Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2139
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: 53950
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Found at i:1111 original size:21 final size:21
Alignment explanation
Indices: 1085--1125 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1075 GTGAGACGGC
* *
1085 TAATTTTTTTATTTTTTATTA
1 TAATTTTTTTAATTATTATTA
1106 TAATTTTTTTAATTATTATT
1 TAATTTTTTTAATTATTATT
1126 TATTTTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TAATTTTTTTAATTATTATTA
Found at i:2003 original size:137 final size:132
Alignment explanation
Indices: 1676--2085 Score: 408
Period size: 136 Copynumber: 3.0 Consensus size: 132
1666 ACAATATCAG
* *
1676 CTGTTCTGGATTGTGACTTGTGGAGAAAGAAAGAGGAAGGCTAAATGCTAAATCT-ACATATAGT
1 CTGTTCT-GATTGTGACTTGTGGAGAAAG-AAGAGGAAGGCTAAACGCTAAATCTAATATATAGT
* ** *
1740 GT-CCGACTGGTGACTAAGTATACTGTCCTAACTCCTACGCAACTTACTCTTTCTAAGAA-A-CA
64 GTCCCGACTGGTGACTAAGTATA-TGTCCTAA-T-CAACTTAA---ACTCTTTCTAAGAACATAA
*
1802 --GC-AGTGA
123 TGGCAAGTAA
* * * * *
1809 CTGTTTCTGTTTATGAACTTGTGGAGAAAGAGGAGTAAGGCCTAAACGCTATATCTAATATATAG
1 CTG-TTCTGATTGTG-ACTTGTGGAGAAAGAAGAGGAAGG-CTAAACGCTAAATCTAATATATAG
* *
1874 TGGTCCCGACTTGGTGACTGAGTATATGTCCTAATCAACTTTAAAGTCTTTCTAAGAACATAATG
63 T-GTCCCGAC-TGGTGACTAAGTATATGTCCTAATCAAC-TTAAACTCTTTCTAAGAACATAATG
1939 GCAAGTTTAA
125 GCAAG--TAA
*
1949 CTGTTCTGATTGTGACTTGTGG-GAGAAGAAGAGGAAGGCTCAACGCTAAATCTAATATATAGTG
1 CTGTTCTGATTGTGACTTGTGGAGA-AAGAAGAGGAAGGCTAAACGCTAAATCTAATATATAGTG
* * * *
2013 CCCCTCACTGGTGACTAAGTATATGTCCTAAGCAACTTAAACTCTTTCTAAAGAACATGATGGC-
65 TCCC-GACTGGTGACTAAGTATATGTCCTAATCAACTTAAACTCTTTCT-AAGAACATAATGGCA
2077 AGT-A
128 AGTAA
2081 CTGTT
1 CTGTT
2086 GTAATATCTG
Statistics
Matches: 233, Mismatches: 26, Indels: 37
0.79 0.09 0.12
Matches are distributed among these distances:
132 6 0.03
133 30 0.13
134 32 0.14
135 26 0.11
136 48 0.21
137 42 0.18
138 35 0.15
139 9 0.04
140 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (132 bp):
CTGTTCTGATTGTGACTTGTGGAGAAAGAAGAGGAAGGCTAAACGCTAAATCTAATATATAGTGT
CCCGACTGGTGACTAAGTATATGTCCTAATCAACTTAAACTCTTTCTAAGAACATAATGGCAAGT
AA
Found at i:8984 original size:13 final size:15
Alignment explanation
Indices: 8962--8999 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
8952 TACTTCATTC
*
8962 CTTTAATCAT-GTAA
1 CTTTAGTCATAGTAA
8976 -TTTAGTCATAGTAA
1 CTTTAGTCATAGTAA
8990 CTTTAGTCAT
1 CTTTAGTCAT
9000 TGCTTGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 8 0.38
14 4 0.19
15 9 0.43
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (15 bp):
CTTTAGTCATAGTAA
Found at i:24187 original size:70 final size:74
Alignment explanation
Indices: 24062--24204 Score: 190
Period size: 72 Copynumber: 2.0 Consensus size: 74
24052 GCTACCTACT
*
24062 ATTCATTGATCAGGTAGCCGGAGCTACCCATTTTTTATCTACAAAGGTAGCCGGAGCTA-CC-AC
1 ATTCACTGATCAGGTAGCCGGAGCTACCCATTTTTTATCTACAAAGGTAGCCGGAGCTACCCAAC
24125 TTTTCACTA
66 TTTTCACTA
* **
