Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022758.1 Corchorus olitorius cultivar O-4 contig22791, 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: 26205
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:178 original size:68 final size:67
Alignment explanation
Indices: 106--259 Score: 186
Period size: 68 Copynumber: 2.3 Consensus size: 67
96 AGGCCAAATA
* * *
106 AGAATAAAACATTGAAAACAGGGAC-GAAATATTGAAAACAATACCTTCCGGCCG-GGAAGGGCA
1 AGAATAAAACATTGAAAACA-GGACTAAAATATTGAAAACAACACCTTCC-GACGAGGAAGGGCA
169 AAACG
64 AAA-G
* * *
174 AGAATAAAGCATTGAAGACAGGACTAAAATATTGAAGACAACACCTTCCGACGAGGAAGGGCAAA
1 AGAATAAAACATTGAAAACAGGACTAAAATATTGAAAACAACACCTTCCGACGAGGAAGGGCAAA
*
239 AT
66 AG
*
241 ATGAATAAAAGATTGAAAA
1 A-GAATAAAACATTGAAAA
260 TAATACCTTC
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
67 8 0.11
68 65 0.89
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (67 bp):
AGAATAAAACATTGAAAACAGGACTAAAATATTGAAAACAACACCTTCCGACGAGGAAGGGCAAA
AG
Found at i:256 original size:48 final size:48
Alignment explanation
Indices: 191--789 Score: 809
Period size: 48 Copynumber: 12.5 Consensus size: 48
181 AGCATTGAAG
* * *
191 ACAGGACTAAAATATTGAAGACAACACCTTCCGA-CGAGGAAGGGCAAA
1 ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCG-GGAAGGGCAAA
* * * * * *
239 ATATGAATAAAA-GATTGAAAATAATACCTTCCGGCCGAGAAGGG-AAA
1 ACAGGAATAAAATG-TTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
* *
286 ACATGAATAAAATGTTGAAAAACAACACCTTCCGATCGGGAAGGGCAAA
1 ACAGGAATAAAATGTTG-AAAACAACACCTTCCGACCGGGAAGGGCAAA
* * * *
335 AC-GGGATAAAATATTGAAGACAACACCTTCCGACCAGGAAGGGCAAA
1 ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
*
382 A-TGAGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
1 ACAG-GAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
* *
430 ACGGGAATTAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
1 ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
478 ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
1 ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
* * * * *
526 ACTA-GAATAAAATATTGAAGACAACCCCTTTCGACTGGGAAGGGCAAA
1 AC-AGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
*
574 ACAGGAATAAAATGTTGAAAACAACACCTTTCGACCGGGAAGGGCAAA
1 ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
* * *
622 ACTGGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAA
1 ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
670 ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
1 ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
* *
718 ACGGGAATAAAATGTTGAAAACAACAACTTCCGACCGGGAAGGGCAAA
1 ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
*
766 ACGGGCAATAAACA--TTGAAAACAA
1 ACAGG-AATAAA-ATGTTGAAAACAA
790 ACCATTCATT
Statistics
Matches: 492, Mismatches: 47, Indels: 24
0.87 0.08 0.04
Matches are distributed among these distances:
47 48 0.10
48 428 0.87
49 15 0.03
50 1 0.00
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (48 bp):
ACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
Found at i:1526 original size:50 final size:50
Alignment explanation
Indices: 1369--1866 Score: 534
Period size: 50 Copynumber: 9.7 Consensus size: 50
1359 AAAATTTCAT
** * * * *
1369 CTTTATTTACAAATTAGTTAAAAGTTCAATATTTTAACTTAAAGATTTC-AT
1 CTTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAA-TTAAA-AGTCCAAC
* * * * *
1420 TTTTATTTACAAATTGCTTAAAAGGTTTCAA-CTTTTCATTAAAAATCCAAT
