Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1089
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: 79684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1311 original size:9 final size:9
Alignment explanation
Indices: 1293--1422 Score: 115
Period size: 9 Copynumber: 14.2 Consensus size: 9
1283 AAATCTTCAC
1293 TTTT-TTTT
1 TTTTGTTTT
1301 TTTTGTTTT
1 TTTTGTTTT
1310 TTTT-TTTT
1 TTTTGTTTT
1318 TTTT-TTCGTT
1 TTTTGTT--TT
1328 TTTTGTTTT
1 TTTTGTTTT
*
1337 GTTT-TTTT
1 TTTTGTTTT
*
1345 TTTTCTTTCT
1 TTTTGTTT-T
*
1355 TTTTCCCTTTT
1 TTTT--GTTTT
1366 TTTTGTTTT
1 TTTTGTTTT
*
1375 GTTTGTTTCT
1 TTTTGTTT-T
*
1385 TTTTTTTTT
1 TTTTGTTTT
1394 TTTTGTTTT
1 TTTTGTTTT
**
1403 GGTTGTTTT
1 TTTTGTTTT
1412 TTTTGTTTT
1 TTTTGTTTT
1421 TT
1 TT
1423 CCTTTGTTTT
Statistics
Matches: 102, Mismatches: 11, Indels: 17
0.78 0.08 0.13
Matches are distributed among these distances:
8 21 0.21
9 52 0.51
10 18 0.18
11 7 0.07
12 4 0.04
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.85
Consensus pattern (9 bp):
TTTTGTTTT
Found at i:1409 original size:70 final size:68
Alignment explanation
Indices: 1292--1423 Score: 180
Period size: 70 Copynumber: 1.9 Consensus size: 68
1282 AAAATCTTCA
*
1292 CTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTCGTTTTTTGTTTTGTTTTTTTT-TTTCTTTCTT
1 CTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTC-TTTTTTGTGTTGTTTTTTTTGTTT-TTTCTT
1356 TTTCC
64 TTTCC
1361 CTTTTTTTTGTTTTGTTTGTTTCTTTTTTTTTTTT-TTGTTTTG-GTTGTTTTTTTTGTTTTTTC
1 CTTTTTTTT-TTTTGTTT-TTT-TTTTTTTTTTTTCTT-TTTTGTGTTGTTTTTTTTGTTTTTTC
1424 CTTTGTTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
69 9 0.16
70 25 0.44
71 11 0.19
72 12 0.21
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (68 bp):
CTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTCTTTTTTGTGTTGTTTTTTTTGTTTTTTCTTTT
TCC
Found at i:1439 original size:1 final size:1
Alignment explanation
Indices: 1293--1422 Score: 89
Period size: 1 Copynumber: 130.0 Consensus size: 1
1283 AAATCTTCAC
* ** * * * *
1293 TTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTCGTTTTTTGTTTTGTTTTTTTTTTTCTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*** * * * * * ** * *
1358 TCCCTTTTTTTTGTTTTGTTTGTTTCTTTTTTTTTTTTTTGTTTTGGTTGTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1423 CCTTTGTTTT
Statistics
Matches: 98, Mismatches: 31, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 98 1.00
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:1439 original size:70 final size:71
Alignment explanation
Indices: 1293--1449 Score: 171
Period size: 74 Copynumber: 2.2 Consensus size: 71
1283 AAATCTTCAC
* * * *
1293 TTTTT-TTTTTTTGTTTTTTTTTTTTTTTTTTCGTTTTTTGTTTTGTTTTTTTTTTTCTTTCTTT
1 TTTTTGTTTTTTTGTTTCTTTTTTTTTTTTTTCGTTTTTTGTTTTGTTTTGTTTTTTCCTTCTGT
*
1357 TTCCCTTT
66 TT--CTTG
1365 TTTTTGTTTTGTTTGTTTCTTTTTTTTTTTTTT-GTTTTGGTTGTTTT-TTTTGTTTTTTCCTT-
1 TTTTTGTTTT-TTTGTTTCTTTTTTTTTTTTTTCGTTTT--TTGTTTTGTTTTGTTTTTTCCTTC
1427 TGTTT-TTG
63 TGTTTCTTG
1435 TTTTTGGGTTTTTTT
1 TTTTT--GTTTTTTT
1450 CTTTTCCATT
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
70 7 0.09
71 3 0.04
72 10 0.14
73 13 0.18
74 34 0.46
75 7 0.09
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (71 bp):
TTTTTGTTTTTTTGTTTCTTTTTTTTTTTTTTCGTTTTTTGTTTTGTTTTGTTTTTTCCTTCTGT
TTCTTG
Found at i:12853 original size:24 final size:24
Alignment explanation
Indices: 12804--12863 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
12794 ACAAGCGATT
* * *
12804 AATAAAAGTAAAATTATTAATATA
1 AATAAAAATCAAATTATCAATATA
12828 AATAAAAATCAAATTATCAAGT-TA
1 AATAAAAATCAAATTATCAA-TATA
*
12852 AATGAAAATCAA
1 AATAAAAATCAA
12864 TCTTACCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (24 bp):
AATAAAAATCAAATTATCAATATA
Found at i:17004 original size:26 final size:26
Alignment explanation
Indices: 16943--17004 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
16933 AATTCTATAG
* *
16943 ATATAGTATTGAAAAAGTTTAACTTT
1 ATATAGGATTGAAAAAGTTCAACTTT
* * * *
16969 CTCTAAGATTGATAAAGTTCAACTTT