24134 ATTCACTGATCAAGGTAG-CGGAGC-A-CTATTTTATTATCTA-TTAGGTAGCCGGAGCTACCCA
1 ATTCACTGATC-AGGTAGCCGGAGCTACCCATTTT-TTATCTACAAAGGTAGCCGGAGCTACCCA
24195 ACTTTTCACT
64 ACTTTTCACT
24205 GATCAAGTAG
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
70 21 0.33
71 10 0.16
72 26 0.41
73 6 0.10
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (74 bp):
ATTCACTGATCAGGTAGCCGGAGCTACCCATTTTTTATCTACAAAGGTAGCCGGAGCTACCCAAC
TTTTCACTA
Found at i:25636 original size:41 final size:40
Alignment explanation
Indices: 25556--25642 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 40
25546 AGACCTTTAA
*
25556 CGGCGCTTATAAGGAAACGCCGCTATATGTTGAGAATTAG
1 CGGCGCTTATAAGGAAACGCCGCTATATGTTGACAATTAG
* * *
25596 TGGCGCTTATATGAGAAACGCCGCTATA-GCTTGACCATTAG
1 CGGCGCTTATAAG-GAAACGCCGCTATATG-TTGACAATTAG
25637 CGGCGC
1 CGGCGC
25643 CTTGGAGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
40 12 0.30
41 28 0.70
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
CGGCGCTTATAAGGAAACGCCGCTATATGTTGACAATTAG
Found at i:27186 original size:79 final size:78
Alignment explanation
Indices: 27103--27352 Score: 222
Period size: 79 Copynumber: 3.2 Consensus size: 78
27093 TGGATAGAGT
* * * * *
27103 ATTAGTGGCGTTTTGAAAAACGCCGCAACAGAAGTAAAGTGTACTGGAAGCGTTGTCGTTTTAGT
1 ATTAGTGGCGTTTTCAAAAACGCCGCAAAAGAAGTAAAGTTTACT-GAAACGTCGTCGTTTTAGT
27168 TGAATATATAGGGG
65 TGAATATATAGGGG
* * ** ** * *
27182 ATTAGTGGCGTTTTTATAGAAAACGCCACAAAAGACAGTTTAGTTTAAAGAAAACGGCGCCGTTT
1 ATTAGTGGCG-TTTT-CA-AAAACGCCGCAAAAGA-AGTAAAGTTTACTG-AAACGTCGTCGTTT
* *
27247 TAG-T--ATAT-GAGGGT
61 TAGTTGAATATATAGGGG
* * * *
27261 ATTAGTGGCGCTTTCAAAAACGCCGCAAAATAATTAAAGTTTACTGTACACGTCGTCGTTTTAGT
1 ATTAGTGGCGTTTTCAAAAACGCCGCAAAAGAAGTAAAGTTTACTG-AAACGTCGTCGTTTTAGT
27326 TGAATATATA-GGG
65 TGAATATATAGGGG
*
27339 ATTAGCGGCGTTTT
1 ATTAGTGGCGTTTT
27353 TTAAATAAAC
Statistics
Matches: 131, Mismatches: 31, Indels: 19
0.72 0.17 0.10
Matches are distributed among these distances:
75 23 0.18
76 15 0.11
77 1 0.01
78 21 0.16
79 25 0.19
80 8 0.06
81 1 0.01
82 16 0.12
83 21 0.16
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (78 bp):
ATTAGTGGCGTTTTCAAAAACGCCGCAAAAGAAGTAAAGTTTACTGAAACGTCGTCGTTTTAGTT
GAATATATAGGGG
Found at i:27263 original size:158 final size:156
Alignment explanation
Indices: 27023--27375 Score: 451
Period size: 158 Copynumber: 2.2 Consensus size: 156
27013 AAAATTAAGA
** *
27023 GATTAGTGGCGTTTTTTAAAAAAACACCGTAAAAAACAGTATAGTTGAAAGAAAACGGCGTCGTT
1 GATTAGTGGCGTTTTTTAAAAAAACACCACAAAAAACAGTATAGTTGAAAGAAAACGGCGCCGTT
* * *
27088 TTAGTTGGATAGAGTATTAGTGGCGTTTTGAAAAACGCCGCAACAGAAGTAAAGTGTACTGGA-A
66 TTAGTT-GATAGAGTATTAGTGGCGCTTTCAAAAACGCCGCAAAAGAAGTAAAGTGTACTGGACA
*
27152 GCGTTGTCGTTTTAGTTGAATATATAGGG
130 -CGTCGTCGTTTTAGTTGAATATATA-GG
* * * * *
27181 GATTAGTGGCG-TTTTTATAGAAAACGCCACAAAAGACAGTTTAGTTTAAAGAAAACGGCGCCGT
1 GATTAGTGGCGTTTTTTA-AAAAAACACCACAAAAAACAGTATAGTTGAAAGAAAACGGCGCCGT
* * * * *
27245 TTTAGTAT-ATGAGGGTATTAGTGGCGCTTTCAAAAACGCCGCAAAATAATTAAAGTTTACTGTA
