Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003485.1 Hibiscus syriacus cultivar Beakdansim tig00007369_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: 123182
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1281 original size:33 final size:33
Alignment explanation
Indices: 1244--1325 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
1234 TACAAATCCC
1244 CACCACCACCAAGC-CCCACATACATTTACAAGT
1 CACCACCACCAA-CACCCACATACATTTACAAGT
* * **
1277 CACCACCACCAACACCTACCTATGTTTACAAGT
1 CACCACCACCAACACCCACATACATTTACAAGT
* *
1310 CACCACCTCCACCACC
1 CACCACCACCAACACC
1326 ATACTACTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 1 0.02
33 41 0.98
ACGTcount: A:0.33, C:0.46, G:0.05, T:0.16
Consensus pattern (33 bp):
CACCACCACCAACACCCACATACATTTACAAGT
Found at i:1283 original size:147 final size:148
Alignment explanation
Indices: 988--1652 Score: 771
Period size: 147 Copynumber: 4.5 Consensus size: 148
978 TACAAGTCTT
** * * *
988 CACCACCAAGTCCCACCTATGTTTACAAGTCACCACCTCCTCCGCCGTATTACTAC-AA-GTCCA
1 CACCACCAACACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTACTACAAATCTCCA
* * * * * * *
1051 CCACCACCGAAGCATGTTGTGAACCCCCCGTACTACTAC-AGTCTCCACC-CCACCGAGTCCC-T
66 CCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCACCACCAAGCCCCAC
* *
1113 TTACGTTTACAAGTCACCAC
131 ATACATTTACAAGT--CCAC
* * * *
1133 CACCACCGACGCCCACCTATGTTTACAAGTCACCACCTCCACCACCATACTACTACAAATCTCCA
1 CACCACCAACACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTACTACAAATCTCCA
* *
1198 CCACCACCGAAGCATGTAGAGATTCCCCCGTACTACTACAAATCCCCACCACCACCAAGCCCCAC
66 CCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCACCACCAAGCCCCAC
1263 ATACATTTACAAGT-CAC
131 ATACATTTACAAGTCCAC
* * *
1280 CACCACCAACACCTACCTATGTTTACAAGTCACCACCTCCACCACCATACTACTACAAATCT---
1 CACCACCAACACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTACTACAAATCTCCA
1342 CCACCACCGAAGCATGTAGAGAAT-CCCCGTACTACTACAAGTCCCCACCACCACCAAGCCCCAC
66 CCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCACCACCAAGCCCCAC
*
1406 ATACGTTTACAAGTCACCAC
131 ATACATTTACAAGT--CCAC
* *
1426 CAACCACCAACACCCACCTA--TTTACAAGTCACCACCTCCTCCCCCGTACTACTACAAGTCTCC
1 C-ACCACCAACACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTACTACAAATCTCC
* * * * *
1489 ACCACCACCGAAGCATGTAGAGAATCCCCCATACTACTACAAGTCCACACCACCAAAACACGTCG
65 ACCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCACC--ACCAAG-CC
** * * * *
1554 AAAAACCACCATACTACTAACTCCAC
127 CCACA-TA-CAT-TTAC-AAGTCCAC
* *
1580 CACCACCAAGC-CCCACCTATGTTTACAAGTCACCACCACCTCCTCCGTACTACTACAAATCTCC
1 CACCACCAA-CACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTACTACAAATCTCC
1644 ACCACCACC
65 ACCACCACC
1653 AGTCCACTCT
Statistics
Matches: 452, Mismatches: 45, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
143 52 0.12
144 23 0.05
145 86 0.19
146 6 0.01
147 118 0.26
148 32 0.07
149 36 0.08
150 12 0.03
151 4 0.01
152 3 0.01
153 17 0.04
154 8 0.02
155 52 0.12
156 3 0.01
ACGTcount: A:0.31, C:0.43, G:0.08, T:0.18
Consensus pattern (148 bp):
CACCACCAACACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTACTACAAATCTCCA
CCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCACCACCAAGCCCCAC
ATACATTTACAAGTCCAC
Found at i:1457 original size:35 final size:35
Alignment explanation
Indices: 1377--1461 Score: 111
Period size: 35 Copynumber: 2.4 Consensus size: 35
1367 CCCGTACTAC
*
1377 TACAAGTCCCCACCACCACCAAGCCCCACATACGTT
1 TACAAGTCACCACCACCACCAAGCCCCACATAC-TT
*
1413 TACAAGTCACCACCAACCACCAA-CACCCACCTA-TT
1 TACAAGTCACCACC-ACCACCAAGC-CCCACATACTT
1448 TACAAGTCACCACC
1 TACAAGTCACCACC
1462 TCCTCCCCCG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
35 16 0.36
36 14 0.31
37 15 0.33
ACGTcount: A:0.34, C:0.46, G:0.06, T:0.14
Consensus pattern (35 bp):
TACAAGTCACCACCACCACCAAGCCCCACATACTT
Found at i:1502 original size:292 final size:291
Alignment explanation
Indices: 978--1543 Score: 805
Period size: 292 Copynumber: 1.9 Consensus size: 291
968 TACTTATGTA
** ** * * * *
978 TACAAGTCTTCACCACCAAGTCCCACCTATGTTTACAAGTCACCACCTCCTCCGCCGTATTACTA
1 TACAAGTCACCACCACCAACACCCACCTATGTTTACAAGTCACCACCTCCACCACCATACTACTA
* * * * *
1043 CAAGTCCACCACCACCGAAGCATGTTGTGAACCCCCCGTACTACTACAGTCTCCACCCCACCGAG
