Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011904.1 Corchorus capsularis cultivar CVL-1 contig11925, 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: 93445
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:260 original size:32 final size:32
Alignment explanation
Indices: 199--260 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
189 TCGAAAGGAA
** **
199 AATTACAGCTAGCTAAAAAAGGGGGGGGGGGT
1 AATTACAGCTAGCTAAAAAAAAGAAGGGGGGT
*
231 AATTGCAGCTAGCTAAAAAAAAGAAGGGGG
1 AATTACAGCTAGCTAAAAAAAAGAAGGGGG
261 AATGGATTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15
Consensus pattern (32 bp):
AATTACAGCTAGCTAAAAAAAAGAAGGGGGGT
Found at i:2321 original size:13 final size:14
Alignment explanation
Indices: 2303--2344 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
2293 AGAAAAAGCA
*
2303 AAAAAGAAGAAA-G
1 AAAAAGAAAAAATG
2316 AAAAAGAAAAAATG
1 AAAAAGAAAAAATG
2330 AAAAATGGAAAAAAT
1 AAAAA--GAAAAAAT
2345 CAGAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 11 0.44
14 6 0.24
16 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAAAGAAAAAATG
Found at i:7829 original size:11 final size:10
Alignment explanation
Indices: 7814--7844 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
7804 TGAAAATGAT
7814 GAAAAAAAAA
1 GAAAAAAAAA
7824 GAAAAAAAAA
1 GAAAAAAAAA
*
7834 GAAAAAGAAA
1 GAAAAAAAAA
7844 G
1 G
7845 GAAGGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:7923 original size:45 final size:45
Alignment explanation
Indices: 7867--7993 Score: 170
Period size: 44 Copynumber: 2.9 Consensus size: 45
7857 AGAAGCAACG
* *
7867 ATGG-TTTTCAAAAAAGGTCATGATTTTCAAAAAGTTTTGATAAA
1 ATGGTTTTTCAAAAAAGGTCATGGTTTTCAAAAGGTTTTGATAAA
*
7911 ATGGTTTTTCAAAAGA-GTCATGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTTCAAAAAAGGTCATGGTTTTCAAAAGGTTTTGATAAA
* * *
7955 ACGATTTTTC-AAAAAGAGTAATGGTTTTCAAAAGGTTTT
1 ATGGTTTTTCAAAAAAG-GTCATGGTTTTCAAAAGGTTTT
7994 CCAAAGTTGT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
43 4 0.05
44 38 0.52
45 31 0.42
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (45 bp):
ATGGTTTTTCAAAAAAGGTCATGGTTTTCAAAAGGTTTTGATAAA
Found at i:8712 original size:12 final size:12
Alignment explanation
Indices: 8695--8732 Score: 58
Period size: 12 Copynumber: 3.0 Consensus size: 12
8685 GGAAGAAAAG
8695 AAGAAAAGAGAA
1 AAGAAAAGAGAA
8707 AAGAAAAGAGAAA
1 AAGAAAAGAG-AA
8720 AAGAAAAAGAGAA
1 AAG-AAAAGAGAA
8733 TGAAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.42
13 7 0.29
14 7 0.29
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAAAAGAGAA
Found at i:8712 original size:20 final size:20
Alignment explanation
Indices: 8687--8743 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
8677 AGGTGCATGG
8687 AAGAAAAGAAG-AAAAGAGAA
1 AAGAAAAGAAGAAAAAGA-AA
8707 AAGAAAAG-AGAAAAAGAAA
1 AAGAAAAGAAGAAAAAGAAA
*
8726 AAGAGAATGAAGAAAAAG
1 AAGA-AAAGAAGAAAAAG
8744 GCTCTAGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 8 0.24
20 17 0.52
21 8 0.24
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (20 bp):
AAGAAAAGAAGAAAAAGAAA
Found at i:8729 original size:14 final size:14
Alignment explanation
Indices: 8698--8743 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
8688 AGAAAAGAAG
8698 AAAAGAG-AAAAG-
1 AAAAGAGAAAAAGA
8710 AAAAGAGAAAAAGA
1 AAAAGAGAAAAAGA
*
8724 AAAAGAGAATGAAGA
1 AAAAGAGAA-AAAGA
8739 AAAAG
1 AAAAG
8744 GCTCTAGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 7 0.23
13 5 0.17
14 9 0.30
15 9 0.30
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (14 bp):
AAAAGAGAAAAAGA
Found at i:9334 original size:29 final size:29
Alignment explanation
Indices: 9292--9352 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
9282 GATCAGTAAA
*
9292 AGAATCTTTCAAAGCATACTATTCAAGTC
1 AGAATCTTTCAAAGCATACTATTCAAGAC
9321 AGAATCTTTCAAAGCATACTATTCAAGAC
1 AGAATCTTTCAAAGCATACTATTCAAGAC
9350 AGA
1 AGA
9353 TCTGGGGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (29 bp):
AGAATCTTTCAAAGCATACTATTCAAGAC
Found at i:9685 original size:69 final size:69
Alignment explanation
Indices: 9595--9959 Score: 353
Period size: 69 Copynumber: 5.3 Consensus size: 69
9585 CGAATGCTCT
**
9595 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATTTAGCCTTGGTTCCATCCAAGCATT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATTTAGATTTGGTTCCATCCAAGCATT
9660 CAGG
66 CAGG
** * * *
9664 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCTAGGCA-
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCA-ATTTAGATTTGGTTCCATCCAAGCAT
** *
9728 AGAGA
65 TCAGG
* * *
9733 GGCTTTTCCATAAGCCAAACTCGCTTT-CACGCGAGAT-AGTTTCAGATTTGGTTCCATCCAAGC
1 GGCTTTTCCACAAGCCAAACTCG-TTTCCACACGAG-TCAATTT-AGATTTGGTTCCATCCAAGC
