Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013987.1 Corchorus capsularis cultivar CVL-1 contig14008, 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: 132834
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1783 original size:16 final size:18
Alignment explanation
Indices: 1744--1784 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
1734 TCTCCCAAAG
1744 ATCTCAAGTACAAGTTTT
1 ATCTCAAGTACAAGTTTT
*
1762 AGCTCAA-TACAA-TTTT
1 ATCTCAAGTACAAGTTTT
*
1778 CTCTCAA
1 ATCTCAA
1785 AAATAGTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 9 0.45
17 5 0.25
18 6 0.30
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (18 bp):
ATCTCAAGTACAAGTTTT
Found at i:5988 original size:87 final size:84
Alignment explanation
Indices: 5802--6033 Score: 311
Period size: 87 Copynumber: 2.7 Consensus size: 84
5792 ATTAAATCTA
* * * * * * **
5802 AAAATATCTCCTAAACCTTCCACAATTTGACAAGATTCATAAAATATTCTCTTTACAAATTAAAT
1 AAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTA-TTATTAAAT
*
5867 TCTTATAATTTTTATTTCTT
65 CCTTATAATTTTTATTTCTT
* *
5887 AAAATATCTTCTAAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTATTATTCAAT
1 AAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGA-AAATATTCTCATTATTATTAAAT
*
5952 CCTTATTATTTATTTATTTCTT
65 CCTTA-TAATT-TTTATTTCTT
*
5974 AAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTTATTATTATT
1 AAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATT
6034 TTAATAATTT
Statistics
Matches: 130, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
85 45 0.35
86 35 0.27
87 50 0.38
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (84 bp):
AAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTAAATC
CTTATAATTTTTATTTCTT
Found at i:11344 original size:20 final size:22
Alignment explanation
Indices: 11319--11374 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
11309 TCTCTCCTTG
*
11319 TTTCTCATCTCCTT-CT-TCTA
1 TTTCTCATCACCTTCCTCTCTA
11339 TTTCTCAT-ACCTTCCTCTCTA
1 TTTCTCATCACCTTCCTCTCTA
*
11360 TTCTCTCATCCCCTT
1 TT-TCTCATCACCTT
11375 TCTATTATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.13
20 10 0.33
21 6 0.20
22 6 0.20
23 4 0.13
ACGTcount: A:0.11, C:0.39, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTCTCATCACCTTCCTCTCTA
Found at i:11380 original size:19 final size:20
Alignment explanation
Indices: 11334--11380 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
11324 CATCTCCTTC
11334 TTCTATTTCTCATACCTTCCT
1 TTCTATTTCTCATACC-TCCT
*
11355 CTCTATTCTCTCAT-CC-CCT
1 TTCTATT-TCTCATACCTCCT
11374 TTCTATT
1 TTCTATT
11381 ATTCTATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 9 0.39
21 8 0.35
22 6 0.26
ACGTcount: A:0.13, C:0.36, G:0.00, T:0.51
Consensus pattern (20 bp):
TTCTATTTCTCATACCTCCT
Found at i:15368 original size:21 final size:20
Alignment explanation
Indices: 15331--15369 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
15321 AATTATACTT
*
15331 TATTAATTTCTAGAAAATTA
1 TATTAATTTCTAAAAAATTA
*
15351 TATTATATTTTTAAAAAAT
1 TATTA-ATTTCTAAAAAAT
15370 ACATAAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATTAATTTCTAAAAAATTA
Found at i:21283 original size:17 final size:16
Alignment explanation
Indices: 21261--21299 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
21251 GTCTAAGACA
21261 TTTTGTCATTAGTGGGG
1 TTTTGTCATTAGT-GGG
**
21278 TTTTGTTGTTAGTGGG
1 TTTTGTCATTAGTGGG
21294 TTTTGT
1 TTTTGT
21300 TAGTAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.08, C:0.03, G:0.33, T:0.56
Consensus pattern (16 bp):
TTTTGTCATTAGTGGG
Found at i:21296 original size:16 final size:17
Alignment explanation
Indices: 21269--21300 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