66 CAAATCCACCACCACCGAAGCATGTAGAGAACCCCCCGTACTACTACAGTCCCCACCCCACCAAG
* ** * *
1108 TCCCTTTACGTTTACAAGTCACCACCACCACCGACGCCCACCTATGTTTACAAGTCACCACCTCC
131 CCCCCATACGTTTACAAGTCACCACCACCACCAACACCCACCTA-GTTTACAAGTCACCACCTCC
* *
1173 ACCACCATACTACTACAAATCTCCACCACCACCGAAGCATGTAGAGATTCCCCCGTACTACTACA
195 ACCACCATACTACTACAAATCTCCACCACCACCGAAGCATGTAGAGAATCCCCCATACTACTACA
*
1238 AATCCCCACCACCACCAAGCCCCACATACATT
260 AATCCACACCACCACCAAGCCCCACATACATT
*
1270 TACAAGTCACCACCACCAACACCTACCTATGTTTACAAGTCACCACCTCCACCACCATACTACTA
1 TACAAGTCACCACCACCAACACCCACCTATGTTTACAAGTCACCACCTCCACCACCATACTACTA
* *
1335 CAAAT-CTCCACCACCGAAGCATGTAGAGAA-TCCCCGTACTACTACAAGTCCCCACCACCACCA
66 CAAATCCACCACCACCGAAGCATGTAGAGAACCCCCCGTACTACTAC-AGTCCCCACC-CCACCA
1398 AGCCCCACATACGTTTACAAGTCACCACCAACCACCAACACCCACCTA-TTTACAAGTCACCACC
129 AGCCCC-CATACGTTTACAAGTCACCACC-ACCACCAACACCCACCTAGTTTACAAGTCACCACC
* * * *
1462 TCCTCCCCCGTACTACTACAAGTCTCCACCACCACCGAAGCATGTAGAGAATCCCCCATACTACT
192 TCCACCACCATACTACTACAAATCTCCACCACCACCGAAGCATGTAGAGAATCCCCCATACTACT
*
1527 ACAAGTCCACACCACCA
257 ACAAATCCACACCACCA
1544 AAACACGTCG
Statistics
Matches: 241, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
290 14 0.06
291 31 0.13
292 160 0.66
293 20 0.08
294 16 0.07
ACGTcount: A:0.31, C:0.42, G:0.09, T:0.18
Consensus pattern (291 bp):
TACAAGTCACCACCACCAACACCCACCTATGTTTACAAGTCACCACCTCCACCACCATACTACTA
CAAATCCACCACCACCGAAGCATGTAGAGAACCCCCCGTACTACTACAGTCCCCACCCCACCAAG
CCCCCATACGTTTACAAGTCACCACCACCACCAACACCCACCTAGTTTACAAGTCACCACCTCCA
CCACCATACTACTACAAATCTCCACCACCACCGAAGCATGTAGAGAATCCCCCATACTACTACAA
ATCCACACCACCACCAAGCCCCACATACATT
Found at i:1566 original size:45 final size:46
Alignment explanation
Indices: 1472--1588 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 46
1462 TCCTCCCCCG
* * * * * *
1472 TACTACTACAAGTCTCCACCACCACCGAAGCATGTAGAGAATCCCCCA
1 TACTACTACAAG--TCCACCACCACCAAAACACGTAGAAAAACCACCA
*
1520 TACTACTACAAGTCCA-CACCACCAAAACACGTCGAAAAACCACCA
1 TACTACTACAAGTCCACCACCACCAAAACACGTAGAAAAACCACCA
*
1565 TACTACT--AACTCCACCACCACCAA
1 TACTACTACAAGTCCACCACCACCAA
1589 GCCCCACCTA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
43 6 0.10
44 9 0.15
45 29 0.48
46 4 0.07
48 12 0.20
ACGTcount: A:0.38, C:0.39, G:0.08, T:0.15
Consensus pattern (46 bp):
TACTACTACAAGTCCACCACCACCAAAACACGTAGAAAAACCACCA
Found at i:1797 original size:98 final size:98
Alignment explanation
Indices: 1621--1798 Score: 227
Period size: 98 Copynumber: 1.8 Consensus size: 98
1611 ACCACCACCT
* * *
1621 CCTCCGTACTACTACAAATCTCCACCACCACCAGTCCACTCTCACCACCACCATACTATTACAAG
1 CCTCCATACTACTACAAATCTCCACCACCACCAGTCCACTCTCACCACCACCATACTACTACAAA
*
1686 TCCCCACCTCCACCACCAAAACACGAAGAACAA
66 TCCCCACCACCACCACCAAAACACGAAGAACAA
* * * *
1719 CCTCCATACTACTACAAATCTCCTCCCCCACCA-TCGC-CATCTC-CTCTCCACCATATTACTAC
1 CCTCCATACTACTACAAATCTCCACCACCACCAGTC-CAC-TCTCAC-CACCACCATACTACTAC
*
1781 AAATCCCCGCCACCACCA
63 AAATCCCCACCACCACCA
1799 GTACACTCCA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
97 4 0.06
98 64 0.94
ACGTcount: A:0.31, C:0.47, G:0.04, T:0.18
Consensus pattern (98 bp):
CCTCCATACTACTACAAATCTCCACCACCACCAGTCCACTCTCACCACCACCATACTACTACAAA
TCCCCACCACCACCACCAAAACACGAAGAACAA
Found at i:1956 original size:48 final size:48
Alignment explanation
Indices: 1865--2280 Score: 232
Period size: 48 Copynumber: 8.7 Consensus size: 48
1855 CGAAGAGCAA
* * *
1865 CCACCGTACTACTACAAATCACCTCCACCACCA-T-CACTGTCTCCTCCT
1 CCACCATACTACTACAAATCACCACCACCACCAGTCCA-T-TCTCCACCT
* *
1913 CCACCATACTATTACAAATCACCTCCACCACCAGTCCATTCTCCACCT
1 CCACCATACTACTACAAATCACCACCACCACCAGTCCATTCTCCACCT
* * ** *** **
1961 CCA-C--ACTACTACAAGTCCCCACCACCACC-G-CCAAAACAAAGAGCAA
1 CCACCATACTACTACAAATCACCACCACCACCAGTCC-ATTC-TCCA-CCT
* * * *
2007 CCCCCATACTACTACAAATCTCCTCCACCACCATTGT-CA-TCTCCTCCT
1 CCACCATACTACTACAAATCACCACCACCACCA--GTCCATTCTCCACCT
* * * * * *
2055 CCACCATATTATTACAAGTCTCCACCACCACCAGCCCACTCTCCACCT
1 CCACCATACTACTACAAATCACCACCACCACCAGTCCATTCTCCACCT
* * * * *
2103 CCACCTTACTACTACAAATCACCCCCACCTCCA-TCGCGGTT-TCCTCCAT
1 CCACCATACTACTACAAATCACCACCACCACCAGTC-C-ATTCTCCACC-T
* * * * * *
2152 -CACCATATTACTACAAATCCCCACCACCTCCA-TCTCCTTCACCACCC
1 CCACCATACTACTACAAATCACCACCACCACCAGTC-CATTCTCCACCT
* ** *
