Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1700
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: 79381
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:292 original size:16 final size:17
Alignment explanation
Indices: 268--313 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
258 TTGCGCCGCC
*
268 GGGGCGGGGCGGG-GCG
1 GGGGGGGGGCGGGAGCG
*
284 GGGGGGGGGCGGGAGGG
1 GGGGGGGGGCGGGAGCG
301 GGGGGGGGGCGGG
1 GGGGGGGGGCGGG
314 CGGCGGGCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.02, C:0.11, G:0.87, T:0.00
Consensus pattern (17 bp):
GGGGGGGGGCGGGAGCG
Found at i:292 original size:21 final size:20
Alignment explanation
Indices: 268--316 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
258 TTGCGCCGCC
268 GGGGCGGG-GCGGGGCGGGGGG
1 GGGGCGGGAG-GGGG-GGGGGG
289 GGGGCGGGAGGGGGGGGGGG
1 GGGGCGGGAGGGGGGGGGGG
309 GCGGGCGG
1 G-GGGCGG
317 CGGGCGCGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.27
21 18 0.69
22 1 0.04
ACGTcount: A:0.02, C:0.12, G:0.86, T:0.00
Consensus pattern (20 bp):
GGGGCGGGAGGGGGGGGGGG
Found at i:327 original size:17 final size:16
Alignment explanation
Indices: 268--327 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
258 TTGCGCCGCC
268 GGGGC-GGGGCGGGGCG
1 GGGGCGGGGGC-GGGCG
*
284 GGGG-GGGGGCGGGAGG
1 GGGGCGGGGGCGGG-CG
*
300 GGGGGGGGGGCGGGCG
1 GGGGCGGGGGCGGGCG
*
316 GCGGGCGCGGGC
1 G-GGGCGGGGGC
328 AGCGCCCTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
15 3 0.08
16 16 0.44
17 17 0.47
ACGTcount: A:0.02, C:0.17, G:0.82, T:0.00
Consensus pattern (16 bp):
GGGGCGGGGGCGGGCG
Found at i:4164 original size:25 final size:23
Alignment explanation
Indices: 4121--4183 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
4111 AGTGAAAGGC
* *
4121 ATACGAAATGGTATTTGAATTGGTT
1 ATACG-AATGGT-TTTGAAATGATT
4146 ATACGAATTGGTTTGTGAAATGATT
1 ATACGAA-TGGTTT-TGAAATGATT
*
4171 ATAAGAATGGTTT
1 ATACGAATGGTTT
4184 AAAATGGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 10 0.30
25 23 0.70
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.40
Consensus pattern (23 bp):
ATACGAATGGTTTTGAAATGATT
Found at i:10662 original size:26 final size:25
Alignment explanation
Indices: 10584--10690 Score: 153
Period size: 26 Copynumber: 4.2 Consensus size: 25
10574 TGAAATTCCC
*
10584 ATCAAGGAACATTACCTAACCCATT
1 ATCATGGAACATTACCTAACCCATT
10609 -TCATGGAACATTTACCTAACCCATTT
1 ATCATGGAACA-TTACCTAACCCA-TT
*
10635 ATCATGAAACATTACCTAAACCCATT
1 ATCATGGAACATTACCT-AACCCATT
10661 ATCATGGAACATTACCTAACCCTATT
1 ATCATGGAACATTACCTAACCC-ATT
10687 ATCA
1 ATCA
10691 ATTTGTATCA
Statistics
Matches: 74, Mismatches: 3, Indels: 9
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.12
25 17 0.23
26 33 0.45
27 15 0.20
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (25 bp):
ATCATGGAACATTACCTAACCCATT
Found at i:17825 original size:27 final size:26
Alignment explanation
Indices: 17730--17835 Score: 137
Period size: 25 Copynumber: 4.1 Consensus size: 26
17720 CTGAAATCCC
17730 TCATGG-ACAGTTTACCT-ACCCATTA
1 TCATGGAACA-TTTACCTAACCCATTA
*
17755 TCATGGAACATTTACCTAA-CTATTA
1 TCATGGAACATTTACCTAACCCATTA
* * *
17780 TCATGAAAAATTTACCTAACCCTTTA
1 TCATGGAACATTTACCTAACCCATTA
