Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3491.1
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: 125874
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:13417 original size:25 final size:25
Alignment explanation
Indices: 13388--13444 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
13378 ATTGGACACA
*
13388 AGTCATAGAATAGTCACATTTGCAT
1 AGTCAAAGAATAGTCACATTTGCAT
*
13413 AGTCAAAGAATAGTCACGTTTGCAT
1 AGTCAAAGAATAGTCACATTTGCAT
13438 AGTCAAA
1 AGTCAAA
13445 TCTCATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (25 bp):
AGTCAAAGAATAGTCACATTTGCAT
Found at i:26012 original size:40 final size:40
Alignment explanation
Indices: 25957--26158 Score: 275
Period size: 40 Copynumber: 5.0 Consensus size: 40
25947 GATGATAACG
* *
25957 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
*
25997 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
26037 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* * **
26077 GGGCTAAATCCCGAAGGCATTTGTACGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* *
26117 GGGCTAAGTCCCAAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
26157 GG
1 GG
26159 TTAAATCCTG
Statistics
Matches: 147, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 144 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:33058 original size:25 final size:25
Alignment explanation
Indices: 33030--33079 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
33020 ACTCTTAAAA
*
33030 ATTTTTAAAAT-ATAATTAATATATT
1 ATTTTAAAAATCA-AATTAATATATT
*
33055 ATTTTAAAAATCAAATTAATGTATT
1 ATTTTAAAAATCAAATTAATATATT
33080 TAAATATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTTTAAAAATCAAATTAATATATT
Found at i:36800 original size:31 final size:31
Alignment explanation
Indices: 36739--36800 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
36729 AATTATAAAA
* *
36739 TAATCACTTAATTATTTAATTTTTTATTTTT
1 TAATCACTTAATTATTAAATTTTCTATTTTT
36770 TAATCA-TCTAATTATTCAAATTTTCT-TTTTT
1 TAATCACT-TAATTATT-AAATTTTCTATTTTT
36801 GGTCATCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 1 0.04
31 19 0.70
32 7 0.26
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (31 bp):
TAATCACTTAATTATTAAATTTTCTATTTTT
Found at i:36964 original size:25 final size:23
Alignment explanation
Indices: 36926--36976 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
36916 AAAACCTCAA
36926 TTTTTATACATTGTGTAATTTTATT
1 TTTTTATACA-T-TGTAATTTTATT
** *
36951 TTTTTATTTATTGTAGTTTTATT
1 TTTTTATACATTGTAATTTTATT
36974 TTT
1 TTT
36977 ATTTGTGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 14 0.61
24 1 0.04
25 8 0.35
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.71
Consensus pattern (23 bp):
TTTTTATACATTGTAATTTTATT
Found at i:38634 original size:16 final size:16
Alignment explanation
Indices: 38585--38648 Score: 71
Period size: 16 Copynumber: 4.2 Consensus size: 16
38575 TACAACTAAT
38585 ATTAAATATTT-TTAA
1 ATTAAATATTTATTAA
* *
38600 ACTAAA-ATTAATT-A
1 ATTAAATATTTATTAA
* *
38614 ATTAATTTTTTATTAA
1 ATTAAATATTTATTAA
38630 ATTAAATATTTATTAA
1 ATTAAATATTTATTAA
38646 ATT
1 ATT
38649 TCTCTATTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 8 0.21
15 12 0.32
16 18 0.47
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTAAATATTTATTAA
Found at i:42052 original size:18 final size:18
Alignment explanation
Indices: 42010--42048 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42000 TGCATGAAAA
*
42010 CCCTATAGTATACGGATC
1 CCCTATAGTATACAGATC
*
42028 CCCTATAGTATGCAGA-C
1 CCCTATAGTATACAGATC
42045 CCCT
1 CCCT
42049 TATAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (18 bp):
CCCTATAGTATACAGATC
Found at i:42307 original size:22 final size:22
Alignment explanation
Indices: 42281--42344 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 22
42271 CAGACCTTAC
42281 ATGTTATTTATGTGAACCCAAT
1 ATGTTATTTATGTGAACCCAAT
* ** ** *
42303 CTGTTCAAATATACGAACCCTAT
1 ATGTT-ATTTATGTGAACCCAAT
*
42326 ATGTTGTTTATGTGAACCC
1 ATGTTATTTATGTGAACCC
42345 TACATGTAGT
