Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1040
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: 39901
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:198 original size:52 final size:51
Alignment explanation
Indices: 138--326 Score: 267
Period size: 51 Copynumber: 3.7 Consensus size: 51
128 ATTTAACTAG
* *
138 ATGTATCGATACATTGAAGAATGTATCGATACATTTAGG-TCAAAAACCTAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTT-GGATC-AAAACCCAGA
* *
190 ATATATCGATACAATGAAGAATGTATCGATACATTTGGATCAAAACCCAAA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTGGATCAAAACCCAGA
* *
241 ATGTATCAATATAATGAAGAATGTATCGATACATTTGGATCAAAACCCAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTGGATCAAAACCCAGA
*
292 ATGTATC-AGTACAGTGAA-AATGTATCGATACATTT
1 ATGTATCGA-TACAATGAAGAATGTATCGATACATTT
327 TCTTTCCAAA
Statistics
Matches: 125, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
50 18 0.14
51 71 0.57
52 36 0.29
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACAATGAAGAATGTATCGATACATTTGGATCAAAACCCAGA
Found at i:345 original size:103 final size:103
Alignment explanation
Indices: 138--326 Score: 269
Period size: 103 Copynumber: 1.9 Consensus size: 103
128 ATTTAACTAG
* * *
138 ATGTATCGATACATTGAAGAATGTATCGATACATTTAGGTCAAAAACCTAGAATATATCGATACA
1 ATGTATCAATACAATGAAGAATGTATCGATACATTTAGGTCAAAAACCCAGAATATATCGATACA
*
203 ATGAAGAATGTATCGATACATTTGGATCAAAACCCAAA
66 ATGAAGAATGTATCGATACATTTCGATCAAAACCCAAA
* *
241 ATGTATCAATATAATGAAGAATGTATCGATACATTT-GGATC-AAAACCCAGAATGTATC-AGTA
1 ATGTATCAATACAATGAAGAATGTATCGATACATTTAGG-TCAAAAACCCAGAATATATCGA-TA
*
303 CAGTGAA-AATGTATCGATACATTT
64 CAATGAAGAATGTATCGATACATTT
327 TCTTTCCAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
101 18 0.23
102 25 0.32
103 35 0.45
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (103 bp):
ATGTATCAATACAATGAAGAATGTATCGATACATTTAGGTCAAAAACCCAGAATATATCGATACA
ATGAAGAATGTATCGATACATTTCGATCAAAACCCAAA
Found at i:406 original size:20 final size:21
Alignment explanation
Indices: 383--436 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
373 CATTTCAAAC
383 ATGTATTGATACATTCACTT-
1 ATGTATTGATACATTCACTTG
*
403 ATGTATCGATACATTCACTTG
1 ATGTATTGATACATTCACTTG
*
424 TTGTATTGATACA
1 ATGTATTGATACA
437 AATTATAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (21 bp):
ATGTATTGATACATTCACTTG
Found at i:1231 original size:104 final size:104
Alignment explanation
Indices: 1051--1438 Score: 322
Period size: 104 Copynumber: 3.7 Consensus size: 104
1041 AAATGATAAG
* * * * * * * *
1051 GATGAGAAAAGTGCCAATGTGCTGATTCAAGGCTAGCGATATTGGGCTTCAAA-GTGATAAGGGT
1 GATGACAAAAGTGCCAATATGCTGATTCAAGGCCAACAACATTGGGCTTAAAATG-GATAAGAGT
*
1115 GCCAATATGCTGATTCCAAGCTAGTGATATCAAACTTAAA
65 GCCAATATGCTGATTCCAAGCTAGTGATATCAGACTTAAA
* *
1155 GATGACAAAAGTGCCAATATGCTGATTCAAGGCCAGCAACATTGGGATTAAAGATGGA-AAGAGT
1 GATGACAAAAGTGCCAATATGCTGATTCAAGGCCAACAACATTGGGCTTAAA-ATGGATAAGAGT
* * **
1219 GCTAATATGCTGATT-CAAGGCTAGTGACATTGGACTTAAAAAGA
65 GCCAATATGCTGATTCCAA-GCTAGTGATATCAGACTT---AA-A
** * * * * * *
1263 GATGGTTTGAGACGTG-CAATTTGTTGATTCAAGG-CAACGACATTGGGCTTAAAA-GTGATAAC
1 GAT-G--ACAAAAGTGCCAATATGCTGATTCAAGGCCAACAACATTGGGCTTAAAATG-GATAAG
* *
1325 AATGCCAATATGCTGATTCAAAGCTAGTGATATCAGACTTAAA
62 AGTGCCAATATGCTGATTCCAAGCTAGTGATATCAGACTTAAA
** * * ** * *
1368 GATGACAATGGTGTCAATATGTTGATTCAAGAACAACAACATTGGGTTTAAAAT-GAAAAGAGTG
1 GATGACAAAAGTGCCAATATGCTGATTCAAGGCCAACAACATTGGGCTTAAAATGGATAAGAGTG
*
1432 CTAATAT
66 CCAATAT
1439 ACTATTTAGA
Statistics
Matches: 226, Mismatches: 42, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
102 4 0.02
103 32 0.14
104 97 0.43
105 7 0.03
106 3 0.01
107 3 0.01
108 7 0.03
109 50 0.22
110 18 0.08
111 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (104 bp):
