Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1212
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: 115892
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:3911 original size:15 final size:17
Alignment explanation
Indices: 3881--3912 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3871 AAATCGGCAC
3881 AAGTATAAGCAAAGAAA
1 AAGTATAAGCAAAGAAA
3898 AAGTA-AAG-AAAGAAA
1 AAGTATAAGCAAAGAAA
3913 TCGAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09
Consensus pattern (17 bp):
AAGTATAAGCAAAGAAA
Found at i:8455 original size:14 final size:14
Alignment explanation
Indices: 8435--8487 Score: 81
Period size: 14 Copynumber: 3.7 Consensus size: 14
8425 ACTAGCTTCT
8435 TTTTTTTTCACGAAA
1 TTTTTTTTCACG-AA
8450 TTTTTTTTTCACGAA
1 -TTTTTTTTCACGAA
8465 TTTTTTTTCACG-A
1 TTTTTTTTCACGAA
8478 TTTTTTTTCA
1 TTTTTTTTCA
8488 ACTTGATATC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
13 11 0.30
14 12 0.32
15 2 0.05
16 12 0.32
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.62
Consensus pattern (14 bp):
TTTTTTTTCACGAA
Found at i:8543 original size:10 final size:10
Alignment explanation
Indices: 8528--8576 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
8518 GAAACCAATT
8528 TTTTTTTGAA
1 TTTTTTTGAA
8538 TTTTTTT---
1 TTTTTTTGAA
8545 TGTTTTTTGAA
1 T-TTTTTTGAA
8556 TTTTTTTTGAA
1 -TTTTTTTGAA
8567 TTTTTTTGAA
1 TTTTTTTGAA
8577 GAAACTACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
7 1 0.03
8 6 0.18
10 17 0.50
11 9 0.26
12 1 0.03
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.73
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:8543 original size:11 final size:11
Alignment explanation
Indices: 8527--8573 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
8517 GGAAACCAAT
8527 TTTTTTTTGAA
1 TTTTTTTTGAA
8538 TTTTTTTTG--
1 TTTTTTTTGAA
8547 --TTTTTTGAA
1 TTTTTTTTGAA
8556 TTTTTTTTGAA
1 TTTTTTTTGAA
8567 TTTTTTT
1 TTTTTTT
8574 GAAGAAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 7 0.22
11 25 0.78
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:8552 original size:18 final size:18
Alignment explanation
Indices: 8529--8564 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
8519 AAACCAATTT
8529 TTTTTTGAATTTTTTTTG
1 TTTTTTGAATTTTTTTTG
8547 TTTTTTGAATTTTTTTTG
1 TTTTTTGAATTTTTTTTG
8565 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTTTGAATTTTTTTTG
Found at i:8570 original size:18 final size:18
Alignment explanation
Indices: 8531--8570 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
8521 ACCAATTTTT
**
8531 TTTTGAATTTTTTTTGTT
1 TTTTGAATTTTTTTTGAA
8549 TTTTGAATTTTTTTTGAA
1 TTTTGAATTTTTTTTGAA
8567 TTTT
1 TTTT
8571 TTTGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.75
Consensus pattern (18 bp):
TTTTGAATTTTTTTTGAA
Found at i:10684 original size:24 final size:26
Alignment explanation
Indices: 10630--10680 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
10620 TCATCTTAGT
* *
10630 TTTAATTAATAAGTGTTTTTGTTGAAC
1 TTTAATTAATAAGTGTTGTTCTT-AAC
*
10657 TTTATTTAATAAGTGTTGTTCTTA
1 TTTAATTAATAAGTGTTGTTCTTA
10681 TTTAATCTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.05
27 20 0.95
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (26 bp):
TTTAATTAATAAGTGTTGTTCTTAAC
Found at i:12499 original size:17 final size:16
Alignment explanation
Indices: 12477--12516 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 16
12467 TAGCTTCTTC
12477 TTTTTTTTCACGAAATT
1 TTTTTTTTCACG-AATT
12494 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAATT
12510 TTTTTTT
1 TTTTTTT
12517 CAACTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTTTTTTCACGAATT
Found at i:12575 original size:12 final size:12
Alignment explanation
Indices: 12558--12601 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
12548 AGAAACCAAT
12558 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
12570 TTTTTTTTTGCA
1 TTTTTTTTTGAA
12582 TTTTTTTTTGAA
1 TTTTTTTTTGAA
12594 TTTTTTTT
1 TTTTTTTT
12602 GAAGAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:19067 original size:39 final size:39
Alignment explanation
Indices: 18863--19085 Score: 223
Period size: 40 Copynumber: 5.6 Consensus size: 39
18853 TTGAATGCTG
* * * * * **
18863 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATTTA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
18903 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
*
