Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019045.1 Corchorus olitorius cultivar O-4 contig19078, 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: 79130
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9402 original size:29 final size:29
Alignment explanation
Indices: 9357--9444 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
9347 TTTTTCTGGT
*
9357 TTTGTTTAAGTGCGGGTTGTGCACTTGTG
1 TTTGTTTAAGTGTGGGTTGTGCACTTGTG
* * *
9386 TTTGTTCAAGTGTGGGTTGTACACTTGGG
1 TTTGTTTAAGTGTGGGTTGTGCACTTGTG
* *
9415 CTTGTTTTGAGTGTGGGTT-TGCACTTGTG
1 TTTG-TTTAAGTGTGGGTTGTGCACTTGTG
9444 T
1 T
9445 CAAAGCTTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 36 0.75
30 12 0.25
ACGTcount: A:0.10, C:0.10, G:0.34, T:0.45
Consensus pattern (29 bp):
TTTGTTTAAGTGTGGGTTGTGCACTTGTG
Found at i:11356 original size:26 final size:26
Alignment explanation
Indices: 11316--11378 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
11306 AACACAACAG
*
11316 CCGCCGCTCAGTCTTCCTTACCCTCA
1 CCGCCGCTCACTCTTCCTTACCCTCA
11342 CCGCCGCTCACTCTTCCTTACCCTCA
1 CCGCCGCTCACTCTTCCTTACCCTCA
11368 CCGCCGCTCAC
1 CCGCCGCTCAC
11379 ACTCAAACAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.11, C:0.54, G:0.11, T:0.24
Consensus pattern (26 bp):
CCGCCGCTCACTCTTCCTTACCCTCA
Found at i:12587 original size:72 final size:72
Alignment explanation
Indices: 12470--12661 Score: 303
Period size: 72 Copynumber: 2.8 Consensus size: 72
12460 ACATTTTGAG
*
12470 CCCAACGTATCTTTAGTTTTCAACTTCCAAATACTTGCTTTCAAACTTGAATATGTTCAAATAAT
1 CCCAACGTATCTTTAGTTTTCAATTTCCAAATACTTGCTTTCAAACTTGAATATGTTCAAATAAT
12535 AAATGTT
66 AAATGTT
12542 CCCAACGTATCTTTAGTTTTCAATTTCCAAATACTTGCTTTCAAACTTGAATATGTTCAAATAAT
1 CCCAACGTATCTTTAGTTTTCAATTTCCAAATACTTGCTTTCAAACTTGAATATGTTCAAATAAT
12607 AAATGTT
66 AAATGTT
*
12614 CCCAACG------TA---TTCAATTTCCAAGTACTTGCTTTCAAACTTGAATATGTT
1 CCCAACGTATCTTTAGTTTTCAATTTCCAAATACTTGCTTTCAAACTTGAATATGTT
12662 TGTTTGTGTA
Statistics
Matches: 118, Mismatches: 2, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
63 38 0.32
66 2 0.02
72 78 0.66
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (72 bp):
CCCAACGTATCTTTAGTTTTCAATTTCCAAATACTTGCTTTCAAACTTGAATATGTTCAAATAAT
AAATGTT
Found at i:13793 original size:26 final size:26
Alignment explanation
Indices: 13741--13790 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
13731 AAACTTTCTG
*
13741 TTTTTTGTTCAAACTTGCTGTTTTTC
1 TTTTTTGCTCAAACTTGCTGTTTTTC
*
13767 TTTTTTGCTCATACTTG-TGTTTTT
1 TTTTTTGCTCAAACTTGCTGTTTTT
13791 TCTGAAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.10, C:0.14, G:0.12, T:0.64
Consensus pattern (26 bp):
TTTTTTGCTCAAACTTGCTGTTTTTC
Found at i:13902 original size:137 final size:139
Alignment explanation
Indices: 13655--14051 Score: 762
Period size: 137 Copynumber: 2.9 Consensus size: 139
13645 AAGGTTAGTT
13655 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
*
13720 CAAAGTTGCTGAAACTTTCTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCTCATACTTG-
66 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCTCATACTTGT
13784 TGTTTTTTC
131 TGTTTTTTC
13793 TGAAACTTGCTGAAATTT-CTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
13857 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCTCATACTTGT
66 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCTCATACTTGT
13922 TGTTTTTTC
131 TGTTTTTTC
13931 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
*
13996 CAAAGTTGTTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCT
66 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCT
14052 ATATTTCTGT
Statistics
Matches: 255, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
137 109 0.43
138 45 0.18
139 101 0.40
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (139 bp):
TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCTCATACTTGT
TGTTTTTTC
Found at i:13919 original size:26 final size:26
Alignment explanation
Indices: 13878--13928 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
13868 AAACTTACTG
*
13878 TTTTTTGTTCAAACTTGCTGTTTTTC
1 TTTTTTGCTCAAACTTGCTGTTTTTC
* *
13904 TTTTTTGCTCATACTTGTTGTTTTT
1 TTTTTTGCTCAAACTTGCTGTTTTT
13929 TCTGAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.10, C:0.14, G:0.12, T:0.65
Consensus pattern (26 bp):
TTTTTTGCTCAAACTTGCTGTTTTTC
Found at i:14030 original size:20 final size:20
Alignment explanation
Indices: 14001--14041 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13991 TTGCTCAAAG
*
14001 TTGTTGAAACTTACTGTTTT
1 TTGTTCAAACTTACTGTTTT
*
14021 TTGTTCAAACTTGCTGTTTT
1 TTGTTCAAACTTACTGTTTT
14041 T
1 T
14042 CTTTTTTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.56
Consensus pattern (20 bp):
TTGTTCAAACTTACTGTTTT
Found at i:16540 original size:21 final size:21
Alignment explanation
Indices: 16503--16551 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
16493 TATTCTTATA
16503 TGCTACGAGCTTATTTACAGT
1 TGCTACGAGCTTATTTACAGT
*
16524 TGCTACGAGCTTATTTACATT
1 TGCTACGAGCTTATTTACAGT
16545 TGCTACG
1 TGCTACG
16552 GACATTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (21 bp):
TGCTACGAGCTTATTTACAGT
Found at i:18880 original size:23 final size:23
Alignment explanation
Indices: 18854--18899 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
18844 ATTTGTGACG
*
18854 AAAAACTAATGTCATGTAT-TAAT
1 AAAAAATAATGTCAT-TATGTAAT
*
18877 AAAAAATCATGTCATTATGTAAT
1 AAAAAATAATGTCATTATGTAAT
18900 CTTGTCACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (23 bp):
AAAAAATAATGTCATTATGTAAT
Found at i:30894 original size:27 final size:28
Alignment explanation
Indices: 30860--30938 Score: 103
Period size: 27 Copynumber: 2.9 Consensus size: 28
30850 GCATTAGGGT
30860 CATC-TAGGGGCATTTTGGTCATTTTTA
1 CATCTTAGGGGCATTTTGGTCATTTTTA
*
30887 CA-CTTAGGGGCATTTTGGTCA--TTTG
1 CATCTTAGGGGCATTTTGGTCATTTTTA
*
30912 CATGTTCAGGGGCATTTTGGTCATTTT
1 CATCTT-AGGGGCATTTTGGTCATTTT
30939 CGGTTCACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
25 5 0.11
26 3 0.07
27 35 0.78
29 2 0.04
ACGTcount: A:0.16, C:0.15, G:0.25, T:0.43
Consensus pattern (28 bp):
CATCTTAGGGGCATTTTGGTCATTTTTA
Found at i:33365 original size:25 final size:25
Alignment explanation
Indices: 33337--33384 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
33327 CATCTACACC
33337 CTCCCCTCTGACC-TCTCTCTAGAAG
1 CTCCCCTCT-ACCTTCTCTCTAGAAG
*
33362 CTCCCCTCTTCCTTCTCTCTAGA
1 CTCCCCTCTACCTTCTCTCTAGA
33385 TTGAGACTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.12, C:0.46, G:0.08, T:0.33
Consensus pattern (25 bp):
CTCCCCTCTACCTTCTCTCTAGAAG
Found at i:39920 original size:76 final size:72
Alignment explanation
Indices: 39790--39931 Score: 176
Period size: 76 Copynumber: 1.9 Consensus size: 72
39780 ATATGGACTA
* * *
39790 TGAGCAAAGGAATGATGAGTTTTAATAAAAATCTTCAAAATCAGTTTCAATCAAAGCTATGATTT
1 TGAGCAAAGGAATGAGGAGTTTTAATAAAAATCTTCAAAATCAGTTTCAATCAAAACAATGATTT
39855 CGAGCTG
66 CGAGCTG
* * ***
39862 TGAGCAAAGGAATGACGGTGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTGGTCAAAACAATG
1 TGAGCAAAGGAATGA-GGAGTTTTAAT-AAAA-AT-CTTCAAAATCAGTTTCAATCAAAACAATG
