Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020869.1 Corchorus olitorius cultivar O-4 contig20902, 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: 121932
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2422 original size:21 final size:21
Alignment explanation
Indices: 2396--2435 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2386 AAGATGCTGC
2396 AATCACTCACTGAACAAGTAG
1 AATCACTCACTGAACAAGTAG
*
2417 AATCACTCACTGAAGAAGT
1 AATCACTCACTGAACAAGT
2436 TGCATGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (21 bp):
AATCACTCACTGAACAAGTAG
Found at i:14538 original size:31 final size:31
Alignment explanation
Indices: 14503--14564 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
14493 CCCACATGAG
** *
14503 CTCCAACGGATCTTCAAGTATTAACCTTCAA
1 CTCCAACAAATCTTCAAGCATTAACCTTCAA
*
14534 CTCCATCAAATCTTCAAGCATTAACCTTCAA
1 CTCCAACAAATCTTCAAGCATTAACCTTCAA
14565 ACCAATCCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.29
Consensus pattern (31 bp):
CTCCAACAAATCTTCAAGCATTAACCTTCAA
Found at i:15106 original size:24 final size:24
Alignment explanation
Indices: 15074--15122 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
15064 TTTGTCCCAG
15074 ATTCTCACAATTCAAATCTCCTCC
1 ATTCTCACAATTCAAATCTCCTCC
*
15098 ATTCTCACATTTCAAATCTCCTCC
1 ATTCTCACAATTCAAATCTCCTCC
15122 A
1 A
15123 CAAGTAACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.35
Consensus pattern (24 bp):
ATTCTCACAATTCAAATCTCCTCC
Found at i:15411 original size:21 final size:22
Alignment explanation
Indices: 15379--15421 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
15369 AAATCCTCAA
*
15379 AAATAGGAGGTTTTTTAGGCTC
1 AAATAGGAGGTTTTGTAGGCTC
15401 AAATA-GAGGTTTTGTAGGCTC
1 AAATAGGAGGTTTTGTAGGCTC
15422 GTAATCCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (22 bp):
AAATAGGAGGTTTTGTAGGCTC
Found at i:15436 original size:138 final size:139
Alignment explanation
Indices: 15181--15566 Score: 600
Period size: 138 Copynumber: 2.8 Consensus size: 139
15171 AGTGCGTAAT
*
15181 CCCAGCCGGAAATAGGAG-CCCATCCACTTTGTCCCAGATTCTCACATTTCAAATCCCCAAGAAT
1 CCCAGCCGGAAATAGGAGCCCCATCCACTTTGTCCCAGATTCTCACATTTCAAATCCCCAAAAAT
* * *
15245 AGGAGGTTTTTCAGGCTCAAATACAGGTTTTGTAGGCTTGTAATCCTCGTAATCCCCACCAGAAA
66 AGGAGGTTTTTTAGGCTCAAATAGAGGTTTTGTAGGCTTGTAATCCTCATAATCCCCACCAGAAA
15310 TAGGAGGAA
131 TAGGAGGAA
* * * * * *
15319 CCCGGCCGGAAATAGTAGCCCCAT-CACTTTTTCCCAGATTTTCAAATTTCAAATCCTCAAAAAT
1 CCCAGCCGGAAATAGGAGCCCCATCCACTTTGTCCCAGATTCTCACATTTCAAATCCCCAAAAAT
*
15383 AGGAGGTTTTTTAGGCTCAAATAGAGGTTTTGTAGGCTCGTAATCCTCATAATCCCCACCAGAAA
66 AGGAGGTTTTTTAGGCTCAAATAGAGGTTTTGTAGGCTTGTAATCCTCATAATCCCCACCAGAAA
15448 TAGGAGGAA
131 TAGGAGGAA
*
15457 CCCAGCCGGAAATAGGAGCCCC-TCCACTTTGTCCTAGATTCTCACATTTCAAATCCCCAAAAAT
