Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012339.1 Corchorus capsularis cultivar CVL-1 contig12360, 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: 41069
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2237 original size:796 final size:797
Alignment explanation
Indices: 687--2286 Score: 2733
Period size: 797 Copynumber: 2.0 Consensus size: 797
677 AATCAAAACA
687 TTAAAATTGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTATCTTCTAATAGACACT
1 TTAAAATTGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTATCTTCTAATAGACACT
* *
752 TGAATCACCTTAATCGGACAAATAGAACAAAAAATACAAAAATAAAAGCTAATGCGTTAAATCGT
66 TGAATCACCTTAATCGGACAAATAGAACAAAAAATACAAAAATAAAAGCCAACGCGTTAAATCGT
* *
817 CCAACCCATAATTGTAAAGGGTTAAATAGAATAAAGTATAAAAGTATGAGGATCATTTGATAAAT
131 CCAACCCATAATTGTAAAGGATTAAATAGAATAAAGCATAAAAGTATGAGGATCATTTGATAAAT
* *
882 AATCCAGCAAAAAAAAATTGTTTATGGAGACCAAACATAAAAATTACCTCTTGAATCCTCCACGA
196 AATCCAGCAAAAAAAAATTGTTTATAGAGACCAAACATAAAAATTACCTCTTGAATCATCCACGA
*
947 AACTCATTAATCAAATTCAGCTTTCAAGCCCTTAATGAAATTCGTAGATCACACAATAACCTTTT
261 AACTCATTAATCAAATTCAGCTTTCAAGCCCTTAATGAAAGTCGTAGATCACACAATAACCTTTT
** *
1012 AACCGACACTTGAACAAGCTCAATCGGACAATTGGATTGAAAATTATATAATATTAGATAGACTG
326 AACCGACACTTGAACAAGCTCAATCGGACAATTGGACCGAAAATTATATAATATTAGATAGACAG
1077 GCAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAACCAAAACATTAAAATTGGTTTTTGAA
391 GCAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAACCAAAACATTAAAATTGGTTTTTGAA
* *
1142 ACCTTAATGGAAGTTGTGGATCATGAAATTACCTTTTAATAGATACTTGAATCACTTTGATCGGA
456 ACCTTAATGGAAGTTGTGGATCATGAAATTACCTTTCAATAGACACTTGAATCACTTTGATCGGA
* * * * *
1207 CAAGCAAAACAAATCATAGAAGAATTAAAGCCGAAATGTTTAGTCATCTAACCCATAATTATAAA
521 CAAACAAAACAAAACATAGAAGAATTAAAGCCGAAACGTTCAGTCATCCAACCCATAATTATAAA
* * *
1272 GGATTAAATAGCATAAAGTATAAAAGTACGAGGATCATTTGATAAATAATCCAGTAAAAAAATGA
586 GGATTAAATAGCATAAAGCATAAAAGTACGAGGACCATTTGATAAATAATCCAGCAAAAAAATGA
1337 TTTGTTTATTGAGAGTGGGACCCACCAAATAGTAACTTTATCATAAAGTTCCAAAAACACCCTTA
651 TTTGTTTATTGAGAGTGGGACCCACCAAATAGTAACTTTATCATAAAGTTCCAAAAACACCCTTA
*
1402 ACAATCAATAATAATAACGAAAATACTGAGCATAAAAATACC-TACCCCTGACAATTTGTTCTTG
716 ACAATCAACAATAATAACGAAAATACTGAGCATAAAAATACCATACCCCTGACAATTTGTTCTTG
1466 GGTGAATGTGGTGCATC
781 GGTGAATGTGGTGCATC
* *
1483 TTAAAATTGGCTTCTGAGTTCTTCATGAAAGTTGTAGGTCATGAAATTATCTTTTAATAGACACT
1 TTAAAATTGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTATCTTCTAATAGACACT
* *
1548 TGAATCACCTTAATCGGACAAATATAACAAAAAATACAAAAATAAAAGCCAACGTGTTAAATCGT
66 TGAATCACCTTAATCGGACAAATAGAACAAAAAATACAAAAATAAAAGCCAACGCGTTAAATCGT
*
1613 CCAACCTATAATTGTAAAGGATTAAATAGAATAAAGCATAAAAGTATGAGGATCATTTGATAAAT
131 CCAACCCATAATTGTAAAGGATTAAATAGAATAAAGCATAAAAGTATGAGGATCATTTGATAAAT
* *
