Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005534.1 Hibiscus syriacus cultivar Beakdansim tig00012802_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: 71878
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2752 original size:21 final size:21
Alignment explanation
Indices: 2728--2783 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
2718 GTTGCCATCG
* *
2728 ATTGATCGTCGAAAGTAGTCA
1 ATTGATCGTCGAAAGCAATCA
2749 ATTGATCGTCGAAAGCAATCA
1 ATTGATCGTCGAAAGCAATCA
2770 ATTGATCGTCGAAA
1 ATTGATCGTCGAAA
2784 TTGCATGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (21 bp):
ATTGATCGTCGAAAGCAATCA
Found at i:3003 original size:2 final size:2
Alignment explanation
Indices: 2996--3026 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2986 TGTTTTTAAA
2996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3027 ATTTTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4093 original size:17 final size:17
Alignment explanation
Indices: 4073--4107 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4063 TAAAAATAGA
4073 AAAAATAGAAAAAATAT
1 AAAAATAGAAAAAATAT
*
4090 AAAAATATAAAAAATAT
1 AAAAATAGAAAAAATAT
4107 A
1 A
4108 TAATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAAATAGAAAAAATAT
Found at i:4106 original size:9 final size:9
Alignment explanation
Indices: 4064--4176 Score: 68
Period size: 9 Copynumber: 12.4 Consensus size: 9
4054 ATTTTTCATT
*
4064 AAAAATAGA
1 AAAAATATA
*
4073 AAAAATAGA
1 AAAAATATA
4082 AAAAATAT-
1 AAAAATATA
4090 AAAAATATA
1 AAAAATATA
4099 AAAAATATA
1 AAAAATATA
* *
4108 TAATATTATA
1 -AAAAATATA
* *
4118 TATAATTAATA
1 -AAAAAT-ATA
*
4129 TAAAATATA
1 AAAAATATA
* *
4138 TAAAATATT
1 AAAAATATA
* *
4147 ATATATATA
1 AAAAATATA
**
4156 ATTAATATA
1 AAAAATATA
4165 AAAAATA-A
1 AAAAATATA
4173 AAAA
1 AAAA
4177 TATTATATAT
Statistics
Matches: 84, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
8 13 0.15
9 53 0.63
10 15 0.18
11 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATATA
Found at i:4157 original size:34 final size:34
Alignment explanation
Indices: 4093--4189 Score: 153
Period size: 34 Copynumber: 2.9 Consensus size: 34
4083 AAAATATAAA
*
4093 AATATAAAAAATATATAATA-T-TATATATAATT
1 AATATAAAAAATATAAAATATTATATATATAATT
*
4125 AATATAAAATATATAAAATATTATATATATAATT
1 AATATAAAAAATATAAAATATTATATATATAATT
*
4159 AATATAAAAAATAAAAAATATTATATATATA
1 AATATAAAAAATATAAAATATTATATATATA
4190 TAATCGGGGC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.31
33 1 0.02
34 40 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
AATATAAAAAATATAAAATATTATATATATAATT
Found at i:5606 original size:2 final size:2
Alignment explanation
Indices: 5599--5647 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
5589 CTCTTATGTA
5599 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5640 AT AT AT AT
1 AT AT AT AT
5648 TAATAAATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7351 original size:78 final size:79
Alignment explanation
Indices: 7221--7420 Score: 233
Period size: 78 Copynumber: 2.5 Consensus size: 79
7211 TTAATGGTTT
* * ** *
7221 TTATACAAATGCCGTATAGGGTTCATCTATAGTGGTGTTTTTTAACAAACGCCGCAACAGAGTAG
1 TTATACAAAAGCCGTATAGGGTTCATATATAGTGGCATTTTTCAACAAACGCCGCAACAGAGTAG
7286 TACTTTAGTAGTTA
66 TACTTTAGTAGTTA
* *
7300 TTATACAAAAGTCGTA-AGGGTTCATATATAGTGGCATTTTTCAACAAACGCCGCAATAGAGTAG
1 TTATACAAAAGCCGTATAGGGTTCATATATAGTGGCATTTTTCAACAAACGCCGCAACAGAGTAG
* *
7364 TACTTTAGCGACGTTT
66 TACTTTAG-TA-GTTA
* * * * *
7380 TTATACAAACGCCATAATATGTTTCAT-TATAGTGACATTTT
1 TTATACAAAAGCCGT-ATAGGGTTCATATATAGTGGCATTTT
7421 GTTGAGTTAA
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 51 0.50
79 15 0.15
80 15 0.15
81 14 0.14
82 7 0.07
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (79 bp):
TTATACAAAAGCCGTATAGGGTTCATATATAGTGGCATTTTTCAACAAACGCCGCAACAGAGTAG
TACTTTAGTAGTTA
Found at i:8102 original size:21 final size:21
Alignment explanation
Indices: 8078--8134 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
8068 ATGGACTAGG
8078 GGTATCGGTACCATCCAGGGA
1 GGTATCGGTACCATCCAGGGA
*
8099 GGTATTGGTACCATCCAGGGA
1 GGTATCGGTACCATCCAGGGA
*
8120 GGTATCGGTATCATC
1 GGTATCGGTACCATC
8135 TGAACATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (21 bp):
GGTATCGGTACCATCCAGGGA
Found at i:10323 original size:14 final size:13
Alignment explanation
Indices: 10283--10323 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
10273 ATGGGCAAAT
*
10283 TTTGAAAACTATG
1 TTTGAAAACAATG