1 CTTTATTTACAAATTTCTTAAAA-G-TTCAATCTTTTAATTAAAAGTCCAAC
* ** * *
1471 CTTTATTTACAAATTACTTAAAAGTTTGATCTTTTAATCTAAAA-CCCAAT
1 CTTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAAT-TAAAAGTCCAAC
* *
1521 CTTTATTTACAAACTACTTAAAAGCTTCAATCTTTTAATTAAAAGTCCAAC
1 CTTTATTTACAAATTTCTTAAAAG-TTCAATCTTTTAATTAAAAGTCCAAC
* *
1572 CTTTATTTACAAATTCCCTAAAAGTTTCAATCTTTTAATTAAAAGTCCAAC
1 CTTTATTTACAAATTTCTTAAAAG-TTCAATCTTTTAATTAAAAGTCCAAC
* * ** * *
1623 CTTTATTTACAAATTGCTTAAAGGTTTGATCTTTTAATTGAAAGTTCAAC
1 CTTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAAC
* *
1673 CTTCATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTTCAAC
1 CTTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAAC
* * *
1723 CTTTATTTAAAAATTTCTTAAAAGTTCAACCTTTATTTACAAATTTCTTAAAAGTTCAAC
1 CTTTATTTACAAATTTCTTAAAAGTTCAA--TCT-TTT---AA----TTAAAAGTCCAAC
1783 CTTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAAC
1 CTTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAAC
*
1833 CTTTATTTACAAATTTCTTAAAAGTTCAACCTTT
1 CTTTATTTACAAATTTCTTAAAAGTTCAATCTTT
1867 ATTTACAAAT
Statistics
Matches: 388, Mismatches: 42, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
49 3 0.01
50 182 0.47
51 137 0.35
52 8 0.02
53 8 0.02
54 2 0.01
56 2 0.01
57 3 0.01
58 2 0.01
60 41 0.11
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.42
Consensus pattern (50 bp):
CTTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAAC
Found at i:1699 original size:30 final size:30
Alignment explanation
Indices: 1663--1884 Score: 250
Period size: 30 Copynumber: 8.1 Consensus size: 30
1653 CTTTTAATTG
*
1663 AAAGTTCAACCTTCATTTACAAATTTCTTA
1 AAAGTTCAACCTTTATTTACAAATTTCTTA
*
1693 AAAGTTCAA--TCT-TTT---AA----TTA
1 AAAGTTCAACCTTTATTTACAAATTTCTTA
*
1713 AAAGTTCAACCTTTATTTAAAAATTTCTTA
1 AAAGTTCAACCTTTATTTACAAATTTCTTA
1743 AAAGTTCAACCTTTATTTACAAATTTCTTA
1 AAAGTTCAACCTTTATTTACAAATTTCTTA
1773 AAAGTTCAACCTTTATTTACAAATTTCTTA
1 AAAGTTCAACCTTTATTTACAAATTTCTTA
*
1803 AAAGTTCAA--TCT-TTT---AA----TTA
1 AAAGTTCAACCTTTATTTACAAATTTCTTA
*
1823 AAAGTCCAACCTTTATTTACAAATTTCTTA
1 AAAGTTCAACCTTTATTTACAAATTTCTTA
*
1853 AAAGTTCAACCTTTATTTACAAATTGCTTA
1 AAAGTTCAACCTTTATTTACAAATTTCTTA
1883 AA
1 AA
1885 GGTTTGATCT
Statistics
Matches: 163, Mismatches: 9, Indels: 40
0.77 0.04 0.19
Matches are distributed among these distances:
20 23 0.14
22 4 0.02
23 6 0.04
24 4 0.02
26 4 0.02
27 6 0.04
28 3 0.02
30 113 0.69
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (30 bp):
AAAGTTCAACCTTTATTTACAAATTTCTTA
Found at i:1735 original size:20 final size:20
Alignment explanation
Indices: 1690--1734 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1680 TACAAATTTC
*
1690 TTAAAAGTTCAATCTTTTAA
1 TTAAAAGTTCAATCCTTTAA
*
1710 TTAAAAGTTCAA-CCTTTAT
1 TTAAAAGTTCAATCCTTTAA
1729 TTAAAA
1 TTAAAA
1735 ATTTCTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (20 bp):
TTAAAAGTTCAATCCTTTAA
Found at i:1856 original size:110 final size:110
Alignment explanation
Indices: 1663--1884 Score: 408
Period size: 110 Copynumber: 2.0 Consensus size: 110
1653 CTTTTAATTG
*
1663 AAAGTTCAACCTTCATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTTCAACCTTTA
1 AAAGTTCAACCTTCATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAACCTTTA
*
1728 TTTAAAAATTTCTTAAAAGTTCAACCTTTATTTACAAATTTCTTA
66 TTTAAAAATTTCTTAAAAGTTCAACCTTTATTTACAAATTGCTTA
*
1773 AAAGTTCAACCTTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAACCTTTA
1 AAAGTTCAACCTTCATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAACCTTTA
*
1838 TTTACAAATTTCTTAAAAGTTCAACCTTTATTTACAAATTGCTTA
66 TTTAAAAATTTCTTAAAAGTTCAACCTTTATTTACAAATTGCTTA
1883 AA
1 AA
1885 GGTTTGATCT
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (110 bp):
AAAGTTCAACCTTCATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAACCTTTA
TTTAAAAATTTCTTAAAAGTTCAACCTTTATTTACAAATTGCTTA
Found at i:1919 original size:80 final size:80
Alignment explanation
Indices: 1610--1904 Score: 359
Period size: 80 Copynumber: 3.7 Consensus size: 80
1600 AATCTTTTAA
* *
1610 TTAAAAGTCCAACCTTTATTTACAAATTGCTTAAAGGTTTGATCTTTTAATTGAAAGTTCAACCT
1 TTAAAAGTTCAACCTTTATTTACAAATTGCTTAAAGGTTTGATCTTTTAATTAAAAGTTCAACCT
*
1675 TCATTTACAAATTTC
66 TTATTTACAAATTTC
* * * ** **
1690 TTAAAAGTTCAATCTTTTAATTA-AAA--G-TTCAACCTTT-AT-TTAAAAATTTCTTAAAAGTT
1 TTAAAAGTTCAA-CCTTTATTTACAAATTGCTTAAAGGTTTGATCTT-----TTAATTAAAAGTT
1749 CAACCTTTATTTACAAATTTC
60 CAACCTTTATTTACAAATTTC
* * ** *
1770 TTAAAAGTTCAACCTTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAACCT
1 TTAAAAGTTCAACCTTTATTTACAAATTGCTTAAAGGTTTGATCTTTTAATTAAAAGTTCAACCT
1835 TTATTTACAAATTTC
66 TTATTTACAAATTTC
1850 TTAAAAGTTCAACCTTTATTTACAAATTGCTTAAAGGTTTGATCTTTTAATTAAA
1 TTAAAAGTTCAACCTTTATTTACAAATTGCTTAAAGGTTTGATCTTTTAATTAAA
1905 GATTATATTT
Statistics
Matches: 179, Mismatches: 24, Indels: 24
0.79 0.11 0.11
Matches are distributed among these distances:
75 2 0.01
76 2 0.01
77 7 0.04
78 1 0.01
79 8 0.04
80 141 0.79
81 8 0.04
83 6 0.03
84 2 0.01
85 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (80 bp):
TTAAAAGTTCAACCTTTATTTACAAATTGCTTAAAGGTTTGATCTTTTAATTAAAAGTTCAACCT
TTATTTACAAATTTC
Found at i:5965 original size:18 final size:18
Alignment explanation
Indices: 5927--5965 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
5917 AAGAATAAAT
*
5927 AAAAATGAAAAAATGGAA
1 AAAAATGAAAAAAAGGAA
5945 AAAAATGAAAAAAAAGGAA
1 AAAAATG-AAAAAAAGGAA
5964 AA
1 AA
5966 GAATCAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (18 bp):
AAAAATGAAAAAAAGGAA
Found at i:9940 original size:9 final size:9
Alignment explanation
Indices: 9918--9956 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
9908 AAATTCCAAT
9918 AAAAAATG-
1 AAAAAATGA
*
9926 ATAAAATGAA
1 AAAAAATG-A
9936 AAAAAATGA
1 AAAAAATGA
9945 AAAAAATGA
1 AAAAAATGA
9954 AAA
1 AAA
9957 TAAGGGCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 7 0.26
9 13 0.48
10 7 0.26
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (9 bp):
AAAAAATGA
Found at i:9941 original size:18 final size:19
Alignment explanation
Indices: 9918--9956 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9908 AAATTCCAAT
*
9918 AAAAAATG-ATAAAATGAA
1 AAAAAATGAAAAAAATGAA
9936 AAAAAATGAAAAAAATGAA
1 AAAAAATGAAAAAAATGAA
9955 AA
1 AA
9957 TAAGGGCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (19 bp):
AAAAAATGAAAAAAATGAA
Found at i:10353 original size:14 final size:14
Alignment explanation
Indices: 10334--10363 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10324 CAAGAAATTC
10334 AATCAAAAACAAAA
1 AATCAAAAACAAAA
*
10348 AATCAAAAATAAAA
1 AATCAAAAACAAAA
10362 AA
1 AA
10364 AATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (14 bp):
AATCAAAAACAAAA
Found at i:10361 original size:19 final size:18
Alignment explanation
Indices: 10339--10409 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
