Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013756.1 Corchorus olitorius cultivar O-4 contig13789, 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: 34453
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:243 original size:18 final size:18
Alignment explanation
Indices: 220--259 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
210 AAATTAAATA
**
220 TTTTTATTTTAATATATT
1 TTTTTATTGAAATATATT
*
238 TTTTTATTGAAATTTATT
1 TTTTTATTGAAATATATT
256 TTTT
1 TTTT
260 AATAATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTATTGAAATATATT
Found at i:1630 original size:2 final size:2
Alignment explanation
Indices: 1623--1669 Score: 67
Period size: 2 Copynumber: 22.5 Consensus size: 2
1613 TACTTTTAGC
*
1623 AT AT AT AT AT AT AT AGT AT AG AT AGT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT
1667 AT A
1 AT A
1670 ATCTTTTCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 37 0.90
3 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2038 original size:25 final size:25
Alignment explanation
Indices: 2004--2054 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1994 TTATAGTAGC
2004 AGGTTAAAACATCTAGTAAATCAGA
1 AGGTTAAAACATCTAGTAAATCAGA
2029 AGGTTAAAACATCTAGTAAATCAGA
1 AGGTTAAAACATCTAGTAAATCAGA
2054 A
1 A
2055 AGTAGAGCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.24
Consensus pattern (25 bp):
AGGTTAAAACATCTAGTAAATCAGA
Found at i:2267 original size:16 final size:16
Alignment explanation
Indices: 2246--2279 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2236 TAAGCCCAGT
2246 TTAAGCAGGTCTCGGG
1 TTAAGCAGGTCTCGGG
2262 TTAAGCAGGTCTCGGG
1 TTAAGCAGGTCTCGGG
2278 TT
1 TT
2280 TGAGACCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (16 bp):
TTAAGCAGGTCTCGGG
Found at i:7049 original size:190 final size:190
Alignment explanation
Indices: 6726--7100 Score: 741
Period size: 190 Copynumber: 2.0 Consensus size: 190
6716 CTATATATAA
6726 TTTAGGGTGTTTGTTTTCTTTTTTGGTGGTAATAAAAGGCTAGTTGTTGGATATGCAGGCAACTT
1 TTTAGGGTGTTTGTTTTCTTTTTTGGTGGTAATAAAAGGCTAGTTGTTGGATATGCAGGCAACTT
6791 TTGAGGAGGGAATGGATGGAGAGGCCATAGCCAAAAACCACAGCACAACAAAGGAGGCAATAGAA
66 TTGAGGAGGGAATGGATGGAGAGGCCATAGCCAAAAACCACAGCACAACAAAGGAGGCAATAGAA
6856 GTGGGAGATTCAGCAGCTGCATATCGCATAATTCTTGCCCATTTCAGCCAAAGGTGTTTG
131 GTGGGAGATTCAGCAGCTGCATATCGCATAATTCTTGCCCATTTCAGCCAAAGGTGTTTG
*
6916 TTTAGGGTGTTTGTTTTCTTTTTTGGTTGTAATAAAAGGCTAGTTGTTGGATATGCAGGCAACTT
1 TTTAGGGTGTTTGTTTTCTTTTTTGGTGGTAATAAAAGGCTAGTTGTTGGATATGCAGGCAACTT
6981 TTGAGGAGGGAATGGATGGAGAGGCCATAGCCAAAAACCACAGCACAACAAAGGAGGCAATAGAA
66 TTGAGGAGGGAATGGATGGAGAGGCCATAGCCAAAAACCACAGCACAACAAAGGAGGCAATAGAA
7046 GTGGGAGATTCAGCAGCTGCATATCGCATAATTCTTGCCCATTTCAGCCAAAGGT
131 GTGGGAGATTCAGCAGCTGCATATCGCATAATTCTTGCCCATTTCAGCCAAAGGT
7101 ACCCAAAGAT
Statistics
Matches: 184, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
190 184 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (190 bp):