18943 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
18983 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
* *
19023 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
19062 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
19086 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 108 0.69
41 10 0.06
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:19105 original size:79 final size:80
Alignment explanation
Indices: 18938--19120 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
18928 GTGCGAGATA
* * *
18938 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
19003 CAGTCGTGCGAGTTG
66 CAGTCGAACGAGGAG
* * * *
19018 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
19082 CATTTGAACGAGGAG
66 CAGTCGAACGAGGAG
* *
19097 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
19121 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGGAG
Found at i:24248 original size:22 final size:22
Alignment explanation
Indices: 24218--24261 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
24208 TTTGGTATTT
24218 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
24240 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
24262 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:28327 original size:13 final size:13
Alignment explanation
Indices: 28309--28333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28299 GACCGTATGC
28309 AATTTTTTTTTCA
1 AATTTTTTTTTCA
28322 AATTTTTTTTTC
1 AATTTTTTTTTC
28334 GAACTCCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
AATTTTTTTTTCA
Found at i:28678 original size:22 final size:22
Alignment explanation
Indices: 28648--28691 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28638 TTTGGTATTT
28648 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
28670 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
28692 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:31212 original size:13 final size:13
Alignment explanation
Indices: 31194--31221 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31184 CATCAACAAA
31194 GCAAATAAGGGGC
1 GCAAATAAGGGGC
31207 GCAAATAAGGGGC
1 GCAAATAAGGGGC
31220 GC
1 GC
31222 GGATCATGGC
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:0.18, G:0.39, T:0.07
Consensus pattern (13 bp):
GCAAATAAGGGGC
Found at i:32435 original size:13 final size:14
Alignment explanation
Indices: 32408--32440 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
32398 CCGTATGCAA
32408 TTTTTTTTCAAAATT
1 TTTTTTTTC-AAATT
32423 TTTTTTTTC-AATT
1 TTTTTTTTCAAATT
32436 TTTTT
1 TTTTT
32441 CGATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
15 9 0.50
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTTTCAAATT
Found at i:32437 original size:12 final size:12
Alignment explanation
Indices: 32408--32463 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
32398 CCGTATGCAA
32408 TTTTTTTTCAAAATT
1 TTTTTTTTC--AA-T
32423 TTTTTTTTCAA-
1 TTTTTTTTCAAT
*
32434 -TTTTTTTCGAT
1 TTTTTTTTCAAT
*
32445 TTTTTTTTCGAT
1 TTTTTTTTCAAT
32457 TTTTTTT
1 TTTTTTT
32464 GAATCTACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
10 9 0.24
12 18 0.47
13 2 0.05
15 9 0.24
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:32459 original size:10 final size:10
Alignment explanation
Indices: 32424--32462 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
32414 TTCAAAATTT
*
32424 TTTTTTTCAA
1 TTTTTTTCGA
32434 TTTTTTTCGA
1 TTTTTTTCGA
32444 TTTTTTTTTCGA
1 --TTTTTTTCGA
32456 TTTTTTT
1 TTTTTTT
32463 TGAATCTACA
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:0.10, C:0.08, G:0.05, T:0.77
Consensus pattern (10 bp):
TTTTTTTCGA
Found at i:45488 original size:10 final size:10
Alignment explanation
Indices: 45472--45529 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
45462 CAACTCCGAC
45472 CAGCTCAATT
1 CAGCTCAATT
* *
45482 GAGCTCATTT
1 CAGCTCAATT
45492 CAGCTCAA-T
1 CAGCTCAATT
45501 CGAGCTCAATT
1 C-AGCTCAATT
*
45512 TAGCTACAATT
1 CAGCT-CAATT
45523 CAGCTCA
1 CAGCTCA
45530 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:45495 original size:20 final size:20
Alignment explanation
Indices: 45472--45532 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
45462 CAACTCCGAC
45472 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
45492 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
45513 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