1 CCCAGCCGGAAATAGGAGCCCCATCCACTTTGTCCCAGATTCTCACATTTCAAATCCCCAAAAAT
* * *
15521 AGGAGGTTTTGTAGACTCAAAT-GTAGGTTTTGAAGGCTTGTAATCC
66 AGGAGGTTTTTTAGGCTCAAATAG-AGGTTTTGTAGGCTTGTAATCC
15567 CCAAGAGGAA
Statistics
Matches: 223, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
137 2 0.01
138 216 0.97
139 5 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (139 bp):
CCCAGCCGGAAATAGGAGCCCCATCCACTTTGTCCCAGATTCTCACATTTCAAATCCCCAAAAAT
AGGAGGTTTTTTAGGCTCAAATAGAGGTTTTGTAGGCTTGTAATCCTCATAATCCCCACCAGAAA
TAGGAGGAA
Found at i:15792 original size:168 final size:168
Alignment explanation
Indices: 15514--16002 Score: 750
Period size: 168 Copynumber: 3.0 Consensus size: 168
15504 TTCAAATCCC
* * * *
15514 CAAAAATAGGAGGTTTTGTAGACTCAAATGTAGGTTTTGAAGGCTTGTAATCCCCAAGAGGAACA
1 CAAAAATGGGAGGTTTTGTAGGCTCAAATGTAAGTTTTGTAGGCTTGTAATCCCCAAGAGGAACA
15579 CAACCGAAAATAGAAGGTTTTTGAGGCGCAAGTACATAATCCTCAAAATCCCCACCACAAATAGG
66 CAACCGAAAATAGAAGGTTTTTGAGGCGCAAGTACATAATCCTCAAAATCCCCACCACAAATAGG
15644 AGGAATAGGAGGAGCCCAGTTGGAAATAGACCTTTCCT
131 AGGAATAGGAGGAGCCCAGTTGGAAATAGACCTTTCCT
*
15682 CAAAAATGGGAGGTTTTGTAGGCTCAAATGTAAGTTTTGTAGGCTTATAATCCCCAAGAGGAACA
1 CAAAAATGGGAGGTTTTGTAGGCTCAAATGTAAGTTTTGTAGGCTTGTAATCCCCAAGAGGAACA
15747 CAACCGAAAATAGAAGGTTTTTGAGGCGCAAGTACATAATCCTCAAAATCCCCACCACAAATAGG
66 CAACCGAAAATAGAAGGTTTTTGAGGCGCAAGTACATAATCCTCAAAATCCCCACCACAAATAGG
15812 AGGAATAGGAGGAGCCCAGTTGGAAATAGACCTTTCCT
131 AGGAATAGGAGGAGCCCAGTTGGAAATAGACCTTTCCT
15850 CAAAAATGGGAGGTTTTGTAGGCTCAAATGTAAGTTTTGTAGGCTTGTAATCCCC---AGG----
1 CAAAAATGGGAGGTTTTGTAGGCTCAAATGTAAGTTTTGTAGGCTTGTAATCCCCAAGAGGAACA
* * * * ** **
15908 --A---AAAATGGGAGGTTTTTTAGGCTCAAGTATGTAATCCTCGTAATCCCCACCACAAATAGG
66 CAACCGAAAATAGAAGGTTTTTGAGGCGCAAGTACATAATCCTCAAAATCCCCACCACAAATAGG
** *
15968 AGGAATAGGAGGAGCCCAGCCGGAAATAGGCCTTT
131 AGGAATAGGAGGAGCCCAGTTGGAAATAGACCTTT
16003 TTCTCAGATT
Statistics
Matches: 304, Mismatches: 17, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
156 83 0.27
159 1 0.00
165 3 0.01
168 217 0.71
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (168 bp):
CAAAAATGGGAGGTTTTGTAGGCTCAAATGTAAGTTTTGTAGGCTTGTAATCCCCAAGAGGAACA
CAACCGAAAATAGAAGGTTTTTGAGGCGCAAGTACATAATCCTCAAAATCCCCACCACAAATAGG
AGGAATAGGAGGAGCCCAGTTGGAAATAGACCTTTCCT
Found at i:16066 original size:21 final size:21
Alignment explanation
Indices: 16040--16086 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
16030 AAAAAATGGG
16040 AGGCTCAAATGTAGGTTTTGT
1 AGGCTCAAATGTAGGTTTTGT
16061 AGGCTCAAATGTAGGTTTTGT
1 AGGCTCAAATGTAGGTTTTGT
16082 AGGCT
1 AGGCT
16087 TGTAATCCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (21 bp):
AGGCTCAAATGTAGGTTTTGT
Found at i:16228 original size:14 final size:14
Alignment explanation
Indices: 16209--16236 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16199 AGCTAGTCAC
