Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018210.1 Corchorus olitorius cultivar O-4 contig18243, 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: 82051
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:37119 original size:21 final size:21
Alignment explanation
Indices: 37093--37163 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
37083 TGCTAGGAGA
37093 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
37114 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
37135 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
37156 TCATTGGA
1 TCATTGGA
37164 ATTGCCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:41488 original size:10 final size:10
Alignment explanation
Indices: 41473--41497 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41463 TTAACACAAA
41473 TCACATACCT
1 TCACATACCT
41483 TCACATACCT
1 TCACATACCT
41493 TCACA
1 TCACA
41498 CACCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (10 bp):
TCACATACCT
Found at i:42344 original size:15 final size:16
Alignment explanation
Indices: 42311--42344 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42301 TTACTTTGCT
42311 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
42327 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
42342 TTG
1 TTG
42345 CTTCCTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:47043 original size:18 final size:19
Alignment explanation
Indices: 47020--47057 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
47010 GTGCATGGGT
*
47020 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
47038 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
47057 T
1 T
47058 AACGATGGAC
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:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:50795 original size:18 final size:18
Alignment explanation
Indices: 50772--50809 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
50762 AAAGGCAGTC
* *
50772 AACGGGACCGAGAGGTCA
1 AACGGGACCAAGAGGGCA
50790 AACGGGACCAAGAGGGCA
1 AACGGGACCAAGAGGGCA
50808 AA
1 AA
50810 AGCATAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.21, G:0.37, T:0.03
Consensus pattern (18 bp):
AACGGGACCAAGAGGGCA
Found at i:52467 original size:21 final size:21
Alignment explanation
Indices: 52443--52509 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
52433 AATTCTCTGT
52443 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
52464 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
52485 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
52506 AAAT
1 AAAT
52510 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:52489 original size:42 final size:42
Alignment explanation
Indices: 52430--52510 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
52420 GCTAAGTCTT
52430 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
52472 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
52511 CTGATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:53382 original size:174 final size:166
Alignment explanation
Indices: 53084--53411 Score: 426
Period size: 174 Copynumber: 1.9 Consensus size: 166
53074 TGAGTCATTT
* *
53084 GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATAAAATGTTAGGGTAT
1 GTCAATTGAGAAATGACCAAAAAGTCTAATTATTTAATCCCCTCAAAAATAAAATGTTAGGGTAT
* * * * *
53149 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCCAACTCATCATTAATCCGGG
66 TTAAGTAATCTACCAAGTAGGAAAAGACGAAAAAAATTAGTTATCCAACTCATCATTAATCAGGG
53214 GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
