Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3133
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: 60781
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3281 original size:12 final size:12
Alignment explanation
Indices: 3264--3288 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3254 CAGAGGCTAT
3264 TAACAATATTTA
1 TAACAATATTTA
3276 TAACAATATTTA
1 TAACAATATTTA
3288 T
1 T
3289 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:5836 original size:21 final size:20
Alignment explanation
Indices: 5807--5845 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
5797 ACGCCTACGA
5807 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
5827 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
5846 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:6045 original size:15 final size:15
Alignment explanation
Indices: 6025--6063 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
6015 TATCATTTCA
6025 ATATATAATTAAAAT
1 ATATATAATTAAAAT
*
6040 ATATATAAATTTAAAT
1 ATATAT-AATTAAAAT
6056 ATAT-TAAT
1 ATATATAAT
6064 AATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 7 0.32
16 12 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATATAATTAAAAT
Found at i:6081 original size:18 final size:18
Alignment explanation
Indices: 6031--6082 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 18
6021 TTCAATATAT
*
6031 AATTAAAATAT-AT-ATA
1 AATTTAAATATAATAATA
*
6047 AATTTAAATATATTAATA
1 AATTTAAATATAATAATA
6065 ATATTTAAATA-AATAATA
1 A-ATTTAAATATAATAATA
6083 TTAATAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 10 0.33
17 1 0.03
18 10 0.33
19 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTAAATATAATAATA
Found at i:7822 original size:13 final size:13
Alignment explanation
Indices: 7804--7837 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
7794 ACCTCCTTGG
7804 ATTAAATTATTAA
1 ATTAAATTATTAA
7817 ATTAAAATTATTAA
1 ATT-AAATTATTAA
7831 A-TAAATT
1 ATTAAATT
7838 GAAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 4 0.20
14 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATTATTAA
Found at i:15088 original size:17 final size:17
Alignment explanation
Indices: 15068--15101 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15058 TTCGTATATT
*
15068 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
15085 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
15102 GCGAATCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:19745 original size:20 final size:19
Alignment explanation
Indices: 19675--19758 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
19665 ATAGATAAGA
19675 AATAGATAAATAATATAA-A-
1 AATA-ATAAAT-ATATAATAG
*
19694 AATAATACTAATATATATTAG
1 AATAATA--AATATATAATAG
19715 AAT-AT--ATATATAATAG
1 AATAATAAATATATAATAG
19731 AATAGATAAATATATAATAG
1 AATA-ATAAATATATAATAG
19751 AATTAATA
1 AA-TAATA
19759 TTCTAACATC
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
16 13 0.24
18 5 0.09
19 9 0.17
20 22 0.41
21 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (19 bp):
AATAATAAATATATAATAG
Found at i:23203 original size:15 final size:15
Alignment explanation
