Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold734
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: 8088
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.23
Warning! 2115 characters in sequence are not A, C, G, or T
Found at i:1209 original size:62 final size:62
Alignment explanation
Indices: 1106--1230 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
1096 TCTCTTTTTT
*
1106 GCATTCATGCATCAACATTACATTTCATCGCATGCAATAAATTTCCTAAAATCCAAAAATAC
1 GCATTCATGCATCAACATTACATTTCATCGCATACAATAAATTTCCTAAAATCCAAAAATAC
* * * *
1168 GCATTCATGCATCAACATTACGTTTCATTGCATACAGTAAATTTCCTAAAATCCAAAAGTAC
1 GCATTCATGCATCAACATTACATTTCATCGCATACAATAAATTTCCTAAAATCCAAAAATAC
1230 G
1 G
1231 TCAAGTTTAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (62 bp):
GCATTCATGCATCAACATTACATTTCATCGCATACAATAAATTTCCTAAAATCCAAAAATAC
Found at i:3026 original size:22 final size:22
Alignment explanation
Indices: 3001--3043 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2991 TCACTTGAAA
3001 AAAAGAA-ATAAAAAAAGAAAAG
1 AAAAGAAGA-AAAAAAAGAAAAG
*
3023 AAAAGAAGAACAAAAAGAAAA
1 AAAAGAAGAAAAAAAAGAAAA
3044 AGGAGAGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAGAAGAAAAAAAAGAAAAG
Found at i:3895 original size:15 final size:15
Alignment explanation
Indices: 3875--3915 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
3865 TGACATTCTG
3875 CATTCATACAAATAT
1 CATTCATACAAATAT
*
3890 CATTCAATGCAAATAT
1 CATTC-ATACAAATAT
3906 CATTCATACA
1 CATTCATACA
3916 CATCTAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.32
Consensus pattern (15 bp):
CATTCATACAAATAT
Found at i:4162 original size:44 final size:45
Alignment explanation
Indices: 4082--4404 Score: 285
Period size: 44 Copynumber: 7.5 Consensus size: 45
4072 TCATTAAAGT
* * * *
4082 AGATCTTGTCTTCCTGTGTTGGCAGTGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGC
* * *
4127 AGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGC
* * * * * *
4170 AGATCTTGTCTTCCCATATTAGTGGCGGAGTAGATCGAAGAAAGT
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGC
* *
4215 AGATATTGTCTTCCTATGTT-G--GC-----AGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGC
* * * * *
4252 AGGTCCTATCTTCTTATATTGGTAG-GAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGC
* * * * *
4295 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGC
* * * *
4340 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGC
*
4384 AGGTCTTGTCTTCCTATATTG
1 AGATCTTGTCTTCCTATATTG
4405 TGGAACAGAT
Statistics
Matches: 218, Mismatches: 48, Indels: 25
0.75 0.16 0.09
Matches are distributed among these distances:
37 26 0.12
38 1 0.00
40 1 0.00
42 2 0.01
43 42 0.19
44 88 0.40
45 58 0.27
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (45 bp):
AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGC
Found at i:4307 original size:125 final size:125
Alignment explanation
Indices: 4113--4352 Score: 408
Period size: 125 Copynumber: 1.9 Consensus size: 125
4103 GCAGTGAAGT
*
4113 AGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTG
1 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTG
* * * *
4178 TCTTCCCATATTAGTGGCGGAGTAGATCGAAGAAAGTAGATATTGTCTTCCTATGTTGGC
66 TCTTCCCATACTAGTGGCGAAGTAGATCCAAGAAAGCAGATATTGTCTTCCTATGTTGGC
*
4238 AGATCGAAGATAGCAGGTCCTATCTTCTTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTG
1 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTG
* *
4303 TCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATCTTGTCTTC
66 TCTTCCCATACTAGTGGCGAAGTAGATCCAAGAAAGCAGATATTGTCTTC
4353 ATGTATTGGC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 107 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (125 bp):
AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTG
TCTTCCCATACTAGTGGCGAAGTAGATCCAAGAAAGCAGATATTGTCTTCCTATGTTGGC
Found at i:4362 original size:125 final size:125
Alignment explanation
Indices: 4113--4404 Score: 404
