Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012014.1 Corchorus olitorius cultivar O-4 contig12047, 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: 70033
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:780 original size:36 final size:36
Alignment explanation
Indices: 733--802 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
723 TTCAATAACC
*
733 TTACACTTTTTGTAATTTTGGTTATCATATTTCTTA
1 TTACACTTTTTGTAATTTTGATTATCATATTTCTTA
*
769 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACACTTTTTGTAATTTTGATTATCATATTTCT
803 CCAAAATCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (36 bp):
TTACACTTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:12176 original size:1 final size:1
Alignment explanation
Indices: 12170--12223 Score: 108
Period size: 1 Copynumber: 54.0 Consensus size: 1
12160 TTGAAAACTG
12170 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12224 CCGAAAACCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13731 original size:15 final size:15
Alignment explanation
Indices: 13711--13739 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13701 GCATAGGTTG
13711 AAAGAAAACAATTAA
1 AAAGAAAACAATTAA
13726 AAAGAAAACAATTA
1 AAAGAAAACAATTA
13740 TACTAGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAGAAAACAATTAA
Found at i:17526 original size:104 final size:102
Alignment explanation
Indices: 17344--17703 Score: 479
Period size: 103 Copynumber: 3.5 Consensus size: 102
17334 GCATAAATTG
* *
17344 AGCATGCCTACATGTTTTATCATTTTTTATGGTAGTATATGCCTAATACTTGCTCATATACACAT
1 AGCATGCCTACATGTTTTATCATTTTTTATGGTAGTATATGCCTAATACTTGATCGTATACACAT
* *
17409 AAATTGAGTTAACATGATCATGCAAAAGCATTGTTTA
66 AAATTGAGCTAACATGATCATGCAAGAGCATTGTTTA
*
17446 AGTATGCCTACATGTTTTTATCATTTTTTGATGGTAGTATATGCCTAATACTTGATCGTATACAC
1 AGCATGCCTACATG-TTTTATCATTTTTT-ATGGTAGTATATGCCTAATACTTGATCGTATACAC
* *
17511 ATAAATTGAGCTAACATGATCGTGCATGAGCATTGTTTA
64 ATAAATTGAGCTAACATGATCATGCAAGAGCATTGTTTA
* * * ***
17550 AGCATGCCTACATGTTTTATCATTCTTTGATGGTAGTATATGCTTGATACTTGCA-CGTATTTGC
1 AGCATGCCTACATGTTTTATCATT-TTTTATGGTAGTATATGCCTAATACTTG-ATCGTATACAC
** *
17614 ATAAATTGAGCTATTATGATCATGCAAGAGCATAGTTTA
64 ATAAATTGAGCTAACATGATCATGCAAGAGCATTGTTTA
* * * * *
17653 AGCATGCTTACAAGCTTTATTAATTTTTTATGGTAGTATATGCCTAGTACT
1 AGCATGCCTACATGTTTTA-TCATTTTTTATGGTAGTATATGCCTAATACT
17704 CGTACGTACA
Statistics
Matches: 226, Mismatches: 27, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
102 13 0.06
103 124 0.55
104 89 0.39
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.39
Consensus pattern (102 bp):
AGCATGCCTACATGTTTTATCATTTTTTATGGTAGTATATGCCTAATACTTGATCGTATACACAT
AAATTGAGCTAACATGATCATGCAAGAGCATTGTTTA
Found at i:17898 original size:20 final size:20
Alignment explanation
Indices: 17862--17959 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 20
17852 GATCATTCTC
* * *
17862 GGCCGTAAAACCTTATGATG
1 GGCCGTAAGACCCTATGACG
*
17882 GGCTGTAAGACCCTATGACG
1 GGCCGTAAGACCCTATGACG
*
17902 GGCCGTAAGACCGACGA-GCATCG
1 GGCCGTAAGACC--CTATG-A-CG
17925 ATCGGCCGTAAGACCCTATGACG
1 ---GGCCGTAAGACCCTATGACG
*
17948 GGTCGTAAGACC
1 GGCCGTAAGACC
17960 GACGAGCATT
