Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1879
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: 52938
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:843 original size:13 final size:14
Alignment explanation
Indices: 819--852 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
809 AAGATATGAT
819 ATAAATATAATTAAA
1 ATAAA-ATAATTAAA
834 A-AAAATAATTAAA
1 ATAAAATAATTAAA
847 ATAAAA
1 ATAAAA
853 AATGACATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.56
14 7 0.39
15 1 0.06
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAATAATTAAA
Found at i:1256 original size:17 final size:18
Alignment explanation
Indices: 1234--1278 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
1224 TTCATTCTTT
*
1234 TTTTCCTTT-TTTTTTTC
1 TTTTCCTTTCTTCTTTTC
1251 TTTTCCTTTCTTCTTTTC
1 TTTTCCTTTCTTCTTTTC
1269 --TTCCTTTCTT
1 TTTTCCTTTCTT
1279 TCCTTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 10 0.38
17 9 0.35
18 7 0.27
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCCTTTCTTCTTTTC
Found at i:6966 original size:30 final size:27
Alignment explanation
Indices: 6932--6998 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 27
6922 TATGTTTGAG
6932 TAAAATATTTTGTAATTTAAATTTATTTATTA
1 TAAAATATTTT-T-ATTTAAATTTA---ATTA
*
6964 AAAAATATTTTTATTTAAATTTAATTA
1 TAAAATATTTTTATTTAAATTTAATTA
6991 T-AAATATT
1 TAAAATATT
6999 AATAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 7 0.21
27 4 0.12
30 11 0.33
31 1 0.03
32 10 0.30
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
TAAAATATTTTTATTTAAATTTAATTA
Found at i:10579 original size:11 final size:11
Alignment explanation
Indices: 10563--10648 Score: 58
Period size: 11 Copynumber: 8.2 Consensus size: 11
10553 TTGATAATTT
10563 TAAATATAATA
1 TAAATATAATA
*
10574 TAAATAAAATA
1 TAAATATAATA
*
10585 TATAAAATAAT-
1 TA-AATATAATA
10596 TAAAT-T-ATGA
1 TAAATATAAT-A
* *
10606 TATAT-TTATA
1 TAAATATAATA
10616 -AAAT-TAATA
1 TAAATATAATA
10625 TAAATATAATA
1 TAAATATAATA
* *
10636 AAAATAAAATA
1 TAAATATAATA
10647 TA
1 TA
10649 TTATCATATT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
8 2 0.03
9 8 0.14
10 12 0.20
11 31 0.53
12 6 0.10
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (11 bp):
TAAATATAATA
Found at i:11010 original size:20 final size:20
Alignment explanation
Indices: 10981--11042 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
10971 ACATAAAATA
10981 TAATAAATATTATATATATT
1 TAATAAATATTATATATATT
* *
11001 TAATATATATTATTTATATT
1 TAATAAATATTATATATATT
*
11021 T-A-AAATTTTA-ATATA-T
1 TAATAAATATTATATATATT
11037 TAATAA
1 TAATAA
11043 TTTATTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 2 0.06
17 5 0.14
18 8 0.23
19 1 0.03
20 19 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATAAATATTATATATATT
Found at i:12760 original size:20 final size:20
Alignment explanation
Indices: 12707--12765 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
12697 GTACCCAGAT
* *
12707 TGTATCGATACATGTATGAA
1 TGTATCGATACATTTATCAA
*
12727 TGTATCGATACATTTTTCAA
1 TGTATCGATACATTTATCAA
12747 TGTATCGATACATTCTATC
1 TGTATCGATACATT-TATC
12766 TTTTTACCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 31 0.91
21 3 0.09
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTATCAA
Found at i:13689 original size:23 final size:23
Alignment explanation
Indices: 13658--13713 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
13648 AGCCTTTGAC
13658 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
*
13681 CATGTA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
13703 CATGCATTTTT
1 CATGCATTTTT
13714 AATATGTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:13712 original size:19 final size:20
Alignment explanation
Indices: 13667--13720 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
13657 CCATGCATTT
*
13667 TTTTTATTATGTTTCATGTA
1 TTTTTATTATGTTTCATGCA
13687 TTTTTTTATTATGTTTCATGCA
1 --TTTTTATTATGTTTCATGCA
*
13709 TTTTTAATATGT
1 TTTTTATTATGT
13721 CCAGCATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.37
22 19 0.63
ACGTcount: A:0.20, C:0.06, G:0.09, T:0.65