17806 TCATGGAACATATTACCTAACCCATTA
1 TCATGGAACAT-TTACCTAACCCATTA
17833 TCA
1 TCA
17836 ATTTGATCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
25 35 0.51
26 17 0.25
27 17 0.25
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.33
Consensus pattern (26 bp):
TCATGGAACATTTACCTAACCCATTA
Found at i:22343 original size:44 final size:44
Alignment explanation
Indices: 22171--22488 Score: 196
Period size: 44 Copynumber: 7.2 Consensus size: 44
22161 CAAAGAAACA
*
22171 AGATTTGGCATCCCTGTGTTTATAGGGAAACAGATCGAAGATAAC
1 AGATTTGGCATCCCTGTGTTTATAGGG-AACAGATCGAAGATAGC
* * * ** * * **
22216 AGATCT-GAAACTCCTGTGCCTACAGCGAAGCAGATCGAAGATTTC
1 AGATTTGGCATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
* * * * *
22261 AG-TATGGCATCCCTATATTTATAGGGAGCA-AGTTGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
*
22304 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGA
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* ** * * * * * ***
22348 AGATCTAACATTCCTGTGCTTACAGCGAAACAGATCAAAGATTTT
1 AGATTTGGCATCCCTGTGTTTATAG-GGAACAGATCGAAGATAGC
** * *
22393 A-ACCTGGCATCTCTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
* * * * * *
22436 ATATTTGGCATCCTTGTGTTTACAAGGAACAAACCGAAGACATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAG--ATAGC
22482 AGATTTG
1 AGATTTG
22489 ACTTTCAGAT
Statistics
Matches: 200, Mismatches: 61, Indels: 23
0.70 0.21 0.08
Matches are distributed among these distances:
42 2 0.01
43 24 0.12
44 112 0.56
45 51 0.25
46 11 0.05
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
Found at i:22414 original size:132 final size:132
Alignment explanation
Indices: 22171--22475 Score: 407
Period size: 132 Copynumber: 2.3 Consensus size: 132
22161 CAAAGAAACA
22171 AGATTTGGCATCCCTGTGTTTATAGGGAAACAGATCGAAGATAACAGATCTGAAACTCCTGTGCC
1 AGATTTGGCATCCCTGTGTTTATAGGG-AACAGATCGAAGATAACAGATCTGAAACTCCTGTGCC
* * ** *
22236 TACAGCGAAGCAGATCGAAGATTTCAGTATGGCATCCCTATATTTATAGGGAGCAAGTTGAAGAT
65 TACAGCGAAACAGATCAAAGATTTCAACATGGCATCCCTATATTTATAGGGAACAAGTTGAAGAT
22301 AGC
130 AGC
*
22304 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGA-AGATCT-AACATTCCTGTGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATA-ACAGATCTGAA-ACTCCTGTGC
* * * * * *
22367 TTACAGCGAAACAGATCAAAGATTTTAACCTGGCATCTCTGTGTTTATAGGGAACAAGTTGAAGA
64 CTACAGCGAAACAGATCAAAGATTTCAACATGGCATCCCTATATTTATAGGGAACAAGTTGAAGA
22432 TAGC
129 TAGC
* * * * * *
22436 ATATTTGGCATCCTTGTGTTTACAAGGAACAAACCGAAGA
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGA
22476 CATAGCAGAT
Statistics
Matches: 152, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
131 2 0.01
132 122 0.80
133 28 0.18
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGAAACTCCTGTGCCT
ACAGCGAAACAGATCAAAGATTTCAACATGGCATCCCTATATTTATAGGGAACAAGTTGAAGATA
GC
Found at i:22641 original size:175 final size:175
Alignment explanation
Indices: 22438--23020 Score: 934
Period size: 175 Copynumber: 3.3 Consensus size: 175
22428 AAGATAGCAT
*
22438 ATTTGGCATCCTTGTGTTTACAAGGAACAAACCGAAGACATAGCAGATTTGACTTTCAGATGTTC
1 ATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCAGATGTTC
* *
22503 TTACACCAAAGCAGATCCAAGATAACAGATTTGGCATCTCCATTTCGACGGAGAGCAGGTAGATA
