Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013040.1 Corchorus olitorius cultivar O-4 contig13073, 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: 134614
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1222 original size:20 final size:21
Alignment explanation
Indices: 1189--1227 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1179 AAAAAATGCC
1189 AAAATTTAACTTTCAAAATTG
1 AAAATTTAACTTTCAAAATTG
1210 AAAATTT-ACTTTCAAAAT
1 AAAATTTAACTTTCAAAAT
1228 GGGGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAATTTAACTTTCAAAATTG
Found at i:2199 original size:52 final size:52
Alignment explanation
Indices: 2120--2664 Score: 764
Period size: 52 Copynumber: 10.6 Consensus size: 52
2110 ATTAAGAACT
* *
2120 AAAACCTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTG
1 AAAA-CTGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
* *
2173 AAAACTGATGGAAACTTTCCCAATTTG-AAAAGAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
* *
2224 AAAACTTGATGGGAACTTTCCCAA-TTCAAAAAGAGCTAATTTGAATACTTTG
1 AAAAC-TGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
*
2276 AAAACTGATGGGAACTTTCCCAATTTG-AAAAGAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
* * *
2327 AAAACTGGTGGGAACATTCCCGACTTGAAAAAGAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
*
2379 AAAACTGATGGGAACTTTCCCAATTTG-AAAAGAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
* * *
2430 AAAACTGTTGGGAACTTTCCCGACTTGAAAAATAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
* ** * *
2482 AAGACTGATGGGAACTTTTTCGACTTG-AAAAGAGCTAGATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
* * *
2533 AAAACTGGTGGGAACTTTCCCGACTTGAAAAGGAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
* * ** *
2585 AAGACTGATGGGAACTTTCCCGACTTG-AAAA-ATTTAAATTGAATAC-TTA
1 AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
*
2634 AAAACTGATGGGAACTTTCCCAATTTGAAAA
1 AAAACTGATGGGAACTTTCCCAACTTGAAAA
2665 CTTAAACCTG
Statistics
Matches: 445, Mismatches: 40, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
49 26 0.06
50 16 0.04
51 190 0.43
52 209 0.47
53 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (52 bp):
AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGCTAAATTGAATACTTTG
Found at i:2300 original size:103 final size:103
Alignment explanation
Indices: 2120--2664 Score: 794
Period size: 103 Copynumber: 5.3 Consensus size: 103
2110 ATTAAGAACT
*
2120 AAAACCTGATGGGAACTTTCCC-AATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACTGATGG
1 AAAA-CTGATGGGAACTTTCCCGAA-TTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGATGG
*
2184 AAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
64 GAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
* *
2224 AAAACTTGATGGGAACTTTCCC-AATTCAAAAAGAGCTAATTTGAATACTTTGAAAACTGATGGG
1 AAAAC-TGATGGGAACTTTCCCGAATTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGATGGG
2288 AACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
65 AACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
* * *
2327 AAAACTGGTGGGAACATTCCCGACTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGATGGGA
1 AAAACTGATGGGAACTTTCCCGAATTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGATGGGA
2392 ACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
66 ACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
* * * *
2430 AAAACTGTTGGGAACTTTCCCGACTTGAAAAATAGCTAAATTGAATACTTTGAAGACTGATGGGA
1 AAAACTGATGGGAACTTTCCCGAATTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGATGGGA
** * * *
2495 ACTTTTTCGACTTGAAAAGAGCTAGATTGAATACTTTG
66 ACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
* * * *
2533 AAAACTGGTGGGAACTTTCCCGACTTGAAAAGGAGCTAAATTGAATACTTTGAAGACTGATGGGA
1 AAAACTGATGGGAACTTTCCCGAATTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGATGGGA
* * ** *