21259 CATTTTGTCA
21269 TTAGTGGGGTTTTGTTG
1 TTAGTGGGGTTTTGTTG
21286 TTAGT-GGGTTTTGTT
1 TTAGTGGGGTTTTGTT
21301 AGTAAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.06, C:0.00, G:0.38, T:0.56
Consensus pattern (17 bp):
TTAGTGGGGTTTTGTTG
Found at i:23379 original size:69 final size:70
Alignment explanation
Indices: 23248--23391 Score: 168
Period size: 69 Copynumber: 2.1 Consensus size: 70
23238 TTCAGTCGAT
* * *
23248 TAGAATTTACTCAGAAAGCTTAGATTGAATTTGAGGAATTTCAGTCGATTAGAAGTTCATTACAA
1 TAGAATTTACTCAGAAAGCTTAGATTGAATTTGAAGAATTCCAGTCGATTAAAAGTTCATTACAA
23313 TCAAC
66 TCAAC
* * * *
23318 TAGAATTTACTCAG-AAGAC-TCGATTTAGTTTGAAGACTTCCAGTCGATTAAAAGCTT-ATTAC
1 TAGAATTTACTCAGAAAG-CTTAGATTGAATTTGAAGAATTCCAGTCGATTAAAAG-TTCATTAC
* *
23380 AGTCAAG
64 AATCAAC
23387 TAGAA
1 TAGAA
23392 GAAGATATTC
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
69 46 0.73
70 17 0.27
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (70 bp):
TAGAATTTACTCAGAAAGCTTAGATTGAATTTGAAGAATTCCAGTCGATTAAAAGTTCATTACAA
TCAAC
Found at i:23808 original size:12 final size:12
Alignment explanation
Indices: 23793--23822 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23783 GGAAACAAAT
23793 TAACAACAACAA
1 TAACAACAACAA
23805 TAACAACAACAA
1 TAACAACAACAA
*
23817 CAACAA
1 TAACAA
23823 TCTCATCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.27, G:0.00, T:0.07
Consensus pattern (12 bp):
TAACAACAACAA
Found at i:26601 original size:18 final size:19
Alignment explanation
Indices: 26578--26615 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
26568 TTATGTGATA
*
26578 GCTTAATTAA-TTGATTGG
1 GCTTAATGAATTTGATTGG
26596 GCTTAATGAATTTGATTGG
1 GCTTAATGAATTTGATTGG
26615 G
1 G
26616 TGAGTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (19 bp):
GCTTAATGAATTTGATTGG
Found at i:26825 original size:13 final size:14
Alignment explanation
Indices: 26807--26835 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
26797 TCCAATTAAT
26807 TTAGTTTAA-TTAG
1 TTAGTTTAATTTAG
26820 TTAGTTTAATTTAG
1 TTAGTTTAATTTAG
26834 TT
1 TT
26836 TATTAGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTAGTTTAATTTAG
Found at i:26828 original size:23 final size:22
Alignment explanation
Indices: 26802--26844 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
26792 AATTGTCCAA
26802 TTAATTTAGTTTAATTAGTTAGT
1 TTAATTTAGTTT-ATTAGTTAGT
26825 TTAATTTAGTTTATTAGTTA
1 TTAATTTAGTTTATTAGTTA
26845 ATTGAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (22 bp):
TTAATTTAGTTTATTAGTTAGT
Found at i:27006 original size:16 final size:17
Alignment explanation
Indices: 26985--27017 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
26975 GGAATCCGTC
26985 GATCA-TGTATCCATTA
1 GATCATTGTATCCATTA
*
27001 GATCATTGTATGCATTA
1 GATCATTGTATCCATTA
27018 TATACAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (17 bp):
GATCATTGTATCCATTA
Found at i:27759 original size:18 final size:19
Alignment explanation
Indices: 27736--27774 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
27726 AAGTTCCAAA
27736 AACCGACCAAACCGA-TTG
1 AACCGACCAAACCGACTTG
*
27754 AACCGACCGAACCGACTTG
1 AACCGACCAAACCGACTTG
27773 AA
1 AA
27775 ATGGTACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.38, C:0.33, G:0.18, T:0.10
Consensus pattern (19 bp):
AACCGACCAAACCGACTTG
Found at i:28038 original size:23 final size:22
Alignment explanation
Indices: 28012--28099 Score: 74
Period size: 23 Copynumber: 4.0 Consensus size: 22
28002 ACTTTATTAG
28012 TTATAATAAACTAATAATCTACC
1 TTATAATAAACTAATAATCTA-C
* *
28035 TTATTAT-AACTAAT-ATATA-
1 TTATAATAAACTAATAATCTAC
* *
28054 TGATGATTAAACTAATAATCTAC
1 TTAT-AATAAACTAATAATCTAC
* *
