Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold643
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: 40929
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1181 original size:9 final size:9
Alignment explanation
Indices: 1155--1192 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1145 TTTTTTCTCC
1155 AAAACCCTA
1 AAAACCCTA
**
1164 AAAGTCCTA
1 AAAACCCTA
1173 AAAACCCT-
1 AAAACCCTA
1181 AAAACCCTA
1 AAAACCCTA
1190 AAA
1 AAA
1193 CTTAAAATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.55, C:0.29, G:0.03, T:0.13
Consensus pattern (9 bp):
AAAACCCTA
Found at i:1184 original size:8 final size:8
Alignment explanation
Indices: 1155--1193 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
1145 TTTTTTCTCC
1155 AAAACCCT
1 AAAACCCT
*
1163 AAAAGTCCT
1 AAAA-CCCT
1172 AAAAACCCT
1 -AAAACCCT
1181 AAAACCCT
1 AAAACCCT
1189 AAAAC
1 AAAAC
1194 TTAAAATCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 17 0.63
9 6 0.22
10 4 0.15
ACGTcount: A:0.54, C:0.31, G:0.03, T:0.13
Consensus pattern (8 bp):
AAAACCCT
Found at i:4752 original size:48 final size:48
Alignment explanation
Indices: 4699--4858 Score: 194
Period size: 48 Copynumber: 3.3 Consensus size: 48
4689 AACCAAAAAT
*
4699 TCAAGACCAACTAGAGGAGGATGAACCCAAGGGAACCAAACAACTGAA
1 TCAAGACCAACTAGAGGAAGATGAACCCAAGGGAACCAAACAACTGAA
* * * * *
4747 CCAAGACCAACTAGAGGAAGATGAATCGAAGGGGACCAAACAACTAAA
1 TCAAGACCAACTAGAGGAAGATGAACCCAAGGGAACCAAACAACTGAA
* * * * * *
4795 TCAAGATCAACTAGAGCAAGATGAACACAAGGGAAACAAACTACAGAA
1 TCAAGACCAACTAGAGGAAGATGAACCCAAGGGAACCAAACAACTGAA
* *
4843 TCATGACCAACAAGAG
1 TCAAGACCAACTAGAG
4859 TCGCAGGTGC
Statistics
Matches: 92, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 92 1.00
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.09
Consensus pattern (48 bp):
TCAAGACCAACTAGAGGAAGATGAACCCAAGGGAACCAAACAACTGAA
Found at i:7534 original size:21 final size:21
Alignment explanation
Indices: 7495--7534 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
7485 ATGGAAATAT
*
7495 AATTTATAATTATAGTTTTCA
1 AATTTATAATTATAATTTTCA
7516 AATTTATTAATT-TAATTTT
1 AATTTA-TAATTATAATTTT
7535 TTTGGTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
AATTTATAATTATAATTTTCA
Found at i:8041 original size:30 final size:28
Alignment explanation
Indices: 8022--8080 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 28
8012 ATATTTATAT
8022 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATATTTAATAATTTTA
* *
8050 TATATT-TTTT--TATTGAATATTTTTA
1 TATATTATTTTAATATTTAATAATTTTA
8075 TATATT
1 TATATT
8081 CATCTTAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 19 0.66
27 4 0.14
28 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
TATATTATTTTAATATTTAATAATTTTA
Found at i:8629 original size:51 final size:51
Alignment explanation
Indices: 8573--8675 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
8563 CAATGGAAAG
8573 TAAAAATTCAACAAGTATAATTATTTATTTTTAAAATTTTAAAATTATTTT
1 TAAAAATTCAACAAGTATAATTATTTATTTTTAAAATTTTAAAATTATTTT
8624 TAAAAATTCAACAAGTATAATTATTTATTTTTAAAATTTTAAAATTATTTT
1 TAAAAATTCAACAAGTATAATTATTTATTTTTAAAATTTTAAAATTATTTT
8675 T
1 T
8676 TAGATTTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (51 bp):
TAAAAATTCAACAAGTATAATTATTTATTTTTAAAATTTTAAAATTATTTT
Found at i:8673 original size:24 final size:24
Alignment explanation
Indices: 8591--8673 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 24
8581 CAACAAGTAT
8591 AATTATTTATTTTTAAAATTTTAA
1 AATTATTTATTTTTAAAATTTTAA
* * *
8615 AATTA--T-TTTTAAAAATTCAACAAGTAT
1 AATTATTTATTTTTAAAATT------TTAA
8642 AATTATTTATTTTTAAAATTTTAA
1 AATTATTTATTTTTAAAATTTTAA
8666 AATTATTT
1 AATTATTT
8674 TTTAGATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
21 10 0.23
22 1 0.02
24 15 0.34
27 7 0.16
29 1 0.02
30 10 0.23
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (24 bp):
AATTATTTATTTTTAAAATTTTAA
Found at i:9971 original size:43 final size:45
Alignment explanation
Indices: 9919--10020 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
9909 AAAATGAATA
* * *
9919 AAATTATAAGAAT-GTAAAAAGATATATGTATGTACATATATAT-
1 AAATTATAAGAATAATAAAAAGATATAAGCATGTACATATATATG
* *
9962 AAATTATAAGATATAATAAAAATATATAAGCATGTATATATATATG
1 AAATTATAAGA-ATAATAAAAAGATATAAGCATGTACATATATATG
*
10008 AAAAT-TAAGAATA
1 AAATTATAAGAATA
10021 TGTATATAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 11 0.22
44 5 0.10
45 30 0.60
46 4 0.08
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (45 bp):
AAATTATAAGAATAATAAAAAGATATAAGCATGTACATATATATG
Found at i:10097 original size:47 final size:46
Alignment explanation
Indices: 9959--10113 Score: 107
