Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015900.1 Corchorus capsularis cultivar CVL-1 contig15921, 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: 69483
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1366 original size:3 final size:3
Alignment explanation
Indices: 1352--1383 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
1342 AAACCCAAAA
1352 AAG AAGG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG A
1384 GTAACATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:8714 original size:1 final size:1
Alignment explanation
Indices: 8708--8750 Score: 86
Period size: 1 Copynumber: 43.0 Consensus size: 1
8698 AAGCTGTCCC
8708 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8751 CCACCTTCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10215 original size:1 final size:1
Alignment explanation
Indices: 10211--10241 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
10201 AAAAAAGTTT
10211 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10242 CTTTGAACAA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10752 original size:2 final size:2
Alignment explanation
Indices: 10745--10769 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10735 TTCAAAAAGA
10745 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
10770 AATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15343 original size:109 final size:109
Alignment explanation
Indices: 15211--15485 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 109
15201 AAAAAAATTA
15211 TATAAA-ATATT-GAATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
15274 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
*
15319 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
*
15384 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* *
15428 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAATTTCTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATAAAAATAGAGTTTTTAGTAGAATAAAA
15486 CTATAATAGT
Statistics
Matches: 155, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
108 6 0.04
109 118 0.76
110 3 0.02
111 1 0.01
114 27 0.17
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:15809 original size:16 final size:16
Alignment explanation
Indices: 15788--15847 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
15778 AATTTCCCGA
15788 ACCCGAACCC-AAAATT
1 ACCCGAACCCGAAAA-T
15804 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
15820 ACCCGAACCCGAGACA-
1 ACCCGAACCCGA-AAAT
15836 ACCCGAACCCGA
1 ACCCGAACCCGA
15848 CCCGAGTCCC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
16 35 0.85
17 6 0.15
ACGTcount: A:0.40, C:0.42, G:0.13, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:17300 original size:15 final size:16
Alignment explanation
Indices: 17268--17308 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
17258 CCCAAACCGA
*
17268 ACCCAAATCCGAAAAT
1 ACCCAAACCCGAAAAT
17284 ACCCAAACCCG-AAAT
1 ACCCAAACCCGAAAAT
*
17299 ACTCAAACCC
1 ACCCAAACCC
17309 AAACCCCGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.46, C:0.39, G:0.05, T:0.10
Consensus pattern (16 bp):
ACCCAAACCCGAAAAT
Found at i:20720 original size:12 final size:12
Alignment explanation
Indices: 20703--20728 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20693 CACATTAAAT
20703 TATAGAAAAGTA
1 TATAGAAAAGTA
20715 TATAGAAAAGTA
1 TATAGAAAAGTA
20727 TA
1 TA
20729 CCCAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (12 bp):
TATAGAAAAGTA
Found at i:22157 original size:2 final size:2
