGACTA
39957 TCGCAATGCGAACA-TGGACTA
1 TCGCAATGCGAA-ATTGGACTA
* *
39978 TCGCAATGCG-AATATGTA-AA
1 TCGCAATGCGAAAT-TGGACTA
* * *
39998 TCGCAATGCGAACTTGTA-AA
1 TCGCAATGCGAAATTGGACTA
40018 TCGCAATGCGA
1 TCGCAATGCGA
40029 TAGTCGAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
19 1 0.01
20 29 0.30
21 66 0.68
22 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAAATTGGACTA
Found at i:39959 original size:42 final size:42
Alignment explanation
Indices: 39910--40035 Score: 161
Period size: 42 Copynumber: 3.0 Consensus size: 42
39900 CGCGAAATTG
*
39910 GACTATCGCAATGCGAACTTGGACTATTGCAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTC
*
39952 GACTATCGCAATGCGAACATGGACTATCGCAATGCGAATA-T-
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCG-ATAGTC
* * *
39993 GTA-AATCGCAATGCGAACTTGTA-AATCGCAATGCGATAGTC
1 G-ACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTC
40034 GA
1 GA
40036 ATTTGCGATT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
39 3 0.04
40 13 0.18
41 19 0.26
42 36 0.49
43 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (42 bp):
GACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTC
Found at i:40002 original size:20 final size:20
Alignment explanation
Indices: 39956--40028 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
39946 ATAGTCGACT
* * *
39956 ATCGCAATGCGAACATGGACT
1 ATCGCAATGCGAATATGTA-A
39977 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
39997 ATCGCAATGCGAACT-TGTAA
1 ATCGCAATGCGAA-TATGTAA
40017 ATCGCAATGCGA
1 ATCGCAATGCGA
40029 TAGTCGAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.62
21 18 0.38
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:40805 original size:42 final size:42
Alignment explanation
Indices: 40746--40889 Score: 216
Period size: 42 Copynumber: 3.4 Consensus size: 42
40736 CGTTGCGATT
40746 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* * * *
40788 TTGGACTATCGCAACGAATTTGGAATAAATTGTAACGTGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* * *
40830 TTCGACTATTGCAACGAACTTGGAATAAATCGCAACACGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
40872 TTAGACTATCGCAACGAA
1 TTGGACTATCGCAACGAA
40890 TTTTGGTTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:40810 original size:19 final size:19
Alignment explanation
Indices: 40746--40889 Score: 99
Period size: 21 Copynumber: 6.9 Consensus size: 19
40736 CGTTGCGATT
40746 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
40765 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
40788 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
* * *
40807 TTGGAATAAATTGTAACGTGAAC
1 TTGGACT--ATCGCAAC--GAAC
* *
40830 TTCGACTATTGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
40849 TTGGAATAAATCGCAACACGAAC
1 TTGGACT--ATCGC-A-ACGAAC
*
40872 TTAGACTATCGCAACGAA
1 TTGGACTATCGCAACGAA
40890 TTTTGGTTAA
Statistics
Matches: 98, Mismatches: 15, Indels: 24
0.72 0.11 0.18
Matches are distributed among these distances:
19 30 0.31
20 1 0.01
21 36 0.37
22 1 0.01
23 30 0.31
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:42210 original size:24 final size:23
Alignment explanation
Indices: 42174--42244 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 23
42164 TTATATATAG
**
42174 TAACTTAAAAAATATTTTTTGTAT
1 TAACTTATTAAATATTTTTT-TAT
42198 TAACTTATTAAATATATTTTATTAT
1 TAACTTATTAAATAT-TTTT-TTAT
* *
42223 TAATTTAATTTAAAGATTTTTT
1 TAACTT-A-TTAAATATTTTTT
42245 ATTTTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 13 0.33
25 13 0.33
26 6 0.15
27 7 0.18
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (23 bp):
TAACTTATTAAATATTTTTTTAT
Found at i:42235 original size:27 final size:27
