Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011703.1 Corchorus capsularis cultivar CVL-1 contig11724, 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: 8549
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:90 original size:54 final size:54
Alignment explanation
Indices: 8--215 Score: 326
Period size: 54 Copynumber: 3.8 Consensus size: 54
1 AGTGGTA
*
8 TTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTACAGTTGT
1 TTAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAAGTTTACAGTTGT
* * *
62 TTAAGTTTATCTTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGT
1 TTAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAAGTTTACAGTTGT
*
116 ATTAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAATTTTACAGTTGT
1 -TTAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAAGTTTACAGTTGT
* * * *
171 TTAAGTTTATCTTCGAGTGATCCAGTGCGGTCAATCAAGTAAGTT
1 TTAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAAGTT
216 CATCTTCGAG
Statistics
Matches: 140, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
54 90 0.64
55 50 0.36
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (54 bp):
TTAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAAGTTTACAGTTGT
Found at i:194 original size:109 final size:109
Alignment explanation
Indices: 1--215 Score: 367
Period size: 109 Copynumber: 2.0 Consensus size: 109
*
1 AGTGGTATTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTACAGTTGTTTAA
1 AGTGGTATTAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAAGTTTACAGTTGTTTAA
*
66 GTTTATCTTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTCC
66 GTTTATCTTCAAGTAATCCAGTGCGATCAATCAAGAAAGTTTCC
*
110 AGTGGTATTAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAATTTTACAGTTGTTTAA
1 AGTGGTATTAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAAGTTTACAGTTGTTTAA
* * * *
175 GTTTATCTTCGAGTGATCCAGTGCGGTCAATCAAGTAAGTT
66 GTTTATCTTCAAGTAATCCAGTGCGATCAATCAAGAAAGTT
216 CATCTTCGAG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 99 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (109 bp):
AGTGGTATTAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAAGTTTACAGTTGTTTAA
GTTTATCTTCAAGTAATCCAGTGCGATCAATCAAGAAAGTTTCC
Found at i:223 original size:38 final size:38
Alignment explanation
Indices: 172--253 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
162 TACAGTTGTT
* *
172 TAAGTTTATCTTCGAGTGATCCAGTGCGGTCAATCAAG
1 TAAGTTCATCTTCGAGTGATCCAGTGCGATCAATCAAG
*
210 TAAGTTCATCTTCGAGTGATCCAGTGCGATCAGTCAAG
1 TAAGTTCATCTTCGAGTGATCCAGTGCGATCAATCAAG
*
248 AAAGTT
1 TAAGTT
254 TCCAGTGGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (38 bp):
TAAGTTCATCTTCGAGTGATCCAGTGCGATCAATCAAG
Found at i:294 original size:55 final size:54
Alignment explanation
Indices: 210--363 Score: 236
Period size: 55 Copynumber: 2.8 Consensus size: 54
200 GTCAATCAAG
*
210 TAAGTTCATCTTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGTAT
1 TAAGTTTATCTTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGG-AT
265 TAAGTTTATCTTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGAT
