Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021550.1 Corchorus olitorius cultivar O-4 contig21583, 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: 47694
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:8119 original size:33 final size:31
Alignment explanation
Indices: 8046--8145 Score: 119
Period size: 33 Copynumber: 3.1 Consensus size: 31
8036 GCTATGATCA
** *
8046 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
8078 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
8111 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
8144 AC
1 AC
8146 TGAAATTAGG
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
32 7 0.12
33 48 0.80
34 5 0.08
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:8160 original size:33 final size:33
Alignment explanation
Indices: 8082--8193 Score: 120
Period size: 33 Copynumber: 3.4 Consensus size: 33
8072 ATTAGCATCC
*
8082 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTATCATCACAAACAACACCT
*
8115 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTATCATCACAAACAACACCT
** * * * *
8147 GAAATTAGGTTTAGTATTATCGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCACAAACAACACCT
8181 AAAACAGATTTAG
1 AAAACAGATTTAG
8194 AATTACTCTT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
32 6 0.09
33 58 0.88
34 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACCT
Found at i:10532 original size:20 final size:21
Alignment explanation
Indices: 10490--10532 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
10480 TCCTTTGTTG
10490 ATGATCTCCAATGGGCTTCAA
1 ATGATCTCCAATGGGCTTCAA
* *
10511 ATGATCTCCGAT-GGCTTTAA
1 ATGATCTCCAATGGGCTTCAA
10531 AT
1 AT
10533 TCTTCAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGATCTCCAATGGGCTTCAA
Found at i:12919 original size:93 final size:92
Alignment explanation
Indices: 12749--12922 Score: 269
Period size: 92 Copynumber: 1.9 Consensus size: 92
12739 AGCACCATGT
* * * **
12749 GCGGTCTTTCATAGAAGTTTTCAGAGATTCAAGTTGATCTTAAGAGACCCTTTGCGGTCTTTCAT
1 GCGGTCTTTCATAAAAGCTTTCAGAGATTCAAGTTGATCTTAAAAGACCCAGTGCGGTCTTTCAT
12814 AGAAGCTTTCAGAGATTTAAGCCCTGG
66 AGAAGCTTTCAGAGATTTAAGCCCTGG
*
12841 GCGGTCTTTCATAAAAGCTTTCAGAGA-TCTAAGTTGATTTTAAAATGACCCAGTGCGGTCTTTC
1 GCGGTCTTTCATAAAAGCTTTCAGAGATTC-AAGTTGATCTTAAAA-GACCCAGTGCGGTCTTTC
12905 ATAGAAGCTTTCAGAGAT
64 ATAGAAGCTTTCAGAGAT
12923 AAGTGATCTT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
91 2 0.03
92 38 0.51
93 34 0.46
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (92 bp):
GCGGTCTTTCATAAAAGCTTTCAGAGATTCAAGTTGATCTTAAAAGACCCAGTGCGGTCTTTCAT
AGAAGCTTTCAGAGATTTAAGCCCTGG
Found at i:13020 original size:54 final size:54
Alignment explanation
Indices: 12962--13363 Score: 436
Period size: 54 Copynumber: 7.4 Consensus size: 54
12952 TTTCATAGAT
* * *
12962 GTTTTTAGAGATCAGAGTTGATCCCCAGATGGTCCAGTGAGATCATTCCAAGAA
1 GTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAA
* * * * * *
13016 GTTTTGA-ATGATTAGAGTTGATCCCCAAATGATCTAGTGCGATCATTTCAAGAA
1 GTTTTTAGA-GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAA
* * *
13070 GTTTTCAGTGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCCAAGAA
1 GTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAA
