Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1588
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: 67652
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:415 original size:21 final size:20
Alignment explanation
Indices: 381--421 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
371 TCAAATATAC
* *
381 CAAAGTAGCCTAAATCAGCA
1 CAAAGTAGCATAAAACAGCA
401 CAAAGCTAGCATAAAACAGCA
1 CAAAG-TAGCATAAAACAGCA
422 TAAAAAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.49, C:0.24, G:0.15, T:0.12
Consensus pattern (20 bp):
CAAAGTAGCATAAAACAGCA
Found at i:3097 original size:29 final size:28
Alignment explanation
Indices: 3029--3098 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 28
3019 TTATGGCACG
3029 AAAAACCT-ACAAATGACTTAAGCAAAAC
1 AAAAA-CTAACAAATGACTTAAGCAAAAC
* *
3057 CAAGACTCAACAAATGACTT-AGACAAAAC
1 AAAAACT-AACAAATGACTTAAG-CAAAAC
3086 AAAAACATAACAA
1 AAAAAC-TAACAA
3099 CGATTTAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
27 2 0.06
28 5 0.15
29 26 0.76
30 1 0.03
ACGTcount: A:0.59, C:0.21, G:0.07, T:0.13
Consensus pattern (28 bp):
AAAAACTAACAAATGACTTAAGCAAAAC
Found at i:4225 original size:21 final size:21
Alignment explanation
Indices: 4192--4231 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4182 AATAATAAAT
*
4192 TTAGAATATTATTTTAATACA
1 TTAGAATATTATTTAAATACA
4213 TTAGAAT-TATATTTAAATA
1 TTAGAATAT-TATTTAAATA
4232 TCAGATAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (21 bp):
TTAGAATATTATTTAAATACA
Found at i:5992 original size:19 final size:20
Alignment explanation
Indices: 5956--6011 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
5946 CTAGCCCAAG
5956 TAAA-ATAATTATACTTAAT-A
1 TAAATATAATTA-A-TTAATCA
5976 TAAATATAATTAATTAATCA
1 TAAATATAATTAATTAATCA
* *
5996 -ACATATAATTATTTAA
1 TAAATATAATTAATTAA
6012 ATTGCTAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 19 0.59
20 6 0.19
21 7 0.22
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATATAATTAATTAATCA
Found at i:12172 original size:10 final size:10
Alignment explanation
Indices: 12157--12194 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
12147 TTTTTCTGCC
12157 TCTTTATTTT
1 TCTTTATTTT
*
12167 TCTTTATTAT
1 TCTTTATTTT
12177 TCTTTATTATT
1 TCTTTATT-TT
12188 T-TTTATT
1 TCTTTATT
12195 GTAGTGCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 23 0.92
11 2 0.08
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (10 bp):
TCTTTATTTT
Found at i:12182 original size:20 final size:20
Alignment explanation
Indices: 12157--12194 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12147 TTTTTCTGCC
12157 TCTTTATT-TTTCTTTATTAT
1 TCTTTATTATTT-TTTATTAT
12177 TCTTTATTATTTTTTATT
1 TCTTTATTATTTTTTATT
12195 GTAGTGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTTATTATTTTTTATTAT
Found at i:14755 original size:2 final size:2
Alignment explanation
Indices: 14742--14784 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
14732 TCTCTATTAG
14742 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14785 ATAAATACCC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15796 original size:13 final size:13
Alignment explanation
Indices: 15778--15802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15768 CATAAAGTGT
15778 TGTATCGATACAA
1 TGTATCGATACAA
15791 TGTATCGATACA
1 TGTATCGATACA
15803 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:15818 original size:32 final size:33
Alignment explanation
Indices: 15758--15826 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
15748 TTCAACGATT
15758 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
15791 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
15823 TGTA
1 TGTA
15827 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:15882 original size:13 final size:13
