Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1086
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: 51957
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3023 original size:20 final size:20
Alignment explanation
Indices: 2980--3025 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2970 AAATCTTTTG
2980 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3001 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3021 CAAAA
1 CAAAA
3026 CCAGTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:5427 original size:13 final size:13
Alignment explanation
Indices: 5409--5434 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5399 TACAGCAAGT
5409 ATGTATCGATACA
1 ATGTATCGATACA
5422 ATGTATCGATACA
1 ATGTATCGATACA
5435 CAAAAAAAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9831 original size:22 final size:21
Alignment explanation
Indices: 9799--9853 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 21
9789 CTTATTTTTT
*
9799 TCTTTGTTTCTATTTCTTCTC
1 TCTTTTTTTCTATTTCTTCTC
* * * *
9820 TCTTTTCTTTCTCTTTTTTTTT
1 TCTTTT-TTTCTATTTCTTCTC
9842 TCTTTTTTTCTA
1 TCTTTTTTTCTA
9854 GTTTAACCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (21 bp):
TCTTTTTTTCTATTTCTTCTC
Found at i:9834 original size:11 final size:11
Alignment explanation
Indices: 9811--9852 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
9801 TTTGTTTCTA
9811 TTTCTTCTCTCT
1 TTTCTT-TCTCT
9823 TTTCTTTCTCT
1 TTTCTTTCTCT
* *
9834 TTTTTTTTTCT
1 TTTCTTTCTCT
9845 TTT-TTTCT
1 TTTCTTTCT
9853 AGTTTAACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 4 0.15
11 17 0.63
12 6 0.22
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTCTCT
Found at i:11236 original size:32 final size:31
Alignment explanation
Indices: 11176--11394 Score: 191
Period size: 32 Copynumber: 7.0 Consensus size: 31
11166 GGTGCCATCA
* **** *
11176 ACTTGTGTGGGCTTTGAAAAAAAATGCCACAA
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCAC-G
*
11208 ACTTGTGTGGGCTTTGAAGGGGGTTGCCAGCG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCA-CG
* *
11240 ACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCA-CG
*
11272 ACTTGTGTGGGCTTTGAATG-GGGTTGCTAGCG
1 ACTTGTGTGGGCTTTGAA-GAGGGTTGCCA-CG
* *
11304 ACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCA-CG
11336 ACTTGTGTGGGCTTT-AGAGAAGGG-TGCCACTG
1 ACTTGTGTGGGCTTTGA-AG-AGGGTTGCCAC-G
*
11368 AC-T-TGTGGGTTTTGAA-AGGG-TGCCACG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCACG
11395 GAGTTGTGGA
Statistics
Matches: 158, Mismatches: 22, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
27 1 0.01
28 10 0.06
30 10 0.06
31 4 0.03
32 127 0.80
33 6 0.04
ACGTcount: A:0.19, C:0.16, G:0.37, T:0.29
Consensus pattern (31 bp):
ACTTGTGTGGGCTTTGAAGAGGGTTGCCACG
Found at i:11374 original size:64 final size:64
Alignment explanation
Indices: 11208--11350 Score: 268
Period size: 64 Copynumber: 2.2 Consensus size: 64
11198 AATGCCACAA
11208 ACTTGTGTGGGCTTTGAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
* *
11272 ACTTGTGTGGGCTTTGAATGGGGTTGCTAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
11336 ACTTGTGTGGGCTTT
1 ACTTGTGTGGGCTTT
11351 AGAGAAGGGT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 77 1.00
ACGTcount: A:0.13, C:0.16, G:0.39, T:0.31
Consensus pattern (64 bp):
ACTTGTGTGGGCTTTGAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
Found at i:11487 original size:32 final size:28
Alignment explanation
Indices: 11341--13691 Score: 667
Period size: 27 Copynumber: 85.9 Consensus size: 28
11331 CACCGACTTG
* *
11341 TGTGGGCTTTAGAGAAGGGTGCCACTGACT
1 TGTGGGCTTTA-A-AAGGATGCCACTAACT
* * * ** *
11371 TGTGGGTTTTGAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
*
11399 TGTGGAC-TTAAAACGGATGCCACTAACT
1 TGTGGGCTTTAAAA-GGATGCCACTAACT
* * *
11427 TGTGGACTTTAAAAGGGTGTCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
11455 TGTGGGCTTTAAAAAAGAAGATGCCACTAACT
1 TGTGGGCTTT--AAAAG--GATGCCACTAACT
* * *
11487 TGTGGGCTTTTGAAAA-GATACCATTGACT
1 TGTGGGC-TTT-AAAAGGATGCCACTAACT
* * *
11516 TGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
11544 TGTGAGCTTTGAAAGGGTGTCACTAA-T
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
11571 TCGTGGGCTTTGAAAGGATGTCACTGAC-
1 T-GTGGGCTTTAAAAGGATGCCACTAACT
* * *
11599 TGTGGACTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
