Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018770.1 Corchorus olitorius cultivar O-4 contig18803, 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: 68301
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:10137 original size:22 final size:22
Alignment explanation
Indices: 10112--10153 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10102 TGCAGCCATT
* *
10112 TTTGCTAATGTGCTTGATCTGA
1 TTTGCTAATGGGCTTCATCTGA
*
10134 TTTGTTAATGGGCTTCATCT
1 TTTGCTAATGGGCTTCATCT
10154 TTATATAGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (22 bp):
TTTGCTAATGGGCTTCATCTGA
Found at i:10218 original size:24 final size:24
Alignment explanation
Indices: 10186--10236 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
10176 ACTTTCCGCC
10186 CAATAGAAATAAAGTCTTCTAAAG
1 CAATAGAAATAAAGTCTTCTAAAG
10210 CAATAGAAATAAAGTCTTCTAAAG
1 CAATAGAAATAAAGTCTTCTAAAG
10234 CAA
1 CAA
10237 ACAAGGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (24 bp):
CAATAGAAATAAAGTCTTCTAAAG
Found at i:19001 original size:16 final size:16
Alignment explanation
Indices: 18980--19014 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
18970 TAAATTCAGA
18980 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
18996 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
19012 AAG
1 AAG
19015 TATTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:19161 original size:41 final size:41
Alignment explanation
Indices: 19104--19213 Score: 193
Period size: 41 Copynumber: 2.7 Consensus size: 41
19094 TTTTCGTTTG
19104 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
19145 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
19186 TTCAAGAACAAGTCATCGAGACCCTTGA
1 TTCAAGATCAAGTCATCGAGACCCTTGA
19214 TGAGTATACG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:23491 original size:73 final size:76
Alignment explanation
Indices: 23357--23512 Score: 264
Period size: 74 Copynumber: 2.1 Consensus size: 76
23347 AATTCTAACG
*
23357 TTTTTTTGCAGAAAACTTGAATTGGTAATTCTATTCTTCTTGTTTTTTTTTTCAACTCCTTTCAT
1 TTTTTTTGCAGAAAACTTGAATTGGTAAGTCTATTCTTCTTGTTTTTTTTTTCAACTCCTTTCAT
23422 TTTTTT-TT-A
66 TTTTTTATTAA
* *
23431 TTTTTTTGCCGAAAACTTGAATTGGTAAGTCTGTTCTTCTTG-TTTTTTTTTCAACTCCTTTCAT
1 TTTTTTTGCAGAAAACTTGAATTGGTAAGTCTATTCTTCTTGTTTTTTTTTTCAACTCCTTTCAT
23495 TTTTTTATTAA
66 TTTTTTATTAA
23506 TTTTTTT
1 TTTTTTT
23513 TTATTTTAAT
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
73 28 0.36
74 41 0.53
75 8 0.10
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (76 bp):
TTTTTTTGCAGAAAACTTGAATTGGTAAGTCTATTCTTCTTGTTTTTTTTTTCAACTCCTTTCAT
TTTTTTATTAA
Found at i:24076 original size:19 final size:21
Alignment explanation
Indices: 24023--24079 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
24013 ATTCGAAATT
24023 TCTCTATTTGGTACCCACATCC
1 TCTCTATTTGGTACCCACA-CC
*
24045 TCTCTATTCGGTACCCAC-CC
1 TCTCTATTTGGTACCCACACC
*
24065 -CTCTGTTTGGTACCC