1678 AATTCAGCAAAAAAATATTTGTTTATAGAGACCAAACATAAAAATTACCTCTTGAATCATCCACG
196 AATCCAGCAAAAAAA-AATTGTTTATAGAGACCAAACATAAAAATTACCTCTTGAATCATCCACG
*
1743 AAACTCATTAATCAAATTCAGCTTTCAAGCTCTTAATGAAAGTCGTAGATCACACAATAACCTTT
260 AAACTCATTAATCAAATTCAGCTTTCAAGCCCTTAATGAAAGTCGTAGATCACACAATAACCTTT
* *
1808 TAACCGACACTTGAACAA-CTTCAATTGGACAATTGGACCGAAAATTATATAATATTTGATAGAC
325 TAACCGACACTTGAACAAGC-TCAATCGGACAATTGGACCGAAAATTATATAATATTAGATAGAC
* * *
1872 AGGTAATCGAGACCCCAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGTTTTTG
389 AGGCAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAACCAAAACATTAAAATTGGTTTTTG
** *
1937 AGTCCTTCATGGAAGTTGTGGATCATGAAATTACCTTTCAATAGACACTTGAATCA-TCTTGATC
454 AAACCTTAATGGAAGTTGTGGATCATGAAATTACCTTTCAATAGACACTTGAATCACT-TTGATC
* * *
2001 GGACAAACAAAACAAAACATAGAAGAATTAAAGTCGAAACGTTCAGTCGTCCAACCCATAATTGT
518 GGACAAACAAAACAAAACATAGAAGAATTAAAGCCGAAACGTTCAGTCATCCAACCCATAATTAT
*
2066 AAAGGATTAAATAGCATAAAGCATAAAAGTATGAGGACCATTTGATAAATAATCCAGCAAAAAAA
583 AAAGGATTAAATAGCATAAAGCATAAAAGTACGAGGACCATTTGATAAATAATCCAGCAAAAAAA
2131 T-ATTTGTTTATTGAGAGTGGGACCCACCAAATAGTAACTTTATCATAAAGTTCCAAAAA-AGCC
648 TGATTTGTTTATTGAGAGTGGGACCCACCAAATAGTAACTTTATCATAAAGTTCCAAAAACA-CC
2194 CTTAACAATCAACAATAATAACGAAAATACTGAGCATAAAAATACCGAAATACCCCTGACAATTT
712 CTTAACAATCAACAATAATAACGAAAATACTGAGCATAAAAATACC---ATACCCCTGACAATTT
2259 GTTCTTGGGTGAATGTGGTGCATC
774 GTTCTTGGGTGAATGTGGTGCATC
2283 TTAA
1 TTAA
2287 GGCTGGACAA
Statistics
Matches: 755, Mismatches: 41, Indels: 12
0.93 0.05 0.01
Matches are distributed among these distances:
795 1 0.00
796 307 0.41
797 404 0.54
800 43 0.06
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.28
Consensus pattern (797 bp):
TTAAAATTGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTATCTTCTAATAGACACT
TGAATCACCTTAATCGGACAAATAGAACAAAAAATACAAAAATAAAAGCCAACGCGTTAAATCGT
CCAACCCATAATTGTAAAGGATTAAATAGAATAAAGCATAAAAGTATGAGGATCATTTGATAAAT
AATCCAGCAAAAAAAAATTGTTTATAGAGACCAAACATAAAAATTACCTCTTGAATCATCCACGA
AACTCATTAATCAAATTCAGCTTTCAAGCCCTTAATGAAAGTCGTAGATCACACAATAACCTTTT
AACCGACACTTGAACAAGCTCAATCGGACAATTGGACCGAAAATTATATAATATTAGATAGACAG
GCAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAACCAAAACATTAAAATTGGTTTTTGAA
ACCTTAATGGAAGTTGTGGATCATGAAATTACCTTTCAATAGACACTTGAATCACTTTGATCGGA
CAAACAAAACAAAACATAGAAGAATTAAAGCCGAAACGTTCAGTCATCCAACCCATAATTATAAA
GGATTAAATAGCATAAAGCATAAAAGTACGAGGACCATTTGATAAATAATCCAGCAAAAAAATGA
TTTGTTTATTGAGAGTGGGACCCACCAAATAGTAACTTTATCATAAAGTTCCAAAAACACCCTTA
ACAATCAACAATAATAACGAAAATACTGAGCATAAAAATACCATACCCCTGACAATTTGTTCTTG
GGTGAATGTGGTGCATC
Found at i:5878 original size:38 final size:37
Alignment explanation
Indices: 5807--6191 Score: 440
Period size: 38 Copynumber: 10.3 Consensus size: 37
5797 AATTCAGGGT
