Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014827.1 Corchorus capsularis cultivar CVL-1 contig14848, 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: 19874
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Found at i:3279 original size:33 final size:33
Alignment explanation
Indices: 3240--3341 Score: 127
Period size: 33 Copynumber: 3.1 Consensus size: 33
3230 CGTAGAAAGA
3240 CCATAACTTTCAGCTCAGATGTCCGTTTTAAAC
1 CCATAACTTTCAGCTCAGATGTCCGTTTTAAAC
* * * ** *
3273 CCATAACTTTCAGCGCAG-TCTTCG-TAGAAAGA
1 CCATAACTTTCAGCTCAGATGTCCGTTTTAAA-C
3305 CCATAACTTTCAGCTCAGATGTCCGTTTTAAAC
1 CCATAACTTTCAGCTCAGATGTCCGTTTTAAAC
3338 CCAT
1 CCAT
3342 GAGTAGCCGT
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
31 4 0.07
32 21 0.39
33 25 0.46
34 4 0.07
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (33 bp):
CCATAACTTTCAGCTCAGATGTCCGTTTTAAAC
Found at i:3314 original size:32 final size:32
Alignment explanation
Indices: 3215--3318 Score: 129
Period size: 32 Copynumber: 3.2 Consensus size: 32
3205 ATTAGCCCGG
3215 TTTCAGCGCAGTCTTCGTAGAAAGACCATAAC
1 TTTCAGCGCAGTCTTCGTAGAAAGACCATAAC
* * * ** *
3247 TTTCAGCTCAGATGTCCGTTTTAAA-CCCATAAC
1 TTTCAGCGCAG-TCTTCG-TAGAAAGACCATAAC
3280 TTTCAGCGCAGTCTTCGTAGAAAGACCATAAC
1 TTTCAGCGCAGTCTTCGTAGAAAGACCATAAC
3312 TTTCAGC
1 TTTCAGC
3319 TCAGATGTCC
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
31 4 0.07
32 28 0.49
33 21 0.37
34 4 0.07
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (32 bp):
TTTCAGCGCAGTCTTCGTAGAAAGACCATAAC
Found at i:3319 original size:65 final size:65
Alignment explanation
Indices: 3215--3341 Score: 254
Period size: 65 Copynumber: 2.0 Consensus size: 65
3205 ATTAGCCCGG
3215 TTTCAGCGCAGTCTTCGTAGAAAGACCATAACTTTCAGCTCAGATGTCCGTTTTAAACCCATAAC
1 TTTCAGCGCAGTCTTCGTAGAAAGACCATAACTTTCAGCTCAGATGTCCGTTTTAAACCCATAAC
3280 TTTCAGCGCAGTCTTCGTAGAAAGACCATAACTTTCAGCTCAGATGTCCGTTTTAAACCCAT
1 TTTCAGCGCAGTCTTCGTAGAAAGACCATAACTTTCAGCTCAGATGTCCGTTTTAAACCCAT
3342 GAGTAGCCGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (65 bp):
TTTCAGCGCAGTCTTCGTAGAAAGACCATAACTTTCAGCTCAGATGTCCGTTTTAAACCCATAAC
Found at i:4438 original size:12 final size:13
Alignment explanation
Indices: 4397--4441 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
4387 AATTATTGTT
*
4397 TGCTTTTTTAATC
1 TGCTTTATTAATC
*
4410 TGCTTTATTAATT
1 TGCTTTATTAATC
4423 TGCTTTA-TAATC
1 TGCTTTATTAATC
4435 TGCTTTA
1 TGCTTTA
4442 GATTTAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.58
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:9271 original size:37 final size:37
Alignment explanation
Indices: 9229--9418 Score: 244
Period size: 37 Copynumber: 5.2 Consensus size: 37
9219 CATGTGCATC
*
9229 AGTAAAACCAGTTAAAGAACTTAATTCAGGGAAATTA
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGAAATTA
*
9266 AGTAAAAGCAGTTAAAGAACTTAATTTA-GGACAATT-
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGA-AATTA
* *
9302 AGTAAAAGTAGTTAAAGAACTTAATTCAGGGCAATTA
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGAAATTA
* * *
9339 AGTAAAATCGGTTAAAGAACTTAATTCAGGGCAATTA
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGAAATTA
* * * *
9376 AGTAAAAGCAGTTAAAG-TCTTTATTTAGGGTAATTA
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGAAATTA
9412 AG-AAAAG
1 AGTAAAAG
9419 AAAGTACAGT
Statistics
Matches: 136, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
35 5 0.04
36 50 0.37
37 81 0.60
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.27
Consensus pattern (37 bp):
AGTAAAAGCAGTTAAAGAACTTAATTCAGGGAAATTA
Found at i:9322 original size:73 final size:74
Alignment explanation
Indices: 9229--9418 Score: 260
Period size: 73 Copynumber: 2.6 Consensus size: 74
9219 CATGTGCATC
* *
9229 AGTAAAACCAGTTAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAAGAACTTAATTTA
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAAGAACTTAATTCA
9294 GGACAATT-
66 GGACAATTA
* * * *
9302 AGTAAAAGTAGTTAAAGAACTTAATTCAGGGCAATTAAGTAAAATCGGTTAAAGAACTTAATTCA
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAAGAACTTAATTCA
*
9367 GGGCAATTA
66 GGACAATTA
* * * *
9376 AGTAAAAGCAGTTAAAG-TCTTTATTTAGGGTAATTAAG-AAAAG
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGAAATTAAGTAAAAG
9419 AAAGTACAGT
Statistics
Matches: 103, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
72 4 0.04
73 83 0.81
74 16 0.16
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.27
Consensus pattern (74 bp):
AGTAAAAGCAGTTAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAAGAACTTAATTCA
GGACAATTA
Found at i:9477 original size:71 final size:71
Alignment explanation
Indices: 9388--9777 Score: 602
Period size: 71 Copynumber: 5.4 Consensus size: 71
9378 TAAAAGCAGT
* *
9388 TAAAGTCTTTATTTAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGCAATTAA
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGCAATTAA
9453 GAAGAG
66 GAAGAG
*
9459 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAA
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGCAATTAA
*
9524 GAAGGG
66 GAAGAG
* *
9530 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTTAAGGTCCTAAGTAGGGCAATTAA
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGCAATTAA
*
9595 GAAGGG
66 GAAGAG
* *
9601 TAAAGTCTTAATTCAGGGAAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTT-GGAAGATTA
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGCA-ATTA
9665 AGAAGAG
65 AGAAGAG
* *
9672 TAAGAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGACAATTA
1 TAA-AGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGCAATTA
*
9737 AAAAGAG
65 AGAAGAG
* *
9744 TAAGAGAACTTAATTCTGGGTAATTAAGTAAAAG
1 TAA-AG-TCTTAATTCAGGGTAATTAAG-AAAAG
9778 CAGGTAAAGA
Statistics
Matches: 295, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
70 3 0.01
71 200 0.68
72 66 0.22
73 21 0.07
74 5 0.02
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.25
Consensus pattern (71 bp):
TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGCAATTAA
GAAGAG
Found at i:9549 original size:31 final size:31
Alignment explanation
Indices: 9514--9628 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 31
9504 GTCCTAAGTT
9514 GGGTAATTAAGAAGGGTAAAGTCTTAATTCA
1 GGGTAATTAAGAAGGGTAAAGTCTTAATTCA
** *
9545 GGGTAATTAAGAAAAG-AAAGTACAGTTAAGGTCCTAAGTA
1 GGGTAATTAAGAAGGGTAAAGT-C--TTAA--T--T---CA
