Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018679.1 Corchorus olitorius cultivar O-4 contig18712, 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: 64836
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:5629 original size:50 final size:51
Alignment explanation
Indices: 5552--5653 Score: 197
Period size: 50 Copynumber: 2.0 Consensus size: 51
5542 AAATATAGAT
5552 GAGACAAGTAATAAAACTCTTTTGACTATACTATTCTAAGATTTTATACAC
1 GAGACAAGTAATAAAACTCTTTTGACTATACTATTCTAAGATTTTATACAC
5603 GAGACAAGTAAT-AAACTCTTTTGACTATACTATTCTAAGATTTTATACAC
1 GAGACAAGTAATAAAACTCTTTTGACTATACTATTCTAAGATTTTATACAC
5653 G
1 G
5654 GTTGAGAACT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 39 0.76
51 12 0.24
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (51 bp):
GAGACAAGTAATAAAACTCTTTTGACTATACTATTCTAAGATTTTATACAC
Found at i:12040 original size:21 final size:23
Alignment explanation
Indices: 12004--12046 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11994 ATTTCCTGTT
*
12004 TCAACCTTGCAAAA-GGTTGAAC
1 TCAACCTTGAAAAAGGGTTGAAC
12026 TCAACC-TGAAAAAGGGTTGAA
1 TCAACCTTGAAAAAGGGTTGAA
12047 ACATCCCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (23 bp):
TCAACCTTGAAAAAGGGTTGAAC
Found at i:16825 original size:51 final size:51
Alignment explanation
Indices: 16749--16852 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
16739 ACCCACATAG
16749 GTTGAGTGCAAACACGAGAGCAAATTATGGTAAATAGGTGTGTGTGTGTGT
1 GTTGAGTGCAAACACGAGAGCAAATTATGGTAAATAGGTGTGTGTGTGTGT
16800 GTTGAGTGCAAACACGAGAGCAAATTATGGTAAATAGGTGTGTGTGTGTGT
1 GTTGAGTGCAAACACGAGAGCAAATTATGGTAAATAGGTGTGTGTGTGTGT
16851 GT
1 GT
16853 GTGTGTATGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.29, C:0.08, G:0.34, T:0.30
Consensus pattern (51 bp):
GTTGAGTGCAAACACGAGAGCAAATTATGGTAAATAGGTGTGTGTGTGTGT
Found at i:19484 original size:41 final size:43
Alignment explanation
Indices: 19439--19524 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 43
19429 GGGATCTTTC
19439 CCTAAATCGAAAACTTT-G-AAAAAAACTTGAATTGGATACTT
1 CCTAAATCGAAAACTTTGGAAAAAAAACTTGAATTGGATACTT
*
19480 CCTAAATTGAAAACTTTGGAAAAAAAAAACTTGAATTGGATACTT
1 CCTAAATCGAAAACTTTGG--AAAAAAAACTTGAATTGGATACTT
19525 TGAAAACTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
41 16 0.40
42 1 0.03
45 23 0.57
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (43 bp):
CCTAAATCGAAAACTTTGGAAAAAAAACTTGAATTGGATACTT
Found at i:19555 original size:38 final size:37
Alignment explanation
Indices: 19513--19603 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 37
19503 AAAAAACTTG
*
19513 AATTGGATACTTTGAAAACTTGATGGGAACTTTCCCTA
1 AATTGAATACTTTGAAAACTTGAT-GGAACTTTCCCTA
*
19551 AATTGAATGCTTTGAAAACTTGATGGAACTTTCCC-A
1 AATTGAATACTTTGAAAACTTGATGGAACTTTCCCTA
* *
19587 ATTTGAAAAACTTTGAA
1 AATTG-AATACTTTGAA
19604 GGAAATTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
36 5 0.11
37 20 0.43
38 22 0.47
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (37 bp):
AATTGAATACTTTGAAAACTTGATGGAACTTTCCCTA
Found at i:19601 original size:37 final size:38
Alignment explanation
Indices: 19521--19603 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 38
19511 TGAATTGGAT
*
19521 ACTTTGAAAACTTGATGGGAACTTTCCCTAAATTGAAT
1 ACTTTGAAAACTTGATGGGAACTTTCCCTAAATTGAAA
* *
19559 GCTTTGAAAACTTGAT-GGAACTTTCCC-AATTTGAAAA
