Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 20 of 20
Found at i:3542368 original size:15 final size:14
Alignment explanation
Indices: 3542305--3542371 Score: 64
Period size: 15 Copynumber: 4.6 Consensus size: 14
3542295 ATTAATTTTA
3542305 AATAAATATAAATAT
1 AATAAATAT-AATAT
**
3542320 TTTAAATATAATTAT
1 AATAAATATAA-TAT
*
3542335 AATATAATAAAATAT
1 AATA-AATATAATAT
3542350 -ATAAATATAATAT
1 AATAAATATAATAT
3542363 CAATAAATA
1 -AATAAATA
3542372 ACAAACGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 9 0.21
14 5 0.12
15 22 0.52
16 6 0.14
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAAATATAATAT
Found at i:3543665 original size:3 final size:3
Alignment explanation
Indices: 3543657--3543696 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3543647 TTTAACACTT
3543657 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3543697 GTCATAGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3547827 original size:26 final size:26
Alignment explanation
Indices: 3547793--3547864 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 26
3547783 ATGAATTCAT
* *
3547793 ATTTTTATTATTTTTTATATTTAA-A
1 ATTTATATTATTTTATATATTTAATA
3547818 ATATTATA-T-TTTTATATA-TTAATA
1 AT-TTATATTATTTTATATATTTAATA
*
3547842 ATTTATTTTATTTTATATATTTA
1 ATTTATATTATTTTATATATTTA
3547865 TATGTATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 8 0.21
24 12 0.31
25 12 0.31
26 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTTATATTATTTTATATATTTAATA
Found at i:3547839 original size:23 final size:23
Alignment explanation
Indices: 3547798--3547859 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
3547788 TTCATATTTT
3547798 TATTATTTTTTATAT-TTAA-AA
1 TATTATTTTTTATATATTAATAA
3547819 TATTATATTTTTATATATTAATAA
1 TATTAT-TTTTTATATATTAATAA
*
3547843 T-TTATTTTATTTTATAT
1 TATTATTTT-TTATATAT
3547860 ATTTATATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 6 0.17
22 12 0.33
23 15 0.42
24 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTATTTTTTATATATTAATAA
Found at i:3548242 original size:8 final size:8
Alignment explanation
Indices: 3548214--3548270 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
3548204 TAAAGCTGGA
3548214 AAAAAAAG
1 AAAAAAAG
3548222 AAAGAAAGGAG
1 AAA-AAA--AG
3548233 AAAAAAAG
1 AAAAAAAG
*
3548241 -AAAAATG
1 AAAAAAAG
*
3548248 AAAGAAAG
1 AAAAAAAG
*
3548256 AAAAAGAG
1 AAAAAAAG
3548264 AAAAAAA
1 AAAAAAA
3548271 ATTTATGTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
7 6 0.15
8 22 0.56
9 3 0.08
10 3 0.08
11 5 0.13
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:3548270 original size:26 final size:27
Alignment explanation
Indices: 3548212--3548272 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
3548202 GGTAAAGCTG
3548212 GAAAAAAAA-GAAAGAAAGGAGAAAAA
1 GAAAAAAAATGAAAGAAAGGAGAAAAA
*
3548238 -AAGAAAAATGAAAGAAA-GA-AAAAGA
1 GAAAAAAAATGAAAGAAAGGAGAAAA-A
3548263 GAAAAAAAAT
1 GAAAAAAAAT
3548273 TTATGTGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 4 0.13
25 10 0.33
26 16 0.53
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (27 bp):
GAAAAAAAATGAAAGAAAGGAGAAAAA
Found at i:3549236 original size:16 final size:17
Alignment explanation
Indices: 3549209--3549248 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
3549199 TATTTTTATC
3549209 ATATTAATATTAT-TTTT
1 ATATT-ATATTATATTTT
3549226 ATATTATATTATATTTT
1 ATATTATATTATATTTT
3549243 A-ATTAT
1 ATATTAT
3549249 TTTTTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATATTATATTTT
Found at i:3549239 original size:27 final size:26
Alignment explanation
Indices: 3549168--3549240 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
3549158 ACATTAATAA
* *
3549168 TTTATTTTATATAAATATTTATATATT
1 TTTATATTATAT-AATATTAATATATT