TTTAGGGTGTTTGTTTTCTTTTTTGGTGGTAATAAAAGGCTAGTTGTTGGATATGCAGGCAACTT
TTGAGGAGGGAATGGATGGAGAGGCCATAGCCAAAAACCACAGCACAACAAAGGAGGCAATAGAA
GTGGGAGATTCAGCAGCTGCATATCGCATAATTCTTGCCCATTTCAGCCAAAGGTGTTTG
Found at i:9289 original size:183 final size:182
Alignment explanation
Indices: 8982--9352 Score: 652
Period size: 183 Copynumber: 2.0 Consensus size: 182
8972 AGTCCCAATC
*
8982 AGTTTTCAAAATATTATTGATGACTTATGGGTTTGCCAATGAGGACGATGACCAATTGTTTTAGG
1 AGTTTTCAAAATATTATTGATGACTTATGGGTTTGCCAATGAGGACGATGACCAATTGCTTTAGG
*
9047 TCATGTATTTTGAAAGATTTGGATTTAAGTAAGGATCCAACAAAAAAACCGGTCTAAAGAATTAG
66 TCATGTATTTTGAAAGATTTGGATTTAAGTAAGAATCCAACAAAAAAACCGGTCTAAAGAATTAG
*
9112 CGTCATTAATCTAAGAACAAATTGATAGGGGTATTTCGGTTATTCCATGCTT
131 CATCATTAATCTAAGAACAAATTGATAGGGGTATTTCGGTTATTCCATGCTT
* * *
9164 AGTTTTCAACATATTATTGGTGACTTATGGGTTTGCCAAATGAGGATGATGACCAATTGCTTTAG
1 AGTTTTCAAAATATTATTGATGACTTATGGGTTTGCC-AATGAGGACGATGACCAATTGCTTTAG
*
9229 GTCATGTGTTTTGAAAGATTTGGATTTAAGTAAGAATCCAACAAAAAAACCGGTCTAAAGAATTA
65 GTCATGTATTTTGAAAGATTTGGATTTAAGTAAGAATCCAACAAAAAAACCGGTCTAAAGAATTA
*
9294 GCATCGTTAATCTAAGAACAAATTGATAGGGGTATTTCGGTTATTCCATGCTT
130 GCATCATTAATCTAAGAACAAATTGATAGGGGTATTTCGGTTATTCCATGCTT
*
9347 AATTTT
1 AGTTTT
9353 TTTTATTTGA
Statistics
Matches: 179, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
182 35 0.20
183 144 0.80
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (182 bp):
AGTTTTCAAAATATTATTGATGACTTATGGGTTTGCCAATGAGGACGATGACCAATTGCTTTAGG
TCATGTATTTTGAAAGATTTGGATTTAAGTAAGAATCCAACAAAAAAACCGGTCTAAAGAATTAG
CATCATTAATCTAAGAACAAATTGATAGGGGTATTTCGGTTATTCCATGCTT
Found at i:9801 original size:178 final size:177
Alignment explanation
Indices: 9433--9766 Score: 449
Period size: 178 Copynumber: 1.9 Consensus size: 177
9423 TTATAAGCTC
* * * *
9433 AAATTATGTAATATTAAGTAGACCGTCTATTTTCCGTTAACCGAAACAACTAATTGTTTGGAAGC
1 AAATTATATAATATTAAGTAGACCGTCTA-TGTCCGTTAACCGAAACAACAAATTGTTCGGAAGC
* *
9498 ATTTTTTATACCTTGAATATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAA
65 ATTTTTGATACCTTGAATATTAAATTTAGTTTTCGAGTCCTTAATGAAAGTTGTAGATCATGGAA
* * * *
9563 CAACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTAGAGCA
130 CAACCTTTCAAGAGACACTTAAATCATCTCAATCAGAAACCAAGAGCA
* ** *
9611 AAAGTTATATAATATTAAGTGGATTGTCTA-GTCCTGTTAACCGAAATAACAAATT-TTCCGGAA
1 AAA-TTATATAATATTAAGTAGACCGTCTATGTCC-GTTAACCGAAACAACAAATTGTT-CGGAA
9674 GCATTTTTGATA-CTTGAAATATTAAATTTAGTTTTCGAGTCCTTAATGAAAGTTGTAGATCATG
63 GCATTTTTGATACCTTG-AATATTAAATTTAGTTTTCGAGTCCTTAATGAAAGTTGTAGATCATG
* * *
9738 GAACAATCTTTTAATAGACACTTAAATCA
127 GAACAACCTTTCAAGAGACACTTAAATCA
9767 CTTTTATTGG
Statistics
Matches: 138, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
177 9 0.07
178 107 0.78
179 22 0.16
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCGTCTATGTCCGTTAACCGAAACAACAAATTGTTCGGAAGCA
TTTTTGATACCTTGAATATTAAATTTAGTTTTCGAGTCCTTAATGAAAGTTGTAGATCATGGAAC
AACCTTTCAAGAGACACTTAAATCATCTCAATCAGAAACCAAGAGCA
Found at i:14949 original size:16 final size:16