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
20 38 0.61
21 1 0.02
22 3 0.05
23 4 0.06
24 3 0.05
25 1 0.02
26 12 0.19
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.17
Consensus pattern (20 bp):
GGCCGTAAGACCCTATGACG
Found at i:17955 original size:46 final size:49
Alignment explanation
Indices: 17877--18007 Score: 180
Period size: 46 Copynumber: 2.7 Consensus size: 49
17867 TAAAACCTTA
* *
17877 TGATGGGCTGTAAGACCCTATGACGGGCCGTAAGACCGACGAGCA-T-C
1 TGATCGGCCGTAAGACCCTATGACGGGCCGTAAGACCGACGAGCATTAC
*
17924 -GATCGGCCGTAAGACCCTATGACGGGTCGTAAGACCGACGAGCATTGAC
1 TGATCGGCCGTAAGACCCTATGACGGGCCGTAAGACCGACGAGCATT-AC
*
17973 TGATCGGCCGTAAGA-CCTCATGACGAGCCGTAAGA
1 TGATCGGCCGTAAGACCCT-ATGACGGGCCGTAAGA
18008 GTGACAAGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
46 41 0.55
47 1 0.01
49 4 0.05
50 28 0.38
ACGTcount: A:0.27, C:0.26, G:0.31, T:0.17
Consensus pattern (49 bp):
TGATCGGCCGTAAGACCCTATGACGGGCCGTAAGACCGACGAGCATTAC
Found at i:17996 original size:50 final size:47
Alignment explanation
Indices: 17877--18069 Score: 176
Period size: 50 Copynumber: 4.0 Consensus size: 47
17867 TAAAACCTTA
* *
17877 TGATGGGCTGTAAGACCCTATGACGGGCCGTAAGACCGACGAGCATC
1 TGATCGGCCGTAAGACCCTATGACGGGCCGTAAGACCGACGAGCATC
*
17924 -GATCGGCCGTAAGACCCTATGACGGGTCGTAAGACCGACGAGCATTGAC
1 TGATCGGCCGTAAGACCCTATGACGGGCCGTAAGACCGACGAGCA-T--C
* ** *
17973 TGATCGGCCGTAAGA-CCTCATGACGAGCCGTAAGAGTGACAAGCA-C
1 TGATCGGCCGTAAGACCCT-ATGACGGGCCGTAAGACCGACGAGCATC
* * * * * *
18019 TTATCGAACCACAGTAAGACCCCACGACAGGCCGTAAGACCGAAGAGCATC
1 TGATCG--GC-C-GTAAGACCCTATGACGGGCCGTAAGACCGACGAGCATC
18070 ATCAACAGCG
Statistics
Matches: 117, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
46 47 0.40
47 1 0.01
48 1 0.01
49 5 0.04
50 60 0.51
51 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.28, T:0.15
Consensus pattern (47 bp):
TGATCGGCCGTAAGACCCTATGACGGGCCGTAAGACCGACGAGCATC
Found at i:18327 original size:74 final size:74
Alignment explanation
Indices: 18246--18415 Score: 232
Period size: 74 Copynumber: 2.3 Consensus size: 74
18236 CGGTGGAGAG
* ** *
18246 CCGACCTCGACCAAGCACGGATGAACAACCCTCTTAAGGGTCCAGTGAAACTGGCTGGCGAGCGA
1 CCGACCTCGACCAAGCACGGATGAACAACCCTCTTAAGGGTCAAGTGAAACCAGATGGCGAGCGA
18311 CCAGCACGA
66 CCAGCACGA
* * * *
18320 CCGACCTCGACCAAGCACGAATGAAGAACCCTCTTAAGGGTTAAGTGGAACCAGATGGCGAGCGA
1 CCGACCTCGACCAAGCACGGATGAACAACCCTCTTAAGGGTCAAGTGAAACCAGATGGCGAGCGA
* *
18385 TCGGCACGA
66 CCAGCACGA
* *
18394 CCGACCTCGTCCAAGCATGGAT
1 CCGACCTCGACCAAGCACGGAT
18416 CAAAAACGAA
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
74 83 1.00
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.14
Consensus pattern (74 bp):
CCGACCTCGACCAAGCACGGATGAACAACCCTCTTAAGGGTCAAGTGAAACCAGATGGCGAGCGA
CCAGCACGA
Found at i:18734 original size:22 final size:22
Alignment explanation
Indices: 18708--18749 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18698 AGATTGCGGA
* *
18708 GATCACCCAAATGAAGAATGTC
1 GATCACCCAAACGAAAAATGTC
*
18730 GATCACGCAAACGAAAAATG
1 GATCACCCAAACGAAAAATG
18750 CTCCTCAAAA
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:0.45, C:0.21, G:0.19, T:0.14
Consensus pattern (22 bp):
