Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold956
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: 57354
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:9187 original size:2 final size:2
Alignment explanation
Indices: 9180--9223 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
9170 AGCCCCCACT
* *
9180 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AT AG AG AT 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
9222 AG
1 AG
9224 TCTTCCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (2 bp):
AG
Found at i:10516 original size:26 final size:25
Alignment explanation
Indices: 10469--10526 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 25
10459 TAGATTGAAT
* *
10469 TGATAAAGAATACATAAGAGCATGG
1 TGATAGAGAATACATAAAAGCATGG
10494 TGATAGAGAAGTACATAAAAGCATGG
1 TGATAGAGAA-TACATAAAAGCATGG
10520 TGATAGA
1 TGATAGA
10527 AAAATAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.47, C:0.07, G:0.26, T:0.21
Consensus pattern (25 bp):
TGATAGAGAATACATAAAAGCATGG
Found at i:14159 original size:128 final size:128
Alignment explanation
Indices: 13931--14184 Score: 377
Period size: 128 Copynumber: 2.0 Consensus size: 128
13921 CATTATAAAT
* *
13931 ATTATCATAACTTAGTCAAAACTCTGAAAAACTACTACCAGTTCAAATAAGTAAAATTTACAGTA
1 ATTATCATAACTTAGTCAAAACTCTGAAAAACTACCACCAGTTCAAATAAGTAAAATTTACAGGA
* * * * *
13996 CACAAAATGCTTAAATATACGGAGAATATTCTGATCCCAAAGATAATCTGAAGGTAAAGAGTA
66 CACAAAATGCTTAAATATACAGAGAAGATTCTGATCCAAAAGATAATCTGAAAGAAAAGAGTA
* * *
14059 ATTATCATAATTTAGTCAAAAGTCTGAAAAACTACCACTAGTT-AAGA-AATGTAAAATTTACAG
1 ATTATCATAACTTAGTCAAAACTCTGAAAAACTACCACCAGTTCAA-ATAA-GTAAAATTTACAG
*
14122 GACACAAAATGCTTAAATATACAGAGAAGATTCTGATCCAAAAGATGATCTGAAAGAAAAGAG
64 GACACAAAATGCTTAAATATACAGAGAAGATTCTGATCCAAAAGATAATCTGAAAGAAAAGAG
14185 CTTTTTATGT
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
127 4 0.04
128 109 0.96
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (128 bp):
ATTATCATAACTTAGTCAAAACTCTGAAAAACTACCACCAGTTCAAATAAGTAAAATTTACAGGA
CACAAAATGCTTAAATATACAGAGAAGATTCTGATCCAAAAGATAATCTGAAAGAAAAGAGTA
Found at i:16320 original size:14 final size:14
Alignment explanation
Indices: 16289--16331 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
16279 AAAATAAAAA
*
16289 TATATTTTATTATAT
1 TATATTTTAAT-TAT
16304 TATATTTTAATTAT
1 TATATTTTAATTAT
16318 TAT-TTTTATATTAT
1 TATATTTTA-ATTAT
16332 ATCTATCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 11 0.42
15 10 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATATTTTAATTAT
Found at i:17788 original size:25 final size:24
Alignment explanation
Indices: 17760--17845 Score: 91
Period size: 25 Copynumber: 3.3 Consensus size: 24
17750 TAATTTTAAA
17760 TATAATAAATATTATTATAATTAAT
1 TATAATAAATATTATTATAATT-AT
*
17785 TATAATAAATATTAATTATAAATAT
1 TATAATAAATATT-ATTATAATTAT
*
17810 TAATAATATAAAAATTATTAAATAATTAT
1 T-AT-A-ATAAATATTATT--ATAATTAT
17839 TATAATA
1 TATAATA
17846 TAACGTAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
25 16 0.31
26 13 0.25
27 5 0.10
28 10 0.19
29 8 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAATAAATATTATTATAATTAT
Found at i:17800 original size:16 final size:15
Alignment explanation
Indices: 17779--17840 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 15
17769 TATTATTATA
17779 ATTAATTATAATAAAT
1 ATTAATTAT-ATAAAT
17795 ATTAA-T-TATAAAT
1 ATTAATTATATAAAT
* *
17808 ATTAATAATATAAAA
1 ATTAATTATATAAAT
* *
