Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018045.1 Corchorus olitorius cultivar O-4 contig18078, 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: 93575
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:8959 original size:28 final size:27
Alignment explanation
Indices: 8892--8985 Score: 134
Period size: 27 Copynumber: 3.4 Consensus size: 27
8882 AATGTACCTG
* *
8892 AAATGACTAAAATGGCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGGACGTGC
*
8919 AAATGACCAAAATGTCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGGACGTGC
* *
8946 AAAATGACCAAAATGCCCCTAGACATGC
1 -AAATGACCAAAATGCCCCTGGACGTGC
8974 AAATGACCAAAA
1 AAATGACCAAAA
8986 GAAGTAAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 37 0.61
28 24 0.39
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGACGTGC
Found at i:9461 original size:35 final size:35
Alignment explanation
Indices: 9377--9688 Score: 396
Period size: 35 Copynumber: 8.9 Consensus size: 35
9367 CTGAATCAAC
*
9377 CTTTAAAGATGCTACACCGAGTCATCTG-ATTCCAATGT
1 CTTTGAAGATGCTACACCGAGTCATCTGAATT-C-A--T
* * * *
9415 CTTTGGAGATGCTGCACCGAGTCATCTAAATTCAA
1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAT
*
9450 CTTTGAAGATGCT--ACCGAGTCATCCGAATTCAT
1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAT
* *
9483 CTTTTAAGATGCTACACCGAGTCATCCGAATTCAT
1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAT
9518 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAT
1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAT
* **
9553 CTTTGAAGATGCAACACCGAGTCATCCAAATTCAT
1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAT
* ** *
9588 CTTTGAAGACGCTACAATGAGTCATCTGAATTCAA
1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAT
* *
9623 CTTTGGAGATGCTACACCGAGTCATCTGACTTCAT
1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAT
* *
9658 CTTTGAAAATGCTACACTGAGTCATCTGAAT
1 CTTTGAAGATGCTACACCGAGTCATCTGAAT
9689 CCCTGAAAAT
Statistics
Matches: 239, Mismatches: 32, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
33 29 0.12
35 181 0.76
37 1 0.00
38 25 0.10
39 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (35 bp):
CTTTGAAGATGCTACACCGAGTCATCTGAATTCAT
Found at i:10632 original size:1 final size:1
Alignment explanation
Indices: 10626--10658 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
10616 GGCTGTATGC
*
10626 TTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10659 AAAGGACAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:18016 original size:21 final size:21
Alignment explanation
Indices: 17992--18032 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17982 AGCTTCTTCG
17992 CGGCG-CTTCGCCTCTTCATCT
1 CGGCGCCTT-GCCTCTTCATCT
*
18013 CGGCGCCTTGCTTCTTCATC
1 CGGCGCCTTGCCTCTTCATC
18033 CTGACGCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.05, C:0.41, G:0.20, T:0.34
Consensus pattern (21 bp):
CGGCGCCTTGCCTCTTCATCT
Found at i:29055 original size:3 final size:3
Alignment explanation
Indices: 29049--29088 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
29039 ATATATATAT
29049 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29089 GGTTAGTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29182 original size:26 final size:26
Alignment explanation
