Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3238
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: 34032
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Found at i:371 original size:56 final size:56
Alignment explanation
Indices: 285--404 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
275 ACAAGGGATG
285 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
341 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
397 ATGGGCAA
1 ATGGGCAA
405 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:1678 original size:40 final size:40
Alignment explanation
Indices: 1532--1709 Score: 199
Period size: 40 Copynumber: 4.5 Consensus size: 40
1522 AATGATGTCC
* * * *
1532 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCG
* * *
1572 GACTAAGAT-CCG--GGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
1610 GGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
1648 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
*
1688 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
1710 AACGAGTAGC
Statistics
Matches: 117, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
37 3 0.03
38 43 0.37
39 21 0.18
40 47 0.40
41 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
Found at i:1716 original size:40 final size:38
Alignment explanation
Indices: 1532--1709 Score: 150
Period size: 38 Copynumber: 4.6 Consensus size: 38
1522 AATGATGTCC
* * * * *
1532 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATT-TGC-GAGTTACTAAATCCG
* * *
1572 GACTAAGAT-CCG--GGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCA-TT-TGCGAGTTACTAAATCCG
1610 GGCTAAG-CCCGAAGGCATTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATT-TGCGAGTTACTAAATCCG
*
1648 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCA-TT-TGCGAGTTACTA-AATCCG
*
1688 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
1710 AACGAGTAGC
Statistics
Matches: 116, Mismatches: 14, Indels: 18
0.78 0.09 0.12
Matches are distributed among these distances:
37 3 0.03
38 45 0.39
39 22 0.19
40 43 0.37
41 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
GGCTAAGTCCCGAAGGCATTTGCGAGTTACTAAATCCG
Found at i:7566 original size:56 final size:56
Alignment explanation
Indices: 7480--7599 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
7470 ACAAGGGATG
7480 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
7536 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
7592 ATGGGCAA
1 ATGGGCAA
7600 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:8810 original size:40 final size:39
Alignment explanation
Indices: 8726--8910 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 39
8716 TCGAATGATG
* * *
8726 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
8765 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAT
*
8806 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAT
*
8845 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAT
* *
8884 AACCGGGCTATGACCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
8911 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
39 36 0.29
40 79 0.64
41 9 0.07
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:8862 original size:79 final size:81
Alignment explanation
Indices: 8726--8910 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
8716 TCGAATGATG
* *
8726 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
8790 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
8805 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGACCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
8867 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
8885 ACCGGGCTATGACCCGAAGGCATTTG
1 TCCGGGCTAAGACCCGAAGGCATTTG
8911 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGACCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:8932 original size:79 final size:79
Alignment explanation
Indices: 8779--8943 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
8769 GGACTAAGAT
* **
8779 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
8844 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
8858 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGACCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
8921 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
8937 CCGAAGG
1 CCGAAGG
8944 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:14539 original size:25 final size:25
Alignment explanation
Indices: 14511--14568 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
14501 TTTGAAACCA
* *
14511 GTAAGCTCTAACGAGCTGCAAATCG
1 GTAAGCTCTAACGAGATACAAATCG
*
14536 GTAAGGTCTAACGAGATACAAATCG
1 GTAAGCTCTAACGAGATACAAATCG
*
14561 ATAAGCTC
1 GTAAGCTC
14569 ATATGAGCTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (25 bp):
GTAAGCTCTAACGAGATACAAATCG
Found at i:16738 original size:27 final size:27
Alignment explanation
Indices: 16605--16738 Score: 189
Period size: 27 Copynumber: 5.0 Consensus size: 27
16595 CAAAATTATT
*
16605 GAAATACCC-TGTAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAATTACC
16631 GAAATACCCTTGTAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
16658 AAAATACCCTTGTAGGGTAGAAATATC
1 GAAATACCCTTGTAGGGTAGAATTACC
16685 GAAATACCCTTGTAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * * *
16712 GAGATACCTTTGTGGGGTAAAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
16739 ATTTTGCCCT
Statistics
Matches: 96, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 9 0.09
27 87 0.91
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (27 bp):
GAAATACCCTTGTAGGGTAGAATTACC
Found at i:17342 original size:6 final size:6
Alignment explanation
Indices: 17333--17418 Score: 77
Period size: 6 Copynumber: 14.0 Consensus size: 6
17323 TTGCATTCAC
* * *
17333 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
* *
17383 ATTCTA ATTCTG ATTCTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
17419 TCACCTGATT
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
5 3 0.05
6 56 0.85
7 5 0.08
8 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:17364 original size:25 final size:25
Alignment explanation
Indices: 17336--17400 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
17326 CATTCACATT
* *
17336 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTCACCTAATA
*
17361 CTGATTCTGATTCTGTCACCTAATT
1 CTGATTCTGATTCTGTCACCTAATA
*
17386 CTAATTCTGATTCTG
1 CTGATTCTGATTCTG
17401 ATTCTGATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.45
Consensus pattern (25 bp):
CTGATTCTGATTCTGTCACCTAATA
Found at i:17409 original size:43 final size:43
Alignment explanation
Indices: 17355--17451 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
17345 ATTCTGTTAC
* * *
17355 CTGATACTGATTCTGATTCTGTCACCTAATTCTAATTCTGATT
1 CTGATTCTGATTCTAATTCTGTCACCTAATTCTAATTCTAATT
* *
17398 CTGATTCTGATTCTAATTCTGTCACCTGATTCTAATTTTAATT
1 CTGATTCTGATTCTAATTCTGTCACCTAATTCTAATTCTAATT
17441 CT-AGTTCTGAT
1 CTGA-TTCTGAT
17452 AATGTTTCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.02
43 47 0.98
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (43 bp):
CTGATTCTGATTCTAATTCTGTCACCTAATTCTAATTCTAATT
Found at i:19440 original size:27 final size:26
Alignment explanation
Indices: 19376--19480 Score: 86
Period size: 27 Copynumber: 3.9 Consensus size: 26
19366 AATACTTTAG
*
19376 TTTACCAAATTACTAAAATACCCTCAA
1 TTTA-CAAATTACCAAAATACCCTCAA
*
19403 CTTGTA-AAATTACCAAAGTACCCTCAA
1 -TT-TACAAATTACCAAAATACCCTCAA
*** *
19430 TTTACAGAATTACCATTTTACCCTCGA
1 TTTACA-AATTACCAAAATACCCTCAA
**
19457 TTTACAAAATTATTAAAATACCCT
1 TTTAC-AAATTACCAAAATACCCT
19481 TGTAGGGTAG
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
25 2 0.03
26 3 0.05
27 52 0.84
28 3 0.05
29 2 0.03
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (26 bp):
TTTACAAATTACCAAAATACCCTCAA
Found at i:19528 original size:27 final size:27
Alignment explanation
Indices: 19471--19605 Score: 155
Period size: 27 Copynumber: 5.0 Consensus size: 27
19461 CAAAATTATT
*
19471 AAAATACCCTTGTAGGGTAGAA-TACT
1 AAAATACCCTTGTAGGGTAGAATTACC
* *
19497 GAAATACCCCTGTAGGGTAGAATTACC
1 AAAATACCCTTGTAGGGTAGAATTACC
* *
19524 AAAATACCCTTGTAGGGTAGAAATATC
1 AAAATACCCTTGTAGGGTAGAATTACC
*
19551 AAAATGCCCTTGTAGGGTAGAATTACC
1 AAAATACCCTTGTAGGGTAGAATTACC
* * * * * *
19578 GAGATACCTTTATGGGGTAAAATTACC
1 AAAATACCCTTGTAGGGTAGAATTACC
19605 A
1 A
19606 TTTTGCCCTA
Statistics
Matches: 90, Mismatches: 18, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
26 20 0.22
27 70 0.78
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (27 bp):
AAAATACCCTTGTAGGGTAGAATTACC
Found at i:20236 original size:6 final size:6
Alignment explanation
Indices: 20225--20330 Score: 60
Period size: 6 Copynumber: 17.3 Consensus size: 6
20215 TCACAATCTA
* * * *
20225 ATTCTG ATTCTG -TTACCTG ATACTG ATTCT- ATTCTG -TCACCTA ATTCTT
1 ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
* *
20274 ATTCTG ATTCTG ATTATG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCT-
1 ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG
20322 AGTTCTG AT
1 A-TTCTG AT
20331 AATGTTTCTT
Statistics
Matches: 77, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
5 10 0.13
6 55 0.71
7 9 0.12
8 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:20259 original size:24 final size:25
Alignment explanation
Indices: 20225--20285 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
20215 TCACAATCTA
* *
20225 ATTCTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGTCACCTAATACTG
* *
20250 ATTCT-ATTCTGTCACCTAATTCTT
1 ATTCTGATTCTGTCACCTAATACTG
20274 ATTCTGATTCTG
1 ATTCTGATTCTG
20286 ATTATGATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 20 0.65
25 11 0.35
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.48
Consensus pattern (25 bp):
ATTCTGATTCTGTCACCTAATACTG
Found at i:20296 original size:37 final size:36
Alignment explanation
Indices: 20241--20321 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 36
20231 ATTCTGTTAC
* * *
20241 CTGATACTGATTCTATTCTGTCACCTAATTCTTATT
1 CTGATTCTGATTATATTCTGTCACCTAATTCTGATT
*
20277 CTGATTCTGATTATGATTCTGTCACCTGATTCTGATT
1 CTGATTCTGATTAT-ATTCTGTCACCTAATTCTGATT
20314 CTGATTCT
1 CTGATTCT
20322 AGTTCTGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 12 0.30
37 28 0.70
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.47
Consensus pattern (36 bp):
CTGATTCTGATTATATTCTGTCACCTAATTCTGATT
Found at i:22357 original size:27 final size:27
Alignment explanation
Indices: 22255--22359 Score: 93
Period size: 27 Copynumber: 3.9 Consensus size: 27