11627 TGTGGGCTTTGCAAAGG-TGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTAACT
* * * *
11655 TGTGAGC-TTAAAAGAATGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* * * ** *
11682 TGTGGTC-ATGAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
11709 TGTGGAC-TTAAAAGGATGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * ** * *
11736 TATAGAATTTAAAA-GATGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* * * *
11763 TGTGGAC-TTAAAAGGGTGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* * *
11790 TGTGGAC-TTAAAAGGGTGCCA-TGAAGT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* * ****
11817 TGTGGACTTTAAAAGGGTGCCACGGGGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * **
11845 TATGGAC-TTAAAAAGATGCCACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
11872 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
11899 TGTGGAC-TTAAAAGGATGCCACGAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * * *
11926 TGTGGACTTTAAAAGGGTACCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
11954 TGTGGAC-TTAAAAGGATACCAC-AGACT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * * ** *
11981 TCT-GGATTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
12008 TGTGGAC-TTAAAAAGATGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * *
12035 TGTGGAG--TTAAAAGGGTGCCACGAAGT
1 TGTGG-GCTTTAAAAGGATGCCACTAACT
* * * ** *
12062 TGTGGACTTTAAAAGGGTGTCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
12090 TGTGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * **
12118 TGTGGAC-TTAAAAGGATGCTACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
** *
12145 TGTGAAC-TTAAAA-GAGTGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGA-TGCCACTA-ACT
* ** *
12172 TGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
12199 TATGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ****
12227 TCTGGAC-TTAAAAGGATGCCACGGTGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * **
12254 TGTGGAC-TTAAAAGGATACCACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
12281 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* **
12308 TGTGGAC-TTAAAAGGATGCCACGCACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
12335 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
12362 TGTGGAC-TTAAAA-GATGCCACGAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * * *
12388 TGTGGACTTTAAAAGGGTACCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
12416 TGTGGAC-TTAAAAGGATACCAC-AGACT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * * ** *
12443 TCT-GGATTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
12470 TGTGGAC-TTAAAAAGATGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * *
12497 TGTGGAG--TTAAAAGGGTGCCACGAAGT
1 TGTGG-GCTTTAAAAGGATGCCACTAACT
* * * ** *
12524 TGTGGACTTTAAAAGGGTGTCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
12552 TGTGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * **
12580 TGTGGAC-TTAAAAGGATGCTACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
12607 TGTGGAC-TTAAAA-GAGTGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGA-TGCCACTA-ACT
* ** *
12634 TGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
12661 TGTGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ****
12689 TCTGGAC-TTAAAAGGATGCCACGGTGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * **
12716 TGTGGAC-TTAAAAGGATACCACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
12743 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* **
12770 TGTGGAC-TTAAAAGGATGCCACGCACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
12797 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* **
12824 TGTGGAC-TTAAAAGGATGCCACGCACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
12851 TGTGGAC-TTAATAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * ** *
12878 TGTGGTC-ATGAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
12905 TATGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** ** *
12932 TATAGAATTTAAAA-GATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
12959 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
** * * *
12986 TGTGAAC-TTAAAA-GAGCGCCACGAAGT
1 TGTGGGCTTTAAAAGGA-TGCCACTAACT
* * *
13013 TGTGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ****
13041 TCTGGAC-TTAAAAGGATGCCACGGTGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