*
9585 GGGCAATTAAGAAGGGTAAAGTCTTAATTCA
1 GGGTAATTAAGAAGGGTAAAGTCTTAATTCA
*
9616 GGGAAATTAAGAA
1 GGGTAATTAAGAA
9629 AAGAAAGTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
30 5 0.08
31 28 0.43
33 4 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 4 0.06
40 15 0.23
41 5 0.08
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (31 bp):
GGGTAATTAAGAAGGGTAAAGTCTTAATTCA
Found at i:9789 original size:37 final size:37
Alignment explanation
Indices: 9743--10128 Score: 252
Period size: 37 Copynumber: 10.1 Consensus size: 37
9733 ATTAAAAAGA
*
9743 GTAAGAGAACTTAATTCTGGGTAATTAAGTAAAAGCAG
1 GTAA-AGAACTTAATTCAGGGTAATTAAGTAAAAGCAG
* * *
9781 GTAAAGAACTTATTTCAGGGTAGTTAAGTGAAGGAGCA-
1 GTAAAGAACTTAATTCAGGGTAATTAAGT-AA-AAGCAG
* * *
9819 GTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGGAG
1 GTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAG
* * *
9856 GTTAAAAAAACTTAATTCAGGGCAATTAAGTAAAAACA-
1 G-T-AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAG
*
9894 GTCAAA-ATCTTAATTCAGGGTAATTAAG-AAAAGTAAACATAG
1 GT-AAAGAACTTAATTCAGGGTAATTAAGTAAAAG----C--AG
* * *
9936 TCAGTCAAA-ATCTTAATTCATGG-AAATAAGGTAAAAGCAG
1 ---GT-AAAGAACTTAATTCAGGGTAATTAA-GTAAAAGCAG
* * * *
9976 GCAAAGGAGCTTAATTCAGGGAAATTAGGT-AAA-CACG
1 GTAAA-GAACTTAATTCAGGGTAATTAAGTAAAAGCA-G
*
10013 GTCAAAGAACTTAATTCAGGATAATTAAGTAAAAAGCA-
1 GT-AAAGAACTTAATTCAGGGTAATTAAGT-AAAAGCAG
* * * * **
10051 GTTAAGACCTTAGTTCATGACAATTAAGTAAAAGCA-
1 GTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAG
* * *
10087 GTTAAGAACTTAATTCATGGTAATTAAGTAAAAACAG
1 GTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAG
*
10124 TTAAA
1 GTAAA
10129 AGGTAAGGAT
Statistics
Matches: 280, Mismatches: 42, Indels: 53
0.75 0.11 0.14
Matches are distributed among these distances:
35 4 0.01
36 66 0.24
37 80 0.29
38 52 0.19
39 42 0.15
40 4 0.01
41 1 0.00
42 1 0.00
44 5 0.02
45 20 0.07
46 5 0.02
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (37 bp):
GTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAG
Found at i:9833 original size:75 final size:75
Alignment explanation
Indices: 9748--10124 Score: 236
Period size: 75 Copynumber: 5.0 Consensus size: 75
9738 AAAGAGTAAG
* * * * *
9748 AGAACTTAATTCTGGGTAATTAAGTAAAAGCAGG-T-AAAGAACTTATTTCAGGGTAGTTAAGTG
1 AGAACTTAATTCAGGGTAATTAAGTAAAAGCAGGTTAAAAAAACTTAATTCAGGGCAATTAAGT-
* * *
9811 AAGGAGCAGTTA
65 AA-AAACAGTCA
* *
9823 AGAACTTAATTCAGGGCAATTAAGTAAAAGGAGGTTAAAAAAACTTAATTCAGGGCAATTAAGTA
1 AGAACTTAATTCAGGGTAATTAAGTAAAAGCAGGTTAAAAAAACTTAATTCAGGGCAATTAAGTA
9888 AAAACAGTCA
66 AAAACAGTCA
* * * * *
9898 A-AATCTTAATTCAGGGTAATTAAG-AAAAGTAAACATAGTCAGTCAAAATCTTAATTCATGG-A
1 AGAA-CTTAATTCAGGGTAATTAAGTAAAAG----CA-GGTTA--AAAAAACTTAATTCAGGGCA
* * *
9960 AATAAGGTAAAAGCAGGCAA
58 ATTAA-GTAAAAACAGTC-A
* * * * * **
9980 AGGAGCTTAATTCAGGGAAATTAGGT-AAA-CACGG-TCAAAGAACTTAATTCAGGATAATTAAG
1 A-GAACTTAATTCAGGGTAATTAAGTAAAAGCA-GGTTAAAAAAACTTAATTCAGGGCAATTAAG
*
10042 TAAAAAGCAGTTA
64 TAAAAA-CAGTCA
* * * ** * * *
10055 AGACCTTAGTTCATGACAATTAAGTAAAAGCA-GTT--AAGAACTTAATTCATGGTAATTAAGTA
1 AGAACTTAATTCAGGGTAATTAAGTAAAAGCAGGTTAAAAAAACTTAATTCAGGGCAATTAAGTA
10117 AAAACAGT
