Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1169
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: 27127
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4591 original size:2 final size:2
Alignment explanation
Indices: 4584--4618 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4574 AAGCTGCAGC
4584 AT 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 AT A
4619 AAGAGAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6875 original size:4 final size:4
Alignment explanation
Indices: 6866--6891 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6856 AAAAAATTAA
6866 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
6892 GCACAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:7212 original size:15 final size:14
Alignment explanation
Indices: 7177--7217 Score: 64
Period size: 15 Copynumber: 2.8 Consensus size: 14
7167 TTAATTAAAT
7177 AATTAATAAATATTA
1 AATTAA-AAATATTA
7192 AATTAAAAATATTA
1 AATTAAAAATATTA
7206 AATTTAAAAATA
1 AA-TTAAAAATA
7218 ATTTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTAAAAATATTA
Found at i:7259 original size:28 final size:28
Alignment explanation
Indices: 7203--7270 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
7193 ATTAAAAATA
7203 TTAAATTTAAAAATAATTTTAATTACTTT
1 TTAAATTTAAAAATAATTTT-ATTACTTT
*
7232 TTAATATTTAAATAAT-ATTTT-TTTCTTT
1 TTAA-ATTTAAA-AATAATTTTATTACTTT
7260 TTAAAGTTTAA
1 TTAAA-TTTAA
7271 TATAAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
27 1 0.03
28 15 0.43
29 4 0.11
30 12 0.34
31 3 0.09
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (28 bp):
TTAAATTTAAAAATAATTTTATTACTTT
Found at i:7952 original size:17 final size:17
Alignment explanation
Indices: 7895--7966 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 17
7885 ATTTATTTCA
*
7895 AAATTAATATATAA-TT
1 AAATTAAAATATAATTT
*
7911 GAATTAATAATA-AATTTAAT
1 AAATTAA-AATATAA-TT--T
*
7931 AAATTTAACATAT-ATTT
1 AAA-TTAAAATATAATTT
7948 AAATTAAAATATAATTT
1 AAATTAAAATATAATTT
7965 AA
1 AA
7967 TAATAATTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
16 16 0.37
17 13 0.30
18 1 0.02
19 2 0.05
20 7 0.16
21 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
AAATTAAAATATAATTT
Found at i:7953 original size:37 final size:37
Alignment explanation
Indices: 7879--7990 Score: 109
Period size: 37 Copynumber: 2.9 Consensus size: 37
7869 AAAAATATTT
* * *
7879 TAATAAATTTATTTCAAAATTAATATATAATTGAATTAA
1 TAATAAATTTA-AT-AAAATTAACATATAATTAAATTAA
* *
7918 TAATAAATTTAATAAATTTAACATATATTTAAATTAA
1 TAATAAATTTAATAAAATTAACATATAATTAAATTAA
*
7955 -AATATAATTTAATAATAATTTAATATAATAATTAAA
1 TAATA-AATTTAATAA-AA-TTAACAT-ATAATTAAA
7991 GATAATTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
36 4 0.07
37 30 0.49
38 2 0.03
39 17 0.28
40 8 0.13
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (37 bp):
TAATAAATTTAATAAAATTAACATATAATTAAATTAA
Found at i:7989 original size:23 final size:21
Alignment explanation
Indices: 7955--7998 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
7945 TTTAAATTAA
7955 AATATAATTTAATA-ATAATTT
1 AATATAATTTAA-AGATAATTT
7976 AATATAATAATTAAAGATAATTT
1 AATATAAT--TTAAAGATAATTT
7999 TAAGCTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATAATTTAAAGATAATTT
Found at i:8625 original size:26 final size:27
Alignment explanation
Indices: 8585--8643 Score: 111
Period size: 26 Copynumber: 2.2 Consensus size: 27
8575 AATAAATTGT
8585 TAATAATATTAATATTTATTTTTAAAA
1 TAATAATATTAATATTTATTTTTAAAA
8612 TAATAAT-TTAATATTTATTTTTAAAA