Period size: 47 Copynumber: 3.3 Consensus size: 46
9949 TGTACATATA
* ** *
9959 TATAAATTATAAGATATAATAAAAATATATAAGCATGTATATATATAT
1 TATAAATTATAAAATATAA-AAAAATATATAAAAATGTATATATGT-T
* * * * * * * * *
10007 GA-AAATTA-AGAATATGTATATAGATATATATATATATAGATATGTT
1 TATAAATTATA-AA-ATATAAAAAAATATATAAAAATGTATATATGTT
*
10053 TATAAATTATAAAATATAAAAAATATATATAAAAATGTATATATGTA
1 TATAAATTATAAAATATAAAAAA-ATATATAAAAATGTATATATGTT
* *
10100 TACAAGTTATAAAA
1 TATAAATTATAAAA
10114 AATATGTACG
Statistics
Matches: 78, Mismatches: 24, Indels: 11
0.69 0.21 0.10
Matches are distributed among these distances:
46 9 0.12
47 63 0.81
48 6 0.08
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (46 bp):
TATAAATTATAAAATATAAAAAAATATATAAAAATGTATATATGTT
Found at i:11730 original size:31 final size:28
Alignment explanation
Indices: 11664--11731 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
11654 ATATAAAAAT
**
11664 ATAAATTAATTATAAAGTATATTATTAA
1 ATAAATTAATTATAAAGTATATTAAGAA
* *
11692 ATTAATTACATTATAAATATTATATTAAGAA
1 ATAAATTA-ATTAT-AA-AGTATATTAAGAA
11723 ATAAATTAA
1 ATAAATTAA
11732 ATAAAGACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 5 0.16
30 3 0.09
31 17 0.53
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
ATAAATTAATTATAAAGTATATTAAGAA
Found at i:11894 original size:20 final size:19
Alignment explanation
Indices: 11862--11900 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
11852 TAAATAAAAG
*
11862 GAAATAAAAAGAAAAGAAA
1 GAAACAAAAAGAAAAGAAA
11881 GAAACAAAACAGAAAAGAAA
1 GAAACAAAA-AGAAAAGAAA
11901 CAGAATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (19 bp):
GAAACAAAAAGAAAAGAAA
Found at i:12626 original size:18 final size:18
Alignment explanation
Indices: 12603--12645 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12593 ATGTGAGGTA
12603 AGTATTAATATTAGTATT
1 AGTATTAATATTAGTATT
*
12621 AGTATTATTATTAGTATT
1 AGTATTAATATTAGTATT
*
12639 ATTATTA
1 AGTATTA
12646 TTATGAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
AGTATTAATATTAGTATT
Found at i:12631 original size:3 final size:3
Alignment explanation
Indices: 12605--12649 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
12595 GTGAGGTAAG
* * * *
12605 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12650 GAGTGGGAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:12844 original size:24 final size:24
Alignment explanation
Indices: 12790--12860 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
12780 TGTGTGAAGT
*
12790 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
12813 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
*
12838 TGTGAAAATTGTAATTGAATTGA
1 TGTGAAAAATG--ATTGAATTGA
12861 GAATATATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 9 0.23
24 15 0.38
25 5 0.13
26 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.34
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:13063 original size:37 final size:39
Alignment explanation
Indices: 13004--13099 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
12994 CGGATAGATT
* * * *
13004 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
13041 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
13080 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
13100 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:19121 original size:28 final size:29
Alignment explanation
Indices: 19090--19167 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 29
19080 TATTATTATT
*
19090 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
19118 TATATTATTAAATTAATTACATTATAAA-
1 TATATAAATAAATAAATTACATTATAAAG
*
19146 TATTATATTAAGAAATAAATTA
1 TA-TATA--AATAAATAAATTA
19168 AATAAAGACA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
28 17 0.45
29 11 0.29
31 10 0.26
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:19167 original size:31 final size:28
Alignment explanation
Indices: 19101--19168 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
19091 ATATAAATAT
**
19101 ATAAATTAATTATAAAGTATATTATTAA
1 ATAAATTAATTATAAAGTATATTAAGAA
* *
19129 ATTAATTACATTATAAATATTATATTAAGAA
1 ATAAATTA-ATTAT-AA-AGTATATTAAGAA
19160 ATAAATTAA
1 ATAAATTAA
19169 ATAAAGACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 5 0.16
30 3 0.09
31 17 0.53
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
ATAAATTAATTATAAAGTATATTAAGAA
Found at i:20065 original size:18 final size:18
Alignment explanation
Indices: 20042--20090 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
20032 ATGTGAGGTA
*
20042 AGTATTAATATTAGTATT
1 AGTATTATTATTAGTATT
20060 AGTATTATTATTAGTATT
1 AGTATTATTATTAGTATT
*
20078 ATTATTATTATTA