*
9796 ATTTAGG
63 ATTCAGG
* * ** * * *
9803 GGCTTTTCCACAAGCCAAGCTTGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCAGGCA-
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCA-ATTTAGATTTGGTTCCATCCAAGCAT
** *
9867 AGAGA
65 TCAGG
* * * * * *
9872 GACTTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTAAGATTTGGTTCCATCCGAGCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAG-TCAATTT-AGATTTGGTTCCATCCAAGCA
9936 TTCAGG
64 TTCAGG
*
9942 GGCTTTTCCATAAGCCAA
1 GGCTTTTCCACAAGCCAA
9960 GTTCAGTGAG
Statistics
Matches: 236, Mismatches: 49, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
68 2 0.01
69 141 0.60
70 92 0.39
71 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATTTAGATTTGGTTCCATCCAAGCATT
CAGG
Found at i:9844 original size:139 final size:138
Alignment explanation
Indices: 9595--9960 Score: 556
Period size: 139 Copynumber: 2.6 Consensus size: 138
9585 CGAATGCTCT
* * * **
9595 GGCTTTTCCACAAGCCAAACTCG-TTTCCACACGAG-TCAATTTAGCCTTGGTTCCATCCAAGCA
1 GGCTTTTCCATAAGCCAAACTCGCTTT-CACGCGAGAT-AGTTTAGATTTGGTTCCATCCAAGCA
* * *
9658 TTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCT
64 TTCAGGGGCTTTTCCACAAGCCAAGCTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCC
9723 AGGCAAGAGA
129 AGGCAAGAGA
9733 GGCTTTTCCATAAGCCAAACTCGCTTTCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGCTTTCACGCGAGATAGTTT-AGATTTGGTTCCATCCAAGCAT
* *
9798 TTAGGGGCTTTTCCACAAGCCAAGCTTGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCA
65 TCAGGGGCTTTTCCACAAGCCAAGCTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCA
9863 GGCAAGAGA
130 GGCAAGAGA
* * *
9872 GACTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAAGATTTGGTTCCATCCGAGCAT
1 GGCTTTTCCATAAGCCAAACTCGCTTTCACGCGAGATAGTTT-AGATTTGGTTCCATCCAAGCAT
*
9937 TCAGGGGCTTTTCCATAAGCCAAG
65 TCAGGGGCTTTTCCACAAGCCAAG
9961 TTCAGTGAGG
Statistics
Matches: 209, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
138 33 0.16
139 176 0.84
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (138 bp):
GGCTTTTCCATAAGCCAAACTCGCTTTCACGCGAGATAGTTTAGATTTGGTTCCATCCAAGCATT
CAGGGGCTTTTCCACAAGCCAAGCTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCAG
GCAAGAGA
Found at i:10220 original size:48 final size:47
Alignment explanation
Indices: 10069--10298 Score: 336
Period size: 47 Copynumber: 4.9 Consensus size: 47
10059 ATCTAGGCAA
* *
10069 TCTTGTCTCGCTTCCACGCGAGTTTTCAATTTAGTGATCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
**
10116 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTGGGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* *
10163 TCTTTTCTCGCTTCCATGCGAGTTTTCAAATCTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTC-AATTTAGTGACCAAAGATGG
10211 TCTTTTCTCGCTTCCACGC-AGGTTTTCAATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGA-GTTTTCAATTTAGTGACCAAAGATGG
* * * *
10258 TCTTTCTCTCGCTTCCATGTGAGTCTGCAATTTAGTGACCA
1 TCTTT-TCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCA
10299 GAGTTAGTCA
Statistics
Matches: 165, Mismatches: 14, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
47 94 0.57
48 70 0.42
49 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
Found at i:10236 original size:95 final size:94
Alignment explanation
Indices: 10069--10298 Score: 345
Period size: 95 Copynumber: 2.4 Consensus size: 94
10059 ATCTAGGCAA
* * *
10069 TCTTGTCTCGCTTCCACGCGAGTTTTCAATTTAGTGATCAAAGATGGTCTTTTCTCGCTTCCACG
1 TCTTTTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGGTCTTTTCTCGCTTCCACG
*
10134 CGAGTTTTCAATTGGGTGACCAAAGATGG
66 CGAGTTTTCAATTGAGTGACCAAAGATGG
*
10163 TCTTTTCTCGCTTCCATGCGAGTTTTCAAATCTAGTGACCAAAGATGGTCTTTTCTCGCTTCCAC
1 TCTTTTCTCGCTTCCATGCGAGTTTTC-AATTTAGTGACCAAAGATGGTCTTTTCTCGCTTCCAC
*
10228 GC-AGGTTTTCAATTTAGTGACCAAAGATGG
65 GCGA-GTTTTCAATTGAGTGACCAAAGATGG
* * *
10258 TCTTTCTCTCGCTTCCATGTGAGTCTGCAATTTAGTGACCA
1 TCTTT-TCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCA
10299 GAGTTAGTCA
Statistics
Matches: 123, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
94 26 0.21
95 78 0.63
96 19 0.15
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (94 bp):
TCTTTTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGGTCTTTTCTCGCTTCCACG
CGAGTTTTCAATTGAGTGACCAAAGATGG
Found at i:10661 original size:28 final size:28
Alignment explanation
Indices: 10623--10696 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
10613 GGTCACATAA
10623 GGGCATTTTGGTCATTTTT-CATGTTCA-G
1 GGGCATTTTGGTCATTTTTGCAT-TT-AGG
10651 GGGCATTTTGGTCATTTTTGCATTTAGG
1 GGGCATTTTGGTCATTTTTGCATTTAGG
*
10679 GGGTATTTTGGTCATTTT
1 GGGCATTTTGGTCATTTT
10697 AAGTTCACTT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