65 TTTAGT-TGAT-AGAGTATTAGTGGCGCTTTCAAAAACGCCGCAAAAGAAGTAAAGTGTACTGGA
27309 CACGTCGTCGTTTTAGTTGAATATATAGG
128 CACGTCGTCGTTTTAGTTGAATATATAGG
* * *
27338 GATTAGCGGCGTTTTTTAAATAAACACCGCAAAAAACA
1 GATTAGTGGCGTTTTTTAAAAAAACACCACAAAAAACA
27376 TTTGTGCTTA
Statistics
Matches: 167, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
157 35 0.21
158 130 0.78
159 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (156 bp):
GATTAGTGGCGTTTTTTAAAAAAACACCACAAAAAACAGTATAGTTGAAAGAAAACGGCGCCGTT
TTAGTTGATAGAGTATTAGTGGCGCTTTCAAAAACGCCGCAAAAGAAGTAAAGTGTACTGGACAC
GTCGTCGTTTTAGTTGAATATATAGG
Found at i:29131 original size:8 final size:8
Alignment explanation
Indices: 29118--29175 Score: 66
Period size: 8 Copynumber: 7.4 Consensus size: 8
29108 TGATTATGAT
29118 AATAGTGG
1 AATAGTGG
29126 AATAGTGG
1 AATAGTGG
*
29134 AATAGTGT
1 AATAGTGG
29142 AAT--TGCG
1 AATAGTG-G
* *
29149 TATAGTGT
1 AATAGTGG
29157 AATAGTGG
1 AATAGTGG
29165 AATAGTGG
1 AATAGTGG
29173 AAT
1 AAT
29176 TTTTTGATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
6 2 0.05
7 2 0.05
8 35 0.85
9 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.31, T:0.31
Consensus pattern (8 bp):
AATAGTGG
Found at i:29733 original size:24 final size:23
Alignment explanation
Indices: 29706--29751 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
29696 AACATTATTG
*
29706 AAATATTCTCATCCGTTTTATCAC
1 AAATATTATCATCC-TTTTATCAC
* *
29730 AAATGTTATCATTCTTTTATCA
1 AAATATTATCATCCTTTTATCA
29752 TTTAAGTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (23 bp):
AAATATTATCATCCTTTTATCAC
Found at i:30004 original size:99 final size:99
Alignment explanation
Indices: 29833--30112 Score: 435
Period size: 99 Copynumber: 2.9 Consensus size: 99
29823 TGTTTACTTT
29833 AAATTAATAAATGCAAATTAAAAGAAAGACTTAACAAGTTGAATGTCATTAATTTAAATATTTTA
1 AAATTAATAAATGCAAATTAAAAGAAAGACTTAACAAGTTGAATGTCATTAATTTAAATATTTTA
*
29898 TTTTATTTTTATATTACCTAATTTTTAAATTAAC
66 TTTTATTTTTAAATTACCTAATTTTTAAATTAAC
29932 AAATTAATAAATGCAAATTAAAAGAAAGACTTAACAAGTTGAATGTCATTAATTTAAATATTTTA
1 AAATTAATAAATGCAAATTAAAAGAAAGACTTAACAAGTTGAATGTCATTAATTTAAATATTTTA
29997 TTTTATTTTTAAATTACCTAATTTTTAAATTAAC
66 TTTTATTTTTAAATTACCTAATTTTTAAATTAAC
* * * ** * *
30031 -AATTAATAAATACAAATTAAAAGAAAAACTTAACAATGTTTAAAAT-ATT--TTGTCAA-CTTT
1 AAATTAATAAATGCAAATTAAAAGAAAGACTTAACAA-GTTGAATGTCATTAATT-TAAATATTT
30091 TATTTTATTTTTAAATTACCTA
64 TATTTTATTTTTAAATTACCTA
30113 CTTAAATTAA
Statistics
Matches: 171, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
96 27 0.16
97 3 0.02
98 37 0.22
99 104 0.61
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (99 bp):
AAATTAATAAATGCAAATTAAAAGAAAGACTTAACAAGTTGAATGTCATTAATTTAAATATTTTA
TTTTATTTTTAAATTACCTAATTTTTAAATTAAC
Found at i:30034 original size:15 final size:16
Alignment explanation
Indices: 30001--30034 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29991 ATTTTATTTT
*
30001 ATTTTTAAATTACCTA
1 ATTTTTAAATTAACTA
30017 ATTTTTAAATTAAC-A
1 ATTTTTAAATTAACTA
