Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005387.1 Hibiscus syriacus cultivar Beakdansim tig00012351_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: 77565
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2548 original size:85 final size:85
Alignment explanation
Indices: 2392--3051 Score: 857
Period size: 85 Copynumber: 7.8 Consensus size: 85
2382 TGTGGTTATC
* * * * ** * * *
2392 GAGCTGAATGGAATCAAACTCGATA-GTTTTTTTTGACAGATAGCTTTTCTCGGCTTAAGATATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATG
* * * *
2456 CTATAAATTTGACATGCCCTT
65 TTGTAAATTTGATATGTCCTT
* *
2477 GAGCTGAATAG-AATCGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
1 GAGCTGAAT-GTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATG
2541 TTGTAAATTTGATATGTCCTT
65 TTGTAAATTTGATATGTCCTT
*
2562 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGATATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGT
*
2627 TGTAAATTTTATATG-CCTTT
66 TGTAAATTTGATATGTCC-TT
* * *
2647 GAGCTGAATGTAATCGAACTCGAAGGTCTTTATTGTA-AGATAGCCCTTCTCTCCTTGAGCTAT-
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTG-ACAGATAGCCCTTCTCGCCTTGAGTTATG
*
2710 TCTGTAAATTTGATTTG-CCTTT
65 T-TGTAAATTTGATATGTCC-TT
* * ** *
2732 GAGCTGAATGTAATCAAACTCGAAGGTCTTTATTGACAGATAATCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGT
2797 TGTAAATTTGATATGTCCTT
66 TGTAAATTTGATATGTCCTT
* *
2817 GAGCTGAATGTAATCAAACTTGAAGGT-TTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTT-GTTGACAGATAGCCCTTCTCGCCTTGAGTTATG
*
2881 CTGTAAATTTGATATGTCCTT
65 TTGTAAATTTGATATGTCCTT
* * * * *
2902 GAGCTGAATGTAATCGAACTCAAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTAAGTTTTGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGT
2967 TGTAAATTTGATATGTCCTT
66 TGTAAATTTGATATGTCCTT
* * * *
2987 GAGCTGAATGTAATTGAACTCGAAGGTCTTTTGCTGGCAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATG
3052 CTGCAAATAG
Statistics
Matches: 513, Mismatches: 50, Indels: 23
0.88 0.09 0.04
Matches are distributed among these distances:
84 9 0.02
85 469 0.91
86 35 0.07
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGT
TGTAAATTTGATATGTCCTT
Found at i:3237 original size:86 final size:86
Alignment explanation
Indices: 3082--3270 Score: 315
Period size: 86 Copynumber: 2.2 Consensus size: 86
3072 GAAAAATGGA
* *
3082 TCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTAGTTCCCCTTAGCGGGTCTTAACCAA
1 TCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTAGTTCCCCTCAGCGGGTCTGAACCAA
*
3147 GTGAGATGATCTTTGGATGAC
66 GTGAGATGATCTTTGGATAAC
* * *
3168 TCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTCAGCGGGTCTGAACTAG
1 TCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTAGTTCCCCTCAGCGGGTCTGAACCAA
3233 GTGAGATGATCTTTGGATAAC
66 GTGAGATGATCTTTGGATAAC
*
3254 TCCCCTTCACAGGAAAG
1 TCCCCTTCACGGGAAAG
3271 TCACGTGAGA
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 96 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (86 bp):
TCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTAGTTCCCCTCAGCGGGTCTGAACCAA
GTGAGATGATCTTTGGATAAC
Found at i:7359 original size:20 final size:21
Alignment explanation
Indices: 7325--7363 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
7315 AAAGAAAACA
*
7325 AAAAAAAGAATAGAAACAATG
1 AAAAAAAGAAGAGAAACAATG
7346 AAAAAAAG-AGAGAAACAA
1 AAAAAAAGAAGAGAAACAA
7364 AAGCAGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.05
Consensus pattern (21 bp):
AAAAAAAGAAGAGAAACAATG
Found at i:7571 original size:2 final size:2
Alignment explanation
Indices: 7564--7627 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
7554 AAATGTTAGG
7564 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7606 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
7628 AAAATAAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7796 original size:20 final size:20
Alignment explanation
Indices: 7758--7803 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
7748 AAACCGAAAC
7758 AAAA-AAATAGTATAAAATA
1 AAAATAAATAGTATAAAATA
7777 AAAATAAATA-TATAATAATA
1 AAAATAAATAGTATAA-AATA
*
7797 ATAATAA
1 AAAATAA
7804 TAACAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAATAAATAGTATAAAATA
Found at i:10546 original size:19 final size:19
Alignment explanation
Indices: 10522--10567 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
10512 AATGTAACAC
10522 CTCGCATCGGATCGAGTCA
1 CTCGCATCGGATCGAGTCA
10541 CTCGCATCGGATCGAGTCA
1 CTCGCATCGGATCGAGTCA
10560 CTCGCATC
1 CTCGCATC
10568 AGTCTGTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.22
Consensus pattern (19 bp):
CTCGCATCGGATCGAGTCA
Found at i:11059 original size:21 final size:19
Alignment explanation
Indices: 11033--11089 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
11023 GACTATCGCA
*
11033 TTGCGATAGTCCAAGTTTGCG
1 TTGCGATAGTCCAA-ATT-CG
*
11054 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAATTCG
11075 TTGCGATAGTCCAAA
1 TTGCGATAGTCCAAA
11090 ATCGCAACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.26
21 14 0.45
22 2 0.06
23 7 0.23
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (19 bp):
TTGCGATAGTCCAAATTCG
Found at i:11838 original size:6 final size:6
Alignment explanation
Indices: 11818--11864 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
11808 CCGTCTCGTC
* * *