1 TAATAATATTAATATTTATTTTTAAAA
8638 TAATAA
1 TAATAA
8644 CGTAATAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 25 0.78
27 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAATAATATTAATATTTATTTTTAAAA
Found at i:8649 original size:26 final size:26
Alignment explanation
Indices: 8594--8650 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
8584 TTAATAATAT
**
8594 TAATATTTATTTTTAAAATAATAATT
1 TAATATTTATTTTTAAAATAATAACG
8620 TAATATTTATTTTTAAAATAATAACG
1 TAATATTTATTTTTAAAATAATAACG
8646 TAATA
1 TAATA
8651 AGTTAACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TAATATTTATTTTTAAAATAATAACG
Found at i:8879 original size:17 final size:17
Alignment explanation
Indices: 8844--8876 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
8834 ATTTTATGTG
8844 AAATAAATTTTATTTTT
1 AAATAAATTTTATTTTT
8861 AAATAAA-TTTATTTTT
1 AAATAAATTTTATTTTT
8877 TAATTTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATAAATTTTATTTTT
Found at i:9039 original size:23 final size:23
Alignment explanation
Indices: 9011--9054 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
9001 TACTTTTTGC
*
9011 TTATAATA-ATAATTTGTATTTCT
1 TTATAATATAAAATTT-TATTTCT
9034 TTATAATATAAAATTTTATTT
1 TTATAATATAAAATTTTATTT
9055 AGCACTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTATAATATAAAATTTTATTTCT
Found at i:12616 original size:6 final size:6
Alignment explanation
Indices: 12605--12641 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
12595 TTTGGGGGAA
12605 TGAGAT TGAGAT TGAGAT TGAGAT TGAGATT TGAGAT
1 TGAGAT TGAGAT TGAGAT TGAGAT TGAGA-T TGAGAT
12642 AGGCGCAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGAGAT
Found at i:12657 original size:6 final size:6
Alignment explanation
Indices: 12648--12702 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
12638 AGATAGGCGC
*
12648 AGGCAT AGGCAT AGGCAT AGGCGT AGGCAT AGGCAT AGGCAT AGGCAT
1 AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT
12696 AGGCAT A
1 AGGCAT A
12703 TGCTCGGAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.33, C:0.16, G:0.35, T:0.16
Consensus pattern (6 bp):
AGGCAT
Found at i:12891 original size:22 final size:22
Alignment explanation
Indices: 12863--12930 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 22
12853 TTTCCCCCCT
12863 ATTTTTATTTTTATTTTTTAAC
1 ATTTTTATTTTTATTTTTTAAC
*
12885 ATTTTTA-ATTTACTTTTTCT-AC
1 ATTTTTATTTTTA-TTTTT-TAAC
12907 ATTATTTATGTATTTATTTATTTA
1 ATT-TTTAT-T-TTTATTT-TTTA
12931 TTTATTTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
21 4 0.11
22 17 0.47
23 5 0.14
25 4 0.11
26 6 0.17
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (22 bp):
ATTTTTATTTTTATTTTTTAAC
Found at i:12924 original size:4 final size:4
Alignment explanation
Indices: 12908--12937 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
12898 TTTTTCTACA
*
12908 TTAT TTAT GTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
12938 TCCCACCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:13378 original size:19 final size:22
Alignment explanation
Indices: 13337--13412 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
13327 TGATTTGGAT
13337 TAAATTATTATGTAAATAATAA
1 TAAATTATTATGTAAATAATAA
13359 TAAATTATT-T-TAAATTTAATAA
1 TAAATTATTATGTAAA--TAATAA
*
13381 TAAA-TATTAATATAAA-AATAA
1 TAAATTATT-ATGTAAATAATAA
**
13402 TATTTTATTAT
1 TAAATTATTAT
13413 TTTAAATAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
20 4 0.09
21 14 0.30
22 23 0.50
23 1 0.02
24 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (22 bp):