17823 ATT-ATTAAATAATT
1 ATTAATTATATAAAT
17837 ATTA
1 ATTA
17841 TAATATAACG
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
13 11 0.30
14 11 0.30
15 10 0.27
16 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATTATATAAAT
Found at i:17843 original size:28 final size:30
Alignment explanation
Indices: 17758--17848 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 30
17748 TATAATTTTA
*
17758 AATATAATAAATATT-AT-TATA-ATTAAT
1 AATATAATAAATATTAATATAAATATTAAT
17785 --TATAATAAATATTAATTATAAATATTAAT
1 AATATAATAAATATTAA-TATAAATATTAAT
*
17814 AATATAA-AAATTATTAA-ATAATTATT-AT
1 AATATAATAAA-TATTAATATAAATATTAAT
17842 AATATAA
1 AATATAA
17849 CGTAATAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
25 13 0.24
26 1 0.02
27 1 0.02
28 12 0.22
29 14 0.25
30 3 0.05
31 11 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AATATAATAAATATTAATATAAATATTAAT
Found at i:20745 original size:26 final size:23
Alignment explanation
Indices: 20695--20749 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
20685 ATACGTACGG
*
20695 ATAATATTAAGATATATTTAGAT
1 ATAATATTAAGATATATTTACAT
*
20718 ATAATTTTAAGTATATATGTTTACAT
1 ATAATATTAAG-ATATA--TTTACAT
20744 ATAATA
1 ATAATA
20750 ATAGTATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 10 0.38
24 5 0.19
26 11 0.42
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (23 bp):
ATAATATTAAGATATATTTACAT
Found at i:20793 original size:2 final size:2
Alignment explanation
Indices: 20742--20778 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
20732 ATATGTTTAC
20742 AT AT A- AT A- AT AGT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
20779 GATTTTAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 28 0.88
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:22016 original size:25 final size:25
Alignment explanation
Indices: 21987--22036 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
21977 CCAAGTGTTA
21987 GTAATAATAATGCTGCAGCCAACCC
1 GTAATAATAATGCTGCAGCCAACCC
22012 GTAATAATAATGCTGCAGCCAACCC
1 GTAATAATAATGCTGCAGCCAACCC
22037 TTCCCCTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (25 bp):
GTAATAATAATGCTGCAGCCAACCC
Found at i:22963 original size:16 final size:16
Alignment explanation
Indices: 22942--22975 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
22932 TAGGATCAAA
22942 CTTTCAGGGAACTGTC
1 CTTTCAGGGAACTGTC
22958 CTTTCAGGGAACTGTC
1 CTTTCAGGGAACTGTC
22974 CT
1 CT
22976 GTTGGATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (16 bp):
CTTTCAGGGAACTGTC
Found at i:29675 original size:6 final size:6
Alignment explanation
Indices: 29664--29694 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
29654 CATAATAAAT
29664 ATTATA ATTATA ATTATA ATTATA A-TATA AT
1 ATTATA ATTATA ATTATA ATTATA ATTATA AT
29695 ACGAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTATA
Found at i:30166 original size:64 final size:64
Alignment explanation
Indices: 30038--30167 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
30028 TGCAAGGCTG
* * *
30038 TTTTTTCGACTTAAAGAATTACCCAATGGGTAAAAATGTTAGATATTCAAATTCAGAATCTAAT
1 TTTTTTCGACTTAAAGAATTACCCAATGAGTAAAAATGTTAGATATTCAAATTCAAAATATAAT
* *
30102 TTTTTTCGACTTAAAGAATTACCCAATGAGTAAAAATGTTAGATATTTAAATTTAAAATATAAT
1 TTTTTTCGACTTAAAGAATTACCCAATGAGTAAAAATGTTAGATATTCAAATTCAAAATATAAT
30166 TT
1 TT
30168 ATTTAGTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (64 bp):
TTTTTTCGACTTAAAGAATTACCCAATGAGTAAAAATGTTAGATATTCAAATTCAAAATATAAT