30032 ATT
1 ATT
30035 AATAAATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTTAAATTAACTA
Found at i:30144 original size:5 final size:5
Alignment explanation
Indices: 30136--30160 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
30126 GTATTTAAAG
30136 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
30161 ATCACGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:30247 original size:91 final size:91
Alignment explanation
Indices: 30078--30523 Score: 655
Period size: 91 Copynumber: 4.8 Consensus size: 91
30068 GTTTAAAATA
* *
30078 TTTTGTCAACTTTTATTTTATTTTTAAATTACCTACTTAAATTAAATTGTATTTAAAGTTTTATT
1 TTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAG-----TT
30143 TTATTTTATTTTATTTTAATCACGAAAAAAC
61 TTATTTTATTTTATTTTAATCACGAAAAAAC
* * * *
30174 TTTTGTCAAATTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTTTATTTAAATTTTTATT
1 TTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATT
* *
30239 TTATTTTATTTTATTCTAATTAGGAAAAAAC
66 TTATTTTA---T-TT-TAATCACGAAAAAAC
30270 --TTGTCTACTTTTATTTTA-TTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATT
1 TTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATT
30332 TTATTTTATTTTAATCACGAAAAAAC
66 TTATTTTATTTTAATCACGAAAAAAC
* *
30358 ATTTTTTCTACTTTTATTTTATTTTTAAATTACCTAATTAAAGTAAATTGTATTTAAAGTTTTAT
1 -TTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTAT
*
30423 TTTATTTTATTTTAATCAGGAAAAAAC
65 TTTATTTTATTTTAATCACGAAAAAAC
* *
30450 TTTTGTCTACTTTTATTTTATTTTTAAATTACCTAAATAAATTAAATTTTATTTAAAGTTTTATT
1 TTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATT
30515 TTATTTTAT
66 TTATTTTAT
30524 ATTATTTTAT
Statistics
Matches: 322, Mismatches: 19, Indels: 23
0.88 0.05 0.06
Matches are distributed among these distances:
88 13 0.04
89 2 0.01
90 1 0.00
91 102 0.32
92 68 0.21
93 50 0.16
94 17 0.05
95 2 0.01
96 67 0.21
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (91 bp):
TTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATT
TTATTTTATTTTAATCACGAAAAAAC
Found at i:30516 original size:5 final size:5
Alignment explanation
Indices: 30508--30537 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
30498 TTATTTAAAG
*
30508 TTTTA TTTTA TTTTA TATTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
30538 ATCACGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:30722 original size:9 final size:9
Alignment explanation
Indices: 30710--30825 Score: 92
Period size: 9 Copynumber: 12.7 Consensus size: 9
30700 AAATATATAT
*
30710 CATATTTTA
1 CATAATTTA
30719 CATAATTTA
1 CATAATTTA
*
30728 CATAACTTA
1 CATAATTTA
30737 CATAA--TA
1 CATAATTTA
30744 CATAAATATATA
1 CAT-AAT-T-TA
*
30756 TCATATTTTA
1 -CATAATTTA
30766 CATAATTTA
1 CATAATTTA
**
30775 CATAATTCG
1 CATAATTTA
* *
30784 GATAACTTA
1 CATAATTTA
* *
30793 CTTAATTAA
1 CATAATTTA
30802 CATAATTTA
1 CATAATTTA
*
30811 CATAACTTA
1 CATAATTTA
30820 CATAAT
1 CATAAT
30826 ACACAAATAT
Statistics
Matches: 83, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