11818 TCGT-G TCGT-G TCGTGG TCGTGC TTGTGG TCGTGG TAGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
11864 T
1 T
11865 AATACGTGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.02, C:0.15, G:0.45, T:0.38
Consensus pattern (6 bp):
TCGTGG
Found at i:11981 original size:21 final size:21
Alignment explanation
Indices: 11955--12045 Score: 75
Period size: 19 Copynumber: 4.4 Consensus size: 21
11945 GTTGGAATAA
*
11955 ATCGCAACGCGAACTTCTACT
1 ATCGCAACGCGAACTTCGACT
*
11976 ATCGCAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * *
11995 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
12014 AAATCGCAACGCGAACTT-GAACT
1 --ATCGCAACGCGAACTTCG-ACT
12037 ATCGCAACG
1 ATCGCAACG
12046 AATTTGGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 27 0.46
21 23 0.39
22 1 0.02
23 8 0.14
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:12030 original size:42 final size:38
Alignment explanation
Indices: 11976--12061 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 38
11966 AACTTCTACT
*
11976 ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGAACTATCGCAACGAATTTGG-A-AA
12016 ATCGCAACGCGAACTTGAACTATCGCAACGAATTTGGAAA
1 ATCGCAA--CGAACTTGAACTATCGCAACGAATTTGGAAA
12056 ATCGCA
1 ATCGCA
12062 TTGCGATAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
40 15 0.35
41 1 0.02
42 27 0.63
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (38 bp):
ATCGCAACGAACTTGAACTATCGCAACGAATTTGGAAA
Found at i:12059 original size:19 final size:19
Alignment explanation
Indices: 11976--12061 Score: 75
Period size: 19 Copynumber: 4.3 Consensus size: 19
11966 AACTTCTACT
**
11976 ATCGCAACGAACTTGGACT
1 ATCGCAACGAACTTGGAAA
*
11995 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGG-A-AA
*
12016 ATCGCAACGCGAACTT-GAACT
1 ATCGCAA--CGAACTTGGAA-A
*
12037 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAACTTGGAAA
12056 ATCGCA
1 ATCGCA
12062 TTGCGATAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
19 27 0.50
20 5 0.09
21 15 0.28
22 1 0.02
23 6 0.11
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAACTTGGAAA
Found at i:12060 original size:61 final size:61
Alignment explanation
Indices: 11946--12061 Score: 187
Period size: 61 Copynumber: 1.9 Consensus size: 61
11936 CCACCAGTCG
* **
11946 TTGGAATAAATCGCAACGCGAACTTCTACTATCGCAACGAACTTGGACTATCGCAACGAAT
1 TTGGAATAAATCGCAACGCGAACTTCAACTATCGCAACGAACTTGGAAAATCGCAACGAAT
* *
12007 TTGGAATAAATCGCAACGCGAACTTGAACTATCGCAACGAATTTGGAAAATCGCA
1 TTGGAATAAATCGCAACGCGAACTTCAACTATCGCAACGAACTTGGAAAATCGCA
12062 TTGCGATAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (61 bp):
TTGGAATAAATCGCAACGCGAACTTCAACTATCGCAACGAACTTGGAAAATCGCAACGAAT
Found at i:12091 original size:21 final size:21
Alignment explanation
Indices: 12062--12107 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
12052 GAAAATCGCA
* *
12062 TTGCGATAGTTGAAGTTCACG
1 TTGCAATAGTCGAAGTTCACG
* *
12083 TTGCAATAGTCGATGTTCGCG
1 TTGCAATAGTCGAAGTTCACG
12104 TTGC
1 TTGC
12108 GAATCTAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (21 bp):
TTGCAATAGTCGAAGTTCACG
Found at i:13444 original size:22 final size:21
Alignment explanation
Indices: 13420--13461 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
13410 TGAAATCGAG
13420 GGGGAATAAAATTTTGAACTC
1 GGGGAATAAAATTTTGAACTC
13441 GGGGAATAAAATTTTGAACTC
1 GGGGAATAAAATTTTGAACTC
13462 TTTGTACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
GGGGAATAAAATTTTGAACTC
Found at i:19396 original size:24 final size:24
Alignment explanation
Indices: 19369--19468 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
19359 GATATCAAAA
*
19369 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
19393 ATCAGAAA-AGAATCCAGGTTAGGA-
1 ATCA-AAACAGAATTCAGATCA-GAT
* *
19417 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
19441 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
19465 ATCA
1 ATCA
19469 GATAAAATAT
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
23 4 0.07
24 48 0.84
25 5 0.09
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:19468 original size:48 final size:48
Alignment explanation
Indices: 19362--19470 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 48
19352 AAACGGAGAT
* * * *
19362 ATCAAAAATCAAAACATAATTCAGATCAGATATCAGAAAAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAGAAAAGAATCCAA
* * * * * *
19410 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCA-AAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAGAAA-AGAATCCAA
19458 ATCAGAAATCAGA
1 ATCAGAAATCAGA
19471 TAAAATATTC
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
47 3 0.06
48 44 0.94
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAGAAAAGAATCCAA
Found at i:21747 original size:27 final size:27
Alignment explanation
Indices: 21711--21823 Score: 136
Period size: 27 Copynumber: 4.1 Consensus size: 27
21701 TCTCAATTGT
*
21711 TTTTTTACTTTTTCTATTTCTCTTTCA
1 TTTTTAACTTTTTCTATTTCTCTTTCA
** * *
21738 TTTTTAACTTTACCCATTTCTCTCTCA
1 TTTTTAACTTTTTCTATTTCTCTTTCA
*
21765 TTTTTTTAACTTTTTCTTTTTCTCTTTCA
1 --TTTTTAACTTTTTCTATTTCTCTTTCA
* *
21794 TTTGTAACTTTTTCTTTTTCTCTTTCA
1 TTTTTAACTTTTTCTATTTCTCTTTCA
21821 TTT
1 TTT
21824 CTTCGTCTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
27 51 0.70
29 22 0.30
ACGTcount: A:0.12, C:0.20, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTTTAACTTTTTCTATTTCTCTTTCA
