Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018539.1 Corchorus olitorius cultivar O-4 contig18572, 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: 48441
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:222 original size:46 final size:46
Alignment explanation
Indices: 157--255 Score: 132
Period size: 47 Copynumber: 2.2 Consensus size: 46
147 TGTTATTACT
*
157 TTTTAC-TTTTTAGCTTAATTAACTCT-A-CTACTGATTACTCTTGC
1 TTTTACTTTTTTAGCTTAATT-ACTCTAATCTACTGATTAATCTTGC
* *
201 TTTTACTTGTTTTAGCTTAATTACTCTAATCTTCTGATTAATCTTTC
1 TTTTACTT-TTTTAGCTTAATTACTCTAATCTACTGATTAATCTTGC
248 TTTTACTT
1 TTTTACTT
256 CTGATTACTC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 6 0.12
45 6 0.12
46 14 0.29
47 22 0.46
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.55
Consensus pattern (46 bp):
TTTTACTTTTTTAGCTTAATTACTCTAATCTACTGATTAATCTTGC
Found at i:257 original size:22 final size:22
Alignment explanation
Indices: 231--360 Score: 160
Period size: 22 Copynumber: 6.1 Consensus size: 22
221 TTACTCTAAT
*
231 CTTCTGATTAATCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
253 CTTCTGATTACTCTTTC--TT-
1 CTTCTGATTACTCTTTCTTTTA
**
272 CTTCTGATTACTCTTTCTTTGG
1 CTTCTGATTACTCTTTCTTTTA
* * *
294 CTTTTGATTATTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
*
316 C-TCTGATTACTCTTTCTATTA
1 CTTCTGATTACTCTTTCTTTTA
*
337 CTTCTGATTACGCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
359 CT
1 CT
361 GCTTAGCTTG
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
19 17 0.19
20 2 0.02
21 18 0.20
22 54 0.59
ACGTcount: A:0.14, C:0.22, G:0.07, T:0.57
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTTTA
Found at i:281 original size:41 final size:41
Alignment explanation
Indices: 230--355 Score: 153
Period size: 41 Copynumber: 3.0 Consensus size: 41
220 ATTACTCTAA
*
230 TCTTCTGATTAATCTTTCTTTTACTTCTGATTACTCTTTCT
1 TCTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCT
** * * *
271 TCTTCTGATTACTCTTTCTTTGGCTTTTGATTATTCTTCCT
1 TCTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCT
* * *
312 TTTACTCTGATTACTCTTTCTATTACTTCTGATTACGCTTTCT
1 TCT--TCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCT
355 T
1 T
356 TTACTGCTTA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
41 37 0.54
43 32 0.46
ACGTcount: A:0.13, C:0.22, G:0.07, T:0.57
Consensus pattern (41 bp):
TCTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCT
Found at i:345 original size:43 final size:42
Alignment explanation
Indices: 233--360 Score: 152
Period size: 43 Copynumber: 3.0 Consensus size: 42
223 ACTCTAATCT
* *
233 TCTGATTAATCTTTCTTTTACTTCTGATTACTCTTTCTTCT--
1 TCTGATTACTCTTTC-TTTACTTCTGATTACTCTTTCTTTTAC
* * * *
274 TCTGATTACTCTTTCTTTGGCTTTTGATTATTCTTCCTTTTAC
1 TCTGATTACTCTTTCTTT-ACTTCTGATTACTCTTTCTTTTAC
*
317 TCTGATTACTCTTTCTATTACTTCTGATTACGCTTTCTTTTAC
1 TCTGATTACTCTTTCT-TTACTTCTGATTACTCTTTCTTTTAC
360 T
1 T
361 GCTTAGCTTG
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.04
41 31 0.43
43 36 0.50
44 2 0.03
ACGTcount: A:0.14, C:0.22, G:0.07, T:0.57
Consensus pattern (42 bp):
TCTGATTACTCTTTCTTTACTTCTGATTACTCTTTCTTTTAC
Found at i:424 original size:47 final size:47
Alignment explanation
Indices: 371--1401 Score: 707
Period size: 47 Copynumber: 22.1 Consensus size: 47
361 GCTTAGCTTG
* *
371 ATTACCCAGAATCAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * * * *
418 ATTACCCTGAATTAAACTCTTTTCTTCCTCTTTTACTTTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * *
465 ATTACCTAGAATTAAACTAGCCTCTGTGTACTTCTTCTTTTACTCTTTAGTTTG
1 ATTACCCAGAATTAAACT-G--T-T-T-T-CTTCTTCTCTTACTCTTTAGTTTA
* *
519 ATTACCAAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * * *
566 ATTACCCTGAATTAAACTCTTTTCTTCTTCTCTTACTTTTTGGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * *
613 GTTACCCAGAATTAAAATGTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * *
660 ATTACCCAGAATTAAATTGTTTTCTTCTTCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * * * *
707 ATTACCCGGAATTAAACTCTTTTCATCTTCTCTTAATTTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * *
754 GTTACCCAGAATTAAAATGTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
** * * *
801 ATTACCTGGAATTAAACTCTTTTCTTCTTCTCTTAATTTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * * * *
848 ATTAACCCAG--TT--TCTGTTTACTTCTTCTTTTCCTCTTTAATTTA
1 ATT-ACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * *
892 ATTACCCATG-ATTAAACTAATTGCTTGTTCTTCAT-TTGCTAC-TTAGTTTA
1 ATTACCCA-GAATTAAACT-GTT--TTCTTCTTC-TCTTACT-CTTTAGTTTA
* * **
942 ATTTCCTAGAATTAAAC-----T-AAC--CTCTT-CT-TTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
** ** * * *
979 ATTACCTGGAATTAAACTAATCTCTTCTTCTTTTACTAC-TAAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGTTTA
* ** * **
