Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014278.1 Corchorus capsularis cultivar CVL-1 contig14299, 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: 24126
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:3744 original size:9 final size:9
Alignment explanation
Indices: 3730--3754 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3720 AGGGATAGGC
3730 GAGGAAGGA
1 GAGGAAGGA
3739 GAGGAAGGA
1 GAGGAAGGA
3748 GAGGAAG
1 GAGGAAG
3755 TGGGGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (9 bp):
GAGGAAGGA
Found at i:4676 original size:20 final size:21
Alignment explanation
Indices: 4627--4683 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
4617 AAGAGAAAAA
*
4627 GCAATCAGTAAAGAGTAAGGTG
1 GCAATCAGTAAAAAGTAA-GTG
*
4649 GTAATCAGTAAAAAGTAA-TG
1 GCAATCAGTAAAAAGTAAGTG
4669 GCAATCAGTAAAAAG
1 GCAATCAGTAAAAAG
4684 AGAAAAGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 16 0.50
22 16 0.50
ACGTcount: A:0.47, C:0.09, G:0.25, T:0.19
Consensus pattern (21 bp):
GCAATCAGTAAAAAGTAAGTG
Found at i:4738 original size:21 final size:20
Alignment explanation
Indices: 4714--4790 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 20
4704 TTCAGTAAAA
4714 TCAGTAAGAGTGAAATAGTAG
1 TCAGTAAGAGT-AAATAGTAG
*
4735 TCAGTAAGAGTAAA-AGGTAA
1 TCAGTAAGAGTAAATA-GTAG
*
4755 TCATTAAGAGTAAGATAGTAG
1 TCAGTAAGAGTAA-ATAGTAG
4776 TCAGTAAGAAGTAAA
1 TCAGTAAG-AGTAAA
4791 GGTAATCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.02
20 18 0.38
21 23 0.48
22 6 0.12
ACGTcount: A:0.47, C:0.05, G:0.25, T:0.23
Consensus pattern (20 bp):
TCAGTAAGAGTAAATAGTAG
Found at i:4764 original size:20 final size:20
Alignment explanation
Indices: 4712--4863 Score: 78
Period size: 20 Copynumber: 7.2 Consensus size: 20
4702 ATTTCAGTAA
*
4712 AATCAGTAAGAGTGAAATA-GT
1 AATCATTAAGAGT-AAA-AGGT
* *
4733 AGTCAGTAAGAGTAAAAGGT
1 AATCATTAAGAGTAAAAGGT
4753 AATCATTAAGAGTAAGATA-GT
1 AATCATTAAGAGTAA-A-AGGT
* *
4774 AGTCAGTAAGAAGT-AAAGGT
1 AATCATTAAG-AGTAAAAGGT
*
4794 AATCATTAAAAGAATAAAATGGT
1 AATCATT--AAGAGTAAAA-GGT
* *
4817 AATCAGTAAAGAGTAATA-GT
1 AATCA-TTAAGAGTAAAAGGT
* * *
4837 AAACAGTAAAAAGTAAAAAGGT
1 AATCA-TTAAGAGT-AAAAGGT
4859 AATCA
1 AATCA
4864 GTAAAAAGTA
Statistics
Matches: 104, Mismatches: 15, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
19 2 0.02
20 40 0.38
21 29 0.28
22 24 0.23
23 8 0.08
24 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.21, T:0.22
Consensus pattern (20 bp):
AATCATTAAGAGTAAAAGGT
Found at i:4799 original size:41 final size:41
Alignment explanation