13068 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * * *
13095 TGTGGAC-TTAAAAGGGTGTCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* * ** *
13122 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
13150 TATGGAC-TTAAAAGGATGCCAC-AGACT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * * *
13177 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
13204 TGTGGACTTAAAAAGG-TGCCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * ** *
13231 TGTGGAC-TTAAAAGGGTACCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
13258 TGTGGACTTTAAAAGGTTACCAC-AGACT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
*
13286 TGTGGAC-TTAAAAGGATGCCAC-AGACT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * *
13313 TGTGGAC-TTAAAAGGGTGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* *
13340 TGTGGAC-TTAAAAGGATGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * *
13367 TGTGGAG--TTAAAAGGGTGCCACGAAGT
1 TGTGG-GCTTTAAAAGGATGCCACTAACT
* * * *
13394 TGTGGACTTTAAAAGGGTGTCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * ** *
13422 TGTGGACTTTAAAAGGGTGTTA-TGGACT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* **
13450 TGTGGAC-TTAAAA-GAGTGCCAC-AGAGG
1 TGTGGGCTTTAAAAGGA-TGCCACTA-ACT
* *
13477 TGTGGAC-TTAAAAGGATGCCA-TAGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * **
13504 TGTGGACTTTAAAAGGGTGCCACGCACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
13532 TATGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
13559 TGTGGAC-TTAAAAGGATACCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
13586 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
13613 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* **
13640 TGTGGAC-TTAAAAGGATGCCACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
13667 TATGGACTTTAAAAGGAATGCCACT
1 TGTGGGCTTTAAAAGG-ATGCCACT
13692 GAATCGTGGA
Statistics
Matches: 1952, Mismatches: 286, Indels: 167
0.81 0.12 0.07
Matches are distributed among these distances:
26 52 0.03
27 1302 0.67
28 523 0.27
29 36 0.02
30 14 0.01
32 22 0.01
33 3 0.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (28 bp):
TGTGGGCTTTAAAAGGATGCCACTAACT
Found at i:11516 original size:29 final size:28
Alignment explanation
Indices: 11362--11663 Score: 137
Period size: 28 Copynumber: 10.6 Consensus size: 28
11352 GAGAAGGGTG
* * * *
11362 CCACTGACTTGTGGGTTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGATA
* * * *
11390 CCACGGAGTTGTGGAC-TT-AAAACGGATG
1 CCACTGACTTGTGGGCTTTGAAAA--GATA
* * * *
11418 CCACTAACTTGTGGACTTT-AAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAA-GATA
* * * *
11446 TCACTAACTTGTGGGCTTTAAAAAAGAAGATG
1 CCACTGACTTGTGGGCTTT---GAA-AAGATA
*
11478 CCACTAACTTGTGGGCTTTTGAAAAGATA
1 CCACTGACTTGTGGGC-TTTGAAAAGATA
* * * *
11507 CCATTGACTTGTGGACTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAAGATA
* * * *
11535 CCACTGACTTGTGAGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGATA
* * * *
11563 TCACT-AATTCGTGGGCTTTGAAAGGATG
1 CCACTGACTT-GTGGGCTTTGAAAAGATA
* * * * *
11591 TCACTGAC-TGTGGACTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGATA
* * * *
11618 CCACTAACTTGTGGGCTTTGCAAAGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGATA
*
11646 CCACTGACTTGTGAGCTT
1 CCACTGACTTGTGGGCTT
11664 AAAAGAATGC
Statistics
Matches: 223, Mismatches: 39, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
26 3 0.01
27 27 0.12
28 141 0.63
29 25 0.11
30 2 0.01
32 20 0.09
33 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (28 bp):
CCACTGACTTGTGGGCTTTGAAAAGATA
Found at i:11519 original size:117 final size:116
Alignment explanation
Indices: 11360--11581 Score: 297
Period size: 117 Copynumber: 1.9 Consensus size: 116
11350 TAGAGAAGGG
* * * * *
11360 TGCCACTGACTTGTGGGTTTTGAAAGGGTGCCACGGAGTTGTGGAC-TTAAAACGGATGCCACTA
1 TGCCACTAACTTGTGGGTTTTGAAAAGATACCACGGACTTGTGGACTTTAAAA-GGATGCCACTA
11424 ACTTGTG-GACTTTAAAAGGGTGTCACTAACTT-GTGGGCTTTAAAAAAGAAGA
65 ACTTGTGAG-CTTTAAAAGGGTGTCACTAA-TTCGTGGGCTTTAAAAAAGAAGA
** * *
11476 TGCCACTAACTTGTGGGCTTTTGAAAAGATACCATTGACTTGTGGACTTTGAAAGGATGCCACTG
1 TGCCACTAACTTGTGGG-TTTTGAAAAGATACCACGGACTTGTGGACTTTAAAAGGATGCCACTA
*
11541 ACTTGTGAGCTTTGAAAGGGTGTCACTAATTCGTGGGCTTT
65 ACTTGTGAGCTTTAAAAGGGTGTCACTAATTCGTGGGCTTT
11582 GAAAGGATGT
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
