Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3357
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: 39267
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:3050 original size:52 final size:52
Alignment explanation
Indices: 2966--3069 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 52
2956 GTGCCAATCT
2966 CACAACCGTGAACACTTAATGCCCGCACACTTA-TGCCAATCTCACAACCGTGA
1 CACAACCGTGAACACTTAATGCCCGCACACTTAGTG-CAATCTCA-AACCGTGA
*
3019 CACAACCGTGAACA-TTATTGCCCGCACACTTAGTGCAATCTCAAACCGTGA
1 CACAACCGTGAACACTTAATGCCCGCACACTTAGTGCAATCTCAAACCGTGA
3070 ACACTATTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
51 8 0.16
52 25 0.51
53 16 0.33
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (52 bp):
CACAACCGTGAACACTTAATGCCCGCACACTTAGTGCAATCTCAAACCGTGA
Found at i:5233 original size:48 final size:49
Alignment explanation
Indices: 5138--5650 Score: 603
Period size: 46 Copynumber: 10.8 Consensus size: 49
5128 CTTATCACAT
* * * * * *
5138 TATACAC-TTCACATCCATCACGTTGGCCACTCA-GCCCTGTCACATATA
1 TATACACTTTCACATTCATCACATCGGCCA-TTAGGCCTTATCACATATA
5186 TATACAC-TTC-CATTCATCACATC-GCCATTAGGCCTTATCACATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
* *
5232 TA-AC-CTTTCACATTCATCACATCAGCCATTAGGCCTTATCAC--GTA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
5277 TATACAC-TTCACATTCATCACATCGGCCATTA-GCCTTATCAACATA-A
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC-ACATATA
5324 TATACACTTTTCACA-TCATCACATCGGCCATTAGG-C-TATCACATATA
1 TATACAC-TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
* *
5371 TATACACTTTCACATACATCAACATCGGCCATTAGGCCTTATCTC--ATA
1 TATACACTTTCACATTCATC-ACATCGGCCATTAGGCCTTATCACATATA
5419 TATACACTTTTCACATTCATCACATC-G-CATTAGGGCCTTATCAACA-ATA
1 TATACAC-TTTCACATTCATCACATCGGCCATTA-GGCCTTATC-ACATATA
* *
5468 TACACACTTTCA-ATTCATCACATCGGCCATTAGGCCCCTATCACATAATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGG-CCTTATCACAT-ATA
5518 TATACAC-TTCACATTCATCACATCGGCCATTAAGGCCTTATCACA-ATA
1 TATACACTTTCACATTCATCACATCGGCCATT-AGGCCTTATCACATATA
* *
5566 TATACACTTTCACATTCATCACATCGGCCATTAGGCCCTA-CAC--GTA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
*
5612 TATACACTTTCACATTCATCACAATCGGTCATTA-GCCTT
1 TATACACTTTCACATTCATCAC-ATCGGCCATTAGGCCTT
5651 CTATCATTTC
Statistics
Matches: 414, Mismatches: 21, Indels: 62
0.83 0.04 0.12
Matches are distributed among these distances:
44 1 0.00
45 19 0.05
46 105 0.25
47 88 0.21
48 88 0.21
49 68 0.16
50 42 0.10
51 3 0.01
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (49 bp):
TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
Found at i:5579 original size:241 final size:232
Alignment explanation
Indices: 5183--5650 Score: 646
Period size: 241 Copynumber: 2.0 Consensus size: 232
5173 CCTGTCACAT
5183 ATATATACACTTCCATTCATCACATCGCCATTAGGCCTTATCACATATATAACCTTTCACATTCA
1 ATATATACACTTCCATTCATCACATCGCCATTAGGCCTTATCACATATATAACCTTTCACATTCA
* *
5248 TCACATCAGCCATTAGGCCTTATCACGTATATACACTTCACATTCATCACATCGGCCATTAGCCT
66 TCACATCAGCCATTAGGCCCTATCACATATATACACTTCACATTCATCACATCGGCCATTAGCCT
* *
5313 TATCAACATAATATACACTTTTCACA-TCATCACATCGGCCATTAGGCTATCACATATATATACA
131 TATCAACATAATATACACTTTTCACATTCATCACATCGGCCATTAGGCCAT-ACACATATATACA
5377 CTTTCACATACATCA-ACATCGGCCATTAGGCCTTATCTC
195 CTTTCACATACATCACA-ATCGGCCATTA-GCCTTATCTC
5416 ATATATACACTTTTCACATTCATCACATCG-CATTAGGGCCTTATCAACA-ATATACACACTTTC
1 ATATATACAC--TTC-CATTCATCACATCGCCATTA-GGCCTTATC-ACATATATA-AC-CTTTC
*
5479 A-ATTCATCACATCGGCCATTAGGCCCCTATCACATAATATATACACTTCACATTCATCACATCG
59 ACATTCATCACATCAGCCATTAGG-CCCTATCAC---ATATATACACTTCACATTCATCACATCG
*
5543 GCCATTAAGGCCTTATC-ACA-ATATATACAC-TTTCACATTCATCACATCGGCCATTAGGCCCT
120 GCCATT-A-GCCTTATCAACATA-ATATACACTTTTCACATTCATCACATCGGCCATTAGGCCAT
* * *
5605 ACACGTATATACACTTTCACATTCATCACAATCGGTCATTAGCCTT