1 TAAGTTTATCTTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGAT
* * * * * *
319 TAAATTTATCTTCAAGTGATCCAATGCGGTCAGTCGAGGAAGTTT
1 TAAGTTTATCTTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTT
364 TCAATGATTT
Statistics
Matches: 92, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
54 41 0.45
55 51 0.55
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (54 bp):
TAAGTTTATCTTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGAT
Found at i:302 original size:93 final size:92
Alignment explanation
Indices: 118--308 Score: 283
Period size: 92 Copynumber: 2.1 Consensus size: 92
108 CCAGTGGTAT
* * * *
118 TAAGTTTATCTTCAAGTAATCCAGTGCGGTCAGTCAAGAAATTTTACAGTTGTTTAAGTTTATCT
1 TAAGTTCATCTTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTACAGTGGTTTAAGTTTATCT
*
183 TCGAGTGATCCAGTGCGGTCAATCAAG
66 TCGAGTGATCCAGTGCGATCAATCAAG
* * *
210 TAAGTTCATCTTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGTATTAAGTTTATC
1 TAAGTTCATCTTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTACAGTGGT-TTAAGTTTATC
*
275 TTCGAGTGATCCAGTGCGATCAGTCAAG
65 TTCGAGTGATCCAGTGCGATCAATCAAG
*
303 AAAGTT
1 TAAGTT
309 TCCAGTGGAT
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
92 46 0.52
93 42 0.48
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (92 bp):
TAAGTTCATCTTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTACAGTGGTTTAAGTTTATCT
TCGAGTGATCCAGTGCGATCAATCAAG
Found at i:330 original size:147 final size:147
Alignment explanation
Indices: 63--350 Score: 459
Period size: 147 Copynumber: 2.0 Consensus size: 147
53 TACAGTTGTT
*
63 TAAGTTTATCTTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGTATTAAGTTTATC
1 TAAGTTCATCTTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGTATTAAGTTTATC
* * * * * *
128 TTCAAGTAATCCAGTGCGGTCAGTCAAGAAATTTTACAGTTGTTTAAGTTTATCTTCGAGTGATC
66 TTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTACAGTGGATTAAATTTATCTTCAAGTGATC
*
193 CAGTGCGGTCAATCAAG
131 CAATGCGGTCAATCAAG
* *
210 TAAGTTCATCTTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGTATTAAGTTTATC
1 TAAGTTCATCTTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGTATTAAGTTTATC
* * *
275 TTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGATTAAATTTATCTTCAAGTGATC
66 TTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTACAGTGGATTAAATTTATCTTCAAGTGATC
340 CAATGCGGTCA
131 CAATGCGGTCA
351 GTCGAGGAAG
Statistics
Matches: 128, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
147 128 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (147 bp):
TAAGTTCATCTTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGTATTAAGTTTATC
TTCAAGTAATCCAGTGCGATCAGTCAAGAAAGTTTACAGTGGATTAAATTTATCTTCAAGTGATC
CAATGCGGTCAATCAAG
Found at i:383 original size:54 final size:54
Alignment explanation
Indices: 210--390 Score: 220
Period size: 54 Copynumber: 3.3 Consensus size: 54
200 GTCAATCAAG
* * *
210 TAAGTTCATCTTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGTAT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGAT-T