1026 ATTACCTAGAATTAAACTAATCTCTTCTTCGATTACTAC-TTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGTTTA
* * * * * * *
1073 ACTACCTAGAATTAAACTAATATT-TTCCTCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACT-GTTTTCTTCTTCTCTTACTCTTTAGTTTA
* **** * * *
1120 ATTACCAAGAATTAAACTAACATCTTCTCCTTTTGCTAC-TTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGTTTA
* ** * *
1167 ATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC-TTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGTTTA
* ** * * * *
1214 ATTACCTAGAATTAAACTAATCTCTTCTCCTTTTA--C-TTGGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
** ** **
1258 ATTACCTGGAATTAAACTAATCCCTTCTTCAT-TTACTAC-TTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTC-TCTTACT-CTTTAGTTTA
* **** * *
1305 ATTACCTAGAATTAAACTAACCTCTTCTTCTTTTGCTAC-TTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGTTTA
* ** * *
1352 ATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC-TTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGTTTA
1399 ATT
1 ATT
1402 CTAGGTAATT
Statistics
Matches: 822, Mismatches: 122, Indels: 80
0.80 0.12 0.08
Matches are distributed among these distances:
37 23 0.03
38 3 0.00
39 3 0.00
41 1 0.00
42 2 0.00
43 6 0.01
44 66 0.08
45 7 0.01
46 7 0.01
47 615 0.75
48 9 0.01
49 2 0.00
50 33 0.04
51 4 0.00
52 1 0.00
53 2 0.00
54 38 0.05
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.48
Consensus pattern (47 bp):
ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
Found at i:476 original size:94 final size:94
Alignment explanation
Indices: 351--1817 Score: 878
Period size: 94 Copynumber: 15.3 Consensus size: 94
341 TGATTACGCT
* * * * * *
351 TTCTTTTACTGCTTAGCTTGATTACCCAGAATCAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTT
1 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTT
*
416 TAATTACCCT-GAATTAAACTCTTTTCTTC
66 TAATTA-CCTAGAATTAAACTATTTTCTTC
* ** *
445 CTCTTTTACTTTTTAGTTTAATTACCTAGAATTAAACTAGCCTCTGTGTACTTCTTCTTTTACTC
1 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACT-G--T-T-T-T-CTTCTTCTCTTACTC
* * *
510 TTTAGTTTGATTACCAAGAATTAAACTGTTTTCTTC
59 TTTAGTTTAATTACCTAGAATTAAACTATTTTCTTC
* * * * *
546 TTCTCTTGCT-CTTTAGTTTAATTACCCT-GAATTAAACTCTTTTCTTCTTCTCTTACTTTTTGG
1 TTCTTTTACTAC-TTAGTTTAATTA-CCTAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAG
* * * *
609 TTTAGTTACCCAGAATTAAAATGTTTTCTTC
64 TTTAATTACCTAGAATTAAACTATTTTCTTC
* * * * * *
640 TTCTCTTGCT-CTTTAGTTTAATTACCCAGAATTAAATTGTTTTCTTCTTCTTTTACTATTTAGT
1 TTCTTTTACTAC-TTAGTTTAATTACCTAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGT
** * *
704 TTAATTACCCGGAATTAAACTCTTTTCATC
65 TTAATTACCTAGAATTAAACTATTTTCTTC
* * ** * * * *
734 TTCTCTTAATTTTTAGTTTAGTTACCCAGAATTAAAATGTTTTCTTCTTCTCTTGCTCTTTAGTT
1 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTT
* *
799 TAATTACCTGGAATTAAACTCTTTTCTTC
66 TAATTACCTAGAATTAAACTATTTTCTTC
* * ** * * * * * *
828 TTCTCTTAATTTTTAGTTTAATTAACCCAG--TT--TCTGTTTACTTCTTCTTTTCCTCTTTAAT
1 TTCTTTTACTACTTAGTTTAATT-ACCTAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGT
* *
889 TTAATTACCCATG-ATTAAACTAATTGCTTGTTC
65 TTAATTACCTA-GAATTAAACT-ATT--TTCTTC
* * * **
922 TTCATTTGCTACTTAGTTTAATTTCCTAGAATTAAAC-----T-AAC--CTCTT-CT-TTTAGTT
1 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTT
* * *
977 TAATTACCTGGAATTAAACTAATCTCTTC
66 TAATTACCTAGAATTAAACTATTTTCTTC
* ** * **
1006 TTCTTTTACTACTAAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCGATTACTAC-TTAGT
1 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGT
* *
1070 TTAACTACCTAGAATTAAACTAATATT-TTC
65 TTAATTACCTAGAATTAAACT-ATTTTCTTC
* * * **** * * *
1100 CTCTTTTACTATTTAGTTTAATTACCAAGAATTAAACTAACATCTTCTCCTTTTGCTAC-TTAGT
1 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGT
* *
1164 TTAATTACCTAGAATTAAACTAATCTCTTC
65 TTAATTACCTAGAATTAAACTATTTTCTTC
** * * * *
1194 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTCCTTTTA--C-TTGGTT
1 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTT
* * **
1256 TAATTACCTGGAATTAAACTAATCCCTTC
66 TAATTACCTAGAATTAAACTATTTTCTTC
* **** * *
1285 TTCATTTACTACTTAGTTTAATTACCTAGAATTAAACTAACCTCTTCTTCTTTTGCTAC-TTAGT
1 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGT
* *
1349 TTAATTACCTAGAATTAAACTAATCTCTTC
65 TTAATTACCTAGAATTAAACTATTTTCTTC
*
1379 TTCTTTTACTACTTAGTTTAATT--CTAGGTAATTAAACTAATCTCTTCTCCTTTTACTTTCTTC
1 TTCTTTTACTACTTAGTTTAATTACCTA-G-AATTAAAC---TGT-TT-T-C--TT-C-TTC-TC
*
1442 TTTTACTAC-TTAGTTTAATTACCTAGAGTTAAACTAATCTCTTCTCCTTTTAACTTC
53 --TTACT-CTTTAGTTTAATTACCTAGAATTAAACT-A----------TTTT--CTTC
* * *
1499 TTCTTTTACTACTTAGTTTAATTACCCAGGATTAAACTAATCTCTTCTCGTTTTACTTTCTTCTT
1 TTCTTTTACTACTTAGTTTAATTACCTAGAATT-A---AA------CT-GTTTT-C-TTCTTCTC
* * * * *
1564 TTACTAC-TTAGTTTAATTATCTTGAATTAAACTAATCTGTTC
53 TTACT-CTTTAGTTTAATTACCTAGAATTAAACTATTTTCTTC