10329 AATTCAATCA
10339 AAAACAAAAAATCAAAAAT
1 AAAA-AAAAAATCAAAAAT
10358 AAAAAAAATAAT-AAAAA-
1 AAAAAAAA-AATCAAAAAT
* *
10375 ATAAAAAAAATCAAAATT
1 AAAAAAAAAATCAAAAAT
**
10393 AAAATCAAAATCAAAAA
1 AAAAAAAAAATCAAAAA
10410 GGGAATGGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
16 3 0.07
17 11 0.26
18 22 0.51
19 7 0.16
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAAAAAAATCAAAAAT
Found at i:10373 original size:10 final size:9
Alignment explanation
Indices: 10352--10390 Score: 60
Period size: 9 Copynumber: 4.1 Consensus size: 9
10342 ACAAAAAATC
10352 AAAAATAAA
1 AAAAATAAA
10361 AAAAATAATA
1 AAAAATAA-A
10371 AAAAATAAA
1 AAAAATAAA
10380 AAAAATCAAA
1 AAAAAT-AAA
10390 A
1 A
10391 TTAAAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 15 0.54
10 13 0.46
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAATAAA
Found at i:12071 original size:19 final size:18
Alignment explanation
Indices: 12038--12073 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12028 TTGAAATTAT
12038 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
12056 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
12074 TAAGTCTTCA
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:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:13525 original size:30 final size:29
Alignment explanation
Indices: 13480--13536 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
13470 GTTTATTAAT
*
13480 GAAACTTGAACATTAAAGACATAAGATAAAG
1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG
13511 GAAA-TTGAAAATTAAAGCATAAATAA
1 GAAACTTGAAAATTAAAGCATAAATAA
13537 CTAATCCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 12 0.48
31 4 0.16
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.21
Consensus pattern (29 bp):
GAAACTTGAAAATTAAAGCATAAATAAAG
Found at i:22048 original size:19 final size:18
Alignment explanation
Indices: 22015--22050 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22005 TTGAAATTAT
22015 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
22033 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
22051 TAAGTCTTCA
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:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:24194 original size:168 final size:168
Alignment explanation
Indices: 23916--24419 Score: 762
Period size: 168 Copynumber: 3.0 Consensus size: 168
23906 TTATTTCCAT
*
23916 TTGATAAAACCTTCGGGTATCATTTCATTTTATCAAGTTTTTC-TCCAAAAATTCATGTTTAAG-
1 TTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCAT-C-AAAATTCATGTTTAAGT
* *
23979 TTAAAATCCTTGATCAAAGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGAGCACAAATTCA
64 TTAAAATCCTTGATCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCA
*
24044 GAAACCTCTAGGTATTAATTCTGATAAGTCCTCCGGGCAA
129 GAAACCTCTGGGTATTAATTCTGATAAGTCCTCCGGGCAA
*
24084 TTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAATTCATGTTTAAGTTT
1 TTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCATCAAAATTCATGTTTAAGTTT
* * * ** * *
24149 AAAATCCTTGTTTAAGGTCTC-ATTTCAAAGTTCACATTGGTAAGTCCTCCGGGCACAAGTTCAA
66 AAAATCCTTGATCAAGGTCTCTA-TTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAG
* *
24213 AAACCTCCGGGTATTAATTCTGATAAGTCCTTCGGGCAA
130 AAACCTCTGGGTATTAATTCTGATAAGTCCTCCGGGCAA
* * * *
24252 TTGATAAAACCTCCGGGTACCATTTCATTTTATCAAGTTTTTCATTAAAAATCCATGTTTAAATT
1 TTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCA-TCAAAATTCATGTTTAAGTT