10296 TTTGAAAACAATG
1 TTTGAAAACAATG
10309 TTTGAAAATCAATG
1 TTTGAAAA-CAATG
10323 T
1 T
10324 GTAGTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:10842 original size:23 final size:22
Alignment explanation
Indices: 10791--10842 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
10781 TACCCTTATA
10791 GGGGTATCGGTACCCATTCAAG
1 GGGGTATCGGTACCCATTCAAG
*
10813 GATGGTATCGGTACCCATTCAAAG
1 G-GGGTATCGGTACCCATTC-AAG
10837 GGGGTA
1 GGGGTA
10843 CGATACCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 1 0.04
23 21 0.81
24 4 0.15
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (22 bp):
GGGGTATCGGTACCCATTCAAG
Found at i:14667 original size:22 final size:21
Alignment explanation
Indices: 14625--14664 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
14615 AAGACTATTT
14625 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
14646 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
14665 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:15707 original size:45 final size:46
Alignment explanation
Indices: 15611--15727 Score: 157
Period size: 45 Copynumber: 2.5 Consensus size: 46
15601 TCCATGCACC
*
15611 AATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCG
1 AATGCATT-T-CATGCATCGATGCACTCAGAATATTTTCAAAACATCG
* **
15659 AATGCATTTGATGCATCGATGCAC-CAGGCTATTTTTC-AAACATCG
1 AATGCATTTCATGCATCGATGCACTCAGAATA-TTTTCAAAACATCG
15704 AATGCATTTCATGCATCGATGCAC
1 AATGCATTTCATGCATCGATGCAC
15728 ACTTGGTGCA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
45 35 0.56
46 19 0.30
47 1 0.02
48 8 0.13
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (46 bp):
AATGCATTTCATGCATCGATGCACTCAGAATATTTTCAAAACATCG
Found at i:21541 original size:20 final size:21
Alignment explanation
Indices: 21512--21567 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
21502 TTTGTGCTTC
*
21512 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
21532 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
21554 ATGCATCGATGCAT
1 ATGCATCGATGCAT
21568 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:22309 original size:21 final size:21
Alignment explanation
Indices: 22285--22348 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
22275 AAAACCGTCC
22285 TCCCGTTCCTCAACATCCTAA
1 TCCCGTTCCTCAACATCCTAA
** *
22306 TCCCGTTCCTCCTCAACCTAA
1 TCCCGTTCCTCAACATCCTAA
* *
22327 TCCTGATCCTCAAGC-TCCTAA
1 TCCCGTTCCTCAA-CATCCTAA
22348 T
1 T
22349 GGCTTATTGA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.22, C:0.42, G:0.06, T:0.30
Consensus pattern (21 bp):
TCCCGTTCCTCAACATCCTAA
Found at i:23175 original size:21 final size:21
Alignment explanation
Indices: 23149--23192 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
23139 ACTCCGGGAG
*
23149 CTAGTTCTTCTCGAGCTGCTC
1 CTAGTTCTTCTCGAGCTCCTC
*
23170 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCTCGAGCTCCTC
23191 CT
1 CT
23193 CCTCCTCCAG
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:0.07, C:0.36, G:0.16, T:0.41
Consensus pattern (21 bp):
CTAGTTCTTCTCGAGCTCCTC
Found at i:24377 original size:64 final size:65
Alignment explanation
Indices: 24199--24362 Score: 215
Period size: 65 Copynumber: 2.5 Consensus size: 65
24189 GAATTAATTG
* * ** *
24199 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* ** **
24264 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTC
24328 -
65 A
24328 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
24363 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:26970 original size:41 final size:41
Alignment explanation
Indices: 26878--27068 Score: 147
Period size: 41 Copynumber: 4.7 Consensus size: 41
26868 CGTTTTTTAT
* ** * *
26878 CAAACGCCGCAAAAGAC-TCCACTTTAGCGGCGTTTGTATA
1 CAAACGCCGCTAAAGACTTAGACTTTAGTGGTGTTTGTATA
* ** *
26918 GAAATTCCGCTAAAGACTTAGACTTTCGTGGTGTTTGTATA
1 CAAACGCCGCTAAAGACTTAGACTTTAGTGGTGTTTGTATA
* * * * *
26959 TAAACGTCGCTATAA-AC-TCGTTCTTTAGTGGCGTTTGTATA
1 CAAACGCCGCTA-AAGACTTAG-ACTTTAGTGGTGTTTGTATA
* * * * *
27000 CAAACGCCTCTATAGACTCATACTTTAGTGGTGTTTTTATA
1 CAAACGCCGCTAAAGACTTAGACTTTAGTGGTGTTTGTATA
*
27041 CAAACGCCGCTATAGACTT-GTACTTTAG
1 CAAACGCCGCTAAAGACTTAG-ACTTTAG
27069 CGATATTTTT
Statistics
Matches: 115, Mismatches: 30, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
40 16 0.14
41 97 0.84
42 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
CAAACGCCGCTAAAGACTTAGACTTTAGTGGTGTTTGTATA
Found at i:27046 original size:82 final size:82
Alignment explanation