2598 ACTTTCCCGACTTGAAAA-ATTTAAATTGAATAC-TTA
66 ACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
2634 AAAACTGATGGGAACTTTCCC-AATTTGAAAA
1 AAAACTGATGGGAACTTTCCCGAA-TTGAAAA
2665 CTTAAACCTG
Statistics
Matches: 409, Mismatches: 29, Indels: 9
0.91 0.06 0.02
Matches are distributed among these distances:
100 1 0.00
101 29 0.07
102 26 0.06
103 331 0.81
104 22 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (103 bp):
AAAACTGATGGGAACTTTCCCGAATTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGATGGGA
ACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
Found at i:6604 original size:63 final size:63
Alignment explanation
Indices: 6496--6625 Score: 235
Period size: 63 Copynumber: 2.1 Consensus size: 63
6486 TTCAATTAAC
*
6496 AAATAAAGGTCCAAAGCAGATAGTAATGGAAAGGCCCGAAAAGGATTAAAAGAAAACCCAAAG
1 AAATAAAGGTCCAAAGCAGATAGTAATGGAAAGACCCGAAAAGGATTAAAAGAAAACCCAAAG
6559 AAATAAAGGTCCAAAGCAGATAGTAATGGAAAGACCC-AAAGAGGATTAAAAGAAAACCCAAAG
1 AAATAAAGGTCCAAAGCAGATAGTAATGGAAAGACCCGAAA-AGGATTAAAAGAAAACCCAAAG
6622 AAAT
1 AAAT
6626 GAACTTGACC
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
62 3 0.05
63 62 0.95
ACGTcount: A:0.54, C:0.14, G:0.21, T:0.12
Consensus pattern (63 bp):
AAATAAAGGTCCAAAGCAGATAGTAATGGAAAGACCCGAAAAGGATTAAAAGAAAACCCAAAG
Found at i:9064 original size:20 final size:21
Alignment explanation
Indices: 9041--9084 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
9031 CGCGGAGATT
*
9041 TTTG-AGAAAAAGCACGGAGC
1 TTTGAAGAAAAAGCACGAAGC
*
9061 TTTGAAAGAATAAGCACGAAGC
1 TTTG-AAGAAAAAGCACGAAGC
9083 TT
1 TT
9085 GATTTTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
22 16 0.80
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (21 bp):
TTTGAAGAAAAAGCACGAAGC
Found at i:10270 original size:19 final size:19
Alignment explanation
Indices: 10248--10299 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
10238 TAATTAGGAG
* *
10248 TAATTTTTAAGTAAAAATA
1 TAATATTTAAATAAAAATA
* *
10267 TAATATATAAATAAAAATT
1 TAATATTTAAATAAAAATA
10286 TAATATTTAAATAA
1 TAATATTTAAATAA
10300 TTAATTAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TAATATTTAAATAAAAATA
Found at i:10862 original size:21 final size:22
Alignment explanation
Indices: 10838--10878 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
10828 CATATATTGG
10838 GAAAATAA-TATTAATTATTTC
1 GAAAATAATTATTAATTATTTC
*
10859 GAAAATAATTATTATTTATT
1 GAAAATAATTATTAATTATT
10879 AATAATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (22 bp):
GAAAATAATTATTAATTATTTC
Found at i:13946 original size:17 final size:17
Alignment explanation
Indices: 13924--13957 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13914 ACCTTAATGA
13924 GCACCTCTGGCATTCTT
1 GCACCTCTGGCATTCTT
*
13941 GCACCTTTGGCATTCTT
1 GCACCTCTGGCATTCTT
13958 ACGTATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.32, G:0.18, T:0.38
Consensus pattern (17 bp):
GCACCTCTGGCATTCTT
Found at i:15346 original size:13 final size:13
Alignment explanation
Indices: 15330--15370 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
15320 ATTCATCTAC
15330 ACATTCCATCACT
1 ACATTCCATCACT
15343 ACATT-CATCTAC-
1 ACATTCCATC-ACT
*
15355 ACACTCCATCACT
1 ACATTCCATCACT
15368 ACA
1 ACA
15371 GATCCCACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.27
Consensus pattern (13 bp):
ACATTCCATCACT
Found at i:15350 original size:25 final size:25
Alignment explanation
Indices: 15320--15370 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
15310 TCGACAGAGA
*
15320 ATTCATCTACACATTCCATCACTAC
1 ATTCATCTACACACTCCATCACTAC
15345 ATTCATCTACACACTCCATCACTAC
1 ATTCATCTACACACTCCATCACTAC
15370 A
1 A
15371 GATCCCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.29
Consensus pattern (25 bp):
ATTCATCTACACACTCCATCACTAC
Found at i:15351 original size:12 final size:12