16209 TAGAGTGATTGAAT
1 TAGAGTGATTGAAT
16223 TAGAGTGATTGAAT
1 TAGAGTGATTGAAT
16237 GACACTGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (14 bp):
TAGAGTGATTGAAT
Found at i:18314 original size:54 final size:55
Alignment explanation
Indices: 18210--18320 Score: 152
Period size: 54 Copynumber: 2.0 Consensus size: 55
18200 CCATAATTAG
* *
18210 AATTATTTTCGAAGATATAAAAGTTATTTTAATAAAATTATGTACAAAAAAAAAGC
1 AATTATTTTCGAAGATATAAAAG-AATTTGAATAAAATTATGTACAAAAAAAAAGC
* * * *
18266 AATTGTTTTCGAAGATATAAAA-AATTTGGATAAAGTTATGTACGAAAAAAAAGC
1 AATTATTTTCGAAGATATAAAAGAATTTGAATAAAATTATGTACAAAAAAAAAGC
18320 A
1 A
18321 CTAAGATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
54 28 0.57
56 21 0.43
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (55 bp):
AATTATTTTCGAAGATATAAAAGAATTTGAATAAAATTATGTACAAAAAAAAAGC
Found at i:29273 original size:16 final size:16
Alignment explanation
Indices: 29252--29283 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29242 TTTGCCAGAA
29252 TTGCTAACACTTTTTT
1 TTGCTAACACTTTTTT
29268 TTGCTAACACTTTTTT
1 TTGCTAACACTTTTTT
29284 ATAACGTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (16 bp):
TTGCTAACACTTTTTT
Found at i:36625 original size:103 final size:105
Alignment explanation
Indices: 36512--36765 Score: 386
Period size: 106 Copynumber: 2.4 Consensus size: 105
36502 AATTTTTCTA
* ** * *
36512 ACCCTTAAAATAAAATTTTAATTTTAATTTGGGCTAAATTTAGTGAA-TTAGTTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAATGAATTTAGTTATATATTTTAT
*
36576 TTCTAAAATCCTATAACAAT-ATTATTAATTATGAAATTT
66 TTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* * *
36615 ACCCTTAAAATAAAAATAAAATTTTAATTTGGACTAAACTTAATGAATTTAGTTTTGTATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAATGAATTTAGTTATATATTTTAT
*
36680 TTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
36721 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAAT
36766 AAAAAGAATA
Statistics
Matches: 136, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
103 41 0.30
104 34 0.25
106 48 0.35
107 13 0.10
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAATGAATTTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:38304 original size:22 final size:22
Alignment explanation
Indices: 38279--38344 Score: 98
Period size: 22 Copynumber: 2.9 Consensus size: 22
38269 GATCAAACAT
38279 TTTACATTTTATTATTTATTTA
1 TTTACATTTTATTATTTATTTA
38301 TTTACATTTTATTATTTATTTA
1 TTTACATTTTATTATTTATTTA
38323 TTTACTCAATTTTATT-TTTATT
1 TTTA--C-ATTTTATTATTTATT
38345 AAGAACTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 26 0.63
24 7 0.17
25 8 0.20
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTACATTTTATTATTTATTTA
Found at i:38345 original size:31 final size:31
Alignment explanation
Indices: 38307--38418 Score: 80
