Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1166
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: 40609
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:2822 original size:19 final size:16
Alignment explanation
Indices: 2777--2835 Score: 61
Period size: 15 Copynumber: 3.7 Consensus size: 16
2767 TCAAATTCGA
2777 AATT-ATTAAATTAAT
1 AATTAATTAAATTAAT
2792 AATTAA-TAAATTAAT
1 AATTAATTAAATTAAT
2807 ATATTTAACTTAAATTAA-
1 A-A-TTAA-TTAAATTAAT
*
2825 AATTAAATAAA
1 AATTAATTAAA
2836 AATAAATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 18 0.47
16 6 0.16
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAATTAAATTAAT
Found at i:2848 original size:3 final size:3
Alignment explanation
Indices: 2830--3021 Score: 61
Period size: 3 Copynumber: 65.3 Consensus size: 3
2820 ATTAAAATTA
* * * * *
2830 AAT AAA AAT AAAT AAT AAT ATT TA- AAT AAT AAT AAT ATT TA- AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
2874 AAAT AAT AAT AAT ATT TA- AAT -AT AA- AAT AAT -TT AA- ATAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * * * *
2916 TA- AAT AAT AAT AAT ATT TA- AAT AAAT AAT AAT ATT TA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* *
2959 -AT AAAT AAT ATAT AAAT AAT -AT AAT AAT AAT -AT ATT ATAT ATT AAT
1 AAT -AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
3005 AAAT AAT -AT AAAT AAT A
1 -AAT AAT AAT -AAT AAT A
3022 TAGAAATATA
Statistics
Matches: 135, Mismatches: 30, Indels: 48
0.63 0.14 0.23
Matches are distributed among these distances:
2 20 0.15
3 91 0.67
4 23 0.17
5 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2857 original size:11 final size:10
Alignment explanation
Indices: 2843--3022 Score: 97
Period size: 11 Copynumber: 18.8 Consensus size: 10
2833 AAAAATAAAT
2843 AATAATATTTA
1 AATAATA-TTA
*
2854 AATAATAAT-
1 AATAATATTA
2863 AAT-AT-TTA
1 AATAATATTA
*
2871 AATAA-ATAA
1 AATAATATTA
2880 TAATAATATTTA
1 -AATAATA-TTA
2892 AAT-ATA--A
1 AATAATATTA
2899 AATAAT-TTA
1 AATAATATTA
2908 AAT-ATAATTA
1 AATAAT-ATTA
*
2918 AATAATAAT-
1 AATAATATTA
2927 AAT-AT-TTA
1 AATAATATTA
2935 AATAA-A-T-
1 AATAATATTA
2942 AATAATATTTA
1 AATAATA-TTA
2953 AATAATA-TA
1 AATAATATTA
2962 AATAATATATA
1 AATAATAT-TA
*
2973 AATAATATAA
1 AATAATATTA
2983 TAATAATATATTA
1 -AAT-A-ATATTA
* * *
2996 TATATTAATA
1 AATAATATTA
3006 AATAATA-TA
1 AATAATATTA
3015 AATAATAT
1 AATAATAT
3023 AGAAATATAG
Statistics
Matches: 131, Mismatches: 13, Indels: 51
0.67 0.07 0.26
Matches are distributed among these distances:
7 11 0.08
8 16 0.12
9 32 0.24
10 28 0.21
11 34 0.26
12 5 0.04
13 5 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATAATATTA
Found at i:2900 original size:64 final size:63
Alignment explanation
Indices: 2830--3021 Score: 197
Period size: 64 Copynumber: 3.1 Consensus size: 63
2820 ATTAAAATTA
2830 AATAAAAATAAATAATAATATTTAAATAATAATAATATTTAAATAAATAATAATAATATTTAAAT
1 AATAAAAATAAATAATAATA-TTAAATAATAATAATATTTAAAT-AATAATAATAATATTTAAAT
*
2895 -AT-AAAATAATTTAA-ATATAATTAAATAATAATAATATTTAAAT-A-AATAATAATATTTAAA
1 AATAAAAATAA-ATAATA-AT-ATTAAATAATAATAATATTTAAATAATAATAATAATATTTAAA
2955 T
63 T
* * *
2956 AATATAAAT-AATATATAA-A-TAATATAATAATAATATATTATATATTAATAAATAATA--TAA
1 AATAAAAATAAATA-ATAATATTAA-ATAATAATAATAT-TTAAATAATAAT-AATAATATTTAA
3016 AT
