Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold339
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: 94545
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3593 original size:24 final size:25
Alignment explanation
Indices: 3540--3593 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
3530 AACAAATTCT
* *
3540 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
3565 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
3588 TTTTTT
1 TTTTTT
3594 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:3595 original size:68 final size:69
Alignment explanation
Indices: 3516--3643 Score: 154
Period size: 68 Copynumber: 1.9 Consensus size: 69
3506 TTTCGAACTT
3516 TCTCTTCTTTTA-CAAACAAATTCTTTTTTTCAT-TTTCATCACTCGTTTCTTT-TTCTTTTGAA
1 TCTCTTCTTTTATCAAACAAATT-TTTTTTTCATCTTTCATCACTC-TTTCTTTATTCTTTTGAA
3578 TCACTC
64 TCACTC
* ** ** * *
3584 TCTCTTTTTTTATCACTCATCTTTTTTTTTCTTCTTTCTTCACTCTTTCTTTATTCTTTT
1 TCTCTTCTTTTATCAAACAAATTTTTTTTTCATCTTTCATCACTCTTTCTTTATTCTTTT
3644 CATTTTTTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
68 27 0.54
69 23 0.46
ACGTcount: A:0.14, C:0.23, G:0.02, T:0.61
Consensus pattern (69 bp):
TCTCTTCTTTTATCAAACAAATTTTTTTTTCATCTTTCATCACTCTTTCTTTATTCTTTTGAATC
ACTC
Found at i:3598 original size:18 final size:18
Alignment explanation
Indices: 3577--3612 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3567 TTTCTTTTGA
3577 ATCACTC-TCTCTTTTTTT
1 ATCACTCATCT-TTTTTTT
3595 ATCACTCATCTTTTTTTT
1 ATCACTCATCTTTTTTTT
3613 TCTTCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (18 bp):
ATCACTCATCTTTTTTTT
Found at i:9409 original size:22 final size:22
Alignment explanation
Indices: 9379--9422 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9369 TTTGGTATTT
9379 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
9401 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
9423 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:13018 original size:14 final size:13
Alignment explanation
Indices: 12999--13048 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
12989 TAGCTCTCTC
12999 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
13012 TTTTTTTTCACAAT
1 TTTTTTTTCA-AAT
*
13026 TTTTTTTTCAAAA
1 TTTTTTTTCAAAT
13039 TTTTTTTTCA
1 TTTTTTTTCA
13049 CAACTTGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
13 22 0.63
14 13 0.37
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:13036 original size:27 final size:27
Alignment explanation
Indices: 12999--13051 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
12989 TAGCTCTCTC
*
12999 TTTTTTTTCAAATTTTTTTTTCACAAT
1 TTTTTTTTCAAAATTTTTTTTCACAAT
13026 TTTTTTTTCAAAATTTTTTTTCACAA
1 TTTTTTTTCAAAATTTTTTTTCACAA
13052 CTTGATATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTTTTCAAAATTTTTTTTCACAAT
Found at i:13107 original size:13 final size:13
Alignment explanation
Indices: 13089--13119 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13079 TGGAAACTAG
*
13089 TTTTTTTCGAATT
1 TTTTTTTCAAATT
13102 TTTTTTTCAAATT
1 TTTTTTTCAAATT
13115 TTTTT
1 TTTTT
13120 GAGCTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTTTCAAATT
Found at i:21220 original size:10 final size:10
Alignment explanation
Indices: 21205--21266 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
21195 TTTGAACCAT
*
21205 TACCAATTCG
1 TACCAATTCA
*
21215 TACCAAATACCA
1 TACC-AAT-TCA
*
21227 TACCATTTCA
1 TACCAATTCA
21237 TACCAATTCCA
1 TACCAATT-CA
* *
21248 TACCATTTCG
1 TACCAATTCA
21258 TACCAATTC
1 TACCAATTC
21267 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:21250 original size:21 final size:21
Alignment explanation
Indices: 21205--21267 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
21195 TTTGAACCAT
* *
21205 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
21227 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
21248 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