5807 AATTAAGTAAAGAGCAGTTAAAAGGGCTTAATTTAGGA
1 AATTAAGTAAAGAGCAGTT-AAAGGGCTTAATTTAGGA
5845 CAATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTAGGA
1 -AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTAGGA
** * *
5883 AATTAAGTAAAG-GCAG-TAAAGTACTTAATTCAGGGT
1 AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTA-GGA
5919 AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTAGGA
1 AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTAGGA
*
5956 CAATTAAGTAAAGAGCGGTTAAAGGGCTTAATTTAGGA
1 -AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTAGGA
*
5994 CAATTAAGTAAAGAGTAGTTAAAGGGCTTAATTTAGGA
1 -AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTAGGA
* * *** * *
6032 CAATTAAGCAAA-AACAG-TAAAATACTTAATTCAGGGT
1 -AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTA-GGA
*
6069 AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTAAGGGA
1 AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTA-GGA
* * *
6107 AATTAAGTAAA-AGCAGTTAAAAGACTTAATTCAGGGA
1 AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTA-GGA
* * ** *
6144 AATTAAGT-AACAGCAGTCAAAGTACTTAATTCAAGGA
1 AATTAAGTAAAGAGCAGTTAAAGGGCTTAATT-TAGGA
6181 AATTAAGTAAA
1 AATTAAGTAAA
6192 ATCACAAAGA
Statistics
Matches: 303, Mismatches: 33, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
35 13 0.04
36 42 0.14
37 86 0.28
38 143 0.47
39 19 0.06
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (37 bp):
AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTAGGA
Found at i:5905 original size:112 final size:112
Alignment explanation
Indices: 5788--6191 Score: 505
Period size: 112 Copynumber: 3.6 Consensus size: 112
5778 AGAACAGTAA
*
5788 AAAGTACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAAGGGCTTAATTTAGGACAATTAAG
1 AAAGTACTTAATTCAGGGTAATTAAGTAAAGAGCAG-TAAAAGGACTTAATTTAGGACAATTAAG
5853 TAAAGAGCAGTTAAAGGGCTTAATTTAGGAAATTAAGTAAAGGCAG-T
65 TAAAGAGCAGTTAAAGGGCTTAATTTAGGAAATTAAGTAAAGGCAGTT
* *
5900 AAAGTACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTAGGACAATTAAGT
1 AAAGTACTTAATTCAGGGTAATTAAGTAAAGAGCAGTAAAAGGACTTAATTTAGGACAATTAAGT
* *
5965 AAAGAGCGGTTAAAGGGCTTAATTTAGGACAATTAAGTAAAGAGTAGTT
66 AAAGAGCAGTTAAAGGGCTTAATTTAGGA-AATTAAGTAAAG-GCAGTT
** * ** * * * * **
6014 AAAGGGCTTAATTTAGGACAATTAAGCAAA-AACAGTAAAA-TACTTAATTCAGGGTAATTAAGT
1 AAAGTACTTAATTCAGGGTAATTAAGTAAAGAGCAGTAAAAGGACTTAATTTAGGACAATTAAGT
* *
6077 AAAGAGCAGTTAAAGGGCTTAATTAAGGGAAATTAAGTAAAAGCAGTT
66 AAAGAGCAGTTAAAGGGCTTAATTTA-GGAAATTAAGTAAAGGCAGTT
* * * * *
6125 AAAAG-ACTTAATTCAGGGAAATTAAGT-AACAGCAGTCAAAGTACTTAATTCAAGGA-AATTAA
1 -AAAGTACTTAATTCAGGGTAATTAAGTAAAGAGCAGTAAAAGGACTTAATT-TAGGACAATTAA
6187 GTAAA
64 GTAAA
6192 ATCACAAAGA
Statistics
Matches: 255, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