131 GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
53250 GTCAATTGAGAAATGAGCAAAAAGTCTAGTTATTTAATCCCCTCAAAAATCAAAA-GTTAGGACA
1 GTCAATTGAGAAATGACCAAAAAGTCTAATTATTTAATCCCCTCAAAAAT-AAAATGTTAGG---
* * * * *
53314 TTTATTTATTTAAGTAATCTATCAAGTGGGAAAAGACGAAAAAAATTAGTTATCTC-GCTCCTCA
62 -----GTATTTAAGTAATCTACCAAGTAGGAAAAGACGAAAAAAATTAGTTATC-CAACTCATCA
53378 TTAATCAGGGGTAGGGATCTTTTAGTAATTCCAC
121 TTAATCAGGGGTAGGGATCTTTTAGTAATTCCAC
53412 ATGTTTATTC
Statistics
Matches: 138, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
166 52 0.38
167 4 0.03
174 81 0.59
175 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAGTCTAATTATTTAATCCCCTCAAAAATAAAATGTTAGGGTAT
TTAAGTAATCTACCAAGTAGGAAAAGACGAAAAAAATTAGTTATCCAACTCATCATTAATCAGGG
GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:54252 original size:2 final size:2
Alignment explanation
Indices: 54245--54301 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
54235 TGATACTAAT
54245 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
54287 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
54302 ATATATATAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:54306 original size:2 final size:2
Alignment explanation
Indices: 54301--54334 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54291 TCTCTCTCTC
54301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54335 CCTTCATTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55296 original size:13 final size:13
Alignment explanation
Indices: 55278--55302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55268 TTTGGAATTC
55278 TAAATAATATTTA
1 TAAATAATATTTA
55291 TAAATAATATTT
1 TAAATAATATTT
55303 GAAACAATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATAATATTTA
Found at i:55893 original size:5 final size:5
Alignment explanation
Indices: 55883--55918 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
55873 GTGCGGGAAA
55883 AATAT AATAT AAT-T -ATAT AATAT AATAT AATAT AAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT
55919 TATACTCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 25 0.86
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:55902 original size:13 final size:13
Alignment explanation
Indices: 55884--55922 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
55874 TGCGGGAAAA
55884 ATATAATATAATT
1 ATATAATATAATT
55897 ATATAATAT-A--
1 ATATAATATAATT
55907 ATATAATATAATT
1 ATATAATATAATT
55920 ATA
1 ATA
55923 CTCTCTCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
12 1 0.04
13 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATAATATAATT
Found at i:57543 original size:57 final size:57
Alignment explanation
Indices: 57481--57599 Score: 202
Period size: 57 Copynumber: 2.1 Consensus size: 57
57471 AATGGTAAAA
* * * *
57481 TAAAATAGTTATAAGGATATTAGATTTAATTAAATAAATATAGAGTTTTTAGTTGAG
1 TAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAATGTTTAGTTGAG
57538 TAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAATGTTTAGTTGAG
1 TAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAATGTTTAGTTGAG
57595 TAAAA
1 TAAAA
57600 CTATAAAAGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (57 bp):
TAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAATGTTTAGTTGAG
Found at i:57560 original size:28 final size:29
Alignment explanation
Indices: 57479--57573 Score: 84
Period size: 29 Copynumber: 3.3 Consensus size: 29
57469 AAAATGGTAA
* *
57479 AATAAAATAGTTATAAGGATATTAGATTT
1 AATAAAATAGTTATAAAGATATTAGATTG
* ** * * *