Indices: 29146--29195 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
29136 TGTCCCTTTG
*
29146 AAAAAAAAAAGAGTGTTAGTAACCTC
1 AAAAAAAAAAGAGAGTTAGTAACCTC
* *
29172 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAAAAAAAAGAGAGTTAGTAACC
29196 CCTAAATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.20, T:0.16
Consensus pattern (26 bp):
AAAAAAAAAAGAGAGTTAGTAACCTC
Found at i:33646 original size:29 final size:31
Alignment explanation
Indices: 33612--33675 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
33602 TAATAAACGC
*
33612 CACTA-TT-TAGCGGCGTTTTCTTCAATAGA
1 CACTATTTATAGCGGCGTTTTCTTCAATAAA
* *
33641 CACTATTTTATAGGGGTGTTTTCTTCAATAAA
1 CACTA-TTTATAGCGGCGTTTTCTTCAATAAA
33673 CAC
1 CAC
33676 CGCTATTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 5 0.17
31 2 0.07
32 22 0.76
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (31 bp):
CACTATTTATAGCGGCGTTTTCTTCAATAAA
Found at i:38818 original size:163 final size:162
Alignment explanation
Indices: 38570--38950 Score: 566
Period size: 163 Copynumber: 2.3 Consensus size: 162
38560 TATTATAGGC
* * * * * *
38570 GAGGGAATTTTTCCCTCCAAAACAAAGAAAAAAAAATTCTATCACTCCATATATTATAATTGCGG
1 GAGGGAATTTTTCCCT-CAAAAAAAAGGAAAAAAAA-TCTCTCCCTCCATATATTAAAATGGCGG
* * *
38635 CGTTTCCTAACCTAGACGCCACTAATTAGCGGCGTCTGATGAGAAAACGCCGCTATATATTATAG
64 CATTTCCTAACCTAGACGCCACTAATTACCGGCGTCTGATGACAAAACGCCGCTATATATTATAG
* *
38700 GCGTAGAGTTGGAAACTTTCTTTGTTTTAGGGGG
129 GCGTAGAGTTGAAAACTTTCTTTGTTTTAGGAGG
*
38734 GAGGGAATTTTTCCCTACAAAAAAAAGGAAAAAAAATCTCTCCCTCCATATGTTAAAATGGCGGC
1 GAGGGAATTTTTCCCT-CAAAAAAAAGGAAAAAAAATCTCTCCCTCCATATATTAAAATGGCGGC
*** * *
38799 ATTTCCTTTTCTAGACGCCACTACTTACCGGCGTCTGATGTCAAAACGCCGCTATATATTATAGG
65 ATTTCCTAACCTAGACGCCACTAATTACCGGCGTCTGATGACAAAACGCCGCTATATATTATAGG
38864 CGTAGAGTTGAAAACTTTCTTTGTTTTAGGAGG
130 CGTAGAGTTGAAAACTTTCTTTGTTTTAGGAGG
*
38897 GAGGGAATTTTTCCCTCCAAAAAAA-GAAAAAAAATCTCTCCCTCCATATATTAA
1 GAGGGAATTTTTCCCTCAAAAAAAAGGAAAAAAAATCTCTCCCTCCATATATTAA
38951 TATAGCAATG
Statistics
Matches: 197, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
161 28 0.14
162 8 0.04
163 128 0.65
164 33 0.17
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (162 bp):
GAGGGAATTTTTCCCTCAAAAAAAAGGAAAAAAAATCTCTCCCTCCATATATTAAAATGGCGGCA
TTTCCTAACCTAGACGCCACTAATTACCGGCGTCTGATGACAAAACGCCGCTATATATTATAGGC
GTAGAGTTGAAAACTTTCTTTGTTTTAGGAGG
Found at i:40232 original size:22 final size:22
Alignment explanation
Indices: 40207--40257 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
40197 AGTAGATAAC
40207 AGCTTCCAGGAAGGTGCAGTGA
1 AGCTTCCAGGAAGGTGCAGTGA
* *
40229 AGCTTCAAGGAATGTGCAGTGA
1 AGCTTCCAGGAAGGTGCAGTGA
40251 AGCTTCC
1 AGCTTCC
40258 TTCTTCTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (22 bp):
AGCTTCCAGGAAGGTGCAGTGA
Found at i:45648 original size:19 final size:19
Alignment explanation
Indices: 45624--45664 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
45614 CCACCACCCC
45624 ATCCCCTTCTTCTCCCTGG
1 ATCCCCTTCTTCTCCCTGG
45643 ATCCCCTTCTTCTCCCTGG
1 ATCCCCTTCTTCTCCCTGG
45662 ATC
1 ATC
45665 GAGAGTCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.46, G:0.10, T:0.37
Consensus pattern (19 bp):
ATCCCCTTCTTCTCCCTGG
Found at i:46156 original size:2 final size:2
Alignment explanation