110 2 0.01
111 86 0.34
112 125 0.49
113 17 0.07
114 25 0.10
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (112 bp):
AAAGTACTTAATTCAGGGTAATTAAGTAAAGAGCAGTAAAAGGACTTAATTTAGGACAATTAAGT
AAAGAGCAGTTAAAGGGCTTAATTTAGGAAATTAAGTAAAGGCAGTT
Found at i:6066 original size:150 final size:149
Alignment explanation
Indices: 5794--6262 Score: 571
Period size: 150 Copynumber: 3.2 Consensus size: 149
5784 GTAAAAAGTA
* *
5794 CTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAAGGGCTTAATTTAGGACAATTAAGTAAAGA
1 CTTAATTAAGGGAAATTAAGTAAAGAGCAGTT-AAAGGGCTTAATTTAGGACAATTAAGTAAAGA
* ** *
5859 GCAGTTAAAGGGCTTAATTTAGGAAATTAAGTAAAGGCAGTAAAGTACTTAATTCAGGGTAATTA
65 GCAGTTAAAGGGCTTAATTTAGGAAATTAAGCAAAAACAGTAAAATACTTAATTCAGGGTAATTA
5924 AGTAAAGAGCAGTTAAAGGG
130 AGTAAAGAGCAGTTAAAGGG
* *
5944 CTTAATTTA-GGACAATTAAGTAAAGAGCGGTTAAAGGGCTTAATTTAGGACAATTAAGTAAAGA
1 CTTAATTAAGGGA-AATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTAGGACAATTAAGTAAAGA
*
6008 GTAGTTAAAGGGCTTAATTTAGGACAATTAAGCAAAAACAGTAAAATACTTAATTCAGGGTAATT
65 GCAGTTAAAGGGCTTAATTTAGGA-AATTAAGCAAAAACAGTAAAATACTTAATTCAGGGTAATT
6073 AAGTAAAGAGCAGTTAAAGGG
129 AAGTAAAGAGCAGTTAAAGGG
* * * *
6094 CTTAATTAAGGGAAATTAAGTAAA-AGCAGTTAAAAGACTTAATTCAGGGA-AATTAAGT-AACA
1 CTTAATTAAGGGAAATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTA-GGACAATTAAGTAAAGA
* ** * * * * * *
6156 GCAGTCAAAGTACTTAATTCAAGGAAATTAAGTAAAATCA--CAAAGACTTAATTCCA-AGTAAT
65 GCAGTTAAAGGGCTTAATT-TAGGAAATTAAGCAAAAACAGTAAAATACTTAATT-CAGGGTAAT
* **
6218 TAAGTAACA-A-CAGTCAAAGTA
128 TAAGTAA-AGAGCAGTTAAAGGG
6239 CTTAATTCAA-GGAAATTAAGTAAA
1 CTTAATT-AAGGGAAATTAAGTAAA
6263 ATCAGCCAGG
Statistics
Matches: 284, Mismatches: 27, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
145 29 0.10
146 26 0.09
147 3 0.01
148 31 0.11
149 87 0.31
150 105 0.37
151 3 0.01
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (149 bp):
CTTAATTAAGGGAAATTAAGTAAAGAGCAGTTAAAGGGCTTAATTTAGGACAATTAAGTAAAGAG
CAGTTAAAGGGCTTAATTTAGGAAATTAAGCAAAAACAGTAAAATACTTAATTCAGGGTAATTAA
GTAAAGAGCAGTTAAAGGG
Found at i:6092 original size:74 final size:74
Alignment explanation
Indices: 5807--6263 Score: 484
Period size: 74 Copynumber: 6.2 Consensus size: 74
5797 AATTCAGGGT
* * **
5807 AATTAAGTAAAGAGCAGTTAAAAGGGCTTAATTTAGGACAATTAAGTAAAGAGCAGTTAAAGGGC
1 AATTAAGTAAA-AGCAGTTAAAA-GACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAGGGC
5872 TTAATTTAGGA
64 TTAATTTAGGA
*
5883 AATTAAGTAAAGGCAG-T-AAAGTACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAGGGCT
1 AATTAAGTAAAAGCAGTTAAAAG-ACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAGGGCT
5946 TAATTTAGGA
65 TAATTTAGGA
* * * * ** *
5956 CAATTAAGTAAAGAGCGGTTAAAGGGCTTAATTTAGGACAATTAAGTAAAGAGTAGTTAAAGGGC
