Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006831.1 Corchorus capsularis cultivar CVL-1 contig06852, 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: 12007
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Found at i:62 original size:20 final size:21
Alignment explanation
Indices: 34--73 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
24 TGATATCATG
*
34 ATAATATATT-TTAAGTTAGA
1 ATAAGATATTATTAAGTTAGA
*
54 ATAAGATATTATTATGTTAG
1 ATAAGATATTATTAAGTTAG
74 TAATTTTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (21 bp):
ATAAGATATTATTAAGTTAGA
Found at i:188 original size:2 final size:2
Alignment explanation
Indices: 172--215 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
162 TAGTAGTCTA
172 AT AT -T AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
212 AT AT
1 AT AT
216 TGCTAGTGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4715 original size:35 final size:36
Alignment explanation
Indices: 4676--4750 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
4666 AGGACAATCA
* *
4676 GTAAAAAGTAAAAAGGT-ATCTG-AAAGGGTAAAATG
1 GTAAAAAGT-AAAAGGTAATCAGTAAAGGATAAAATG
4711 GTAAAAAGTAAAAGGTAATCAGTAAAGGATAAAATG
1 GTAAAAAGTAAAAGGTAATCAGTAAAGGATAAAATG
4747 GTAA
1 GTAA
4751 TTAGTAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 7 0.19
35 13 0.36
36 16 0.44
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.20
Consensus pattern (36 bp):
GTAAAAAGTAAAAGGTAATCAGTAAAGGATAAAATG
Found at i:4749 original size:22 final size:21
Alignment explanation
Indices: 4715--4943 Score: 154
Period size: 22 Copynumber: 10.8 Consensus size: 21
4705 AAAATGGTAA
4715 AAAG-TAAAA-GGTAATCAGT
1 AAAGATAAAATGGTAATCAGT
*
4734 AAAGGATAAAATGGTAATTAGT
1 AAA-GATAAAATGGTAATCAGT
4756 AAAGAGTAAAATGGTAATCAGT
1 AAAGA-TAAAATGGTAATCAGT
*
4778 GAAA-ATTAAAA-GAGTAATCCGT
1 -AAAGA-TAAAATG-GTAATCAGT
*
4800 --AGA-AAGTAATAGTAATCAGT
1 AAAGATAA--AATGGTAATCAGT
*
4820 -AAGA-AGCAATGGTAATCAGT
1 AAAGATA-AAATGGTAATCAGT
* *
4840 AAAAAGTAAAAAGGTAATCAGT
1 AAAGA-TAAAATGGTAATCAGT
* * * *
4862 AAAAGGTAAAGTAGTAATCAAT
1 -AAAGATAAAATGGTAATCAGT
*
4884 AAAGGGTAAAATGGTAATCAGT
1 AAA-GATAAAATGGTAATCAGT
*
4906 AAAAAGTAAAA-GAGTAATCAGT
1 AAAGA-TAAAATG-GTAATCAGT
*
4928 AAAGAGAAAATGGTAA
1 AAAGATAAAATGGTAA
4944 AGGGTAAAGA
Statistics
Matches: 166, Mismatches: 24, Indels: 38
0.73 0.11 0.17
Matches are distributed among these distances:
18 2 0.01
19 4 0.02
20 24 0.14
21 27 0.16
22 102 0.61
23 7 0.04
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (21 bp):
AAAGATAAAATGGTAATCAGT
Found at i:4774 original size:44 final size:43
Alignment explanation
Indices: 4711--4943 Score: 198
Period size: 44 Copynumber: 5.4 Consensus size: 43
4701 GGGTAAAATG
* *
4711 GTAAAAAGTAAAA-GGTAATCAGTAAAGGATAAAATGGTAATTA
1 GTAAAGAGTAAAATGGTAATCAGTAAA-GATAAAATGGTAATCA
*
4754 GTAAAGAGTAAAATGGTAATCAGTGAAA-ATTAAAA-GAGTAATCC
1 GTAAAGAGTAAAATGGTAATCAGT-AAAGA-TAAAATG-GTAATCA
* *
4798 GTAGAA-AGT--AATAGTAATCAGT-AAGA-AGCAATGGTAATCA
1 GTA-AAGAGTAAAATGGTAATCAGTAAAGATA-AAATGGTAATCA
* * * * *
4838 GTAAAAAGTAAAAAGGTAATCAGTAAAAGGTAAAGTAGTAATCA
1 GTAAAGAGTAAAATGGTAATCAGT-AAAGATAAAATGGTAATCA
* * *
4882 ATAAAGGGTAAAATGGTAATCAGTAAAAAGTAAAA-GAGTAATCA
1 GTAAAGAGTAAAATGGTAATCAGTAAAGA-TAAAATG-GTAATCA