182 ACACATATATACACTTTCACATACATCACAATCGGCCATTAGCCTT
5651 CTATCATTTC
Statistics
Matches: 210, Mismatches: 9, Indels: 25
0.86 0.04 0.10
Matches are distributed among these distances:
233 10 0.05
235 8 0.04
236 28 0.13
237 26 0.12
238 14 0.07
240 5 0.02
241 76 0.36
242 35 0.17
243 8 0.04
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.31
Consensus pattern (232 bp):
ATATATACACTTCCATTCATCACATCGCCATTAGGCCTTATCACATATATAACCTTTCACATTCA
TCACATCAGCCATTAGGCCCTATCACATATATACACTTCACATTCATCACATCGGCCATTAGCCT
TATCAACATAATATACACTTTTCACATTCATCACATCGGCCATTAGGCCATACACATATATACAC
TTTCACATACATCACAATCGGCCATTAGCCTTATCTC
Found at i:10047 original size:25 final size:24
Alignment explanation
Indices: 10012--10063 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 24
10002 CTTATCTAAC
10012 AACCAAGTTAATAATCTTTCATCA
1 AACCAAGTTAATAATCTTTCATCA
10036 AACCAAGCTTAATAATCTTTCATCA
1 AACCAAG-TTAATAATCTTTCATCA
10061 AAC
1 AAC
10064 TTCAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.42, C:0.23, G:0.04, T:0.31
Consensus pattern (24 bp):
AACCAAGTTAATAATCTTTCATCA
Found at i:15025 original size:17 final size:17
Alignment explanation
Indices: 15005--15056 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
14995 TTCTAAAATT
15005 TAAAAATTATAAAAAAA
1 TAAAAATTATAAAAAAA
*
15022 TAAAATTTATATAAAAGTAAA
1 TAAAA-AT-TATAAAA--AAA
15043 TAAAAATTA-AAAAA
1 TAAAAATTATAAAAA
15057 TAAAATAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 1 0.03
17 5 0.17
18 5 0.17
19 9 0.31
20 1 0.03
21 8 0.28
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAAATTATAAAAAAA
Found at i:17902 original size:18 final size:21
Alignment explanation
Indices: 17860--17902 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 21
17850 ATAAATTATT
*
17860 TAAAATTATCACTATAAAAAT
1 TAAAATTATCACTATAAAAAA
17881 TAAAATTA-C-CT-TAAAAAA
1 TAAAATTATCACTATAAAAAA
17899 TAAA
1 TAAA
17903 TTGAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 1 0.05
21 8 0.38
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAATTATCACTATAAAAAA
Found at i:20822 original size:25 final size:25
Alignment explanation
Indices: 20791--20843 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
20781 TTTTTTTGAA
20791 GTTTGATGAAAGATTATTAAGCTTG
1 GTTTGATGAAAGATTATTAAGCTTG
20816 GTTTGATGAAAGATTATTAAGCTTG
1 GTTTGATGAAAGATTATTAAGCTTG
20841 GTT
1 GTT
20844 GTTAGATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.42
Consensus pattern (25 bp):
GTTTGATGAAAGATTATTAAGCTTG
Found at i:25368 original size:49 final size:48
Alignment explanation
Indices: 25213--25742 Score: 833
Period size: 47 Copynumber: 11.1 Consensus size: 48
25203 GAAATGATAG
*
25213 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTTATATATGTGA
*
25260 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTTATATATGTGA
25307 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-TATATATGTGA
*
25356 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-TATATATGTGA
*
25405 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTTATATATGTGA
25452 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-TATATATGTGA
25501 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-TATATATGTGA
*
25549 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTTATATATGTGA
25596 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTTATATATGTGA
*
25643 TAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-TATATATGTGA
* * * * * * *
25692 -CAGGGCTGAGTGGCCAACGTGATGGATGTGAAAGTG-TATAAATGTGA
1 TAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTTATATATGTGA
25739 TAAG
1 TAAG
25743 TCCCGAAGGG
Statistics
Matches: 454, Mismatches: 20, Indels: 17
0.92 0.04 0.03
Matches are distributed among these distances:
47 227 0.50
48 55 0.12
49 172 0.38