Alignment explanation
Indices: 15864--15888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15854 ATTACTCAAA
15864 TGTATCGATACAT
1 TGTATCGATACAT
15877 TGTATCGATACA
1 TGTATCGATACA
15889 CTCATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:15941 original size:52 final size:52
Alignment explanation
Indices: 15897--16025 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
15887 CACTCATCTT
15897 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * * *
15949 TGTATCGATACATACAGGCAAATTTGCCCAGATATACCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
16001 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
16026 TCATATTTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:21479 original size:20 final size:20
Alignment explanation
Indices: 21434--21485 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
21424 GTAGCCAAAC
**
21434 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
21454 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
21473 TTGTATCGATACA
1 TTGTATCGATACA
21486 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:27498 original size:27 final size:27
Alignment explanation
Indices: 27415--27498 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
27405 TTAAAAGACA
27415 TGGTTATTTAATTAAAAGTTATGTCTCT
1 TGGTTATTT-ATTAAAAGTTATGTCTCT
**
27443 TAATTATTTATTAAGAA-TTATGTCTCT
1 TGGTTATTTATTAA-AAGTTATGTCTCT
*
27470 TGGTTATTTATTAAAAGTTGTGTCTCT
1 TGGTTATTTATTAAAAGTTATGTCTCT
27497 TG
1 TG
27499 AAAATTTAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
26 2 0.04
27 38 0.78
28 9 0.18
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.51
Consensus pattern (27 bp):
TGGTTATTTATTAAAAGTTATGTCTCT
Found at i:30788 original size:19 final size:18
Alignment explanation
Indices: 30763--30859 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
30753 ATTTCAACGA
30763 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
30781 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
30797 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
30813 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
30829 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
30845 TTTTGTATCGATACA
1 -TTTGTATCGATACA
30860 ATGTATCGCT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
18 1 0.02
19 35 0.53
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:30801 original size:32 final size:32
Alignment explanation
Indices: 30765--30872 Score: 198
Period size: 32 Copynumber: 3.4 Consensus size: 32
30755 TTCAACGATT
30765 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
30797 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
30829 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
30861 TGTATCGCTACA
1 TGTATCGATACA
30873 AAGCTACTGC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 74 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:30802 original size:13 final size:13
Alignment explanation
Indices: 30784--30873 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
30774 ACATAAGTGT
30784 TGTATCGATACAA
1 TGTATCGATACAA
30797 TGTATCGATACATAA
1 TGTATCGATAC--AA
30812 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
30829 TGTATCGATACATAA
1 TGTATCGATAC--AA
30844 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
30861 TGTATCGCTACAA
1 TGTATCGATACAA
30874 AGCTACTGCC
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:30930 original size:13 final size:13
Alignment explanation
Indices: 30912--30936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30902 ATTACTCAAA
30912 TGTATCGATACAT
1 TGTATCGATACAT
30925 TGTATCGATACA
1 TGTATCGATACA
30937 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:30989 original size:52 final size:52
Alignment explanation
