Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012045.1 Corchorus capsularis cultivar CVL-1 contig12066, 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: 20984
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Found at i:80 original size:43 final size:43
Alignment explanation
Indices: 33--213 Score: 143
Period size: 43 Copynumber: 4.0 Consensus size: 43
23 AATCAACAAG
*
33 AAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGTAAA
1 AAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGTAATCAGTAAA
*
76 AAGT-AAAAGAGTAATCAGTAAAAAAGGAGCAGAAAATAGTAATCAGTAAA
1 AAGTAAAAAG-GTAATCAGT--AAAA--AGC--AAAA-GGTAATCAGTAAA
* * *
126 AGAGTAAAATGGTAATCAGTAAAAAGTAAAAAGGTAATCAAT-AA
1 A-AGTAAAAAGGTAATCAGTAAAAAG-CAAAAGGTAATCAGTAAA
* ** * * *
170 GAGTAAAATTGTAATCAGTACAAAGTAAATA-ATAATCAGTAAA
1 AAGTAAAAAGGTAATCAGTAAAAAGCAAA-AGGTAATCAGTAAA
213 A
1 A
214 TAGTGATGGT
Statistics
Matches: 112, Mismatches: 13, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
42 15 0.13
43 38 0.34
44 2 0.02
45 12 0.11
46 4 0.04
47 5 0.04
49 8 0.07
50 12 0.11
51 12 0.11
52 4 0.04
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.19
Consensus pattern (43 bp):
AAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGTAATCAGTAAA
Found at i:95 original size:15 final size:15
Alignment explanation
Indices: 77--132 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
67 ATCAGTAAAA
77 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
92 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
106 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
120 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
133 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:175 original size:21 final size:22
Alignment explanation
Indices: 2--186 Score: 90
Period size: 22 Copynumber: 8.2 Consensus size: 22
1 G
* * *
2 ATCAATAAACAGTAAAAAGCTA
1 ATCAATAAAGAGTAAAATGGTA
* *
24 ATCAA-CAAGAAGTAAAAAGGTA
1 ATCAATAAAG-AGTAAAATGGTA
* * * *
46 ATCAGTAAAAAGCAAAA-GGCA
1 ATCAATAAAGAGTAAAATGGTA
* *
67 ATCAGTAAAAAGTAAAA-GAGTA
1 ATCAATAAAGAGTAAAATG-GTA
* * *
89 ATCAGTAAAAAAGGAGCAGAAAATAGTA
1 ATC---AATAAA-GAG--TAAAATGGTA
*
117 ATCAGTAAAAGAGTAAAATGGTA
1 ATCAAT-AAAGAGTAAAATGGTA
* * *
140 ATCAGTAAAAAGTAAAAAGGTA
1 ATCAATAAAGAGTAAAATGGTA
*
162 ATCAAT-AAGAGTAAAATTGTA
1 ATCAATAAAGAGTAAAATGGTA
183 ATCA
1 ATCA
187 GTACAAAGTA
Statistics
Matches: 127, Mismatches: 25, Indels: 23
0.73 0.14 0.13
Matches are distributed among these distances:
21 38 0.30
22 50 0.39
23 16 0.13
25 8 0.06
26 5 0.04
28 10 0.08
ACGTcount: A:0.57, C:0.08, G:0.17, T:0.18
Consensus pattern (22 bp):
ATCAATAAAGAGTAAAATGGTA
Found at i:199 original size:21 final size:22
Alignment explanation
Indices: 33--213 Score: 147
Period size: 21 Copynumber: 8.0 Consensus size: 22
23 AATCAACAAG
33 AAGTAAAA-AGGTAATCAGTAAA
1 AAGTAAAATA-GTAATCAGTAAA
* * *
55 AAGCAAAA-GGCAATCAGTAAA
1 AAGTAAAATAGTAATCAGTAAA
*
76 AAGTAAAAGAGTAATCAGTAAAAA
1 AAGTAAAATAGTAATCAGT--AAA
*
100 AGGAGCAGAAAATAGTAATCAGTAAA
1 A--AG--TAAAATAGTAATCAGTAAA
*
126 AGAGTAAAATGGTAATCAGTAAA
1 A-AGTAAAATAGTAATCAGTAAA
*
149 AAGTAAAA-AGGTAATCAAT-AA
1 AAGTAAAATA-GTAATCAGTAAA
* * *
170 GAGTAAAATTGTAATCAGTACA
1 AAGTAAAATAGTAATCAGTAAA
*
192 AAGT-AAATAATAATCAGTAAA
1 AAGTAAAATAGTAATCAGTAAA
213 A
1 A
214 TAGTGATGGT
Statistics
Matches: 129, Mismatches: 20, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