1 AGTATTATTATTA
20091 TGAGTGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (18 bp):
AGTATTATTATTAGTATT
Found at i:20070 original size:3 final size:3
Alignment explanation
Indices: 20044--20091 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
20034 GTGAGGTAAG
* * * *
20044 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20092 GAGTGGGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:20091 original size:12 final size:12
Alignment explanation
Indices: 20044--20091 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
20034 GTGAGGTAAG
* *
20044 TATTAATATTAG
1 TATTAGTATTAT
20056 TATTAGTATTAT
1 TATTAGTATTAT
20068 TATTAGTATTAT
1 TATTAGTATTAT
*
20080 TATTATTATTAT
1 TATTAGTATTAT
20092 GAGTGGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:20286 original size:24 final size:24
Alignment explanation
Indices: 20232--20303 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
20222 TGTGTGAAGT
*
20232 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
20255 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
20280 TGTGAAAAATTGTAATTGAATTGA
1 TGTGAAAAA-TG--ATTGAATTGA
20304 GAATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.22
24 14 0.35
25 7 0.17
27 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:20700 original size:12 final size:12
Alignment explanation
Indices: 20665--20704 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
20655 ATGAAAAAGT
*
20665 TGAATTGTGAAT
1 TGAATTGTGAAA
*
20677 TGAAATGTGAAA
1 TGAATTGTGAAA
*
20689 TGAATTGAGAAA
1 TGAATTGTGAAA
20701 TGAA
1 TGAA
20705 CCTAAGGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (12 bp):
TGAATTGTGAAA
Found at i:25379 original size:44 final size:44
Alignment explanation
Indices: 25153--25380 Score: 357
Period size: 44 Copynumber: 5.2 Consensus size: 44
25143 AACACCGATA
* * * *
25153 TGTTATTTTCGATCTACTCTCCTCCACTACAGAGACGCCAAATC
1 TGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC
* * *
25197 TGTCATCTTCGATCTGTTCTCCGCCACTACAGAGACGCCAAATC
1 TGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC
* *
25241 TGTCATCTTCGATCTGCTCTCCGCTGCTACAGAGACGCCAAATC
1 TGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC
25285 TGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC
1 TGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC
*
25329 TGTTATCTTCGATCTACTCTCCGCCGCTACAGAGACGCCAAATC
1 TGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC
*
25373 TATTATCT
1 TGTTATCT
25381 GCTTAAATGA
Statistics
Matches: 172, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 172 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.29
Consensus pattern (44 bp):
TGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC
Found at i:29427 original size:19 final size:19
Alignment explanation
Indices: 29398--29445 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
29388 GGGAAAATCT
29398 AATGCAAATGATGCAATGC
1 AATGCAAATGATGCAATGC
* *
29417 AGTGCACATGATGCAATGC
1 AATGCAAATGATGCAATGC
29436 AATGCAAATG
1 AATGCAAATG
29446 CATGGGATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (19 bp):
AATGCAAATGATGCAATGC
Found at i:31040 original size:46 final size:46
Alignment explanation
Indices: 30980--31299 Score: 444
Period size: 46 Copynumber: 7.0 Consensus size: 46
30970 TTTGACATGA
* * * * * *
30980 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
31026 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*** *** *
31072 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
31118 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
31164 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
31210 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
31256 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
31300 AGAGCACACT
Statistics
Matches: 251, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 247 0.98
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:33024 original size:10 final size:11
Alignment explanation
Indices: 32998--33030 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
32988 TTCTGCACCA
32998 TTTCTCTTCAC
1 TTTCTCTTCAC
*
33009 TTTCTCTT-AT
1 TTTCTCTTCAC
33019 TTTCTCTTCAC
1 TTTCTCTTCAC
33030 T
1 T
33031 AACATATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTCTCTTCAC
Found at i:33463 original size:18 final size:20
Alignment explanation
Indices: 33448--33484 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33438 TAATAATAAA
*
33448 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
33468 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
33485 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Done.