Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_813
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: 45801
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:1308 original size:93 final size:93
Alignment explanation
Indices: 1195--1366 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
1185 GCCCATAAGT
*
1195 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1260 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
1288 GAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
1353 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
1367 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:1362 original size:46 final size:46
Alignment explanation
Indices: 1187--1362 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
1177 TGTAACCCGC
*
1187 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
1233 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** * *
1279 ACATCTCTCGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
1326 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1363 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 69 0.63
47 31 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:9081 original size:9 final size:9
Alignment explanation
Indices: 9067--9107 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
9057 TTCTATTTCA
9067 AAAAAAAAG
1 AAAAAAAAG
9076 AAAAAAAAG
1 AAAAAAAAG
*
9085 AAAAACAAG
1 AAAAAAAAG
* *
9094 AGAAAAAAT
1 AAAAAAAAG
9103 AAAAA
1 AAAAA
9108 GAAAAATGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:10264 original size:132 final size:132
Alignment explanation
Indices: 10097--10454 Score: 581
Period size: 132 Copynumber: 2.7 Consensus size: 132
10087 AGGGAACAAG
* *
10097 TTGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTCGAAGATAGCAGATTTGGCAT
1 TTGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCAT
* *
10162 CCCTGTGTTTATAGGGAACAAATCGAAGATAGCAAATCTGACATTCTTGTGCTTACAGTGAAGCA
66 CCCTGTGTTTATAGGGAACAAATCGAAGATAGCAAATCTGACATTCCTGTGCTTACAGCGAAGCA
10227 GA
131 GA
*
10229 TTGAAGATTTCAGCATGGCATCCTTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCAT
1 TTGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCAT
* *
10294 CCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTATAGCGAAGCA
66 CCCTGTGTTTATAGGGAACAAATCGAAGATAGCAAATCTGACATTCCTGTGCTTACAGCGAAGCA
10359 GA
131 GA
** *
10361 TCAAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGTAGATTTGGCAT
1 TTGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCAT
* * * * *
10426 CCTTGTGCTTACAAGGAACAAATTGAAGA
66 CCCTGTGTTTATAGGGAACAAATCGAAGA
10455 CATAGCTGAT
Statistics
Matches: 210, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 210 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (132 bp):
TTGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCAT
CCCTGTGTTTATAGGGAACAAATCGAAGATAGCAAATCTGACATTCCTGTGCTTACAGCGAAGCA
GA
Found at i:10267 original size:175 final size:175
Alignment explanation
Indices: 9976--10351 Score: 574
Period size: 175 Copynumber: 2.1 Consensus size: 175
9966 CACAGAAACA
* * *
9976 AGATTTGGTATCCCTGTGTTTACAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAAATCTGACACTCCTGTGCTT
*
10041 ACAGCAAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATT
66 ACAGCAAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
* *
10106 TCAGCA-TGGCATCCCTGTGCTTATAGGGAACAAGTCGAAGATAGC
131 GCAG-ATTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
* *
10151 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAAATCTGACATTCTTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAAATCTGACACTCCTGTGCTT
** * *
10216 ACAGTGAAGCAGATTGAAGATTTCAGCATGGCATCCTTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCAAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
*
10281 GCAGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
131 GCAGA-TTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
* * * *
10327 AGATCTGACATTCCTGTGCTTATAG
1 AGATTTGGCATCCCTGTGTTTATAG
10352 CGAAGCAGAT
Statistics
Matches: 182, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
174 1 0.01
175 123 0.68
176 58 0.32
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (175 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAAATCTGACACTCCTGTGCTT
ACAGCAAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GCAGATTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