** * * * ** * * *
1606 TTCGGTTACTACTTAGTTTAACTACCCATAATTAAACTAATCTCTTCTT-TTTTACTATTTAGTT
1 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTT
* ***
1670 TAATTACCCAGAATTAAACTAACATCTTC
66 TAATTACCTAGAATTAAACTATTTTCTTC
* ** * * * *
1699 TTCTTTTACTATTTAGTTTAATTACCCT-GAATTAAACTAATTTCTTCTCCTTTTACTGTCTAGT
1 TTCTTTTACTACTTAGTTTAATTA-CCTAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGT
* *
1763 TTAATTACCCT-GAATTAAACTAATCTCTTC
65 TTAATTA-CCTAGAATTAAACTATTTTCTTC
*
1793 TCCTTTTACTA-TTCAGTTTAATTAC
1 TTCTTTTACTACTT-AGTTTAATTAC
1818 TCTTCTAATT
Statistics
Matches: 1121, Mismatches: 168, Indels: 169
0.77 0.12 0.12
Matches are distributed among these distances:
84 37 0.03
86 3 0.00
87 22 0.02
88 2 0.00
89 5 0.00
90 1 0.00
91 125 0.11
92 9 0.01
93 90 0.08
94 561 0.50
95 15 0.01
96 3 0.00
97 6 0.01
98 2 0.00
99 2 0.00
100 4 0.00
101 72 0.06
102 5 0.00
103 3 0.00
104 3 0.00
105 1 0.00
106 1 0.00
107 62 0.06
108 1 0.00
109 2 0.00
118 2 0.00
119 1 0.00
120 60 0.05
121 2 0.00
122 3 0.00
123 3 0.00
124 3 0.00
125 3 0.00
126 2 0.00
127 3 0.00
128 1 0.00
130 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.48
Consensus pattern (94 bp):
TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTT
TAATTACCTAGAATTAAACTATTTTCTTC
Found at i:1446 original size:60 final size:60
Alignment explanation
Indices: 1376--1606 Score: 337
Period size: 60 Copynumber: 3.9 Consensus size: 60
1366 AACTAATCTC
1376 TTCTTCTTTTACTACTTAGTTTAATT-CTAGGTAATTAAACTAATCTCTTCTCCTTTTACT
1 TTCTTCTTTTACTACTTAGTTTAATTACTAGG-AATTAAACTAATCTCTTCTCCTTTTACT
*
1436 TTCTTCTTTTACTACTTAGTTTAATTACCTA-GAGTTAAACTAATCTCTTCTCCTTTTAAC-
1 TTCTTCTTTTACTACTTAGTTTAATTA-CTAGGAATTAAACTAATCTCTTCTCCTTTT-ACT
* *
1496 TTCTTCTTTTACTACTTAGTTTAATTACCCAGG-ATTAAACTAATCTCTTCTCGTTTTACT
1 TTCTTCTTTTACTACTTAGTTTAATTA-CTAGGAATTAAACTAATCTCTTCTCCTTTTACT
* *
1556 TTCTTCTTTTACTACTTAGTTTAATTATCT-TGAATTAAACTAATCTGTTCT
1 TTCTTCTTTTACTACTTAGTTTAATTA-CTAGGAATTAAACTAATCTCTTCT
1607 TCGGTTACTA
Statistics
Matches: 157, Mismatches: 8, Indels: 12
0.89 0.05 0.07
Matches are distributed among these distances:
59 3 0.02
60 147 0.94
61 4 0.03
62 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (60 bp):
TTCTTCTTTTACTACTTAGTTTAATTACTAGGAATTAAACTAATCTCTTCTCCTTTTACT
Found at i:1455 original size:107 final size:108
Alignment explanation
Indices: 1329--1755 Score: 417
Period size: 120 Copynumber: 4.0 Consensus size: 108
1319 AACTAACCTC
*
1329 TTCTTCTTTTGCTACTTAGTTTAATTACCTAGAATTAAACTAATC-TCTTCTTCTTTTACTACTT
1 TTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCTTTTACTACTT
*
1393 AGTTTAATT-CTAGGTAATTAAACTAATCTCTTCTCCTTTTACT
66 AGTTTAATTACCAGG-AATTAAACTAATCTCTTCTCCTTTTACT
*
1436 TTCTTCTTTTACTACTTAGTTTAATTACCTAGAGTTAAACTAATCTCTTCTCCTTTTAACTTCTT
1 TTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAA-------T-C--TT--CTTCTT
*
1501 CTTTTACTACTTAGTTTAATTACCCAGG-ATTAAACTAATCTCTTCTCGTTTTACT
54 CTTTTACTACTTAGTTTAATTA-CCAGGAATTAAACTAATCTCTTCTCCTTTTACT
* * * **
1556 TTCTTCTTTTACTACTTAGTTTAATTATCTTGAATTAAACTAATC-TGTTCTTCGGTTACTACTT
1 TTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCTTTTACTACTT
* *
1620 AGTTTAACTACCCA-TAATTAAACTAA-------T-C---T-C-
66 AGTTTAATTA-CCAGGAATTAAACTAATCTCTTCTCCTTTTACT
* * * *
1650 TTCTT-TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-CATCTTCTTCTTTTACTATTT
1 TTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCTTTTACTACTT
** *
1713 AGTTTAATTACCCTGAATTAAACTAATTTCTTCTCCTTTTACT
66 AGTTTAATTACCAGGAATTAAACTAATCTCTTCTCCTTTTACT
1756 GTCTAGTTTA
Statistics
Matches: 265, Mismatches: 24, Indels: 63
0.75 0.07 0.18
Matches are distributed among these distances:
92 3 0.01
93 68 0.26
94 5 0.02
95 1 0.00
96 1 0.00
100 2 0.01
101 1 0.00
104 1 0.00
105 1 0.00
107 79 0.30
109 1 0.00
112 1 0.00
113 1 0.00
114 1 0.00
115 1 0.00
118 1 0.00
120 93 0.35
122 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.05, T:0.48
Consensus pattern (108 bp):
TTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCTTTTACTACTT
AGTTTAATTACCAGGAATTAAACTAATCTCTTCTCCTTTTACT
Found at i:1625 original size:47 final size:47
Alignment explanation
Indices: 1556--1817 Score: 336
Period size: 47 Copynumber: 5.6 Consensus size: 47
1546 TCGTTTTACT
* * *
1556 TTCTTCTTTTACTACTTAGTTTAATTATCTTGAATTAAACTAATCTG
1 TTCTTCTTTTACTACTTAGTTTAATTACCCTGAATTAAACTAATCTC
** *
1603 TTCTTCGGTTACTACTTAGTTTAACTACCCAT-AATTAAACTAATCTC
1 TTCTTCTTTTACTACTTAGTTTAATTACCC-TGAATTAAACTAATCTC
* *
1650 TTCTT-TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-CATC
1 TTCTTCTTTTACTACTTAGTTTAATTACCCTGAATTAAACTAATC-TC
* *
1696 TTCTTCTTTTACTATTTAGTTTAATTACCCTGAATTAAACTAATTTC
1 TTCTTCTTTTACTACTTAGTTTAATTACCCTGAATTAAACTAATCTC
* *
1743 TTCTCCTTTTACT-GTCTAGTTTAATTACCCTGAATTAAACTAATCTC
1 TTCTTCTTTTACTACT-TAGTTTAATTACCCTGAATTAAACTAATCTC
*