66 TTACACCAAAGCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
*
22568 GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAAATCCAAGATG
131 GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATG
* **
22613 ATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTTGGATGTTC
1 ATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCAGATGTTC
* * *
22678 TCACACCAAAGCAGATCCAAGATAACAGATCTGGCATCTCTATTTTGACGGAGAGCAGGTACATA
66 TTACACCAAAGCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
22743 GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATG
131 GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATG
* ** *
22788 ATTTGGCATTCTTGTGTTTACAAGGAACAAATTAAAGACATAGCAGATTTGACTTTCGGATGTTC
1 ATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCAGATGTTC
* * * *
22853 TTACACCAAAACAGATCCAAGATAATAGATCTGGCATCTCCATTTCGACGGAGAGTAGATACATA
66 TTACACCAAAGCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
* * *
22918 GCAGATGTAACCTTTAGATGATTT-TACTGAAGCAGATCCAAGATG
131 GCAGGTCTAACCTTCAGATG-TTTATACTGAAGCAGATCCAAGATG
* * *
22963 ATTTGGCATCCTTGTGTTCACAAGGAGCAAATCGAAGACATAGCAGATTTGGCTTTCA
1 ATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCA
23021 CGTGTTTACG
Statistics
Matches: 377, Mismatches: 30, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
175 374 0.99
176 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (175 bp):
ATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCAGATGTTC
TTACACCAAAGCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATG
Found at i:22851 original size:87 final size:87
Alignment explanation
Indices: 22438--23054 Score: 278
Period size: 87 Copynumber: 7.1 Consensus size: 87
22428 AAGATAGCAT
* ***
22438 ATTTGGCATCCTTGTGTTTACAAGGAACAAACCGAAGACATAGCAGATTTGACTTTCAGATGTTC
1 ATTTGGCATTCTTGTGTTTACAAGGAACAAATTAAAGACATAGCAGATTTGACTTTCAGATG-T-
**
22503 TTACACCAAAGCAGATCCAAGATAACAG
64 TTACACTGAAGCAGATCCAAGAT----G
*** * ** * * * *
22531 ATTTGGCA-TC-TCCATTT-CGACGGAGAGC-AGGT--AG--ATAGCAGGTCTAACCTTCAGATG
1 ATTTGGCATTCTTGTGTTTAC-AAGGA-A-CAAATTAAAGACATAGCAGATTTGACTTTCAGATG
* *
22588 TTTATACTGAAGCAAATCCAAGATG
63 TTTACACTGAAGCAGATCCAAGATG
** **
22613 ATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTTGGATGTTC
1 ATTTGGCATTCTTGTGTTTACAAGGAACAAATTAAAGACATAGCAGATTTGACTTTCAGATGTT-
**
22678 TCACACCAAAGCAGATCCAAGATAACAG
65 T-ACACTGAAGCAGATCCAAGAT----G
* * ** * * * *
22706 ATCTGGCATCTCTAT-T-TTGAC--GGAGAGC-AGGT----ACATAGCAGGTCTAACCTTCAGAT
1 ATTTGGCAT-TCT-TGTGTTTACAAGGA-A-CAAATTAAAGACATAGCAGATTTGACTTTCAGAT
*
22762 GTTTATACTGAAGCAGATCCAAGATG
62 GTTTACACTGAAGCAGATCCAAGATG
*
22788 ATTTGGCATTCTTGTGTTTACAAGGAACAAATTAAAGACATAGCAGATTTGACTTTCGGATGTTC
1 ATTTGGCATTCTTGTGTTTACAAGGAACAAATTAAAGACATAGCAGATTTGACTTTCAGATG-T-
** *
22853 TTACACCAAAACAGATCCAAGATAATAG
64 TTACACTGAAGCAGATCCAAG---AT-G
* *** * * * * * * *
22881 ATCTGGCA-TC-TCCATTT-CGACGG---AGAGTAGATACATAGCAGATGTAACCTTT-AGATGA
1 ATTTGGCATTCTTGTGTTTAC-AAGGAACAAATTAAAGACATAGCAGATTTGA-CTTTCAGATG-
*
22939 TTT-TACTGAAGCAGATCCAAGATG
63 TTTACACTGAAGCAGATCCAAGATG
* * * ** *
22963 ATTTGGCATCCTTGTGTTCACAAGGAGCAAATCGAAGACATAGCAGATTTGGCTTTCACG-TGTT
