Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008623.1 Hibiscus syriacus cultivar Beakdansim tig00111586_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: 78635
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:3074 original size:5 final size:5
Alignment explanation
Indices: 3055--3103 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
3045 GTCCGTCCGT
* * * *
3055 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTTGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
3104 TGGTCGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.04, C:0.39, G:0.37, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:3112 original size:6 final size:6
Alignment explanation
Indices: 3101--3177 Score: 86
Period size: 6 Copynumber: 13.2 Consensus size: 6
3091 TCGGCTTGGC
* * *
3101 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCG-AG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* * *
3148 TCGAGT TCGT-G TCATGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
3178 AATACGTGTC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
5 7 0.12
6 53 0.88
ACGTcount: A:0.06, C:0.17, G:0.45, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:3167 original size:23 final size:22
Alignment explanation
Indices: 3105--3173 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
3095 CTTGGCTCGT
3105 GGTCGTGGTCGTGGTCGTGGTCGA
1 GGTCGT-GTC-TGGTCGTGGTCGA
*
3129 GGTCGAGGTC-GAGTCGTGGTCGA
1 GGTCG-TGTCTG-GTCGTGGTCGA
*
3152 GTTCGTGTCATGGTCGTGGTCG
1 GGTCGTGTC-TGGTCGTGGTCG
3174 TGGTAATACG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 4 0.11
23 25 0.66
24 9 0.24
ACGTcount: A:0.07, C:0.17, G:0.46, T:0.29
Consensus pattern (22 bp):
GGTCGTGTCTGGTCGTGGTCGA
Found at i:8974 original size:5 final size:5
Alignment explanation
Indices: 8966--9009 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
8956 TCCGTCTAGT
* * *
8966 CTCGG CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTTGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
9010 TGTCGTGGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.05, C:0.39, G:0.39, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:9022 original size:6 final size:6
Alignment explanation
Indices: 9007--9137 Score: 176
Period size: 6 Copynumber: 22.2 Consensus size: 6
8997 TCGGCTTGGC
* * *
9007 TCGT-G TCGTGG TCGTGG TCGT-G TCGTGG TCGAGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* * *
9053 TCGAGG TCGTGG TCGTGG TCGAGT TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* *
9101 TCGAGT TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
9138 AATACGTGTC
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
5 9 0.08
6 105 0.92
ACGTcount: A:0.05, C:0.17, G:0.47, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:15253 original size:15 final size:15
Alignment explanation
Indices: 15235--15269 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
15225 CGAGGGTTTT
15235 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
15250 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
15265 GTAGT
1 GTAGT
15270 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:22115 original size:15 final size:15
Alignment explanation
Indices: 22097--22146 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
22087 CGAGGGTTCT
22097 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
22112 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
*
22127 GTAGTCCTTCAGGAC
1 GTAGTCCTTCGGGAC
22142 GTAGT
1 GTAGT
22147 AGTCCTACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.16, C:0.24, G:0.32, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:23977 original size:5 final size:5
Alignment explanation
Indices: 23965--24008 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
23955 GTCCGTCCGT
* * * *
23965 CTCGG CACGG CACGG CTCGG CTCGG CTCGG CTCAG CTCGA CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
24009 TGGTCGTGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.09, C:0.41, G:0.34, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:24017 original size:6 final size:6