Indices: 4712--4802 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
4702 ATTTCAGTAA
*
4712 AATCAGTAAGAGTGAAATAGTAGTCAGTAAGAGTAAAAGGT
1 AATCATTAAGAGTGAAATAGTAGTCAGTAAGAGTAAAAGGT
4753 AATCATTAAGAGT-AAGATAGTAGTCAGTAAGAAGT-AAAGGT
1 AATCATTAAGAGTGAA-ATAGTAGTCAGTAAG-AGTAAAAGGT
4794 AATCATTAA
1 AATCATTAA
4803 AAGAATAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
40 2 0.04
41 42 0.89
42 3 0.06
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.24
Consensus pattern (41 bp):
AATCATTAAGAGTGAAATAGTAGTCAGTAAGAGTAAAAGGT
Found at i:4831 original size:7 final size:7
Alignment explanation
Indices: 4821--4878 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
4811 AATGGTAATC
*
4821 AGTAAAG
1 AGTAAAA
*
4828 AGT-AAT
1 AGTAAAA
*
4834 AGTAAAC
1 AGTAAAA
4841 AGTAAAA
1 AGTAAAA
4848 AGTAAAA
1 AGTAAAA
**
4855 AGGTAATC
1 A-GTAAAA
4863 AGTAAAA
1 AGTAAAA
4870 AGTAAAA
1 AGTAAAA
4877 AG
1 AG
4879 GTATCTGAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
6 5 0.12
7 32 0.76
8 5 0.12
ACGTcount: A:0.60, C:0.03, G:0.19, T:0.17
Consensus pattern (7 bp):
AGTAAAA
Found at i:4870 original size:22 final size:22
Alignment explanation
Indices: 4746--5215 Score: 200
Period size: 22 Copynumber: 21.8 Consensus size: 22
4736 CAGTAAGAGT
* *
4746 AAAAGGTAATCA-TTAAGAGTA
1 AAAAGGTAATCAGTAAAAAGTA
* * *
4767 AGATA-GTAGTCAGTAAGAAGT-
1 A-AAAGGTAATCAGTAAAAAGTA
* *
4788 -AAAGGTAATCATTAAAAGAATA
1 AAAAGGTAATCAGTAAAA-AGTA
* *
4810 AAATGGTAATCAGTAAAGAGT-
1 AAAAGGTAATCAGTAAAAAGTA
* *
4831 AATA-GTAAACAGTAAAAAGTA
1 AAAAGGTAATCAGTAAAAAGTA
4852 AAAAGGTAATCAGTAAAAAGTA
1 AAAAGGTAATCAGTAAAAAGTA
* ** *
4874 AAAAGGT-ATCTG-AAAGGGCA
1 AAAAGGTAATCAGTAAAAAGTA
* *
4894 AAATGGTAATTAG-AAAAGAGTA
1 AAAAGGTAATCAGTAAAA-AGTA
* * *
4916 AAGA-GTAATCAGTGGAAGAGTA
1 AAAAGGTAATCAGT-AAAAAGTA
** *
4938 ATCA-GTAA--AGACAAAAATGGTAA
1 AAAAGGTAATCAG-TAAAAA--GT-A
*
4961 AGAAAGAGTAAT-AGT-AAGAGTA
1 A-AAAG-GTAATCAGTAAAAAGTA
*
4983 AAAAGGTAAAAT-GGTAAAAAGT-
1 AAAAGGT--AATCAGTAAAAAGTA
* **
5005 AAAAGGTAATCATTAAAGGGTA
1 AAAAGGTAATCAGTAAAAAGTA
* *
5027 AAATGGTAATTAGTAAAAAGTA
1 AAAAGGTAATCAGTAAAAAGTA
* * * *
5049 AAATGGTAATTAGTGAAAA-TT
1 AAAAGGTAATCAGTAAAAAGTA
* *
5070 AAAAGAGTAGTCAGTAAAGAGT-
1 AAAAG-GTAATCAGTAAAAAGTA
* * *
5092 AATA-GTGATCAGTAAGAAGT-
1 AAAAGGTAATCAGTAAAAAGTA
*
5112 -AATGGTAATCAGTAAAAAGT-
1 AAAAGGTAATCAGTAAAAAGTA
* *
5132 ACAAGGATAATCAGTAAAAGGTA
1 AAAAGG-TAATCAGTAAAAAGTA
*
5155 AAATA-GTAATTAG-AAAAGAGTA
1 AAA-AGGTAATCAGTAAAA-AGTA
*
5177 AAATGGTAATCAGTAAAAAGT-
1 AAAAGGTAATCAGTAAAAAGTA
*
5198 AAATGAGTAATCAGTAAA
1 AAAAG-GTAATCAGTAAA