21268 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:23473 original size:12 final size:11
Alignment explanation
Indices: 23456--23513 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 11
23446 AGTTTCTCGT
*
23456 AAAAAAAACTTG
1 AAAAAAAA-TTC
23468 AAAAAAAATTC
1 AAAAAAAATTC
23479 AAAAAAAAAATTC
1 --AAAAAAAATTC
23492 AAAAAAAAAAATTC
1 ---AAAAAAAATTC
23506 AAAAAAAA
1 AAAAAAAA
23514 AATTTTGGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
11 10 0.24
12 8 0.19
13 11 0.26
14 13 0.31
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:23475 original size:14 final size:13
Alignment explanation
Indices: 23468--23517 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
23458 AAAAAACTTG
23468 AAAAAAAATTCAA
1 AAAAAAAATTCAA
23481 AAAAAAAATTCAAA
1 AAAAAAAATTC-AA
23495 AAAAAAAATTCAA
1 AAAAAAAATTCAA
23508 AAAAAAAATT
1 AAAAAAAATT
23518 TTGGTTTCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 23 0.64
14 13 0.36
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:23584 original size:13 final size:13
Alignment explanation
Indices: 23555--23604 Score: 70
Period size: 14 Copynumber: 4.0 Consensus size: 13
23545 GGATATCAAG
23555 TTGTG-AAAAAAA
1 TTGTGAAAAAAAA
23567 -T-TGAAAAAAAA
1 TTGTGAAAAAAAA
23578 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
23591 TTTGTGAAAAAAAA
1 -TTGTGAAAAAAAA
23605 GAGAGCTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.06
11 8 0.24
12 1 0.03
13 10 0.29
14 13 0.38
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:24364 original size:18 final size:17
Alignment explanation
Indices: 24338--24381 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
24328 GAGTGACGAG
24338 AGAAAAAAAACCGAAAA
1 AGAAAAAAAACCGAAAA
**
24355 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACCGAAAA
24373 AGAGAAAAA
1 AGA-AAAAA
24382 GATTGGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 16 0.70
19 2 0.09
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.05
Consensus pattern (17 bp):
AGAAAAAAAACCGAAAA
Found at i:34888 original size:21 final size:23
Alignment explanation
Indices: 34843--34889 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
34833 TCACCTGCAA
* *
34843 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
34866 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
34887 TAA
1 TAA
34890 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39031 original size:11 final size:11
Alignment explanation
Indices: 39013--39057 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
39003 AAGAGGAAAT
39013 TTGAAAAAAAA
1 TTGAAAAAAAA
*
39024 TCGAAAAAAAA
1 TTGAAAAAAAA
39035 TTGAAAAAAAAA
1 TTG-AAAAAAAA
39047 TTGAAAAAAAA
1 TTGAAAAAAAA
39058 ATTCGAAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (11 bp):
TTGAAAAAAAA
Found at i:39031 original size:12 final size:12
Alignment explanation
Indices: 39016--39064 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
39006 AGGAAATTTG
39016 AAAAAAAATCG-
1 AAAAAAAATCGA
*
39027 AAAAAAAATTGA
1 AAAAAAAATCGA
*
39039 AAAAAAAATTGA
1 AAAAAAAATCGA
39051 AAAAAAAATTCGA
1 AAAAAAAA-TCGA
39064 A
1 A
39065 GTATTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 10 0.29
12 20 0.59
13 4 0.12
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:43499 original size:12 final size:12
Alignment explanation
Indices: 43482--43531 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
43472 GAGGAAATTT
43482 GAAAAAAAAATC
1 GAAAAAAAAATC
*
43494 G--AAAAAAATT
1 GAAAAAAAAATC
*
43504 GAAAAAAAAATT
1 GAAAAAAAAATC
43516 GAAAAAAAAATTC
1 GAAAAAAAAA-TC
43529 GAA
1 GAA
43532 GTATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 9 0.27
12 20 0.61
13 4 0.12
ACGTcount: A:0.72, C:0.04, G:0.10, T:0.14
Consensus pattern (12 bp):
GAAAAAAAAATC
Found at i:43505 original size:22 final size:22
Alignment explanation
Indices: 43480--43523 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43470 AAGAGGAAAT
43480 TTGAAAAAAAAATCGAAAAAAA
1 TTGAAAAAAAAATCGAAAAAAA
*
43502 TTGAAAAAAAAATTGAAAAAAA