* * *
3549195 TGTATATTTTTATCATATTAATATTATT
1 TTTATA-TTATATAATATTAATA-TATT
*
3549223 TTTATATTATATTATATT
1 TTTATATTATATAATATT
3549241 TTAATTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (26 bp):
TTTATATTATATAATATTAATATATT
Found at i:3549344 original size:27 final size:29
Alignment explanation
Indices: 3549295--3549382 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 29
3549285 TTTATATTTT
* *
3549295 ATTTAAATTT-TTTATATAATAAAATTTTAA
1 ATTTAAATTTATTTAT-TAA-ATATTTTTAA
3549325 ATTTAAATTTATTTATTAAATATTTTTAA
1 ATTTAAATTTATTTATTAAATATTTTTAA
*
3549354 A--TAAATTTATTAATTATAATATTATTTAA
1 ATTTAAATTTATTTATTA-AATATT-TTTAA
3549383 TTAAAAATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 14 0.27
28 6 0.12
29 14 0.27
30 13 0.25
31 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTTAAATTTATTTATTAAATATTTTTAA
Found at i:3551264 original size:21 final size:21
Alignment explanation
Indices: 3551239--3551293 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3551229 AATAAATTAA
*
3551239 AAATATATTTAATTATTTATT
1 AAATATATTTAATTAATTATT
* ***
3551260 CAATATAAAAAATTAATTATT
1 AAATATATTTAATTAATTATT
3551281 AAATATATATTAA
1 AAATATAT-TTAA
3551294 AAATAATATT
Statistics
Matches: 24, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATATATTTAATTAATTATT
Found at i:3552580 original size:15 final size:16
Alignment explanation
Indices: 3552559--3552596 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
3552549 TTTAATTACT
3552559 TATTTAAATTGATTTA
1 TATTTAAATTGATTTA
*
3552575 -ATTTAATTTGATTTA
1 TATTTAAATTGATTTA
3552590 TATTTAA
1 TATTTAA
3552597 TAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (16 bp):
TATTTAAATTGATTTA
Found at i:3552695 original size:27 final size:25
Alignment explanation
Indices: 3552665--3552719 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
3552655 AATTTTAATT
3552665 ATTTTTAATAATAAATTAATTT-TTTG
1 ATTTTTAA-AA-AAATTAATTTATTTG
*
3552691 A-ATTTAAAAAAATTAATTTATTTG
1 ATTTTTAAAAAAATTAATTTATTTG
3552715 ATTTT
1 ATTTT
3552720 ACTTATAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 10 0.40
24 7 0.28
25 7 0.28
26 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
ATTTTTAAAAAAATTAATTTATTTG
Found at i:3552703 original size:23 final size:26
Alignment explanation
Indices: 3552668--3552720 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
3552658 TTTAATTATT
3552668 TTTAATAATAAATTAATTT-TTTGAA
1 TTTAATAATAAATTAATTTATTTGAA
*
3552693 TTTAA-AA-AAATTAATTTATTTGAT
1 TTTAATAATAAATTAATTTATTTGAA
3552717 TTTA
1 TTTA
3552721 CTTATAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 11 0.42
25 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTAATAATAAATTAATTTATTTGAA
Found at i:3553564 original size:3 final size:3
Alignment explanation
Indices: 3553556--3553633 Score: 60
Period size: 3 Copynumber: 26.3 Consensus size: 3
3553546 GCCCACCTTT
*
3553556 TTA TTA TTA TTA TTA TTA TTA TTG TT- TT- TTA TTA TTTA TTTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA
3553600 TATA TCTA -TA TTTA TTA TTA TTA TT- TT- TTA TTA T
1 T-TA T-TA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T
3553634 CTATCTATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
2 11 0.17
3 43 0.65
4 12 0.18
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:3553615 original size:43 final size:43
Alignment explanation
Indices: 3553568--3553651 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
3553558 ATTATTATTA
* * * *
3553568 TTATTATTATTGTTTTTTATTATTTATTTATTTATATCTATAT
1 TTATTATTATTATTTTTTATTATCTATCTATTTATACCTATAT
3553611 TTATTATTATTATTTTTTATTATCTATCTATTTATACCTAT
1 TTATTATTATTATTTTTTATTATCTATCTATTTATACCTAT
3553652 CTACGTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (43 bp):