7 5 0.06
8 2 0.02
9 66 0.80
10 2 0.02
11 1 0.01
12 4 0.05
13 3 0.04
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.41
Consensus pattern (9 bp):
CATAATTTA
Found at i:30740 original size:27 final size:27
Alignment explanation
Indices: 30710--30825 Score: 110
Period size: 27 Copynumber: 4.2 Consensus size: 27
30700 AAATATATAT
*
30710 CATATTTTACATAATTTACATAACTTA
1 CATAATTTACATAATTTACATAACTTA
**
30737 CATAA--TACATAAATATATATCATATTTTA
1 CATAATTTACAT-AAT-T-TA-CATAACTTA
***
30766 CATAATTTACATAATTCGGATAACTTA
1 CATAATTTACATAATTTACATAACTTA
* *
30793 CTTAATTAACATAATTTACATAACTTA
1 CATAATTTACATAATTTACATAACTTA
30820 CATAAT
1 CATAAT
30826 ACACAAATAT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
25 5 0.07
26 3 0.04
27 38 0.55
28 2 0.03
29 13 0.19
30 3 0.04
31 5 0.07
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.41
Consensus pattern (27 bp):
CATAATTTACATAATTTACATAACTTA
Found at i:35034 original size:51 final size:52
Alignment explanation
Indices: 34952--35059 Score: 182
Period size: 51 Copynumber: 2.1 Consensus size: 52
34942 TGCCAATAGA
* * *
34952 CAGAACCCCACCTTCAACGCCGGCGTCTGGTTCACTGCCATCTCTTCTATCT
1 CAGAGCCCCACCTTCAACACCGCCGTCTGGTTCACTGCCATCTCTTCTATCT
35004 CAGAGCCCCACCTT-AACACCGCCGTCTGGTTCACTGCCATCTCTTCTATCT
1 CAGAGCCCCACCTTCAACACCGCCGTCTGGTTCACTGCCATCTCTTCTATCT
35055 CAGAG
1 CAGAG
35060 TCTAACTGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 40 0.75
52 13 0.25
ACGTcount: A:0.19, C:0.40, G:0.16, T:0.26
Consensus pattern (52 bp):
CAGAGCCCCACCTTCAACACCGCCGTCTGGTTCACTGCCATCTCTTCTATCT
Found at i:36168 original size:15 final size:13
Alignment explanation
Indices: 36132--36161 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
36122 ATAAAACATA
*
36132 AACCTTAACCCCC
1 AACCTTAAACCCC
36145 AACCTTAAACCCC
1 AACCTTAAACCCC
36158 AACC
1 AACC
36162 CCTTAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.50, G:0.00, T:0.13
Consensus pattern (13 bp):
AACCTTAAACCCC
Found at i:36309 original size:19 final size:18
Alignment explanation
Indices: 36285--36327 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
36275 CTATAATGAT
36285 AATTAATTCAATATTTTAA
1 AATTAATT-AATATTTTAA
36304 AATTAA-TAATATTTTAA
1 AATTAATTAATATTTTAA
36321 AATTAAT
1 AATTAAT
36328 ACTATATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 16 0.70
18 1 0.04
19 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTAATTAATATTTTAA
Found at i:36530 original size:40 final size:40
Alignment explanation
Indices: 36454--36597 Score: 152
Period size: 39 Copynumber: 3.6 Consensus size: 40
36444 TATTTGTGGT
* * * * *
36454 GTTTTTCAAAAAACGCCGCTAAAGATC-AGCATTAGCGGC
1 GTTTTTTAAAAAGCGCCGCTAAAGCTCGATCTTTAGCGGC
*
36493 GTTTTTTAAAAAGCGCCGCTAAAGGT-G-TACTTATAGCGGC
1 GTTTTTTAAAAAGCGCCGCTAAAGCTCGAT-CTT-TAGCGGC
* *
36533 GTTTCTTAAAAAAGCGCCGCTAATGCTCGATCTTTAGCGGC
1 GTTT-TTTAAAAAGCGCCGCTAAAGCTCGATCTTTAGCGGC
*
36574 G-TTTTTAAAAAGCGCCGCGAAAGC
1 GTTTTTTAAAAAGCGCCGCTAAAGC
36598 CACTAAAATC
