Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015659.1 Corchorus capsularis cultivar CVL-1 contig15680, 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: 70275
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:2849 original size:27 final size:27
Alignment explanation
Indices: 2791--2875 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
2781 CCGTTTAGTA
* **
2791 ATATATATAATTA-AATATATATTTTGT
1 ATATATATAATAATAATATATATAAT-T
* *
2818 GTATATAATAATATTAGATATATATAATT
1 ATATAT-ATAATAATA-ATATATATAATT
*
2847 ATATATATAATAATAATATATATTATT
1 ATATATATAATAATAATATATATAATT
2874 AT
1 AT
2876 TAAACGGTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
27 18 0.38
28 13 0.28
29 7 0.15
30 9 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (27 bp):
ATATATATAATAATAATATATATAATT
Found at i:2852 original size:12 final size:12
Alignment explanation
Indices: 2835--2872 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2825 ATAATATTAG
2835 ATATATATAATT
1 ATATATATAATT
*
2847 ATATATATAATA
1 ATATATATAATT
2859 ATA-ATATATATT
1 ATATATATA-ATT
2871 AT
1 AT
2873 TATTAAACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATATAATT
Found at i:3208 original size:16 final size:16
Alignment explanation
Indices: 3179--3222 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3169 TATTTGGTAG
3179 GGAA-GAAA-GAAATA
1 GGAAGGAAAGGAAATA
3193 GGAAGGAAAGGAAATA
1 GGAAGGAAAGGAAATA
*
3209 GCAAGGAAAAGGAA
1 GGAAGG-AAAGGAA
3223 GTCACATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 4 0.15
15 4 0.15
16 11 0.42
17 7 0.27
ACGTcount: A:0.59, C:0.02, G:0.34, T:0.05
Consensus pattern (16 bp):
GGAAGGAAAGGAAATA
Found at i:4296 original size:20 final size:20
Alignment explanation
Indices: 4251--4298 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4241 TTAAACTTAG
* *
4251 CAACCTTTCTCGATCATCTT
1 CAACCTTTCTCCATCATCCT
*
4271 CAACCTTTCTCCATCGTCCT
1 CAACCTTTCTCCATCATCCT
*
4291 CGACCTTT
1 CAACCTTT
4299 TTTTTTCTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.40, G:0.06, T:0.38
Consensus pattern (20 bp):
CAACCTTTCTCCATCATCCT
Found at i:4545 original size:15 final size:15
Alignment explanation
Indices: 4525--4567 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4515 AGTCTCTTCC
4525 TTCCCTCCCATTTCT
1 TTCCCTCCCATTTCT
4540 TTCCCTCCC-TCTTCT
1 TTCCCTCCCAT-TTCT
*
4555 TTCCTTCCCATTT
1 TTCCCTCCCATTT
4568 GCTCTGTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.05, C:0.47, G:0.00, T:0.49
Consensus pattern (15 bp):
TTCCCTCCCATTTCT
Found at i:4909 original size:72 final size:72
Alignment explanation
Indices: 4804--4944 Score: 221
Period size: 72 Copynumber: 2.0 Consensus size: 72
4794 TCGAATATCT
* *
4804 ATATCTATACTATATATAAAATTATGAGCTTTGTAAAACTTTTGAATCAACCATTATA-CTCTTA
1 ATATCTATACTATATATAAAAGTACGAGCTTTGTAAAACTTTTGAATCAACCATTATATC-CTTA
4868 TTTTTTGG
65 TTTTTTGG
* * *
4876 ATATCTATACTATATATAAAAGTACGAGTTTTGTAAAACTTTTGAATCGATCATTATATCCTTAT
1 ATATCTATACTATATATAAAAGTACGAGCTTTGTAAAACTTTTGAATCAACCATTATATCCTTAT
4941 TTTT
66 TTTT
4945 CGAATACATT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 62 0.98
73 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.45
Consensus pattern (72 bp):
ATATCTATACTATATATAAAAGTACGAGCTTTGTAAAACTTTTGAATCAACCATTATATCCTTAT
TTTTTGG
Found at i:5176 original size:31 final size:31
Alignment explanation
Indices: 5141--5206 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
5131 AACTTTATGT
*
5141 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTA-CCTTATTCTTTAAAACATA
*
5172 TTTCCAATTGTACCTTTTTCTTTAAAACATA
1 TTTCCAATTGTACCTTATTCTTTAAAACATA
5203 TTTC
1 TTTC
5207 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCTTATTCTTTAAAACATA
Found at i:6071 original size:22 final size:22
Alignment explanation
Indices: 5931--6071 Score: 104
Period size: 22 Copynumber: 6.3 Consensus size: 22
5921 GTGATATTAA
*
5931 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATCAAAATTTCATAGG
* * *