Alignment explanation
Indices: 24006--24102 Score: 140
Period size: 6 Copynumber: 16.2 Consensus size: 6
23996 TCAGCTCGAC
* * * *
24006 TCGTGG TCGTGG CCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
**
24054 TCGTGG TCGTGG TCAAGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
24102 T
1 T
24103 AATACGTGTC
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.05, C:0.18, G:0.48, T:0.29
Consensus pattern (6 bp):
TCGTGG
Found at i:29993 original size:6 final size:6
Alignment explanation
Indices: 29982--30045 Score: 101
Period size: 6 Copynumber: 10.7 Consensus size: 6
29972 GCTCGGCTCA
* * *
29982 TGGTCG TGGTCG AGGTCG AGGTCG TGGTCG TGGTCG AGGTCG TGGTCG
1 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG
30030 TGGTCG TGGTCG TGGT
1 TGGTCG TGGTCG TGGT
30046 AATACGTGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.05, C:0.16, G:0.50, T:0.30
Consensus pattern (6 bp):
TGGTCG
Found at i:32296 original size:31 final size:28
Alignment explanation
Indices: 32201--32296 Score: 75
Period size: 32 Copynumber: 3.2 Consensus size: 28
32191 AACATAGCTA
** *
32201 AGGGACTAAAATCGAACATAAGTTAACATCT
1 AGGGACTAAAATCGAACGGAA--TAACGT-T
*
32232 AAGGGACTAAAATCGAACGGAATAATGTT
1 -AGGGACTAAAATCGAACGGAATAACGTT
* *
32261 AGGGACTAAAATTGGACGGATCGATAACGTT
1 AGGGACTAAAATCGAACGGA---ATAACGTT
32292 AGGGA
1 AGGGA
32297 TTATCCCTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
28 18 0.33
29 1 0.02
30 4 0.07
31 12 0.22
32 19 0.35
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (28 bp):
AGGGACTAAAATCGAACGGAATAACGTT
Found at i:36642 original size:2 final size:2
Alignment explanation
Indices: 36635--36662 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36625 ACTTCATGTG
36635 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
36663 CCTATCTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39508 original size:2 final size:2
Alignment explanation
Indices: 39501--39549 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
39491 AGTCGCTAAT
39501 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
39543 TA TA TA T
1 TA TA TA T
39550 GTATTTATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46520 original size:21 final size:22
Alignment explanation
Indices: 46494--46538 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
46484 GCCACTCATG
46494 TTGCCAT-AAGGACGGCTAATC
1 TTGCCATCAAGGACGGCTAATC
*
46515 TTGCCATCAGGGACGGCTAATC
1 TTGCCATCAAGGACGGCTAATC
46537 TT
1 TT
46539 TATCTGGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (22 bp):
TTGCCATCAAGGACGGCTAATC
Found at i:51352 original size:20 final size:20
Alignment explanation
Indices: 51327--51461 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
51317 AATTGGGAAA
51327 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
51347 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
51367 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
51388 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
51408 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
51428 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
51448 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
51462 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:51371 original size:61 final size:61
Alignment explanation
Indices: 51324--51455 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
51314 GCGAATTGGG
* * * * *
51324 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
51385 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
51446 ATAATCGCAA
1 AAAATCGCAA
51456 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:51989 original size:20 final size:20
Alignment explanation
Indices: 51935--51993 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
51925 GCGATTATCT
**
51935 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
51955 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
51975 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