1 ACTTTGAAAACTTGATGGGAACTTTCCCTAAATTG-AAA
19596 ACTTTGAA
1 ACTTTGAA
19604 GGAAATTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 5 0.12
37 20 0.50
38 15 0.38
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (38 bp):
ACTTTGAAAACTTGATGGGAACTTTCCCTAAATTGAAA
Found at i:23896 original size:23 final size:23
Alignment explanation
Indices: 23869--23913 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
23859 CATTGAAGTA
*
23869 AATTGGAGCATTGAAGAATTGAG
1 AATTGGAACATTGAAGAATTGAG
*
23892 AATTGGAACATTGAATAATTGA
1 AATTGGAACATTGAAGAATTGA
23914 AGAAAGACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.29
Consensus pattern (23 bp):
AATTGGAACATTGAAGAATTGAG
Found at i:23916 original size:73 final size:74
Alignment explanation
Indices: 23829--23970 Score: 241
Period size: 73 Copynumber: 1.9 Consensus size: 74
23819 CGAGAATAAG
*
23829 TTGAAGAATTGAAGAAAGACCACCCAGGATCATTGAAGTAAATTGGAGCATTGAAGAATTG-AGA
1 TTGAAGAATTGAAGAAAGACCACCCAGGATCATTGAAGTAAATTGAAGCATTGAAGAATTGAAGA
23893 ATTGGAACA
66 ATTGGAACA
* * *
23902 TTGAATAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATAATTGAAGA
1 TTGAAGAATTGAAGAAAGACCACCCAGGATCATTGAAGTAAATTGAAGCATTGAAGAATTGAAGA
23967 ATTG
66 ATTG
23971 AAGAAAGACC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 57 0.89
74 7 0.11
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (74 bp):
TTGAAGAATTGAAGAAAGACCACCCAGGATCATTGAAGTAAATTGAAGCATTGAAGAATTGAAGA
ATTGGAACA
Found at i:23956 original size:8 final size:8
Alignment explanation
Indices: 23942--23975 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
23932 CATTGAAGTA
23942 AATTGAAG
1 AATTGAAG
* *
23950 CATTGAAT
1 AATTGAAG
23958 AATTGAAG
1 AATTGAAG
23966 AATTGAAG
1 AATTGAAG
23974 AA
1 AA
23976 AGACCACCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (8 bp):
AATTGAAG
Found at i:23963 original size:16 final size:18
Alignment explanation
Indices: 23932--23973 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
23922 CACCCTGGAT
23932 CATTGAAGTAAATTGAAG
1 CATTGAAGTAAATTGAAG
23950 CATTGAA-T-AATTGAAG
1 CATTGAAGTAAATTGAAG
*
23966 AATTGAAG
1 CATTGAAG
23974 AAAGACCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 14 0.64
17 1 0.05
18 7 0.32
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (18 bp):
CATTGAAGTAAATTGAAG
Found at i:23970 original size:58 final size:58
Alignment explanation
Indices: 23901--24145 Score: 361
Period size: 58 Copynumber: 4.3 Consensus size: 58
23891 GAATTGGAAC
*
23901 ATTGAATAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATA
1 ATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATA
*
23959 ATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGGAGTAAATTGAAGCATTGAATA
1 ATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATA
*
24017 ATTGAAGAATTGAAGAAAGACCATCCTGGATCATTCG-AGTAAATTGAAGCATTGAATA
1 ATTGAAGAATTGAAGAAAGACCACCCTGGATCATT-GAAGTAAATTGAAGCATTGAATA
* * ** * * * *
24075 ACTGAAGAGTTGAAGAAAGACCACTATGGATAATTGAAGTAAATTGAAACATTAAAGA
1 ATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATA
24133 ATTG-A-AATTGAAG
1 ATTGAAGAATTGAAG
24146 CATTGAAGTA
Statistics
Matches: 171, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
56 7 0.04
57 2 0.01
58 161 0.94
59 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.25
Consensus pattern (58 bp):
ATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATA
Found at i:24012 original size:8 final size:8
Alignment explanation
Indices: 24000--24033 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
23990 CATTGGAGTA
24000 AATTGAAG
1 AATTGAAG
* *
24008 CATTGAAT
1 AATTGAAG
24016 AATTGAAG
1 AATTGAAG
24024 AATTGAAG
1 AATTGAAG
24032 AA
1 AA
24034 AGACCATCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (8 bp):
AATTGAAG
Found at i:24167 original size:22 final size:22
Alignment explanation
Indices: 24115--24167 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
24105 TAATTGAAGT
*
24115 AAATTGAAACATTAAAGAATTG
1 AAATTGAAGCATTAAAGAATTG
* *
24137 AAATTGAAGCATTGAAGTATTG
1 AAATTGAAGCATTAAAGAATTG
24159 AAATTGAAG
1 AAATTGAAG
24168 AAAGACTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (22 bp):
AAATTGAAGCATTAAAGAATTG
Found at i:24184 original size:136 final size:137
Alignment explanation
Indices: 23999--24304 Score: 436
Period size: 136 Copynumber: 2.2 Consensus size: 137
23989 TCATTGGAGT
* *
23999 AAATTGAAGCATTGAA-TAATTGAAGAATTGAAGAAAGACCATCCTGGATCATTCGAGTAAATTG
1 AAATTGAAGCATTGAAGT-ATTG-A-AATTGAAGAAAGACCACCCTGGATCATTCGAGTAAATTA
* *
24063 AAGCATTGAATAACTGAAGAGTTGAAGAAAGACCACTATGGATAATTGAAGTAAATTGAAACATT
63 AAGCATTGAATAACTGAAGAATTGAAGAAAGACCACCATGGATAATTGAAGTAAATTGAAACATT
24128 -AAAGAATTG
128 GAAAGAATTG
* *
24137 AAATTGAAGCATTGAAGTATTGAAATTGAAGAAAGACTACCCTGGATCATTGGAGTAAATTAAAG
1 AAATTGAAGCATTGAAGTATTGAAATTGAAGAAAGACCACCCTGGATCATTCGAGTAAATTAAAG
* * * * * *
24202 TATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGGAGTAAATTGAAGCATTGAA
66 CATTGAATAACTGAAGAATTGAAGAAAGACCACCATGGATAATTGAAGTAAATTGAAACATTGAA
*
24267 GGAATTG
131 AGAATTG
* *
24274 AAATTGAAGCATTAAAGAATTGAAATTGAAG
1 AAATTGAAGCATTGAAGTATTGAAATTGAAG
24305 CATTGAAGAA
Statistics
Matches: 151, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
136 92 0.61
137 38 0.25
138 20 0.13
139 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (137 bp):
AAATTGAAGCATTGAAGTATTGAAATTGAAGAAAGACCACCCTGGATCATTCGAGTAAATTAAAG
CATTGAATAACTGAAGAATTGAAGAAAGACCACCATGGATAATTGAAGTAAATTGAAACATTGAA
AGAATTG
Found at i:24214 original size:78 final size:81
Alignment explanation
Indices: 24057--24225 Score: 195
Period size: 78 Copynumber: 2.1 Consensus size: 81
24047 TCATTCGAGT
*
24057 AAATTGAAGCATTGAATAACTGAAGAGTTGAAGAAAGACCACTATGGATAATTGAAGTAAATTGA
1 AAATTGAAGCATTGAATAACTGAAGAGTTGAAGAAAGACCACCATGGATAATTGAAGTAAATTGA
24122 AACATTAAAGAATTG-
66 AACATTAAAGAATTGA
* * * * *
24137 AAATTGAAGCATTGAAGT-ATTGAA-A-TTGAAGAAAGACTACCCTGGATCATTGGAGTAAATT-
1 AAATTGAAGCATTGAA-TAACTGAAGAGTTGAAGAAAGACCACCATGGATAATTGAAGTAAATTG
* * *
24198 AAAGTATTGAATAATTGA
65 AAA-CATTAAAGAATTGA
24216 AGAATTGAAG
1 A-AATTGAAG
24226 AAAGACCACC
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
77 3 0.04
78 41 0.54
79 2 0.03
80 29 0.38
81 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.27
Consensus pattern (81 bp):
AAATTGAAGCATTGAATAACTGAAGAGTTGAAGAAAGACCACCATGGATAATTGAAGTAAATTGA
AACATTAAAGAATTGA
Found at i:24237 original size:58 final size:57
Alignment explanation
Indices: 24137--24282 Score: 206
Period size: 58 Copynumber: 2.6 Consensus size: 57
24127 TAAAGAATTG
* * *
24137 AAATTGAAGCATTGAA-GTATTGAAATTGAAGAAAGACTACCCTGGATCATTGGAGT