Period size: 31 Copynumber: 3.3 Consensus size: 31
38297 TTTATTTACA
38307 TTTTATTATTTATTTATTTACTCAATTTTAT
1 TTTTATTATTTATTTATTTACTCAATTTTAT
* * * * *
38338 TTTTATTAAGAACTTAGGTTATATCAGATCAAACATTTTACA
1 TTTTATT----ATTTA-TTTAT-TTA-CTC--A-ATTTTA-T
38380 TTTTATTATTTATTTATTTACTCAATTTTAT
1 TTTTATTATTTATTTATTTACTCAATTTTAT
38411 TTTTATTA
1 TTTTATTA
38419 AGAACAAAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 22
0.65 0.11 0.24
Matches are distributed among these distances:
31 15 0.25
32 6 0.10
33 1 0.02
35 6 0.10
36 6 0.10
37 6 0.10
38 6 0.10
40 1 0.02
41 6 0.10
42 7 0.12
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (31 bp):
TTTTATTATTTATTTATTTACTCAATTTTAT
Found at i:108211 original size:76 final size:76
Alignment explanation
Indices: 108085--108238 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 76
108075 GACCCATTTT
*
108085 TGAGATTTACGGACCCGTTGGATTTTCACCTGCGGGCTTTTCGGAATTTACTGATCGCCTACCAA
1 TGAGATTTACGGACCCGTTGGATTTTCACCTGCGGGCTTTTCGAAATTTACTGATCGCCTACCAA
108150 ATAGGAGACTG
66 ATAGGAGACTG
*
108161 TGAGATTTACGGATCCGTTGGACTTTT-ACCTGCGGGCTTTTCGAAATTTACTGATCGCCTACCA
1 TGAGATTTACGGACCCGTTGGA-TTTTCACCTGCGGGCTTTTCGAAATTTACTGATCGCCTACCA
108225 AATAGGAGACTG
65 AATAGGAGACTG
108237 TG
1 TG
108239 GTCAACGGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
76 71 0.95
77 4 0.05
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (76 bp):
TGAGATTTACGGACCCGTTGGATTTTCACCTGCGGGCTTTTCGAAATTTACTGATCGCCTACCAA
ATAGGAGACTG
Found at i:110132 original size:15 final size:15
Alignment explanation
Indices: 110112--110142 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
110102 TCATCCAACT
110112 CTAATGAAGTCTCTA
1 CTAATGAAGTCTCTA
110127 CTAATGAAGTCTCTA
1 CTAATGAAGTCTCTA
110142 C
1 C
110143 CAAGGAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (15 bp):
CTAATGAAGTCTCTA
Found at i:110839 original size:5 final size:5
Alignment explanation
Indices: 110829--110853 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
110819 TGGAACTTTT
110829 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
110854 TAACTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:112880 original size:2 final size:2
Alignment explanation
Indices: 112832--112861 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
112822 CATGTGTGTC
112832 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
112862 TTGTGTGTGT
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:115531 original size:1 final size:1
Alignment explanation
Indices: 115525--115549 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
115515 AAGTTTACTC
115525 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
115550 CCTAAAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:116755 original size:16 final size:16
Alignment explanation