51994 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:52184 original size:25 final size:24
Alignment explanation
Indices: 52130--52184 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
52120 TGTTTATTAT
* *
52130 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
52154 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
52180 TGTTT
1 TGTTT
52185 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:53331 original size:18 final size:18
Alignment explanation
Indices: 53310--53354 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
53300 TCCACTTCGG
*
53310 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
53328 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
53346 GAGCCATCA
1 GAGCCATCA
53355 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:53861 original size:20 final size:20
Alignment explanation
Indices: 53836--53881 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
53826 TAGTTTACTT
53836 TCGCAACACGAAAATAACTA
1 TCGCAACACGAAAATAACTA
* * **
53856 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATAACTA
53876 TCGCAA
1 TCGCAA
53882 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATAACTA
Found at i:53890 original size:19 final size:20
Alignment explanation
Indices: 53853--53890 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53843 ACGAAAATAA
53853 CTATCGCAACGCGGAAATGG
1 CTATCGCAACGCGGAAATGG
*
53873 CTATCGCAATGC-GAAATG
1 CTATCGCAACGCGGAAATG
53891 AAAATCGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGGAAATGG
Found at i:53910 original size:14 final size:14
Alignment explanation
Indices: 53891--53948 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
53881 ATGCGAAATG
53891 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
53905 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
53921 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
53937 AAAATCGCAACG
1 AAAATCGCAACG
53949 TGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:53933 original size:32 final size:33
Alignment explanation
Indices: 53875--53965 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
53865 GGAAATGGCT
53875 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
53908 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
53940 ATCGCAACGTGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
53966 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:53982 original size:19 final size:18
Alignment explanation
Indices: 53977--54041 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
53967 GCGATTTGTG
*
53977 TTTCGCGTTGCGATTTCA
1 TTTCGCATTGCGATTTCA
53995 TTTCGCATTGCGATTT--
1 TTTCGCATTGCGATTTCA
*
54011 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGA-TTTCA
54028 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
54042 AGCCATTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.15
15 3 0.08
16 4 0.10
17 4 0.10
18 16 0.41
19 6 0.15
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (18 bp):
TTTCGCATTGCGATTTCA
Found at i:54060 original size:20 final size:19
Alignment explanation
Indices: 54026--54081 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
54016 TTGCGATTTT
*
54026 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
54045 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
54065 CATTTTTGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
54082 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:54061 original size:39 final size:33
Alignment explanation
Indices: 53977--54041 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
53967 GCGATTTGTG
53977 TTTCGCGTTGCGA-TTTCATTTCGCATTGCGAT
1 TTTCGCGTTGCGATTTTCATTTCGCATTGCGAT
54009 TTT-GTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TTTCG-CGTTGCGATTTTCATTTCGCATTGCGAT
54042 AGCCATTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 1 0.03
32 11 0.35
33 19 0.61
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTCATTTCGCATTGCGAT
Found at i:55972 original size:14 final size:14
Alignment explanation
Indices: 55953--55988 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
55943 ATTGTTTAAT