Consensus pattern (20 bp):
TTTTTATTATGTTTCATGCA
Found at i:15970 original size:22 final size:23
Alignment explanation
Indices: 15922--15971 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
15912 AATATTTTTT
* *
15922 ATTTTTTAAAACAAATAAAGATC
1 ATTTTTTAAAACAAATAAACATA
15945 ATTTTTTAAAA-AAA-AAACATA
1 ATTTTTTAAAACAAATAAACATA
*
15966 AATTTT
1 ATTTTT
15972 GAACTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 11 0.46
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTTTTTAAAACAAATAAACATA
Found at i:16117 original size:2 final size:2
Alignment explanation
Indices: 16110--16134 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16100 GATTTTCAAA
16110 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16135 CATACAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16524 original size:10 final size:10
Alignment explanation
Indices: 16511--16540 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
16501 CCATTTCATA
16511 TTTTTTCTTT
1 TTTTTTCTTT
16521 TTTTTTCTTT
1 TTTTTTCTTT
*
16531 TTCTTTCTTT
1 TTTTTTCTTT
16541 CTTCTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:16533 original size:16 final size:17
Alignment explanation
Indices: 16512--16546 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16502 CATTTCATAT
*
16512 TTTTTCTTT-TTTTTTC
1 TTTTTCTTTCTTTCTTC
16528 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
16545 TT
1 TT
16547 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:19664 original size:3 final size:3
Alignment explanation
Indices: 19656--19684 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19646 TTCAAGAGAT
19656 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
19685 AAAGCTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20553 original size:22 final size:22
Alignment explanation
Indices: 20525--20568 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20515 AGGATACAAA
20525 AGAATGTATACTAGAATTCTTT
1 AGAATGTATACTAGAATTCTTT
20547 AGAATGTATACTAGAATTCTTT
1 AGAATGTATACTAGAATTCTTT
20569 CTTCACTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (22 bp):
AGAATGTATACTAGAATTCTTT
Found at i:20626 original size:25 final size:26
Alignment explanation
Indices: 20591--20640 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
20581 TGAAAGATTT
* *
20591 TTAATATTTATA-AATTTTAATTAAG
1 TTAATAATTATATAATTTAAATTAAG
20616 TTAATAATTATATAATTTAAATTAA
1 TTAATAATTATATAATTTAAATTAA
20641 ATTATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TTAATAATTATATAATTTAAATTAAG
Found at i:20794 original size:22 final size:21
Alignment explanation
Indices: 20769--20816 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
20759 AATTAAGTAC
*
20769 AATAT-AATATAAAAATAATATA
1 AATATGAA-ATAAAAAT-ATAAA
*
20791 AATATGAAATAAATATATAAA
1 AATATGAAATAAAAATATAAA
20812 AATAT
1 AATAT
20817 TAGAATCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 12 0.52
23 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AATATGAAATAAAAATATAAA
Found at i:22845 original size:16 final size:17
Alignment explanation
Indices: 22810--22847 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
22800 TAATTAAAAC
* *
22810 ATAAAACAATATAGAAA
1 ATAAAACAATACACAAA
22827 ATAAAACAA-ACACAAA
1 ATAAAACAATACACAAA
22843 ATAAA
1 ATAAA
22848 TACATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.74, C:0.11, G:0.03, T:0.13
Consensus pattern (17 bp):
ATAAAACAATACACAAA
Found at i:23216 original size:21 final size:20
Alignment explanation
Indices: 23184--23222 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
23174 TTCTATTTTC
23184 CTTTTTTGCCTTTCCTTTCTT
1 CTTTTTTGCCTTT-CTTTCTT
23205 CTTTTCTT-CCTTTCTTTC
1 CTTTT-TTGCCTTTCTTTC
23223 CTTAATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 10 0.59
22 2 0.12
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.67
Consensus pattern (20 bp):
CTTTTTTGCCTTTCTTTCTT
Found at i:25606 original size:22 final size:21
Alignment explanation
Indices: 25581--25625 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
25571 TCCTTTGAAT
25581 ATTACTAAAAATAATTTAATAA
1 ATTACTAAAAATAA-TTAATAA