Indices: 23183--23213 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
23173 CTGTATCAGT
23183 AATGAATCAGAGCAC
1 AATGAATCAGAGCAC
23198 AATGAATCAGAGCAC
1 AATGAATCAGAGCAC
23213 A
1 A
23214 CGGAACCGTC
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:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (15 bp):
AATGAATCAGAGCAC
Found at i:27926 original size:16 final size:17
Alignment explanation
Indices: 27905--27937 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27895 TTAGGATGCC
*
27905 CCTCC-TTCCCCTTTCT
1 CCTCCTTTCCCCCTTCT
27921 CCTCCTTTCCCCCTTCT
1 CCTCCTTTCCCCCTTCT
27938 TTCATTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (17 bp):
CCTCCTTTCCCCCTTCT
Found at i:27957 original size:18 final size:18
Alignment explanation
Indices: 27934--27976 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
27924 CCTTTCCCCC
*
27934 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
27952 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
*
27970 TGCTTTC
1 TTCTTTC
27977 TTTTTATGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:28619 original size:15 final size:17
Alignment explanation
Indices: 28599--28630 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
28589 ACGTTTCATT
28599 TATATAA-T-CATAAAA
1 TATATAACTGCATAAAA
28614 TATATAACTGCATAAAA
1 TATATAACTGCATAAAA
28631 AGATTTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (17 bp):
TATATAACTGCATAAAA
Found at i:28712 original size:31 final size:31
Alignment explanation
Indices: 28677--28736 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
28667 AACTAAATAG
*
28677 AAATAAATTTAATCTATATTAAATCTATTCA
1 AAATAAATTGAATCTATATTAAATCTATTCA
28708 AAATAAATTGAATCTATATTAAATCTATT
1 AAATAAATTGAATCTATATTAAATCTATT
28737 AAATCGATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (31 bp):
AAATAAATTGAATCTATATTAAATCTATTCA
Found at i:28819 original size:17 final size:17
Alignment explanation
Indices: 28797--28835 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
28787 AATTTAGATG
*
28797 TAAAATATACTA-AAATA
1 TAAAATAAACTAGAAA-A
28814 TAAAATAAACTAGAAAA
1 TAAAATAAACTAGAAAA
28831 TAAAA
1 TAAAA
28836 ATGGAGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAATAAACTAGAAAA
Found at i:28913 original size:9 final size:9
Alignment explanation
Indices: 28899--28929 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28889 ATAAAAAAAG
28899 ATATTAAAT
1 ATATTAAAT
28908 ATATTAAAT
1 ATATTAAAT
*
28917 ATATAAAAT
1 ATATTAAAT
28926 ATAT
1 ATAT
28930 AGATAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATATTAAAT
Found at i:28946 original size:19 final size:21
Alignment explanation
Indices: 28912--28955 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
28902 TTAAATATAT
28912 TAAATATATAAAATATATAGA
1 TAAATATATAAAATATATAGA
*
28933 TAAATA-AT-AAATATATATA
1 TAAATATATAAAATATATAGA
28952 TAAA
1 TAAA
28956 ATTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 2 0.09
21 6 0.27
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAATATATAAAATATATAGA
Found at i:29125 original size:13 final size:13
Alignment explanation
Indices: 29109--29136 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29099 ATTCGAGTCT