Indices: 116734--116766 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
116724 CTAAATCTAA
116734 TCTTTTGAATAAAAAT
1 TCTTTTGAATAAAAAT
116750 TCTTTTGAATAAAAAT
1 TCTTTTGAATAAAAAT
116766 T
1 T
116767 GCAGGGGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TCTTTTGAATAAAAAT
Found at i:118652 original size:228 final size:228
Alignment explanation
Indices: 118249--119159 Score: 1035
Period size: 228 Copynumber: 4.0 Consensus size: 228
118239 ACCAAACAAG
* * * * * * * *
118249 ATGCAGATCTTCGTCAAGACCCTCACCGGCAAGACCATCA-CTCTCGAGGTCGAGAGTTCCGATA
1 ATGCAGATCTTCGTCAAAACCTTGACCGGAAAGACCATCACCT-TGGAAGTCGAGAGCTCCGACA
* * * * * *
118313 CCATCGATAATGTTAAGGCTAAGATTCAAGACAAGGAGGGAA-TCCCTCCAGATCAGCAGCGTCT
65 CCATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAGGGAATTCCC-CCAGACCAGCAGCGTCT
* *
118377 GATCTTCGCCGGGAAGCAACTCGAGGACGGCCGAACCTTGGCCGATTATAACATCCAGAAGGAGT
129 CATCTTCGCCGGGAAGCAACTCGAGGACGGCCGAACCTTGGCCGATTACAACATCCAGAAGGAGT
*
118442 CAACCCTCCACCTTGTCCTCCGTCTCCGTGGTGGC
194 CCACCCTCCACCTTGTCCTCCGTCTCCGTGGTGGC
* * *
118477 ATGCAAATCTTCGTCAAAACCTTGACCGGCAAGACCATAACCTTGGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTCAAAACCTTGACCGGAAAGACCATCACCTTGGAAGTCGAGAGCTCCGACAC
*
118542 CATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAGGGAATTCCCCCAGACCAACAGCGTCTCA
66 CATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAGGGAATTCCCCCAGACCAGCAGCGTCTCA
* *
118607 TCTTCGCCGGAAAACAACTCGAGGACGGCCGAACCTTGGCCGATTACAACATCCAGAAGGAGTCC
131 TCTTCGCCGGGAAGCAACTCGAGGACGGCCGAACCTTGGCCGATTACAACATCCAGAAGGAGTCC
*
118672 ACCCTCCACCTTGTCCTCCGTCTCCGTGGTGGT
196 ACCCTCCACCTTGTCCTCCGTCTCCGTGGTGGC
* *
118705 ATGCAGATCTTTGTCAAAACCCTT-ACCGGAAAAACCATCACCTTGGAAGTCGAGAGCTCCGACA
1 ATGCAGATCTTCGTCAAAA-CCTTGACCGGAAAGACCATCACCTTGGAAGTCGAGAGCTCCGACA
* * * * * *
118769 CGATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAGGGGATCCCCCCAGACCAGCAGAGGCTT
65 CCATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAGGGAATTCCCCCAGACCAGCAGCGTCTC
* * *
118834 ATCTTTGCCGGGAAGCAACTCGAGGACGGCCGAACTTTGGCCGATTACAACATCCAGAAGGAATC
130 ATCTTCGCCGGGAAGCAACTCGAGGACGGCCGAACCTTGGCCGATTACAACATCCAGAAGGAGTC
* * * ** * * *
118899 CACCCTTCATCTTGTCTTGAGGCTTCGTGGTGGG
195 CACCCTCCACCTTGTCCTCCGTCTCCGTGGTGGC
* * * * * * * * * *
118933 ATGCAGATTTTTGTCAAGACTTTGACCGGAAAGACCATCACTTTGGAGGTGGAAAGCTCGGATAC
1 ATGCAGATCTTCGTCAAAACCTTGACCGGAAAGACCATCACCTTGGAAGTCGAGAGCTCCGACAC
* * * * * * *
118998 AATTGATAACGTTAAGGCCAAAATTCAAGACAAGGAAGGG-ATTCCTCCAGACCAGCAAAG-GT-
66 CATCGACAACGTCAAGGCCAAGATCCAAGACAAGG-AGGGAATTCCCCCAGACCAGC--AGCGTC
* * * * * * * ** * * *
119060 TGATTTTCGCTGGGAAGCAATTGGAAGATGGAAGGACCCTT-GCTGATTACAACATTCAGAAGGA
128 TCATCTTCGCCGGGAAGCAACTCGAGGACGG-CCGAACCTTGGCCGATTACAACATCCAGAAGGA
* * *
119124 GTCCACTCTCCACCTTGTCTTGCGTCTCCGTGGTGG