62 AT
3018 AATA
1 AATA
3022 TAGAAATATA
Statistics
Matches: 110, Mismatches: 5, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
59 3 0.03
60 14 0.13
61 24 0.22
62 15 0.14
63 16 0.15
64 37 0.34
65 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (63 bp):
AATAAAAATAAATAATAATATTAAATAATAATAATATTTAAATAATAATAATAATATTTAAAT
Found at i:2930 original size:43 final size:44
Alignment explanation
Indices: 2820--3021 Score: 179
Period size: 43 Copynumber: 4.5 Consensus size: 44
2810 TTTAACTTAA
*
2820 ATTAAAATTAAATAAAAATAAATAATAATATTTAAAT-AATAATAAT
1 ATTAAAA-T-AATATAAAT-AATAATAATATTTAAATAAATAATAAT
2866 ATT----TAA-ATAAATAATAATAATATTTAAATATAA-AATAAT
1 ATTAAAATAATATAAATAATAATAATATTTAAATA-AATAATAAT
2905 -TTAAATATAAT-TAAATAATAATAATATTTAAATAAATAATAAT
1 ATTAAA-ATAATATAAATAATAATAATATTTAAATAAATAATAAT
* * *
2948 ATTTAAATAATATAAATAATATATAAATAATATAATAATAATATATTATAT
1 ATTAAAATAATATAAATAATA-AT-AAT-AT-TTA-AATAA-ATAATA-AT
2999 ATTAATAAATAATATAAATAATA
1 ATT-A-AAATAATATAAATAATA
3022 TAGAAATATA
Statistics
Matches: 131, Mismatches: 5, Indels: 33
0.78 0.03 0.20
Matches are distributed among these distances:
38 19 0.15
39 11 0.08
40 4 0.03
41 1 0.01
42 2 0.02
43 37 0.28
44 13 0.10
45 2 0.02
46 6 0.05
47 2 0.02
48 2 0.02
49 5 0.04
50 5 0.04
51 5 0.04
53 17 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (44 bp):
ATTAAAATAATATAAATAATAATAATATTTAAATAAATAATAAT
Found at i:3041 original size:21 final size:20
Alignment explanation
Indices: 3015--3053 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3005 AAATAATATA
3015 AATAATATAGAAATATAGATT
1 AATAATATAGAAAT-TAGATT
3036 AATAATATAGAAATTAGA
1 AATAATATAGAAATTAGA
3054 AATATAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (20 bp):
AATAATATAGAAATTAGATT
Found at i:3044 original size:13 final size:13
Alignment explanation
Indices: 3026--3074 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
3016 ATAATATAGA
3026 AATATAGATTAAT
1 AATATAGATTAAT
3039 AATATAGAAATTAGA-
1 AATATAG--ATTA-AT
3054 AATATAGATTAAT
1 AATATAGATTAAT
3067 AATATAGA
1 AATATAGA
3075 AATATAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.03
13 19 0.59
15 11 0.34
16 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (13 bp):
AATATAGATTAAT
Found at i:3058 original size:28 final size:29
Alignment explanation
Indices: 3006--3082 Score: 129
Period size: 28 Copynumber: 2.7 Consensus size: 29
2996 TATATTAATA
*
3006 AATAATATAAATAATATAGAAATATAGATT
1 AATAATATAGA-AATATAGAAATATAGATT
3036 AATAATATAGAAAT-TAGAAATATAGATT
1 AATAATATAGAAATATAGAAATATAGATT
3064 AATAATATAGAAATATAGA
1 AATAATATAGAAATATAGA
3083 TTTCGAAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 28 0.62
29 7 0.16
30 10 0.22
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (29 bp):
AATAATATAGAAATATAGAAATATAGATT
Found at i:3142 original size:10 final size:11
Alignment explanation
Indices: 3124--3158 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
3114 AATATAAATA
3124 TTAATAATTAC
1 TTAATAATTAC
3135 TTAA-AATTA-
1 TTAATAATTAC
3144 TTAATAATTAC
1 TTAATAATTAC
3155 TTAA
1 TTAA
3159 ATTAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.18
10 10 0.45
11 8 0.36
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAATAATTAC
Found at i:3147 original size:20 final size:20