Indices: 30945--31073 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
30935 CACTGATCTT
*
30945 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
*
30997 TGTATCGATACATACAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
31049 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
31074 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
Found at i:35323 original size:80 final size:80
Alignment explanation
Indices: 35190--35350 Score: 241
Period size: 80 Copynumber: 2.0 Consensus size: 80
35180 AGAGCATGAT
* * * * * *
35190 ATAGTGTTTACATTTAGCCTTATCCATATTAGTCTTATAGCTCCTATATATTAACTCCACTAGTA
1 ATAGTGTCTACATTTAGCCTTATCCATATTAGTCCTACAACTCCTACATATTAAATCCACTAGTA
35255 TTTTCTTAGCCAAGG
66 TTTTCTTAGCCAAGG
* *
35270 ATAGTGTCTACATTTAGCCTTATCCATATTAGTCCTGCAACTCCTACATATTAAATCCTCTAGTA
1 ATAGTGTCTACATTTAGCCTTATCCATATTAGTCCTACAACTCCTACATATTAAATCCACTAGTA
*
35335 TTTTCTTAGCGAAGG
66 TTTTCTTAGCCAAGG
35350 A
1 A
35351 CTTTTAATGA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (80 bp):
ATAGTGTCTACATTTAGCCTTATCCATATTAGTCCTACAACTCCTACATATTAAATCCACTAGTA
TTTTCTTAGCCAAGG
Found at i:36384 original size:2 final size:2
Alignment explanation
Indices: 36377--36409 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36367 ACCCTAGTGC
36377 AT AT AT AT 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 AT AT AT AT A
36410 AATTCATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36434 original size:31 final size:34
Alignment explanation
Indices: 36394--36489 Score: 115
Period size: 35 Copynumber: 2.8 Consensus size: 34
36384 TATATATATA
* *
36394 TATATATATATATATAA-ATT-CATATTATTTAAT
1 TATATATACATA-ATAAGATTGAATATTATTTAAT
*
36427 TATATATACATAATAAGTTTTGAATATTATTTAAT
1 TATATATACATAATAAG-ATTGAATATTATTTAAT
*
36462 TATATATACATAATAAGTTTTGAATATT
1 TATATATACATAATAAG-ATTGAATATT
36490 GTGCATTGGC
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 4 0.07
33 11 0.19
34 2 0.04
35 40 0.70
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (34 bp):
TATATATACATAATAAGATTGAATATTATTTAAT
Found at i:37569 original size:28 final size:27
Alignment explanation
Indices: 37517--37569 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
37507 TGCATCTTAA
* *
37517 TTATTTATTAAGAATTGTGTTTCTTGG
1 TTATTTATTAAGAATTATGTCTCTTGG
37544 TTATTTAATTAAGAATTATGTCTCTT
1 TTATTT-ATTAAGAATTATGTCTCTT
37570 AAGTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (27 bp):
TTATTTATTAAGAATTATGTCTCTTGG
Found at i:45712 original size:3 final size:3
Alignment explanation
Indices: 45704--45748 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
45694 TAAAAAACAG
45704 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45749 CAACCAATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:46449 original size:30 final size:30
Alignment explanation
Indices: 46413--46516 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 30
46403 TGATGGATTT
* * *
46413 AATTAAAGGTTAAATGCTTATTTGAATATA
1 AATTAAAGATTAAAAGCTTGTTTGAATATA
*
46443 AATTAAA-ATTAAGAAG-TTGTTTGGATATA
1 AATTAAAGATTAA-AAGCTTGTTTGAATATA
* *
46472 AATTAAATG-TTAAAGGAC-TGTTTGAATGTA
1 AATTAAA-GATTAAAAG-CTTGTTTGAATATA
46502 AATTAAAGATTAAAA
1 AATTAAAGATTAAAA
46517 AAATATGAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
29 25 0.42
30 35 0.58
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (30 bp):
AATTAAAGATTAAAAGCTTGTTTGAATATA
Found at i:47919 original size:34 final size:36
Alignment explanation
Indices: 47857--47926 Score: 117
Period size: 34 Copynumber: 2.0 Consensus size: 36
47847 ACTTATTAAA
47857 ATTTTTTCTACCATCAATATATATAAAATAATTATT
1 ATTTTTTCTACCATCAATATATATAAAATAATTATT
*
47893 ATTTTTTCTATCATC-AT-TATATAAAATAATTATT
1 ATTTTTTCTACCATCAATATATATAAAATAATTATT