39927 ATTTC
62 ATTTC
39932 TAGGTGATTG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
72 15 0.26
73 9 0.16
74 4 0.07
75 2 0.03
76 28 0.48
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (72 bp):
TGAGCAAAGGAATGAGGAGTTTTAATAAAAATCTTCAAAATCAGTTTCAATCAAAACAATGATTT
CGAGCTG
Found at i:40764 original size:31 final size:33
Alignment explanation
Indices: 40726--40797 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 33
40716 TAAGAAATTC
40726 AAAAAC-AAAATCAATCAA-AAAAATAA-AAAAT
1 AAAAACAAAAATCAATCAACAAAAA-AATAAAAT
40757 AAAAACAAAAAAATCAATCAATCAAAAAAATAAAAT
1 AAAAAC--AAAAATCAATCAA-CAAAAAAATAAAAT
40793 AAAAA
1 AAAAA
40798 ATCGAAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
31 6 0.17
34 12 0.34
35 2 0.06
36 15 0.43
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (33 bp):
AAAAACAAAAATCAATCAACAAAAAAATAAAAT
Found at i:40798 original size:13 final size:14
Alignment explanation
Indices: 40744--40798 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
40734 AATCAATCAA
40744 AAAAAT-AAAAAAT
1 AAAAATAAAAAAAT
*
40757 AAAAACAAAAAAAT
1 AAAAATAAAAAAAT
*
40771 CAATCAATCAAAAAAAT
1 -AA-AAAT-AAAAAAAT
40788 -AAAATAAAAAA
1 AAAAATAAAAAA
40799 TCGAAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 11 0.32
14 10 0.29
15 3 0.09
16 2 0.06
17 8 0.24
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:40810 original size:14 final size:13
Alignment explanation
Indices: 40726--40810 Score: 50
Period size: 14 Copynumber: 6.2 Consensus size: 13
40716 TAAGAAATTC
*
40726 AAAAACAAAATCA
1 AAAAATAAAATCA
*
40739 ATCAAA-AAAAT-A
1 A-AAAATAAAATCA
*
40751 AAAAATAAAAACAA
1 AAAAATAAAATC-A
40765 AAAAATCAATCAATCAA
1 AAAAAT-AA--AATC-A
40782 AAAAATAAAAT-A
1 AAAAATAAAATCA
*
40794 AAAAATCGAAATCA
1 AAAAAT-AAAATCA
40808 AAA
1 AAA
40811 GAGAATTGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
11 3 0.05
12 13 0.22
13 10 0.17
14 17 0.29
15 2 0.03
16 2 0.03
17 11 0.19
ACGTcount: A:0.75, C:0.11, G:0.01, T:0.13
Consensus pattern (13 bp):
AAAAATAAAATCA
Found at i:41449 original size:50 final size:50
Alignment explanation
Indices: 41383--41557 Score: 224
Period size: 50 Copynumber: 3.5 Consensus size: 50
41373 AAAGATTTAG
* * * * *
41383 AATAAGATTGCATTCCATTTCTGCGCCCAAGACCAAAATTCGCTTTTCAA
1 AATAAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
* * * *
41433 AGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCTAAATTCGCTTTTCAA
1 AATAAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
**
41483 AACGAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
1 AATAAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
* * *
41533 AATAAGATTGCACTCCATTGGTGAG
1 AATAAAATTGCATTCCATTTGTGAG
41558 AAAAAGACCA
Statistics
Matches: 105, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 105 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (50 bp):
AATAAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
Found at i:41580 original size:100 final size:100
Alignment explanation
Indices: 41389--41580 Score: 233
Period size: 100 Copynumber: 1.9 Consensus size: 100
41379 TTAGAATAAG
* * ** *
41389 ATTGCATTCCATTTCTGCGCCCAAGACCAAAATTCGCTTTTCAAAGTAAAATTGCTTTCCATTTG
1 ATTGCATTCCATTTCTGAGCCCAAGACCAAAATTCGCTTTTCAAAATAAAATTGCACTCCATTGG
*** * * *
41454 TGAGTTCAAGATCTAAATTCGCTTTTCAAAACGAA
66 TGAGAAAAAGATCCAAAGTCGATTTTCAAAACGAA
* * * *
41489 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAATAAGATTGCACTCCATTGG
1 ATTGCATTCCATTTCTGAGCCCAAGACCAAAATTCGCTTTTCAAAATAAAATTGCACTCCATTGG