5216 GAAAAAATGG
Statistics
Matches: 334, Mismatches: 79, Indels: 71
0.69 0.16 0.15
Matches are distributed among these distances:
19 3 0.01
20 71 0.21
21 58 0.17
22 158 0.47
23 33 0.10
24 2 0.01
25 3 0.01
26 4 0.01
27 2 0.01
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.22
Consensus pattern (22 bp):
AAAAGGTAATCAGTAAAAAGTA
Found at i:5073 original size:44 final size:43
Alignment explanation
Indices: 4712--5243 Score: 222
Period size: 42 Copynumber: 12.9 Consensus size: 43
4702 ATTTCAGTAA
* * * * *
4712 AATCAGTAAGAGTGAAATAGTAGTCAGT-AAGAGTAAAA-GGT
1 AATCAGTAAAAGTAAAATGGTAATCAGTAAAAAGTAAAATGGT
* * * * * *
4753 AATCATTAAGAGTAAGATAGTAGTCAGTAAGAAGT-AAA-GGT
1 AATCAGTAAAAGTAAAATGGTAATCAGTAAAAAGTAAAATGGT
* * *
4794 AATCATTAAAAGAATAAAATGGTAATCAGTAAAGAGT--AATAGT
1 AATCAGTAAAAG--TAAAATGGTAATCAGTAAAAAGTAAAATGGT
* * *
4837 AAACAGTAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAAGGT
1 AATCAGT-AAAAGTAAAATGGTAATCAGTAAAAAGTAAAATGGT
* * * *
4881 -ATCTG-AAAGGGCAAAATGGTAATTAG-AAAAGAGT-AAA-GAGT
1 AATCAGTAAA-AGTAAAATGGTAATCAGTAAAA-AGTAAAATG-GT
* * * **
4922 AATCAGT----GGAAGA--GTAATCAGTAAAGACAAAAATGGT
1 AATCAGTAAAAGTAAAATGGTAATCAGTAAAAAGTAAAATGGT
* *
4959 AA--AG-AAAGAGT--AATAGTAA-GAGTAAAAAGGTAAAATGG-
1 AATCAGTAAA-AGTAAAATGGTAATCAGTAAAAA-GTAAAATGGT
* **
4997 --T-A--AAAAGTAAAA-GGTAATCATTAAAGGGTAAAATGGT
1 AATCAGTAAAAGTAAAATGGTAATCAGTAAAAAGTAAAATGGT
* * * *
5034 AATTAGTAAAAAGTAAAATGGTAATTAGTGAAAATTAAAA-GAGT
1 AATCAGT-AAAAGTAAAATGGTAATCAGTAAAAAGTAAAATG-GT
* * * *
5078 AGTCAGTAAAGAGT--AATAGTGATCAGTAAGAAGT--AATGGT
1 AATCAGTAAA-AGTAAAATGGTAATCAGTAAAAAGTAAAATGGT
* * *
5118 AATCAGTAAAAAGTACAA-GGATAATCAGTAAAAGGTAAAATAGT
1 AATCAGT-AAAAGTAAAATGG-TAATCAGTAAAAAGTAAAATGGT
* *
5162 AATTAGAAAAGAGTAAAATGGTAATCAGTAAAAAGT-AAATGAGT
1 AATCAGTAAA-AGTAAAATGGTAATCAGTAAAAAGTAAAATG-GT
* ** *
5206 AATCAGT-AAAGAAAAAATGGTAAAGAGTAAAGAGTAAA
1 AATCAGTAAAAG-TAAAATGGTAATCAGTAAAAAGTAAA
5244 GAGTAAAGAG
Statistics
Matches: 369, Mismatches: 73, Indels: 95
0.69 0.14 0.18
Matches are distributed among these distances:
35 5 0.01
36 24 0.07
37 19 0.05
38 12 0.03
39 13 0.04
40 15 0.04
41 59 0.16
42 77 0.21
43 70 0.19
44 73 0.20
45 2 0.01
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.21
Consensus pattern (43 bp):
AATCAGTAAAAGTAAAATGGTAATCAGTAAAAAGTAAAATGGT
Found at i:5105 original size:20 final size:20
Alignment explanation
Indices: 5075--5271 Score: 99
Period size: 22 Copynumber: 9.8 Consensus size: 20
5065 AAATTAAAAG
*
5075 AGTAGTCAGTAAAGAGTAAT
1 AGTAATCAGTAAAGAGTAAT
*
5095 AGTGATCAGT-AAGAAGTAAT