Found at i:10452 original size:44 final size:44
Alignment explanation
Indices: 9976--10469 Score: 376
Period size: 44 Copynumber: 11.2 Consensus size: 44
9966 CACAGAAACA
* * *
9976 AGATTTGGTATCCCTGTGTTTACAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
* * * ** * **
10020 AGATCTGACA-CTCCTGTGCTTACAGCAAAGCAGATCGAAGATTTC
1 AGATTTGGCATC-CCTGTGCTTATAGGGAA-CAAATCGAAGATAGC
* * * **
10065 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATTTC
1 AG-ATTTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
*
10108 AGCA--TGGCATCCCTGTGCTTATAGGGAACAAGTCGAAGATAGC
1 AG-ATTTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
*
10151 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
* * * * * * * * * **
10195 AAATCTGACATTCTTGTGCTTACAGTGAAGCAGATTGAAGATTTC
1 AGATTTGGCATCCCTGTGCTTATAGGGAA-CAAATCGAAGATAGC
* * * *
10240 AGCA--TGGCATCCTTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
*
10283 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
* * * * * * **
10327 AGATCTGACATTCCTGTGCTTATAGCGAAGCAGATCAAAGATTTC
1 AGATTTGGCATCCCTGTGCTTATAGGGAA-CAAATCGAAGATAGC
* * * *
10372 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGT
1 AG-ATTTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
* * * *
10415 AGATTTGGCATCCTTGTGCTTACAAGGAACAAATTGAAGACATAGC
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAAATCGAAG--ATAGC
*
10461 TGATTTGGC
1 AGATTTGGC
10470 TTTCACGTGC
Statistics
Matches: 359, Mismatches: 75, Indels: 30
0.77 0.16 0.06
Matches are distributed among these distances:
42 3 0.01
43 77 0.21
44 224 0.62
45 40 0.11
46 15 0.04
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAGC
Found at i:10770 original size:206 final size:206
Alignment explanation
Indices: 10416--10944 Score: 828
Period size: 206 Copynumber: 2.6 Consensus size: 206
10406 GAAGATAGTA
*
10416 GATTTGGCATCCTTGTGCTTACAAGGAACAAATTGAAGACATAGCTGATTTGGCTTTCACGTGCT
1 GATTTGGCATTCTTGTGCTTACAAGGAACAAATTGAAGACATAGCTGATTTGGCTTTCACGTGCT
10481 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGG
* * * * *
10546 CGTCTCCATATTCGATGGAGAGCAGACACATAGCAGGTTTGACCTTCAGATGTTTATACTGAAGC
131 CGTCTCCATATTCGATGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGATTAGACTGAAGC
10611 AGATCCAAGAT
196 AGATCCAAGAT
* *
10622 GATTTGGCATTCTTGTGCTTACAAGGAACAAATCGAAAACATAGCTGATTTGGCTTTCACGTGCT
1 GATTTGGCATTCTTGTGCTTACAAGGAACAAATTGAAGACATAGCTGATTTGGCTTTCACGTGCT
10687 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGG
* * *
10752 CGTCTCCATATTCGATGGAGGGCAGACACATAGCAGATCTAACCTTTAGATGATTAGACTGAAGT
131 CGTCTCCATATTCGATGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGATTAGACTGAAGC
10817 AGATCCAAGAT
196 AGATCCAAGAT
* * * * * * * *
10828 -AGTTTGGTA-TCATTATGCTTGCAAGGAGCAAATTGAAGACATAGTTGATTTGGTTTTCGCGTA
1 GA-TTTGGCATTC-TTGTGCTTACAAGGAACAAATTGAAGACATAGCTGATTTGGCTTTCACGTG
* * *
10891 CTTACGATGAAGCAAATCTAAGATGATTTGACATCTTTGTATTGTCAGAAAACA
64 CTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACA
10945 GATCGAAGAT
Statistics
Matches: 297, Mismatches: 24, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
205 3 0.01
206 294 0.99
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (206 bp):
GATTTGGCATTCTTGTGCTTACAAGGAACAAATTGAAGACATAGCTGATTTGGCTTTCACGTGCT
TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGG
CGTCTCCATATTCGATGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGATTAGACTGAAGC
AGATCCAAGAT
Found at i:11363 original size:19 final size:19
Alignment explanation
Indices: 11339--11436 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
11329 AATCTTTAAG
11339 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11358 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11377 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11394 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11413 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
11434 GAT
1 GAT
11437 CTTGTAATCT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:11369 original size:36 final size:35
Alignment explanation
Indices: 11329--11436 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 35
11319 ATGGAAATAT
11329 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
11365 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
11401 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
