Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008237.1 Hibiscus syriacus cultivar Beakdansim tig00110883_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: 70346
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:10215 original size:105 final size:105
Alignment explanation
Indices: 10033--10489 Score: 688
Period size: 105 Copynumber: 4.4 Consensus size: 105
10023 AGGTTTTACC
10033 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
10098 ACGAAGGGACCGCTGGTTGTCTACAAGCGTTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
10138 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
10203 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
10243 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCGACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
10308 ACGAAGGGACCGCTGGTTGTCAAC-AACA--TCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
10345 CAGAGCC-ATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
10409 ACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* ** *
10450 CAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
10490 GGAACAATAC
Statistics
Matches: 319, Mismatches: 28, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
101 75 0.24
102 18 0.06
103 1 0.00
104 4 0.01
105 193 0.61
106 28 0.09
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:13118 original size:39 final size:38
Alignment explanation
Indices: 13045--13449 Score: 259
Period size: 39 Copynumber: 10.6 Consensus size: 38
13035 ATATACATAT
* *
13045 ATATCTATATATTATATAG--TTTACAAATGGTTTTTGAAA
1 ATAT-TATATAATATATAGTTTTTA-AAAT-ATTTTTGAAA
*
13084 ATATGTATATAATATATAATTTTTAAAATATTTTTGAAA
1 ATAT-TATATAATATATAGTTTTTAAAATATTTTTGAAA
* *
13123 AAATATATATATTATATAGTTTTTAAAAATATTTTTG-AA
1 ATAT-TATATAATATATAGTTTTT-AAAATATTTTTGAAA
* * * *
13162 A-ATTATATATTGTATAGTTTTTAAAACATTTTAGAATATATATA
1 ATATTATATAATATATAGTTTTTAAAATATTTT----T-GA-A-A
**
13206 ATATATATATATATATATAGTTTTTAAAATCATTTTGAAA
1 ATAT-TATATA-ATATATAGTTTTTAAAATATTTTTGAAA
* *
13246 A-A-TATATAATACATAGTTTTTTGAAATCATTTTTGAAA
1 ATATTATATAATATATAG-TTTTTAAAAT-ATTTTTGAAA
* * *
13284 ACA-TATAT--TATATAGTTTTGAAAATATTTTTTAAA
1 ATATTATATAATATATAGTTTTTAAAATATTTTTGAAA
* *
13319 ATA-TATATAATATATAGGTTTTGAAAACATTTTTG-AA
1 ATATTATATAATATATA-GTTTTTAAAATATTTTTGAAA
* * * *
13356 A-ACT-TAT--TATATAGTTTTGAAAACATTTTCGAAA
1 ATATTATATAATATATAGTTTTTAAAATATTTTTGAAA
* * * * *
13390 ACATTTATATATTTTATAATTTTT-AAATGTTTTTGAAA
1 ATA-TTATATAATATATAGTTTTTAAAATATTTTTGAAA
13428 ACT-TATATATAATATATAGTTT
1 A-TAT-TATATAATATATAGTTT
13450 ATATTATAAT
Statistics
Matches: 297, Mismatches: 40, Indels: 59
0.75 0.10 0.15
Matches are distributed among these distances:
33 17 0.06
34 9 0.03
35 17 0.06
36 29 0.10
37 53 0.18
38 53 0.18
39 64 0.22
40 19 0.06
41 5 0.02
42 1 0.00
43 2 0.01
44 2 0.01
45 2 0.01
46 6 0.02
47 18 0.06
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (38 bp):
ATATTATATAATATATAGTTTTTAAAATATTTTTGAAA
Found at i:13215 original size:46 final size:48
Alignment explanation
Indices: 13165--13256 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
13155 TTTTGAAAAT
* *
13165 TATATAT-TGTATAGTTTTTAAAA-CATTTT-AGAATATATATAATATA
1 TATATATATATATAGTTTTTAAAATCATTTTGA-AAAATATATAATATA
13211 TATATATATATATAGTTTTTAAAATCATTTTGAAAAATATATAATA
1 TATATATATATATAGTTTTTAAAATCATTTTGAAAAATATATAATA
13257 CATAGTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
46 7 0.17
47 15 0.37
48 18 0.44
49 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (48 bp):
TATATATATATATAGTTTTTAAAATCATTTTGAAAAATATATAATATA
Found at i:13298 original size:120 final size:123
Alignment explanation
Indices: 13083--13334 Score: 336
Period size: 122 Copynumber: 2.1 Consensus size: 123
13073 GGTTTTTGAA
* *
13083 AATATGTATATAATATATAATTTTTAAAATATTTTTGAAAAAATATATATATTATATAGTTTTTA
1 AATATATATATAATATATAATTTTTAAAATATTTTTGAAAAAATATATATATTACATAGTTTTTA
* * * *
13148 AAAATATTTTTGAAAATTATATATTGTATAGTTTTTAAAACA-TTTTAGAATATATAT
66 AAAATATTTTTGAAAATCATATATTATATAGTTTTGAAAACATTTTTAAAATATATAT
*
13205 AATATATATATATATATATAGTTTTTAAAATCA-TTTTG-AAAAATATATA-A-TACATAGTTTT
1 AATATATATATA-ATATATAATTTTTAAAAT-ATTTTTGAAAAAATATATATATTACATAGTTTT
** *
13266 TTGAAATCATTTTTGAAAA-CATATATTATATAGTTTTGAAAATATTTTTTAAAATATATAT
64 TAAAAAT-ATTTTTGAAAATCATATATTATATAGTTTTGAAAACA-TTTTTAAAATATATAT
13327 AATATATA
1 AATATATA
13335 GGTTTTGAAA
Statistics
Matches: 115, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
120 36 0.31
121 12 0.10
122 44 0.38
123 22 0.19
124 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (123 bp):
AATATATATATAATATATAATTTTTAAAATATTTTTGAAAAAATATATATATTACATAGTTTTTA
AAAATATTTTTGAAAATCATATATTATATAGTTTTGAAAACATTTTTAAAATATATAT
Found at i:13302 original size:73 final size:73