1 ATTTGGCATTCTTGTGTTTACAAGGAACAAATTAAAGACATAGCAGATTTGACTTTCA-GATGTT
* *
23027 TACGCTGAAGCAGATCTAAGATG
65 TACACTGAAGCAGATCCAAGATG
23050 ATTTG
1 ATTTG
23055 ACATCTCTGT
Statistics
Matches: 381, Mismatches: 96, Indels: 100
0.66 0.17 0.17
Matches are distributed among these distances:
80 1 0.00
81 4 0.01
82 32 0.08
83 10 0.03
84 17 0.04
85 4 0.01
86 58 0.15
87 84 0.22
88 66 0.17
89 38 0.10
90 4 0.01
91 18 0.05
92 9 0.02
93 31 0.08
94 4 0.01
95 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (87 bp):
ATTTGGCATTCTTGTGTTTACAAGGAACAAATTAAAGACATAGCAGATTTGACTTTCAGATGTTT
ACACTGAAGCAGATCCAAGATG
Found at i:23488 original size:14 final size:15
Alignment explanation
Indices: 23469--23525 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
23459 AATCTTTAAG
23469 GATATG-CAATCTTA
1 GATATGACAATCTTA
23483 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
23500 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
23519 GATATGA
1 GATATGA
23526 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:23510 original size:36 final size:38
Alignment explanation
Indices: 23469--23558 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 38
23459 AATCTTTAAG
23469 GATATGCAATCTTAGATATGATA-CAATCTT-AGATAT
1 GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
23505 GATATGCAATCTTAGATATGATATGCAATCTTGAAGATAT
1 GATATGCAATCTTAGATATGATA-GCAATCTT-AAGATAT
*
23545 GATATTGTAATCTT
1 GATA-TGCAATCTT
23559 GGAGATTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
36 23 0.48
38 7 0.15
40 10 0.21
41 8 0.17
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
Found at i:23516 original size:19 final size:19
Alignment explanation
Indices: 23469--23549 Score: 130
Period size: 19 Copynumber: 4.3 Consensus size: 19
23459 AATCTTTAAG
23469 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23488 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23505 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23524 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
23545 GATAT
1 GATAT
23550 TGTAATCTTG
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.29
19 30 0.52
21 11 0.19
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:34891 original size:28 final size:28
Alignment explanation
Indices: 34853--35017 Score: 133
Period size: 28 Copynumber: 5.9 Consensus size: 28
34843 CTTTAGAAAA
* *
34853 TGCCACGAAGGTGTTCCTTTCCATAGAT
1 TGCCACAAAGGTGTTCCTTTTCATAGAT
* * *
34881 TGCCACAAAGG-CTTCTGTTTTCCTAGAT
1 TGCCACAAAGGTGTTC-CTTTTCATAGAT
* *
34909 TGCCACAAAGGTG-TCTATTTTCATATAT
1 TGCCACAAAGGTGTTC-CTTTTCATAGAT
* * *
34937 TGTCACAAAGGT-CTCCATTTTCATATAT
1 TGCCACAAAGGTGTTCC-TTTTCATAGAT
* * *
34965 TGTCATAAAGGTG-TCCATTTTCATAAAT
1 TGCCACAAAGGTGTTCC-TTTTCATAGAT
34993 TGCCACAAAGGTG-TCCATTTTCATA
1 TGCCACAAAGGTGTTCC-TTTTCATA
35018 CATTTTCACG
Statistics
Matches: 117, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.03
28 114 0.97
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (28 bp):
TGCCACAAAGGTGTTCCTTTTCATAGAT
Found at i:34920 original size:56 final size:55
Alignment explanation
Indices: 34853--35017 Score: 170
Period size: 56 Copynumber: 2.9 Consensus size: 55
34843 CTTTAGAAAA
* * * ** *