4926 GTAAAGAG-AAAATGGTAA
1 GTAAAGAGTAAAATGGTAA
4944 AGGGTAAAGA
Statistics
Matches: 152, Mismatches: 22, Indels: 32
0.74 0.11 0.16
Matches are distributed among these distances:
39 3 0.02
40 16 0.11
41 2 0.01
42 23 0.15
43 27 0.18
44 75 0.49
45 6 0.04
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (43 bp):
GTAAAGAGTAAAATGGTAATCAGTAAAGATAAAATGGTAATCA
Found at i:4921 original size:15 final size:14
Alignment explanation
Indices: 4837--5232 Score: 58
Period size: 14 Copynumber: 27.9 Consensus size: 14
4827 AATGGTAATC
*
4837 AGTAAAAAGTAAAA
1 AGTAAAGAGTAAAA
**
4851 AGGTAATCAGTAAAA
1 A-GTAAAGAGTAAAA
* *
4866 GGTAAAGTAGTAATCA
1 AGTAAAG-AGTAA-AA
*
4882 A-TAAAGGGTAAAA
1 AGTAAAGAGTAAAA
* **
4895 TGGTAATCAGTAAAA
1 -AGTAAAGAGTAAAA
**
4910 AGTAAAAGAGTAATC
1 AGT-AAAGAGTAAAA
4925 AGTAAAGAG-AAAA
1 AGTAAAGAGTAAAA
* * *
4938 TGGTAAAGGGTAAAG
1 -AGTAAAGAGTAAAA
***
4953 AGTAAAAGAGTATTC
1 AGT-AAAGAGTAAAA
**
4968 AG-ACAAGAGTAATC
1 AGTA-AAGAGTAAAA
4982 AGT-AA-AG-AAAA
1 AGTAAAGAGTAAAA
***
4993 AGTAAAAGAGTATTC
1 AGT-AAAGAGTAAAA
**
5008 AG-ACAAGAGTAATC
1 AGTA-AAGAGTAAAA
5022 AGTAAAGA--AAAA
1 AGTAAAGAGTAAAA
* * *
5034 TGGTAAAGAGTATAG
1 -AGTAAAGAGTAAAA
5049 AGTAAAGAGT--AA
1 AGTAAAGAGTAAAA
5061 AGTAAAGAGTAATCAGCAA
1 AGTAAAGAGT-A--A--AA
5080 AGTAAA-ATGGTAAAA
1 AGTAAAGA--GTAAAA
* **
5095 AGTAAAAGAATAATC
1 AGT-AAAGAGTAAAA
5110 AGTAAAGA--AAAA
1 AGTAAAGAGTAAAA
*
5122 ATGGTAAAGAGTAAAG
1 A--GTAAAGAGTAAAA
*
5138 AGT-AA-AGTAAAG
1 AGTAAAGAGTAAAA
** *
5150 AGTAATCAG--CAA
1 AGTAAAGAGTAAAA
5162 AGTAAA-ATGGTAAAA
1 AGTAAAGA--GTAAAA
* **
5177 AGTAAAAGAATAATC
1 AGT-AAAGAGTAAAA
*
5192 AGTAAAGA-AAAAA
1 AGTAAAGAGTAAAA
*
5205 ATGGTAAAGAGTAAAG
1 A--GTAAAGAGTAAAA
5221 AGTAAAGAGTAA
1 AGTAAAGAGTAA
5233 TCAGTAAAGG
Statistics
Matches: 275, Mismatches: 61, Indels: 92
0.64 0.14 0.21
Matches are distributed among these distances:
11 6 0.02
12 34 0.12
13 23 0.08
14 95 0.35
15 87 0.32
16 15 0.05
17 3 0.01
18 1 0.00
19 9 0.03
20 2 0.01
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (14 bp):
AGTAAAGAGTAAAA
Found at i:4931 original size:14 final size:14
Alignment explanation
Indices: 4914--5081 Score: 95
Period size: 14 Copynumber: 12.3 Consensus size: 14
4904 GTAAAAAGTA
4914 AAAGAGTAATCAGT
1 AAAGAGTAATCAGT
* *
4928 AAAGAGAAAAT-GGT
1 AAAGAG-TAATCAGT
* **
4942 AAAGGGTAAAGAGT
1 AAAGAGTAATCAGT
*
4956 AAAAGAGTATTCAG-
1 -AAAGAGTAATCAGT
4970 ACAAGAGTAATCAGT
1 A-AAGAGTAATCAGT
*
4985 AAAGA--AA-AAGT
1 AAAGAGTAATCAGT
*
4996 AAAAGAGTATTCAG-
1 -AAAGAGTAATCAGT
5010 ACAAGAGTAATCAGT
1 A-AAGAGTAATCAGT
** *
5025 AAAGAAAAAT-GGT
1 AAAGAGTAATCAGT
*
5038 AAAGAGT-ATAGAGT
1 AAAGAGTAAT-CAGT
5052 AAAGAGTAA--AGT
1 AAAGAGTAATCAGT
*
5064 AAAGAGTAATCAGC
1 AAAGAGTAATCAGT
5078 AAAG
1 AAAG
5082 TAAAATGGTA
Statistics
Matches: 116, Mismatches: 22, Indels: 32
0.68 0.13 0.19
Matches are distributed among these distances:
11 3 0.03
12 21 0.18
13 11 0.09
14 64 0.55
15 17 0.15
ACGTcount: A:0.54, C:0.05, G:0.24, T:0.17
Consensus pattern (14 bp):
AAAGAGTAATCAGT
Found at i:5007 original size:40 final size:40
Alignment explanation
Indices: 4953--5046 Score: 163
Period size: 40 Copynumber: 2.3 Consensus size: 40
4943 AAGGGTAAAG
4953 AGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAA
1 AGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAA
4993 AGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAA
1 AGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAA
5033 ATGGT-AAAGAGTAT
1 A--GTAAAAGAGTAT
5047 AGAGTAAAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
40 41 0.79
41 9 0.17
42 2 0.04
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.19
Consensus pattern (40 bp):
AGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAA
Found at i:5052 original size:7 final size:7
Alignment explanation
Indices: 5036--5458 Score: 76
Period size: 7 Copynumber: 62.0 Consensus size: 7
5026 AAGAAAAATG
5036 GTAAAGA
1 GTAAAGA
*
5043 GTATAGA
1 GTAAAGA
5050 GTAAAGA
1 GTAAAGA
5057 GT-AA-A
1 GTAAAGA
5062 GTAAAGA
1 GTAAAGA
**
5069 GTAATCA
1 GTAAAGA
*
5076 G-CAA-A
1 GTAAAGA
5081 GTAAA-A
1 GTAAAGA
*
5087 TGGTAAAAA
1 --GTAAAGA
5096 GTAAAAGA
1 GT-AAAGA
* **
5104 ATAATCA
1 GTAAAGA
5111 GTAAAGA
1 GTAAAGA
**
5118 AAAAATG-
1 GTAAA-GA
5125 GTAAAGA
1 GTAAAGA
5132 GTAAAGA
1 GTAAAGA
5139 GT-AA-A
1 GTAAAGA
5144 GTAAAGA
1 GTAAAGA
**
5151 GTAATCA
1 GTAAAGA
*
5158 G-CAA-A
1 GTAAAGA
5163 GTAAA-A
1 GTAAAGA
*
5169 TGGTAAAAA
1 --GTAAAGA
5178 GTAAAAGA
1 GT-AAAGA
* **
5186 ATAATCA
1 GTAAAGA
5193 GTAAAGA
1 GTAAAGA
* *
5200 -AAAAAA
1 GTAAAGA
5206 TGGTAAAGA
1 --GTAAAGA
5215 GTAAAGA
1 GTAAAGA
5222 GTAAAGA
1 GTAAAGA
**
5229 GTAATCA
1 GTAAAGA
5236 GTAAAG-
1 GTAAAGA
5242 G-AAATG-
1 GTAAA-GA
* **
5248 GCAATCA
1 GTAAAGA
5255 GTAAAGA
1 GTAAAGA
5262 --AAA-A
1 GTAAAGA
5266 GTAAAAGA
1 GT-AAAGA
***
5274 GTATTCA
1 GTAAAGA
5281 G-ACAAGA
1 GTA-AAGA
**
5288 GTAATCA
1 GTAAAGA
5295 GTAAAG-
1 GTAAAGA
*
5301 GAAAATG-
1 GTAAA-GA
*
5308 GTAAAGG
1 GTAAAGA
5315 GTAAAGA
1 GTAAAGA
5322 GT-AA-A
1 GTAAAGA
5327 GTAAAGA
1 GTAAAGA
**
5334 GTAATCA
1 GTAAAGA
*
5341 G-CAA-A
1 GTAAAGA
5346 GTAAA-A
1 GTAAAGA
*
5352 TGGTAAAAA
1 --GTAAAGA
5361 GTAAAAGA
1 GT-AAAGA
**
5369 GTAATCA
1 GTAAAGA
5376 GTAAAGA
1 GTAAAGA
* *
5383 -AAAAGG
1 GTAAAGA
5389 GTAAAGA
1 GTAAAGA
5396 GTAAAGA
1 GTAAAGA
5403 GTAAAGA
1 GTAAAGA
** *
5410 AAAAAAA
1 GTAAAGA
*
5417 TGGTAAAGG
1 --GTAAAGA
5426 GTAAAGA
1 GTAAAGA
5433 GT--AGA
1 GTAAAGA
5438 GTAAAGA
1 GTAAAGA
**
5445 GTAATCA
1 GTAAAGA
5452 GTAAAGA
1 GTAAAGA
5459 AAAATGGTAA
Statistics
Matches: 292, Mismatches: 82, Indels: 84
0.64 0.18 0.18
Matches are distributed among these distances:
4 1 0.00
5 26 0.09
6 42 0.14
7 177 0.61
8 36 0.12
9 10 0.03
ACGTcount: A:0.56, C:0.04, G:0.23, T:0.17
Consensus pattern (7 bp):
GTAAAGA
Found at i:5066 original size:12 final size:13
Alignment explanation
Indices: 5036--5072 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
5026 AAGAAAAATG
5036 GTAAAGAGTATAGA
1 GTAAAGAGTA-AGA
5050 GTAAAGAGTAA-A
1 GTAAAGAGTAAGA
5062 GTAAAGAGTAA
1 GTAAAGAGTAA
5073 TCAGCAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.52
13 1 0.04
14 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.19
Consensus pattern (13 bp):
GTAAAGAGTAAGA
Found at i:5110 original size:35 final size:36
Alignment explanation
Indices: 5059--5136 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
5049 AGTAAAGAGT
* *
5059 AAAGT-AAAGAGTAATCAGCAAAG-TAAAATGGTAA
1 AAAGTAAAAGAATAATCAGCAAAGAAAAAATGGTAA
*
5093 AAAGTAAAAGAATAATCAGTAAAGAAAAAATGGTAA
1 AAAGTAAAAGAATAATCAGCAAAGAAAAAATGGTAA