Found at i:32267 original size:35 final size:40
Alignment explanation
Indices: 32219--32299 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 40
32209 ACGGCTTTGG
*
32219 ATATGATACAAAAAATAAT-T-AA-AT-TATAATATA-AA
1 ATATGACACAAAAAATAATATGAATATATATAATATACAA
*
32254 ATATGACATAAAAAATAATATGAATATGATATAATATACAA
1 ATATGACACAAAAAATAATATGAATAT-ATATAATATACAA
32295 ATATG
1 ATATG
32300 TCAAAATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 17 0.45
36 1 0.03
37 2 0.05
38 2 0.05
40 9 0.24
41 7 0.18
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (40 bp):
ATATGACACAAAAAATAATATGAATATATATAATATACAA
Found at i:36177 original size:30 final size:32
Alignment explanation
Indices: 36143--36211 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 32
36133 GTAATATTTT
36143 TAAAATAAT-ATGAATA-TAATATAATTTATA
1 TAAAATAATGATGAATATTAATATAATTTATA
* *
36173 TAAAATAAATGATTAATATTATTATAATTTATA
1 TAAAAT-AATGATGAATATTAATATAATTTATA
36206 -AAAATA
1 TAAAATA
36212 TAAAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 6 0.18
31 4 0.12
32 11 0.32
33 13 0.38
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (32 bp):
TAAAATAATGATGAATATTAATATAATTTATA
Found at i:36339 original size:16 final size:16
Alignment explanation
Indices: 36311--36370 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
36301 TTTAACTATT
*
36311 AAAT-TAAATTAATTA
1 AAATCTAAAATAATTA
36326 AAATCTAAAATAATTAA
1 AAATCTAAAATAATT-A
36343 AAATC-AAAATAAATTA
1 AAATCTAAAAT-AATTA
* *
36359 AACTCAAAAATA
1 AAATCTAAAATA
36371 TTATAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.10
16 20 0.51
17 15 0.38
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATCTAAAATAATTA
Found at i:36369 original size:33 final size:34
Alignment explanation
Indices: 36316--36380 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
36306 CTATTAAATT
* *
36316 AAATTAATTAAAATCTAAAATAAT-TAAAAATCA
1 AAATAAATTAAAATCAAAAATAATATAAAAATCA
* *
36349 AAATAAATTAAACTCAAAAATATTATAAAAAT
1 AAATAAATTAAAATCAAAAATAATATAAAAAT
36381 TTTAAAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (34 bp):
AAATAAATTAAAATCAAAAATAATATAAAAATCA
Found at i:39968 original size:14 final size:15
Alignment explanation
Indices: 39940--39969 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39930 ATTTATATAA
39940 AAATTATTCAAAATT
1 AAATTATTCAAAATT
39955 AAATTATT-AAAATT
1 AAATTATTCAAAATT
39969 A
1 A
39970 TTTATATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTATTCAAAATT
Found at i:40043 original size:21 final size:21
Alignment explanation
Indices: 40002--40066 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
39992 TATAATAATT
**
40002 TTTTATTT-ATTAAATTTAAAA
1 TTTTATTTAATT-AATAAAAAA
40023 TTTTATTTAATTAATAAAAAA
1 TTTTATTTAATTAATAAAAAA
40044 TATTTAAATTTAATT-ATAAAAAA
1 T-TTT--ATTTAATTAATAAAAAA
40067 ATATAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 16 0.42
22 6 0.16
23 8 0.21
24 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTATTTAATTAATAAAAAA
Found at i:40048 original size:23 final size:23
Alignment explanation
Indices: 40027--40090 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 23
40017 TTAAAATTTT
40027 ATTTAATTAATAAAAAATATTTAA
1 ATTTAATT-ATAAAAAATATTTAA
*
40051 ATTTAATTATAAAAAA-ATATAA
1 ATTTAATTATAAAAAATATTTAA
40073 ATATTAAATTA-AAAAAAT
1 AT-TT-AATTATAAAAAAT
40091 TAAATTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 7 0.19
23 16 0.44