GATGACAAAAGTGCCAATATGCTGATTCAAGGCCAACAACATTGGGCTTAAAATGGATAAGAGTG
CCAATATGCTGATTCCAAGCTAGTGATATCAGACTTAAA
Found at i:1258 original size:52 final size:53
Alignment explanation
Indices: 1060--1471 Score: 208
Period size: 52 Copynumber: 7.8 Consensus size: 53
1050 GGATGAGAAA
* * * *
1060 AGTGCCAATGTGCTGATTCAAGGCTAGCGATATTGGGCTTCAAAG-T-GATAAG
1 AGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTT-AAAGATGGACAAG
* * * *** *
1112 GGTGCCAATATGCTGATTCCAA-GCTAGTGATATCAAACTTAAAGAT-GACAAA
1 AGTGCCAATATGCTGATT-CAAGGCTAGCGACATTGGACTTAAAGATGGACAAG
* *
1164 AGTGCCAATATGCTGATTCAAGGCCAGCAACATTGGGA-TTAAAGATGGA-AAG
1 AGTGCCAATATGCTGATTCAAGGCTAGCGACATT-GGACTTAAAGATGGACAAG
* * ***
1216 AGTGCTAATATGCTGATTCAAGGCTAGTGACATTGGACTTAAAAAGAGATGGTTTGAG
1 AGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTT---AA-AGATGG-ACAAG
* * * * * *
1274 ACGTG-CAATTTGTTGATTCAAGGC-AACGACATTGGGCTTAAA-A-GTGATAAC
1 A-GTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATG-GACAAG
* * * * **
1325 AATGCCAATATGCTGATTCAAAGCTAGTGATATCAGACTTAAAGAT-GACAATG
1 AGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGGACAA-G
* * * * * ** *
1378 -GTGTCAATATGTTGATTCAAGAAC-AACAACATTGGGTTTAAA-AT-GAAAAG
1 AGTGCCAATATGCTGATTCAAG-GCTAGCGACATTGGACTTAAAGATGGACAAG
* * * *
1428 AGTGCTAATATACT-ATTTAGAGTGCTAGTGACATTGGACTTAAA
1 AGTGCCAATATGCTGATTCA-AG-GCTAGCGACATTGGACTTAAA
1472 AAGAGATGGT
Statistics
Matches: 266, Mismatches: 71, Indels: 46
0.69 0.19 0.12
Matches are distributed among these distances:
50 7 0.03
51 48 0.18
52 158 0.59
53 9 0.03
54 2 0.01
55 2 0.01
56 6 0.02
57 12 0.05
58 19 0.07
59 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (53 bp):
AGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGGACAAG
Found at i:1338 original size:109 final size:106
Alignment explanation
Indices: 1163--1528 Score: 305
Period size: 109 Copynumber: 3.4 Consensus size: 106
1153 AAGATGACAA
* * * * * * * *
1163 AAGTGCCAATATGCTGATTCAAGGCCAGCAACATTGGGATTAAAGATGGAAAGAGTGCTAATATG
1 AAGTG-CAATATGTTGATTCAAGG-CAACGACATTGGGCTTAAA-ATGAAAACAATGCCAATATG
1228 CTGATTCAAGGCTAGTGACATTGGACTTAAAAAGAGATGGTTTG
63 CTGATTCAAGGCTAGTGACATTGGACTTAAAAAGAGATGGTTTG
* *
1272 AGACGTGCAATTTGTTGATTCAAGGCAACGACATTGGGCTTAAAAGTGATAACAATGCCAATATG
1 A-A-GTGCAATATGTTGATTCAAGGCAACGACATTGGGCTTAAAA-TGAAAACAATGCCAATATG
* * ** * *
1337 CTGATTCAAAGCTAGTGATATCAGACTTAAAGATGACAATGG--T-
63 CTGATTCAAGGCTAGTGACATTGGACTTAAA-AAGA-GATGGTTTG
* * * * * * *
1380 --GT-CAATATGTTGATTCAAGAACAACAACATTGGGTTTAAAATGAAAAGAGTGCTAATATACT
1 AAGTGCAATATGTTGATTCAAG-GCAACGACATTGGGCTTAAAATGAAAACAATGCCAATATGCT
*
1442 -ATTTAGAGTGCTAGTGACATTGGACTTAAAAAGAGATGGTTTG
65 GATTCA-AG-GCTAGTGACATTGGACTTAAAAAGAGATGGTTTG
* * *
1485 ACATGTGCTAATGTGTTGATTTAAGGCCAATGACATTGGGCTTA
1 A-A-GTGC-AATATGTTGATTCAAGG-CAACGACATTGGGCTTA
1529 GAAGGAGATG
Statistics
Matches: 201, Mismatches: 38, Indels: 34
0.74 0.14 0.12
Matches are distributed among these distances:
102 8 0.04
103 36 0.18
104 39 0.19
108 1 0.00
109 61 0.30
110 21 0.10
111 35 0.17
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (106 bp):
AAGTGCAATATGTTGATTCAAGGCAACGACATTGGGCTTAAAATGAAAACAATGCCAATATGCTG
ATTCAAGGCTAGTGACATTGGACTTAAAAAGAGATGGTTTG
Found at i:1371 original size:213 final size:214
Alignment explanation
Indices: 1061--1528 Score: 645
Period size: 213 Copynumber: 2.2 Consensus size: 214
1051 GATGAGAAAA
* * * * * ***
1061 GTGCCAATGTGCTGATTCAAGGCTAGCGATATTGGGCTTCAAAGTGATAAGGGTGCCAATATGCT
1 GTGCTAATGTGTTGATTCAAGGC-AACGACATTGGGCTTAAAAGTGATAACAATGCCAATATGCT
* ** *
1126 GATTCCAAGCTAGTGATATCAAACTTAAAGATGACAAAAGTGCCAATATGCTGATTCAAGGCCAG
65 GATTCAAAGCTAGTGATATCAAACTTAAAGATGACAAAAGTGCCAATATGCTGATTCAAGAACAA
* *
1191 CAACATTGGGATTAAAGATGGAAAGAGTGCTAATATGCTGATTCA-AG-GCTAGTGACATTGGAC