Indices: 46144--46182 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
46134 ATACTTTTTA
*
46144 AT AT A- AT AT AT AT AT AT AT AT A- AT AT AT AG 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
46183 GGTAGGTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:46166 original size:17 final size:17
Alignment explanation
Indices: 46144--46182 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
46134 ATACTTTTTA
*
46144 ATATAATATATATATAT
1 ATATAATATATAGATAT
46161 ATATAATATATAGATAT
1 ATATAATATATAGATAT
46178 ATATA
1 ATATA
46183 GGTAGGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATAATATATAGATAT
Found at i:46169 original size:15 final size:15
Alignment explanation
Indices: 46151--46180 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46141 TTAATATAAT
*
46151 ATATATATATATATA
1 ATATATAGATATATA
46166 ATATATAGATATATA
1 ATATATAGATATATA
46181 TAGGTAGGTA
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:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
ATATATAGATATATA
Found at i:48906 original size:41 final size:41
Alignment explanation
Indices: 48855--49012 Score: 244
Period size: 41 Copynumber: 3.9 Consensus size: 41
48845 GTTTGATTTG
* * * ***
48855 ATTTGATTCAACGGTCTCGAGGACTTGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
48896 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
48937 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
**
48978 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAA
49013 CAAATAAAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
Found at i:49133 original size:16 final size:16
Alignment explanation
Indices: 49108--49142 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49098 TCTGAAAATA
* *
49108 CTTCAGAGCTTTTCTG
1 CTTCAAAGCTATTCTG
49124 CTTCAAAGCTATTCTG
1 CTTCAAAGCTATTCTG
49140 CTT
1 CTT
49143 TCTGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (16 bp):
CTTCAAAGCTATTCTG
Found at i:52069 original size:21 final size:21
Alignment explanation
Indices: 52045--52085 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52035 GTTGTGGTCC
* *
52045 TTCTTGGTTGTTTGTACCTTT
1 TTCTTGGTTGTCTGAACCTTT
*
52066 TTCTTGTTTGTCTGAACCTT
1 TTCTTGGTTGTCTGAACCTT
52086 GGTTTCCCTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.17, G:0.17, T:0.59
Consensus pattern (21 bp):
TTCTTGGTTGTCTGAACCTTT
Found at i:54346 original size:51 final size:51
Alignment explanation
Indices: 54291--54472 Score: 168
Period size: 51 Copynumber: 3.4 Consensus size: 51
54281 TACACGGCGC
* *
54291 TGCAGTAGTCGGGGAAGGACTTGGAGGACGAGAATTGCCAGGGAGGCTTGT
1 TGCAGTAGTCGGGGAAGGACTTGGAGGACGGGAAATGCCAGGGAGGCTTGT
* * * * *
54342 TGCAGTAGTCGGGTCGGGGAAGGAGTTGGAGAATGGGAAATGCCAGCTGAATTAG-TTGT
1 TGCAGTA-----GTCGGGGAAGGACTTGGAGGACGGGAAATGCCAG--GGA--GGCTTGT
* * * *
54401 TGTAGTAGTCGGGGAAGGACTTAGAGGACGGGAAATGCCAAGGAGGCTTGC
1 TGCAGTAGTCGGGGAAGGACTTGGAGGACGGGAAATGCCAGGGAGGCTTGT
*
54452 TGCAGTAGTCGGTGAAGGACT
1 TGCAGTAGTCGGGGAAGGACT
54473 CGGATTCTGT
Statistics
Matches: 103, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
50 1 0.01
51 29 0.28
52 2 0.02
54 29 0.28
56 29 0.28
58 2 0.02
59 10 0.10
60 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.41, T:0.21
Consensus pattern (51 bp):
TGCAGTAGTCGGGGAAGGACTTGGAGGACGGGAAATGCCAGGGAGGCTTGT