1 TTGAAAAAAAAATCGAAAAAAA
43524 AATTCGAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (22 bp):
TTGAAAAAAAAATCGAAAAAAA
Found at i:43518 original size:34 final size:35
Alignment explanation
Indices: 43444--43531 Score: 99
Period size: 34 Copynumber: 2.5 Consensus size: 35
43434 AGCATATTGT
* **
43444 AATTGAACAAAAAATC-AAAAAAAAAGAAGAGGAA
1 AATTGAAAAAAAAATCGAAAAAAAAAGAAGAAAAA
* **
43478 ATTTGAAAAAAAAATCGAAAAAAATTGAA-AAAAA
1 AATTGAAAAAAAAATCGAAAAAAAAAGAAGAAAAA
43512 AATTGAAAAAAAAATTCGAA
1 AATTGAAAAAAAAA-TCGAA
43532 GTATTAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 30 0.67
35 15 0.33
ACGTcount: A:0.69, C:0.05, G:0.11, T:0.15
Consensus pattern (35 bp):
AATTGAAAAAAAAATCGAAAAAAAAAGAAGAAAAA
Found at i:43520 original size:10 final size:10
Alignment explanation
Indices: 43485--43523 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
43475 GAAATTTGAA
*
43485 AAAAAAATCG
1 AAAAAAATTG
43495 AAAAAAATTG
1 AAAAAAATTG
43505 AAAAAAAAATTG
1 --AAAAAAATTG
43517 AAAAAAA
1 AAAAAAA
43524 AATTCGAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 16 0.62
12 10 0.38
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:52320 original size:21 final size:23
Alignment explanation
Indices: 52275--52321 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
52265 TCACCTGCAA
* *
52275 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
52298 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
52319 TAA
1 TAA
52322 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:57290 original size:15 final size:14
Alignment explanation
Indices: 57253--57287 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
57243 CTTCTTCTTC
57253 TTTTTTTCACGAAT
1 TTTTTTTCACGAAT
57267 TTTTTTTCACGAAT
1 TTTTTTTCACGAAT
57281 TTTTTTT
1 TTTTTTT
57288 TCAACTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (14 bp):
TTTTTTTCACGAAT
Found at i:57346 original size:11 final size:11
Alignment explanation
Indices: 57330--57375 Score: 74
Period size: 11 Copynumber: 4.0 Consensus size: 11
57320 GCAAACCAAT
57330 TTTTTTTTTGA
1 TTTTTTTTTGA
57341 TTTTTTTTTGAA
1 TTTTTTTTTG-A
57353 TTTTTTTTTTGA
1 -TTTTTTTTTGA
57365 TTTTTTTTTGA
1 TTTTTTTTTGA
57376 AGAAACTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 21 0.64
12 2 0.06
13 10 0.30
ACGTcount: A:0.11, C:0.00, G:0.09, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:57347 original size:13 final size:12
Alignment explanation
Indices: 57328--57373 Score: 76
Period size: 12 Copynumber: 3.8 Consensus size: 12
57318 AAGCAAACCA
57328 ATTTTTTTTTTG
1 ATTTTTTTTTTG
57340 A-TTTTTTTTTG
1 ATTTTTTTTTTG
57351 AATTTTTTTTTTG
1 -ATTTTTTTTTTG
57364 ATTTTTTTTT
1 ATTTTTTTTT
57374 GAAGAAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.31
12 12 0.38
13 10 0.31
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.83
Consensus pattern (12 bp):
ATTTTTTTTTTG
Found at i:57355 original size:24 final size:24
Alignment explanation
Indices: 57327--57376 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
57317 AAAGCAAACC
57327 AATTTTTTTTTTGATTTTTTTTTG
1 AATTTTTTTTTTGATTTTTTTTTG
57351 AATTTTTTTTTTGATTTTTTTTTG
1 AATTTTTTTTTTGATTTTTTTTTG
57375 AA
1 AA
57377 GAAACTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (24 bp):
AATTTTTTTTTTGATTTTTTTTTG
Found at i:62066 original size:15 final size:15
Alignment explanation
Indices: 62023--62071 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 15
62013 TTTTTTTCAC
62023 TTTTTTTT-G-AA-T
1 TTTTTTTTCGAAATT
*
62035 TTTTTTTTCAATCAATT
1 TTTTTTTTCGA--AATT
62052 TTTTTTTTCGAAATT
1 TTTTTTTTCGAAATT
62067 TTTTT
1 TTTTT
62072 GATTTTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 8 0.27
15 9 0.30
16 2 0.07
17 11 0.37
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.71
Consensus pattern (15 bp):
TTTTTTTTCGAAATT
Found at i:64658 original size:11 final size:11
Alignment explanation
Indices: 64642--64671 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