Alignment explanation
Indices: 13212--13390 Score: 242
Period size: 73 Copynumber: 2.5 Consensus size: 73
13202 TATAATATAT
* * *
13212 ATATATATATATAGTTTTTAAAATCATTTTGAAAA-ATATATAATACATAGTTTTTTGAAATCAT
1 ATATAT-TATATAGTTTTGAAAATCATTTTGAAAATATATATAATACATAG-GTTTTGAAAACAT
13276 TTTTGAAAAC
64 TTTTGAAAAC
* *
13286 ATATATTATATAGTTTTGAAAAT-ATTTTTTAAAATATATATAATATATAGGTTTTGAAAACATT
1 ATATATTATATAGTTTTGAAAATCA-TTTTGAAAATATATATAATACATAGGTTTTGAAAACATT
13350 TTTGAAAAC
65 TTTGAAAAC
13359 -T-TATTATATAGTTTTGAAAA-CATTTTCGAAAA
1 ATATATTATATAGTTTTGAAAATCATTTT-GAAAA
13391 CATTTATATA
Statistics
Matches: 95, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
70 4 0.04
71 24 0.25
72 2 0.02
73 45 0.47
74 20 0.21
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (73 bp):
ATATATTATATAGTTTTGAAAATCATTTTGAAAATATATATAATACATAGGTTTTGAAAACATTT
TTGAAAAC
Found at i:13354 original size:12 final size:12
Alignment explanation
Indices: 13337--13395 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
13327 AATATATAGG
13337 TTTTGAAAACAT
1 TTTTGAAAACAT
13349 TTTTGAAAAC-T
1 TTTTGAAAACAT
* * * *
13360 TATT--ATATAG
1 TTTTGAAAACAT
13370 TTTTGAAAACAT
1 TTTTGAAAACAT
*
13382 TTTCGAAAACAT
1 TTTTGAAAACAT
13394 TT
1 TT
13396 ATATATTTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
9 2 0.06
10 3 0.09
11 4 0.11
12 26 0.74
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:13423 original size:71 final size:71
Alignment explanation
Indices: 13219--13438 Score: 225
Period size: 73 Copynumber: 3.1 Consensus size: 71
13209 TATATATATA
* * * *
13219 TATATAGTTTTTAAAATCATTTTG-AAAA-ATATATAATACATAGTTTTTTGAAATCATTTTTGA
1 TATATAGTTTTGAAAA-CATTTTGAAAAATATATATAATATATAG-ATTTTGAAAACATTTTTGA
13282 AAACATATAT
64 AAAC-T-TAT
* ** *
13292 TATATAGTTTTGAAAATATTTTTTAAAATATATATAATATATAGGTTTTGAAAACATTTTTGAAA
1 TATATAGTTTTGAAAACATTTTGAAAAATATATATAATATATAGATTTTGAAAACATTTTTGAAA
13357 ACTTAT
66 ACTTAT
* * * * **
13363 TATATAGTTTTGAAAACATTTTCGAAAACATTTATATATTTTATA-ATTTT-TAAATGTTTTTGA
1 TATATAGTTTTGAAAACATTTT-GAAAA-ATATATATAATATATAGATTTTGAAAACATTTTTGA
13426 AAACTTA-
64 AAACTTAT
13433 TATATA
1 TATATA
13439 ATATATAGTT
Statistics
Matches: 127, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
70 6 0.05
71 41 0.32
72 13 0.10
73 53 0.42
74 14 0.11
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (71 bp):
TATATAGTTTTGAAAACATTTTGAAAAATATATATAATATATAGATTTTGAAAACATTTTTGAAA
ACTTAT
Found at i:14611 original size:19 final size:18
Alignment explanation
Indices: 14579--14618 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
14569 TATTTGTTTA
*
14579 TTTGTTTTTTATTTCATT
1 TTTGTTTTTCATTTCATT
14597 TTTGTTATTTCATTTCATT
1 TTTGTT-TTTCATTTCATT
14616 TTT
1 TTT
14619 ATTGTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTGTTTTTCATTTCATT
Found at i:14739 original size:8 final size:8
Alignment explanation
Indices: 14721--14785 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
14711 TTAAAAAAAC
14721 TTTTTCA-
1 TTTTTCAT
14728 TTTTTCAT
1 TTTTTCAT
14736 TTTTT-ACT
1 TTTTTCA-T
14744 TTTTTCA-
1 TTTTTCAT
*
14751 TTTATC-T
1 TTTTTCAT
14758 TTTTT-ATTT
1 TTTTTCA--T
14767 TTTTTCAT
1 TTTTTCAT
*
14775 TTTTTCCT
1 TTTTTCAT
14783 TTT
1 TTT
14786 ATTATTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
7 17 0.36
8 22 0.47
9 7 0.15
10 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:14751 original size:23 final size:23
Alignment explanation
Indices: 14721--14810 Score: 83
Period size: 23 Copynumber: 3.7 Consensus size: 23
14711 TTAAAAAAAC
14721 TTTTTCATTTTTCATTTTTTA-CT
1 TTTTTCATTTTTC-TTTTTTATCT
* *
14744 TTTTTCATTTATCTTTTTTATTT
1 TTTTTCATTTTTCTTTTTTATCT
*
14767 TTTTTCATTTTTTCCTTTTATTATTATT
1 TTTTTCA-TTTTT-CTTTT-TTA-T-CT
*
14795 TTTTTCCTTTTTCTTT
1 TTTTTCATTTTTCTTT
14811 CTCCTTTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
22 7 0.12
23 20 0.35
24 4 0.07
25 5 0.09
26 7 0.12
27 6 0.11
28 8 0.14
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTCATTTTTCTTTTTTATCT
Found at i:14857 original size:10 final size:10
Alignment explanation
Indices: 14840--14890 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
14830 TTATTTGGTG
*
14840 TATATATGTA
1 TATATATATA
* *
14850 TGTATATGTA
1 TATATATATA
14860 TATATATATA
1 TATATATATA
14870 TATATATATA
1 TATATATATA
14880 TATATATATA
1 TATATATATA
14890 T
1 T
14891 TATTTTACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (10 bp):
TATATATATA
Found at i:14859 original size:6 final size:6
Alignment explanation
Indices: 14840--14890 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
14830 TTATTTGGTG
* * *
14840 TATATA TGTATG TATATG TATATA TATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
14888 TAT
1 TAT
14891 TATTTTACTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:14865 original size:4 final size:4