21 50 0.39
22 34 0.26
23 18 0.14
24 4 0.03
25 3 0.02
26 6 0.05
28 14 0.11
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.19
Consensus pattern (22 bp):
AAGTAAAATAGTAATCAGTAAA
Found at i:3638 original size:6 final size:6
Alignment explanation
Indices: 3605--3654 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
3595 CAACTCAAGG
* *
3605 AAAAGA AGAAAG- AAAA-A AGAAGA GAAAGA AAAAGA AAAAG- AAAAGA
1 AAAAGA A-AAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
3651 AAAA
1 AAAA
3655 CCTTGGCCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
5 11 0.31
6 21 0.58
7 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:3646 original size:16 final size:16
Alignment explanation
Indices: 3610--3654 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3600 CAAGGAAAAG
3610 AAGAAAGAAAAAAGAA
1 AAGAAAGAAAAAAGAA
*
3626 GAGAAAG-AAAAAGAAA
1 AAGAAAGAAAAAAG-AA
3642 AAGAAAAGAAAAA
1 AAG-AAAGAAAAA
3655 CCTTGGCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.25
16 10 0.42
17 4 0.17
18 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAAAAAGAA
Found at i:5487 original size:55 final size:55
Alignment explanation
Indices: 5315--5519 Score: 222
Period size: 54 Copynumber: 3.8 Consensus size: 55
5305 CTTAGTCGAG
** * * **
5315 TTTCAAGTGATCTGGTGCGGTCAATTAA-AAAGTTTCCAAAGGTATTAAGTTTAT-
1 TTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTCCAGTGGT-TTAAGTTTATC
* * * * *
5369 TTTCAAGTGATCCAGTGCGGCCAATTAAGAAAG-TTCGTAGTGGTTTAGGTTTATC
1 TTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTC-CAGTGGTTTAAGTTTATC
*
5424 -TTCAAGTGATCCAGTGCGGTTAGTCAAGAAAAGTTTCCAGTGGTTTAAGTTTATC
1 TTTCAAGTGATCCAGTGCGGTCAGTCAAG-AAAGTTTCCAGTGGTTTAAGTTTATC
* *
5479 TTTC-AGTGATCCAGTGCGATCAGTCAAGAAAGTTTGCAGTG
1 TTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTCCAGTG
5520 CGCTCAATTA
Statistics
Matches: 129, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
54 73 0.57
55 50 0.39
56 6 0.05
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (55 bp):
TTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
Found at i:5508 original size:109 final size:113
Alignment explanation
Indices: 5342--5545 Score: 274
Period size: 109 Copynumber: 1.8 Consensus size: 113
5332 CGGTCAATTA
* * *
5342 AAAAGTTTCCAAAGGTATTAAGTTTATTTTCAAGTGATCCAGTGCGGCCAATTAAGAAAGTTCGT
1 AAAAGTTTCCAAAGGTATTAAGTTTATTTTCAAGTGATCCAGTGCGACCAATCAAGAAAGTTCGC
5407 AGTG-G-T-TTAGGTTTATCTTCAAGTGATCCAGTGCGGTTAGTCAAG
66 AGTGCGCTATTAGGTTTATCTTCAAGTGATCCAGTGCGGTTAGTCAAG
** * * *
5452 AAAAGTTTCCAGTGGT-TTAAGTTTATCTTTC-AGTGATCCAGTGCGATCAGTCAAGAAAGTTTG
1 AAAAGTTTCCAAAGGTATTAAGTTTAT-TTTCAAGTGATCCAGTGCGACCAATCAAGAAAGTTCG
5515 CAGTGCGCTCAATTAGGTTTATCTTCAAGTG
65 CAGTGCGCT--ATTAGGTTTATCTTCAAGTG
5546 GTTCGGTAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
109 41 0.51
110 19 0.24
111 1 0.01
114 19 0.24
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (113 bp):
AAAAGTTTCCAAAGGTATTAAGTTTATTTTCAAGTGATCCAGTGCGACCAATCAAGAAAGTTCGC
AGTGCGCTATTAGGTTTATCTTCAAGTGATCCAGTGCGGTTAGTCAAG
Found at i:5802 original size:89 final size:85
Alignment explanation
Indices: 5631--5987 Score: 292
Period size: 79 Copynumber: 4.2 Consensus size: 85
5621 TCCAAAATTG
* * * *
5631 GATTCGGTAAATCAAGTCAATGCGGTGCATTTCTTCAAAGATTGGAATTCGGTGAGCTTGGTGCA
1 GATTCGGTGAATCAAGGCAATGC-GTGCATTTCTTCAAAGATCGG-ATTCGGTGAGCTCGGTGCA
