Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017594.1 Corchorus olitorius cultivar O-4 contig17627, 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: 44424
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Found at i:4190 original size:69 final size:69
Alignment explanation
Indices: 4063--4357 Score: 412
Period size: 69 Copynumber: 4.3 Consensus size: 69
4053 TATTGTAGCA
* * * * * * *
4063 CTTGGTCTTGGCTCAAAATC-TAATTCGCAAATGATTTAAGACCGACATCGTCAGTATACGCTGT
1 CTTGGCCTCGGCTCGAAATCTTTATTCGCAATTGATTTAAGCCCAACATCGTCAGTATACGCTGT
*
4127 AACA
66 AACG
* * * *
4131 CTTGGCCTCGGCTCGAAATCTTTATTCGCAATTGATTTAAGCCCAGCATTGTCAATATACACTGT
1 CTTGGCCTCGGCTCGAAATCTTTATTCGCAATTGATTTAAGCCCAACATCGTCAGTATACGCTGT
*
4196 AATG
66 AACG
* *
4200 CTTGGCCTCAGCTCGAAATCTTTATTTGCAATTGATTTAAGCCCAACATCGTCAGTATACGCTGT
1 CTTGGCCTCGGCTCGAAATCTTTATTCGCAATTGATTTAAGCCCAACATCGTCAGTATACGCTGT
4265 AACG
66 AACG
* * *
4269 CTAGGCCTCGGCTCGAAATCTTTATTTGCAATTGATTTAAGCCCAACATCGTTAGTATACGCTGT
1 CTTGGCCTCGGCTCGAAATCTTTATTCGCAATTGATTTAAGCCCAACATCGTCAGTATACGCTGT
4334 AACG
66 AACG
*
4338 CTAGGCCTCGGCTCGAAATC
1 CTTGGCCTCGGCTCGAAATC
4358 AGTAGCAATC
Statistics
Matches: 203, Mismatches: 23, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
68 17 0.08
69 186 0.92
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (69 bp):
CTTGGCCTCGGCTCGAAATCTTTATTCGCAATTGATTTAAGCCCAACATCGTCAGTATACGCTGT
AACG
Found at i:5421 original size:17 final size:17
Alignment explanation
Indices: 5396--5429 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5386 AGTGTGCGAC
*
5396 CTGAGTCGAATCCGGAT
1 CTGAATCGAATCCGGAT
5413 CTGAATCGAATCCGGAT
1 CTGAATCGAATCCGGAT
5430 TAATCAGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (17 bp):
CTGAATCGAATCCGGAT
Found at i:7253 original size:25 final size:26
Alignment explanation
Indices: 7219--7275 Score: 98
Period size: 25 Copynumber: 2.2 Consensus size: 26
7209 CCCAATTTAA
7219 AAAGTCATAGAGTCTGCCATAAAACT
1 AAAGTCATAGAGTCTGCCATAAAACT
*
7245 AAAG-CATAGAGTCTGCCGTAAAACT
1 AAAGTCATAGAGTCTGCCATAAAACT
7270 AAAGTC
1 AAAGTC
7276 TAAACCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (26 bp):
AAAGTCATAGAGTCTGCCATAAAACT
Found at i:15685 original size:136 final size:136
Alignment explanation
Indices: 15523--15779 Score: 487
Period size: 136 Copynumber: 1.9 Consensus size: 136
15513 TTGAAAGAAT
*
15523 TAATGCTCTGCAAAGTGAAAGGAATCTCTGCAACAAGAGGTTGAAATTGAAGAAAATAATGCTCT
1 TAATGCTCTGCAAAGTGAAAGGAATCTCTGCAACAAGAAGTTGAAATTGAAGAAAATAATGCTCT
*
15588 GCAAAGTGGAAAGAATCTCTGCAAAAATATTTCCAATTATGTCAATAGTGCAAAGCTGAAATTGA
66 GCAAAGTGGAAAGAATCTCTGCAAAAATATTTCCAATTATGTCAACAGTGCAAAGCTGAAATTGA
15653 AGAAAA
131 AGAAAA
*
15659 TAATGCTTTGCAAAGTGAAAGGAATCTCTGCAACAAGAAGTTGAAATTGAAGAAAATAATGCTCT
1 TAATGCTCTGCAAAGTGAAAGGAATCTCTGCAACAAGAAGTTGAAATTGAAGAAAATAATGCTCT
15724 GCAAAGTGGAAAGAATCTCTGCAAAAATATTTCCAATTATGTCAACAGTGCAAAGC
66 GCAAAGTGGAAAGAATCTCTGCAAAAATATTTCCAATTATGTCAACAGTGCAAAGC
15780 ACATAGAGTG
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 118 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (136 bp):
TAATGCTCTGCAAAGTGAAAGGAATCTCTGCAACAAGAAGTTGAAATTGAAGAAAATAATGCTCT
GCAAAGTGGAAAGAATCTCTGCAAAAATATTTCCAATTATGTCAACAGTGCAAAGCTGAAATTGA
AGAAAA