Alignment explanation
Indices: 42181--42268 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
42171 TAGTAACTTA
* *
42181 AAAAATATTTTTTGTATTAACTT-A-TT
1 AAAAATATTTTAT-TATTAATTTAATTT
*
42207 AAATATATTTTATTATTAATTTAATTT
1 AAAAATATTTTATTATTAATTTAATTT
* * * * *
42234 AAAGATTTTTTATTTTTATTTTCATTT
1 AAAAATATTTTATTATTAATTTAATTT
42261 AAAAATAT
1 AAAAATAT
42269 ATATTTTTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
25 8 0.16
26 12 0.24
27 30 0.60
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
AAAAATATTTTATTATTAATTTAATTT
Found at i:42438 original size:31 final size:31
Alignment explanation
Indices: 42403--42477 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
42393 TGACCCGTAA
*
42403 TGATCACCTCTTAATTAAATAAAAACAAAAG
1 TGATCACATCTTAATTAAATAAAAACAAAAG
* **
42434 TGATCATATCTTAATTAAATAAAAATGAAAG
1 TGATCACATCTTAATTAAATAAAAACAAAAG
*
42465 TGATCATATCTTA
1 TGATCACATCTTA
42478 TTTTTTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (31 bp):
TGATCACATCTTAATTAAATAAAAACAAAAG
Found at i:52051 original size:39 final size:39
Alignment explanation
Indices: 51982--52118 Score: 177
Period size: 39 Copynumber: 3.5 Consensus size: 39
51972 AACCAAAGCA
* * * *
51982 GGACTTGCCA-CTCTTGACGCAGCAGAATGCTCATCATCC
1 GGACTTG-CAGCTCTCGATGCAACAGGATGCTCATCATCC
* *
52021 GGACTTGCAACTCTCGATGTAACAGGATGCTCATCATCC
1 GGACTTGCAGCTCTCGATGCAACAGGATGCTCATCATCC
* *
52060 GGACTTGCAGCTCTCGATGCAGCAGGATGCTCATCACCC
1 GGACTTGCAGCTCTCGATGCAACAGGATGCTCATCATCC
*
52099 GGGCTTGCAGCTCTCGATGC
1 GGACTTGCAGCTCTCGATGC
52119 TCCAACATGT
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 2 0.02
39 85 0.98
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.23
Consensus pattern (39 bp):
GGACTTGCAGCTCTCGATGCAACAGGATGCTCATCATCC
Found at i:52133 original size:39 final size:39
Alignment explanation
Indices: 52008--52134 Score: 137
Period size: 39 Copynumber: 3.3 Consensus size: 39
51998 ACGCAGCAGA
* * * * **
52008 ATGCTCATCATCCGGACTTGCAACTCTCGATGTAACAGG
1 ATGCTCATCACCCGGACTTGCAGCTCTCGATGCACCAAC
* * **
52047 ATGCTCATCATCCGGACTTGCAGCTCTCGATGCAGCAGG
1 ATGCTCATCACCCGGACTTGCAGCTCTCGATGCACCAAC
* *
52086 ATGCTCATCACCCGGGCTTGCAGCTCTCGATGCTCCAAC
1 ATGCTCATCACCCGGACTTGCAGCTCTCGATGCACCAAC
*
52125 ATGTTCATCA
1 ATGCTCATCA
52135 ACTGCGCCTG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.25
Consensus pattern (39 bp):
ATGCTCATCACCCGGACTTGCAGCTCTCGATGCACCAAC
Found at i:52133 original size:78 final size:78
Alignment explanation
Indices: 51982--52134 Score: 184
Period size: 78 Copynumber: 2.0 Consensus size: 78
51972 AACCAAAGCA
* * **
51982 GGACTTGCCACTCTTGACGCAGCAGAATGCTCATCATCCGGACTTGCAACTCTCGATGTAACAGG
1 GGACTTGCCACTCTCGACGCAGCAGAATGCTCATCACCCGGACTTGCAACTCTCGATGTAACAAC
52047 ATGCTCATCATCC
66 ATGCTCATCATCC
* * * * *
52060 GGACTTG-CAGCTCTCGATGCAGCAGGATGCTCATCACCCGGGCTTGCAGCTCTCGATGCT-CCA
1 GGACTTGCCA-CTCTCGACGCAGCAGAATGCTCATCACCCGGACTTGCAACTCTCGATG-TAACA
*
52123 ACATGTTCATCA
64 ACATGCTCATCA
52135 ACTGCGCCTG
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
77 2 0.03
78 60 0.95
79 1 0.02
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (78 bp):
GGACTTGCCACTCTCGACGCAGCAGAATGCTCATCACCCGGACTTGCAACTCTCGATGTAACAAC
ATGCTCATCATCC
Found at i:60787 original size:22 final size:22
Alignment explanation
Indices: 60762--60816 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
60752 TCAGGAGTTA
* *
60762 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
60784 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
60806 CAGGAGTTATA
1 CAGGAGTTATA
60817 ACAGCTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Done.