** * * * * *
13124 GTTTTCT-TTGATCAGAGTTGAT-TCCAGATG-GCCTAGTGTGGTCATTCCTATAA
1 GTTTT-TAGAGATCAGAGTTGATCCCCAGATGATCC-AGTGCGGTCATTCCAAGAA
* * *
13177 G-TTTTAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGATCATTCAAAAGAA
1 GTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTC-CAAGAA
* ** *
13231 GTTTTCACTGATCGGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAA
1 GTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAA
* * *
13285 GTTTTTAGAGATCAGAGTTGATCCCCAGATGAACCGGTGCGGTCATTCCATGAA
1 GTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAA
**
13339 GTTTTTTTTATGATCAGAGTTGATC
1 G-TTTTTAGA-GATCAGAGTTGATC
13364 TCGTTTCAAG
Statistics
Matches: 288, Mismatches: 49, Indels: 20
0.81 0.14 0.06
Matches are distributed among these distances:
51 1 0.00
52 18 0.06
53 41 0.14
54 168 0.58
55 46 0.16
56 14 0.05
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (54 bp):
GTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAA
Found at i:13232 original size:161 final size:162
Alignment explanation
Indices: 12962--13363 Score: 501
Period size: 161 Copynumber: 2.5 Consensus size: 162
12952 TTTCATAGAT
12962 GTTTTTAGAGATCAGAGTTGATCCCCAGATGGTCCAGTGAGATCATTCCAAGAAGTTTTGAATGA
1 GTTTTTAGAGATCAGAGTTGATCCCCAGATGGTCCAGTGAGATCATTCCAAGAAGTTTTGAATGA
* * *
13027 TTAGAGTTGATCCCCAAATGATCTAGTGCGATCATTTCAAGAAGTTTTCAGTGATCAGAGTTGAT
66 TCAGAGTTGATCCCCAAATGATCCAGTGCGATCATTTCAAGAAGTTTTCACTGATCAGAGTTGAT
*
13092 CCCTAGATGATCCAGTGCGGTCATTCCAAGAA
131 CCCCAGATGATCCAGTGCGGTCATTCCAAGAA
** * * * * *
13124 GTTTTCT-TTGATCAGAGTTGAT-TCCAGATGG-CCTAGTGTGGTCATTCCTATAAGTTTT-AGA
1 GTTTT-TAGAGATCAGAGTTGATCCCCAGATGGTCC-AGTGAGATCATTCCAAGAAGTTTTGA-A
* * *
13185 -GATCAGAGTTGATCCCTAGATGATCCAGTGCGATCA-TTCAAAAGAAGTTTTCACTGATCGGAG
63 TGATCAGAGTTGATCCCCAAATGATCCAGTGCGATCATTTC--AAGAAGTTTTCACTGATCAGAG
13248 TTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAA
126 TTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAA
** * * * * **
13285 GTTTTTAGAGATCAGAGTTGATCCCCAGATGAACCGGTGCGGTCATTCCATGAAGTTTTTTTTAT
1 GTTTTTAGAGATCAGAGTTGATCCCCAGATGGTCCAGTGAGATCATTCCAAGAAG--TTTTGAAT
13350 GATCAGAGTTGATC
64 GATCAGAGTTGATC
13364 TCGTTTCAAG
Statistics
Matches: 204, Mismatches: 24, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
159 3 0.01
160 36 0.18
161 103 0.50
162 40 0.20
163 3 0.01
164 5 0.02
165 14 0.07
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (162 bp):
GTTTTTAGAGATCAGAGTTGATCCCCAGATGGTCCAGTGAGATCATTCCAAGAAGTTTTGAATGA
TCAGAGTTGATCCCCAAATGATCCAGTGCGATCATTTCAAGAAGTTTTCACTGATCAGAGTTGAT
CCCCAGATGATCCAGTGCGGTCATTCCAAGAA
Found at i:13300 original size:215 final size:216
Alignment explanation
Indices: 12964--13362 Score: 604
Period size: 215 Copynumber: 1.9 Consensus size: 216
12954 TCATAGATGT
* * * *
12964 TTTTAGAGATCAGAGTTGATCCCCAGATGGTCCAGTGAGATCATTCCAAGAAGTTTTGAATGATT
1 TTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGAGATCATTCAAAGAAGTTTTCAATGATC
* * *
13029 AGAGTTGATCCCCAAATGATCTAGTGCGATCATTTCAAGAAGTTTTCAGTGATCAGAGTTGATCC
66 AGAGTTGATCCCCAAATGATCCAGTGCGATCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCC
* *
13094 CTAGATGATCCAGTGCGGTCATTCCAAGAAG-TTTTCTT-TGATCAGAGTTGATTCCAGATGGCC