5696 GCGAATTTTCAAACAGTTCAAGGAT
64 GC-AATTTTCAAACAGTT-AAGG-T
*
5721 GATTCGGTGAATCAAGGCAATGCAGTGCATTTCTTCAAGGATCGGATTCGGTGAGCTCGGTGCAG
1 GATTCGGTGAATCAAGGCAATGC-GTGCATTTCTTCAAAGATCGGATTCGGTGAGCTCGGTGCAG
5786 CAAATTTTCAAACAGTTAACGGT
65 C-AATTTTCAAACAGTTAA-GGT
* * * * * * *
5809 AAATC----AAGTTAAGGCGATGCCT-TATTTCTTCAAAGATTGGGATTCGGTGAGCTCGGTGCA
1 GATTCGGTGAA-TCAAGGCAATGCGTGCATTTCTTCAAAGA-TCGGATTCGGTGAGCTCGGTGCA
*
5869 GCACTTTCTCAAACAGTTAAGGGT
64 GCAATTT-TCAAACAGTTAA-GGT
* ** * * *
5893 GATTCGGTGAATTAAGTTATTGCGGTGCA----TT-----ATTGGATTCGGTGAGCTCAGTGCAG
1 GATTCGGTGAATCAAGGCAATGC-GTGCATTTCTTCAAAGATCGGATTCGGTGAGCTCGGTGCAG
*
5949 CACATTTTCAAACAGTTTAGAGT
65 CA-ATTTTCAAACAGTTAAG-GT
*
5972 GATTCGGTGGATCAAG
1 GATTCGGTGAATCAAG
5988 TTAGTGCGGT
Statistics
Matches: 224, Mismatches: 31, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
78 1 0.00
79 51 0.23
80 4 0.02
83 16 0.07
84 45 0.20
85 12 0.05
87 8 0.04
88 9 0.04
89 38 0.17
90 40 0.18
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (85 bp):
GATTCGGTGAATCAAGGCAATGCGTGCATTTCTTCAAAGATCGGATTCGGTGAGCTCGGTGCAGC
AATTTTCAAACAGTTAAGGT
Found at i:5949 original size:163 final size:163
Alignment explanation
Indices: 5635--5965 Score: 400
Period size: 173 Copynumber: 2.0 Consensus size: 163
5625 AAATTGGATT
* * *
5635 CGGTAAATCAAGTCAATGCGGTGCATTTCTTCAAAGATTGGAATTCGGTGAGCTTGGTGCAGCGA
1 CGGTAAATCAAGTCAAGGCGATGCATTTCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCGA
5700 ATTTTCAAACAGTTCAAGGATGATTCGGTGAATCAAGGCAATGCAGTGCATTTCTTCAAGGATCG
66 ATTTTCAAACAGTTCAAGGATGATTCGGTGAATCAAGGCAATGCAGTGCA--T-TT--A--ATCG
*
5765 GATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTAA
124 GATTCGGTGAGCTCAGTGCAGCAAATTTTCAAACAGTTAA
* *
5805 CGGTAAATCAAGTTAAGGCGATGCCTTATTTCTTCAAAGATTGGGATTCGGTGAGCTCGGTGCAG
1 CGGTAAATCAAGTCAAGGCGATG-C--ATTTCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAG
* * * ** * * *
5870 C-ACTTTCTCAAACAGTT-AAGGGTGATTCGGTGAATTAAGTTATTGCGGTGCA-TT-ATTGGAT
63 CGAATTT-TCAAACAGTTCAAGGATGATTCGGTGAATCAAGGCAATGCAGTGCATTTAATCGGAT
*
5931 TCGGTGAGCTCAGTGCAGCACATTTTCAAACAGTT
127 TCGGTGAGCTCAGTGCAGCAAATTTTCAAACAGTT
5966 TAGAGTGATT
Statistics
Matches: 142, Mismatches: 15, Indels: 15
0.83 0.09 0.09
Matches are distributed among these distances:
163 39 0.27
168 2 0.01
170 20 0.14
171 1 0.01
172 33 0.23
173 47 0.33
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (163 bp):
CGGTAAATCAAGTCAAGGCGATGCATTTCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCGA
ATTTTCAAACAGTTCAAGGATGATTCGGTGAATCAAGGCAATGCAGTGCATTTAATCGGATTCGG
TGAGCTCAGTGCAGCAAATTTTCAAACAGTTAA
Found at i:6024 original size:46 final size:46
Alignment explanation
Indices: 5971--6077 Score: 160
Period size: 46 Copynumber: 2.3 Consensus size: 46
5961 CAGTTTAGAG
* **
5971 TGATTCGGTGGATCAAGTTAGTGCGGTACACTATTTCTTCAAAGTT
1 TGATTCGGTGAATCAAGTTACCGCGGTACACTATTTCTTCAAAGTT
* * *
6017 TGATTCGGTGAATCAAGTTACCGCGTTGCAGTATTTCTTCAAAGTT
1 TGATTCGGTGAATCAAGTTACCGCGGTACACTATTTCTTCAAAGTT
6063 TGATTCGGTGAATCA
1 TGATTCGGTGAATCA
6078 GATTTGTTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (46 bp):
TGATTCGGTGAATCAAGTTACCGCGGTACACTATTTCTTCAAAGTT
Found at i:6375 original size:28 final size:28
Alignment explanation
Indices: 6307--6408 Score: 145
Period size: 28 Copynumber: 3.6 Consensus size: 28
6297 GGGTCATCCA
6307 GGGGCATTTTGGTCATTTTCACATCTAGG