*
5129 AGAGTAAA
1 AAAGTAAA
5137 GAGTAAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.13
35 16 0.42
36 17 0.45
ACGTcount: A:0.60, C:0.04, G:0.19, T:0.17
Consensus pattern (36 bp):
AAAGTAAAAGAATAATCAGCAAAGAAAAAATGGTAA
Found at i:5138 original size:35 final size:35
Alignment explanation
Indices: 5059--5150 Score: 118
Period size: 35 Copynumber: 2.7 Consensus size: 35
5049 AGTAAAGAGT
* *
5059 AAAGTAAAGAGTAATCAGCAAAG-TAAAATGGTAA
1 AAAGTAAAGAGTAATCAGTAAAGAAAAAATGGTAA
*
5093 AAAGTAAAAGAATAATCAGTAAAGAAAAAATGGTAA
1 AAAGT-AAAGAGTAATCAGTAAAGAAAAAATGGTAA
*
5129 AGAGTAAAGAGTAA--AGTAAAGA
1 AAAGTAAAGAGTAATCAGTAAAGA
5151 GTAATCAGCA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 8 0.16
34 5 0.10
35 24 0.47
36 14 0.27
ACGTcount: A:0.60, C:0.03, G:0.21, T:0.16
Consensus pattern (35 bp):
AAAGTAAAGAGTAATCAGTAAAGAAAAAATGGTAA
Found at i:5145 original size:82 final size:83
Alignment explanation
Indices: 5047--5227 Score: 355
Period size: 82 Copynumber: 2.2 Consensus size: 83
5037 TAAAGAGTAT
5047 AGAGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAAAAGAATAATCAG
1 AGAGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAAAAGAATAATCAG
5112 TAAAG-AAAAAATGGTAA
66 TAAAGAAAAAAATGGTAA
5129 AGAGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAAAAGAATAATCAG
1 AGAGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAAAAGAATAATCAG
5194 TAAAGAAAAAAATGGTAA
66 TAAAGAAAAAAATGGTAA
5212 AGAGTAAAGAGTAAAG
1 AGAGTAAAGAGTAAAG
5228 AGTAATCAGT
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 70 0.71
83 28 0.29
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.17
Consensus pattern (83 bp):
AGAGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAAAAGAATAATCAG
TAAAGAAAAAAATGGTAA
Found at i:5163 original size:19 final size:19
Alignment explanation
Indices: 5125--5167 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5115 AGAAAAAATG
* *
5125 GTAAAGAGTAAAGAGTAAA
1 GTAAAGAGTAAACAGCAAA
*
5144 GTAAAGAGTAATCAGCAAA
1 GTAAAGAGTAAACAGCAAA
5163 GTAAA
1 GTAAA
5168 ATGGTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.16
Consensus pattern (19 bp):
GTAAAGAGTAAACAGCAAA
Found at i:5191 original size:35 final size:36
Alignment explanation
Indices: 5141--5219 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 36
5131 AGTAAAGAGT
* *
5141 AAAGT-AAAGAGTAATCAGCAAAG-TAAAATGGTAA
1 AAAGTAAAAGAATAATCAGCAAAGAAAAAATGGTAA
*
5175 AAAGTAAAAGAATAATCAGTAAAGAAAAAAATGGTAA
1 AAAGTAAAAGAATAATCAGCAAAG-AAAAAATGGTAA
*
5212 AGAGTAAA
1 AAAGTAAA
5220 GAGTAAAGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 5 0.13
35 16 0.42
37 17 0.45
ACGTcount: A:0.61, C:0.04, G:0.19, T:0.16
Consensus pattern (36 bp):
AAAGTAAAAGAATAATCAGCAAAGAAAAAATGGTAA
Found at i:5287 original size:272 final size:259
Alignment explanation
Indices: 4904--5408 Score: 789
Period size: 265 Copynumber: 1.9 Consensus size: 259
4894 ATGGTAATCA
* * * *
4904 GTAAAAAGTAAAAGAGTAATCAGTAAAGAGAAAATGGTAAAGGGTAAAGAGTAAAAGAGTATTCA
1 GTAAAAAGTAAAAGAATAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAAAAGAGTAATCA
*
4969 GACAAGAGTAATCAGTAAAGAAAAAGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAAA
66 GACAAGAGCAATCAGTAAAGAAAAAGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAAA
5034 TGGTAAAGAGTATAGAGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTA
131 TGGT-AA-AG----G-GTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTA
*
5099 AAAGAATAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAG
189 AAAGAATAATCAGTAAAG-AAAAAGGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAG
5164 TAAAATG
253 TAAAATG
5171 GTAAAAAGTAAAAGAATAATCAGTAAAGAAAAAAATGGTAAAGAGTAAAGAGT-AAAGAGTAATC
1 GTAAAAAGTAAAAGAATAATCAGTAAAG-AAAAAATGGTAAAGAGTAAAGAGTAAAAGAGTAATC
5235 AGTA-AAGGAAATGGCAATCAGTAAAGAAAAAGTAAAAGAGTATTCAGACAAGAGTAATCAGTAA
65 AG-ACAA-G--A--GCAATCAGTAAAGAAAAAGTAAAAGAGTATTCAGACAAGAGTAATCAGTAA
*
5299 AGGAAAATGGTAAAGGGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTA
124 AGAAAAATGGTAAAGGGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTA
*
5364 AAAGAGTAATCAGTAAAGAAAAAGGGTAAAGAGTAAAGAGTAAAG
189 AAAGAATAATCAGTAAAGAAAAAGGGTAAAGAGTAAAGAGTAAAG
5409 AAAAAAAATG
Statistics
Matches: 223, Mismatches: 8, Indels: 17
0.90 0.03 0.07
Matches are distributed among these distances:
264 26 0.12
265 66 0.30
266 1 0.00
267 41 0.18
268 24 0.11
270 3 0.01
271 2 0.01
272 60 0.27
ACGTcount: A:0.56, C:0.04, G:0.23, T:0.17
Consensus pattern (259 bp):
GTAAAAAGTAAAAGAATAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAAAAGAGTAATCA
GACAAGAGCAATCAGTAAAGAAAAAGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAAA
TGGTAAAGGGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAAAAGAAT
AATCAGTAAAGAAAAAGGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATG
Found at i:5332 original size:19 final size:19
Alignment explanation
Indices: 5308--5365 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
5298 AAGGAAAATG
*
5308 GTAAAGGGTAAAGAGTAAA
1 GTAAAGGGTAAAAAGTAAA
* ** *
5327 GTAAAGAGTAATCAGCAAA
1 GTAAAGGGTAAAAAGTAAA
*
5346 GTAAAATGGTAAAAAGTAAA
1 GT-AAAGGGTAAAAAGTAAA
5366 AGAGTAATCA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.55, C:0.03, G:0.24, T:0.17
Consensus pattern (19 bp):
GTAAAGGGTAAAAAGTAAA
Found at i:5337 original size:46 final size:48
Alignment explanation
Indices: 5099--5382 Score: 201
Period size: 46 Copynumber: 6.1 Consensus size: 48
5089 GTAAAAAGTA
* * * *
5099 AAAGAATAATCAGTAAAGAAAAAATGGTAAAGAGT-AAAGAGTAA-AGT
1 AAAGAGTAATCAGCAAAG-GAAAATGGTAAAAAGTAAAAGAGTAACAGT
* *
5146 AAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAAAAGAATAATCAGT
1 AAAGAGTAATCAGCAAAGGAAAATGGTAAAAAGTAAAAGAGTAA-CAGT
* *
5195 AAAGA--AA--A--AAATGGTAAA-GAGTAAAGAGT-AAAGAGTAATCAGT
1 AAAGAGTAATCAGCAAA-GGAAAATG-GTAAAAAGTAAAAGAGTAA-CAGT
* * * *
5238 AAAG-GAAAT-GGCAATCA-GTAAA--G-AAAAAGTAAAAGAGTATTCAG-
1 AAAGAGTAATCAGCAA--AGGAAAATGGTAAAAAGTAAAAGAGTA-ACAGT
* **
5282 ACAAGAGTAATCAGTAAAGGAAAATGGTAAAGGGT-AAAGAGTAA-AGT
1 A-AAGAGTAATCAGCAAAGGAAAATGGTAAAAAGTAAAAGAGTAACAGT
*
5329 AAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAAAAGAGTAATCAGT
1 AAAGAGTAATCAGCAAAGGAAAATGGTAAAAAGTAAAAGAGTAA-CAGT
5378 AAAGA
1 AAAGA
5383 AAAAGGGTAA
Statistics
Matches: 189, Mismatches: 23, Indels: 48
0.73 0.09 0.18
Matches are distributed among these distances:
43 21 0.11
44 21 0.11
45 17 0.09
46 53 0.28
47 46 0.24
48 9 0.05
49 22 0.12
ACGTcount: A:0.56, C:0.05, G:0.22, T:0.17
Consensus pattern (48 bp):
AAAGAGTAATCAGCAAAGGAAAATGGTAAAAAGTAAAAGAGTAACAGT