131 CCAGATGAACCAGTGCGGTCATTCCAAGAAGTTTTTCTTATGATCAGAGTTGATTCCAGATGGCC
13157 TAGTGTGGTCATTCCTATAAG
196 TAGTGTGGTCATTCCTATAAG
* * *
13178 TTTTAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGATCATTCAAAAGAAGTTTTCACTGAT
1 TTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGAGATCATTC-AAAGAAGTTTTCAATGAT
* * * *
13243 CGGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATC
65 CAGAGTTGATCCCCAAATGATCCAGTGCGATCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATC
* * *
13308 CCCAGATGAACCGGTGCGGTCATTCCATGAAGTTTTTTTTATGATCAGAGTTGAT
130 CCCAGATGAACCAGTGCGGTCATTCCAAGAAGTTTTTCTTATGATCAGAGTTGAT
13363 CTCGTTTCAA
Statistics
Matches: 163, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
214 43 0.26
215 100 0.61
216 6 0.04
217 14 0.09
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (216 bp):
TTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGAGATCATTCAAAGAAGTTTTCAATGATC
AGAGTTGATCCCCAAATGATCCAGTGCGATCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCC
CCAGATGAACCAGTGCGGTCATTCCAAGAAGTTTTTCTTATGATCAGAGTTGATTCCAGATGGCC
TAGTGTGGTCATTCCTATAAG
Found at i:13418 original size:37 final size:35
Alignment explanation
Indices: 13342--13969 Score: 819
Period size: 35 Copynumber: 17.6 Consensus size: 35
13332 CCATGAAGTT
*
13342 TTTTTTATGATCAGAGTTGATCTCGTTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
13377 TTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
13412 TTTTTTTTATGATCATAGTTGATCTCGTTTCAAGAAG
1 --TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* * *
13449 TATTTTATGATCATAGTTGATCTCCTTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
13484 TTTTTTTATGATCAGAGTTGATCTCGTTTCAAGAAG
1 -TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
13520 TTTTTTTTATGATCAGAGTTGATCTCGTTTCAAGAAG
1 --TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
13557 TTTTTTTTATGATCATAGTTGATCTCATTCCAAGAAG
1 --TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
13594 TTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
13629 TTTTCGT-TGATTAGAGTTGATCTCATTTCAAGAAG
1 TTTT-TTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
13664 TTTTTGATGATCAGAGTTAATCTCA-TTCTAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTC-AAGAAG
** * **
13699 TTTTGGATGATCAGAGTTGATCTCGTTTTGAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
13734 TCTTTTATGATCAGAGTTGATCTCCTTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
13769 TTTTTGATGATCAGAGTTGATCTCGTTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
13804 TTTTTGATTATCAGAGTTGATCTCATTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
13839 TTTTTGATGATCAGAGTTGATCTCATTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
13874 TTTTTTTTATGATCAGAGTTGATATTATTTCAAGAAG
1 --TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
13911 TTTTTTTTATGATCAGAGTTGATCTCATTCCAAGAAG
1 --TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
** *
13948 TTTTCAATGGTCAGAGTTGATC
1 TTTTTTATGATCAGAGTTGATC
13970 CCCAAAAGAT
Statistics
Matches: 536, Mismatches: 47, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
34 3 0.01
35 329 0.61
36 35 0.07
37 169 0.32
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (35 bp):
TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
Found at i:14017 original size:54 final size:54
Alignment explanation
Indices: 13935--14235 Score: 360
Period size: 54 Copynumber: 5.6 Consensus size: 54
13925 AGAGTTGATC
13935 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * *
13989 TCATTCTAAGAAGTTTTCAATGGTCAGAGTTCATCCCCAAAAGGTCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * *
14043 TTATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCGCC-AAAGATCCAATTCGG
1 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * * * *
14096 TCATTCCAAGAAGTTTT--ACGATCAGAGTTGATCCTCAGATGATCCCGTGCGG
1 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
** * * * *
14148 TCATTCCAAGAAGTTTTTGATGATCAGAGTTGATCTCCAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* *
14202 TCCTTCCGAA-AAGTTTTCGAA-GTTCAGAGTTGAT
1 TCATTCC-AAGAAGTTTTC-AATGGTCAGAGTTGAT
14236 GATGCGCCAA
Statistics
Matches: 214, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
51 15 0.07
52 27 0.13
53 28 0.13
54 141 0.66
55 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (54 bp):
TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
Found at i:14151 original size:159 final size:160
Alignment explanation
Indices: 13935--14235 Score: 392
Period size: 159 Copynumber: 1.9 Consensus size: 160
13925 AGAGTTGATC
* * *
13935 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGGTCATTCTAAGA
1 TCATTCCAAGAAGTTTT-AACGATCAGAGTTGATCCCCAAAAGATCCAGTGCGGTCATTCCAAGA
* * *
14000 AGTTTTCAATGGTCAGAGTTCATCCCCAAAAGGTCCAGTGCGGTTATTCC-AAGAAGTTTTC-AA
65 AGTTTTCAATGATCAGAGTTCATCCCCAAAAGATCCAGTGCGGTCATTCCGAA-AAGTTTTCGAA
14063 TGGTCAGAGTTGATCGCCAAAGATCCAATTCGG
129 -GGTCAGAGTTGATCGCCAAAGATCCAATTCGG
* * * *
14096 TCATTCCAAGAAGTTTT-ACGATCAGAGTTGATCCTCAGATGATCCCGTGCGGTCATTCCAAGAA
1 TCATTCCAAGAAGTTTTAACGATCAGAGTTGATCCCCAAAAGATCCAGTGCGGTCATTCCAAGAA
** * * * * * *
14160 GTTTTTGATGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCCTTCCGAAAAGTTTTCGAAGT
66 GTTTTCAATGATCAGAGTTCATCCCCAAAAGATCCAGTGCGGTCATTCCGAAAAGTTTTCGAAGG
14225 TCAGAGTTGAT
131 TCAGAGTTGAT
14236 GATGCGCCAA
Statistics
Matches: 120, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
159 99 0.82
160 4 0.03
161 17 0.14
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (160 bp):
TCATTCCAAGAAGTTTTAACGATCAGAGTTGATCCCCAAAAGATCCAGTGCGGTCATTCCAAGAA
GTTTTCAATGATCAGAGTTCATCCCCAAAAGATCCAGTGCGGTCATTCCGAAAAGTTTTCGAAGG
TCAGAGTTGATCGCCAAAGATCCAATTCGG
Found at i:14367 original size:21 final size:21
Alignment explanation
Indices: 14341--14474 Score: 200
Period size: 21 Copynumber: 6.4 Consensus size: 21
14331 TGCTAGAAGT
14341 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
14362 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
14383 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
14404 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
14425 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
14446 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
14467 TCATTGGA
1 TCATTGGA
14475 ATTGCCTAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
20 2 0.02
21 106 0.98
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:15497 original size:53 final size:54