27 1 0.02
28 39 0.91
29 3 0.07
ACGTcount: A:0.14, C:0.11, G:0.27, T:0.49
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTTTGCATTTAGG
Found at i:14357 original size:7 final size:7
Alignment explanation
Indices: 14336--14378 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
14326 AAGATTTGAA
14336 AAAAAAG
1 AAAAAAG
14343 CAAAAAAG
1 -AAAAAAG
*
14351 AAGAAAG
1 AAAAAAG
14358 AAAAAAG
1 AAAAAAG
*
14365 AACAAATG
1 AA-AAAAG
14373 AAAAAA
1 AAAAAA
14379 TGGAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 17 0.57
8 13 0.43
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:16857 original size:41 final size:41
Alignment explanation
Indices: 16794--16902 Score: 139
Period size: 41 Copynumber: 2.7 Consensus size: 41
16784 TATCTTCAAG
*
16794 TCAACTTCGTCTCAGGATGTTAAAATTACTTTT-CTCTACTT
1 TCAACTTCGTCTCAGGACGTTAAAATT-CTTTTCCTCTACTT
* * * *
16835 TCAACTTCGTCTTAGGACGTTAAAAATGTTTTCCTTTACTT
1 TCAACTTCGTCTCAGGACGTTAAAATTCTTTTCCTCTACTT
**
16876 TCTGCTTCGTCTCAGGACGTTAAAATT
1 TCAACTTCGTCTCAGGACGTTAAAATT
16903 GTTACTTCTC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 4 0.07
41 54 0.93
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (41 bp):
TCAACTTCGTCTCAGGACGTTAAAATTCTTTTCCTCTACTT
Found at i:17553 original size:125 final size:125
Alignment explanation
Indices: 17323--17794 Score: 601
Period size: 125 Copynumber: 3.8 Consensus size: 125
17313 CAATATATAT
* * * * * * * *
17323 ACTATACCGATGTGTGTAAATGTCGGAACAAATTTTTCATATCATTTGATTTCGATGTATTCCGA
1 ACTATACCGACGTTTGCAAATGTCAGAACAAGTTCTTCACATCATTTGATTTCGACGTATTCCGA
* * * * * *
17388 CATTTGTAAGCGTTAGTATAGATTTTATATTGTGGA-ATTTATTAAACGTCATTATAGAAT
66 CATTTGTAAGCGTTGGTATAGATATTATATCGT-GACATTTATTAAATGTCACTATAGAAC
* * * *
17448 ACTATACCAACGTTTGCAAAAGTCAGAACAAGTTCTTCACATCATTTGATTTCGGCGCT-TGCCG
1 ACTATACCGACGTTTGCAAATGTCAGAACAAGTTCTTCACATCATTTGATTTCGACG-TATTCCG
*
17512 ACATTTGTAAGCGTCGGTATAGATATTATATCGTGACATTTATTAAATGTCACTATAGAAC
65 ACATTTGTAAGCGTTGGTATAGATATTATATCGTGACATTTATTAAATGTCACTATAGAAC
* * *
17573 AC--TACCGACGTTTGCAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCAACGTATCCCGA
1 ACTATACCGACGTTTGCAAATGTCAGAACAAGTTCTTCACATCATTTGATTTCGACGTATTCCGA
* *** * *
17636 TATTTGTAAGCGTTGGTATAGATATTATATCACAACATTTATTAAATGTCGCTATACAAC
66 CATTTGTAAGCGTTGGTATAGATATTATATCGTGACATTTATTAAATGTCACTATAGAAC
* * *
17696 ACTGTACCGACGTTTACAAATGTCAGAACAAGTTCTTCACATCGTTTGATTTCGACGTATTCCGA
1 ACTATACCGACGTTTGCAAATGTCAGAACAAGTTCTTCACATCATTTGATTTCGACGTATTCCGA
* *
17761 CATTTGTAAGTGTTGGTATAAATATTATATCGTG
66 CATTTGTAAGCGTTGGTATAGATATTATATCGTG
17795 GGGCTGAAAT
Statistics
Matches: 299, Mismatches: 43, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
122 1 0.00
123 108 0.36
124 2 0.01
125 187 0.63
126 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (125 bp):
ACTATACCGACGTTTGCAAATGTCAGAACAAGTTCTTCACATCATTTGATTTCGACGTATTCCGA
CATTTGTAAGCGTTGGTATAGATATTATATCGTGACATTTATTAAATGTCACTATAGAAC
Found at i:17788 original size:248 final size:248
Alignment explanation
Indices: 17340--17794 Score: 626
Period size: 248 Copynumber: 1.8 Consensus size: 248
17330 CGATGTGTGT
* * * * *
17340 AAATGTCGGAACAAATTTTTCATATCATTTGATTTCGATGTATTCCGACATTTGTAAGCGTTAGT
1 AAATGTCGGAACAAATTCTTCACATCATTTGATTTCAACGTATCCCGACATTTGTAAGCGTTAGT
* **** * * * *
17405 ATAGATTTTATATTGTGGAATTTATTAAACGTCATTATAGAATACTATACCAACGTTTGCAAAAG
66 ATAGATATTATATTCACAAATTTATTAAACGTCACTATACAACACTATACCAACGTTTACAAAAG
* *
17470 TCAGAACAAGTTCTTCACATCATTTGATTTCGGCGCTTGCCGACATTTGTAAGCGTCGGTATAGA
131 TCAGAACAAGTTCTTCACATCATTTGATTTCGACGCTTGCCGACATTTGTAAGCGTCGGTATAAA
17535 TATTATATCGTGACATTTATTAAATGTCACTATAGAACACTACCGACGTTTGC
196 TATTATATCGTGACATTTATTAAATGTCACTATAGAACACTACCGACGTTTGC
* * *
17588 AAATGTCGGAACAAGTTCTTCACATCATTTGATTTCAACGTATCCCGATATTTGTAAGCGTTGGT
1 AAATGTCGGAACAAATTCTTCACATCATTTGATTTCAACGTATCCCGACATTTGTAAGCGTTAGT
* * * * *
17653 ATAGATATTATA-TCACAACATTTATTAAATGTCGCTATACAACACTGTACCGACGTTTACAAAT
66 ATAGATATTATATTCACAA-ATTTATTAAACGTCACTATACAACACTATACCAACGTTTACAAAA
* * * *
17717 GTCAGAACAAGTTCTTCACATCGTTTGATTTCGACG-TATTCCGACATTTGTAAGTGTTGGTATA
130 GTCAGAACAAGTTCTTCACATCATTTGATTTCGACGCT-TGCCGACATTTGTAAGCGTCGGTATA
17781 AATATTATATCGTG
194 AATATTATATCGTG
17795 GGGCTGAAAT
Statistics
Matches: 177, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
247 3 0.02
248 174 0.98
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (248 bp):
AAATGTCGGAACAAATTCTTCACATCATTTGATTTCAACGTATCCCGACATTTGTAAGCGTTAGT
ATAGATATTATATTCACAAATTTATTAAACGTCACTATACAACACTATACCAACGTTTACAAAAG
TCAGAACAAGTTCTTCACATCATTTGATTTCGACGCTTGCCGACATTTGTAAGCGTCGGTATAAA