1 GGGGCATTTTGGTCATTTTCACATCTA-G
6336 GGGGCATTTTGGTCATTTTTGCAC-T-TAG
1 GGGGCATTTTGGTCA-TTTT-CACATCTAG
*
6364 GGGGTATTTTGGTCATTTTCACATCTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
*
6392 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
6409 CTTAATCTAC
Statistics
Matches: 68, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
26 3 0.04
27 5 0.07
28 35 0.51
29 17 0.25
30 5 0.07
31 3 0.04
ACGTcount: A:0.16, C:0.14, G:0.28, T:0.42
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTCACATCTAG
Found at i:8149 original size:110 final size:110
Alignment explanation
Indices: 8013--8233 Score: 433
Period size: 110 Copynumber: 2.0 Consensus size: 110
8003 GCACTATTGA
*
8013 TCATATTTAGAATTTAGTTAGCATATAGCATCCACAATTTAGCATTTTCACATTAGAATATAAGC
1 TCATATTTAGAATTTAGTTAGCATATAGCATCCACAATTTAGCATCTTCACATTAGAATATAAGC
8078 ATACATGGCAACCTTCATTACATCATTCCTAGCATCTCATTACAT
66 ATACATGGCAACCTTCATTACATCATTCCTAGCATCTCATTACAT
8123 TCATATTTAGAATTTAGTTAGCATATAGCATCCACAATTTAGCATCTTCACATTAGAATATAAGC
1 TCATATTTAGAATTTAGTTAGCATATAGCATCCACAATTTAGCATCTTCACATTAGAATATAAGC
8188 ATACATGGCAACCTTCATTACATCATTCCTAGCATCTCATTACAT
66 ATACATGGCAACCTTCATTACATCATTCCTAGCATCTCATTACAT
8233 T
1 T
8234 TCACTTCACA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.35
Consensus pattern (110 bp):
TCATATTTAGAATTTAGTTAGCATATAGCATCCACAATTTAGCATCTTCACATTAGAATATAAGC
ATACATGGCAACCTTCATTACATCATTCCTAGCATCTCATTACAT
Found at i:8221 original size:55 final size:55
Alignment explanation
Indices: 8052--8224 Score: 128
Period size: 55 Copynumber: 3.1 Consensus size: 55
8042 ATCCACAATT
*
8052 TAGCATTTTCACATTAGAATATAAGCATACATGGCAACCTTCATTACATCATTCC
1 TAGCATCTTCACATTAGAATATAAGCATACATGGCAACCTTCATTACATCATTCC
* * * * ** * * *
8107 TAGCATCTCATTACATT--CATATTTAGAATTTAGTTAGCATA--TAGCA-TCCA-CAATT--
1 TAGCATCT--TCACATTAGAATA-TAAGCA--TACATGGCA-ACCT-TCATTACATC-ATTCC
8162 TAGCATCTTCACATTAGAATATAAGCATACATGGCAACCTTCATTACATCATTCC
1 TAGCATCTTCACATTAGAATATAAGCATACATGGCAACCTTCATTACATCATTCC
8217 TAGCATCT
1 TAGCATCT
8225 CATTACATTT
Statistics
Matches: 83, Mismatches: 19, Indels: 32
0.62 0.14 0.24
Matches are distributed among these distances:
51 1 0.01
52 8 0.10
53 13 0.16
54 5 0.06
55 29 0.35
56 5 0.06
57 13 0.16
58 8 0.10
59 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (55 bp):
TAGCATCTTCACATTAGAATATAAGCATACATGGCAACCTTCATTACATCATTCC
Found at i:9073 original size:23 final size:24
Alignment explanation
Indices: 9022--9078 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
9012 AGGAGAGTTT
* * *
9022 AGAGAAGGCAAGGAAGAGAAAGAG
1 AGAGGAGGCAAGGAAAAAAAAGAG
*
9046 GGAGGAGGCAA-GAAAAAAAAGAG
1 AGAGGAGGCAAGGAAAAAAAAGAG
9069 AGAGGAGGCA
1 AGAGGAGGCA
9079 GTGAGGATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.53, C:0.05, G:0.42, T:0.00
Consensus pattern (24 bp):
AGAGGAGGCAAGGAAAAAAAAGAG
Found at i:10286 original size:22 final size:22
Alignment explanation
Indices: 10258--10313 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
10248 AGAAAGATGC
10258 AATCAGTAAA-ATGTAAAATGAT
1 AATCAGTAAAGA-GTAAAATGAT
*
10280 AATCAGTAAAGAGTAAAGTGAT
1 AATCAGTAAAGAGTAAAATGAT
10302 AATCAGTAAAGA
1 AATCAGTAAAGA
10314 AATTAGTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.54, C:0.05, G:0.18, T:0.23
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATGAT
Found at i:10382 original size:55 final size:55