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (22 bp):
ATGTTATTTATGTGAACCCAAT
Found at i:42345 original size:22 final size:22
Alignment explanation
Indices: 42316--42382 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
42306 TTCAAATATA
42316 CGAACCCTATATGTTGTTTATG
1 CGAACCCTATATGTTGTTTATG
* * * *
42338 TGAACCCTACATGTAGTATATG
1 CGAACCCTATATGTTGTTTATG
* * *
42360 CAAACCCTATTTGTTGATTATG
1 CGAACCCTATATGTTGTTTATG
42382 C
1 C
42383 AAACTATATG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (22 bp):
CGAACCCTATATGTTGTTTATG
Found at i:43755 original size:13 final size:13
Alignment explanation
Indices: 43739--43763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43729 GTTTTAAAAC
43739 TTTTAAAGGAGTA
1 TTTTAAAGGAGTA
43752 TTTTAAAGGAGT
1 TTTTAAAGGAGT
43764 GTGCATGCAT
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (13 bp):
TTTTAAAGGAGTA
Found at i:44720 original size:21 final size:21
Alignment explanation
Indices: 44694--44737 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
44684 GAGTGGGAAA
*
44694 AAAAGGCAAA-AAGTTTCAAAT
1 AAAAGG-AAATAAGGTTCAAAT
*
44715 AAAAGGAAATCAGGTTCAAAT
1 AAAAGGAAATAAGGTTCAAAT
44736 AA
1 AA
44738 TCCAACCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.57, C:0.09, G:0.16, T:0.18
Consensus pattern (21 bp):
AAAAGGAAATAAGGTTCAAAT
Found at i:45478 original size:13 final size:11
Alignment explanation
Indices: 45450--45492 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
45440 AGTTAAATAT
45450 TATTTTATTAA
1 TATTTTATTAA
45461 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
45474 TA-TTTATTAT
1 TATTTTATTAA
45484 TATTTTATT
1 TATTTTATT
45493 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:45479 original size:23 final size:23
Alignment explanation
Indices: 45453--45496 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
45443 TAAATATTAT
45453 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
45476 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
45497 AAATGGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:48691 original size:35 final size:35
Alignment explanation
Indices: 48651--48721 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
48641 ATGTGCTCAC
48651 ATAGTTTTCTTTCCTATGTTTTATATATAATTGGA
1 ATAGTTTTCTTTCCTATGTTTTATATATAATTGGA
*
48686 ATAGTTTTCTTTCTTATGTTTTATATATAATTGGA
1 ATAGTTTTCTTTCCTATGTTTTATATATAATTGGA
48721 A
1 A
48722 GCTCGTCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (35 bp):
ATAGTTTTCTTTCCTATGTTTTATATATAATTGGA
Found at i:50799 original size:27 final size:27
Alignment explanation
Indices: 50768--50820 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
50758 TTGTGACACG
50768 GAAAAAAGGATTATGGGAAAGTCATAT
1 GAAAAAAGGATTATGGGAAAGTCATAT
*
50795 GAAAAAAGGCTTATGGGAAAGTCATA
1 GAAAAAAGGATTATGGGAAAGTCATA
50821 CTCATCGTCG
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:0.47, C:0.06, G:0.26, T:0.21
Consensus pattern (27 bp):
GAAAAAAGGATTATGGGAAAGTCATAT
Found at i:55088 original size:112 final size:112
Alignment explanation
Indices: 54891--55228 Score: 649
Period size: 112 Copynumber: 3.0 Consensus size: 112
54881 TAGACCATTC
54891 AATATGTTAGTGGACTTTTATGGACACAAATTTAAATGATTTTTAAGTTAAAATCTAAGGTTAAG
1 AATATGTTAGTGGACTTTTATGGACACAAATTTAAATGATTTTTAAGTTAAAATCTAAGGTTAAG
54956 ATAGTAAATTAATAAATATACTTAAAATTAAAGTGGAGAAAAGATGT
66 ATAGTAAATTAATAAATATACTTAAAATTAAAGTGGAGAAAAGATGT
55003 AATATGTTAGTGGACTTTTATGGACACAAATTTAAATGATTTTTAAGTTAAAATCTAAGGTTAAG
1 AATATGTTAGTGGACTTTTATGGACACAAATTTAAATGATTTTTAAGTTAAAATCTAAGGTTAAG
55068 ATAGTAAATTAATAAATATACTTAAAATTAAAGTGGAGAAAAGATGT
66 ATAGTAAATTAATAAATATACTTAAAATTAAAGTGGAGAAAAGATGT
*
55115 AATATGTTAGTGGACTTTTATGGACACAAATTTAAATGATTTTTAAGTTAAAATCTAAGGTTAAA
1 AATATGTTAGTGGACTTTTATGGACACAAATTTAAATGATTTTTAAGTTAAAATCTAAGGTTAAG
*
55180 ATAGTAAATTAATAAATATACTTAAAATTAAAGTAGAGAAAAAGATGT
66 ATAGTAAATTAATAAATATACTTAAAATTAAAGTGGAG-AAAAGATGT
55228 A
1 A
55229 TCATCTTCTC
Statistics
Matches: 223, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