Alignment explanation
Indices: 15320--15357 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
15310 TCGACAGAGA
15320 ATTCATCTACAC
1 ATTCATCTACAC
15332 ATTCCATC-ACTAC
1 ATT-CATCTAC-AC
15345 ATTCATCTACAC
1 ATTCATCTACAC
15357 A
1 A
15358 CTCCATCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTCATCTACAC
Found at i:20352 original size:22 final size:23
Alignment explanation
Indices: 20321--20364 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
20311 TAGTGGTTCT
* *
20321 TTCAACCCTTTTTCCAGGTTGAG
1 TTCAACCCTTTTGCAAGGTTGAG
20344 TTCAA-CCTTTTGCAAGGTTGA
1 TTCAACCCTTTTGCAAGGTTGA
20365 AACAGGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (23 bp):
TTCAACCCTTTTGCAAGGTTGAG
Found at i:23345 original size:34 final size:32
Alignment explanation
Indices: 23285--23368 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 32
23275 CAAACTTCCC
** * *
23285 TTTTCTCTTTTTACCATATTACCAAATTTCATT
1 TTTTCTCTTTTTACTTTATTACCAAATGTCA-A
23318 TTTTCTCTTTTTACTTTGATTACCAAATGTCAA
1 TTTTCTCTTTTTACTTT-ATTACCAAATGTCAA
* *
23351 TTTACTCTTTTTCCTTTA
1 TTTTCTCTTTTTACTTTA
23369 ATATTTAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.02
33 30 0.68
34 13 0.30
ACGTcount: A:0.21, C:0.20, G:0.02, T:0.56
Consensus pattern (32 bp):
TTTTCTCTTTTTACTTTATTACCAAATGTCAA
Found at i:23437 original size:24 final size:25
Alignment explanation
Indices: 23399--23466 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 25
23389 AGTTTTATTT
**
23399 TTACCAAATACCATTTA-ACTTTAA
1 TTACCAAATTTCATTTACACTTTAA
* *
23423 TTACCGAATTTCATTTTTTACTCTTTAA
1 TTACCAAATTTCA---TTTACACTTTAA
23451 TTACCAAATTTCATTT
1 TTACCAAATTTCATTT
23467 TTGATCTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
24 10 0.29
25 3 0.09
27 4 0.11
28 18 0.51
ACGTcount: A:0.32, C:0.19, G:0.01, T:0.47
Consensus pattern (25 bp):
TTACCAAATTTCATTTACACTTTAA
Found at i:23451 original size:28 final size:28
Alignment explanation
Indices: 23417--23662 Score: 167
Period size: 28 Copynumber: 8.9 Consensus size: 28
23407 TACCATTTAA
*
23417 CTTTAATTACCGAATTTCATTTTTTACT
1 CTTTAATTACCAAATTTCATTTTTTACT
*
23445 CTTTAATTACCAAATTTCATTTTTGA-T
1 CTTTAATTACCAAATTTCATTTTTTACT
* ** *
23472 CTTTAAATACTTTAATTATCAAATTCATTT--T
1 CTTTAATTAC-CAAATT-TC--ATT-TTTTACT
* * * *
23503 CTTTAATTGCCATATTCCA--TATTACT
1 CTTTAATTACCAAATTTCATTTTTTACT
*
23529 CCTTT-A-T--CAAATTCCA--TTTTACT
1 -CTTTAATTACCAAATTTCATTTTTTACT
* *
23552 CCTTTTACTTACCAAATTTCA-CTTTTACT
1 -C-TTTAATTACCAAATTTCATTTTTTACT
*
23581 TTTTAATTACCCAAATTTCATTTTTTACT
1 CTTTAATTA-CCAAATTTCATTTTTTACT
*
23610 TTTTAATTACCCAAA-TTCATTTTTTACT
1 CTTTAATTA-CCAAATTTCATTTTTTACT
23638 CTTTAATTACCCAAATTTCATTTTT
1 CTTTAATTA-CCAAATTTCATTTTT
23663 ACCAAATACC
Statistics
Matches: 178, Mismatches: 23, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
23 16 0.09
24 5 0.03
25 1 0.01
26 3 0.02
27 22 0.12
28 73 0.41
29 41 0.23
30 3 0.02
31 12 0.07
32 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.01, T:0.51
Consensus pattern (28 bp):
CTTTAATTACCAAATTTCATTTTTTACT
Found at i:23693 original size:40 final size:40
Alignment explanation
Indices: 23640--23837 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 40
23630 TTTTTACTCT
*
23640 TTAATTACCCAAATTTCATTTTTACCAAATACCATTTAACC
1 TTAATTA-CCAAATTTCATTTTTACTAAATACCATTTAACC
* *
23681 TTAGTTACCAAATTTCATTTTTACTTTTTAATTACCGAATTTCATTTTTACTC
1 TTAATTACCAAATTTCATTTTTAC----TAAATACC--ATTT-A-----AC-C
* * * *
23734 TTTAATTACCAAATTTCATCTTTATTTAATACCATTTAACT
1 -TTAATTACCAAATTTCATTTTTACTAAATACCATTTAACC
*
23775 TTAATTACCAAATTTCATTTTTACTTAATACCATTTAACC
1 TTAATTACCAAATTTCATTTTTACTAAATACCATTTAACC
*
23815 TTAGTTACCAAATTTCATTTTTA
1 TTAATTACCAAATTTCATTTTTA
23838 ATTTTTTAAT
Statistics
Matches: 130, Mismatches: 13, Indels: 29
0.76 0.08 0.17
Matches are distributed among these distances:
40 76 0.58
41 6 0.05
42 2 0.02
44 6 0.05
46 4 0.03
47 2 0.02
48 4 0.03
50 6 0.05
52 2 0.02
53 1 0.01
54 21 0.16
ACGTcount: A:0.32, C:0.19, G:0.02, T:0.47
Consensus pattern (40 bp):
TTAATTACCAAATTTCATTTTTACTAAATACCATTTAACC
Found at i:23705 original size:68 final size:67
Alignment explanation
Indices: 23620--23919 Score: 296
Period size: 68 Copynumber: 4.4 Consensus size: 67
23610 TTTTAATTAC
23620 CCAAA-TTCATTTTTTACTCTTTAATTACCCAAATTTCATTTTTACCAAATACCATTTAACCTTA
1 CCAAATTTCA-TTTTTACTCTTTAATTA-CCAAATTTCATTTTTACCAAATACCATTTAACCTTA
23684 GTTA
64 GTTA
* * * *
23688 CCAAATTTCATTTTTACTTTTTAATTACCGAATTTCATTTTTACTCTTTAATTACCAAATTTCAT
1 CCAAATTTCATTTTTACTCTTTAATTACCAAATTTCATTTTTAC-C---AAATACC--ATTT-AA
*
23753 CTTTA-TT-
59 CCTTAGTTA
* ** * **
23760 --TAATACCA--TTTA-ACTTTAATTACCAAATTTCATTTTTACTTAATACCATTTAACCTTAGT
1 CCAAATTTCATTTTTACTCTTTAATTACCAAATTTCATTTTTACCAAATACCATTTAACCTTAGT
23820 TA
66 TA
* *
23822 CCAAATTTCATTTTTAATTTTTTAATTACCAAATTTCATTTTTA-CATAATACCATTTAACCTTA
1 CCAAATTTCATTTTT-ACTCTTTAATTACCAAATTTCATTTTTACCA-AATACCATTTAACCTTA
23886 GTTA
64 GTTA
23890 CCAAATTTCATTTTTTACAT-TTTAATTACC
1 CCAAATTTCA-TTTTTAC-TCTTTAATTACC
23920 CTCTTTTTTA
Statistics
Matches: 189, Mismatches: 24, Indels: 38
0.75 0.10 0.15
Matches are distributed among these distances:
60 5 0.03
61 6 0.03
63 5 0.03
64 5 0.03
66 3 0.02
67 41 0.22
68 92 0.49
69 10 0.05
70 5 0.03
71 6 0.03
73 6 0.03
74 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.01, T:0.48
Consensus pattern (67 bp):
CCAAATTTCATTTTTACTCTTTAATTACCAAATTTCATTTTTACCAAATACCATTTAACCTTAGT
TA
Found at i:23721 original size:27 final size:27
Alignment explanation
Indices: 23685--23757 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
23675 TTAACCTTAG
*
23685 TTACCAAATTTCATTTTTACTTTTTAA
1 TTACCAAATTTCATTTTTACTCTTTAA
*
23712 TTACCGAATTTCATTTTTACTCTTTAA
1 TTACCAAATTTCATTTTTACTCTTTAA
*
23739 TTACCAAATTTCATCTTTA
1 TTACCAAATTTCATTTTTA
23758 TTTAATACCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.29, C:0.18, G:0.01, T:0.52
Consensus pattern (27 bp):
TTACCAAATTTCATTTTTACTCTTTAA
Found at i:23757 original size:20 final size:20
Alignment explanation
Indices: 23732--23797 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
23722 TCATTTTTAC
23732 TCTTTAATTACCAAATTTCA
1 TCTTTAATTACCAAATTTCA
* ** *
23752 TCTTTATTTAATACCATTT-A
1 TCTTTAATTACCA-AATTTCA
*
23772 ACTTTAATTACCAAATTTCA
1 TCTTTAATTACCAAATTTCA
*
23792 TTTTTA
1 TCTTTA
23798 CTTAATACCA
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
19 4 0.12
20 25 0.76
21 4 0.12
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (20 bp):
TCTTTAATTACCAAATTTCA
Found at i:23783 original size:94 final size:96
Alignment explanation
Indices: 23582--23920 Score: 353
Period size: 108 Copynumber: 3.4 Consensus size: 96
23572 ACTTTTACTT
23582 TTTAATTACCCAAATTTCATTTTTTACTTTTTAATTACCCAAATTCATTTTTTACTCTTTAATTA
1 TTTAATTA-CCAAATTTCA-TTTTTACTTTTTAATTACCCAAATTCATTTTTTACTCTTTAATTA
*
23647 CCCAAATTTCATTTTTACCAAATACCATTTAAC
64 CCCAAATTTCATCTTTACCAAATACCATTTAAC
* * * *
23680 CTTAGTTACCAAATTTCATTTTTACTTTTTAATTACCGAATTTCA-TTTTTACTCTTTAATTA-C
1 TTTAATTACCAAATTTCATTTTTACTTTTTAATTACCCAAATTCATTTTTTACTCTTTAATTACC
***
23743 CAAATTTCATCTTTATTTAATACCATTTAAC
66 CAAATTTCATCTTTACCAAATACCATTTAAC
* *
23774 TTTAATTACCAAATTTCATTTTTACTTAATACCATTTAACCTTAGTTACCAAATTTCATTTTTAA
1 TTTAATTACCAAATTTCATTTTTAC-T--T----TTTAA--TTA---CCCAAA-TTCATTTTTTA
* * *
23839 TTTTTTAATTA-CCAAATTTCATTTTTA-CATAATACCATTTAAC
53 CTCTTTAATTACCCAAATTTCATCTTTACCA-AATACCATTTAAC
* * *
23882 CTTAGTTACCAAATTTCATTTTTTACATTTTAATTACCC
1 TTTAATTACCAAATTTCA-TTTTTACTTTTTAATTACCC
23921 TCTTTTTTAC
Statistics
Matches: 202, Mismatches: 23, Indels: 33
0.78 0.09 0.13
Matches are distributed among these distances:
94 51 0.25