* * *
25603 ATTATTAATATTAATTAATAA
1 ATTACTAAAAATAATTAATAA
25624 AT
1 AT
25626 AACATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTACTAAAAATAATTAATAA
Found at i:31316 original size:17 final size:16
Alignment explanation
Indices: 31276--31308 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31266 ATATATTAAC
31276 TGTTAAAGTCATTTTA
1 TGTTAAAGTCATTTTA
*
31292 TGTTAAAGTTATTTTA
1 TGTTAAAGTCATTTTA
31308 T
1 T
31309 TTTTAAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (16 bp):
TGTTAAAGTCATTTTA
Found at i:32489 original size:3 final size:3
Alignment explanation
Indices: 32474--32517 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
32464 TCTATCTTTC
*
32474 ATT ATT AGT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
32518 GACATCATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:32624 original size:38 final size:36
Alignment explanation
Indices: 32555--32627 Score: 92
Period size: 38 Copynumber: 2.0 Consensus size: 36
32545 TATAATATAA
* * *
32555 ATAAAATATAAAAAATAATTAAATTATAATATATTT
1 ATAAAATATAAAAAATAATAAAAATAAAATATATTT
*
32591 ATAAAATTAATAAAATATAATAAAAATAAAATATATT
1 ATAAAA-T-ATAAAAAATAATAAAAATAAAATATATT
32628 AACATATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 6 0.19
37 1 0.03
38 24 0.77
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (36 bp):
ATAAAATATAAAAAATAATAAAAATAAAATATATTT
Found at i:32653 original size:46 final size:45
Alignment explanation
Indices: 32554--32655 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 45
32544 ATATAATATA
* * *
32554 AATAAAATATAAAAAATAATTAAATTATAATATATTTATAAAATT
1 AATAAAATATAAAAAATAATAAAATTATAACATATTAATAAAATT
* *
32599 AATAAAATATAATAAA-AATAAAATATATTAACATATTAATAAATTT
1 AATAAAATATAAAAAATAATAAAAT-TA-TAACATATTAATAAAATT
* *
32645 ATTTAAATATA
1 AATAAAATATA
32656 TAATTATGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 7 0.15
45 17 0.35
46 24 0.50
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (45 bp):
AATAAAATATAAAAAATAATAAAATTATAACATATTAATAAAATT
Found at i:32982 original size:18 final size:17
Alignment explanation
Indices: 32941--33029 Score: 60
Period size: 18 Copynumber: 5.2 Consensus size: 17
32931 AAATATAAGA
* *
32941 TATAATTAATA-TTATA
1 TATATTTAATATTTATT
*
32957 TATTTTTAATATGTTATT
1 TATATTTAATAT-TTATT
*
32975 TATATTTAA-AATT-TT
1 TATATTTAATATTTATT
*
32990 AATATATTAATAATTTATTT
1 TATAT-TTAAT-ATTTA-TT
33010 TATATTTAA-ATTTAATT
1 TATATTTAATATTT-ATT
33027 TAT
1 TAT
33030 TGATCTAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
15 6 0.11
16 15 0.26
17 10 0.18
18 16 0.28
19 4 0.07
20 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (17 bp):
TATATTTAATATTTATT
Found at i:33021 original size:17 final size:17
Alignment explanation
Indices: 32973--33029 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
32963 TAATATGTTA
32973 TTTATATTTAAAATTT-T
1 TTTATATTT-AAATTTAT
** *
32990 AATATATTAATAATTTAT
1 TTTATATTTA-AATTTAT
*
33008 TTTATATTTAAATTTAA
1 TTTATATTTAAATTTAT
33025 TTTAT
1 TTTAT
33030 TGATCTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
16 1 0.03
17 22 0.71
18 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATTTAAATTTAT
Found at i:35663 original size:25 final size:26
Alignment explanation
Indices: 35628--35681 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
35618 GGAAAGAATT
* * *
35628 TTAATATTTATA-AATTTTAATTAAA
1 TTAATAATTATATAATTTAAAATAAA
35653 TTAATAATTATATAATTTAAAATAAA
1 TTAATAATTATATAATTTAAAATAAA
35679 TTA
1 TTA
35682 TGTTAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATAATTATATAATTTAAAATAAA
Found at i:35870 original size:28 final size:28
Alignment explanation
Indices: 35817--35873 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
35807 GTATAATCTG
*
35817 ATATAAAAATAATATGAATATGACATAA
1 ATATAAAAATAATATGAAAATGACATAA
* *
35845 ATATAAAAAT-ATATTAAAATCTACATAA
1 ATATAAAAATAATATGAAAAT-GACATAA
35873 A
1 A
35874 ATGAATTACG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (28 bp):
ATATAAAAATAATATGAAAATGACATAA
Found at i:36780 original size:20 final size:19
Alignment explanation