1 AAATTAAAGCATTGAAGGAATTGAAATTGAAGAAAGACCACCCTGGATCATTGGAGT
* *
24193 AAATTAAAGTATTGAA-TAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGGAGT
1 AAATTAAAGCATTGAAGGAATTG-A-AATTGAAGAAAGACCACCCTGGATCATTGGAGT
*
24251 AAATTGAAGCATTGAAGGAATTGAAATTGAAG
1 AAATTAAAGCATTGAAGGAATTGAAATTGAAG
24283 CATTAAAGAA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
56 18 0.23
57 9 0.11
58 47 0.59
59 5 0.06
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (57 bp):
AAATTAAAGCATTGAAGGAATTGAAATTGAAGAAAGACCACCCTGGATCATTGGAGT
Found at i:24275 original size:9 final size:8
Alignment explanation
Indices: 24252--24617 Score: 106
Period size: 8 Copynumber: 49.9 Consensus size: 8
24242 CATTGGAGTA
24252 AATTGAAG
1 AATTGAAG
*
24260 CATTGAAGG
1 AATTGAA-G
24269 AATTG-A-
1 AATTGAAG
24275 AATTGAAG
1 AATTGAAG
* *
24283 CATTAAAG
1 AATTGAAG
24291 AATTG-A-
1 AATTGAAG
24297 AATTGAAG
1 AATTGAAG
*
24305 CATTGAAG
1 AATTGAAG
24313 AATTG-A-
1 AATTGAAG
24319 AATTGAAG
1 AATTGAAG
*
24327 CATTG-A-
1 AATTGAAG
24333 AATTGAAG
1 AATTGAAG
*
24341 CATTGACA-
1 AATTGA-AG
*
24349 TATTG-A-
1 AATTGAAG
24355 AATTGAA-
1 AATTGAAG
24362 ACATTGAA-
1 A-ATTGAAG
24370 AGATTG-A-
1 A-ATTGAAG
*
24377 ATTTGAAG
1 AATTGAAG
24385 AATTG-A-
1 AATTGAAG
24391 AATTGAA-
1 AATTGAAG
24398 ACATTGAA-
1 A-ATTGAAG
24406 ATATTG-A-
1 A-ATTGAAG
24413 AATTGAA-
1 AATTGAAG
24420 ACATTGAAG
1 A-ATTGAAG
24429 AATTG-A-
1 AATTGAAG
*
24435 ATTTGAAG
1 AATTGAAG
*
24443 CATTGAA-
1 AATTGAAG
24450 ATATTG-A-
1 A-ATTGAAG
24457 AATTGAA-
1 AATTGAAG
24464 ACATTGAAG
1 A-ATTGAAG
*
24473 GATTG-A-
1 AATTGAAG
*
24479 ATTTGAAG
1 AATTGAAG
*
24487 AACTG-A-
1 AATTGAAG
24493 AATTGAA-
1 AATTGAAG
24500 ACATTGAA-
1 A-ATTGAAG
24508 ATATTG-A-
1 A-ATTGAAG
24515 AATTGAA-
1 AATTGAAG
*
24522 ACATTAAAG
1 A-ATTGAAG
*
24531 GATTG-A-
1 AATTGAAG
*
24537 ATTTGAAG
1 AATTGAAG
24545 AATTG-A-
1 AATTGAAG
24551 AATTGAA-
1 AATTGAAG
24558 ACATTGAAG
1 A-ATTGAAG
*
24567 GATTG-A-
1 AATTGAAG
*
24573 ATTTGAAG
1 AATTGAAG
24581 AATTG-A-
1 AATTGAAG
24587 AATTGAA-
1 AATTGAAG
24594 ACATTGAAG
1 A-ATTGAAG
*
24603 CATTGAAG
1 AATTGAAG
24611 AATTGAA
1 AATTGAA
24618 ATTGAGATCA
Statistics
Matches: 276, Mismatches: 40, Indels: 84
0.69 0.10 0.21
Matches are distributed among these distances:
6 71 0.26
7 44 0.16
8 154 0.56
9 7 0.03
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.30
Consensus pattern (8 bp):
AATTGAAG
Found at i:24331 original size:22 final size:22
Alignment explanation
Indices: 24251--24333 Score: 148
Period size: 22 Copynumber: 3.7 Consensus size: 22
24241 TCATTGGAGT
24251 AAATTGAAGCATTGAAGGAATTG
1 AAATTGAAGCATTGAA-GAATTG
*
24274 AAATTGAAGCATTAAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
24296 AAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
24318 AAATTGAAGCATTGAA
1 AAATTGAAGCATTGAA
24334 ATTGAAGCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
22 43 0.74
23 15 0.26
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.27
Consensus pattern (22 bp):
AAATTGAAGCATTGAAGAATTG
Found at i:24332 original size:36 final size:37
Alignment explanation
Indices: 24292--24617 Score: 244
Period size: 36 Copynumber: 8.6 Consensus size: 37
24282 GCATTAAAGA
*
24292 ATTGAA-ATTGAAGCATTGAAGAATTGAAATTGAAGC
1 ATTGAAGATTGAAGCATTGAAGAATTGAAATTGAAAC
*
24328 ATTGAA-ATTGAAGCATTGACA-TATTGAAATTGAAAC