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
39 43 0.49
40 13 0.15
41 27 0.31
42 4 0.05
43 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (40 bp):
GTTTTTTAAAAAGCGCCGCTAAAGCTCGATCTTTAGCGGC
Found at i:36764 original size:39 final size:40
Alignment explanation
Indices: 36686--36773 Score: 124
Period size: 39 Copynumber: 2.2 Consensus size: 40
36676 TACATATTGC
* *
36686 GGCGTTTTTACAAAAGCGCCGCTAATACTCAATCTTTAGT
1 GGCGTTTTTACAAAAGCGCCGCAAATACTCAATCCTTAGT
* **
36726 GGCGTTTTTA-AAAAGCGCCGCAAATGCTCGCTCCTTAGT
1 GGCGTTTTTACAAAAGCGCCGCAAATACTCAATCCTTAGT
36765 GGCGTTTTT
1 GGCGTTTTT
36774 CATTCAAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 33 0.77
40 10 0.23
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (40 bp):
GGCGTTTTTACAAAAGCGCCGCAAATACTCAATCCTTAGT
Found at i:41833 original size:450 final size:439
Alignment explanation
Indices: 40943--41869 Score: 1055
Period size: 450 Copynumber: 2.1 Consensus size: 439
40933 CAAAAAAAAA
* * *
40943 TTATTGAACCGAAATGGGTCGAGGATAAATCAGTTATTTTTGCGCTGATGCTGTTGCTTGAATGG
1 TTATTGAACCGAAATGGGTCGAGGATAAATCACTTATTGTTGCGCTGATGCTCTTGCTTGAATGG
*
41008 GAAGTAATCCTAGTTTGCTTTCAAATTTCAATTCTAGGAACTCAACTATGTTTGTCATTTTGATA
66 GAAGTAATCCTAGTTTGCTTTCAAACTTCAATTCTAGGAACTCAACTATGTTTGTCATTTTGATA
*
41073 TGCCAAACTTTATGGCTAGCTAAGTAAAAGCCGATAAAGCTAGAGCTCCTATGCATTGTACAATT
131 TGCCAAACTTTATGGCTAGCTAAGTAAAAGCCGATAAAGCTAGAGCTCCTACGCATTGT--AA--
* * *
41138 TTCTTTTTTCTTTTTTACTTATGAATGCATTTTCCTTTTTAGAAAAAAAAGTTTGTTTACATTAA
192 -TC--TTGTCTTTTTAACTTATGAATGCATGTTCCTTTTTAGAAAAAAAA--TTG-TTACATTAA
* * * * *
41203 TTATATAATGATAGAGAAAATATGGAGAAAAAATTAAAAATTTTATCATTAAGGGTATGCATGTA
251 TTATATAAT-ATAGACAAAATATAGAGAAAAAATTAAAAATTCTATCAATAAGGGTATCCATGTA
* *
41268 ATTTTATAGGTTCTGGACAAATTTTGGACATATAACTCTTATTTATAAAATGAATGATTATATTA
315 ATTTTATAGGTTCTGGACAAATGTTGGACATATAACTCTCATTTATAAAATGAATGATTATATTA
*
41333 TTATATATGTCATATTTTTTAGATTTTATTTTTTATGAAATTTAAATTTTTTTGTAATTT
380 TTATATATGTCATATTTTTTAAATTTTATTTTTTATGAAATTTAAATTTTTTTGTAATTT
* * *
41393 TTATTGAACCGAAATGGGTCGCGGGTAAATCACTTATTGTTGCGGTGATGCTCTTGCTTGAATGG
1 TTATTGAACCGAAATGGGTCGAGGATAAATCACTTATTGTTGCGCTGATGCTCTTGCTTGAATGG
**
41458 GAAGTAATCCTAGTTTGCTTTCAAACTTCAATTCTAGGGGCTCTGCTAATGACTATGTTTGTCAT
66 GAAGTAATCCTAGTTTGCTTTCAAACTTCAATTCTA--GGAACT-C--A--ACTATGTTTGTCAT
* * * * *
41523 TTTGATATGCCAAACTTTATGGCTAGCTATGTAAAAGCTGGTAAGGCTAG-GCCTCCTACGTATT
124 TTTGATATGCCAAACTTTATGGCTAGCTAAGTAAAAGCCGATAAAGCTAGAG-CTCCTACGCATT
* *
41587 GT-A-C-TGT-TTTTTAACTTATGAATGCATGTTCCTTTTTAGAAAAAGAAA-TG-TACGTTTA-
188 GTAATCTTGTCTTTTTAACTTATGAATGCATGTTCCTTTTTAGAAAAA-AAATTGTTACATTAAT
* *
41645 TAT-TAAT-T-G-CATAATGATAGAGAAAAAATTACAAATTCTATCAATAAGGGTATCCATGTAA
252 TATATAATATAGACAAAAT-ATAGAGAAAAAATTAAAAATTCTATCAATAAGGGTATCCATGTAA
** * * *
41706 TTTTATAGGTTCTGGACAAATGTTGGACATATAA-TACCTCCA-TTA-ATTATTATTTATT-TGA
316 TTTTATAGGTTCTGGACAAATGTTGGACATATAACT--CT-CATTTATAAAATGAATGATTAT-A
* * * * * * *