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (48 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTTATATATGTGA
Found at i:25387 original size:96 final size:94
Alignment explanation
Indices: 25213--25742 Score: 830
Period size: 96 Copynumber: 5.5 Consensus size: 94
25203 GAAATGATAG
* *
25213 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAGGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
25278 GTGATGAATGTGAAAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
*
25307 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
25372 ATGTGATGAATGTGAAAGTGTGTATATATGTGA
64 ATGTGATGAATGTGAAA--GTGTATATATGTGA
*
25405 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
25470 GTGATGAATGTGAAAGTGTATATATATGTGA
66 GTGATGAATGTGAAAGTG--TATATATGTGA
25501 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
25565 ATGTGATGAATGTGAAAGTGTATATACGTGA
64 ATGTGATGAATGTGAAAGTGTATATATGTGA
25596 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
25661 GTGATGAATGTGGAAGTGTATATATATGTGA
66 GTGATGAATGTGAAAGTG--TATATATGTGA
* * * * * * *
25692 -CAGGGCTGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
25743 TCCCGAAGGG
Statistics
Matches: 410, Mismatches: 14, Indels: 22
0.92 0.03 0.05
Matches are distributed among these distances:
94 85 0.21
95 50 0.12
96 179 0.44
97 46 0.11
98 50 0.12
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (94 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGA
Found at i:25917 original size:37 final size:37
Alignment explanation
Indices: 25861--25939 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
25851 CCGAGCTCTA
* * *
25861 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
25898 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
25935 AAGAC
1 AAGAC
25940 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:27851 original size:43 final size:43
Alignment explanation
Indices: 27803--27960 Score: 208
Period size: 43 Copynumber: 3.4 Consensus size: 43
27793 TTGGTTTTCA
27803 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
27846 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAAT-A------A-----GTGTTCACGGTTGTGAGATTG
27901 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
27944 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
27961 TTGAAATGCA
Statistics
Matches: 103, Mismatches: 0, Indels: 24
0.81 0.00 0.19
Matches are distributed among these distances:
43 58 0.56
44 1 0.01
48 1 0.01
50 1 0.01
54 1 0.01
55 41 0.40
ACGTcount: A:0.22, C:0.15, G:0.35, T:0.28
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:27885 original size:12 final size:12
Alignment explanation
Indices: 27868--27894 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27858 CGGGCAATAA
27868 GTGTTCACGGTT
1 GTGTTCACGGTT
27880 GTGTTCACGGTT
1 GTGTTCACGGTT
27892 GTG
1 GTG
27895 AGATTGGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.37, T:0.41
Consensus pattern (12 bp):
GTGTTCACGGTT
Found at i:27894 original size:55 final size:55
Alignment explanation
Indices: 27825--27937 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
27815 CGGGCAATAA
27825 GTGTTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGCAATAAGTGTTCACGGTT
1 GTGTTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGCAATAAGTGTTCACGGTT
27880 GTGTTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGCAATAAGTGTTCACGGTT
1 GTGTTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGCAATAAGTGTTCACGGTT
27935 GTG
1 GTG
27938 AGATTGGCAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.19, C:0.14, G:0.35, T:0.31
Consensus pattern (55 bp):
GTGTTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGCAATAAGTGTTCACGGTT
Found at i:27977 original size:29 final size:29
Alignment explanation
Indices: 27942--28015 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