55953 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
55967 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
55981 TGATTTGT
1 TGATTTGT
55989 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:56096 original size:20 final size:20
Alignment explanation
Indices: 56071--56109 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56061 ATGTTGAAGG
*
56071 CAAAACAGACTATCGCAACA
1 CAAAACAGACAATCGCAACA
*
56091 CAAAACTGACAATCGCAAC
1 CAAAACAGACAATCGCAAC
56110 GAGAGAATCG
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:0.49, C:0.31, G:0.10, T:0.10
Consensus pattern (20 bp):
CAAAACAGACAATCGCAACA
Found at i:56139 original size:19 final size:19
Alignment explanation
Indices: 56115--56165 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
56105 GCAACGAGAG
56115 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56134 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56153 AATCGCAATGCGA
1 AATCGCAATGCGA
56166 GTTTCAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:56913 original size:24 final size:24
Alignment explanation
Indices: 56886--56939 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
56876 GTATTCGAAA
*
56886 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
56910 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
56934 TTTGAT
1 TTTGAT
56940 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:59450 original size:33 final size:33
Alignment explanation
Indices: 59408--59534 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
59398 GGAAATTACT
59408 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
59441 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
59473 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
59507 ATCGCAATGCGAAATGAAAATCGTAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
59535 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:59515 original size:66 final size:66
Alignment explanation
Indices: 59409--59541 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
59399 GAAATTACTA
*
59409 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
59474 T
66 T
* *
59475 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGTAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
59540 T
66 T
59541 T
1 T
59542 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:59566 original size:14 final size:14
Alignment explanation
Indices: 59549--59605 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
59539 TTTAATTTCG
59549 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
59563 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
59582 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
59596 CGTTGCGATT
1 CGTTGCGATT
59606 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:59585 original size:33 final size:33
Alignment explanation
Indices: 59534--59623 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
59524 AAATCGTAAC
* *
59534 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
59567 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
59600 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
59624 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:59587 original size:19 final size:19
Alignment explanation
Indices: 59563--59623 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
59553 GCGATTCTCT
59563 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
59582 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
59596 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
59615 CATTGCGAT
1 CGTTGCGAT
59624 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:59748 original size:14 final size:14
Alignment explanation
Indices: 59729--59765 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
59719 CATCAATTAA
59729 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
59743 ACAAATCACCTTTT
1 ACAAATCAACTTTT
59757 ACAAATCAA
1 ACAAATCAA
59766 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:63321 original size:20 final size:19
Alignment explanation
Indices: 63292--63448 Score: 111
