Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2360
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: 52046
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:6506 original size:74 final size:73
Alignment explanation
Indices: 6409--6615 Score: 231
Period size: 73 Copynumber: 2.8 Consensus size: 73
6399 ATTTCTGTTC
* ** * *
6409 CAAAGATCAACTTATAGGGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCAAATT
1 CAAAAATCAACTTATACTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTC-AA-T
6474 C-TT-TTT-T
64 CGTTGTTTGT
* * * * *
6481 CAAAAAAATCAACTTATATTACGAGAGGTGAGTTGAGCCTCGGGGCACGGTGAGGAATTTTCAAT
1 C--AAAAATCAACTTATACTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAT
6546 CGTTGTTTGT
64 CGTTGTTTGT
* * * *
6556 CAAAAATCAACTCATACTGCCAGAGGAGAGTTAAGCCTCAGGGCACGCTGAGGTATTTTC
1 CAAAAATCAACTTATACTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTC
6616 GATTTCCGCT
Statistics
Matches: 112, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
72 3 0.03
73 54 0.48
74 53 0.47
75 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (73 bp):
CAAAAATCAACTTATACTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATCG
TTGTTTGT
Found at i:6816 original size:164 final size:163
Alignment explanation
Indices: 6462--7108 Score: 610
Period size: 164 Copynumber: 4.0 Consensus size: 163
6452 CATGCTGAGG
* * * * * *
6462 TATTTTCAAATTCT-TTTTTCAAAAAAATCAACTTATATTACGAGAGGTGAGTTGAGCCTCGGGG
1 TATTTTCAATTTCTGTTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
* * * * *
6526 CACGGTGAGG-AATTTTCAATCGT-TGTTTGTC-AAAAATCAACTCATA-CTGCCAGAGGAGAGT
66 CACGCTGAGGTAACTTTCAAT-TTCTGTTTGTCAAAAAATCAACTCATATC-GCGAGAGGTGAGT
* *
6587 TAAGCCTCAGGGCACGCTGAGGTATTTTCGATTTCC
129 TGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT-C
** * **
6623 GCTTTCCAATTTCTCCTCTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
1 TATTTTCAATTTCTGTTCTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
*
6688 GAAACGCTGAGGTAA-TTTCAATTTCTGTTTGTC-AAAAATCAACTCATATCGCGAGAGGTGAGT
64 GACACGCTGAGGTAACTTTCAATTTCTGTTTGTCAAAAAATCAACTCATATCGCGAGAGGTGAGT
* *
6751 TGAGCCTC-GGCTCACATGCTGAGGTCTTTTCAATTTC
129 TGAGCCTCAGG-GCAC--GCTGAGGTATTTTCAATTTC
*
6788 TATTTTTCAATTTCTGTTCGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TA-TTTTCAATTTCTGTTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
*
6853 GCACGCTGAGGTATTTTCGATTTCTACTTTCCAATTTCTGTCTT-TCAAAATAATCAACTCATAT
65 ACACGCTGAGG-----T--A-----ACTTT-CAATTTCTGT-TTGTCAAAA-AATCAACTCATAT
* *
6917 TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG-----T-AATTT-
115 CGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTC
* *
6959 TGA---TC----TCCGTT-TTC--GAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 T-ATTTTCAATTTCTGTTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* *
7014 ACACGCTGAGGTAAC-TTCAATTTCTGTTTGTCAAAAAATCAACTCATATTGCGGGAGGTGAGTT
65 ACACGCTGAGGTAACTTTCAATTTCTGTTTGTCAAAAAATCAACTCATATCGCGAGAGGTGAGTT
*
7078 GAGCCTCGGGGCACGCTGAGGTATTTTCAAT
130 GAGCCTCAGGGCACGCTGAGGTATTTTCAAT
7109 CATTGTTTTT
Statistics
Matches: 414, Mismatches: 36, Indels: 81
0.78 0.07 0.15
Matches are distributed among these distances:
146 48 0.12
147 16 0.04
148 2 0.00
149 2 0.00
151 1 0.00
152 3 0.01
154 1 0.00
156 1 0.00
161 60 0.14
162 4 0.01
163 5 0.01
164 156 0.38
165 4 0.01
166 32 0.08
168 2 0.00
169 1 0.00
171 2 0.00
172 6 0.01
173 1 0.00
176 1 0.00
177 3 0.01
178 19 0.05
179 5 0.01
180 37 0.09
181 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (163 bp):
TATTTTCAATTTCTGTTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
CACGCTGAGGTAACTTTCAATTTCTGTTTGTCAAAAAATCAACTCATATCGCGAGAGGTGAGTTG