1 -AATTAAGTAAA-AGCAGTTAAAAGACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAGGGC
6021 TTAATTTAGGA
64 TTAATTTAGGA
* * *
6032 CAATTAAGCAAAAACAG-TAAAATACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAGGGCT
1 -AATTAAGTAAAAGCAGTTAAAAGACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAGGGCT
*
6096 TAATTAAGGGA
65 TAATTTA-GGA
* * * **
6107 AATTAAGTAAAAGCAGTTAAAAGACTTAATTCAGGGAAATTAAGT-AACAGCAGTCAAAGTACTT
1 AATTAAGTAAAAGCAGTTAAAAGACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAGGGCTT
*
6171 AATTCAAGGA
66 AATT-TAGGA
* * * * **
6181 AATTAAGTAAAATCA---CAAAGACTTAATTCCA-AGTAATTAAGTAACA-A-CAGTCAAAGTAC
1 AATTAAGTAAAAGCAGTTAAAAGACTTAATT-CAGGGTAATTAAGTAA-AGAGCAGTTAAAGGGC
*
6240 TTAATTCAAGGA
64 TTAATT-TAGGA
6252 AATTAAGTAAAA
1 AATTAAGTAAAA
6264 TCAGCCAGGC
Statistics
Matches: 334, Mismatches: 36, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
71 57 0.17
72 5 0.01
73 51 0.15
74 108 0.32
75 41 0.12
76 69 0.21
77 3 0.01
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (74 bp):
AATTAAGTAAAAGCAGTTAAAAGACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAGGGCTT
AATTTAGGA
Found at i:6219 original size:34 final size:34
Alignment explanation
Indices: 6105--6297 Score: 176
Period size: 37 Copynumber: 5.4 Consensus size: 34
6095 TTAATTAAGG
* * *
6105 GAAATTAAGTAAAAGCAGTTAAAAGACTTAATTCAGG
1 GAAATTAAGTAAAATCAG--CAAAGACTTAATTCA-A
* *
6142 GAAATTAAGTAACAGCAGTCAAAGTACTTAATTCAA
1 GAAATTAAGTAAAATCAG-CAAAG-ACTTAATTCAA
6178 GGAAATTAAGTAAAATCA-CAAAGACTTAATTCCAA
1 -GAAATTAAGTAAAATCAGCAAAGACTTAATT-CAA
*
6213 GTAATTAAGTAACAA-CAGTCAAAGTACTTAATTCAA
1 GAAATTAAGTAA-AATCAG-CAAAG-ACTTAATTCAA
* *
6249 GGAAATTAAGTAAAATCAGC-CAGGCTTAATTCATA
1 -GAAATTAAGTAAAATCAGCAAAGACTTAATTCA-A
*
6284 GTAATTAAGTAAAA
1 GAAATTAAGTAAAA
6298 ACATTAGAAA
Statistics
Matches: 136, Mismatches: 10, Indels: 23
0.80 0.06 0.14
Matches are distributed among these distances:
34 43 0.32
35 13 0.10
36 16 0.12
37 64 0.47
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (34 bp):
GAAATTAAGTAAAATCAGCAAAGACTTAATTCAA
Found at i:6311 original size:108 final size:108
Alignment explanation
Indices: 5995--6263 Score: 262
Period size: 108 Copynumber: 2.5 Consensus size: 108
5985 AATTTAGGAC
* * * * * * *
5995 AATTAAGTAAAGAGTAGTTAAAGGGCTTAATT-TAGGACAATTAAGCAAAAACAGT-AAAATACT
1 AATTAAGTAAA-AGCAGTTAAAAGACTTAATTCAAGGA-AATTAAGTAAAAGCAGTCAAAGTACT
* * * * * *
6058 TAATTCAGGGTAATTAAGTAAAGAGCAGTTAAAGGGCTTAATT--AAGGGA
64 TAATTCAAGGAAATTAAGTAAA-ATCA--CAAA-GACTTAATTCCAA--GT
* *
6107 AATTAAGTAAAAGCAGTTAAAAGACTTAATTCAGGGAAATTAAGTAACAGCAGTCAAAGTACTTA
1 AATTAAGTAAAAGCAGTTAAAAGACTTAATTCAAGGAAATTAAGTAAAAGCAGTCAAAGTACTTA
6172 ATTCAAGGAAATTAAGTAAAATCACAAAGACTTAATTCCAAGT
66 ATTCAAGGAAATTAAGTAAAATCACAAAGACTTAATTCCAAGT
*