Alignment explanation
Indices: 14928--14978 Score: 102
Period size: 16 Copynumber: 3.2 Consensus size: 16
14918 AGAAATTGTA
14928 TGCTAACCTTAAGAAG
1 TGCTAACCTTAAGAAG
14944 TGCTAACCTTAAGAAG
1 TGCTAACCTTAAGAAG
14960 TGCTAACCTTAAGAAG
1 TGCTAACCTTAAGAAG
14976 TGC
1 TGC
14979 ACCATTTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (16 bp):
TGCTAACCTTAAGAAG
Found at i:18267 original size:16 final size:16
Alignment explanation
Indices: 18238--18308 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
18228 GCCTTTTGTA
18238 GGTGAGTA-TGTACTG
1 GGTGAGTATTGTACTG
18253 GGTGAGTATTGTACTG
1 GGTGAGTATTGTACTG
*
18269 GGTGAGTGTTGTACTG
1 GGTGAGTATTGTACTG
* *
18285 GGTGAGTGTTGTATTG
1 GGTGAGTATTGTACTG
18301 GGTGAGTA
1 GGTGAGTA
18309 GGGTAGGAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 8 0.15
16 44 0.85
ACGTcount: A:0.17, C:0.04, G:0.42, T:0.37
Consensus pattern (16 bp):
GGTGAGTATTGTACTG
Found at i:18771 original size:47 final size:46
Alignment explanation
Indices: 18692--18853 Score: 186
Period size: 47 Copynumber: 3.6 Consensus size: 46
18682 TTGGCTTCTT
* * * * *
18692 AGGGAGCGCTCCGCGCAAGAGTTGGGTTAGCCTCCACGCGAGAGCA
1 AGGGAGTGCTCCGCGCAAGAGCTGGGTGAGCCTCCGCGCAAGAGCA
* * *
18738 GGGGAGTGCTCCGTGCAAAGAGCTGGGTGAGCCTCTGCGCAAGAGCA
1 AGGGAGTGCTCCGCGC-AAGAGCTGGGTGAGCCTCCGCGCAAGAGCA
* * *
18785 AGGGAGTTCTCCGCACAAGAGCTGAGTGAG---CCGCGCAAGAGCA
1 AGGGAGTGCTCCGCGCAAGAGCTGGGTGAGCCTCCGCGCAAGAGCA
*
18828 AGAGAGTGCTCCGCGCAAGAGCTGGG
1 AGGGAGTGCTCCGCGCAAGAGCTGGG
18854 GACTAATATA
Statistics
Matches: 97, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
43 34 0.35
46 26 0.27
47 37 0.38
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.13
Consensus pattern (46 bp):
AGGGAGTGCTCCGCGCAAGAGCTGGGTGAGCCTCCGCGCAAGAGCA
Found at i:18841 original size:23 final size:23
Alignment explanation
Indices: 18774--18849 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
18764 GTGAGCCTCT
* *
18774 GCGCAAGAGCAAGGGAGTTCTCC
1 GCGCAAGAGCAAGAGAGTGCTCC
* * **
18797 GCACAAGAGC---TGAGTGAGCC
1 GCGCAAGAGCAAGAGAGTGCTCC
18817 GCGCAAGAGCAAGAGAGTGCTCC
1 GCGCAAGAGCAAGAGAGTGCTCC
18840 GCGCAAGAGC
1 GCGCAAGAGC
18850 TGGGGACTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
20 15 0.37
23 26 0.63
ACGTcount: A:0.29, C:0.26, G:0.36, T:0.09
Consensus pattern (23 bp):
GCGCAAGAGCAAGAGAGTGCTCC
Found at i:19728 original size:40 final size:40
Alignment explanation
Indices: 19683--20406 Score: 416
Period size: 40 Copynumber: 16.7 Consensus size: 40
19673 AGGGAATAGG
* *
19683 AACAACACCTTCCGATGAGGAAGGACAGACTGGAAATTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATTTA
* * *
19723 GACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTGGACTTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GG--AA----A-TTTA
*
19771 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATTTA
* * *
19811 AACAACACCTTCTGGTGGGGAAGGGCAAACTGGGAAAAGTGGGCTTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GG-AAA------TTTA