1790 TTCTCCTTTTACTA-TTCAGTTTAATTAC
1 TTCTTCTTTTACTACTT-AGTTTAATTAC
1818 TCTTCTAATT
Statistics
Matches: 191, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
45 1 0.01
46 40 0.21
47 149 0.78
48 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.47
Consensus pattern (47 bp):
TTCTTCTTTTACTACTTAGTTTAATTACCCTGAATTAAACTAATCTC
Found at i:1725 original size:93 final size:93
Alignment explanation
Indices: 1556--1817 Score: 339
Period size: 93 Copynumber: 2.8 Consensus size: 93
1546 TCGTTTTACT
* * * * ** *
1556 TTCTTCTTTTACTACTTAGTTTAATTATCTTGAATTAAACTAATCTGTTCTTCGGTTACTACTTA
1 TTCTT-TTTTACTATTTAGTTTAATTACCCTGAATTAAACTAATCTCTTCTTCTTTTACTATTTA
*
1621 GTTTAACTACCCAT-AATTAAACTAATCTC
65 GTTTAATTACCC-TGAATTAAACTAATCTC
*
1650 TTCTTTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-CATCTTCTTCTTTTACTATTTA
1 TTCTTTTTTACTATTTAGTTTAATTACCCTGAATTAAACTAATC-TCTTCTTCTTTTACTATTTA
*
1714 GTTTAATTACCCTGAATTAAACTAATTTC
65 GTTTAATTACCCTGAATTAAACTAATCTC
* * * * *
1743 TTCTCCTTTTACTGTCTAGTTTAATTACCCTGAATTAAACTAATCTCTTCTCCTTTTACTATTCA
1 TTCT-TTTTTACTATTTAGTTTAATTACCCTGAATTAAACTAATCTCTTCTTCTTTTACTATTTA
1808 GTTTAATTAC
65 GTTTAATTAC
1818 TCTTCTAATT
Statistics
Matches: 148, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
92 2 0.01
93 78 0.53
94 67 0.45
95 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.47
Consensus pattern (93 bp):
TTCTTTTTTACTATTTAGTTTAATTACCCTGAATTAAACTAATCTCTTCTTCTTTTACTATTTAG
TTTAATTACCCTGAATTAAACTAATCTC
Found at i:1839 original size:140 final size:138
Alignment explanation
Indices: 1556--1817 Score: 357
Period size: 140 Copynumber: 1.9 Consensus size: 138
1546 TCGTTTTACT
* * * *
1556 TTCTTCTTTTACTACTTAGTTTAATTATCTTGAATTAAACTAATCTGTTCTTCGGTTACTACTTA
1 TTCTTCTTTTACTACTTAGTTTAATTACCCTGAATTAAACTAATCTCTTCTCCGGTTACTACTTA
* *
1621 GTTTAACTACCCATAATTAAACTAATCTCTTCTTTTTTACTATTTAGTTTAATTACCCAGAATTA
66 GTTTAACTACCCATAATTAAACTAATCTCTTCTCTTTTACTATTCAGTTTAATTACCCAGAATT-
1686 AACTAACATC
130 AACT-ACATC
* * ** *
1696 TTCTTCTTTTACTATTTAGTTTAATTACCCTGAATTAAACTAATTTCTTCTCCTTTTACT-GTCT
1 TTCTTCTTTTACTACTTAGTTTAATTACCCTGAATTAAACTAATCTCTTCTCCGGTTACTACT-T
*
1760 AGTTTAATTACCC-TGAATTAAACTAATCTCTTCTCCTTTTACTATTCAGTTTAATTAC
65 AGTTTAACTACCCAT-AATTAAACTAATCTCTTCT-CTTTTACTATTCAGTTTAATTAC
1818 TCTTCTAATT
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
139 2 0.02
140 84 0.79
141 21 0.20
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.47
Consensus pattern (138 bp):
TTCTTCTTTTACTACTTAGTTTAATTACCCTGAATTAAACTAATCTCTTCTCCGGTTACTACTTA
GTTTAACTACCCATAATTAAACTAATCTCTTCTCTTTTACTATTCAGTTTAATTACCCAGAATTA
ACTACATC
Found at i:2983 original size:22 final size:22
Alignment explanation
Indices: 2953--2999 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2943 TCCCCTTGTA
*
2953 CCCGAACCTCAAACCACCAAAT
1 CCCGAACCTAAAACCACCAAAT
*
2975 CCCGTACCTAAAACCACCAAAT
1 CCCGAACCTAAAACCACCAAAT
2997 CCC
1 CCC
3000 AGCGGCACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.47, G:0.04, T:0.11
Consensus pattern (22 bp):
CCCGAACCTAAAACCACCAAAT
Found at i:8359 original size:26 final size:26
Alignment explanation
Indices: 8304--8360 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
8294 CAGCCGATCT
***
8304 AGCTAGGTTGGCTCGATCAAAATTTG
1 AGCTAGGTTGGCTCGATCAAAAACCG
8330 -GCTAGGTTGGCTCGATCAAAAACCG
1 AGCTAGGTTGGCTCGATCAAAAACCG
8355 AGCTAG
1 AGCTAG
8361 CTAGGTTGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (26 bp):
AGCTAGGTTGGCTCGATCAAAAACCG
Found at i:11437 original size:308 final size:307
Alignment explanation
Indices: 10856--11474 Score: 1168
Period size: 308 Copynumber: 2.0 Consensus size: 307
10846 GATCCTCAAT
10856 TTAAAAGATGAATTCAATACTAAATACTTGATGATAACTGGCCTAGGGAAACCCTAACATGCTAT
1 TTAAAAGATGAATTCAATACTAAATACTTGATGATAACTGGCCTAGGGAAACCCTAACATGCTAT
*
10921 TTAGTAAAATCTCGGTTAAGACTTATTTTACCCTTTTATTTCTTAACTATTCAATTATCGGTTAA
66 TTAGTAAAATCTCGGTTAAGACTTATTTTACCCTTTTATTTCTTAACTAATCAATTATCGGTTAA
10986 GACTTAAAAATTTGCTAGGAAACAAAGCATTAAGAGCAACTTTAATATTAGTTCTTCCACACATG
131 GACTTAAAAATTTGCTAGGAAACAAAGCATTAAGAGCAACTTTAATATTAGTTCTTCCACACATG
* *
11051 CTTAACAAGTAAAACCATACAACAATTAAATAAATCTGATCACTGGCATGCTAAACCCATTGACG
196 CTTAACAAGTAAAACCATACAACAATCAAATAAATATGATCACTGGCATGCTAAACCCATTGACG
11116 CGACGTCAATCGTCATCAATTTGTTACCAAACAATCAAACTCATGTG
261 CGACGTCAATCGTCATCAATTTGTTACCAAACAATCAAACTCATGTG
11163 TTAAAAGATGAATTCAATACTAAATACTTGATGATAACTGGCCTAGGGAAACCCTAACATGCTAT
1 TTAAAAGATGAATTCAATACTAAATACTTGATGATAACTGGCCTAGGGAAACCCTAACATGCTAT
11228 TTAGTAAAATCTCGGTTAAGACTTATTTTACCCTTTTATTTCTTAACTAATCAATTA-CTGGTTA
66 TTAGTAAAATCTCGGTTAAGACTTATTTTACCCTTTTATTTCTTAACTAATCAATTATC-GGTTA
* *
11292 AGGCTTAAAAAATTTGCTAGGAAACAAAGCATTAAGAGCAACTTTAATATTAGTTCTTTCACACA
130 AGACTT-AAAAATTTGCTAGGAAACAAAGCATTAAGAGCAACTTTAATATTAGTTCTTCCACACA