Alignment explanation
Indices: 3122--3159 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3112 TTAATATAAA
3122 TATTAATAATTACTTAAAAT
1 TATTAATAATTACTTAAAAT
3142 TATTAATAATTACTTAAA
1 TATTAATAATTACTTAAA
3160 TTAATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAATAATTACTTAAAAT
Found at i:3165 original size:16 final size:18
Alignment explanation
Indices: 3118--3160 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 18
3108 TATATTAATA
3118 TAAATATTAATAATTACT
1 TAAATATTAATAATTACT
3136 TAAAATTATTAATAATTACT
1 T-AAA-TATTAATAATTACT
3156 TAAAT
1 TAAAT
3161 TAATATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.09
19 6 0.26
20 15 0.65
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATATTAATAATTACT
Found at i:3170 original size:19 final size:20
Alignment explanation
Indices: 3125--3170 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
3115 ATATAAATAT
*
3125 TAATAATTACTTAAAATTAT
1 TAATAATTACTTAAAATTAA
3145 TAATAATTACTT-AAATTAA
1 TAATAATTACTTAAAATTAA
*
3164 TATTAAT
1 TAATAAT
3171 AACATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATAATTACTTAAAATTAA
Found at i:8871 original size:15 final size:15
Alignment explanation
Indices: 8853--8883 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8843 ATCTCTCATC
8853 TATCTATCTATTTTT
1 TATCTATCTATTTTT
8868 TATCTATCTATTTTT
1 TATCTATCTATTTTT
8883 T
1 T
8884 CTTTAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (15 bp):
TATCTATCTATTTTT
Found at i:10494 original size:16 final size:16
Alignment explanation
Indices: 10475--10525 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
10465 TTTCTAGTAT
10475 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
*
10491 TTTATTTACTAGCATA
1 TTTATTTACTAGCGTA
*
10507 TTCATTTACTAGCGTA
1 TTTATTTACTAGCGTA
10523 TTT
1 TTT
10526 GCTCTTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:12517 original size:12 final size:12
Alignment explanation
Indices: 12500--12526 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12490 GAGGCTAAAG
12500 AAAAAGTGATGA
1 AAAAAGTGATGA
12512 AAAAAGTGATGA
1 AAAAAGTGATGA
12524 AAA
1 AAA
12527 GTTTTCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (12 bp):
AAAAAGTGATGA
Found at i:13813 original size:9 final size:9
Alignment explanation
Indices: 13799--13889 Score: 61
Period size: 9 Copynumber: 10.6 Consensus size: 9
13789 ATTAAAAGAA
13799 AATATATAT
1 AATATATAT
13808 AATATATAT
1 AATATATAT
13817 AATATATA-
1 AATATATAT
*
13825 AATAAAT-T
1 AATATATAT
13833 GAATATATA-
1 -AATATATAT
*
13842 AATAAAT-T
1 AATATATAT
*
13850 GAATA-AAAT
1 -AATATATAT
13859 AATATATA-
1 AATATATAT
*
13867 AATAAAT-T
1 AATATATAT
*
13875 GAATATATTT
1 -AATATATAT
13885 AATAT
1 AATAT
13890 TAAATAGAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
8 23 0.35
9 41 0.63
10 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (9 bp):
AATATATAT
Found at i:13882 original size:17 final size:17
Alignment explanation
Indices: 13799--13854 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 17
13789 ATTAAAAGAA
*
13799 AATATATATAATATATAT-
1 AATATATA-AATAAAT-TG
13817 AATATATAAATAAATTG
1 AATATATAAATAAATTG
13834 AATATATAAATAAATTG
1 AATATATAAATAAATTG
13851 AATA
1 AATA
13855 AAATAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