AGCCTCAGGGCACGCTGAGGTATTTTCAATTTC
Found at i:6870 original size:89 final size:89
Alignment explanation
Indices: 6703--6959 Score: 351
Period size: 89 Copynumber: 2.9 Consensus size: 89
6693 GCTGAGGTAA
* *
6703 TTTCAATTTCTGTTTGTC--AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTC-GGCTCA
1 TTTCAATTTCTGTTCGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---A
* * *
6765 CATGCTGAGGTCTTTTCAATTTCTATT
63 CACGCTGAGGTATTTTCAATTTCTACT
*
6792 TTTCAATTTCTGTTCGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
1 TTTCAATTTCTGTTCGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
*
6857 GCTGAGGTATTTTCGATTTCTACT
66 GCTGAGGTATTTTCAATTTCTACT
* * *
6881 TTCCAATTTCTG-TCTTTCAAAATAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTCAATTTCTGTTC-GTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
6945 CGCTGAGGTAATTTT
65 CGCTGAGGT-ATTTT
6960 GATCTCCGTT
Statistics
Matches: 152, Mismatches: 11, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
88 2 0.01
89 106 0.70
90 5 0.03
91 37 0.24
92 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (89 bp):
TTTCAATTTCTGTTCGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTATTTTCAATTTCTACT
Found at i:7021 original size:72 final size:71
Alignment explanation
Indices: 6904--7161 Score: 322
Period size: 72 Copynumber: 3.5 Consensus size: 71
6894 CTTTCAAAAT
* *
6904 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTGATCTCCGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAATCTCTGT
6969 TTTCGAA
66 TTTC-AA
* * *
6976 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAACTTCAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAATCTCTGT
7041 TTGTCAAAA
66 TT-TC--AA
* * *
7050 AATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGT-ATTTTCAATCAT-T
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTT-AATC-TCT
7113 GTTTTTCAA
64 G-TTTTCAA
* * * *
7122 GAATTAATTCATATTGCTAGAGGTGAATTGAGCCTCAGGA
1 -AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
7162 TCACACACCG
Statistics
Matches: 161, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
72 64 0.40
73 37 0.23
74 56 0.35
75 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (71 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAATCTCTGT
TTTCAA
Found at i:7095 original size:74 final size:72
Alignment explanation
Indices: 6884--7161 Score: 342
Period size: 74 Copynumber: 3.8 Consensus size: 72
6874 TTCTACTTTC
6884 CAATTTCTGTCTTTCAAAATAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1 CAATTTCTGT-TTTC-AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
6949 GAGGTAATTT
63 GAGGTAATTT
** * * *
6959 TGATCTCCGTTTTCGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 CAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
7024 GTAACTT
66 GTAATTT
* * *
7031 CAATTTCTGTTTGTCAAAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTG
1 CAATTTCTGTTT-TC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
7096 AGGTATTTT
64 AGGTAATTT
* * * * * *
7105 CAATCAT-TGTTTTTCAAGAATTAATTCATATTGCTAGAGGTGAATTGAGCCTCAGGA
1 CAAT-TTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
7162 TCACACACCG
Statistics
Matches: 174, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
72 62 0.36
73 38 0.22
74 64 0.37
75 10 0.06
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (72 bp):
CAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
GTAATTT
Found at i:7177 original size:14 final size:14
Alignment explanation
Indices: 7158--7187 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
7148 ATTGAGCCTC
7158 AGGATCACACACCG
1 AGGATCACACACCG
7172 AGGATCACACACCG
1 AGGATCACACACCG
7186 AG
1 AG