Alignment explanation
Indices: 15275--15501 Score: 262
Period size: 54 Copynumber: 4.2 Consensus size: 54
15265 GATTCGTATC
* ** * * * * *
15275 AGTTGATGTCCAGATGATCTAGTGCGGTTC-TTCCTAGAAGTTTTCAAAGATCAA
1 AGTTGATCTCCAGATGATCCGGTGTGG-TCGTTTCAAGAAGTTTTCGAAGATCAG
*
15329 AGTTGATCTCCAGATGATCCGGTGCT-GTCGTTTCAAGAAATTTTCGAAGATCAG
1 AGTTGATCTCCAGATGATCCGGTG-TGGTCGTTTCAAGAAGTTTTCGAAGATCAG
* * *
15383 AGTTGATCTTCAGATGATCCGGTATGGTCGTTTTAAGAAGTTTTCGAAGATCAG
1 AGTTGATCTCCAGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
* * * * *
15437 AGTTGATCTCCGGATGATCCAGTGTGGTCG-TTCAAGAAGTTTCCGATGACCAG
1 AGTTGATCTCCAGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
15490 AGTTGATCTCCA
1 AGTTGATCTCCA
15502 ATTTGATCCA
Statistics
Matches: 148, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
53 33 0.22
54 115 0.78
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (54 bp):
AGTTGATCTCCAGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
Found at i:15529 original size:108 final size:108
Alignment explanation
Indices: 15275--15529 Score: 266
Period size: 108 Copynumber: 2.4 Consensus size: 108
15265 GATTCGTATC
* * ** * *
15275 AGTTGATGTCCAGATGATCTAGTGCGGTTC-TTCCTAGAAGTTTTCAAAGATCAAAGTTGATCTC
1 AGTTGATCTCCAGATGATCCAGTATGG-TCACTCCAAGAAGTTTTCAAAGATCAAAGTTGATCTC
* * *
15339 CAGATGATCCGGTGCTGTCGTTTCAAGAAATTTTCGAAGATCAG
65 CAGATGATCCAGTGCTGTCGTTTCAAGAAATTTCCGAAGACCAG
* * ** ** * *
15383 AGTTGATCTTCAGATGATCCGGTATGGTCGTTTTAAGAAGTTTTCGAAGATCAGAGTTGATCTCC
1 AGTTGATCTCCAGATGATCCAGTATGGTCACTCCAAGAAGTTTTCAAAGATCAAAGTTGATCTCC
* * *
15448 GGATGATCCAGTG-TGGTCG-TTCAAGAAGTTTCCGATGACCAG
66 AGATGATCCAGTGCT-GTCGTTTCAAGAAATTTCCGAAGACCAG
15490 AGTTGATCTCCA-ATTTGATCCAGTATGGTCACTCCAAGAA
1 AGTTGATCTCCAGA--TGATCCAGTATGGTCACTCCAAGAA
15530 AGGTTTCCGT
Statistics
Matches: 120, Mismatches: 23, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
106 1 0.01
107 33 0.28
108 86 0.72
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (108 bp):
AGTTGATCTCCAGATGATCCAGTATGGTCACTCCAAGAAGTTTTCAAAGATCAAAGTTGATCTCC
AGATGATCCAGTGCTGTCGTTTCAAGAAATTTCCGAAGACCAG
Found at i:17107 original size:4 final size:4
Alignment explanation
Indices: 17096--17293 Score: 89
Period size: 4 Copynumber: 52.5 Consensus size: 4
17086 AAAGATTTTT
* * * **
17096 TTTA -TTA TTTA TTCA CT-A TTTA TTT- TTT- TGTTA TTTT TTTA ACTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA
* * * * *
17141 -TTA TCTA TTTA TTTA -CTA TTCA TCTA TTTA TTTA -TT- TTTA ATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
17185 -TTA TCTA TTTA TTTA -CTA TTTA TCTA TTTA TTTA TTAA TTTA ATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* ** ** * *
17231 -TTA TCTA TTTA TTTA -CAA TTTA TCGA TTTA TTTA TTAA TTTA GTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
17277 -TTA TCTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TT
17294 ATTATTATTT
Statistics
Matches: 140, Mismatches: 41, Indels: 26
0.68 0.20 0.13
Matches are distributed among these distances:
3 29 0.21
4 110 0.79
5 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (4 bp):
TTTA
Found at i:17149 original size:19 final size:20
Alignment explanation
Indices: 17127--17218 Score: 75