*
265 TAAGTTTATCTTCGAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGA-T
1 TAAGTTTATCTTCAAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGT-GATT
* * * * * * *
319 TAAATTTATCTTCAAGTGATCCAATGCGGTCAGTCGAGGAAGTTTTCAATGATT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGATT
* *
373 TGAGTATATCTTCAAGTG
1 TAAGTTTATCTTCAAGTG
391 GTTCGGTGAA
Statistics
Matches: 111, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
53 2 0.02
54 59 0.53
55 49 0.44
56 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (54 bp):
TAAGTTTATCTTCAAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGATT
Found at i:446 original size:43 final size:40
Alignment explanation
Indices: 380--472 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 40
370 ATTTGAGTAT
*
380 ATCTTCAAGTGGTTCGGTGAATCAGATGACTCGGTGTAGC
1 ATCTTCAAGTGGTTCGGTGAATCAGAGGACTCGGTGTAGC
* *
420 ATCTTCAAGGTTGGATTTGGTGAATCAGAGGGCTCGGTGTAGC
1 ATCTTCAA-G-TGG-TTCGGTGAATCAGAGGACTCGGTGTAGC
*
463 ATCTTTAAGT
1 ATCTTCAAGT
473 ATTGGAATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 8 0.17
41 2 0.04
42 4 0.09
43 32 0.70
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (40 bp):
ATCTTCAAGTGGTTCGGTGAATCAGAGGACTCGGTGTAGC
Found at i:692 original size:90 final size:91
Alignment explanation
Indices: 479--776 Score: 322
Period size: 90 Copynumber: 3.3 Consensus size: 91
469 AAGTATTGGA
* * * * * *** * * *
479 ATTCGGTGAGCTCGGTGCAGCACATCTTCAAATAGATCATTGTGATTCGGTGAATCGAGTTAATG
1 ATTCAGTGAGCTCGGTGCAGCACATTTTCGAACAGTTCAGAATGATTCGGTGAATCAAGTTGAGG
544 CGGTG-C--ATTTCTTCAAAGATAGG
66 CGGTGCCTTATTTCTTCAAAGATAGG
* *
567 AAGTT-AGTGAGCTCGGTGCAGCATATTCT-GAAACAGTTCAGAATGATTCGGTGAATCAAGTTG
1 -A-TTCAGTGAGCTCGGTGCAGCACATTTTCG-AACAGTTCAGAATGATTCGGTGAATCAAGTTG
* *
630 AGGCGGTGCCTTATTTTTTCAAAG-TCGG
63 AGGCGGTGCCTTATTTCTTCAAAGATAGG
* *
658 ATTCAGTGAGCTCGGTGCAGCACATTTTCGAACAGTTCAGGATGAATCGGTGAATCAAGTTGAGG
1 ATTCAGTGAGCTCGGTGCAGCACATTTTCGAACAGTTCAGAATGATTCGGTGAATCAAGTTGAGG
** *
723 TAGTGCCTTATTTCTTC-AAGATTGG
66 CGGTGCCTTATTTCTTCAAAGATAGG
* *
748 ATTTAGTGAGCTCGGTGCAACACATTTTC
1 ATTCAGTGAGCTCGGTGCAGCACATTTTC
777 AGCTAATTAG
Statistics
Matches: 176, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
89 58 0.33
90 103 0.59
91 4 0.02
92 11 0.06
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (91 bp):
ATTCAGTGAGCTCGGTGCAGCACATTTTCGAACAGTTCAGAATGATTCGGTGAATCAAGTTGAGG
CGGTGCCTTATTTCTTCAAAGATAGG
Found at i:1120 original size:26 final size:26
Alignment explanation
Indices: 1074--1124 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1064 CATATCAAAT
*
1074 CATATCCTATTAATTCGCATTAGAAC
1 CATATCCTATTAATTCACATTAGAAC
* *
1100 CATATCCTATTAGTTTACATTAGAA
1 CATATCCTATTAATTCACATTAGAA
1125 TCATGTTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (26 bp):
CATATCCTATTAATTCACATTAGAAC
Found at i:3142 original size:135 final size:135
Alignment explanation
Indices: 2900--3172 Score: 528
Period size: 135 Copynumber: 2.0 Consensus size: 135
2890 GTAGAATTTA
*
2900 GCATACACCTTGCACCAATTTAGCATGCATTTAGGCACACAATCACATCTCAAACACACTCCCTA