Period size: 125 Copynumber: 2.3 Consensus size: 125
4103 GCAGTGAAGT
*
4113 AGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTG
1 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTG
* * * * * *
4178 TCTTCCCATATTAGTGGCGGAGTAGATCGAAGAAAGTAGATATTGTCTTCCTATGTTGGC
66 TCTTCCCATACTAGTGGCGAAGTAGATCCAAGAAAGCAGATATTGTCTTCATATATTGGC
*
4238 AGATCGAAGATAGCAGGTCCTATCTTCTTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTG
1 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTG
* * *
4303 TCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTCCCATACTAGTGGCGAAGTAGATCCAAGAAAGCAGATATTGTCTTCATATATTGGC
* *
4363 GTGAAGTAGATCGAAGATAGCAGGTCTTGTCTTCCTATATTG
1 -------AGATCGAAGATAGCAGGTCCTATCTTCCTATATTG
4405 TGGAACAGAT
Statistics
Matches: 146, Mismatches: 14, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
125 114 0.78
132 32 0.22
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (125 bp):
AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTG
TCTTCCCATACTAGTGGCGAAGTAGATCCAAGAAAGCAGATATTGTCTTCATATATTGGC
Found at i:4470 original size:50 final size:50
Alignment explanation
Indices: 4411--4989 Score: 283
Period size: 50 Copynumber: 11.6 Consensus size: 50
4401 ATTGTGGAAC
* * *
4411 AGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTACAATTTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTTAAA
* *** * * * *****
4461 AGATTGAAGCTGCAACAATGAATCTTACTTCCATGGCGA-TGCAGTGGGGC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGAC-ATTGCAATTTAAA
* * * * *
4511 AGATTAAAGCTACAACAGCGAATCTTGCTT-CCTCAACATTACAATTTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCT-GACATTGCAATTTAAA
** * * * * * * * * **
4561 AGATTGAAGCCGCAACGACGAATCTCACTTCTCTGGCAGTACAGTGTAGC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTTAAA
* * * * * *
4611 AGATTAAAGCTACGACGGCGAATCTTGCTTTCTTGATATTGCAATTTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTTAAA
** * * * * ** **
4661 AGATTGAAGCCGCAACGGCGAATCTTACTTTCTTGGCGA-TGCAGTGGATC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGAC-ATTGCAATTTAAA
*
4711 AGATTGAAGCTACAACGGCGAATCTTA-TTCCCCGACATTGCAA-TTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTTAAA
* * * * * * * * * ** **
4759 GAGATTGAAGCCACAACGGTGAATCTCATTTCTCTGGCAGTACAGTGCAGC
1 -AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTTAAA
* * * * ** *
4810 AGATTAAAGCTACGACGGTGAATATTGTTTCCCTGATATTGCAATTTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTTAAA
** * * * * ** **
4860 AGATTGAAGCCGCAACGGCGAATCTTACTTTCTTGGCGA-TGCAGTGGATC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGAC-ATTGCAATTTAAA
* * * *
4910 AGATTGAAGCTACAACGGTGAATCTT-GTTCCCCGACATTGTAA-TTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTTAAA
* *
4958 GAGATTGAAGCCACAACGGCGAATCTCACTTC
1 -AGATTGAAGCTACAACGGCGAATCTTACTTC
4990 TCTAGCAAAC
Statistics
Matches: 368, Mismatches: 148, Indels: 26
0.68 0.27 0.05
Matches are distributed among these distances:
48 4 0.01
49 67 0.18
50 291 0.79
51 6 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTTAAA
Found at i:4584 original size:100 final size:99
Alignment explanation
Indices: 4404--4989 Score: 635
Period size: 100 Copynumber: 5.9 Consensus size: 99
4394 TTCCTATATT
* * * * *
4404 GTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTACAATTTAAAAGATTGAA
1 GTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAA
* *** *
4469 GCTGCAACAATGAATCTTACTTCCATGGCGATGCA
66 GCCGCAACGGCGAATCTCACTTCC-TGGCGATGCA
* * * * *
4504 GTGGGGCAGATTAAAGCTACAACAGCGAATCTTGCTTCCTCAACATTACAATTTAAAAGATTGAA
1 GTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAA
* *
4569 GCCGCAACGACGAATCTCACTTCTCTGGC-AGTACA
66 GCCGCAACGGCGAATCTCACTTC-CTGGCGA-TGCA
* * * ** *
4604 GTGTAGCAGATTAAAGCTACGACGGCGAATCTTGCTTTCTTGATATTGCAATTTAAAAGATTGAA
1 GTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAA
* *
4669 GCCGCAACGGCGAATCTTACTTTCTTGGCGATGCA
66 GCCGCAACGGCGAATCTCAC-TTCCTGGCGATGCA