1 ATATAGGATTGAAAAAGTTCAACTTT
16995 ATATAGGATT
1 ATATAGGATT
17005 TTAGATTTTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (26 bp):
ATATAGGATTGAAAAAGTTCAACTTT
Found at i:17717 original size:6 final size:6
Alignment explanation
Indices: 17708--17737 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
17698 TTTTCTTTTT
*
17708 CCCTTG CCCTTC CCCTTC CCCTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
17738 GCTTCGCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.63, G:0.03, T:0.33
Consensus pattern (6 bp):
CCCTTC
Found at i:19941 original size:12 final size:13
Alignment explanation
Indices: 19920--19945 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19910 CACCCATCAC
19920 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
19933 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
19946 TGAAACGATG
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAA
Found at i:22057 original size:17 final size:18
Alignment explanation
Indices: 22029--22093 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
22019 AAAATCTAAT
*
22029 GATTCTTAAAAAAATTGA
1 GATTCTTAAAAAATTTGA
*
22047 GATTCTTAAAAAATTTAA
1 GATTCTTAAAAAATTTGA
* *
22065 AATT-TTAAAAAATTATGT
1 GATTCTTAAAAAATT-TGA
22083 GATTCTTAAAA
1 GATTCTTAAAA
22094 TCTATGATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
17 10 0.26
18 23 0.59
19 6 0.15
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
GATTCTTAAAAAATTTGA
Found at i:23358 original size:21 final size:18
Alignment explanation
Indices: 23310--23348 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
23300 GGGCGTGATT
*
23310 TCTTCATCAAATACTGGC
1 TCTTCATCAAATACGGGC
23328 TCTTCATCAAATACGGGC
1 TCTTCATCAAATACGGGC
23346 TCT
1 TCT
23349 CTATCATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (18 bp):
TCTTCATCAAATACGGGC
Found at i:24930 original size:18 final size:17
Alignment explanation
Indices: 24907--24974 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 17
24897 GTGATTCTTA
24907 ATAATTTTTAAAAAATT
1 ATAATTTTTAAAAAATT
*
24924 CATAATTCTTAAAAAATT
1 -ATAATTTTTAAAAAATT
24942 -TAAATTTTTTTAAAAAAATT
1 AT-AA--TTTTT-AAAAAATT
24962 ATAATTTTTAAAA
1 ATAATTTTTAAAA
24975 TCTGTGATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
16 1 0.02
17 6 0.14
18 21 0.49
19 4 0.09
20 10 0.23
21 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAATTTTTAAAAAATT
Found at i:25930 original size:2 final size:2
Alignment explanation
Indices: 25919--25952 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
25909 TCATTCCATA
25919 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25953 TCATCTAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:27122 original size:3 final size:3
Alignment explanation
Indices: 27114--27152 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
27104 AGTTCATTTG
27114 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
27153 CATGGATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:32145 original size:2 final size:2
Alignment explanation
Indices: 32138--32168 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32128 CTTTTCCGTT
32138 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
32169 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:43085 original size:21 final size:21
Alignment explanation
Indices: 43052--43094 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
43042 CTAAGTAAAA
43052 ATACGTATTGTATCAATACAC
1 ATACGTATTGTATCAATACAC
*
43073 ATAC-TATTGGTATTAATACAC
1 ATACGTATT-GTATCAATACAC
43094 A
1 A
43095 AGATTGACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAC
Found at i:43157 original size:20 final size:19
Alignment explanation
Indices: 43132--43202 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
43122 ACCATGAAAA
43132 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
43152 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
43171 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
43192 GTATCGATACA
1 GTATCGATACA
43203 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:43256 original size:53 final size:53