2199 CCACCATACTACTACAAATCACC-CC-CCACCCGGTTTATTCTCCACCA
1 CCACCATACTACTACAAATCACCACCACCA-CCAGTCCATTCTCCACCT
* * * *
2246 CCACCATACTACTACAAGTCTCCCCCACCTCCAGT
1 CCACCATACTACTACAAATCACCACCACCACCAGT
2281 AGAAGTTCCA
Statistics
Matches: 280, Mismatches: 65, Indels: 46
0.72 0.17 0.12
Matches are distributed among these distances:
43 2 0.01
44 3 0.01
45 22 0.08
46 6 0.02
47 40 0.14
48 173 0.62
49 28 0.10
50 3 0.01
51 1 0.00
52 2 0.01
ACGTcount: A:0.28, C:0.47, G:0.04, T:0.21
Consensus pattern (48 bp):
CCACCATACTACTACAAATCACCACCACCACCAGTCCATTCTCCACCT
Found at i:2131 original size:142 final size:144
Alignment explanation
Indices: 1633--2119 Score: 560
Period size: 142 Copynumber: 3.4 Consensus size: 144
1623 TCCGTACTAC
* * *
1633 TACAAATCTCCACCACCACCAGTCCACTCT-CACCACCACCATACTATTACAAGTCCCCACCTCC
1 TACAAATCTCCACCACCACCAGTCCACTCTCCACCTCCACCATACTACTACAAGT--CCACCACC
* * * * *
1697 ACCACCAAAACACGAAGAACAACCTCCATACTACTACAAATCTCCTCCCCCACCATCGCCATCTC
64 ACCACCAAAACAC-AAGAGCAACCACCATACTACTACAAATCTCCTCCACCACCATTGACATCTC
*
1762 CT-CTCCACCATATTAC
128 CTCCTCCACCATATTAT
* * * * *
1778 TACAAATCCCCGCCACCACCAGT--ACACTCCACCTTCACCATACTACTACAAGTCCCCACCGCC
1 TACAAATCTCCACCACCACCAGTCCACTCTCCACCTCCACCATACTACTACAAGT--CCACCACC
* * * *
1841 ATCCCACCAAAACACGAAGAGCAACCACCGTACTACTACAAATCACCTCCACCACCA-TCACTGT
64 A--CCACCAAAACAC-AAGAGCAACCACCATACTACTACAAATCTCCTCCACCACCATTGAC-AT
*
1905 CTCCTCCTCCACCATACTAT
125 CTCCTCCTCCACCATATTAT
* * *
1925 TACAAATCACCTCCACCACCAGTCCATTCTCCACCTCCA-C--ACTACTACAAGTCCCCACCACC
1 TACAAATCTCCACCACCACCAGTCCACTCTCCACCTCCACCATACTACTACAAGT--CCACCACC
* * *
1987 ACCGCCAAAACA-AAGAGCAACCCCCATACTACTACAAATCTCCTCCACCACCATTGTCATCTCC
64 ACCACCAAAACACAAGAGCAACCACCATACTACTACAAATCTCCTCCACCACCATTGACATCTCC
2051 TCCTCCACCATATTAT
129 TCCTCCACCATATTAT
* * *
2067 TACAAGTCTCCACCACCACCAGCCCACTCTCCACCTCCACCTTACTACTACAA
1 TACAAATCTCCACCACCACCAGTCCACTCTCCACCTCCACCATACTACTACAA
2120 ATCACCCCCA
Statistics
Matches: 294, Mismatches: 37, Indels: 22
0.83 0.10 0.06
Matches are distributed among these distances:
142 92 0.31
143 7 0.02
144 41 0.14
145 32 0.11
146 77 0.26
147 33 0.11
148 1 0.00
149 11 0.04
ACGTcount: A:0.31, C:0.46, G:0.05, T:0.18
Consensus pattern (144 bp):
TACAAATCTCCACCACCACCAGTCCACTCTCCACCTCCACCATACTACTACAAGTCCACCACCAC
CACCAAAACACAAGAGCAACCACCATACTACTACAAATCTCCTCCACCACCATTGACATCTCCTC
CTCCACCATATTAT
Found at i:2340 original size:18 final size:18
Alignment explanation
Indices: 2317--2363 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
2307 ACAAGTCCCC
2317 ACCACCACCATCTCCTTT
1 ACCACCACCATCTCCTTT
2335 ACCACCACCATCTCCTTT
1 ACCACCACCATCTCCTTT
2353 ACCACCACCAT
1 ACCACCACCAT
2364 ACTACTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.51, G:0.00, T:0.23
Consensus pattern (18 bp):
ACCACCACCATCTCCTTT
Found at i:2500 original size:46 final size:48
Alignment explanation
Indices: 2404--2526 Score: 124
Period size: 46 Copynumber: 2.6 Consensus size: 48
2394 CCAGCACCTG
* * * * *
2404 CATACCACTACAATTCCCCTCCTCCACCATCACCATCTCCTCCTCTCC
1 CATACCACTACAAATCCCCTCCACCACCATCACCATCACCCCCTCCCC
* *
2452 CATACCACTACAAAT-CCC-CCACCACCATCTCCCTCACCCCCTCCCC
1 CATACCACTACAAATCCCCTCCACCACCATCACCATCACCCCCTCCCC
* * * * *
2498 CATACTACTACCACTCACCTCCTCCACCA
1 CATACCACTACAAATCCCCTCCACCACCA
2527 GTGAATCACC
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
46 34 0.56
47 5 0.08
48 22 0.36
ACGTcount: A:0.24, C:0.56, G:0.00, T:0.20
Consensus pattern (48 bp):
CATACCACTACAAATCCCCTCCACCACCATCACCATCACCCCCTCCCC
Found at i:16302 original size:41 final size:39
Alignment explanation
Indices: 16220--16303 Score: 105
Period size: 41 Copynumber: 2.1 Consensus size: 39
16210 CTACGGCCTG
* *
16220 GCCTATTTAATAAAAAGGCCAGACCAGGCCTTTTTAAAA
1 GCCTATTTAATAAAAAGGCCAGACCAGGCCTATTAAAAA
* * *
16259 GCCTATTTAATTAAACAGGCCAGGCTTAGGCCTATTAAAAA
1 GCCTATTTAA-TAAAAAGGCCAGAC-CAGGCCTATTAAAAA
16300 GCCT
1 GCCT
16304 TATAAGCTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 10 0.26
40 12 0.32
41 16 0.42
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (39 bp):
GCCTATTTAATAAAAAGGCCAGACCAGGCCTATTAAAAA
Found at i:16469 original size:17 final size:17
Alignment explanation
Indices: 16447--16479 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16437 TTTTAAACAT