7188 TAAAGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.33, G:0.23, T:0.07
Consensus pattern (14 bp):
AGGATCACACACCG
Found at i:9357 original size:24 final size:24
Alignment explanation
Indices: 9320--9427 Score: 73
Period size: 24 Copynumber: 4.4 Consensus size: 24
9310 GTATATATTG
*
9320 TATATGTTTTATA-TATGTTATGTA
1 TATAT-TTTTATACCATGTTATGTA
**
9344 TATATTTTTAATATTACTAGTTA--TA
1 TATATTTTT-ATACCA-T-GTTATGTA
9369 TATATTTCTTATA-CAT-TTCCATGTA
1 TATATTT-TTATACCATGTT--ATGTA
* *
9394 CATATTTTTATACCATCTTATGTA
1 TATATTTTTATACCATGTTATGTA
9418 TATATTTTTA
1 TATATTTTTA
9428 AATACTATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
21 2 0.03
23 6 0.09
24 28 0.40
25 25 0.36
26 5 0.07
27 4 0.06
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.56
Consensus pattern (24 bp):
TATATTTTTATACCATGTTATGTA
Found at i:9490 original size:36 final size:33
Alignment explanation
Indices: 9411--9493 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 33
9401 TTATACCATC
*
9411 TTATGTATATATTTTTAAATACTATATTGTATA
1 TTATGTATATATTCTTAAATACTATATTGTATA
* *
9444 TGTATATATATATTCTT-AGTACTATATTACGCATATA
1 T-TATGTATATATTCTTAAATACTATATT--G--TATA
9481 TTATGTATATATT
1 TTATGTATATATT
9494 TATTTTTACC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
33 11 0.27
34 13 0.32
35 1 0.02
36 11 0.27
37 5 0.12
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (33 bp):
TTATGTATATATTCTTAAATACTATATTGTATA
Found at i:18908 original size:19 final size:20
Alignment explanation
Indices: 18884--18922 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
18874 TTATAAAACT
*
18884 TAATGCATATG-ATGAAATG
1 TAATGCAGATGAATGAAATG
18903 TAATGCAGATGAATGAAATG
1 TAATGCAGATGAATGAAATG
18923 GATACAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (20 bp):
TAATGCAGATGAATGAAATG
Found at i:26027 original size:6 final size:6
Alignment explanation
Indices: 26016--26052 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
26006 AGAAGTTGTG
26016 ATAATT ATAATT AT-A-T ATAATT ATAATTT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT ATAA-TT ATAATT AT
26053 TATTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 3 0.11
5 2 0.07
6 17 0.61
7 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATAATT
Found at i:26055 original size:16 final size:16
Alignment explanation
Indices: 26016--26047 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
26006 AGAAGTTGTG
26016 ATAATTATAATTATAT
1 ATAATTATAATTATAT
26032 ATAATTATAATT-TAT
1 ATAATTATAATTATAT
26047 A
1 A
26048 ATTATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATTATAATTATAT
Found at i:29808 original size:19 final size:21
Alignment explanation
Indices: 29777--29815 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
29767 AGGCCCATAC
29777 CAAAACTAAAATAA-AAAATG
1 CAAAACTAAAATAACAAAATG
29797 CAAAAC-AAAATAACAAAAT
1 CAAAACTAAAATAACAAAAT
29816 AAAATCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.72, C:0.13, G:0.03, T:0.13
Consensus pattern (21 bp):
CAAAACTAAAATAACAAAATG
Found at i:31309 original size:29 final size:27
Alignment explanation
Indices: 31263--31333 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 27
31253 TGATTTCGTG
* *
31263 TTATTT-TATATAA-ATTCTTTTAAAT
1 TTATTTATATATAATTTTCTTTTAAAC
31288 TTATTATATATATATATTTTCTTTTAAAC
1 TTATT-TATATATA-ATTTTCTTTTAAAC
*
31317 TTATTTATGTATAATTT
1 TTATTTATATATAATTT
31334 GTTTCCTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 5 0.13
26 1 0.03
27 10 0.26
28 8 0.21
29 15 0.38
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (27 bp):
TTATTTATATATAATTTTCTTTTAAAC
Found at i:36930 original size:50 final size:50
Alignment explanation
Indices: 36855--37031 Score: 300
