Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022598.1 Corchorus olitorius cultivar O-4 contig22631, 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: 94351
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:268 original size:19 final size:18
Alignment explanation
Indices: 235--270 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
225 TTGAAATTAT
235 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
253 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
271 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:11067 original size:10 final size:10
Alignment explanation
Indices: 11052--11076 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11042 CAGAGTACAT
11052 AAACATAATG
1 AAACATAATG
11062 AAACATAATG
1 AAACATAATG
11072 AAACA
1 AAACA
11077 ACACTAAAAT
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:0.64, C:0.12, G:0.08, T:0.16
Consensus pattern (10 bp):
AAACATAATG
Found at i:11730 original size:17 final size:16
Alignment explanation
Indices: 11676--11726 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
11666 GATCACCCCC
*
11676 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
11693 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
11710 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
11726 A
1 A
11727 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:15284 original size:18 final size:19
Alignment explanation
Indices: 15257--15295 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
15247 CGTAGGAACG
**
15257 AAAAGAAGAAGGCAAGGAA
1 AAAAGAAGAAAACAAGGAA
15276 AAAAG-AGAAAACAAGGAA
1 AAAAGAAGAAAACAAGGAA
15294 AA
1 AA
15296 CGGAGATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.69, C:0.05, G:0.26, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAAAACAAGGAA
Found at i:17289 original size:37 final size:34
Alignment explanation
Indices: 17247--17315 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
17237 AAATTATCTA
17247 AGAAAGCAATCAAGAAAATTAAAGAAAACAATTAATC
1 AGAAAGCAATCAA-AAAATT--AGAAAACAATTAATC
* * *
17284 AGAAAGCAGTGAATAAATTAGAAAACAATTAA
1 AGAAAGCAATCAAAAAATTAGAAAACAATTAA
17316 ATTAAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 13 0.45
36 5 0.17
37 11 0.38
ACGTcount: A:0.61, C:0.09, G:0.13, T:0.17
Consensus pattern (34 bp):
AGAAAGCAATCAAAAAATTAGAAAACAATTAATC
Found at i:18640 original size:10 final size:10
Alignment explanation
Indices: 18625--18654 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
18615 TCTTGAAATA
18625 ATTCTTCAAT
1 ATTCTTCAAT
18635 ATTCTTCAAT
1 ATTCTTCAAT
*
18645 AGTCTTCAAT
1 ATTCTTCAAT
18655 TCTTCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (10 bp):
ATTCTTCAAT
Found at i:19002 original size:21 final size:21
Alignment explanation
Indices: 18976--19018 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18966 TGAGACTTAT
18976 ACTACTATACGACCCAAATGA
1 ACTACTATACGACCCAAATGA
*
18997 ACTACTATATGACCCAAATGA
1 ACTACTATACGACCCAAATGA
19018 A
1 A
19019 ATGAAAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (21 bp):
ACTACTATACGACCCAAATGA
Found at i:22381 original size:41 final size:40
Alignment explanation
Indices: 22312--22391 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
22302 TGTTTTTCCT
*
22312 TTTTATCTCACCTAGGGTTTAATGTGTTTTTTGAGGGTTTC
1 TTTTATCTCACCTAGGGTTTAATGTGTTTGTT-AGGGTTTC
* *
22353 TTTTATCTCACTTAGGGTTTGTAT-TGTTTGTTAGGGTTT
1 TTTTATCTCACCTAGGGTTT-AATGTGTTTGTTAGGGTTT
22392 GGGTTTCATG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 7 0.20
41 26 0.74
42 2 0.06
ACGTcount: A:0.14, C:0.10, G:0.23, T:0.54