24 13 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTTAATTATAAAAAATATTTAA
Found at i:40058 original size:24 final size:23
Alignment explanation
Indices: 40027--40096 Score: 76
Period size: 22 Copynumber: 3.1 Consensus size: 23
40017 TTAAAATTTT
*
40027 ATTTAATTAATAAAAAATATTTAA
1 ATTTAATTAATAAAAAA-ATATAA
40051 ATTTAATT-ATAAAAAAATATAA
1 ATTTAATTAATAAAAAAATATAA
*
40073 ATATTAA--ATTAAAAAAAT-TAA
1 AT-TTAATTAATAAAAAAATATAA
40094 ATT
1 ATT
40097 AAAATTTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 1 0.02
21 5 0.12
22 16 0.38
23 12 0.29
24 8 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATTTAATTAATAAAAAAATATAA
Found at i:45176 original size:20 final size:20
Alignment explanation
Indices: 45146--45183 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
45136 TTTGCTTATT
45146 TAAATTTAATA-AAAATATA
1 TAAATTTAATATAAAATATA
45165 TAAATATTAATATAAAATA
1 TAAAT-TTAATATAAAATA
45184 ATATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAATTTAATATAAAATATA
Found at i:55818 original size:19 final size:21
Alignment explanation
Indices: 55763--55819 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
55753 GTTTAAACAC
55763 TATTAAAATAAA-A-AATATA
1 TATTAAAATAAATATAATATA
*
55782 TATTTAAATATAATATAATAT-
1 TATTAAAATA-AATATAATATA
55803 T-TTAAAATAAATATAAT
1 TATTAAAATAAATATAAT
55820 TAATTTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 17 0.52
20 9 0.27
21 2 0.06
22 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTAAAATAAATATAATATA
Found at i:56144 original size:10 final size:10
Alignment explanation
Indices: 56131--56160 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
56121 ATTTTTATTT
56131 ATTTAAATAA
1 ATTTAAATAA
*
56141 ATTTATATAA
1 ATTTAAATAA
56151 ATTTAAATAA
1 ATTTAAATAA
56161 TAATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:56252 original size:61 final size:63
Alignment explanation
Indices: 56182--56310 Score: 199
Period size: 62 Copynumber: 2.1 Consensus size: 63
56172 CGATATAATC
* *
56182 TATATAAAATAA-ATTTTTCGACATAAATGTTACTATTTATTATGAGGTTTTTTATAGAGA-A
1 TATATAAAATAAGATTTTTCGACATAAATGTTAATATTTATTATGAAGTTTTTTATAGAGATA
* * *
56243 TATATAAAATAAGTTTTTTTGACATAAATGTTAATATTTATTATGAATTTTTTTATAGAGATA
1 TATATAAAATAAGATTTTTCGACATAAATGTTAATATTTATTATGAAGTTTTTTATAGAGATA
56306 TATAT
1 TATAT
56311 TCATTAATTT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 12 0.20
62 43 0.70
63 6 0.10
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (63 bp):
TATATAAAATAAGATTTTTCGACATAAATGTTAATATTTATTATGAAGTTTTTTATAGAGATA
Found at i:56359 original size:30 final size:31
Alignment explanation
Indices: 56305--56371 Score: 127
Period size: 30 Copynumber: 2.2 Consensus size: 31
56295 TTATAGAGAT
56305 ATATATTCATTAATTTTAAATTAATTAATAG
1 ATATATTCATTAATTTTAAATTAATTAATAG
56336 ATATATTCATTAATTTT-AATTAATTAATAG
1 ATATATTCATTAATTTTAAATTAATTAATAG
56366 ATATAT
1 ATATAT
56372 AGATTCATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 19 0.53
31 17 0.47
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (31 bp):
ATATATTCATTAATTTTAAATTAATTAATAG
Found at i:56392 original size:31 final size:30
Alignment explanation
Indices: 56297--56393 Score: 88
Period size: 31 Copynumber: 3.0 Consensus size: 30
56287 GAATTTTTTT
* *
56297 ATAGAGATATATATTCATTAATTTTAAATTA
1 ATAGATATATATATTCATTAATATT-AATTA
*
56328 ATTA-ATAGATATATTCATTAATTTTAATTAATTA
1 A-TAGATATATATATTCATTAA---T-ATTAATTA
*
56362 ATAGATATATAGATTCATTAAGTATTAATTA