Alignment explanation
Indices: 43172--43305 Score: 232
Period size: 53 Copynumber: 2.5 Consensus size: 53
43162 AAATTGCATA
43172 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
* *
43226 GTATCGATACACACAATATATATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
43279 GTATCGATACACAAAATATGTATCGAT
1 GTATCGATACACACAATATGTATCGAT
43306 GCATTGGAAG
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 62 0.82
54 14 0.18
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:43351 original size:10 final size:10
Alignment explanation
Indices: 43332--43362 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
43322 AATCTCATTT
43332 TCACTGTTCA
1 TCACTGTTCA
*
43342 TCACTATTCA
1 TCACTGTTCA
43352 TCACTGTTCA
1 TCACTGTTCA
43362 T
1 T
43363 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:43384 original size:21 final size:22
Alignment explanation
Indices: 43350--43405 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
43340 CATCACTATT
43350 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
43372 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
43393 CATCACTGTTCAT
1 CATCACTGTTCAT
43406 AGGTCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:43513 original size:13 final size:13
Alignment explanation
Indices: 43495--43520 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43485 ACATATTTGT
43495 GTGTATCGATACA
1 GTGTATCGATACA
43508 GTGTATCGATACA
1 GTGTATCGATACA
43521 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:46608 original size:29 final size:30
Alignment explanation
Indices: 46566--46675 Score: 104
Period size: 29 Copynumber: 3.8 Consensus size: 30
46556 TATTGTCAAG
*
46566 AAGTAT-TGTTGCCAAAAGTACATATG-CAA
1 AAGTATCTG-TGCCAAAAGTACTTATGACAA
* *
46595 AATGTA-CTGTGCC-AGAGTACTTGTGACAA
1 AA-GTATCTGTGCCAAAAGTACTTATGACAA
** *
46624 AAGTATCTGTG-TGAAAGTACTTATGTCAA
1 AAGTATCTGTGCCAAAAGTACTTATGACAA
*
46653 AAGTATCTGTGCCAAAAGAACTT
1 AAGTATCTGTGCCAAAAGTACTT
46676 GTGTTAAATT
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
28 12 0.18
29 40 0.62
30 13 0.20
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (30 bp):
AAGTATCTGTGCCAAAAGTACTTATGACAA
Found at i:46745 original size:14 final size:14
Alignment explanation
Indices: 46723--46764 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
46713 GTACCTATGA
46723 CAAAGGTACTTGTAC
1 CAAA-GTACTTGTAC
*
46738 CAAAGTACTTGTGC
1 CAAAGTACTTGTAC
*
46752 CAAAGTACCTGTA
1 CAAAGTACTTGTA
46765 GTAAATAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (14 bp):
CAAAGTACTTGTAC
Found at i:47597 original size:14 final size:14
Alignment explanation
Indices: 47578--47604 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47568 GATAAAAATA
47578 GAAAAAAAAAGAAG
1 GAAAAAAAAAGAAG
47592 GAAAAAAAAAGAA
1 GAAAAAAAAAGAA
47605 AAAATATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAGAAG
Found at i:48776 original size:29 final size:29
Alignment explanation
Indices: 48733--48791 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
48723 ACGTATGTGA
* *
48733 TTTTTTTGTTTTGA-TTTGAAAAGTGATTT
1 TTTTTTTGATATGATTTTG-AAAGTGATTT
*
48762 TTTTTTTGATATGATTTTGAAGGTGATTT
1 TTTTTTTGATATGATTTTGAAAGTGATTT
48791 T
1 T
48792 GTTAAAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.19, T:0.61
Consensus pattern (29 bp):
TTTTTTTGATATGATTTTGAAAGTGATTT
Found at i:49118 original size:37 final size:37
Alignment explanation
Indices: 49046--49127 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
49036 TAGAAATCGA
* * * *
49046 TTTCAACCGTGCCACCAGTAGAGAATAGTGGTTTTTG
1 TTTCGACCGTGCCACCAATAGAGAATAATGATTTTTG
49083 TTTCGACCTGTGCCACCAATA-AGAATAATGATTTTTG
1 TTTCGACC-GTGCCACCAATAGAGAATAATGATTTTTG
49120 TTTCGACC
1 TTTCGACC
49128 CATACCATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 29 0.73
38 11 0.28
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (37 bp):
TTTCGACCGTGCCACCAATAGAGAATAATGATTTTTG
Found at i:49192 original size:37 final size:37
Alignment explanation
Indices: 49095--49194 Score: 110
