Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1790
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: 32933
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Found at i:113 original size:21 final size:20
Alignment explanation
Indices: 84--126 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
74 GACTAGTGTG
* *
84 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
105 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
125 GG
1 GG
127 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:575 original size:13 final size:13
Alignment explanation
Indices: 557--594 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
547 ATAATCCCCC
557 TGTATCGATACAG
1 TGTATCGATACAG
*
570 TGTATCGATACAT
1 TGTATCGATACAG
583 TGTATCGATACA
1 TGTATCGATACA
595 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2675 original size:15 final size:15
Alignment explanation
Indices: 2655--2685 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2645 ATTTCGTTTG
*
2655 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2670 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2685 G
1 G
2686 GATATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4514 original size:21 final size:21
Alignment explanation
Indices: 4485--4529 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4475 AAGTTTTTAT
*
4485 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
4505 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
4527 TTT
1 TTT
4530 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:6749 original size:13 final size:13
Alignment explanation
Indices: 6731--6756 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6721 AATTTTTTTG
6731 TGTATCGATACAT
1 TGTATCGATACAT
6744 TGTATCGATACAT
1 TGTATCGATACAT
6757 ATTTTTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6772 original size:32 final size:34
Alignment explanation
Indices: 6710--6774 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
6700 TACAAGCCAA
*
6710 TGTATCGATACAATTTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTTGTGTATCGATACAT
6744 TGTATCGATAC-ATATTTTT-TGTATCGATACA
1 TGTATCGATACAATATTTTTGTGTATCGATACA
6775 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 12 0.40
33 7 0.23
34 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (34 bp):
TGTATCGATACAATATTTTTGTGTATCGATACAT
Found at i:21552 original size:19 final size:19
Alignment explanation
Indices: 21528--21578 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
21518 TTTCAATGAT
21528 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
21547 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
21566 TTGTATCGATACA
1 TTGTATCGATACA
21579 ATGTATCGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:21649 original size:13 final size:13
Alignment explanation
Indices: 21631--21655 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21621 ATTACTCAAA
21631 TGTATCGATACAT
1 TGTATCGATACAT
21644 TGTATCGATACA
1 TGTATCGATACA
21656 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:21708 original size:52 final size:52
Alignment explanation
Indices: 21664--21792 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
21654 CACTGATCTT
21664 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATGAAA
* *
21716 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATGAAA
21768 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
21793 TCATATTTTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATGAAA
Found at i:23901 original size:31 final size:32
Alignment explanation
Indices: 23819--23907 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 32
23809 AAGTGGCATT
* * *
23819 TTGAAAAGGGTTGCCACTGACTTGTGTAGGCC
1 TTGAAAAAGGTTGCCACCGATTTGTGTAGGCC
* * *
23851 TTTAAAAAGAAG-TACCACCGATTTGTGT-GGGC
1 TTGAAAAAG--GTTGCCACCGATTTGTGTAGGCC
23883 TTGAAAAAGGTTGCCACCGATTTGT
1 TTGAAAAAGGTTGCCACCGATTTGT
23908 ATGGACTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
30 1 0.02
31 13 0.28
32 18 0.39
33 13 0.28
34 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (32 bp):
TTGAAAAAGGTTGCCACCGATTTGTGTAGGCC
Found at i:23958 original size:60 final size:56
Alignment explanation
Indices: 23889--24042 Score: 148
Period size: 56 Copynumber: 2.7 Consensus size: 56
23879 GGGCTTGAAA
* * * *
23889 AAGGTTGCCACCGATTTGTATGGACTTTAAGAAGATGTGCCACTAACCT-GTGGGCTTTGG
1 AAGGGTGCCACCGACTTG--TGGAC-TTAA-AAAAAGTGCCA-TAACCTCGTGGGCTTTGG
* * ***
23949 AAGGGTGCCATCGACTTGTGGGCTTAAAAAAAGTGCCATTTGCTCGTGGGCTTTGG
1 AAGGGTGCCACCGACTTGTGGACTTAAAAAAAGTGCCATAACCTCGTGGGCTTTGG
* * *
24005 AAGGGTGCCACCGACTTATGGGCTTAAAAAAAATGCCA
1 AAGGGTGCCACCGACTTGTGGACTTAAAAAAAGTGCCA
24043 CTTGCTTGGG
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
55 3 0.04
56 55 0.68
57 4 0.05
58 4 0.05
60 15 0.19
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (56 bp):
AAGGGTGCCACCGACTTGTGGACTTAAAAAAAGTGCCATAACCTCGTGGGCTTTGG
Found at i:23968 original size:28 final size:27
Alignment explanation
Indices: 23937--24760 Score: 348
Period size: 28 Copynumber: 29.5 Consensus size: 27
23927 GCCACTAACC
*
23937 TGTGGGCTTTGGAAGGGTGCCATCGACT
1 TGTGGGCTTTGAAAGGGTGCCA-CGACT
** ** *
23965 TGTGGGCTTAAAAAAAGTGCCATTTG-CT
1 TGTGGGCTTTGAAAGGGTGCCA--CGACT
* *
23993 CGTGGGCTTTGGAAGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGGTGCCA-CGACT
* ** ***
24021 TATGGGCTTAAAAAAAATGCCACTTG-CT
1 TGTGGGCTTTGAAAGGGTGCCAC--GACT
* *
24049 TGGGGGCTTT-AGAAGGGTGCC-CTTAACT
1 TGTGGGCTTTGA-AAGGGTGCCAC--GACT
*** *
24077 TGTGGGCTGAAAAAGGGTGCTACTTG-CT
1 TGTGGGCTTTGAAAGGGTGCCAC--GACT
* * * *
24105 TGT-GGATTTGAAAAGATGCCACTGAAT
1 TGTGGGCTTTGAAAGGGTGCCAC-GACT
* *
24132 TGTGGGCTTCGAAAAGGGGTGCCACTAGCT
1 TGTGGGCTTTG-AAA-GGGTGCCACGA-CT
* * *
24162 TGTGGGTTTTGGATA-GGAGCCACTGACT
1 TGTGGGCTTT-GAAAGGGTGCCAC-GACT
* ** * *
24190 TATGGGCTTAAAAAGGGTGCCACCAATT
1 TGTGGGCTTTGAAAGGGTGCCA-CGACT
*
24218 TGTGGGCTTTGAAAGGGTGCCACCAACT
1 TGTGGGCTTTGAAAGGGTGCCA-CGACT
** * *
24246 TGTGGGCTTAAAAAGGATGCCACCTACT
1 TGTGGGCTTTGAAAGGGTGCCA-CGACT
* *
24274 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCAC-GACT
** *
24302 TACGGGCTTTGAAAAGGGTGCCACTTACT
1 TGTGGGCTTTG-AAAGGGTGCCAC-GACT
* * * *
24331 TGTGGACTTTGAAAAGATACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCAC-GACT
24359 TGTGGGCTTTGAAAAGGGTGCCACTTG-CT
1 TGTGGGCTTTG-AAAGGGTGCCAC--GACT
* * * *
24388 TATGGGCTTTGGAATGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCAC-GACT
* *
24416 TATGGGCTTAGAAAGGGT-CCACTTG-CT
1 TGTGGGCTTTGAAAGGGTGCCAC--GACT
* * *