1 AGTAATCAGTAAAG-AGTAAT
* *
5115 GGTAATCAGTAAAAAGTACA-
1 AGTAATCAGTAAAGAGTA-AT
5135 AGGATAATCAGTAAA-AGGTAAAAT
1 A-G-TAATCAGTAAAGA-GT--AAT
* *
5159 AGTAATTAGAAAAGAGTAAAAT
1 AGTAATCAGTAAAGAGT--AAT
* *
5181 GGTAATCAGTAAAAAGTAAAT
1 AGTAATCAGTAAAGAGT-AAT
5202 GAGTAATCAGTAAAGA--AA-
1 -AGTAATCAGTAAAGAGTAAT
* *
5220 A--AAT-GGTAAAGAGTAAAG
1 AGTAATCAGTAAAGAGT-AAT
** *
5238 AGTAAAGAGTAAAGAG-AAG
1 AGTAATCAGTAAAGAGTAAT
5257 AGTAATCAGTAAAGA
1 AGTAATCAGTAAAGA
5272 AAAAAATGGT
Statistics
Matches: 140, Mismatches: 19, Indels: 37
0.71 0.10 0.19
Matches are distributed among these distances:
14 7 0.05
15 3 0.02
17 3 0.02
18 1 0.01
19 21 0.15
20 28 0.20
21 17 0.12
22 55 0.39
23 3 0.02
24 2 0.01
ACGTcount: A:0.53, C:0.04, G:0.23, T:0.20
Consensus pattern (20 bp):
AGTAATCAGTAAAGAGTAAT
Found at i:5223 original size:22 final size:21
Alignment explanation
Indices: 5026--5238 Score: 82
Period size: 22 Copynumber: 10.0 Consensus size: 21
5016 ATTAAAGGGT
*
5026 AAAATGGTAATTAGTAAA-AA
1 AAAATGGTAATCAGTAAAGAA
* *
5046 GTAAAATGGTAATTAGTGAAA-ATT
1 --AAAATGGTAATCAGT-AAAGA-A
*
5070 AAAA-GAGTAGTCAGTAAAG-A
1 AAAATG-GTAATCAGTAAAGAA
** * *
5090 GTAATAGTGATCAGT-AAGAA
1 AAAATGGTAATCAGTAAAGAA
**
5110 GTAATGGTAATCAGTAAA-AA
1 AAAATGGTAATCAGTAAAGAA
* **
5130 GTACAA-GGATAATCAGTAAAAGGT
1 --AAAATGG-TAATCAGT-AAAGAA
* * * *
5154 AAAATAGTAATTAGAAAAGAGT
1 AAAATGGTAATCAGTAAAGA-A
5176 AAAATGGTAATCAGTAAA-AA
1 AAAATGGTAATCAGTAAAGAA
*
5196 GTAAATGAGTAATCAGTAAAGAA
1 -AAAATG-GTAATCAGTAAAGAA
**
5219 AAAATGGTAAAGAGTAAAGA
1 AAAATGGTAATCAGTAAAGA
5239 GTAAAGAGTA
Statistics
Matches: 146, Mismatches: 28, Indels: 35
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.02
20 25 0.17
21 30 0.21
22 78 0.53
23 10 0.07
ACGTcount: A:0.53, C:0.03, G:0.21, T:0.23
Consensus pattern (21 bp):
AAAATGGTAATCAGTAAAGAA
Found at i:5237 original size:7 final size:7
Alignment explanation
Indices: 5188--5493 Score: 139
Period size: 7 Copynumber: 45.1 Consensus size: 7
5178 AATGGTAATC
*
5188 AGTAAAA
1 AGTAAAG
5195 AGTAAATG
1 AGTAAA-G
**
5203 AGTAATC
1 AGTAAAG
5210 AGTAAAG
1 AGTAAAG
**
5217 AAAAAATG
1 AGTAAA-G
5225 -GTAAAG
1 AGTAAAG
5231 AGTAAAG
1 AGTAAAG
5238 AGTAAAG
1 AGTAAAG
5245 AGTAAAG
1 AGTAAAG
5252 AG--AAG
1 AGTAAAG
**
5257 AGTAATC
1 AGTAAAG
5264 AGTAAAG
1 AGTAAAG
* *
5271 A-AAAAA
1 AGTAAAG
5277 ATGGTAAAG
1 A--GTAAAG
*
5286 GGTAAAG
1 AGTAAAG
5293 AGT--AG
1 AGTAAAG
5298 AGTAAAG
1 AGTAAAG
**
5305 AGTAATC
1 AGTAAAG
5312 AGTAAAG
1 AGTAAAG
*
5319 A-AAAATG
1 AGTAAA-G
5326 -GTAAAG
1 AGTAAAG
5332 AGTAAAG
1 AGTAAAG
5339 AGT-AA-
1 AGTAAAG