1 ATTGAAGATTGAAGCATTGA-AGAATTGAAATTGAAAC
*
24364 ATTGAAAGATTGAA--TTTGAAGAATTGAAATTGAAAC
1 ATTG-AAGATTGAAGCATTGAAGAATTGAAATTGAAAC
* * *
24400 ATTGAAATATTGAAATTGAAACATTGAAGAATTGAATTTGAAGC
1 ATTG--A-A--G--ATTGAAGCATTGAAGAATTGAAATTGAAAC
* * *
24444 ATTGAAATATTGAAATTGAAACATTGAAGGATTGAATTTGAAGA-
1 ATTG--A-A--G--ATTGAAGCATTGAAGAATTGAAATTGAA-AC
* *
24488 ACTGAA-ATTGAAACATTGAA-ATATTGAAATTGAAAC
1 ATTGAAGATTGAAGCATTGAAGA-ATTGAAATTGAAAC
* *
24524 ATTAAAGGATTGAA--TTTGAAGAATTGAAATTGAAAC
1 ATTGAA-GATTGAAGCATTGAAGAATTGAAATTGAAAC
*
24560 ATTGAAGGATTGAA--TTTGAAGAATTGAAATTGAAAC
1 ATTGAA-GATTGAAGCATTGAAGAATTGAAATTGAAAC
*
24596 ATTGAAGCATTGAAGAATTGAA
1 ATTGAAG-ATTGAAGCATTGAA
24618 ATTGAGATCA
Statistics
Matches: 252, Mismatches: 17, Indels: 40
0.82 0.06 0.13
Matches are distributed among these distances:
35 3 0.01
36 153 0.61
37 6 0.02
38 18 0.07
40 1 0.00
41 1 0.00
42 7 0.03
44 63 0.25
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (37 bp):
ATTGAAGATTGAAGCATTGAAGAATTGAAATTGAAAC
Found at i:24340 original size:58 final size:56
Alignment explanation
Indices: 24251--24622 Score: 266
Period size: 58 Copynumber: 6.2 Consensus size: 56
24241 TCATTGGAGT
24251 AAATTGAAGCATTGAAGGAATTGAAATTGAAGCATTAAAGAATTGAAATTGAAGCATTGA
1 AAATTGAA--ATTGAA-GAATTGAAATTGAAGCATTAAA-AATTGAAATTGAAGCATTGA
* * * *
24311 AGAATTGAAATTGAAGCATTGAAATTGAAGCATTGACATATTGAAATTGAAACATTGA
1 A-AATTGAAATTGAAGAATTGAAATTGAAGCATT-AAAAATTGAAATTGAAGCATTGA
* * * *
24369 AAGATTGAATTTGAAGAATTGAAATTGAAACATTGAAATATTGAAATTGAAACATTGA
1 AA-ATTGAAATTGAAGAATTGAAATTGAAGCATT-AAAAATTGAAATTGAAGCATTGA
* * ** * * *
24427 AGAATTGAATTTGAAGCATTGAAATATTGAAATTGAAACATTGAAGGATTGAATTTGAAGAACTG
1 A-AATTGAAATTG-A--A--G--A-ATTGAAATTGAAGCATT-AAAAATTGAAATTGAAGCATTG
24492 -
56 A
* * * *
24492 AAATTGAAACATTGAA-ATATTGAAATTGAAACATTAAAGGATTGAATTTGAAGAATTG-
1 AAATTG-AA-ATTGAAGA-ATTGAAATTGAAGCATTAAA-AATTGAAATTGAAGCATTGA
* * * *
24550 AAATTGAAACATTGAAGGATTGAATTTGAAGAATT-GAAATTGAAACATTGAAGCATTGA
1 AAATTG-AA-ATTGAAGAATTGAAATTGAAGCATTAAAAATTG-AA-ATTGAAGCATTGA
24609 AGAATTGAAATTGA
1 A-AATTGAAATTGA
24623 GATCATGTTG
Statistics
Matches: 267, Mismatches: 25, Indels: 42
0.80 0.07 0.13
Matches are distributed among these distances:
56 4 0.01
57 6 0.02
58 181 0.68
59 13 0.05
60 6 0.02
61 8 0.03
63 2 0.01
64 5 0.02
65 5 0.02
66 37 0.14
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.30
Consensus pattern (56 bp):
AAATTGAAATTGAAGAATTGAAATTGAAGCATTAAAAATTGAAATTGAAGCATTGA
Found at i:24345 original size:22 final size:19
Alignment explanation
Indices: 24269--24622 Score: 130
Period size: 22 Copynumber: 16.6 Consensus size: 19
24259 GCATTGAAGG
*
24269 AATTGAAATTGAAGCATTAAA
1 AATTGAAATTGAAG-ATT-GA
24290 GAATTGAAATTGAAGCATTG-
1 -AATTGAAATTGAAG-ATTGA
24310 AA--G-AATTGAA-ATTGA
1 AATTGAAATTGAAGATTGA
24325 AGCATTGAAATTGAAGCATTGA
1 A--ATTGAAATTGAAG-ATTGA
*
24347 CATATTGAAATTGAAACATTGAA
1 -A-ATTGAAATTG-AAGATTG-A
*
24370 AGATTGAATTTGAAGAATTGA
1 A-ATTGAAATTGAAG-ATTGA
*
24391 AATTGAAACATTGAAATATTGA
1 AATTG-AA-ATTG-AAGATTGA
24413 AATTGAAACATTGAAGAATTGA
1 AATTG-AA-ATTGAAG-ATTGA
* *
24435 ATTTGAAGCATTGAAATATTGA
1 AATTGAA--ATTG-AAGATTGA
24457 AATTGAAACATTGAAGGATTGA
1 AATTG-AA-ATTGAA-GATTGA
* *
24479 ATTTGAAGAACTGAA-ATTGAA
1 AATTG-A-AATTGAAGATTG-A
24500 ACATTGAAATATTGAA-ATTGAA
1 A-ATTG-AA-ATTGAAGATTG-A