5953 ATGGTTATTATAATTTCAT-GAG
1 GTGGTTATCAAAATTTCATAG-G
* * *
5975 GAGGTTATCAAAATTCCATAGT
1 GTGGTTATCAAAATTTCATAGG
*
5997 GTGGTTACCAAAATTTCATAGG
1 GTGGTTATCAAAATTTCATAGG
* * * *
6019 ATCAGGTTATTAAAATCTCTTAGG
1 GT--GGTTATCAAAATTTCATAGG
* * **
6043 TTAGTTATTGAAATTTCATAGG
1 GTGGTTATCAAAATTTCATAGG
6065 GTGGTTA
1 GTGGTTA
6072 ATTATCACAA
Statistics
Matches: 89, Mismatches: 26, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
22 71 0.80
23 1 0.01
24 17 0.19
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAAAATTTCATAGG
Found at i:6166 original size:22 final size:23
Alignment explanation
Indices: 6107--6167 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
6097 ATCAAAGAGA
*
6107 TTAT-CAAAATGTCATAGCGAGG
1 TTATACAAAATTTCATAGCGAGG
* * *
6129 TTATATAAGAATTTCATAGTGTGG
1 TTATACAA-AATTTCATAGCGAGG
6153 TTA-ACAAAATTTCAT
1 TTATACAAAATTTCAT
6168 TAAATATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 12 0.38
23 5 0.16
24 15 0.47
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (23 bp):
TTATACAAAATTTCATAGCGAGG
Found at i:6198 original size:22 final size:22
Alignment explanation
Indices: 6173--6238 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
6163 TTCATTAAAT
*
6173 ATTTAATGGGGAGGTTATCAAA
1 ATTTAATAGGGAGGTTATCAAA
* * *
6195 ATTTTATAGTGTGGTTATCAAA
1 ATTTAATAGGGAGGTTATCAAA
* * *
6217 ATTTCATATGAAGGTTAT-AAA
1 ATTTAATAGGGAGGTTATCAAA
6238 A
1 A
6239 GTCTCAATTT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (22 bp):
ATTTAATAGGGAGGTTATCAAA
Found at i:6200 original size:23 final size:22
Alignment explanation
Indices: 6181--6488 Score: 65
Period size: 22 Copynumber: 13.9 Consensus size: 22
6171 ATATTTAATG
6181 GGGAGGTTATCAAAATTTTATA
1 GGGAGGTTATCAAAATTTTATA
* * *
6203 GTGTGGTTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* *
6225 TGAAGGTTAT-AAAAGTCTCAATTTCATA
1 GGGAGGTTATCAAAA---T---TTT-ATA
* *
6253 GGGA-G-TACCAAAATTTGATA
1 GGGAGGTTATCAAAATTTTATA
* * *
6273 -GAAGGTTATC-AAATCTCATA
1 GGGAGGTTATCAAAATTTTATA
* * * * *
6293 GAGTGATTATCGAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
*
6315 GAGATCGGATTATCAAAA-TTTATA
1 GGGA--GG-TTATCAAAATTTTATA
** * *
6339 GAAAGATTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* ** * *
6361 GTGTTGTTATCAAAATTTCAAA
1 GGGAGGTTATCAAAATTTTATA
* * **
6383 GCGAGGTTATCAGAATTACATA
1 GGGAGGTTATCAAAATTTTATA
** * * * *
6405 ATGCGATTATCAGAATTTCATAA
1 GGGAGGTTATCAAAATTTTAT-A
* * *
6428 AGG-GGTCAACAAAATTTTATA
1 GGGAGGTTATCAAAATTTTATA
** *
6449 AAGAGGTTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
** *
6471 AAGAAGTTATC-AAATTTT
1 GGGAGGTTATCAAAATTTT
6489 CAAAATGTGA
Statistics
Matches: 211, Mismatches: 57, Indels: 37
0.69 0.19 0.12
Matches are distributed among these distances:
19 2 0.01
20 12 0.06
21 33 0.16
22 128 0.61
23 3 0.01
24 11 0.05
25 8 0.04
26 2 0.01
27 7 0.03
28 5 0.02
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
GGGAGGTTATCAAAATTTTATA
Found at i:6313 original size:22 final size:23
Alignment explanation
Indices: 6261--6515 Score: 119
Period size: 22 Copynumber: 11.6 Consensus size: 23
6251 TAGGGAGTAC
* *
6261 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
6282 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
6303 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
*
6328 CAAAATTT-ATAGA-AAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
6349 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
6371 CAAAATTTCAAAGCGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
6393 CAGAATTACATA-ATG-CGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * * * *
6415 CAGAATTTCATAAAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* * *
6437 CAAAATTTTATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
6459 CAAAATTTCATAAAGAAG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* *
6481 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
6502 CAAAAATTTCATAG
1 C-AAAATTTCATAG
6516 TGGTATTTCT