Indices: 36719--36777 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
36709 ATTTTTAAAA
*
36719 ATTTTTAATTTTTAATGATT
1 ATTTTTAATTTTT-ATAATT
* * *
36739 ATTTTAAAAGTTTTAAAATT
1 ATTTT-TAATTTTTATAATT
36759 ATTTTTAATTTTTATAATT
1 ATTTTTAATTTTTATAATT
36778 TATAATTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 11 0.35
20 14 0.45
21 6 0.19
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
ATTTTTAATTTTTATAATT
Found at i:36783 original size:16 final size:16
Alignment explanation
Indices: 36759--36789 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36749 TTTTAAAATT
*
36759 ATTTTTAATTTTTATA
1 ATTTATAATTTTTATA
36775 ATTTATAATTTTTAT
1 ATTTATAATTTTTAT
36790 TATTATTAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTATAATTTTTATA
Found at i:37288 original size:16 final size:16
Alignment explanation
Indices: 37267--37303 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
37257 GATATTTTTT
37267 ATATAATATAAT-TAAA
1 ATATAATATAATAT-AA
37283 ATATAATATAATATAA
1 ATATAATATAATATAA
37299 ATATA
1 ATATA
37304 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAATATAATATAA
Found at i:37308 original size:27 final size:27
Alignment explanation
Indices: 37266--37331 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
37256 AGATATTTTT
*
37266 TATATAATATAATTAAAATATAATATAA
1 TATA-AATATATTTAAAATATAATATAA
* *
37294 TATAAATATATTTAAAATTTTATATAA
1 TATAAATATATTTAAAATATAATATAA
*
37321 TAAAAAT-TATT
1 TATAAATATATT
37332 GATATATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.12
27 26 0.76
28 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TATAAATATATTTAAAATATAATATAA
Found at i:37319 original size:32 final size:31
Alignment explanation
Indices: 37283--37369 Score: 85
Period size: 32 Copynumber: 2.9 Consensus size: 31
37273 TATAATTAAA
37283 ATATAATATAATATAAATATATTTAAAATTTT
1 ATATAATATAATATAAATATATTTAAAA-TTT
* * *
37315 ATATAATA-AAAATTATTGATATATTAAAATTT
1 ATATAATATAATATAAAT-ATAT-TTAAAATTT
37347 ATATAA-AT-ATA-AAATAT-TTTAAA
1 ATATAATATAATATAAATATATTTAAA
37370 TTAATTATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
27 5 0.11
28 1 0.02
29 2 0.04
30 2 0.04
31 9 0.20
32 21 0.46
33 6 0.13
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (31 bp):
ATATAATATAATATAAATATATTTAAAATTT
Found at i:37342 original size:18 final size:17
Alignment explanation
Indices: 37299--37348 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
37289 TATAATATAA
*
37299 ATATATTTAAAATT-TT
1 ATATATTAAAAATTATT
*
37315 ATATAATAAAAATTATT
1 ATATATTAAAAATTATT
*
37332 GATATATTAAAATTTAT
1 -ATATATTAAAAATTAT
37349 ATAAATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 12 0.43
17 2 0.07
18 14 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATATATTAAAAATTATT
Found at i:38157 original size:16 final size:15
Alignment explanation
Indices: 38127--38169 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
38117 AATATAAATA
*
38127 ATTTTTATTTTTTTCT
1 ATTTTT-TTTCTTTCT
38143 ATTTTTTGTTCTTTCT
1 ATTTTTT-TTCTTTCT
*
38159 CTTTTTTTTCT
1 ATTTTTTTTCT
38170 CCTTTCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (15 bp):
ATTTTTTTTCTTTCT
Found at i:40741 original size:22 final size:21
Alignment explanation
Indices: 40716--40760 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
40706 TCCTTTGAAT
40716 ATTACTAAAAATAATTTAATAA
1 ATTACTAAAAATAA-TTAATAA
* * *
40738 ATTATTAATATTAATTAATAA
1 ATTACTAAAAATAATTAATAA
40759 AT
1 AT
40761 AATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTACTAAAAATAATTAATAA
Found at i:40763 original size:17 final size:17
Alignment explanation
Indices: 40724--40765 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
40714 ATATTACTAA
40724 AAATAAT-TTAATAAAT
1 AAATAATATTAATAAAT
* * *
40740 TATTAATATTAATTAAT
1 AAATAATATTAATAAAT
40757 AAATAATAT
1 AAATAATAT
40766 ATATAAAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAATATTAATAAAT
Found at i:42668 original size:23 final size:23
Alignment explanation
Indices: 42642--42692 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
42632 TAAAATAAAA
42642 AATTTAATTAAAAA-TATTAATAT
