Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2624
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: 22500
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:756 original size:91 final size:91
Alignment explanation
Indices: 618--825 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
608 TTGATTTTAG
* *
618 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
683 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
710 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
775 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
801 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
826 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:794 original size:26 final size:28
Alignment explanation
Indices: 740--800 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
730 TATTATCAAG
* *
740 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
768 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
794 AATTATA
1 AATTATA
801 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:800 original size:44 final size:43
Alignment explanation
Indices: 658--800 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
648 GAATTTTATG
* *
658 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
702 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
749 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
793 AAATTATA
1 AAATTATA
801 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:918 original size:59 final size:57
Alignment explanation
Indices: 852--1040 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
842 ATTTTATTAA
852 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
911 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
972 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
1031 ATCATATATT
1 ATCATATATT
1041 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:949 original size:66 final size:64
Alignment explanation
Indices: 879--1077 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
869 AAATATATTT
879 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
944 G
64 G
* * * * * **
945 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
999 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1064 G
64 G
*
1065 AATATTGATTATT
1 AATATTAATTATT
1078 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:965 original size:120 final size:120
Alignment explanation
Indices: 841--1138 Score: 517
Period size: 120 Copynumber: 2.5 Consensus size: 120
831 AATTATTTTA
* * *
841 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
905 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
961 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
1026 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
1081 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
1139 ATGATTAAAT
Statistics
Matches: 168, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
120 161 0.96
121 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:981 original size:61 final size:61
Alignment explanation
Indices: 914--1101 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
904 TTATAGTATC
914 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
975 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
1033 C
61 T
*
1034 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1095 ATATATT
1 ATATATT
1102 TTAATTAAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.17
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:1001 original size:15 final size:15
Alignment explanation
Indices: 966--1017 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
956 TTAAGAATTT
*
966 TATTAAATTAT-ATA
1 TATTTAATTATAATA
980 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
994 TATTTAATAATAAT-
1 TATTTAATTATAATA
1008 TATGTTAATT
1 TAT-TTAATT
1018 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:1110 original size:18 final size:17
Alignment explanation
Indices: 1082--1116 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1072 ATTATTAAGA
*
1082 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1099 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1117 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1401 original size:16 final size:16
Alignment explanation
Indices: 1352--1403 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
1342 GATTTGCTAT
* * *
1352 TACACATCTATTCCAT
1 TACACCTCTAATCCAA