11357 TGCTTAACAAGTAAAACCATACAACAATCAAATAAATATGATCACTGGCATGCTAAACCCATTGA
194 TGCTTAACAAGTAAAACCATACAACAATCAAATAAATATGATCACTGGCATGCTAAACCCATTGA
11422 CGCGACGTCAATCGTCATCAATTTGTTACCAAACAATCAAACTCATGTG
259 CGCGACGTCAATCGTCATCAATTTGTTACCAAACAATCAAACTCATGTG
11471 TTAA
1 TTAA
11475 CAGTCTTGTT
Statistics
Matches: 305, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
306 1 0.00
307 131 0.43
308 173 0.57
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (307 bp):
TTAAAAGATGAATTCAATACTAAATACTTGATGATAACTGGCCTAGGGAAACCCTAACATGCTAT
TTAGTAAAATCTCGGTTAAGACTTATTTTACCCTTTTATTTCTTAACTAATCAATTATCGGTTAA
GACTTAAAAATTTGCTAGGAAACAAAGCATTAAGAGCAACTTTAATATTAGTTCTTCCACACATG
CTTAACAAGTAAAACCATACAACAATCAAATAAATATGATCACTGGCATGCTAAACCCATTGACG
CGACGTCAATCGTCATCAATTTGTTACCAAACAATCAAACTCATGTG
Found at i:18941 original size:14 final size:15
Alignment explanation
Indices: 18922--18952 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
18912 CCCTATATGC
18922 AATGCGAAAA-AGGA
1 AATGCGAAAAGAGGA
18936 AATGCGAAAAGAGGA
1 AATGCGAAAAGAGGA
18951 AA
1 AA
18953 GTGACAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.58, C:0.06, G:0.29, T:0.06
Consensus pattern (15 bp):
AATGCGAAAAGAGGA
Found at i:20900 original size:11 final size:11
Alignment explanation
Indices: 20884--20931 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
20874 GAAGTTCGTG
20884 TTTGAAGACTA
1 TTTGAAGACTA
20895 TTTGAAGA-TAA
1 TTTGAAGACT-A
20906 TTTGAAGAC--
1 TTTGAAGACTA
20915 -TTGAAGACTA
1 TTTGAAGACTA
20925 -TTGAAGA
1 TTTGAAGA
20932 ATTAATTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.24
10 8 0.24
11 17 0.52
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (11 bp):
TTTGAAGACTA
Found at i:24138 original size:27 final size:27
Alignment explanation
Indices: 24081--24145 Score: 114
Period size: 26 Copynumber: 2.4 Consensus size: 27
24071 ATTGATTACC
24081 CTTACTCTTTTTACTGATTACCATTTT
1 CTTACTCTTTTTACTGATTACCATTTT
*
24108 -TTACTCTTTTTACTTATTACCATTTT
1 CTTACTCTTTTTACTGATTACCATTTT
24134 CTTACTCTTTTT
1 CTTACTCTTTTT
24146 TTTACTGGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 25 0.69
27 11 0.31
ACGTcount: A:0.17, C:0.22, G:0.02, T:0.60
Consensus pattern (27 bp):
CTTACTCTTTTTACTGATTACCATTTT
Found at i:24196 original size:35 final size:36
Alignment explanation
Indices: 24157--24242 Score: 115
Period size: 35 Copynumber: 2.4 Consensus size: 36
24147 TTACTGGTTT
*
24157 CCATTTTTTGCCTTTT-TTACTTTAATTACTGAATA
1 CCATTTTTTACCTTTTCTTACTTTAATTACTGAATA
*
24192 CCA-TTTTTACTTTTTCTTACTTTAATTACTGAATA
1 CCATTTTTTACCTTTTCTTACTTTAATTACTGAATA
*
24227 TCA-TTTTTACTCTTTT
1 CCATTTTTTAC-CTTTT
24243 TAATCTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
34 10 0.22
35 31 0.69
36 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.03, T:0.57
Consensus pattern (36 bp):
CCATTTTTTACCTTTTCTTACTTTAATTACTGAATA
Found at i:24244 original size:9 final size:9
Alignment explanation
Indices: 24230--24268 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
24220 CTGAATATCA
24230 TTTTTACTC
1 TTTTTACTC
*
24239 TTTTTAATC
1 TTTTTACTC
24248 TTTTTAC-C
1 TTTTTACTC
24256 ATTTTTACTC
1 -TTTTTACTC
24266 TTT
1 TTT
24269 GAATTTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 24 0.92
10 1 0.04
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTTACTC
Found at i:24345 original size:35 final size:36
Alignment explanation
Indices: 24306--24618 Score: 141
Period size: 35 Copynumber: 8.5 Consensus size: 36
24296 ATTTTACTAA
24306 TTACTCTTTACTCTTTACTGATTACTATTA-TCATT
1 TTACTCTTTACTCTTTACTGATTACTATTACTCATT
** *
24341 TTACTTTTTACTTTTTACTCTTTTAAAGATTATTATTACTC---
1 TTAC----T-C--TTTACTC-TTTACTGATTACTATTACTCATT
* * *
24382 TTCCT-TGATTACTCTTTACTGACTATTATTACTCA-T
1 TTACTCT--TTACTCTTTACTGATTACTATTACTCATT
* *
24418 TTACTCTTTACTCTTTACTGATTATTATTACTCTTTCTT
1 TTACTCTTTACTCTTTACTGATTACTATTACTC---ATT
* * * *
24457 GATTACTCTTTACGCTTTACTTACTATTATTACTC-TT
1 --TTACTCTTTACTCTTTACTGATTACTATTACTCATT
** * * *
24494 TTACTGATTACTCTTTAC-CATTTCTTGATTAGTC--T
1 TTACTCTTTACTCTTTACTGATTAC-T-ATTACTCATT
** * *
24529 TTACTCTTTACTGATTACT-ATTACTCTTTTACTGA--
1 TTACTCTTTACTCTTTACTGATTA--CTATTACTCATT
24564 TTACTCTTTACTCTTTTACTGATTACTATTAC-CATT
1 TTACTCTTTACTC-TTTACTGATTACTATTACTCATT
**
24600 TTACTGATTACTCTTTACT
1 TTACTCTTTACTCTTTACT
24619 TTTCTTTGAA
Statistics
Matches: 213, Mismatches: 35, Indels: 60
0.69 0.11 0.19
Matches are distributed among these distances:
33 1 0.00
34 20 0.09
35 97 0.46
36 27 0.13
37 9 0.04
39 2 0.01
40 1 0.00
41 33 0.15
42 7 0.03
43 14 0.07
44 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.54
Consensus pattern (36 bp):
TTACTCTTTACTCTTTACTGATTACTATTACTCATT
Found at i:24429 original size:7 final size:7
Alignment explanation
Indices: 24410--24579 Score: 56
Period size: 7 Copynumber: 24.3 Consensus size: 7