1 GCATACACCTTGCACCAATTCAGCATGCATTTAGGCACACAATCACATCTCAAACACACTCCCTA
*
2965 TTTGCACATTTACACTTTCACAATCATTGCATATAACAGACTCTAGCAGTGCAAAACAAGGCAAT
66 TTTGCACATTTACACTTTCACAATCATTGCATATAACAGACTCTAGCAGTGCAAAACAAGACAAT
3030 CAAGT
131 CAAGT
3035 GCATACACCTTGCACCAATTCAGCATGCATTTAGGCACACAATCACATCTCAAACACACTCCCTA
1 GCATACACCTTGCACCAATTCAGCATGCATTTAGGCACACAATCACATCTCAAACACACTCCCTA
3100 TTTGCACATTTACACTTTCACAATCATTGCATATAACAGACTCTAGCAGTGCAAAACAAGACAAT
66 TTTGCACATTTACACTTTCACAATCATTGCATATAACAGACTCTAGCAGTGCAAAACAAGACAAT
3165 CAAGT
131 CAAGT
3170 GCA
1 GCA
3173 GCAAAGCATT
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 136 1.00
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.25
Consensus pattern (135 bp):
GCATACACCTTGCACCAATTCAGCATGCATTTAGGCACACAATCACATCTCAAACACACTCCCTA
TTTGCACATTTACACTTTCACAATCATTGCATATAACAGACTCTAGCAGTGCAAAACAAGACAAT
CAAGT
Found at i:5124 original size:36 final size:33
Alignment explanation
Indices: 5068--5187 Score: 99
Period size: 30 Copynumber: 3.7 Consensus size: 33
5058 GGTCAGTCAG
** *
5068 AAAAGTAAAAAGGGTGATCAGAGTGATTAAGTTCCA
1 AAAAGTAAAAAGGGCAATC--AGTAATTAAGTT-CA
5104 AAAAGTAAAAAGGGCAATCAGTAATTAAGTTCA
1 AAAAGTAAAAAGGGCAATCAGTAATTAAGTTCA
* * * *
5137 ATAAG-AAAAA--GTAATCAGTGATTAAATTCA
1 AAAAGTAAAAAGGGCAATCAGTAATTAAGTTCA
*
5167 ATAAG-AAAAA--GCAATCAGTAA
1 AAAAGTAAAAAGGGCAATCAGTAA
5188 AGAGTAAAGT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
30 36 0.48
32 5 0.07
33 6 0.08
34 11 0.15
36 17 0.23
ACGTcount: A:0.52, C:0.08, G:0.18, T:0.22
Consensus pattern (33 bp):
AAAAGTAAAAAGGGCAATCAGTAATTAAGTTCA
Found at i:5154 original size:30 final size:30
Alignment explanation
Indices: 5117--5187 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
5107 AGTAAAAAGG
*
5117 GCAATCAGTAATTAAGTTCAATAAGAAAAA
1 GCAATCAGTAATTAAATTCAATAAGAAAAA
* *
5147 GTAATCAGTGATTAAATTCAATAAGAAAAA
1 GCAATCAGTAATTAAATTCAATAAGAAAAA
5177 GCAATCAGTAA
1 GCAATCAGTAA
5188 AGAGTAAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (30 bp):
GCAATCAGTAATTAAATTCAATAAGAAAAA
Found at i:5257 original size:20 final size:20
Alignment explanation
Indices: 5229--5350 Score: 68
Period size: 20 Copynumber: 5.9 Consensus size: 20
5219 CAAATAGTAA
*
5229 AATAGTAATCAGTAAAAAAT
1 AATAATAATCAGTAAAAAAT
*
5249 AATAATAATCAATAAAAGGTAA-
1 AATAATAATCAGTAAAA---AAT
** *
5271 AATGGTAATTAGTAAAGAGCAAT
1 AATAATAATCAGTAAA-A--AAT
* * *
5294 -ATGATAATCAGTAAAGAGT
1 AATAATAATCAGTAAAAAAT
* * *
5313 AATAGTAATCAGTAAGAAGT
1 AATAATAATCAGTAAAAAAT
*
5333 AATGATAATCAGTAAAAA
1 AATAATAATCAGTAAAAA
5351 GAAAAAAGGT
Statistics
Matches: 78, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.03
20 45 0.58
22 28 0.36
23 3 0.04
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.25
Consensus pattern (20 bp):
AATAATAATCAGTAAAAAAT
Found at i:5286 original size:22 final size:22
Alignment explanation
Indices: 5225--5584 Score: 177
Period size: 22 Copynumber: 16.9 Consensus size: 22
5215 AATTCAAATA
*
5225 GTAAAATAGTAATCAGTAAAA-
1 GTAAAATGGTAATCAGTAAAAG