Period size: 50 Copynumber: 3.5 Consensus size: 50
36845 CCATGGCAAC
36855 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
36905 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
36955 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
37006 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
37032 TTGATCAATG
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
50 97 0.81
51 23 0.19
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:37049 original size:31 final size:31
Alignment explanation
Indices: 37011--37069 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
37001 ATGGCAAGTA
*
37011 AAAAGTGGTAGCTTCGGCTACTTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
37042 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
37070 TCGGCTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:37076 original size:46 final size:46
Alignment explanation
Indices: 37024--37115 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
37014 AGTGGTAGCT
* *
37024 TCGGCTACTTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACTTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
* *
37070 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACTTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
37116 GTGAATAGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (46 bp):
TCGGCTACTTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
Found at i:37119 original size:31 final size:31
Alignment explanation
Indices: 37071--37139 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
37061 ACCTGATCAT
* * *
37071 CGGCTACTTGATTAGTGAAAAATGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
* * *
37102 CGGCTACCTGATCAGTGAATAGTGATAGCTT
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
37133 CGGCTAC
1 CGGCTAC
37140 AAGTGACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAAAAATGATAGCTC
Found at i:40196 original size:16 final size:16
Alignment explanation
Indices: 40175--40218 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
40165 TCTTGAGGCC
*
40175 TTAAAAAAATTAAAAA
1 TTAAAAAAAATAAAAA
40191 TTAAAAAAAATAAAAA
1 TTAAAAAAAATAAAAA
40207 TTCAAACAAAAA
1 TT-AAA-AAAAA
40219 ATCAATCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 17 0.68
17 3 0.12
18 5 0.20
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (16 bp):
TTAAAAAAAATAAAAA
Found at i:41529 original size:64 final size:64
Alignment explanation
Indices: 41341--41530 Score: 308
Period size: 64 Copynumber: 3.0 Consensus size: 64
41331 TCATTCATAA
* *
41341 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCTTAATTATTTGACATAAACAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
* ** *
41405 CACATCTAGTTAGGAACATTTGATTCATTTCGATCATAGTGTCCTAATTAGTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
* *
41469 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGTCATAAGC
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGC
41531 GTAGATACAT
Statistics
Matches: 114, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 114 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:42019 original size:177 final size:177
Alignment explanation
Indices: 41826--42162 Score: 505
Period size: 177 Copynumber: 1.9 Consensus size: 177
41816 AAAATTACAG
* * *
41826 ATCTTATCCCCCTAAGCAGTAGTGGAGCAGATCGAAAAGGGCGAATCTTATCTCCATGTATCGGC
1 ATCTTATCCCCCTAAGCAGTAGTGGAGCAGATCGAAAAGGACAAATCTTATCTCCATGTATAGGC
* *
41891 AATAGAGCATATTTTAACCA-TCAGCCTTATCTCTCTAAGGTAGCAAAAGAGCAGGTTGGCGATT
66 AATAGAGCAGATTTTAACCACT-AGCCTTATCTCTCTAAGGTAGCAAAAGAGCAGGTAGGCGATT
*
41955 GTAGTCTTATCTTTCTGAGGTAACAAGGAAGCAGACTGAAGATTGAAA
130 GTAGTCTTATCTTCCTGAGGTAACAAGGAAGCAGACTGAAGATTGAAA