22245 AATAATTTAG
* *
22255 TTTACCAAATTACTAAAATACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* ** * *
22282 CTTGGAAAATTACCAAAGTACCCCCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* ***
22309 TTTACAGAATTACCATTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
**
22336 TTTACAAAATTATTAAAATACCCT
1 TTTACAAAATTACCAAAATACCCT
22360 TGTAAGGTAG
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTCGA
Found at i:22436 original size:26 final size:27
Alignment explanation
Indices: 22351--22482 Score: 178
Period size: 27 Copynumber: 4.9 Consensus size: 27
22341 AAAATTATTA
* *
22351 AAATACCCTTGTAAGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACTG
22378 AAATACCCCTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACTG
22405 AAATACCCCTGTAGGGTAGAA-TACTG
1 AAATACCCCTGTAGGGTAGAATTACTG
*
22431 AAATACCTCTGTAGGGTAGAATTA-TCG
1 AAATACCCCTGTAGGGTAGAATTACT-G
* * * *
22458 ACATACCCTTGTGGGGTAAAATTAC
1 AAATACCCCTGTAGGGTAGAATTAC
22483 CATTTTGCCC
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 26 0.28
27 68 0.72
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACTG
Found at i:22464 original size:53 final size:54
Alignment explanation
Indices: 22351--22482 Score: 187
Period size: 53 Copynumber: 2.5 Consensus size: 54
22341 AAAATTATTA
*
22351 AAATACCCTTGTAAGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACTG
1 AAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACTG
* *
22405 AAATACCCCTGTAGGGTAGAA-TACTGAAATACCTCTGTAGGGTAGAATTA-TCG
1 AAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACT-G
* * *
22458 ACATACCCTTGTGGGGTAAAATTAC
1 AAATACCCTTGTAGGGTAGAATTAC
22483 CATTTTGCCC
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
52 1 0.01
53 46 0.67
54 22 0.32
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (54 bp):
AAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACTG
Found at i:22646 original size:16 final size:16
Alignment explanation
Indices: 22625--22655 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22615 CAAATATGGG
*
22625 CATGACATTTTGCATA
1 CATGACATGTTGCATA
22641 CATGACATGTTGCAT
1 CATGACATGTTGCAT
22656 GGGTTGGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (16 bp):
CATGACATGTTGCATA
Found at i:24433 original size:79 final size:80
Alignment explanation
Indices: 24298--24481 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 80
24288 TTGAATGATG
* *
24298 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCGGACTAAGATCCGAAGGCAATT
24362 GTGCGAGATACTA-A
66 GTGCGAGATACTATA
* * * **
24376 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAAT-CGGACTAAGAT-CCGAAGGCA
*
24438 ATTGTGCGAGTTACTATA
63 ATTGTGCGAGATACTATA
* *
24456 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
24482 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
78 18 0.20
79 57 0.63
80 15 0.17
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATA
Found at i:24488 original size:40 final size:39
Alignment explanation
Indices: 24299--24481 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 39
24289 TGAATGATGT
* * * *
24299 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
24338 TCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
24378 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
24416 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
24457 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
24482 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
39 55 0.46
40 63 0.52
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:24503 original size:79 final size:79
Alignment explanation
Indices: 24350--24514 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
24340 GGACTAAGAT
* * **
24350 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
24415 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
24429 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
24492 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
24508 CCGAAGG
1 CCGAAGG
24515 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:32375 original size:39 final size:39
Alignment explanation
Indices: 32326--32453 Score: 143
Period size: 39 Copynumber: 3.2 Consensus size: 39
32316 CTAAGATCCG
*
32326 AGGCATTTGTGCGAGATACTAATTCCCGGGCTAAG-CCCA
1 AGGCATTTGTGCGAGTTACTAATT-CCGGGCTAAGTCCCA
* * *
32365 AGGCATTTGTGCGAGTTACTAAAATCCGGGTTAAGTCCGA
1 AGGCATTTGTGCGAGTTACT-AATTCCGGGCTAAGTCCCA
* * *
32405 AGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGA
1 AGGCATTTGTGCGAGTTACTAAT-TCCGGGCTAAGTCCC-A
32445 AGGCATTTG
1 AGGCATTTG
32454 AATGAGTAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 39 0.53
40 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
AGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCA
Found at i:33996 original size:20 final size:21
Alignment explanation
Indices: 33973--34031 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
33963 ATGTTATCGA
*
33973 GGGCTTTGTGCCG-TTATTGT
1 GGGCTTCGTGCCGATTATTGT
**
33993 GGGCTTCGTATCGATTATTGT
1 GGGCTTCGTGCCGATTATTGT
34014 GGGCTTCGTGCCGATTAT
1 GGGCTTCGTGCCGATTAT
34032 C
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 10 0.30
21 23 0.70
ACGTcount: A:0.10, C:0.17, G:0.32, T:0.41
Consensus pattern (21 bp):
GGGCTTCGTGCCGATTATTGT
Done.