112 213 0.96
113 10 0.04
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (112 bp):
AATATGTTAGTGGACTTTTATGGACACAAATTTAAATGATTTTTAAGTTAAAATCTAAGGTTAAG
ATAGTAAATTAATAAATATACTTAAAATTAAAGTGGAGAAAAGATGT
Found at i:57178 original size:12 final size:12
Alignment explanation
Indices: 57161--57190 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
57151 TCAGGCAGTT
57161 ACATGGCCTAGC
1 ACATGGCCTAGC
*
57173 ACATGGCCTGGC
1 ACATGGCCTAGC
57185 ACATGG
1 ACATGG
57191 GCGTGTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (12 bp):
ACATGGCCTAGC
Found at i:57251 original size:13 final size:13
Alignment explanation
Indices: 57235--57273 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
57225 ACACACGGGC
57235 GTGTGACACGACT
1 GTGTGACACGACT
* *
57248 GTGTGACGCGACC
1 GTGTGACACGACT
*
57261 GTGTGACCCGACT
1 GTGTGACACGACT
57274 CAGAGAGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (13 bp):
GTGTGACACGACT
Found at i:58983 original size:25 final size:25
Alignment explanation
Indices: 58955--59036 Score: 130
Period size: 25 Copynumber: 3.3 Consensus size: 25
58945 TCATTAGAGT
*
58955 TACCGATTTATAGCTCGTGAGAGCA
1 TACCGATTTATAGCTCATGAGAGCA
58980 TACCGATTTATAGCTCATGAGAGCA
1 TACCGATTTATAGCTCATGAGAGCA
*
59005 TACCAATTTATTA-CTCATGAGAGCA
1 TACCGATTTA-TAGCTCATGAGAGCA
59030 TACCGAT
1 TACCGAT
59037 CTTCCACTCG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
25 51 0.96
26 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (25 bp):
TACCGATTTATAGCTCATGAGAGCA
Found at i:59053 original size:25 final size:25
Alignment explanation
Indices: 59025--59082 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
59015 TTACTCATGA
59025 GAGCATACCGATCTTC-CA-CTCGTAT
1 GAGCATACCGA--TTCACAGCTCGTAT
*
59050 GAGCATACTGATTCACAGCTCGTAT
1 GAGCATACCGATTCACAGCTCGTAT
59075 GAGCATAC
1 GAGCATAC
59083 ATGTACATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 3 0.10
24 2 0.07
25 25 0.83
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (25 bp):
GAGCATACCGATTCACAGCTCGTAT
Found at i:66564 original size:16 final size:16
Alignment explanation
Indices: 66545--66575 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
66535 CTTCTTCACT
66545 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
66561 TACTTACTTACTTAA
1 TACTCACTTACTTAA
66576 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:66581 original size:20 final size:20
Alignment explanation
Indices: 66542--66581 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
66532 AAACTTCTTC
* *
66542 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
66562 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
66582 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:73895 original size:16 final size:16
Alignment explanation
Indices: 73876--73906 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73866 CTTCTTCACT
73876 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
73892 TACTTACTTACTTAA
1 TACTCACTTACTTAA
73907 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:73912 original size:20 final size:20
Alignment explanation
Indices: 73873--73912 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
73863 AAACTTCTTC
* *
73873 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
73893 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
73913 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:78327 original size:47 final size:47
Alignment explanation
Indices: 78273--78399 Score: 159
Period size: 47 Copynumber: 2.7 Consensus size: 47
78263 AATCGATAAG
*
78273 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATC-CTGGAA
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCT-GAA
* * ** *
78320 TACCTATACTATTGCCTATAGCCAAATCAAGGTAACTCCTCTCTGAA
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCTGAA
* *
78367 TACCTATACCATGG-TCGTAGCCAAATTAAGGTA
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTA
78400 TTATTCACAC
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
46 15 0.22
47 50 0.75