* *
24522 ACATTAAAGGATTGAA-TTTGAA
1 A-ATTGAA--ATTGAAGATTG-A
*
24544 GAATTGAAATTGAAACATTGA
1 -AATTGAAATTG-AAGATTGA
*
24565 AGGATTGAATTTGAAGAATTGA
1 A--ATTGAAATTGAAG-ATTGA
24587 AATTGAAACATTGAAGCATTGAA
1 AATTG-AA-ATTGAAG-ATTG-A
24610 GAATTGAAATTGA
1 -AATTGAAATTGA
24623 GATCATGTTG
Statistics
Matches: 271, Mismatches: 26, Indels: 70
0.74 0.07 0.19
Matches are distributed among these distances:
14 4 0.01
15 1 0.00
16 7 0.03
17 2 0.01
19 3 0.01
20 24 0.09
21 24 0.09
22 186 0.69
23 15 0.06
24 5 0.02
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (19 bp):
AATTGAAATTGAAGATTGA
Found at i:25848 original size:50 final size:50
Alignment explanation
Indices: 25784--25884 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
25774 TAAATTGCCC
*
25784 TTTGAAAAGAGAATTTCGATCTTGGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAGAGAATTTCGATCCTGGACTCACAAATGGAATGCAATCTTAT
* *
25834 TTTGAAAAGCGAATTTTGATCCTGGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAGAGAATTTCGATCCTGGACTCACAAATGGAATGCAATCTTAT
25884 T
1 T
25885 ATAAAACTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (50 bp):
TTTGAAAAGAGAATTTCGATCCTGGACTCACAAATGGAATGCAATCTTAT
Found at i:26831 original size:15 final size:15
Alignment explanation
Indices: 26811--26840 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26801 ATCAGGCTGC
*
26811 CACGATACACGATAT
1 CACGATACACAATAT
26826 CACGATACACAATAT
1 CACGATACACAATAT
26841 TTCAACCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:28499 original size:19 final size:20
Alignment explanation
Indices: 28472--28520 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
28462 CATATTTTTA
*
28472 TTTGATTTTTTTGTTTTTGT
1 TTTGATTTTGTTGTTTTTGT
*
28492 TTTG-TTTTGTTGTTTTTTT
1 TTTGATTTTGTTGTTTTTGT
28511 TTTGAATTTT
1 TTTG-ATTTT
28521 TTGATGGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 17 0.68
20 4 0.16
21 4 0.16
ACGTcount: A:0.06, C:0.00, G:0.14, T:0.80
Consensus pattern (20 bp):
TTTGATTTTGTTGTTTTTGT
Found at i:29332 original size:75 final size:75
Alignment explanation
Indices: 29209--29373 Score: 251
Period size: 75 Copynumber: 2.2 Consensus size: 75
29199 TTGTCTCCTT
* *
29209 AGTCCTTTGCTCACACCTTGAAACCATTACTTTGACTAAAACCGATTTTCAAACAT-TTTTCGAT
1 AGTCCTTTGCTCACACCTCGAAACCATTACTTTGACTAAAACCGATTTTCAAACATCCTTT-GAT
29273 TAAAACTCATC
65 TAAAACTCATC
* * *
29284 AGTCCTTTGCTCACACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCCTTTGATT
1 AGTCCTTTGCTCACACCTCGAAACCATTACTTTGACTAAAACCGATTTTCAAACATCCTTTGATT
29349 AAAACTCATC
66 AAAACTCATC
* *
29359 ATTCCTTTTCTCACA
1 AGTCCTTTGCTCACA
29374 ATCCAGATAA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
75 79 0.96
76 3 0.04
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.35
Consensus pattern (75 bp):
AGTCCTTTGCTCACACCTCGAAACCATTACTTTGACTAAAACCGATTTTCAAACATCCTTTGATT
AAAACTCATC
Found at i:34317 original size:13 final size:12
Alignment explanation
Indices: 34301--34330 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
34291 TTGTATTGGC
34301 TTTTTCTCTTTTT
1 TTTTTCT-TTTTT
34314 TTTTTCTTTTTT
1 TTTTTCTTTTTT
34326 TTTTT
1 TTTTT
34331 GCTGAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:48530 original size:15 final size:15
Alignment explanation
Indices: 48510--48540 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