41554 TGAGAAAAAGA-CCAAAGGTCGATTTTC
66 TGAGAAAAAGATCCAAA-GTCGATTTTC
41581 GAAAGGCATT
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
99 4 0.05
100 72 0.95
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (100 bp):
ATTGCATTCCATTTCTGAGCCCAAGACCAAAATTCGCTTTTCAAAATAAAATTGCACTCCATTGG
TGAGAAAAAGATCCAAAGTCGATTTTCAAAACGAA
Found at i:42299 original size:50 final size:50
Alignment explanation
Indices: 42221--42696 Score: 844
Period size: 50 Copynumber: 9.5 Consensus size: 50
42211 CCATCTGAAC
* *
42221 ACATAGGCTTTTCCACAAGCCAACCTCGTTTCCATACGAGTCAGTTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
*
42271 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
*
42321 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
42371 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
*
42421 ACATAGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
* * *
42471 AGATAGGATTTTCCACAAGCCAAACTCGTTTCCGTACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
* *
42521 ACTTAGGCTTTTCCACAAGGCAAACTCGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
42571 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
* *
42621 ACATAGGCTTGTCCACAAGCCAAACTAGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
42671 ACATAGGCTTTTCCACAAGCCAAACT
1 ACATAGGCTTTTCCACAAGCCAAACT
42697 TGAACATTGG
Statistics
Matches: 409, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 409 1.00
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.28
Consensus pattern (50 bp):
ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
Found at i:43199 original size:27 final size:28
Alignment explanation
Indices: 43169--43244 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
43159 CTAGGGTCAT
43169 CTAGGGGCATTTTGGTCATTTTTGCA-C
1 CTAGGGGCATTTTGGTCATTTTTGCATC
* *
43196 CTAGGGGCAATTTGGTCA--TTTGCATG
1 CTAGGGGCATTTTGGTCATTTTTGCATC
*
43222 TTCAGGGGCATTTTGGTCATTTT
1 CT-AGGGGCATTTTGGTCATTTT
43245 CGGTTCACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 6 0.15
26 1 0.02
27 32 0.78
29 2 0.05
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.41
Consensus pattern (28 bp):
CTAGGGGCATTTTGGTCATTTTTGCATC
Found at i:51458 original size:76 final size:72
Alignment explanation
Indices: 51328--51472 Score: 191
Period size: 76 Copynumber: 2.0 Consensus size: 72
51318 ATATGGACTA
* * *
51328 TGAGCAAAGGAATGATGAGTTTTAATCAAAATCTTCAAAATCAGTTTCGATCAAAGCTATGATTT
1 TGAGCAAAGGAATGAGGAGTTTTAATCAAAATCTTCAAAATCAGTTTCGATCAAAACAATGATTT
51393 CGAGCTG
66 CGAGCTG
* * * *
51400 TGAGCAAAGGAATGACGGTGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTGGTCAAAACAATG
1 TGAGCAAAGGAATGA-GGAGTTTTAATC-AAA-AT-CTTCAAAATCAGTTTCGATCAAAACAATG
51465 ATTTCGAG
62 ATTTCGAG
51473 GTGACTGAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
72 15 0.24
73 10 0.16
74 3 0.05
75 2 0.03
76 32 0.52
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (72 bp):
TGAGCAAAGGAATGAGGAGTTTTAATCAAAATCTTCAAAATCAGTTTCGATCAAAACAATGATTT
CGAGCTG
Found at i:51880 original size:6 final size:7
Alignment explanation
Indices: 51863--51888 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
51853 AATAATCCAA
51863 AAAAATG
1 AAAAATG
51870 AAAAATG
1 AAAAATG
51877 AAAAATG
1 AAAAATG
51884 AAAAA
1 AAAAA
51889 AAAAAGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:52352 original size:14 final size:13
Alignment explanation
Indices: 52268--52352 Score: 59
Period size: 14 Copynumber: 6.2 Consensus size: 13
52258 TAAGAAATTC
52268 AAAAA-AAAATCA
1 AAAAATAAAATCA
*
52280 ATAAAAAAAAAT-A