* * ** *
42003 ATCTTATCTCCCTAAGCAGTTGTGGAGCAGATCGAGGATGACAAATCTTATCTCCATGTATAGGC
1 ATCTTATCCCCCTAAGCAGTAGTGGAGCAGATCGAAAAGGACAAATCTTATCTCCATGTATAGGC
* * * * *
42068 AATGGAGCAGATTTTAGCCACTAGCCTTGTCTCTCTGAGGTAGCAAGAGAGCAGGTAGGCGATTG
66 AATAGAGCAGATTTTAACCACTAGCCTTATCTCTCTAAGGTAGCAAAAGAGCAGGTAGGCGATTG
*
42133 TAGTCTTATCTTCCTGAGGTAGCAAGGAAG
131 TAGTCTTATCTTCCTGAGGTAACAAGGAAG
42163 TCGAGGATGA
Statistics
Matches: 142, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
177 141 0.99
178 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (177 bp):
ATCTTATCCCCCTAAGCAGTAGTGGAGCAGATCGAAAAGGACAAATCTTATCTCCATGTATAGGC
AATAGAGCAGATTTTAACCACTAGCCTTATCTCTCTAAGGTAGCAAAAGAGCAGGTAGGCGATTG
TAGTCTTATCTTCCTGAGGTAACAAGGAAGCAGACTGAAGATTGAAA
Found at i:42189 original size:129 final size:129
Alignment explanation
Indices: 42034--42291 Score: 498
Period size: 129 Copynumber: 2.0 Consensus size: 129
42024 GTGGAGCAGA
* *
42034 TCGAGGATGACAAATCTTATCTCCATGTATAGGCAATGGAGCAGATTTTAGCCACTAGCCTTGTC
1 TCGAGGATGACAAATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAGCCACTAGCCTTGTC
42099 TCTCTGAGGTAGCAAGAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAG
66 TCTCTGAGGTAGCAAGAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAG
42163 TCGAGGATGACAAATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAGCCACTAGCCTTGTC
1 TCGAGGATGACAAATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAGCCACTAGCCTTGTC
42228 TCTCTGAGGTAGCAAGAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAG
66 TCTCTGAGGTAGCAAGAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAG
42292 CAGACTGAAG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 127 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (129 bp):
TCGAGGATGACAAATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAGCCACTAGCCTTGTC
TCTCTGAGGTAGCAAGAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAG
Found at i:42281 original size:306 final size:306
Alignment explanation
Indices: 41869--42464 Score: 978
Period size: 306 Copynumber: 1.9 Consensus size: 306
41859 GAAAAGGGCG
* * *
41869 AATCTTATCTCCATGTATCGGCAATAGAGCATATTTTAACCATCAGCCTTATCTCTCTAAGGTAG
1 AATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAACCATCAGCCTTATCTCTCTAAGGTAG
* *
41934 CAAAAGAGCAGGTTGGCGATTGTAGTCTTATCTTTCTGAGGTAACAAGGAAGCAGACTGAAGATT
66 CAAAAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAACAAGGAAGCAGACTGAAGATT
* * *
41999 GAAAATCTTATCTCCCTAAGCAGTTGTGGAGCAGATCGAGGATGACAAATCTTATCTCCATGTAT
131 GAAAATCTTATCTCCCTAAGCAGTTGTGGAACAGATCGAAGATGACAAATATTATCTCCATGTAT
*
42064 AGGCAATGGAGCAGATTTTAGCCACTAGCCTTGTCTCTCTGAGGTAGCAAGAGAGCAGGTAGGCG
196 AGGCAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTAGGCG
42129 ATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGTCGAGGATGACA
261 ATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGTCGAGGATGACA
* * *
42175 AATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAGCCA-CTAGCCTTGTCTCTCTGAGGTA
1 AATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAACCATC-AGCCTTATCTCTCTAAGGTA
* *
42239 GCAAGAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGAT
65 GCAAAAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAACAAGGAAGCAGACTGAAGAT
* * *
42304 TGAAGATCTTATCTCTCTAAGCAGTTGTGGAACAGATCGAAGATGGCAAATATTATCTCCATGTA
130 TGAAAATCTTATCTCCCTAAGCAGTTGTGGAACAGATCGAAGATGACAAATATTATCTCCATGTA
* * * *
42369 TCGGCAATGGAGCAGATTTTAGCCATTAGCCTTATCTCTTTGAGGTAGCAAGAGAGCAGGTTGGC
195 TAGGCAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTAGGC
*
42434 GATTGTAGTCTTATCTTCCTGATGTAGCAAG
260 GATTGTAGTCTTATCTTCCTGAGGTAGCAAG
42465 AAAGCAGACT
Statistics