1368 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
1384 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
1400 TACA
1 TACA
1404 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12789 original size:22 final size:22
Alignment explanation
Indices: 12755--12816 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
12745 GGCTCGGCCC
12755 ATTTTTAATTAAAATTAAAATTA
1 ATTTTTAA-TAAAATTAAAATTA
*
12778 TTTTTTAATAAAATTAAAATTA
1 ATTTTTAATAAAATTAAAATTA
* *
12800 ATTGTTATTAAAATTAA
1 ATTTTTAATAAAATTAA
12817 TTGTTAGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 28 0.80
23 7 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTTTAATAAAATTAAAATTA
Found at i:12809 original size:16 final size:16
Alignment explanation
Indices: 12790--12831 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
12780 TTTTAATAAA
12790 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
12806 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
12822 AGTAAAATTA
1 ATTAAAATTA
12832 TCAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:12933 original size:68 final size:69
Alignment explanation
Indices: 12820--13030 Score: 360
Period size: 68 Copynumber: 3.1 Consensus size: 69
12810 AAATTAATTG
12820 TTAGTAAAA-TTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACAT
1 TTAGTAAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
12882 TTGA
66 TTGA
12886 TTAG-AAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
1 TTAGTAAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
12950 TTGA
66 TTGA
* *
12954 TTAGT-AAATTTGTCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACAT
1 TTAGTAAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
*
13018 TTAA
66 TTGA
13022 TTAGTAAAA
1 TTAGTAAAA
13031 CAAACTTGAT
Statistics
Matches: 137, Mismatches: 3, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
65 4 0.03
66 22 0.16
68 108 0.79
69 3 0.02
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (69 bp):
TTAGTAAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
TTGA
Found at i:12937 original size:9 final size:9
Alignment explanation
Indices: 12904--12931 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12894 TTTATCAAAT
12904 TATTAATTG
1 TATTAATTG
12913 TATTAATTG
1 TATTAATTG
12922 TATTAATTG
1 TATTAATTG
12931 T
1 T
12932 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:12984 original size:9 final size:9
Alignment explanation
Indices: 12972--12999 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12962 TTTGTCAAAT
12972 TATTAATTG
1 TATTAATTG
12981 TATTAATTG
1 TATTAATTG
12990 TATTAATTG
1 TATTAATTG
12999 T
1 T
13000 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:13136 original size:22 final size:24
Alignment explanation
Indices: 13096--13139 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
13086 AAATAAACTT
13096 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
13120 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
13140 AATATTTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:13878 original size:3 final size:3
Alignment explanation
Indices: 13870--13909 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
13860 AACCATATAA
13870 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
13910 CAAAAGCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:14442 original size:10 final size:11
Alignment explanation
Indices: 14419--14448 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
14409 TCAGTGATCA
*
14419 TTTTATAACTT
1 TTTTAAAACTT
14430 TTTTAAAACTT
1 TTTTAAAACTT
14441 TTTTAAAA
1 TTTTAAAA
14449 TTGAGTGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAACTT
Found at i:15609 original size:121 final size:116
Alignment explanation
Indices: 15482--15719 Score: 386
Period size: 121 Copynumber: 2.0 Consensus size: 116
15472 CAATTGCATC
* * *
15482 TAAAAAAATCAAGAATTTTGCGGCTAAAATTTTCACATTCAATCTCATCAAAAACCAGTCTTTTA
1 TAAAAAAACCAAGAATTTTACGGCTAAAATTTTCACATTCAATCTCATCAAAAACCAATCTTTTA
15547 ACTTTCACAAAAAAAAAAATATATATATATATCCATTCACTTTTATCTTACTCGTT
66 ACTTTCAC-AAAAAAAAAA-A-ATA-A-ATATCCATTCACTTTTATCTTACTCGTT
*
15603 TAAAAAAACCAAGAATTTTACGGCTAAAATTTTCACATTCAATCTCATCAAAAATCAATCTTTTA
1 TAAAAAAACCAAGAATTTTACGGCTAAAATTTTCACATTCAATCTCATCAAAAACCAATCTTTTA
*
15668 ACTTTCACAAAAAAATAAAATAAATATCCATTCACTTTTATCTTACTCGTT
66 ACTTTCACAAAAAAAAAAAATAAATATCCATTCACTTTTATCTTACTCGTT
15719 T
1 T
15720 TTCATTGTTT
Statistics
Matches: 112, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