Found at i:5386 original size:20 final size:20
Alignment explanation
Indices: 5358--5402 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5348 AAAATGGTAA
* *
5358 AAAGTAAAAGAGTAATCAGT
1 AAAGAAAAAGAGTAAACAGT
* *
5378 AAAGAAAAAGGGTAAAGAGT
1 AAAGAAAAAGAGTAAACAGT
5398 AAAGA
1 AAAGA
5403 GTAAAGAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.13
Consensus pattern (20 bp):
AAAGAAAAAGAGTAAACAGT
Found at i:5386 original size:27 final size:26
Alignment explanation
Indices: 5356--5473 Score: 89
Period size: 27 Copynumber: 4.5 Consensus size: 26
5346 GTAAAATGGT
*
5356 AAAAAGTAAAAGAGTAATCAGTAAAGA
1 AAAAAGT-AAAGAGTAAACAGTAAAGA
* *
5383 AAAAGGGTAAAGAGTAAAGAGTAAAGA
1 AAAA-AGTAAAGAGTAAACAGTAAAGA
* **
5410 AAAAA--AATG-GTAAAGGGTAAAGA
1 AAAAAGTAAAGAGTAAACAGTAAAGA
** * *
5433 GTAGAGTAAAGAGTAATCAGTAAAGA
1 AAAAAGTAAAGAGTAAACAGTAAAGA
*
5459 AAAATGGTAAAGAGT
1 AAAA-AGTAAAGAGT
5474 GAAGGGAAGT
Statistics
Matches: 69, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
23 15 0.22
24 3 0.04
25 3 0.04
26 12 0.17
27 34 0.49
28 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (26 bp):
AAAAAGTAAAGAGTAAACAGTAAAGA
Found at i:5422 original size:30 final size:33
Alignment explanation
Indices: 5326--5444 Score: 129
Period size: 35 Copynumber: 3.6 Consensus size: 33
5316 TAAAGAGTAA
* * *
5326 AGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAA
1 AGTAAAGAGTAA-CAGTAAAGAAAAATGGTAAAG
*
5360 AGTAAAAGAGTAATCAGTAAAGAAAAAGGGTAAAG
1 AGT-AAAGAGTAA-CAGTAAAGAAAAATGGTAAAG
5395 AGTAAAGAGTAA-AG-AAA-AAAAATGGTAAAG
1 AGTAAAGAGTAACAGTAAAGAAAAATGGTAAAG
* *
5425 GGTAAAGAGT-AGAGTAAAGA
1 AGTAAAGAGTAACAGTAAAGA
5445 GTAATCAGTA
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
29 1 0.01
30 23 0.31
31 6 0.08
32 3 0.04
34 12 0.16
35 30 0.40
ACGTcount: A:0.57, C:0.03, G:0.25, T:0.15
Consensus pattern (33 bp):
AGTAAAGAGTAACAGTAAAGAAAAATGGTAAAG
Found at i:5434 original size:111 final size:110
Alignment explanation
Indices: 5302--5516 Score: 324
Period size: 111 Copynumber: 1.9 Consensus size: 110
5292 TCAGTAAAGG
*
5302 AAAATGGTAAAGGGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAAAA
1 AAAATGGTAAAGGGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGAAAAATGGTAAAAAGT-AAA
*
5367 GAGTAA-TCAGTAAAGAAAAAGGGTAAAGAGTAAAGAGTAAAGAAAA
65 G-GGAAGTCAGTAAAGAAAAAGGGTAAAGAGTAAAGAGTAAAGAAAA
* * * *
5413 AAAATGGTAAAGGGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTGAAG
1 AAAATGGTAAAGGGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGAAAAATGGTAAAAAGTAAAG
* * *
5478 GGAAGTCAGTAAAGAAGAATGGTGAAGAGTAAAGAGTAA
66 GGAAGTCAGTAAAGAAAAAGGGTAAAGAGTAAAGAGTAA
5517 TCCAGTAAAG
Statistics
Matches: 94, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
109 3 0.03
110 34 0.36
111 57 0.61
ACGTcount: A:0.54, C:0.02, G:0.27, T:0.16
Consensus pattern (110 bp):
AAAATGGTAAAGGGTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGAAAAATGGTAAAAAGTAAAG
GGAAGTCAGTAAAGAAAAAGGGTAAAGAGTAAAGAGTAAAGAAAA
Found at i:5487 original size:34 final size:34
Alignment explanation
Indices: 5435--5547 Score: 138
Period size: 34 Copynumber: 3.2 Consensus size: 34
5425 GGTAAAGAGT
*
5435 AGAGTAAAGAGTAATCAGTAAAGAAAAATGGTAA
1 AGAGTAAAGAGGAATCAGTAAAGAAAAATGGTAA
* * *
5469 AGAGTGAAG-GGAAGTCAGTAAAGAAGAATGGTGA