34853 TGCCACGAAGGTGTTCCTTTCCATAGATTGCCACAAAGG-CTTCTGTTTTCCTAGAT
1 TGCCACAAAGGTG-TCCTTTTCATAAATTGCCACAAAGGTC-TCCATTTTCATAGAT
* * * *
34909 TGCCACAAAGGTGTCTATTTTCATATATTGTCACAAAGGTCTCCATTTTCATATAT
1 TGCCACAAAGGTGTC-CTTTTCATAAATTGCCACAAAGGTCTCCATTTTCATAGAT
* * *
34965 TGTCATAAAGGTGTCCATTTTCATAAATTGCCACAAAGGTGTCCATTTTCATA
1 TGCCACAAAGGTGTCC-TTTTCATAAATTGCCACAAAGGTCTCCATTTTCATA
35018 CATTTTCACG
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
55 2 0.02
56 88 0.97
57 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (55 bp):
TGCCACAAAGGTGTCCTTTTCATAAATTGCCACAAAGGTCTCCATTTTCATAGAT
Found at i:46159 original size:17 final size:17
Alignment explanation
Indices: 46137--46169 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
46127 AGCCAAGTAC
46137 GACTCAGTATAATAACG
1 GACTCAGTATAATAACG
46154 GACTCAGTATAATAAC
1 GACTCAGTATAATAAC
46170 CTCACCAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (17 bp):
GACTCAGTATAATAACG
Found at i:50647 original size:46 final size:46
Alignment explanation
Indices: 50591--50724 Score: 198
Period size: 46 Copynumber: 2.9 Consensus size: 46
50581 ATTTATGGTT
* * *
50591 TCTTCCATCCATCCCACTACAAATCAAGGGTATAGGATTTGTACCA
1 TCTTCAATCCATCCCACTACAACTCAGGGGTATAGGATTTGTACCA
* **
50637 TCTTCAATCCATCCCACTGCAACTCAGGGGTAT-GAGATTTGTATTA
1 TCTTCAATCCATCCCACTACAACTCAGGGGTATAG-GATTTGTACCA
50683 TCTTCAATCCATCCCACTACAACTCAGGGGTATAGGATTTGT
1 TCTTCAATCCATCCCACTACAACTCAGGGGTATAGGATTTGT
50725 GGCTTCTTCA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
45 1 0.01
46 77 0.97
47 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (46 bp):
TCTTCAATCCATCCCACTACAACTCAGGGGTATAGGATTTGTACCA
Found at i:50733 original size:46 final size:46
Alignment explanation
Indices: 50581--50737 Score: 183
Period size: 46 Copynumber: 3.4 Consensus size: 46
50571 GGGAGATAAA
* * * * *
50581 ATTTATGGTTTCTTCCATCCATCCCACTACAAATCAAGGGTATAGG
1 ATTTGTGGCTTCTTCAATCCATCCCACTACAACTCAGGGGTATAGG
** * *
50627 ATTTGTACCATCTTCAATCCATCCCACTGCAACTCAGGGGTAT-GAG
1 ATTTGTGGCTTCTTCAATCCATCCCACTACAACTCAGGGGTATAG-G
**
50673 ATTTGT-ATTATCTTCAATCCATCCCACTACAACTCAGGGGTATAGG
1 ATTTGTGGCT-TCTTCAATCCATCCCACTACAACTCAGGGGTATAGG
50719 ATTTGTGGCTTCTTCAATC
1 ATTTGTGGCTTCTTCAATC
50738 AATTTGATCT
Statistics
Matches: 92, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
45 1 0.01
46 89 0.97
47 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (46 bp):
ATTTGTGGCTTCTTCAATCCATCCCACTACAACTCAGGGGTATAGG
Found at i:51229 original size:53 final size:53
Alignment explanation
Indices: 51149--51251 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
51139 AGGAGCATAG
*
51149 CTCGAAATGAATAAATTAATTAAAGATAACAAATGCAATAAGAAGGAAATCAA
1 CTCGAAATGAATAAATTAATCAAAGATAACAAATGCAATAAGAAGGAAATCAA
* * ** *
51202 CTCGAAATGAATGAGTTAATCAAAGATAGTAAATGTAATAAGAAGGAAAT
1 CTCGAAATGAATAAATTAATCAAAGATAACAAATGCAATAAGAAGGAAAT
51252 TGATTGGTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.22
Consensus pattern (53 bp):
CTCGAAATGAATAAATTAATCAAAGATAACAAATGCAATAAGAAGGAAATCAA
Found at i:61347 original size:45 final size:43
Alignment explanation
Indices: 61265--61378 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 43
61255 TAACTTCGAT
* * *