** *
5246 --AATAATAATAATCAATAAAAG
1 GTAA-AATGGTAATCAGTAAAAG
*
5267 GTAAAATGGTAATTAGT-AAAG
1 GTAAAATGGTAATCAGTAAAAG
* * *
5288 AGCAATATGATAATCAGT-AAAG
1 -GTAAAATGGTAATCAGTAAAAG
*
5310 AGT--AATAGTAATCAGTAAGAA-
1 -GTAAAATGGTAATCAGTAA-AAG
* *
5331 GT--AATGATAATCAGTAAAAA
1 GTAAAATGGTAATCAGTAAAAG
* * * **
5351 GAAAAAAGGTAGTCAGTAATGG
1 GTAAAATGGTAATCAGTAAAAG
* *
5373 GTACAATGGTAATTAGT-AAAG
1 GTAAAATGGTAATCAGTAAAAG
* * * *
5394 AGTAAAGTGATAATTAGTAATAG
1 -GTAAAATGGTAATCAGTAAAAG
*
5417 AGT--AATAGTAATCAGTAAGAA-
1 -GTAAAATGGTAATCAGTAA-AAG
* * *
5438 GT--AATAGTAAACAGTAAAAAA
1 GTAAAATGGTAATCAGT-AAAAG
* *
5459 GTAAAAAGGTAATCAGTAAAAA
1 GTAAAATGGTAATCAGTAAAAG
** *
5481 GTAAAGA-GGT-ATTTGTAAAGG
1 GTAAA-ATGGTAATCAGTAAAAG
*
5502 GTAAAATGGTAATTAGT-AAAG
1 GTAAAATGGTAATCAGTAAAAG
5523 AGTAAAATGGTAATCAGTAAAA-
1 -GTAAAATGGTAATCAGTAAAAG
*
5545 GTAAAAGGGTAATCAGTAAAA-
1 GTAAAATGGTAATCAGTAAAAG
*
5566 GTAAAAGGGTAATCAGTAA
1 GTAAAATGGTAATCAGTAA
5585 TCAAGTTCAA
Statistics
Matches: 266, Mismatches: 51, Indels: 44
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.02
20 58 0.22
21 79 0.30
22 103 0.39
23 22 0.08
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.24
Consensus pattern (22 bp):
GTAAAATGGTAATCAGTAAAAG
Found at i:5442 original size:20 final size:20
Alignment explanation
Indices: 5417--5484 Score: 82
Period size: 20 Copynumber: 3.2 Consensus size: 20
5407 TTAGTAATAG
*
5417 AGTAATAGTAATCAGTAAGA
1 AGTAATAGTAATCAGTAAAA
*
5437 AGTAATAGTAAACAGTAAAAA
1 AGTAATAGTAATCAGT-AAAA
*
5458 AGTAAAAAGGTAATCAGTAAAA
1 AGT-AATA-GTAATCAGTAAAA
5480 AGTAA
1 AGTAA
5485 AGAGGTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.37
21 8 0.20
22 10 0.24
23 8 0.20
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.21
Consensus pattern (20 bp):
AGTAATAGTAATCAGTAAAA
Found at i:5453 original size:107 final size:104
Alignment explanation
Indices: 5229--5585 Score: 384
Period size: 107 Copynumber: 3.4 Consensus size: 104
5219 CAAATAGTAA
* * * * *
5229 AATAGTAATCAGTAAAAAATAATAA--TAATCAATAAAAGGTAAAATGGTAATTAGTAAAGAGCA
1 AATAGTAATCAGTAAAAAGTAAAAAGGTAATCAGTAATAGGT-AAATGGTAATTAGTAAAGAGTA
*
5292 ATATGATAATCAGTAAAGAGTAATAGTAATCAGTAAGAAGT
65 A-ATGATAATTAGTAAAGAGTAATAGTAATCAGTAAGAAGT
* * *
5333 AAT-GATAATCAGTAAAAAGAAAAAAGGTAGTCAGTAATGGGTACAATGGTAATTAGTAAAGAGT
1 AATAG-TAATCAGTAAAAAGTAAAAAGGTAATCAGTAATAGGTA-AATGGTAATTAGTAAAGAGT
5397 AAAGTGATAATTAGTAATAGAGTAATAGTAATCAGTAAGAAGT
64 AAA-TGATAATTAGTAA-AGAGTAATAGTAATCAGTAAGAAGT
* * * * * *
5440 AATAGTAAACAGTAAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAGAGGT-ATTTGTAAAGGGT
1 AATAGTAATCAGT-AAAAAGTAAAAAGGTAATCAGTAATAGGTAAA-TGGTAATTAGTAAAGAGT
* *
5504 AAAATGGTAATTAGTAAAGAGTAAAATGGTAATCAGTAA-AAGT
64 -AAATGATAATTAGTAAAGAGT--AATAGTAATCAGTAAGAAGT
* *
5547 AAAAGGGTAATCAGT-AAAAGTAAAAGGGTAATCAGTAAT
1 AATA--GTAATCAGTAAAAAGTAAAAAGGTAATCAGTAAT
5586 CAAGTTCAAA
Statistics
Matches: 215, Mismatches: 24, Indels: 25
0.81 0.09 0.09
Matches are distributed among these distances:
103 1 0.00
104 20 0.09
105 2 0.01
106 49 0.23
107 89 0.41
108 46 0.21