27932 GTTGTGAGAT
* *
27942 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
27971 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
28000 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28016 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:28376 original size:40 final size:40
Alignment explanation
Indices: 28328--28430 Score: 152
Period size: 40 Copynumber: 2.6 Consensus size: 40
28318 TCGAATGATG
*
28328 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
* *
28368 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
* * *
28408 TCCGGGCTAGGTCCCGAAGAGCA
1 TCCGGACTAAGTTCCGAAGAGCA
28431 ATCATGCTGG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
Found at i:28439 original size:40 final size:40
Alignment explanation
Indices: 28328--28443 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 40
28318 TCGAATGATG
* * *
28328 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGACTAAGTCCCGAAGAGCATTCGTGCTGGTGATATA
* *
28368 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGACTAAGTCCCGAAGAGCATTCGTGCTGGTGATATA
* * * *
28408 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGACTAAGTCCCGAAGAGCATTCGTGCTGGTGA
28444 AGTGTATTCG
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGAGCATTCGTGCTGGTGATATA
Found at i:32337 original size:49 final size:47
Alignment explanation
Indices: 32182--32705 Score: 835
Period size: 47 Copynumber: 11.1 Consensus size: 47
32172 GAAATGATAG
*
32182 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
32229 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
32276 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
32325 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTGTATATATGTGA
32374 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
32421 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
32470 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
32518 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
32565 TAAGGCCTAATGGCTGATGTGATGAATGTG-AAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
32611 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * *
32657 -CAGGGCTGAGTGGCCAACGTGATGGATGTG-AAGTGTA-AAATGTGA
1 TAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
32702 TAAG
1 TAAG
32706 TCCCGAAGGG
Statistics
Matches: 455, Mismatches: 13, Indels: 19
0.93 0.03 0.04
Matches are distributed among these distances:
45 12 0.03
46 88 0.19
47 170 0.37
48 48 0.11
49 134 0.29
51 3 0.01
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.30
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:32357 original size:96 final size:94
Alignment explanation
Indices: 32182--32705 Score: 835
Period size: 96 Copynumber: 5.5 Consensus size: 94
32172 GAAATGATAG
* *
32182 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAGGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
32247 GTGATGAATGTGAAAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
32276 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
32341 ATGTGATGAATGTGAAAGTGTGTATATATGTGA
64 ATGTGATGAATGTGAAA--GTGTATATATGTGA
32374 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
32439 GTGATGAATGTGAAAGTGTATATATATGTGA
66 GTGATGAATGTGAAAGTG--TATATATGTGA
32470 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
32534 ATGTGATGAATGTGAAAGTGTATATATGTGA
64 ATGTGATGAATGTGAAAGTGTATATATGTGA
*
32565 TAAGGCCTAATGGCTGATGTGATGAATGTG-AAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
32629 GTGATGAATGTG-AAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * *
32657 -CAGGGCTGAGTGGCCAACGTGATGGATGTG-AAGTGTA-AAATGTGATAAG
1 TAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
32706 TCCCGAAGGG
Statistics
Matches: 409, Mismatches: 11, Indels: 23
0.92 0.02 0.05