Period size: 37 Copynumber: 2.7 Consensus size: 37
49085 TCGACCTGTG
* * *
49095 CCACCAATAAGAATAATGATTTTTGTTTCGACCCATA
1 CCACCGATAAGAATAATGATTTTTATTCCGACCCATA
** * * * *
49132 CCATTGGTAATAATAGTGATTTTTATTCCGATCCATA
1 CCACCGATAAGAATAATGATTTTTATTCCGACCCATA
*
49169 CCACCGATAAGAATAATGGTTTTTAT
1 CCACCGATAAGAATAATGATTTTTAT
49195 CTCGAATCGT
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (37 bp):
CCACCGATAAGAATAATGATTTTTATTCCGACCCATA
Found at i:50282 original size:133 final size:133
Alignment explanation
Indices: 50139--50379 Score: 310
Period size: 132 Copynumber: 1.8 Consensus size: 133
50129 TGGTAGTAGG
* * *
50139 GCATGGGACCATAATGGTCGACTTCTTTATGGGAAA-AACTTGTATATA-GAAGAGTGACAAAAG
1 GCATGGGACCACAACGATCGACTT-TTTAT-GGAAAGAACTTGTATATAGGAA-AGTGACAAAAG
* *
50202 TGGAGCATAAGACCACAA-GGTTGACTTCTCTATTAAGAA-TACTTGAATTAGAGAGAGTGTTGG
63 TGGAGCATAAGACCACAACGATTAACTTCTCTATTAA-AAGTACTTGAATTAGAGAGAGTGTTGG
50265 AAATAGC
127 AAATAGC
* * * *
50272 GCATGGGACCACAACGATTGGCTTTTTATTGAAAGAACTTGTATATAGGAAAGTGACAGAAGTGG
1 GCATGGGACCACAACGATCGACTTTTTATGGAAAGAACTTGTATATAGGAAAGTGACAAAAGTGG
* * *
50337 AGTATAGGAGCACAACGATTAACTTCTCTATTAAAAGTACTTG
66 AGCATAAGACCACAACGATTAACTTCTCTATTAAAAGTACTTG
50380 TGAATGTGAG
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
131 4 0.04
132 44 0.48
133 44 0.48
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (133 bp):
GCATGGGACCACAACGATCGACTTTTTATGGAAAGAACTTGTATATAGGAAAGTGACAAAAGTGG
AGCATAAGACCACAACGATTAACTTCTCTATTAAAAGTACTTGAATTAGAGAGAGTGTTGGAAAT
AGC
Found at i:52466 original size:15 final size:14
Alignment explanation
Indices: 52415--52479 Score: 58
Period size: 15 Copynumber: 4.5 Consensus size: 14
52405 ATTGCTATTG
*
52415 AAAGTACATGTGCA
1 AAAGTACTTGTGCA
* * *
52429 AAAGGTAATTATGCT
1 AAA-GTACTTGTGCA
*
52444 AGAGTACTTGTGACA
1 AAAGTACTTGTG-CA
*
52459 AAAGTACTTGTGCC
1 AAAGTACTTGTGCA
52473 AAAGTAC
1 AAAGTAC
52480 CTATATCAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
14 18 0.46
15 21 0.54
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (14 bp):
AAAGTACTTGTGCA
Found at i:52478 original size:29 final size:29
Alignment explanation
Indices: 52415--52479 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
52405 ATTGCTATTG
*
52415 AAAGTACATGTGCAAAAGGTAATTATGCT
1 AAAGTACATGTGCAAAAGGTAATTATGCC
* * * *
52444 AGAGTACTTGTGACAAAA-GTACTTGTGCC
1 AAAGTACATGTG-CAAAAGGTAATTATGCC
52473 AAAGTAC
1 AAAGTAC
52480 CTATATCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (29 bp):
AAAGTACATGTGCAAAAGGTAATTATGCC
Found at i:63202 original size:21 final size:21
Alignment explanation
Indices: 63169--63217 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
63159 TACATCCTTC
* *
63169 TATCTAATAAATGTATTATTT
1 TATCTAATAAATGCATCATTT
63190 TATCTAACT-AATGCATCATTT
1 TATCTAA-TAAATGCATCATTT
*
63211 AATCTAA
1 TATCTAA
63218 ATGCTTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (21 bp):
TATCTAATAAATGCATCATTT
Found at i:70299 original size:19 final size:18
Alignment explanation
Indices: 70253--70306 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
70243 ATTCAACAAT
70253 TTGTATCGATACAAACTG
1 TTGTATCGATACAAACTG
*
70271 TAACTGTATCGATACATAAGTG
1 T---TGTATCGATACA-AACTG
70293 TTGTATCGATACAA
1 TTGTATCGATACAA
70307 TGTATACATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.06
19 12 0.39
21 12 0.39
22 5 0.16
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (18 bp):
TTGTATCGATACAAACTG
Found at i:70314 original size:28 final size:28
Alignment explanation
Indices: 70282--70399 Score: 200
Period size: 28 Copynumber: 4.1 Consensus size: 28
70272 AACTGTATCG
70282 ATACATAAGTGTTGTATCGATACAATGT
1 ATACATAAGTGTTGTATCGATACAATGT
70310 ATACATAAGTGTTGTATCGATACAATGT
1 ATACATAAGTGTTGTATCGATACAATGT
70338 ATACATAAGTGTTGTATCGATACAATGTAT
1 ATACATAAGTGTTGTATCGATACAATG--T
70368 CGATACATAAGTGTTGTATCGATACAATGT
1 --ATACATAAGTGTTGTATCGATACAATGT
70398 AT
1 AT
70400 CGCTACAAAG
Statistics
Matches: 86, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
28 57 0.66
30 2 0.02
32 27 0.31