Found at i:25735 original size:13 final size:13
Alignment explanation
Indices: 25697--25738 Score: 66
Period size: 14 Copynumber: 3.1 Consensus size: 13
25687 AAAATTGTTA
25697 TCAAGAAAAGGTTT
1 TCAA-AAAAGGTTT
25711 TCAAAAATAGGTTT
1 TCAAAAA-AGGTTT
25725 TCAAAAAAGGTTT
1 TCAAAAAAGGTTT
25738 T
1 T
25739 GAGTCTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (13 bp):
TCAAAAAAGGTTT
Found at i:28126 original size:67 final size:67
Alignment explanation
Indices: 27960--28290 Score: 463
Period size: 67 Copynumber: 5.0 Consensus size: 67
27950 AGAGGATTTT
* * * *
27960 AGAAGAACGCCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTGGATTGGAAGACAATCTCAC
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCAT
28025 TA
66 TA
* **
28027 AGGAA-T--ACCGGAAGACGGTTTGCAAGAAAGAATTTTCAAAAATTGATT-GAAGACAATCTCA
1 A-GAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCA
28088 TTAA
65 TT-A
* * *
28092 AGAAGTACACCGGAAGACGGCTTGTTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCAT
28157 TA
66 TA
* *
28159 AGAAGTACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTAT
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCAT
28224 TA
66 TA
* * * * *
28226 AGGAGAACCCCGGAAGACGGTTTCCTAGAAAGGATTTTCAAATGTTGATTGGAAGACAATCTCAT
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCAT
28291 CGGAAGACGG
Statistics
Matches: 237, Mismatches: 21, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
64 17 0.07
65 40 0.17
67 162 0.68
68 18 0.08
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (67 bp):
AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCAT
TA
Found at i:28320 original size:55 final size:55
Alignment explanation
Indices: 28236--28342 Score: 144
Period size: 55 Copynumber: 1.9 Consensus size: 55
28226 AGGAGAACCC
** *
28236 CGGAAGACGGTTTCCTAGAAAGGATTTTCA-AATGTTGATTGGAAGACAATCTCAT
1 CGGAAGACGGTTTCCTAGAAACAATTTTCAGAA-GTTGATCGGAAGACAATCTCAT
* * *
28291 CGGAAGACGGTTTGCTAGAAACAATTTTCAGGAGTTGATCGGAAGACGATCT
1 CGGAAGACGGTTTCCTAGAAACAATTTTCAGAAGTTGATCGGAAGACAATCT
28343 TGTCAAGAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
55 44 0.98
56 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (55 bp):
CGGAAGACGGTTTCCTAGAAACAATTTTCAGAAGTTGATCGGAAGACAATCTCAT
Found at i:28397 original size:64 final size:64
Alignment explanation
Indices: 28323--28670 Score: 439
Period size: 64 Copynumber: 5.4 Consensus size: 64
28313 AATTTTCAGG
* **
28323 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCCTA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAGTTTTCAAA
* * * * *
28387 AGTTGATCGGAAGACGATCTTGTCAAAAAGCACACCAGAAGATAGTTTC-CTAATAGTTTTCAGA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAAAGTTTTCAAA
* * *
28451 AGTTGATCGGAAGATGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACAGTTTTCAGA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAGTTTTCAAA
* * * *
28515 AGTTGATCGGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGATTCTTAAAA-TTTTCAAA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAGTTTTCAAA
* * * * * * *
28578 AGTCGGTCGGAAGACGATCTTGTTAAAAAGCACACCAGAAGATAGTTTCTCGAAAAGGTTTCAAA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAAAGTTTTCAAA
* * *
28643 AGTGGGTCGGAAGACGATCTTGTTAAGA
1 AGTTGATCGGAAGACGATCTTGTCAAGA