57508 AATTAAATAAATATAGAGTTTTTAG-TTG
1 AATAAAATAGTTATAAAGATATTAGATTG
* *
57536 AGTAAAATAGTTATAAAGATATTAGATTT
1 AATAAAATAGTTATAAAGATATTAGATTG
*
57565 AATTAAATA
1 AATAAAATA
57574 AAAATAGAAT
Statistics
Matches: 47, Mismatches: 18, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
28 20 0.43
29 27 0.57
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (29 bp):
AATAAAATAGTTATAAAGATATTAGATTG
Found at i:60262 original size:6 final size:6
Alignment explanation
Indices: 60251--60280 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
60241 CACGAGGGCG
*
60251 GCCACA GCCACA GCCACA GCCGCA GCCACA
1 GCCACA GCCACA GCCACA GCCACA GCCACA
60281 ACCGCAGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.50, G:0.20, T:0.00
Consensus pattern (6 bp):
GCCACA
Found at i:60285 original size:12 final size:12
Alignment explanation
Indices: 60251--60289 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
60241 CACGAGGGCG
*
60251 GCCACAGCCACA
1 GCCACAGCCGCA
60263 GCCACAGCCGCA
1 GCCACAGCCGCA
*
60275 GCCACAACCGCA
1 GCCACAGCCGCA
60287 GCC
1 GCC
60290 TAAAAAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.28, C:0.51, G:0.21, T:0.00
Consensus pattern (12 bp):
GCCACAGCCGCA
Found at i:60288 original size:18 final size:18
Alignment explanation
Indices: 60255--60289 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60245 AGGGCGGCCA
*
60255 CAGCCACAGCCACAGCCG
1 CAGCCACAACCACAGCCG
*
60273 CAGCCACAACCGCAGCC
1 CAGCCACAACCACAGCC
60290 TAAAAAGGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.51, G:0.20, T:0.00
Consensus pattern (18 bp):
CAGCCACAACCACAGCCG
Found at i:61313 original size:13 final size:13
Alignment explanation
Indices: 61295--61321 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
61285 CTCCGTCCCA
61295 AAAGTATAAGCTC
1 AAAGTATAAGCTC
61308 AAAGTATAAGCTC
1 AAAGTATAAGCTC
61321 A
1 A
61322 TTTGCTTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (13 bp):
AAAGTATAAGCTC
Found at i:62938 original size:45 final size:45
Alignment explanation
Indices: 62839--62947 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 45
62829 AAAACTAAAC
** ** * *
62839 CCTATACAAAATAAAGGCCTTTTCTAGATCATTGCAAGTTAGTGA
1 CCTATACAAAATAAAGGCCTCATCTAGAAAATGGCAAATTAGTGA
* * *
62884 TCTACACAAAATAAATGCCTCATCTAGAAAATGGCAAATTAAG-GA
1 CCTATACAAAATAAAGGCCTCATCTAGAAAATGGCAAATT-AGTGA
62929 CCTATACAAAATAAGAGGC
1 CCTATACAAAATAA-AGGC
62948 TGCTTTTCTA
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
45 45 0.90
46 5 0.10
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (45 bp):
CCTATACAAAATAAAGGCCTCATCTAGAAAATGGCAAATTAGTGA
Found at i:66176 original size:95 final size:97
Alignment explanation
Indices: 65942--66224 Score: 394
Period size: 95 Copynumber: 2.9 Consensus size: 97
65932 TTATTAAATG
* *
65942 TATTATC-ATTTGGAAGCGGATTTAAACACGGATATGTAGTTTCCCTGTTAAATTCCGTTT-CAA
1 TATTATCAATTT-GAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
66005 ATGAAATAAAAGATTTATTTATAGAATAATTTTAT
65 ATGAAATAAAA-ATTTATTTATAGAAT-ATTTTAT
* ** *
66040 TATTATCAATTAGAAGCGGATTTAGACACAAATATGTAGTTTCCGTGTTAAATTTCGTTTCCAAA
1 TATTATCAATTTGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAAA
66105 TGAAAT-AAAATTTATTTATAGAAT-TTTTAT
66 TGAAATAAAAATTTATTTATAGAATATTTTAT
* * * * *
66135 TATTATCAATTTGAATCGGATTTTGACACGGATATGCAGTTTCCGTGTTAAATTCCGTTGCCAAG
1 TATTATCAATTTGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAAA
*
66200 TGAAATAGAAAATTAATTTATAGAA
66 TGAAATA-AAAATTTATTTATAGAA
66225 GATAGTATTT
Statistics