16447 GCTTTTAAACAGGCCAA
1 GCTTTTAAACAGGCCAA
*
16464 GCTTTTAAATAGGCCA
1 GCTTTTAAACAGGCCA
16480 GGCCAGTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (17 bp):
GCTTTTAAACAGGCCAA
Found at i:16962 original size:25 final size:25
Alignment explanation
Indices: 16943--16994 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
16933 GATTATTGTT
16943 TTCTATTTAGTATCGTATTATGGAC
1 TTCTATTTAGTATCGTATTATGGAC
16968 TTCTATTTAGTATCGTATTATGGAC
1 TTCTATTTAGTATCGTATTATGGAC
16993 TT
1 TT
16995 GAAATTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (25 bp):
TTCTATTTAGTATCGTATTATGGAC
Found at i:17280 original size:2 final size:2
Alignment explanation
Indices: 17273--17305 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17263 CTTTTAAACT
17273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17306 TTGAGGCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22088 original size:22 final size:24
Alignment explanation
Indices: 22063--22109 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
22053 GTTTAACAGA
*
22063 AAAT-ATA-TTTTGTTTTCGTGAT
1 AAATAATACTTTTGTTGTCGTGAT
22085 AAATAATATCTTTTGTTGTCGTGAT
1 AAATAATA-CTTTTGTTGTCGTGAT
22110 CGGAAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 3 0.14
25 14 0.67
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (24 bp):
AAATAATACTTTTGTTGTCGTGAT
Found at i:28677 original size:33 final size:33
Alignment explanation
Indices: 28650--28950 Score: 532
Period size: 33 Copynumber: 9.1 Consensus size: 33
28640 TGCTAATCCC
* * *
28650 TATGGCCAACCCT-CACAGCCAAATGCTAATCCA
1 TATGGTCAA-CCTGCACAGCCAAATGCCAGTCCA
28683 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
*
28716 TATGGTCAACCTGCTCAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
28749 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
28782 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
*
28815 TATGGTCAACCTGCTCAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
28848 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
*
28881 TATGGTCAACCTGCACAGCCAAATGCCAGTTCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
28914 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
28947 TATG
1 TATG
28951 CCCAAACCAT
Statistics
Matches: 258, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
32 3 0.01
33 255 0.99
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.20
Consensus pattern (33 bp):
TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
Found at i:29682 original size:15 final size:15
Alignment explanation
Indices: 29658--29716 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
29648 GGGCATGGGA
29658 ATGGGGATGAACAAC
1 ATGGGGATGAACAAC
*
29673 ATGGGAATGAATCCAGGA-
1 ATGGGGATGAA--CA--AC
29691 ATGGGGATGAACAAC
1 ATGGGGATGAACAAC
*
29706 ATGGGCATGAA
1 ATGGGGATGAA
29717 TCCGGGAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 1 0.03
15 20 0.56
16 2 0.06
17 2 0.06
18 10 0.28
19 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.34, T:0.15
Consensus pattern (15 bp):
ATGGGGATGAACAAC
Found at i:29692 original size:33 final size:33
Alignment explanation
Indices: 29655--29729 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
29645 TATGGGCATG
29655 GGAATGGGGATGAACAACATGGGAATGAATCCA
1 GGAATGGGGATGAACAACATGGGAATGAATCCA
* *
29688 GGAATGGGGATGAACAACATGGGCATGAATCCG
1 GGAATGGGGATGAACAACATGGGAATGAATCCA
29721 GGAATGGGG
1 GGAATGGGG
29730 CAGAGACCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.39, T:0.15
Consensus pattern (33 bp):
GGAATGGGGATGAACAACATGGGAATGAATCCA
Found at i:29700 original size:18 final size:18
Alignment explanation
Indices: 29673--29729 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
29663 GATGAACAAC
*
29673 ATGGGAATGAATCCAGGA
1 ATGGGGATGAATCCAGGA
29691 ATGGGGATGAA--CA--A
1 ATGGGGATGAATCCAGGA
* *
29705 CATGGGCATGAATCCGGGA
1 -ATGGGGATGAATCCAGGA
29724 ATGGGG
1 ATGGGG
29730 CAGAGACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 1 0.03
15 10 0.33
16 2 0.07
17 1 0.03
18 15 0.50
19 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.39, T:0.16
Consensus pattern (18 bp):
ATGGGGATGAATCCAGGA
Found at i:30259 original size:27 final size:27
Alignment explanation
Indices: 30221--30272 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