48 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (47 bp):
TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCTGAA
Found at i:79024 original size:29 final size:29
Alignment explanation
Indices: 78964--79018 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
78954 ATTTATTTCA
*
78964 CAATTTAATCCCTCAATTTACACTTTTTT
1 CAATTTAATCCCTCAATATACACTTTTTT
*
78993 CAATTTAATCCCT-AATATGCA-TTTTT
1 CAATTTAATCCCTCAATATACACTTTTT
79019 ACTCAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 6 0.25
29 13 0.54
ACGTcount: A:0.29, C:0.22, G:0.02, T:0.47
Consensus pattern (29 bp):
CAATTTAATCCCTCAATATACACTTTTTT
Found at i:79624 original size:12 final size:12
Alignment explanation
Indices: 79607--79635 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
79597 GCCATAAGCA
79607 TTAAAAATAATT
1 TTAAAAATAATT
79619 TT-AAAATAATT
1 TTAAAAATAATT
79630 TTAAAA
1 TTAAAA
79636 CATCATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTAAAAATAATT
Found at i:79626 original size:11 final size:11
Alignment explanation
Indices: 79610--79635 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
79600 ATAAGCATTA
79610 AAAATAATTTT
1 AAAATAATTTT
79621 AAAATAATTTT
1 AAAATAATTTT
79632 AAAA
1 AAAA
79636 CATCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:84271 original size:47 final size:47
Alignment explanation
Indices: 84218--84411 Score: 271
Period size: 47 Copynumber: 4.1 Consensus size: 47
84208 TTAGGATTTT
* ** * * *
84218 ATGTGATGAACGTGAATGTGTATATATGAGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
84265 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
84312 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
84359 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
84406 ATGTGA
1 ATGTGA
84412 AATATGTATG
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:84367 original size:25 final size:25
Alignment explanation
Indices: 84292--84367 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
84282 ATGCATATAT
84292 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
84317 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
84339 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
84364 GTGA
1 GTGA
84368 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:84445 original size:48 final size:48
Alignment explanation
Indices: 84382--84517 Score: 211
Period size: 50 Copynumber: 2.8 Consensus size: 48
84372 GAACATGCAT
84382 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGC
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGC
* *
84430 ATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATGT
1 ATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATGC
*
84480 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
84518 GGCGATGTGC
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
47 1 0.01
48 33 0.41
49 4 0.05
50 41 0.51
51 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.30
Consensus pattern (48 bp):
ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGC
Found at i:84532 original size:50 final size:50
Alignment explanation
Indices: 84376--84538 Score: 201
Period size: 50 Copynumber: 3.3 Consensus size: 50
84366 GAATATGAAC
*
84376 ATGCATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
1 ATGCGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
*
84426 ATGC--ATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGAT
1 ATGCGTATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGAT
* * *
84476 AT--GTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGCGAT
1 ATGCGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
*
84524 GTGCGTATATTGTGG
1 ATGCGTATA-TGTGG
84539 CCAAACGACT
Statistics
Matches: 98, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
47 1 0.01
48 38 0.39
49 4 0.04
50 49 0.50
51 6 0.06
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (50 bp):
ATGCGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
Found at i:84772 original size:37 final size:37
Alignment explanation