Matches: 165, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
95 68 0.41
97 31 0.19
98 53 0.32
99 13 0.08
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (97 bp):
TATTATCAATTTGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAAA
TGAAATAAAAATTTATTTATAGAATATTTTAT
Found at i:66564 original size:99 final size:99
Alignment explanation
Indices: 66413--66601 Score: 360
Period size: 99 Copynumber: 1.9 Consensus size: 99
66403 ATATTATCAT
* *
66413 TTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAAATGAAATAGA
1 TTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTATTAAATTCCGTTTCCAAATGAAATAAA
66478 AAAATTATTTATAGAATTTAGTACTTATTACCGG
66 AAAATTATTTATAGAATTTAGTACTTATTACCGG
66512 TTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTATTAAATTCCGTTTCCAAATGAAATAAA
1 TTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTATTAAATTCCGTTTCCAAATGAAATAAA
66577 AAAATTATTTATAGAATTTAGTACT
66 AAAATTATTTATAGAATTTAGTACT
66602 CATCTTCATC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 88 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (99 bp):
TTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTATTAAATTCCGTTTCCAAATGAAATAAA
AAAATTATTTATAGAATTTAGTACTTATTACCGG
Found at i:70884 original size:18 final size:19
Alignment explanation
Indices: 70861--70898 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
70851 GTGCATGGGT
*
70861 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
70879 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
70898 T
1 T
70899 AACGATGGAC
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:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:74727 original size:2 final size:2
Alignment explanation
Indices: 74722--74746 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
74712 AAGTCCAAGC
74722 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 A
74747 CATAAAGCTC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76006 original size:13 final size:12
Alignment explanation
Indices: 75975--76013 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
75965 CCTCCTCTGT
75975 TTTCTTTTTGTA
1 TTTCTTTTTGTA
75987 TTT-TTTTTGTA
1 TTTCTTTTTGTA
*
75998 TCTTCTTTTGGTA
1 T-TTCTTTTTGTA
76011 TTT
1 TTT
76014 TTTCTACTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 9 0.38
12 7 0.29
13 8 0.33
ACGTcount: A:0.08, C:0.08, G:0.10, T:0.74
Consensus pattern (12 bp):
TTTCTTTTTGTA
Found at i:77869 original size:47 final size:46
Alignment explanation
Indices: 77800--77892 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 46
77790 AGACTATTCA
* *
77800 ACCATAAGAGAATTAAAAGGAATAACACCCAAAATTAAAAGGAGGAT
1 ACCATAAGAAAATTAAAAGGAATAA-AACCAAAATTAAAAGGAGGAT
*
77847 ACCATAAGAAAATTAAAAGGAATAAAACCAACATTAAAAGGAGGAT
1 ACCATAAGAAAATTAAAAGGAATAAAACCAAAATTAAAAGGAGGAT
77893 TGGATTGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
46 19 0.44
47 24 0.56
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.15
Consensus pattern (46 bp):
ACCATAAGAAAATTAAAAGGAATAAAACCAAAATTAAAAGGAGGAT
Found at i:78449 original size:39 final size:38
Alignment explanation
Indices: 78361--78940 Score: 273
Period size: 39 Copynumber: 15.0 Consensus size: 38
78351 GTTTGATTCG
* * * *
78361 ACGAAAC-TCTAAGCATAGACCTAAACAGGTTCACTTAA
1 ACGAAACTTCTAAACA-GGACCTAAGCAGGTTTACTTAA
*
78399 GCGAGAA-TTCTAAACACGGACCTAAGCAGGTTTGA-TTAA
1 ACGA-AACTTCTAAACA-GGACCTAAGCAGGTTT-ACTTAA
**
78438 ACGAAACTTCTAAA-AGAAGACCTAAGCAGGTTTACTCGA
1 ACGAAACTTCTAAACAG--GACCTAAGCAGGTTTACTTAA
*
78477 ATG-AAC-TC-AAAGCAGAGATCCTAAGCAGGTTTACTTAA