1 TCTCTATTTGGTACCC
24080 GTTTCCACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.41
20 2 0.06
22 17 0.53
ACGTcount: A:0.14, C:0.39, G:0.12, T:0.35
Consensus pattern (21 bp):
TCTCTATTTGGTACCCACACC
Found at i:28110 original size:2 final size:2
Alignment explanation
Indices: 28105--28141 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28095 TGTGTGCTAC
28105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28142 GTCAATTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32344 original size:46 final size:46
Alignment explanation
Indices: 32277--32371 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
32267 AGTAAGGTTC
32277 CTTGAATTGATTTAATTGGAGTCTCAATTGTTAACGTTTGTTTGTT
1 CTTGAATTGATTTAATTGGAGTCTCAATTGTTAACGTTTGTTTGTT
32323 CTTGAATTGATTTAATTGGAGTCTCAATTGTTAACGTTTGTTTGTT
1 CTTGAATTGATTTAATTGGAGTCTCAATTGTTAACGTTTGTTTGTT
32369 CTT
1 CTT
32372 ATTTGCGCTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (46 bp):
CTTGAATTGATTTAATTGGAGTCTCAATTGTTAACGTTTGTTTGTT
Found at i:34031 original size:65 final size:64
Alignment explanation
Indices: 33951--34138 Score: 321
Period size: 60 Copynumber: 3.0 Consensus size: 64
33941 TTTCCCAAAT
33951 CCGATATAAAGGAACAAGTCTGCGGTGAAGCGCTAGCTTCCGATATTTTGATTAAAACTCCTTAC
1 CCGATATAAAGGAACAAGTCTGCGG-GAAGCGCTAGCTTCCGATATTTTGATTAAAACTCCTTAC
34016 CCGATATAAAGGAACAAGTCTGC--G--GCGCTAGCTTCCGATATTTTGATTAAAACTCCTTAC
1 CCGATATAAAGGAACAAGTCTGCGGGAAGCGCTAGCTTCCGATATTTTGATTAAAACTCCTTAC
*
34076 CCGATATAAAGGAACAAGTCTGCGGCGAAGCGCTAGCTTCCAATATTTTGATTAAAACTCCTT
1 CCGATATAAAGGAACAAGTCTGCGG-GAAGCGCTAGCTTCCGATATTTTGATTAAAACTCCTT
34139 GATCTCATGC
Statistics
Matches: 117, Mismatches: 1, Indels: 10
0.91 0.01 0.08
Matches are distributed among these distances:
60 59 0.50
62 1 0.01
63 1 0.01
65 56 0.48
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (64 bp):
CCGATATAAAGGAACAAGTCTGCGGGAAGCGCTAGCTTCCGATATTTTGATTAAAACTCCTTAC
Found at i:36255 original size:29 final size:29
Alignment explanation
Indices: 36195--36256 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
36185 AAGGGATTAA
*
36195 TTTGTCCCAAAAAAAACATAAAGAGTTAT
1 TTTGTCCCAAAAAAAACATAAAGAGATAT
*
36224 TTTGTCCCAAAAGAAAAACAT-AAGAGATTT
1 TTTGTCCC-AAA-AAAAACATAAAGAGATAT
36254 TTT
1 TTT
36257 TGGGTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 8 0.28
30 13 0.45
31 8 0.28
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (29 bp):
TTTGTCCCAAAAAAAACATAAAGAGATAT
Found at i:39453 original size:36 final size:36
Alignment explanation
Indices: 39406--39495 Score: 171
Period size: 36 Copynumber: 2.5 Consensus size: 36
39396 GCAATCAACT
39406 TAATTCAGGGTAATTAAGTAAGTCAATAAAATGACC
1 TAATTCAGGGTAATTAAGTAAGTCAATAAAATGACC
*
39442 TAATTCAGGGTAATTAAGTAAGTCAATAAAATGGCC
1 TAATTCAGGGTAATTAAGTAAGTCAATAAAATGACC
39478 TAATTCAGGGTAATTAAG
1 TAATTCAGGGTAATTAAG
39496 CAATTCATTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (36 bp):