45533 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:46883 original size:11 final size:12
Alignment explanation
Indices: 46860--46896 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
46850 AAAAAAATCG
46860 AAATTCAAAAAA
1 AAATTCAAAAAA
46872 AAATTCAAAAAA
1 AAATTCAAAAAA
* *
46884 AAAGTGAAAAAA
1 AAATTCAAAAAA
46896 A
1 A
46897 TCGAGCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:47852 original size:18 final size:18
Alignment explanation
Indices: 47831--47865 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
47821 AGAAAAGAAA
47831 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
47849 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
47866 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:49952 original size:10 final size:10
Alignment explanation
Indices: 49936--49993 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
49926 CAACTCCGAC
49936 CAGCTCAATT
1 CAGCTCAATT
* *
49946 GAGCTCATTT
1 CAGCTCAATT
49956 CAGCTCAA-T
1 CAGCTCAATT
49965 CGAGCTCAATT
1 C-AGCTCAATT
*
49976 TAGCTACAATT
1 CAGCT-CAATT
49987 CAGCTCA
1 CAGCTCA
49994 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:49959 original size:20 final size:20
Alignment explanation
Indices: 49936--49996 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
49926 CAACTCCGAC
49936 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
49956 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
49977 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
49997 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:52162 original size:21 final size:23
Alignment explanation
Indices: 52117--52163 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
52107 TCACCTGCAA
* *
52117 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
52140 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
52161 TAA
1 TAA
52164 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:59205 original size:13 final size:13
Alignment explanation
Indices: 59187--59246 Score: 88
Period size: 13 Copynumber: 4.8 Consensus size: 13
59177 AATGGAAACC
59187 AATTTTTTTTTTG
1 AATTTTTTTTTTG
59200 AA--TTTTTTTTG
1 AATTTTTTTTTTG
59211 AATTTTTTTTTTG
1 AATTTTTTTTTTG
*
59224 AATTTTTTTTTCG
1 AATTTTTTTTTTG
*
59237 AGTTTTTTTT
1 AATTTTTTTT
59247 CGAGAAACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.26
13 32 0.74
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:59207 original size:11 final size:11
Alignment explanation
Indices: 59191--59233 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
59181 GAAACCAATT
59191 TTTTTTTTGAA
1 TTTTTTTTGAA
59202 TTTTTTTTGAA
1 TTTTTTTTGAA
59213 TTTTTTTTTTGAA
1 --TTTTTTTTGAA
59226 TTTTTTTT
1 TTTTTTTT
59234 TCGAGTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:59219 original size:24 final size:24
Alignment explanation
Indices: 59187--59233 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
59177 AATGGAAACC
59187 AATTTTTTTTTTGAATTTTTTTTG
1 AATTTTTTTTTTGAATTTTTTTTG
59211 AATTTTTTTTTTGAATTTTTTTT
1 AATTTTTTTTTTGAATTTTTTTT
59234 TCGAGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (24 bp):
AATTTTTTTTTTGAATTTTTTTTG
Found at i:59247 original size:12 final size:12
Alignment explanation
Indices: 59190--59250 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
59180 GGAAACCAAT
* *
59190 TTTTTTTTTGAA
1 TTTTTTTTCGAG
*
59202 TTTTTTTT-GAAT
1 TTTTTTTTCG-AG
* *
59214 TTTTTTTTTGAAT
1 TTTTTTTTCG-AG
59227 TTTTTTTTCGAG
1 TTTTTTTTCGAG
59239 TTTTTTTTCGAG
1 TTTTTTTTCGAG
59251 AAACTACTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
11 1 0.02
12 30 0.68
13 13 0.30
ACGTcount: A:0.13, C:0.03, G:0.11, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCGAG
Found at i:60278 original size:21 final size:23
Alignment explanation
Indices: 60233--60279 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
60223 TCACCTACAA
* *
60233 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
60256 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
60277 TAA
1 TAA
60280 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:63246 original size:11 final size:11
Alignment explanation
Indices: 63232--63263 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
63222 AAACTGAAAC
63232 TTTTTTTCAAG
1 TTTTTTTCAAG
*
63243 TTTTTTTCAAT
1 TTTTTTTCAAG
63254 TTTTTTTCAA
1 TTTTTTTCAA
63264 ATCGAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.09, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTTTTTCAAG
Found at i:70928 original size:17 final size:17
Alignment explanation
Indices: 70883--70936 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
70873 AGAAAAGAGC
* *
70883 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
70900 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
70917 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
70934 GAA
1 GAA
70937 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:77232 original size:23 final size:22
Alignment explanation
Indices: 77181--77232 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
77171 CCTCGTCTTT
*
77181 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
77203 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
77226 TTCTTTT
1 TTCTTTT
77233 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:80627 original size:21 final size:23
Alignment explanation
Indices: 80582--80628 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
80572 TCACCTCCAA
* *
80582 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
80605 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
80626 TAA
1 TAA
80629 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:82229 original size:11 final size:10
Alignment explanation
Indices: 82204--82264 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
82194 ACCAATAAAA
82204 TAAA-TGAGC
1 TAAATTGAGC
*
82213 TGAATTGTAGC
1 TAAATTG-AGC
82224 TAAATTGAGC
1 TAAATTGAGC
**
82234 TCGATTGAGC
1 TAAATTGAGC
82244 TGAAA-TGAGC
1 T-AAATTGAGC
*
82254 TTAATTGAGC
1 TAAATTGAGC
82264 T
1 T
82265 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:82265 original size:20 final size:20
Alignment explanation
Indices: 82205--82265 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
82195 CCAATAAAAT
*
82205 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
82225 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
*
82246 AAATGAGCTTAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
82266 GTCGGAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:84350 original size:18 final size:18
Alignment explanation
Indices: 84329--84363 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
84319 TTTTTCTTTT
84329 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
84347 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
84364 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:84422 original size:18 final size:18
Alignment explanation
Indices: 84401--84467 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
84391 CACTATTTTG
*
84401 ATTTCTTTTTCTTTTGCA
1 ATTTCTTTTTCTTTTTCA
*
84419 ATTTCTTTTTCTTTTTCG
1 ATTTCTTTTTCTTTTTCA
* *
84437 TTTTCTTTTGTTTTCTTTCA
1 ATTTCTTTT-TCTT-TTTCA
84457 ATTTCTTTTTC
1 ATTTCTTTTTC
84468 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:0.07, C:0.16, G:0.04, T:0.72
Consensus pattern (18 bp):
ATTTCTTTTTCTTTTTCA
Found at i:84467 original size:6 final size:6
Alignment explanation
Indices: 84402--84445 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
84392 ACTATTTTGA
* ** *
84402 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
84446 GTTTTCTTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:85653 original size:10 final size:11
Alignment explanation
Indices: 85638--85666 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
85628 TAACTCAAAT
85638 TTTTTTTTGA-
1 TTTTTTTTGAC
85648 TTTTTTTTGAC
1 TTTTTTTTGAC
85659 TTTTTTTT
1 TTTTTTTT
85667 ACGTTACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:86947 original size:11 final size:10
Alignment explanation
Indices: 86922--86982 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
86912 ACCAATAAAA
86922 TAAA-TGAGC
1 TAAATTGAGC
*
86931 TGAATTGTAGC
1 TAAATTG-AGC
86942 TAAATTGAGC
1 TAAATTGAGC
**
86952 TCGATTGAGC
1 TAAATTGAGC
86962 TGAAA-TGAGC
1 T-AAATTGAGC
*
86972 TCAATTGAGC
1 TAAATTGAGC
86982 T
1 T
86983 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:86983 original size:20 final size:20
Alignment explanation
Indices: 86923--86983 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
86913 CCAATAAAAT
*
86923 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
86943 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
86964 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
86984 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:90254 original size:26 final size:26
Alignment explanation
Indices: 90204--90254 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