16 1 0.03
17 27 0.75
18 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (17 bp):
AATATATAAATAAATTG
Found at i:13908 original size:24 final size:24
Alignment explanation
Indices: 13881--13943 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
13871 AATTGAATAT
13881 ATTTAATATTAAATAGAATTTCGA
1 ATTTAATATTAAATAGAATTTCGA
*
13905 ATTTAATATTTAATAGAATTTCGA
1 ATTTAATATTAAATAGAATTTCGA
*
13929 ATTTAATATAAAATA
1 ATTTAATATTAAATA
13944 TATAAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (24 bp):
ATTTAATATTAAATAGAATTTCGA
Found at i:14672 original size:16 final size:16
Alignment explanation
Indices: 14653--14703 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
14643 TTTCTAGTAT
14653 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
*
14669 TTTATTTACTAGCATA
1 TTTATTTACTAGCGTA
*
14685 TTCATTTACTAGCGTA
1 TTTATTTACTAGCGTA
14701 TTT
1 TTT
14704 GCTCTTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:25040 original size:13 final size:12
Alignment explanation
Indices: 25022--25054 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
25012 TAATTTATGG
25022 GAACAAATAAATA
1 GAACAAATAAA-A
25035 GAACAAATAAAA
1 GAACAAATAAAA
25047 -AACAAATA
1 GAACAAATA
25055 GCGGTAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 1 0.05
13 11 0.55
ACGTcount: A:0.73, C:0.09, G:0.06, T:0.12
Consensus pattern (12 bp):
GAACAAATAAAA
Found at i:27099 original size:15 final size:15
Alignment explanation
Indices: 27079--27112 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
27069 TCCTATTACC
27079 TATTATTTAATTTAA
1 TATTATTTAATTTAA
27094 TATTATTTAATTTAA
1 TATTATTTAATTTAA
27109 TATT
1 TATT
27113 GATATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTTAATTTAA
Found at i:31383 original size:19 final size:16
Alignment explanation
Indices: 31338--31396 Score: 61
Period size: 15 Copynumber: 3.7 Consensus size: 16
31328 TCAAATTCGA
31338 AATT-ATTAAATTAAT
1 AATTAATTAAATTAAT
31353 AATTAA-TAAATTAAT
1 AATTAATTAAATTAAT
31368 ATATTTAACTTAAATTAA-
1 A-A-TTAA-TTAAATTAAT
*
31386 AATTAAATAAA
1 AATTAATTAAA
31397 AATAAATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 18 0.47
16 6 0.16
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAATTAAATTAAT
Found at i:31409 original size:3 final size:3
Alignment explanation
Indices: 31391--31582 Score: 61
Period size: 3 Copynumber: 65.3 Consensus size: 3
31381 ATTAAAATTA
* * * * *
31391 AAT AAA AAT AAAT AAT AAT ATT TA- AAT AAT AAT AAT ATT TA- AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
31435 AAAT AAT AAT AAT ATT TA- AAT -AT AA- AAT AAT -TT AA- ATAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * * * *
31477 TA- AAT AAT AAT AAT ATT TA- AAT AAAT AAT AAT ATT TA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* *
31520 -AT AAAT AAT ATAT AAAT AAT -AT AAT AAT AAT -AT ATT ATAT ATT AAT
1 AAT -AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
31566 AAAT AAT -AT AAAT AAT A
1 -AAT AAT AAT -AAT AAT A
31583 TAGAAATATA
Statistics
Matches: 135, Mismatches: 30, Indels: 48
0.63 0.14 0.23
Matches are distributed among these distances:
2 20 0.15
3 91 0.67
4 23 0.17
5 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:31418 original size:11 final size:10
Alignment explanation
Indices: 31404--31583 Score: 97