48500 GATTAACCTG
48510 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
48525 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
48540 T
1 T
48541 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:51177 original size:16 final size:16
Alignment explanation
Indices: 51152--51223 Score: 72
Period size: 16 Copynumber: 4.5 Consensus size: 16
51142 AAAAAGATCG
*
51152 AACCCAAAAAAACTCA
1 AACCCGAAAAAACTCA
* * *
51168 AATCCGAAAAATCTGA
1 AACCCGAAAAAACTCA
* *
51184 TACCCGATAAAACTCA
1 AACCCGAAAAAACTCA
* *
51200 AACCCGAAAAAACCCG
1 AACCCGAAAAAACTCA
51216 AACCCGAA
1 AACCCGAA
51224 CCTGAAAAAA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.51, C:0.31, G:0.08, T:0.10
Consensus pattern (16 bp):
AACCCGAAAAAACTCA
Found at i:51221 original size:32 final size:31
Alignment explanation
Indices: 51150--51223 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
51140 AAAAAAAGAT
* * *
51150 CGAACCCAAAAAAACTCAAATCCGAAAAATC
1 CGAACCCGAAAAAACTCAAACCCGAAAAACC
* *
51181 TGATACCCGATAAAACTCAAACCCGAAAAAACC
1 CGA-ACCCGAAAAAACTCAAACCCG-AAAAACC
51214 CGAACCCGAA
1 CGAACCCGAA
51224 CCTGAAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
31 2 0.06
32 24 0.71
33 8 0.24
ACGTcount: A:0.50, C:0.31, G:0.09, T:0.09
Consensus pattern (31 bp):
CGAACCCGAAAAAACTCAAACCCGAAAAACC
Found at i:51541 original size:123 final size:128
Alignment explanation
Indices: 51412--51666 Score: 394
Period size: 131 Copynumber: 2.0 Consensus size: 128
51402 CATTGTTTAA
* *
51412 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATATAATATCCTTATCTA
51473 -TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
51535 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATATAATATCCTTAT--C
* * *
51600 TATTTTATTTTTACCATTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATA
64 TA-TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
51665 T
128 T
51666 A
1 A
51667 TTTCTTAAAT
Statistics
Matches: 118, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
123 53 0.45
124 1 0.01
125 1 0.01
126 1 0.01
129 2 0.02
131 60 0.51
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (128 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATATAATATCCTTATCTA
TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:51688 original size:14 final size:13
Alignment explanation
Indices: 51652--51690 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
51642 TATATATTAG
51652 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
51665 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
51679 AATTTTTTAAAT
1 AATTTTTTAAAT
51691 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:52583 original size:15 final size:15
Alignment explanation
Indices: 52563--52643 Score: 72
Period size: 16 Copynumber: 5.1 Consensus size: 15
52553 GTCAAAACCT
*
52563 AACCCGAACCGAATC
1 AACCCGAACCAAATC
* *
52578 AACCCGATCCAAATTT
1 AACCCGAACCAAA-TC
52594 AACCCGAATCCAAATC
1 AACCCGAA-CCAAATC
* * *
52610 AACCTGACCCAAATTT
1 AACCCGAACCAAA-TC
52626 AACCCGAATCCAAATC
1 AACCCGAA-CCAAATC
52642 AA
1 AA
52644 TCCAACCCAA
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
15 16 0.31
16 25 0.49
17 10 0.20
ACGTcount: A:0.42, C:0.35, G:0.07, T:0.16
Consensus pattern (15 bp):
AACCCGAACCAAATC
Found at i:52599 original size:16 final size:17
Alignment explanation