Indices: 26898--27070 Score: 211
Period size: 82 Copynumber: 2.1 Consensus size: 82
26888 AAAAGACTCC
* ** * * *
26898 ACTTTAGCGGCGTTTGTATAGAAATTCCGCTAAAGACTTAGACTTTCGTGGTGTTTGTATATAAA
1 ACTTTAGCGGCGTTTGTATACAAACGCCGCTAAAGACTCAGACTTTAGTGGTGTTTGTATACAAA
*
26963 CGTCGCTATAAACTCGT
66 CGCCGCTATAAACTCGT
* * * * * *
26980 TCTTTAGTGGCGTTTGTATACAAACGCCTCTATAGACTCATACTTTAGTGGTGTTTTTATACAAA
1 ACTTTAGCGGCGTTTGTATACAAACGCCGCTAAAGACTCAGACTTTAGTGGTGTTTGTATACAAA
* *
27045 CGCCGCTATAGACTTGT
66 CGCCGCTATAAACTCGT
27062 ACTTTAGCG
1 ACTTTAGCG
27071 ATATTTTTGT
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (82 bp):
ACTTTAGCGGCGTTTGTATACAAACGCCGCTAAAGACTCAGACTTTAGTGGTGTTTGTATACAAA
CGCCGCTATAAACTCGT
Found at i:27119 original size:41 final size:41
Alignment explanation
Indices: 26981--27214 Score: 150
Period size: 41 Copynumber: 5.6 Consensus size: 41
26971 TAAACTCGTT
* * * * *
26981 CTTTAGTGGCGTTTGTATACAAACGCCTCTATAGACTCA--TA
1 CTTTAGTGGCGTTTTTGTATAAACGCCGCAATAG--TCATGTA
* * * * * *
27022 CTTTAGTGGTGTTTTTATACAAACGCCGCTATAGACTTGTA
1 CTTTAGTGGCGTTTTTGTATAAACGCCGCAATAGTCATGTA
* *** * *
27063 CTTTAGCGATATTTTTGT-TCAAATGTCGCAATAGTCATGTA
1 CTTTAGTGGCGTTTTTGTAT-AAACGCCGCAATAGTCATGTA
** * *
27104 CTTTAGTGGCGTTTTTGTAATAAACATCACAATAATCATGTA
1 CTTTAGTGGCGTTTTTGT-ATAAACGCCGCAATAGTCATGTA
* *
27146 ATTTAGTGGCATTTTTTGTAATAAACGCCGCAATAGTCATGTA
1 CTTTAGTGGC-GTTTTTGT-ATAAACGCCGCAATAGTCATGTA
* * *
27189 CCTTAGTGACGTTTTTATTATAAACG
1 CTTTAGTGGCGTTTTT-GTATAAACG
27215 TTGCGATTGT
Statistics
Matches: 152, Mismatches: 34, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
39 1 0.01
41 77 0.51
42 38 0.25
43 36 0.24
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (41 bp):
CTTTAGTGGCGTTTTTGTATAAACGCCGCAATAGTCATGTA
Found at i:27151 original size:42 final size:42
Alignment explanation
Indices: 27091--27213 Score: 147
Period size: 43 Copynumber: 2.9 Consensus size: 42
27081 TCAAATGTCG
*
27091 CAATAGTCATGTACTTTAGTGGCGTTTTTGTAATAAACATCA
1 CAATAGTCATGTACTTTAGTGGCGTTTTTGTAATAAACACCA
* * * * *
27133 CAATAATCATGTAATTTAGTGGCATTTTTTGTAATAAACGCCG
1 CAATAGTCATGTACTTTAGTGGC-GTTTTTGTAATAAACACCA
* * * *
27176 CAATAGTCATGTACCTTAGTGACGTTTTTATTATAAAC
1 CAATAGTCATGTACTTTAGTGGCGTTTTTGTAATAAAC
27214 GTTGCGATTG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 33 0.49
43 34 0.51
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (42 bp):
CAATAGTCATGTACTTTAGTGGCGTTTTTGTAATAAACACCA
Found at i:27180 original size:43 final size:42
Alignment explanation
Indices: 27089--27213 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 42
27079 GTTCAAATGT
* *
27089 CGCAATAGTCATGTACTTTAGTGGCGTTTTTGTAATAAACAT
1 CGCAATAGTCATGTAATTTAGTGGCGTTTTTGTAATAAACAC
* * * *
27131 CACAATAATCATGTAATTTAGTGGCATTTTTTGTAATAAACGC
1 CGCAATAGTCATGTAATTTAGTGGC-GTTTTTGTAATAAACAC
** * * *
27174 CGCAATAGTCATGTACCTTAGTGACGTTTTTATTATAAAC
1 CGCAATAGTCATGTAATTTAGTGGCGTTTTTGTAATAAAC
27214 GTTGCGATTG
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 34 0.50
43 34 0.50
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (42 bp):
CGCAATAGTCATGTAATTTAGTGGCGTTTTTGTAATAAACAC
Found at i:29118 original size:21 final size:21
Alignment explanation
Indices: 29092--29162 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
29082 TGATTTATTA
*
29092 TTATGGATTTCAAGTTGGTTG
1 TTATGGATTTCAAGTTTGTTG
29113 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTGTTG
29134 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTGTTG
29155 TTATGGAT
1 TTATGGAT
29163 GTCATGCTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.20, C:0.04, G:0.25, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTGTTG
Found at i:36851 original size:20 final size:20
Alignment explanation
Indices: 36826--36874 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
36816 TGAACTTGGC
36826 ATCGATACCAC-CCTGAGAGT
1 ATCGATACCACACCT-AGAGT
* *
36846 ATCGATACCTCACCTATAGT
1 ATCGATACCACACCTAGAGT
36866 ATCGATACC
1 ATCGATACC
36875 CCTTGTATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (20 bp):
ATCGATACCACACCTAGAGT
Found at i:38984 original size:30 final size:29
Alignment explanation
Indices: 38945--39003 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
38935 GAGAATTTAC
* *
38945 ATGAACTACGTGATTAAATGTATATGTGA
1 ATGAACTACGAGATTAAATGAATATGTGA
* *
38974 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTAAATGAATATGTGA
39004 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTAAATGAATATGTGA
Found at i:39261 original size:23 final size:23
Alignment explanation
Indices: 39234--39301 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
39224 CATTTTATAT
39234 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
39257 GGCACTTAGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
39280 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
39302 AGATGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:39738 original size:2 final size:2
Alignment explanation
Indices: 39731--39762 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39721 AAAGGAAATG
39731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39763 TTATGTTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46695 original size:42 final size:42
Alignment explanation
Indices: 46648--46737 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
46638 GTGCATGGCG
*
46648 GCATGGCAACGTGGCATGTGTCTGGGCGAGGTTGGAGTCTCT
1 GCATGGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCT
46690 GCATGGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCT
1 GCATGGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCT
46732 GCATGG
1 GCATGG
46738 TTGTGCATGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.14, C:0.19, G:0.42, T:0.24
Consensus pattern (42 bp):
GCATGGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCT
Found at i:46810 original size:29 final size:29
Alignment explanation
Indices: 46763--46846 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
46753 TGCAACGTGG
* *
46763 GTAGGTCGCCAGGGAATCCCAGCGACATT
1 GTAGGTCGCCAGAGAATCCCAACGACATT
* *
46792 GTAGGTCGCTAGAGCATCCCAACGACATT
1 GTAGGTCGCCAGAGAATCCCAACGACATT
*
46821 GTAGGTCGCCA-AGGGATCCCAACGAC
1 GTAGGTCGCCAGA-GAATCCCAACGAC
46847 CTATGCCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
28 1 0.02
29 47 0.98
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.17
Consensus pattern (29 bp):
GTAGGTCGCCAGAGAATCCCAACGACATT
Found at i:47159 original size:8 final size:9
Alignment explanation
Indices: 47129--47166 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
47119 GGTAAGTTTT
47129 TTTTAATTA
1 TTTTAATTA
47138 TTTTAATTA
1 TTTTAATTA
*
47147 GTTT-ATTA
1 TTTTAATTA
47155 TTTTAAATTA
1 TTTT-AATTA
47165 TT
1 TT
47167 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:47288 original size:28 final size:27
Alignment explanation
Indices: 47249--47301 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
47239 ATATTAAAAA
47249 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
47277 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
47302 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:47307 original size:27 final size:29
Alignment explanation
Indices: 47248--47312 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
47238 TATATTAAAA
47248 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
47277 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
47303 AAATAGTTAA
1 AAATAATTAA
47313 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:47451 original size:18 final size:18
Alignment explanation
Indices: 47428--47482 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
47418 AATAATTATT
47428 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
47446 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
47458 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
47475 TAAATTAG
1 TAAATTAG
47483 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:47537 original size:21 final size:20
Alignment explanation
Indices: 47507--47550 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
47497 ATTAGTTAAT
47507 TATTTTGTTAGTTTAAGTTA
1 TATTTTGTTAGTTTAAGTTA
47527 TATTATTGTTAGTTTAAGTTA
1 TATT-TTGTTAGTTTAAGTTA
47548 TAT
1 TAT
47551 CATATAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (20 bp):
TATTTTGTTAGTTTAAGTTA
Found at i:47797 original size:30 final size:30
Alignment explanation
Indices: 47729--47832 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 30
47719 ATTAGTTAAT
* *
47729 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAATTAT-ATTAAAGAA
*
47760 TCA-TTTATTAGTTTAATTTATATTAAAGAA
1 T-AGTTTATTAGTTTAAATTATATTAAAGAA
*
47790 TAGTTTATTAG-TTAACGTTATATTAAAGAA
1 TAGTTTATTAGTTTAA-ATTATATTAAAGAA
47820 TAGTTTATTAGTT
1 TAGTTTATTAGTT
47833 GTTTAAGGGG
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
29 11 0.17
30 42 0.66
31 10 0.16
32 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAATTATATTAAAGAA
Found at i:47906 original size:16 final size:16
Alignment explanation
Indices: 47874--47920 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
47864 TTTAAAAAGT
47874 TTAGTTTATTAGT-TTA
1 TTAGTTTATTA-TATTA
*
47890 TTAGTTTAATATATTA
1 TTAGTTTATTATATTA
*
47906 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
47921 AATTTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:49152 original size:22 final size:21
Alignment explanation
Indices: 49107--49152 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
49097 GTTATTTTTA
* *
49107 ATTATTATTTAAATTAACTAT
1 ATTATTATTTAAATAAAATAT
*
49128 ATTATTGATTTAAATAAAATTT
1 ATTATT-ATTTAAATAAAATAT
49150 ATT
1 ATT
49153 GTTTTTGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTATTATTTAAATAAAATAT
Found at i:50166 original size:14 final size:14
Alignment explanation
Indices: 50147--50194 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
50137 TTCAAGTCGT
50147 AAATCATTACTATC
1 AAATCATTACTATC
50161 AAATCATTAC--T-
1 AAATCATTACTATC
* *
50172 AAATTATTAATATC
1 AAATCATTACTATC
50186 AAATCATTA
1 AAATCATTA
50195 AATATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 8 0.29
12 1 0.04
13 1 0.04
14 18 0.64
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:50174 original size:25 final size:25
Alignment explanation
Indices: 50146--50194 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
50136 GTTCAAGTCG
*
50146 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
*
50171 TAAATTATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
50195 AATATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:50210 original size:21 final size:22
Alignment explanation
Indices: 50146--50204 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 22
50136 GTTCAAGTCG
* *
50146 TAAATCATTACTATCAAATCATT
1 TAAATTATTAATATCAAATCA-T
50169 ACTAAATTATTAATATCAAATCAT
1 --TAAATTATTAATATCAAATCAT
50193 TAAA-TATTAATA
1 TAAATTATTAATA
50205 ATAAATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 8 0.25
22 4 0.12
24 1 0.03
25 19 0.59
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTATTAATATCAAATCAT
Found at i:50215 original size:21 final size:22
Alignment explanation
Indices: 50166--50215 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
50156 CTATCAAATC
*
50166 ATTACTAAATTATTAATATCAA
1 ATTATTAAATTATTAATATCAA
*
50188 ATCATTAAA-TATTAATAAT-AA
1 ATTATTAAATTATTAAT-ATCAA
50209 ATTATTA
1 ATTATTA
50216 TTACTAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTATTAAATTATTAATATCAA
Found at i:50227 original size:59 final size:60
Alignment explanation
Indices: 50162--50290 Score: 208
Period size: 58 Copynumber: 2.2 Consensus size: 60
50152 ATTACTATCA
* *
50162 AATCATTACTAAATTATTAATATCAAATCATTAAATATTAATAATAA-ATTATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATATTATTATTACT
* *
50221 AATCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATATTATTATTACT
50280 AATCATTACTA
1 AATCATTACTA
50291 TCAAATCATT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
58 33 0.52
59 31 0.48
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (60 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATATTATTATTACT
Found at i:50230 original size:10 final size:10
Alignment explanation
Indices: 50215--50241 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
50205 ATAAATTATT
50215 ATTACTAATC
1 ATTACTAATC
50225 ATTACTAATC
1 ATTACTAATC
50235 ATTACTA
1 ATTACTA
50242 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:50281 original size:49 final size:49
Alignment explanation
Indices: 50225--50388 Score: 310
Period size: 49 Copynumber: 3.3 Consensus size: 49
50215 ATTACTAATC
*
50225 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
50274 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
50323 ATTACTAATCATTACTATCAAATTATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
50372 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
50389 ATCATTATTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 113 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:50385 original size:10 final size:10
Alignment explanation
Indices: 50372--50408 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
50362 TAATTTCATT
50372 ATTACTAATC
1 ATTACTAATC
50382 ATTACTAATC
1 ATTACTAATC
*
50392 ATTATTAATC
1 ATTACTAATC
50402 ATTACTA
1 ATTACTA
50409 TCAAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (10 bp):
ATTACTAATC
Found at i:50405 original size:69 final size:69
Alignment explanation