Alignment explanation
Indices: 22150--22174 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22140 TAGCTTCTAT
22150 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 T
22175 TCTATAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23794 original size:236 final size:236
Alignment explanation
Indices: 23381--23851 Score: 924
Period size: 236 Copynumber: 2.0 Consensus size: 236
23371 TTGATCTAGA
23381 GCTCCGTTTGAGGCAAATGAATAACCGTTGGAAAGCTAACTCCAAGATCTACAACTTTTGTGTTT
1 GCTCCGTTTGAGGCAAATGAATAACCGTTGGAAAGCTAACTCCAAGATCTACAACTTTTGTGTTT
23446 TGGTCGAAGCCCAGTTCAAACATTTTCATGGACAAAAATGCCCCTGAAGTCAGCGGACAGAATCT
66 TGGTCGAAGCCCAGTTCAAACATTTTCATGGACAAAAATGCCCCTGAAGTCAGCGGACAGAATCT
23511 GTCTTGGGCATTTCTTGCGGGATTGATCCAATTGAGCCCAAATTCTTATTTGGGCTAGCTTGAAG
131 GTCTTGGGCATTTCTTGCGGGATTGATCCAATTGAGCCCAAATTCTTATTTGGGCTAGCTTGAAG
*
23576 ACTTGGAGAGCAGCCCAGCACGTCCTTAGGGTTTGTTTAGG
196 ACTTGGAGAGCAGCCCAACACGTCCTTAGGGTTTGTTTAGG
23617 GCTCCGTTTGAGGCAAATGAATAACCGTTGGAAAGCTAACTCCAAGATCTACAACTTTTGTGTTT
1 GCTCCGTTTGAGGCAAATGAATAACCGTTGGAAAGCTAACTCCAAGATCTACAACTTTTGTGTTT
*
23682 TGGTCGAAGCCCAGTTCGAACATTTTCATGGACAAAAATGCCCCTGAAGTCAGCGGACAGAATCT
66 TGGTCGAAGCCCAGTTCAAACATTTTCATGGACAAAAATGCCCCTGAAGTCAGCGGACAGAATCT
23747 GTCTTGGGCATTTCTTGCGGGATTGATCCAATTGAGCCCAAATTCTTATTTGGGCTAGCTTGAAG
131 GTCTTGGGCATTTCTTGCGGGATTGATCCAATTGAGCCCAAATTCTTATTTGGGCTAGCTTGAAG
23812 ACTTGGAGAGCAGCCCAACACGTCCTTAGGGTTTGTTTAG
196 ACTTGGAGAGCAGCCCAACACGTCCTTAGGGTTTGTTTAG
23852 CTCTAAATTA
Statistics
Matches: 233, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
236 233 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (236 bp):
GCTCCGTTTGAGGCAAATGAATAACCGTTGGAAAGCTAACTCCAAGATCTACAACTTTTGTGTTT
TGGTCGAAGCCCAGTTCAAACATTTTCATGGACAAAAATGCCCCTGAAGTCAGCGGACAGAATCT
GTCTTGGGCATTTCTTGCGGGATTGATCCAATTGAGCCCAAATTCTTATTTGGGCTAGCTTGAAG
ACTTGGAGAGCAGCCCAACACGTCCTTAGGGTTTGTTTAGG
Found at i:26031 original size:13 final size:13
Alignment explanation
Indices: 26015--26046 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
26005 ATATTAAACA
26015 TTAGTTTTAACCT
1 TTAGTTTTAACCT
26028 TTAGTTTTAACCT
1 TTAGTTTTAACCT
26041 TTAGTT
1 TTAGTT
26047 GTTAGTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.56
Consensus pattern (13 bp):
TTAGTTTTAACCT
Found at i:26412 original size:102 final size:101
Alignment explanation
Indices: 26230--26431 Score: 359
Period size: 102 Copynumber: 2.0 Consensus size: 101
26220 ATCACCACAT
*
26230 CCTCCTGATGTGGGATCTTGGGGCGTCACAATCTACCCCCTTGTAGACTTGTCGTCCCCAACAAG
1 CCTCCTGATGTGGGATCTTGGGGCGTCACAATCTACCCCCTTATAGACTTGTCGTCCCCAACAAG
26295 CCCACACAATCACAATCACCAGGACCCACCGGGCGG
66 CCCACACAATCACAATCACCAGGACCCACCGGGCGG
* *
26331 CCTCCTGATGTGGGATCTTGGGGCGTCACAATCTACCCCCCTTATAGGCTTGTCGTCCCCGACAA
1 CCTCCTGATGTGGGATCTTGGGGCGTCACAATCTA-CCCCCTTATAGACTTGTCGTCCCCAACAA
*
26396 GCCCACACAATCACAATCACCAGGACCCACTGGGCG
65 GCCCACACAATCACAATCACCAGGACCCACCGGGCG
26432 CCGGGATTCT
Statistics
Matches: 96, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
101 35 0.36
102 61 0.64
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.19
Consensus pattern (101 bp):
CCTCCTGATGTGGGATCTTGGGGCGTCACAATCTACCCCCTTATAGACTTGTCGTCCCCAACAAG
CCCACACAATCACAATCACCAGGACCCACCGGGCGG
Found at i:29530 original size:31 final size:32
Alignment explanation
Indices: 29471--29535 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
29461 TATTCAAGTA
29471 CTTAATATCCTAAAACATAACACACCAATTTC
1 CTTAATATCCTAAAACATAACACACCAATTTC