Matches: 267, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
305 1 0.00
306 266 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (306 bp):
AATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAACCATCAGCCTTATCTCTCTAAGGTAG
CAAAAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAACAAGGAAGCAGACTGAAGATT
GAAAATCTTATCTCCCTAAGCAGTTGTGGAACAGATCGAAGATGACAAATATTATCTCCATGTAT
AGGCAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTAGGCG
ATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGTCGAGGATGACA
Found at i:42401 original size:177 final size:177
Alignment explanation
Indices: 42163--42539 Score: 603
Period size: 177 Copynumber: 2.1 Consensus size: 177
42153 AGCAAGGAAG
* * *
42163 TCGAGGATGACAAATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAGCCACTAGCCTTGTC
1 TCGAAGATGGCAAATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAGCCACTAGCCTTATC
*
42228 TCTCTGAGGTAGCAAGAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGC
66 TCTCTGAGGTAGCAAGAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGAAAGC
42293 AGACTGAAGATTGAAGATCTTATCT-CTCTAAGCAGTTGTGGAACAGA
131 AGACTGAAGATTGAAGATCTTATCTCCT-TAAGCAGTTGTGGAACAGA
* * * * *
42340 TCGAAGATGGCAAATATTATCTCCATGTATCGGCAATGGAGCAGATTTTAGCCATTAGCCTTATC
1 TCGAAGATGGCAAATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAGCCACTAGCCTTATC
* * *
42405 TCTTTGAGGTAGCAAGAGAGCAGGTTGGCGATTGTAGTCTTATCTTCCTGATGTAGCAAGAAAGC
66 TCTCTGAGGTAGCAAGAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGAAAGC
*
42470 AGACTGAAGATTGAAGATCTTATCTCCTTAAGCAGTTGTGGAGCAGA
131 AGACTGAAGATTGAAGATCTTATCTCCTTAAGCAGTTGTGGAACAGA
* *
42517 TCAAAGATGGCGAATCTTATCTC
1 TCGAAGATGGCAAATCTTATCTC
42540 GAAAGAGAGA
Statistics
Matches: 183, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
177 181 0.99
178 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (177 bp):
TCGAAGATGGCAAATCTTATCTCCATGTATAGGCAATAGAACAGATTTTAGCCACTAGCCTTATC
TCTCTGAGGTAGCAAGAGAGCAGGTAGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGAAAGC
AGACTGAAGATTGAAGATCTTATCTCCTTAAGCAGTTGTGGAACAGA
Found at i:43930 original size:16 final size:16
Alignment explanation
Indices: 43909--43949 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
43899 TTTTTTTATG
*
43909 TTGGGCTAGTTGAGTA-
1 TTGGGCTAGGTG-GTAT
43925 TTGGGCT-GGTGGTAT
1 TTGGGCTAGGTGGTAT
43940 TTGGGCTAGG
1 TTGGGCTAGG
43950 GGATTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.12, C:0.07, G:0.44, T:0.37
Consensus pattern (16 bp):
TTGGGCTAGGTGGTAT
Found at i:47595 original size:27 final size:26
Alignment explanation
Indices: 47535--47603 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 26
47525 TAAAGGAAAC
* *
47535 AAATTATACATAAATAAGTTTAAAAG
1 AAATTATATATAAATAAATTTAAAAG
*
47561 AAAATATATATATAATAAATTTAAAAG
1 AAATTATATATA-AATAAATTTAAAAG
*
47588 AATTTATATA-AAATAA
1 AAATTATATATAAATAA
47604 CACGAAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.14
26 11 0.30
27 21 0.57
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (26 bp):
AAATTATATATAAATAAATTTAAAAG
Found at i:47602 original size:25 final size:26
Alignment explanation
Indices: 47546--47603 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
47536 AATTATACAT
*
47546 AAATAAGTTTAAAAGAAAATATATATA
1 AAATAAATTTAAAAG-AAATATATATA
* *
47573 TAATAAATTTAAAAG-AATTTATATA
1 AAATAAATTTAAAAGAAATATATATA
47598 AAATAA
1 AAATAA
47604 CACGAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 14 0.52
27 13 0.48
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AAATAAATTTAAAAGAAATATATATA
Found at i:48722 original size:177 final size:177
Alignment explanation
Indices: 48426--48791 Score: 590