6215 AATTAAGTAACAA-CAG-TCAAAGTACTTAATTCAAGGAAATTAAGTAAAA
1 AATTAAGTAA-AAGCAGTTAAAAG-ACTTAATTCAAGGAAATTAAGTAAAA
6264 TCAGCCAGGC
Statistics
Matches: 133, Mismatches: 18, Indels: 16
0.80 0.11 0.10
Matches are distributed among these distances:
107 5 0.04
108 46 0.35
109 5 0.04
110 2 0.02
111 34 0.26
112 41 0.31
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (108 bp):
AATTAAGTAAAAGCAGTTAAAAGACTTAATTCAAGGAAATTAAGTAAAAGCAGTCAAAGTACTTA
ATTCAAGGAAATTAAGTAAAATCACAAAGACTTAATTCCAAGT
Found at i:6348 original size:39 final size:39
Alignment explanation
Indices: 6303--6508 Score: 358
Period size: 39 Copynumber: 5.3 Consensus size: 39
6293 TAAAAACATT
*
6303 AGAAAGACTGACTTAATTTCAAAGAAGGAAATTAGGTAA
1 AGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAA
* *
6342 AGAAAGACTGACTTGATTTCAAGGAAGGGAATTAGGTAA
1 AGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
6381 AGAAAGATTGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
6420 AGAAAGACTGACTTAATTTCAAGGAAGGGAATTAGGTAA
1 AGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
6459 AGAAAGACTGACTTAATTTCAAGGAAGGAAATTTGGTAA
1 AGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAA
6498 AGAAAGACTGA
1 AGAAAGACTGA
6509 GGCACATGCT
Statistics
Matches: 157, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 157 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.23
Consensus pattern (39 bp):
AGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAA
Found at i:7919 original size:28 final size:30
Alignment explanation
Indices: 7860--7932 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 30
7850 AAAAAAAAAT
7860 TTCCTTATGTTTTTCTTTTGGGACAAAATAA
1 TTCCTTATG-TTTTCTTTTGGGACAAAATAA
*
7891 TTCCTTATG-TTT-TTTTGGGACAAATTAA
1 TTCCTTATGTTTTCTTTTGGGACAAAATAA
*
7919 -TCTCTTACGTTTTC
1 TTC-CTTATGTTTTC
7933 AAAAGTGAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 2 0.05
28 20 0.54
29 6 0.16
31 9 0.24
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (30 bp):
TTCCTTATGTTTTCTTTTGGGACAAAATAA
Found at i:9265 original size:2 final size:2
Alignment explanation
Indices: 9258--9296 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
9248 AAGACAAGAT
*
9258 TA TA TA TA AA TA TA -A 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 TA TA TA TA TA TA TA
9297 AATCCAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:10134 original size:35 final size:35
Alignment explanation
Indices: 10078--11092 Score: 1542
Period size: 35 Copynumber: 28.9 Consensus size: 35
10068 AGTCGTACTG
*
10078 GATCAACTCTGATCATC-GAAAACTTCTTGAAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
*
10113 TATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
10148 GATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