* * *
4704 GTGGATCAGATTGAAGCTACAACGGCGAATCTT-ATTCCCCGACATTGCAA-TTAAAGAGATTGA
1 GTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAA-AGATTGA
* * * *
4767 AGCCACAACGGTGAATCTCATTTCTCTGGC-AGTACA
65 AGCCGCAACGGCGAATCTCACTTC-CTGGCGA-TGCA
* * * * * * *
4803 GTGCAGCAGATTAAAGCTACGACGGTGAATATTGTTTCCCTGATATTGCAATTTAAAAGATTGAA
1 GTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAA
* *
4868 GCCGCAACGGCGAATCTTACTTTCTTGGCGATGCA
66 GCCGCAACGGCGAATCTCAC-TTCCTGGCGATGCA
* * * *
4903 GTGGATCAGATTGAAGCTACAACGGTGAATCTTG-TTCCCCGACATTGTAA-TTAAAGAGATTGA
1 GTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAA-AGATTGA
*
4966 AGCCACAACGGCGAATCTCACTTC
65 AGCCGCAACGGCGAATCTCACTTC
4990 TCTAGCAAAC
Statistics
Matches: 408, Mismatches: 66, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
98 17 0.04
99 110 0.27
100 267 0.65
101 14 0.03
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (99 bp):
GTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAA
GCCGCAACGGCGAATCTCACTTCCTGGCGATGCA
Found at i:4849 original size:199 final size:199
Alignment explanation
Indices: 4410--4992 Score: 837
Period size: 199 Copynumber: 2.9 Consensus size: 199
4400 TATTGTGGAA
* * ** * * * *
4410 CAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTACAATTTAAAAGATTGAAGCTGCA
1 CAGATTAAAGCTACGACGGTGAATCTTGTTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCA
*** * * ** * * *
4475 ACAATGAATCTTACTTCCATGGCGATGCAGTGGGGCAGATTAAAGCTACAACAGCGAATCTTGCT
66 ACGGCGAATCTTACTTTCTTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTT-AT
* * * * *
4540 TCCTCAACATTACAATTTAAA-AGATTGAAGCCGCAACGACGAATCTCACTTCTCTGGCAGTACA
130 TCCCCGACATTGCAA-TTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACA
*
4604 GTGTAG
194 GTGCAG
* *
4610 CAGATTAAAGCTACGACGGCGAATCTTGCTTT-CTTGATATTGCAATTTAAAAGATTGAAGCCGC
1 CAGATTAAAGCTACGACGGTGAATCTTG-TTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGC
4674 AACGGCGAATCTTACTTTCTTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTTAT
65 AACGGCGAATCTTACTTTCTTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTTAT
* *
4739 TCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGTGAATCTCATTTCTCTGGCAGTACAG
130 TCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAG
4804 TGCAG
195 TGCAG
*
4809 CAGATTAAAGCTACGACGGTGAATATTGTTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCA
1 CAGATTAAAGCTACGACGGTGAATCTTGTTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCA
* *
4874 ACGGCGAATCTTACTTTCTTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGTGAATCTTGTT
66 ACGGCGAATCTTACTTTCTTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTTATT
*
4939 CCCCGACATTGTAATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCT
131 CCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCT
4993 AGCAAACAGA
Statistics
Matches: 344, Mismatches: 36, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
198 8 0.02
199 229 0.67
200 105 0.31
201 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (199 bp):
CAGATTAAAGCTACGACGGTGAATCTTGTTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCA
ACGGCGAATCTTACTTTCTTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTTATT
CCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGT
GCAG
Found at i:5065 original size:40 final size:41
Alignment explanation
Indices: 4993--5288 Score: 343
Period size: 40 Copynumber: 7.2 Consensus size: 41
4983 TCACTTCTCT
* * * * *
4993 AGCAAACAGAAACCAGATCTTATCTCTCTAAGCAGTAGTGG
1 AGCAGACAGAATCAAGATCTTATCTCCCTAAGCAATAGTGG
* *
5034 AGCAGATC-GCATCAAG-TCTTACCTCCCTAAGCAATAGTGG
1 AGCAGA-CAGAATCAAGATCTTATCTCCCTAAGCAATAGTGG
*
5074 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGG
1 AGCAGACAGAATCA-AGATCTTATCTCCCTAAGCAATAGTGG
* *
5116 AGCAGATC-GCATCAAG-TCTTATCTCCCTAAACAATAGTGG
1 AGCAGA-CAGAATCAAGATCTTATCTCCCTAAGCAATAGTGG
*
5156 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGG
1 AGCAGACAGAATCA-AGATCTTATCTCCCTAAGCAATAGTGG
* ** *
5198 AGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGG
1 AGCAGACAGAATCAA--GATCTTATCTCCCTAAGCAATAGTGG
*
5241 AGCAGATCA-CATCAAG-TCTTATCTCCCTAAGCAATAGTGG
1 AGCAGA-CAGAATCAAGATCTTATCTCCCTAAGCAATAGTGG
5281 AGCAGACA
1 AGCAGACA
5289 NNNNNNNNNN
Statistics
Matches: 220, Mismatches: 24, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
39 4 0.02
40 93 0.42
41 18 0.08
42 68 0.31
43 35 0.16
44 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (41 bp):
AGCAGACAGAATCAAGATCTTATCTCCCTAAGCAATAGTGG
Found at i:5143 original size:82 final size:82
Alignment explanation
Indices: 4993--5286 Score: 391
Period size: 82 Copynumber: 3.6 Consensus size: 82
4983 TCACTTCTCT
* * * * *
4993 AGCAAACAGAAAC-CAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTACC
1 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATC
5057 TCCCTAAGCAATAGTGG
66 TCCCTAAGCAATAGTGG
5074 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATC
1 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATC
*
5139 TCCCTAAACAATAGTGG
66 TCCCTAAGCAATAGTGG
** **
5156 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGA-CAAAAGAAACCGATCT
1 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATC-GCATCAA--G-TCT
*
5220 TATCTCCCTAAGCAGTAGTGG
62 TATCTCCCTAAGCAATAGTGG
* *
5241 AGCAGATCA-CATCA-AG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA
1 AGCAGA-CAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGA
5287 CANNNNNNNN
Statistics
Matches: 193, Mismatches: 14, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
81 12 0.06
82 115 0.60
83 30 0.16
84 3 0.02
85 31 0.16
86 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (82 bp):
AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATC
TCCCTAAGCAATAGTGG
Found at i:5246 original size:125 final size:122
Alignment explanation
Indices: 5010--5288 Score: 407
Period size: 125 Copynumber: 2.3 Consensus size: 122
5000 AGAAACCAGA
* * * *
5010 TCTTATCTCTCTAAGCAGTAGTGGAGCAGATC-GCATCAAGTCTTACCTCCCTAAGCAATAGTGG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CAGAACCAAGTCTTACCTCCCTAAGCAATAGTGG
* ** *
5074 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAG
65 AGCAGACAAAAAAACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCACATCAAG
* *
5132 TCTTATCTCCCTAAACAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCA-AG-TCTTACCTCCCTAAGCAATAGTG
* *
5197 GAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
64 GAGCAGACAAAA-AAACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCACATCAAG
5257 TCTTATCTCCCTAAGCAATAGTGGAGCAGACA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACA
5289 NNNNNNNNNN
Statistics
Matches: 140, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
121 1 0.01
122 31 0.22
123 2 0.01
124 33 0.24
125 73 0.52
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (122 bp):
TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCAAGTCTTACCTCCCTAAGCAATAGTGGA
GCAGACAAAAAAACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCACATCAAG
Found at i:7417 original size:2 final size:2
Alignment explanation
Indices: 7410--7436 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7400 NNNNTTTTCT
7410 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7437 CATTTCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7574 original size:31 final size:29
Alignment explanation
Indices: 7530--7604 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
7520 TCTATTTTAA
* * *
7530 ATATACTATTTATTTTTTAATTGTTTCTATT
1 ATATTCTATTTATTTTCTAATT-TTTATA-T
*
7561 ATTATT-TATTTATTGTCTAATTTTTATAT
1 A-TATTCTATTTATTTTCTAATTTTTATAT
7590 ATATTCTATTTATTT
1 ATATTCTATTTATTT
7605 GAAACGTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 4 0.11
29 10 0.27
30 5 0.14
31 15 0.41
32 3 0.08
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (29 bp):
ATATTCTATTTATTTTCTAATTTTTATAT
Done.