TAAATTATTATGTAAATAATAA
Found at i:18035 original size:36 final size:36
Alignment explanation
Indices: 17995--18113 Score: 220
Period size: 36 Copynumber: 3.3 Consensus size: 36
17985 TACAAACTTG
*
17995 TGAATCAGTGGGCTCGTTAGTTTCATCATGAATTTC
1 TGAATCATTGGGCTCGTTAGTTTCATCATGAATTTC
*
18031 TGAATCATTGAGCTCGTTAGTTTCATCATGAATTTC
1 TGAATCATTGGGCTCGTTAGTTTCATCATGAATTTC
18067 TGAATCATTGGGCTCGTTAGTTTCATCATGAATTTC
1 TGAATCATTGGGCTCGTTAGTTTCATCATGAATTTC
18103 TGAATCATTGG
1 TGAATCATTGG
18114 TATCATTGGT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (36 bp):
TGAATCATTGGGCTCGTTAGTTTCATCATGAATTTC
Found at i:22978 original size:19 final size:18
Alignment explanation
Indices: 22950--23001 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
22940 TATATAGAAA
*
22950 AAAATTTATATGAAGATT
1 AAAATATATATGAAGATT
22968 AAAATACTATATGAA-A--
1 AAAATA-TATATGAAGATT
22984 AAAATA-ATATGAAGATT
1 AAAATATATATGAAGATT
23001 A
1 A
23002 TATAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
14 7 0.24
15 1 0.03
16 6 0.21
17 1 0.03
18 6 0.21
19 8 0.28
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.31
Consensus pattern (18 bp):
AAAATATATATGAAGATT
Found at i:23199 original size:293 final size:293
Alignment explanation
Indices: 22672--23228 Score: 1033
Period size: 293 Copynumber: 1.9 Consensus size: 293
22662 ATAGAAAAAA
22672 ATTAAAATACTATATGAAAAAAATAATATGAAAATTATATAAATATATAAATATGTCAGAATATA
1 ATTAAAATACTATATGAAAAAAATAATATGAAAATTATATAAATATATAAATATGTCAGAATATA
*
22737 TATAATACTAATTATTGATGTTTAAAAATTTATATAAATTCATAATGCTTTGCACGCAAAAAATA
66 CATAATACTAATTATTGATGTTTAAAAATTTATATAAATTCATAATGCTTTGCACGCAAAAAATA
22802 ACACAAACATGTTATTAACATACAAAATTTTTGCTAAATTAAATCACTACGATAAATTAGGTAAA
131 ACACAAACATGTTATTAACATACAAAATTTTTGCTAAATTAAATCACTACGATAAATTAGGTAAA
* *
22867 TATTCATGAATTGAAATAGAACACAATCACGATATAAATACGAATTTTTTCAGAATTGAATTACA
196 TATTCATGAATTGAAATAGAACACAATCACGATATAAATACGAATTTTCTCAAAATTGAATTACA
22932 ATGAAGATTATATAGAAAAAAATTTATATGAAG
261 ATGAAGATTATATAGAAAAAAATTTATATGAAG
*
22965 ATTAAAATACTATATGAAAAAAATAATATGAAGATTATATAAATATATAAATATGTCAGAATATA
1 ATTAAAATACTATATGAAAAAAATAATATGAAAATTATATAAATATATAAATATGTCAGAATATA
* *
23030 CATAATACTAATTATTGATGTTTAAAAATTTATGTAAATTCATAATGCTTTGCATGCAAAAAATA
66 CATAATACTAATTATTGATGTTTAAAAATTTATATAAATTCATAATGCTTTGCACGCAAAAAATA
23095 ACACAAACATGTTATTAACATACAAAATTTTTGCTAAATTAAATCACTACGATAAATTAGGTAAA
131 ACACAAACATGTTATTAACATACAAAATTTTTGCTAAATTAAATCACTACGATAAATTAGGTAAA
* * *
23160 TATTTATGAATTGAAATAGAACACGATCATGATATAAATACGAATTTTCTCAAAATTGAATTACA
196 TATTCATGAATTGAAATAGAACACAATCACGATATAAATACGAATTTTCTCAAAATTGAATTACA
23225 ATGA
261 ATGA
23229 TCACATTATA
Statistics
Matches: 255, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
293 255 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (293 bp):
ATTAAAATACTATATGAAAAAAATAATATGAAAATTATATAAATATATAAATATGTCAGAATATA
CATAATACTAATTATTGATGTTTAAAAATTTATATAAATTCATAATGCTTTGCACGCAAAAAATA
ACACAAACATGTTATTAACATACAAAATTTTTGCTAAATTAAATCACTACGATAAATTAGGTAAA
TATTCATGAATTGAAATAGAACACAATCACGATATAAATACGAATTTTCTCAAAATTGAATTACA
ATGAAGATTATATAGAAAAAAATTTATATGAAG
Found at i:23479 original size:22 final size:21
Alignment explanation
Indices: 23430--23479 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
23420 ACACAAATAC
* *
23430 TAAATTAAAAATTAATTAAAA
1 TAAATAAAAAATAAATTAAAA
*
23451 TATAATAAAAAATAAATATAACA
1 TA-AATAAAAAATAAAT-TAAAA
23474 TAAATA
1 TAAATA
23480 TACAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.67