TTATTATTATTATTTTTTATTATCTATCTATTTATACCTATAT
Found at i:3553836 original size:24 final size:26
Alignment explanation
Indices: 3553808--3553857 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
3553798 TTATACGTAA
3553808 TTAAATTATTAA-T-AAATAA-TATTT
1 TTAAATT-TTAATTAAAATAATTATTT
3553832 TTAAATTTTAATTAAAATAATTATTT
1 TTAAATTTTAATTAAAATAATTATTT
3553858 ATAATCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.17
24 8 0.35
25 6 0.26
26 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAAATTTTAATTAAAATAATTATTT
Found at i:3554100 original size:2 final size:2
Alignment explanation
Indices: 3554093--3554129 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3554083 CATATAGATT
3554093 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3554130 GCAAAAGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3554791 original size:11 final size:11
Alignment explanation
Indices: 3554775--3554824 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
3554765 AAATTTATAT
*
3554775 TTTTATATTCA
1 TTTTATATTTA
3554786 TTTTATATTTA
1 TTTTATATTTA
3554797 TATTTATATTTTA
1 T-TTTATA-TTTA
*
3554810 TTTTA-ATTAA
1 TTTTATATTTA
3554820 TTTTA
1 TTTTA
3554825 AATATTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 8 0.23
11 12 0.34
12 10 0.29
13 5 0.14
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTATATTTA
Found at i:3554797 original size:25 final size:24
Alignment explanation
Indices: 3554767--3554814 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
3554757 ATATAAAAAA
*
3554767 ATTTATATTTTTATATTCATTTTAT
1 ATTTATATTTATAT-TTCATTTTAT
*
3554792 ATTTATATTTATATTTTATTTTA
1 ATTTATATTTATATTTCATTTTA
3554815 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (24 bp):
ATTTATATTTATATTTCATTTTAT
Found at i:3554798 original size:6 final size:6
Alignment explanation
Indices: 3554776--3554812 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3554766 AATTTATATT
*
3554776 TTTATA TTCAT- TTTATA TTTATA TTTATA TTT-TA TTT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTT
3554813 TAATTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 9 0.32
6 19 0.68
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTATA
Found at i:3554811 original size:17 final size:17
Alignment explanation
Indices: 3554776--3554824 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
3554766 AATTTATATT
*
3554776 TTTATATTCAT-TTTATA
1 TTTATATTTATATTT-TA
3554793 TTTATATTTATATTTTA
1 TTTATATTTATATTTTA
*
3554810 TTT-TAATTA-ATTTTA
1 TTTATATTTATATTTTA
3554825 AATATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 6 0.21
16 5 0.17
17 15 0.52
18 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTTATATTTTA
Found at i:3554814 original size:35 final size:36
Alignment explanation
Indices: 3554769--3554865 Score: 96
Period size: 34 Copynumber: 2.8 Consensus size: 36
3554759 ATAAAAAAAT
* * **
3554769 TTATATTTTTATATTCATTTTATAT-TTATATTTATA
1 TTAT-TTTTTATATTAATTTTAAATATTATATACATA
3554805 TT-TTATTTTA-ATTAATTTTAAATATTATATACATA
1 TTATT-TTTTATATTAATTTTAAATATTATATACATA
*
3554840 TTATTTTTTATA-T-ATTTAAAATATTA
1 TTATTTTTTATATTAATTTTAAATATTA
3554866 AAAATTTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
34 24 0.46
35 23 0.44
36 5 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (36 bp):
TTATTTTTTATATTAATTTTAAATATTATATACATA
Found at i:3555961 original size:14 final size:13
Alignment explanation
Indices: 3555942--3555987 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
3555932 AGAAACTTCA
3555942 TATTTTTTAATTT
1 TATTTTTTAATTT
3555955 GTATTTTTTAATTT
1 -TATTTTTTAATTT
*
3555969 T-TAATTTTAATTT
1 TAT-TTTTTAATTT
3555982 TATTTT
1 TATTTT
3555988 AGAATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 1 0.04
13 13 0.46
14 14 0.50