GATCACCCAAACGAAAAATGTC
Found at i:18925 original size:117 final size:118
Alignment explanation
Indices: 18715--19074 Score: 546
Period size: 118 Copynumber: 3.1 Consensus size: 118
18705 GGAGATCACC
* * * *
18715 CAAATGAAGAATGTCGATCACGCAAACGAAAAATGCTCCTCA-AAACGAGTTGAATGCACAAGTG
1 CAAATGAAGAATGTCGATCGCGCAAACGAAAAATGCTCCTCAGAAGCGAGTAGAATGCCCAAGTG
** *
18779 AAGATCACTCACCATAAGGGAGTAGATCGTGTGATGGAGAA-CGACGTTCGCG
66 AAGATCACTCACCATAAGGGAGTAGATCGTGCAATGGAGAATCGACGATCGCG
*
18831 CAAATGAAGAATGTCGATCGCGCAAACGAAAAATGCTCCTCAGAAGGGAGTAGAATGCCCAAGTG
1 CAAATGAAGAATGTCGATCGCGCAAACGAAAAATGCTCCTCAGAAGCGAGTAGAATGCCCAAGTG
* *
18896 AAGATCACTCACCATAAAGGAGTAGATCGTGCAATGGAGAATCGTCGATCGCG
66 AAGATCACTCACCATAAGGGAGTAGATCGTGCAATGGAGAATCGACGATCGCG
*
18949 CAAATGAAGAATGTCGATCGCGCAAACGGAAAATGCTCCTCAGAAGCGAGTAGAATGCCCAAGTG
1 CAAATGAAGAATGTCGATCGCGCAAACGAAAAATGCTCCTCAGAAGCGAGTAGAATGCCCAAGTG
* * * *
19014 AAGATCACTCACCATAAGGGAGTAGATCGCGAAATTGAAGAAT-GACGATTGCG
66 AAGATCACTCACCATAAGGGAGTAGATCGTGCAA-TGGAGAATCGACGATCGCG
*
19067 AAAATGAA
1 CAAATGAA
19075 TAACGCTCCT
Statistics
Matches: 222, Mismatches: 19, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
116 41 0.18
117 56 0.25
118 118 0.53
119 7 0.03
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (118 bp):
CAAATGAAGAATGTCGATCGCGCAAACGAAAAATGCTCCTCAGAAGCGAGTAGAATGCCCAAGTG
AAGATCACTCACCATAAGGGAGTAGATCGTGCAATGGAGAATCGACGATCGCG
Found at i:18974 original size:22 final size:23
Alignment explanation
Indices: 18920--18974 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
18910 TAAAGGAGTA
* *
18920 GATCGTGC-AATGGAGAATCGTC
1 GATCGCGCAAATGAAGAATCGTC
18942 GATCGCGCAAATGAAGAAT-GTC
1 GATCGCGCAAATGAAGAATCGTC
18964 GATCGCGCAAA
1 GATCGCGCAAA
18975 CGGAAAATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (23 bp):
GATCGCGCAAATGAAGAATCGTC
Found at i:18983 original size:22 final size:22
Alignment explanation
Indices: 18920--18983 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
18910 TAAAGGAGTA
* *
18920 GATCGTGCAATGG-AGAATCGTC
1 GATCGCGCAAAGGAAGAAT-GTC
*
18942 GATCGCGCAAATGAAGAATGTC
1 GATCGCGCAAAGGAAGAATGTC
18964 GATCGCGCAAACGGAA-AATG
1 GATCGCGCAAA-GGAAGAATG
18984 CTCCTCAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 28 0.78
23 8 0.22
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (22 bp):
GATCGCGCAAAGGAAGAATGTC
Found at i:19087 original size:96 final size:96
Alignment explanation
Indices: 18942--19152 Score: 282
Period size: 96 Copynumber: 2.2 Consensus size: 96
18932 GAGAATCGTC
* * *
18942 GATCGCGCAAATGAAGAATGTCGATCGCGCAAACGGAAAATGCTCCTCAGAAGCGAGTAGAATGC
1 GATCGCGCAAATGAAGAATGACGATCGCGCAAAAGGAAAACGCTCCTCAGAAGCGAGTAGAATGC
**
19007 CCAAGTGAAGATCACTCACCATAAGGGAGTA
66 CCAAGTGAAGATCACTCACCATAAGAAAGTA
* * *
19038 GATCGCG-AAATTGAAGAATGACGATTGCG-AAAATGAATAACGCTCCTCAGAAGGGAGTAGAAT
1 GATCGCGCAAA-TGAAGAATGACGATCGCGCAAAAGGAA-AACGCTCCTCAGAAGCGAGTAGAAT
** * *
19101 GGGCAAGTGAAGATCACTTACCATAAGAAAGTC
64 GCCCAAGTGAAGATCACTCACCATAAGAAAGTA
19134 GATCGCGCAAATGAAGAAT
1 GATCGCGCAAATGAAGAAT
19153 AATGTTGATC
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
95 9 0.09
96 88 0.88