Consensus pattern (40 bp):
TTTTATCTCACCTAGGGTTTAATGTGTTTGTTAGGGTTTC
Found at i:29766 original size:44 final size:44
Alignment explanation
Indices: 29703--29791 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
29693 AACCTTTAAC
29703 TAATATGTTTACAGGATATAACATCCTTCAAAATATGCAAAACT
1 TAATATGTTTACAGGATATAACATCCTTCAAAATATGCAAAACT
29747 TAATATGTTTACAGGATATAACATCCTTCAAAATATGCAAAACT
1 TAATATGTTTACAGGATATAACATCCTTCAAAATATGCAAAACT
29791 T
1 T
29792 TGTATTTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (44 bp):
TAATATGTTTACAGGATATAACATCCTTCAAAATATGCAAAACT
Found at i:34679 original size:14 final size:14
Alignment explanation
Indices: 34660--34695 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
34650 ATAACGTTGG
34660 AAACCCCTACGGTT
1 AAACCCCTACGGTT
34674 AAACCCCTACGGTT
1 AAACCCCTACGGTT
34688 AAACCCCT
1 AAACCCCT
34696 TGTCGGAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.39, G:0.11, T:0.19
Consensus pattern (14 bp):
AAACCCCTACGGTT
Found at i:37004 original size:23 final size:23
Alignment explanation
Indices: 36977--37031 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
36967 AGGCTCATAT
36977 TAAAAGAAATAATAATTAAAATA
1 TAAAAGAAATAATAATTAAAATA
37000 TAAAAGAAATAATAATTAAAATA
1 TAAAAGAAATAATAATTAAAATA
37023 TAAAAGAAA
1 TAAAAGAAA
37032 AGAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (23 bp):
TAAAAGAAATAATAATTAAAATA
Found at i:41103 original size:24 final size:21
Alignment explanation
Indices: 41052--41101 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
41042 CTCATTAGCA
41052 GCATCATCTTCCTTGTGGCTT
1 GCATCATCTTCCTTGTGGCTT
* *
41073 GCATCATCTTCCTTTTTGCTT
1 GCATCATCTTCCTTGTGGCTT
41094 GCATCATC
1 GCATCATC
41102 ATTCTGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.12, C:0.30, G:0.14, T:0.44
Consensus pattern (21 bp):
GCATCATCTTCCTTGTGGCTT
Found at i:46645 original size:26 final size:26
Alignment explanation
Indices: 46609--46686 Score: 156
Period size: 26 Copynumber: 3.0 Consensus size: 26
46599 GCTTCTTCTC
46609 GGCTTTATGGTAGAAAGATGAGAAGG
1 GGCTTTATGGTAGAAAGATGAGAAGG
46635 GGCTTTATGGTAGAAAGATGAGAAGG
1 GGCTTTATGGTAGAAAGATGAGAAGG
46661 GGCTTTATGGTAGAAAGATGAGAAGG
1 GGCTTTATGGTAGAAAGATGAGAAGG
46687 CAAGCGAAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.35, C:0.04, G:0.38, T:0.23
Consensus pattern (26 bp):
GGCTTTATGGTAGAAAGATGAGAAGG
Found at i:49110 original size:109 final size:109
Alignment explanation
Indices: 48919--49135 Score: 398
Period size: 109 Copynumber: 2.0 Consensus size: 109
48909 TTATATATAC
* *
48919 ATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCGCACATACCAAACAATAC
1 ATTATTATTAATTGTGTGGTTTATTCAATTAAACCTATTAAATAAGCACACATACCAAACAATAC
48984 AAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCT
66 AAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCT
*
49028 ATTATTATTAATTGTGTTGTTTATTCAATTAAACCTATTAAATAAGCACACATACCAAACAATAC
1 ATTATTATTAATTGTGTGGTTTATTCAATTAAACCTATTAAATAAGCACACATACCAAACAATAC
*
49093 AAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 AAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
49136 AAAATGACTA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (109 bp):
ATTATTATTAATTGTGTGGTTTATTCAATTAAACCTATTAAATAAGCACACATACCAAACAATAC
AAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCT
Found at i:50387 original size:33 final size:33
Alignment explanation
Indices: 50316--50388 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
50306 GATGTACATT
* *
50316 AAAAAAACATCTTTTCTCCATTAATAAATCATA
1 AAAAAAACATCTTTTCTCCAATAATAAATCAAA
* * *
50349 GAAAAAACAATCTTTTCTCCAATAA-AATTTAAA