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (28 bp):
ATACATAAGTGTTGTATCGATACAATGT
Found at i:70344 original size:56 final size:58
Alignment explanation
Indices: 70282--70399 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 58
70272 AACTGTATCG
70282 ATACATAAGTGTTGTATCGATACAATG-T-ATACATAAGTGTTGTATCGATACAATGT
1 ATACATAAGTGTTGTATCGATACAATGATCATACATAAGTGTTGTATCGATACAATGT
70338 ATACATAAGTGTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGT
1 ATACATAAGTGTTGTATCGATACAATG-ATC-ATACATAAGTGTTGTATCGATACAATGT
70398 AT
1 AT
70400 CGCTACAAAG
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
56 27 0.47
58 1 0.02
60 30 0.52
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (58 bp):
ATACATAAGTGTTGTATCGATACAATGATCATACATAAGTGTTGTATCGATACAATGT
Found at i:70368 original size:13 final size:13
Alignment explanation
Indices: 70350--70407 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
70340 ACATAAGTGT
70350 TGTATCGATACAA
1 TGTATCGATACAA
70363 TGTATCGATACATAA
1 TGTATCGATAC--AA
70378 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
70395 TGTATCGCTACAA
1 TGTATCGATACAA
70408 AGCTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:70379 original size:32 final size:32
Alignment explanation
Indices: 70275--70406 Score: 199
Period size: 28 Copynumber: 4.4 Consensus size: 32
70265 AAACTGTAAC
70275 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
70307 TG--T--ATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
70335 TG--T--ATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
70363 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
70395 TGTATCGCTACA
1 TGTATCGATACA
70407 AAGCTACTGC
Statistics
Matches: 95, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
28 55 0.58
30 2 0.02
32 38 0.40
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:70387 original size:19 final size:19
Alignment explanation
Indices: 70338--70393 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
70328 GATACAATGT
70338 ATACATAAGTGTTGTATCG
1 ATACATAAGTGTTGTATCG
70357 ATAC--AA----TGTATCG
1 ATACATAAGTGTTGTATCG
70370 ATACATAAGTGTTGTATCG
1 ATACATAAGTGTTGTATCG
70389 ATACA
1 ATACA
70394 ATGTATCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 11 0.35
15 2 0.06
17 2 0.06
19 16 0.52
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (19 bp):
ATACATAAGTGTTGTATCG
Found at i:70463 original size:13 final size:13
Alignment explanation
Indices: 70445--70472 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
70435 CATTACTCAA
70445 TGTATCAATACAT
1 TGTATCAATACAT
70458 TGTATCAATACAT
1 TGTATCAATACAT
70471 TG
1 TG
70473 ATCTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:75674 original size:34 final size:33
Alignment explanation
Indices: 75626--75842 Score: 258
Period size: 34 Copynumber: 6.4 Consensus size: 33
75616 TGGTAAAAAC
*
75626 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
75659 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
75693 CATCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
75727 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
75761 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
75795 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
75829 CACCATTTAATCAA
1 CACCATTTAATCAA
75843 TAATTCTCCC
Statistics
Matches: 158, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 19 0.12
34 133 0.84
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:75769 original size:102 final size:101
Alignment explanation
Indices: 75626--75842 Score: 335
Period size: 102 Copynumber: 2.1 Consensus size: 101
75616 TGGTAAAAAC
* *
75626 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* * *
75691 ATCATCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
75727 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
75792 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
75829 CACCATTTAATCAA
1 CACCATTTAATCAA
75843 TAATTCTCCC
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 12 0.12
102 91 0.88
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Done.