97 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.17
Consensus pattern (96 bp):
GATCGCGCAAATGAAGAATGACGATCGCGCAAAAGGAAAACGCTCCTCAGAAGCGAGTAGAATGC
CCAAGTGAAGATCACTCACCATAAGAAAGTA
Found at i:20128 original size:12 final size:12
Alignment explanation
Indices: 20111--20144 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20101 ATCATTCCGA
20111 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
20123 AAAAAACAAAAC
1 AAAAAAAAAAAC
20135 AAAACAAAAA
1 AAAA-AAAAA
20145 GCCCAAAGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:20138 original size:17 final size:15
Alignment explanation
Indices: 20110--20144 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
20100 TATCATTCCG
20110 AAAAAAAAAAAACAA
1 AAAAAAAAAAAACAA
20125 AAAACAAAACAAAACAA
1 AAAA-AAAA-AAAACAA
20142 AAA
1 AAA
20145 GCCCAAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 4 0.22
17 10 0.56
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAACAA
Found at i:23959 original size:11 final size:11
Alignment explanation
Indices: 23943--23968 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23933 TAATTAGCTA
23943 ACTTAATAAGC
1 ACTTAATAAGC
23954 ACTTAATAAGC
1 ACTTAATAAGC
23965 ACTT
1 ACTT
23969 TAGAACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (11 bp):
ACTTAATAAGC
Found at i:31925 original size:2 final size:2
Alignment explanation
Indices: 31912--31960 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
31902 CATAAAAATA
31912 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31955 AT AT AT
1 AT AT AT
31961 TAGAGAATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52380 original size:2 final size:2
Alignment explanation
Indices: 52373--52405 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52363 TAATTTGTAA
52373 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
52406 AAAGAATGGT
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:57962 original size:2 final size:2
Alignment explanation
Indices: 57955--58002 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
57945 AAAATAGATT
57955 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
57997 CA CA CA
1 CA CA CA
58003 TATATATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:59468 original size:20 final size:20
Alignment explanation
Indices: 59445--59518 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
59435 TTTCTGATAT
*
59445 ATTATATATAAATATAACTA
1 ATTATATATAAATATAAATA
* *
59465 ATTAAATATAATATAAAATATA
1 ATTATATATAA-ATATAA-ATA
* *
59487 AATATATAATATATATAAATA
1 ATTATAT-ATAAATATAAATA
59508 ATTATATATAA
1 ATTATATATAA
59519 TACCTCAGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
20 13 0.31
21 14 0.33
22 12 0.29
23 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATATATAAATATAAATA
Found at i:59508 original size:13 final size:13
Alignment explanation
Indices: 59469--59518 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
59459 TAACTAATTA
59469 AATATA-ATATAA-
1 AATATATATA-AAT
* *
59481 AATATAAATATAT
1 AATATATATAAAT
59494 AATATATATAAAT
1 AATATATATAAAT
59507 AATTATATATAA
1 AA-TATATATAA
59519 TACCTCAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 7 0.22
13 16 0.50