5344 AGTAAAG
1 AGTAAAG
**
5351 AGTAATC
1 AGTAAAG
5358 A--ACAA-
1 AGTA-AAG
5363 AGTAAA-
1 AGTAAAG
*
5369 ATGGTAAAA
1 A--GTAAAG
5378 AGTAAAAG
1 AGT-AAAG
**
5386 AGTAATC
1 AGTAAAG
5393 AGTAAAG
1 AGTAAAG
*
5400 A-AAAAG
1 AGTAAAG
*
5406 GGTAAAG
1 AGTAAAG
5413 AGTAAAG
1 AGTAAAG
5420 AGTAAAG
1 AGTAAAG
5427 AG--AAG
1 AGTAAAG
**
5432 AGTAATC
1 AGTAAAG
5439 AGTAAAG
1 AGTAAAG
**
5446 AAAAAATG
1 AGTAAA-G
5454 -GTAAAG
1 AGTAAAG
*
5460 GGTAAAG
1 AGTAAAG
5467 AGT--AG
1 AGTAAAG
5472 AGTAAAG
1 AGTAAAG
**
5479 AGTAATC
1 AGTAAAG
5486 AGTAAAG
1 AGTAAAG
5493 A
1 A
5494 AAAAATGGTA
Statistics
Matches: 220, Mismatches: 50, Indels: 58
0.67 0.15 0.18
Matches are distributed among these distances:
5 25 0.11
6 22 0.10
7 151 0.69
8 18 0.08
9 4 0.02
ACGTcount: A:0.56, C:0.03, G:0.25, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:5340 original size:46 final size:47
Alignment explanation
Indices: 5232--5509 Score: 266
Period size: 46 Copynumber: 6.2 Consensus size: 47
5222 ATGGTAAAGA
*
5232 GTAAAGAGTAAAGAGTAAAG-AGAAGAGTAATCAGTAAAGAAAAAAATG
1 GTAAAGAGTAAAGAGTAGAGTA-AAGAGTAATCAGTAAAG-AAAAAATG
*
5280 GTAAAGGGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAG-AAAAATG
1 GTAAAGAGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
* ** *
5326 GTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAG-TAAAATG
1 GTAAAGAGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
* ** * ***
5372 GTAAAAAGT-AA-A--AGAGTAATCAGTAA--AGAAAAAGGGTAAA-G
1 GTAAAGAGTAAAGAGTAGAGTAAAGAGTAATCAG-TAAAGAAAAAATG
*
5413 AGTAAAGAGTAAAGAGAAGAGT----A---ATCAGTAAAGAAAAAATG
1 -GTAAAGAGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
*
5454 GTAAAGGGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
1 GTAAAGAGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
5501 GTAAAGAGT
1 GTAAAGAGT
5510 GAAGGGAAGT
Statistics
Matches: 189, Mismatches: 23, Indels: 37
0.76 0.09 0.15
Matches are distributed among these distances:
39 1 0.01
40 27 0.14
41 8 0.04
42 23 0.12
43 2 0.01
44 3 0.02
45 2 0.01
46 61 0.32
47 26 0.14
48 35 0.19
49 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.16
Consensus pattern (47 bp):
GTAAAGAGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
Found at i:5398 original size:81 final size:79
Alignment explanation
Indices: 5296--5582 Score: 296
Period size: 81 Copynumber: 3.5 Consensus size: 79
5286 GGTAAAGAGT
**
5296 AGAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAAC
1 AGAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAGT
5361 AAAGTAAAATGGTAA
66 AAAG-AAAATGGTAA
* *