116 18 0.20
117 68 0.74
118 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (116 bp):
TGCCACTAACTTGTGGGTTTTGAAAAGATACCACGGACTTGTGGACTTTAAAAGGATGCCACTAA
CTTGTGAGCTTTAAAAGGGTGTCACTAATTCGTGGGCTTTAAAAAAGAAGA
Found at i:11684 original size:27 final size:27
Alignment explanation
Indices: 11639--13704 Score: 2316
Period size: 27 Copynumber: 76.0 Consensus size: 27
11629 TGGGCTTTGC
* *
11639 AAAGG-TGCCACTGACTTGT-GAGCTTA
1 AAAGGATGCCACGGAGTTGTGGA-CTTA
* * * * *
11665 AAAGAATGCCATGGAGTTGTGGTCATG
1 AAAGGATGCCACGGAGTTGTGGACTTA
11692 AAAGGATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * * *
11719 AAAGGATGCCACAGAGTTATAGAATTTA
1 AAAGGATGCCACGGAGTTGT-GGACTTA
*
11747 AAA-GATGCCATGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
11773 AAAGGGTGCCATGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
11800 AAAGGGTGCCATGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
11828 AAAGGGTGCCACGGGGTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
11855 AAAAGATGCCACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* **
11882 AAAGGGTGCCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
11909 AAAGGATGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * **
11937 AAAGGGTACCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * * * *
11964 AAAGGATACCACAGACTTCTGGATTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
11991 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
12018 AAAAGATGCCACAGAGTTGTGGAGTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
12045 AAAGGGTGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* *
12073 AAAGGGTGTCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
12101 AAAGGGTGCCACGAACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
12128 AAAGGATGCTACGGACTTGTGAACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12155 AAA-GAGTGCCACAGAGTTGTGGACTTA
1 AAAGGA-TGCCACGGAGTTGTGGACTTA
*
12182 AAAGGATGCCACGGAGTTATGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
12210 AAAGGGTGCCACGAACTTCTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12237 AAAGGATGCCACGGTGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
12264 AAAGGATACCACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12291 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
12318 AAAGGATGCCACGCACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12345 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12372 AAA-GATGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * **
12399 AAAGGGTACCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * * * *
12426 AAAGGATACCACAGACTTCTGGATTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12453 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
12480 AAAAGATGCCACAGAGTTGTGGAGTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
12507 AAAGGGTGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* *
12535 AAAGGGTGTCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
12563 AAAGGGTGCCACGAACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
12590 AAAGGATGCTACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12617 AAA-GAGTGCCACAGAGTTGTGGACTTA
1 AAAGGA-TGCCACGGAGTTGTGGACTTA
12644 AAAGGATGCCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
12672 AAAGGGTGCCACGAACTTCTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12699 AAAGGATGCCACGGTGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
12726 AAAGGATACCACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12753 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
12780 AAAGGATGCCACGCACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12807 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
12834 AAAGGATGCCACGCACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * * *
12861 ATAGGATGCCACGGAGTTGTGGTCATG
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
12888 AAAGGATGCCACGGAGTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
12915 AAAGGATGCCACGGAGTTATAGAATTTA
1 AAAGGATGCCACGGAGTTGT-GGACTTA
12943 AAA-GATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
12969 AAAGGGTGCCACGGAGTTGTGAACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
12996 AAA-GAGCGCCACGAAGTTGTGGACTTTA
1 AAAGGA-TGCCACGGAGTTGTGGAC-TTA
* * * *
13024 AAAGGGTGCCACGAACTTCTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
13051 AAAGGATGCCACGGTGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* **
13078 AAAGGGTGCCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
13105 AAAGGGTGTCATGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* *
13133 AAAGGGTGCCACGGAGTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
13160 AAAGGATGCCACAGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* **
13187 AAAGGGTGCCACAAAGTTGTGGACTTAA
1 AAAGGATGCCACGGAGTTGTGGACTT-A
**
13215 AAAGG-TGCCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
13241 AAAGGGTACCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
13269 AAAGGTTACCACAGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
13296 AAAGGATGCCACAGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
13323 AAAGGGTGCCACAGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
13350 AAAGGATGCCACAGAGTTGTGGAGTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
13377 AAAGGGTGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
13405 AAAGGGTGTCACAGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* ** * *
13433 AAAGGGTGTTATGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
13460 AAA-GAGTGCCACAGAGGTGTGGACTTA
1 AAAGGA-TGCCACGGAGTTGTGGACTTA
**
13487 AAAGGATGCCATAGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
13515 AAAGGGTGCCACGCACTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
13542 AAAGGATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
13569 AAAGGATACCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
13596 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
13623 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
13650 AAAGGATGCCACGGACTTATGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
13678 AAAGGAATGCCACTGAATCGTGGACTT
1 AAAGG-ATGCCACGGAGTTGTGGACTT
13705 TGAAAAGGTT
Statistics
Matches: 1749, Mismatches: 260, Indels: 60
0.85 0.13 0.03
Matches are distributed among these distances:
26 50 0.03
27 1296 0.74
28 387 0.22
29 16 0.01
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (27 bp):
AAAGGATGCCACGGAGTTGTGGACTTA
Found at i:11884 original size:109 final size:108
Alignment explanation
Indices: 11639--13704 Score: 2384
Period size: 109 Copynumber: 19.0 Consensus size: 108
11629 TGGGCTTTGC
* * ** * * * * *
11639 AAAGG-TGCCACTGACTTGT-GAGCTTAAAAGAATGCCATGGAGTTGTGGTCATGAAAGGATGCC
1 AAAGGATGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * * *
11702 ACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTATAGAATTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT-GGACTTA
* *
11747 AAA-GATGCCATGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * * *
11811 TGAAGTTGTGGACTTTAAAAGGGTGCCACGGGGTTATGGACTTA
66 CGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTA
* * ** *
11855 AAAAGATGCCACGGACTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTAAAAGGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * **
11920 CGAAGTTGTGGACTTTAAAAGGGTACCACAAAGTTGTGGACTTA
66 CGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * * * *
11964 AAAGGATACCACAGACTTCTGGATTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * *
12029 CAGAGTTGTGGAGTTAAAAGGGTGCCACGAAGTTGTGGACTTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* * * * * *
12073 AAAGGGTGTCACGGAGTTGTGGACTTTAAAAGGGTGCCACGAACTTGTGGACTTAAAAGGATGCT
1 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * *
12138 ACGGACTTGTGAACTTAAAA-GAGTGCCACAGAGTTGTGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGA-TGCCACGGAGTTGTGGACTTA
* * * * *
12182 AAAGGATGCCACGGAGTTATGGACTTTAAAAGGGTGCCACGAACTTCTGGACTTAAAAGGATGCC
1 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * *
12247 ACGGTGTTGTGGACTTAAAAGGATACCACGGACTTGTGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * *
12291 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGCACTTGTGGACTTAAAAGGGTGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
*
12356 CGGAGTTGTGGACTTAAAA-GATGCCACGAAGTTGTGGACTTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* * ** * * * * * *
12399 AAAGGGTACCACAAAGTTGTGGACTTAAAAGGATACCACAGACTTCTGGATTTAAAAGGGTGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * *
12464 CGGAGTTGTGGACTTAAAAAGATGCCACAGAGTTGTGGAGTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * *
12507 AAAGGGTGCCACGAAGTTGTGGACTTTAAAAGGGTGTCACGGAGTTGTGGACTTTAAAAGGGTGC