Period size: 19 Copynumber: 4.5 Consensus size: 20
17117 ATTTTTTTGT
*
17127 TATTTTTTTAACTATT-ATC
1 TATTTATTTAACTATTCATC
17146 TATTTATTT-ACTATTCATC
1 TATTTATTTAACTATTCATC
*
17165 TATTTATTTATTTTTAATTATT-ATC
1 ----TATTTA--TTTAACTATTCATC
*
17190 TATTTATTT-ACTATTTATC
1 TATTTATTTAACTATTCATC
17209 TATTTATTTA
1 TATTTATTTA
17219 TTAATTTAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
18 11 0.18
19 26 0.43
21 6 0.10
23 6 0.10
25 6 0.10
26 5 0.08
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTATTTAACTATTCATC
Found at i:17234 original size:27 final size:27
Alignment explanation
Indices: 17204--17294 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 27
17194 TATTTACTAT
17204 TTATCTATTTATTTATTAATTTAATTA
1 TTATCTATTTATTTATTAATTTAATTA
*
17231 TTATCTATTTA--T-TT-A--CAA-T-
1 TTATCTATTTATTTATTAATTTAATTA
* *
17250 TTATCGATTTATTTATTAATTTAGTTA
1 TTATCTATTTATTTATTAATTTAATTA
17277 TTATCTATTTATTTATTA
1 TTATCTATTTATTTATTA
17295 TTATTATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
19 10 0.20
20 1 0.02
21 3 0.06
22 2 0.04
23 2 0.04
24 2 0.04
25 2 0.04
26 1 0.02
27 28 0.55
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (27 bp):
TTATCTATTTATTTATTAATTTAATTA
Found at i:17244 original size:46 final size:46
Alignment explanation
Indices: 17097--17303 Score: 266
Period size: 46 Copynumber: 4.6 Consensus size: 46
17087 AAGATTTTTT
* * ** *
17097 TTAT-TATTTATTCACTATTTAT-T-TTTTTGTTATTTTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTAT-TTATTAATTTAATTA
*
17141 TTATCTATTTATTTACTATTCATCTATTTATTTATT--TTTAATTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTAATTTAATTA
17185 TTATCTATTTATTTACTATTTATCTATTTATTTATTAATTTAATTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTAATTTAATTA
* * *
17231 TTATCTATTTATTTACAATTTATCGATTTATTTATTAATTTAGTTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTAATTTAATTA
*
17277 TTATCTATTTATTTATTA-TTAT-TATTT
1 TTATCTATTTATTTACTATTTATCTATTT
17304 TTAGCTACCT
Statistics
Matches: 147, Mismatches: 11, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
44 50 0.34
45 20 0.14
46 73 0.50
47 4 0.03
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (46 bp):
TTATCTATTTATTTACTATTTATCTATTTATTTATTAATTTAATTA
Found at i:17306 original size:15 final size:15
Alignment explanation
Indices: 17139--17368 Score: 125
Period size: 15 Copynumber: 15.0 Consensus size: 15
17129 TTTTTTTAAC
17139 TATTATCTATTTATT
1 TATTATCTATTTATT
* *
17154 TACTAT-TCATCTATT
1 TATTATCT-ATTTATT
*
17169 TATTTAT-T-TTTAAT
1 TA-TTATCTATTTATT
17183 TATTATCTATTTATT
1 TATTATCTATTTATT
* * *
17198 TACTATTTATCTATT
1 TATTATCTATTTATT
*
17213 TATTTAT-TAATTTAAT
1 TA-TTATCT-ATTTATT
17229 TATTATCTATTTATT
1 TATTATCTATTTATT
*
17244 TACAATTTATCGATTTATT
1 T---A-TTATCTATTTATT
*
17263 TATTA---ATTTAGT
1 TATTATCTATTTATT
17275 TATTATCTATTTATT
1 TATTATCTATTTATT
*
17290 TATTAT-TATTATTTT
1 TATTATCTATT-TATT
* * *
17305 TAGCTACCTATTTATC
1 TA-TTATCTATTTATT
* * *
17321 TATTATTCTCTGTATC
1 TATTA-TCTATTTATT
17337 TATTTATCTATTTATT
1 TA-TTATCTATTTATT
* *
17353 TCTATATCTTTTTATT
1 TAT-TATCTATTTATT
17369 ATTTTATTTT
Statistics
Matches: 165, Mismatches: 30, Indels: 39
0.71 0.13 0.17
Matches are distributed among these distances:
12 11 0.07
13 4 0.02
14 12 0.07
15 67 0.41
16 50 0.30
17 7 0.04
18 1 0.01
19 13 0.08
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTATCTATTTATT
Found at i:17346 original size:8 final size:8
Alignment explanation
Indices: 17150--17351 Score: 81
Period size: 8 Copynumber: 26.9 Consensus size: 8
17140 ATTATCTATT
17150 TATTTA-C
1 TATTTATC
*
17157 TATTCATC
1 TATTTATC
*
17165 TATTTATT
1 TATTTATC
17173 TATTT-T-
1 TATTTATC
*
17179 TAATTAT-
1 TATTTATC
* *
17186 TATCTATT
1 TATTTATC
17194 TATTTA-C
1 TATTTATC
17201 TATTTATC
1 TATTTATC
*
17209 TATTTATT
1 TATTTATC
* *
17217 TATTAATT
1 TATTTATC
*
17225 TAATTAT-
1 TATTTATC
* *
17232 TATCTATT
1 TATTTATC
17240 TATTTA-C
1 TATTTATC
*
17247 AATTTATC
1 TATTTATC
* *
17255 GATTTATT
1 TATTTATC
* *
17263 TATTAATT
1 TATTTATC
*
17271 TAGTTAT-
1 TATTTATC
* *
17278 TATCTATT
1 TATTTATC
17286 TATTTAT-
1 TATTTATC
17293 TA-TTAT-
1 TATTTATC
17299 TATTT-T-
1 TATTTATC
** *
17305 TAGCTACC
1 TATTTATC
17313 TATTTATC
1 TATTTATC
17321 TA-TTATTC
1 TATTTA-TC
* *
17329 TCTGTATC
1 TATTTATC
17337 TATTTATC
1 TATTTATC
17345 TATTTAT
1 TATTTAT
17352 TTCTATATCT
Statistics
Matches: 147, Mismatches: 36, Indels: 23
0.71 0.17 0.11
Matches are distributed among these distances:
6 14 0.10
7 40 0.27
8 91 0.62
9 2 0.01
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.61
Consensus pattern (8 bp):
TATTTATC
Found at i:17374 original size:24 final size:24
Alignment explanation
Indices: 17312--17377 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
17302 TTTTAGCTAC
*
17312 CTATTTATCTA-TTATTCTCTGTAT
1 CTATTTATCTATTTATT-TCTATAT
17336 CTATTTATCTATTTATTTCTATAT
1 CTATTTATCTATTTATTTCTATAT
*
17360 CTTTTTAT-TATTTTATTT
1 CTATTTATCTA-TTTATTT
17378 TTTTTAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 2 0.05
24 31 0.82
25 5 0.13
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (24 bp):
CTATTTATCTATTTATTTCTATAT
Found at i:18025 original size:29 final size:30
Alignment explanation
Indices: 17966--18025 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
17956 GAAGTTCGTG
* * *
17966 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATCTCAAGA
17997 TTTGAAGA-CATTGAAGAATTATCTCAAGA
1 TTTGAAGACCATTGAAGAATTATCTCAAGA
18026 GCTAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 18 0.69
31 8 0.31
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATCTCAAGA
Found at i:21631 original size:20 final size:22
Alignment explanation
Indices: 21580--21635 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
21570 AACAAAGGTT
21580 AAGCAATTAAGATTAAATTAAGC
1 AAGCAATTAA-ATTAAATTAAGC
*
21603 AA--AAGTAAATTAAA-TAAG-
1 AAGCAATTAAATTAAATTAAGC
21621 AAGCAATTAAATTAA
1 AAGCAATTAAATTAA
21636 GAAAAACAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 2 0.07
19 4 0.14
20 16 0.55
21 5 0.17
23 2 0.07
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (22 bp):
AAGCAATTAAATTAAATTAAGC
Found at i:23418 original size:29 final size:29
Alignment explanation
Indices: 23374--23453 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
23364 TCCCTCTGAA
* *
23374 AAAAAAAAGAGTGTTAGTAACCTCAAAAG
1 AAAAAAAAGTGAGTTAGTAACCTCAAAAG
23403 AAAAAAAAGTGAGTTAGTAACCTCAAAAG