Found at i:28434 original size:27 final size:28
Alignment explanation
Indices: 28363--28420 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
28353 TCCATTAAAT
*
28363 GAGGGAAAATGAATTCCATCCAAGAATG
1 GAGGGAAAGTGAATTCCATCCAAGAATG
28391 GAGGGAAAGTGAATTCCATCCAAGAATG
1 GAGGGAAAGTGAATTCCATCCAAGAATG
28419 GA
1 GA
28421 TGAAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.28, T:0.17
Consensus pattern (28 bp):
GAGGGAAAGTGAATTCCATCCAAGAATG
Found at i:28838 original size:193 final size:191
Alignment explanation
Indices: 28612--28960 Score: 510
Period size: 193 Copynumber: 1.8 Consensus size: 191
28602 TAAGTGTGAA
*
28612 ATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATA-C-CCGA-CC-AAAAATATATATATA
1 ATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCGCCGACCCGAAAAA-A-ATATATA
* * * *
28673 GTTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTCTCTATATATATATTTTCCAA
64 ATTTTACCTTATATATTTAGGAATAATTACAATAATA-CCC-CTATATATATA-AAATTTT-CAA
*
28738 TTAAGT-AGTAGTTTTTATTGAATAAAAATATATTTTTATTATTTCGGATCGGGTTTCTAATTTA
125 TTAAGTCAAT-GTTTTTATTGAATAAAAATATATTTTTATTATTTCGGATCGGGTTTCTAATTTA
28802 TAT
189 TAT
*
28805 ATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAAAAATATATA
1 ATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACC-G-CCGACCCGAAAAAAATATATA
*
28870 ATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATAAAATTTTCAATTTA
64 ATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATAAAATTTTCAATTAA
28935 GTCAATGTTTTTATTGAATAAAAATA
129 GTCAATGTTTTTATTGAATAAAAATA
28961 GTTTTTGGTA
Statistics
Matches: 141, Mismatches: 8, Indels: 14
0.87 0.05 0.09
Matches are distributed among these distances:
193 65 0.46
194 9 0.06
195 9 0.06
196 3 0.02
197 47 0.33
198 3 0.02
199 5 0.04
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (191 bp):
ATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCGCCGACCCGAAAAAAATATATAAT
TTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATAAAATTTTCAATTAAGT
CAATGTTTTTATTGAATAAAAATATATTTTTATTATTTCGGATCGGGTTTCTAATTTATAT
Found at i:35925 original size:21 final size:22
Alignment explanation
Indices: 35842--35924 Score: 105
Period size: 23 Copynumber: 3.8 Consensus size: 22
35832 CCAGAACCCC
* *
35842 AGGGGGTATCGATTCCCCTAC-
1 AGGGGGAATCGATTCCCCTTCA
*
35863 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
*
35886 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
35908 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
35925 TCTGCACTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 18 0.33
22 16 0.29
23 21 0.38
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:38834 original size:53 final size:53
Alignment explanation
Indices: 38754--38860 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
38744 ATCACAAATT
*
38754 TTATCATTATCAAATTTTAGTTTAGGCAGCCCTCGAACCAAATCTCCTTGAAC
1 TTATCATTATCAAATTTTAGTTTAGGCAGCCCTCGAACCAAATCTCATTGAAC
*
38807 TTATCATTATCAAATTTTAGTTTAGGCAGCCCTCTAACCAAATCTCATTGAAC
1 TTATCATTATCAAATTTTAGTTTAGGCAGCCCTCGAACCAAATCTCATTGAAC
38860 T
1 T
38861 AACCATTGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (53 bp):
TTATCATTATCAAATTTTAGTTTAGGCAGCCCTCGAACCAAATCTCATTGAAC
Found at i:43529 original size:17 final size:18
Alignment explanation
Indices: 43496--43529 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43486 ATTAACTTAA
*
43496 TCAATTTTAACTAATTAT
1 TCAATTTGAACTAATTAT
43514 TCAATTTGAA-TAATTA
1 TCAATTTGAACTAATTA
43530 AAATGAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (18 bp):
TCAATTTGAACTAATTAT
Found at i:43925 original size:137 final size:137
Alignment explanation
Indices: 43330--44070 Score: 755
Period size: 137 Copynumber: 5.4 Consensus size: 137
43320 GAAACTAAAA
* * * * * * * * *
43330 AAAATGTAGGCTCTAAGATTAATCCTAGTTATTTTTTAGT-AATTAT-TGAATCGAATAGTCAAA
1 AAAATGGAGACTCTAATATTAATCCTAATTA-ATTTTAATCAATTATGTGATTCGAATAATTAAA
* * * * ** * *
43393 ATGGAACCTCAAGCATAAGCGAGGACCAAATCAAAAATTCTCCTAGATAAAAGGACTAGGTGTGA
65 ATGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAATTC-CCTA-ATTTAAGGACTAAGTTTGA
43458 AATTGAA-CCT
128 AATT-AAGCCT
* * * * * * *
43468 ATAATGGA-ATCTTTAAAAATTAA-CTTAATCAATTTTAA-CTAATTAT-TCAATTTGAATAATT
1 AAAATGGAGA-CTCT-AATATTAATCCTAATTAATTTTAATC-AATTATGT-GATTCGAATAATT
* * * * * *
43529 AAAATGAAACCTCGATCGAAAGCGATGACCAAATTAAAAATTTCCCTAATTTAAGGACTAAGTTA
62 AAAATGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAA-TTCCCTAATTTAAGGACTAAGTTT
43594 GAAATTAAGCCT
126 GAAATTAAGCCT
* * *
43606 AAAATGGA-AGCTCTAATATTAATCCTGATTAATTTTAGTCAATTATGTGATTCGAATAATGAAA
1 AAAATGGAGA-CTCTAATATTAATCCTAATTAATTTTAATCAATTATGTGATTCGAATAATTAAA
* * * *
43670 ATGGAACCTTGATCAAAAGCGAGGATCGAATTAAAAATTCATCTAAATTTAAGGACTAAGTTTGA
65 ATGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAATTC-CCT-AATTTAAGGACTAAGTTTGA
*
43735 AATTAAACCT
128 AATTAAGCCT
**
43745 AAAATGGAGGTTCTAATATTAATCCTAATTAATTTTAATCAATTATGTGATTCGAATAATTAAAA
1 AAAATGGAGACTCTAATATTAATCCTAATTAATTTTAATCAATTATGTGATTCGAATAATTAAAA
* *** * * *
43810 TAGAACCTCGAGCAAAAATAAGGATTAAATTAAAAACT-CCTAATTTTAAGGACTAAATTTGAAA
66 TGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAATTCCCTAA-TTTAAGGACTAAGTTTGAAA
43874 TTAAGCCT
130 TTAAGCCT
* * * *
43882 AAAATGGAGACTCTAATTATTAA-CCTAGTCAATTTTAACCAATTATTTGATTCGAATAATTAAA