Matches are distributed among these distances:
91 16 0.04
92 40 0.10
93 41 0.10
94 39 0.10
95 51 0.12
96 125 0.31
97 47 0.11
98 50 0.12
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.30
Consensus pattern (94 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGA
Found at i:32880 original size:37 final size:37
Alignment explanation
Indices: 32824--32902 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
32814 CCGAGCTCTA
* * *
32824 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
32861 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
32898 AAGAC
1 AAGAC
32903 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:34841 original size:43 final size:43
Alignment explanation
Indices: 34756--34887 Score: 250
Period size: 43 Copynumber: 3.1 Consensus size: 43
34746 TTGGTTTTCA
34756 GCACTAAGTGTGCGGGCAATAAGT-TTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
34798 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
34841 GCACTAAGTGTGCGGGCAATAAGTGTTCAC-GTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
34883 GCACT
1 GCACT
34888 GTGGCGGGCT
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
42 41 0.46
43 48 0.54
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.28
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:35308 original size:39 final size:39
Alignment explanation
Indices: 35259--35375 Score: 144
Period size: 39 Copynumber: 2.9 Consensus size: 39
35249 AATGATGTCC
*
35259 GACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG
1 GACT-AGTTCCGAAGAGCATTCGTGCTGGTGATGTATCCG
* *
35299 GACTAGTTCCGAAGAGCATTCGTGCTGGTGTTATATCCG
1 GACTAGTTCCGAAGAGCATTCGTGCTGGTGATGTATCCG
* * * *
35338 GGCTAGGTCCCGAAGAGCAATCATGCTGGTGAGTGTAT
1 GACTA-GTTCCGAAGAGCATTCGTGCTGGTGA-TGTAT
35376 TCGGCCTTCG
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
39 36 0.55
40 26 0.39
41 4 0.06
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (39 bp):
GACTAGTTCCGAAGAGCATTCGTGCTGGTGATGTATCCG
Found at i:39215 original size:88 final size:91
Alignment explanation
Indices: 39103--39267 Score: 275
Period size: 88 Copynumber: 1.8 Consensus size: 91
39093 ATGAAATGAA
39103 GTAAGGCCTAATGCCGATGTGATGAATGTGAAAGTG-TATA-ACGTGATA-GGCCTAATGGCGA-
1 GTAAGGCCTAATGCCGATGTGATGAATGTGAAAGTGTTATATACGTGATAGGGCCTAATGGCGAG
39164 TGATGAATGTGAAAGTGTATATATGT
66 TGATGAATGTGAAAGTGTATATATGT
*
39190 GTAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCGA
1 GTAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTTATATACGTGATAGGGCCTAATGGCGA
39255 TGTGATGAATGTG
65 -GTGATGAATGTG
Statistics
Matches: 71, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
87 12 0.17
88 24 0.34
89 4 0.06
90 7 0.10
91 13 0.18
93 11 0.15
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (91 bp):
GTAAGGCCTAATGCCGATGTGATGAATGTGAAAGTGTTATATACGTGATAGGGCCTAATGGCGAG
TGATGAATGTGAAAGTGTATATATGT
Found at i:39256 original size:47 final size:45
Alignment explanation
Indices: 39106--39267 Score: 242
Period size: 47 Copynumber: 3.6 Consensus size: 45
39096 AAATGAAGTA
* *
39106 AGGCCTAATGCCGATGTGATGAATGTGAAAGTGTATA-ACGTGAT
1 AGGCCTAATGGCGATGTGATGAATGTGAAAGTGTATATATGTGAT
39150 AGGCCTAATGGCGA--TGATGAATGTGAAAGTGTATATATGTG-T
1 AGGCCTAATGGCGATGTGATGAATGTGAAAGTGTATATATGTGAT
39192 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTTATATATGTGAT
1 -AGGCCTAATGG-CGATGTGATGAATGTGAAAGTG-TATATATGTGAT
39240 AGGGCCTAATGGCGATGTGATGAATGTG
1 A-GGCCTAATGGCGATGTGATGAATGTG
Statistics
Matches: 108, Mismatches: 2, Indels: 13
0.88 0.02 0.11
Matches are distributed among these distances:
42 22 0.20
43 15 0.14
44 16 0.15
46 17 0.16
47 27 0.25
48 11 0.10
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.29
Consensus pattern (45 bp):
AGGCCTAATGGCGATGTGATGAATGTGAAAGTGTATATATGTGAT
Done.