66 AAAACAGT
10125 TAAAAGGTAA
Statistics
Matches: 238, Mismatches: 44, Indels: 43
0.73 0.14 0.13
Matches are distributed among these distances:
72 4 0.02
73 29 0.12
74 26 0.11
75 82 0.34
76 13 0.05
77 23 0.10
78 4 0.02
79 3 0.01
80 5 0.02
81 25 0.11
82 2 0.01
83 21 0.09
84 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (75 bp):
AGAACTTAATTCAGGGTAATTAAGTAAAAGCAGGTTAAAAAAACTTAATTCAGGGCAATTAAGTA
AAAACAGTCA
Found at i:10268 original size:76 final size:76
Alignment explanation
Indices: 10142--10423 Score: 512
Period size: 76 Copynumber: 3.7 Consensus size: 76
10132 TAAGGATAGT
*
10142 CACAGAGTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATTA
1 CACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATTA
10207 AGTAAAGTAAG
66 AGTAAAGTAAG
10218 CACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATTA
1 CACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATTA
10283 AGTAAAGTAAG
66 AGTAAAGTAAG
* *
10294 CACAGACTTAATTTCAAGGAAGGAAGTTACGTAAAGACAAGCATAGACTTAATTCAGGGTAATTA
1 CACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATTA
10359 AGTAAAGTAAG
66 AGTAAAGTAAG
*
10370 CACAGACTTAATTTC-AGTGAAGGAAATTAGGTAAACACAAGCATAGACTTAATT
1 CACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAAGACAAGCATAGACTTAATT
10424 TCAAGGAAGG
Statistics
Matches: 199, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
75 2 0.01
76 197 0.99
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (76 bp):
CACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATTA
AGTAAAGTAAG
Found at i:10446 original size:41 final size:38
Alignment explanation
Indices: 10149--10468 Score: 243
Period size: 41 Copynumber: 8.3 Consensus size: 38
10139 AGTCACAGAG
10149 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGAC
1 TTAATTTC-AGGAAGGAAATTA-GTAAA-ACAAGCATAGAC
* ** *
10190 TTAA-TTCA-G--GGTAATTAAGTAAAGTAAGCACAGAC
1 TTAATTTCAGGAAGGAAATT-AGTAAAACAAGCATAGAC
10225 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGAC
1 TTAATTTC-AGGAAGGAAATTA-GTAAA-ACAAGCATAGAC
* ** *
10266 TTAA-TTCA-G--GGTAATTAAGTAAAGTAAGCACAGAC
1 TTAATTTCAGGAAGGAAATT-AGTAAAACAAGCATAGAC
*
10301 TTAATTTCAAGGAAGGAAGTTACGTAAAGACAAGCATAGAC
1 TTAATTTC-AGGAAGGAAATTA-GTAAA-ACAAGCATAGAC
* ** *
10342 TTAA-TTCA-G--GGTAATTAAGTAAAGTAAGCACAGAC
1 TTAATTTCAGGAAGGAAATT-AGTAAAACAAGCATAGAC
10377 TTAATTTCAGTGAAGGAAATTAGGTAAACACAAGCATAGAC
1 TTAATTTCAG-GAAGGAAATTA-GTAAA-ACAAGCATAGAC
* * *
10418 TTAATTTCAAGGAAGGAAATTAGTTAAACGCAAGCAAATAC
1 TTAATTTC-AGGAAGGAAATTAG-TAAA-ACAAGCATAGAC
10459 TTAA-TTCAGG
1 TTAATTTCAGG
10469 GTAATTAAGT
Statistics
Matches: 224, Mismatches: 29, Indels: 54
0.73 0.09 0.18
Matches are distributed among these distances:
35 39 0.17
36 42 0.19
37 5 0.02
38 6 0.03
39 9 0.04
40 45 0.20
41 76 0.34
42 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.24
Consensus pattern (38 bp):
TTAATTTCAGGAAGGAAATTAGTAAAACAAGCATAGAC
Found at i:10533 original size:152 final size:151
Alignment explanation
Indices: 10149--10516 Score: 412
Period size: 152 Copynumber: 2.4 Consensus size: 151
10139 AGTCACAGAG
* * * **
10149 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATTAAGTAAAG
1 TTAATTTCAAGG-AGGAAGTTAAGTAAAGACAAGCAAAGACTTAATTCAAAGTAATTAAGTAAAG
* *
10214 TAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTA
65 TAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAACACAAGCATAGACTTAATTCAGGGAA
* *
10279 ATTAAGTAAAGTAAGCACAGAC
130 ATTAAGTAAAGCAAGCAAAGAC
* * **
10301 TTAATTTCAAGGAAGGAAGTTACGTAAAGACAAGCATAGACTTAATTCAGGGTAATTAAGTAAAG
1 TTAATTTCAAGG-AGGAAGTTAAGTAAAGACAAGCAAAGACTTAATTCAAAGTAATTAAGTAAAG
10366 TAAGCACAGACTTAATTTC-AGTGAAGGAAATTAGGTAAACACAAGCATAGACTTAATTTCAAGG
65 TAAGCACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAACACAAGCATAGACTTAA-TTC-A-G
*
10430 AAGGAAATT-AGTTAAACGCAAGCAAATAC
126 --GGAAATTAAG-TAAA-GCAAGCAAAGAC
* **
10459 TTAA-TTC-AGG-GTAA-TTAAGT-AA-ATTAGCAAAGACTTAATTTCATAAG-AATTAAGTAAA
1 TTAATTTCAAGGAGGAAGTTAAGTAAAGACAAGCAAAGACTTAA-TTCA-AAGTAATTAAGTAAA
10517 ATCATCAAAG
Statistics
Matches: 192, Mismatches: 14, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
151 15 0.08
152 132 0.69
153 9 0.05
154 4 0.02
155 1 0.01
156 5 0.03
157 13 0.07
158 13 0.07
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (151 bp):
TTAATTTCAAGGAGGAAGTTAAGTAAAGACAAGCAAAGACTTAATTCAAAGTAATTAAGTAAAGT
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAACACAAGCATAGACTTAATTCAGGGAAA
TTAAGTAAAGCAAGCAAAGAC
Found at i:10547 original size:36 final size:35
Alignment explanation
Indices: 10471--10569 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 35
10461 AATTCAGGGT
*
10471 AATTAAGT-AAATTAGCAAAGACTTAATTTCATAAG
1 AATTAAGTAAAATCAGCAAAGACTTAA-TTCATAAG
* *
10506 AATTAAGTAAAATCATCAAAGACTTAA-TCCTAAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTCATAAG
* *
10540 ATGATTAAGTAAGATCAGACAAAAACTTAA
1 A--ATTAAGTAAAATCAG-CAAAGACTTAA
10570 CCTCCGGGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 7 0.13
35 8 0.15
36 29 0.54
37 10 0.19
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (35 bp):
AATTAAGTAAAATCAGCAAAGACTTAATTCATAAG
Found at i:10636 original size:37 final size:37
Alignment explanation
Indices: 10592--10989 Score: 581
Period size: 37 Copynumber: 10.9 Consensus size: 37
10582 AAGTAAAGAA
* *
10592 AAAGGACTTGGTTCCAAGGAAGGGAATTAAGTAGAGC
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
* *
10629 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAAAGA
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
* *
10666 AAAGGACTTGGTTCCAAGGAAGGGAATTAAGTAGAGC
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
*
10703 AAAGGACTTGATTCCAAGGAAGGGAATCAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
*
10740 AGAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
10777 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
*
10814 AAGGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
*
10851 GAAGGACTTGATTCCAAGGAAGGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAA-GGGAATTAAGTAGAGT
* * * *
10889 TAAGGACTTAATTTCAAGGAAGGAAATTAAGT--AG-
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
*
10923 --AGGATTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
* * * *
10958 TAAGGACTTAATTTCAAGGATGGGAATTAAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGT
10990 CAAGTTGGGG
Statistics