95 18 0.09
96 25 0.12
97 13 0.06
98 6 0.03
100 3 0.01
101 5 0.02
102 5 0.02
103 3 0.01
106 4 0.02
107 4 0.02
108 58 0.29
109 7 0.03
ACGTcount: A:0.32, C:0.19, G:0.01, T:0.49
Consensus pattern (96 bp):
TTTAATTACCAAATTTCATTTTTACTTTTTAATTACCCAAATTCATTTTTTACTCTTTAATTACC
CAAATTTCATCTTTACCAAATACCATTTAAC
Found at i:28626 original size:2 final size:2
Alignment explanation
Indices: 28619--28643 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28609 ACCGATCTAA
28619 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28644 CAATAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33271 original size:17 final size:17
Alignment explanation
Indices: 33231--33273 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
33221 TAGTCGGGTT
* *
33231 CGGGTCTTAATAAGTCT
1 CGGGTCTTAACAAGTCA
* *
33248 CGAGTCTTAACAGGTCA
1 CGGGTCTTAACAAGTCA
33265 CGGGTCTTA
1 CGGGTCTTA
33274 TCAGATCGGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (17 bp):
CGGGTCTTAACAAGTCA
Found at i:46524 original size:14 final size:14
Alignment explanation
Indices: 46505--46532 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46495 AAAAATCCTA
46505 AAGAAACTAGGTTT
1 AAGAAACTAGGTTT
46519 AAGAAACTAGGTTT
1 AAGAAACTAGGTTT
46533 CTACACCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
AAGAAACTAGGTTT
Found at i:58733 original size:19 final size:18
Alignment explanation
Indices: 58700--58735 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
58690 TTGAAATAAT
58700 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
58718 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
58736 TGACTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:58743 original size:11 final size:10
Alignment explanation
Indices: 58700--58746 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
58690 TTGAAATAAT
58700 TCTTCAATGA
1 TCTTCAATGA
58710 TCTTCAA--A
1 TCTTCAATGA
*
58718 TCTTCAAATTA
1 TCTTC-AATGA
58729 TCTTCAATGA
1 TCTTCAATGA
58739 CTCTTCAA
1 -TCTTCAA
58747 ACACGAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:59910 original size:29 final size:29
Alignment explanation
Indices: 59861--59919 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
59851 TAAGGCATAC
*
59861 ATTTATTAATCTGGCTCTACACCTTCCAT
1 ATTTATTAATCTAGCTCTACACCTTCCAT
*
59890 ATTTATTAATCTAGCTTTACACCTTCCAT
1 ATTTATTAATCTAGCTCTACACCTTCCAT
59919 A
1 A
59920 CCACACTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.05, T:0.42
Consensus pattern (29 bp):
ATTTATTAATCTAGCTCTACACCTTCCAT
Found at i:73135 original size:27 final size:26
Alignment explanation
Indices: 73098--73203 Score: 140
Period size: 27 Copynumber: 4.0 Consensus size: 26
73088 GCATTAGGGT
* **
73098 CACATAAGGGGCATTTTATTCATTTG
1 CACATCAGGGGCATTTTGGTCATTTG
73124 CACATCCAGGGGCATTTTGGTCATTTG
1 CACAT-CAGGGGCATTTTGGTCATTTG
*
73151 CACAGTCAGGGGCATTTTGGACATTTG
1 CACA-TCAGGGGCATTTTGGTCATTTG
*
73178 CACATTCAAGGGCATTTTGGTCATTT
1 CACA-TCAGGGGCATTTTGGTCATTT
73204 TAAGTTCACA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
26 5 0.07
27 65 0.92
28 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (26 bp):
CACATCAGGGGCATTTTGGTCATTTG
Found at i:73332 original size:17 final size:17
Alignment explanation
Indices: 73290--73325 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
73280 TTTTTTCTTC
*
73290 TTAGTTTTGTACTACAA
1 TTAGCTTTGTACTACAA
73307 TTAGCTTTGTACTACAA
1 TTAGCTTTGTACTACAA
73324 TT
1 TT
73326 GCATTTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (17 bp):
TTAGCTTTGTACTACAA
Found at i:76284 original size:21 final size:22
Alignment explanation
Indices: 76260--76300 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
76250 TAATTAAATG
*
76260 CAATTTGATCCCTG-TTTTATT
1 CAATTTGACCCCTGATTTTATT
76281 CAATTTGACCCCTGATTTTA
1 CAATTTGACCCCTGATTTTA