Alignment explanation
Indices: 10318--10794 Score: 758
Period size: 55 Copynumber: 8.7 Consensus size: 55
10308 TAAAGAAATT
* *
10318 AGTCAAGGTAATAGAAATCAGTAAATCAGTAATTAAGTGAAAAGAAATTAATCAG
1 AGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
* * * *
10373 AGTCAAGGTAATAGAAATCAGTAATTCAATAATTAAGTGAAAAGAAATTAATCAG
1 AGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
* * *
10428 AGTCAAGGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAATCAG
1 AGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
10483 AGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
1 AGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
* *
10538 AGTCAAGGTAATAGTAATCAGTAAATCAGTGATTAAGTAAAAAGAGATTAATCAG
1 AGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
* * *
10593 AGTCAAAGTAATAGTATTCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAG
1 AGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
* *
10648 AGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTTAAAAGAGATTAATCAG
1 AGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
* * * *
10703 AGTCAAAGTAGTAGTAATCAGTAAATCAATAATTAAGTAAAAAGAGATTAATCAG
1 AGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
10758 AGTCAAGGTAATAGTAATCAGTAAATC-GATAATTAAG
1 AGTCAAGGTAATAGTAATCAGTAAATCAG-TAATTAAG
10795 AGTTAAAATG
Statistics
Matches: 402, Mismatches: 19, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
55 402 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (55 bp):
AGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
Found at i:10419 original size:30 final size:29
Alignment explanation
Indices: 10330--10475 Score: 96
Period size: 30 Copynumber: 5.2 Consensus size: 29
10320 TCAAGGTAAT
*
10330 AGAAATCAGTAAATCAGTAATTAAGTGAAA
1 AGAAATCAGT-AATCAATAATTAAGTGAAA
* * * *
10360 AGAAAT---TAATC-AGAGTCAAG-GTAAT
1 AGAAATCAGTAATCAATAATTAAGTG-AAA
10385 AGAAATCAGTAATTCAATAATTAAGTGAAA
1 AGAAATCAGTAA-TCAATAATTAAGTGAAA
* * * *
10415 AGAAAT---TAATC-AGAGTCAAG-GTAAT
1 AGAAATCAGTAATCAATAATTAAGTG-AAA
10440 AGAAATCAGTAAATCAATAATTAAGTGAAA
1 AGAAATCAGT-AATCAATAATTAAGTGAAA
10470 AGAAAT
1 AGAAAT
10476 TAATCAGAGT
Statistics
Matches: 85, Mismatches: 17, Indels: 28
0.65 0.13 0.22
Matches are distributed among these distances:
24 2 0.02
25 27 0.32
26 6 0.07
27 4 0.05
28 4 0.05
29 6 0.07
30 34 0.40
31 2 0.02
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.24
Consensus pattern (29 bp):
AGAAATCAGTAATCAATAATTAAGTGAAA
Found at i:10730 original size:29 final size:28
Alignment explanation
Indices: 10532--10730 Score: 71
Period size: 29 Copynumber: 7.2 Consensus size: 28
10522 AAAAGAGATT
*
10532 AATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGAGTCAAAGT-ATAGTAATCAGTA
* * ** *
10561 AATCAGTGAT-TAAGTA-A--AAAGAGATT
1 AATCAGAG-TCAAAGTATAGTAATCAG-TA
*
10587 AATCAGAGTCAAAGTAATAGTATTCAGTA
1 AATCAGAGTCAAAGT-ATAGTAATCAGTA
* * ** *
10616 AATCAGTAAT-TAAGTA-A--AAAGAGATT
1 AATCAG-AGTCAAAGTATAGTAATCAG-TA
10642 AATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGAGTCAAAGT-ATAGTAATCAGTA
* * ** *
10671 AATCAGTAAT-TAAGT-TA--AAAGAGATT
1 AATCAG-AGTCAAAGTATAGTAATCAG-TA
10697 AATCAGAGTCAAAGTAGTAGTAATCAGTA
1 AATCAGAGTCAAAGTA-TAGTAATCAGTA
10726 AATCA
1 AATCA
10731 ATAATTAAGT
Statistics
Matches: 116, Mismatches: 33, Indels: 42
0.61 0.17 0.22
Matches are distributed among these distances:
25 16 0.14
26 34 0.29