Period size: 11 Copynumber: 18.8 Consensus size: 10
31394 AAAAATAAAT
31404 AATAATATTTA
1 AATAATA-TTA
*
31415 AATAATAAT-
1 AATAATATTA
31424 AAT-AT-TTA
1 AATAATATTA
*
31432 AATAA-ATAA
1 AATAATATTA
31441 TAATAATATTTA
1 -AATAATA-TTA
31453 AAT-ATA--A
1 AATAATATTA
31460 AATAAT-TTA
1 AATAATATTA
31469 AAT-ATAATTA
1 AATAAT-ATTA
*
31479 AATAATAAT-
1 AATAATATTA
31488 AAT-AT-TTA
1 AATAATATTA
31496 AATAA-A-T-
1 AATAATATTA
31503 AATAATATTTA
1 AATAATA-TTA
31514 AATAATA-TA
1 AATAATATTA
31523 AATAATATATA
1 AATAATAT-TA
*
31534 AATAATATAA
1 AATAATATTA
31544 TAATAATATATTA
1 -AAT-A-ATATTA
* * *
31557 TATATTAATA
1 AATAATATTA
31567 AATAATA-TA
1 AATAATATTA
31576 AATAATAT
1 AATAATAT
31584 AGAAATATAG
Statistics
Matches: 131, Mismatches: 13, Indels: 51
0.67 0.07 0.26
Matches are distributed among these distances:
7 11 0.08
8 16 0.12
9 32 0.24
10 28 0.21
11 34 0.26
12 5 0.04
13 5 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATAATATTA
Found at i:31461 original size:64 final size:63
Alignment explanation
Indices: 31391--31582 Score: 197
Period size: 64 Copynumber: 3.1 Consensus size: 63
31381 ATTAAAATTA
31391 AATAAAAATAAATAATAATATTTAAATAATAATAATATTTAAATAAATAATAATAATATTTAAAT
1 AATAAAAATAAATAATAATA-TTAAATAATAATAATATTTAAAT-AATAATAATAATATTTAAAT
*
31456 -AT-AAAATAATTTAA-ATATAATTAAATAATAATAATATTTAAAT-A-AATAATAATATTTAAA
1 AATAAAAATAA-ATAATA-AT-ATTAAATAATAATAATATTTAAATAATAATAATAATATTTAAA
31516 T
63 T
* * *
31517 AATATAAAT-AATATATAA-A-TAATATAATAATAATATATTATATATTAATAAATAATA--TAA
1 AATAAAAATAAATA-ATAATATTAA-ATAATAATAATAT-TTAAATAATAAT-AATAATATTTAA
31577 AT
62 AT
31579 AATA
1 AATA
31583 TAGAAATATA
Statistics
Matches: 110, Mismatches: 5, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
59 3 0.03
60 14 0.13
61 24 0.22
62 15 0.14
63 16 0.15
64 37 0.34
65 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (63 bp):
AATAAAAATAAATAATAATATTAAATAATAATAATATTTAAATAATAATAATAATATTTAAAT
Found at i:31491 original size:43 final size:44
Alignment explanation
Indices: 31381--31582 Score: 179
Period size: 43 Copynumber: 4.5 Consensus size: 44
31371 TTTAACTTAA
*
31381 ATTAAAATTAAATAAAAATAAATAATAATATTTAAAT-AATAATAAT
1 ATTAAAA-T-AATATAAAT-AATAATAATATTTAAATAAATAATAAT
31427 ATT----TAA-ATAAATAATAATAATATTTAAATATAA-AATAAT
1 ATTAAAATAATATAAATAATAATAATATTTAAATA-AATAATAAT
31466 -TTAAATATAAT-TAAATAATAATAATATTTAAATAAATAATAAT
1 ATTAAA-ATAATATAAATAATAATAATATTTAAATAAATAATAAT
* * *
31509 ATTTAAATAATATAAATAATATATAAATAATATAATAATAATATATTATAT
1 ATTAAAATAATATAAATAATA-AT-AAT-AT-TTA-AATAA-ATAATA-AT
31560 ATTAATAAATAATATAAATAATA
1 ATT-A-AAATAATATAAATAATA
31583 TAGAAATATA
Statistics
Matches: 131, Mismatches: 5, Indels: 33
0.78 0.03 0.20
Matches are distributed among these distances:
38 19 0.15
39 11 0.08
40 4 0.03
41 1 0.01
42 2 0.02
43 37 0.28
44 13 0.10
45 2 0.02
46 6 0.05
47 2 0.02
48 2 0.02
49 5 0.04
50 5 0.04
51 5 0.04
53 17 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (44 bp):
ATTAAAATAATATAAATAATAATAATATTTAAATAAATAATAAT
Found at i:31602 original size:21 final size:20
Alignment explanation
Indices: 31576--31614 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
31566 AAATAATATA
31576 AATAATATAGAAATATAGATT
1 AATAATATAGAAAT-TAGATT
31597 AATAATATAGAAATTAGA