28077 TGTAAAAAAAACTAATAATCTAC
1 T-TATAATAAACTAATAATCTAC
28100 ATAAACCGAA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
19 3 0.06
20 1 0.02
21 11 0.22
22 11 0.22
23 23 0.46
24 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.35
Consensus pattern (22 bp):
TTATAATAAACTAATAATCTAC
Found at i:35369 original size:396 final size:399
Alignment explanation
Indices: 34625--36239 Score: 1809
Period size: 396 Copynumber: 4.0 Consensus size: 399
34615 TCAAATCACT
* * * * * * * *
34625 TTATATAATTTTTCTTATAGGATTACTATACAACACACTTTTTCAGTGTGAATTTTACATTTCAT
1 TTATATAATTTTTCTTATAGGATTATTATACAACACGC--TGTCAATGTAAATTTTAGACTCCAT
* * * *
34690 AAGCGGGTTAAGAAGTTGCCACATACCCTATTTCATAATCAATTAAATTTTTAATATCAGTACAT
64 AAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATCAATACAT
* * * * * * **
34755 A-TCCCTTAAGGGGACACATCTCAAACCTTAAACCATGCACGTGCAATCTGCTAAATTTGACTGA
129 ATTCCC-TAAGGGGACACATGTCAACCCTTAACCCCTGCACGTGCAGTCTGCTAAAATCCACTGA
* *
34819 CGGTGTA-TAGTATAATTTTTCTTATAAGATTACTT-TACTGTATACAATCCAATGTCAGTGTAA
193 CGGTGTATTA-TATAATTTTTCTTATAGGATTA-TTATAC---A-ACAA-AC-ATGTCAGTGTAA
* * * *
34882 ATTTTGGACTCCATAAGCGGCTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATT
250 ATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATA
* * * *
34947 TAAAATTAATACATATTCCCTAAGGGGATACATGTCAACCCTTAAACCCCGCTCGTGCAGTCTGC
315 TAATATTAATACATATTCCTTAAGGGGAAACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
*
35012 TAAAATTCACTGACGGTATA
380 TAAAATCCACTGACGGTATA
* * *
35032 TTATATAATTTTTCTGATAGGATTATTGTACAACACGCTGTCAATGTAAATTTTAGACTCTATAA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACGCTGTCAATGTAAATTTTAGACTCCATAA
* ** * *
35097 GCGGGTTAAGAAGTTGACACATATCTTATTTCATCATCAATTAAATATATAAT-T-AATACATAT
66 GCGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATCAATACATAT
* * * * *
35160 TCCCTAAGAGGACACATGTCAACCCTTAACCCCTGCACGTGCAGTCTGTTAAACTCCACTTACAG
131 TCCCTAAGGGGACACATGTCAACCCTTAACCCCTGCACGTGCAGTCTGCTAAAATCCACTGACGG
* *
35225 TGTA-TAGTATAATTTTTCTTATAGGATTATTATACAATAAAC-TGCCAGTGTAAATTTTGGACT
196 TGTATTA-TATAATTTTTCTTATAGGATTATTATACAACAAACATGTCAGTGTAAATTTTGGACT
* * * *
35288 CCATAATCGGGTTATGAAGTTGACACATACCTCATTTCATAATTAATAAAATATTTAATATTAAT
260 CCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATATAATATTAAT
* * * ** * * *
35353 ACATATTCCTTAAGGGGAGACATGTCAATCCTTAAAGCCCGCATATGCAGTTTGCTAAACTCCAT
325 ACATATTCCTTAAGGGGAAACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAAATCCAC
* *
35418 TGACTGTGTA
390 TGACGGTATA
* * *** * *
35428 TTATATAATTGTTCTTATAGGATTATTATACAATAATTTGTCAATGTAAATTTTGGACGCCATAA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACGCTGTCAATGTAAATTTTAGACTCCATAA
** * * * *
35493 ATGGATTAAGAAGTTGACATATACCGCATTTCATAATTAATTAAATATTTAATAGT-AATACATA
66 GCGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATA-TCAATACATA
* * *
35557 TTCTCTAAGGGGACACATGTCAACCTTTAAACCCC-GCACGTGCAGCCTGCTAAAATCCACTGAC
130 TTCCCTAAGGGGACACATGTCAACCCTT-AACCCCTGCACGTGCAGTCTGCTAAAATCCACTGAC
* **
35621 GGTGTATTATATAATTTTCCTTATAGGATTATTATACAACACGCTATGATCAGTGTAAATTTTGG
194 GGTGTATTATATAATTTTTCTTATAGGATTATTATACAACAAAC-ATG-TCAGTGTAAATTTTGG
* * * *
35686 ACTCTATAAGCGTGTTAAGAAGTTGACACATACCTAATTTCATCATTAATTAAATATATAATA-T
257 ACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATATAATATT
* * *
35750 --TACATATTCTCTT-ATGGGACACATGTCAACCCTT-AACCCTGCACGTGCAGTCTGCTAAAAT
322 AATACATATTC-CTTAAGGGGAAACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAAAT
*
35811 CCACTGACGGTGTA
386 CCACTGACGGTATA
* * ** *
35825 TTATATTATTTTTCTTATAGGATTATTATACAATACAG-TGTCTGTGTAAAATTT-GAACTCCAT
1 TTATATAATTTTTCTTATAGGATTATTATACAACAC-GCTGTCAATGTAAATTTTAG-ACTCCAT
* * *