24443 TGTGGGCTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCAC-GACT
24471 TGTGGGCTTTGAAAAGGGTGCCACTTG-CT
1 TGTGGGCTTTG-AAAGGGTGCCAC--GACT
* *
24500 TATGGGCTTTGGAAGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGGTGCCA-CGACT
* **
24528 TATGGGCTTAAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCAC-GACT
* * *
24556 TGTGGGCTTTGAAAAGATACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCAC-GACT
* * * *
24584 TGGGGGCTTTGAAA---AGCCACTAATT
1 TGTGGGCTTTGAAAGGGTGCCAC-GACT
* * * * *
24609 TGTGGACTTGGAAAAGATGCCACTGAGT
1 TGTGGGCTTTGAAAGGGTGCCAC-GACT
* * *
24637 TGTGGACTTTGAAAGGATGCCACTA-T
1 TGTGGGCTTTGAAAGGGTGCCACGACT
* * *
24663 AAGTGGGCTTTGAAGGGGTGCCACTAACT
1 -TGTGGGCTTTGAAAGGGTGCCAC-GACT
*** * *
24692 TGTAAACTTT-AAAGAGATGCCACTTACT
1 TGTGGGCTTTGAAAG-GGTGCCAC-GACT
* *
24720 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCAC-GACT
*
24748 TGTAGGCTTTGAA
1 TGTGGGCTTTGAA
24761 GATATGAACG
Statistics
Matches: 611, Mismatches: 147, Indels: 76
0.73 0.18 0.09
Matches are distributed among these distances:
25 18 0.03
26 3 0.00
27 72 0.12
28 412 0.67
29 84 0.14
30 21 0.03
31 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.28
Consensus pattern (27 bp):
TGTGGGCTTTGAAAGGGTGCCACGACT
Found at i:23998 original size:56 final size:56
Alignment explanation
Indices: 23937--24592 Score: 604
Period size: 56 Copynumber: 11.7 Consensus size: 56
23927 GCCACTAACC
** *
23937 TGTGGGCTTTGGAAGGGTGCCA-TCGACTTGTGGGCTTAAAAAAAGTGCCATTTGCT
1 TGTGGGCTTTGGAAGGGTGCCACT-GACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
* * * ***
23993 CGTGGGCTTTGGAAGGGTGCCACCGACTTATGGGCTTAAAAAAAATGCCACTTGCT
1 TGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
* * * * *
24049 TGGGGGCTTTAGAAGGGTGCC-CTTAACTTGTGGGCTGAAAAAGGGTGCTACTTGCT
1 TGTGGGCTTTGGAAGGGTGCCAC-TGACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
* * * * * * *
24105 TGT-GGATTTGAAAAGATGCCACTGAATTGTGGGCTTCGAAAAGGGGTGCCACTAGCT
1 TGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGCTT--AAAAAGGGTGCCACTTGCT
* * * ****
24162 TGTGGGTTTTGGATA-GGAGCCACTGACTTATGGGCTTAAAAAGGGTGCCACCAATT
1 TGTGGGCTTTGGA-AGGGTGCCACTGACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
* ** * * *
24218 TGTGGGCTTTGAAAGGGTGCCACCAACTTGTGGGCTTAAAAAGGATGCCACCTACT
1 TGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
* * * ** * *
24274 TGTGGGCTTTGAAAAGATGCCACTGACTTACGGGCTTTGAAAAGGGTGCCACTTACT
1 TGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGC-TTAAAAAGGGTGCCACTTGCT
* * * * * *
24331 TGTGGACTTTGAAAAGATACCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTTGCT
1 TGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGC-TTAAAAAGGGTGCCACTTGCT
* * * * *
24388 TATGGGCTTTGGAATGGTGCCACTAACTTATGGGCTTAGAAAGGGT-CCACTTGCT
1 TGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
* * * * *
24443 TGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTTGCT
1 TGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGC-TTAAAAAGGGTGCCACTTGCT
* * *
24500 TATGGGCTTTGGAAGGGTGCCACCGACTTATGGGCTTAAAAAGGGTGCCAC-TGACT
1 TGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGGTGCCACTTG-CT
* * * * *
24556 TGTGGGCTTTGAAAAGATACCACTGACTTGGGGGCTT
1 TGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGCTT
24593 TGAAAAGCCA
Statistics
Matches: 494, Mismatches: 94, Indels: 24
0.81 0.15 0.04
Matches are distributed among these distances:
55 66 0.13
56 249 0.50
57 153 0.31
58 25 0.05
59 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (56 bp):
TGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
Found at i:24163 original size:57 final size:57
Alignment explanation
Indices: 23925--24760 Score: 592
Period size: 56 Copynumber: 14.9 Consensus size: 57
23915 TTAAGAAGAT
* * * * * * **
23925 GTGCCACTAACCTGTGGGCTTTGGAAGGGTGCCA-TCGACTTGTGGGC-TTAAAAAAA
1 GTGCCACTAGCTTGTGGGCTTTGAAAAGATGCCACT-GACTTGTGGGCTTTGAAAAGG
* * * * * * * * * **
23981 GTGCCATTTGCTCGTGGGCTTTGGAAGGGTGCCACCGACTTATGGGC-TTAAAAAAA
1 GTGCCACTAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
* * * * * *
24037 ATGCCACTTGCTTGGGGGCTTT-AGAAGGGTGCC-CTTAACTTGTGGGC--TGAAAAAGG
1 GTGCCACTAGCTTGTGGGCTTTGA-AAAGATGCCAC-TGACTTGTGGGCTTTG-AAAAGG
* * * * *
24093 GTGCTACTTGCTTGT-GGATTTGAAAAGATGCCACTGAATTGTGGGCTTCGAAAAGGG
1 GTGCCACTAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAA-GG
* * * * *
24150 GTGCCACTAGCTTGTGGGTTTTGGATAGGA-GCCACTGACTTATGGGC-TTAAAAAGG
1 GTGCCACTAGCTTGTGGGCTTT-GAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
* ** * * ** *
24206 GTGCCACCAATTTGTGGGCTTTGAAAGGGTGCCACCAACTTGTGGGC-TTAAAAAGG
1 GTGCCACTAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
* **
24262 ATGCCACCTA-CTTGTGGGCTTTGAAAAGATGCCACTGACTTACGGGCTTTGAAAAGG
1 GTGCCA-CTAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
* *
24319 GTGCCACTTA-CTTGTGGACTTTGAAAAGATACCACTGACTTGTGGGCTTTGAAAAGG
1 GTGCCAC-TAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
* * * * * * * *
24376 GTGCCACTTGCTTATGGGCTTTGGAATGGTGCCACTAACTTATGGGCTTAG-AAAGG
1 GTGCCACTAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
* *
24432 GT-CCACTTGCTTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAAGG
1 GTGCCACTAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
* * * * * * * *
24488 GTGCCACTTGCTTATGGGCTTTGGAAGGGTGCCACCGACTTATGGGC-TTAAAAAGG
1 GTGCCACTAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
* *
24544 GTGCCACT-GACTTGTGGGCTTTGAAAAGATACCACTGACTTGGGGGCTTTGAAAA--
1 GTGCCACTAG-CTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
** * * * *
24599 --GCCACTAATTTGTGGACTTGGAAAAGATGCCACTGAGTTGTGGACTTTG-AAAGG
1 GTGCCACTAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
* * ** * * ***
24653 ATGCCACTA--TAAGTGGGCTTTGAAGGGGTGCCACTAACTTGTAAACTTT--AAAGAG
1 GTGCCACTAGCT-TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAG-G
* * * *
24708 ATGCCACTTA-CTTGTGGGCTTTGAAAGGATGCCACTAACTTGTAGGCTTTGAA
1 GTGCCAC-TAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAA
24761 GATATGAACG
Statistics
Matches: 633, Mismatches: 116, Indels: 60
0.78 0.14 0.07
Matches are distributed among these distances:
52 3 0.00
53 40 0.06
54 5 0.01
55 108 0.17
56 287 0.45
57 164 0.26
58 21 0.03
59 5 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (57 bp):
GTGCCACTAGCTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
Found at i:24323 original size:169 final size:169
Alignment explanation
Indices: 23937--24756 Score: 731
Period size: 169 Copynumber: 4.9 Consensus size: 169