130 CAACATTGGGATTAAA-ATGAAAAGAGTGCTAATATACT-ATTCAGAGTGCTAGTGACATTGGAC
*
1254 TTAAAAAGAGATGGTTTGAGAC
193 TTAAAAAGAGATGGTTTGACAC
*
1276 GTGC-AATTTGTTGATTCAAGGCAACGACATTGGGCTTAAAAGTGATAACAATGCCAATATGCTG
1 GTGCTAATGTGTTGATTCAAGGCAACGACATTGGGCTTAAAAGTGATAACAATGCCAATATGCTG
* ** * *
1340 ATTCAAAGCTAGTGATATCAGACTTAAAGATGACAATGGTGTCAATATGTTGATTCAAGAACAAC
66 ATTCAAAGCTAGTGATATCAAACTTAAAGATGACAAAAGTGCCAATATGCTGATTCAAGAACAAC
* *
1405 AACATTGGGTTTAAAATGAAAAGAGTGCTAATATACTATTTAGAGTGCTAGTGACATTGGACTTA
131 AACATTGGGATTAAAATGAAAAGAGTGCTAATATACTATTCAGAGTGCTAGTGACATTGGACTTA
*
1470 AAAAGAGATGGTTTGACAT
196 AAAAGAGATGGTTTGACAC
* *
1489 GTGCTAATGTGTTGATTTAAGGCCAATGACATTGGGCTTA
1 GTGCTAATGTGTTGATTCAAGG-CAACGACATTGGGCTTA
1529 GAAGGAGATG
Statistics
Matches: 223, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
211 4 0.02
212 22 0.10
213 146 0.65
214 31 0.14
215 20 0.09
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (214 bp):
GTGCTAATGTGTTGATTCAAGGCAACGACATTGGGCTTAAAAGTGATAACAATGCCAATATGCTG
ATTCAAAGCTAGTGATATCAAACTTAAAGATGACAAAAGTGCCAATATGCTGATTCAAGAACAAC
AACATTGGGATTAAAATGAAAAGAGTGCTAATATACTATTCAGAGTGCTAGTGACATTGGACTTA
AAAAGAGATGGTTTGACAC
Found at i:1575 original size:32 final size:32
Alignment explanation
Indices: 1537--1728 Score: 191
Period size: 31 Copynumber: 6.1 Consensus size: 32
1527 TAGAAGGAGA
*
1537 TGCCACCGACTTATGTGGGCTTTTAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTAAAAGGGT
1569 TGCCACCGACTTGTGTGGGC-TTTAGAAA-GGT
1 TGCCACCGACTTGTGTGGGCTTTTA-AAAGGGT
* * * *
1600 TGCCATCAACTTGTAT--GCTTTTGAAA-GGT
1 TGCCACCGACTTGTGTGGGCTTTTAAAAGGGT
* *
1629 TGCCACTGACTTGTGTGGGCTTTT-GAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTAAAAGGGT
* ***
1660 TGCGACCGACTTGTGTGGGC-TTTAAAAAAAT
1 TGCCACCGACTTGTGTGGGCTTTTAAAAGGGT
*
1691 GTGCCATCGACTTGTGTGGGCTTTTGAAAAGGGAT
1 -TGCCACCGACTTGTGTGGGCTTTT-AAAAGGG-T
1726 TGC
1 TGC
1729 TCATATGGGG
Statistics
Matches: 129, Mismatches: 21, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
29 20 0.16
30 8 0.06
31 50 0.39
32 40 0.31
33 3 0.02
34 7 0.05
35 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTTAAAAGGGT
Found at i:1672 original size:60 final size:61
Alignment explanation
Indices: 1554--1719 Score: 183
Period size: 60 Copynumber: 2.7 Consensus size: 61
1544 GACTTATGTG
* * *
1554 GGCTTTTAAAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAAGGTTGCCATCAACTTGTAT
1 GGCTTTTAAAA-GGTTGCCACTGACTTGTGTGGGCTTTTGAAAGGTTGCCACCAACTTGTAT
* * * * *
1616 -GCTTTTGAAAGGTTGCCACTGACTTGTGTGGGCTTTTGAAGGGTTGCGACCGACTTGTGT
1 GGCTTTTAAAAGGTTGCCACTGACTTGTGTGGGCTTTTGAAAGGTTGCCACCAACTTGTAT
* **
1676 GGGCTTTAAAAAAATGTGCCA-TCGACTTGTGTGGGCTTTTGAAA
1 -GGCTTTTAAAAGGT-TGCCACT-GACTTGTGTGGGCTTTTGAAA
1720 AGGGATTGCT
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
60 43 0.49
61 9 0.10
62 10 0.11
63 25 0.29
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (61 bp):
GGCTTTTAAAAGGTTGCCACTGACTTGTGTGGGCTTTTGAAAGGTTGCCACCAACTTGTAT
Found at i:3488 original size:20 final size:20
Alignment explanation
Indices: 3471--3508 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3461 TGTGTTTTGT
3471 TTTTTTTG-CTTTTCTTTTTC
1 TTTTTTTGCCTTTT-TTTTTC
3491 TTTTTTTGCCTTTTTTTT
1 TTTTTTTGCCTTTTTTTT
3509 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTTTTGCCTTTTTTTTTC
Found at i:3516 original size:12 final size:12
Alignment explanation
Indices: 3501--3544 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3491 TTTTTTTGCC
3501 TTTTTTTTAAAT
1 TTTTTTTTAAAT
* **
3513 TTTTTTCTACTT
1 TTTTTTTTAAAT
3525 TTTTTTTTAAAAT
1 TTTTTTTT-AAAT
3538 TTTTTTT
1 TTTTTTT
3545 GACTTTTGAC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTTAAAT
Found at i:3529 original size:25 final size:25
Alignment explanation