1 AAAAAAAAGTGAGTTAGTAACCTCAAAAG
23432 AAAAAAAAGTGAGTTAGTAACC
1 AAAAAAAAGTGAGTTAGTAACC
23454 CCTAAGTCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (29 bp):
AAAAAAAAGTGAGTTAGTAACCTCAAAAG
Found at i:24541 original size:25 final size:24
Alignment explanation
Indices: 24505--24551 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
24495 TCCTTCTATT
24505 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
24528 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
24552 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:34190 original size:15 final size:15
Alignment explanation
Indices: 34144--34204 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
34134 AGGTTGTCAC
* *
34144 AATAGAAATCAAGTA
1 AATAGAAAGCAATTA
*
34159 AACAGAAAGCAAATTA
1 AATAGAAAGC-AATTA
34175 AATAGAAAGCAATTAA
1 AATAGAAAGCAATT-A
34191 AATAGAATAGCAAT
1 AATAGAA-AGCAAT
34205 AGATAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
15 12 0.31
16 21 0.54
17 6 0.15
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.18
Consensus pattern (15 bp):
AATAGAAAGCAATTA
Found at i:38189 original size:21 final size:21
Alignment explanation
Indices: 38163--38203 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
38153 ACAGCTAGAA
*
38163 AACCTTGCCTAGGCGCGGCCC
1 AACCTTGCCCAGGCGCGGCCC
38184 AACCTTGCCCAGGCGCGGCC
1 AACCTTGCCCAGGCGCGGCC
38204 TATACCAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (21 bp):
AACCTTGCCCAGGCGCGGCCC
Found at i:39798 original size:20 final size:20
Alignment explanation
Indices: 39773--39811 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39763 AATTTATATA
39773 ATTATAT-AATTAATTAATTG
1 ATTATATAAATTAA-TAATTG
39793 ATTATATAAATTAATAATT
1 ATTATATAAATTAATAATT
39812 TACATGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTATATAAATTAATAATTG
Found at i:40212 original size:19 final size:18
Alignment explanation
Indices: 40179--40214 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40169 TTGAAATAAT
40179 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
40197 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
40215 TGAGTCTTCA
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:40222 original size:11 final size:10
Alignment explanation
Indices: 40179--40225 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
40169 TTGAAATAAT
40179 TCTTCAATGA
1 TCTTCAATGA
40189 TCTTCAA--A
1 TCTTCAATGA
*
40197 TCTTCAAATTA
1 TCTTC-AATGA
40208 TCTTCAATGA
1 TCTTCAATGA
40218 GTCTTCAA
1 -TCTTCAA
40226 ACACGAACTT
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:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:47338 original size:27 final size:27
Alignment explanation
Indices: 47277--47352 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 27
47267 AGGGTCATCT
* *
47277 AGGGGAATTTTGGTCATTTTTTTTACATTC
1 AGGGGCATTTTGGTCA---TTTGTACATTC
47307 AGGGGCATTTTGGTCATTTGTACATTC
1 AGGGGCATTTTGGTCATTTGTACATTC
47334 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
47353 TAAGTTCACT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 29 0.66
30 15 0.34
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.45
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGTACATTC
Done.