1 ACGAAACTTCTAAA-CAG-GA-CCTAAGCAGGTTTACTTAA
* *
78515 ACGGAGA-TTCTAAACAAAGACCTAAGCAGGTTTACTTGAA
1 AC-GAAACTTCTAAAC-AGGACCTAAGCAGGTTTACTT-AA
** * * ** *
78555 TGGCAAC-TCAAAATGGGGACCTAAGCAGGTTTACTTGA
1 ACGAAACTTCTAAA-CAGGACCTAAGCAGGTTTACTTAA
* * *
78593 TC-AAAGC-TCTAAGCGGAGATCCTAAGCAGGTTTA-TATAA
1 ACGAAA-CTTCTAAACAG-GA-CCTAAGCAGGTTTACT-TAA
*
78632 ACGGAAA-TTCTAAACAAGGACATAAGCAGGTTTGA-TTAA
1 AC-GAAACTTCTAAAC-AGGACCTAAGCAGGTTT-ACTTAA
* * *
78671 ACGAAACTCCTAAA-TGTAGACCTAAGCGGGTTTACTTAA
1 ACGAAACTTCTAAACAG--GACCTAAGCAGGTTTACTTAA
* * * * * *
78710 ACGGAAGTTCAAAACAAGGACGTAAGCAGGTTCACTGAA
1 ACGAAACTTCTAAAC-AGGACCTAAGCAGGTTTACTTAA
* * **
78749 ACGAAAATTATAAACAGAGACCTAAGCAGGTTTAAC-CGA
1 ACGAAACTTCTAAACAG-GACCTAAGCAGGTTT-ACTTAA
* * * * *
78788 GCGAGA-TTCTAAGCGGGGACCTAAGCAGGTTTTCTTAA
1 ACGAAACTTCTAAAC-AGGACCTAAGCAGGTTTACTTAA
* * *
78826 AC-AGAACTTCTAAGCAGAGACCTAAGCAGGTTTTCTTAT
1 ACGA-AACTTCTAAACAG-GACCTAAGCAGGTTTACTTAA
* * * * *
78865 ATGAGA-TTCTGAACATAGACCTAAACAGGTTTACTTAA
1 ACGAAACTTCTAAACA-GGACCTAAGCAGGTTTACTTAA
* * ***
78903 ATGGCAACTT-TGAATGGGGACCTAAGCAGGTTTACTTA
1 A-CGAAACTTCT-AAACAGGACCTAAGCAGGTTTACTTA
78941 GACAAAGACC
Statistics
Matches: 413, Mismatches: 84, Indels: 89
0.70 0.14 0.15
Matches are distributed among these distances:
36 3 0.01
37 13 0.03
38 98 0.24
39 265 0.64
40 25 0.06
41 9 0.02
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (38 bp):
ACGAAACTTCTAAACAGGACCTAAGCAGGTTTACTTAA
Found at i:78646 original size:117 final size:117
Alignment explanation
Indices: 78367--78956 Score: 413
Period size: 116 Copynumber: 5.1 Consensus size: 117
78357 TTCGACGAAA
* * * * **
78367 CTCTAAGCATAGACCTAAACAGGTTCACTTAAGC-GAGAATTCTAAACACGGACCTAAGCAGGTT
1 CTCTAAGCAGAGACCTAAGCAGGTTTACTTAAACGGA-AATTCTAAACAAAGACCTAAGCAGGTT
* ** * * ** * **
78431 TGA-TT-AAACGAAACTTCTAAAAGAAGACCTAAGCAGGTTTACTCGAATGAA-
65 TAACTTGAATGGCAAC-TCTAAATGGGGACCTAAGCAGGTTTACTTGAACAAAG
* *
78482 CTCAAAGCAGAGATCCTAAGCAGGTTTACTTAAACGGAGATTCTAAACAAAGACCTAAGCAGGTT
1 CTCTAAGCAGAGA-CCTAAGCAGGTTTACTTAAACGGAAATTCTAAACAAAGACCTAAGCAGGTT
* *
78547 T-ACTTGAATGGCAACTCAAAATGGGGACCTAAGCAGGTTTACTTGATCAAAG
65 TAACTTGAATGGCAACTCTAAATGGGGACCTAAGCAGGTTTACTTGAACAAAG
* * *
78599 CTCTAAGCGGAGATCCTAAGCAGGTTTA-TATAAACGGAAATTCTAAACAAGGACATAAGCAGGT
1 CTCTAAGCAGAGA-CCTAAGCAGGTTTACT-TAAACGGAAATTCTAAACAAAGACCTAAGCAGGT
* ** * ** * * *
78663 TTGA-TT-AAACGAAACTCCTAAATGTAGACCTAAGCGGGTTTACTTAAACGGAAG
64 TTAACTTGAATGGCAACT-CTAAATGGGGACCTAAGCAGGTTTACTTGAAC-AAAG
* * * * * * * * *
78717 TTCAAAACA-AGGACGTAAGCAGGTTCACTGAAACGAAAATTATAAACAGAGACCTAAGCAGGTT
1 CTCTAAGCAGA-GACCTAAGCAGGTTTACTTAAACGGAAATTCTAAACAAAGACCTAAGCAGGTT
* * ** * *
78781 TAAC-CG-A--GCGAGATTCTAAGCGGGGACCTAAGCAGGTTTTCTTAAACAGAA-
65 TAACTTGAATGGC-A-ACTCTAAATGGGGACCTAAGCAGGTTTACTTGAACA-AAG
* * * * * * *
78832 CTTCTAAGCAGAGACCTAAGCAGGTTTTCTTATA-TGAGATTCTGAACATAGACCTAAACAGGTT
1 C-TCTAAGCAGAGACCTAAGCAGGTTTACTTAAACGGAAATTCTAAACAAAGACCTAAGCAGGTT
* * *
78896 T-ACTTAAATGGCAACTTTGAATGGGGACCTAAGCAGGTTTACTT-AGACAAAG
65 TAACTTGAATGGCAACTCTAAATGGGGACCTAAGCAGGTTTACTTGA-ACAAAG
*
78948 ACCCTAAGC
1 -CTCTAAGC
78957 CAAGAGAAAC
Statistics
Matches: 369, Mismatches: 81, Indels: 49
0.74 0.16 0.10
Matches are distributed among these distances:
114 2 0.01
115 40 0.11
116 168 0.46
117 145 0.39
118 14 0.04
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (117 bp):
CTCTAAGCAGAGACCTAAGCAGGTTTACTTAAACGGAAATTCTAAACAAAGACCTAAGCAGGTTT
AACTTGAATGGCAACTCTAAATGGGGACCTAAGCAGGTTTACTTGAACAAAG
Done.