1 A-AAAATAAAATCA
*
52293 AAAAATAAAAACAA
1 AAAAATAAAATC-A
52307 AAAAATCAATCAATCAA
1 AAAAAT-AA--AATC-A
52324 AAAAATAAAAT-A
1 AAAAATAAAATCA
*
52336 AAAAATCGAAATCA
1 AAAAAT-AAAATCA
52350 AAA
1 AAA
52353 GAGAATTGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
12 16 0.27
13 10 0.17
14 19 0.32
15 2 0.03
16 2 0.03
17 11 0.18
ACGTcount: A:0.78, C:0.08, G:0.01, T:0.13
Consensus pattern (13 bp):
AAAAATAAAATCA
Found at i:52993 original size:50 final size:51
Alignment explanation
Indices: 52914--53098 Score: 232
Period size: 50 Copynumber: 3.7 Consensus size: 51
52904 AGATTTACAA
* *
52914 TAAAATAGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTC-AAAC
1 TAAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAAC
* * *
52964 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCTAAATTCGCTTTTCAAAAC
1 TAAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAAC
* *
53015 -GAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTT-AAAAA
1 TAAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAAC
** * * * *
53064 TAGGATTGCACTCCATTGGTGAGACCAAGACCAAA
1 TAAAATTGCATTCCATTTGTGAGTCCAAGATCAAA
53099 GGTCGATTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 4 0.03
50 108 0.93
51 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (51 bp):
TAAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAAC
Found at i:54645 original size:50 final size:50
Alignment explanation
Indices: 53754--54642 Score: 1562
Period size: 50 Copynumber: 17.8 Consensus size: 50
53744 CTGAATACAA
*
53754 AGGCTTTTCCACAAGCCAACCTCGTTTCCATACGAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
* *
53804 AGGCTTTTCCACAAGCCAACCTCGTTTCCATACGAGTCAATTATTAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
53854 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
53904 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
* *
53954 AGACTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
54004 AGACTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
54054 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
54104 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
54154 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
54204 AGGCTTTTCCACAAGCCAAACTCGTTTTCATACGAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
* *
54254 AGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATTATCAACTT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
* *
54304 GGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
* *
54354 AGGATTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
54404 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
54454 AGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
54504 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
* * *
54554 AGACTTTTCCACAAGCCAAAGTCGTTTCCATACGAGTCAGTTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
**
54604 AAACTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
54643 GTTCAAGCCT
Statistics
Matches: 809, Mismatches: 30, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 809 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (50 bp):
AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
Found at i:54802 original size:69 final size:69
Alignment explanation
Indices: 54606--54783 Score: 302
Period size: 69 Copynumber: 2.6 Consensus size: 69
54596 ATCAACATAA
54606 ACTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTTCATCCAAGCCAT
1 ACTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTTCATCCAAGCCAT
54671 ATAG
66 ATAG
* * *