Indices: 84664--84772 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
84654 GGAAATATAT
*
84664 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
84701 TCCGGGTAAGACCCGATGACTACGCGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
84738 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
84773 CGTCTGAGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:87470 original size:79 final size:82
Alignment explanation
Indices: 87359--87543 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
87349 GCTACTCGTT
* * *
87359 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
87422 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
87439 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
87502 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
87519 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
87544 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:87543 original size:40 final size:40
Alignment explanation
Indices: 87340--87543 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
87330 CGGAATTTAA
** *
87340 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
87380 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
87420 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
87459 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
87499 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
87539 CCGGA
1 CCGGA
87544 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:93153 original size:54 final size:54
Alignment explanation
Indices: 93096--93208 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 54
93086 GCTCAATATC
* *
93096 TTTTCTCTCTTCAAACTCAATTTCTTTTTCAATTTTCTTTTTC-TTTTCACATTCT
1 TTTTCACTC-TCAAACTCAATTTCTTTTTC-ATTCTCTTTTTCTTTTTCACATTCT
* * ** * *
93151 TTTTCACTCTCGATCTCTTTTTCTTTTTCCTTCTCTTTTTCTTTTTCACTTTCT
1 TTTTCACTCTCAAACTCAATTTCTTTTTCATTCTCTTTTTCTTTTTCACATTCT
93205 TTTT
1 TTTT
93209 GCTTTCTTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
53 10 0.20
54 31 0.63
55 8 0.16
ACGTcount: A:0.11, C:0.25, G:0.01, T:0.64
Consensus pattern (54 bp):
TTTTCACTCTCAAACTCAATTTCTTTTTCATTCTCTTTTTCTTTTTCACATTCT
Found at i:93175 original size:6 final size:6
Alignment explanation
Indices: 93166--93213 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
93156 ACTCTCGATC
* * **
93166 TCTTTT TCTTTT TCCTTC TCTTTT TCTTTT TCACTT TCTTTT TGCTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T-CTTT
93214 CTTTCACACT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (6 bp):
TCTTTT
Found at i:93185 original size:18 final size:19
Alignment explanation
Indices: 93116--93233 Score: 88
Period size: 18 Copynumber: 6.4 Consensus size: 19
93106 TCAAACTCAA
* *
93116 TTTCTTTTTCAATTTTCTT
1 TTTCTTTTTCACTTCTCTT
*
93135 TTTC-TTTTCACAT-TCTT
1 TTTCTTTTTCACTTCTCTT
** *
93152 TTTCACTCTCGA--TCTCTT
1 TTTCTTTTTC-ACTTCTCTT
93170 TTTCTTTTTC-CTTCTCTT
1 TTTCTTTTTCACTTCTCTT
93188 TTTCTTTTTCACTT-TCTT
1 TTTCTTTTTCACTTCTCTT
*
93206 TTTGCTTTCTTTCAC-ACTCTT
1 TTT-C-TT-TTTCACTTCTCTT
93227 TTTCTTT
1 TTTCTTT
93234 GATTTCTTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
17 9 0.11
18 45 0.56
19 11 0.14
20 3 0.04
21 13 0.16
ACGTcount: A:0.08, C:0.25, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTCTTTTTCACTTCTCTT
Found at i:93220 original size:21 final size:20
Alignment explanation
Indices: 93183--93233 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
93173 CTTTTTCCTT
*
93183 CTCTTTTTC-TT-TTTCACT
1 CTCTTTTTCTTTCTTTCACA
*
93201 TTCTTTTTGCTTTCTTTCACA
1 CTCTTTTT-CTTTCTTTCACA
93222 CTCTTTTTCTTT
1 CTCTTTTTCTTT
93234 GATTTCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 7 0.26
19 1 0.04
20 6 0.22
21 13 0.48
ACGTcount: A:0.06, C:0.25, G:0.02, T:0.67
Consensus pattern (20 bp):
CTCTTTTTCTTTCTTTCACA
Found at i:95773 original size:10 final size:10
Alignment explanation
Indices: 95760--95794 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
95750 AAGCTCGGTT
95760 GAGCTCAAAC
1 GAGCTCAAAC
*
95770 GAGCTGAAAC
1 GAGCTCAAAC
*
95780 GAGCTCAAAT