Indices: 3501--3551 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
3491 TTTTTTTGCC
3501 TTTTTTTT-AAATTTTTTTCT-ACTT
1 TTTTTTTTAAAATTTTTTT-TGACTT
3525 TTTTTTTTAAAATTTTTTTTGACTT
1 TTTTTTTTAAAATTTTTTTTGACTT
3550 TT
1 TT
3552 GACTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTTTTTAAAATTTTTTTTGACTT
Found at i:3551 original size:11 final size:10
Alignment explanation
Indices: 3470--3530 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 10
3460 TTGTGTTTTG
*
3470 TTTTTTTTGC
1 TTTTTTTTAC
*
3480 TTTTCTTTTTC
1 TTTT-TTTTAC
**
3491 TTTTTTTGCC
1 TTTTTTTTAC
*
3501 TTTTTTTTAAA
1 TTTTTTTT-AC
3512 TTTTTTTCTAC
1 TTTTTTT-TAC
3523 TTTTTTTT
1 TTTTTTTT
3531 TTAAAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 16 0.39
11 24 0.59
12 1 0.02
ACGTcount: A:0.07, C:0.11, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTTTTTTAC
Found at i:3560 original size:20 final size:19
Alignment explanation
Indices: 3537--3581 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3527 TTTTTTAAAA
3537 TTTTTTTTGACTTTTGACTT
1 TTTTTTTTGACTTTTGA-TT
* *
3557 TTTTATTTGATTTTTGATT
1 TTTTTTTTGACTTTTGATT
3576 TTTTTT
1 TTTTTT
3582 ACATGGGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.76
Consensus pattern (19 bp):
TTTTTTTTGACTTTTGATT
Found at i:7861 original size:21 final size:21
Alignment explanation
Indices: 7814--7871 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
7804 CATTTTTATC
*
7814 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
7835 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
7856 CAAATGTATCGATACA
1 CAAATGTATCGATACA
7872 AGGTCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:7937 original size:19 final size:18
Alignment explanation
Indices: 7913--7975 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
7903 ATAATTTGTA
7913 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
7932 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
7945 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
7964 TGTATCGATACA
1 TGTATCGATACA
7976 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:7950 original size:13 final size:13
Alignment explanation
Indices: 7932--7956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7922 ACATAAGTGT
7932 TGTATCGATACAA
1 TGTATCGATACAA
7945 TGTATCGATACA
1 TGTATCGATACA
7957 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:7953 original size:32 final size:32
Alignment explanation
Indices: 7912--7983 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
7902 AATAATTTGT
7912 ATGTATCGATACATAAGTGTTGTATCGATACA
1 ATGTATCGATACATAAGTGTTGTATCGATACA
*
7944 ATGTATCGATACATAAGTTTTGTATCGATACA
1 ATGTATCGATACATAAGTGTTGTATCGATACA
7976 ATGTATCG
1 ATGTATCG
7984 CTAGGAAGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
ATGTATCGATACATAAGTGTTGTATCGATACA
Found at i:8051 original size:21 final size:21
Alignment explanation
Indices: 8007--8063 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
7997 GCCAAGGAAA
*
8007 TGTATCGATACAT-TTTTCTG
1 TGTATCGATACATCTATTCTG
*
8027 TGTATCGATACATCTATTCTT
1 TGTATCGATACATCTATTCTG
8048 TGTATCGATACATCTA
1 TGTATCGATACATCTA
8064 GGAAGTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (21 bp):
TGTATCGATACATCTATTCTG
Found at i:10523 original size:28 final size:28
Alignment explanation
Indices: 10491--10561 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
10481 TCACAATCAA
* * **
10491 GGATACTCCAACCTCATTATCTCATTGG
1 GGATACTCCAACCCCATTACCTCAGAGG
* *
10519 GGATACTCCAACCCCGTTACCTCCGAGG
1 GGATACTCCAACCCCATTACCTCAGAGG
10547 GGATACTCCAACCCC
1 GGATACTCCAACCCC
10562 GGCTTTATTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (28 bp):
GGATACTCCAACCCCATTACCTCAGAGG
Found at i:10608 original size:51 final size:51
Alignment explanation
Indices: 10545--10765 Score: 248