1 ATAGATATATATATTCATTAA-TATTAATTA
56393 A
1 A
56394 ATATTATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
31 25 0.46
32 3 0.06
33 2 0.04
34 22 0.41
35 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (30 bp):
ATAGATATATATATTCATTAATATTAATTA
Found at i:56633 original size:150 final size:150
Alignment explanation
Indices: 56296--56633 Score: 358
Period size: 150 Copynumber: 2.3 Consensus size: 150
56286 TGAATTTTTT
* *
56296 TATAGAGATATATATTCATTAATTTTAAATTAATTAAT--AGATATATTCATTAATTTTAATTAA
1 TATAGAGATATATA-TAATTGATTTTAAATTAATTAATAGAGATATATTCATTAATTTTAATTAA
*
56359 TTAATAGATATATAGATTCATTAAGTATTAATTAAATATTATTTATTATGAATTTTTTTTAGAGA
65 TTAATAGATATATAGATTCATTAAGTATTAATTAAATATTATTTATTATGAAGTTTTTTTA-AGA
* ***
56424 ATATATAAAATAATTTTTTTGA
129 ATATATAAAATAATATAGATGA
* * * * *
56446 CATAAATGTTAATATTTATTATGAGTTTT---TT--TT-ATAGAGATATATTCATTAATTTTAAA
1 TATAGA-GAT-ATATATAAT-TGA-TTTTAAATTAATTAATAGAGATATATTCATTAATTTT-AA
*
56505 TTAATTAATAGATATATAGATTGATTAAGTATTAATTAAATATAAATATTTATTATG-AGTTTTT
61 TTAATTAATAGATATATAGATTCATTAAGTATTAATTAAATAT---TATTTATTATGAAGTTTTT
** *
56569 TT-ATCATAT-TAAATTAATATAGATG-
123 TTAAGAATATATAAAATAATATAGATGA
56594 TATAGAGATATATATAATTGATTTTAAATTAATTAATAGA
1 TATAGAGATATATATAATTGATTTTAAATTAATTAATAGA
56634 TACATAGATA
Statistics
Matches: 151, Mismatches: 21, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
144 4 0.03
145 3 0.02
146 7 0.05
147 6 0.04
148 6 0.04
149 32 0.21
150 60 0.40
151 4 0.03
152 14 0.09
153 15 0.10
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (150 bp):
TATAGAGATATATATAATTGATTTTAAATTAATTAATAGAGATATATTCATTAATTTTAATTAAT
TAATAGATATATAGATTCATTAAGTATTAATTAAATATTATTTATTATGAAGTTTTTTTAAGAAT
ATATAAAATAATATAGATGA
Found at i:56672 original size:31 final size:31
Alignment explanation
Indices: 56628--56686 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
56618 TAAATTAATT
*
56628 AATAGATACATAGATATATAGATTCATTAAG
1 AATAGATACATAGAGATATAGATTCATTAAG
** *
56659 AATAGATGTATAGAGATATATATTCATT
1 AATAGATACATAGAGATATAGATTCATT
56687 GATTTTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.36
Consensus pattern (31 bp):
AATAGATACATAGAGATATAGATTCATTAAG
Found at i:56752 original size:74 final size:73
Alignment explanation
Indices: 56587--56732 Score: 247
Period size: 74 Copynumber: 2.0 Consensus size: 73
56577 TTAAATTAAT
56587 ATAGATGTATAGAGATATATATAATTGATTTTAAATTAATTAATAGATACATAGATATATAGATT
1 ATAGATGTATAGAGATATATATAATTGATTTTAAATTAATTAATAGATACATAGATATATAGATT
*
56652 CATTAAGA
66 CAATAAGA
* * *
56660 ATAGATGTATAGAGATATATATTCATTGATTTTAAATTAATTAATAGATATATAGCTATATAGAT
1 ATAGATGTATAGAGATATATA-TAATTGATTTTAAATTAATTAATAGATACATAGATATATAGAT
56725 TCAATAAG
65 TCAATAAG
56733 TAATTAATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
73 21 0.31
74 47 0.69
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.39
Consensus pattern (73 bp):
ATAGATGTATAGAGATATATATAATTGATTTTAAATTAATTAATAGATACATAGATATATAGATT
CAATAAGA
Found at i:56875 original size:2 final size:2
Alignment explanation
Indices: 56845--56905 Score: 81
Period size: 2 Copynumber: 31.0 Consensus size: 2
56835 TAATTAATAG
* *
56845 AT AT AT AG AT AT AG A- AT A- AT AT GAT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
56886 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
56906 TCATTGAATC
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.04
2 49 0.92
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Done.