Indices: 52578--52661 Score: 79
Period size: 16 Copynumber: 5.2 Consensus size: 17
52568 GAACCGAATC
52578 AACCCG-ATCCAAATTT
1 AACCCGAATCCAAATTT
*
52594 AACCCGAATCCAAA-TC
1 AACCCGAATCCAAATTT
* *
52610 AACCTG-ACCCAAATTT
1 AACCCGAATCCAAATTT
*
52626 AACCCGAATCCAAA-TC
1 AACCCGAATCCAAATTT
* *
52642 AATCC-AACCCAAATTT
1 AACCCGAATCCAAATTT
52658 AACC
1 AACC
52662 TGATCTAACT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
15 13 0.25
16 27 0.51
17 13 0.25
ACGTcount: A:0.42, C:0.35, G:0.05, T:0.19
Consensus pattern (17 bp):
AACCCGAATCCAAATTT
Found at i:52622 original size:32 final size:31
Alignment explanation
Indices: 52562--52661 Score: 139
Period size: 32 Copynumber: 3.2 Consensus size: 31
52552 GGTCAAAACC
* *
52562 TAACCCGAA-CCGAATCAACCCGATCCAAATT
1 TAACCCGAATCCAAATCAA-CCGACCCAAATT
52593 TAACCCGAATCCAAATCAACCTGACCCAAATT
1 TAACCCGAATCCAAATCAACC-GACCCAAATT
*
52625 TAACCCGAATCCAAATCAATCCAACCCAAATT
1 TAACCCGAATCCAAATCAA-CCGACCCAAATT
52657 TAACC
1 TAACC
52662 TGATCTAACT
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
31 11 0.17
32 50 0.79
33 2 0.03
ACGTcount: A:0.41, C:0.35, G:0.06, T:0.18
Consensus pattern (31 bp):
TAACCCGAATCCAAATCAACCGACCCAAATT
Found at i:55414 original size:208 final size:202
Alignment explanation
Indices: 55033--55429 Score: 580
Period size: 205 Copynumber: 1.9 Consensus size: 202
55023 AATACTTTAG
* * * * *
55033 GCTCTTCATCATCATTAATATGATCAAAGAGTTCATGATTTTGGTTCAGAAGAACTACTAAAAGA
1 GCTCCTCATCATCACTAATATGATCAAAGAGTTAATGATTTTGATTCAGAAGAACTACTAAAAAA
* *
55098 TTTAGACCTTCAAATTCACCAATTTCTACAGTATTAGCTATAATTTGTTACATCAAACAGATAAT
66 TTTAGACCTTCAAATTCACCAATGTCTACAGTATTAGCTATAATGTGTTACATCAAACAGATAAT
** ** *
55163 GCCTGCTATGGTATAGCCAAACCTAGAAATCAACAAAGTGGAATGGGCAAAACACCAGCACCTTA
131 GCAGGCTACAGAATAGCCAAACCTAGAAATCAACAAAGTGGAATGGGC--AACACCAGCACCTTA
55228 TGCAGTCAT
194 TGCAGTCAT
* *
55237 GCTCCTCATCTTCACTAATATGATCAAAGAGTTAAATGATTTTGATTCAGAAGCAACTATTAAAA
1 GCTCCTCATCATCACTAATATGATCAAAGAGTT-AATGATTTTGATTCAGAAG-AACTACTAAAA
* *
55302 AATTTAGACCTTCAAATTCA-CAATGTCTACAGTATTAGCTTTAATGTGTTCAGCTTCAAACAGA
64 AATTTAGACCTTCAAATTCACCAATGTCTACAGTATTAGCTATAATGTGTT-A-CATCAAACAGA
55366 TAATGTCAGGCTACAGAATAGCCAAACCTAGAAATCAACAAAGTGGAATGGGCAACACCAGCAC
127 TAATG-CAGGCTACAGAATAGCCAAACCTAGAAATCAACAAAGTGGAATGGGCAACACCAGCAC
55430 TGGCAGTGGT
Statistics
Matches: 172, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
204 30 0.17
205 44 0.26
206 41 0.24
207 15 0.09
208 42 0.24
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (202 bp):
GCTCCTCATCATCACTAATATGATCAAAGAGTTAATGATTTTGATTCAGAAGAACTACTAAAAAA
TTTAGACCTTCAAATTCACCAATGTCTACAGTATTAGCTATAATGTGTTACATCAAACAGATAAT
GCAGGCTACAGAATAGCCAAACCTAGAAATCAACAAAGTGGAATGGGCAACACCAGCACCTTATG
CAGTCAT
Found at i:64143 original size:29 final size:31
Alignment explanation
Indices: 64108--64173 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
64098 AAATCAATTC
64108 AGGATATAACATT-T-CAAAAACGTCAAAAA
1 AGGATATAACATTATCCAAAAACGTCAAAAA
* * *
64137 AGGATATAACGTTATCCAAAAGCGTCAAATA
1 AGGATATAACATTATCCAAAAACGTCAAAAA
64168 AGGATA
1 AGGATA
64174 ATTTTGGACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 12 0.38
30 1 0.03
31 19 0.59
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.21
Consensus pattern (31 bp):
AGGATATAACATTATCCAAAAACGTCAAAAA
Done.