Alignment explanation
Indices: 14840--14890 Score: 75
Period size: 4 Copynumber: 12.8 Consensus size: 4
14830 TTATTTGGTG
* * *
14840 TATA TATG TATG TATA TGTA TATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
14888 TAT
1 TAT
14891 TATTTTACTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:15481 original size:19 final size:19
Alignment explanation
Indices: 15459--15496 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
15449 ATATTTTTAG
15459 AAATTTAAAATAAT-TAATT
1 AAATTT-AAATAATATAATT
*
15478 AAATTTTAATAATATAATT
1 AAATTTAAATAATATAATT
15497 TTTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTTAAATAATATAATT
Found at i:15938 original size:21 final size:21
Alignment explanation
Indices: 15914--15953 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
15904 ATCGTCAAAG
* *
15914 TGTACTAACATGTCATCATAA
1 TGTAATAACATATCATCATAA
*
15935 TGTAATGACATATCATCAT
1 TGTAATAACATATCATCAT
15954 TGGAAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (21 bp):
TGTAATAACATATCATCATAA
Found at i:19484 original size:2 final size:2
Alignment explanation
Indices: 19477--19517 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
19467 TTCATATACT
19477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19517 T
1 T
19518 TTAATCATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21043 original size:21 final size:21
Alignment explanation
Indices: 21015--21062 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
21005 TCTTAAATGC
*
21015 AATAAAATATTTTAAATACAAA
1 AATAAATTATTTTAAA-ACAAA
* *
21037 AATAAATTATTTTTAAACAAT
1 AATAAATTATTTTAAAACAAA
21058 AATAA
1 AATAA
21063 TTAGTTTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAAATTATTTTAAAACAAA
Found at i:21794 original size:168 final size:164
Alignment explanation
Indices: 21491--21822 Score: 612
Period size: 168 Copynumber: 2.0 Consensus size: 164
21481 AATATAAAAA
21491 ATAGATATCGTTATAATAGAATAAAATATACAAAAATAAGATAAACTCATCATTATGTGTTAAGC
1 ATAGATATCGTTATAATAGAATAAAATATACAAAAATAAGATAAACTCATCATTATGTGTTAAGC
21556 TAACAATATCAATTTTTATTTTTTTTTTCTCAAAAAAATTTTTAGGAATGTTTGTAGTCTCTTTA
66 TAACAATATCAATTTTTATTTTTTTTTTCTCAAAAAAATTTTTAGGAATGTTTGTAGTCTCTTTA
21621 TTATCTTACAATTTTAGATTTC-TTTTTCTATTT
131 TTATCTTACAATTTTAGATTTCTTTTTTCTATTT
21654 ATAGAATATCGTTATAATAGAATAAAATATACAAAAATAAGATAAACTCATCAATTATCGTGTCT
1 ATAG-ATATCGTTATAATAGAATAAAATATACAAAAATAAGATAAACTCATC-ATTAT-GTGT-T
21719 AAGCTAACAATATCAATTTTTATTTTTATTTTTCTCAAAAAAATTTTTAGGAATGTTTGTAGTCT
62 AAGCTAACAATATCAATTTTTATTTTT-TTTTTCTCAAAAAAATTTTTAGGAATGTTTGTAGTCT
21784 CTTTATTATCTTACAATTTTAGATTTCTTTTTTCTATTT
126 CTTTATTATCTTACAATTTTAGATTTCTTTTTTCTATTT
21823 TAATTTGTCA
Statistics
Matches: 163, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
163 4 0.02
164 47 0.29
165 5 0.03
166 4 0.02
167 28 0.17
168 64 0.39
169 11 0.07
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.45
Consensus pattern (164 bp):
ATAGATATCGTTATAATAGAATAAAATATACAAAAATAAGATAAACTCATCATTATGTGTTAAGC
TAACAATATCAATTTTTATTTTTTTTTTCTCAAAAAAATTTTTAGGAATGTTTGTAGTCTCTTTA
TTATCTTACAATTTTAGATTTCTTTTTTCTATTT
Found at i:22294 original size:58 final size:58
Alignment explanation
Indices: 22204--22320 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
22194 CACTAATGTT
22204 ATCGACTTGCAATAAAATGGTCACTCGATGTTAATAGTCGTTAATCTCGATAACAAAA
1 ATCGACTTGCAATAAAATGGTCACTCGATGTTAATAGTCGTTAATCTCGATAACAAAA
22262 ATCGACTTGCAATAAAATGGTCACTCGATGTTAATAGTCGTTAATCTCGATAACAAAA
1 ATCGACTTGCAATAAAATGGTCACTCGATGTTAATAGTCGTTAATCTCGATAACAAAA
22320 A
1 A
22321 ACTGAGATGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (58 bp):
ATCGACTTGCAATAAAATGGTCACTCGATGTTAATAGTCGTTAATCTCGATAACAAAA
Found at i:22789 original size:2 final size:2
Alignment explanation
Indices: 22782--22830 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
22772 ATTACAAATT
22782 TA TA TA TA -A TA TA TA TA TA TA TA TA -A 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
22822 TA TA TA TA T
1 TA TA TA TA T
22831 GTAAATAGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22804 original size:17 final size:17
Alignment explanation
Indices: 22782--22830 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
22772 ATTACAAATT
22782 TATATATAATATATATA
1 TATATATAATATATATA
22799 TATATATAATATATATA
1 TATATATAATATATATA
22816 TATATAT-ATATATAT
1 TATATATAATATATAT
22831 GTAAATAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 8 0.25
17 24 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATATAATATATATA
Found at i:33067 original size:184 final size:183
Alignment explanation
Indices: 32740--33126 Score: 638
Period size: 184 Copynumber: 2.1 Consensus size: 183
32730 TTTTCTAATT
* *