30211 TACATGTGGG
*
30221 GATTACGCTATTCAAACCTGGGTTAAA
1 GATTACGCTATTCAAACCCGGGTTAAA
* *
30248 GATTACGTTATTCGAACCCGGGTTA
1 GATTACGCTATTCAAACCCGGGTTA
30273 TCAAGGGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (27 bp):
GATTACGCTATTCAAACCCGGGTTAAA
Found at i:33167 original size:2 final size:2
Alignment explanation
Indices: 33160--33187 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33150 AATAAAATGA
33160 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
33188 TAGGTCAAAT
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):
AT
Found at i:37703 original size:42 final size:42
Alignment explanation
Indices: 37645--37747 Score: 170
Period size: 42 Copynumber: 2.5 Consensus size: 42
37635 TTTGTACAAG
*
37645 AAGTATTGATATTGTTCTTTGCAGCATCAATACCACATGAAC
1 AAGTATCGATATTGTTCTTTGCAGCATCAATACCACATGAAC
* * *
37687 AAGTATCGATACTGTTCTTTGCAGTATCGATACCACATGAAC
1 AAGTATCGATATTGTTCTTTGCAGCATCAATACCACATGAAC
37729 AAGTATCGATATTGTTCTT
1 AAGTATCGATATTGTTCTT
37748 AGGGTATCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (42 bp):
AAGTATCGATATTGTTCTTTGCAGCATCAATACCACATGAAC
Found at i:41874 original size:26 final size:26
Alignment explanation
Indices: 41825--41876 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
41815 TTATTTACCG
* *
41825 TTCTTTATTTTCTTTAATTGTTTTTC
1 TTCTTTAATTTCTTTAAATGTTTTTC
41851 TTCTTTAATTTCTTTACAAT-TTTTTC
1 TTCTTTAATTTCTTTA-AATGTTTTTC
41877 AATTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.69
Consensus pattern (26 bp):
TTCTTTAATTTCTTTAAATGTTTTTC
Found at i:45991 original size:2 final size:2
Alignment explanation
Indices: 45984--46016 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
45974 GTTTTTAAAG
*
45984 TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
46017 ATCTATGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:46021 original size:10 final size:10
Alignment explanation
Indices: 45984--46022 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
45974 GTTTTTAAAG
*
45984 TCTCTCTCTC
1 TCTCTCTATC
*
45994 TCTCTCTCTC
1 TCTCTCTATC
46004 TCTCTCTATC
1 TCTCTCTATC
*
46014 TCTATCTAT
1 TCTCTCTAT
46023 GCTGCTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.08, C:0.41, G:0.00, T:0.51
Consensus pattern (10 bp):
TCTCTCTATC
Found at i:51717 original size:29 final size:29
Alignment explanation
Indices: 51683--51741 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
51673 CCTAAATTAA
51683 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
51712 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
51741 T
1 T
51742 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:56402 original size:29 final size:29
Alignment explanation
Indices: 56368--56426 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
56358 CCTAAATTAA
56368 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
56397 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
56426 T
1 T
56427 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:59138 original size:3 final size:3
Alignment explanation
Indices: 59118--59217 Score: 130
Period size: 3 Copynumber: 33.7 Consensus size: 3
59108 TTTTTATCCA
* * * *
59118 TAT TGT TAT TAA TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
59166 TAT TAA TAT TAT TAT TAT TTT TAT TAT TAT TTT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
59213 TAT TA
1 TAT TA
59218 AATATATATT
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
2 2 0.02
3 80 0.98
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:60883 original size:32 final size:32
Alignment explanation
Indices: 60828--60899 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
60818 CGGATATTTT
*
60828 TAAATAAATATTTTTTTACAATTTTGAAATTA
1 TAAATAAATATATTTTTACAATTTTGAAATTA
* * *
60860 TAAATTAAATATATTTTT-GAATTTTTAAATTTT
1 TAAA-TAAATATATTTTTACAATTTTGAAA-TTA
60893 TAAATAA
1 TAAATAA
60900 TAGAGACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
32 16 0.47
33 18 0.53
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (32 bp):
TAAATAAATATATTTTTACAATTTTGAAATTA
Found at i:72004 original size:9 final size:9
Alignment explanation
Indices: 71990--72023 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
71980 CTTGAAGAAA
71990 AAAAAAGAG