29109 ATAATTCATATTA
1 ATAATTCATATTA
29122 ATAATTCATATTA
1 ATAATTCATATTA
29135 AT
1 AT
29137 TATGAATAAC
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:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATTCATATTA
Found at i:29591 original size:18 final size:18
Alignment explanation
Indices: 29570--29614 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
29560 ATATCTATTT
29570 TATTATATATATTCTAAA
1 TATTATATATATTCTAAA
* * *
29588 TATTTTATATATTTTATA
1 TATTATATATATTCTAAA
29606 T-TTATATAT
1 TATTATATAT
29615 TAATATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATATATATTCTAAA
Found at i:29603 original size:32 final size:35
Alignment explanation
Indices: 29565--29651 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 35
29555 TCTATATATC
29565 TATTTTATTATATATAT-TCTAA-A-T-ATTTTATA
1 TATTTTATTATATATATAT-TAATATTCATTTTATA
* *
29597 TATTTTA-TATTTATATATTAATATTCTTTTTATA
1 TATTTTATTATATATATATTAATATTCATTTTATA
29631 TATTATTATTATATATATATT
1 TATT-TTATTATATATATATT
29652 TATTTCTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
31 11 0.24
32 9 0.20
33 1 0.02
34 11 0.24
35 3 0.07
36 11 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (35 bp):
TATTTTATTATATATATATTAATATTCATTTTATA
Found at i:29605 original size:7 final size:8
Alignment explanation
Indices: 29516--29654 Score: 70
Period size: 8 Copynumber: 16.9 Consensus size: 8
29506 TGGTTTAATT
*
29516 TATTTATC
1 TATTTATA
29524 TATTTA-A
1 TATTTATA
29531 TA-TTATA
1 TATTTATA
** *
29538 T-TCAATT
1 TATTTATA
29545 TATTTATA
1 TATTTATA
*
29553 TATCTATA
1 TATTTATA
* *
29561 TATCTATTT
1 TATTTA-TA
29570 TATTATATA
1 TATT-TATA
*
29579 TATTCTAAA
1 TATT-TATA
29588 TATTTTATA
1 TA-TTTATA
29597 TATTT-TA
1 TATTTATA
29604 TATTTATA
1 TATTTATA
*
29612 TATTAATA
1 TATTTATA
* *
29620 TTCTTTTTA
1 -TATTTATA
29629 TATATTATTA
1 TAT-TTA-TA
*
29639 TTATATATA
1 -TATTTATA
29648 TATTTAT
1 TATTTAT
29655 TTCTATTTTT
Statistics
Matches: 98, Mismatches: 22, Indels: 22
0.69 0.15 0.15
Matches are distributed among these distances:
6 3 0.03
7 14 0.14
8 42 0.43
9 28 0.29
10 8 0.08
11 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTTATA
Found at i:29653 original size:25 final size:25
Alignment explanation
Indices: 29544--29654 Score: 78
Period size: 25 Copynumber: 4.6 Consensus size: 25
29534 TATATTCAAT
* *
29544 TTATTTATATATCTATATATCTATT-
1 TTATATATATATTTATATAT-TATTA
*
29569 TTATTATATATATTCTAAATATT-TTA
1 TTA-TATATATATT-TATATATTATTA
*
29595 -TATATTTTATATTTATATATTA--A
1 TTATA-TATATATTTATATATTATTA
*
29618 -TAT-TCT-T-TTTATATATTATTA
1 TTATATATATATTTATATATTATTA
29639 TTATATATATATTTAT
1 TTATATATATATTTAT
29655 TTCTATTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
19 11 0.16
20 1 0.01
21 3 0.04
22 3 0.04
23 6 0.09
24 10 0.15
25 19 0.28
26 9 0.13
27 6 0.09
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATATATATATTTATATATTATTA
Found at i:30947 original size:14 final size:14
Alignment explanation
Indices: 30925--30958 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
30915 AATAGAAAAC
*
30925 TTTTCATCACTTTT
1 TTTTTATCACTTTT
30939 TTTTTATCACTTTT
1 TTTTTATCACTTTT
*
30953 TCTTTA
1 TTTTTA