TATTATATCGTGACATTTATTAAATGTCACTATAGAACACTACCGACGTTTGC
Found at i:18020 original size:17 final size:16
Alignment explanation
Indices: 18000--18051 Score: 70
Period size: 17 Copynumber: 3.2 Consensus size: 16
17990 ATTTTATTAT
18000 TTTTTAATTTTTAAATA
1 TTTTTAATTTTT-AATA
18017 TTTTTAATTTTTAAT-
1 TTTTTAATTTTTAATA
*
18032 TTTTATTATTTTTAATA
1 TTTT-TAATTTTTAATA
18049 TTT
1 TTT
18052 ATAAATCAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 4 0.12
16 13 0.41
17 15 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTAATTTTTAATA
Found at i:18027 original size:6 final size:7
Alignment explanation
Indices: 18000--18052 Score: 52
Period size: 7 Copynumber: 6.9 Consensus size: 7
17990 ATTTTATTAT
18000 TTTTTAA
1 TTTTTAA
18007 TTTTTAAATA
1 TTTTT--A-A
18017 TTTTTAA
1 TTTTTAA
18024 TTTTTAA
1 TTTTTAA
18031 TTTTTATTA
1 TTTTTA--A
18040 TTTTTAA
1 TTTTTAA
*
18047 TATTTA
1 TTTTTA
18053 TAAATCAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
7 25 0.62
8 1 0.03
9 8 0.20
10 6 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTTAA
Found at i:18052 original size:16 final size:17
Alignment explanation
Indices: 17991--18053 Score: 76
Period size: 16 Copynumber: 3.8 Consensus size: 17
17981 TTAAAATATA
* *
17991 TTTTATTATTTTTTAAT
1 TTTTAATATTTATTAAT
18008 TTTTAAATATTT-TTAAT
1 TTTT-AATATTTATTAAT
*
18025 TTTTAATTTTTATT-AT
1 TTTTAATATTTATTAAT
18041 TTTTAATATTTAT
1 TTTTAATATTTAT
18054 AAATCAGCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
16 20 0.49
17 15 0.37
18 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAATATTTATTAAT
Found at i:19876 original size:17 final size:18
Alignment explanation
Indices: 19852--19919 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
19842 TCTGTTTTGG
*
19852 AGAAGAAAAGAGAAGGAA
1 AGAAGAAAAGAAAAGGAA
* *
19870 A-AAGAAAATACAAGGAAA
1 AGAAGAAAAGAAAAGG-AA
19888 AGAAGAAAAGAAAAGGAA
1 AGAAGAAAAGAAAAGGAA
19906 GAGAA-AAAAGAAAA
1 -AGAAGAAAAGAAAA
19920 TAGGGGTGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
17 12 0.28
18 15 0.35
19 16 0.37
ACGTcount: A:0.72, C:0.01, G:0.25, T:0.01
Consensus pattern (18 bp):
AGAAGAAAAGAAAAGGAA
Found at i:28723 original size:12 final size:11
Alignment explanation
Indices: 28695--28720 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28685 ATATAAAATC
28695 AAAATTTTCGA
1 AAAATTTTCGA
28706 AAAATTTTCGA
1 AAAATTTTCGA
28717 AAAA
1 AAAA
28721 ATTATACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (11 bp):
AAAATTTTCGA
Found at i:32726 original size:12 final size:12
Alignment explanation
Indices: 32709--32734 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
32699 AATCATAAAA
32709 TTATTCTAGGGT
1 TTATTCTAGGGT
32721 TTATTCTAGGGT
1 TTATTCTAGGGT
32733 TT
1 TT
32735 GACAACAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (12 bp):
TTATTCTAGGGT
Found at i:33808 original size:22 final size:22
Alignment explanation
Indices: 33782--33834 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
33772 CAAAATAGGG
33782 TAAAAACATATATAAAAGTAG-TA
1 TAAAAACATATA-AAAA-TAGCTA
*
33805 -AAAAGCATATAAAAATAGCTA
1 TAAAAACATATAAAAATAGCTA
33826 TAAAAACAT
1 TAAAAACAT
33835 GCATAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.12
21 6 0.23
22 17 0.65
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (22 bp):
TAAAAACATATAAAAATAGCTA
Found at i:43435 original size:16 final size:17
Alignment explanation
Indices: 43414--43447 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
43404 CCTCAACCTA
43414 AACTAGAAG-AAAATAG
1 AACTAGAAGAAAAATAG
43430 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
43447 A
1 A
43448 TGAAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.65, C:0.06, G:0.18, T:0.12
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:50291 original size:15 final size:15
Alignment explanation
Indices: 50268--50307 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
50258 TTAACTAACC
*
50268 TTTAATTTTCATGTT
1 TTTATTTTTCATGTT
50283 TTTATTTTTCATGTT
1 TTTATTTTTCATGTT
50298 TTTCATTTTT
1 TTT-ATTTTT
50308 GTAGGGTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.15, C:0.07, G:0.05, T:0.72
Consensus pattern (15 bp):
TTTATTTTTCATGTT
Found at i:54602 original size:37 final size:37
Alignment explanation
Indices: 54507--54621 Score: 153
Period size: 36 Copynumber: 3.2 Consensus size: 37
54497 CTATTTTTAG
* * * **
54507 ATTAAG-CTCTTTATTGACTCCACTTAATTACCCAAA
1 ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
*
54543 ATTAAGCC-TTTTATTGATGCTACTTAATTACCCTGA
1 ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
*
54579 ATTAAGCCTTTTTATTGACGCTACTTAATTACCATGA
1 ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
54616 ATTAAG
1 ATTAAG