192 GTCCACCCTCCACCTTGTCCTCCGTCTCCGTGGTGG
119160 TTTCTAAGCT
Statistics
Matches: 588, Mismatches: 87, Indels: 16
0.85 0.13 0.02
Matches are distributed among these distances:
227 3 0.01
228 563 0.96
229 20 0.03
230 2 0.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (228 bp):
ATGCAGATCTTCGTCAAAACCTTGACCGGAAAGACCATCACCTTGGAAGTCGAGAGCTCCGACAC
CATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAGGGAATTCCCCCAGACCAGCAGCGTCTCA
TCTTCGCCGGGAAGCAACTCGAGGACGGCCGAACCTTGGCCGATTACAACATCCAGAAGGAGTCC
ACCCTCCACCTTGTCCTCCGTCTCCGTGGTGGC
Found at i:119276 original size:11 final size:11
Alignment explanation
Indices: 119260--119284 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
119250 GTCTCTCTGT
119260 CTTTACCTTTC
1 CTTTACCTTTC
119271 CTTTACCTTTC
1 CTTTACCTTTC
119282 CTT
1 CTT
119285 GTGTTATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (11 bp):
CTTTACCTTTC
Found at i:121407 original size:426 final size:426
Alignment explanation
Indices: 120289--121913 Score: 2714
Period size: 427 Copynumber: 3.8 Consensus size: 426
120279 TTAAAACTGT
* *
120289 GAATGGGGTCACCGGGAGACAGGGAGAGAAGAGTAATTTTTTTTAATAGAAAAAAAGTGAGAAAT
1 GAATGGGGTCACCGGGAGACAAGGAGAGAAGAGTAGTTTTTTTTAATAGAAAAAAAGTGAGAAAT
* * *
120354 TAGAATTGAGCTGAGAAGGGAATGCAGACCTTTTTGGTGAAATTAACGTCAATGTAAGGATTGGC
66 CAGAATTGAGCTGAGAAGGGAATGCAGACCTTTTTGGTGAAATTAACGTCAGTGTAGGGATTGGC
* * *
120419 AGCGGCAGAACATGACTTTATCTCGTATTGTAGAGGAGCGTAAGGGAGCTATAGGATCTCATCGT
131 GGCGGCAGAACATGACTTTTTCTCGTATTGTAGAGGAGCGTAAGGGAGCTCTAGGATCTCATCGT
120484 TCGAGCAGATCGGAGCGATGCAAGTGGCCAACGAAATGACACACTTGCTAGCTTCTTCTTTCGTT
196 TCGAGCAGATCGGAGCGATGCAAGTGGCCAACGAAATGACACACTTGCTAGCTTCTTCTTTCGTT
* * * *
120549 CTTGGTCAAACGTTCCAAGTCATCCGTAGGGCATCTCGATTTTCACTACCCATGTTCAACCATCT
261 CTTGGCCAAACGTTCCATGTCATCCGTAGGGCATCTCGGTTTTCGCTACCCATGTTCAACCATCT
* * *
120614 CGGATTGAACTCAAATTTTTGGGATTACTTTTTTCTTGAGTCTCTTTTTCTTTTCACCATTTGGT
326 CGGATTGAACTCAAATTTCTGGGATTACTTTTTTCCTCAGTCTCTTTTTCTTTTCACCATTTGGT
*
120679 TTGTCTGATTTTGGAAGACCGAGGAGAAACTGTAGA
391 TTGTCTGATTTTGGGAGACCGAGGAGAAACTGTAGA
* * * *
120715 GAAAGGGGTCACCGGGAGACAAGGAGAGAAAAGTAGTTTTCTTTGAAAAGAAAAAAAGTGAGAAA
1 GAATGGGGTCACCGGGAGACAAGGAGAGAAGAGTAGTTTT-TTTTAATAGAAAAAAAGTGAGAAA
* *
120780 TCAGAATTGAGCTGCGAAGGGAATGCAGATCTTTTTGGTGAAATTAACGTCAGTGTAGGGATTGG
65 TCAGAATTGAGCTGAGAAGGGAATGCAGACCTTTTTGGTGAAATTAACGTCAGTGTAGGGATTGG
* *
120845 CGGCGGCGGAACATGACTTTTTCTCGCATTGTAGAGGAGCGTAAGGGAGCTCTAGGATCTCATCG
130 CGGCGGCAGAACATGACTTTTTCTCGTATTGTAGAGGAGCGTAAGGGAGCTCTAGGATCTCATCG
*
120910 TTCGAGCAGATCGGAGCGATGCAAGTGGCCAACGAAATGACACACTTTCTAGCTTCTTCTTTCGT
195 TTCGAGCAGATCGGAGCGATGCAAGTGGCCAACGAAATGACACACTTGCTAGCTTCTTCTTTCGT
*
120975 TCTTGGCCAAACGTTCCTTGTCATCCGTAGGGCATCTCGGTTTTCGCTACCCATGTTCAACCATC
260 TCTTGGCCAAACGTTCCATGTCATCCGTAGGGCATCTCGGTTTTCGCTACCCATGTTCAACCATC
