Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1899
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: 38309
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1740 original size:153 final size:154
Alignment explanation
Indices: 1476--1759 Score: 342
Period size: 153 Copynumber: 1.9 Consensus size: 154
1466 TCGTTCTTAT
* * * *
1476 TTTTTGGTGTCTTTTAAGGTTATCGGGATACTTTCGTGTCAAAGATATACTGTAAGGGCATTTTG
1 TTTTTGGTGTCTTTTAAGGTTATCGGGATACTTTCATATCAAAGATATACTGTAAGGGCATGTTA
* * * * * * * ** *
1541 GTAATTTTTTAAAATTGAGTTTTAAGTAGTTATTGGGTCTTTTTTATGTCAAAAGTGTGCATTTA
66 ATAATTTTCTAAAATTGAGTCTTAAGTAATCACTGAGTCTCCTTTATGCCAAAAGTGTGCATTTA
1606 GGATAAGTTTATCCATTTATGATC
131 GGATAAGTTTATCCATTTATGATC
* * * *
1630 TTTTT-GTGTCTTTTAAGGTTATTGGGATATTTTCATATCGAAGATATACCT-TAAGGGTATGTT
1 TTTTTGGTGTCTTTTAAGGTTATCGGGATACTTTCATATCAAAGATATA-CTGTAAGGGCATGTT
*
1693 AATAATTTCTCTAAAATTGAGTCTT-AGATAATCACTGAGT-TCCTTTATGCCAAAAGTGTGCGT
65 AATAATTT-TCTAAAATTGAGTCTTAAG-TAATCACTGAGTCTCCTTTATGCCAAAAGTGTGCAT
1756 TTAG
128 TTAG
1760 TATAGGTTCA
Statistics
Matches: 108, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
153 79 0.73
154 29 0.27
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (154 bp):
TTTTTGGTGTCTTTTAAGGTTATCGGGATACTTTCATATCAAAGATATACTGTAAGGGCATGTTA
ATAATTTTCTAAAATTGAGTCTTAAGTAATCACTGAGTCTCCTTTATGCCAAAAGTGTGCATTTA
GGATAAGTTTATCCATTTATGATC
Found at i:2124 original size:25 final size:25
Alignment explanation
Indices: 2096--2144 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
2086 TTCTTCAAAA
2096 TGGGAATTTCAAATTTCATGAAACG
1 TGGGAATTTCAAATTTCATGAAACG
2121 TGGGAATTTCAAATTTCATGAAAC
1 TGGGAATTTCAAATTTCATGAAAC
2145 AAAACCTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (25 bp):
TGGGAATTTCAAATTTCATGAAACG
Found at i:11580 original size:97 final size:97
Alignment explanation
Indices: 11412--11676 Score: 354
Period size: 97 Copynumber: 2.7 Consensus size: 97
11402 TTTAATTTTT
* * ** * * * *
11412 AGTTAAAAAACGAGGTTGGAGTAT-CCCTCGGAGGAATGGGGTTAGAGTATTCCT-GATGATGAT
1 AGTTTAAAAACAAGGTTGGAGTATCCCCTAAGAAGAATGGGGTTGGAGTA-TCCTCGATGATAAA
*
11475 AATTTAAGCAAAAATAAGGTTTAAATATAGATG
65 AATTTAAGCAAAAATAAGATTTAAATATAGATG
* *
11508 AGTTTAAAAATAAGGTTGGAGTATCCCCTAAGAAGAATGGGGTTGGAGTACCCTCGATGATAAAA
1 AGTTTAAAAACAAGGTTGGAGTATCCCCTAAGAAGAATGGGGTTGGAGTATCCTCGATGATAAAA
* *
11573 ATTTAAGCAAAAATGAGATTTAAATCTAGATG
66 ATTTAAGCAAAAATAAGATTTAAATATAGATG
* * *
11605 AGTTTAAAAACAGGGTTGGAGTTTCCCCTTAGAAGAATGGGGTTGGAGTATCCTCGATGATAAAA
1 AGTTTAAAAACAAGGTTGGAGTATCCCCTAAGAAGAATGGGGTTGGAGTATCCTCGATGAT-AAA
11670 AATTTAA
65 AATTTAA
11677 TACTTTTTTT
Statistics
Matches: 148, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
96 24 0.16
97 114 0.77
98 10 0.07
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (97 bp):
AGTTTAAAAACAAGGTTGGAGTATCCCCTAAGAAGAATGGGGTTGGAGTATCCTCGATGATAAAA
ATTTAAGCAAAAATAAGATTTAAATATAGATG
Found at i:14150 original size:20 final size:21
Alignment explanation
Indices: 14122--14176 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
14112 ATGTTTTAGG
14122 TATGTATCGATACATTCACT-
1 TATGTATCGATACATTCACTA
* * *
14142 TATGCATCGATATATTTACTA
1 TATGTATCGATACATTCACTA
*