30959 GCCTCCGGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTATCACTTTT
Found at i:32297 original size:16 final size:16
Alignment explanation
Indices: 32276--32326 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
32266 AAGAAAGAGC
32276 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
32292 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
*
32308 AAACACGCTAGTAAAT
1 AAATACGCTAGTAAAT
32324 AAA
1 AAA
32327 ATACTAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (16 bp):
AAATACGCTAGTAAAT
Found at i:33266 original size:16 final size:17
Alignment explanation
Indices: 33245--33278 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
33235 AATTAGAGAA
33245 TTCTATTTAA-TTCTAT
1 TTCTATTTAATTTCTAT
33261 TTCTATTTAATTTCTAT
1 TTCTATTTAATTTCTAT
33278 T
1 T
33279 AAATCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTATTTAATTTCTAT
Found at i:33971 original size:15 final size:15
Alignment explanation
Indices: 33953--33983 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33943 ATAACTAAAG
33953 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
33968 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
33983 A
1 A
33984 GATGAGAGAT
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:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (15 bp):
AAAAAATAGATAGAT
Found at i:39696 original size:23 final size:22
Alignment explanation
Indices: 39670--39714 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
39660 AATATTCAGA
39670 ATATTAAGTA-ATTAATAATATTT
1 ATATT-AGTATATTAAT-ATATTT
*
39693 ATATTATTATATTAATATATTT
1 ATATTAGTATATTAATATATTT
39715 CGATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATTAGTATATTAATATATTT
Found at i:39702 original size:8 final size:8
Alignment explanation
Indices: 39691--39912 Score: 79
Period size: 8 Copynumber: 28.2 Consensus size: 8
39681 TTAATAATAT
39691 TTATATTA
1 TTATATTA
39699 TTATATTA
1 TTATATTA
*
39707 ATATATTTCGA
1 TTATA-TT--A
*
39718 TT-TATAAA
1 TTATAT-TA
39726 TCTATATT-
1 T-TATATTA
39734 TCTATATTA
1 T-TATATTA
39743 TT-TATT-
1 TTATATTA
*
39749 TTATTATTC
1 TTA-TATTA
*
39758 TATCTATTA
1 T-TATATTA
39767 TTATATTA
1 TTATATTA
*
39775 -TCTATTA
1 TTATATTA
39782 TTATATTA
1 TTATATTA
39790 TCTAT-TTA
1 T-TATATTA
*
39798 TAAT-TTA
1 TTATATTA
39805 -TATATTA
1 TTATATTA
39812 TT-T-TTA
1 TTATATTA
39818 -TAT-TTA
1 TTATATTA
*
39824 TAAT-TTA
1 TTATATTA
39831 TATATTATTA
1 T-TA-TATTA
39841 TTATATATA
1 TTATAT-TA
39850 TT-T-TTA
1 TTATATTA
39856 TATATATTA
1 T-TATATTA
*
39865 -TATATTT
1 TTATATTA
*
39872 TTATTTCTA
1 TTATAT-TA
39881 TT-TAGTTA
1 TTATA-TTA
39889 TTAT-TTA
1 TTATATTA
39896 TT-TAGTTA
1 TTATA-TTA
39904 TTAT-TTA
1 TTATATTA
39911 TT
1 TT
39913 TTTATTTCTA
Statistics
Matches: 166, Mismatches: 17, Indels: 63
0.67 0.07 0.26
Matches are distributed among these distances:
5 1 0.01
6 15 0.09
7 43 0.26
8 65 0.39
9 30 0.18
10 10 0.06
11 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (8 bp):
TTATATTA
Found at i:39756 original size:15 final size:15
Alignment explanation
Indices: 39738--39959 Score: 81
Period size: 15 Copynumber: 14.3 Consensus size: 15
39728 TATATTTCTA
39738 TATTATTTATTTTAT