76301 GAAATTATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (22 bp):
CAATTTGACCCCTGATTTTATT
Found at i:77128 original size:17 final size:18
Alignment explanation
Indices: 77106--77141 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
77096 TCCTAATTTG
*
77106 GAGAAAAATAAA-CAAAA
1 GAGAAAAAAAAATCAAAA
77123 GAGAAAAAAAAATCAAAA
1 GAGAAAAAAAAATCAAAA
77141 G
1 G
77142 TGTTTTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.06
Consensus pattern (18 bp):
GAGAAAAAAAAATCAAAA
Found at i:78068 original size:17 final size:17
Alignment explanation
Indices: 78048--78082 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
78038 GATTAATTTG
*
78048 ATTTGCTTTATTTTTTC
1 ATTTGCTCTATTTTTTC
*
78065 ATTTTCTCTATTTTTTC
1 ATTTGCTCTATTTTTTC
78082 A
1 A
78083 AACTGTCCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.69
Consensus pattern (17 bp):
ATTTGCTCTATTTTTTC
Found at i:78492 original size:137 final size:136
Alignment explanation
Indices: 78333--78589 Score: 333
Period size: 137 Copynumber: 1.9 Consensus size: 136
78323 ACTTTTATAG
78333 TTTTACTCAAATAAAAAATCTA-TTTTTATTTAATTAAATCTAATATCCTTATAACTA-TTTAAT
1 TTTTACTCAAATAAAAAATCTATTTTTTATTTAATT--A--TAATATCCTTATAACTATTTTAAT
* * * * *
78396 TTTCACCATTTTAC-AATTTTAATTAAAAAACTT-ATATATTATAATTTTTTAAATATACTTTTA
62 TTTCACCATTATACTAA-TTTAATTAAAAAAATTAACATATTAGAATTTTTAAAATATACTTTTA
78459 TAGTTTTACAC
126 TAGTTTTACAC
* * * * *
78470 TTTTACTCAACTAAAAACTCTATTTTTTATTTAATTATAATATCCTTATACCTATTTTATTTTTT
1 TTTTACTCAAATAAAAAATCTATTTTTTATTTAATTATAATATCCTTATAACTATTTTAATTTTC
*
78535 ATCATTATACTAATTTAATTAAAAAAATTAGACATATTAGAATTTTTAAAATATA
66 ACCATTATACTAATTTAATTAAAAAAATTA-ACATATTAGAATTTTTAAAATATA
78590 TTTGTTAAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
134 16 0.15
135 31 0.30
136 3 0.03
137 41 0.39
138 13 0.12
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.49
Consensus pattern (136 bp):
TTTTACTCAAATAAAAAATCTATTTTTTATTTAATTATAATATCCTTATAACTATTTTAATTTTC
ACCATTATACTAATTTAATTAAAAAAATTAACATATTAGAATTTTTAAAATATACTTTTATAGTT
TTACAC
Found at i:79675 original size:3 final size:3
Alignment explanation
Indices: 79667--79699 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
79657 TCATAGGTAA
79667 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
79700 ATTTTATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:83518 original size:13 final size:13
Alignment explanation
Indices: 83500--83524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83490 TTGTAACAGT
83500 TTATCTGGATCAA
1 TTATCTGGATCAA
83513 TTATCTGGATCA
1 TTATCTGGATCA
83525 GATATTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TTATCTGGATCAA
Found at i:87225 original size:23 final size:24
Alignment explanation
Indices: 87176--87225 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
87166 AGCTTATTAA
** **
87176 TTATTTAATGTAAAGAAATTATGT
1 TTATTTAAAATAAAGAAATTACAT
87200 TTATTTAAAATAAA-AAATTACAT
1 TTATTTAAAATAAAGAAATTACAT
87223 TTA
1 TTA
87226 CGAAAGTAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (24 bp):
TTATTTAAAATAAAGAAATTACAT
Found at i:93188 original size:24 final size:23
Alignment explanation
Indices: 93161--93211 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
93151 GAATGTTCTG
*
93161 TTTCTTTAATTTATTAGTGGCTT
1 TTTCTTTAATTTATTAGTAGCTT
93184 ATTTCTTTAATTTATTAGTAGCTT
1 -TTTCTTTAATTTATTAGTAGCTT
93208 TTTC
1 TTTC
93212 GTGGCGTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.61
Consensus pattern (23 bp):
TTTCTTTAATTTATTAGTAGCTT
Found at i:94818 original size:51 final size:52
Alignment explanation
Indices: 94600--94827 Score: 370
Period size: 52 Copynumber: 4.4 Consensus size: 52
94590 TGAAATCCTA
* *
94600 ATGGGAACTTTCCCACTTTGAAATGACCTAAATCAAACACTTTGAAAACTTG
1 ATGGGAACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTG
*
94652 ATGGGAACTTTCTCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTG
1 ATGGGAACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTG
94704 ATGGGAACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTG
1 ATGGGAACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTG
* * *
94756 ATGGGAACTTTCACACTTTGAATAGACCTAAATTGAA-ACTTTGAAAACATT-
1 ATGGGAACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAAC-TTG
*
94807 ATGGGAACTTTCCTACTTTGA
1 ATGGGAACTTTCCCACTTTGA
94828 GAACTTTGAA
Statistics
Matches: 166, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
51 30 0.18
52 136 0.82
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (52 bp):
ATGGGAACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTG
Found at i:94883 original size:7 final size:7
Alignment explanation
Indices: 94847--94871 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
94837 AGGAAATTCT
94847 TTTTGAA
1 TTTTGAA
94854 TTTTGAA
1 TTTTGAA
94861 TTTTGAA
1 TTTTGAA
94868 TTTT
1 TTTT
94872 TTTTGGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (7 bp):
TTTTGAA
Found at i:95386 original size:5 final size:6
Alignment explanation
Indices: 95370--95405 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
95360 TAATCTAACC
95370 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTCT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTT-T CTTTT
95406 ATTAATCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:103544 original size:27 final size:27
Alignment explanation
Indices: 103502--103592 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
103492 AACTTCTGAC
*
103502 TTTGGGCTTTTAAATTGTTTTAATGCA
1 TTTGGGCTTTTAAATTGTTTTTATGCA
* *
103529 TTTGGGCTTCTT-AATTATTTTTGTGCA
1 TTTGGGCTT-TTAAATTGTTTTTATGCA
* *
103556 CTTGGGCTTTTAAATAGTTTTTATGCA
1 TTTGGGCTTTTAAATTGTTTTTATGCA
103583 TTTGGGCTTT
1 TTTGGGCTTT
103593 GTTGAGACTT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.04
27 50 0.93
28 2 0.04
ACGTcount: A:0.18, C:0.10, G:0.20, T:0.53
Consensus pattern (27 bp):
TTTGGGCTTTTAAATTGTTTTTATGCA
Found at i:104498 original size:52 final size:52
Alignment explanation
Indices: 104418--104557 Score: 208
Period size: 52 Copynumber: 2.7 Consensus size: 52
104408 TCTTTCAAAG
* * **
104418 TTTTCAAAGTGAGAAAGTTCCCAACAAGTTTTCAAAGTGTTCAGTTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAACTTAGGTC
* * *
104470 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTCCAAAGTGTTCAACTTAGTTT
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAACTTAGGTC
*
104522 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAA
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAA
104558 TTAAGAAAGT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (52 bp):
TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAACTTAGGTC
Found at i:104565 original size:28 final size:27
Alignment explanation
Indices: 104522--104580 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
104512 AACTTAGTTT
**
104522 TTTTCAAATTGGGAAAGTTCCCATCAAG
1 TTTTCAAATTAAGAAAGTTCCCATC-AG
104550 TTTTCAAATTAAGAAAGTTCCCATCAG
1 TTTTCAAATTAAGAAAGTTCCCATCAG
104577 TTTT
1 TTTT
104581 TAAAGCATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (27 bp):
TTTTCAAATTAAGAAAGTTCCCATCAG
Found at i:105813 original size:18 final size:18
Alignment explanation
Indices: 105790--105828 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
105780 ACATGTTAGA
105790 AATGGCAAC-GGAAATGGC
1 AATGGCAACAGG-AATGGC
*
105808 AATGGCATCAGGAATGGC
1 AATGGCAACAGGAATGGC
105826 AAT
1 AAT
105829 CCACTCCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (18 bp):
AATGGCAACAGGAATGGC
Found at i:112288 original size:16 final size:14
Alignment explanation
Indices: 112254--112284 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
112244 TCTTACAAAC
112254 TTTGAAGCCCATCT