Period size: 51 Copynumber: 4.3 Consensus size: 51
10535 TTACCTCCGA
* * * * *
10545 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTC-CATAATC
* *
10596 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTCCATAATC
* * * *
10647 GGGGATACTCCAACCCCGGTTTCATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTCC-ATAATC
* * * *
10699 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAAAATTT-CACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCC-AAAACA-CTAATTTTCCATAATC
*
10751 GAGGATACTCCAACC
1 GGGGATACTCCAACC
10766 TCGTTATTTC
Statistics
Matches: 145, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
51 80 0.55
52 52 0.36
53 7 0.05
54 6 0.04
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.29
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTCCATAATC
Found at i:10731 original size:52 final size:52
Alignment explanation
Indices: 10379--10765 Score: 254
Period size: 52 Copynumber: 7.4 Consensus size: 52
10369 TCAATTGTTC
* * * *
10379 ATAATCGGGGATACACCAACCTCAATTTTATTTTCAAAACACCAATTTTCCT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
* * *
10431 TTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTCCT
* ** * **** * * **
10483 ACAATCAAGGATACTCCAACCTC-ATTATCTCATTGGGGATACTCCAA--CCCCGT
1 ATAATCGGGGATACTCCAACCCCGATT-T-T-ATTTCCAAAACACCAATTTTCC-T
* ** * * ***
10536 -TACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGA-TTT-CT
1 ATA-AT-C--GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
* * *
10589 CATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCC-
1 -ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
* * * *
10641 ACAATCGGGGATACTCCAACCCCGGTTTCATTTTCAAAACACCAATTTTCCT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
* *
10693 TTAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAAAATTT-C-
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACC-AATTTTCCT
* *
10745 ACAATCGAGGATACTCCAACC
1 ATAATCGGGGATACTCCAACC
10766 TCGTTATTTC
Statistics
Matches: 254, Mismatches: 62, Indels: 38
0.72 0.18 0.11
Matches are distributed among these distances:
51 83 0.33
52 99 0.39
53 36 0.14
54 17 0.07
55 3 0.01
56 15 0.06
57 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.29
Consensus pattern (52 bp):
ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
Found at i:10775 original size:31 final size:28
Alignment explanation
Indices: 10748--10824 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
10738 AAATTTCACA
*
10748 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
**
10776 ATCGAGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
10804 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
10825 GCTTTATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
28 41 0.93
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:10846 original size:262 final size:262
Alignment explanation
Indices: 10381--10875 Score: 846
Period size: 262 Copynumber: 1.9 Consensus size: 262
10371 AATTGTTCAT
* *
10381 AATCGGGGATACACCAACCTCAATTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACACCAACCCCAATTTCATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
* **
10446 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCAAGGATACTCCAACCTCATTAT
66 CCAACCCCGATTTTATTTCCAAAAACACCAAAATTTCACAATCAAGGATACTCCAACCTCATTAT
* *
10511 CTCATTGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
131 CTCATCGAGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
*
10576 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCC
196 AATATTGATTTCTCATAATCAGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCC
10641 AC
261 AC
* **
10643 AATCGGGGATACTCCAACCCCGGTTTCATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACACCAACCCCAATTTCATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