1 AATTT-ATTAAAAATTATTAATAT
* *
42665 AATTTTTTAAAAATTTTTAATAT
1 AATTTATTAAAAATTATTAATAT
*
42688 TATTT
1 AATTT
42693 TATATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTTATTAAAAATTATTAATAT
Found at i:42676 original size:22 final size:23
Alignment explanation
Indices: 42649--42693 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42639 AAAAATTTAA
42649 TTAAAAA-TATTAATATAATTTT
1 TTAAAAATTATTAATATAATTTT
* *
42671 TTAAAAATTTTTAATATTATTTT
1 TTAAAAATTATTAATATAATTTT
42694 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAAAAATTATTAATATAATTTT
Found at i:43360 original size:15 final size:15
Alignment explanation
Indices: 43317--43353 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
43307 TTTTCACTTC
43317 TTTTCTACTTTATCT
1 TTTTCTACTTTATCT
*
43332 CTTTCTACTTTATCT
1 TTTTCTACTTTATCT
43347 TTTTCTA
1 TTTTCTA
43354 TTCTATCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTCTACTTTATCT
Found at i:46053 original size:15 final size:15
Alignment explanation
Indices: 46032--46075 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
46022 TTTTCTCTTT
*
46032 TTTTCTACTCTAT-C
1 TTTTCTATTCTATCC
*
46046 TCTTTCTATTTTATCC
1 T-TTTCTATTCTATCC
46062 TTTTCTATTCTATC
1 TTTTCTATTCTATC
46076 ACTATCAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 22 0.88
16 2 0.08
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTCTATTCTATCC
Found at i:48202 original size:79 final size:80
Alignment explanation
Indices: 48131--48298 Score: 232
Period size: 79 Copynumber: 2.1 Consensus size: 80
48121 AAAAATAGGT
* *
48131 TTGGAGTATCCTCTCGAAAATAATGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGA
1 TTGGAGTATCCTCTCGAAAATAACGGGATTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGA
*
48196 AAAT-AAAACCGGAG
66 AAATAAAAACAGGAG
* * * * *
48210 TTGGAGTATCCTTTCGAAAATAACGGGATTAGAGTATCCTCGATTGTGAAAAATTGGTGTTTTGA
1 TTGGAGTATCCTCTCGAAAATAACGGGATTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGA
* *
48275 AAATAAAATC-GGGG
66 AAATAAAAACAGGAG
48289 TTGGAGTATC
1 TTGGAGTATC
48299 TTCGATTATG
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 75 0.95
80 4 0.05
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (80 bp):
TTGGAGTATCCTCTCGAAAATAACGGGATTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGA
AAATAAAAACAGGAG
Found at i:48304 original size:51 final size:51
Alignment explanation
Indices: 48241--48351 Score: 161
Period size: 51 Copynumber: 2.2 Consensus size: 51
48231 AACGGGATTA
* *
48241 GAGTATCCTCGATTGTGAAAAATTGGTGTTTTGAAAATAAAA-TCGGGGTTG
1 GAGTATCCTCGATTATGAAAAATTAGTGTTTTGAAAATAAAACT-GGGGTTG
* *
48292 GAGTATCTTCGATTATGAAAAATTAGTGTTTTGAAAATAAAACTGGGGTTA
1 GAGTATCCTCGATTATGAAAAATTAGTGTTTTGAAAATAAAACTGGGGTTG
*
48343 GATTATCCT
1 GAGTATCCT
48352 TTCAGAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 52 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.35
Consensus pattern (51 bp):
GAGTATCCTCGATTATGAAAAATTAGTGTTTTGAAAATAAAACTGGGGTTG
Found at i:50852 original size:50 final size:50
Alignment explanation
Indices: 50738--50845 Score: 173
Period size: 50 Copynumber: 2.2 Consensus size: 50
50728 AAAAATGTCT
* *
50738 GAATGTATCGATACATTTGGGTAAAACCTAGAATGTATCGATACAATGAA
1 GAATGTATCGATACATCTGGGTAAAACCTAGAATGTATCAATACAATGAA
*
50788 TAATGTATCGATACATCTGGGTAAAAGCC-AGAATGTATCAATACAATGAA
1 GAATGTATCGATACATCTGGGTAAAA-CCTAGAATGTATCAATACAATGAA
50838 GAATGTAT
1 GAATGTAT
50846 TAATACAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 51 0.96
51 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (50 bp):
GAATGTATCGATACATCTGGGTAAAACCTAGAATGTATCAATACAATGAA
Found at i:52773 original size:20 final size:20
Alignment explanation
Indices: 52748--52796 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
52738 AAATAGAGGC
52748 TCCCTCTTCCCTCTCAAGCA
1 TCCCTCTTCCCTCTCAAGCA
* ** *
52768 TCCCTCATCCCTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGCA
52788 TCCCTCTTC
1 TCCCTCTTC
52797 AATTCTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.49, G:0.04, T:0.37
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGCA
Done.