14 9 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATATATAAAT
Found at i:60327 original size:4 final size:4
Alignment explanation
Indices: 60318--60361 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
60308 AGACGCATGT
* *
60318 ATAC ATAC ATAC ATAC GTAC ATAC ATAC ATAT ATAC AATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -ATAC ATA
60362 AATATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 31 0.89
5 4 0.11
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:61859 original size:45 final size:45
Alignment explanation
Indices: 61795--61924 Score: 233
Period size: 45 Copynumber: 2.9 Consensus size: 45
61785 AAGCAACAAT
* * *
61795 TAATATTAGTTTTATTTTGATGAATTATCTAGAGATGGAGGAGTA
1 TAATATTAGCTTTAATTTGATGAATTACCTAGAGATGGAGGAGTA
61840 TAATATTAGCTTTAATTTGATGAATTACCTAGAGATGGAGGAGTA
1 TAATATTAGCTTTAATTTGATGAATTACCTAGAGATGGAGGAGTA
61885 TAATATTAGCTTTAATTTGATGAATTACCTAGAGATGGAG
1 TAATATTAGCTTTAATTTGATGAATTACCTAGAGATGGAG
61925 TATAATTTAG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (45 bp):
TAATATTAGCTTTAATTTGATGAATTACCTAGAGATGGAGGAGTA
Found at i:64000 original size:2 final size:2
Alignment explanation
Indices: 63993--64033 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
63983 ATATTAAGCC
* *
63993 AT AT AT AT AC AC 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 AT AT A
64034 CTTTGTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:64453 original size:33 final size:33
Alignment explanation
Indices: 64413--64481 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
64403 CAAAATAAAG
*
64413 TTTGGAATGTGCAATTTTTTAAAATAAATTATT
1 TTTGGAATGTGCAATTTTTCAAAATAAATTATT
*
64446 TTTGGAATTTGCAATTTTTCAAAATAAATTATT
1 TTTGGAATGTGCAATTTTTCAAAATAAATTATT
64479 TTT
1 TTT
64482 TGAAGTAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (33 bp):
TTTGGAATGTGCAATTTTTCAAAATAAATTATT
Found at i:64498 original size:30 final size:32
Alignment explanation
Indices: 64413--64503 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 32
64403 CAAAATAAAG
*
64413 TTTGGAATGT-GCAATTTTTTAAAATAAATTATT
1 TTTGGAA-GTAGCAA-TTTTCAAAATAAATTATT
* *
64446 TTTGGAATTTGCAATTTTTCAAAATAAATTATT
1 TTTGGAAGTAGCAA-TTTTCAAAATAAATTATT
*
64479 TTTTGAAGTAG-AA-TTTCAAAATAAA
1 TTTGGAAGTAGCAATTTTCAAAATAAA
64504 GTTTTGTATC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
30 12 0.23
32 3 0.06
33 37 0.71
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (32 bp):
TTTGGAAGTAGCAATTTTCAAAATAAATTATT
Found at i:68929 original size:50 final size:49
Alignment explanation
Indices: 68846--68948 Score: 120
Period size: 50 Copynumber: 2.1 Consensus size: 49
68836 CTTCATATTT
* *
68846 TCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGTTTTC
1 TCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTG-TTTC
* * *
68896 TCTTGTTTCA-ATCTTGTCTCCGGAC-ATAAAAACACTGTATTCGTGTTTC
1 TCTTGTTT-AGATCTTGTCTCAGGACAAT-AAAACACTCTATTAGTGTTTC
68945 TCTT
1 TCTT
68949 TTAGAAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
49 10 0.22
50 35 0.76
51 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (49 bp):
TCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGTTTC
Done.