61265 CTACTCCGCTGAAACTTAAAGGAGATAAAAATTGTGTATTTCATC
1 CTACTCCACTGCAACTTCAAGGAGATAAAAATTGTGTATTT--TC
**
61310 CTACTCCACTGCAACTTCAAGGAGAT-AAGGTTCGTGTATTTTC
1 CTACTCCACTGCAACTTCAAGGAGATAAAAATT-GTGTATTTTC
* * *
61353 CTGCCCCACTGCAACTTCAAGAAGAT
1 CTACTCCACTGCAACTTCAAGGAGAT
61379 TATGGCTTCC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 25 0.42
44 4 0.07
45 31 0.52
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (43 bp):
CTACTCCACTGCAACTTCAAGGAGATAAAAATTGTGTATTTTC
Found at i:61549 original size:45 final size:46
Alignment explanation
Indices: 61493--61612 Score: 127
Period size: 46 Copynumber: 2.6 Consensus size: 46
61483 AATCTATTCC
* * *
61493 ACTGGAACTTCAAAGAGGTAAGAATTG-GTAATTTCAACCTGCTCT
1 ACTGCAACTTCAGAGAGATAAGAATTGTGTAATTTCAACCTGCTCT
* ** * * *
61538 ACTGCAACTTCAGGGAGATAAGGCTTGTGTATTTTTATCCTGCTCT
1 ACTGCAACTTCAGAGAGATAAGAATTGTGTAATTTCAACCTGCTCT
*
61584 ACTGTAACTTCAGAGAGATAA-AGATTGTG
1 ACTGCAACTTCAGAGAGATAAGA-ATTGTG
61613 GCCTCGATCT
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
45 21 0.35
46 39 0.65
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (46 bp):
ACTGCAACTTCAGAGAGATAAGAATTGTGTAATTTCAACCTGCTCT
Found at i:61912 original size:143 final size:143
Alignment explanation
Indices: 61710--62070 Score: 463
Period size: 143 Copynumber: 2.5 Consensus size: 143
61700 TAATTTCAAC
* * * ** * *
61710 CTGCTCCACTGCAACTTTAAGGAGATAAGGCTAGTGGCTTTGATCTACTTCACTACAACTTCAGG
1 CTGCTCCGCTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGG
* ** * *
61775 AAGATAAGATCTGCCATAATTTGTAGCTTCAATCTGTTCCACTGTAACTTCAGGGAAATAAGATT
66 GAGATAAGATCTGCCATAATTTGTAGCTTCAATCTGTTCCACTACAACATCAGGGAAATAAGATC
** *
61840 TGCTATCTTTAGT
131 CACTATCTTCAGT
* * *
61853 CTGCTCTGCTGCAACTTCAGGGAGATAAGACTGGTGGCTTCAATCTACTCCACTGCAACTTCAGG
1 CTGCTCCGCTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGG
* * * *
61918 GAGATAA-AGTTTTCCATAATTTGTAGCTTTAATCTGTTCCACTACAACATCATGGAAATAAGAT
66 GAGATAAGA-TCTGCCATAATTTGTAGCTTCAATCTGTTCCACTACAACATCAGGGAAATAAGAT
61982 CCACTATCTTCAGT
130 CCACTATCTTCAGT
* * * * *
61996 CTGCTCCGCAGCAACTTCAAGAAGAAAAGGCTGGTGGCTGCAATCTGCTCCACTGCAACTTCAGG
1 CTGCTCCGCTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGG
62061 GAGATAAGAT
66 GAGATAAGAT
62071 TCACCATTAT
Statistics
Matches: 186, Mismatches: 30, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
142 1 0.01
143 184 0.99
144 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (143 bp):
CTGCTCCGCTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGG
GAGATAAGATCTGCCATAATTTGTAGCTTCAATCTGTTCCACTACAACATCAGGGAAATAAGATC
CACTATCTTCAGT
Found at i:66245 original size:20 final size:20
Alignment explanation
Indices: 66209--66247 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
66199 CCCACGTTGA
*
66209 CCCATTTTCTCTGCTTTTTG
1 CCCATTTTCGCTGCTTTTTG
66229 CCCATTTCTCGCT-CTTTTT
1 CCCATTT-TCGCTGCTTTTT
66248 ACTCTCCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.05, C:0.33, G:0.08, T:0.54
Consensus pattern (20 bp):
CCCATTTTCGCTGCTTTTTG
Found at i:66888 original size:17 final size:16
Alignment explanation
Indices: 66865--66906 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
66855 GAGATTGAAT