1 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
* * * *
12572 CACGAACTTGTGGACTTAAAAGGATGCTACGGACTTGTGGACTTA
64 CACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* *
12617 AAA-GAGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGC
1 AAAGGA-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
* * * *
12681 CACGAACTTCTGGACTTAAAAGGATGCCACGGTGTTGTGGACTTA
64 CACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * *
12726 AAAGGATACCACGGACTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * *
12791 CGCACTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * * * * *
12834 AAAGGATGCCACGCACTTGTGGACTTAATAGGATGCCACGGAGTTGTGGTCATGAAAGGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * *
12899 CGGAGTTATGGACTTAAAAGGATGCCACGGAGTTATAGAATTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT-GGACTTA
* * *
12943 AAA-GATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGAACTTAAAAGAGCGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * * *
13007 CGAAGTTGTGGACTTTAAAAGGGTGCCACGAACTTCTGGACTTA
66 CGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTA
* ** *
13051 AAAGGATGCCACGGTGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTAAAAGGGTGTCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * *
13116 TGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTATGGACTTA
66 CGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTA
* * ** *
13160 AAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTAAAAAGGTGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
** * *
13225 CAAAGTTGTGGACTTAAAAGGGTACCACGGAGTTGTGGACTTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* * * * * * *
13269 AAAGGTTACCACAGACTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * *
13334 CAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGAGTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * *
13377 AAAGGGTGCCACGAAGTTGTGGACTTTAAAAGGGTGTCACAGAGTTGTGGACTTTAAAAGGGTGT
1 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
* * * * *
13442 TATGGACTTGTGGACTTAAAA-GAGTGCCACAGAGGTGTGGACTTA
64 CACGGAGTTGTGGACTTAAAAGGA-TGCCACGGAGTTGTGGACTTA
** * * * *
13487 AAAGGATGCCATAGAGTTGTGGACTTTAAAAGGGTGCCACGCACTTATGGACTTAAAAGGATGCC
1 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
*
13552 ACGGAGTTGTGGACTTAAAAGGATACCACGGAGTTGTGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* *
13596 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * * *
13661 CGGACTTATGGACTTTAAAAGGAATGCCACTGAATCGTGGACTT
66 CGGAGTTGTGGAC-TTAAAAGG-ATGCCACGGAGTTGTGGACTT
13705 TGAAAAGGTT
Statistics
Matches: 1699, Mismatches: 235, Indels: 46
0.86 0.12 0.02
Matches are distributed among these distances:
107 18 0.01
108 559 0.33
109 872 0.51
110 250 0.15
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (108 bp):
AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
Found at i:15039 original size:20 final size:18
Alignment explanation
Indices: 15014--15076 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 18
15004 TGTCCTTGTT
15014 TTTTTATTTTTGTTGTTCCA
1 TTTTTATTTTTGTT-TT-CA
15034 TTTTTA-TTTTGTTTTTGCA
1 TTTTTATTTTTG-TTTT-CA
*
15053 CTTTTTATTTTTCTTTTCA
1 -TTTTTATTTTTGTTTTCA
15072 TTTTT
1 TTTTT
15077 TGTGCTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 5 0.13
19 11 0.29
20 18 0.47
21 4 0.11
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTTATTTTTGTTTTCA
Found at i:15043 original size:19 final size:20
Alignment explanation
Indices: 15014--15063 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
15004 TGTCCTTGTT
15014 TTTTTATTTTTGTTGTTCCA-
1 TTTTTA-TTTTGTTGTTCCAC
* *
15034 TTTTTATTTTGTTTTTGCAC
1 TTTTTATTTTGTTGTTCCAC
15054 TTTTTATTTT
1 TTTTTATTTT
15064 TCTTTTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.74
Consensus pattern (20 bp):
TTTTTATTTTGTTGTTCCAC
Found at i:17623 original size:33 final size:33
Alignment explanation
Indices: 17586--17652 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
17576 TTCAACGATT
17586 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
17619 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
17652 T
1 T
17653 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:17624 original size:13 final size:13
Alignment explanation
Indices: 17606--17630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17596 CATAAAATGT
17606 TGTATCGATACAA