TAATTCAGGGTAATTAAGTAAGTCAATAAAATGACC
Found at i:42094 original size:35 final size:35
Alignment explanation
Indices: 42055--42563 Score: 600
Period size: 35 Copynumber: 14.5 Consensus size: 35
42045 AAACGGCCCC
*
42055 TAAGTAACTTAATTCAGAGTAATTAAGTAAGTCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
42090 TAAGTAACTTAATTCAGGGTAATTAAGAAAGTCAA
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
42125 TAAGTAACTTAATTTAGGGTAATTAAGTGAGTCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
42160 TAAATAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
42195 TAAATAACTTAATTCGGGGT-AGT-A--AAG-CTAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTC-AG
*
42226 TAAATAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
42261 TAAATAACTTGATTCAGGGTAATTAAGTAAAGCCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGT-AAGTCAG
* *
42297 TAAGTAACTTAATTTAGGGTAATTAAGTAAAGTTAG
1 TAAGTAACTTAATTCAGGGTAATTAAGT-AAGTCAG
*
42333 TTAGTAACTTAATTCAGGGTAATTAAGTAAAGTCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGT-AAGTCAG
* *
42369 TTAGTAAC-TAATTCAGGGTAATTAAGTAAAGTCAT
1 TAAGTAACTTAATTCAGGGTAATTAAGT-AAGTCAG
* * * * *
42404 TTAGTAATTTAATTCAGGATAGTTAAGTAAATCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
42439 T-AGTCAACTTAATTCAGGGTAATTAAGAAAGTTAA
1 TAAGT-AACTTAATTCAGGGTAATTAAGTAAGTCAG
42474 TAAGTAACTTAATTCTCAGGGTAATTAAGTAAGTCAG
1 TAAGTAACTTAA-T-TCAGGGTAATTAAGTAAGTCAG
* * * * *
42511 TAAATAATTTAATTCATGGTAATTAAGTAAATCAA
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
42546 TAAATGACTTAATTCAGG
1 TAAGTAACTTAATTCAGG
42564 ATAAATTGAG
Statistics
Matches: 414, Mismatches: 48, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.00
31 24 0.06
32 2 0.00
33 2 0.00
34 5 0.01
35 250 0.60
36 101 0.24
37 29 0.07
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (35 bp):
TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
Found at i:42556 original size:107 final size:104
Alignment explanation
Indices: 42055--42563 Score: 582
Period size: 107 Copynumber: 4.8 Consensus size: 104
42045 AAACGGCCCC
*
42055 TAAGTAACTTAATTCAGAGTAATTAAGTAAGTCAGTAAGTAACTTAATTCAGGGTAATTAAG-AA
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAGTAACTTAATTCA-GGTAATTAAGTAA
* * **
42119 AGTCAATAAGTAACTTAATTTAGGGTAATTAAGTGAGTCAG
65 A-TCAGTAAGTAACTTAATTCAGGGTAATTAAGAAAGTCAG
* * **
42160 TAAATAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAATAACTTAATTC-GG--GGT-AGTAAA
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAGTAACTTAATTCAGGTAATTAAGTAAA
* * *
42221 GCTAGTAAATAACTTAATTCAGGGTAATTAAGTAAGTCAG
66 TC-AGTAAGTAACTTAATTCAGGGTAATTAAGAAAGTCAG
* * * *
42261 TAAATAACTTGATTCAGGGTAATTAAGTAAAGCCAGTAAGTAACTTAATTTAGGGTAATTAAGTA
1 TAAGTAACTTAATTCAGGGTAATTAAGT-AAGTCAGTAAGTAACTTAATTCA-GGTAATTAAGTA
* *
42326 AAGTTAGTTAGTAACTTAATTCAGGGTAATTAAGTAAAGTCAG
64 AA-TCAGTAAGTAACTTAATTCAGGGTAATTAAG-AAAGTCAG
* * * * *