1 AAAATGGAGACTCTAA-TATTAATCCTAATTAATTTTAATCAATTATGTGATTCGAATAATTAAA
* *
43946 ATGGAACCTCGAGCAAAAGCGAGGACCAAATTAAAAATTCCCTAATATAAGGACTAAGTTTGAAA
65 ATGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAATTCCCTAATTTAAGGACTAAGTTTGAAA
* *
44011 CTAGGCCT
130 TTAAGCCT
* * * *
44019 AAAGTGAAGGCTCTAATATCAATCCTAATTAATTTTAATCAATTATGTGATT
1 AAAATGGAGACTCTAATATTAATCCTAATTAATTTTAATCAATTATGTGATT
44071 ATTCATCTAA
Statistics
Matches: 497, Mismatches: 89, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
136 7 0.01
137 190 0.38
138 127 0.26
139 170 0.34
140 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (137 bp):
AAAATGGAGACTCTAATATTAATCCTAATTAATTTTAATCAATTATGTGATTCGAATAATTAAAA
TGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAATTCCCTAATTTAAGGACTAAGTTTGAAAT
TAAGCCT
Found at i:44464 original size:14 final size:14
Alignment explanation
Indices: 44438--44480 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
44428 TAATTTAAGG
*
44438 AAAAAAA-TGAAAT
1 AAAAAAATTTAAAT
44451 AAAAAAATTTAAAT
1 AAAAAAATTTAAAT
**
44465 GGAAAAATTTAAAT
1 AAAAAAATTTAAAT
44479 AA
1 AA
44481 TGAAAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAAAAATTTAAAT
Found at i:44490 original size:18 final size:19
Alignment explanation
Indices: 44467--44509 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
44457 ATTTAAATGG
44467 AAAAATTTAAATAAT-GAA
1 AAAAATTTAAATAATCGAA
*
44485 AAAAA-TTAATTAATCGAA
1 AAAAATTTAAATAATCGAA
*
44503 TAAAATT
1 AAAAATT
44510 ATTAGTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 12 0.57
19 1 0.05
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAATTTAAATAATCGAA
Found at i:44510 original size:18 final size:17
Alignment explanation
Indices: 44462--44510 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
44452 AAAAAATTTA
* *
44462 AATGGAAAAATTTAAAT
1 AATGAAAAAAATTAAAT
*
44479 AATGAAAAAAATTAATT
1 AATGAAAAAAATTAAAT
*
44496 AATCGAATAAAATTA
1 AAT-GAAAAAAATTA
44511 TTAGTTAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (17 bp):
AATGAAAAAAATTAAAT
Found at i:46335 original size:3 final size:3
Alignment explanation
Indices: 46327--46361 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
46317 TATATTTTGA
*
46327 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
46362 AAAATGGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:46515 original size:17 final size:17
Alignment explanation
Indices: 46493--46525 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
46483 AACCCTTCTG
46493 TTGGAAATGATGATCTA
1 TTGGAAATGATGATCTA
46510 TTGGAAATGATGATCT
1 TTGGAAATGATGATCT
46526 GCTTTCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (17 bp):
TTGGAAATGATGATCTA
Found at i:46792 original size:97 final size:97
Alignment explanation
Indices: 46605--46794 Score: 240
Period size: 97 Copynumber: 2.0 Consensus size: 97
46595 TTCGGACGAG
* * *
46605 TTCTTCTCATTATGAACTCCTCCATTGAAAATGTTGATCCAACTCCTTTTATGATGAATTTGAGC
1 TTCTTCTCATTATGAACTCCTCAATTGAAAATGTCGATCCAACTCCTTCTATGATGAATTTGAGC
** * *
46670 AAAAGGTTGAACAAGATCTTTTCATTATGAAT
66 AAAAGGTCAAAAAAGATCTTCTCATTATGAAT
* * *
46702 TTCTTCTCATTATGAAC-CCTTCAATTGGAAATGTCGATCC-ACATCCTTCTGTGATGGATTTGA
1 TTCTTCTCATTATGAACTCC-TCAATTGAAAATGTCGATCCAAC-TCCTTCTATGATGAATTTGA
* *
46765 GTAAAAGGTCAAAAAAGCTCTTCTCATTAT
64 GCAAAAGGTCAAAAAAGATCTTCTCATTAT
46795 AAACTTATTC
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
96 4 0.05
97 75 0.95
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (97 bp):
TTCTTCTCATTATGAACTCCTCAATTGAAAATGTCGATCCAACTCCTTCTATGATGAATTTGAGC
AAAAGGTCAAAAAAGATCTTCTCATTATGAAT
Found at i:46884 original size:216 final size:216
Alignment explanation
Indices: 46531--46925 Score: 526
Period size: 216 Copynumber: 1.8 Consensus size: 216
46521 GATCTGCTTT
* * * * *
46531 CTTCTGTGATTGATTTGAACAAAAAGTCGAATAAGTTCTTCTCATTATGAAATTTCTCTCTCTCT
1 CTTCTGTGATGGATTTGAACAAAAAGTCAAAAAAGCTCTTCTCATTATGAAATTTCTCTCCCTCT
** *
46596 TCGGACGAGTTCTTCTCATTATGAACTCCTCCATTGAAAATGTTGATCCAACTCCTTTTATGATG
66 TCGGACGAGTTCTTCTCATTATGAACTCCTCCATTGAAAATGTCAATCCAACTCCTTCTATGATG
** * *
46661 AATTTGAGCAAAAGGTTGAACAAGATCTTTTCATTATGAATTTCTTCTCATTATGAACCCTTCAA
131 AATTTGAGCAAAAGGTCAAACAAGATCTTCTCATTATGAACTTCTTCTCATTATGAACCCTTCAA
46726 TTGGAAATGTCGATCCACATC
196 TTGGAAATGTCGATCCACATC
** *
46747 CTTCTGTGATGGATTTGAGTAAAAGGTCAAAAAAGCTCTTCTCATTAT-AAACTTAT-TCTCCCT
1 CTTCTGTGATGGATTTGAACAAAAAGTCAAAAAAGCTCTTCTCATTATGAAA-TT-TCTCTCCCT
* * * * * *
46810 CTTCGGATGAGTTCTTCTCATTATGAAC-CTTTCTATTGGAAATGTCAATCCACCTCCTTCTGTG
64 CTTCGGACGAGTTCTTCTCATTATGAACTC-CTCCATTGAAAATGTCAATCCAACTCCTTCTATG
* * *
46874 ATGGATTTGAGCAAAAGGTCAAACATGTTCTTCTCATTATGAACTTCTTCTC
128 ATGAATTTGAGCAAAAGGTCAAACAAGATCTTCTCATTATGAACTTCTTCTC
46926 CCTCTTCGAA
Statistics
Matches: 152, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
215 4 0.03
216 147 0.97
217 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (216 bp):
CTTCTGTGATGGATTTGAACAAAAAGTCAAAAAAGCTCTTCTCATTATGAAATTTCTCTCCCTCT
TCGGACGAGTTCTTCTCATTATGAACTCCTCCATTGAAAATGTCAATCCAACTCCTTCTATGATG
AATTTGAGCAAAAGGTCAAACAAGATCTTCTCATTATGAACTTCTTCTCATTATGAACCCTTCAA
TTGGAAATGTCGATCCACATC
Found at i:46913 original size:119 final size:119
Alignment explanation
Indices: 46702--46999 Score: 440
Period size: 119 Copynumber: 2.5 Consensus size: 119