Matches: 328, Mismatches: 27, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
32 26 0.08
34 2 0.01
35 2 0.01
37 264 0.80
38 34 0.10
ACGTcount: A:0.39, C:0.08, G:0.30, T:0.22
Consensus pattern (37 bp):
AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
Found at i:11029 original size:37 final size:37
Alignment explanation
Indices: 10997--11189 Score: 275
Period size: 37 Copynumber: 5.3 Consensus size: 37
10987 AGTCAAGTTG
*
10997 GGGACTTAATTCAGGTTAATTAAGTAGCGTCAATAAA
1 GGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
* *
11034 GGGACTTAATTCAGGATAATTAAGTAGAGTCAATAAA
1 GGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
*
11071 GGGACTTAATTCAGGGTAATTAAGTAGTGTCAATAAAA
1 GGGACTTAATTCAGGGTAATTAAGTAGCGTCAAT-AAA
*
11109 AGG-CTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
1 GGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
* * *
11145 AGG-CTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
1 GGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
*
11181 GAG-CTTAAT
1 GGGACTTAAT
11190 CTAAGAAGAG
Statistics
Matches: 145, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
36 44 0.30
37 96 0.66
38 5 0.03
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.28
Consensus pattern (37 bp):
GGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
Found at i:11216 original size:110 final size:111
Alignment explanation
Indices: 11001--11224 Score: 285
Period size: 110 Copynumber: 2.0 Consensus size: 111
10991 AAGTTGGGGA
* *
11001 CTTAATTCAGGTTAATTAAGTAGCGTCAATAAAGGGACTTAATTCAGGATAATTAAGTAGAGTCA
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGGACTTAATTCAGGATAATTAAGTAGAGTCA
* * * * ***
11066 ATAAAGGGACTTAATTCAGGGTAATTAAGTAGTGTCAATAAAAAGG
66 ATAAAGAGACTTAATTAAGAGTAATTAAGCAGAAACAATAAAAAGG
* *
11112 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG-CTTAATTCAGGGTAATTAAGTGGAGTCA
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGGACTTAATTCAGGATAATTAAGTAGAGTCA
*
11176 ATAAAGAG-CTTAATCTAAGAAG-AGATTAAGCA-AAACAATAAAAGGG
66 ATAAAGAGACTTAAT-TAAG-AGTA-ATTAAGCAGAAACAATAAAAAGG
11222 CTT
1 CTT
11225 GATTTATAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
109 6 0.06
110 50 0.51
111 42 0.43
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (111 bp):
CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGGACTTAATTCAGGATAATTAAGTAGAGTCA
ATAAAGAGACTTAATTAAGAGTAATTAAGCAGAAACAATAAAAAGG
Found at i:15070 original size:2 final size:2
Alignment explanation
Indices: 15063--15087 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15053 TGAATATAAA
15063 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 A
15088 GCGGCGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19761 original size:32 final size:32
Alignment explanation
Indices: 19725--19793 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
19715 CACAATAGCA
*
19725 GCGTCTAATGATTAAAACGCCACTATTTAACG
1 GCGTCTAATGATTAAAACGCCACAATTTAACG
** * * *
19757 GCGTCTTTTGATTCATACGCCACAATTTAGCG
1 GCGTCTAATGATTAAAACGCCACAATTTAACG
19789 GCGTC
1 GCGTC
19794 CAAACGCTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (32 bp):
GCGTCTAATGATTAAAACGCCACAATTTAACG
Done.