47927 CCTACTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 17 0.52
35 2 0.06
36 14 0.42
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (36 bp):
ATTTTTTCTACCATCAATATATATAAAATAATTATT
Found at i:48350 original size:21 final size:20
Alignment explanation
Indices: 48313--48355 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
48303 ATTTTATAAA
48313 TAAATAAAATTTAAATTGTAT
1 TAAATAAAATTTAAATT-TAT
*
48334 TAAA-AAAATTTTTAATTTAT
1 TAAATAAAA-TTTAAATTTAT
48354 TA
1 TA
48356 GTTTAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TAAATAAAATTTAAATTTAT
Found at i:48419 original size:88 final size:90
Alignment explanation
Indices: 48327--48511 Score: 197
Period size: 88 Copynumber: 2.1 Consensus size: 90
48317 TAAAATTTAA
** *
48327 ATTGTATTAAAAAAATT-TTTAATTTATT-AGTTTAATGTAAATTA-AAAATAAAAAAT-AAATA
1 ATTGTATTAAAAAAATTATTT-ATTTATTAAG-TTAATAAAAAGTAGAAAATAAAAAATAAAAT-
48388 AATTTAATGTAAATTTTAATTA-TTTTT
63 AATTTAATGTAAATTTTAATTATTTTTT
* * * ** *
48415 ATTG--TCAAATAAATTATTTATTTTTTAAAGTTAATAAAAAGTAGAACTTTAAAAATAAAATAA
1 ATTGTATTAAAAAAATTATTTATTTATT-AAGTTAATAAAAAGTAGAAAATAAAAAATAAAATAA
48478 TTTAATGTAAATTTTAATTATTTTTT
65 TTTAATGTAAATTTTAATTATTTTTT
48504 ATT-TATTA
1 ATTGTATTA
48512 TTAAATAAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
86 15 0.19
87 13 0.16
88 37 0.47
89 12 0.15
90 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (90 bp):
ATTGTATTAAAAAAATTATTTATTTATTAAGTTAATAAAAAGTAGAAAATAAAAAATAAAATAAT
TTAATGTAAATTTTAATTATTTTTT
Found at i:49751 original size:29 final size:29
Alignment explanation
Indices: 49707--49782 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
49697 CTTACTCATA
49707 ATTTATAAATTTTTAATAAACCTT-TATT-TT
1 ATTTAT-AATTTTTAATAAA--TTATATTATT
*
49737 TTTTATAATTTTTAA-AAATTATATTAATT
1 ATTTATAATTTTTAATAAATTATATT-ATT
49766 ATTTATAATTTTTAATA
1 ATTTATAATTTTTAATA
49783 TCTTATTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 3 0.08
29 25 0.62
30 6 0.15
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTTATAATTTTTAATAAATTATATTATT
Found at i:49902 original size:30 final size:29
Alignment explanation
Indices: 49830--49899 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
49820 ATTTATCTAA
49830 AACTTTCAAAAATTATATTTACCATTAAT
1 AACTTTCAAAAATTATATTTACCATTAAT
* * * *
49859 AATTTTTAAAAATTATATTTATCATTCAT
1 AACTTTCAAAAATTATATTTACCATTAAT
49888 AACTTTCAAAAA
1 AACTTTCAAAAA
49900 ATTTTATCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (29 bp):
AACTTTCAAAAATTATATTTACCATTAAT
Found at i:51218 original size:20 final size:20
Alignment explanation
Indices: 51195--51232 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51185 AGAACGCATA
51195 AGAAGATATAAGAAAATCAT
1 AGAAGATATAAGAAAATCAT
* *
51215 AGAATATATGAGAAAATC
1 AGAAGATATAAGAAAATC
51233 TTACCTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (20 bp):
AGAAGATATAAGAAAATCAT
Found at i:51342 original size:2 final size:2
Alignment explanation
Indices: 51335--51359 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51325 TAAACATCAA
51335 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
51360 AAGTGAATTA
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:55766 original size:24 final size:24
Alignment explanation
Indices: 55703--55766 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
55693 CGTAATGTGA
*
55703 AAAATAATATTAATAAAATATAAAT
1 AAAATAA-ATTATTAAAATATAAAT
* * * *
55728 -ATATAAATATGTTAAAATTTATAT
1 AAAATAAAT-TATTAAAATATAAAT
55752 AAAATAAATTATTAA
1 AAAATAAATTATTAA
55767 CGTATAAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
23 2 0.07
24 21 0.70
25 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATAAATTATTAAAATATAAAT
Found at i:56207 original size:18 final size:15
Alignment explanation