* * *
121040 TCGGATTGAACTCAAATTTCGGGGGTTTCTTTTTTCCTCAGTCTCTTTTTCTTTTCACCATTTGG
325 TCGGATTGAACTCAAATTTCTGGGATTACTTTTTTCCTCAGTCTCTTTTTCTTTTCACCATTTGG
121105 TTTGTCTGATTTTGGGAGACCGAGGAGAAACTGTAGA
390 TTTGTCTGATTTTGGGAGACCGAGGAGAAACTGTAGA
121142 GAATGGGGTCACCGGGAGACAAGGAGAGAAGAGTAGTTTTTTTTAATAGAAAAAAAGTGAGAAAT
1 GAATGGGGTCACCGGGAGACAAGGAGAGAAGAGTAGTTTTTTTTAATAGAAAAAAAGTGAGAAAT
*
121207 CAGAATTGAGCTGAGAAGGGAATGCATACCTTTTTGGTGAAATTAACGTCAGTGTAGGGATTGGC
66 CAGAATTGAGCTGAGAAGGGAATGCAGACCTTTTTGGTGAAATTAACGTCAGTGTAGGGATTGGC
* *
121272 GGTGGCAGAACATGACTTTTTCTCGTATTGTAGAGGAGGGTAAGGGAGCTCTAGGATCTCATCGT
131 GGCGGCAGAACATGACTTTTTCTCGTATTGTAGAGGAGCGTAAGGGAGCTCTAGGATCTCATCGT
* * *
121337 TCGAGCAGATCGGAGCGATGCAAGTGGCCAACGAAGTGAGACACTTGCTAGCTTTTTCTTTCGTT
196 TCGAGCAGATCGGAGCGATGCAAGTGGCCAACGAAATGACACACTTGCTAGCTTCTTCTTTCGTT
*
121402 CTTGGCCAAACGTTCTATGGT-ATCCGTAGGGCATCTCGGTTTTCGCT-CCCTATGTTCAACCAT
261 CTTGGCCAAACGTTCCAT-GTCATCCGTAGGGCATCTCGGTTTTCGCTACCC-ATGTTCAACCAT
* * *
121465 CTCGGATTGAACTCAAATTTTTGGGATTACTTTTTTCTTGAGTCTCTTTTTCTTTTCACCATTTG
324 CTCGGATTGAACTCAAATTTCTGGGATTACTTTTTTCCTCAGTCTCTTTTTCTTTTCACCATTTG
121530 GTTTGTCTGATTTTGGGAGACCGAGGAGAAACTGTAGA
389 GTTTGTCTGATTTTGGGAGACCGAGGAGAAACTGTAGA
121568 GAATGAGGGTCACCGGGAGACAAGGAGAGAAGAGTAGTTTTTTTTTAATAGAAAAAAAAGTGAGA
1 GAATG-GGGTCACCGGGAGACAAGGAGAGAAGAGTAG-TTTTTTTTAATAG-AAAAAAAGTGAGA
* * *
121633 AATCAGAAATAAGCTGAGAAGGGAATGCATACCTTTTTGGTGAAATTAACGTCAGTGTAGGGATT
63 AATCAGAATTGAGCTGAGAAGGGAATGCAGACCTTTTTGGTGAAATTAACGTCAGTGTAGGGATT
*
121698 GGCGGCGGCAGAACATGACTTTTTCTCGTATTGTAGAGGAGGGTAAGGGAGCTCTAGGATCTCAT
128 GGCGGCGGCAGAACATGACTTTTTCTCGTATTGTAGAGGAGCGTAAGGGAGCTCTAGGATCTCAT
* * * * * * *
121763 TGTTCGAACAGATCGGAGCGATGCAAGTGGCCAAAGAAGTGAGACGCTTGCTAGCTTTTTCTTTC
193 CGTTCGAGCAGATCGGAGCGATGCAAGTGGCCAACGAAATGACACACTTGCTAGCTTCTTCTTTC
* *
121828 GTTCTTCGCTAAACGTTCCATGTCATCCGTAGGGCATCTCGGTTTTCGCTACCCATGTTCAACCA
258 GTTCTTGGCCAAACGTTCCATGTCATCCGTAGGGCATCTCGGTTTTCGCTACCCATGTTCAACCA
121893 TCTCGGATTGAACTCAAATTT
323 TCTCGGATTGAACTCAAATTT
121914 TCGTGTTTCT
Statistics
Matches: 1129, Mismatches: 62, Indels: 13
0.94 0.05 0.01
Matches are distributed among these distances:
425 3 0.00
426 399 0.35
427 432 0.38
428 15 0.01
429 277 0.25
430 3 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (426 bp):
GAATGGGGTCACCGGGAGACAAGGAGAGAAGAGTAGTTTTTTTTAATAGAAAAAAAGTGAGAAAT
CAGAATTGAGCTGAGAAGGGAATGCAGACCTTTTTGGTGAAATTAACGTCAGTGTAGGGATTGGC
GGCGGCAGAACATGACTTTTTCTCGTATTGTAGAGGAGCGTAAGGGAGCTCTAGGATCTCATCGT
TCGAGCAGATCGGAGCGATGCAAGTGGCCAACGAAATGACACACTTGCTAGCTTCTTCTTTCGTT
CTTGGCCAAACGTTCCATGTCATCCGTAGGGCATCTCGGTTTTCGCTACCCATGTTCAACCATCT
CGGATTGAACTCAAATTTCTGGGATTACTTTTTTCCTCAGTCTCTTTTTCTTTTCACCATTTGGT
TTGTCTGATTTTGGGAGACCGAGGAGAAACTGTAGA
Done.