42369 TTAGTAAC-TAATTCAGGGTAATTAAGTAAAGTCATTTAGTAATTTAATTCAGGATAGTTAAGTA
1 TAAGTAACTTAATTCAGGGTAATTAAGT-AAGTCAGTAAGTAACTTAATTCAGG-TAATTAAGTA
* *
42433 AATCAGT-AGTCAACTTAATTCAGGGTAATTAAGAAAGTTAA
64 AATCAGTAAGT-AACTTAATTCAGGGTAATTAAGAAAGTCAG
* *
42474 TAAGTAACTTAATTCTCAGGGTAATTAAGTAAGTCAGTAAATAATTTAATTCATGGTAATTAAGT
1 TAAGTAACTTAA-T-TCAGGGTAATTAAGTAAGTCAGTAAGTAACTTAATTCA-GGTAATTAAGT
* * *
42539 AAATCAATAAATGACTTAATTCAGG
63 AAATCAGTAAGTAACTTAATTCAGG
42564 ATAAATTGAG
Statistics
Matches: 346, Mismatches: 41, Indels: 32
0.83 0.10 0.08
Matches are distributed among these distances:
100 3 0.01
101 64 0.18
102 19 0.05
103 2 0.01
104 2 0.01
105 63 0.18
106 32 0.09
107 129 0.37
108 32 0.09
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (104 bp):
TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAGTAACTTAATTCAGGTAATTAAGTAAA
TCAGTAAGTAACTTAATTCAGGGTAATTAAGAAAGTCAG
Found at i:43629 original size:35 final size:33
Alignment explanation
Indices: 43540--43717 Score: 140
Period size: 40 Copynumber: 4.8 Consensus size: 33
43530 AAGATGCTTT
*
43540 TGATGGGAACTTTCCCATTTTGAAAACTAAAAC
1 TGATGGGAACTTTCCCAATTTGAAAACTAAAAC
*
43573 TGAAAATGACGGGAACTTTCCCTAAATTGAAAACTAAAATC
1 TG---AT---GGGAACTTTCCC-AATTTGAAAACTAAAA-C
43614 TGATGGGAACTTTCCCAATTTTGAAAACTGAAAGCGGAAC
1 TGATGGGAACTTTCCCAA-TTTGAAAACT--AA----AAC
*
43654 TGATGGGAACTTTCCCTGAATTTAAAAAGACTAAAACC
1 TGATGGGAACTTTCCC--AATTT-GAAA-ACTAAAA-C
*
43692 TGGTGGGAACTTTCCCAATTTGAAAA
1 TGATGGGAACTTTCCCAATTTGAAAA
43718 AGAGCTAAAT
Statistics
Matches: 119, Mismatches: 6, Indels: 39
0.73 0.04 0.24
Matches are distributed among these distances:
33 2 0.02
34 3 0.03
35 24 0.20
36 7 0.06
37 4 0.03
38 18 0.15
39 12 0.10
40 31 0.26
41 10 0.08
42 5 0.04
43 3 0.03
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (33 bp):
TGATGGGAACTTTCCCAATTTGAAAACTAAAAC
Found at i:43657 original size:40 final size:37
Alignment explanation
Indices: 43540--43717 Score: 145
Period size: 35 Copynumber: 4.7 Consensus size: 37
43530 AAGATGCTTT
*
43540 TGATGGGAACTTTCCC-ATTTTGAAAACTAAAACTGAAAA
1 TGATGGGAACTTTCCCAATTTTGAAAACT-AAAC-G-AAC
* * *
43579 TGACGGGAACTTTCCCTAA-ATTGAAAACTAAA--ATC
1 TGATGGGAACTTTCCC-AATTTTGAAAACTAAACGAAC
43614 TGATGGGAACTTTCCCAATTTTGAAAACTGAAAGCGGAAC
1 TGATGGGAACTTTCCCAATTTTGAAAACT-AAA-C-GAAC
** *
43654 TGATGGGAACTTTCCCTGAATTTAAAAAGACTAAA--ACC
1 TGATGGGAACTTTCCC--AATTTTGAAA-ACTAAACGAAC
*
43692 TGGTGGGAACTTTCCCAA-TTTGAAAA
1 TGATGGGAACTTTCCCAATTTTGAAAA
43718 AGAGCTAAAT
Statistics
Matches: 115, Mismatches: 13, Indels: 27
0.74 0.08 0.17
Matches are distributed among these distances:
34 3 0.03
35 30 0.26
36 5 0.04
38 17 0.15
39 18 0.16
40 27 0.23
41 1 0.01
42 11 0.10
43 3 0.03
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (37 bp):
TGATGGGAACTTTCCCAATTTTGAAAACTAAACGAAC
Found at i:43662 original size:75 final size:78
Alignment explanation
Indices: 43540--43717 Score: 233