1 TTTGAAGCCCATCT
112268 TTTGAAGCCCATCT
1 TTTGAAGCCCATCT
112282 TTT
1 TTT
112285 TTGAGAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (14 bp):
TTTGAAGCCCATCT
Found at i:118461 original size:19 final size:18
Alignment explanation
Indices: 118437--118472 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
118427 TGAAGACTTA
118437 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
118456 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
118473 ACTATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:120025 original size:5 final size:6
Alignment explanation
Indices: 120010--120034 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
120000 TTGTGTATTA
120010 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
120035 ATTTGATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:125713 original size:12 final size:12
Alignment explanation
Indices: 125696--125725 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
125686 GCACATAATA
125696 AACAGAATTTTC
1 AACAGAATTTTC
125708 AACAGAATTTTC
1 AACAGAATTTTC
125720 AACAGA
1 AACAGA
125726 CTTTATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (12 bp):
AACAGAATTTTC
Found at i:127314 original size:1 final size:1
Alignment explanation
Indices: 127308--127332 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
127298 TTGAGTCGGC
127308 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
127333 GAAGCTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:131272 original size:52 final size:52
Alignment explanation
Indices: 131215--131319 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
131205 TTTTTCTTTC
* *
131215 CGCAACAACTTATGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTATGCCCCGAAGTTGAACAAGCTCTGGGCCGAAGTTGTCCTG
*
131267 CGCAACAACTTCTGCCCCGAAGTTGAACAAGCTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTATGCCCCGAAGTTGAACAAGCTCTGGGCCGAAGTTGTCCTG
131319 C
1 C
131320 AATTCTTGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.23
Consensus pattern (52 bp):
CGCAACAACTTATGCCCCGAAGTTGAACAAGCTCTGGGCCGAAGTTGTCCTG
Found at i:131369 original size:21 final size:21
Alignment explanation
Indices: 131345--131385 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
131335 TTCGACAGGC
*
131345 CAACTTCTGGGCAGAAGTTGA
1 CAACATCTGGGCAGAAGTTGA
*
131366 CAACATCTGGGCCGAAGTTG
1 CAACATCTGGGCAGAAGTTG
131386 TCCTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (21 bp):
CAACATCTGGGCAGAAGTTGA
Found at i:133470 original size:33 final size:32
Alignment explanation
Indices: 133433--133562 Score: 125
Period size: 33 Copynumber: 3.9 Consensus size: 32
133423 ATGATCAACC
** * *
133433 AAAACAGATTTGTATTCATCACAATTAGCATCT
1 AAAACAGATTTGTA-TCATCACAAACAACACCT
133466 AAAACAGAATTTGTATCATCACAAACAACACCT
1 AAAACAG-ATTTGTATCATCACAAACAACACCT
* * *
133499 AAAACAGATTTAGTGTCATCACTAACAACATCT
1 AAAACAGATTT-GTATCATCACAAACAACACCT
* * **
133532 AAAACATATTTCGTGTCATTGCAAACAACAC
1 AAAACAGATTT-GTATCATCACAAACAACAC
133563 TCAAATTAGG
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
32 4 0.05
33 71 0.87
34 7 0.09
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (32 bp):
AAAACAGATTTGTATCATCACAAACAACACCT
Found at i:133646 original size:60 final size:60
Alignment explanation
Indices: 133568--133691 Score: 203
Period size: 60 Copynumber: 2.1 Consensus size: 60
133558 AACACTCAAA
* * *
133568 TTAGGTTCATAATTACTCTTTGAAAATAAGGTTGTTTTATGATCAAAACAATCAACAATT
1 TTAGGTTCAGAATTACTCTTTGAAAATAAGGTTGTTTTATCATCAAAACAATCAACAAGT
* *
133628 TTAGGTTCGGAATTACTCTTTGAAAATAAGGTTGTTTTATCATCAAAACAATCAGCAAGT
1 TTAGGTTCAGAATTACTCTTTGAAAATAAGGTTGTTTTATCATCAAAACAATCAACAAGT
133688 TTAG
1 TTAG
133692 AATCGGTGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (60 bp):
TTAGGTTCAGAATTACTCTTTGAAAATAAGGTTGTTTTATCATCAAAACAATCAACAAGT
Done.