1 AAAAAAGAG
*
71999 AAAAAAGAAA
1 AAAAAAG-AG
72009 AAAAAAGAG
1 AAAAAAGAG
72018 AAAAAA
1 AAAAAA
72024 AAAGGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:72008 original size:19 final size:19
Alignment explanation
Indices: 71984--72052 Score: 88
Period size: 19 Copynumber: 3.6 Consensus size: 19
71974 ATTATGCTTG
71984 AAGAAAAAAAAAGAGAAAA
1 AAGAAAAAAAAAGAGAAAA
72003 AAGAAAAAAAAAGAGAAAA
1 AAGAAAAAAAAAGAGAAAA
**
72022 AA-AAAGGAAAAGA-AGAAA
1 AAGAAAAAAAAAGAGA-AAA
72040 AAGAAAAAGAAAA
1 AAGAAAAA-AAAA
72053 AAAGGGGTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
17 1 0.02
18 14 0.33
19 24 0.56
20 4 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAAAGAGAAAA
Found at i:72013 original size:21 final size:21
Alignment explanation
Indices: 71987--72055 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
71977 ATGCTTGAAG
71987 AAAAAAAAAGAGAAAAAAGAA
1 AAAAAAAAAGAGAAAAAAGAA
* *
72008 AAAAAAAGAGAAAAAAAAAGGAA
1 AAAAAAAAAG-AGAAAAAA-GAA
*
72031 AAGAAGAAAA-AG-AAAAAGAA
1 AA-AAAAAAAGAGAAAAAAGAA
72051 AAAAA
1 AAAAA
72056 GGGGTCAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.05
20 5 0.13
21 14 0.36
22 8 0.21
23 5 0.13
24 5 0.13
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGAGAAAAAAGAA
Found at i:72023 original size:31 final size:31
Alignment explanation
Indices: 71984--72055 Score: 112
Period size: 31 Copynumber: 2.3 Consensus size: 31
71974 ATTATGCTTG
71984 AAGAAAAAAAAAGAGAAAA-AAGAAAAA-AAA
1 AAGAAAAAAAAAG-GAAAAGAAGAAAAAGAAA
72014 AGAGAAAAAAAAAGGAAAAGAAGAAAAAGAAA
1 A-AGAAAAAAAAAGGAAAAGAAGAAAAAGAAA
72046 AAGAAAAAAA
1 AAGAAAAAAA
72056 GGGGTCAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
30 6 0.15
31 29 0.74
32 4 0.10
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (31 bp):
AAGAAAAAAAAAGGAAAAGAAGAAAAAGAAA
Found at i:72053 original size:12 final size:12
Alignment explanation
Indices: 71984--72053 Score: 65
Period size: 12 Copynumber: 5.7 Consensus size: 12
71974 ATTATGCTTG
71984 AAGAAAAA-AAA
1 AAGAAAAAGAAA
71995 AGAGAAAAAAGAAA
1 A-AG-AAAAAGAAA
72009 AA-AAAAGAGAAA
1 AAGAAAA-AGAAA
*
72021 AA-AAAAGGAAAA
1 AAGAAAAAG-AAA
72033 GAAGAAAAAGAAA
1 -AAGAAAAAGAAA
72046 AAGAAAAA
1 AAGAAAAA
72054 AAGGGGTCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
11 6 0.12
12 24 0.48
13 11 0.22
14 9 0.18
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAA
Found at i:73278 original size:52 final size:52
Alignment explanation
Indices: 73200--73672 Score: 840
Period size: 52 Copynumber: 9.1 Consensus size: 52
73190 AATATGCTCA
73200 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
*
73252 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAAAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
73304 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
* *
73356 AGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTAGACAGAAAAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
*
73408 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGATAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
73460 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
73512 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
* * *
73564 AGCATATTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
* * *
73616 AGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGATTGGACAGAATCA-
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA-CAT
73668 AGCAT
1 AGCAT
73673 TGAATTTAAA
Statistics
Matches: 405, Mismatches: 15, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
52 403 1.00
53 2 0.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (52 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
Found at i:74505 original size:114 final size:114
Alignment explanation
Indices: 74290--74861 Score: 968
Period size: 114 Copynumber: 5.0 Consensus size: 114
74280 TAGCAAAGAT
*
74290 TTGAATTCATCAGACTTGATGGATCATTGTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCT
1 TTGAATTCATCA-AATTGATGGATCATTGTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCT
74355 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
74405 TTGAATTCATCAAATTGATGGATCATTGTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
1 TTGAATTCATCAAATTGATGGATCATTGTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