Period size: 75 Copynumber: 2.3 Consensus size: 78
43530 AAGATGCTTT
*
43540 TGATGGGAACTTTCCC-ATTTTGAAAACTAAAACTGAAAATGACGGGAACTTTCCCT-AAATT-G
1 TGATGGGAACTTTCCCAATTTTGAAAACTAAAACTGAAAATGACGGGAACTTTCCCTGAAATTAA
*
43602 AAA-ACTAAAATC
66 AAAGACTAAAACC
* * * * *
43614 TGATGGGAACTTTCCCAATTTTGAAAACTGAAAGC-GGAACTGATGGGAACTTTCCCTGAATTTA
1 TGATGGGAACTTTCCCAATTTTGAAAACT-AAAACTGAAAATGACGGGAACTTTCCCTGAAATTA
43678 AAAAGACTAAAACC
65 AAAAGACTAAAACC
*
43692 TGGTGGGAACTTTCCCAA-TTTGAAAA
1 TGATGGGAACTTTCCCAATTTTGAAAA
43718 AGAGCTAAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
74 16 0.18
75 31 0.34
76 8 0.09
77 11 0.12
78 25 0.27
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (78 bp):
TGATGGGAACTTTCCCAATTTTGAAAACTAAAACTGAAAATGACGGGAACTTTCCCTGAAATTAA
AAAGACTAAAACC
Found at i:43776 original size:52 final size:52
Alignment explanation
Indices: 43686--43936 Score: 250
Period size: 52 Copynumber: 4.6 Consensus size: 52
43676 TAAAAAGACT
* * * *
43686 AAAACCTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
1 AAAA-CTGATGGGAACTTTCCCGACTTGAAAAAAAGCTAAATTGAATACTTTG
*
43739 AAAGCTGATGGGAACTTTCCCGACTTGAAAAAAAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCGACTTGAAAAAAAGCTAAATTGAATACTTTG
* * * *
43791 AAAGCTGATGGGAACTTTCCCGACTTGAAAAACCTTTGAAAAAAACTTGAGTTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCGACTTG----A------AAAAAAGC-TAAATTGAATACTTTG
* * * *
43854 AAAACTGGTGGGAACTTTCCCGACTTGAAAAAGAGCTAAATCGAATATTTTG
1 AAAACTGATGGGAACTTTCCCGACTTGAAAAAAAGCTAAATTGAATACTTTG
* * *
43906 AAAACTGGTGGGAACTTTCCCAATTTGAAAA
1 AAAACTGATGGGAACTTTCCCGACTTGAAAA
43937 CTTAAACCTA
Statistics
Matches: 169, Mismatches: 18, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
52 112 0.66
53 9 0.05
56 1 0.01
59 1 0.01
62 7 0.04
63 39 0.23
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (52 bp):
AAAACTGATGGGAACTTTCCCGACTTGAAAAAAAGCTAAATTGAATACTTTG
Found at i:43835 original size:63 final size:63
Alignment explanation
Indices: 43763--43885 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
43753 CTTTCCCGAC
*
43763 TTGAAAAAAAGC-TAAATTGAATACTTTGAAAGCTGATGGGAACTTTCCCGACTTGAAAAACCT
1 TTGAAAAAAA-CTTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAACCT
* * *
43826 TTGAAAAAAACTTGAGTTGAATACTTTGAAAACTGGTGGGAACTTTCCCGACTTGAAAAA
1 TTGAAAAAAACTTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAA
43886 GAGCTAAATC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 1 0.02
63 54 0.98
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (63 bp):
TTGAAAAAAACTTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAACCT
Found at i:43918 original size:115 final size:115
Alignment explanation
Indices: 43727--43936 Score: 339
Period size: 115 Copynumber: 1.8 Consensus size: 115
43717 AAGAGCTAAA
* *
43727 TTGAATACTTTGAAAGCTGATGGGAACTTTCCCGACTTGAAAAAAAGCTAAATTGAATACTTTGA
