Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006598.1 Hibiscus syriacus cultivar Beakdansim tig00016186_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: 63052
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1035 original size:48 final size:49
Alignment explanation
Indices: 982--1151 Score: 220
Period size: 48 Copynumber: 3.3 Consensus size: 49
972 TAAGATTTAG
982 TAATGATTAGTAATGATGAAATTA-TATTAATATTTAATGATTTGATAT
1 TAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAT
* *
1030 TAATGATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGATAG
1 TAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAT
1078 TAATGATTAGTAATGATTAGTAATAATAATTATTATTAATATTTAATGA-TTGATAT
1 TAATGATTAGTAATGA-T-G-----A-AATTATTATTAATATTTAATGATTTGATAT
1134 TAATGATTTAGTAATGAT
1 TAATGA-TTAGTAATGAT
1152 TTGATAGTAA
Statistics
Matches: 107, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
48 53 0.50
49 8 0.07
50 1 0.01
55 1 0.01
56 26 0.24
57 18 0.17
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (49 bp):
TAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAT
Found at i:1090 original size:10 final size:10
Alignment explanation
Indices: 1075--1101 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1065 AATGATTTGA
1075 TAGTAATGAT
1 TAGTAATGAT
1085 TAGTAATGAT
1 TAGTAATGAT
1095 TAGTAAT
1 TAGTAAT
1102 AATAATTATT
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:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:1091 original size:24 final size:24
Alignment explanation
Indices: 982--1095 Score: 76
Period size: 24 Copynumber: 4.8 Consensus size: 24
972 TAAGATTTAG
982 TAATGATTAGTAATGATGAAATT-ATAT
1 TAATGATTAGTAATGAT----TTGATAT
1009 TAAT-ATT--TAATGATTTGATAT
1 TAATGATTAGTAATGATTTGATAT
* ***
1030 TAATGATTAGTAATAATGAAATTAT
1 TAATGATTAGTAATGATTTGA-TAT
* * * *
1055 TATTAATT-TTAATGATTTGATAG
1 TAATGATTAGTAATGATTTGATAT
1078 TAATGATTAGTAATGATT
1 TAATGATTAGTAATGATT
1096 AGTAATAATA
Statistics
Matches: 66, Mismatches: 15, Indels: 15
0.69 0.16 0.16
Matches are distributed among these distances:
20 2 0.03
21 8 0.12
22 3 0.05
23 8 0.12
24 29 0.44
25 9 0.14
26 3 0.05
27 4 0.06
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (24 bp):
TAATGATTAGTAATGATTTGATAT
Found at i:1162 original size:25 final size:24
Alignment explanation
Indices: 1121--1168 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
1111 TATTAATATT
*
1121 TAATGATTGATATTAATGATTTAG
1 TAATGATTGATAGTAATGATTTAG
1145 TAATGATTTGATAGTAATGATTTA
1 TAATGA-TTGATAGTAATGATTTA
1169 CGACTTGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (24 bp):
TAATGATTGATAGTAATGATTTAG
Found at i:1167 original size:14 final size:13
Alignment explanation
Indices: 1121--1166 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
1111 TATTAATATT
*
1121 TAATGATTGATAT
1 TAATGATTGATAG
1134 TAATGATT--TAG
1 TAATGATTGATAG
1145 TAATGATTTGATAG
1 TAATGA-TTGATAG
1159 TAATGATT
1 TAATGATT
1167 TACGACTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 10 0.34
14 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (13 bp):
TAATGATTGATAG
Found at i:1368 original size:11 final size:11
Alignment explanation
Indices: 1352--1438 Score: 52
Period size: 11 Copynumber: 7.6 Consensus size: 11
1342 AATGATTTGA
1352 TAGTAATGATT