46692 CATTATGAAT
* * *
46702 TTCTTCTCATTATGAACCCTTCAATTGGAAATGTCGATCCACATCCTTCTGTGATGGATTTGAGT
1 TTCTTCTCATTATGAACCCTTCTATTGGAAATGTCGATCCACCTCCTTCTGTGATGGATTTGAGC
* *
46767 AAAAGGTCAAAAAAGCTCTTCTCATTATAAACTTATTCTCCCTCTTCGGATGAG
66 AAAAGGTCAAAAAAGCTCTTCTCATTATAAACTTATTCTCCCTCTTCGAACGAG
* *
46821 TTCTTCTCATTATGAACCTTTCTATTGGAAATGTCAATCCACCTCCTTCTGTGATGGATTTGAGC
1 TTCTTCTCATTATGAACCCTTCTATTGGAAATGTCGATCCACCTCCTTCTGTGATGGATTTGAGC
* * * * *
46886 AAAAGGTCAAACATGTTCTTCTCATTATGAACTTCTTCTCCCTCTTCGAACGAG
66 AAAAGGTCAAAAAAGCTCTTCTCATTATAAACTTATTCTCCCTCTTCGAACGAG
* * *
46940 TTC-T-T-ATTATGAACCCTTCTATTGTAAATGTCGGTCCACCTCCTTCTGTGATAGATTTGA
1 TTCTTCTCATTATGAACCCTTCTATTGGAAATGTCGATCCACCTCCTTCTGTGATGGATTTGA
47000 ATCTGTAAAA
Statistics
Matches: 162, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
116 50 0.31
117 1 0.01
118 1 0.01
119 110 0.68
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (119 bp):
TTCTTCTCATTATGAACCCTTCTATTGGAAATGTCGATCCACCTCCTTCTGTGATGGATTTGAGC
AAAAGGTCAAAAAAGCTCTTCTCATTATAAACTTATTCTCCCTCTTCGAACGAG
Found at i:48163 original size:15 final size:15
Alignment explanation
Indices: 48145--48173 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48135 CTCCTTTTAA
48145 TTTTTT-CTTTTTTC
1 TTTTTTCCTTTTTTC
48159 TTTTTTCCTTTTTTC
1 TTTTTTCCTTTTTTC
48174 CTTATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTCCTTTTTTC
Found at i:51518 original size:23 final size:23
Alignment explanation
Indices: 51466--51526 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
51456 AAATTTATGA
*
51466 AATGAATGTAAAGAATGAAGAAT
1 AATGAATGTAAAGAATGAAAAAT
*
51489 AACGAATGTAAAGAATGTAAAAAT
1 AATGAATGTAAAGAATG-AAAAAT
*
51513 -ATGAATGCAAAGAA
1 AATGAATGTAAAGAA
51527 CGATTTCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 28 0.85
24 5 0.15
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (23 bp):
AATGAATGTAAAGAATGAAAAAT
Found at i:63901 original size:136 final size:138
Alignment explanation
Indices: 63535--63938 Score: 456
Period size: 139 Copynumber: 2.9 Consensus size: 138
63525 CCAGTATTAG
* * * * ** * * * * *
63535 CGAGGATCAAATAAAAAATTCTCCTAGATAAAAGGACTAGGTGTGAAACTAAACCTACAATGGAG
1 CGAGGACCAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAACATAAAATGGAG
* * * *
63600 GCTCTAAAAATTAACTTAATCAATTTTAACCAATTATTTAATTCAAATAATTAAAATGGAACCTC
66 GCTCT-AATATTAACCTAATCAATTTTAACCAATTATTTGATTCGAATAATTAAAATGGAACCTC
*
63665 GAGCAAAAA
130 AAGCAAAAA
** ** * **
63674 CGAGGACTTAATTAAAAATTTGCCTAAATTTAAGGACTAAGTTTGAAATTAAACCTAAAATTAAG
1 CGAGGACCAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAACATAAAATGGAG
* * * *
63739 GCTCTAATATTAATCCTAATTAATTTTAATCATTTATGTGATTCGAATAATTAAAATGGAACCTC
66 GCTCTAATATTAA-CCTAATCAATTTTAACCAATTATTTGATTCGAATAATTAAAATGGAACCTC
**
63804 AAGCAAACG
130 AAGCAAAAA
* * *
63813 CGATGACCAAATTAAAAA-TCCCCT-AA-TTAAGGATTAAGTTTGAAATTAAGCATAAAATGGAG
1 CGAGGACCAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAACATAAAATGGAG
*
63875 GCTCTAATTATTAACCTAGTCAATTTTAACCAATTATTTGATTCG-ATAATTAAAATGGAACCTC
66 GCTCTAA-TATTAACCTAATCAATTTTAACCAATTATTTGATTCGAATAATTAAAATGGAACCTC
63939 TACTAGATCC
Statistics
Matches: 222, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
135 19 0.09
136 64 0.29
137 8 0.04
138 11 0.05
139 120 0.54
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (138 bp):
CGAGGACCAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAACATAAAATGGAG
GCTCTAATATTAACCTAATCAATTTTAACCAATTATTTGATTCGAATAATTAAAATGGAACCTCA
AGCAAAAA
Found at i:65041 original size:22 final size:22
Alignment explanation
Indices: 65009--65062 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
64999 TGAATATATT
*
65009 TTAAAAGTTAG-ATGTTAGAAG
1 TTAAAAATTAGCATGTTAGAAG
**
65030 TTAGAAAATTAGCATGTTAGCGG
1 TTA-AAAATTAGCATGTTAGAAG
65053 TTAAAAATTA
1 TTAAAAATTA
65063 AAATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 14 0.50
23 11 0.39
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (22 bp):
TTAAAAATTAGCATGTTAGAAG
Found at i:67125 original size:42 final size:41
Alignment explanation
Indices: 67077--67296 Score: 118
Period size: 43 Copynumber: 5.2 Consensus size: 41
67067 AACTAAAGAA
67077 AAATAAAAAAAAGGAAATAAAAAT-AAATAAA-A-AAGGAAAAT
1 AAATAAAAAAAA-GAAATAAAAATAAAATAAAGATAA--AAAAT
* *
67118 AAGATAAAGAAAAGACATAAAAAATAAAATAAAGATAAAAAAT
1 AA-ATAAAAAAAAGAAAT-AAAAATAAAATAAAGATAAAAAAT
* *
67161 AAATAAAATAAAGAACAT-AAAA-AACA-AAAGA-AATAAAA-
1 AAATAAAAAAAAGAA-ATAAAAATAAAATAAAGATAA-AAAAT
* * *
67199 AAATGAAGAAAAATAAATAAAATAATCAAAATAAAGATAACGAACA-
1 AAAT-AAAAAAAAGAAAT-AAA-AAT-AAAATAAAGATAA--AAAAT
* * * *
67245 AAATAAAATAAAATAAA-AAATAATTAAATAATAAATAATAAAT
1 AAATAAAA-AAAAGAAATAAA-AATAAAATAA-AGATAAAAAAT
*
67288 AAATGAAAA
1 AAATAAAAA
67297 TACTAATAAT
Statistics
Matches: 142, Mismatches: 18, Indels: 37
0.72 0.09 0.19
Matches are distributed among these distances:
38 8 0.06
39 17 0.12
40 5 0.04
41 12 0.08
42 28 0.20
43 32 0.23
44 18 0.13
45 7 0.05
46 15 0.11
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (41 bp):
AAATAAAAAAAAGAAATAAAAATAAAATAAAGATAAAAAAT
Found at i:67149 original size:25 final size:22
Alignment explanation
Indices: 67081--67261 Score: 96
Period size: 22 Copynumber: 8.0 Consensus size: 22
67071 AAAGAAAAAT
* *
67081 AAAAAAAAGGAAATAAAAATAAAT
1 AAAAAAAA-AAAAT-AAAATAAAG