24400 CTGACTATTA
24410 TTACTCAT
1 TTACTC-T
24418 TTACTCT
1 TTACTCT
24425 TTACTCT
1 TTACTCT
**
24432 TTACTGA
1 TTACTCT
24439 TTA-T-T
1 TTACTCT
24444 ATTACTCT
1 -TTACTCT
24452 TT-CT-T
1 TTACTCT
24457 GATTACTCT
1 --TTACTCT
*
24466 TTACGCT
1 TTACTCT
24473 TTA--C-
1 TTACTCT
*
24477 TTACTATT
1 TTACT-CT
24485 ATTACTCTT
1 -TTACTC-T
**
24494 TTACTGA
1 TTACTCT
24501 TTACTCT
1 TTACTCT
24508 TTAC-CAT
1 TTACTC-T
24515 TT-CT-T
1 TTACTCT
*
24520 GATTAGTCT
1 --TTACTCT
24529 TTACTCT
1 TTACTCT
**
24536 TTACTGA
1 TTACTCT
*
24543 TTACT-A
1 TTACTCT
24549 TTACTCTT
1 TTACTC-T
**
24557 TTACTGA
1 TTACTCT
24564 TTACTCT
1 TTACTCT
24571 TTACTCT
1 TTACTCT
24578 TT
1 TT
24580 TACTGATTAC
Statistics
Matches: 122, Mismatches: 19, Indels: 43
0.66 0.10 0.23
Matches are distributed among these distances:
4 3 0.02
5 3 0.02
6 14 0.11
7 74 0.61
8 20 0.16
9 8 0.07
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.54
Consensus pattern (7 bp):
TTACTCT
Found at i:24477 original size:63 final size:63
Alignment explanation
Indices: 24297--24579 Score: 233
Period size: 63 Copynumber: 4.4 Consensus size: 63
24287 ACCATTACCA
* * ** **
24297 TTTTACTAATTACTCTTTACTCTTTAC-TGATTACT-ATTATCATTTTACTTTTTACTTTTTACT
1 TTTTACTGATTACTCTTTACTCTTT-CTTGATTACTCTTTA-CGCTTTACTCATTAC-TTTTACT
24360 C
63 C
** *
24361 TTTTAAAGATTA-T-TATTACTCTTCCTTGATTACTCTTTACTGACTATTATTACTCATTTACTC
1 TTTTACTGATTACTCT-TTACTCTTTCTTGATTACTCTTTAC-G-C---T-TTACTCA-TTACT-
24424 TTTACTC
57 TTTACTC
* *
24431 -TTTACTGATTA-T-TATTACTCTTTCTTGATTACTCTTTACGCTTTACTTACTA-TTATTACTC
1 TTTTACTGATTACTCT-TTACTCTTTCTTGATTACTCTTTACGCTTTACTCATTACTT-TTACTC
* * * *
24492 TTTTACTGATTACTCTTTAC-CATTTCTTGATTAGTCTTTACTCTTTACTGATTACTATTACTC
1 TTTTACTGATTACTCTTTACTC-TTTCTTGATTACTCTTTACGCTTTACTCATTACTTTTACTC
24555 TTTTACTGATTACTCTTTACTCTTT
1 TTTTACTGATTACTCTTTACTCTTT
24580 TACTGATTAC
Statistics
Matches: 182, Mismatches: 19, Indels: 37
0.76 0.08 0.16
Matches are distributed among these distances:
60 1 0.01
61 7 0.04
62 16 0.09
63 86 0.47
64 16 0.09
67 1 0.01
68 2 0.01
69 42 0.23
70 11 0.06
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.54
Consensus pattern (63 bp):
TTTTACTGATTACTCTTTACTCTTTCTTGATTACTCTTTACGCTTTACTCATTACTTTTACTC
Found at i:24497 original size:69 final size:71
Alignment explanation
Indices: 24341--24498 Score: 206
Period size: 69 Copynumber: 2.3 Consensus size: 71
24331 TATTATCATT
24341 TTACT-TTTTACT-TTTTACTCTTTTAAAGATTATTATTACTCTTCCTTGATTACTCTTTACTGA
1 TTACTATTTTACTCTTTTACTCTTTTAAAGATTATTATTACTCTTCCTTGATTACTCTTTACTGA
24404 CTATTA
66 CTATTA
** *
24410 TTACTCA-TTTACTC-TTTACTC-TTTACTGATTATTATTACTCTTTCTTGATTACTCTTTAC-G
1 TTACT-ATTTTACTCTTTTACTCTTTTAAAGATTATTATTACTCTTCCTTGATTACTCTTTACTG
24471 -CT-TTA
65 ACTATTA
24476 CTTACTATTATTACTCTTTTACT
1 -TTACTATT-TTACTCTTTTACT
24499 GATTACTCTT
Statistics
Matches: 79, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
66 4 0.05
67 8 0.10
68 7 0.09
69 47 0.59
70 13 0.16
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.55
Consensus pattern (71 bp):
TTACTATTTTACTCTTTTACTCTTTTAAAGATTATTATTACTCTTCCTTGATTACTCTTTACTGA
CTATTA
Found at i:24589 original size:15 final size:14
Alignment explanation
Indices: 24543--24615 Score: 53
Period size: 15 Copynumber: 5.1 Consensus size: 14
24533 TCTTTACTGA
24543 TTACTATTACTCTT
1 TTACTATTACTCTT
24557 TTACTGATTACTC-T
1 TTACT-ATTACTCTT
* **
24571 TTACTCTTTTACT-GA
1 TTA--CTATTACTCTT
24586 TTACTATTAC-CATT
1 TTACTATTACTC-TT
24600 TTACTGATTACTCTT
1 TTACT-ATTACTCTT
24615 T
1 T
24616 ACTTTTCTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
13 6 0.13
14 14 0.30
15 23 0.50
16 3 0.07
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (14 bp):
TTACTATTACTCTT
Found at i:24610 original size:21 final size:21
Alignment explanation
Indices: 24278--24611 Score: 174
Period size: 21 Copynumber: 15.6 Consensus size: 21
24268 TGAATTTTAG
* *
24278 TTACCGATTACCATTAC-CATT
1 TTACTGATTACTATTACTC-TT
* *
24299 TTACTAATTACTCTTTACTC-T
1 TTACTGATTACT-ATTACTCTT
24320 TTACTGATTACTATTA-TCATT
1 TTACTGATTACTATTACTC-TT
** *
24341 TTACTTTTTACTTTTTACTCTT
1 TTACTGATTAC-TATTACTCTT
** *
24363 TTAAAGATTATTATTACTC--
1 TTACTGATTACTATTACTCTT
* *
24382 TTCCTTGATTACTCTTTACTGACTATT
1 TTAC-TGATTACT-ATTACT--C--TT
* *
24409 ATTACTCATTTACTCTTTACTC-T
1 -TTACTGA-TTACT-ATTACTCTT
*
24432 TTACTGATTATTATTACTC-T
1 TTACTGATTACTATTACTCTT
* *
24452 TT-CTTGATTACTCTTTACGC-T
1 TTAC-TGATTACT-ATTACTCTT
* * *
24473 TTACTTACTATTATTACTCTT
1 TTACTGATTACTATTACTCTT
* *
24494 TTACTGATTACTCTTTAC-CAT
1 TTACTGATTACT-ATTACTCTT
24515 TT-CTTGATTAGTCT-TTACTC-T
1 TTAC-TGATTA--CTATTACTCTT
24536 TTACTGATTACTATTACTCTT
1 TTACTGATTACTATTACTCTT
*
24557 TTACTGATTACTCTTTACTCTT
1 TTACTGATTACT-ATTACTCTT
24579 TTACTGATTACTATTAC-CATT
1 TTACTGATTACTATTACTC-TT
24600 TTACTGATTACT