1 TAGTAATGATT
1363 TAGTAATGA-T
1 TAGTAATGATT
* *
1373 TAGTAATAATG
1 TAGTAATGATT
* * * *
1384 AAATTATTATT
1 TAGTAATGATT
*
1395 AATATTAATGATTT
1 --TAGTAATGA-TT
1409 GATAGTAATGATT
1 --TAGTAATGATT
1422 TAGTAATGA-T
1 TAGTAATGATT
1432 TAGTAAT
1 TAGTAAT
1439 AATGAAATTG
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
10 17 0.29
11 24 0.41
13 7 0.12
14 11 0.19
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:1376 original size:21 final size:19
Alignment explanation
Indices: 1352--1439 Score: 54
Period size: 21 Copynumber: 4.4 Consensus size: 19
1342 AATGATTTGA
1352 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-A-TTAGTAATGAT
* * *
1373 TAGTAATAAT-GAAATTAT
1 TAGTAATATTAGTAATGAT
* * *
1391 TATTAATATTAATGATTTGA-
1 TAGTAATATTAGT-A-ATGAT
1411 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-A-TTAGTAATGAT
1432 TAGTAATA
1 TAGTAATA
1440 ATGAAATTGT
Statistics
Matches: 49, Mismatches: 12, Indels: 13
0.66 0.16 0.18
Matches are distributed among these distances:
18 14 0.29
19 1 0.02
20 12 0.24
21 18 0.37
22 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (19 bp):
TAGTAATATTAGTAATGAT
Found at i:1489 original size:58 final size:59
Alignment explanation
Indices: 1240--1874 Score: 821
Period size: 58 Copynumber: 11.3 Consensus size: 59
1230 GAACTTATAA
*
1240 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATT-ATATTTAATGATTTGATAG
*
1300 TAATGA-TTAG---T-ATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATT-ATATTTAATGATTTGATAG
1355 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTA-ATATTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTATAT-TTAATGATTTGATAG
*
1414 TAATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTA-ATTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTATATTTAATGATTTGATAG
1472 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGA-TTGATA-
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATT-ATATTTAATGATTTGATAG
* *
1530 T-ATGATTT-G-AGT-ATTAG---TAATGAAATTA-TATTAATTTTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATT-ATATTTAATGATTTGATAG
*
1582 TAATGA-TTAGT-ATGATTAGTAATAATG-AATTATTATTAATATTTAATGA-TTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATT-ATATTTAATGATTTGATAG
*
1638 TAATGATTTAGTAATGATTAGT-ATAATGAAATTGTTATTA-ATATTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTATAT-TTAATGATTTGATAG
1696 TAATGATTTAGTAATGATTAG-AATAATGAAATT-TTATTTATATTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTA-TTATATTTAATGATTTGATAG
1754 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTA-T-T-TTT-A--A-TT-AT--
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTATATTTAATGATTTGATAG
* * *
1803 T--TGA--TAGTAATGATTAGTAATAAT-AATTTATT-TAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTATATTTAATGATTTGATAG
1856 TAATGATTTAGTAATGATT
1 TAATGATTTAGTAATGATT
1875 TGATAGTAAC
Statistics
Matches: 519, Mismatches: 14, Indels: 87
0.84 0.02 0.14
Matches are distributed among these distances:
44 7 0.01
45 21 0.04
46 3 0.01
47 4 0.01
49 2 0.00
50 17 0.03
51 21 0.04
52 5 0.01
53 8 0.02
54 10 0.02
55 54 0.10
56 28 0.05
57 61 0.12
58 153 0.29
59 84 0.16
60 41 0.08
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (59 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTATATTTAATGATTTGATAG
Found at i:1666 original size:282 final size:279
Alignment explanation
Indices: 979--1874 Score: 1015
Period size: 282 Copynumber: 3.2 Consensus size: 279
969 TTATAAGATT
*
979 TAGTAATGATTAGTAATGATGAAATTATATTAATATTTAATGATTTG------AT-ATTA--ATG
1 TAGTAATGATTAGTAATAATGAAATTATATTAATATTTAATGATTTGATATTAATGATTAGTATG
1035 ATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGATAGTAATGA-TTAGTAATGATTAG
66 ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAG
* *
1098 TAATAAT--AATTATTATTAATATTTAATGA-TTGATATTAATGATTTAGTAATGATTTGATAGT
131 TAATAATGAAATTATTATTAATA-TTAATGATTTGATAGTAATGATTTAGTAATGATTAGA-A-T
* * * ** * * * ** * *
1160 AATG--ATTTACGACTTGAACAATGAACAATG-TTTGGT--TCA--ATTAACCATAT-TTTCGTT
193 AATGAAATTT--TA-TT-TA-TAT--TTAATGATTTGATAGTAATGATTTAGTA-ATGATTAG-T
* * **
1217 ACATAACTGTAATGAACTTA-TAATAATGA-TT--
249 A-ATAA-TGAAAT-TA-TTATTTTTAATGATTTGA
1248 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTAG--T
1 TAGTAATGATTAGTAATAATGAAATTA-TATTAATATTTAATGATTTGATATTAATGATTAGTAT
*
1311 -ATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTA
65 GATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTA
1375 GTAATAATGAAATTATTATTAATATTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATA
130 GTAATAATGAAATTATTATTAATATTAATGATTTGATAGTAATGATTTAGTAATGATTAG-AATA
1440 ATGAAATTGTTA-TTA-ATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAA
194 ATGAAATT-TTATTTATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAA
1503 ATTATTATTAATATTTAATGA-TTGA
258 ATTATTA-T--T-TTTAATGATTTGA
* *
1528 TA-T-ATGATTTGAGTATTAGTAATGAAATTATATTAATTTTTAATGATTTGATAGTAATGATTA
1 TAGTAATGA-TT-AGTA--A-TAATGAAATTATATTAATATTTAATGATTTGATATTAATGATTA
*
1591 GTATGATTAGTAATAATG-AATTATTATTAATATTTAATGA-TTGATATTAATGATTTAGTAATG
61 GTATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATG
*
1654 ATTAGT-ATAATGAAATTGTTATTAATATTAATGATTTGATAGTAATGATTTAGTAATGATTAGA
126 ATTAGTAATAATGAAATTATTATTAATATTAATGATTTGATAGTAATGATTTAGTAATGATTAGA
1718 ATAATGAAATTTTATTTATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATG
191 ATAATGAAATTTTATTTATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATG
*
1783 AAATTATTATTTTTAATTATTTGA
256 AAATTATTATTTTTAATGATTTGA
*
1807 TAGTAATGATTAGTAATAAT-AATTTAT-TTAATATTTAATGATTTGATATTAATGATTTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATATTAATATTTAATGATTTGATATTAATGA-TTAGT-A
1870 TGATT
64 TGATT
1875 TGATAGTAAC
Statistics
Matches: 553, Mismatches: 28, Indels: 85
0.83 0.04 0.13
Matches are distributed among these distances:
269 26 0.05
270 20 0.04
273 7 0.01
274 32 0.06
275 18 0.03
276 44 0.08
277 34 0.06
278 49 0.09
279 26 0.05
280 54 0.10
281 24 0.04
282 145 0.26
283 39 0.07
284 22 0.04
285 13 0.02
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.45
Consensus pattern (279 bp):
TAGTAATGATTAGTAATAATGAAATTATATTAATATTTAATGATTTGATATTAATGATTAGTATG
ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAG
TAATAATGAAATTATTATTAATATTAATGATTTGATAGTAATGATTTAGTAATGATTAGAATAAT
GAAATTTTATTTATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATT
ATTATTTTTAATGATTTGA
Found at i:1757 original size:14 final size:14
Alignment explanation
Indices: 1740--1883 Score: 59
Period size: 14 Copynumber: 10.2 Consensus size: 14
1730 TATTTATATT
1740 TAATGATTTGATAG