1 TATTATTTATTTTAT
*
39753 TATTCTATCTATTATTA-
1 TA-T-TATTTATT-TTAT
*
39770 TATTATCTATTATTATAT
1 TATTA--T-TTATTTTAT
39788 TATCTATTTATAATTTAT
1 TAT-TATTTAT--TTTAT
*
39806 ATATTATTT-TTATATT
1 -TATTATTTATTTTA-T
*
39822 TATAATTTATATATTAT
1 TATTATTTAT-T-TTAT
*
39839 TATTATATATATTT-T
1 TATTATTTAT-TTTAT
*
39854 TATATATATTA-TATAT
1 TAT-TAT-TTATTTTAT
* *
39870 TTTTATTTCTATTTAGT
1 TATTATTTAT-TTTA-T
39887 TATTATTTA-TTTAGT
1 TATTATTTATTTTA-T
39902 TATTATTTA-TTT-T
1 TATTATTTATTTTAT
*
39915 TATT-TCTATTTT-T
1 TATTATTTATTTTAT
*
39928 TATT-TCTA-TTTAGT
1 TATTATTTATTTTA-T
*
39942 TATTATTTA-GTTAT
1 TATTATTTATTTTAT
39956 TATT
1 TATT
39960 TATATTTAGT
Statistics
Matches: 163, Mismatches: 19, Indels: 51
0.70 0.08 0.22
Matches are distributed among these distances:
12 6 0.04
13 17 0.10
14 12 0.07
15 47 0.29
16 19 0.12
17 36 0.22
18 21 0.13
19 5 0.03
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (15 bp):
TATTATTTATTTTAT
Found at i:39795 original size:27 final size:30
Alignment explanation
Indices: 39750--39907 Score: 116
Period size: 26 Copynumber: 5.3 Consensus size: 30
39740 TTATTTATTT
* *
39750 TATTATTCTATCTATTA-TTAT-A-TTATC
1 TATTATTATATCTATTATTTATAATTTATA
39777 TATTATTATAT-TATCTATTTATAATTTATA
1 TATTATTATATCTAT-TATTTATAATTTATA
39807 TATTATT-T-T-TA-TATTTATAATTTATA
1 TATTATTATATCTATTATTTATAATTTATA
* *
39833 TATTATTATTATATATATTTTTATATATATTATA
1 TATTATTA-TATCTAT-TATTTATA-AT-TTATA
* * * * *
39867 TATTTTTATTTCTATTTAGTTATTATTTATT
1 TATTATTATATCTA-TTATTTATAATTTATA
39898 TAGTTATTAT
1 TA-TTATTAT
39908 TTATTTTTAT
Statistics
Matches: 106, Mismatches: 11, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
26 25 0.24
27 12 0.11
28 8 0.08
29 3 0.03
30 13 0.12
31 6 0.06
32 15 0.14
33 11 0.10
34 13 0.12
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (30 bp):
TATTATTATATCTATTATTTATAATTTATA
Found at i:39803 original size:7 final size:6
Alignment explanation
Indices: 39782--39884 Score: 68
Period size: 6 Copynumber: 16.5 Consensus size: 6
39772 TTATCTATTA
* *
39782 TTATAT TATCTAT TTATAAT TTATAT ATTATTT TTATAT TTATAAT TTATAT
1 TTATAT T-TATAT TTAT-AT TTATAT -TTATAT TTATAT TTAT-AT TTATAT
* * * *
39834 ATTAT-T ATTATA- -TATAT TTTTAT ATATAT TATATAT TTTTAT TTCTAT
1 -TTATAT -TTATAT TTATAT TTATAT TTATAT T-TATAT TTATAT TTATAT
39882 TTA
1 TTA
39885 GTTATTATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
4 4 0.05
6 41 0.53
7 32 0.42
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (6 bp):
TTATAT
Found at i:39860 original size:51 final size:48
Alignment explanation
Indices: 39787--39994 Score: 122
Period size: 55 Copynumber: 4.1 Consensus size: 48
39777 TATTATTATA
*
39787 TTATCTATTTATAATTTATATATTATTTTTATATTTATAATTTATATATTA-
1 TTAT-TATTTAT-TTTTATATATTATTTTTATATTT-TAATTTATAT-TTAG
* * *
39838 TTATTATATATATTTTTATATA-TA-TTATATATTTTTATTTCTATTTAG
1 TTATTAT-T-TATTTTTATATATTATTTTTATATTTTAATTTATATTTAG
* *
39886 TTATTATTTATTTAGTTAT-TATTTATTTTTATTTCTATTTTTTATTTCTATTTAG
1 TTATTATTTATTT--TTATATA-TTATTTTTA----TA-TTTTAATTTATATTTAG
* * * *
39941 TTATTATTTAGTTATTATTTA-TATTTAGTATATTTAGAATTTATTATTTA-
1 TTATTATTTA-TTTTTATATATTATTT-TTATATTT-TAATTTA-TATTTAG