Indices: 50323--50457 Score: 252
Period size: 69 Copynumber: 2.0 Consensus size: 69
50313 TAATTTCATT
*
50323 ATTACTAATCATTACTATCAAATTATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
50388 AATC
66 AATC
*
50392 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
50457 A
66 A
50458 TCAAATCATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (69 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
AATC
Found at i:50406 original size:177 final size:173
Alignment explanation
Indices: 50244--50926 Score: 765
Period size: 177 Copynumber: 3.9 Consensus size: 173
50234 CATTACTATC
* * *
50244 AAATCATTAAAAATTAATAATAATT-TTATTATTACT-AATCATTACTATCAAATCATTAAAAAT
1 AAATCAATAAAAATT--TAATAATTATAATCATTACTAAATCATTACTATCAAATCATTAAAAAT
50307 TAATAATAATTTCATTATTACTAATCATTACT-ATCA-A-AT-T-ATTAAAAATTAATAATAATT
64 TAATAATAATTTCATTATTACTAATCATTACTAATCATATATATCATTAAAAATTAATAATAATT
50367 TCATTATTACTAATCATTACT-AATCATTA-T-T--AATCATTACTA
129 TCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTA--A
* * *
50409 TCAAATCATTAAAAATTAATAATAATT-TCATTATTACT-AATCATTACTATCAAATCATT-AAA
1 --AAATCAATAAAAATT--TAATAATTATAATCATTACTAAATCATTACTATCAAATCATTAAAA
*
50471 TTTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAA
62 ATTAATAATAATTTCATTATTACTAATCATTACT-AATCA-TA-TAT---ATCATTAAAAATTAA
*
50536 TAATAATTTCATTATTACTAATCATTACTAAATCATTATTATCAAATCATTAA
121 TAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAA
* ** * * *
50589 AAATTAATAATGATTTCATTATTACTAATCATGACTAAATCATTACTATCAAATCATTAAAAA-T
1 AAATCAATAAAAATTTAATAATTA-TAATCATTACTAAATCATTACTATCAAATCATTAAAAATT
50653 AATAAT--TTTCATTATTACTAATCATTACTAAATCATTATTATCAAATCATTAAAAATTAATAA
65 AATAATAATTTCATTATTACTAATCATTACT-AATCA-TA-TAT---ATCATTAAAAATTAATAA
*
50716 TGATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAA
124 TAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAA
* * * * * *
50766 AAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATT
1 AAATCAATAAAAATTTAATAATTA-TAATCATTACTAAATCATTACTATCAAATCATTAAAAATT
*
50831 AATAATAATTTCATTATTACTAATCATTACT-ATCAAATTACTATCAAATCATTAAATATTAATA
65 AATAATAATTTCATTATTACTAATCATTACTAATC--A-TA-TAT---ATCATTAAAAATTAATA
*
50895 ATAATTTCATCATTACTAATCATTACTAAATC
123 ATAATTTCATTATTACTAATCATTACTAAATC
50927 TTATAAATAC
Statistics
Matches: 468, Mismatches: 23, Indels: 37
0.89 0.04 0.07
Matches are distributed among these distances:
166 36 0.08
167 56 0.12
168 4 0.01
170 1 0.00
172 2 0.00
176 7 0.01
177 204 0.44
178 37 0.08
179 29 0.06
180 84 0.18
182 8 0.02
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (173 bp):
AAATCAATAAAAATTTAATAATTATAATCATTACTAAATCATTACTATCAAATCATTAAAAATTA
ATAATAATTTCATTATTACTAATCATTACTAATCATATATATCATTAAAAATTAATAATAATTTC
ATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAA
Found at i:50592 original size:24 final size:24
Alignment explanation
Indices: 50544--50592 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
50534 AATAATAATT
* *
50544 TCATTATTACTAATCATTACTAAA
1 TCATTATTACAAATCATTACAAAA
50568 TCATTATTATCAAATCATTA-AAAA
1 TCATTATTA-CAAATCATTACAAAA
50592 T
1 T
50593 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (24 bp):
TCATTATTACAAATCATTACAAAA
Found at i:50639 original size:60 final size:60
Alignment explanation
Indices: 50634--50926 Score: 479
Period size: 60 Copynumber: 4.9 Consensus size: 60
50624 TAAATCATTA
50634 CTATCAAATCATTAAAAA-TAATAAT--TTTCATTATTACTAATCATTACTAAATCATTA
1 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
* *
50691 TTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTACTAAATCATTA
1 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
50751 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
1 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
* *
50811 ATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT--ATCAAATTA
1 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC--ATTA
* *
50871 CTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTAAATC
1 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
50927 TTATAAATAC
Statistics
Matches: 222, Mismatches: 7, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
57 17 0.08
58 10 0.05
60 192 0.86
62 3 0.01
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
Found at i:50709 original size:24 final size:24
Alignment explanation
Indices: 50661--50709 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
50651 ATAATAATTT
* *
50661 TCATTATTACTAATCATTACTAAA
1 TCATTATTACAAATCATTACAAAA