1 TAATGATTTGATAG
1754 TAATGA-TT--TAG
1 TAATGATTTGATAG
* *
1765 TAATGATTAG-TAA
1 TAATGATTTGATAG
* **
1778 TAATGAAATTATTATTTT
1 TAATG--ATT-TGA-TAG
*
1796 TAATTATTTGATAG
1 TAATGATTTGATAG
* *
1810 TAATGATTAGTAATAA
1 TAATGATT--TGATAG
* * *
1826 TAATTTATTTAATATT
1 TAA-TGATTTGATA-G
*
1842 TAATGATTTGATAT
1 TAATGATTTGATAG
1856 TAATGA-TT--TAG
1 TAATGATTTGATAG
1867 TAATGATTTGATAG
1 TAATGATTTGATAG
1881 TAA
1 TAA
1884 CTATTTTCCA
Statistics
Matches: 98, Mismatches: 18, Indels: 28
0.68 0.12 0.19
Matches are distributed among these distances:
11 17 0.17
12 3 0.03
13 11 0.11
14 27 0.28
15 18 0.18
16 13 0.13
17 4 0.04
18 5 0.05
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:1769 original size:25 final size:25
Alignment explanation
Indices: 1740--1883 Score: 86
Period size: 25 Copynumber: 5.7 Consensus size: 25
1730 TATTTATATT
1740 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
* * *
1765 TAATGATTAG-TAATAATGAAATTATTATTTT
1 TAATGATTTGATAGTAATG--A-T-TTA---G
*
1796 TAATTATTTGATAGTAATGA-TTAG
1 TAATGATTTGATAGTAATGATTTAG
* * *
1820 TAATAATAATTTAT-TTAAT-A-TT--
1 TAATGAT--TTGATAGTAATGATTTAG
*
1842 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
1867 TAATGATTTGATAGTAA
1 TAATGATTTGATAGTAA
1884 CTATTTTCCA
Statistics
Matches: 91, Mismatches: 13, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
20 4 0.04
21 5 0.05
22 7 0.08
23 2 0.02
24 16 0.18
25 29 0.32
26 5 0.05
27 4 0.04
28 3 0.03
30 1 0.01
31 8 0.09
32 7 0.08
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:1812 original size:45 final size:46
Alignment explanation
Indices: 1762--1870 Score: 150
Period size: 45 Copynumber: 2.4 Consensus size: 46
1752 AGTAATGATT
* *
1762 TAGTAATGATTAGTAATAATGAAATTA-TT-ATTTTTAATTATTTGA
1 TAGTAATGATTAGTAATAAT-AAATTATTTAATATTTAATGATTTGA
*
1807 TAGTAATGATTAGTAATAATAATTTATTTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAATTATTTAATATTTAATGATTTGA
*
1853 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
1871 GATTTGATAG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
44 5 0.09
45 22 0.39
46 22 0.39
47 8 0.14
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (46 bp):
TAGTAATGATTAGTAATAATAAATTATTTAATATTTAATGATTTGA
Found at i:1859 original size:116 final size:112
Alignment explanation
Indices: 1240--1875 Score: 607
Period size: 115 Copynumber: 5.6 Consensus size: 112
1230 GAACTTATAA
* * *
1240 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
1 TAATGATTTAGTAATGAATAG-AATAATGAAATT-TTATTTATATTTAATGA-TT--TAGTAATG
*
1305 A-TTAG---T-ATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAG
61 ATTTAGTAATGATTAGT-ATAATGAAATTATTATT-ATA-TTAATGATTTGATAG
* *
1355 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATA-TTAATGATTTGATAGTAATG
1 TAATGATTTAGTAATGAATAG-AATAATGAAATT-TTATTTATATTTAATGA-TT--TAGTAATG
*
1419 ATTTAGTAATGATTAGTAATAATGAAATTGTTATTA-ATTTAATGATTTGATAG
61 ATTTAGTAATGATTAGT-ATAATGAAATTATTATTATA-TTAATGATTTGATAG
* * *
1472 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTGA-TATATGAT
1 TAATGATTTAGTAATGAATAG-AATAATGAAATT-TTATTTATATTTAATGATTTAGTA-ATGAT
* *
1536 TT-G-AGT-ATTAG--TAATGAAATTA-TATTAATTTTTAATGATTTGATAG
63 TTAGTAATGATTAGTATAATGAAATTATTATT-A-TATTAATGATTTGATAG
* * *
1582 TAATGA-TTAGT-ATGATTAGTAATAATG-AATTATTATTAATATTTAATGATTGATATTAATGA