Period size: 19 Copynumber: 8.7 Consensus size: 19
63282 CTTTTGGTTG
63292 AATGAAAATCGCAACGAGA
1 AATGAAAATCGCAACGAGA
*
63311 TAATGAGAATCGCAACGCAG-
1 -AATGAAAATCGCAACG-AGA
**
63331 AATGACTATCGCAACGAG-
1 AATGAAAATCGCAACGAGA
* *
63349 -A-G--AATTGCAACGCGA
1 AATGAAAATCGCAACGAGA
** *
63364 AATGACTATCGCGACGAG-
1 AATGAAAATCGCAACGAGA
*
63382 -A-G--AATCGCAACGCGA
1 AATGAAAATCGCAACGAGA
* *
63397 AATAAAAATCGCAACGCGA
1 AATGAAAATCGCAACGAGA
*
63416 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGAGA
63435 AATGAAAATCGCAA
1 AATGAAAATCGCAA
63449 TGCGATTTTG
Statistics
Matches: 111, Mismatches: 15, Indels: 23
0.74 0.10 0.15
Matches are distributed among these distances:
14 18 0.16
16 4 0.04
17 3 0.03
18 2 0.02
19 67 0.60
20 15 0.14
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
AATGAAAATCGCAACGAGA
Found at i:63359 original size:33 final size:33
Alignment explanation
Indices: 63315--63399 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
63305 ACGAGATAAT
63315 GAGAATCGCAACGC-AGAATGACTATCGCAACGA
1 GAGAATCGCAACGCGA-AATGACTATCGCAACGA
* *
63348 GAGAATTGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
63381 GAGAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
63400 AAAAATCGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
33 47 0.98
34 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:63406 original size:19 final size:19
Alignment explanation
Indices: 63384--63453 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
63374 GCGACGAGAG
*
63384 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
63403 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
63422 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
63441 AATCGCAATGCGA
1 AATCGCAACGCGA
63454 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:63408 original size:33 final size:33
Alignment explanation
Indices: 63315--63448 Score: 135
Period size: 33 Copynumber: 3.9 Consensus size: 33
63305 ACGAGATAAT
**
63315 GAGAATCGCAACGC-AGAATGACTATCGCAACGA
1 GAGAATCGCAACGCGA-AATGAAAATCGCAACGA
* ** *
63348 GAGAATTGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
*
63381 GAGAATCGCAACGCGAAATAAAAATCGCAACGCGAAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA--CG--A
*
63418 TGAAAATCGCAACGCGAAATGAAAATCGCAA
1 -GAGAATCGCAACGCGAAATGAAAATCGCAA
63449 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
33 54 0.63
34 1 0.01
35 2 0.02
37 1 0.01
38 28 0.33
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:63482 original size:19 final size:19
Alignment explanation
Indices: 63449--63513 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
63439 AAAATCGCAA
**
63449 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
63468 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
63487 TGCGATAGTTATTTC-CGT
1 TGCGATTTTTATTTCGCGT
63505 TGCGATTTT
1 TGCGATTTT
63514 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
18 10 0.25
19 30 0.75
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:64052 original size:20 final size:20
Alignment explanation
Indices: 64027--64079 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
64017 GCGCTATGTA
64027 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
64047 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
64067 TATCTCGTTGCGA
1 AATCGCGTTGCGA
64080 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:64113 original size:20 final size:20
Alignment explanation
Indices: 64088--64141 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
64078 GATTTTGTAT
64088 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
64108 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
64128 TATCGCATTGCGAT
1 TATCGCATTGCGAT
64142 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:64126 original size:61 final size:61
Alignment explanation
Indices: 64028--64144 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
64018 CGCTATGTAA
* * * * *
64028 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
64089 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