10183 GATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
10218 GATCAACTCTGACCACTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
10253 GATCAACTCTGACATCTGAAAACTTCTTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
10288 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
10323 GATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
10358 GATCAACTCTGACCTCTGAAAACTTCTTTAAAATGA
1 GATCAACTCTGACCTCTGAAAACTTC-TTGAAATGA
* * ** * *
10394 GATCAACTCTGATCAT-TGGAAACTTAATGGAATGT
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
*
10429 GATCAACTCTGACCTCTGAAAACTTCTTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
10464 GATCAACTCTGACCTCTGGAAACTTCTTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
10499 GATTAACTATGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* * *
10534 GATCAACTCTGACCTCTGAAAACGTCATGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
10569 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
10604 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
10639 GATCAACTCTGACCTCTGAAAACTTCTT-AATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAA-ATGA
*
10674 GATCAACTCTGACCTCTGAAAACTTCTTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
10709 GTTCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* ** * *
10744 GATCAACTTTGATAAT-TGGAAACTTCTTGGAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
10779 GATCAACTCTGACCT-TGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
10813 GATCAACTCTGACCTCTGAAAACTTCTT-AATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAA-ATGA
*
10848 GTTCAACTCTGACCTACTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCT-CTGAAAACTTCTTGAAATGA
*
10884 GATCAACTCTGACCTCTGAAAACTTCTTTAAAATGA
1 GATCAACTCTGACCTCTGAAAACTTC-TTGAAATGA
* *
10920 GATCAACTTTGATCGT-TGAAAACTTCTTGAAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
10955 GATCAACTCTGACCTCTGAAAACTTCTT-AGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGA-AATGA
* * *
10990 GATCAACTCCGACCTCTGAAAACTTTTTGAAATGT
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
11025 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
11060 GATCAACTCTGACCTCTGAAAACTTCTATGAAA
1 GATCAACTCTGACCTCTGAAAACTTCT-TGAAA
11093 AGACCACCCT
Statistics
Matches: 894, Mismatches: 69, Indels: 33
0.90 0.07 0.03
Matches are distributed among these distances:
34 45 0.05
35 748 0.84
36 95 0.11
37 6 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (35 bp):
GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
Found at i:11230 original size:22 final size:22
Alignment explanation
Indices: 11203--11250 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11193 AACACCTTAA
*
11203 CTTGAC-TCTTCATCTACCCTTT
1 CTTGACTTCTTC-TCTACCCATT
*
11225 CTTGACTTCTTCTTTACCCATT