1 AAAAAAAC-ATCTTTTCTCCAATAATAAATCAAA
50382 AAAAAAA
1 AAAAAAA
50389 TTTTGCTGCA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
33 18 0.55
34 15 0.45
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (33 bp):
AAAAAAACATCTTTTCTCCAATAATAAATCAAA
Found at i:50734 original size:104 final size:104
Alignment explanation
Indices: 50578--50771 Score: 293
Period size: 104 Copynumber: 1.9 Consensus size: 104
50568 ATTTAATATG
* * * * *
50578 TACACCTCGATGGAGTTTAGCTGACTACACAAGCGGGTTTTGAAGGGTGACATGTG-CCCCTAGG
1 TACACCTCAATGGAGTTTAGCAGACTACACAAACGGATTTTGAAGAGTGACATGTGTCCCCTAGG
*
50642 GACTAGATTGAAATATTTAAAATTTGGGTTTATATATAA
66 GACTAAATTGAAATATTTAAAATTTGGGTTTATATATAA
*
50681 TACACCGTCAATGGAGTTTAGCAGACTGCACAAACGGATCTTT-AAGAGTGACATGTGTCCCCTA
1 TACACC-TCAATGGAGTTTAGCAGACTACACAAACGGAT-TTTGAAGAGTGACATGTGTCCCCTA
50745 GGGACTAAATTGAAATATTTAAAATTT
64 GGGACTAAATTGAAATATTTAAAATTT
50772 AATTAATTCA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
103 6 0.07
104 40 0.49
105 35 0.43
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (104 bp):
TACACCTCAATGGAGTTTAGCAGACTACACAAACGGATTTTGAAGAGTGACATGTGTCCCCTAGG
GACTAAATTGAAATATTTAAAATTTGGGTTTATATATAA
Found at i:50905 original size:27 final size:25
Alignment explanation
Indices: 50871--50968 Score: 126
Period size: 27 Copynumber: 3.7 Consensus size: 25
50861 GGTCATCCAT
*
50871 GGGG-ATTTTAGTCATTTGCATGTCAA
1 GGGGCATTTTGGTCATTTGCAT-TC-A
50897 GGGGCATTTTGGTCATTTGCATATTCA
1 GGGGCATTTTGGTCATTTGC--ATTCA
50924 GGGGCATTTTGGTCATTTGCACATTCA
1 GGGGCATTTTGGTCATTTG--CATTCA
50951 GGGGCATTTTGGTCATTT
1 GGGGCATTTTGGTCATTT
50969 TAAGTTCACT
Statistics
Matches: 66, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
26 4 0.06
27 57 0.86
28 2 0.03
29 3 0.05
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.40
Consensus pattern (25 bp):
GGGGCATTTTGGTCATTTGCATTCA
Found at i:61058 original size:3 final size:3
Alignment explanation
Indices: 61052--61090 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
61042 GAAGTAATGA
*
61052 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG CAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
61091 GTTGTATTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:62025 original size:52 final size:52
Alignment explanation
Indices: 61963--62088 Score: 234
Period size: 52 Copynumber: 2.4 Consensus size: 52
61953 AAGATTAGCT
*
61963 TTTGAGGTGAAAATTAGCTTTTGATACAAATCATTACTTATTTGGCATTATG
1 TTTGAGGTGAAAAGTAGCTTTTGATACAAATCATTACTTATTTGGCATTATG
*
62015 TTTGAGGTGAAAAGTAGCTTTTGATACAAATCATTACTTATTTGGCATTGTG
1 TTTGAGGTGAAAAGTAGCTTTTGATACAAATCATTACTTATTTGGCATTATG
62067 TTTGAGGTGAAAAGTAGCTTTT
1 TTTGAGGTGAAAAGTAGCTTTT
62089 TTATCTCCAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (52 bp):
TTTGAGGTGAAAAGTAGCTTTTGATACAAATCATTACTTATTTGGCATTATG
Found at i:62550 original size:3 final size:3
Alignment explanation
Indices: 62542--62615 Score: 78
Period size: 3 Copynumber: 24.7 Consensus size: 3
62532 ATCTTGGTTC
* * *
62542 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCT TCA TCT TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
* **
62590 TAA TCA T-A TTCA TCA AGA TCA TCA TC
1 TCA TCA TCA -TCA TCA TCA TCA TCA TC
62616 GTCTTTGTTG
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
2 1 0.02
3 55 0.96
4 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.01, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:62679 original size:24 final size:24
Alignment explanation
Indices: 62647--62693 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
62637 CTGATCTTCA