1 TAATGATTTAGTAATGAATAG-AATAATGAAATT-TTATTTATATTTAATGATT--TAGTAATGA
*
1644 TTTAGTAATGATTAGTATAATGAAATTGTTATTAATATTAATGATTTGATAG
62 TTTAGTAATGATTAGTATAATGAAATTATTATT-ATATTAATGATTTGATAG
*
1696 TAATGATTTAGTAATGATTAGAATAATGAAATTTTATTTATATTTAATGATTTGATAGTAATGAT
1 TAATGATTTAGTAATGAATAGAATAATGAAATTTTATTTATATTTAATGA-TT--TAGTAATGAT
*
1761 TTAGTAATGATTAGTAATAATGAAATTATTATT-T-TTAATTATTTGATAG
63 TTAGTAATGATTAGT-ATAATGAAATTATTATTATATTAATGATTTGATAG
* * *
1810 TAATGA-TTAGTAAT-AATA-ATTTATTTAATATTTAATGATTTGATA-TTAATGATTTAGTAAT
1 TAATGATTTAGTAATGAATAGA-ATAATGAA-ATTT--T-ATTT-ATATTTAATGATTTAGTAAT
1871 GATTT
60 GATTT
1876 GATAGTAACT
Statistics
Matches: 474, Mismatches: 17, Indels: 62
0.86 0.03 0.11
Matches are distributed among these distances:
107 24 0.05
108 20 0.04
109 24 0.05
110 24 0.05
111 3 0.01
112 18 0.04
113 26 0.05
114 75 0.16
115 94 0.20
116 51 0.11
117 82 0.17
118 9 0.02
119 24 0.05
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (112 bp):
TAATGATTTAGTAATGAATAGAATAATGAAATTTTATTTATATTTAATGATTTAGTAATGATTTA
GTAATGATTAGTATAATGAAATTATTATTATATTAATGATTTGATAG
Found at i:4217 original size:35 final size:37
Alignment explanation
Indices: 4177--4252 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 37
4167 AATATTCTTT
4177 TATATAACTAA-AAC-TAATAAACT-ATTTTTCAT-TAA
1 TATAT-ACTAATAACTTAAT-AACTAATTTTTCATATAA
* *
4212 TATATACTAATAACTTACTAACTAATTTTTTATATAA
1 TATATACTAATAACTTAATAACTAATTTTTCATATAA
4249 TATA
1 TATA
4253 AATTCAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 5 0.14
35 12 0.34
36 11 0.31
37 7 0.20
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (37 bp):
TATATACTAATAACTTAATAACTAATTTTTCATATAA
Found at i:4628 original size:26 final size:26
Alignment explanation
Indices: 4580--4639 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
4570 TTCTCCCTTT
* *
4580 CTTTCTTTCGGCTGTAATTTCTTCTCC
1 CTTTC-TTCGGCTGCAATCTCTTCTCC
*
4607 CTTTCTTCTGCTGCAATCTCTTCTCC
1 CTTTCTTCGGCTGCAATCTCTTCTCC
4633 CTTTCTT
1 CTTTCTT
4640 TCTTTTATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.07, C:0.33, G:0.08, T:0.52
Consensus pattern (26 bp):
CTTTCTTCGGCTGCAATCTCTTCTCC
Found at i:4725 original size:33 final size:33
Alignment explanation
Indices: 4683--4749 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
4673 ATAATTTAGG
4683 TGTCACCGGCTGCCTCAATTATTTCACCAATAA
1 TGTCACCGGCTGCCTCAATTATTTCACCAATAA
4716 TGTCACCGGCTGCCTCAATTATTTCACCAATAA
1 TGTCACCGGCTGCCTCAATTATTTCACCAATAA
4749 T
1 T
4750 TGTGCAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (33 bp):
TGTCACCGGCTGCCTCAATTATTTCACCAATAA
Found at i:4898 original size:18 final size:19
Alignment explanation
Indices: 4866--4904 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
4856 AGACATGCAG
4866 CGGGAGCAGGAGGGGAGCA
1 CGGGAGCAGGAGGGGAGCA
4885 CGGGAGCA-GAGGGGAGCA
1 CGGGAGCAGGAGGGGAGCA
4903 CG
1 CG
4905 TGAAGCTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.26, C:0.18, G:0.56, T:0.00
Consensus pattern (19 bp):
CGGGAGCAGGAGGGGAGCA
Found at i:8876 original size:47 final size:45
Alignment explanation
Indices: 8806--8930 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
8796 TATAAAATCC
* *
8806 CTTACCATTTATCCCATAAGCTCGTAGGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