1 TTACTGATTACT
24612 CTTTACTTTT
Statistics
Matches: 243, Mismatches: 40, Indels: 60
0.71 0.12 0.17
Matches are distributed among these distances:
19 7 0.03
20 38 0.16
21 124 0.51
22 49 0.20
23 7 0.03
26 1 0.00
27 2 0.01
28 15 0.06
ACGTcount: A:0.23, C:0.20, G:0.04, T:0.52
Consensus pattern (21 bp):
TTACTGATTACTATTACTCTT
Found at i:24638 original size:43 final size:43
Alignment explanation
Indices: 24278--24618 Score: 239
Period size: 42 Copynumber: 7.9 Consensus size: 43
24268 TGAATTTTAG
* * *
24278 TTACCGATTACCATTACCATTTTACTAATTACTCTTTACTC-T
1 TTACTGATTACTATTACCATTTTACTGATTACTCTTTACTCTT
* ** *
24320 TTACTGATTACTATTATCATTTTACTTTTTACTTTTTACTCTT
1 TTACTGATTACTATTACCATTTTACTGATTACTCTTTACTCTT
** * * *
24363 TTAAAGATTATTATTA-C-TCTTCCTTGATTACTCTTTACTGACTATT
1 TTACTGATTACTATTACCATTTTAC-TGATTACTCTTTACT--C--TT
* *
24409 ATTACTCATTTACTCTTTA-C-TCTTTACTGATTA-T-TATTACTC-T
1 -TTACTGA-TTACT-ATTACCAT-TTTACTGATTACTCT-TTACTCTT
* * *
24452 TT-CTTGATTACTCTTTACGC--TTTACTTACTA-T-TATTACTCTT
1 TTAC-TGATTACT-ATTAC-CATTTTACTGATTACTCT-TTACTCTT
* *
24494 TTACTGATTACTCTTTACCA-TTT-CTTGATTAGTCTTTACTC-T
1 TTACTGATTACT-ATTACCATTTTAC-TGATTACTCTTTACTCTT
24536 TTACTGATTACTATTACTC-TTTTACTGATTACTCTTTACTCTT
1 TTACTGATTACTATTAC-CATTTTACTGATTACTCTTTACTCTT
24579 TTACTGATTACTATTACCATTTTACTGATTACTCTTTACT
1 TTACTGATTACTATTACCATTTTACTGATTACTCTTTACT
24619 TTTCTTTGAA
Statistics
Matches: 246, Mismatches: 28, Indels: 49
0.76 0.09 0.15
Matches are distributed among these distances:
41 39 0.16
42 109 0.44
43 64 0.26
44 2 0.01
46 3 0.01
47 5 0.02
48 10 0.04
49 11 0.04
50 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.04, T:0.52
Consensus pattern (43 bp):
TTACTGATTACTATTACCATTTTACTGATTACTCTTTACTCTT
Found at i:24697 original size:59 final size:56
Alignment explanation
Indices: 24579--24705 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 56
24569 CTTTACTCTT
* * *
24579 TTACTG-ATTACTATTACCATTTTACTGATTACTCTTTACTTTTCTTTGAATTTTAA
1 TTACTGAATTACCATTACCATTTTACTGATTACTCTTTA-TATTCTTTGAATATTAA
*
24635 TTACTCTGAATTACCATTACCATTTTACTGATTACTCTTT-TATTCTTT-ACTGATTACTA
1 TTA--CTGAATTACCATTACCATTTTACTGATTACTCTTTATATTCTTTGAAT-ATTA--A
24694 TTACTGAATTAC
1 TTACTGAATTAC
24706 TACTTATCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
56 5 0.08
57 19 0.31
58 3 0.05
59 34 0.56
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (56 bp):
TTACTGAATTACCATTACCATTTTACTGATTACTCTTTATATTCTTTGAATATTAA
Found at i:26224 original size:6 final size:6
Alignment explanation
Indices: 26213--26251 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
26203 ATCATTTTCC
26213 TTCTTT TTC-TT TTCTTT TTCTTTT TTCTCTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTC-TTT TTCT-TT TTCTTT TT
26252 TTTAATGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 13 0.43
7 12 0.40
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:26237 original size:27 final size:25
Alignment explanation
Indices: 26192--26254 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 25
26182 ACCCTAGAGC
**
26192 TTCTTTTCTTCATCATTTTCCTTCTTT
1 TTCTTTTCTTTTTCATTTTCC-TC-TT
* *
26219 TTCTTTTCTTTTTCTTTTTTCTCTT
1 TTCTTTTCTTTTTCATTTTCCTCTT
26244 TTCTTTT-TTTT
1 TTCTTTTCTTTT
26255 AATGCACTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 4 0.12
25 9 0.28
26 2 0.06
27 17 0.53
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (25 bp):
TTCTTTTCTTTTTCATTTTCCTCTT
Found at i:26247 original size:14 final size:13
Alignment explanation
Indices: 26213--26252 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
26203 ATCATTTTCC
26213 TTCTTTTTC--TT
1 TTCTTTTTCTTTT
26224 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
26237 TTCTCTTTTCTTTT
1 TTCT-TTTTCTTTT
26251 TT
1 TT
26253 TTAATGCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.35
13 6 0.23
14 11 0.42
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:26925 original size:12 final size:12
Alignment explanation
Indices: 26887--26933 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
26877 AGCATCCTCG
*
26887 TGAAAACAAATTT
1 TGAAAAC-ATTTT
26900 TGAAAACCATTTT
1 TGAAAA-CATTTT
26913 TGAAAA-ATCTTT
1 TGAAAACAT-TTT
26925 TGAAAACAT
1 TGAAAACAT
26934 GTGACTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 2 0.07
12 9 0.30
13 18 0.60
14 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.34
Consensus pattern (12 bp):
TGAAAACATTTT
Found at i:30864 original size:5 final size:5
Alignment explanation
Indices: 30856--30892 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
30846 ACATCAAAGC
* *
30856 AAACA AAACA AAACA AACCG AAACA AAACA AAACA AA
1 AAACA AAACA AAACA AAACA AAACA AAACA AAACA AA
30893 GCAACCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.76, C:0.22, G:0.03, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:33331 original size:24 final size:23