1 TTGAATACTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAAAAGCTAAATCGAATACTTTGA
* *
43792 AAGCTGATGGGAACTTTCCCGACTTGAAAAACCTTTGAAAAAAACTTGAG
66 AAACTGATGGGAACTTTCCCAACTTGAAAAACCTTTGAAAAAAACTTGAG
* * *
43842 TTGAATACTTTGAAAACTGGTGGGAACTTTCCCGACTTGAAAAAGAGCTAAATCGAATATTTTGA
1 TTGAATACTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAAAAGCTAAATCGAATACTTTGA
* *
43907 AAACTGGTGGGAACTTTCCCAATTTGAAAA
66 AAACTGATGGGAACTTTCCCAACTTGAAAA
43937 CTTAAACCTA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 86 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (115 bp):
TTGAATACTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAAAAGCTAAATCGAATACTTTGA
AAACTGATGGGAACTTTCCCAACTTGAAAAACCTTTGAAAAAAACTTGAG
Found at i:44645 original size:24 final size:24
Alignment explanation
Indices: 44626--44673 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
44616 TAATTAAATT
44626 TTGAAAGCCCAAACAGATTAAGAA
1 TTGAAAGCCCAAACAGATTAAGAA
44650 TTGAAAGCCCAAACCA-ATTAAGAA
1 TTGAAAGCCCAAA-CAGATTAAGAA
44674 CCAAATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.17
Consensus pattern (24 bp):
TTGAAAGCCCAAACAGATTAAGAA
Found at i:50614 original size:22 final size:23
Alignment explanation
Indices: 50566--50611 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
50556 CTTACCCTTA
50566 TCTTTTTATTTTTCGTTATTTTT
1 TCTTTTTATTTTTCGTTATTTTT
50589 TCTTTTTATTTTT-GTTTATTTTT
1 TCTTTTTATTTTTCG-TTATTTTT
50612 CTTAAGTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.80
Consensus pattern (23 bp):
TCTTTTTATTTTTCGTTATTTTT
Found at i:51783 original size:21 final size:20
Alignment explanation
Indices: 51744--51792 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
51734 TCAATGCTTT
**
51744 AAGAATGCAAGAGGGATTTCA
1 AAGAA-GCAAGAGCCATTTCA
*
51765 AAGGAAGCAAGAGCCATTTCC
1 AA-GAAGCAAGAGCCATTTCA
51786 AAGAAGC
1 AAGAAGC
51793 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 16 0.67
22 3 0.12
ACGTcount: A:0.43, C:0.16, G:0.27, T:0.14
Consensus pattern (20 bp):
AAGAAGCAAGAGCCATTTCA
Found at i:54343 original size:21 final size:21
Alignment explanation
Indices: 54319--54363 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
54309 CTTCTATTAC
*
54319 CTTTATTCA-CAAATTCACTCA
1 CTTTAATCATCAAATTCACT-A
*
54340 CTTTAATCATCAATTTCACTA
1 CTTTAATCATCAAATTCACTA
54361 CTT
1 CTT
54364 CATCACTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (21 bp):
CTTTAATCATCAAATTCACTA
Found at i:56683 original size:2 final size:2
Alignment explanation
Indices: 56676--56708 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
56666 TTTAATCAGA
56676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56709 ATAAGGTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60146 original size:36 final size:36
Alignment explanation
Indices: 60117--60209 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
60107 CAGCATCAGA
60117 CTGATCAGCCACCATCTCCTGTTGTGCAGCCTCAAT
1 CTGATCAGCCACCATCTCCTGTTGTGCAGCCTCAAT