8851 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
**
8898 CTTGTCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
8931 GCATACTTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 21 0.29
44 3 0.04
45 10 0.14
46 2 0.03
47 36 0.50
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:12829 original size:17 final size:17
Alignment explanation
Indices: 12786--12847 Score: 72
Period size: 18 Copynumber: 3.6 Consensus size: 17
12776 CAAGTGAAAT
* *
12786 ATTTTTTTTTCATCTCTC
1 ATTTTTTTCTCAT-TTTC
*
12804 ATTTTTTTCTC-TTTTT
1 ATTTTTTTCTCATTTTC
12820 ATTTTCTTTCTCATTTTC
1 ATTTT-TTTCTCATTTTC
12838 ATTTTTTTCT
1 ATTTTTTTCT
12848 TCTTCGTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
16 7 0.18
17 12 0.32
18 19 0.50
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTTTCTCATTTTC
Found at i:12847 original size:21 final size:22
Alignment explanation
Indices: 12821--12881 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 22
12811 TCTCTTTTTA
12821 TTTTCTT-TCTCATTTTC-ATTT
1 TTTTCTTCT-TCATTTTCTATTT
*
12842 TTTTCTTCTTCGTTTTCTATTTT
1 TTTTCTTCTTCATTTTCTA-TTT
12865 TTTTCTTCTTCTATTTT
1 TTTTCTTCTTC-ATTTT
12882 TTTTCTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 14 0.41
22 2 0.06
23 14 0.41
24 4 0.12
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTCTTCTTCATTTTCTATTT
Found at i:12870 original size:40 final size:38
Alignment explanation
Indices: 12785--12891 Score: 93
Period size: 40 Copynumber: 2.9 Consensus size: 38
12775 ACAAGTGAAA
*
12785 TATTTTTTTT-TCATCTCTCA--TTTTT-TTC-TCTTTT
1 TATTTTTTTTCTCAT-TTTCATTTTTTTCTTCTTCTTTT
*
12819 TATTTTCTTTCTCATTTTCATTTTTTTCTTCTTCGTTTT
1 TATTTTTTTTCTCATTTTCATTTTTTTCTTCTTC-TTTT
*
12858 CTATTTTTTTTCT--TCTTCTATTTTTTTTCTTCTT
1 -TATTTTTTTTCTCATTTTC-A-TTTTTTTCTTCTT
12892 ATAATATATA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
34 13 0.22
35 4 0.07
36 5 0.08
37 3 0.05
38 6 0.10
39 5 0.08
40 24 0.40
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (38 bp):
TATTTTTTTTCTCATTTTCATTTTTTTCTTCTTCTTTT
Found at i:12878 original size:17 final size:17
Alignment explanation
Indices: 12788--12891 Score: 74
Period size: 17 Copynumber: 5.8 Consensus size: 17
12778 AGTGAAATAT
*
12788 TTTTTTTTCATC-TCTCA
1 TTTTTTTTCTTCTTCT-A
12805 TTTTTTTCTCTT-TT-TA
1 TTTTTTT-TCTTCTTCTA
12821 TTTTCTTTCTCATT-TTC-A
1 TTTT-TTT-TC-TTCTTCTA
12839 TTTTTTTCTTCTTCGTTTTCTA
1 -TTTTTT-TTCTTC---TTCTA
12861 TTTTTTTTCTTCTTCTA
1 TTTTTTTTCTTCTTCTA
12878 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
12892 ATAATATATA
Statistics
Matches: 74, Mismatches: 1, Indels: 24
0.75 0.01 0.24
Matches are distributed among these distances:
16 5 0.07
17 35 0.47
18 13 0.18
19 5 0.07
20 6 0.08
21 9 0.12
22 1 0.01
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (17 bp):
TTTTTTTTCTTCTTCTA
Found at i:15629 original size:47 final size:45
Alignment explanation
Indices: 15559--15683 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
15549 TATAAAATCT
* *
15559 CTTACCATTTATCCCATAAGCTCGTAGGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
15604 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
15651 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
15684 GCATACTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