66865 TGAAAAATTACCTAAC
1 TGAAAAATTACCTAAC
66881 TAGAAAAA-TA-CTAAC
1 T-GAAAAATTACCTAAC
66896 TGAAAAATTAC
1 TGAAAAATTAC
66907 ATTCCTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.26
15 8 0.35
16 3 0.13
17 6 0.26
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (16 bp):
TGAAAAATTACCTAAC
Found at i:66896 original size:15 final size:15
Alignment explanation
Indices: 66865--66903 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 15
66855 GAGATTGAAT
66865 TGAAAAATTACCTAAC
1 TGAAAAA-TACCTAAC
66881 TAGAAAAATA-CTAAC
1 T-GAAAAATACCTAAC
66896 TGAAAAAT
1 TGAAAAAT
66904 TACATTCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.32
15 6 0.27
16 3 0.14
17 6 0.27
ACGTcount: A:0.56, C:0.13, G:0.08, T:0.23
Consensus pattern (15 bp):
TGAAAAATACCTAAC
Found at i:68216 original size:20 final size:21
Alignment explanation
Indices: 68186--68224 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
68176 AGTAAGTTAA
*
68186 AAAATAAATAAAGATAAAAGT
1 AAAATAAATAAAAATAAAAGT
68207 AAAA-AAATAAAAATAAAA
1 AAAATAAATAAAAATAAAA
68225 AGTCTTCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAATAAATAAAAATAAAAGT
Found at i:68218 original size:14 final size:15
Alignment explanation
Indices: 68185--68225 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
68175 AAGTAAGTTA
68185 AAAAATAAATAAAGAT
1 AAAAATAAA-AAAGAT
*
68201 AAAAGTAAAAAA-AT
1 AAAAATAAAAAAGAT
68215 AAAAATAAAAA
1 AAAAATAAAAA
68226 GTCTTCAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 3 0.13
16 8 0.35
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (15 bp):
AAAAATAAAAAAGAT
Found at i:71031 original size:24 final size:24
Alignment explanation
Indices: 70999--71053 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
70989 GGCATGGGTT
70999 AGGCTCCATCACGTTCTTCCTAAG
1 AGGCTCCATCACGTTCTTCCTAAG
71023 AGGCTCCATCACGTTCTTCCTAAG
1 AGGCTCCATCACGTTCTTCCTAAG
71047 AGGCTCC
1 AGGCTCC
71054 TGCAAAGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (24 bp):
AGGCTCCATCACGTTCTTCCTAAG
Found at i:76698 original size:40 final size:40
Alignment explanation
Indices: 76642--76988 Score: 601
Period size: 40 Copynumber: 8.7 Consensus size: 40
76632 TGAGCATTGG
76642 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
76682 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
76722 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
76762 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
76802 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
76842 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* *
76882 AATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAG--
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
76920 -ATGATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTT
1 AAT-ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
76960 GATATGTCCGGGTTAAGACCCGAAGGCAA
1 AATATATCCGGGCTAAGACCCGAAGGCAA
76989 AGGTGTTTGC
Statistics
Matches: 294, Mismatches: 9, Indels: 8
0.95 0.03 0.03
Matches are distributed among these distances:
37 2 0.01
38 32 0.11
40 258 0.88
41 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (40 bp):
AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
Done.