Indices: 56181--56226 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
56171 TCCCTATTTC
*
56181 CTTTTT-TTTCCTTT
1 CTTTTTCTTTTCTTT
56195 CTGTTCTTCTTTTCTTT
1 CT-TT-TTCTTTTCTTT
56212 CTTTTTCTTTT-TTT
1 CTTTTTCTTTTCTTT
56226 C
1 C
56227 CATAATAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.21
15 9 0.32
16 4 0.14
17 9 0.32
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (15 bp):
CTTTTTCTTTTCTTT
Found at i:56472 original size:14 final size:13
Alignment explanation
Indices: 56450--56536 Score: 57
Period size: 14 Copynumber: 5.8 Consensus size: 13
56440 TTTTCAATAT
56450 TTTTCTTTCTTTATC
1 TTTT-TTTCTTT-TC
*
56465 TTTTTTTCTTTTT
1 TTTTTTTCTTTTC
56478 TTTTTTTCACTTTTC
1 TTTTTTT--CTTTTC
*
56493 TTTCCTTTCCTCTCTTCC
1 TTT--TTT--TCT-TTTC
56511 TTTTCTTTCTTTTC
1 TTTT-TTTCTTTTC
56525 TTTATTTTCTTT
1 TTT-TTTTCTTT
56537 CCTCAATAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
13 8 0.14
14 20 0.34
15 16 0.27
16 1 0.02
17 7 0.12
18 6 0.10
19 1 0.02
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:56491 original size:11 final size:10
Alignment explanation
Indices: 56450--56539 Score: 66
Period size: 9 Copynumber: 9.1 Consensus size: 10
56440 TTTTCAATAT
56450 TTTTCTTT-C
1 TTTTCTTTCC
56459 TTTATCTTT--
1 TTT-TCTTTCC
*
56468 TTTTCTTT-T
1 TTTTCTTTCC
*
56477 TTTTTTTTCAC
1 TTTTCTTTC-C
56488 TTTTCTTTCC
1 TTTTCTTTCC
56498 TTTCCTCTCTTCC
1 TTT--TCT-TTCC
56511 TTTTCTTT-C
1 TTTTCTTTCC
*
56520 TTTTCTTT-A
1 TTTTCTTTCC
56529 TTTTCTTTCC
1 TTTTCTTTCC
56539 T
1 T
56540 CAATAAATCA
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
8 5 0.07
9 30 0.44
10 12 0.18
11 11 0.16
12 3 0.04
13 7 0.10
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTCTTTCC
Found at i:56690 original size:14 final size:13
Alignment explanation
Indices: 56667--56696 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
56657 ACTTTTATAA
56667 ATAGTTATAAATT
1 ATAGTTATAAATT
56680 ATAGATTATAAATT
1 ATAG-TTATAAATT
56694 ATA
1 ATA
56697 CATTTGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (13 bp):
ATAGTTATAAATT
Found at i:57103 original size:21 final size:22
Alignment explanation
Indices: 57079--57124 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
57069 AAGTATTTGG
57079 AAAAATATAT-AAAAATAAAAT
1 AAAAATATATCAAAAATAAAAT
* *
57100 -AAAATTTATCAAAATTAAAAT
1 AAAAATATATCAAAAATAAAAT
57121 AAAA
1 AAAA
57125 GAAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 8 0.38
21 10 0.48
22 3 0.14
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAATATATCAAAAATAAAAT
Found at i:57113 original size:20 final size:21
Alignment explanation
Indices: 57080--57124 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
57070 AGTATTTGGA
57080 AAAATATATAAAAA-TAAAAT
1 AAAATATATAAAAATTAAAAT
* *
57100 AAAATTTATCAAAATTAAAAT
1 AAAATATATAAAAATTAAAAT
57121 AAAA
1 AAAA
57125 GAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATATATAAAAATTAAAAT
Found at i:58055 original size:26 final size:27
Alignment explanation
Indices: 58011--58119 Score: 95
Period size: 26 Copynumber: 4.1 Consensus size: 27
58001 TATAATTTTA
*
58011 ATAATTTT-TAATTATTATTCAATATAT
1 ATAATTTTAT-ATTATTATTTAATATAT
* *
58038 ATAATTTTATTTTA-TATTTTATAT-T
1 ATAATTTTATATTATTATTTAATATAT
*
58063 TTATATTTTATATTATTATTTAATATAAAT
1 ATA-ATTTTATATTATTATTTAATAT--AT
*
58093 ATAATTTT-TA--ATTATTTATTATAT
1 ATAATTTTATATTATTATTTAATATAT
58117 ATA
1 ATA
58120 CATATATTCT
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
24 5 0.07
25 3 0.04
26 29 0.43
27 20 0.29
28 3 0.04
29 5 0.07
30 3 0.04
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (27 bp):
ATAATTTTATATTATTATTTAATATAT
Found at i:58057 original size:7 final size:7
Alignment explanation
Indices: 58045--58081 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