41767 GTT-TTCTGTTTCGTCTTATTTTTTAAATTTTATTTTTTATGAATTTTGAAGTTTTTTTTTAATT
377 -TTATTATATAT-GTCATATTTTTTAAATTTTATTTTTTATGAAATTT-AAATTTTTTTGTAA-T
41831 TT
438 TT
* *
41833 TTATTGAACCGAAATAGGTC-ACGAGT-AATCACTTATT
1 TTATTGAACCGAAATGGGTCGAGGA-TAAATCACTTATT
41870 TTTTTGCTGA
Statistics
Matches: 412, Mismatches: 46, Indels: 49
0.81 0.09 0.10
Matches are distributed among these distances:
436 6 0.01
437 88 0.21
438 40 0.10
439 25 0.06
440 27 0.07
441 3 0.01
442 6 0.01
444 2 0.00
446 35 0.08
447 5 0.01
450 95 0.23
452 4 0.01
453 1 0.00
454 1 0.00
455 1 0.00
456 1 0.00
457 72 0.17
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.42
Consensus pattern (439 bp):
TTATTGAACCGAAATGGGTCGAGGATAAATCACTTATTGTTGCGCTGATGCTCTTGCTTGAATGG
GAAGTAATCCTAGTTTGCTTTCAAACTTCAATTCTAGGAACTCAACTATGTTTGTCATTTTGATA
TGCCAAACTTTATGGCTAGCTAAGTAAAAGCCGATAAAGCTAGAGCTCCTACGCATTGTAATCTT
GTCTTTTTAACTTATGAATGCATGTTCCTTTTTAGAAAAAAAATTGTTACATTAATTATATAATA
TAGACAAAATATAGAGAAAAAATTAAAAATTCTATCAATAAGGGTATCCATGTAATTTTATAGGT
TCTGGACAAATGTTGGACATATAACTCTCATTTATAAAATGAATGATTATATTATTATATATGTC
ATATTTTTTAAATTTTATTTTTTATGAAATTTAAATTTTTTTGTAATTT
Found at i:43983 original size:43 final size:43
Alignment explanation
Indices: 43921--44004 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
43911 CGAACCATAA
* *
43921 AAATTAATAGAACATAGATCATACCTGCATAAATCACATACGT
1 AAATTAATAGAACACAGATCATACCTACATAAATCACATACGT
*
43964 AAATTAATAGAACACAGATCATACCTACATAAATTACATAC
1 AAATTAATAGAACACAGATCATACCTACATAAATCACATAC
44005 CTTAAACACG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.25
Consensus pattern (43 bp):
AAATTAATAGAACACAGATCATACCTACATAAATCACATACGT
Found at i:46871 original size:39 final size:39
Alignment explanation
Indices: 46810--46977 Score: 273
Period size: 39 Copynumber: 4.3 Consensus size: 39
46800 GCTCTGATGA
* * *
46810 GCTTCAGTTAGCCTTCGGGCTTCCGATTAGCACTTATGT
1 GCTTCAATTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
*
46849 GCTTTAATTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAATTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
* *
46888 GCTTCAGTTAACCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAATTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
46927 GCTTCAATTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAATTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
*
46966 GCTTCAGTTAGC
1 GCTTCAATTAGC
46978 ACAAATTTCG
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 119 1.00
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.36
Consensus pattern (39 bp):
GCTTCAATTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
Found at i:48380 original size:32 final size:32
Alignment explanation
Indices: 48336--48463 Score: 159
Period size: 32 Copynumber: 3.8 Consensus size: 32
48326 TTGATCAGTG
* *
48336 AAAAGTGGTAGCTCCGGCTACCTAATAGATAA
1 AAAAATGGTAGCTCCGGCTACCTGATAGATAA
*
48368 AAAAATAGTAGCTCCGGCTACCTGATCAG-TGAA
1 AAAAATGGTAGCTCCGGCTACCTGAT-AGAT-AA
48401 TAGTGAAAAGTGGTAGCTCCGGCTACCTGATAGATAA