23 6 0.25
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAATAAAAAATAAATTAAAA
Found at i:23505 original size:19 final size:19
Alignment explanation
Indices: 23462--23559 Score: 55
Period size: 19 Copynumber: 5.3 Consensus size: 19
23452 ATAATAAAAA
23462 ATAAATATAACATAAATAT
1 ATAAATATAACATAAATAT
*
23481 ACAAATATAA-A-AAATATTT
1 ATAAATATAACATAAATA--T
* * *
23500 ATAAATATTATATAAATTT
1 ATAAATATAACATAAATAT
*
23519 ATAATATTTTAA-AT-AATA-
1 ATAA-A-TATAACATAAATAT
* *
23537 AAAAATATAA-ATAAAAAT
1 ATAAATATAACATAAATAT
23555 ATAAA
1 ATAAA
23560 CACTTAAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 17
0.68 0.12 0.19
Matches are distributed among these distances:
16 6 0.10
17 9 0.15
18 8 0.13
19 26 0.43
20 4 0.07
21 7 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAATATAACATAAATAT
Found at i:24028 original size:11 final size:11
Alignment explanation
Indices: 24012--24057 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
24002 AATTTTTTCC
24012 TCTTTTCTTTT
1 TCTTTTCTTTT
24023 TCTTTT-TTTCT
1 TCTTTTCTTT-T
*
24034 TCTTTTTTTCTT
1 TCTTTTCTT-TT
24046 TC-TTTCTTTT
1 TCTTTTCTTTT
24056 TC
1 TC
24058 AGCTGAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.23
11 18 0.58
12 5 0.16
13 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:24030 original size:8 final size:8
Alignment explanation
Indices: 24014--24056 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
24004 TTTTTTCCTC
24014 TTTTCTTT
1 TTTTCTTT
24022 TTCTT-TTT
1 TT-TTCTTT
24030 TTCTTCTTT
1 TT-TTCTTT
24039 TTTTCTTT
1 TTTTCTTT
*
24047 CTTTCTTT
1 TTTTCTTT
24055 TT
1 TT
24057 CAGCTGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 24 0.77
9 7 0.23
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTCTTT
Found at i:24034 original size:19 final size:18
Alignment explanation
Indices: 24012--24056 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
24002 AATTTTTTCC
*
24012 TCTTTTCTTTTTCTTTTTT
1 TCTTTT-TTTTTCTTTCTT
24031 TCTTCTTTTTTTCTTTCTT
1 TCTT-TTTTTTTCTTTCTT
24050 TCTTTTT
1 TCTTTTT
24057 CAGCTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 3 0.12
19 19 0.79
20 2 0.08
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TCTTTTTTTTTCTTTCTT
Found at i:24457 original size:11 final size:11
Alignment explanation
Indices: 24441--24485 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
24431 TAATAGTTTA
24441 TATATTTATAT
1 TATATTTATAT
24452 TATATTTATA-
1 TATATTTATAT
*
24462 TATTTTATATAT
1 TATATT-TATAT
*
24474 TATTTTTATAT
1 TATATTTATAT
24485 T
1 T
24486 TAAAATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 5 0.16
11 20 0.65
12 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTATAT
Found at i:24493 original size:20 final size:21
Alignment explanation
Indices: 24448--24506 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
24438 TTATATATTT
* *
24448 ATATTATATTTATATATTTTAT
1 ATATTATATTT-TATATTTAAA
24470 ATATTAT-TTTTATATTTAAA
1 ATATTATATTTTATATTTAAA
24490 ATATTATATATTTATAT
1 ATATTATAT-TTTATAT
24507 AAATTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.45
21 4 0.12
22 14 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTATATTTTATATTTAAA
Found at i:24509 original size:20 final size:20
Alignment explanation
Indices: 24438--24509 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
24428 ATTTAATAGT
* *
24438 TTATATATTTATATTATAT-
1 TTATATATTTATATAAAATA
24457 TTATATATTT-TAT---ATA
1 TTATATATTTATATAAAATA
24473 TTAT-T-TTTATATTTAAAATA
1 TTATATATTTATA--TAAAATA
24493 TTATATATTTATATAAA