Period size: 177 Copynumber: 2.1 Consensus size: 177
48416 GGCCTTGTTC
** *
48426 GAGATAAGATTCGCCATCTTTGATCTGCTCCACAACTGCTTAAGGAGATAAGATCTTCAATCTTC
1 GAGATAAGATTTTCCATCTTCGATCTGCTCCACAACTGCTTAAGGAGATAAGATCTTCAATCTTC
*
48491 AGTCTGCTTTCTTGCTACATCAGGAAGATAAGACTACAATCGCCAACCTGCTCTCTTGCTACCTC
66 AGTCTGCTTCCTTGCTACATCAGGAAGATAAGACTACAATCGCCAACCTGCTCTCTTGCTACCTC
*
48556 AAAGAGATAAGGCTAATGGCTAAAATCTGCTCCATTGCCGATACATG
131 AAAGAGACAAGGCTAATGGCTAAAATCTGCTCCATTGCCGATACATG
* *
48603 GAGATAATATTTTCCATCTTCGATCTGTTCCACAACTGCTT-AGAGAGATAAGATCTTCAATCTT
1 GAGATAAGATTTTCCATCTTCGATCTGCTCCACAACTGCTTAAG-GAGATAAGATCTTCAATCTT
* *
48667 CAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCTACCTGCTCTCTTGCTACCT
65 CAGTCTGCTTCCTTGCTACATCAGGAAGATAAGACTACAATCGCCAACCTGCTCTCTTGCTACCT
* * * * *
48732 CAGAGAGACAAGGCTAGTGGCTAAAATCTGTTCTATTGCCTATACATG
130 CAAAGAGACAAGGCTAATGGCTAAAATCTGCTCCATTGCCGATACATG
48780 GAGATAAGATTT
1 GAGATAAGATTT
48792 GTCATCCTCG
Statistics
Matches: 173, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 2 0.01
177 171 0.99
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (177 bp):
GAGATAAGATTTTCCATCTTCGATCTGCTCCACAACTGCTTAAGGAGATAAGATCTTCAATCTTC
AGTCTGCTTCCTTGCTACATCAGGAAGATAAGACTACAATCGCCAACCTGCTCTCTTGCTACCTC
AAAGAGACAAGGCTAATGGCTAAAATCTGCTCCATTGCCGATACATG
Found at i:48825 original size:129 final size:129
Alignment explanation
Indices: 48674--48931 Score: 498
Period size: 129 Copynumber: 2.0 Consensus size: 129
48664 CTTCAGTCTG
48674 CTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCTACCTGCTCTCTTGCTACCTCAGAGAG
1 CTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCTACCTGCTCTCTTGCTACCTCAGAGAG
* *
48739 ACAAGGCTAGTGGCTAAAATCTGTTCTATTGCCTATACATGGAGATAAGATTTGTCATCCTCGA
66 ACAAGGCTAGTGGCTAAAATCTGCTCCATTGCCTATACATGGAGATAAGATTTGTCATCCTCGA
48803 CTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCTACCTGCTCTCTTGCTACCTCAGAGAG
1 CTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCTACCTGCTCTCTTGCTACCTCAGAGAG
48868 ACAAGGCTAGTGGCTAAAATCTGCTCCATTGCCTATACATGGAGATAAGATTTGTCATCCTCGA
66 ACAAGGCTAGTGGCTAAAATCTGCTCCATTGCCTATACATGGAGATAAGATTTGTCATCCTCGA
48932 TCTCTCCAGC
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 127 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (129 bp):
CTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCTACCTGCTCTCTTGCTACCTCAGAGAG
ACAAGGCTAGTGGCTAAAATCTGCTCCATTGCCTATACATGGAGATAAGATTTGTCATCCTCGA
Found at i:49621 original size:64 final size:64
Alignment explanation
Indices: 49436--49624 Score: 299
Period size: 63 Copynumber: 3.0 Consensus size: 64
49426 ATGTATCTAC
* *
49436 GCTTATGACAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTGAT
1 GCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGAT
* ** *
49500 GCTTATGTCAACTAATTAGGACAC-ATGATCGAAATGAATCAAATGTTCCTAACTAGATGTGAT
1 GCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGAT
* *
49563 GTTTATGTCAAATAATTAAGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 GCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
49625 TTATGAATGA
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
63 56 0.50
64 56 0.50
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (64 bp):
GCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGAT
Found at i:51353 original size:18 final size:17
Alignment explanation
Indices: 51323--51363 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
51313 ATGACCTTTG
*
51323 TTTATTGTTTTTTCTCT
1 TTTATTGTTTTTTCTAT
*
51340 TTTATTGTTTTTTTGTAT
1 TTTATTG-TTTTTTCTAT
51358 TTTATT
1 TTTATT
51364 TTTCTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (17 bp):
TTTATTGTTTTTTCTAT
Done.