32740 TATATAA-A-AATTAAATGTTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATAGAA
1 TATATAATATAATT-AATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATAGAA
*
32803 TTATAAAATAAAAATTTCAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
65 TTATAAAATAAAAATTTCAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGCTATT
32868 GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCAC-ATATGTTA
130 GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGC-CTATATGTTA
*
32922 TATATAATATAATTAATATTTTTTAATT-AAAAAATAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATAATTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATAGAA
* *
32986 TTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGCTAT
65 TTATAAAATAAAAATTTCA-ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGCTAT
*
33051 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGGTGAGCCTATATGTTA
129 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCTATATGTTA
*
33106 TATATAATATATTTAATATTT
1 TATATAATATAATTAATATTT
33127 AAAATTTAAT
Statistics
Matches: 192, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
182 13 0.07
183 60 0.31
184 119 0.62
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (183 bp):
TATATAATATAATTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATAGAAT
TATAAAATAAAAATTTCAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGCTATTG
GATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCTATATGTTA
Found at i:34614 original size:543 final size:541
Alignment explanation
Indices: 33589--34670 Score: 2047
Period size: 543 Copynumber: 2.0 Consensus size: 541
33579 TCTTAATCTT
33589 TGAAGTTGGTTTTCAACTTCATATTTATAGAAAATAATTTTCTCTATAAATTCACTTTTGCTCTT
1 TGAAGTTGGTTTTCAACTTCATATTTATAGAAAATAATTTTCTCTATAAATTCACTTTTGCTCTT
*
33654 TTAACAAATATACATAGCAATACTTTTGTTATCATTAAGAGAGGAAATAAAATATTTATTCTCCT
66 TTAACAAATACACATAGCAATACTTTTGTTATCATTAAGAGAGGAAATAAAATATTTATTCTCCT
*
33719 CATCTGCCATTATTACAAATTTTAAGAACTTGATCACTAAAACTTCTTTAGTGTCAGCATCTTTC
131 CATCTGCCATTATTACAAATTTTAAGAACTTGACCACTAAAACTTCTTTAGTGTCAGCATCTTTC
33784 ATTTCATATTTATGGTCTAAAGTCATCCATAATTATTTTATTCATATTATGGATACTATACACTT
196 ATTTCATATTTATGGTCTAAAGTCATCCATAATTATTTTATTCATATTATGGATACTATACACTT
*
33849 TATAATGTGTATCTGATAATCCATTTAGGATATATTTTCAATATAAGAAGTTAGAATACTCCCAA
261 TATAATGTGTATCTGATAATCCATTTAGGATATATTTTCAATATAAGAAGTTAAAATACTCCCAA
33914 ACTTTAATATCAATAAATATGGTAATAATGTTTACCTCATCCTCTCTAATAATAGAAGGATCATC
326 ACTTTAATATCAATAAATATGGTAATAATGTTTACCTCATCCTCTCTAATAATAGAAGGATCATC
*
33979 CGTTATTTGGCCAAATTTACCAAATAAAATAACATCACATGTTATTACATCTTGAAATTTTATCC
391 CGTTATTTGGCCAAATTTACCAAATAAAATAACATCACATGTTATTACATCTTGAAATTCTATCC
*
34044 ATAGAACTTTAAAAAATTCTCATTGTGGCTCATGACTACCGACAATCATTACACACGAAATTAGA
456 ATAGAACTTTAAAAAATTCTCATTGTGGCTCATGACTACCGACAACCATTACACACGAAATTAGA
34109 ATTAATAATAATTCTAACATG
521 ATTAATAATAATTCTAACATG
*
34130 TGAAGTTGGTTTTCAACTTCATATTTATAGAAAATAATTTTCTCTATAAATTCTCTTTTGCTCTT
1 TGAAGTTGGTTTTCAACTTCATATTTATAGAAAATAATTTTCTCTATAAATTCACTTTTGCTCTT
* * *
34195 TTAATAAATACACATAGCAATACTTTTGTTATCATTAAGAGAGGCAATAAAATATTTATTGTCCT
66 TTAACAAATACACATAGCAATACTTTTGTTATCATTAAGAGAGGAAATAAAATATTTATTCTCCT
* *
34260 CATTTGTGCCATTATTACAAATTTTAAGAACTTGACCACTAAAACTTCTTTAGTGTTAGCATCTT
131 CA--TCTGCCATTATTACAAATTTTAAGAACTTGACCACTAAAACTTCTTTAGTGTCAGCATCTT
34325 TCATTTCATATTTATGGTCTAAAGTCATCCATAATTATTTTATTCATATTATGGATACTATACAC
194 TCATTTCATATTTATGGTCTAAAGTCATCCATAATTATTTTATTCATATTATGGATACTATACAC
34390 TTTATAATGTGTATCTGATAATCCATTTAGGATATATTTTCAATATAAGAAGTTAAAATACTCCC
259 TTTATAATGTGTATCTGATAATCCATTTAGGATATATTTTCAATATAAGAAGTTAAAATACTCCC
34455 AAACTTTAATATCAATAAATATGGTAATAATGTTTACCTCATCCTCTCTAATAATAGAAGGATCA
324 AAACTTTAATATCAATAAATATGGTAATAATGTTTACCTCATCCTCTCTAATAATAGAAGGATCA
34520 TCCGTTATTTGGCCAAATTTACCAAATAAAATAACATCACATGTTATTACATCTTGAAATTCTAT
389 TCCGTTATTTGGCCAAATTTACCAAATAAAATAACATCACATGTTATTACATCTTGAAATTCTAT
34585 CCATAGAACTTTAAAAAATTCTCATTGTGGCTCATGACTACCGACAACCATTACACACGAAATTA
454 CCATAGAACTTTAAAAAATTCTCATTGTGGCTCATGACTACCGACAACCATTACACACGAAATTA
34650 GAATTAATAATAATTCTAACA
519 GAATTAATAATAATTCTAACA
34671 ATAAACTGAA
Statistics
Matches: 528, Mismatches: 11, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
541 127 0.24
543 401 0.76
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (541 bp):
TGAAGTTGGTTTTCAACTTCATATTTATAGAAAATAATTTTCTCTATAAATTCACTTTTGCTCTT
TTAACAAATACACATAGCAATACTTTTGTTATCATTAAGAGAGGAAATAAAATATTTATTCTCCT
CATCTGCCATTATTACAAATTTTAAGAACTTGACCACTAAAACTTCTTTAGTGTCAGCATCTTTC
ATTTCATATTTATGGTCTAAAGTCATCCATAATTATTTTATTCATATTATGGATACTATACACTT
TATAATGTGTATCTGATAATCCATTTAGGATATATTTTCAATATAAGAAGTTAAAATACTCCCAA
ACTTTAATATCAATAAATATGGTAATAATGTTTACCTCATCCTCTCTAATAATAGAAGGATCATC
CGTTATTTGGCCAAATTTACCAAATAAAATAACATCACATGTTATTACATCTTGAAATTCTATCC