1 AGAGTAAAGAGGAA-TCAGTAAAGAAAAATGGTAA
*
5503 AGAGTAAAGAGTAATCCAGTAAAGAAAAAAATGGTAA
1 AGAGTAAAGAGGAAT-CAGTAAAG--AAAAATGGTAA
5540 AGAGTAAA
1 AGAGTAAA
5548 ATATTAATCA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
33 3 0.05
34 35 0.53
35 11 0.17
37 17 0.26
ACGTcount: A:0.53, C:0.04, G:0.27, T:0.16
Consensus pattern (34 bp):
AGAGTAAAGAGGAATCAGTAAAGAAAAATGGTAA
Found at i:5560 original size:37 final size:34
Alignment explanation
Indices: 5435--5562 Score: 118
Period size: 34 Copynumber: 3.6 Consensus size: 34
5425 GGTAAAGAGT
5435 AGAGT-AAAGAGTAATCAGTAAAGAAAAATGGTAA
1 AGAGTAAAAGA-TAATCAGTAAAGAAAAATGGTAA
** * * *
5469 AGAGTGAAGGGA-AGTCAGTAAAGAAGAATGGTGA
1 AGAGT-AAAAGATAATCAGTAAAGAAAAATGGTAA
5503 AGAGT-AAAGAGTAATCCAGTAAAGAAAAAAATGGTAA
1 AGAGTAAAAGA-TAAT-CAGTAAAG--AAAAATGGTAA
*
5540 AGAGTAAAATATTAATCAGTAAA
1 AGAGTAAAAGA-TAATCAGTAAA
5563 AAGTAATGGC
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
32 3 0.04
34 31 0.42
35 8 0.11
36 3 0.04
37 21 0.28
38 8 0.11
ACGTcount: A:0.53, C:0.04, G:0.25, T:0.18
Consensus pattern (34 bp):
AGAGTAAAAGATAATCAGTAAAGAAAAATGGTAA
Found at i:5646 original size:21 final size:21
Alignment explanation
Indices: 5586--5652 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
5576 CAGCAAAGAA
* *
5586 TAAAATGGTAACTAGTAATCAG
1 TAAAATAGTAA-TGGTAATCAG
* * *
5608 TACAA-AGTAAAGAATAATCAG
1 TAAAATAGTAATG-GTAATCAG
5629 TAAAATAGTAATGGTAATCAG
1 TAAAATAGTAATGGTAATCAG
5650 TAA
1 TAA
5653 TTCAGTAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 25 0.71
22 10 0.29
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.25
Consensus pattern (21 bp):
TAAAATAGTAATGGTAATCAG
Found at i:6569 original size:26 final size:26
Alignment explanation
Indices: 6540--6594 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
6530 TTCTTTCAAA
*
6540 GAAGATTCAATTATTGGAGAATTACT
1 GAAGACTCAATTATTGGAGAATTACT
* * *
6566 GAAGACTCAGTTATTGGGGAATTATT
1 GAAGACTCAATTATTGGAGAATTACT
6592 GAA
1 GAA
6595 AGAAGATCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (26 bp):
GAAGACTCAATTATTGGAGAATTACT
Found at i:6824 original size:51 final size:50
Alignment explanation
Indices: 6769--6864 Score: 138
Period size: 51 Copynumber: 1.9 Consensus size: 50
6759 AGTCAAATCA
*
6769 TCATCAATTCGAGATCAAGTCATCAAGACCCTCGAATCAAATCAAACTCCC
1 TCATCAATTCAAGATCAAGTCAT-AAGACCCTCGAATCAAATCAAACTCCC
** * *
6820 TCATCAATTCAAGATCAAGTCATTTGACCCTTGAATCGAATCAAA
1 TCATCAATTCAAGATCAAGTCATAAGACCCTCGAATCAAATCAAA
6865 TCAAATCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 18 0.45
51 22 0.55
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (50 bp):
TCATCAATTCAAGATCAAGTCATAAGACCCTCGAATCAAATCAAACTCCC
Found at i:8706 original size:72 final size:73
Alignment explanation
Indices: 8576--8738 Score: 190
Period size: 72 Copynumber: 2.2 Consensus size: 73
8566 TGCACACAAT
*
8576 AAAAAAGAAAAGAAAAAAAAAAGCTCACTAAGTTGAAAATCCTGTAAAGGAAAGCTTAGGAAAAA
1 AAAAAAGAAAAGAAAAAAAAAAGCTCACTAAGTTGAAAATCCTGCAAAGGAAAGCTTAGGAAAAA
*
8641 GTCAGAGC
66 CTCAGAGC
* * * *
8649 AAAAAA-AAAA-AAAAAAAAGAGGCTCGCTAAGTTGAAAATCCTGCAAAGG-ACGACTTAGGCAA
1 AAAAAAGAAAAGAAAAAAAA-AAGCTCACTAAGTTGAAAATCCTGCAAAGGAAAG-CTTAGGAAA
*
8711 AACTTAGAGC
64 AACTCAGAGC
*
8721 ACAATAATGAAAA-AAAAA
1 A-AA-AAAGAAAAGAAAAA