58035 TATATAATTT
58045 TATTTTA
1 TATTTTA
58052 TATTTTA
1 TATTTTA
58059 TATTTTA
1 TATTTTA
58066 TATTTTA
1 TATTTTA
58073 TATTATTA
1 TATT-TTA
58081 T
1 T
58082 TTAATATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 25 0.86
8 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TATTTTA
Found at i:58058 original size:12 final size:12
Alignment explanation
Indices: 58041--58083 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
58031 AATATATATA
58041 ATTTTATTTTAT
1 ATTTTATTTTAT
58053 ATTTTATATTTTAT
1 A-TTT-TATTTTAT
*
58067 ATTTTATATTATT
1 ATTTTATTTTA-T
58080 ATTT
1 ATTT
58084 AATATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.26
13 11 0.41
14 9 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTATTTTAT
Found at i:58084 original size:12 final size:14
Alignment explanation
Indices: 58035--58088 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
58025 TTATTCAATA
58035 TATATAATTTTAT-T
1 TATAT-ATTTTATAT
58049 T-TATATTTTATAT
1 TATATATTTTATAT
*
58062 TTTATATTTTATAT
1 TATATATTTTATAT
*
58076 TAT-TATTTAATAT
1 TATATATTTTATAT
58089 AAATATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
12 7 0.19
13 14 0.39
14 15 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATATATTTTATAT
Found at i:58789 original size:10 final size:10
Alignment explanation
Indices: 58748--58796 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
58738 TTTTAGAATA
58748 TTTAATAAA-
1 TTTAATAAAT
58757 -TT-ATAAAT
1 TTTAATAAAT
*
58765 TTTAAAAATAT
1 TTTAATAA-AT
*
58776 TTTAGTAAAT
1 TTTAATAAAT
58786 TTTAATAAAT
1 TTTAATAAAT
58796 T
1 T
58797 ATATTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
7 5 0.16
8 2 0.06
9 2 0.06
10 15 0.47
11 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (10 bp):
TTTAATAAAT
Found at i:58805 original size:21 final size:20
Alignment explanation
Indices: 58751--58805 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
58741 TAGAATATTT
*
58751 AATAAATTATAAATTTTAAA
1 AATATATTATAAATTTTAAA
*
58771 AATATTTTAGTAAATTTTAATA
1 AATATATTA-TAAATTTTAA-A
58793 AATTATATT-TAAA
1 AA-TATATTATAAA
58806 ATAATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 7 0.24
21 14 0.48
22 3 0.10
23 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AATATATTATAAATTTTAAA
Found at i:58821 original size:23 final size:22
Alignment explanation
Indices: 58791--58863 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
58781 TAAATTTTAA
58791 TAAATTATATTTAAAATAATTTT
1 TAAATTAT-TTTAAAATAATTTT
* *
58814 TAAATTATGTTGAAAATAATATT
1 TAAATTAT-TTTAAAATAATTTT
* *
58837 AAAATTATTATTAATAATAATTAT
1 TAAATTATT-TTAA-AATAATTTT
58861 TAA
1 TAA
58864 TATACTTTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
22 1 0.03
23 30 0.75
24 9 0.22
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
TAAATTATTTTAAAATAATTTT
Found at i:58861 original size:13 final size:13
Alignment explanation
Indices: 58828--58865 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
58818 TTATGTTGAA
58828 AATAA-TATTAA-
1 AATAATTATTAAT
*
58839 AATTATTATTAAT
1 AATAATTATTAAT
58852 AATAATTATTAAT
1 AATAATTATTAAT
58865 A
1 A
58866 TACTTTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 4 0.17
12 6 0.26
13 13 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATAATTATTAAT
Found at i:60862 original size:17 final size:15
Alignment explanation
Indices: 60816--60862 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 15
60806 TTAATTAATA
60816 AATATAAAATATAAAT
1 AATATAAAA-ATAAAT
60832 CAATAT-AAAATAAAT
1 -AATATAAAAATAAAT
60847 AATTATAAAAACTAAA
1 AA-TATAAAAA-TAAA
60863 AAAACATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.07
15 9 0.33
16 7 0.26
17 9 0.33
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (15 bp):
AATATAAAAATAAAT
Done.