Found at i:54386 original size:56 final size:56
Alignment explanation
Indices: 54298--54463 Score: 169
Period size: 56 Copynumber: 3.0 Consensus size: 56
54288 CGCTGCAGTA
* *
54298 GTCGGGGAAGGACTTGGAGGACGAGAATTGCCAGGGAGGCTTGTTGCAGTAGTCGG
1 GTCGGGGAAGGACTTGGAGGACGGGAAATGCCAGGGAGGCTTGTTGCAGTAGTCGG
* * * * * ** *
54354 GTCGGGGAAGGAGTTGGAGAATGGGAAATGCCAGCTGA--ATTAGTTGTTGTAGT--A
1 GTCGGGGAAGGACTTGGAGGACGGGAAATGCCAG-GGAGGCTT-GTTGCAGTAGTCGG
* * *
54408 GTCGGGGAAGGACTTAGAGGACGGGAAATGCCAAGGAGGCTTGCTGCAGTAGTCGG
1 GTCGGGGAAGGACTTGGAGGACGGGAAATGCCAGGGAGGCTTGTTGCAGTAGTCGG
54464 TGAAGGACTC
Statistics
Matches: 83, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
53 2 0.02
54 37 0.45
55 4 0.05
56 38 0.46
57 2 0.02
ACGTcount: A:0.25, C:0.13, G:0.42, T:0.20
Consensus pattern (56 bp):
GTCGGGGAAGGACTTGGAGGACGGGAAATGCCAGGGAGGCTTGTTGCAGTAGTCGG
Found at i:54460 original size:54 final size:54
Alignment explanation
Indices: 54294--54460 Score: 165
Period size: 54 Copynumber: 3.1 Consensus size: 54
54284 ACGGCGCTGC
* * *
54294 AGTAGTCGGGGAAGGACTTGGAGGACGAGAATTGCCAGGGAGGCTTGTTGCAGT
1 AGTAGTCGGGGAAGGACTTGGAGGACGGGAAATGCCAAGGAGGCTTGTTGCAGT
* * * * ** ** **
54348 AGTCGGGTCGGGGAAGGAGTTGGAGAATGGGAAATGCC-AGCTGAATTAGTTGTTGT
1 AGT--AGTCGGGGAAGGACTTGGAGGACGGGAAATGCCAAGGAGGCTT-GTTGCAGT
* *
54404 AGTAGTCGGGGAAGGACTTAGAGGACGGGAAATGCCAAGGAGGCTTGCTGCAGT
1 AGTAGTCGGGGAAGGACTTGGAGGACGGGAAATGCCAAGGAGGCTTGTTGCAGT
54458 AGT
1 AGT
54461 CGGTGAAGGA
Statistics
Matches: 84, Mismatches: 25, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
54 39 0.46
55 9 0.11
56 36 0.43
ACGTcount: A:0.26, C:0.12, G:0.41, T:0.21
Consensus pattern (54 bp):
AGTAGTCGGGGAAGGACTTGGAGGACGGGAAATGCCAAGGAGGCTTGTTGCAGT
Found at i:63768 original size:20 final size:20
Alignment explanation
Indices: 63745--63798 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
63735 TACAACTAAT
* *
63745 TCAAATCAAGGAATAGGCAA
1 TCAAATCAAGCAATAAGCAA
*
63765 TC-AATCAAAGCAATAATCAA
1 TCAAATC-AAGCAATAAGCAA
63785 TCAAATCAAAGCAA
1 TCAAATC-AAGCAA
63799 AAGAAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.54, C:0.19, G:0.11, T:0.17
Consensus pattern (20 bp):
TCAAATCAAGCAATAAGCAA
Found at i:66165 original size:6 final size:6
Alignment explanation
Indices: 66154--66184 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
66144 CAAATCAAAT
66154 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
66185 TAATACACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:67752 original size:22 final size:22
Alignment explanation
Indices: 67727--67794 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
67717 AATTTATTTA
67727 TGGTATAGTTTCTAGTTTGGGT
1 TGGTATAGTTTCTAGTTTGGGT
* *** ***
67749 TGGTA-GGTAGGTAGTTTATTT
1 TGGTATAGTTTCTAGTTTGGGT
67770 ATGGTATAGTTTCTAGTTTGGGT
1 -TGGTATAGTTTCTAGTTTGGGT
67793 TG
1 TG
67795 AATTCTCCTT
Statistics
Matches: 30, Mismatches: 14, Indels: 4
0.62 0.29 0.08
Matches are distributed among these distances:
21 9 0.30
22 12 0.40
23 9 0.30
ACGTcount: A:0.16, C:0.03, G:0.32, T:0.49
Consensus pattern (22 bp):
TGGTATAGTTTCTAGTTTGGGT
Found at i:67760 original size:44 final size:44
Alignment explanation
Indices: 67704--67794 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