14163 TTTGTATCGATACA
1 TATGTATCGATACA
14177 AATTGTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (21 bp):
TATGTATCGATACATTCACTA
Found at i:14993 original size:54 final size:53
Alignment explanation
Indices: 14847--14994 Score: 147
Period size: 53 Copynumber: 2.8 Consensus size: 53
14837 AACGAGAGAG
* * * * * *
14847 TGCCAATG-AGCTGATTCAAGGCCAATGATATTGGACTTGAAGATAAGAAAAA
1 TGCCAATGTGGCTAATTAAAGGCCAACGACATTGGACTTAAAGATAAGAAAAA
* * * * * *
14899 TGCCAATGTGGCTGATTCAAGGCCAAGGACATTGGGCTTAAAGATGAGAAGAA
1 TGCCAATGTGGCTAATTAAAGGCCAACGACATTGGACTTAAAGATAAGAAAAA
*
14952 TGCTAATGT-GCTAATTTAAGAGGCCAACGACATTGGACTTAAA
1 TGCCAATGTGGCTAA-TTAA-AGGCCAACGACATTGGACTTAAA
14995 CTTGATAATG
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 12 0.15
53 48 0.59
54 21 0.26
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (53 bp):
TGCCAATGTGGCTAATTAAAGGCCAACGACATTGGACTTAAAGATAAGAAAAA
Found at i:15045 original size:52 final size:52
Alignment explanation
Indices: 14845--15198 Score: 283
Period size: 52 Copynumber: 6.8 Consensus size: 52
14835 AAAACGAGAG
* ** * * * *
14845 AGTGCCAATGAGCTGATTCAAGGCCAATGATATT-GGACTTGAAGATAAGAAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGG-CTTAAAGATGATAAA
* * *
14897 AATGCCAATGTGGCTGATTCAAGGCCAAG-GACATTGGGCTTAAAGATGAGAAGA
1 AGTGCCAATGT-GCTGATTCAAGGCC-AGCGACATTAGGCTTAAAGATGATAA-A
* * * * ** *
14951 A-TGCTAATGTGCTAATTTAAGAGGCCAACGACATT-GGACTTAAACTTGATAAT
1 AGTGCCAATGTGCTGA-TTCA-AGGCCAGCGACATTAGG-CTTAAAGATGATAAA
* * * * *
15004 GGTGCTAATGTGTTGATTCAAGGCCAGCAACATTAGGCTTAAAAATGAT-AA
1 AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTTAAAGATGATAAA
* * **
15055 AG-GCCAATATGCTGATTCAAGGCTAGCGACATTAGATTTAAAGATGATAAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTTAAAGATGATAAA
*
15106 AGTGCCAATGTGCTGATTCAAGGCCAGTGACATT-GGACTTAAAGATGA-AAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGG-CTTAAAGATGATAAA
* * * * *
15157 GAATACCAATGTGTTGATTCAAGGCCAGCAACATTAGACTTA
1 -AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTTA
15199 GAAAGAGATG
Statistics
Matches: 244, Mismatches: 43, Indels: 30
0.77 0.14 0.09
Matches are distributed among these distances:
50 38 0.16
51 10 0.04
52 106 0.43
53 51 0.21
54 39 0.16
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.25
Consensus pattern (52 bp):
AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTTAAAGATGATAAA
Found at i:15123 original size:102 final size:102
Alignment explanation
Indices: 14894--15194 Score: 248
Period size: 102 Copynumber: 2.9 Consensus size: 102
14884 TGAAGATAAG
* * * * * *
14894 AAAAATGCCAATGTGGCTGATTCAAGGCCAAG-GACATTGGGCTTAAAGATGAGAAGAATGCTAA
1 AAAAGTGCCAATGT-GCTGATTCAAGGCC-AGCAACATTGGACTTAAAAATGAAAAGAA--CCAA
* * * * * * * **
14958 TGTGCTAATTTAAGAGGCCAACGACATTGGACTTAAACTTGAT
62 TATGCTGA-TTCA-AGGCCAGCAACATTAGATTTAAAGATGAT
** * * *
15001 AATGGTGCTAATGTGTTGATTCAAGGCCAGCAACATTAGG-CTTAAAAATGATAAAG-GCCAATA
1 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCAACATT-GGACTTAAAAATGA-AAAGAACCAATA
* *
15064 TGCTGATTCAAGGCTAGCGACATTAGATTTAAAGATGAT
64 TGCTGATTCAAGGCCAGCAACATTAGATTTAAAGATGAT
** * *
15103 AAAAGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGAAAAGAATACCAATG
1 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAAATGAAAAG-A-ACCAATA
*
15168 TGTTGATTCAAGGCCAGCAACATTAGA
64 TGCTGATTCAAGGCCAGCAACATTAGA
15195 CTTAGAAAGA
Statistics
Matches: 156, Mismatches: 31, Indels: 17
0.76 0.15 0.08
Matches are distributed among these distances:
101 6 0.04
102 64 0.41
103 3 0.02
104 38 0.24
105 2 0.01
106 28 0.18
107 15 0.10
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (102 bp):
AAAAGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAAATGAAAAGAACCAATATG
CTGATTCAAGGCCAGCAACATTAGATTTAAAGATGAT
Found at i:15306 original size:32 final size:32
Alignment explanation
Indices: 15265--15357 Score: 118
Period size: 32 Copynumber: 2.9 Consensus size: 32
15255 TTAAAGGAGA
* * *
15265 TGCCACCAACTTGTGTGGGCTTT-TAAGAGGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAAAAGG
**
15296 TTGCCACCAACTCATGTGGGCTTTGAAAAAAGG
1 -TGCCACCAACTTGTGTGGGCTTTGAAAAAAGG
15329 TGCCACCAACTTGTGTGGGC-TTGAAAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAAAA
15358 AAAGATGCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 9 0.17
32 39 0.74
33 5 0.09
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAAAAGG
Found at i:15367 original size:34 final size:31
Alignment explanation
Indices: 15262--15376 Score: 104
Period size: 32 Copynumber: 3.5 Consensus size: 31
15252 AGCTTAAAGG
* * *
15262 AGATGCCACCAACTTGTGTGGGCTTTTAAGAG
1 AGATGCCACCAACTTGTGTGGGC-TTGAAAAA
* * **
15294 GGTTGCCACCAACTCATGTGGGCTTTGAAAAA
1 AGATGCCACCAACTTGTGTGGGC-TTGAAAAA
*
15326 AGGTGCCACCAACTTGTGTGGGCTTGAAAAAAAA
1 AGATGCCACCAACTTGTGTGGGCTTG---AAAAA
*
15360 AGATGCCACTAACTTGT
1 AGATGCCACCAACTTGT
15377 AAAGGATGCC
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
31 3 0.04
32 44 0.66
34 20 0.30
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AGATGCCACCAACTTGTGTGGGCTTGAAAAA
Found at i:15419 original size:31 final size:29
Alignment explanation
Indices: 15381--15442 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
15371 ACTTGTAAAG
*
15381 GATGCCACC-GACTTGTATGGGCTTTGAAAAA
1 GATGCCACCAG-CTTATATGGGC-TT-AAAAA
15412 GATGCCACCAGCTTATATGGGCTTAAAAA
1 GATGCCACCAGCTTATATGGGCTTAAAAA
15441 GA
1 GA
15443 GGTCACCACC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 2 0.07
31 19 0.66
32 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (29 bp):
GATGCCACCAGCTTATATGGGCTTAAAAA
Found at i:16051 original size:14 final size:14
Alignment explanation
Indices: 16028--16079 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
16018 ATGGTAATGT
16028 GAATGCATGATATG
1 GAATGCATGATATG
* *
16042 GAATGTATGATGTG
1 GAATGCATGATATG
* *
16056 GAATGCATGATGTT
1 GAATGCATGATATG
16070 GAATGCATGA
1 GAATGCATGA
16080 CATGAAGTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.33, C:0.06, G:0.31, T:0.31
Consensus pattern (14 bp):
GAATGCATGATATG
Found at i:16073 original size:28 final size:27
Alignment explanation
Indices: 16024--16079 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
16014 TGTGATGGTA
*
16024 ATGTGAATGCATGATATGGAATGTATG
1 ATGTGAATGCATGATATGGAATGCATG
* *
16051 ATGTGGAATGCATGATGTTGAATGCATG
1 ATGT-GAATGCATGATATGGAATGCATG
16079 A
1 A