ATAGAACTTTAAAAAATTCTCATTGTGGCTCATGACTACCGACAACCATTACACACGAAATTAGA
ATTAATAATAATTCTAACATG
Found at i:40295 original size:3 final size:3
Alignment explanation
Indices: 40287--40370 Score: 123
Period size: 3 Copynumber: 27.7 Consensus size: 3
40277 TTTTTATCCA
* * *
40287 TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT AAA TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
40335 TATT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40371 AATATATATT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:40302 original size:9 final size:9
Alignment explanation
Indices: 40290--40382 Score: 73
Period size: 9 Copynumber: 10.0 Consensus size: 9
40280 TTATCCATAT
40290 TATTATTAA
1 TATTATTAA
40299 TATTATTATTA
1 TATTATTA--A
*
40310 TTATTATAAA
1 -TATTATTAA
*
40320 TATTATTAT
1 TATTATTAA
40329 TATTATT-A
1 TATTATTAA
*
40337 T-TTATTAT
1 TATTATTAA
* *
40345 TATTATCAT
1 TATTATTAA
*
40354 TATTATTAT
1 TATTATTAA
40363 TATTATTAAA
1 TATTATT-AA
40373 TATATATTAA
1 TAT-TATTAA
40383 ACATATATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
7 5 0.07
8 2 0.03
9 43 0.62
10 7 0.10
11 5 0.07
12 7 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAA
Found at i:40868 original size:26 final size:26
Alignment explanation
Indices: 40839--40908 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 26
40829 CGAACCTGAA
*
40839 AAAAAAAAAAAAGAGAAGGGAGACAG
1 AAAAAAAAAAAAGAGAAGGAAGACAG
**
40865 ---AAAAAACGA-AGAAGGAAGACAG
1 AAAAAAAAAAAAGAGAAGGAAGACAG
*
40887 AAAAAAAAAACAGAGAAAGGAA
1 AAAAAAAAAAAAGAG-AAGGAA
40909 AAAAAACTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
22 12 0.35
23 7 0.21
25 7 0.21
26 2 0.06
27 6 0.18
ACGTcount: A:0.70, C:0.06, G:0.24, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAAAAGAGAAGGAAGACAG
Found at i:40870 original size:21 final size:22
Alignment explanation
Indices: 40844--40893 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
40834 CTGAAAAAAA
*
40844 AAAAAAAG-AGAAGGGAGACAG
1 AAAAAAAGAAGAAGGAAGACAG
*
40865 AAAAAACGAAGAAGGAAGACAG
1 AAAAAAAGAAGAAGGAAGACAG
40887 AAAAAAA
1 AAAAAAA
40894 AAACAGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.68, C:0.06, G:0.26, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAGAAGGAAGACAG
Found at i:40976 original size:15 final size:15
Alignment explanation
Indices: 40956--40987 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40946 AGCAACCAAG
40956 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
40971 AAAAGAAAGAAGAGA
1 AAAAGAAAGAAAAGA
40986 AA
1 AA
40988 CTTACTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:41858 original size:13 final size:13
Alignment explanation
Indices: 41842--41887 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
41832 ATATAATAAA
41842 TAAATATTTATTT
1 TAAATATTTATTT
*
41855 TAAATAAATTATTT
1 TAAAT-ATTTATTT
41869 T-AATATTTATTT
1 TAAATATTTATTT
*
41881 TTAATAT
1 TAAATAT
41888 CGAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:42540 original size:26 final size:26
Alignment explanation
Indices: 42511--42592 Score: 60
Period size: 26 Copynumber: 3.0 Consensus size: 26
42501 AAATTAAAAG
*
42511 TTCATATATTTAATTT-TTTCTTTCTT
1 TTCATATATTTAATTTATTT-TTTATT
* * *
42537 TTCAAATTTTTTATTTATTTTTTATT
1 TTCATATATTTAATTTATTTTTTATT
*
42563 TTTATAATATTTATATGTT-TTATTTTATT
1 TTCAT-ATATTTA-AT-TTATT-TTTTATT
42592 T
1 T
42593 GCAAGTATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
26 21 0.49
27 8 0.19
28 4 0.09
29 10 0.23
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (26 bp):
TTCATATATTTAATTTATTTTTTATT
Found at i:42614 original size:13 final size:15
Alignment explanation
Indices: 42583--42619 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
42573 TTATATGTTT
42583 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
42598 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
42611 TA-TTTATTT
1 TATTTTATTT
42620 TTCTGTCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:53238 original size:1 final size:1
Alignment explanation
Indices: 53228--53297 Score: 95
Period size: 1 Copynumber: 70.0 Consensus size: 1
53218 GAAAAGAAAG
* * * * *
53228 AAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAGAAGAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53293 AAAAA
1 AAAAA
53298 GGGGGTCAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:53298 original size:14 final size:14
Alignment explanation
Indices: 53216--53297 Score: 101
Period size: 14 Copynumber: 5.7 Consensus size: 14
53206 ATTATGCTTG
*
53216 AAGAAAAGAAAGAAA
1 AAGAAAA-AAAAAAA
53231 AAGAAAAAAAAAAAA
1 AAG-AAAAAAAAAAA
*
53246 AAAAAAAAAAAAAA
1 AAGAAAAAAAAAAA
*
53260 AAAAAAAAAAAAAA
1 AAGAAAAAAAAAAA
* *
53274 AAGAAAAAAAGAAG
1 AAGAAAAAAAAAAA
53288 AAGAAAAAAA
1 AAGAAAAAAA