74470 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
74519 TTGAATTCATCAAATTGATGGATCATTGTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
1 TTGAATTCATCAAATTGATGGATCATTGTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
74584 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
74633 TTGAATTCATCAAATTGATGGATCATCGTTTCCAGAGGAAGAGTTCACAATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATTGTTTCCAGA-GAAG-GTTCATAATGAGAAGAA--C-TC
*
74698 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
61 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *** * *
74752 TTGAATTCATC-ATTTGATGGATCAACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCT
1 TTGAATTCATCAAATTGATGGATCATTGTTTCCAGAG-AAGGTTCATAATGAGAAGAACTCATCT
*
74815 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
74862 GTTTGATGCT
Statistics
Matches: 439, Mismatches: 12, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
113 51 0.12
114 251 0.57
115 16 0.04
116 33 0.08
117 2 0.00
118 20 0.05
119 66 0.15
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (114 bp):
TTGAATTCATCAAATTGATGGATCATTGTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:75197 original size:3 final size:3
Alignment explanation
Indices: 75177--75273 Score: 115
Period size: 3 Copynumber: 32.7 Consensus size: 3
75167 TTTTTATCCA
* * * *
75177 TAT TGT TAT TAA TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
75225 TAA TAT TAT TAT TAT TTT TAT TTT TAT TTT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
75272 TA
1 TA
75274 AATATATTAA
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:76973 original size:32 final size:32
Alignment explanation
Indices: 76918--76989 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
76908 CGGATATTTT
*
76918 TAAATAAATATTTTTTTACAATTTTGAAATTA
1 TAAATAAATATATTTTTACAATTTTGAAATTA
* * *
76950 TAAATTAAATATATTTTT-GAATTTTTAAATTTT
1 TAAA-TAAATATATTTTTACAATTTTGAAA-TTA
76983 TAAATAA
1 TAAATAA
76990 TAGAGACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
32 16 0.47
33 18 0.53
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (32 bp):
TAAATAAATATATTTTTACAATTTTGAAATTA
Found at i:78293 original size:14 final size:15
Alignment explanation
Indices: 78266--78297 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
78256 TTAGTTGAAA
78266 ATTTAAAGATAAAAT
1 ATTTAAAGATAAAAT
78281 ATTTAAA-ATAAAAT
1 ATTTAAAGATAAAAT
78295 ATT
1 ATT
78298 AATTACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
ATTTAAAGATAAAAT
Found at i:78299 original size:13 final size:14
Alignment explanation
Indices: 78263--78299 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
78253 AAATTAGTTG
78263 AAAAT-TTAAAGAT
1 AAAATATTAAAGAT
78276 AAAATATTTAAA-AT
1 AAAATA-TTAAAGAT
78290 AAAATATTAA
1 AAAATATTAA
78300 TTACATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
14 8 0.36
15 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AAAATATTAAAGAT
Found at i:84181 original size:25 final size:25
Alignment explanation
Indices: 84147--84200 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
84137 AAACCCAAAC
*
84147 TCGACGAGTTTCGACTCAATCTGAT
1 TCGACGAGTTTCGACTCAATCCGAT
*
84172 TCGACGAGTTTCGACTCGATCCGAT
1 TCGACGAGTTTCGACTCAATCCGAT
84197 TCGA
1 TCGA
84201 TCGGGTAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (25 bp):
TCGACGAGTTTCGACTCAATCCGAT
Found at i:84437 original size:18 final size:19
Alignment explanation
Indices: 84393--84440 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
84383 AATTAAATCC
*
84393 TTATTTTTATTGAATAAAAA
1 TTATTTTT-TTCAATAAAAA
*
84413 TTATTTTTTTCAATAAATA
1 TTATTTTTTTCAATAAAAA
84432 -TATTTTTTT
1 TTATTTTTTT
84441 GGGTCGGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 9 0.35
19 9 0.35
20 8 0.31
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATTTTTTTCAATAAAAA
Found at i:86515 original size:10 final size:11
Alignment explanation
Indices: 86490--86516 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
86480 AACCTAATTT
86490 TTTTTATTTAA
1 TTTTTATTTAA
86501 TTTTTATTTAA
1 TTTTTATTTAA
86512 TTTTT
1 TTTTT
86517 TAAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTATTTAA
Found at i:87088 original size:189 final size:185
Alignment explanation