1 TTATATATTTATATAAA
24510 TTTAATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
14 3 0.07
15 5 0.11
16 4 0.09
17 1 0.02
18 3 0.07
19 10 0.23
20 11 0.25
21 1 0.02
22 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATATATTTATATAAAATA
Found at i:24862 original size:18 final size:16
Alignment explanation
Indices: 24851--24898 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
24841 ATATTTATTA
24851 TTAAAATAATATTAAT
1 TTAAAATAATATTAAT
24867 TTAAAATAA-ATT-A-
1 TTAAAATAATATTAAT
* *
24880 TTAAAATATTATTATT
1 TTAAAATAATATTAAT
24896 TTA
1 TTA
24899 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 8 0.30
14 4 0.15
15 3 0.11
16 12 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAATAATATTAAT
Found at i:24879 original size:29 final size:28
Alignment explanation
Indices: 24847--24972 Score: 92
Period size: 29 Copynumber: 4.1 Consensus size: 28
24837 TTTAATATTT
24847 ATTATTAAAATAATATTAATTTAAAATAA
1 ATTATTAAAATAATATTAATTTAAAA-AA
* *
24876 ATTATTAAAATATTATTATTTTATTTAAAAA
1 ATTATTAAAATAATATTAATTTA---AAAAA
*
24907 ATTATTAAATTAATTGATGT-ATTTAATAAAAA
1 ATTATTAAAATAA-T-AT-TAATTT-A-AAAAA
* * *
24939 ATTATTAAAATGATTAATAATTTGATAAAA
1 ATTATTAAAAT-AATATTAATTT-AAAAAA
24969 ATTA
1 ATTA
24973 CTAGAGTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
29 21 0.27
30 9 0.12
31 19 0.24
32 21 0.27
33 6 0.08
34 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (28 bp):
ATTATTAAAATAATATTAATTTAAAAAA
Found at i:25640 original size:28 final size:27
Alignment explanation
Indices: 25571--25641 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 27
25561 TAAAATAATT
25571 AAATAATAATAATTAAAATTAAAATTTCA
1 AAATAAT-ATAATT-AAATTAAAATTTCA
* * *
25600 AATTAA-ATAAATTAAATTCAATATTTTA
1 AAATAATAT-AATTAAATT-AAAATTTCA
25628 AAATAATATAATTA
1 AAATAATATAATTA
25642 CATTTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
27 7 0.20
28 21 0.60
29 7 0.20
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATAATATAATTAAATTAAAATTTCA
Found at i:25663 original size:21 final size:21
Alignment explanation
Indices: 25602--25663 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
25592 AAATTTCAAA
* *
25602 TTAAATAAATTAAATTCAATATT
1 TTAAATAAA-TAAATT-TACATT
25625 TTAAA-ATAATATAA-TTACATT
1 TTAAATA-AATA-AATTTACATT
25646 TTAAATAAATAAATTTAC
1 TTAAATAAATAAATTTAC
25664 GATTAATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
20 2 0.06
21 17 0.52
22 5 0.15
23 9 0.27
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAATAAATAAATTTACATT
Found at i:25686 original size:26 final size:25
Alignment explanation
Indices: 25626--25686 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
25616 TTCAATATTT
* *
25626 TAAAATAATATAATTACATTTTAAA
1 TAAAATAATTTAATTACATTGTAAA
25651 T-AAATAAATTTACGATTA-ATTGTAAA
1 TAAAAT-AATTTA--ATTACATTGTAAA
25677 TAAAATAATT
1 TAAAATAATT
25687 GTTTAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 4 0.13
25 6 0.20
26 12 0.40
27 8 0.27
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (25 bp):
TAAAATAATTTAATTACATTGTAAA
Found at i:25887 original size:29 final size:29
Alignment explanation
Indices: 25855--25919 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
25845 TTTTTTTAAA
*
25855 TTAAAATAATAGTATATTAATAATTTATT
1 TTAAAATAATAGTATATTAATAACTTATT
* * *
25884 TTAAACTAATATTATTTTAATAACTTATT
1 TTAAAATAATAGTATATTAATAACTTATT
*
25913 TAAAAAT
1 TTAAAAT
25920 TAAGAGCACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (29 bp):
TTAAAATAATAGTATATTAATAACTTATT
Done.