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TATTTTTTAATTT
Found at i:3555971 original size:7 final size:7
Alignment explanation
Indices: 3555945--3555982 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
3555935 AACTTCATAT
3555945 TTTTTAA
1 TTTTTAA
* *
3555952 TTTGTAT
1 TTTTTAA
3555959 TTTTTAA
1 TTTTTAA
3555966 TTTTTAA
1 TTTTTAA
3555973 -TTTTAA
1 TTTTTAA
3555979 TTTT
1 TTTT
3555983 ATTTTAGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:3556001 original size:26 final size:27
Alignment explanation
Indices: 3555941--3556005 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
3555931 TAGAAACTTC
* **
3555941 ATATTTTTTAATTTGTATTTTTTAATT
1 ATATATTTTAATTTGTATTTTAGAATT
*
3555968 -TTTAATTTTAATTT-TATTTTAGAATT
1 ATAT-ATTTTAATTTGTATTTTAGAATT
3555994 ATATATTTTAAT
1 ATATATTTTAAT
3556006 GTTAATTTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (27 bp):
ATATATTTTAATTTGTATTTTAGAATT
Found at i:3556110 original size:26 final size:27
Alignment explanation
Indices: 3556076--3556126 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
3556066 TAATATTTTT
*
3556076 TTTAGTTTTTTATATTTTAAATTTAGA
1 TTTAGTTTTTAATATTTTAAATTTAGA
* *
3556103 TTTA-TTTTTAATTTTTTAATTTTA
1 TTTAGTTTTTAATATTTTAAATTTA
3556127 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTAGTTTTTAATATTTTAAATTTAGA
Found at i:3556377 original size:18 final size:18
Alignment explanation
Indices: 3556349--3556384 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3556339 ATTTTAAATT
3556349 TTTTATATTTAAGTTTTTA
1 TTTTATATTTAA-TTTTTA
3556368 TTTT-TATTTAATTTTTA
1 TTTTATATTTAATTTTTA
3556385 AATGATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTATATTTAATTTTTA
Found at i:3557756 original size:58 final size:59
Alignment explanation
Indices: 3557645--3557757 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 59
3557635 TGTCATATTC
* * *
3557645 GTATCGTATTTCCATTCATGACATATTTTACATAATTTTTCTTAATAATTTAATTTAAT
1 GTATCGTATCTCAATTCATGACATATTTTACATAATTTTTCATAATAATTTAATTTAAT
* * *
3557704 GTATCGTATCTCAATTCGTGACAT-TTTTTCATAATTTGTT-ATAATGATTTAATT
1 GTATCGTATCTCAATTCATGACATATTTTACATAATTT-TTCATAATAATTTAATT
3557758 AAAAAAATTG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 24 0.51
59 23 0.49
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (59 bp):
GTATCGTATCTCAATTCATGACATATTTTACATAATTTTTCATAATAATTTAATTTAAT
Found at i:3557902 original size:10 final size:10
Alignment explanation
Indices: 3557887--3557931 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
3557877 TTGTCAAGAG
3557887 AAAAAGAAAA
1 AAAAAGAAAA
3557897 AAAAAGATAGAA
1 AAAAAGA-A-AA
* *
3557909 AAAAGGAGAA
1 AAAAAGAAAA
3557919 AAAAAGAAAA
1 AAAAAGAAAA
3557929 AAA
1 AAA
3557932 TTATGTATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 20 0.69
11 1 0.03
12 8 0.28
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:3558801 original size:21 final size:22
Alignment explanation
Indices: 3558777--3558818 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3558767 ATTTATTTTT
3558777 TTTATT-TTT-TTATAATTAAAA
1 TTTATTATTTATTA-AATTAAAA
3558798 TTTATTATTTATTAAATTAAA
1 TTTATTATTTATTAAATTAAA
3558819 TATAATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTATTATTTATTAAATTAAAA
Found at i:3559383 original size:5 final size:5
Alignment explanation
Indices: 3559373--3559403 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
3559363 TTAATTATTA
3559373 AATAT AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT A
3559404 TATTTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:3559733 original size:21 final size:20
Alignment explanation
Indices: 3559704--3559755 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
3559694 AAATATAACA
*
3559704 AATTAAATATAAAATTATTTAT
1 AATT-AATATAAAATAATTT-T