* * *
19859 AACAACACCTTCTGATGAGGAAGGACAAACTGGGAATTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATTTA
* *
19899 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTACACTTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GG---A--A-A-TTTA
* * * *
19947 TACAACACATTCCGATGAGTAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATTTA
* * *
19987 AACAACACCTTCCGGTGGGGAAGGGTAAACTGGGAAAAGTAGTCTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GG--AA--A-T-TTA
* * *
20034 GACAACACCTTCCGATGAGAAAGAGCAAACT-GAGAATTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGA-AATTTA
* **
20074 AACAACACCTTCCGGTGAGGAAAAGCAAACTGGGAAAAGTGGGCTTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GG-AAA------TTTA
*
20122 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATTTA
* * * *
20162 AGCAACACCTTTCGGTGGGGAAGGGCAAACTGGGAAAAGTAGACTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GG-AAA-T----TTA
* * * *
20209 GACAACACTTTCCGATGGGGAAGGGCAAACTAGGAAA-GTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GGAAATTTA
* * * * * *
20249 AACAACACCTTCC-AGTGGGGAAGAGCATATTGGGTTAATTGGACAAA
1 AACAACACCTTCCGA-TGAGGAAGGGCAAACT-GG-AAATT-----TA
* * *
20296 GGCAACAACACCTCCCGATGAGGAAGGGCAAATTGG-AATACT-
1 ---AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAAT-TTA
* *
20338 AACAACACCTTCCGATGAGGAAGGGCAAACTGAAAATGCT-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAAT-TTA
* *
20378 GACAACACCTTCCGATGAGGAAAGGCAAA
1 AACAACACCTTCCGATGAGGAAGGGCAAA
20407 ATAGGAAGTA
Statistics
Matches: 540, Mismatches: 82, Indels: 124
0.72 0.11 0.17
Matches are distributed among these distances:
39 31 0.06
40 239 0.44
41 15 0.03
42 9 0.02
43 6 0.01
44 1 0.00
45 3 0.01
46 9 0.02
47 73 0.14
48 126 0.23
49 2 0.00
50 25 0.05
51 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (40 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATTTA
Found at i:19832 original size:88 final size:87
Alignment explanation
Indices: 19683--20406 Score: 872
Period size: 88 Copynumber: 8.3 Consensus size: 87
19673 AGGGAATAGG
* * * *
19683 AACAACACCTTCCGATGAGGAAGGACAGACTGGAAATTTAGACAACACCTTCCGGTGGGGAAGGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
19748 CAAACTGGGAAAAGTGGACTTTA
66 CAAACTGGGAAAAGTGGAC-TTA
*
19771 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCTGGTGGGGAAGGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
*
19836 CAAACTGGGAAAAGTGGGCTTTA
66 CAAACTGGGAAAAGTGGAC-TTA
* *
19859 AACAACACCTTCTGATGAGGAAGGACAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
**
19924 CAAACTGGGAAAAGTACACTTTA
66 CAAACTGGGAAAAGTGGAC-TTA
* * *
19947 TACAACACATTCCGATGAGTAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
* * *
20012 TAAACTGGGAAAAGTAGTCTTA
66 CAAACTGGGAAAAGTGGACTTA
* * * * * **
20034 GACAACACCTTCCGATGAGAAAGAGCAAACTGAGAATTTAAACAACACCTTCCGGTGAGGAAAAG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
*
20099 CAAACTGGGAAAAGTGGGCTTTA
66 CAAACTGGGAAAAGTGGAC-TTA