53298 GGGGGTCAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
14 46 0.75
15 11 0.18
16 4 0.07
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAAA
Found at i:54571 original size:83 final size:83
Alignment explanation
Indices: 54428--54888 Score: 807
Period size: 83 Copynumber: 5.6 Consensus size: 83
54418 AATAGAACAA
*
54428 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
* * *
54493 AATCATTGAATTTGGAAG
66 AAGCATTGAGTTTAGAAG
*
54511 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
54576 AAGCATTGAGTTTAGAAG
66 AAGCATTGAGTTTAGAAG
* *
54594 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGATATCTGATCTGGTTGGACAGAA-C
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
*
54658 AATCATTGAGTTTAGAAG
66 AAGCATTGAGTTTAGAAG
**
54676 ATGAATTCACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
* *
54741 AAGCATTGAATTTGGAAG
66 AAGCATTGAGTTTAGAAG
54759 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
54824 AAGCATTGAGTTTAGAAG
66 AAGCATTGAGTTTAGAAG
54842 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
54889 GTTTGGTATG
Statistics
Matches: 357, Mismatches: 20, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
82 77 0.22
83 280 0.78
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (83 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
AAGCATTGAGTTTAGAAG
Found at i:54725 original size:165 final size:166
Alignment explanation
Indices: 54428--54888 Score: 825
Period size: 165 Copynumber: 2.8 Consensus size: 166
54418 AATAGAACAA
54428 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
* *
54493 AATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
66 AATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
*
54558 ATCTGATTAGACAGAATCAAGCATTGAGTTTAGAAG
131 ATCTGATTAGACAGAATCAAGCATTGAATTTAGAAG
*
54594 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGATATCTGATCTGGTTGGACAGAA-C
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
**
54658 AATCATTGAGTTTAGAAGATGAATTCACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
66 AATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* *
54723 ATCTGATTGGACAGAATCAAGCATTGAATTTGGAAG
131 ATCTGATTAGACAGAATCAAGCATTGAATTTAGAAG
*
54759 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
*
54824 AAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
66 AATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
54889 GTTTGGTATG
Statistics
Matches: 281, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
165 156 0.56
166 125 0.44
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (166 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
AATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
ATCTGATTAGACAGAATCAAGCATTGAATTTAGAAG
Found at i:54866 original size:248 final size:248
Alignment explanation
Indices: 54428--54888 Score: 868
Period size: 248 Copynumber: 1.9 Consensus size: 248
54418 AATAGAACAA
** *
54428 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
1 ATGAATTCACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
*
54493 AATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
66 AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
54558 ATCTGATTAGACAGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAG
131 ATCTGATTAGACAGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAG
54623 TGTTCTTTGAGATATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
196 TGTTCTTTGAGATATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
54676 ATGAATTCACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATGAATTCACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
54741 AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
66 AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
*
54806 ATCTGATTGGACAGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAG
131 ATCTGATTAGACAGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAG
*
54871 TGTTCTTTGAGTTATCTG
196 TGTTCTTTGAGATATCTG
54889 GTTTGGTATG
Statistics
Matches: 207, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
248 207 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (248 bp):
ATGAATTCACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
ATCTGATTAGACAGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAG
TGTTCTTTGAGATATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
Found at i:55935 original size:113 final size:113
Alignment explanation
Indices: 55754--56403 Score: 1122
Period size: 113 Copynumber: 5.8 Consensus size: 113
55744 GAAAGATTAG
*
55754 CTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
55819 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAA
66 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAGGGATCAA
55867 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