3559726 AATTAATAATAAAATAATTTT
1 AATTAAT-ATAAAATAATTTT
3559747 AATTAATAT
1 AATTAATAT
3559756 TTTATTTACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 11 0.39
22 15 0.54
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTAATATAAAATAATTTT
Found at i:3562416 original size:176 final size:177
Alignment explanation
Indices: 3562173--3562491 Score: 437
Period size: 176 Copynumber: 1.8 Consensus size: 177
3562163 ATTCTGGAAT
*
3562173 ATATGTATTGATTAAATTGCAGCCACAGTAATGATTTTGAACTTTCTATTAAAGAAGAGGAATTT
1 ATATATATTGATTAAATTGCAGCCACAGTAATGATTTTGAACTTTCTATTAAAGAAGAGGAATTT
* * *
3562238 TTTTAGCACGAAATTTAGTGGGA-ATAACATGTAAAGAAGATAGCTA-TAATTCCAGAATTCACT
66 TTTTAGCACAAAATTTAGTGGGAGA-AACATGTAAAGAAGATAGC-ACAAATTCCAGAATACACT
3562301 TAAACAGTCTTCTAAATTATTTATGCTGATTCTTCTTGCTTGTTCTTAA
129 TAAACAGTCTTCTAAATTATTTATGCTGATTCTTCTTGCTTGTTCTTAA
* * ** * * *
3562350 ATATATATTGATTAAATTGCAG-CACGGTAATGGTTTTGCTCTTTCTATTGAAGACGATGAATTT
1 ATATATATTGATTAAATTGCAGCCACAGTAATGATTTTGAACTTTCTATTAAAGAAGAGGAATTT
* * * *
3562414 TTTTGGCATAAAATTTAGTGGGAGAAATATGTAAATAAGATAGCAGCAAATTCCAGAATACACTT
66 TTTTAGCACAAAATTTAGTGGGAGAAACATGTAAAGAAGATAGCA-CAAATTCCAGAATACACTT
**
3562479 AAAGTGTCTTCTA
130 AAACAGTCTTCTA
3562492 TGTCATTTTT
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
175 1 0.01
176 72 0.59
177 49 0.40
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (177 bp):
ATATATATTGATTAAATTGCAGCCACAGTAATGATTTTGAACTTTCTATTAAAGAAGAGGAATTT
TTTTAGCACAAAATTTAGTGGGAGAAACATGTAAAGAAGATAGCACAAATTCCAGAATACACTTA
AACAGTCTTCTAAATTATTTATGCTGATTCTTCTTGCTTGTTCTTAA
Found at i:3566885 original size:23 final size:23
Alignment explanation
Indices: 3566857--3566911 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
3566847 TATAAATTAA
3566857 TATTTTTATA-CATATTTTATAT
1 TATTTTTATATCATATTTTATAT
*
3566879 TATTTTTATATCCTATTTTATAT
1 TATTTTTATATCATATTTTATAT
3566902 TATATTTTAT
1 TAT-TTTTAT
3566912 CCATTTGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 10 0.33
23 14 0.47
24 6 0.20
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTTTTATATCATATTTTATAT
Found at i:3566899 original size:12 final size:12
Alignment explanation
Indices: 3566860--3566911 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
3566850 AAATTAATAT
3566860 TTTTATA-CATA
1 TTTTATATCATA
*
3566871 TTTTATATTAT-
1 TTTTATATCATA
*
3566882 TTTTATATCCTA
1 TTTTATATCATA
*
3566894 TTTTATATTATA
1 TTTTATATCATA
3566906 TTTTAT
1 TTTTAT
3566912 CCATTTGCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 16 0.47
12 18 0.53
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTTATATCATA
Found at i:3576195 original size:13 final size:13
Alignment explanation
Indices: 3576177--3576240 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 13
3576167 TATAATATAC
*
3576177 TTAAAATATAAAT
1 TTAAAAAATAAAT
3576190 TTAAAAAAT-AA-
1 TTAAAAAATAAAT
*
3576201 --AAATAA-AAAT
1 TTAAAAAATAAAT
*
3576211 TTAAAAAATAAAG
1 TTAAAAAATAAAT
*
3576224 TTAAAAAATATAT
1 TTAAAAAATAAAT
3576237 TTAA
1 TTAA
3576241 GATTAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
9 7 0.17
12 7 0.17
13 26 0.65
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (13 bp):
TTAAAAAATAAAT
Found at i:3576230 original size:21 final size:21
Alignment explanation
Indices: 3576179--3576222 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3576169 TAATATACTT
*
3576179 AAAATATAAATTTAAAAAATA
1 AAAATAAAAATTTAAAAAATA
3576200 AAAATAAAAATTTAAAAAATA
1 AAAATAAAAATTTAAAAAATA
3576221 AA
1 AA
3576223 GTTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAATAAAAATTTAAAAAATA
Found at i:3578329 original size:13 final size:13
Alignment explanation
Indices: 3578311--3578335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3578301 ATATTAACTG