1 AATAATATAGAAATTAGA
31615 AATATAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (20 bp):
AATAATATAGAAATTAGATT
Found at i:31605 original size:13 final size:13
Alignment explanation
Indices: 31587--31635 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
31577 ATAATATAGA
31587 AATATAGATTAAT
1 AATATAGATTAAT
31600 AATATAGAAATTAGA-
1 AATATAG--ATTA-AT
31615 AATATAGATTAAT
1 AATATAGATTAAT
31628 AATATAGA
1 AATATAGA
31636 AATATAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.03
13 19 0.59
15 11 0.34
16 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (13 bp):
AATATAGATTAAT
Found at i:31619 original size:28 final size:29
Alignment explanation
Indices: 31567--31643 Score: 129
Period size: 28 Copynumber: 2.7 Consensus size: 29
31557 TATATTAATA
*
31567 AATAATATAAATAATATAGAAATATAGATT
1 AATAATATAGA-AATATAGAAATATAGATT
31597 AATAATATAGAAAT-TAGAAATATAGATT
1 AATAATATAGAAATATAGAAATATAGATT
31625 AATAATATAGAAATATAGA
1 AATAATATAGAAATATAGA
31644 TTTCGAAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 28 0.62
29 7 0.16
30 10 0.22
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (29 bp):
AATAATATAGAAATATAGAAATATAGATT
Found at i:31699 original size:23 final size:22
Alignment explanation
Indices: 31673--31734 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 22
31663 TAATTTTATA
31673 TTAATATAAATATTAATAATTAC
1 TTAA-ATAAATATTAATAATTAC
*
31696 TT-AA-AATTATTAATAATTAC
1 TTAAATAAATATTAATAATTAC
*
31716 TTAAAATTAATATTAATAA
1 TT-AAATAAATATTAATAA
31735 CATTAATAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 17 0.52
21 1 0.03
22 3 0.09
23 12 0.36
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAAATAAATATTAATAATTAC
Found at i:31703 original size:10 final size:11
Alignment explanation
Indices: 31685--31724 Score: 59
Period size: 10 Copynumber: 3.9 Consensus size: 11
31675 AATATAAATA
31685 TTAATAATTAC
1 TTAATAATTAC
31696 TTAA-AATTA-
1 TTAATAATTAC
31705 TTAATAATTAC
1 TTAATAATTAC
31716 TTAA-AATTA
1 TTAATAATTA
31725 ATATTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.15
10 15 0.56
11 8 0.30
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAATAATTAC
Found at i:31708 original size:20 final size:20
Alignment explanation
Indices: 31683--31724 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31673 TTAATATAAA
31683 TATTAATAATTACTTAAAAT
1 TATTAATAATTACTTAAAAT
31703 TATTAATAATTACTTAAAAT
1 TATTAATAATTACTTAAAAT
31723 TA
1 TA
31725 ATATTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAATAATTACTTAAAAT
Found at i:31732 original size:20 final size:20
Alignment explanation
Indices: 31686--31732 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
31676 ATATAAATAT
*
31686 TAATAATTACTTAAAATTAT
1 TAATAATTACTTAAAATTAA
31706 TAATAATTACTTAAAATTAA
1 TAATAATTACTTAAAATTAA
*
31726 TATTAAT
1 TAATAAT
31733 AACATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATAATTACTTAAAATTAA
Found at i:37436 original size:15 final size:15
Alignment explanation
Indices: 37418--37448 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
37408 ATCTCTCATC
37418 TATCTATCTATTTTT
1 TATCTATCTATTTTT
37433 TATCTATCTATTTTT
1 TATCTATCTATTTTT
37448 T
1 T
37449 CTTTAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (15 bp):
TATCTATCTATTTTT
Done.