1 TGTATCGATACAA
17619 TGTATCGATACA
1 TGTATCGATACA
17631 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:17711 original size:13 final size:13
Alignment explanation
Indices: 17693--17717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17683 ATTACTCAAA
17693 TGTATCGATACAT
1 TGTATCGATACAT
17706 TGTATCGATACA
1 TGTATCGATACA
17718 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:17819 original size:52 final size:51
Alignment explanation
Indices: 17726--17849 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 51
17716 CACTGATCTT
*
17726 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACACTATT-AAA
17777 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACACTATTAAA
17829 TGTATCGATACATGCA-GCAAT
1 TGTATCGATACATGCAGGCAAT
17850 GCCAATTTAT
Statistics
Matches: 70, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
50 3 0.04
51 21 0.30
52 43 0.61
53 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:25320 original size:22 final size:22
Alignment explanation
Indices: 25294--25349 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
25284 TTTTTCTTTG
25294 TTTCT-ATTTCTTCTCTCTTTTT
1 TTTCTCATTT-TTCTCTCTTTTT
* *
25316 TTTCTCCTTTTTTTCTCTTTTT
1 TTTCTCATTTTTCTCTCTTTTT
* *
25338 TTTTTCTTTTTT
1 TTTCTCATTTTT
25350 TTAGTTGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCTCATTTTTCTCTCTTTTT
Found at i:25351 original size:11 final size:11
Alignment explanation
Indices: 25307--25351 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
25297 CTATTTCTTC
25307 TCTCTTTTTTT
1 TCTCTTTTTTT
*
25318 TCTCCTTTTTT
1 TCTCTTTTTTT
25329 TCTCTTTTTTT
1 TCTCTTTTTTT
*
25340 TTTCTTTTTTT
1 TCTCTTTTTTT
25351 T
1 T
25352 AGTTGAACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTCTTTTTTT
Found at i:27238 original size:20 final size:21
Alignment explanation
Indices: 27213--27261 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
27203 GCACTCGTTA
27213 GATGAAAAGACATACTT-TTG
1 GATGAAAAGACATACTTGTTG
**
27233 GATGAAAAGATGTACTTGTTG
1 GATGAAAAGACATACTTGTTG
*
27254 GACGAAAA
1 GATGAAAA
27262 AAATTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (21 bp):
GATGAAAAGACATACTTGTTG
Found at i:30497 original size:3 final size:3
Alignment explanation
Indices: 30489--30550 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
30479 CTTATTAATA
*
30489 TCT TCT TCT GTCT TCT TC- TCT T-T TTT TCT GT-T TCT TCT TCTT TCT
1 TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TC-T TCT
30534 TCT TC- TCT TGCT TCT TC
1 TCT TCT TCT T-CT TCT TC
30551 AAATACTTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
2 7 0.14
3 33 0.66
4 10 0.20
ACGTcount: A:0.00, C:0.29, G:0.05, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:30519 original size:20 final size:20
Alignment explanation
Indices: 30494--30550 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
30484 TAATATCTTC
30494 TTCTGTCTTCTTC-TCTTTTT
1 TTCTGT-TTCTTCTTCTTTTT
30514 TTCTGTTTCTTCTTCTTTCTT
1 TTCTGTTTCTTCTTCTTT-TT
* *
30535 CTTCTCTTGCTTCTTC
1 -TTCTGTTTCTTCTTC
30551 AAATACTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.19
20 11 0.34
21 2 0.06
22 13 0.41
ACGTcount: A:0.00, C:0.28, G:0.05, T:0.67
Consensus pattern (20 bp):
TTCTGTTTCTTCTTCTTTTT
Found at i:32835 original size:20 final size:20
Alignment explanation
Indices: 32810--32863 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
32800 CTACCACTGT
* *
32810 TTGTATCGATACATGGTCCA
1 TTGTATCGATACATGATCAA
*
32830 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATCAA
32850 TTGTATCGATACAT
1 TTGTATCGATACAT
32864 TGCTTGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATCAA
Found at i:35113 original size:21 final size:20
Alignment explanation
Indices: 35079--35121 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
35069 TATTAAAAAG
*
35079 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
35100 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
35120 TT
1 TT
35122 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:35120 original size:20 final size:21
Alignment explanation
Indices: 35079--35121 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
35069 TATTAAAAAG
*
35079 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
35100 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
35120 TT
1 TT
35122 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:37464 original size:33 final size:34