Statistics
Matches: 185, Mismatches: 31, Indels: 34
0.74 0.12 0.14
Matches are distributed among these distances:
20 10 0.05
21 27 0.15
22 124 0.67
23 6 0.03
24 5 0.03
25 13 0.07
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:14190 original size:2 final size:2
Alignment explanation
Indices: 14183--14226 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
14173 GTTTGTTATG
* *
14183 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA 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 TA
14225 TA
1 TA
14227 CACATGAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:14227 original size:14 final size:14
Alignment explanation
Indices: 14188--14231 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
14178 TTATGTATAT
* *
14188 ATATATATATATAT
1 ATATATATATACAC
14202 ATATATATATACAC
1 ATATATATATACAC
14216 ATATATATATACAC
1 ATATATATATACAC
14230 AT
1 AT
14232 GAAATAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATATACAC
Found at i:18839 original size:1 final size:1
Alignment explanation
Indices: 18835--18862 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
18825 TATTCGGATG
18835 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
18863 GCGTAAATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:19975 original size:4 final size:4
Alignment explanation
Indices: 19966--19999 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
19956 CGCTGCTCTT
19966 TTTC TTTC TTTC TTTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC T
20000 CCCTCATCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:19981 original size:13 final size:13
Alignment explanation
Indices: 19965--19999 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
19955 TCGCTGCTCT
19965 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
19978 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
19991 -TTTCTTTCT
1 TTTTCTTTCT
20000 CCCTCATCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTTCTTTC
Found at i:21117 original size:32 final size:33
Alignment explanation
Indices: 21062--21124 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
21052 GTTTGAGTTG
*
21062 ATTTTGCTGGTATTTTTTTTGTTAAATTTTGCTA
1 ATTTTCCTGGTA-TTTTTTTGTTAAATTTTGCTA
*
21096 ATTTTCCTGGTA-TTTTTTGTTACATTTTG
1 ATTTTCCTGGTATTTTTTTGTTAAATTTTG
21125 TTGAGTGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 16 0.59
34 11 0.41
ACGTcount: A:0.16, C:0.08, G:0.14, T:0.62
Consensus pattern (33 bp):
ATTTTCCTGGTATTTTTTTGTTAAATTTTGCTA
Found at i:21699 original size:17 final size:17
Alignment explanation
Indices: 21677--21726 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
21667 AAAATTTGAG
21677 AAACATTACTAGTCATA
1 AAACATTACTAGTCATA
* *
21694 AAACATGATTAGTTC-TA
1 AAACATTACTAG-TCATA
21711 AAACATTACTAGTCAT
1 AAACATTACTAGTCAT
21727 GTGGTATGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 23 0.85
18 2 0.07
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (17 bp):
AAACATTACTAGTCATA
Found at i:22234 original size:31 final size:31
Alignment explanation
Indices: 22196--22299 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 31
22186 TTAATTTGGC
22196 CAAATAAGGGTCTAACCTTATCGAAAATGCT
1 CAAATAAGGGTCTAACCTTATCGAAAATGCT
* * * **
22227 CAAATAAGGGTCTGATCTT-T-TAATTTGGC-
1 CAAATAAGGGTCTAACCTTATCGAAAAT-GCT
** *
22256 CAAATAAGGACCTAACGTTATCGAAAATGCT
1 CAAATAAGGGTCTAACCTTATCGAAAATGCT
22287 CAAATAAGGGTCT
1 CAAATAAGGGTCT
22300 GGCGTCAGTT
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
29 17 0.31
30 6 0.11
31 31 0.57
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (31 bp):
CAAATAAGGGTCTAACCTTATCGAAAATGCT
Found at i:22297 original size:60 final size:60
Alignment explanation
Indices: 22136--22300 Score: 251
Period size: 60 Copynumber: 2.8 Consensus size: 60
22126 GCTAATTGCT
* * * *
22136 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCCCGGTCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
* *
22196 CAAATAAGGGTCTAACCTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
*
22256 CAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAAGGGTCTG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTG
22301 GCGTCAGTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
Found at i:22377 original size:31 final size:30
Alignment explanation
Indices: 22339--22505 Score: 146
Period size: 31 Copynumber: 5.5 Consensus size: 30
22329 TTCGACGCCG
22339 GGCCCTTATTTGAGCATTTTGGCAAACGTTA
1 GGCCCTTATTTGAGCATTTT-GCAAACGTTA
** * * **
22370 GGCCCTTATTTG-GCCAAATT-AAAAGGTCG
1 GGCCCTTATTTGAG-CATTTTGCAAACGTTA
22399 GGCCCTTATTTGAGCATTTTGACAAACGTTA
1 GGCCCTTATTTGAGCATTTTG-CAAACGTTA
** * *
22430 GGCCCTTATTTG-GCCAAATT--AAAAGATCA
1 GGCCCTTATTTGAG-CATTTTGCAAACG-TTA
*
22459 GGCCCTTATTTGAGCATTTTGACAAACATTA
1 GGCCCTTATTTGAGCATTTTG-CAAACGTTA
22490 GGCCCTTATTTGAGCA
1 GGCCCTTATTTGAGCA
22506 ATTAGCCAAA
Statistics
Matches: 105, Mismatches: 21, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
28 4 0.04
29 39 0.37
30 4 0.04
31 55 0.52
32 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (30 bp):
GGCCCTTATTTGAGCATTTTGCAAACGTTA
Found at i:22410 original size:29 final size:29
Alignment explanation
Indices: 22369--22470 Score: 116
Period size: 29 Copynumber: 3.4 Consensus size: 29
22359 GGCAAACGTT
22369 AGGCCCTTATTTGGCCAAATTAAAAGGTC
1 AGGCCCTTATTTGGCCAAATTAAAAGGTC
* ** * *
22398 GGGCCCTTATTTGAG-CATTTTGACAAACGTT
1 AGGCCCTTATTTG-GCCAAATT-A-AAAGGTC
*
22429 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGGTC
22458 AGGCCCTTATTTG
1 AGGCCCTTATTTG
22471 AGCATTTTGA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
29 33 0.57
30 4 0.07
31 21 0.36
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGGTC
Found at i:22430 original size:60 final size:60
Alignment explanation
Indices: 22337--22501 Score: 294
Period size: 60 Copynumber: 2.8 Consensus size: 60
22327 TTTTCGACGC
* *
22337 CGGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGGT
1 CGGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
22397 CGGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CGGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* *
22457 CAGGCCCTTATTTGAGCATTTTGACAAACATTAGGCCCTTATTTG
1 CGGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
22502 AGCAATTAGC
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 101 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (60 bp):
CGGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:30011 original size:3 final size:3
Alignment explanation
Indices: 30003--30032 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
29993 CCAAGAGCTT
30003 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30033 AAAGCCAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:32407 original size:1 final size:1
Alignment explanation
Indices: 32362--32392 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
32352 CCCCTTTTAG
32362 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32393 GGTACAACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:44256 original size:2 final size:2
Alignment explanation
Indices: 44249--44275 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44239 GGTAAATTAC
44249 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
44276 CCCTGTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55062 original size:66 final size:66
Alignment explanation
Indices: 54956--55087 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
54946 GAAGATCTTT
54956 TAAAGTGTTTAAATTCTTGTAATTTACTGGACATCCCTGGATCTGGACAAAACTTTACATGGACT
1 TAAAGTGTTTAAATTCTTGTAATTTACTGGACATCCCTGGATCTGGACAAAACTTTACATGGACT
55021 A
66 A
55022 TAAAGTGTTTAAATTCTTGTAATTTACTGGACATCCCTGGATCTGGACAAAACTTTACATGGACT
1 TAAAGTGTTTAAATTCTTGTAATTTACTGGACATCCCTGGATCTGGACAAAACTTTACATGGACT
55087 A
66 A
55088 ACAATCGAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (66 bp):
TAAAGTGTTTAAATTCTTGTAATTTACTGGACATCCCTGGATCTGGACAAAACTTTACATGGACT
A
Done.