54622 TCTCTAACTT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 36 0.52
37 33 0.48
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (37 bp):
ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
Found at i:54634 original size:37 final size:37
Alignment explanation
Indices: 54507--54634 Score: 113
Period size: 36 Copynumber: 3.5 Consensus size: 37
54497 CTATTTTTAG
* * *
54507 ATTAAGCTCTT-T-ATTGACTCCACTTAATTACCCA-AA
1 ATTAAGC-CTTCTAATTGACGCTACTTAATTA-CCATGA
* * *
54543 ATTAAGCCTT-TTATTGATGCTACTTAATTACCCTGA
1 ATTAAGCCTTCTAATTGACGCTACTTAATTACCATGA
* *
54579 ATTAAGCCTTTTTATTGACGCTACTTAATTACCATGA
1 ATTAAGCCTTCTAATTGACGCTACTTAATTACCATGA
*
54616 ATTAAGTC-TCTAACTTGAC
1 ATTAAGCCTTCTAA-TTGAC
54635 TTGATTTCTT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
35 6 0.08
36 36 0.46
37 36 0.46
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (37 bp):
ATTAAGCCTTCTAATTGACGCTACTTAATTACCATGA
Found at i:54687 original size:37 final size:37
Alignment explanation
Indices: 54644--54860 Score: 307
Period size: 37 Copynumber: 5.9 Consensus size: 37
54634 CTTGATTTCT
* * *
54644 TTCCTTGAAATTAAATCCTCTACTCTACTTAATTCCC
1 TTCCTTGGAATCAAGTCCTCTACTCTACTTAATTCCC
* *
54681 TCCCTTGGAATCAAGTCCTCTACTCTACTTAATT-TC
1 TTCCTTGGAATCAAGTCCTCTACTCTACTTAATTCCC
54717 TTCCTTGGAATCAAGTCC-CTTACTCTACTTAATTCCC
1 TTCCTTGGAATCAAGTCCTC-TACTCTACTTAATTCCC
54754 TTCCTTGGAATCAAGTCCTCTACTCTACTTAATTCCC
1 TTCCTTGGAATCAAGTCCTCTACTCTACTTAATTCCC
54791 TTCCTTGGAATCAAGTCC-CTTACTCTACTTAATTCCC
1 TTCCTTGGAATCAAGTCCTC-TACTCTACTTAATTCCC
* * *
54828 TTCCTTGGAA-CTAAGTCCTTTTCTTTACTTAAT
1 TTCCTTGGAATC-AAGTCCTCTACTCTACTTAAT
54861 CCCGGAGGTT
Statistics
Matches: 164, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
35 1 0.01
36 34 0.21
37 128 0.78
38 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (37 bp):
TTCCTTGGAATCAAGTCCTCTACTCTACTTAATTCCC
Found at i:54776 original size:110 final size:111
Alignment explanation
Indices: 54644--54860 Score: 323
Period size: 110 Copynumber: 2.0 Consensus size: 111
54634 CTTGATTTCT
*
54644 TTCCTTGAAATTAAATCCTCTACTCTACTTAATTCCCTCCCTTGGAATCAAGT-CCTCTACTCTA
1 TTCCTTGAAATCAAATCCTCTACTCTACTTAATTCCCTCCCTTGGAATCAAGTCCCT-TACTCTA
*
54708 CTTAATT-TCTTCCTTGGAA-TCAAGTCCCTTACTCTACTTAATTCCC
65 CTTAATTCCCTTCCTTGGAACT-AAGTCCCTTACTCTACTTAATTCCC
* * *
54754 TTCCTTGGAATCAAGTCCTCTACTCTACTTAATTCCCTTCCTTGGAATCAAGTCCCTTACTCTAC
1 TTCCTTGAAATCAAATCCTCTACTCTACTTAATTCCCTCCCTTGGAATCAAGTCCCTTACTCTAC
* * *
54819 TTAATTCCCTTCCTTGGAACTAAGTCCTTTTCTTTACTTAAT
66 TTAATTCCCTTCCTTGGAACTAAGTCCCTTACTCTACTTAAT
54861 CCCGGAGGTT
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
110 63 0.66
111 32 0.33
112 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (111 bp):
TTCCTTGAAATCAAATCCTCTACTCTACTTAATTCCCTCCCTTGGAATCAAGTCCCTTACTCTAC
TTAATTCCCTTCCTTGGAACTAAGTCCCTTACTCTACTTAATTCCC
Found at i:55020 original size:41 final size:40
Alignment explanation
Indices: 54969--55156 Score: 199
Period size: 41 Copynumber: 4.8 Consensus size: 40
54959 ACTTAATTAC
* *
54969 CCTG-AATTAAGTATGTGCTTGCCTTTACCTAATTTCCTT
1 CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
* *
55008 CCTTGAAATTAAGTCTATGCTTGTCTTTACCTAATTTTCTT
1 CC-TGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
* * * *
55049 CACTGAAATTAAGTCGGTGCTT-ACTTTACTTAA-TTAC--
1 C-CTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
* *
55086 CCTG-AATTAAGTCTATGCTTGTCTTTACCCAATTTCCTT
1 CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
* *
55125 CCTTGAAATTAAGTCTGTGCCTATCTTTACCT
1 CC-TGAAATTAAGTCTGTGCTTGTCTTTACCT
55157 TTTAACTGTT
Statistics
Matches: 121, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
35 14 0.12
36 11 0.09
37 4 0.03
39 7 0.06
40 13 0.11
41 71 0.59
42 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (40 bp):
CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
Found at i:55086 original size:117 final size:116
Alignment explanation
Indices: 54936--55156 Score: 343
Period size: 117 Copynumber: 1.9 Consensus size: 116
54926 TTAATTCTTA
** * *
54936 TGAAATTAAGTCTTTGCTAATTTACTTAATTACCCTGAATTAAGTATGTGCTTGCCTTTACCTAA
1 TGAAATTAAGTCGGTGCTAATTTACTTAATTACCCTGAATTAAGTATATGCTTGCCTTTACCCAA
* *
55001 TTTCCTTCCTTGAAATTAAGTCTATGCTTGTCTTTACCTAATTTTCTTCAC
66 TTTCCTTCCTTGAAATTAAGTCTATGCCTATCTTTACCTAATTTTCTTCAC
* * *
55052 TGAAATTAAGTCGGTGCTTACTTTACTTAATTACCCTGAATTAAGTCTATGCTTGTCTTTACCCA
1 TGAAATTAAGTCGGTGC-TAATTTACTTAATTACCCTGAATTAAGTATATGCTTGCCTTTACCCA
*
55117 ATTTCCTTCCTTGAAATTAAGTCTGTGCCTATCTTTACCT
65 ATTTCCTTCCTTGAAATTAAGTCTATGCCTATCTTTACCT
55157 TTTAACTGTT
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
116 15 0.16
117 79 0.84