35888 AAGCAGGTTAAGAAGTTGACAGATACCCCATTTCATAATTAATTAAATATTTAATATCAATACAT
64 AAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATCAATACAT
* *
35953 CTTCCCCT-AGGGGACACATGTCAA-CCTTATA-CCCTGCACGTGCAGTCTGCTAAAATCCACCG
129 ATT-CCCTAAGGGGACACATGTCAACCCTTA-ACCCCTGCACGTGCAGTCTGCTAAAATCCACTG
* * **
36015 ACGGTGTATTATATAATTTTTCCTATAGGATTACTATACAACACGC-TGTCAGTGTAAATTTTGG
192 ACGGTGTATTATATAATTTTTCTTATAGGATTATTATACAACAAACATGTCAGTGTAAATTTTGG
* * *
36079 ATTCTATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATCATTAATTAAATATATAATATT
257 ACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATATAATATT
* * * * * * * * *
36144 AATGCATTTTTCC-TAAGGGAAAATATGTCAACCCTTAAACCCTGCAGGTGTAGTCCGCTAAACT
322 AATACA-TATTCCTTAAGGGGAAACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAAAT
* * *
36208 TCACTTAC-ATATA
386 CCACTGACGGTATA
*
36221 -TATTATAATTTTTCATATA
1 TTA-TATAATTTTTCTTATA
36240 TATAATAGAT
Statistics
Matches: 1038, Mismatches: 147, Indels: 57
0.84 0.12 0.05
Matches are distributed among these distances:
393 76 0.07
394 3 0.00
395 7 0.01
396 350 0.34
397 193 0.19
398 126 0.12
399 14 0.01
400 4 0.00
401 70 0.07
402 2 0.00
403 87 0.08
404 5 0.00
405 67 0.06
407 34 0.03
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (399 bp):
TTATATAATTTTTCTTATAGGATTATTATACAACACGCTGTCAATGTAAATTTTAGACTCCATAA
GCGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATCAATACATAT
TCCCTAAGGGGACACATGTCAACCCTTAACCCCTGCACGTGCAGTCTGCTAAAATCCACTGACGG
TGTATTATATAATTTTTCTTATAGGATTATTATACAACAAACATGTCAGTGTAAATTTTGGACTC
CATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATATAATATTAATA
CATATTCCTTAAGGGGAAACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAAATCCACT
GACGGTATA
Found at i:35447 original size:199 final size:198
Alignment explanation
Indices: 34625--36205 Score: 1772
Period size: 199 Copynumber: 7.9 Consensus size: 198
34615 TCAAATCACT
* * * ** * *
34625 TTATATAATTTTTCTTATAGGATTACTATACAACACACTTTTTCAGTGTGAATTTTACATTTCAT
1 TTATATAATTTTTCTTATAGGATTATTATACAACACAC--TGTCAGTGTAAATTTTGGACTCCAT
* * * * *
34690 AAGCGGGTTAAGAAGTTGCCACATACC-CTATTTCATAATCAATTAAATTTTTAATATCAGTACA
64 AAGCGGGTTAAGAAGTTGACACATACCTC-ATTTCATAATTAATTAAATATTTAATATTAATACA
* * * * * * **
34754 TATCCCTTAAGGGGACACATCTCAAACCTTAAACCATGCACGTGCAATCTGCTAAATTTGACTGA
128 TATTCCTTAAGGGGACACATGTCAACCCTTAAACC-CGCACGTGCAGTCTGCTAAAATCCACTGA
34819 CGGTGTA
192 CGGTGTA
* *
34826 -TAGTATAATTTTTCTTATAAGATTACTT-TACTGTATACAATCCAATGTCAGTGTAAATTTTGG
1 TTA-TATAATTTTTCTTATAGGATTA-TTATAC---A-AC-A--CACTGTCAGTGTAAATTTTGG
* * * *
34889 ACTCCATAAGCGGCTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAAAATT
57 ACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATT
* * * *
34954 AATACATATTCCCTAAGGGGATACATGTCAACCCTTAAACCCCGCTCGTGCAGTCTGCTAAAATT
122 AATACATATTCCTTAAGGGGACACATGTCAACCCTTAAA-CCCGCACGTGCAGTCTGCTAAAATC
*
35019 CACTGACGGTATA
186 CACTGACGGTGTA
* * * * * *
35032 TTATATAATTTTTCTGATAGGATTATTGTACAACACGCTGTCAATGTAAATTTTAGACTCTATAA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACACTGTCAGTGTAAATTTTGGACTCCATAA
* * * * *
35097 GCGGGTTAAGAAGTTGACACATATCTTATTTCATCATCAATTAAATATAT-A-ATTAATACATAT
66 GCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATTAATACATAT
* * * * * * *
35160 TCCCTAAGAGGACACATGTCAACCCTTAACCCCTGCACGTGCAGTCTGTTAAACTCCACTTACAG
131 TCCTTAAGGGGACACATGTCAACCCTTAAACCC-GCACGTGCAGTCTGCTAAAATCCACTGACGG
35225 TGTA
195 TGTA
* * *
35229 -TAGTATAATTTTTCTTATAGGATTATTATACAATAAACTGCCAGTGTAAATTTTGGACTCCATA
1 TTA-TATAATTTTTCTTATAGGATTATTATACAACACACTGTCAGTGTAAATTTTGGACTCCATA
* * *
35293 ATCGGGTTATGAAGTTGACACATACCTCATTTCATAATTAATAAAATATTTAATATTAATACATA
65 AGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATTAATACATA
* * ** * * * *
35358 TTCCTTAAGGGGAGACATGTCAATCCTTAAAGCCCGCATATGCAGTTTGCTAAACTCCATTGACT
130 TTCCTTAAGGGGACACATGTCAACCCTTAAA-CCCGCACGTGCAGTCTGCTAAAATCCACTGACG
35423 GTGTA
194 GTGTA
* * * * *
35428 TTATATAATTGTTCTTATAGGATTATTATACAATA-ATTTGTCAATGTAAATTTTGGACGCCATA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACA-CTGTCAGTGTAAATTTTGGACTCCATA
** * * * *
35492 AATGGATTAAGAAGTTGACATATACCGCATTTCATAATTAATTAAATATTTAATAGTAATACATA
65 AGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATTAATACATA
* *
35557 TT-CTCTAAGGGGACACATGTCAACCTTTAAACCCCGCACGTGCAGCCTGCTAAAATCCACTGAC
130 TTCCT-TAAGGGGACACATGTCAACCCTTAAA-CCCGCACGTGCAGTCTGCTAAAATCCACTGAC
35621 GGTGTA
193 GGTGTA
* * *
35627 TTATATAATTTTCCTTATAGGATTATTATACAACACGCTATGATCAGTGTAAATTTTGGACTCTA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACAC--TG-TCAGTGTAAATTTTGGACTCCA
* * * *
35692 TAAGCGTGTTAAGAAGTTGACACATACCTAATTTCATCATTAATTAAATATATAATA-T--TACA
63 TAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATTAATACA
*
35754 TATTCTCTT-ATGGGACACATGTCAACCCTT-AACCCTGCACGTGCAGTCTGCTAAAATCCACTG
128 TATTC-CTTAAGGGGACACATGTCAACCCTTAAACCC-GCACGTGCAGTCTGCTAAAATCCACTG
35817 ACGGTGTA
191 ACGGTGTA
* * * * * *
35825 TTATATTATTTTTCTTATAGGATTATTATACAATACAGTGTCTGTGTAAAATTTGAACTCCATAA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACACTGTCAGTGTAAATTTTGGACTCCATAA
* * * * *
35890 GCAGGTTAAGAAGTTGACAGATACCCCATTTCATAATTAATTAAATATTTAATATCAATACATCT
66 GCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATTAATACATAT
* * *
35955 TCCCCT-AGGGGACACATGTCAA-CCTTATACCCTGCACGTGCAGTCTGCTAAAATCCACCGACG
131 T-CCTTAAGGGGACACATGTCAACCCTTAAACCC-GCACGTGCAGTCTGCTAAAATCCACTGACG
36018 GTGTA
194 GTGTA
* * * * *
36023 TTATATAATTTTTCCTATAGGATTACTATACAACACGCTGTCAGTGTAAATTTTGGATTCTATAA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACACTGTCAGTGTAAATTTTGGACTCCATAA
* * * *
36088 GCGGGTTAAGAAGTTGACACATACCTCATTTCATCATTAATTAAATATATAATATTAATGCATTT
66 GCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATTAATACA-TA
* * * * * *
36153 TTCC-TAAGGGAAAATATGTCAACCCTTAAACCCTGCAGGTGTAGTCCGCTAAA
130 TTCCTTAAGGGGACACATGTCAACCCTTAAACCC-GCACGTGCAGTCTGCTAAA
36206 CTTCACTTAC
Statistics
Matches: 1170, Mismatches: 174, Indels: 74
0.83 0.12 0.05
Matches are distributed among these distances:
195 68 0.06
196 7 0.01
197 170 0.15
198 261 0.22
199 388 0.33
200 8 0.01
201 30 0.03
202 70 0.06
203 1 0.00
204 1 0.00
205 4 0.00
206 155 0.13
207 5 0.00
208 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (198 bp):
TTATATAATTTTTCTTATAGGATTATTATACAACACACTGTCAGTGTAAATTTTGGACTCCATAA
GCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATTAATACATAT
TCCTTAAGGGGACACATGTCAACCCTTAAACCCGCACGTGCAGTCTGCTAAAATCCACTGACGGT
GTA
Found at i:36006 original size:595 final size:592
Alignment explanation
Indices: 34625--36185 Score: 1972
Period size: 595 Copynumber: 2.6 Consensus size: 592
34615 TCAAATCACT
* * * * * * *
34625 TTATATAATTTTTCTTATAGGATTACTATACAACACACTTTTTCAGTGT-GAATTTTACATTTCA
1 TTATATAATTTTTCTTATAGGATTATTATACAATACAC--TGTCAGTGTAAAATTTGA-ACTCCA
* * * * *
34689 TAAGCGGGTTAAGAAGTTGCCACATACCCTATTTCATAATCAATTAAATTTTTAATATCAGTACA
63 TAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATCAATACA
* * * * * **
34754 TATCCCTTAAGGGGACACATCTCAAACCTTAAACCATGCACGTGCAATCTGCTAAATTTGACTGA
128 TTTCCCTTAAGGGGACACATGTC-AACCTTAAACCCTGCACGTGCAGTCTGCTAAAATCCACTGA
*
34819 CGGTGTA-TAGTATAATTTTTCTTATAAGATTACTTTACTGTATACAATCCAATGTCAGTGTAAA
192 CGGTGTATTA-TATAATTTTTCTTAT-AG--GA--TTA-T-TATACAAT--AATGTCAGTGTAAA
*
34883 TTTTGGACTCCATAAGCGGCTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTT
247 TTTTGGACTCCATAAGCGGATTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTT
* * * * *
34948 AAAATTAATACATATTCCCTAAGGGGATACATGTCAACCCTTAAACCCCGCTCGTGCAGTCTGCT
312 AATATTAATACATATTCTCTAAGGGGAAACATGTCAACCCTTAAACCCCGCACGTGCAGCCTGCT
* * *
35013 AAAATTCACTGACGGTATATTATATAATTTTTCTGATAGGATTATTGTACAACACGCTGTCAATG
377 AAAATCCACTGACGGTATATTATATAATTTTCCTGATAGGATTATTATACAACACGCTGTCAATG
* *
35078 TAAATTTTAGACTCTATAAGCGGGTTAAGAAGTTGACACATATCTTATTTCATCATCAATTAAAT
442 TAAATTTTAGACTCTATAAGCGGGTTAAGAAGTTGACACATACCTAATTTCATCATCAATTAAAT
35143 ATATAATTAATACATATTCCCTAAGAGGACACATGTCAACCCTTAACCCCTGCACGTGCAGTCTG
507 ATATAATTAATACATATTCCCTAAGAGGACACATGTCAACCCTTAACCCCTGCACGTGCAGTCTG
* * *
35208 TTAAACTCCACTTACAGTGTA
572 CTAAAATCCACTGACAGTGTA
* * * *
35229 -TAGTATAATTTTTCTTATAGGATTATTATACAATAAACTGCCAGTGTAAATTTTGGACTCCATA
1 TTA-TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAAATTTGAACTCCATA
* * * * *
35293 ATCGGGTTATGAAGTTGACACATACCTCATTTCATAATTAATAAAATATTTAATATTAATACATA
65 AGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATCAATACAT-
* ** * * *
35358 TT-CCTTAAGGGGAGACATGTCAATCCTTAAAGCCC-GCATATGCAGTTTGCTAAACTCCATTGA
129 TTCCCTTAAGGGGACACATGTCAA-CCTTAAA-CCCTGCACGTGCAGTCTGCTAAAATCCACTGA
* * *
35421 CTGTGTATTATATAATTGTTCTTATAGGATTATTATACAATAATTTGTCAATGTAAATTTTGGAC
192 CGGTGTATTATATAATTTTTCTTATAGGATTATTATACAATAA--TGTCAGTGTAAATTTTGGAC
* ** * *
35486 GCCATAAATGGATTAAGAAGTTGACATATACCGCATTTCATAATTAATTAAATATTTAATAGTAA
255 TCCATAAGCGGATTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAA
* *
35551 TACATATTCTCTAAGGGGACACATGTCAACCTTTAAACCCCGCACGTGCAGCCTGCTAAAATCCA
320 TACATATTCTCTAAGGGGAAACATGTCAACCCTTAAACCCCGCACGTGCAGCCTGCTAAAATCCA
* * *
35616 CTGACGGTGTATTATATAATTTTCCTTATAGGATTATTATACAACACGCTATGATCAGTGTAAAT
385 CTGACGGTATATTATATAATTTTCCTGATAGGATTATTATACAACACGC--TG-TCAATGTAAAT
* * *
35681 TTTGGACTCTATAAGCGTGTTAAGAAGTTGACACATACCTAATTTCATCATTAATTAAATATATA
447 TTTAGACTCTATAAGCGGGTTAAGAAGTTGACACATACCTAATTTCATCATCAATTAAATATATA
* * *
35746 A-TATTACATATTCTCTTATG-GGACACATGTCAACCCTTAA-CCCTGCACGTGCAGTCTGCTAA
512 ATTAATACATATTC-CCTAAGAGGACACATGTCAACCCTTAACCCCTGCACGTGCAGTCTGCTAA
*
35808 AATCCACTGACGGTGTA
576 AATCCACTGACAGTGTA
* * *
35825 TTATATTATTTTTCTTATAGGATTATTATACAATACAGTGTCTGTGTAAAATTTGAACTCCATAA
1 TTATATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAAATTTGAACTCCATAA
* *
35890 GCAGGTTAAGAAGTTGACAGATACCCCATTTCATAATTAATTAAATATTTAATATCAATACATCT
66 GCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATCAATACAT-T
* * *
35955 TCCCCT-AGGGGACACATGTCAACCTTATACCCTGCACGTGCAGTCTGCTAAAATCCACCGACGG
130 TCCCTTAAGGGGACACATGTCAACCTTAAACCCTGCACGTGCAGTCTGCTAAAATCCACTGACGG
* * * * * *
36019 TGTATTATATAATTTTTCCTATAGGATTACTATACAACACGCTGTCAGTGTAAATTTTGGATTCT
195 TGTATTATATAATTTTTCTTATAGGATTATTATACAATA--ATGTCAGTGTAAATTTTGGACTCC
* * * * * *
36084 ATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATCATTAATTAAATATATAATATTAATGC
258 ATAAGCGGATTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATAC
* * *
36149 AT-TTTTCCTAAGGGAAAATATGTCAACCCTTAAACCC
323 ATATTCT-CTAAGGGGAAACATGTCAACCCTTAAACCC
36186 TGCAGGTGTA
Statistics
Matches: 824, Mismatches: 115, Indels: 45
0.84 0.12 0.05
Matches are distributed among these distances:
593 2 0.00
594 6 0.01
595 357 0.43
596 164 0.20
597 41 0.05
598 75 0.09
599 1 0.00
601 4 0.00
602 131 0.16
603 11 0.01
604 32 0.04
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35
Consensus pattern (592 bp):
TTATATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAAATTTGAACTCCATAA
GCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATCAATACATTT
CCCTTAAGGGGACACATGTCAACCTTAAACCCTGCACGTGCAGTCTGCTAAAATCCACTGACGGT
GTATTATATAATTTTTCTTATAGGATTATTATACAATAATGTCAGTGTAAATTTTGGACTCCATA
AGCGGATTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATA
TTCTCTAAGGGGAAACATGTCAACCCTTAAACCCCGCACGTGCAGCCTGCTAAAATCCACTGACG
GTATATTATATAATTTTCCTGATAGGATTATTATACAACACGCTGTCAATGTAAATTTTAGACTC
TATAAGCGGGTTAAGAAGTTGACACATACCTAATTTCATCATCAATTAAATATATAATTAATACA
TATTCCCTAAGAGGACACATGTCAACCCTTAACCCCTGCACGTGCAGTCTGCTAAAATCCACTGA
CAGTGTA
Found at i:37535 original size:26 final size:26
Alignment explanation
Indices: 37496--37556 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
37486 TCATAAATTG
**
37496 AGTAACCTCACATTATT-GAAATTTTT
1 AGTAACCTTGCATTATTAGAAA-TTTT
* *
37522 AGTGACCTTGCATTCTTAGAAATTTT
1 AGTAACCTTGCATTATTAGAAATTTT
37548 AGTAACCTT
1 AGTAACCTT
37557 TCATCAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (26 bp):
AGTAACCTTGCATTATTAGAAATTTT
Found at i:38300 original size:3 final size:3
Alignment explanation
Indices: 38292--38316 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38282 GGAGTACTAC
38292 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
38317 CTTAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:56605 original size:16 final size:18
Alignment explanation
Indices: 56579--56614 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
56569 CGGAATGTGA
56579 GTTTAATTTGTA-ATTTG
1 GTTTAATTTGTATATTTG
56596 GTTT-ATTTGTATATTTG
1 GTTTAATTTGTATATTTG
56613 GT
1 GT
56615 AGTGATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (18 bp):
GTTTAATTTGTATATTTG
Found at i:57648 original size:20 final size:21
Alignment explanation
Indices: 57620--57659 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
57610 AAACTTCTAG
* *
57620 TAACTTTA-TAAAGTTTTTAA
1 TAACCTTATTAAACTTTTTAA
57640 TAACCTTATTAAACTTTTTA
1 TAACCTTATTAAACTTTTTA
57660 TACTAATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (21 bp):
TAACCTTATTAAACTTTTTAA
Found at i:58922 original size:45 final size:45
Alignment explanation
Indices: 58871--58959 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
58861 TAATAGAGTA
58871 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
* *
58916 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTG
58960 AAGAAGTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
Found at i:60111 original size:27 final size:28
Alignment explanation
Indices: 60081--60136 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
60071 AAAGAAATAT
60081 GAGGGACAATTAAAAAGGAACA-AGGGA
1 GAGGGACAATTAAAAAGGAACAGAGGGA
60108 GAGGGACAATTAAAAAGGAACAGAGGGA
1 GAGGGACAATTAAAAAGGAACAGAGGGA
60136 G
1 G
60137 TACTATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.50, C:0.07, G:0.36, T:0.07
Consensus pattern (28 bp):
GAGGGACAATTAAAAAGGAACAGAGGGA
Found at i:64852 original size:48 final size:49
Alignment explanation
Indices: 64699--64858 Score: 183
Period size: 48 Copynumber: 3.4 Consensus size: 49
64689 CTGTACGTAC
* * *
64699 TTTGGGCTTTGTGTG-CTTT--A-TACGTTGCCCATG--TGGTATGTGTT
1 TTTGGGCTTTGTGTGTATTTGAAGTACATTGCCCATGTATCGTATGTG-T
* ** *
64743 TTTGGGCCTTGTGCAT-TTTGAAGTACATTGCCCATGTGTCGTATGTGT
1 TTTGGGCTTTGTGTGTATTTGAAGTACATTGCCCATGTATCGTATGTGT
*
64791 TTTGGGCTTTGTGTGTATTTGAAGTACATTG-CCATGTATTGTATGTGT
1 TTTGGGCTTTGTGTGTATTTGAAGTACATTGCCCATGTATCGTATGTGT
64839 TTTGGGCTTTGTGTGTATTT
1 TTTGGGCTTTGTGTGTATTT
64859 TGGAGTGTGG
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
44 15 0.15
46 1 0.01
47 12 0.12
48 49 0.49
49 22 0.22
ACGTcount: A:0.12, C:0.12, G:0.28, T:0.47
Consensus pattern (49 bp):
TTTGGGCTTTGTGTGTATTTGAAGTACATTGCCCATGTATCGTATGTGT
Found at i:65112 original size:30 final size:29
Alignment explanation
Indices: 65050--65118 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
65040 TAACAACCGT
* ***