55932 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAGGGATCAA
66 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAGGGATCAA
* *
55980 CTTTTCCAGAGAAAGTTCATAATAAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
56045 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAGGGATCAA
66 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAGGGATCAA
* *
56093 CTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
56158 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAGGGATCAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAGGGATCAA
* *
56206 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATTA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * *
56271 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAGGGATCAA
* * *
56319 CTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* *
56383 GAAGAACTTGTTCAACTTTTT
66 GAAGAATTTGTTCAACCTTTT
56404 GCATAATTCT
Statistics
Matches: 516, Mismatches: 21, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
112 69 0.13
113 447 0.87
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAGGGATCAA
Found at i:56730 original size:3 final size:3
Alignment explanation
Indices: 56722--56834 Score: 208
Period size: 3 Copynumber: 37.7 Consensus size: 3
56712 TTTTTATCCA
56722 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
56770 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56818 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
56835 AATATATATT
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 108 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:57333 original size:21 final size:22
Alignment explanation
Indices: 57307--57356 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
57297 CCTGAAAAAA
*
57307 AAAAAAAG-AGAAGGGAGACAG
1 AAAAAAAGAAGAAGGAAGACAG
*
57328 AAAAAACGAAGAAGGAAGACAG
1 AAAAAAAGAAGAAGGAAGACAG
57350 AAAAAAA
1 AAAAAAA
57357 AACAGAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.68, C:0.06, G:0.26, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAGAAGGAAGACAG
Found at i:57368 original size:26 final size:26
Alignment explanation
Indices: 57303--57370 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 26
57293 CGAACCTGAA
* *
57303 AAAAAAAAAAAGAG-AAGGGAGACAG
1 AAAAAAAAACAGAGAAAGGAAGACAG
57328 ---AAAAAAC-GA-AGAAGGAAGACAG
1 AAAAAAAAACAGAGA-AAGGAAGACAG
57350 AAAAAAAAACAGAGAAAGGAA
1 AAAAAAAAACAGAGAAAGGAA
57371 AAAAAACTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
21 2 0.06
22 16 0.47
25 7 0.21
26 8 0.24
27 1 0.03
ACGTcount: A:0.69, C:0.06, G:0.25, T:0.00
Consensus pattern (26 bp):
AAAAAAAAACAGAGAAAGGAAGACAG
Found at i:57438 original size:15 final size:15
Alignment explanation
Indices: 57418--57449 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
57408 AGCAACCAAG
57418 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
57433 AAAAGAAAGAAGAGA
1 AAAAGAAAGAAAAGA
57448 AA
1 AA
57450 CTTACTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:58317 original size:13 final size:13
Alignment explanation
Indices: 58301--58346 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
58291 ATATAATAAA
58301 TAAATATTTATTT
1 TAAATATTTATTT
*
58314 TAAATAAATTATTT
1 TAAAT-ATTTATTT
58328 T-AATATTTATTT
1 TAAATATTTATTT
*
58340 TTAATAT
1 TAAATAT
58347 CGAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:59442 original size:24 final size:24
Alignment explanation
Indices: 59402--59487 Score: 88
Period size: 24 Copynumber: 3.6 Consensus size: 24
59392 CATAGGTTTC
* *
59402 GTTCGTTCAT-TTACGTTCGTGAAT
1 GTTCGTTTATGTT-CGTTCGTGTAT
* *
59426 GTTCGGTTATGTTCGTTTG-GTTAT
1 GTTCGTTTATGTTCGTTCGTG-TAT
59450 GTTCGTTTATGTTCGTTCGAT-TAT
1 GTTCGTTTATGTTCGTTCG-TGTAT
59474 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
59488 ATTCATTTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.02
24 49 0.94
25 2 0.04
ACGTcount: A:0.12, C:0.13, G:0.23, T:0.52
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGTGTAT
Found at i:59449 original size:14 final size:14
Alignment explanation
Indices: 59430--59481 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
59420 GTGAATGTTC
59430 GGTTATGTTCGTTT
1 GGTTATGTTCGTTT
59444 GGTTATGTTCG--T
1 GGTTATGTTCGTTT
*
59456 --TTATGTTCGTTC
1 GGTTATGTTCGTTT
*
59468 GATTATGTTCGTTT
1 GGTTATGTTCGTTT
59482 ATGTTCATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 9 0.28
12 1 0.03
14 22 0.69
ACGTcount: A:0.10, C:0.10, G:0.25, T:0.56
Consensus pattern (14 bp):
GGTTATGTTCGTTT
Found at i:59497 original size:24 final size:24
Alignment explanation
Indices: 59424--59500 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
59414 ACGTTCGTGA
* * * *
59424 ATGTTCGGTTATGTTCGTTTGGTT
1 ATGTTCGTTTATGTTCATTCGATT
*
59448 ATGTTCGTTTATGTTCGTTCGATT