8739 TGAACTACAT
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
71 10 0.13
72 48 0.62
73 8 0.10
74 2 0.03
75 9 0.12
ACGTcount: A:0.56, C:0.12, G:0.18, T:0.13
Consensus pattern (73 bp):
AAAAAAGAAAAGAAAAAAAAAAGCTCACTAAGTTGAAAATCCTGCAAAGGAAAGCTTAGGAAAAA
CTCAGAGC
Found at i:9608 original size:26 final size:26
Alignment explanation
Indices: 9579--9633 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
9569 TTCTTTCAAA
*
9579 GAAGATTCAATTATTGGAGAATTACT
1 GAAGACTCAATTATTGGAGAATTACT
* * *
9605 GAAGACTCAGTTATTGGGGAATTATT
1 GAAGACTCAATTATTGGAGAATTACT
9631 GAA
1 GAA
9634 AGAAGATCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (26 bp):
GAAGACTCAATTATTGGAGAATTACT
Found at i:9863 original size:51 final size:50
Alignment explanation
Indices: 9808--9903 Score: 138
Period size: 51 Copynumber: 1.9 Consensus size: 50
9798 AGTCAAATCA
*
9808 TCATCAATTCGAGATCAAGTCATCAAGACCCTCGAATCAAATCAAACTCCC
1 TCATCAATTCAAGATCAAGTCAT-AAGACCCTCGAATCAAATCAAACTCCC
** * *
9859 TCATCAATTCAAGATCAAGTCATTTGACCCTTGAATTAAATCAAA
1 TCATCAATTCAAGATCAAGTCATAAGACCCTCGAATCAAATCAAA
9904 TCAAACTCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 18 0.45
51 22 0.55
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (50 bp):
TCATCAATTCAAGATCAAGTCATAAGACCCTCGAATCAAATCAAACTCCC
Found at i:10539 original size:36 final size:35
Alignment explanation
Indices: 10499--10566 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 35
10489 TTATTTATTT
10499 ATATATAATAAAAACATATATAATATAATATATAAA
1 ATATATAATAAAAACATATATAATATAA-ATATAAA
** * * *
10535 ATATATTTTAAATATATATATTATATAAATAT
1 ATATATAATAAAAACATATATAATATAAATAT
10567 CTATTCGGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 4 0.15
36 23 0.85
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (35 bp):
ATATATAATAAAAACATATATAATATAAATATAAA
Found at i:10571 original size:15 final size:15
Alignment explanation
Indices: 10521--10571 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
10511 AACATATATA
*
10521 ATATAATATATAAA-
1 ATATATTATATAAAT
*
10535 ATATATTTTA-AATAT
1 ATATATTATATAA-AT
10550 ATATATTATATAAAT
1 ATATATTATATAAAT
*
10565 ATCTATT
1 ATATATT
10572 CGGTTTCTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.07
14 9 0.30
15 17 0.57
16 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATTATATAAAT
Found at i:11149 original size:64 final size:64
Alignment explanation
Indices: 11048--11174 Score: 191
Period size: 64 Copynumber: 2.0 Consensus size: 64
11038 CGTCAGACCC
* * *
11048 TTATTTGAGCAATTTCGATAATGTTAGGCCCTTATTTGGTCAAATTAAAAGATCAGCCCCTTAA
1 TTATTTGAGCAATTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGACCCTTAA
* ** *
11112 TTATTTGAGCATTTTCGATAACGTTAGGCTTTTATTTGGCCAAATTAAAAGATCGGACCCTTA
1 TTATTTGAGCAATTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGACCCTTA
11175 TTTGAACATT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (64 bp):
TTATTTGAGCAATTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGACCCTTAA
Found at i:11866 original size:2 final size:2
Alignment explanation
Indices: 11861--11886 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11851 AAAATACTAA
11861 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11887 TAATTTAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.