29503 CTTAATATCCTAAAACATAA-ACACCAATTTC
1 CTTAATATCCTAAAACATAACACACCAATTTC
29534 CT
1 CT
29536 AAACTGTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.29
Consensus pattern (32 bp):
CTTAATATCCTAAAACATAACACACCAATTTC
Found at i:31512 original size:24 final size:24
Alignment explanation
Indices: 31480--31529 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
31470 GGAGTAACTC
31480 TTCAACATTATGATTTGGCATCGT
1 TTCAACATTATGATTTGGCATCGT
31504 TTCAACATTATGATTTGGCATCGT
1 TTCAACATTATGATTTGGCATCGT
31528 TT
1 TT
31530 GACCTTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (24 bp):
TTCAACATTATGATTTGGCATCGT
Found at i:31620 original size:24 final size:24
Alignment explanation
Indices: 31588--31638 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
31578 GTTGCACTGC
*
31588 TTCTCCAACAGCCCTTGGGGCTTG
1 TTCTCCAACAGCCCTTGGGACTTG
*
31612 TTCTCCAACAGCCCTTGGTACTTG
1 TTCTCCAACAGCCCTTGGGACTTG
31636 TTC
1 TTC
31639 ATTGGCAGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.33
Consensus pattern (24 bp):
TTCTCCAACAGCCCTTGGGACTTG
Found at i:31647 original size:24 final size:24
Alignment explanation
Indices: 31620--31675 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
31610 TGTTCTCCAA
31620 CAGCCCTTGGTACTTGTTCATTGG
1 CAGCCCTTGGTACTTGTTCATTGG
31644 CAGCCCTTGGTACTTGTTCATTGG
1 CAGCCCTTGGTACTTGTTCATTGG
31668 CAGCCCTT
1 CAGCCCTT
31676 TTTGAGCGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.12, C:0.29, G:0.23, T:0.36
Consensus pattern (24 bp):
CAGCCCTTGGTACTTGTTCATTGG
Found at i:33358 original size:15 final size:15
Alignment explanation
Indices: 33338--33366 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33328 AAGTAATTTA
33338 ATTATTATTATTAAT
1 ATTATTATTATTAAT
33353 ATTATTATTATTAA
1 ATTATTATTATTAA
33367 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATTATTATTAAT
Found at i:34112 original size:18 final size:18
Alignment explanation
Indices: 34089--34123 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34079 TGGCATCTTA
34089 TTTGGAACATCATTCCTT
1 TTTGGAACATCATTCCTT
*
34107 TTTGGAACATCCTTCCT
1 TTTGGAACATCATTCCT
34124 GGTAAGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.26, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTGGAACATCATTCCTT
Found at i:42491 original size:59 final size:59
Alignment explanation
Indices: 42405--42533 Score: 222
Period size: 59 Copynumber: 2.2 Consensus size: 59
42395 TAAATATTGT
*
42405 TTTTTATATATTATTTACTCTCTTTTCAATATCCAAAAAGTACTACTTATATATAAATA
1 TTTTTATATATTATTTACTCTCTTTTCAATATCCAAAAAGTACAACTTATATATAAATA
*
42464 TTTTTATATATTATTTACTCTCTTTTCAATATCCAAAAAGTACAACTTATATATACATA
1 TTTTTATATATTATTTACTCTCTTTTCAATATCCAAAAAGTACAACTTATATATAAATA
* *
42523 TATATATATAT
1 TTTTTATATAT
42534 CTAAGCTAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 66 1.00
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (59 bp):
TTTTTATATATTATTTACTCTCTTTTCAATATCCAAAAAGTACAACTTATATATAAATA
Found at i:43545 original size:17 final size:17
Alignment explanation
Indices: 43523--43557 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43513 CTCCTCTTGC
43523 ATGAAAAACACTTTTTT
1 ATGAAAAACACTTTTTT
* *
43540 ATGAAAAAGATTTTTTT
1 ATGAAAAACACTTTTTT
43557 A
1 A
43558 ACTACCCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (17 bp):
ATGAAAAACACTTTTTT
Found at i:46132 original size:23 final size:23
Alignment explanation
Indices: 46102--46145 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
46092 AGCTAAAGGA
46102 TCATGTGGCCGGGCATGGCCGAG