50685 TCATTATTATCAAATCATTA-AAAA
1 TCATTATTA-CAAATCATTACAAAA
50709 T
1 T
50710 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (24 bp):
TCATTATTACAAATCATTACAAAA
Found at i:50724 original size:237 final size:236
Alignment explanation
Indices: 50162--50923 Score: 991
Period size: 237 Copynumber: 3.3 Consensus size: 236
50152 ATTACTATCA
* * * *
50162 AATCATTACTAAATTATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCAT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATAATAATAAT-ATTTATTATTACTAATCAT
50227 TACTAATCATTACTATCAAATCATTAAAAATTAATAATA----ATT-TTA-T--T-ATTACT-AA
65 TACTAATCATTACTATCAAATCATTAAAAATTAATAATATTTCATTATTACTAATCATTACTAAA
50282 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT--ATCA--
130 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATT
50343 A--AT----T-ATTAAAAATTAATAATAATTTCATTATTACT
195 ATTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
50378 AATCATTACTAATCATTATTAATCATTACTATCAAATCATTAAA-AATTAATAATA---A-T-TT
1 AATCA-T--T-A-C--TA--AATCATTACTATCAAATCATTAAATAA-TAATAATATTTATTATT
* *
50437 -C--ATTATTACTAATCATTACTATCAAATCATT-AAATTTAATAATAATTTCATTATTACTAAT
56 ACTAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT-ATTTCATTATTACTAAT
50498 CATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
120 CATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
*
50563 CTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACT
185 CTAAATCATTATTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
50615 AATCATGACTAAATCATTACTATCAAATCATTAAA-AATAATAAT-TTTCATTATTACTAATCAT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATAATAATAATATTT-ATTATTACTAATCAT
*
50678 TACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTACTA
65 TACT-AATCATTACTATCAAATCATTAAAAATTAATAAT-ATTTCATTATTACTAATCATTACTA
50743 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
128 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
* *
50808 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
193 TTATTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
50852 AATCATTACT--ATCAAATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAAT
1 AATCATTACTAAATC--ATTACTATCAAATCATTAAATAATAATAAT-ATTT-ATTATTACTAAT
50915 CATTACTAA
62 CATTACTAA
50924 ATCTTATAAA
Statistics
Matches: 481, Mismatches: 17, Indels: 73
0.84 0.03 0.13
Matches are distributed among these distances:
215 11 0.02
216 35 0.07
217 1 0.00
218 1 0.00
219 3 0.01
220 5 0.01
221 5 0.01
222 1 0.00
223 2 0.00
224 3 0.01
225 35 0.07
226 59 0.12
227 7 0.01
228 30 0.06
230 4 0.01
231 1 0.00
232 5 0.01
233 2 0.00
235 11 0.02
236 22 0.05
237 206 0.43
238 8 0.02
239 2 0.00
240 22 0.05
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (236 bp):
AATCATTACTAAATCATTACTATCAAATCATTAAATAATAATAATATTTATTATTACTAATCATT
ACTAATCATTACTATCAAATCATTAAAAATTAATAATATTTCATTATTACTAATCATTACTAAAT
CATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
TTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:50857 original size:35 final size:35
Alignment explanation
Indices: 50817--50919 Score: 91
Period size: 35 Copynumber: 3.2 Consensus size: 35
50807 ATTAATATCA
50817 AATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTAAATATTAATAATAATTTCATTATTACT
* * * *
50852 AATCA-T---TACT-ATCA-AA-TT-ACTA-T-CA
1 AATCATTAAATATTAATAATAATTTCATTATTACT
*
50877 AATCATTAAATATTAATAATAATTTCATCATTACT
1 AATCATTAAATATTAATAATAATTTCATTATTACT
50912 AATCATTA
1 AATCATTA
50920 CTAAATCTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 20
0.63 0.12 0.26
Matches are distributed among these distances:
25 6 0.12
26 2 0.04
27 3 0.06
28 2 0.04
29 5 0.10
30 6 0.12
31 5 0.10
32 2 0.04
33 2 0.04
34 2 0.04
35 14 0.29
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.42
Consensus pattern (35 bp):
AATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:54027 original size:28 final size:28
Alignment explanation
Indices: 53996--54049 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
53986 ATAATCTAAT
*
53996 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
54024 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
54050 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:54056 original size:28 final size:28
Alignment explanation
Indices: 53992--54056 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
53982 TTATATAATC
*
53992 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
54020 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