64145 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:64160 original size:61 final size:61
Alignment explanation
Indices: 64028--64162 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
64018 CGCTATGTAA
* * * * * ** *
64028 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
64089 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
64151 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
64163 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:67376 original size:20 final size:20
Alignment explanation
Indices: 67351--67389 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
67341 TTTGGTTGCT
67351 GGACTAGTCTCCATACCGAG
1 GGACTAGTCTCCATACCGAG
*
67371 GGACTAGTCTCCATGCCGA
1 GGACTAGTCTCCATACCGA
67390 AGATTGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.21
Consensus pattern (20 bp):
GGACTAGTCTCCATACCGAG
Found at i:68300 original size:64 final size:62
Alignment explanation
Indices: 68161--68320 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 62
68151 TTCTGGGCAA
*** * * * *
68161 GGTGTATCGATGCATATTCAATGCATCGATGCACTCTTTAAAGAAGAACATCGAATGCAATT
1 GGTGTATCGATGCATAAGGAGTGCATCGATGCACCCTTAAAAGAAGAACATCGAAGGCAATT
* *
68223 GGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCCTTAAAATGAA-AACATCGAAGGTAATT
1 GGTGTATCGATGCATAAGGAGTGCATCGATGCA--CCCTTAAAA-GAAGAACATCGAAGGCAATT
* *
68287 TGTGTATCGATGCAT-GGGTAGTGCATCGATGCAC
1 GGTGTATCGATGCATAAGG-AGTGCATCGATGCAC
68321 ATGTTAAGAA
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
62 29 0.35
63 2 0.02
64 48 0.59
65 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (62 bp):
GGTGTATCGATGCATAAGGAGTGCATCGATGCACCCTTAAAAGAAGAACATCGAAGGCAATT
Found at i:68352 original size:19 final size:21
Alignment explanation
Indices: 68308--68363 Score: 80
Period size: 19 Copynumber: 2.7 Consensus size: 21
68298 GCATGGGTAG
68308 TGCATCGATGCACATGTTAAGAA
1 TGCATCGATGCAC-TGTT-AGAA
68331 TGCATCGATGCACTG-T-GAA
1 TGCATCGATGCACTGTTAGAA
68350 TGCATCGATGCACT
1 TGCATCGATGCACT
68364 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 17 0.52
21 1 0.03
22 2 0.06
23 13 0.39
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCACTGTTAGAA
Found at i:76294 original size:20 final size:20
Alignment explanation
Indices: 76261--76298 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
76251 ATTACATGTA
76261 CAAATATGACAAACCGGTCC
1 CAAATATGACAAACCGGTCC
76281 CAAA-ATGACAAAACCGGT
1 CAAATATGAC-AAACCGGT
76299 AAACGCTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.45, C:0.26, G:0.16, T:0.13
Consensus pattern (20 bp):
CAAATATGACAAACCGGTCC
Found at i:76691 original size:199 final size:197
Alignment explanation
Indices: 76348--77539 Score: 1540
Period size: 198 Copynumber: 6.1 Consensus size: 197
76338 ATAAGTATTG
* *
76348 AAAACATCGAAAAATATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATATAAACGGTCTAAATATAC
* * *
76413 CGATTTTTGAGAAAACATGTATACAAAAAGTATCGACACAAATCTAACAAGTGTCGATACTTTTT
66 CGGTTTTTGAGAAAACATGTGTAC-AAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
* * * * * *
76478 CTTCATACTGTATTTCAAATCCAAGTGCACTAAAAAGTGTCAATACATATATAACAAGTGTCGAT
130 GTCCAGAATGTATTTCAAAACCAAGTGCAC-AAAAAGTGTCGATACATATATAACAAGTGTCGAT
76543 CCCA
194 CCCA
* * * * *
76547 AAAACATCGAAAACCATAATTATAATGTAATAAGTAAATTA-GCAAAATAATCGGTCTAAATATA
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTC-ATATAAACGGTCTAAATATA
*
76611 CCGGTTTTTGAGAAAACATGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATACTTTT
65 CCGGTTTTTGAGAAAACATGTGTACAAA-AGTATCGACACAAATATAACAAGTGTCGATACTTTT
* * * * *
76676 GGTCCAGAATGTATTTCAGAACCAAGTGCACATAAAGGTGTCGATACATTTAAAACAAGTGTCGA
129 TGTCCAGAATGTATTTCAAAACCAAGTGCACA-AAAAGTGTCGATACATATATAACAAGTGTCGA
*
76741 TCCCG
193 TCCCA
*
76746 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATATAAACGGTCTAAATATAC
* * *
76811 CGGTTTTTGAGAAAATAGGTGTACAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTTC
66 CGGTTTTTGAGAAAACATGTGTACAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTTG
* *
76876 TCCAGACTGTATTTTAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGATC
131 TCCAGAATGTATTTCAAAACCAAGTGCAC-AAAAAGTGTCGATACATATATAACAAGTGTCGATC
76941 CCA
195 CCA
* * * *
76944 AAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTA-ACAATATAACCGGTCTAAATCTA
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTC-ATATAAACGGTCTAAATATA
* *
77008 CCGGTTTTTGAGAAAA-AAGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATACTTTT
65 CCGGTTTTTGAGAAAACATGTGTACAAA-AGTATCGACACAAATATAACAAGTGTCGATACTTTT
* * * * *
77072 GGTCCAGAAAGTATTTCAGAACCAAGTGCACATAAAAGTGTCGATACATTTAAAACAAGTGTCGA
129 TGTCCAGAATGTATTTCAAAACCAAGTGCACA-AAAAGTGTCGATACATATATAACAAGTGTCGA
77137 TCCCGA
193 TCCC-A
*
77143 AAAA-ATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATATAAACGGTCTAAATATAC
77207 CGGTTTTTGAGAAAACA-GTGTTA-AAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
66 CGGTTTTTGAGAAAACATGTG-TACAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
* * *
77270 -CCCAGAATGTATTTCAAAACCAAGTGCACTAAAAGTGTAGATAC--ATATAACAAGTGTCGATC
130 GTCCAGAATGTATTTCAAAACCAAGTGCACAAAAAGTGTCGATACATATATAACAAGTGTCGATC
77332 CCA
195 CCA
* * ** *
77335 AAAAC-TCGAAAACCATAATTATAATGTAATAGGTAAATTA-GCA-ATATAGTGGTCT-AATGTA
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATATA-AACGGTCTAAATATA
* * * * * *
77396 CCGGTTTATGAG-AAACATGTATACATGAAGTATCGACACAAATACATCAA-TTTCGA-ACATTT
65 CCGGTTTTTGAGAAAACATGTGTACA-AAAGTATCGACACAAATATAACAAGTGTCGATAC-TTT
* * * * * * *
77458 TTGTCCAGACTATATTTTAAAAACCAAGTGCACAACAAA-TTTCGATACATTTATAACAATTGTT
128 TTGTCCAGAATGTA-TTTCAAAACCAAGTGCACAA-AAAGTGTCGATACATATATAACAAGTGTC
*
77522 AATCCC-
191 GATCCCA
77528 AAAA-ATCGAAAA
1 AAAACATCGAAAA
77540 TAATTATAAC
Statistics
Matches: 876, Mismatches: 93, Indels: 54
0.86 0.09 0.05
Matches are distributed among these distances:
189 9 0.01
190 31 0.04
191 37 0.04
192 64 0.07
193 32 0.04
194 16 0.02
195 13 0.01
196 26 0.03
197 47 0.05
198 340 0.39
199 260 0.30
200 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (197 bp):
AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATATAAACGGTCTAAATATAC
CGGTTTTTGAGAAAACATGTGTACAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTTG
TCCAGAATGTATTTCAAAACCAAGTGCACAAAAAGTGTCGATACATATATAACAAGTGTCGATCC
CA
Found at i:77194 original size:396 final size:395
Alignment explanation
Indices: 76347--77539 Score: 1815
Period size: 396 Copynumber: 3.0 Consensus size: 395
76337 TATAAGTATT
* *
76347 GAAAACATCGAAAAATATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
1 GAAAAAATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
* * *
76412 CCGATTTTTGAGAAAACATGTATACAAAAAGTATCGACACAAATCTAACAAGTGTCGATACTTTT
66 CCGGTTTTTGAGAAAACA-GTGTAC-AAAAGTATCGACACAAATATAACAAGTGTCGATACTTTT
* * * *
76477 TCTTCATACTGTATTTCAAATCCAAGTGCACTAAAAAGTGTCAATACATATATAACAAGTGTCGA
129 TCTCCAGACTGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGA
* * *
76542 TCCCAAAAACATCGAAAACCATAATTATAATGTAATAAGTAAATTAGCAAAATAATCGGTCTAAA
194 TCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAACCGGTCTAAA
76607 TATACCGGTTTTTGAGAAAACATGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATAC
259 TATACCGGTTTTTGAGAAAA-ATGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATAC
* *
76672 TTTTGGTCCAGAATGTATTTCAGAACCAAGTGCACATAAAGGTGTCGATACATTTAAAACAAGTG
323 TTTTGGTCCAGAAAGTATTTCAGAACCAAGTGCACATAAAAGTGTCGATACATTTAAAACAAGTG
76737 TCGATCCC
388 TCGATCCC
*
76745 GAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
1 GAAAAAATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
*
76810 CCGGTTTTTGAGAAAATAGGTGTACAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
66 CCGGTTTTTGAGAAAACA-GTGTACAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
*
76875 CTCCAGACTGTATTTTAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
130 CTCCAGACTGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
*
76940 CCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAACAATATAACCGGTCTAAAT
195 CCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAACCGGTCTAAAT
* *
77005 CTACCGGTTTTTGAGAAAAAAGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATACTT
260 ATACCGGTTTTTGAGAAAAATGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATACTT
77070 TTGGTCCAGAAAGTATTTCAGAACCAAGTGCACATAAAAGTGTCGATACATTTAAAACAAGTGTC
325 TTGGTCCAGAAAGTATTTCAGAACCAAGTGCACATAAAAGTGTCGATACATTTAAAACAAGTGTC
77135 GATCCC
390 GATCCC
77141 GAAAAAATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
1 GAAAAAATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
77206 CCGGTTTTTGAGAAAACAGTGTTA-AAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
66 CCGGTTTTTGAGAAAACAGTG-TACAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
* *
77270 C-CCAGAATGTATTTCAAAACCAAGTGCACT-AAAAGTGTAGATAC--ATATAACAAGTGTCGAT
130 CTCCAGACTGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
**
77331 CCCAAAAAC-TCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATAT-AGTGGTCT-AAT
195 CCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAACCGGTCTAAAT
* * * * * * * *
77393 GTACCGGTTTATGAGAAACATGTATACATGA-AGTATCGACACAAATACATCAA-TTTCGA-ACA
260 ATACCGGTTTTTGAGAAAAATGTGTACA-AACAGTATCGACACAAATAGAACAAGTGTCGATAC-
* * * * * *
77455 TTTTTGTCCAGACTA-TATTTTAAAAACCAAGTGCACA-ACAAA-TTTCGATACATTTATAACAA
323 TTTTGGTCCAGA-AAGTA-TTTCAGAACCAAGTGCACATA-AAAGTGTCGATACATTTAAAACAA
* **
77517 TTGTTAATCCC
385 GTGTCGATCCC
77528 --AAAAATCGAAAA
1 GAAAAAATCGAAAA
77540 TAATTATAAC
Statistics
Matches: 744, Mismatches: 45, Indels: 25
0.91 0.06 0.03
Matches are distributed among these distances:
385 12 0.02
386 2 0.00
387 45 0.06
388 67 0.09
389 7 0.01
390 41 0.06
391 26 0.03
393 13 0.02
394 27 0.04
395 44 0.06
396 197 0.26
397 178 0.24
398 85 0.11
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (395 bp):
GAAAAAATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
CCGGTTTTTGAGAAAACAGTGTACAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTTC
TCCAGACTGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGATC
CCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAACCGGTCTAAATA
TACCGGTTTTTGAGAAAAATGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATACTTT
TGGTCCAGAAAGTATTTCAGAACCAAGTGCACATAAAAGTGTCGATACATTTAAAACAAGTGTCG
ATCCC
Found at i:77860 original size:284 final size:280
Alignment explanation
Indices: 77385--77916 Score: 874
Period size: 284 Copynumber: 1.9 Consensus size: 280
77375 GCAATATAGT
77385 GGTCTAATGTACCGGTTTATGAGAAACATGTATACATGAAGTATCGACACAAATACATCAATTTC
1 GGTCTAATGTACCGGTTTATGAGAAACATGTATACATGAAGTATCGACACAAATACA-CAATTTC
77450 GAACATTTTTGTCCAGACTATATTTTAAAAACCAAGTGCACAACAAATTTCGATACATTTATAAC
65 GAACATTTTTGTCCAGACTATATTTTAAAAACCAAGTGCACAACAAATTTCGATACATTTATAAC
*
77515 AATTGTTAATCCCAAAAATCGAAAATAATTATAACCAAATGTCTCTAACATCATGTGCTGGAGGT
130 AATTGTTAATCCCAAAAATCGAAAATAATTATAACCAAATGTCTCAAACATCATGTGCTGGAGGT
77580 TCATAACCATTCCATTCCGTCTTCAAAAAATTCAGTTGAAGTAGACTACGTGCTATAATTAATGA
195 TCATAACCATTCCATTCCGTCTTCAAAAAA-TCAGTTGAAGTAGACTACGTGCTATAATTAATGA
77645 ATAGGTAATTAACAATGTAACC
259 ATAGGTAATTAACAATGTAACC
*
77667 GGTCTAAATGTACCCGGTTTATGAGAAAACATGTATACATGAAGTATCGACACAAAT-CA-AGTT
1 GGTCT-AATGTA-CCGGTTTATGAG-AAACATGTATACATGAAGTATCGACACAAATACACAATT
* * *
77730 TCG-ATATTTTTGTCCATACTATATTTTAAAAACCAAGTGCACAATAAAGTTTCGATACATTTAT
63 TCGAACATTTTTGTCCAGACTATATTTTAAAAACCAAGTGCACAACAAA-TTTCGATACATTTAT
* *
77794 AACAATTG-TCATCCCAAAACATTGAAAACATAATTATAACCAAATGTCTCAAACATCATGTGCT
127 AACAATTGTTAATCCCAAAA-ATCG-AAA-ATAATTATAACCAAATGTCTCAAACATCATGTGCT
* *
77858 GGAGGTTCATAACCATTCCATTCCGTCTTCAAAAAATCAGTTGAAGTAGATTGCGTGCT
189 GGAGGTTCATAACCATTCCATTCCGTCTTCAAAAAATCAGTTGAAGTAGACTACGTGCT
77917 TGTATTCAAA
Statistics
Matches: 234, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
281 52 0.22
282 37 0.16
283 30 0.13
284 84 0.36
285 31 0.13
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (280 bp):
GGTCTAATGTACCGGTTTATGAGAAACATGTATACATGAAGTATCGACACAAATACACAATTTCG
AACATTTTTGTCCAGACTATATTTTAAAAACCAAGTGCACAACAAATTTCGATACATTTATAACA
ATTGTTAATCCCAAAAATCGAAAATAATTATAACCAAATGTCTCAAACATCATGTGCTGGAGGTT
CATAACCATTCCATTCCGTCTTCAAAAAATCAGTTGAAGTAGACTACGTGCTATAATTAATGAAT
AGGTAATTAACAATGTAACC
Done.