28671 GATGCACCGG
Statistics
Matches: 248, Mismatches: 32, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
63 49 0.20
64 165 0.67
65 34 0.14
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (64 bp):
AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAGTTTTCAAA
Found at i:28529 original size:192 final size:192
Alignment explanation
Indices: 28310--28670 Score: 535
Period size: 192 Copynumber: 1.9 Consensus size: 192
28300 GTTTGCTAGA
* * *
28310 AACAATTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCA
1 AACAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGATTCT-A
** * *
28375 AAAATTTTCCTAAGTTGATCGGAAGACGATCTTGTCAAAAAGCACACCAGAAGATAGTTTC-CTA
65 AAAATTTTCAAAAGTCGATCGGAAGACGATCTTGTCAAAAAGCACACCAGAAGATAGTTTCTCGA
* * * * *
28439 ATAGTTTTCAGAAGTTGATCGGAAGATGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
130 AAAGGTTTCAAAAGTGGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
* * *
28502 AACAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGATTCTTA
1 AACAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGATTCTAA
* *
28567 AAATTTTCAAAAGTCGGTCGGAAGACGATCTTGTTAAAAAGCACACCAGAAGATAGTTTCTCGAA
66 AAATTTTCAAAAGTCGATCGGAAGACGATCTTGTCAAAAAGCACACCAGAAGATAGTTTCTCGAA
* *
28632 AAGGTTTCAAAAGTGGGTCGGAAGACGATCTTGTTAAGA
131 AAGGTTTCAAAAGTGGATCGGAAGACGATCTTGTCAAGA
28671 GATGCACCGG
Statistics
Matches: 149, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
191 56 0.38
192 93 0.62
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (192 bp):
AACAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGATTCTAA
AAATTTTCAAAAGTCGATCGGAAGACGATCTTGTCAAAAAGCACACCAGAAGATAGTTTCTCGAA
AAGGTTTCAAAAGTGGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
Found at i:29026 original size:50 final size:51
Alignment explanation
Indices: 28900--29143 Score: 332
Period size: 51 Copynumber: 4.8 Consensus size: 51
28890 TGATTTTGTC
* **
28900 AAGATTGAATTGGAAGACAGTTCAAAGAATGGGCGGAAGACGGTCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* * * *
28951 TAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGCAAGACGGTCC-TTCT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
*
29001 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* * * *
29052 AAGATTGAATTAGAAGACAGTTCAAAGGATGAGCGGGAGACAGTCC-TTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* *
29102 AAGATTGAATTGGAAGACAGTTCGAGGGATAAGCAGG-AGACG
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGC-GGAAGACG
29144 ATCCATTCCG
Statistics
Matches: 171, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
50 85 0.50
51 86 0.50
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.24
Consensus pattern (51 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
Found at i:29132 original size:101 final size:101
Alignment explanation
Indices: 28900--29143 Score: 346
Period size: 101 Copynumber: 2.4 Consensus size: 101
28890 TGATTTTGTC
* ** * * *
28900 AAGATTGAATTGGAAGACAGTTCAAAGAATGGGCGGAAGACGGTCCTTTTTTAGATTGAATTGGT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGAATTAGA
*
28965 AGACAGTTCAAAGGATAAGCGCAAGACGGTCCTTCT
66 AGACAGTTCAAAGGATAAGCGCAAGACAGTCCTTCT
*
29001 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGAATTAGA
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGAATTAGA
* ** *
29066 AGACAGTTCAAAGGATGAGCGGGAGACAGTCCTTTT
66 AGACAGTTCAAAGGATAAGCGCAAGACAGTCCTTCT
* *
29102 AAGATTGAATTGGAAGACAGTTCGAGGGATAAGCAGG-AGACG
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGC-GGAAGACG
29144 ATCCATTCCG
Statistics
Matches: 127, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
101 125 0.98
102 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.24
Consensus pattern (101 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGAATTAGA
AGACAGTTCAAAGGATAAGCGCAAGACAGTCCTTCT
Found at i:29440 original size:27 final size:30
Alignment explanation
Indices: 29366--29443 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
29356 TTAGGATCAC
*
29366 CTAGGGGCATTTTGGTCATTTTCAAGAAAT
1 CTAGGGGCATTTTGGTCATTTGCAAGAAAT
* * *
29396 CTAGGGGCATTTTAGTCATTTGC-A-TATT
1 CTAGGGGCATTTTGGTCATTTGCAAGAAAT
29424 C-AGGGGCATTTTGGTCATTT
1 CTAGGGGCATTTTGGTCATTT
29444 TAAGTCCACG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 18 0.42
28 3 0.07
29 1 0.02
30 21 0.49
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (30 bp):
CTAGGGGCATTTTGGTCATTTGCAAGAAAT
Found at i:36372 original size:15 final size:15
Alignment explanation
Indices: 36352--36393 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
36342 AGAAAAACTC
*
36352 AAAAAAATAGAAAAG
1 AAAAAAAGAGAAAAG
* *
36367 AAAAAAAGGGAAAAT
1 AAAAAAAGAGAAAAG
36382 AAAAAAAGAGAA
1 AAAAAAAGAGAA
36394 GGTTTCAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (15 bp):
AAAAAAAGAGAAAAG
Found at i:36653 original size:67 final size:66
Alignment explanation
Indices: 36557--36845 Score: 395
Period size: 67 Copynumber: 4.3 Consensus size: 66
36547 GTAATTTCAA
* *
36557 ATTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTAGTATTTT
1 ATTTCCAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTGCATTCAAGTTTAGTATTTT
36621 C
66 C
* * *
36622 AAATTTCCAAAATACCCTTTCGGTCGAAGGGTCA-TTTCCGTC-ATTTGCATTTAAGTGTAGTAT
1 --ATTTCCAAAATACCCTTTCGGTCGAAGGGTCAGTTT-CGTCTTTTTGCATTCAAGTTTAGTAT
36685 TTTC
63 TTTC
* *
36689 ATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCTTTTTGCATTCAAGTTTAGTATTT
1 ATTTCC-AAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTGCATTCAAGTTTAGTATTT
36754 TC
65 TC
* * * *
36756 GTTTCCAGAAATACCCTTTCGGTCGAAGGGTTAGTTTCGTCTTTTTGCATTCAAGATTAGTAGTT
1 ATTTCCA-AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTGCATTCAAGTTTAGTATTT
36821 TC
65 TC
*
36823 GTTTCCAGAAATACCCTTTCGGT
1 ATTTCCA-AAATACCCTTTCGGT
36846 GAAAAGGGGC
Statistics
Matches: 204, Mismatches: 13, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
65 6 0.03
66 32 0.16
67 166 0.81
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (66 bp):
ATTTCCAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTGCATTCAAGTTTAGTATTTT
C
Found at i:36783 original size:133 final size:130
Alignment explanation
Indices: 36557--37052 Score: 463
Period size: 134 Copynumber: 3.7 Consensus size: 130
36547 GTAATTTCAA
* * *
36557 ATTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC--TTTTGCATTTAAGTTTAGTATTT
1 ATTTCCAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCATTTTTGCATTTAAGTTTAGTATTT
*
36620 TCAAATTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCATTTGCATTTAAGTGTAGTAT
66 TC---TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCATTTGCATTCAAGT-TAGTAT
36685 TTTC
127 TTTC
*
36689 ATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATC-TTTTTGCATTCAAGTTTAGTATT
1 ATTTCC-AAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCATTTTTGCATTTAAGTTTAGTATT
* *
36753 TTCGTTTCCAGAAATACCCTTTCGGTCGAAGGGTTAGTTT-CGTCTTTTTGCATTCAAGATTAGT
65 TTC-TTTCCA-AAATACCCTTTCGGTCGAAGGGTCA-TTTCCGTC-ATTTGCATTCAAG-TTAGT
*
36817 AGTTTC
125 ATTTTC
* * * * * * *
36823 GTTTCCAGAAATACCCTTTCGGTGAAAAGGGGCAGTATCATCAGGTTATTGCATTTTAGTCTAGT
1 ATTTCCA-AAATACCCTTTCGGT-CAAAGGGTCAGTTTCATCA--TTTTTGCATTTAAGTTTAGT
* * * * * *
36888 -CTTTCTTTCCAAAGAATACTCTTTCGGTCAAAGGGTCAATTCTGTCA-TT-C-TTGAAGTTCAG
62 ATTTTCTTTCC-AA-AATACCCTTTCGGTCGAAGGGTCATTTCCGTCATTTGCATTCAAGTT-AG
*
36949 CAATTTTC
124 -TATTTTC
* * * *
36957 AAATTTCCAAAATACCCTTTCGGTGAAAGGGTCAGTTTCATCATTTTCGCATTTCAGTCTA-T-T
1 --ATTTCCAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCATTTTTGCATTTAAGTTTAGTAT
* * * *
37020 CTACTTTCCAAGAATGCCCTTTCGGTCAAAGGG
64 TTTCTTTCCAA-AATACCCTTTCGGTCGAAGGG
37053 CGAACTTTGT
Statistics
Matches: 307, Mismatches: 39, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
130 22 0.07
131 8 0.03
132 29 0.09
133 67 0.22
134 89 0.29
135 33 0.11
136 14 0.05
137 29 0.09
138 16 0.05
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (130 bp):
ATTTCCAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCATTTTTGCATTTAAGTTTAGTATTT
TCTTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCATTTGCATTCAAGTTAGTATTTTC
Found at i:39066 original size:181 final size:181
Alignment explanation
Indices: 38755--39111 Score: 624
Period size: 181 Copynumber: 2.0 Consensus size: 181
38745 TATTAAAAAG
* *
38755 TACGTTTACCTGTAAAACTTTTGAATCACCCATTATACCCTTATTTGTCAAATATATTTCTATTT
1 TACGTTCACCTGTAAAACTTTTGAATCACCCATTATACCCTTATTTATCAAATATATTTCTATTT
* *
38820 TGCCATTCTAGAATTAATATTATTAGATTTTAATTATATATTGTTTATATTTATTATTTAATGAT
66 TGCCATTCTACAATTAATATTATTAGATTTTAATTACATATTGTTTATATTTATTATTTAATGAT
38885 TACTAATAAAATTTAATTTGATTAACAATTATTACCTCACTAGACTCTATT
131 TACTAATAAAATTTAATTTGATTAACAATTATTACCTCACTAGACTCTATT
** * *
38936 TACGTTCACCTGTAAAACTTTTGAATCGTCCATTATATCCTTATTTATCAAATATATTTTTATTT
1 TACGTTCACCTGTAAAACTTTTGAATCACCCATTATACCCTTATTTATCAAATATATTTCTATTT
* *
39001 TGTCATTCTACAATTAATATTATTAGATTTTATTTACATATTGTTTATATTTATTATTTAATGAT
66 TGCCATTCTACAATTAATATTATTAGATTTTAATTACATATTGTTTATATTTATTATTTAATGAT
39066 TACTAATAAAATTTAATTTGATTAACAATTATTACCTCACTAGACT
131 TACTAATAAAATTTAATTTGATTAACAATTATTACCTCACTAGACT
39112 ACTACTCTTA
Statistics
Matches: 166, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
181 166 1.00
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.48
Consensus pattern (181 bp):
TACGTTCACCTGTAAAACTTTTGAATCACCCATTATACCCTTATTTATCAAATATATTTCTATTT
TGCCATTCTACAATTAATATTATTAGATTTTAATTACATATTGTTTATATTTATTATTTAATGAT
TACTAATAAAATTTAATTTGATTAACAATTATTACCTCACTAGACTCTATT
Found at i:42581 original size:13 final size:13
Alignment explanation
Indices: 42563--42589 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42553 GAATATGATG
42563 ATTATTAAAGACA
1 ATTATTAAAGACA
42576 ATTATTAAAGACA
1 ATTATTAAAGACA
42589 A
1 A
42590 AATGGACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
ATTATTAAAGACA
Done.