62647 CCTTCACTATCCTCATCATCATCG
1 CCTTCACTATCCTCATCATCATCG
*
62671 CCTTCACTATCCTCATCCTCATC
1 CCTTCACTATCCTCATCATCATC
62694 ATCAGTGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.45, G:0.02, T:0.34
Consensus pattern (24 bp):
CCTTCACTATCCTCATCATCATCG
Found at i:63563 original size:43 final size:45
Alignment explanation
Indices: 63466--63578 Score: 115
Period size: 49 Copynumber: 2.5 Consensus size: 45
63456 TATTTTGATT
63466 GTATTGGAGTTGGCTCACTCAGTTTTCTTTCTGTTTCTAAACTGTAAC
1 GTATTGGAGTTGGCTCACTCAGTTTTCTTTCTGTTTCTAAAC--T-AC
* *
63514 TATATTGGAGTTGGCTCAGTCA-TTTGTCTTTCTGTTTCTAAAC-A-
1 -GTATTGGAGTTGGCTCACTCAGTTT-TCTTTCTGTTTCTAAACTAC
* * *
63558 GTATTGCACTTGACTCACTCA
1 GTATTGGAGTTGGCTCACTCA
63579 TGCATGTAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
43 16 0.29
45 1 0.02
48 3 0.05
49 36 0.64
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.42
Consensus pattern (45 bp):
GTATTGGAGTTGGCTCACTCAGTTTTCTTTCTGTTTCTAAACTAC
Found at i:64418 original size:10 final size:10
Alignment explanation
Indices: 64403--64431 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
64393 TATAAACCCA
64403 AAAAAAAAAG
1 AAAAAAAAAG
64413 AAAAAAAAAG
1 AAAAAAAAAG
64423 AAAAAAAAA
1 AAAAAAAAA
64432 TCAGGGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:72056 original size:57 final size:57
Alignment explanation
Indices: 71976--72085 Score: 220
Period size: 57 Copynumber: 1.9 Consensus size: 57
71966 GTTTGTTAGA
71976 GAAGGGGTTTCTTGGCTTATAGATTAGCGTTTCGGTAATGTAGTTAATCTTGTTGGG
1 GAAGGGGTTTCTTGGCTTATAGATTAGCGTTTCGGTAATGTAGTTAATCTTGTTGGG
72033 GAAGGGGTTTCTTGGCTTATAGATTAGCGTTTCGGTAATGTAGTTAATCTTGT
1 GAAGGGGTTTCTTGGCTTATAGATTAGCGTTTCGGTAATGTAGTTAATCTTGT
72086 AGCAGTGTAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.20, C:0.09, G:0.30, T:0.41
Consensus pattern (57 bp):
GAAGGGGTTTCTTGGCTTATAGATTAGCGTTTCGGTAATGTAGTTAATCTTGTTGGG
Found at i:72622 original size:67 final size:67
Alignment explanation
Indices: 72510--72645 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 67
72500 CTGCTTAACC
* *
72510 AAATTAAGAGTACGAGACCTAAATTGCGCATTTTCGCATATGTTAGGGCCTTATTTAATCAAATT
1 AAATTAAGAGTACAAGACCTAAATTGCGCATTTTCGCATACGTTAGGGCCTTATTTAATCAAATT
72575 AA
66 AA
*
72577 AAATTAAGAGTACAAGACCTAAATTGCGCATTTTCGCATACGTTAGGGTCTTATTTAATCAAATT
1 AAATTAAGAGTACAAGACCTAAATTGCGCATTTTCGCATACGTTAGGGCCTTATTTAATCAAATT
72642 AA
66 AA
72644 AA
1 AA
72646 CATGGGTCCT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (67 bp):
AAATTAAGAGTACAAGACCTAAATTGCGCATTTTCGCATACGTTAGGGCCTTATTTAATCAAATT
AA
Found at i:73340 original size:2 final size:2
Alignment explanation
Indices: 73333--73365 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
73323 TTTTTCTATC
73333 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
73366 AAATTAAGGT
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:74825 original size:61 final size:61
Alignment explanation
Indices: 74754--74873 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 61
74744 AACGTATATG
* * * *
74754 AAAATGCTCAATTTAGAGCTTATGCTTTTAATTTGGTGAAATAAGACCCTAATGTATGCAA
1 AAAATGCTCAATTCAGAGCTCATGCTTTGAATTTGGTGAAATAAGACCCTAACGTATGCAA
* * *
74815 AAAATGCTCAATTCAGGGCTCATGCTTTGAATTTGGTTAAATAGGACCCTAACGTATGC
1 AAAATGCTCAATTCAGAGCTCATGCTTTGAATTTGGTGAAATAAGACCCTAACGTATGC
74874 GAAATGCTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (61 bp):
AAAATGCTCAATTCAGAGCTCATGCTTTGAATTTGGTGAAATAAGACCCTAACGTATGCAA
Found at i:79159 original size:15 final size:15
Alignment explanation
Indices: 79122--79161 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
79112 TTTCGAATGG