39991 TTAT
1 TTAT
39995 AATATTTAAT
Statistics
Matches: 129, Mismatches: 10, Indels: 37
0.73 0.06 0.21
Matches are distributed among these distances:
46 5 0.04
47 6 0.05
48 19 0.15
49 14 0.11
50 19 0.15
51 19 0.15
52 3 0.02
53 5 0.04
54 8 0.06
55 29 0.22
56 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (48 bp):
TTATTATTTATTTTTATATATTATTTTTATATTTTAATTTATATTTAG
Found at i:39884 original size:80 final size:84
Alignment explanation
Indices: 39742--39914 Score: 191
Period size: 80 Copynumber: 2.1 Consensus size: 84
39732 TTTCTATATT
* * *
39742 ATTTATTTTATTATTCTATCTATTATTATATTATCTATTATTATATTATCTATTTATAATTTA-T
1 ATTTATTTTATTATTATATATATTATTATATTATATATTATTATATTATCTATTTATAATTTAGT
*
39806 ATATTATTT-TTATATTTATA
66 -TATTATTTATT-TAGTTATA
* *
39826 ATTTATATATTATTATTATATATATT-TT-TA-TATATATTA-TATATT-TTTATTTCT-ATTTA
1 ATTTAT-T-TTATTATTATATATATTATTATATTATATATTATTATATTATCTATTTATAATTTA
*
39885 GTTATTATTTATTTAGTTATT
64 GTTATTATTTATTTAGTTATA
39906 ATTTATTTT
1 ATTTATTTT
39915 TATTTCTATT
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
78 2 0.03
79 1 0.01
80 25 0.32
81 10 0.13
82 6 0.08
83 8 0.10
84 8 0.10
85 3 0.04
86 15 0.19
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (84 bp):
ATTTATTTTATTATTATATATATTATTATATTATATATTATTATATTATCTATTTATAATTTAGT
TATTATTTATTTAGTTATA
Found at i:39911 original size:7 final size:7
Alignment explanation
Indices: 39738--39994 Score: 121
Period size: 7 Copynumber: 35.9 Consensus size: 7
39728 TATATTTCTA
39738 TATTATT
1 TATTATT
39745 TA-T-TT
1 TATTATT
39750 TATTATT
1 TATTATT
39757 CTATCTA-T
1 -TAT-TATT
39765 TATTATAT
1 TATTAT-T
39773 TATCTA-T
1 TAT-TATT
39780 TATTATAT
1 TATTAT-T
39788 TATCTATT
1 TAT-TATT
*
39796 TATAATT
1 TATTATT
39803 TA-TATAT
1 TATTAT-T
39810 TATT-TT
1 TATTATT
39816 TA-TATT
1 TATTATT
*
39822 TATAATT
1 TATTATT
39829 TA-TATAT
1 TATTAT-T
39836 TATTATT
1 TATTATT
39843 ATATATATT
1 -TAT-TATT
39852 T-TTATAT
1 TATTAT-T
*
39859 ATATTATA
1 -TATTATT
39867 TATT-TT
1 TATTATT
*
39873 TATT-TC
1 TATTATT
*
39879 TATTTAGT
1 TA-TTATT
39887 TATTATT
1 TATTATT
*
39894 TATTTAGT
1 TA-TTATT
39902 TATTATT
1 TATTATT
39909 TATT-TT
1 TATTATT
39915 TATTTCTATT
1 TA--T-TATT
*
39925 TTTTATT
1 TATTATT
*
39932 T-CTATT
1 TATTATT
39938 TAGTTA-T
1 TA-TTATT
*
39945 TATTTAGT
1 TA-TTATT
39953 TATTATT
1 TATTATT
39960 TA-TATT
1 TATTATT
39966 TAGTATATT
1 TA-T-TATT
**
39975 TAGAATT
1 TATTATT
39982 TATTATT
1 TATTATT
39989 TATTAT
1 TATTAT
39995 AATATTTAAT
Statistics
Matches: 195, Mismatches: 21, Indels: 68
0.69 0.07 0.24
Matches are distributed among these distances:
5 5 0.03
6 43 0.22
7 82 0.42
8 40 0.21
9 22 0.11
10 3 0.02
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (7 bp):
TATTATT
Found at i:39911 original size:55 final size:52
Alignment explanation
Indices: 39779--39959 Score: 158
Period size: 55 Copynumber: 3.4 Consensus size: 52
39769 ATATTATCTA
* * *
39779 TTATTATATTATCTATTTATAATTTATA-TA-TTAT-TTTTATATTTATAATTTA-
1 TTATTAT-TTATTTA-TTATTATTTATATTATTTATATTTT-TATTTCT-ATTTAG
39831 TATATTA-TTATTATATATATT-TTTATATATATTATATATTTTTATTTCTATTTAG
1 T-TATTATTTATT-TAT-TATTATTTATAT-TATT-TATATTTTTATTTCTATTTAG
* *