64632 GGAAATTTGA
64642 AAAAAAAATTC
1 AAAAAAAATTC
64653 AAAAAAAATTC
1 AAAAAAAATTC
64664 AAAAAAAA
1 AAAAAAAA
64672 AATTTTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:70218 original size:20 final size:20
Alignment explanation
Indices: 70172--70218 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
70162 AGCTCGTTTC
*
70172 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
70192 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
70212 CAGCTCA
1 CAGCTCA
70219 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:71739 original size:12 final size:10
Alignment explanation
Indices: 71722--71797 Score: 57
Period size: 9 Copynumber: 7.0 Consensus size: 10
71712 CGAAATTCAA
71722 AAAAAAAAATTG
1 AAAAAAAAA--G
71734 AAAAAAAAAG
1 AAAAAAAAAG
71744 -AAAAAAAAG
1 AAAAAAAAAG
71753 AAGTGAGCAAAAAAG
1 AA---A--AAAAAAG
71768 -AAAAAAAAG
1 AAAAAAAAAG
*
71777 TAAAAAAAAG
1 AAAAAAAAAG
71787 AAGAAAAAAAG
1 AA-AAAAAAAG
71798 TGAAAAGTCT
Statistics
Matches: 55, Mismatches: 1, Indels: 17
0.75 0.01 0.23
Matches are distributed among these distances:
9 16 0.29
10 12 0.22
11 9 0.16
12 9 0.16
13 1 0.02
14 1 0.02
15 7 0.13
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:71748 original size:25 final size:24
Alignment explanation
Indices: 71720--71803 Score: 81
Period size: 24 Copynumber: 3.8 Consensus size: 24
71710 ATCGAAATTC
*
71720 AAAAAAAAAAATTGAAAAAAAAAG
1 AAAAAAAAAAAGTGAAAAAAAAAG
* **
71744 AAAAAAAAGAAGTGAGCAAAAAAG
1 AAAAAAAAAAAGTGAAAAAAAAAG
71768 ---AAAAAAAAGT--AAAAAAAAG
1 AAAAAAAAAAAGTGAAAAAAAAAG
*
71787 -AAGAAAAAAAGTGAAAA
1 AAAAAAAAAAAGTGAAAA
71804 GTCTTGCGAG
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
19 7 0.15
21 18 0.38
23 3 0.06
24 20 0.42
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.06
Consensus pattern (24 bp):
AAAAAAAAAAAGTGAAAAAAAAAG
Found at i:77153 original size:23 final size:23
Alignment explanation
Indices: 77126--77185 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
77116 TCACCTGCAA
77126 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATGAGTTTAT
77149 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATGAGTTTAT
*
77172 TAAACATATTAAAA
1 TAAACACATTAAAA
77186 CACTTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.33
Consensus pattern (23 bp):
TAAACACATTAAAATGAGTTTAT
Found at i:77192 original size:21 final size:23
Alignment explanation
Indices: 77126--77200 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
77116 TCACCTGCAA
* * *
77126 TAAACACATTAAAATGAGTTTAT
1 TAAACATATTAAAATCAGCTTAT
* * *
77149 TAAACACATTAAAATGAGTTTAT
1 TAAACATATTAAAATCAGCTTAT
77172 TAAACATATTAAAA-CA-CTTAT
1 TAAACATATTAAAATCAGCTTAT
*
77193 TAATCATA
1 TAAACATA
77201 ACACATATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.23
22 1 0.02
23 36 0.75
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (23 bp):
TAAACATATTAAAATCAGCTTAT
Found at i:78121 original size:27 final size:27
Alignment explanation
Indices: 78091--78142 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
78081 ACAAGTGAGG
78091 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
78118 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
78143 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:78163 original size:23 final size:22
Alignment explanation
Indices: 78137--78189 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
78127 TTGAGAGTGA
*
78137 AAAAGAAATT-GAAGAAAGAAGAT
1 AAAAGAAATTAGAA-AAAGAA-AC
78160 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
78182 AAAAGAAA
1 AAAAGAAA
78190 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:81332 original size:7 final size:8
Alignment explanation
Indices: 81313--81342 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
81303 AAGTTTGTAA
81313 AAAAAATT
1 AAAAAATT
81321 AAAAAATT
1 AAAAAATT
81329 AAAAAATT
1 AAAAAATT
81337 AAAAAA
1 AAAAAA
81343 GAAAAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAAAATT
Found at i:81348 original size:16 final size:16
Alignment explanation
Indices: 81312--81359 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
81302 TAAGTTTGTA
*
81312 AAAAAAATTAAAAAAT
1 AAAAAAATTAAAAAAG
*
81328 TAAAAAATTAAAAAAG
1 AAAAAAATTAAAAAAG
*
81344 AAAAACATTGAAAAAA
1 AAAAAAATT-AAAAAA
81360 ATTATGGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (16 bp):
AAAAAAATTAAAAAAG
Found at i:84008 original size:23 final size:22
Alignment explanation
Indices: 83956--84008 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
83946 TCCACGTCTT
*
83956 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
83978 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
84001 TTTCTTTT
1 TTTCTTTT
84009 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:88388 original size:33 final size:33
Alignment explanation
Indices: 88350--88412 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
88340 GATTACTCAC
88350 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
88383 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
88413 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:88439 original size:21 final size:21
Alignment explanation
Indices: 88410--88465 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
88400 CAAGCTCTCT
*
88410 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
88431 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
88452 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
88466 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:88458 original size:14 final size:14
Alignment explanation
Indices: 88409--88465 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
88399 TCAAGCTCTC
88409 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
88422 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
88436 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
88450 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
88464 TT
1 TT
88466 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:88495 original size:18 final size:18
Alignment explanation
Indices: 88481--88547 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
88471 ACTTTTTTTG
*
88481 ATTTCTTTTTCTTTTGCA
1 ATTTCTTTTTCTTTTTCA
88499 ATTTCTTTTTCTTTTTCA
1 ATTTCTTTTTCTTTTTCA
* * *
88517 TTTTTTTTTGTTTTCTTTCA
1 ATTTCTTTT-TCTT-TTTCA
88537 ATTTCTTTTTC
1 ATTTCTTTTTC
88548 AATCTCTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 24 0.60
19 4 0.10
20 12 0.30
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.73
Consensus pattern (18 bp):
ATTTCTTTTTCTTTTTCA
Found at i:88547 original size:6 final size:6
Alignment explanation
Indices: 88427--88534 Score: 60
Period size: 6 Copynumber: 17.7 Consensus size: 6
88417 TCTTTTTTCG
* * * **
88427 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* ** *
88478 -TTGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CATTTT -TTTTT
1 CTT--TTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
88526 -GTTTT CTTT
1 CTTTTT CTTT
88535 CAATTTCTTT
Statistics
Matches: 75, Mismatches: 21, Indels: 12
0.69 0.19 0.11
Matches are distributed among these distances:
5 10 0.13
6 48 0.64
7 12 0.16
8 5 0.07
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:89270 original size:20 final size:20
Alignment explanation
Indices: 89228--89272 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
89218 CCACAAATCT
* **
89228 CTCAAGTTAGCTCATTCGTG
1 CTCAAGTCAGCTCATTCAAG
89248 CTCAAGTCAGCTCATTCAAG
1 CTCAAGTCAGCTCATTCAAG
89268 CTCAA
1 CTCAA
89273 TTTAACTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCAAGTCAGCTCATTCAAG
Found at i:91714 original size:17 final size:18
Alignment explanation
Indices: 91692--91728 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
91682 TGGAATAAAC
91692 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
91709 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
91727 TT
1 TT
91729 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Done.