109 8 0.04
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.24
Consensus pattern (104 bp):
AATAGTAATCAGTAAAAAGTAAAAAGGTAATCAGTAATAGGTAAATGGTAATTAGTAAAGAGTAA
ATGATAATTAGTAAAGAGTAATAGTAATCAGTAAGAAGT
Found at i:5476 original size:15 final size:14
Alignment explanation
Indices: 5423--5484 Score: 63
Period size: 15 Copynumber: 4.4 Consensus size: 14
5413 ATAGAGTAAT
*
5423 AGTAATCAGTAAGA
1 AGTAATCAGTAAAA
*
5437 AGTAAT-AGTAAAC
1 AGTAATCAGTAAAA
**
5450 AGTAAAAAAGTAAAA
1 AGT-AATCAGTAAAA
5465 AGGTAATCAGTAAAA
1 A-GTAATCAGTAAAA
5480 AGTAA
1 AGTAA
5485 AGAGGTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 8 0.21
14 12 0.31
15 17 0.44
16 2 0.05
ACGTcount: A:0.58, C:0.05, G:0.18, T:0.19
Consensus pattern (14 bp):
AGTAATCAGTAAAA
Found at i:5506 original size:43 final size:43
Alignment explanation
Indices: 5224--5680 Score: 213
Period size: 42 Copynumber: 10.5 Consensus size: 43
5214 AAATTCAAAT
* * * *
5224 AGTAAAATAGTAATCAGTAAAAAATAATAA--TAATCAATAAAA
1 AGTAAAATGGTAATCAGT-AAAAGTAAAAAGGTAATCAGTAAAA
* * * * * * *
5266 GGTAAAATGGTAATTAGTAAAGAGCAATATGATAATCAGTAAAG
1 AGTAAAATGGTAATCAGTAAA-AGTAAAAAGGTAATCAGTAAAA
* * *
5310 AGT--AATAGTAATCAGTAAGAAGT--AATGATAATCAGTAAAA
1 AGTAAAATGGTAATCAGTAA-AAGTAAAAAGGTAATCAGTAAAA
* * * ** * * * *
5350 AGAAAAAAGGTAGTCAGTAATGGGTACAATGGTAATTAGTAAAG
1 AGTAAAATGGTAATCAGTAA-AAGTAAAAAGGTAATCAGTAAAA
* * * * *
5394 AGTAAAGTGATAATTAGTAATAGAGT-AATA-GTAATCAGTAAGA
1 AGTAAAATGGTAATCAGTAA-A-AGTAAAAAGGTAATCAGTAAAA
* *
5437 AGT--AATAGTAAACAGTAAAAAAGTAAAAAGGTAATCAGTAAAA
1 AGTAAAATGGTAATCAGT--AAAAGTAAAAAGGTAATCAGTAAAA
** * * * *
5480 AGTAAAGA-GGT-ATTTGTAAAGGGTAAAATGGTAATTAGTAAAG
1 AGTAAA-ATGGTAATCAGTAAA-AGTAAAAAGGTAATCAGTAAAA
*
5523 AGTAAAATGGTAATCAGTAAAAGTAAAAGGGTAATCAGT-AAA
1 AGTAAAATGGTAATCAGTAAAAGTAAAAAGGTAATCAGTAAAA
* *
5565 AGTAAAAGGGTAATCAGTAATCAAGTTCAAAAAGTAATGGTAATCAGT-AAG
1 AGTAAAATGGTAATCAGTAA--AAG-T---AAA--AA-GGTAATCAGTAAAA
* * ** *
5616 AGTAAAATAGTAATCAATAAAAAAGTAAAAAAATAATCAGTAAAG
1 AGTAAAATGGTAATCAGT--AAAAGTAAAAAGGTAATCAGTAAAA
* *
5661 AGTAAAATGATAGTCAGTAA
1 AGTAAAATGGTAATCAGTAA
5681 TTAAATTCAA
Statistics
Matches: 313, Mismatches: 71, Indels: 61
0.70 0.16 0.14
Matches are distributed among these distances:
40 17 0.05
41 14 0.04
42 78 0.25
43 75 0.24
44 63 0.20
45 25 0.08
46 1 0.00
47 3 0.01
48 3 0.01
50 2 0.01
51 30 0.10
53 2 0.01
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.24
Consensus pattern (43 bp):
AGTAAAATGGTAATCAGTAAAAGTAAAAAGGTAATCAGTAAAA
Found at i:5642 original size:23 final size:22
Alignment explanation
Indices: 5616--5668 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
5606 AATCAGTAAG
*
5616 AGTAAAATAGTAATCAATAAAAA
1 AGTAAAATAATAATCAAT-AAAA
* * *
5639 AGTAAAAAAATAATCAGTAAAG
1 AGTAAAATAATAATCAATAAAA
5661 AGTAAAAT
1 AGTAAAAT
5669 GATAGTCAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.64, C:0.04, G:0.11, T:0.21
Consensus pattern (22 bp):
AGTAAAATAATAATCAATAAAA
Found at i:5648 original size:51 final size:50
Alignment explanation