27 6 0.05
28 6 0.05
29 38 0.33
30 16 0.14
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (28 bp):
AATCAGAGTCAAAGTATAGTAATCAGTA
Found at i:11036 original size:22 final size:22
Alignment explanation
Indices: 10979--11367 Score: 227
Period size: 22 Copynumber: 17.8 Consensus size: 22
10969 AATAGCATGC
* *
10979 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAGAGTAAAATGGT
* *
11001 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
* *
11021 AATTAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
*
11043 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAGAGTAA-AATGGT
*
11065 AATCA--ACAAGAGTAAAATAGT
1 AATCAGTA-AAGAGTAAAATGGT
* * *
11086 AGTCAGTAAAAAGT-AAATAGT
1 AATCAGTAAAGAGTAAAATGGT
* * **
11107 AATTAGT-AAGTGTAAAAAAGT
1 AATCAGTAAAGAGTAAAATGGT
*
11128 AA-CAAGT-AAGAAGTAAAA-GGA
1 AATC-AGTAAAG-AGTAAAATGGT
*
11149 AATCAGT-AAGAGTAAAAAGGT
1 AATCAGTAAAGAGTAAAATGGT
* * * *
11170 GATCAATAAAGAGTAAAAAGCT
1 AATCAGTAAAGAGTAAAATGGT
* *
11192 AATCAG-GAAGAAGTAAAAAGGT
1 AATCAGTAAAG-AGTAAAATGGT
* * *
11214 AATCAGTAAAAAG-AAAAAGGC
1 AATCAGTAAAGAGTAAAATGGT
*
11235 AATCAGTAAAAAGTAAAA-GAGT
1 AATCAGTAAAGAGTAAAATG-GT
* *
11257 AATCAGTAAAAAAGGAGCAGAAAATAGT
1 AATCAGT---AAA-GAG--TAAAATGGT
11285 AATCAGTAAAAGAGTAAAATGGT
1 AATCAGT-AAAGAGTAAAATGGT
* *
11308 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAGAGTAAAATGGT
*
11330 AATCA--ACAAGAGTAAAATAGT
1 AATCAGTA-AAGAGTAAAATGGT
*
11351 AATTAGTACAA-AGTAAA
1 AATCAGTA-AAGAGTAAA
11368 GAATAATCAG
Statistics
Matches: 293, Mismatches: 47, Indels: 54
0.74 0.12 0.14
Matches are distributed among these distances:
20 27 0.09
21 101 0.34
22 117 0.40
23 23 0.08
25 6 0.02
26 6 0.02
28 13 0.04
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.19
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATGGT
Found at i:11078 original size:43 final size:43
Alignment explanation
Indices: 11029--11367 Score: 260
Period size: 43 Copynumber: 7.7 Consensus size: 43
11019 GTAATTAGTA
*
11029 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAGGTAATCAAC
* * * **
11072 AAGAGTAAAATAGTAGTCAGTAAAAAGTAAATA-GTAATTAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAGGTAATCAAC
* * * * **
11114 AAGTGTAAAAAAGTAA-CAAGTAAGAAGT-AAAAGGAAATCAGT
1 AAGAGTAAAATAGTAATC-AGTAAAAAGTAAAAAGGTAATCAAC
* * * * **
11156 AAGAGTAAAA-AGGTGATCAATAAAGAGTAAAAAGCTAATCAGG
1 AAGAGTAAAATA-GTAATCAGTAAAAAGTAAAAAGGTAATCAAC
*
11199 AAGAAGTAAAA-AGGTAATCAGTAAAAAG-AAAAAGGCAATCAGTA-
1 AAG-AGTAAAATA-GTAATCAGTAAAAAGTAAAAAGGTAATCA--AC
* * * * *
11243 AAAAGTAAAAGAGTAATCAGTAAAAAAGGAGCAGAAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT--AAAA--AGTA-AAAA-GGTAATCA--AC
*
11294 AAGAGTAAAATGGTAATCAGTAAAAAGTAAAAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAGGTAATCAAC
* *
11337 AAGAGTAAAATAGTAATTAGTACAAAGTAAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA
11368 GAATAATCAG
Statistics
Matches: 240, Mismatches: 39, Indels: 34
0.77 0.12 0.11
Matches are distributed among these distances:
41 5 0.02
42 54 0.22
43 101 0.42
44 24 0.10
45 11 0.05
46 4 0.02
47 5 0.02
48 1 0.00
49 8 0.03
50 9 0.04
51 18 0.08
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (43 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAGGTAATCAAC
Found at i:11145 original size:21 final size:21
Alignment explanation
Indices: 11046--11380 Score: 177