116 29 0.26
117 1 0.01
118 3 0.03
119 1 0.01
120 9 0.08
121 69 0.62
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.35
Consensus pattern (116 bp):
TAAAAAAACCAAGAATTTTACGGCTAAAATTTTCACATTCAATCTCATCAAAAACCAATCTTTTA
ACTTTCACAAAAAAAAAAAATAAATATCCATTCACTTTTATCTTACTCGTT
Found at i:20273 original size:17 final size:17
Alignment explanation
Indices: 20232--20275 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
20222 AAACTCTTTT
20232 ATTTTTATTTGTTTTTAA
1 ATTTTTATTTG-TTTTAA
20250 ATTTTTATTTG-TTTAA
1 ATTTTTATTTGTTTTAA
20266 ATTATTTATT
1 ATT-TTTATT
20276 GTAAACTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 11 0.44
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
ATTTTTATTTGTTTTAA
Found at i:20277 original size:16 final size:16
Alignment explanation
Indices: 20236--20277 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
20226 TCTTTTATTT
*
20236 TTATTTGTT-TTTAAA
1 TTATTTATTGTTTAAA
20251 TT-TTTATTTGTTTAAA
1 TTATTTA-TTGTTTAAA
20267 TTATTTATTGT
1 TTATTTATTGT
20278 AAACTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 3 0.13
15 4 0.17
16 12 0.52
17 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (16 bp):
TTATTTATTGTTTAAA
Found at i:21232 original size:17 final size:17
Alignment explanation
Indices: 21212--21366 Score: 100
Period size: 17 Copynumber: 8.8 Consensus size: 17
21202 CTTAAAAAAA
21212 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
*
21229 TCGTGTTTTCAAAATTTT
1 TCGTG-TTTCAAAAATTT
*** *
21247 TCGTGTCAAAAAAATTC
1 TCGTGTTTCAAAAATTT
* * *
21264 TCATGTATCGAAAA-TT
1 TCGTGTTTCAAAAATTT
*
21280 TCGGTGTTTTCAAAAAAATT
1 TC-GTG-TTTC-AAAAATTT
* *
21300 CCGTGTTTCAAAAATCT
1 TCGTGTTTCAAAAATTT
21317 TCGTGTTTTCAAAAATTATT
1 TCGTG-TTTCAAAAA-T-TT
* *
21337 ATTGTGTTTC-AAAATTC
1 -TCGTGTTTCAAAAATTT
21354 TCGTGTTT-AAAAA
1 TCGTGTTTCAAAAA
21367 CAAAAAAAGT
Statistics
Matches: 105, Mismatches: 23, Indels: 21
0.70 0.15 0.14
Matches are distributed among these distances:
16 14 0.13
17 34 0.32
18 33 0.31
19 12 0.11
20 8 0.08
21 4 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:21240 original size:18 final size:18
Alignment explanation
Indices: 21212--21361 Score: 96
Period size: 18 Copynumber: 8.4 Consensus size: 18
21202 CTTAAAAAAA
21212 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
21229 TCGTGTTTTCAAAATTTT
1 TCGTGTTTTCAAAAATTT
*** *
21247 TCGTG-TCAAAAAAATTC
1 TCGTGTTTTCAAAAATTT
* * *
21264 TCATG-TATCGAAAA-TT
1 TCGTGTTTTCAAAAATTT
*
21280 TCGGTGTTTTCAAAAAAATT
1 TC-GTGTTTTC-AAAAATTT
* *
21300 CCGTG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
21317 TCGTGTTTTCAAAAATTAT
1 TCGTGTTTTCAAAAATT-T
** *
21336 TATTGTGTTTC-AAAATTC
1 TCGTGT-TTTCAAAAATTT
21354 TCGTGTTT
1 TCGTGTTT
21362 AAAAACAAAA
Statistics
Matches: 100, Mismatches: 25, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
16 3 0.03
17 35 0.35
18 37 0.37
19 18 0.18
20 7 0.07
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:21251 original size:35 final size:33
Alignment explanation
Indices: 21212--21366 Score: 98
Period size: 35 Copynumber: 4.4 Consensus size: 33
21202 CTTAAAAAAA
21212 TCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTT
1 TCGTGTTTCAAAAATTTTCGTG-TTTCAAAA-TTT
*** * * *
21247 TCGTGTCAAAAAAATTCTCATGTATCGAAAA-TT
1 TCGTGTTTCAAAAATTTTCGTGTTTC-AAAATTT
* * *
21280 TCGGTGTTTTCAAAAAAATTCCGTGTTTCAAAAATCT
1 TC-GTG-TTTC-AAAAATTTTCGTGTTTC-AAAATTT
* *
21317 TCGTGTTTTCAAAAATTATTATTGTGTTTCAAAATTC
1 TCGTG-TTTCAAAAA-T-TT-TCGTGTTTCAAAATTT
21354 TCGTGTTT-AAAAA
1 TCGTGTTTCAAAAA
21367 CAAAAAAAGT
Statistics
Matches: 91, Mismatches: 21, Indels: 16
0.71 0.16 0.12
Matches are distributed among these distances:
33 4 0.04
34 6 0.07
35 32 0.35
36 27 0.30
37 15 0.16
38 7 0.08
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (33 bp):
TCGTGTTTCAAAAATTTTCGTGTTTCAAAATTT
Found at i:21314 original size:36 final size:37
Alignment explanation
Indices: 21252--21331 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 37
21242 ATTTTTCGTG
*
21252 TCAAAAAAATTCTCATGTATCGAAAAT-TTCGGTGTTT
1 TCAAAAAAATTCTCATGTATCAAAAATCTTC-GTGTTT
* *
21289 TCAAAAAAATTC-CGTGTTTCAAAAATCTTCGTGTTT
1 TCAAAAAAATTCTCATGTATCAAAAATCTTCGTGTTT
21325 TCAAAAA
1 TCAAAAA
21332 TTATTATTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
36 24 0.62
37 15 0.38
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (37 bp):
TCAAAAAAATTCTCATGTATCAAAAATCTTCGTGTTT
Done.