54048 TAATTTATA
1 TAATATATA
54057 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:54059 original size:21 final size:21
Alignment explanation
Indices: 54026--54074 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
54016 TTAATATAAT
54026 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
54047 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
54068 ATTAACT
1 A-TAACT
54075 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:54812 original size:29 final size:29
Alignment explanation
Indices: 54713--54847 Score: 126
Period size: 29 Copynumber: 4.5 Consensus size: 29
54703 GGACGCCGGC
* *
54713 GTGCATGGCGACCTATAAGGTCGCTGGGC
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
* * *
54742 GTACATGGCGACCTACCATCTTGGTCGCCGGGA
1 GTGCATGGCGACCTA-CA---AGGTCGCTGGGA
* *
54775 TTGCTTGGCGACCTACAAGGTCGCTGGGA
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
*** *
54804 GTGCATGGCGACCTTGTAGGTCGCTTGGA
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
*
54833 GTGCTTGGCGACCTA
1 GTGCATGGCGACCTA
54848 TGGTTGGGTT
Statistics
Matches: 84, Mismatches: 18, Indels: 8
0.76 0.16 0.07
Matches are distributed among these distances:
29 60 0.71
30 1 0.01
32 2 0.02
33 21 0.25
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (29 bp):
GTGCATGGCGACCTACAAGGTCGCTGGGA
Found at i:54894 original size:12 final size:12
Alignment explanation
Indices: 54877--54901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54867 CCATGCACGA
54877 CACGATCCTCGT
1 CACGATCCTCGT
54889 CACGATCCTCGT
1 CACGATCCTCGT
54901 C
1 C
54902 GGAAGCAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.44, G:0.16, T:0.24
Consensus pattern (12 bp):
CACGATCCTCGT
Found at i:60910 original size:3 final size:3
Alignment explanation
Indices: 60902--60958 Score: 87
Period size: 3 Copynumber: 18.3 Consensus size: 3
60892 TCGGGTCTTG
*
60902 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
60948 TAAA TAA TAA T
1 T-AA TAA TAA T
60959 CTACTATATA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 45 0.90
4 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:60966 original size:20 final size:19
Alignment explanation
Indices: 60904--60966 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
60894 GGGTCTTGTA
*
60904 ATAATAATAATAATAATAAT
1 ATAATAATAATAAT-ATACT
*
60924 AATAATAATAATAATATATT
1 -ATAATAATAATAATATACT
*
60944 ATAATAAATAATAATCTACT
1 ATAAT-AATAATAATATACT
60964 ATA
1 ATA
60967 TATTATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.13
20 19 0.50
21 14 0.37
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAATAATAATAATATACT
Found at i:61124 original size:35 final size:36
Alignment explanation
Indices: 61078--61390 Score: 339
Period size: 36 Copynumber: 8.6 Consensus size: 36
61068 TCTGATCTTG
* * * *
61078 CTTCACTACTCTTCCATGAAGGCT-AGATTGAAT-TA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATG-ATCTA
* *
61113 CTTCACTACTCTTCCATGAAGGATGAAAATGAT-TAA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATCT-A
*
61149 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATCGA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATCTA
*
61185 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATCGA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATCTA
* * *
61221 CGTCACTACTGTTCCGTGAAGGTTGAAAATGATCGA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATCTA
* ** * *
61257 CTTCACTACTCTTCCATGAAGGTTG-ACTTGTTTTA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATCTA
** *
61292 CTTCACTACTCTTCCGTGAAGGTTG-ACTTGTTCTA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATCTA
* *
61327 CTTCACTACTCTTCCGTGAAGGTTGAAATTACGTTACTTTA
1 CTTCACTACTCTTCCGTGAAGGTTGAAA--A--TGA-TCTA
61368 CTTCACTACTCTTCCGTGAAGGT
1 CTTCACTACTCTTCCGTGAAGGT
61391 CAGATTTGAG
Statistics
Matches: 246, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
35 89 0.36
36 130 0.53
40 1 0.00
41 26 0.11
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.35
Consensus pattern (36 bp):
CTTCACTACTCTTCCGTGAAGGTTGAAAATGATCTA
Found at i:61505 original size:20 final size:20
Alignment explanation
Indices: 61482--61540 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
61472 AGACTAATAG
61482 ATGACCCGAAGGTTTTACAA
1 ATGACCCGAAGGTTTTACAA
*
61502 ATGACCCGGAGGTTTTACAA
1 ATGACCCGAAGGTTTTACAA
*
61522 ATGACCCAAAGGTTTTACA
1 ATGACCCGAAGGTTTTACA
61541 GCTTTGTGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
ATGACCCGAAGGTTTTACAA
Done.