** *
67105 AAAAAAGGAAAATAAGATAAAG
1 AAAAAAAAAAAATAAAATAAAG
67127 AAAAGACATAAAAAATAAAATAAAG
1 AAAA-A-A-AAAAAATAAAATAAAG
* *
67152 ATAAAAAATAAATAAAATAAAG
1 AAAAAAAAAAAATAAAATAAAG
* * * * *
67174 -AACATAAAAAACAAAAGAAAT
1 AAAAAAAAAAAATAAAATAAAG
* * *
67195 AAAAAAATGAAGA-AAAATAAAT
1 AAAAAAA-AAAAATAAAATAAAG
** *
67217 AAAATAATCAAAATAAAGATAACG
1 AAAA-AAAAAAAATAAA-ATAAAG
* *
67241 AACAAAATAAAATAAAATAAA
1 AAAAAAAAAAAATAAAATAAA
67262 AAATAATTAA
Statistics
Matches: 118, Mismatches: 31, Indels: 18
0.71 0.19 0.11
Matches are distributed among these distances:
21 14 0.12
22 49 0.42
23 24 0.20
24 15 0.13
25 16 0.14
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (22 bp):
AAAAAAAAAAAATAAAATAAAG
Found at i:67155 original size:18 final size:17
Alignment explanation
Indices: 67134--67441 Score: 107
Period size: 18 Copynumber: 16.8 Consensus size: 17
67124 AAGAAAAGAC
67134 ATAAAAAATAAAATAAA
1 ATAAAAAATAAAATAAA
67151 GATAAAAAAT-AAATAAA
1 -ATAAAAAATAAAATAAA
67168 ATAAAGAACATAAAA-AACA
1 ATAAA-AA-ATAAAATAA-A
*
67187 A-AAGAAAT-AAA-AAA
1 ATAAAAAATAAAATAAA
67201 ATGAAGAAAA-ATAAATAAA
1 AT-AA-AAAATA-AAATAAA
*
67220 ATAATCAAAATAAAGATAACG
1 ATAA--AAAATAAA-ATAA-A
*
67241 A-ACAAAATAAAATAAA
1 ATAAAAAATAAAATAAA
67257 ATAAAAAATAATTAAATAATAA
1 ATAAAAAAT-A--AAAT-A-AA
*
67279 ATAATAAAT-AAATGAAA
1 ATAAAAAATAAAAT-AAA
* **
67296 ATACTAATAATAGTATATAA
1 ATA--AAAAATAAAATA-AA
* *
67316 ATAATAAATAAAAAAACA
1 ATAAAAAATAAAATAA-A
*
67334 AGAGAAAAATACAAATGAAA
1 ATA-AAAAATA-AAAT-AAA
*
67354 AT-AAATATATAAATAAA
1 ATAAAAAATA-AAATAAA
*
67371 ACTAATATAA-AAAATAAA
1 A-TAA-AAAATAAAATAAA
*
67389 ATAAGAAAAATAATTAAGAAA
1 AT-A-AAAAATAA--AATAAA
*
67410 AGAAAAAA-ATAAATAAA
1 ATAAAAAATA-AAATAAA
67427 ATAAGAAAAATAAAA
1 AT-A-AAAAATAAAA
67442 AGTAAATATG
Statistics
Matches: 219, Mismatches: 31, Indels: 79
0.67 0.09 0.24
Matches are distributed among these distances:
14 2 0.01
15 5 0.02
16 10 0.05
17 41 0.19
18 69 0.32
19 46 0.21
20 26 0.12
21 10 0.05
22 10 0.05
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (17 bp):
ATAAAAAATAAAATAAA
Found at i:67162 original size:43 final size:42
Alignment explanation
Indices: 67113--67238 Score: 120
Period size: 43 Copynumber: 3.0 Consensus size: 42
67103 ATAAAAAAGG
67113 AAAATAAGATAAAGAAAAGACATAAAAAATAAAATAAAGATAA
1 AAAATAAGATAAA-AAAAGACATAAAAAATAAAATAAAGATAA
* * *
67156 AAAATAA-ATAAAATAAAGAACATAAAAAACAAAAGAAATA-AA
1 AAAATAAGATAAAA-AAAG-ACATAAAAAATAAAATAAAGATAA
*
67198 AAAATGAAG--AAAAATA-A-ATAAAATAATCAAAATAAAGATAA
1 AAAAT-AAGATAAAAAAAGACATAAAA-AAT-AAAATAAAGATAA
67239 CGAACAAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
38 6 0.09
39 3 0.04
40 8 0.12
41 5 0.07
42 20 0.29
43 27 0.39
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.14
Consensus pattern (42 bp):
AAAATAAGATAAAAAAAGACATAAAAAATAAAATAAAGATAA
Found at i:67166 original size:4 final size:4
Alignment explanation
Indices: 67134--67449 Score: 53
Period size: 4 Copynumber: 73.8 Consensus size: 4
67124 AAGAAAAGAC
*
67134 ATAA A-AA ATAAA ATAAA GATAA A-AA ATAA ATAAA ATAA AGAA CATAA
1 ATAA ATAA AT-AA AT-AA -ATAA ATAA ATAA AT-AA ATAA ATAA -ATAA
* * * *
67181 A-AA ACAAA AGAA ATAA AAAA ATGAA GAAAA ATAA ATAA A-ATA ATCAAA
1 ATAA A-TAA ATAA ATAA ATAA AT-AA -ATAA ATAA ATAA ATA-A AT--AA
* ** * *
67229 ATAA AGATA ACGA ACAA AATAA AATAA AATAA A-AA ATAA TTAA AT-A
1 ATAA ATA-A ATAA ATAA A-TAA -ATAA -ATAA ATAA ATAA ATAA ATAA
*
67275 ATAA AT-A ATAA ATAA ATGAAA ATACTA ATAA TAGTAT ATAA AT-A ATAA
1 ATAA ATAA ATAA ATAA AT--AA ATA--A ATAA -A-TAA ATAA ATAA ATAA
* * * * *
67323 ATAA AAAA ACAA GAGAA A-AA TACAA ATGAAA ATAA ATAT ATAA ATAAA
1 ATAA ATAA ATAA -ATAA ATAA -ATAA AT--AA ATAA ATAA ATAA AT-AA
* * * *
67371 ACTAA TATAA A-AA ATAAA ATAA GAAAA ATAA TTAA GA-AA AGAA AAAA
1 A-TAA -ATAA ATAA AT-AA ATAA -ATAA ATAA ATAA -ATAA ATAA ATAA
* *
67418 ATAA ATAAA ATAA GAAAA ATAA A-AA GTAA ATA
1 ATAA AT-AA ATAA -ATAA ATAA ATAA ATAA ATA
67450 TGGAAAATAA
Statistics
Matches: 236, Mismatches: 33, Indels: 86
0.66 0.09 0.24
Matches are distributed among these distances:
3 30 0.13
4 118 0.50
5 64 0.27
6 23 0.10
7 1 0.00
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (4 bp):
ATAA
Found at i:67169 original size:52 final size:51
Alignment explanation
Indices: 67091--67398 Score: 143
Period size: 52 Copynumber: 5.8 Consensus size: 51
67081 AAAAAAAAGG
* * *
67091 AAATAAAAATAAATAAA-AAAGGAAAATAAGATAAAGAAAAGACATAAA-AAATA
1 AAATAAAGATAAA-AAATAAA-TAAAATAAGA-AAAGAAAAAACA-AAAGAAATA
* *
67144 AAATAAAGATAAAAAATAAATAAAATAAAGAACATAAAAAACAAAAGAAATA
1 AAATAAAGATAAAAAATAAATAAAAT-AAGAAAAGAAAAAACAAAAGAAATA
* * *
67196 AAA-AAATGA-AGAAAAATAAATAAAATAATCAAAATAAAGATAACGAACA-AAATA
1 AAATAAA-GATA-AAAAATAAATAAAATAA-GAAAAGAAA-A-AAC-AAAAGAAATA
* * * * * *
67250 AAATAAA-ATAAAAAAT-AATTAAATAA-TAAATAATAAATAAATGAAAATA
1 AAATAAAGATAAAAAATAAATAAAATAAGAAAAGAAAAAACAAAAG-AAATA
* * * * *
67299 CTAATAATAGTATATAAATAATAAATAAAAAAACAAGAGAAAAATACAAATGAAAATA
1 -AAATAA-AG-ATA-AAA-AATAAATAAAATAAGAAAAGAAAAA-ACAAAAG-AAATA
67357 AATATATAA-ATAAAACTAATATAA-AAAATAA-AATAAGAAAAA
1 AA-ATA-AAGATAAAA--AATA-AATAAAATAAGAA-AAGAAAAA
67399 TAATTAAGAA
Statistics
Matches: 203, Mismatches: 25, Indels: 51
0.73 0.09 0.18
Matches are distributed among these distances:
47 2 0.01
48 2 0.01
49 6 0.03
50 11 0.05
51 10 0.05
52 58 0.29
53 30 0.15