Alignment explanation
Indices: 37401--37466 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
37391 TATTACAAGC
*
37401 AATGTATCGATACAATTTCATCATGTATCGATAT
1 AATGTATCGATACAATTTCACCATGTATCGATAT
37435 AATGTATCGATAC-ATTGTC-CCATGTATCGATA
1 AATGTATCGATACAATT-TCACCATGTATCGATA
37467 CAAATAGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (34 bp):
AATGTATCGATACAATTTCACCATGTATCGATAT
Found at i:40061 original size:13 final size:13
Alignment explanation
Indices: 40042--40083 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
40032 AAATAGTACC
40042 CAATGTATCGATA
1 CAATGTATCGATA
* *
40055 TAATGTATTGATA
1 CAATGTATCGATA
*
40068 CATTGTATCGATA
1 CAATGTATCGATA
40081 CAA
1 CAA
40084 GGAATGTTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:45589 original size:13 final size:13
Alignment explanation
Indices: 45571--45627 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
45561 CATAAAGTGT
45571 TGTATCGATACAA
1 TGTATCGATACAA
45584 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
45599 GTGTTGTACCGATACAA
1 ----TGTATCGATACAA
45616 TGTATCGATACA
1 TGTATCGATACA
45628 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:45606 original size:32 final size:32
Alignment explanation
Indices: 45553--45648 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
45543 TCAATGATTA
45553 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACAT-AAGTGTTGTATCGATACAATG
*
45586 TATCGATACATAAGTGTTGTACCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
*
45618 TATCGATACATAAGTTTTGTATCGATACAAT
1 TATCGATACATAAGTGTTGTATCGATACAAT
45649 TTAAGCTACT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 49 0.82
33 11 0.18
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATG
Found at i:45640 original size:19 final size:18
Alignment explanation
Indices: 45553--45646 Score: 73
Period size: 19 Copynumber: 5.6 Consensus size: 18
45543 TCAATGATTA
45553 TATCGATACATAAAGTGTTG
1 TATCGATACAT-AAGT-TTG
45573 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
45586 TATCGATACATAAGTGTTG
1 TATCGATACATAAGT-TTG
*
45605 TACCGATAC--AA---TG
1 TATCGATACATAAGTTTG
45618 TATCGATACATAAGTTTTG
1 TATCGATACATAAG-TTTG
45637 TATCGATACA
1 TATCGATACA
45647 ATTTAAGCTA
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
13 21 0.35
15 4 0.07
17 4 0.07
19 22 0.37
20 9 0.15
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
TATCGATACATAAGTTTG
Found at i:45707 original size:13 final size:13
Alignment explanation
Indices: 45689--45713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45679 ATTACTCAAA
45689 TGTATCGATACAT
1 TGTATCGATACAT
45702 TGTATCGATACA
1 TGTATCGATACA
45714 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:45766 original size:52 final size:51
Alignment explanation
Indices: 45702--45850 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
45692 ATCGATACAT
**
45702 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
45754 TGTATCGATACACTA-CAAAATATATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATC--AATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
45806 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTT
45851 CATATTTCGG
Statistics
Matches: 88, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 86 0.98
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:49944 original size:13 final size:13
Alignment explanation
Indices: 49903--49951 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
49893 CCGTTACAAG
49903 CAATGTATCGATA
1 CAATGTATCGATA
49916 CAAT-T-TC-AT-
1 CAATGTATCGATA
49925 C-ATGTATCGATA
1 CAATGTATCGATA
49937 CAATGTATCGATA
1 CAATGTATCGATA
49950 CA
1 CA
49952 TTGTCCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 4 0.13
12 2 0.06
13 17 0.55
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:49967 original size:33 final size:34
Alignment explanation
Indices: 49903--49972 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
49893 CCGTTACAAG
*
49903 CAATGTATCGATACAATTTCATCATGTATCGATA
1 CAATGTATCGATACAATTTCACCATGTATCGATA
49937 CAATGTATCGATAC-ATTGTC-CCATGTATCGATA
1 CAATGTATCGATACAATT-TCACCATGTATCGATA
49970 CAA
1 CAA
49973 ACAGTGGTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 18 0.53
34 16 0.47
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (34 bp):
CAATGTATCGATACAATTTCACCATGTATCGATA
Done.