3578311 TTAAAAATGATTA
1 TTAAAAATGATTA
3578324 TTAAAAATGATT
1 TTAAAAATGATT
3578336 GTATAATTTG
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:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
TTAAAAATGATTA
Found at i:3579802 original size:3 final size:3
Alignment explanation
Indices: 3579794--3579819 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3579784 TTACACCATT
3579794 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
3579820 AAGGTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3581936 original size:45 final size:46
Alignment explanation
Indices: 3581836--3581964 Score: 154
Period size: 48 Copynumber: 2.8 Consensus size: 46
3581826 ATTGGCTGAT
* * * *
3581836 TTTCTTCACTTCATTAACAACTTTGCTAGGCTTATCTTCTTGCAAC
1 TTTCTTCACTTCGTTAACAACTTTGTTAGGCTTTTCTTCTGGCAAC
* *
3581882 TTCTTCTTCACTTCGTTAACAGA-TTTGTTTGGCTTTTCTTCTGGTAA-
1 -T-TTCTTCACTTCGTTAACA-ACTTTGTTAGGCTTTTCTTCTGGCAAC
*
3581929 TTTCTTCACTTCGTTAGCAACTTTGTTAGGCTTTTC
1 TTTCTTCACTTCGTTAACAACTTTGTTAGGCTTTTC
3581965 CTGTATTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
44 1 0.01
45 31 0.44
46 1 0.01
47 1 0.01
48 36 0.51
49 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.48
Consensus pattern (46 bp):
TTTCTTCACTTCGTTAACAACTTTGTTAGGCTTTTCTTCTGGCAAC
Found at i:3582052 original size:9 final size:9
Alignment explanation
Indices: 3582040--3582069 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3582030 CCCCTTCCCA
3582040 TTCCTCCTC
1 TTCCTCCTC
3582049 TTCCTCCTC
1 TTCCTCCTC
*
3582058 CTCCTCCTC
1 TTCCTCCTC
3582067 TTC
1 TTC
3582070 GTCTTCTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (9 bp):
TTCCTCCTC
Found at i:3582077 original size:3 final size:3
Alignment explanation
Indices: 3582065--3582102 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3582055 CTCCTCCTCC
*
3582065 TCT TCG TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
3582103 AGAAAATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:3585137 original size:16 final size:16
Alignment explanation
Indices: 3585116--3585147 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3585106 CTCTAGAAAC
3585116 CTTTTCTCTATATATT
1 CTTTTCTCTATATATT
3585132 CTTTTCTCTATATATT
1 CTTTTCTCTATATATT
3585148 AAATTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTTCTCTATATATT
Found at i:3587273 original size:25 final size:25
Alignment explanation
Indices: 3587239--3587287 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3587229 TAAAAATTAT
* *
3587239 TTATCATTTTAAATTTATTTTTAAG
1 TTATCATTTTAAAATTAATTTTAAG
*
3587264 TTATTATTTTAAAATTAATTTTAA
1 TTATCATTTTAAAATTAATTTTAA
3587288 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TTATCATTTTAAAATTAATTTTAAG
Found at i:3587306 original size:22 final size:23
Alignment explanation
Indices: 3587273--3587330 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
3587263 GTTATTATTT
3587273 TAAA-ATTAATTTTAAATAAAAAA
1 TAAATATT-ATTTTAAATAAAAAA
* * *
3587296 TAAATA-TATTTTAATTAATAAT
1 TAAATATTATTTTAAATAAAAAA
3587318 TAAATATTATTTT
1 TAAATATTATTTT
3587331 TTAATCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 18 0.60
23 11 0.37
24 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATATTATTTTAAATAAAAAA
Found at i:3588339 original size:2 final size:2
Alignment explanation
Indices: 3588332--3588376 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3588322 TATGCAAGAC
3588332 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3588374 AG A
1 AG A
3588377 TTATATTCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3594580 original size:20 final size:20
Alignment explanation
Indices: 3594538--3594581 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3594528 TTACTTAATA
*
3594538 AATTAAAAAATAATATAAAT