79122 ATCATTAGCTGCTAA
1 ATCATTAGCTGCTAA
* *
79137 ATCCTTAGCTGCTAC
1 ATCATTAGCTGCTAA
*
79152 CTCATTAGCT
1 ATCATTAGCT
79162 CAGCTATCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (15 bp):
ATCATTAGCTGCTAA
Found at i:82239 original size:43 final size:43
Alignment explanation
Indices: 82178--82278 Score: 202
Period size: 43 Copynumber: 2.3 Consensus size: 43
82168 AACATGTCAA
82178 ACGGTGTTGAAGCTTGTTGCAACTTTGTTGCAGCCGACGACAG
1 ACGGTGTTGAAGCTTGTTGCAACTTTGTTGCAGCCGACGACAG
82221 ACGGTGTTGAAGCTTGTTGCAACTTTGTTGCAGCCGACGACAG
1 ACGGTGTTGAAGCTTGTTGCAACTTTGTTGCAGCCGACGACAG
82264 ACGGTGTTGAAGCTT
1 ACGGTGTTGAAGCTT
82279 TGCCGATAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (43 bp):
ACGGTGTTGAAGCTTGTTGCAACTTTGTTGCAGCCGACGACAG
Found at i:84434 original size:6 final size:6
Alignment explanation
Indices: 84423--84497 Score: 105
Period size: 6 Copynumber: 11.7 Consensus size: 6
84413 TCACAATTAC
84423 ATATCT ATATCT ATATCTAT ATATCT ATATCT ATATCT ATATCTAT ATATCT
1 ATATCT ATATCT ATATC--T ATATCT ATATCT ATATCT ATATC--T ATATCT
84475 ATATCT ATATCT ATATACT ATAT
1 ATATCT ATATCT ATAT-CT ATAT
84498 AAGTCTAAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
6 46 0.72
7 6 0.09
8 12 0.19
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATCT
Found at i:84448 original size:20 final size:20
Alignment explanation
Indices: 84428--84497 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
84418 ATTACATATC
* *
84428 TATATCTATATCTATATATC
1 TATATCTATATCTATATCTA
84448 TATATCTATATCTATATCTA
1 TATATCTATATCTATATCTA
84468 TATATCTATATCTATATCTA
1 TATATCTATATCTATATCTA
84488 TATA-CTATAT
1 TATATCTATAT
84498 AAGTCTAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 6 0.12
20 42 0.88
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATCTATATCTATATCTA
Found at i:84452 original size:26 final size:26
Alignment explanation
Indices: 84423--84498 Score: 143
Period size: 26 Copynumber: 2.9 Consensus size: 26
84413 TCACAATTAC
84423 ATATCTATATCTATATCTATATATCT
1 ATATCTATATCTATATCTATATATCT
84449 ATATCTATATCTATATCTATATATCT
1 ATATCTATATCTATATCTATATATCT
84475 ATATCTATATCTATATACTATATA
1 ATATCTATATCTATAT-CTATATA
84499 AGTCTAAACT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 42 0.86
27 7 0.14
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATCTATATCTATATCTATATATCT
Found at i:85635 original size:35 final size:36
Alignment explanation
Indices: 85589--85657 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
85579 GAGATTTTGG
*
85589 AGAAATATGATAATCAAAATTAC-AAAAATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
85624 AGAAATATGATAACCAAAATTACAAAAAATGTAA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAA
85658 GGTTATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 22 0.69
36 10 0.31
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Found at i:86411 original size:180 final size:180
Alignment explanation
Indices: 86109--86453 Score: 591
Period size: 180 Copynumber: 1.9 Consensus size: 180
86099 TACTAATGTT
*
86109 ATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAACTTTTTTAGTAGATTACT
1 ATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAACTTTTATAGTAGATTACT
* *
86174 CAAGTAATTAAATTGGTAATTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGTA
66 CAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGTA
86239 AGATTACTTGAATCTAGATAGTACTATAATGTTTTTTGGTAAAAAAAAAA
131 AGATTACTTGAATCTAGATAGTACTATAATGTTTTTTGGTAAAAAAAAAA
* * * *
86289 ATTAAGAATGTAAGGATTGGTAAATACAATTTTAATAACTTTTTTAGCTTTTATAGTAGATTACT
1 ATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAACTTTTATAGTAGATTACT
* * *
86354 TAAGTAATTAAATTGGCAACTTTCATTATTGATCATACAAAGTTACTAAAATTAATAAGGATGTA
66 CAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGTA
*
86419 AGATTATTTGAATCTAGATAGTACTATAATGTTTT
131 AGATTACTTGAATCTAGATAGTACTATAATGTTTT
86454 CATAACTTTT
Statistics
Matches: 154, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
180 154 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (180 bp):
ATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAACTTTTATAGTAGATTACT
CAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGTA
AGATTACTTGAATCTAGATAGTACTATAATGTTTTTTGGTAAAAAAAAAA
Found at i:88175 original size:95 final size:95
Alignment explanation
Indices: 88070--88251 Score: 337
Period size: 95 Copynumber: 1.9 Consensus size: 95
88060 AAATTGATAA
*
88070 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAGTAGCC
1 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCC
88135 CTGTAGTTCTTTTAGTAAATTCTTTCTTCT
66 CTGTAGTTCTTTTAGTAAATTCTTTCTTCT
*
88165 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGCC
1 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCC
*
88230 CTGTAGTTTTTTTAGTAAATTC
66 CTGTAGTTCTTTTAGTAAATTC
88252 AAATAAGAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (95 bp):
TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCC
CTGTAGTTCTTTTAGTAAATTCTTTCTTCT
Found at i:91871 original size:2 final size:2
Alignment explanation
Indices: 91864--91893 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
91854 ATTATATGCG
91864 AT 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 AT
91894 TGTATTGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94202 original size:217 final size:217
Alignment explanation
Indices: 93811--94347 Score: 950
Period size: 217 Copynumber: 2.5 Consensus size: 217
93801 CATAGGTGTC
* * *
93811 ATTATATGACACTAAATTCGTATGGATGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTA
1 ATTAGATGACACTAAATTCGTATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTA
93876 AAGCACGTTTAAAGCCAATTTTGGGTATATAAAAAATGCCAATCTCTAAAGAATTTGGGTATGGT
66 AAGCACGTTTAAAGCCAATTTTGGGTATATAAAAAATGCCAATCTCTAAAGAATTTGGGTATGGT
93941 GCTTATGATTATTTGGGGATGATGAAAAACGATTTAAGTATAAAGTATATCAGTTTGGGGATGCT
131 GCTTATGATTATTTGGGGATGATGAAAAACGATTTAAGTATAAAGTATATCAGTTTGGGGATGCT
94006 GAATTTTGCATTTTGTTTCATT
196 GAATTTTGCATTTTGTTTCATT
94028 ATTAGATGACACTAAATTCGTATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTA
1 ATTAGATGACACTAAATTCGTATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTA
*
94093 AAGCACGTTTAAAGCCAATTTTGGGTATATAAAAAATGCCAATCTTTAAAGAATTTGGGTATGGT
66 AAGCACGTTTAAAGCCAATTTTGGGTATATAAAAAATGCCAATCTCTAAAGAATTTGGGTATGGT
* * * *
94158 TCTTATGATTATTTGGGGATGATGAGAAATGATTT-GGTTATAAAGTATATCAGTTTGGGGATGC
131 GCTTATGATTATTTGGGGATGATGAAAAACGATTTAAG-TATAAAGTATATCAGTTTGGGGATGC
94222 TGAATTTTGCATTTTGTTTCATT
195 TGAATTTTGCATTTTGTTTCATT
* * *
94245 ATTAGTTGACACTAAATTCATATAGACGGGTTTTATTCAATTAATTAGGATGAAAATATGGATTA
1 ATTAGATGACACTAAATTCGTATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTA
94310 AAGCACGTTTAAAAGCCAATTTTGGGTATATAAAAAAT
66 AAGCACGTTT-AAAGCCAATTTTGGGTATATAAAAAAT
94348 TTGT
Statistics
Matches: 307, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
216 1 0.00
217 279 0.91
218 27 0.09
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (217 bp):
ATTAGATGACACTAAATTCGTATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTA
AAGCACGTTTAAAGCCAATTTTGGGTATATAAAAAATGCCAATCTCTAAAGAATTTGGGTATGGT
GCTTATGATTATTTGGGGATGATGAAAAACGATTTAAGTATAAAGTATATCAGTTTGGGGATGCT
GAATTTTGCATTTTGTTTCATT
Done.