* *
10708 CCAACCCCGATTTTATTTCCAAAAACACCAAAATTTCACAATCGAGGATACTCCAACCTCGTTAT
66 CCAACCCCGATTTTATTTCCAAAAACACCAAAATTTCACAATCAAGGATACTCCAACCTCATTAT
* *
10773 TTCATCGAGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAA
131 CTCATCGAGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
*
10838 AATATTGATTTCTCATAATTAGGGATACTCCAACCCCG
196 AATATTGATTTCTCATAATCAGGGATACTCCAACCCCG
10876 TTATTTCCGA
Statistics
Matches: 217, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
262 217 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (262 bp):
AATCGGGGATACACCAACCCCAATTTCATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
CCAACCCCGATTTTATTTCCAAAAACACCAAAATTTCACAATCAAGGATACTCCAACCTCATTAT
CTCATCGAGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
AATATTGATTTCTCATAATCAGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCC
AC
Found at i:10875 original size:79 final size:79
Alignment explanation
Indices: 10781--10982 Score: 253
Period size: 79 Copynumber: 2.6 Consensus size: 79
10771 ATTTCATCGA
** * *
10781 GGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT-ATTG
1 GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCC-AAATCATCG
* **
10845 ATTTCTCATAATTAG
65 ATTTCTCACAACCAG
* * *
10860 GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGA
1 GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAATCATCGA
* *
10925 TTTTTCACAACCGG
66 TTTCTCACAACCAG
* * *
10939 GGATACTCCAACCCCGTTATTTTCAAGGGGACACTCCAACCCCG
1 GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
10983 TTATTATCTC
Statistics
Matches: 106, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 3 0.03
79 103 0.97
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAATCATCGA
TTTCTCACAACCAG
Found at i:16083 original size:20 final size:20
Alignment explanation
Indices: 16058--16130 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
16048 ATTGGGCATA
16058 ATGTATCGATACAATCCTTC
1 ATGTATCGATACAATCCTTC
16078 ATGTATCGATACAATCCTTC
1 ATGTATCGATACAATCCTTC
**
16098 ATGTATCGATACAATGTTTC
1 ATGTATCGATACAATCCTTC
16118 ATGTATCGATACA
1 ATGTATCGATACA
16131 TTTCACTTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATCCTTC
Found at i:16202 original size:19 final size:20
Alignment explanation
Indices: 16162--16211 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
16152 CCAGTTTCAA
* *
16162 GTATCAATACAATTGAGTAT
1 GTATCGATACAATTGAGCAT
16182 GTATCGATACAA-TGAGCAT
1 GTATCGATACAATTGAGCAT
16201 GTATCGATACA
1 GTATCGATACA
16212 TTGTATCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATTGAGCAT
Found at i:16218 original size:13 final size:13
Alignment explanation
Indices: 16200--16224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16190 ACAATGAGCA
16200 TGTATCGATACAT
1 TGTATCGATACAT
16213 TGTATCGATACA
1 TGTATCGATACA
16225 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16241 original size:33 final size:32
Alignment explanation
Indices: 16181--16245 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
16171 CAATTGAGTA
* *
16181 TGTATCGATACAATGAGCATGTATCGATACAT
1 TGTATCGATACAAAGAGAATGTATCGATACAT
*
16213 TGTATCGATACAAAGCATAATGTATCGATACAT
1 TGTATCGATACAAAG-AGAATGTATCGATACAT
16246 CTAGGTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAAGAGAATGTATCGATACAT
Found at i:24386 original size:13 final size:13
Alignment explanation
Indices: 24368--24393 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24358 ACAATTCATC
24368 ATGTATCGATACA
1 ATGTATCGATACA
24381 ATGTATCGATACA
1 ATGTATCGATACA
24394 TCGTACTACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:24407 original size:33 final size:33
Alignment explanation
Indices: 24370--24447 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
24360 AATTCATCAT
* *
24370 GTATCGATACAATGTATCGATACATCGTACTAC