5376 AAAGTAAAAGAGTAATCAGTAAAGAAAAAGGGTAAAGAGTAAAGAGTAAAG-AGAAGAGTAATCA
1 AGAGT-AAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA-AAGAGTAATCA
5440 GTAAAGAAAAAATGGTAA
64 GTAAAG--AAAATGGTAA
* * ** * ** * *
5458 AGGGTAAAGAGT-A-GAGTAAAGAGTAATCAGTAAAGAAAAAATG-GTAAAGAGTGAAG-GGAAG
1 AGAGTAAAGAGTAATCAGTAAAGAAAAAT-GGTAAAGAGTAAA-GAGT-AA-AGTAAAGAGTAA-
*
5519 TCAGTAAAGAAGAATGGTGA
61 TCAGTAAAGAA-AATGGTAA
5539 AGAGTAAAGAGTAATCCAGTAAAGAAAAAATGGTAAAGAGTAAA
1 AGAGTAAAGAGTAAT-CAGTAAAG-AAAAATGGTAAAGAGTAAA
5583 AATATGAATC
Statistics
Matches: 169, Mismatches: 24, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
79 10 0.06
80 20 0.12
81 90 0.53
82 28 0.17
84 17 0.10
85 4 0.02
ACGTcount: A:0.55, C:0.03, G:0.26, T:0.16
Consensus pattern (79 bp):
AGAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAGT
AAAGAAAATGGTAA
Found at i:5523 original size:128 final size:127
Alignment explanation
Indices: 5254--5552 Score: 397
Period size: 128 Copynumber: 2.3 Consensus size: 127
5244 GAGTAAAGAG
* * *
5254 AAGAGTAATCAGTAAAGAAAAAAATGGTAAAGGGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAG
1 AAGAGGAATCAGTAAAG--AAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAGTAAAG
*
5319 AAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGTAAAATGGTAAAAAGTAA
64 AAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGAAAAATGGTAAAAAGTAA
* *
5383 AAGAGTAATCAGTAAAGAAAAAGGGTAAAGAGTAAAGAGTAAAG-AGAAGAGTAATCAGTAAAGA
1 AAGAGGAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA-AAGAGTAATCAGTAAAG-
* * ** * *
5447 AAAAATGGTAAAGGGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGT-G
64 AAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAG-AAAAATGGTAAAAAGTAA
* *
5511 AAG-GGAAGTCAGTAAAGAAGAATGGTGAAGAGTAAAGAGTAA
1 AAGAGGAA-TCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAA
5553 TCCAGTAAAG
Statistics
Matches: 152, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
126 1 0.01
127 44 0.29
128 76 0.50
129 31 0.20
ACGTcount: A:0.55, C:0.03, G:0.26, T:0.16
Consensus pattern (127 bp):
AAGAGGAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAGTAAAGAA
AAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGAAAAATGGTAAAAAGTAA
Found at i:22847 original size:15 final size:15
Alignment explanation
Indices: 22822--22860 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
22812 TACTTTTATC
**
22822 AATTGATTTTCTTTTT
1 AATT-ATTTTCTAGTT
22838 AATTATTTTCTAGTT
1 AATTATTTTCTAGTT
22853 AATTATTT
1 AATTATTT
22861 GTTTGTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (15 bp):
AATTATTTTCTAGTT
Done.