* * *
24317 TAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGACCTCCGGGCACAATTTCAG
65 TAAAATCCTTGATCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAG
24382 AAACCTCTGGGTATTAATTCTGATAAGTCCTCCGGGCA
130 AAACCTCTGGGTATTAATTCTGATAAGTCCTCCGGGCA
24420 TTTCTCATTT
Statistics
Matches: 302, Mismatches: 29, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
167 17 0.06
168 175 0.58
169 109 0.36
170 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (168 bp):
TTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCATCAAAATTCATGTTTAAGTTT
AAAATCCTTGATCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGA
AACCTCTGGGTATTAATTCTGATAAGTCCTCCGGGCAA
Found at i:24638 original size:30 final size:30
Alignment explanation
Indices: 24495--24828 Score: 359
Period size: 30 Copynumber: 11.0 Consensus size: 30
24485 TGCTTATTAG
* * * *
24495 TTTATTTCAATCCGGGTTTAGGATCTTTG-
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
24524 TTTATTTCTCGAGTCCTGGTTTAGGATCATTG-
1 TTTATTT-T--AATCCTGGTTGAGGATCATTGC
*
24556 TTTATTTCTCGAATCCTGGTTTAGGATCATTG-
1 TTTATTT-T--AATCCTGGTTGAGGATCATTGC
* *
24588 TTTTTTTCTCAATCCTAGTTGAGGATCATTGC
1 TTTATTT-T-AATCCTGGTTGAGGATCATTGC
** *
24620 TTTATTTTAATCCCAGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
24650 TTTACTTTAATCTTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
24680 TTCATTTTAATCCTGGTTGAGTATCATTGT
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
24710 TTTATTTTCATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
24740 TTCATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
24770 TTTATTTTCATCCTGGTAGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
24800 TTCATTTTAATCCTAGTTTAGGATCATTG
1 TTTATTTTAATCCTGGTTGAGGATCATTG
24829 TTTCATCAGT
Statistics
Matches: 265, Mismatches: 36, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
29 7 0.03
30 175 0.66
31 20 0.08
32 63 0.24
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.46
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGC
Found at i:24854 original size:32 final size:30
Alignment explanation
Indices: 24669--24861 Score: 133
Period size: 30 Copynumber: 6.4 Consensus size: 30
24659 ATCTTGGTTG
* *
24669 AGGATCATTGCTTCATTTTAATCCTGGT-T
1 AGGATCATTGCTTCATGTTAATCCTGATAT
* * * * * *
24698 GAGTATCATTGTTTTATTTTCATCCTGGT-T
1 -AGGATCATTGCTTCATGTTAATCCTGATAT
* *
24728 GAGGATCATTGCTTCATTTTAATCCTGGT-T
1 -AGGATCATTGCTTCATGTTAATCCTGATAT
* * * * *
24758 GAGGATCATTGCTTTATTTTCATCCTGGTAG
1 -AGGATCATTGCTTCATGTTAATCCTGATAT
* *
24789 AGGATCATTGCTTCATTTTAATCCT-AGTTT
1 AGGATCATTGCTTCATGTTAATCCTGA-TAT
*
24819 AGGATCATTGTTTCATCAGTTAATCCTGATAT
1 AGGATCATTGCTTCAT--GTTAATCCTGATAT
*
24851 AGGATTATTGC
1 AGGATCATTGC
24862 ATTATGAGTT
Statistics
Matches: 137, Mismatches: 21, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
30 117 0.85
32 19 0.14
33 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.45
Consensus pattern (30 bp):
AGGATCATTGCTTCATGTTAATCCTGATAT
Found at i:25985 original size:19 final size:19
Alignment explanation
Indices: 25961--26002 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
25951 AAATACAGGT
25961 ACAAATATTCACCAAGTAC
1 ACAAATATTCACCAAGTAC
25980 ACAAATATTCACCAAGTAC
1 ACAAATATTCACCAAGTAC
25999 ACAA
1 ACAA
26003 GACCATAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.26, G:0.05, T:0.19
Consensus pattern (19 bp):
ACAAATATTCACCAAGTAC
Done.