54 15 0.07
55 14 0.07
56 29 0.14
57 9 0.04
58 16 0.08
59 1 0.00
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (51 bp):
AAATAAAGATAAAAAATAAATAAAATAAGAAAAGAAAAAACAAAAGAAATA
Found at i:67324 original size:7 final size:7
Alignment explanation
Indices: 67255--67326 Score: 58
Period size: 7 Copynumber: 9.9 Consensus size: 7
67245 AAATAAAATA
*
67255 AAATAAA
1 AAATAAT
67262 AAATAATT
1 AAATAA-T
67270 AAATAAT
1 AAATAAT
67277 AAATAAT
1 AAATAAT
67284 AAATAAAT
1 AAAT-AAT
*
67292 GAA-AAT
1 AAATAAT
67298 ACTAATAAT
1 A--AATAAT
*
67307 -AGTATAT
1 AAATA-AT
67314 AAATAAT
1 AAATAAT
67321 AAATAA
1 AAATAA
67327 AAAAACAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
6 6 0.11
7 28 0.53
8 16 0.30
9 3 0.06
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:67419 original size:20 final size:20
Alignment explanation
Indices: 67382--67436 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
67372 CTAATATAAA
67382 AAATAAAATAAG--AAAAAT
1 AAATAAAATAAGAAAAAAAT
*
67400 AATTAAGAA-AAGAAAAAAAT
1 AAATAA-AATAAGAAAAAAAT
67420 AAATAAAATAAGAAAAA
1 AAATAAAATAAGAAAAA
67437 TAAAAAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 8 0.26
19 4 0.13
20 19 0.61
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (20 bp):
AAATAAAATAAGAAAAAAAT
Found at i:67447 original size:21 final size:21
Alignment explanation
Indices: 67377--67447 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
67367 TAAAACTAAT
*
67377 ATAAAAAATAAAATAAGAAAA
1 ATAAAAAGTAAAATAAGAAAA
* *
67398 ATAATTAAG-AAAAGAA-AAAA
1 ATAA-AAAGTAAAATAAGAAAA
67418 AT--AAA-TAAAATAAGAAAA
1 ATAAAAAGTAAAATAAGAAAA
67436 ATAAAAAGTAAA
1 ATAAAAAGTAAA
67448 TATGGAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
17 8 0.21
18 6 0.15
20 9 0.23
21 14 0.36
22 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.15
Consensus pattern (21 bp):
ATAAAAAGTAAAATAAGAAAA
Found at i:67448 original size:20 final size:20
Alignment explanation
Indices: 67377--67459 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
67367 TAAAACTAAT
*
67377 ATAAAAAATAAAATAAGAAAA
1 ATAAAAAGT-AAATAAGAAAA
* * *
67398 ATAATTAAGAAAAGAA-AAAA
1 ATAA-AAAGTAAATAAGAAAA
*
67418 ATAAATA--AAATAAGAAAA
1 ATAAAAAGTAAATAAGAAAA
* *
67436 ATAAAAAGTAAATATGGAAA
1 ATAAAAAGTAAATAAGAAAA
67456 ATAA
1 ATAA
67460 TGATGAGGGT
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
17 5 0.10
18 10 0.21
19 1 0.02
20 21 0.44
21 9 0.19
22 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (20 bp):
ATAAAAAGTAAATAAGAAAA
Found at i:67915 original size:3 final size:3
Alignment explanation
Indices: 67907--67955 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
67897 CATATATTGA
*
67907 AAT AAT AAT AAC AAT AA- AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
67953 AAT
1 AAT
67956 GCTAATAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:67932 original size:20 final size:20
Alignment explanation
Indices: 67907--67955 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
67897 CATATATTGA
67907 AATAATAATAACAATAAAAT
1 AATAATAATAACAATAAAAT
*
67927 AATAATAATAATAATAAAAT
1 AATAATAATAACAATAAAAT
67947 AATAATAAT
1 AATAATAAT
67956 GCTAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAATAATAACAATAAAAT
Found at i:67952 original size:17 final size:17
Alignment explanation
Indices: 67906--67955 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
67896 ACATATATTG
*
67906 AAATAATAATAACAATA
1 AAATAATAATAATAATA
67923 AAATAATAATAATAATA
1 AAATAATAATAATAATA
67940 ATAA-AATAATAATAAT
1 A-AATAATAATAATAAT
67956 GCTAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 29 0.94
18 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAATAATAATAATA
Found at i:67961 original size:20 final size:19
Alignment explanation
Indices: 67906--67965 Score: 79
Period size: 20 Copynumber: 3.2 Consensus size: 19
67896 ACATATATTG
67906 AAATAATAATAA-C-AATA
1 AAATAATAATAATCTAATA
*
67923 AAATAATAATAATAATAATA
1 AAATAATAATAAT-CTAATA
67943 AAATAATAATAATGCTAATA
1 AAATAATAATAAT-CTAATA
67963 AAA
1 AAA
67966 AAAATGGTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.32
20 25 0.68
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATAATAATAATCTAATA
Found at i:68890 original size:20 final size:20
Alignment explanation
Indices: 68861--68899 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
68851 AGAGCCCATG
*
68861 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
68881 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
68900 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:70134 original size:18 final size:17
Alignment explanation
Indices: 70111--70156 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
70101 TGTTTATGAG
70111 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
*
70129 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTAA
70146 GGAATTGGAAT
1 GGAATTGGAAT
70157 ATGAATCTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:70753 original size:20 final size:20
Alignment explanation
Indices: 70699--70829 Score: 72
Period size: 20 Copynumber: 6.5 Consensus size: 20
70689 TAAAATAAAG
*
70699 GAAATAAAAATATATAAGAAAG
1 GAAATAAAAA-ATA-AAGAAAA
* *
70721 GAAA-ATAAGATAAAGAAAA
1 GAAATAAAAAATAAAGAAAA
*
70740 GACATAAAAAATAAA-ATAAA
1 GAAATAAAAAATAAAGA-AAA
* *
70760 GATAA-AAAAACTAAATAAAA
1 GA-AATAAAAAATAAAGAAAA