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.43
Consensus pattern (116 bp):
TGAAATTAAGTCGGTGCTAATTTACTTAATTACCCTGAATTAAGTATATGCTTGCCTTTACCCAA
TTTCCTTCCTTGAAATTAAGTCTATGCCTATCTTTACCTAATTTTCTTCAC
Found at i:55244 original size:36 final size:36
Alignment explanation
Indices: 55158--55305 Score: 206
Period size: 37 Copynumber: 4.1 Consensus size: 36
55148 TCTTTACCTT
* * *
55158 TTAACTGTTTTTACTTAATTACCCTGAATTAAGTCC
1 TTAACTGCTTTTACTTAATTATCCTGAATTAAGTTC
* *
55194 TTCAACTGCTTTTACTTAATTTTCCTAAATTAAGTTC
1 TT-AACTGCTTTTACTTAATTATCCTGAATTAAGTTC
* *
55231 TTAACTGCTTTTACTTAATTGTCCTGAACTAAGTTC
1 TTAACTGCTTTTACTTAATTATCCTGAATTAAGTTC
*
55267 TTAACTGCTTTTTACTTAATTATCCTGACTTAAGTTC
1 TTAACTGC-TTTTACTTAATTATCCTGAATTAAGTTC
55304 TT
1 TT
55306 TGACCATGTT
Statistics
Matches: 99, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
36 41 0.41
37 58 0.59
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (36 bp):
TTAACTGCTTTTACTTAATTATCCTGAATTAAGTTC
Found at i:55245 original size:73 final size:73
Alignment explanation
Indices: 55158--55305 Score: 208
Period size: 73 Copynumber: 2.0 Consensus size: 73
55148 TCTTTACCTT
* * *
55158 TTAACTGTTTTTACTTAATTACCCTGAATTAAGTCCTTCAACTGC-TTTTACTTAATTTTCCTAA
1 TTAACTGCTTTTACTTAATTACCCTGAACTAAGTCCTT-AACTGCTTTTTACTTAATTATCCTAA
55222 ATTAAGTTC
65 ATTAAGTTC
** * * *
55231 TTAACTGCTTTTACTTAATTGTCCTGAACTAAGTTCTTAACTGCTTTTTACTTAATTATCCTGAC
1 TTAACTGCTTTTACTTAATTACCCTGAACTAAGTCCTTAACTGCTTTTTACTTAATTATCCTAAA
55296 TTAAGTTC
66 TTAAGTTC
55304 TT
1 TT
55306 TGACCATGTT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
72 6 0.09
73 60 0.91
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (73 bp):
TTAACTGCTTTTACTTAATTACCCTGAACTAAGTCCTTAACTGCTTTTTACTTAATTATCCTAAA
TTAAGTTC
Found at i:55459 original size:72 final size:71
Alignment explanation
Indices: 55318--55696 Score: 589
Period size: 72 Copynumber: 5.3 Consensus size: 71
55308 ACCATGTTTG
* * * *
55318 CTTAATTACCCAGAATTAAGTTCTCTTACTCTTCTTAATTGTCCAACTTAGGACCTTGACTATAT
1 CTTAATTACCCTGAATTAAG-ACT-TTACTCTTCTTAATTGCCCAACTTAGGACCTTGACTATAC
55383 TTTCTTTT
64 TTTCTTTT
*
55391 CTTAATTACCCTGAATTAAGACTTTACCCTTCTTAATTGCCCAATCTTAGGACCTTGACTATACT
1 CTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAA-CTTAGGACCTTGACTATACT
55456 TTCTTTT
65 TTCTTTT
*
55463 CTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAATCTTAGGACCTTAACTATACT
1 CTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAA-CTTAGGACCTTGACTATACT
55528 TTCTTTT
65 TTCTTTT
* * *
55535 CTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTTAAGATCTTGACTGTACTT
1 CTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTTAGGACCTTGACTATACTT
55600 TCTTTT
66 TCTTTT
* *
55606 CTTAATTACCCTGAATTAAGACTTTACT-TGCTCTTAATTGCCCAACTTAGGACCTTGATTGTAC
1 CTTAATTACCCTGAATTAAGACTTTACTCT--TCTTAATTGCCCAACTTAGGACCTTGACTATAC
*
55670 TTTCCTTT
64 TTTCTTTT
55678 CTTAATTACCCTGAATTAA
1 CTTAATTACCCTGAATTAA
55697 AATTTTAACT
Statistics
Matches: 288, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
70 1 0.00
71 70 0.24
72 198 0.69
73 19 0.07
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (71 bp):
CTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTTAGGACCTTGACTATACTT
TCTTTT
Found at i:55465 original size:41 final size:41
Alignment explanation
Indices: 55420--55541 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 41
55410 GACTTTACCC
55420 TTCTTAATTGCCCAATCTTAGGACCTTGACTATACTTTCTT
1 TTCTTAATTGCCCAATCTTAGGACCTTGACTATACTTTCTT
* *
55461 TTCTTAATTACCCTGAA--TTA--A----GACTTTAC--TC--
1 TTCTTAATTGCCC--AATCTTAGGACCTTGACTATACTTTCTT
*
55492 TTCTTAATTGCCCAATCTTAGGACCTTAACTATACTTTCTT
1 TTCTTAATTGCCCAATCTTAGGACCTTGACTATACTTTCTT
55533 TTCTTAATT
1 TTCTTAATT
55542 ACCCTGAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 28
0.65 0.05 0.29
Matches are distributed among these distances:
29 2 0.03
31 15 0.24
33 3 0.05
35 7 0.11
37 6 0.10
39 3 0.05
41 24 0.39
43 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (41 bp):
TTCTTAATTGCCCAATCTTAGGACCTTGACTATACTTTCTT
Found at i:55497 original size:143 final size:142
Alignment explanation
Indices: 55318--55696 Score: 589
Period size: 143 Copynumber: 2.6 Consensus size: 142
55308 ACCATGTTTG
* * * *
55318 CTTAATTACCCAGAATTAAGTTCTCTTACTCTTCTTAATTGTCCAACTTAGGACCTTGACTATAT
1 CTTAATTACCCTGAATTAAG-ACT-TTACTCTTCTTAATTGCCCAACTTAGGACCTTGACTATAC
*
55383 TTTCTTTTCTTAATTACCCTGAATTAAGACTTTACCCTTCTTAATTGCCCAATCTTAGGACCTTG
64 TTTCTTTTCTTAATTACCCTGAATTAAGACTTTACCCTTCTTAATTGCCCAA-CTTAAGACCTTG
55448 ACTATACTTTCTTTT
128 ACTATACTTTCTTTT
*
55463 CTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAATCTTAGGACCTTAACTATACT
1 CTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAA-CTTAGGACCTTGACTATACT
* *
55528 TTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTTAAGATCTTGAC
65 TTCTTTTCTTAATTACCCTGAATTAAGACTTTACCCTTCTTAATTGCCCAACTTAAGACCTTGAC
*
55593 TGTACTTTCTTTT
130 TATACTTTCTTTT
* *
55606 CTTAATTACCCTGAATTAAGACTTTACT-TGCTCTTAATTGCCCAACTTAGGACCTTGATTGTAC
1 CTTAATTACCCTGAATTAAGACTTTACTCT--TCTTAATTGCCCAACTTAGGACCTTGACTATAC
*
55670 TTTCCTTTCTTAATTACCCTGAATTAA
64 TTTCTTTTCTTAATTACCCTGAATTAA
55697 AATTTTAACT
Statistics
Matches: 218, Mismatches: 13, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
142 1 0.00
143 114 0.52
144 84 0.39
145 19 0.09
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (142 bp):
CTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTTAGGACCTTGACTATACTT
TCTTTTCTTAATTACCCTGAATTAAGACTTTACCCTTCTTAATTGCCCAACTTAAGACCTTGACT
ATACTTTCTTTT
Found at i:55584 original size:30 final size:29
Alignment explanation
Indices: 55525--55585 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
55515 CCTTAACTAT
*
55525 ACTTTCTTTTCTTAATTACCCTGAATTAAG
1 ACTTTCTCTTCTTAATTACCC-GAATTAAG
*
55555 ACTTTACTCTTCTTAATTGCCC-AACTTAAG
1 ACTTT-CTCTTCTTAATTACCCGAA-TTAAG
55585 A
1 A
55586 TCTTGACTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 2 0.07
30 11 0.41
31 14 0.52
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.43
Consensus pattern (29 bp):
ACTTTCTCTTCTTAATTACCCGAATTAAG
Found at i:55608 original size:40 final size:38
Alignment explanation
Indices: 55555--55684 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
55545 CTGAATTAAG
*
55555 ACTTTACTCTTCTTAATTGCCCAACTTAAGATCTTGACTGT
1 ACTTT-CTTTTCTTAATTGCCCAACTTAAGA-CTTGA-TGT
*
55596 ACTTTCTTTTCTTAATTACCCTGAA-TTAAGAC-T--T-T
1 ACTTTCTTTTCTTAATTGCCC--AACTTAAGACTTGATGT
* *
55631 ACTTGC---TCTTAATTGCCCAACTTAGGACCTTGATTGT
1 ACTTTCTTTTCTTAATTGCCCAACTTAAGA-CTTGA-TGT
*
55668 ACTTTCCTTTCTTAATT
1 ACTTTCTTTTCTTAATT
55685 ACCCTGAATT
Statistics
Matches: 71, Mismatches: 6, Indels: 25
0.70 0.06 0.25
Matches are distributed among these distances:
30 2 0.03
31 5 0.07
32 12 0.17
33 1 0.01
35 6 0.08
36 2 0.03
37 6 0.08
39 1 0.01
40 23 0.32
41 11 0.15
42 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (38 bp):
ACTTTCTTTTCTTAATTGCCCAACTTAAGACTTGATGT
Found at i:55772 original size:76 final size:80
Alignment explanation
Indices: 55674--55854 Score: 185
Period size: 76 Copynumber: 2.3 Consensus size: 80
55664 TTGTACTTTC
** * **
55674 CTTTCTTAATTACCCTGAATTAAAATTTTAA-C-TGCTT-TTACTTAATCA-CCTTGGATTGAAA
1 CTTTCTTAATCGCCCTGGATTAAAACCTTAACCGTGCTTATTACTTAAT-AGCCTTGGATT-AAA
*
55735 T-TTTAACTA-ATCTGA
64 TCCTTAACTATATCTGA
* *
55750 CTTTCTTAATCGCCCTGGATTAAAACCTTAACCGTGTTTGACTTTCTTAATAGCCTTGGATTAAA
1 CTTTCTTAATCGCCCTGGATTAAAACCTTAACCGTGCTT-A-TTACTTAATAGCCTTGGATTAAA
* *
55815 TCCTTAACTATGTTTGA
64 TCCTTAACTATATCTGA
*
55832 CCTTCTTAATCGCCCTGGATTAA
1 CTTTCTTAATCGCCCTGGATTAA
55855 GACTTTACTT
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
76 26 0.30
77 1 0.01
78 4 0.05
80 5 0.06
81 24 0.28
82 26 0.30
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (80 bp):
CTTTCTTAATCGCCCTGGATTAAAACCTTAACCGTGCTTATTACTTAATAGCCTTGGATTAAATC
CTTAACTATATCTGA
Found at i:55800 original size:41 final size:41
Alignment explanation
Indices: 55747--55854 Score: 162
Period size: 41 Copynumber: 2.6 Consensus size: 41
55737 TTAACTAATC
*
55747 TGACTTTCTTAATCGCCCTGGATTAAAACCTTAACCGTGTT
1 TGACTTTCTTAATCGCCCTGGATTAAAACCTTAACCATGTT
* * * *
55788 TGACTTTCTTAATAGCCTTGGATTAAATCCTTAACTATGTT
1 TGACTTTCTTAATCGCCCTGGATTAAAACCTTAACCATGTT
*
55829 TGACCTTCTTAATCGCCCTGGATTAA
1 TGACTTTCTTAATCGCCCTGGATTAA
55855 GACTTTACTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (41 bp):
TGACTTTCTTAATCGCCCTGGATTAAAACCTTAACCATGTT
Found at i:59052 original size:25 final size:26
Alignment explanation
Indices: 58994--59057 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
58984 TGGACCTAAA
**
58994 GACAAAAATGCCCTTGAAGTGAAAAT
1 GACAAAAATGCCCTTGAAGACAAAAT
* *
59020 GACCAAAATGCCCTTG-GGACAAAAT
1 GACAAAAATGCCCTTGAAGACAAAAT
59045 GACAAAAATGCCC
1 GACAAAAATGCCC
59058 CTGGCAATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 18 0.55
26 15 0.45
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.16
Consensus pattern (26 bp):
GACAAAAATGCCCTTGAAGACAAAAT
Found at i:71678 original size:2 final size:2
Alignment explanation
Indices: 71671--71700 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
71661 TGTTCATAAC
71671 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71701 TTTTGGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:73543 original size:25 final size:27
Alignment explanation