1 TCATGTGGCCGGGCATGGCCGAG
**
46125 TCATGTGGCCGGTTATGGCCG
1 TCATGTGGCCGGGCATGGCCG
46146 GGCATGGCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.25, G:0.41, T:0.23
Consensus pattern (23 bp):
TCATGTGGCCGGGCATGGCCGAG
Found at i:46149 original size:33 final size:33
Alignment explanation
Indices: 46107--46183 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
46097 AAGGATCATG
* *
46107 TGGCCGGGCATGGCCGA-GTCATGTGGCCGGTTA
1 TGGCCGGGCATGGCC-ATGTCACGTGGCCGGTGA
*
46140 TGGCCGGGCATGGCCATGTCGCGTGGCCGGTGA
1 TGGCCGGGCATGGCCATGTCACGTGGCCGGTGA
46173 TGGCCGGGCAT
1 TGGCCGGGCAT
46184 CTCCAAGTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.03
33 39 0.98
ACGTcount: A:0.10, C:0.26, G:0.44, T:0.19
Consensus pattern (33 bp):
TGGCCGGGCATGGCCATGTCACGTGGCCGGTGA
Found at i:46194 original size:33 final size:33
Alignment explanation
Indices: 46129--46236 Score: 128
Period size: 33 Copynumber: 3.3 Consensus size: 33
46119 GCCGAGTCAT
* ** *
46129 GTGGCCGGTTATGGCCGGGCATGGCCATGTCGC
1 GTGGCCGGTGATGGCCGGGCATCTCCAAGTCGC
46162 GTGGCCGGTGATGGCCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGATGGCCGGGCATCTCCAAGTCGC
* * * *
46195 ATGGCCGGTG-TTGCGTGGGCATTTCCAAGTCGC
1 GTGGCCGGTGATGGC-CGGGCATCTCCAAGTCGC
46228 GTGGCCGGT
1 GTGGCCGGT
46237 CACAATTGCT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
32 3 0.05
33 62 0.95
ACGTcount: A:0.10, C:0.27, G:0.41, T:0.22
Consensus pattern (33 bp):
GTGGCCGGTGATGGCCGGGCATCTCCAAGTCGC
Found at i:49253 original size:19 final size:18
Alignment explanation
Indices: 49229--49264 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
49219 TGAAGATTTC
49229 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
49248 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
49265 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:59146 original size:19 final size:18
Alignment explanation
Indices: 59122--59157 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
59112 TGAAGATTTC
59122 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
59141 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
59158 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:63369 original size:10 final size:10
Alignment explanation
Indices: 63354--63405 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
63344 TCGACACCAA
63354 GCCATGCCCG
1 GCCATGCCCG
63364 GCCATGTCCGCG
1 GCCATG-CC-CG
*
63376 CACCATGCCCG
1 -GCCATGCCCG
63387 GCCATGCCCG
1 GCCATGCCCG
63397 GCCAATGCC
1 GCC-ATGCC
63406 ATACCATCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 18 0.50
11 9 0.25
12 4 0.11
13 5 0.14
ACGTcount: A:0.13, C:0.48, G:0.27, T:0.12
Consensus pattern (10 bp):
GCCATGCCCG
Found at i:64108 original size:23 final size:25
Alignment explanation
Indices: 64069--64115 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
64059 ATATGCTCAT
64069 ATTGATCGATTGATTTG-ATTTTTG
1 ATTGATCGATTGATTTGAATTTTTG
*
64093 ATTGAT-GATTGCTTTGAATTTTT
1 ATTGATCGATTGATTTGAATTTTT
64116 AAGAATGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.21, C:0.04, G:0.19, T:0.55
Consensus pattern (25 bp):
ATTGATCGATTGATTTGAATTTTTG
Found at i:65915 original size:13 final size:13
Alignment explanation
Indices: 65897--65929 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
65887 ATAATTATTG
65897 TTTGCTTTATTAA
1 TTTGCTTTATTAA
65910 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
65923 TCTGCTT
1 TTTGCTT
65930 AGATTTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (13 bp):
TTTGCTTTATTAA
Done.