1 GTATCGACACAATGTATCGATACATCGTACCAC
*
24403 GTATCGACACAATGTATTGATACATCGTACCAC
1 GTATCGACACAATGTATCGATACATCGTACCAC
24436 GTATCGACACAA
1 GTATCGACACAA
24448 ACAGTGGTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (33 bp):
GTATCGACACAATGTATCGATACATCGTACCAC
Found at i:24520 original size:19 final size:19
Alignment explanation
Indices: 24476--24531 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
24466 TTGCCAATTT
**
24476 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
24496 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
24515 CATGTATTGATACAATG
1 CATGTATCGATACAATG
24532 TATTGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:24534 original size:13 final size:13
Alignment explanation
Indices: 24516--24542 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24506 TACAATGAAC
24516 ATGTATTGATACA
1 ATGTATTGATACA
24529 ATGTATTGATACA
1 ATGTATTGATACA
24542 A
1 A
24543 AGCATAATGA
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:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:25161 original size:22 final size:22
Alignment explanation
Indices: 25136--25177 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
25126 AGATAAACAT
25136 ATTTCTCCCCCTTTATCAAAGC
1 ATTTCTCCCCCTTTATCAAAGC
*
25158 ATTTCTCCCCCTTTGTCAAA
1 ATTTCTCCCCCTTTATCAAA
25178 TCTTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.05, T:0.38
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAAGC
Found at i:26698 original size:13 final size:13
Alignment explanation
Indices: 26680--26704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26670 CATGCTGCTT
26680 TGTATCGATACAA
1 TGTATCGATACAA
26693 TGTATCGATACA
1 TGTATCGATACA
26705 TGTTTAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:32936 original size:13 final size:13
Alignment explanation
Indices: 32918--32946 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
32908 ACAACATTCC
32918 TTGTATCGATACA
1 TTGTATCGATACA
32931 TTGTATCGATACA
1 TTGTATCGATACA
32944 TTG
1 TTG
32947 GGTACAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:34829 original size:17 final size:17
Alignment explanation
Indices: 34807--34862 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
34797 ACGGGGAGAA
34807 GATAATCGTTTAAGGGG
1 GATAATCGTTTAAGGGG
** *
34824 GATAATTTTTTTTAAGAGGA
1 GATAA--TCGTTTAAG-GGG
34844 GATAATCGTTTAAGGGG
1 GATAATCGTTTAAGGGG
34861 GA
1 GA
34863 GAATATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
17 9 0.30
18 7 0.23
19 7 0.23
20 7 0.23
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (17 bp):
GATAATCGTTTAAGGGG
Found at i:35490 original size:20 final size:20
Alignment explanation
Indices: 35465--35502 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35455 TATCACTATT
35465 TGTATCGATACATGGTATAA
1 TGTATCGATACATGGTATAA
*
35485 TGTATCGATACATTGTAT
1 TGTATCGATACATGGTAT
35503 CGATACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATGGTATAA
Found at i:35501 original size:13 final size:13
Alignment explanation
Indices: 35485--35543 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
35475 CATGGTATAA
35485 TGTATCGATACAT
1 TGTATCGATACAT
35498 TGTATCGATACA-
1 TGTATCGATACAT
*
35510 TG-A-AGA-A-A-
1 TGTATCGATACAT
35518 TGTATCGATACAT
1 TGTATCGATACAT
35531 TGTATCGATACAT
1 TGTATCGATACAT
35544 GAAGAAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 3 0.08
9 2 0.05
10 4 0.10
11 2 0.05
12 3 0.08
13 25 0.64
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:35501 original size:33 final size:32
Alignment explanation
Indices: 35464--35563 Score: 157
Period size: 33 Copynumber: 3.0 Consensus size: 32
35454 CTATCACTAT
35464 TTGTATCGATACATG-GTATAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
35497 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