Indices: 73491--73543 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
73481 TTACTCAACT
**
73491 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
73518 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
73543 A
1 A
73544 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:76642 original size:53 final size:53
Alignment explanation
Indices: 76557--76657 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 53
76547 GACGTGGCAC
* ** *
76557 GCCACGTGTACCAAAAAATGACATGTGGCACGCCACATGTACCAAAAAATCGT
1 GCCACATGTACCAAAAAATGACACATAGCACGCCACATGTACCAAAAAATCGT
* * *
76610 GCCACATGTACCAAAAAGTGACACATATCACGCCACGTGTACCAAAAA
1 GCCACATGTACCAAAAAATGACACATAGCACGCCACATGTACCAAAAA
76658 GTGACACGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.40, C:0.28, G:0.17, T:0.16
Consensus pattern (53 bp):
GCCACATGTACCAAAAAATGACACATAGCACGCCACATGTACCAAAAAATCGT
Found at i:76676 original size:31 final size:31
Alignment explanation
Indices: 76609--76707 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
76599 CAAAAAATCG
* **
76609 TGCCACATGTACCAAAAAGTGACACATATCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* *
76640 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** * *
76671 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
76702 TGCCAC
1 TGCCAC
76708 GTGCACAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:77703 original size:10 final size:10
Alignment explanation
Indices: 77688--77719 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
77678 CAGAGCTTGT
77688 TTTACTGCTA
1 TTTACTGCTA
77698 TTTACTGCTA
1 TTTACTGCTA
77708 TTT--TGCTA
1 TTTACTGCTA
77716 TTTA
1 TTTA
77720 ATTATATGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (10 bp):
TTTACTGCTA
Found at i:78993 original size:10 final size:10
Alignment explanation
Indices: 78978--79009 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
78968 CAGAGCTTGT
78978 TTTACTGCTA
1 TTTACTGCTA
78988 TTTACTGCTA
1 TTTACTGCTA
78998 TTT--TGCTA
1 TTTACTGCTA
79006 TTTA
1 TTTA
79010 ATTATATGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (10 bp):
TTTACTGCTA
Found at i:79992 original size:30 final size:30
Alignment explanation
Indices: 79957--80013 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
79947 TAAACATTCA
*
79957 ACATTCAACAATGCTTCTTCTTCTTCAACT
1 ACATTCAACAATGCTTCTTCCTCTTCAACT
*
79987 ACATTCAACATTGCTTCTTCCTCTTCA
1 ACATTCAACAATGCTTCTTCCTCTTCA
80014 TTCAGAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.32, G:0.04, T:0.40
Consensus pattern (30 bp):
ACATTCAACAATGCTTCTTCCTCTTCAACT
Found at i:82049 original size:12 final size:13
Alignment explanation
Indices: 82021--82061 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
82011 ATACGAACTA
*
82021 TTATCTTTGT-CT
1 TTATCTTTATACT
*
82033 CTATCTTTATA-T
1 TTATCTTTATACT
82045 TTATCTTTATACT
1 TTATCTTTATACT
82058 TTAT
1 TTAT
82062 AATTCTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.20, C:0.15, G:0.02, T:0.63
Consensus pattern (13 bp):
TTATCTTTATACT
Found at i:82951 original size:45 final size:45
Alignment explanation
Indices: 82900--82985 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
82890 TAATAGAGTA
*
82900 GTGGAATTACTAAAAGATCTCTACCCC-GAATTAATGATGAGGTGG
1 GTGGAATTACTAAAAGATCCCTACCCCAG-ATTAATGATGAGGTGG
82945 GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATGAG
1 GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATGAG
82986 CTGTAGAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 38 0.97
46 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATGAGGTGG
Found at i:87040 original size:2 final size:2
Alignment explanation
Indices: 87033--87058 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
87023 ATCAATTGTG
87033 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
87059 AGTTCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:87590 original size:33 final size:33
Alignment explanation
Indices: 87525--87591 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
87515 ACTTGGATTT
* * ****
87525 AATTCAATTGTGATCTTTTTTTTTTTTTTAAAG
1 AATTCAATTGTGATCTTTATTATTGAAATAAAG
87558 AATTCAATTGTGATCTTTATTATTGAAATAAAG
1 AATTCAATTGTGATCTTTATTATTGAAATAAAG
87591 A
1 A
87592 GGCATCCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (33 bp):
AATTCAATTGTGATCTTTATTATTGAAATAAAG
Found at i:88916 original size:37 final size:37
Alignment explanation
Indices: 88866--88936 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
88856 ATATAATTAT
* *
88866 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
88903 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
88937 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Done.