Period size: 21 Copynumber: 15.3 Consensus size: 21
11036 AAATAGTAAT
* *
11046 CAGTAAAAAGTAAGAAGGTAAT
1 CAGTAAGAAGTAAAAAG-TAAT
** *
11068 CAACAAG-AGTAAAATAGTAGT
1 CAGTAAGAAGTAAAA-AGTAAT
* *
11089 CAGTAAAAAGTAAATAGTAAT
1 CAGTAAGAAGTAAAAAGTAAT
* *
11110 TAGTAAG-TGTAAAAAAGTAA-
1 CAGTAAGAAGT-AAAAAGTAAT
* *
11130 CAAGTAAGAAGTAAAAGGAAAT
1 C-AGTAAGAAGTAAAAAGTAAT
*
11152 CAGTAAG-AGTAAAAAGGTGAT
1 CAGTAAGAAGTAAAAA-GTAAT
*
11173 CAATAA-AGAGTAAAAAGCTAAT
1 CAGTAAGA-AGTAAAAAG-TAAT
*
11195 CAGGAAGAAGTAAAAAGGTAAT
1 CAGTAAGAAGTAAAAA-GTAAT
* *
11217 CAGTAAAAAG-AAAAAGGCAAT
1 CAGTAAGAAGTAAAAA-GTAAT
*
11238 CAGTAAAAAGTAAAAGAGTAAT
1 CAGTAAGAAGTAAAA-AGTAAT
11260 CAGTAAAAAAGGAGCAG-AAAATAGTAAT
1 CAGT----AA-GA--AGTAAAA-AGTAAT
* *
11288 CAGTAAAAGAGTAAAATGGTAAT
1 CAGTAAGA-AGTAAAA-AGTAAT
*
11311 CAGTAAAAAGTAAAAAGGTAAT
1 CAGTAAGAAGTAAAAA-GTAAT
**
11333 CAACAAG-AGTAAAATAGTAAT
1 CAGTAAGAAGTAAAA-AGTAAT
*
11354 TAGTACA-AAGTAAAGAA-TAAT
1 CAGTA-AGAAGTAAA-AAGTAAT
11375 CAGTAA
1 CAGTAA
11381 AATAGTGATG
Statistics
Matches: 244, Mismatches: 42, Indels: 56
0.71 0.12 0.16
Matches are distributed among these distances:
20 10 0.04
21 101 0.41
22 89 0.36
23 23 0.09
24 2 0.01
26 2 0.01
27 1 0.00
28 14 0.06
29 2 0.01
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (21 bp):
CAGTAAGAAGTAAAAAGTAAT
Found at i:11264 original size:15 final size:15
Alignment explanation
Indices: 11246--11301 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
11236 ATCAGTAAAA
11246 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
11261 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
11275 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
11289 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
11302 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:13932 original size:21 final size:19
Alignment explanation
Indices: 13907--13945 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
13897 TATGACTCAT
13907 ATGCTATGAATGCTATGATTG
1 ATGCTATGAAT-CT-TGATTG
*
13928 ATGCTTTGAATCTTGATT
1 ATGCTATGAATCTTGATT
13946 TGCTTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (19 bp):
ATGCTATGAATCTTGATTG
Found at i:16214 original size:18 final size:17
Alignment explanation
Indices: 16187--16222 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
16177 TTTCTCTTCA
16187 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
16204 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
16222 T
1 T
16223 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:17353 original size:4 final size:4
Alignment explanation
Indices: 17344--17386 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
17334 ACTACGCTTA
17344 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
17387 CTGGGTCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:18637 original size:22 final size:22
Alignment explanation
Indices: 18559--18645 Score: 79
Period size: 22 Copynumber: 4.0 Consensus size: 22
18549 GTCTTCCTTA
18559 GTCTCAGAACAGACTC-CTAAGC
1 GTCTCAGAACAGACTCTC-AAGC
** * *
18581 GTCTCA-AGGTAGACTCCCAAGT
1 GTCTCAGA-ACAGACTCTCAAGC
18603 GTCTCAGAACAGACTCTCAAGC
1 GTCTCAGAACAGACTCTCAAGC
** *
18625 GTCTCAGGGCAGACTTTCAAG
1 GTCTCAGAACAGACTCTCAAG
18646 TATCAGTTGG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.02
22 49 0.94
23 2 0.04
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (22 bp):
GTCTCAGAACAGACTCTCAAGC