Indices: 5552--5652 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 50
5542 AAAGTAAAAG
* * ** * *
5552 GGTAATCAGTAAAAGTAAAAGGGTAATCAGTAATCAAGTTCAAAAAGTAAT
1 GGTAATCAGTAAAAGTAAAAGAGTAATCAATAAAAAAG-TAAAAAAATAAT
* *
5603 GGTAATCAGTAAGAGTAAAATAGTAATCAATAAAAAAGTAAAAAAATAAT
1 GGTAATCAGTAAAAGTAAAAGAGTAATCAATAAAAAAGTAAAAAAATAAT
5653 CAGTAAAGAG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
50 10 0.24
51 32 0.76
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (50 bp):
GGTAATCAGTAAAAGTAAAAGAGTAATCAATAAAAAAGTAAAAAAATAAT
Found at i:5677 original size:22 final size:21
Alignment explanation
Indices: 5605--5680 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 21
5595 AAAGTAATGG
5605 TAATCAGT-AAGAGTAAAATA
1 TAATCAGTAAAGAGTAAAATA
* * *
5625 GTAATCAATAAAAAAGTAAAAAAA
1 -TAATCAGT-AAAGAGT-AAAATA
5649 TAATCAGTAAAGAGTAAAATGA
1 TAATCAGTAAAGAGTAAAAT-A
*
5671 TAGTCAGTAA
1 TAATCAGTAA
5681 TTAAATTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 11 0.25
22 16 0.36
23 12 0.27
24 5 0.11
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.22
Consensus pattern (21 bp):
TAATCAGTAAAGAGTAAAATA
Found at i:5749 original size:39 final size:36
Alignment explanation
Indices: 5689--5772 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 36
5679 AATTAAATTC
* *
5689 AAAGAGTAAAATGGTAGTCAGTAAAAGAGAAAAAGA
1 AAAGAGTAAAATGGTAATCAGTAAAAAAGAAAAAGA
**
5725 AGAAGAGTACAAAGTGGTAATCAGTAAAAAAGAGTAAGA
1 A-AAGAGTA-AAA-TGGTAATCAGTAAAAAAGAAAAAGA
5764 AAAGAGTAA
1 AAAGAGTAA
5773 TCAGTAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 1 0.02
37 8 0.20
38 10 0.24
39 22 0.54
ACGTcount: A:0.57, C:0.04, G:0.25, T:0.14
Consensus pattern (36 bp):
AAAGAGTAAAATGGTAATCAGTAAAAAAGAAAAAGA
Found at i:5781 original size:27 final size:28
Alignment explanation
Indices: 5741--5799 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
5731 GTACAAAGTG
5741 GTAATCAGTAAAAAAGAGTAAGAAAAGA
1 GTAATCAGTAAAAAAGAGTAAGAAAAGA
*
5769 GTAATCAGT-AAAAAGAGTAAGAAATGA
1 GTAATCAGTAAAAAAGAGTAAGAAAAGA
5796 GTAA
1 GTAA
5800 AAAATGGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.58, C:0.03, G:0.22, T:0.17
Consensus pattern (28 bp):
GTAATCAGTAAAAAAGAGTAAGAAAAGA
Found at i:5785 original size:54 final size:51
Alignment explanation
Indices: 5727--6049 Score: 182
Period size: 54 Copynumber: 5.7 Consensus size: 51
5717 GAAAAAGAAG
*
5727 AAGAGTACAAAGTGGTAATCAGTAAAAAAGAGTAAGAAAAGAGTAATCAGTAAA
1 AAGAGTA-AAAATGGTAATCAGT-AAAAAGAGTAA-AAAAGAGTAATCAGTAAA
* * *
5781 AAGAGTAAGAAATGAGTAAAAAATGGTGATCAGTAAAAAAGAGTGAAAGAGAGTAATTAGTAATA
1 AAGAGTAA-AAATG-GT-----A-----ATCAGT-AAAAAGAGTAAAAAAGAGTAATCAGTAA-A
* * *
5846 AAGAGTAAGAAATGGTGATCAGTAAAAAAGAGT-AAAAAGTGGTATTCAGTAAA
1 AAGAGTAA-AAATGGTAATCAGT-AAAAAGAGTAAAAAAG-AGTAATCAGTAAA
* * * *
5899 AAGGGGTAAAAATGGTATTAAGTAAAAAAGGAGAGTAAAAATATG-GTAATTAAGTAAA
1 AA-GAGTAAAAATGGTAATCAGT--AAAA--AGAGTAAAAA-A-GAGTAA-TCAGTAAA
* * * * *
5957 AAGAGTAAAAAGTGGTATTCGGTAAAGACAGTAAGAAAAGGGGTAATCAGTAAAA
1 AAGAGTAAAAA-TGGTAATCAGTAAAAAGAGTAA-AAAA-GAGTAATCAGT-AAA
*
6012 AAGAGTAAAATATGGTAATCAGTACAAAGAGTAAAAAA