* * * *
70780 TAAAGAACATAA-AAACAAAA
1 GAAATAA-AAAATAAAGAAAA
*
70800 GAAATAAAAAATGAAGAAAAA
1 GAAATAAAAAATAAAG-AAAA
*
70821 TAAATAAAA
1 GAAATAAAA
70830 TAATCAAAAT
Statistics
Matches: 83, Mismatches: 18, Indels: 17
0.70 0.15 0.14
Matches are distributed among these distances:
19 15 0.18
20 45 0.54
21 19 0.23
22 4 0.05
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (20 bp):
GAAATAAAAAATAAAGAAAA
Found at i:70779 original size:24 final size:25
Alignment explanation
Indices: 70723--70832 Score: 81
Period size: 25 Copynumber: 4.4 Consensus size: 25
70713 TAAGAAAGGA
* *
70723 AAATAAGATAAAGAAAAGACATAAA--
1 AAATAAAATAAAGATAAGA-A-AAACT
70748 AAATAAAATAAAGATAA-AAAAACT
1 AAATAAAATAAAGATAAGAAAAACT
*
70772 AAATAAAATAAAGA-ACATAAAAAC-
1 AAATAAAATAAAGATA-AGAAAAACT
*
70796 AAA-AGAAATAAAAAATGAAGAAAAA-T
1 AAATA-AAAT-AAAGAT-AAGAAAAACT
70822 AAATAAAATAA
1 AAATAAAATAA
70833 TCAAAATAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
22 3 0.04
23 3 0.04
24 23 0.32
25 27 0.38
26 13 0.18
27 2 0.03
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (25 bp):
AAATAAAATAAAGATAAGAAAAACT
Found at i:70783 original size:9 final size:8
Alignment explanation
Indices: 70745--70842 Score: 56
Period size: 9 Copynumber: 11.2 Consensus size: 8
70735 GAAAAGACAT
70745 AAAAAATAA
1 AAAAAAT-A
70754 AATAAAGATA
1 AA-AAA-ATA
70764 AAAAAACTA
1 AAAAAA-TA
70773 AATAAAATA
1 AA-AAAATA
*
70782 AAGAACATA
1 AA-AAAATA
*
70791 AAAACA-A
1 AAAAAATA
*
70798 AAGAAAT-
1 AAAAAATA
70805 AAAAAATGA
1 AAAAAAT-A
70814 AGAAAAATA
1 A-AAAAATA
70823 AATAAAATA
1 AA-AAAATA
*
70832 ATCAAAATA
1 A-AAAAATA
70841 AA
1 AA
70843 GATAACAAGC
Statistics
Matches: 72, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
7 11 0.15
8 6 0.08
9 37 0.51
10 16 0.22
11 2 0.03
ACGTcount: A:0.77, C:0.04, G:0.05, T:0.14
Consensus pattern (8 bp):
AAAAAATA
Found at i:70816 original size:15 final size:15
Alignment explanation
Indices: 70776--70828 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
70766 AAAACTAAAT
70776 AAAATAAAGAACATAA
1 AAAATAAAGAA-ATAA
70792 AAACA-AAAGAAATAA
1 AAA-ATAAAGAAATAA
*
70807 AAAATGAAGAAA-AA
1 AAAATAAAGAAATAA
*
70821 TAAATAAA
1 AAAATAAA
70829 ATAATCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 9 0.28
15 13 0.41
16 9 0.28
17 1 0.03
ACGTcount: A:0.77, C:0.04, G:0.08, T:0.11
Consensus pattern (15 bp):
AAAATAAAGAAATAA
Found at i:70840 original size:18 final size:17
Alignment explanation
Indices: 70817--70886 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
70807 AAAATGAAGA
70817 AAAATAAATAAAATAATC
1 AAAATAAATAAAATAA-C
* * *
70835 AAAATAAAGATAACAAGC
1 AAAATAAATAAAATAA-C
* *
70853 AACATAAAATAAAATAAG
1 AAAAT-AAATAAAATAAC
70871 AAAATAAATGAAAATA
1 AAAATAAAT-AAAATA
70887 CTAATAATAG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
17 4 0.10
18 28 0.70
19 8 0.20
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAATAAATAAAATAAC
Found at i:70985 original size:21 final size:21
Alignment explanation
Indices: 70962--71025 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
70952 AACTAATATA
* *
70962 AAAATAAAATAAGA-AAGAAA
1 AAAAAAAAATAAAATAAGAAA
*
70982 AAAAACAAATAAAATAAGAAA
1 AAAAAAAAATAAAATAAGAAA
* * *
71003 AATAAAAAGTAAATATAGGAAA
1 AAAAAAAAATAAA-ATAAGAAA
71025 A
1 A
71026 TAATGATGAG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
20 11 0.31
21 16 0.46
22 8 0.23
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (21 bp):
AAAAAAAAATAAAATAAGAAA
Found at i:71015 original size:7 final size:6
Alignment explanation
Indices: 70902--71015 Score: 52
Period size: 6 Copynumber: 18.2 Consensus size: 6
70892 AATAGTATGT
** * * * *
70902 AAATAA TAAATAA AAGAGGA AAATAC AAATGA AAATAA ATATAT AAATAA
1 AAATAA -AAATAA AA-ATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * * * *
70952 AACT-A ATATAA AAAT-A AAATAA GAAAGAA AAAAAA CAAATAAA ATAAGAA
1 AAATAA AAATAA AAATAA AAATAA -AAATAA AAATAA -AAAT-AA A-AATAA
71002 AAATAA AAAGTAA A
1 AAATAA AAA-TAA A
71016 TATAGGAAAA
Statistics
Matches: 78, Mismatches: 21, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
5 8 0.10
6 40 0.51
7 26 0.33
8 4 0.05
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:71016 original size:25 final size:25
Alignment explanation
Indices: 70963--71010 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
70953 ACTAATATAA
70963 AAATAAAATAAGAAAGAAAAAAAAC
1 AAATAAAATAAGAAAGAAAAAAAAC
*
70988 AAATAAAATAAGAAA-AATAAAAA
1 AAATAAAATAAGAAAGAAAAAAAA
71011 GTAAATATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.10
Consensus pattern (25 bp):
AAATAAAATAAGAAAGAAAAAAAAC
Found at i:71532 original size:3 final size:3
Alignment explanation
Indices: 71472--71523 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
71462 TATATATTGA
* *
71472 AAT AAT AAT AAT AAC AAT AAT AA- AAT AA- AAC AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
71518 AAT AAT
1 AAT AAT
71524 GCTAATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:72460 original size:20 final size:20
Alignment explanation
Indices: 72431--72469 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
72421 AGAGCCCATG
*
72431 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
72451 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
72470 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Done.