39886 TTATTATTTATTTAGTTATTATTTATTTTTATTTCTATTTTTTATTTCTATTTAG
1 TTATTATTTATTTA-TTATTATTTA-TATTATTTATA-TTTTTATTTCTATTTAG
*
39941 TTATTATTTAGTTATTATT
1 TTATTATTTATTTATTATT
39960 TATATTTAGT
Statistics
Matches: 109, Mismatches: 6, Indels: 26
0.77 0.04 0.18
Matches are distributed among these distances:
51 11 0.10
52 6 0.06
53 7 0.06
54 25 0.23
55 54 0.50
56 6 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (52 bp):
TTATTATTTATTTATTATTATTTATATTATTTATATTTTTATTTCTATTTAG
Found at i:39924 original size:19 final size:18
Alignment explanation
Indices: 39738--39938 Score: 97
Period size: 19 Copynumber: 10.6 Consensus size: 18
39728 TATATTTCTA
39738 TATTATTTATTTTATTATT
1 TATT-TTTATTTTATTATT
* * *
39757 CTATCTATTATTATATTATC
1 -TAT-TTTTATTTTATTATT
* *
39777 TA---TTATTATATTATC
1 TATTTTTATTTTATTATT
* *
39792 TATTTATAATTTA-TATAT
1 TATTTTTATTTTATTAT-T
*
39810 TATTTTTATATTTATAATT
1 TATTTTTAT-TTTATTATT
* *
39829 TATATATTATTATTA-TATA
1 TAT-TTTTATT-TTATTATT
* *
39848 TATTTTTATATATATTATA
1 TATTTTTAT-TTTATTATT
*
39867 TATTTTTATTTCTATTTAGT
1 TATTTTTATTT-TA-TTATT
39887 TATTATTTATTTAGTTATTATT
1 TATT-TTTA-TT--TTATTATT
*
39909 TATTTTTATTTCTATTTTT
1 TATTTTTATTT-TATTATT
*
39928 TATTTCTATTT
1 TATTTTTATTT
39939 AGTTATTATT
Statistics
Matches: 142, Mismatches: 21, Indels: 37
0.71 0.10 0.19
Matches are distributed among these distances:
15 15 0.11
17 3 0.02
18 21 0.15
19 48 0.34
20 33 0.23
21 9 0.06
22 10 0.07
23 2 0.01
24 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TATTTTTATTTTATTATT
Found at i:39950 original size:11 final size:10
Alignment explanation
Indices: 39738--39962 Score: 121
Period size: 11 Copynumber: 22.0 Consensus size: 10
39728 TATATTTCTA
39738 TATTATTTAT
1 TATTATTTAT
39748 T-TTA-TTAT
1 TATTATTTAT
* *
39756 T-CTATCTAT
1 TATTATTTAT
39765 TATTATATTAT
1 TATTAT-TTAT
39776 CTATTATTATAT
1 -TATTATT-TAT
39788 TATCTATTTA-
1 TAT-TATTTAT
39798 TA--ATTTAT
1 TATTATTTAT
39806 ATATTATTT-T
1 -TATTATTTAT
39816 TA-TATTTAT
1 TATTATTTAT
* *
39825 AATTTATATAT
1 TA-TTATTTAT
39836 TATTATTATAT
1 TATTATT-TAT
*
39847 ATATTTTTATAT
1 -TATTATT-TAT
*
39859 ATATTATATAT
1 -TATTATTTAT
* *
39870 TTTTATTT-C
1 TATTATTTAT
*
39879 TATTTAGTTAT
1 TA-TTATTTAT
39890 TATTTATTTAGT
1 TA-TTATTTA-T
39902 TATTATTTAT
1 TATTATTTAT
* *
39912 TTTTATTT-C
1 TATTATTTAT
*
39921 TATTTTTTAT
1 TATTATTTAT
39931 T-TCTATTTAGT
1 TAT-TATTTA-T
39942 TATTATTTAGT
1 TATTATTTA-T
39953 TATTATTTAT
1 TATTATTTAT
39963 ATTTAGTATA
Statistics
Matches: 169, Mismatches: 24, Indels: 44
0.71 0.10 0.19
Matches are distributed among these distances:
7 5 0.03
8 12 0.07
9 21 0.12
10 37 0.22
11 61 0.36
12 33 0.20
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (10 bp):
TATTATTTAT
Found at i:39990 original size:29 final size:30
Alignment explanation
Indices: 39868--39991 Score: 99
Period size: 29 Copynumber: 4.4 Consensus size: 30
39858 TATATTATAT
*
39868 ATTT-TTATTTCTATTTAGTTATTATTT--
1 ATTTATTATTTATATTTAGTTATTATTTAG
* **
39895 ATTTAGTTA--T-TATTTA-TTTTTATTTCT
1 ATTTA-TTATTTATATTTAGTTATTATTTAG
* *
39922 ATTTTTTATTTCTATTTAGTTATTATTTAG
1 ATTTATTATTTATATTTAGTTATTATTTAG
39952 --TTATTATTTATATTTAG-TA-TATTTAG