1 AAGAGTAAAA-ATGGTAATCAGTAAAAAGAGTAAAAAA
6050 TGGTAAATTA
Statistics
Matches: 215, Mismatches: 27, Indels: 54
0.73 0.09 0.18
Matches are distributed among these distances:
53 20 0.09
54 62 0.29
55 39 0.18
56 9 0.04
57 15 0.07
58 19 0.09
59 1 0.00
60 1 0.00
64 17 0.08
65 32 0.15
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.20
Consensus pattern (51 bp):
AAGAGTAAAAATGGTAATCAGTAAAAAGAGTAAAAAAGAGTAATCAGTAAA
Found at i:5813 original size:37 final size:38
Alignment explanation
Indices: 5747--5836 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 38
5737 AGTGGTAATC
5747 AGTAAAAAAGAGTAAGAAAAGAGTAATCAGT-AAAAAG
1 AGTAAAAAAGAGTAAGAAAAGAGTAATCAGTAAAAAAG
* *
5784 AGTAAGAAATGAGTAA-AAAATG-GTGATCAGTAAAAAAG
1 AGTAA-AAAAGAGTAAGAAAA-GAGTAATCAGTAAAAAAG
* *
5822 AGTGAAAGAGAGTAA
1 AGTAAAAAAGAGTAA
5837 TTAGTAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
37 25 0.56
38 20 0.44
ACGTcount: A:0.58, C:0.02, G:0.24, T:0.16
Consensus pattern (38 bp):
AGTAAAAAAGAGTAAGAAAAGAGTAATCAGTAAAAAAG
Found at i:5815 original size:65 final size:64
Alignment explanation
Indices: 5706--5859 Score: 193
Period size: 65 Copynumber: 2.3 Consensus size: 64
5696 AAAATGGTAG
** * * *
5706 TCAGTAAAAGAGAAAAAGAAGAAGAGTACAAAGTGGTAATCAGTAAAAAAGAGTAAGAAA-AGAG
1 TCAGTAAAA-AGAGTAAGAA-ATGAGTAAAAAATGGTAATCAGTAAAAAAGAGT--GAAAGAGAG
5770 TAA
62 TAA
*
5773 TCAGTAAAAAGAGTAAGAAATGAGTAAAAAATGGTGATCAGTAAAAAAGAGTGAAAGAGAGTAA
1 TCAGTAAAAAGAGTAAGAAATGAGTAAAAAATGGTAATCAGTAAAAAAGAGTGAAAGAGAGTAA
*
5837 TTAGTAATAAAGAGTAAGAAATG
1 TCAGTAA-AAAGAGTAAGAAATG
5860 GTGATCAGTA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
63 4 0.05
64 13 0.17
65 44 0.56
66 8 0.10
67 9 0.12
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.17
Consensus pattern (64 bp):
TCAGTAAAAAGAGTAAGAAATGAGTAAAAAATGGTAATCAGTAAAAAAGAGTGAAAGAGAGTAA
Found at i:5824 original size:27 final size:27
Alignment explanation
Indices: 5784--6055 Score: 221
Period size: 27 Copynumber: 9.9 Consensus size: 27
5774 CAGTAAAAAG
* *
5784 AGTAAGAAATGAGTAAAAAATGGTGATC
1 AGTAA-AAAAGAGTAAAAAATGGTAATC
* * *
5812 AGTAAAAAAGAGTGAAAGA-GAGTAATT
1 AGTAAAAAAGAGTAAAAAATG-GTAATC
* * *
5839 AGTAATAAAGAGTAAGAAATGGTGATC
1 AGTAAAAAAGAGTAAAAAATGGTAATC
* *
5866 AGTAAAAAAGAGTAAAAAGTGGTATTC
1 AGTAAAAAAGAGTAAAAAATGGTAATC
* * * *
5893 AGTAAAAAGGGGT-AAAAATGGTATTA
1 AGTAAAAAAGAGTAAAAAATGGTAATC
*
5919 AGTAAAAAAGGAGAGTAAAAATATGGTAATTA
1 AGT-AAAAA--AGAGTAAAAA-ATGGTAA-TC
* *
5951 AGT-AAAAAGAGTAAAAAGTGGTATTC
1 AGTAAAAAAGAGTAAAAAATGGTAATC
* * * *
5977 GGT-AAAGACAGTAAGAAAAGGGGTAATC
1 AGTAAAAAAGAGTAA-AAAA-TGGTAATC
*
6005 AGTAAAAAAGAGTAAAATATGGTAATC
1 AGTAAAAAAGAGTAAAAAATGGTAATC
*
6032 AGT-ACAAAGAGTAAAAAATGGTAA
1 AGTAAAAAAGAGTAAAAAATGGTAA
6056 ATTAGTAATC
Statistics
Matches: 194, Mismatches: 39, Indels: 24
0.75 0.15 0.09
Matches are distributed among these distances:
26 46 0.24
27 90 0.46
28 27 0.14
29 12 0.06
30 8 0.04
31 6 0.03
32 5 0.03
ACGTcount: A:0.52, C:0.03, G:0.24, T:0.21
Consensus pattern (27 bp):
AGTAAAAAAGAGTAAAAAATGGTAATC
Done.