23927 GCCACTAACC
* * * * ** * * *
23937 TGTGGGCTTTGGAAGGGTGCCA-TCGACTTGTGGGC-TTAAAAAAAGTGCCATTTGCTCGTGGGC
1 TGTGGGCTTTGAAAAGATGCCACT-GACTTGTGGGCTTTGAAAAGGGTGCCACTAGCTTGTGGGC
* *** * *
24000 TTTGGAAGGGTGCCACCGACTTATGGGCTTAAAAAAAATGCCACTTGCTTGGGGGCTTT-AGAAG
65 TTTGGAAGGGAGCCACCGACTTATGGGCTTAAAAAGGGTGCCACTTACTTGTGGGCTTTGA-AAG
* *
24064 GGTGCC-CTTAACTTGTGGGCTGAAAAAGGGTGCTACTTGCT
129 GGTGCCAC-TAACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
* * * *
24105 TGT-GGATTTGAAAAGATGCCACTGAATTGTGGGCTTCGAAAAGGGGTGCCACTAGCTTGTGGGT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAA-GGGTGCCACTAGCTTGTGGGC
* ** *
24169 TTTGGATA-GGAGCCACTGACTTATGGGCTTAAAAAGGGTGCCACCAATTTGTGGGCTTTGAAAG
65 TTTGGA-AGGGAGCCACCGACTTATGGGCTTAAAAAGGGTGCCACTTACTTGTGGGCTTTGAAAG
* * * *
24233 GGTGCCACCAACTTGTGGGCTTAAAAAGGATGCCACCTACT
129 GGTGCCACTAACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
** *
24274 TGTGGGCTTTGAAAAGATGCCACTGACTTACGGGCTTTGAAAAGGGTGCCACTTA-CTTGTGGAC
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCAC-TAGCTTGTGGGC
** * * * * * * *
24338 TTT-GAAAAGATACCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTTGCTTATGGGCTTTGGAA
65 TTTGGAAGGGA-GCCACCGACTTATGGGC-TTAAAAAGGGTGCCACTTACTTGTGGGCTTTGAAA
* * *
24402 TGGTGCCACTAACTTATGGGCTTAGAAAGGGT-CCACTTGCT
128 GGGTGCCACTAACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
* * *
24443 TGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTTGCTTATGGGCT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAGCTTGTGGGCT
* * * *
24508 TTGGAAGGGTGCCACCGACTTATGGGCTTAAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
66 TTGGAAGGGAGCCACCGACTTATGGGCTTAAAAAGGGTGCCACTTACTTGTGGGCTTTGAAAGGG
* * * * ***
24573 TACCACTGACTTGGGGGCTTTGAAAA----GCCACTAATT
131 TGCCACTAACTTGTGGGC-TTAAAAAGGGTGCCACTTGCT
* * * * * *
24609 TGTGGACTTGGAAAAGATGCCACTGAGTTGTGGACTTTG-AAAGGATGCCACTA--TAAGTGGGC
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAGCT-TGTGGGC
* ** * *** * *
24671 TTT-GAAGGGGTGCCACTAACTTGTAAACTT-TAAAGAGATGCCACTTACTTGTGGGCTTTGAAA
65 TTTGGAA-GGGAGCCACCGACTTATGGGCTTAAAAAG-GGTGCCACTTACTTGTGGGCTTTGAAA
* *
24734 GGATGCCACTAACTTGTAGGCTT
128 GGGTGCCACTAACTTGTGGGCTT
24757 TGAAGATATG
Statistics
Matches: 530, Mismatches: 104, Indels: 41
0.79 0.15 0.06
Matches are distributed among these distances:
163 10 0.02
164 66 0.12
165 12 0.02
166 40 0.08
167 25 0.05
168 59 0.11
169 220 0.42
170 98 0.18
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.28
Consensus pattern (169 bp):
TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAGCTTGTGGGCT
TTGGAAGGGAGCCACCGACTTATGGGCTTAAAAAGGGTGCCACTTACTTGTGGGCTTTGAAAGGG
TGCCACTAACTTGTGGGCTTAAAAAGGGTGCCACTTGCT
Found at i:24623 original size:53 final size:53
Alignment explanation
Indices: 24546--24650 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
24536 TAAAAAGGGT
* * * *
24546 GCCACTGACTTGTGGGCTTTGAAAAGATACCACTGACTTGGGGGCTTTGAAAA
1 GCCACTAACTTGTGGACTTGGAAAAGATACCACTGACTTGGGGACTTTGAAAA
* * * *
24599 GCCACTAATTTGTGGACTTGGAAAAGATGCCACTGAGTTGTGGACTTTGAAA
1 GCCACTAACTTGTGGACTTGGAAAAGATACCACTGACTTGGGGACTTTGAAA
24651 GGATGCCACT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (53 bp):
GCCACTAACTTGTGGACTTGGAAAAGATACCACTGACTTGGGGACTTTGAAAA
Done.