Found at i:18765 original size:38 final size:38
Alignment explanation
Indices: 18721--18907 Score: 261
Period size: 38 Copynumber: 5.0 Consensus size: 38
18711 TCAAAGCAGG
* *
18721 TTATCAAGATCGACTAGAAACAGGTCATCTCTCAACAA
1 TTATCAAGATCGACTAGAAACAGGTCATCTTTCAGCAA
* * *
18759 TTATCAA-ATTGATTGGAAACAGGTCATCTTTCAGCAA
1 TTATCAAGATCGACTAGAAACAGGTCATCTTTCAGCAA
* *
18796 TTATCAAGATCGACTGGAAACAGGTCATCTGTCAGCAA
1 TTATCAAGATCGACTAGAAACAGGTCATCTTTCAGCAA
*
18834 TTTTCAAGATCGACTA-AAACAGGTCATCTTTCAGCAA
1 TTATCAAGATCGACTAGAAACAGGTCATCTTTCAGCAA
** *
18871 TTATCAAGATCGGTTAGAAACAGGTCATCTTGCAGCA
1 TTATCAAGATCGACTAGAAACAGGTCATCTTTCAGCA
18908 GTTTTTCAGT
Statistics
Matches: 132, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
37 65 0.49
38 67 0.51
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (38 bp):
TTATCAAGATCGACTAGAAACAGGTCATCTTTCAGCAA
Found at i:18854 original size:75 final size:75
Alignment explanation
Indices: 18721--18900 Score: 263
Period size: 75 Copynumber: 2.4 Consensus size: 75
18711 TCAAAGCAGG
* * *
18721 TTATCAAGATCGACTAGAAACAGGTCATCTCTCAACAATTATCAAATTGATTGGAAACAGGTCAT
1 TTATCAAGATCGACTAGAAACAGGTCATCTCTCAACAATTATCAAATCGACTGAAAACAGGTCAT
18786 CTTTCAGCAA
66 CTTTCAGCAA
* * * *
18796 TTATCAAGATCGACTGGAAACAGGTCATCTGTCAGCAATTTTCAAGATCGACT-AAAACAGGTCA
1 TTATCAAGATCGACTAGAAACAGGTCATCTCTCAACAATTATCAA-ATCGACTGAAAACAGGTCA
18860 TCTTTCAGCAA
65 TCTTTCAGCAA
**
18871 TTATCAAGATCGGTTAGAAACAGGTCATCT
1 TTATCAAGATCGACTAGAAACAGGTCATCT
18901 TGCAGCAGTT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 89 0.95
76 5 0.05
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (75 bp):
TTATCAAGATCGACTAGAAACAGGTCATCTCTCAACAATTATCAAATCGACTGAAAACAGGTCAT
CTTTCAGCAA
Found at i:19056 original size:44 final size:43
Alignment explanation
Indices: 18910--19332 Score: 530
Period size: 44 Copynumber: 9.7 Consensus size: 43
18900 TTGCAGCAGT
*
18910 TTTTCAGTTGCTCCAAAGAGGGGGCATTTCC-ACAACTTTTCAG
1 TTTTCAGTTGCTCCAAGGAGGGGGCA-TTCCAACAACTTTTCAG
* * * *
18953 CTTTACAAGTTGCTCCAAAGAGGGGGCATTCTAACAACTCTTCAG
1 -TTTTC-AGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAG
*
18998 TTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAATTTTTTCAG
1 TTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAA-CTTTTCAG
* *
19042 TTTTCAATTGCTCCAAGGAGTGGGGCATTTCAACAACTTTTCAG
1 TTTTCAGTTGCTCCAAGGAG-GGGGCATTCCAACAACTTTTCAG
* * *
19086 CTTTACAAGTTGCTCCAAAGAGGGGGCATTCTAACAACTTTT-AG
1 -TTTTC-AGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAG
* * *
19130 TTTTCAGTTGCTCCCAGGAGGGGGCAATCCAACAACTTTACAG
1 TTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAG
* * *
19173 TTTTTTAGTTGCTCCAAGGAGAGGGCATTCCAACAACTTTACAG
1 -TTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAG
*
19217 TTTTTCAGTTGCTCCAAGGAGGGGGCAGTCCAACAACTTTTCAG
1 -TTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAG
* **
19261 TTTTCAGTTGCTCCAAAGAGGGGGCATTATAACAACTTTTCAG
1 TTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAG
*
19304 TTTTCAGTTGATCACAA-G-GGGGGCATTCC
1 TTTTCAGTTGCTC-CAAGGAGGGGGCATTCC
19333 TGTGAGTTTC
Statistics
Matches: 333, Mismatches: 37, Indels: 20
0.85 0.09 0.05
Matches are distributed among these distances:
42 39 0.12
43 86 0.26
44 127 0.38
45 68 0.20
46 13 0.04
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (43 bp):
TTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAG
Done.