* *
20122 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAGCAACACCTTTCGGTGGGGAAGGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
*
20187 CAAACTGGGAAAAGTAGACTTA
66 CAAACTGGGAAAAGTGGACTTA
* * * * ** * *
20209 GACAACACTTTCCGATGGGGAAGGGCAAACTAGGAAAGTAAACAACACCTTCCAGTGGGGAAGAG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
* * ** * **
20274 CATATTGGGTTAATTGGACAAA
66 CAAACTGGGAAAAGTGGACTTA
* * * * *
20296 GGCAACAACACCTCCCGATGAGGAAGGGCAAA-TTGGAATACT-AACAACACCTTCCGATGAGGA
1 ---AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-TTAAACAACACCTTCCGGTGGGGA
20359 AGGGCAAACT--GAAAA-T-G-C-T-
62 AGGGCAAACTGGGAAAAGTGGACTTA
* *
20378 GACAACACCTTCCGATGAGGAAAGGCAAA
1 AACAACACCTTCCGATGAGGAAGGGCAAA
20407 ATAGGAAGTA
Statistics
Matches: 552, Mismatches: 79, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
79 26 0.05
84 1 0.00
85 1 0.00
86 1 0.00
87 151 0.27
88 316 0.57
89 30 0.05
90 26 0.05
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (87 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
CAAACTGGGAAAAGTGGACTTA
Found at i:20137 original size:175 final size:173
Alignment explanation
Indices: 19684--20406 Score: 892
Period size: 175 Copynumber: 4.2 Consensus size: 173
19674 GGGAATAGGA
* * *
19684 ACAACACCTTCCGATGAGGAAGGACAGACTG-GAAATTTAGACAACACCTTCCGGTGGGGAAGGG
1 ACAACACCTTCCGATGAGGAAGG-CAAACTGAG-AATTTAAACAACACCTTCCGGTGGGGAAGAG
19748 CAAACTGGGAAAAGTGGACTTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAA
64 CAAACTGGGAAAAGTGGACTTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAA
* * *
19813 CAACACCTTCTGGTGGGGAAGGGCAAACTGGGAAAAGTGGGCTTTAA
129 CAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGT-AGC-TTAG
* * *
19860 ACAACACCTTCTGATGAGGAAGGACAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGC
1 ACAACACCTTCCGATGAGGAAGG-CAAACTGAGAATTTAAACAACACCTTCCGGTGGGGAAGAGC
** * * *
19925 AAACTGGGAAAAGTACACTTTATACAACACATTCCGATGAGTAAGGGCAAACTGGGAATTTAAAC
65 AAACTGGGAAAAGTGGACTTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAAC
*
19990 AACACCTTCCGGTGGGGAAGGGTAAACTGGGAAAAGTAGTCTTAG
130 AACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTAG-CTTAG
* * *
20035 ACAACACCTTCCGATGAGAAAGAGCAAACTGAGAATTTAAACAACACCTTCCGGTGAGGAAAAGC
1 ACAACACCTTCCGATGAGGAAG-GCAAACTGAGAATTTAAACAACACCTTCCGGTGGGGAAGAGC
* *
20100 AAACTGGGAAAAGTGGGCTTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAGC
65 AAACTGGGAAAAGTGGACTTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAAC
*
20165 AACACCTTTCGGTGGGGAAGGGCAAACTGGGAAAAGTAGACTTAG
130 AACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTAG-CTTAG
* * ** *
20210 ACAACACTTTCCGATGGGGAAGGGCAAACT-AGGAAAGTAAACAACACCTTCCAGTGGGGAAGAG
1 ACAACACCTTCCGATGAGGAA-GGCAAACTGA-GAATTTAAACAACACCTTCCGGTGGGGAAGAG
* * ** * ** * * *
20274 CATATTGGGTTAATTGGAC-AAAGGCAACAACACCTCCCGATGAGGAAGGGCAAA-TTGGAATAC
64 CAAACTGGGAAAAGTGGACTTTA---AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-T
* *