65050 CAAATAAGCCCCTGAACTTTTATTTTGGC
1 CAAATAAGCCCCTGAACTCTTATAAAGGC
65079 CAAATAAGCCCCTGAACTCTTATAAAAGGC
1 CAAATAAGCCCCTGAACTCTTAT-AAAGGC
65109 CAAATAAGCC
1 CAAATAAGCC
65119 TTGATGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTCTTATAAAGGC
Found at i:65457 original size:17 final size:17
Alignment explanation
Indices: 65435--65469 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
65425 GGATTCCCTA
65435 ATTTGTAAAAATTTGCT
1 ATTTGTAAAAATTTGCT
65452 ATTTGTAAAAATTTGCT
1 ATTTGTAAAAATTTGCT
65469 A
1 A
65470 AGTATGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (17 bp):
ATTTGTAAAAATTTGCT
Found at i:66595 original size:21 final size:21
Alignment explanation
Indices: 66569--66609 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
66559 AAAAACAGGC
*
66569 GATGGACACGGCGGGACACGG
1 GATGGACACGGCCGGACACGG
66590 GATGGACACGGCCGGACACG
1 GATGGACACGGCCGGACACG
66610 TCGAAACACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.44, T:0.05
Consensus pattern (21 bp):
GATGGACACGGCCGGACACGG
Found at i:66598 original size:11 final size:12
Alignment explanation
Indices: 66566--66601 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
66556 AAAAAAAACA
66566 GGCGATGGACAC
1 GGCGATGGACAC
66578 GGCG--GGACAC
1 GGCGATGGACAC
66588 GG-GATGGACAC
1 GGCGATGGACAC
66599 GGC
1 GGC
66602 CGGACACGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
9 1 0.05
10 8 0.38
11 8 0.38
12 4 0.19
ACGTcount: A:0.22, C:0.25, G:0.47, T:0.06
Consensus pattern (12 bp):
GGCGATGGACAC
Found at i:70679 original size:3 final size:3
Alignment explanation
Indices: 70671--70709 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
70661 TGATTCCTTG
70671 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
70710 GTTAAGAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:76223 original size:19 final size:20
Alignment explanation
Indices: 76180--76223 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
76170 TATTGGCGAT
76180 GTCCTTCTGGCAAGGGAACC
1 GTCCTTCTGGCAAGGGAACC
* *
76200 -ACCTTGTGG-AAGGGAACC
1 GTCCTTCTGGCAAGGGAACC
76218 GTCCTT
1 GTCCTT
76224 TGAGGCAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.23
Consensus pattern (20 bp):
GTCCTTCTGGCAAGGGAACC
Found at i:77915 original size:2 final size:2
Alignment explanation
Indices: 77908--77936 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
77898 AGGTTAACGT
77908 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
77937 AAATTTAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:102952 original size:15 final size:15
Alignment explanation
Indices: 102908--102967 Score: 75
Period size: 15 Copynumber: 3.7 Consensus size: 15
102898 TCCCCAACAC
102908 CAAAGTATTTAAGTG
1 CAAAGTATTTAAGTG
102923 CAAAGAATATATTTAAGTG
1 CAAAG----TATTTAAGTG
*
102942 CAAAGTATTTAAGTC
1 CAAAGTATTTAAGTG
102957 CAAAGTATTTA
1 CAAAGTATTTA
102968 TATTTTCTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
15 25 0.62
19 15 0.38
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.33
Consensus pattern (15 bp):
CAAAGTATTTAAGTG
Found at i:112638 original size:2 final size:2
Alignment explanation
Indices: 112631--112658 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
112621 AAAATATTGA
112631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112659 CCATAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117600 original size:17 final size:16
Alignment explanation
Indices: 117580--117613 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
117570 TTGCACTATA
117580 TTTCTTTTTTTTTCTTT
1 TTTCTTTTTTTTT-TTT
117597 TTTCTTTTTTTTTTTT
1 TTTCTTTTTTTTTTTT
117613 T
1 T
117614 ACATTTGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTCTTTTTTTTTTTT
Done.