35530 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
35563 T
1 T
35564 AGCTTGTAAC
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
33 63 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:35521 original size:20 final size:20
Alignment explanation
Indices: 35498--35563 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
35488 ATCGATACAT
35498 TGTATCGATACATGAAGAAA
1 TGTATCGATACATGAAGAAA
35518 TGTATCGATACAT-------
1 TGTATCGATACATGAAGAAA
35531 TGTATCGATACATGAAGAAA
1 TGTATCGATACATGAAGAAA
35551 TGTATCGATACAT
1 TGTATCGATACAT
35564 AGCTTGTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAA
Found at i:36818 original size:51 final size:51
Alignment explanation
Indices: 36658--36828 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
36648 GAAATAACGA
* * *
36658 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
36710 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
36763 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
36814 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
36829 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:36874 original size:27 final size:28
Alignment explanation
Indices: 36811--36886 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
36801 AAAATAAAGT
*
36811 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
36839 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
36866 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
36887 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:39202 original size:1 final size:1
Alignment explanation
Indices: 39196--39250 Score: 83
Period size: 1 Copynumber: 55.0 Consensus size: 1
39186 TAAAGTTTTG
***
39196 AAAAAAAAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39251 TTTATGTATC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.95, C:0.00, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:39231 original size:27 final size:27
Alignment explanation
Indices: 39193--39246 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
39183 AGATAAAGTT
39193 TTGAAAAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAAAAA
39220 TTGAAAAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAAAAA
39247 AAAATTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.89, C:0.00, G:0.04, T:0.07
Consensus pattern (27 bp):
TTGAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:39284 original size:19 final size:21
Alignment explanation
Indices: 39254--39307 Score: 85
Period size: 19 Copynumber: 2.7 Consensus size: 21
39244 AAAAAAATTT
39254 ATGTATCGATACATTTGTAG-
1 ATGTATCGATACATTTGTAGA
*
39274 ATGTA-CGATACATTTGTGGA
1 ATGTATCGATACATTTGTAGA
39294 ATGTATCGATACAT
1 ATGTATCGATACAT
39308 CCTACAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 13 0.42
20 10 0.32
21 8 0.26
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (21 bp):
ATGTATCGATACATTTGTAGA
Found at i:39414 original size:29 final size:32
Alignment explanation
Indices: 39364--39423 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 32
39354 TCAACAAATT
*
39364 TGTATCGATACATAAGTTTTGT-TCG-TACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
39394 TGTA-CGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
39424 TAATTAGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 16 0.59
30 7 0.26
31 4 0.15
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:39488 original size:33 final size:33
Alignment explanation
Indices: 39446--39509 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
39436 GCCAAGGAAA
***
39446 TGTATCGATACATTTTTCTGTGTATCGATACCT
1 TGTATCGATACATGGATCTGTGTATCGATACCT
*
39479 TGTATCGATACATGGATCTTTGTATCGATAC
1 TGTATCGATACATGGATCTGTGTATCGATAC
39510 ATTTGGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACCT
Done.