90194 TCATCTTAGT
* *
90204 TTTAATTAATAAGTGTTTTTTTTAAC
1 TTTAATTAATAAGTGTTGTTCTTAAC
*
90230 TTTATTTAATAAGTGTTGTTCTTAA
1 TTTAATTAATAAGTGTTGTTCTTAA
90255 TTGATCTAGT
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:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (26 bp):
TTTAATTAATAAGTGTTGTTCTTAAC
Found at i:93764 original size:15 final size:16
Alignment explanation
Indices: 93731--93773 Score: 70
Period size: 15 Copynumber: 2.7 Consensus size: 16
93721 TAGCTTCTTC
93731 TTTTTTTTTCACGATAA
1 TTTTTTTTTCACGA-AA
93748 TTTTTTTTTCACG-AA
1 TTTTTTTTTCACGAAA
93763 TTTTTTTTTCA
1 TTTTTTTTTCA
93774 ACTTGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 13 0.50
17 13 0.50
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.65
Consensus pattern (16 bp):
TTTTTTTTTCACGAAA
Found at i:93830 original size:11 final size:11
Alignment explanation
Indices: 93814--93869 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
93804 GAAACCAAAT
93814 TTTTTTTTGAA
1 TTTTTTTTGAA
*
93825 TTTTTTTTGAG
1 TTTTTTTTGAA
* *
93836 TTTTTTTTTAT
1 TTTTTTTTGAA
93847 TTTTTTTTGGAA
1 TTTTTTTT-GAA
*
93859 ATTTTTTTGAA
1 TTTTTTTTGAA
93870 GAAACTACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 30 0.79
12 8 0.21
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:94903 original size:21 final size:23
Alignment explanation
Indices: 94858--94904 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
94848 TCACCTGCAA
* *
94858 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
94881 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
94902 TAA
1 TAA
94905 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:105035 original size:27 final size:25
Alignment explanation
Indices: 105005--105058 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
104995 GTTAAAACAA
*
105005 CTTGTAAAGAAAACTCAAGAGAGAATT
1 CTTGGAAA-AAAACTCAA-AGAGAATT
*
105032 CTTGGAGAAAAACTCAAAGAGAATT
1 CTTGGAAAAAAACTCAAAGAGAATT
105057 CT
1 CT
105059 GCACTTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.40
26 9 0.36
27 6 0.24
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (25 bp):
CTTGGAAAAAAACTCAAAGAGAATT
Found at i:110811 original size:11 final size:12
Alignment explanation
Indices: 110779--110810 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
110769 AGGAAATTTG
110779 AAAAAAAAATTC
1 AAAAAAAAATTC
110791 AAAAAAAAATTC
1 AAAAAAAAATTC
110803 AAAAAAAA
1 AAAAAAAA
110811 TCGAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:111943 original size:48 final size:47
Alignment explanation
Indices: 111843--111948 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 47
111833 GAGTGTCATG
*
111843 GAAAAAGAAATTGAGATTGAAAAAGGATGGGAAAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATAGAAAAAGGATGGGAAAAAGAG-AAGAAATC
*
111891 GAAAAAGAAATTGAGATAGAACAAAAGTG-TGAGGAAAAAGAG-A-AAATT
1 GAAAAAGAAATTGAGATAG-A-AAAAG-GATG-GGAAAAAGAGAAGAAATC
111939 GAAAAAGAAA
1 GAAAAAGAAA
111949 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
48 32 0.62
49 2 0.04
50 7 0.13
51 11 0.21
ACGTcount: A:0.60, C:0.02, G:0.25, T:0.12
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATAGAAAAAGGATGGGAAAAAGAGAAGAAATC
Found at i:112788 original size:4 final size:4
Alignment explanation
Indices: 112779--112806 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
112769 TTAAACTAAG
112779 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
112807 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:114211 original size:23 final size:22
Alignment explanation
Indices: 114159--114211 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
114149 TCCACGTCTT
*
114159 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
114181 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
114204 TTTCTTTT
1 TTTCTTTT
114212 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:115741 original size:33 final size:34
Alignment explanation
Indices: 115699--115767 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
115689 CAGTTTAGAA
115699 ATCAACCAAGAACACCCAAAACG-CCAAAATCTG
1 ATCAACCAAGAACACCCAAAACGCCCAAAATCTG
115732 ATCAACCAAGAACACCCAAAACGCCCAAAATCTG
1 ATCAACCAAGAACACCCAAAACGCCCAAAATCTG
115766 AT
1 AT
115768 ACCAAATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 23 0.66
34 12 0.34
ACGTcount: A:0.48, C:0.33, G:0.09, T:0.10
Consensus pattern (34 bp):
ATCAACCAAGAACACCCAAAACGCCCAAAATCTG
Done.