Indices: 86682--87099 Score: 439
Period size: 186 Copynumber: 2.2 Consensus size: 185
86672 GACCTCTAAT
* * * ** * * ** *
86682 TTTTTTAATTTTATAAAATAA-TCATTATTTTTTGTTTTTATAGTTGAGGAACAATAATTTAATC
1 TTTTTCAATTTTATAAAATAATTCA-TACTTTCTACTTTTATAATTAAGGGCCCATAATTTAATC
* * * * *
86746 ATTTTCTATGGTTTATTAATTTAATATTAAATTAATTGTTCAAAATAATATAGTCTATTTTCATT
65 ATTTTATATGGTTCATTAATGTAATATTAAATTAATTGTTCAAAATAATATAATATATTTTCATT
** *
86811 CTATAAGACTAATTTTTGAGTTTTCGCTCAAGGTTTATTACTAAGGATCCCTAATGC
130 CTATAAGACT-ATTTTTGAGTTTTCAATCAAGGTTTATAACTAAGGATCCCTAATGC
* *
86868 TTTTTCAATTTTATAAAATAATTCCTACTTTCTTCTTTTATAATTAAGGGCCCATAATTTAATCA
1 TTTTTCAATTTTATAAAATAATTCATACTTTCTACTTTTATAATTAAGGGCCCATAATTTAATCA
* * *
86933 TTTTATATGGTTCATTAATGTAATATTAAATTAGTTTTTTTTTCAAAATAATATAATATATTTTT
66 TTTTATATGGTTCATTAATGTAATATTAAATTA----ATTGTTCAAAATAATATAATATATTTTC
* * * * ** * *
86998 GTTCTATAGGGTCT-TTTTTTAGTTTTCAATTGAGGTTTATAACTAAGG-GCTCCTAAT-T
127 ATTCTATA-AGACTATTTTTGAGTTTTCAATCAAGGTTTATAACTAAGGATC-CCTAATGC
*
87056 TTTTTCCAATTTTATAAAATAGTTCATACTTTCTACTTTTATAA
1 TTTTT-CAATTTTATAAAATAATTCATACTTTCTACTTTTATAA
87100 CCGAGGCTCA
Statistics
Matches: 191, Mismatches: 33, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
186 81 0.42
187 2 0.01
188 6 0.03
189 69 0.36
190 30 0.16
191 3 0.02
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.50
Consensus pattern (185 bp):
TTTTTCAATTTTATAAAATAATTCATACTTTCTACTTTTATAATTAAGGGCCCATAATTTAATCA
TTTTATATGGTTCATTAATGTAATATTAAATTAATTGTTCAAAATAATATAATATATTTTCATTC
TATAAGACTATTTTTGAGTTTTCAATCAAGGTTTATAACTAAGGATCCCTAATGC
Found at i:91183 original size:23 final size:23
Alignment explanation
Indices: 91153--91202 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
91143 ATCCTGTTTT
91153 TTTTTTTTTTGGAACATTTTTCA
1 TTTTTTTTTTGGAACATTTTTCA
91176 TTTTTTTTTTGGAACATTTTTCA
1 TTTTTTTTTTGGAACATTTTTCA
91199 TTTT
1 TTTT
91203 GGAGCAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (23 bp):
TTTTTTTTTTGGAACATTTTTCA
Found at i:93280 original size:2 final size:2
Alignment explanation
Indices: 93273--93322 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
93263 AATTAAATTG
93273 AT AT AT AT AT 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 AT AT AT AT AT
93315 AT AT AT AT
1 AT AT AT AT
93323 TAAATTTTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93777 original size:13 final size:13
Alignment explanation
Indices: 93738--93778 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
93728 ATATGTACAC
93738 AAATGTAATGAAA
1 AAATGTAATGAAA
* **
93751 AATTGTAACAAAA
1 AAATGTAATGAAA
93764 AAATGTAATGAAA
1 AAATGTAATGAAA
93777 AA
1 AA
93779 TAAAGAAATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.22
Consensus pattern (13 bp):
AAATGTAATGAAA
Found at i:97487 original size:22 final size:21
Alignment explanation
Indices: 97462--97502 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
97452 TGAAATTGAG
97462 TGAAAAGATTTGCTGGAAATTC
1 TGAAAAG-TTTGCTGGAAATTC
* *
97484 TGAACAGTTTGCTGTAAAT
1 TGAAAAGTTTGCTGGAAAT
97503 GGTAAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (21 bp):
TGAAAAGTTTGCTGGAAATTC
Found at i:98395 original size:17 final size:17
Alignment explanation
Indices: 98373--98420 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
98363 TATCTGCTTT
98373 ATGAATGTGCTGCTGAC
1 ATGAATGTGCTGCTGAC
98390 ATGAATGTGCTGCTGAC
1 ATGAATGTGCTGCTGAC
98407 ATGAATGTGCTGCT
1 ATGAATGTGCTGCT
98421 TCATGTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (17 bp):
ATGAATGTGCTGCTGAC
Found at i:106229 original size:15 final size:16
Alignment explanation
Indices: 106209--106238 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
106199 TACAAATCTA
106209 TTAAAAGTAA-AACTT
1 TTAAAAGTAATAACTT
106224 TTAAAAGTAATAACT
1 TTAAAAGTAATAACT
106239 GGCGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (16 bp):
TTAAAAGTAATAACTT
Found at i:118334 original size:19 final size:19
Alignment explanation
Indices: 118310--118347 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
118300 ACCGAAGGAA
118310 CTTATGCTTCCTACATATG
1 CTTATGCTTCCTACATATG
118329 CTTATGCTTCCTACATATG
1 CTTATGCTTCCTACATATG
118348 TTCTACATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (19 bp):
CTTATGCTTCCTACATATG
Done.