43 21 0.29
44 3 0.04
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:15691 original size:38 final size:41
Alignment explanation
Indices: 15559--15697 Score: 122
Period size: 47 Copynumber: 3.2 Consensus size: 41
15549 TATAAAATCT
* * *
15559 CTTACCATTTATCCCATAAGCTCGTAGGCTTATTTTACCAAAATA
1 CTTACCA-TTAT-TCATAAGCTCGTAAGCTTATTTTAGC--AATA
*
15604 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCA-TT--ATT-CATAAGCTCGTAAGCTTATTTTAGC-A-ATA
*
15651 CTTGCCATTATTCATAAGCTCGTAAGCTTA-TTT-GC-ATA
1 CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
15689 CTTACCATT
1 CTTACCATT
15698 TATTAACTAA
Statistics
Matches: 84, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
38 11 0.13
41 1 0.01
42 3 0.04
43 18 0.21
44 3 0.04
45 10 0.12
46 4 0.05
47 34 0.40
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (41 bp):
CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
Found at i:23011 original size:20 final size:21
Alignment explanation
Indices: 22986--23025 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
22976 CTTTGAATAG
22986 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
23006 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
23026 CCCAACGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:23658 original size:90 final size:92
Alignment explanation
Indices: 23492--23663 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 92
23482 CTGCTAGACC
* *
23492 TAACACACTCTTTTATAGCAAAGTTACCCTAATCATATTAGGGTTTTTTATTATTTCAAATTAAT
1 TAACAAACTCTTTTATAGCAAAGTTACCCTAATCATATTAGGGTATTTTATTATTTCAAATTAAT
23557 TAAATATATATTTAATTGATTAGAATT
66 TAAATATATATTTAATTGATTAGAATT
* *
23584 TAACAAAC-CTTTTATATCCAAGTTACCCTAATCATATTAGGG-ATTTTATTATTTCAAATTAAT
1 TAACAAACTCTTTTATAGCAAAGTTACCCTAATCATATTAGGGTATTTTATTATTTCAAATTAAT
*
23647 TAAATCTATATTTAATT
66 TAAATATATATTTAATT
23664 AATTGAAATT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
90 36 0.48
91 32 0.43
92 7 0.09
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.44
Consensus pattern (92 bp):
TAACAAACTCTTTTATAGCAAAGTTACCCTAATCATATTAGGGTATTTTATTATTTCAAATTAAT
TAAATATATATTTAATTGATTAGAATT
Found at i:31068 original size:24 final size:24
Alignment explanation
Indices: 31041--31104 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
31031 TTCAATGCAT
*
31041 CATTTCCTTTAGGCTTAGGCTTAC
1 CATTTCCCTTAGGCTTAGGCTTAC
31065 CATTTCCCTTAGGCTTAGGCTTAC
1 CATTTCCCTTAGGCTTAGGCTTAC
31089 CATTTCCCTTAGGCTT
1 CATTTCCCTTAGGCTT
31105 TGTTATTGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.41
Consensus pattern (24 bp):
CATTTCCCTTAGGCTTAGGCTTAC
Found at i:48343 original size:23 final size:24
Alignment explanation
Indices: 48316--48361 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
48306 ATTAGTTGTT
*
48316 ATAATAGATATA-AAATGATAAAA
1 ATAATAGATATATAAATAATAAAA
*
48339 ATAATATATATATAAATAATAAA
1 ATAATAGATATATAAATAATAAA
48362 TAAAAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
ATAATAGATATATAAATAATAAAA
Found at i:49619 original size:2 final size:2
Alignment explanation
Indices: 49612--49643 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49602 TTTTATTTGT
49612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49644 GGCATATTGT
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):
TA
Done.