1 GAGCTCAAAC
95790 GAGCT
1 GAGCT
95795 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:95803 original size:20 final size:20
Alignment explanation
Indices: 95757--95804 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
95747 AGTAAGCTCG
95757 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
95777 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
95797 GTTGAGCT
1 GTTGAGCT
95805 GGACAGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:97260 original size:40 final size:40
Alignment explanation
Indices: 97203--97278 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
97193 GCCAGGCCAA
*
97203 GTGCAAGACACAGCCGTGTGAATGTCGTACGTGTGGCTGT
1 GTGCAAGACACAACCGTGTGAATGTCGTACGTGTGGCTGT
* * * *
97243 GTGCAAGACATAACCGTGTGATTGTTGTAGGTGTGG
1 GTGCAAGACACAACCGTGTGAATGTCGTACGTGTGG
97279 TAGTGCGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.36, T:0.28
Consensus pattern (40 bp):
GTGCAAGACACAACCGTGTGAATGTCGTACGTGTGGCTGT
Found at i:109130 original size:42 final size:42
Alignment explanation
Indices: 109083--109164 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
109073 AGACTGACCA
109083 TCAGTCTGAGGGTTAAAAGCTATGCTAAAGCTCAACTTCGGG
1 TCAGTCTGAGGGTTAAAAGCTATGCTAAAGCTCAACTTCGGG
*
109125 TCAGTCTGAGGGTTAAAAGCTGTGCTAAAGCTCAACTTCG
1 TCAGTCTGAGGGTTAAAAGCTATGCTAAAGCTCAACTTCG
109165 TACCCAAGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (42 bp):
TCAGTCTGAGGGTTAAAAGCTATGCTAAAGCTCAACTTCGGG
Found at i:117148 original size:45 final size:45
Alignment explanation
Indices: 117084--117216 Score: 212
Period size: 45 Copynumber: 3.0 Consensus size: 45
117074 TATCGAACAG
117084 TACTATTCAGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAAA
1 TACTATTCAGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAAA
* *
117129 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAGA
1 TACTATTCAGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAAA
* * * *
117174 TACTATTCAAGCCCTCGAGCCTAGCAGGCTATAATGCCGGTGA
1 TACTATTCAGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGA
117217 TTTGATAATA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (45 bp):
TACTATTCAGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAAA
Found at i:119044 original size:20 final size:20
Alignment explanation
Indices: 119012--119135 Score: 185
Period size: 20 Copynumber: 6.2 Consensus size: 20
119002 GAGGCAATGC
119012 ACACGCCCGTGTGCATTGGG
1 ACACGCCCGTGTGCATTGGG
* * * *
119032 ACATGCTCGTGTGCATTAGC
1 ACACGCCCGTGTGCATTGGG
*
119052 ACACACCCGTGTGCATTGGG
1 ACACGCCCGTGTGCATTGGG
119072 ACACGCCCGTGTGCATTGGG
1 ACACGCCCGTGTGCATTGGG
119092 ACACGCCCGTGTGCATTGGG
1 ACACGCCCGTGTGCATTGGG
* *
119112 ACACACCTGTGTGCATTGGG
1 ACACGCCCGTGTGCATTGGG
119132 ACAC
1 ACAC
119136 ACCTGTGTCC
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 92 1.00
ACGTcount: A:0.19, C:0.29, G:0.31, T:0.22
Consensus pattern (20 bp):
ACACGCCCGTGTGCATTGGG
Found at i:123775 original size:40 final size:40
Alignment explanation
Indices: 123720--124147 Score: 730
Period size: 40 Copynumber: 10.7 Consensus size: 40
123710 GAGCATTGGA
*
123720 ATATATCCGGGCTAAGAGCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
123760 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
123800 ATATACCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
123840 ATATATCCGGGCTAAGACCCGAAGGAAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
123880 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
123920 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
123960 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
124000 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
124040 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
124080 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
124120 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
124148 ATGTGTTTGC
Statistics
Matches: 376, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 376 1.00
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Done.