54675 GCTTTTCCACATGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTTTATCCAAGCCAT
1 ACTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTTCATCCAAGCCAT
54740 ATAG
66 ATAG
* * *
54744 ACTTTTCCATAAGTCAAACTCGTTTCCATGCGAGTCAGTT
1 ACTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT
54784 TGAACATTGG
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 101 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (69 bp):
ACTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTTCATCCAAGCCAT
ATAG
Found at i:54984 original size:13 final size:13
Alignment explanation
Indices: 54966--54991 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54956 AAATCTTTGG
54966 TCAAGGTCTCTTT
1 TCAAGGTCTCTTT
54979 TCAAGGTCTCTTT
1 TCAAGGTCTCTTT
54992 GAGTTTCTTA
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:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
TCAAGGTCTCTTT
Found at i:59760 original size:8 final size:8
Alignment explanation
Indices: 59747--59793 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
59737 CAAAGTTGAA
59747 GAAAAAAT
1 GAAAAAAT
59755 GAAAAAA-
1 GAAAAAAT
59762 GAAGAAAA-
1 GAA-AAAAT
59770 GAAAAAAT
1 GAAAAAAT
*
59778 GAAAAGAT
1 GAAAAAAT
*
59786 GGAAAAAT
1 GAAAAAAT
59794 CAGAAAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 7 0.21
8 27 0.79
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (8 bp):
GAAAAAAT
Found at i:59773 original size:15 final size:15
Alignment explanation
Indices: 59745--59792 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
59735 GTCAAAGTTG
59745 AAGAAAAAATGAAAA
1 AAGAAAAAATGAAAA
59760 AAGAAGAAAA-GAAAA
1 AAGAA-AAAATGAAAA
*
59775 AATGAAAAGATGGAAAA
1 AA-GAAAAAAT-GAAAA
59792 A
1 A
59793 TCAGAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 15 0.54
16 7 0.25
17 6 0.21
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (15 bp):
AAGAAAAAATGAAAA
Found at i:61429 original size:18 final size:17
Alignment explanation
Indices: 61406--61442 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
61396 CTAGCCCTAA
61406 AACTAGAAGAAAAACAAG
1 AACTAGAAGAAAAA-AAG
*
61424 AACTAGAAGAGAAAAAG
1 AACTAGAAGAAAAAAAG
61441 AA
1 AA
61443 GAAGAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.68, C:0.08, G:0.19, T:0.05
Consensus pattern (17 bp):
AACTAGAAGAAAAAAAG
Found at i:62037 original size:19 final size:18
Alignment explanation
Indices: 62004--62039 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
61994 TTGAAATTAT
62004 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
62022 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
62040 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:62905 original size:18 final size:18
Alignment explanation
Indices: 62882--62918 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
62872 CTACTCTATC
*
62882 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
*
62900 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTCTTTTT
62918 A
1 A
62919 ATTACCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:65415 original size:14 final size:14
Alignment explanation
Indices: 65396--65443 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
65386 GCGATTTCTC
65396 CATGAGGTATTTTT
1 CATGAGGTATTTTT
* *
65410 CATGAGGTATGTGAGTC
1 CATGAGGTAT-T--TTT
65427 CATGAGGTATTTTT
1 CATGAGGTATTTTT
65441 CAT
1 CAT
65444 CTCATGGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 14 0.52
15 1 0.04
16 1 0.04
17 11 0.41
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (14 bp):
CATGAGGTATTTTT
Done.