* *
60153 CTGATCAGCCACCACCTCCTGTAGTGCAGCCTCAAT
1 CTGATCAGCCACCATCTCCTGTTGTGCAGCCTCAAT
60189 CTGATCAGCCACC-TCCTCCTG
1 CTGATCAGCCACCAT-CTCCTG
60210 CTCCTGAACG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.19, C:0.40, G:0.16, T:0.25
Consensus pattern (36 bp):
CTGATCAGCCACCATCTCCTGTTGTGCAGCCTCAAT
Found at i:61901 original size:152 final size:151
Alignment explanation
Indices: 61562--62009 Score: 743
Period size: 152 Copynumber: 3.0 Consensus size: 151
61552 ATCATCCATG
* * * * *
61562 TAGTTTTTCATTGTCCAGCTTGGTGTTAGGTAGTAAATAAATTATTAATTTGGGTCTGCTTTGAA
1 TAGTTTTTCTTTGTCCAGCTTGGTGTTAAGTAGTAGATGAATTATTAATTCGGGTCTGCTTTGAA
61627 TCTTTCTTTTTTGTCTTGTGTATGTAGTAGCTTTGCTTATTGATATGGCCTTGTTTTGGCTGGAA
66 TCTTTCTTTTTTGTCTTGTGTATGTAGTAGCTTTGCTTATTGATATGGCCTTGTTTTGGCTGGAA
*
61692 TTGTTATATTTGCTTATAATG
131 TTGTTATATTTGCTTATAATA
* *
61713 TAGTTTTTCTTTGTCCAGCTTGGTGTTAAATAGTAGATGAATTATTAATTCGGGTCTGCGTTGAA
1 TAGTTTTTCTTTGTCCAGCTTGGTGTTAAGTAGTAGATGAATTATTAATTCGGGTCTGCTTTGAA
* *
61778 TCTTTCTTTTTTGTCATGTGTATGTAGTAGCTTTGCTTGTTGATATGGCGCTTGTTTTGGCTGGA
66 TCTTTCTTTTTTGTCTTGTGTATGTAGTAGCTTTGCTTATTGATATGGC-CTTGTTTTGGCTGGA
61843 ATTGTTATATTTGCTTATAATA
130 ATTGTTATATTTGCTTATAATA
* *
61865 TAGTTTTTCTTTGTCCAGCTTGGTGTTAAGTCGTAGATGAATTATTAATTCTGGTCTGCTTTGAA
1 TAGTTTTTCTTTGTCCAGCTTGGTGTTAAGTAGTAGATGAATTATTAATTCGGGTCTGCTTTGAA
* * * *
61930 TCTTTCTTTTCTGACTTGTGTATCTAGTAGCTTTGCTTACTGATATGGCCTTGTTTTGGCTGGAA
66 TCTTTCTTTTTTGTCTTGTGTATGTAGTAGCTTTGCTTATTGATATGGCCTTGTTTTGGCTGGAA
61995 TTGTTATATTTGCTT
131 TTGTTATATTTGCTT
62010 TTGTTTTTCC
Statistics
Matches: 276, Mismatches: 20, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
151 136 0.49
152 140 0.51
ACGTcount: A:0.18, C:0.11, G:0.21, T:0.49
Consensus pattern (151 bp):
TAGTTTTTCTTTGTCCAGCTTGGTGTTAAGTAGTAGATGAATTATTAATTCGGGTCTGCTTTGAA
TCTTTCTTTTTTGTCTTGTGTATGTAGTAGCTTTGCTTATTGATATGGCCTTGTTTTGGCTGGAA
TTGTTATATTTGCTTATAATA
Found at i:64024 original size:15 final size:15
Alignment explanation
Indices: 63997--64035 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
63987 CTTTGCTTTA
63997 TTTTCTAGTTTAATTG
1 TTTTCT-GTTTAATTG
64013 TTTTCTGTTTAATTG
1 TTTTCTGTTTAATTG
*
64028 CTTTCTGT
1 TTTTCTGT
64036 CAACCTCTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.64
Consensus pattern (15 bp):
TTTTCTGTTTAATTG
Found at i:64753 original size:43 final size:43
Alignment explanation
Indices: 64692--64792 Score: 157
Period size: 43 Copynumber: 2.3 Consensus size: 43
64682 CGAAGTAATT
*
64692 ATTCCAAACATTGTTCCTAAAGTTTTGGAATGAGATAAAAGTC
1 ATTCCAAACATTGTTCCTAAAATTTTGGAATGAGATAAAAGTC
* *
64735 ATTCCAAACATTTTTCCTAAAATTTTGGAATGAGGTAAAAGTC
1 ATTCCAAACATTGTTCCTAAAATTTTGGAATGAGATAAAAGTC
* *
64778 ATTCCTAACTTTGTT
1 ATTCCAAACATTGTT
64793 GCTGTTCCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Consensus pattern (43 bp):
ATTCCAAACATTGTTCCTAAAATTTTGGAATGAGATAAAAGTC
Done.