1 ATTTATTATTTATATTTAGTTATTATTTAG
39978 AATTTATTATTTAT
1 -ATTTATTATTTAT
39992 TATAATATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
25 8 0.10
26 16 0.20
27 11 0.14
28 16 0.20
29 20 0.25
30 8 0.10
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (30 bp):
ATTTATTATTTATATTTAGTTATTATTTAG
Found at i:40019 original size:40 final size:40
Alignment explanation
Indices: 39941--40019 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
39931 TTCTATTTAG
**
39941 TTATTATTTAGTTATTATTTATATTTAGTATATTTAGAAT
1 TTATTATTTAGTTATTATTTATATTTAGTATAAATAGAAT
39981 TTATTATTTA-TTATAATATTTA-ATTTAAGT-TAAATAGAA
1 TTATTATTTAGTTAT--TATTTATATTT-AGTATAAATAGAA
40020 AAATTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 4 0.12
40 21 0.62
41 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (40 bp):
TTATTATTTAGTTATTATTTATATTTAGTATAAATAGAAT
Found at i:40033 original size:31 final size:32
Alignment explanation
Indices: 39994--40068 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
39984 TTATTTATTA
39994 TAAT-ATTTAATTTAAGT-TAAATAGAAA-AAT
1 TAATAATTTAATTTAAGTATAAATA-AAACAAT
*
40024 TAATAATTTAATTTAAGTATAATTAAAATCAAT
1 TAATAATTTAATTTAAGTATAAATAAAA-CAAT
*
40057 TATTAATTTAAT
1 TAATAATTTAAT
40069 AATTTTTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 4 0.10
31 16 0.41
32 5 0.13
33 14 0.36
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (32 bp):
TAATAATTTAATTTAAGTATAAATAAAACAAT
Found at i:44948 original size:12 final size:12
Alignment explanation
Indices: 44931--44959 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
44921 TTAAATTATA
44931 CAATTTCTAATT
1 CAATTTCTAATT
44943 CAATTTCTAATT
1 CAATTTCTAATT
44955 CAATT
1 CAATT
44960 ATTATACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (12 bp):
CAATTTCTAATT
Found at i:45749 original size:25 final size:25
Alignment explanation
Indices: 45715--45764 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
45705 ATCTAGTTTC
45715 TTTTTATAATATCTATTTATTTCTA
1 TTTTTATAATATCTATTTATTTCTA
45740 TTTTTATAATATCTATTTATTTCTA
1 TTTTTATAATATCTATTTATTTCTA
45765 ATAAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTTTATAATATCTATTTATTTCTA
Found at i:45756 original size:15 final size:15
Alignment explanation
Indices: 45715--45757 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
45705 ATCTAGTTTC
45715 TTTTTATAATATCTA
1 TTTTTATAATATCTA
45730 --TTTAT--T-TCTA
1 TTTTTATAATATCTA
45740 TTTTTATAATATCTA
1 TTTTTATAATATCTA
45755 TTT
1 TTT
45758 ATTTCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 4 0.17
11 1 0.04
12 5 0.22
13 5 0.22
14 1 0.04
15 7 0.30
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTATAATATCTA
Found at i:45771 original size:21 final size:23
Alignment explanation
Indices: 45719--45772 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
45709 AGTTTCTTTT
*
45719 TATAATATCTATTTATTTCTATTTT
1 TATAATATCTATTTATTTCTA--TA
45744 TATAATATCTATTTATTTCTA-A
1 TATAATATCTATTTATTTCTATA
45766 TA-AATAT
1 TATAATAT
45773 TTATATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 2 0.07
25 21 0.75
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (23 bp):
TATAATATCTATTTATTTCTATA
Done.