1 -A---AAAA-TGGTAGCTCCGGCTACCTGATAGATAA
48438 AAAAATGGTAGCTCCGGCTACCTGAT
1 AAAAATGGTAGCTCCGGCTACCTGAT
48464 CAATGAATAG
Statistics
Matches: 84, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
32 45 0.54
33 8 0.10
34 1 0.01
36 1 0.01
37 8 0.10
38 21 0.25
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (32 bp):
AAAAATGGTAGCTCCGGCTACCTGATAGATAA
Found at i:48417 original size:38 final size:37
Alignment explanation
Indices: 48332--48475 Score: 141
Period size: 32 Copynumber: 4.1 Consensus size: 37
48322 CTACTTGATC
*
48332 AGTGAAAAGTGGTAGCTCCGGCTACCTAAT-AGAT-AA-
1 AGTGAAAA-TGGTAGCTCCGGCTACCTGATCAG-TGAAT
*
48368 A---AAAATAGTAGCTCCGGCTACCTGATCAGTGAAT
1 AGTGAAAATGGTAGCTCCGGCTACCTGATCAGTGAAT
48402 AGTGAAAAGTGGTAGCTCCGGCTACCTGAT-AGAT-AA-
1 AGTGAAAA-TGGTAGCTCCGGCTACCTGATCAG-TGAAT
*
48438 A---AAAATGGTAGCTCCGGCTACCTGATCAATGAAT
1 AGTGAAAATGGTAGCTCCGGCTACCTGATCAGTGAAT
48472 AGTG
1 AGTG
48476 GTAGCTTCGG
Statistics
Matches: 90, Mismatches: 4, Indels: 27
0.74 0.03 0.22
Matches are distributed among these distances:
32 42 0.47
33 15 0.17
34 2 0.02
36 2 0.02
37 8 0.09
38 21 0.23
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (37 bp):
AGTGAAAATGGTAGCTCCGGCTACCTGATCAGTGAAT
Found at i:48449 original size:70 final size:70
Alignment explanation
Indices: 48332--48475 Score: 261
Period size: 70 Copynumber: 2.1 Consensus size: 70
48322 CTACTTGATC
*
48332 AGTGAAAAGTGGTAGCTCCGGCTACCTAATAGATAAAAAAATAGTAGCTCCGGCTACCTGATCAG
1 AGTGAAAAGTGGTAGCTCCGGCTACCTAATAGATAAAAAAATAGTAGCTCCGGCTACCTGATCAA
48397 TGAAT
66 TGAAT
* *
48402 AGTGAAAAGTGGTAGCTCCGGCTACCTGATAGATAAAAAAATGGTAGCTCCGGCTACCTGATCAA
1 AGTGAAAAGTGGTAGCTCCGGCTACCTAATAGATAAAAAAATAGTAGCTCCGGCTACCTGATCAA
48467 TGAAT
66 TGAAT
48472 AGTG
1 AGTG
48476 GTAGCTTCGG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (70 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTAATAGATAAAAAAATAGTAGCTCCGGCTACCTGATCAA
TGAAT
Found at i:51895 original size:39 final size:39
Alignment explanation
Indices: 51834--52001 Score: 291
Period size: 39 Copynumber: 4.3 Consensus size: 39
51824 GCTCTGATGA
*
51834 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
* * *
51873 GCTTTAATTAGCCTCCGGGCTTCCGGTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
*
51912 GCTTCAGTTAACCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
51951 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
51990 GCTTCAGTTAGC
1 GCTTCAGTTAGC
52002 ACAGATTTCG
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 120 1.00
ACGTcount: A:0.14, C:0.27, G:0.23, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
Found at i:52429 original size:24 final size:24
Alignment explanation
Indices: 52402--52453 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52392 TTAGTAAGTC
*
52402 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
52426 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
52450 AAAT
1 AAAT
52454 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Done.