1 CTTGACTTCTTCTCTACCCATT
11247 CTTG
1 CTTG
11251 GCTACTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.12, C:0.33, G:0.06, T:0.48
Consensus pattern (22 bp):
CTTGACTTCTTCTCTACCCATT
Found at i:12540 original size:20 final size:21
Alignment explanation
Indices: 12494--12542 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
12484 TCTATTTTTG
*
12494 TCTTTTTCAACTTCTTTCTTT
1 TCTTTTTCAACTTCTTTCTCT
12515 TCTTTTTCAA-TTCTTT-TCT
1 TCTTTTTCAACTTCTTTCTCT
12534 TCATTTTTC
1 TC-TTTTTC
12543 TTTCCCTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 12 0.46
21 10 0.38
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.67
Consensus pattern (21 bp):
TCTTTTTCAACTTCTTTCTCT
Found at i:17678 original size:87 final size:88
Alignment explanation
Indices: 17570--17793 Score: 353
Period size: 87 Copynumber: 2.6 Consensus size: 88
17560 TTTCCTTTTT
* * *
17570 TATATCTTCTAAATCTCCCACAATTTGACAAGATTTAGAAAATATTCTCATTATT-ATTCAATCT
1 TATATCTCCTAAACCTTCCACAATTTGACAAGATTTAGAAAATATTCTCATTATTAATTCAAT-T
* *
17634 TTATAATTTATTTATTTTTTTAAA
65 TTATAATTTATTTATTTCTTAAAA
*
17658 -ATATCTCCTAAACCTTCCACAATTTGACAAGATTTAGAAAATATTCTCATTATTAATTCTATTT
1 TATATCTCCTAAACCTTCCACAATTTGACAAGATTTAGAAAATATTCTCATTATTAATTCAATTT
*
17722 TTTAATTTATTTATTTCTTAAAA
66 TATAATTTATTTATTTCTTAAAA
*
17745 TATATCTCCTAAACCTTCCACAATTTGGCAAGATTTAGAAAATATTCTC
1 TATATCTCCTAAACCTTCCACAATTTGACAAGATTTAGAAAATATTCTC
17794 TCTTTACAAA
Statistics
Matches: 126, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
87 73 0.58
88 53 0.42
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.44
Consensus pattern (88 bp):
TATATCTCCTAAACCTTCCACAATTTGACAAGATTTAGAAAATATTCTCATTATTAATTCAATTT
TATAATTTATTTATTTCTTAAAA
Found at i:18238 original size:2 final size:2
Alignment explanation
Indices: 18231--18263 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
18221 AAGACAAGAT
*
18231 TA TA TA TA AA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18264 AATCCAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:38475 original size:82 final size:82
Alignment explanation
Indices: 38338--38500 Score: 272
Period size: 82 Copynumber: 2.0 Consensus size: 82
38328 ACCTTTTTGG
* *
38338 TCATGCTAAGTTGTGGTGGCGTTCCAAATTCATAGATGGGGAGTGCCCATTAAGACGTGGAGAGA
1 TCATGCTAAGTTGTGGTAGCGTTCCAAATTCATAGATGAGGAGTGCCCATTAAGACGTGGAGAGA
*
38403 GCTCACGCAGGAGCTTT
66 GCTCAAGCAGGAGCTTT
* * *
38420 TCATGCTAAGTTGTGGTAGTGTTCCAAATTCATAGATGAGGAGTGCTCATTAAGACGTGGAGGGA
1 TCATGCTAAGTTGTGGTAGCGTTCCAAATTCATAGATGAGGAGTGCCCATTAAGACGTGGAGAGA
38485 GCTCAAGCAGGAGCTT
66 GCTCAAGCAGGAGCTT
38501 AAGAATGAGT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (82 bp):
TCATGCTAAGTTGTGGTAGCGTTCCAAATTCATAGATGAGGAGTGCCCATTAAGACGTGGAGAGA
GCTCAAGCAGGAGCTTT
Done.