Alignment explanation
Indices: 33299--33345 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
33289 TTTTCTCTTC
33299 CTTCCTCCTCGACGCTTCTCCCTT
1 CTTCCTCCTCGAC-CTTCTCCCTT
*
33323 CTTCTTCCTCGACCTTCTCCCTT
1 CTTCCTCCTCGACCTTCTCCCTT
33346 TACCAATCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.04, C:0.49, G:0.06, T:0.40
Consensus pattern (23 bp):
CTTCCTCCTCGACCTTCTCCCTT
Found at i:36220 original size:40 final size:39
Alignment explanation
Indices: 36165--36291 Score: 118
Period size: 39 Copynumber: 3.2 Consensus size: 39
36155 ACCGAAACCG
*
36165 AAAC-TGACGGGAACTTTCCCTAAATTGAAAACTTCAAAA
1 AAACTTGACGGAAACTTTCCCTAAATTGAAAACTT-AAAA
* **
36204 AAACTTGATGGAAACTTTCCC-ATTTTGAAAAC-TAAAA
1 AAACTTGACGGAAACTTTCCCTAAATTGAAAACTTAAAA
* *
36241 TTAACAC-TAACGGGAACTTTCCCTAAATTGAAAACTTTGAAAA
1 --AA-ACTTGACGGAAACTTTCCCTAAATTGAAAAC-TT-AAAA
36284 AAACTTGA
1 AAACTTGA
36292 ATCGAATACT
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
37 4 0.06
38 1 0.01
39 28 0.41
40 27 0.39
41 4 0.06
42 1 0.01
43 4 0.06
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (39 bp):
AAACTTGACGGAAACTTTCCCTAAATTGAAAACTTAAAA
Found at i:36229 original size:80 final size:80
Alignment explanation
Indices: 36136--36291 Score: 217
Period size: 79 Copynumber: 1.9 Consensus size: 80
36126 GTTAGACGAT
* *
36136 AACTTTCCCATTTTTAAAAACCGAAACCGAA-ACTGACGGGAACTTTCCCTAAATTGAAAAC-TT
1 AACTTTCCCA-TTTTAAAAA-CGAAAACGAACACTAACGGGAACTTTCCCTAAATTGAAAACTTT
36199 CAAAAAAACTTGATGGA
64 CAAAAAAACTTGATGGA
* * ** *
36216 AACTTTCCCATTTTGAAAACTAAAATTAACACTAACGGGAACTTTCCCTAAATTGAAAACTTTGA
1 AACTTTCCCATTTTAAAAACGAAAACGAACACTAACGGGAACTTTCCCTAAATTGAAAACTTTCA
36281 AAAAAACTTGA
66 AAAAAACTTGA
36292 ATCGAATACT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 6 0.09
79 37 0.55
80 24 0.36
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (80 bp):
AACTTTCCCATTTTAAAAACGAAAACGAACACTAACGGGAACTTTCCCTAAATTGAAAACTTTCA
AAAAAACTTGATGGA
Found at i:36306 original size:34 final size:34
Alignment explanation
Indices: 36268--36375 Score: 207
Period size: 34 Copynumber: 3.2 Consensus size: 34
36258 TTTCCCTAAA
36268 TTGAAAACTTTGAAAAAAACTTGAATCGAATACT
1 TTGAAAACTTTGAAAAAAACTTGAATCGAATACT
36302 TTGAAAACTTTGAAAAAAACTTGAATCGAATACT
1 TTGAAAACTTTGAAAAAAACTTGAATCGAATACT
*
36336 TTGAAAACTTTGAAAAAAACTTGAATAGAATACT
1 TTGAAAACTTTGAAAAAAACTTGAATCGAATACT
36370 TTGAAA
1 TTGAAA
36376 TGAAGGAAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 73 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (34 bp):
TTGAAAACTTTGAAAAAAACTTGAATCGAATACT
Found at i:36423 original size:7 final size:7
Alignment explanation
Indices: 36388--36413 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
36378 AAGGAAATTC
36388 TTTTTGA
1 TTTTTGA
36395 TTTTTGA
1 TTTTTGA
36402 TTTTTGA
1 TTTTTGA
36409 TTTTT
1 TTTTT
36414 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.77
Consensus pattern (7 bp):
TTTTTGA
Found at i:36675 original size:19 final size:19
Alignment explanation
Indices: 36653--36699 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
36643 CAAGGGCTGA
36653 AATTAATTAATTAAATAAT
1 AATTAATTAATTAAATAAT
* * *
36672 AATTATTTTATTGAATAAT
1 AATTAATTAATTAAATAAT
*
36691 TATT-ATTAA
1 AATTAATTAA
36700 AAATCTTATG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
AATTAATTAATTAAATAAT
Found at i:47680 original size:21 final size:21
Alignment explanation
Indices: 47642--47682 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
47632 AAAATTGAGC
*
47642 TTTTCAAAATTAACAAAAAGG
1 TTTTCAAAATTAAAAAAAAGG
*
47663 TTTTCAAAATACAAAAAAAA
1 TTTTCAAAAT-TAAAAAAAA
47683 TTCAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.27
Consensus pattern (21 bp):
TTTTCAAAATTAAAAAAAAGG
Found at i:47758 original size:35 final size:35
Alignment explanation
Indices: 47719--47796 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 35
47709 GAGAATATCA
* * *
47719 TTAAGTTTTTTTTATTAGAAAAGTTCCCACCGGTT
1 TTAAGTTTTTGTAATCAGAAAAGTTCCCACCGGTT
* * *
47754 TTAAG-TTTTGTAATCGGGAAAGTTCCCAGCGGTT
1 TTAAGTTTTTGTAATCAGAAAAGTTCCCACCGGTT
47788 TTAAGTTTT
1 TTAAGTTTT
47797 CAAATTGGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 28 0.78
35 8 0.22
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (35 bp):
TTAAGTTTTTGTAATCAGAAAAGTTCCCACCGGTT
Found at i:47780 original size:34 final size:34
Alignment explanation
Indices: 47738--47815 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
47728 TTTTATTAGA
**
47738 AAAGTTCCCACCGGTTTTAAGTTTTGTAATCGGG
1 AAAGTTCCCACCGGTTTTAAGTTTTCAAATCGGG
* *
47772 AAAGTTCCCAGCGGTTTTAAGTTTTCAAATTGGG
1 AAAGTTCCCACCGGTTTTAAGTTTTCAAATCGGG
47806 AAAGTTCCCA
1 AAAGTTCCCA
47816 TTCAATTTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (34 bp):
AAAGTTCCCACCGGTTTTAAGTTTTCAAATCGGG
Done.