1 AATTAAAAAATAATAAAAAT
3594558 AATTAAAAAAT-ATAAAAATT
1 AATTAAAAAATAATAAAAA-T
3594578 AATT
1 AATT
3594582 TTATTTTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATTAAAAAATAATAAAAAT
Found at i:3596111 original size:32 final size:32
Alignment explanation
Indices: 3596071--3596132 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
3596061 TAAATAATGA
*
3596071 ATTAATTTTAAAAAAAT-ATTAATCAATTAAG
1 ATTAATTTTAAAAAAATAATTAATAAATTAAG
*
3596102 ATTACATTTTAAAAATATAATTAATAAATTA
1 ATTA-ATTTTAAAAAAATAATTAATAAATTA
3596133 CTTTTCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 4 0.15
32 12 0.44
33 11 0.41
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (32 bp):
ATTAATTTTAAAAAAATAATTAATAAATTAAG
Found at i:3598540 original size:2 final size:2
Alignment explanation
Indices: 3598533--3598589 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
3598523 GTGCTTGTTA
*
3598533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3598575 AC AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT A
3598590 AATGGTCAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3603014 original size:2 final size:2
Alignment explanation
Indices: 3603007--3603031 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3602997 ACAACATTCT
3603007 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3603032 GGTCTTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3604001 original size:36 final size:36
Alignment explanation
Indices: 3603929--3604013 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 36
3603919 AAATATGTTC
3603929 TTTTAAAATATAT-TATAATTTATATAAAATAAATTA
1 TTTTAAAA-ATATGTATAATTTATATAAAATAAATTA
3603965 TTTTAAAAATATGTA-ATATTT-TA-AAAATAATTATTA
1 TTTTAAAAATATGTATA-ATTTATATAAAATAA--ATTA
3604001 TATTT-AAAATATG
1 T-TTTAAAAATATG
3604014 AGATTTCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
34 7 0.16
35 7 0.16
36 27 0.61
37 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (36 bp):
TTTTAAAAATATGTATAATTTATATAAAATAAATTA
Found at i:3604006 original size:19 final size:18
Alignment explanation
Indices: 3603961--3604013 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
3603951 TATAAAATAA
3603961 ATTATTTTAAAAATATGT
1 ATTATTTTAAAAATATGT
*
3603979 AATATTTTAAAAATAAT-T
1 ATTATTTTAAAAAT-ATGT
3603997 ATTATATTT-AAAATATG
1 ATTAT-TTTAAAAATATG
3604014 AGATTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 2 0.07
18 23 0.77
19 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
ATTATTTTAAAAATATGT
Found at i:3604427 original size:17 final size:17
Alignment explanation
Indices: 3604405--3604440 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3604395 TTAAGAGTTT
3604405 AAAATAAATTTAAATTA
1 AAAATAAATTTAAATTA
*
3604422 AAAATATATTTAAATTA
1 AAAATAAATTTAAATTA
3604439 AA
1 AA
3604441 TAAAAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATAAATTTAAATTA
Found at i:3604456 original size:18 final size:17
Alignment explanation
Indices: 3604405--3604547 Score: 78
Period size: 18 Copynumber: 8.0 Consensus size: 17
3604395 TTAAGAGTTT
*
3604405 AAAATAAATTTAAATTAA
1 AAAATAAAATTAAA-TAA
3604423 AAATATATTTAAATTAAATAA
1 AAA-ATA---AAATTAAATAA
3604444 AAACATAAAATTAAATAA
1 AAA-ATAAAATTAAATAA
*
3604462 AATAATAAAATTCAATAA
1 AA-AATAAAATTAAATAA
* * *
3604480 TCACAT---TTTAAA-AA
1 -AAAATAAAATTAAATAA
* * *
3604494 TATATTTAAATTAAATAA
1 -AAAATAAAATTAAATAA
3604512 AAATATAAAATTAAATAA
1 AAA-ATAAAATTAAATAA
*
3604530 AATAATAAAATTCAATAA
1 AA-AATAAAATTAAATAA
3604548 TCACATTATT
Statistics
Matches: 97, Mismatches: 16, Indels: 24
0.71 0.12 0.18
Matches are distributed among these distances:
14 4 0.04
15 4 0.04
17 7 0.07
18 60 0.62
19 6 0.06
21 9 0.09
22 7 0.07
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAAAATTAAATAA
Found at i:3604493 original size:68 final size:68
Alignment explanation
Indices: 3604419--3604554 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
3604409 TAAATTTAAA
3604419 TTAAAAATATATTTAAATTAAATAAAAACATAAAATTAAATAAAATAATAAAATTCAATAATCAC
1 TTAAAAATATATTTAAATTAAATAAAAACATAAAATTAAATAAAATAATAAAATTCAATAATCAC
3604484 ATT
66 ATT
*
3604487 TTAAAAATATATTTAAATTAAATAAAAATATAAAATTAAATAAAATAATAAAATTCAATAATCAC
1 TTAAAAATATATTTAAATTAAATAAAAACATAAAATTAAATAAAATAATAAAATTCAATAATCAC
3604552 ATT
66 ATT
3604555 ATTATAACTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (68 bp):
TTAAAAATATATTTAAATTAAATAAAAACATAAAATTAAATAAAATAATAAAATTCAATAATCAC
ATT
Found at i:3609562 original size:2 final size:2
Alignment explanation
Indices: 3609555--3609582 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3609545 AAGAATAAGA
3609555 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
3609583 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3611319 original size:13 final size:13
Alignment explanation
Indices: 3611301--3611328 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3611291 AATCCCATGG
3611301 ACCCCTTTAGGCT
1 ACCCCTTTAGGCT
3611314 ACCCCTTTAGGCT
1 ACCCCTTTAGGCT
3611327 AC
1 AC
3611329 AATCCATGGC
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:0.18, C:0.39, G:0.14, T:0.29
Consensus pattern (13 bp):
ACCCCTTTAGGCT
Found at i:3618041 original size:24 final size:24
Alignment explanation
Indices: 3618014--3618070 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
3618004 TGTCACTGCC
* *
3618014 TTTGCTATTAATGGCCATCTACAA
1 TTTGCCATCAATGGCCATCTACAA
*
3618038 TTTGCCATCAATTGCCATCTACAA
1 TTTGCCATCAATGGCCATCTACAA
3618062 TTTGCCATC
1 TTTGCCATC
3618071 TCTCGGATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (24 bp):
TTTGCCATCAATGGCCATCTACAA
Found at i:3618046 original size:14 final size:14
Alignment explanation
Indices: 3618027--3618071 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
3618017 GCTATTAATG
3618027 GCCATCTACAATTT
1 GCCATCTACAATTT
3618041 GCCA--T-CAA-TT
1 GCCATCTACAATTT
3618051 GCCATCTACAATTT
1 GCCATCTACAATTT
3618065 GCCATCT
1 GCCATCT
3618072 CTCGGATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 6 0.22
11 3 0.11
12 2 0.07
13 3 0.11
14 13 0.48
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (14 bp):
GCCATCTACAATTT
Found at i:3620479 original size:12 final size:12
Alignment explanation
Indices: 3620456--3620487 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3620446 ATTTTTATAC
3620456 ATAATATA--AT
1 ATAATATATTAT
3620466 ATAATATATTAT
1 ATAATATATTAT
3620478 ATAATATATT
1 ATAATATATT
3620488 TTTATAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.40
12 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATAATATATTAT
Found at i:3625294 original size:60 final size:60
Alignment explanation
Indices: 3625220--3625340 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
3625210 AGCACTTCGT
3625220 AAAGCAGTTTCCTCCTCTCCATTATATTTTTTTTGCTGCTTCTGGTTTAAGTCAAACATC
1 AAAGCAGTTTCCTCCTCTCCATTATATTTTTTTTGCTGCTTCTGGTTTAAGTCAAACATC
* *
3625280 AAAGTAGTTTCCTCCTTTCCATTATATTTTTTTTGCTGCTTCTGGTTTAAGTCAAACATC
1 AAAGCAGTTTCCTCCTCTCCATTATATTTTTTTTGCTGCTTCTGGTTTAAGTCAAACATC
3625340 A
1 A
3625341 GAGAAGGATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (60 bp):
AAAGCAGTTTCCTCCTCTCCATTATATTTTTTTTGCTGCTTCTGGTTTAAGTCAAACATC
Found at i:3628611 original size:16 final size:17
Alignment explanation
Indices: 3628581--3628613 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3628571 TTAGAATTAT
*
3628581 TTTTTTATAATAATTTA
1 TTTTATATAATAATTTA
3628598 TTTTATATAA-AATTTA
1 TTTTATATAATAATTTA
3628614 AAGCTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATATAATAATTTA
Done.