20337 T-AACAACACCTTCCGATGAGGAAGGGCAAACT--GAAAA-T-GC-T-G
125 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTAGCTTAG
20379 ACAACACCTTCCGATGAGGAAAGGCAAA
1 ACAACACCTTCCGATGAGG-AAGGCAAA
20407 ATAGGAAGTA
Statistics
Matches: 484, Mismatches: 53, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
169 24 0.05
170 3 0.01
171 1 0.00
172 1 0.00
173 1 0.00
174 7 0.01
175 226 0.47
176 191 0.39
177 30 0.06
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (173 bp):
ACAACACCTTCCGATGAGGAAGGCAAACTGAGAATTTAAACAACACCTTCCGGTGGGGAAGAGCA
AACTGGGAAAAGTGGACTTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACA
ACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTAGCTTAG
Found at i:27338 original size:28 final size:23
Alignment explanation
Indices: 27279--27325 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
27269 GTCCTCTAAT
27279 ACAAAGAAAAGAAGAAGCAAGGC
1 ACAAAGAAAAGAAGAAGCAAGGC
27302 ACAAAGAAAAGAAGAAGCAAGGC
1 ACAAAGAAAAGAAGAAGCAAGGC
27325 A
1 A
27326 GGGAATATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.62, C:0.13, G:0.26, T:0.00
Consensus pattern (23 bp):
ACAAAGAAAAGAAGAAGCAAGGC
Found at i:28293 original size:25 final size:25
Alignment explanation
Indices: 28257--28444 Score: 164
Period size: 25 Copynumber: 7.5 Consensus size: 25
28247 TAGGTTAGGG
* *
28257 GAGTCTTCCCTAGCGCACAGCAGGT
1 GAGTCTCCCCTAGCGCATAGCAGGT
* * *
28282 GAGTCTCACCTAGCGCGTAACAAGG-
1 GAGTCTCCCCTAGCGCATAGC-AGGT
* * * *
28307 GAGTCTCCCTTAGTGCACAGTAGGT
1 GAGTCTCCCCTAGCGCATAGCAGGT
** * *
28332 GAACCTCACCTAGCGCATAGCAGGG
1 GAGTCTCCCCTAGCGCATAGCAGGT
* * * *
28357 GAGTTTCCCCTAGTGCGTTGCAAGG-
1 GAGTCTCCCCTAGCGCATAGC-AGGT
*
28382 GAGTCTCCCCTAGCGCACAGCAGGT
1 GAGTCTCCCCTAGCGCATAGCAGGT
* *
28407 GAGTCTCTCCTAGCGCATAGCAGGG
1 GAGTCTCCCCTAGCGCATAGCAGGT
28432 GAGTCTCCCCTAG
1 GAGTCTCCCCTAG
28445 TATGCAGCAG
Statistics
Matches: 123, Mismatches: 36, Indels: 8
0.74 0.22 0.05
Matches are distributed among these distances:
24 6 0.05
25 111 0.90
26 6 0.05
ACGTcount: A:0.21, C:0.30, G:0.29, T:0.20
Consensus pattern (25 bp):
GAGTCTCCCCTAGCGCATAGCAGGT
Found at i:28388 original size:75 final size:75
Alignment explanation
Indices: 28265--28445 Score: 245
Period size: 75 Copynumber: 2.4 Consensus size: 75
28255 GGGAGTCTTC
* * * * * * *
28265 CCTAGCGCACAGCAGGTGAGTCTCACCTAGCGCGTAACAAGGGAGTCTCCCTTAGTGCACAGTAG
1 CCTAGCGCATAGCAGGGGAGTCTCCCCTAGTGCGTAACAAGGGAGTCTCCCCTAGCGCACAGCAG
28330 GTGAACCTCA
66 GTGAACCTCA
* **
28340 CCTAGCGCATAGCAGGGGAGTTTCCCCTAGTGCGTTGCAAGGGAGTCTCCCCTAGCGCACAGCAG
1 CCTAGCGCATAGCAGGGGAGTCTCCCCTAGTGCGTAACAAGGGAGTCTCCCCTAGCGCACAGCAG
** *
28405 GTGAGTCTCT
66 GTGAACCTCA
28415 CCTAGCGCATAGCAGGGGAGTCTCCCCTAGT
1 CCTAGCGCATAGCAGGGGAGTCTCCCCTAGT
28446 ATGCAGCAGG
Statistics
Matches: 92, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 92 1.00
ACGTcount: A:0.22, C:0.30, G:0.29, T:0.20
Consensus pattern (75 bp):
CCTAGCGCATAGCAGGGGAGTCTCCCCTAGTGCGTAACAAGGGAGTCTCCCCTAGCGCACAGCAG
GTGAACCTCA
Done.