67694 GTTTGTTTAT
67704 TTGGTAGGTAGGTAATTTATTTATGGTATAGTTTCTAGTTTGGG
1 TTGGTAGGTAGGTAATTTATTTATGGTATAGTTTCTAGTTTGGG
*
67748 TTGGTAGGTAGGTAGTTTATTTATGGTATAGTTTCTAGTTTGGG
1 TTGGTAGGTAGGTAATTTATTTATGGTATAGTTTCTAGTTTGGG
67792 TTG
1 TTG
67795 AATTCTCCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (44 bp):
TTGGTAGGTAGGTAATTTATTTATGGTATAGTTTCTAGTTTGGG
Found at i:68746 original size:32 final size:32
Alignment explanation
Indices: 68691--68774 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
68681 CATATATATA
* *
68691 AATGAATTGCAAATTTGTCCCCATCTGCAATT
1 AATGCATTGCAAATTTGTCCCCATATGCAATT
* * *
68723 AATGCATTGTAAATTTGTTCCCATATGTAATT
1 AATGCATTGCAAATTTGTCCCCATATGCAATT
68755 AATGCATTGCAAATTTGTCC
1 AATGCATTGCAAATTTGTCC
68775 TTATTCAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (32 bp):
AATGCATTGCAAATTTGTCCCCATATGCAATT
Found at i:72361 original size:14 final size:14
Alignment explanation
Indices: 72342--72368 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
72332 AAATAAATAA
72342 ATAAATATTTTTGG
1 ATAAATATTTTTGG
72356 ATAAATATTTTTG
1 ATAAATATTTTTG
72369 ATTTATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTTGG
Found at i:82060 original size:30 final size:30
Alignment explanation
Indices: 82004--82061 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
81994 AATTCTTGCT
**
82004 TCTTGAAATAATTCTTCAATGGTCTTCATA
1 TCTTGAAATAATTCTTCAATAATCTTCATA
*
82034 TCTTGAAATTA-TCTTCAATAAATCTTCA
1 TCTTGAAATAATTCTTCAAT-AATCTTCA
82062 ATCACAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (30 bp):
TCTTGAAATAATTCTTCAATAATCTTCATA
Found at i:84145 original size:130 final size:130
Alignment explanation
Indices: 83912--84155 Score: 479
Period size: 130 Copynumber: 1.9 Consensus size: 130
83902 AATGAATTGT
83912 ACAAAAGCAGATAAAAACCACAACAGAGTAGTAGATAATTATACCACCAAAACCAGTAACTGAGA
1 ACAAAAGCAGATAAAAACCACAACAGAGTAGTAGATAATTATACCACCAAAACCAGTAACTGAGA
*
83977 AGAGTTTGTCTATACTTCAAATACCCAGTTGTTACATCAAATTCAATATAAGCACACAACTTGAG
66 AAAGTTTGTCTATACTTCAAATACCCAGTTGTTACATCAAATTCAATATAAGCACACAACTTGAG
84042 ACAAAAGCAGATAAAAACCACAACAGAGTAGTAGATAATTATACCACCAAAACCAGTAACTGAGA
1 ACAAAAGCAGATAAAAACCACAACAGAGTAGTAGATAATTATACCACCAAAACCAGTAACTGAGA
84107 AAAGTTTGTCTATACTTCAAATACCCAGTTGTTACATCAAATTCAATAT
66 AAAGTTTGTCTATACTTCAAATACCCAGTTGTTACATCAAATTCAATAT
84156 TAAAATTTAA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 113 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (130 bp):
ACAAAAGCAGATAAAAACCACAACAGAGTAGTAGATAATTATACCACCAAAACCAGTAACTGAGA
AAAGTTTGTCTATACTTCAAATACCCAGTTGTTACATCAAATTCAATATAAGCACACAACTTGAG
Found at i:93525 original size:33 final size:32
Alignment explanation
Indices: 93453--93547 Score: 99
Period size: 33 Copynumber: 2.9 Consensus size: 32
93443 CTATGATCAA
93453 CTAAAACAGAA-TTGTTTTCATCACAATTAGC-ATC
1 CTAAAACAGAATTTG-TTTCATCACAA--A-CAATC
93487 C-AAAACAGAATTTGTTTCATCACAAACAATAC
1 CTAAAACAGAATTTGTTTCATCACAAACAAT-C
*
93519 CTAAAACAG-ATTTAGTGTCATCACAAACA
1 CTAAAACAGAATTT-GTTTCATCACAAACA
93548 TCACTCAAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
30 1 0.02
31 3 0.05
32 6 0.11
33 41 0.75
34 4 0.07
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.27
Consensus pattern (32 bp):
CTAAAACAGAATTTGTTTCATCACAAACAATC
Done.