1 ATGTTCGTTTATGTTCATTCGATT
59472 ATGTTCGTTTATGTTCATTC-ATTT
1 ATGTTCGTTTATGTTCATTCGA-TT
59496 ATGTT
1 ATGTT
59501 TAACCCAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.02
24 47 0.98
ACGTcount: A:0.13, C:0.10, G:0.21, T:0.56
Consensus pattern (24 bp):
ATGTTCGTTTATGTTCATTCGATT
Found at i:60254 original size:16 final size:16
Alignment explanation
Indices: 60233--60299 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
60223 TTTATATTCG
60233 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
60249 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
60265 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
60281 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
60295 TTTAT
1 TTTAT
60300 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:60270 original size:32 final size:32
Alignment explanation
Indices: 60229--60291 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
60219 AACGTTTATA
60229 TTCGTTTATGTTCGTGTTCATTTATGTTCGTG
1 TTCGTTTATGTTCGTGTTCATTTATGTTCGTG
*
60261 TTCGTTTATGTTCGTGTTCGTTTATGTTCGT
1 TTCGTTTATGTTCGTGTTCATTTATGTTCGT
60292 TTATTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.08, C:0.13, G:0.22, T:0.57
Consensus pattern (32 bp):
TTCGTTTATGTTCGTGTTCATTTATGTTCGTG
Found at i:60382 original size:16 final size:16
Alignment explanation
Indices: 60361--60393 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
60351 AAAAAAATTT
60361 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
60377 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
60393 T
1 T
60394 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:61061 original size:34 final size:34
Alignment explanation
Indices: 61005--61145 Score: 143
Period size: 34 Copynumber: 4.3 Consensus size: 34
60995 GGTTTAAGAT
**
61005 TTATATTATATAATTACTATAAAAAATATAAAAAA
1 TTATA-TATATAATTAAAATAAAAAATATAAAAAA
*
61040 TTATATATCTAATTAAAATAAAAAATA-AAAAATA
1 TTATATATATAATTAAAATAAAAAATATAAAAA-A
* *
61074 TTATATATATAATT--AATATAAAATAT---ATA
1 TTATATATATAATTAAAATAAAAAATATAAAAAA
* *
61103 -TATATATATAATTAATATAAAAAATATATAAATA
1 TTATATATATAATTAAAATAAAAAATATA-AAAAA
61137 TTATATATA
1 TTATATATA
61146 AATATATATA
Statistics
Matches: 89, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
28 13 0.15
29 1 0.01
30 11 0.12
32 10 0.11
33 5 0.06
34 36 0.40
35 13 0.15
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (34 bp):
TTATATATATAATTAAAATAAAAAATATAAAAAA
Found at i:61080 original size:2 final size:2
Alignment explanation
Indices: 61071--61177 Score: 99
Period size: 2 Copynumber: 58.5 Consensus size: 2
61061 AAAATAAAAA
*
61071 AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
61108 AT AT A- AT -T A- AT AT A- AA AA AT AT AT AA AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
61145 AA 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 AT A
61178 ATCGGGGCGG
Statistics
Matches: 89, Mismatches: 6, Indels: 20
0.77 0.05 0.17
Matches are distributed among these distances:
1 10 0.11
2 79 0.89
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:61115 original size:28 final size:28
Alignment explanation
Indices: 61064--61171 Score: 137
Period size: 28 Copynumber: 3.8 Consensus size: 28
61054 AAAATAAAAA
61064 ATAAAAAATAT-TATATATATAATTAAT
1 ATAAAAAATATATATATATATAATTAAT
*
61091 ATAAAATATATATATATATATAATTAAT
1 ATAAAAAATATATATATATATAATTAAT
* *
61119 ATAAAAAATATATAAATATTATATATAAAT
1 ATAAAAAATATATATATA-TATA-ATTAAT
* *
61149 ATATATATATATATATATATATA
1 ATA-AAAAATATATATATATATA
61172 TATATAATCG
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.14
28 32 0.46
29 4 0.06
30 12 0.17
31 12 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATAAAAAATATATATATATATAATTAAT
Found at i:61167 original size:55 final size:55
Alignment explanation
Indices: 61064--61165 Score: 158
Period size: 53 Copynumber: 1.9 Consensus size: 55
61054 AAAATAAAAA
61064 ATAAAAAATATTATATATATAATTAATATAAAATATATATATATATATAATTAAT
1 ATAAAAAATATTATATATATAATTAATATAAAATATATATATATATATAATTAAT
61119 ATAAAAAATA-TATA-A-AT-ATTATATATAAATATATATATATATATATA
1 ATAAAAAATATTATATATATAATTA-ATATAAA-ATATATATATATATATA
61166 TATATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
51 4 0.09
52 9 0.20
53 18 0.40
54 4 0.09
55 10 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (55 bp):
ATAAAAAATATTATATATATAATTAATATAAAATATATATATATATATAATTAAT
Found at i:67850 original size:15 final size:15
Alignment explanation
Indices: 67813--67850 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
67803 CATAGAAATA
* *
67813 AAAATTAATAAAGAT
1 AAAATAAATAAAGAG
67828 AAAA-AAATAAAGAG
1 AAAATAAATAAAGAG
67842 AAAATAAAT
1 AAAATAAAT
67851 GTGTGATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (15 bp):
AAAATAAATAAAGAG
Done.