11437 CTTGTAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 28 0.46
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:15571 original size:47 final size:47
Alignment explanation
Indices: 15511--15977 Score: 673
Period size: 47 Copynumber: 9.9 Consensus size: 47
15501 TTAGGATTTT
* ** * * * * *
15511 ATGTGATGGATGTGAATGTGTATACATGAGCTAAGGCCGAATGACAA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * *
15558 ATGTGATGAATGTGAACATGCATTTGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
*
15605 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
15652 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
15699 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
15746 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * *
15793 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * *
15840 ATGTGAAGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * * *
15887 ATGTGATAAATGTGAACATGCATACATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * ** ** *
15934 ATGTGATGAACGTGGATGTGTATATATGTGGGAAAGCCGAATGG
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGG
15978 TTAATGCGAA
Statistics
Matches: 381, Mismatches: 39, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 381 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
Found at i:15940 original size:22 final size:22
Alignment explanation
Indices: 15865--15940 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
15855 ACATGCATAT
*
15865 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCAGAATGGCCA
*
15887 ATGTGATAAATGTG-A-ACAT-GCATA
1 ATGTGAT-AA-G-GCAGA-ATGGC-CA
15911 CATGTGATAAGGCAGAATGGCCA
1 -ATGTGATAAGGCAGAATGGCCA
15934 ATGTGAT
1 ATGTGAT
15941 GAACGTGGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 15 0.36
23 10 0.24
24 9 0.21
25 8 0.19
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.24
Consensus pattern (22 bp):
ATGTGATAAGGCAGAATGGCCA
Found at i:16010 original size:46 final size:46
Alignment explanation
Indices: 15957--16047 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
15947 GGATGTGTAT
* * **
15957 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
16003 ATATGTGGTAAAGCCAAATGGCTAATGTGAGACATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
16048 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:17808 original size:194 final size:194
Alignment explanation
Indices: 17407--17860 Score: 448
Period size: 194 Copynumber: 2.3 Consensus size: 194
17397 AAAGAACAAT
** * * * * ** ** *
17407 ATTATAATTTATTTAATTTATGGGATTCAAAAATAAATTATTGTGTTCATTCATTCATACACAAT
1 ATTATAATTTATTTAATTTACAGGATTCAAATAGAAATTACTATCATCATTCATTCATACGTAGT
* * * * * ** ** * * * *
17472 TCTTTACATTACACATACTTGTGAAGATTGATTGGATAATTGATTTGATTTTTAGTGTTAAATAC
66 TATTAATATTACTCGTGTTTGTGAAGATCCATCGTATAATTGATTTAATTTTTAGAGTTAAATAC
* ** * * * *
17537 AAACCATAGGCTTTATTTATTTTTATGCAGTTCTTAATATTGCACGTGTTTTGCCAAGATGGAA
131 AAACCATAGGCTTTAGTTATAATTATGCAGTTCTCAATATTACACATGTTTTGCCAAGATCGAA
* * * *
17601 ATTATAATTTATTTAATTTA-TGAGATTCAAATATAAATTACTATCGTCA-TCTATTCATATGTA
1 ATTATAATTTATTTAATTTACAG-GATTCAAATAGAAATTACTATCATCATTC-ATTCATACGTA
17664 GTTATTAATATTACTCGTGTTTGTGAAGATCCATCGTATAATTGATTTAATTTTTAGAGTTCAAA
64 GTTATTAATATTACTCGTGTTTGTGAAGATCCATCGTATAATTGATTTAATTTTTAGAGTT-AAA
* * * * *
17729 TACAAACCATCGTCTTT-GTTATAATTATGCAGTTCTCAATATTACACATGTTTTGTCAATATCT
128 TACAAACCATAGGCTTTAGTTATAATTATGCAGTTCTCAATATTACACATGTTTTGCCAAGATCG
*
17793 ATC
193 A-A
* * *
17796 A-TATAGTTTATTTAATTTACAGGATTCAAATAGAAATTATTGTCATCATTCATTCATACGTAGT
1 ATTATAATTTATTTAATTTACAGGATTCAAATAGAAATTACTATCATCATTCATTCATACGTAGT
17860 T
66 T
17861 CTTTAAATTA
Statistics
Matches: 211, Mismatches: 43, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
193 3 0.01
194 186 0.88
195 22 0.10
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (194 bp):
ATTATAATTTATTTAATTTACAGGATTCAAATAGAAATTACTATCATCATTCATTCATACGTAGT
TATTAATATTACTCGTGTTTGTGAAGATCCATCGTATAATTGATTTAATTTTTAGAGTTAAATAC
AAACCATAGGCTTTAGTTATAATTATGCAGTTCTCAATATTACACATGTTTTGCCAAGATCGAA
Found at i:19737 original size:40 final size:40
Alignment explanation
Indices: 19643--19823 Score: 206
Period size: 40 Copynumber: 4.5 Consensus size: 40
19633 TATTCGAATG
* *
19643 ATATCTGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTGACT
* *
19684 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGTGACT
* *
19724 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * **
19764 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
19803 ATATCC-GGCTAAATCCTGAAG
1 ATATCCGGGCTAAGTCCCGAAG
19824 ATACTTGGGT
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
38 12 0.10
39 16 0.13
40 63 0.52
41 28 0.23
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:25194 original size:40 final size:40
Alignment explanation
Indices: 25100--25280 Score: 206
Period size: 40 Copynumber: 4.5 Consensus size: 40
25090 TATTCGAATG
* *
25100 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTACTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTGACT
* *
25141 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGTGACT
* *
25181 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * **
25221 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
25260 ATATCC-GGCTAAATCCTGAAG
1 ATATCCGGGCTAAGTCCCGAAG
25281 ATACTTGGGT
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
38 12 0.10
39 16 0.13
40 63 0.52
41 28 0.23
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:26914 original size:14 final size:14
Alignment explanation
Indices: 26897--26927 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
26887 TAAATCGCGA
26897 AACCTAAATTAAAT
1 AACCTAAATTAAAT
26911 AACCTAAATTAAAT
1 AACCTAAATTAAAT
26925 AAC
1 AAC
26928 ATCCATCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCTAAATTAAAT
Found at i:28490 original size:26 final size:26
Alignment explanation
Indices: 28461--28510 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
28451 TGAGTTGTCA
* *
28461 AAAATCACATATATGGTTATGAATCC
1 AAAATCAAATATATAGTTATGAATCC
*
28487 AAAATCAAATATTTAGTTATGAAT
1 AAAATCAAATATATAGTTATGAAT
28511 ATGTCCCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (26 bp):
AAAATCAAATATATAGTTATGAATCC
Found at i:37453 original size:97 final size:96
Alignment explanation
Indices: 37185--37475 Score: 259
Period size: 97 Copynumber: 3.0 Consensus size: 96
37175 TTACACGTAC
* ** * * * * *
37185 TTGTGAAGATTGATCGGATGATTGATTT-GATTTTGTGTTAAAATACAAACCATAGTCTTCAATT
1 TTGTGAAGATCGATCATATAATTGATTTAGTTTTTGAGTTCAAATACAAACCATAGTCTTCATTT
* * * *
37249 ATTCTTATGTAATTCTTAATATTA-TACATGT
66 ATTATTATGTAGTTCTCAATATTACT-CGTGT
* * * * * ** *
37280 TTGGTGAAGATGGAT-ATTATAATTTATTTAATTTATGAGATTCAAATATAAATTATTA-TCGTC
1 TT-GTGAAGATCGATCA-TATAATTGATTTAGTTTTTGAG-TTCAAATACAAACCA-TAGTCTTC
* *
37343 ATGTATTCA-TATGTAGTTATCAATATTACTCGTGT
62 ATTTATT-ATTATGTAGTTCTCAATATTACTCGTGT
**
37378 TTGTGAAGATCGATCATATAATTGATTTAGTTTTTAGAGTTCAAATACAAACCAGCGTCTTCATT
1 TTGTGAAGATCGATCATATAATTGATTTAGTTTTT-GAGTTCAAATACAAACCATAGTCTTCATT
*
37443 TATTATTATGTAGTTCTCAATATTACACGTGT
65 TATTATTATGTAGTTCTCAATATTACTCGTGT
37475 T
1 T
37476 CATCTATCAT
Statistics
Matches: 151, Mismatches: 34, Indels: 20
0.74 0.17 0.10
Matches are distributed among these distances:
95 2 0.01
96 21 0.14
97 79 0.52
98 46 0.30
99 3 0.02
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (96 bp):
TTGTGAAGATCGATCATATAATTGATTTAGTTTTTGAGTTCAAATACAAACCATAGTCTTCATTT
ATTATTATGTAGTTCTCAATATTACTCGTGT
Found at i:38493 original size:23 final size:23
Alignment explanation
Indices: 38454--38498 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
38444 TAATTATTTG
*
38454 TAATGTTATTTGGTAACTTTTTT
1 TAATGTTATTTGGTAACATTTTT
*
38477 TAATAGTTATTT-TTAACATTTT
1 TAAT-GTTATTTGGTAACATTTT
38499 CTTTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.27, C:0.04, G:0.09, T:0.60
Consensus pattern (23 bp):
TAATGTTATTTGGTAACATTTTT
Found at i:38586 original size:26 final size:26
Alignment explanation
Indices: 38557--38606 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
38547 TGAGTTGTCA
* *
38557 AAAATCACATATATGGTTATGAATCC
1 AAAATCAAATATATGATTATGAATCC
*
38583 AAAATCAAATATTTGATTATGAAT
1 AAAATCAAATATATGATTATGAAT
38607 ATGTCCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (26 bp):
AAAATCAAATATATGATTATGAATCC
Found at i:44504 original size:3 final size:3
Alignment explanation
Indices: 44496--44545 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
44486 TTTTGTTTTG
* *
44496 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA AAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44543 TAT
1 TAT
44546 GCATTCTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Done.