16080 CATGAAGTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.32
Consensus pattern (27 bp):
ATGTGAATGCATGATATGGAATGCATG
Found at i:16816 original size:25 final size:29
Alignment explanation
Indices: 16783--16839 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 29
16773 TAATAAGTAG
*
16783 AAATCAAAAATTAA-A-AAAT-ATATAAA
1 AAATCAAAAATTAATAGAAATCAAATAAA
16809 AAAT-AAAAATTAATAGAAATCAAATAAA
1 AAATCAAAAATTAATAGAAATCAAATAAA
16837 AAA
1 AAA
16840 AACATCATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 9 0.33
26 5 0.19
27 4 0.15
28 9 0.33
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (29 bp):
AAATCAAAAATTAATAGAAATCAAATAAA
Found at i:16841 original size:42 final size:42
Alignment explanation
Indices: 16760--16841 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
16750 GATTTATTCG
* * *
16760 ATATAAAATATAATAATAAGTAGAAATCAAAAATTAAAAAAT
1 ATATAAAAAATAAAAATAAGTAGAAATCAAAAATAAAAAAAT
*
16802 ATATAAAAAATAAAAATTAA-TAGAAATCAAATA-AAAAAAA
1 ATATAAAAAATAAAAA-TAAGTAGAAATCAAAAATAAAAAAA
16842 CATCATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 6 0.17
42 26 0.74
43 3 0.09
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (42 bp):
ATATAAAAAATAAAAATAAGTAGAAATCAAAAATAAAAAAAT
Found at i:17523 original size:82 final size:82
Alignment explanation
Indices: 17386--17641 Score: 336
Period size: 82 Copynumber: 3.1 Consensus size: 82
17376 AGCAATCGAA
* * * *
17386 AACTCCAGTAGCTTCAAGCAGCAGCGGCATCCATCAATACCGGTA-CTAGCTCGAGCCTCTTCCA
1 AACTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGTAGC-AGCTCGAGCCTTTTCCA
*
17450 GCCCACAAACATGGCAAC
65 GCCCACGAACATGGCAAC
* * *
17468 AACTCTAGCAGCTTCAGGCAACAGCAGCATCCATCAATACCCGTAGCAGCTCGAGCCTTTTCCAG
1 AACTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGTAGCAGCTCGAGCCTTTTCCAG
* *
17533 CCCATGAACATGGCAGC
66 CCCACGAACATGGCAAC
* * *
17550 AGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAG-TGAGAGCCTTTTCCA
1 AACTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGTAGCAGCT-CGAGCCTTTTCCA
* *
17614 TCCCACGAACATGGCAGC
65 GCCCACGAACATGGCAAC
*
17632 AGCTCCAGCA
1 AACTCCAGCA
17642 ATTTCCAGTA
Statistics
Matches: 154, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
81 1 0.01
82 152 0.99
83 1 0.01
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (82 bp):
AACTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGTAGCAGCTCGAGCCTTTTCCAG
CCCACGAACATGGCAAC
Found at i:30192 original size:19 final size:19
Alignment explanation
Indices: 30168--30235 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
30158 AATTCAACAA
30168 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
30187 TTTGTATCAATAC---A--
1 TTTGTATCGATACATAAGT
30201 -TTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
30219 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
30236 TTAGCTATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 11 0.27
16 2 0.05
19 28 0.68
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:30205 original size:32 final size:32
Alignment explanation
Indices: 30169--30233 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
30159 ATTCAACAAT
*
30169 TTGTATCGATACATAAGTTTTGTATCAATACA
1 TTGTATCGATACATAAGTATTGTATCAATACA
*
30201 TTGTATCGATACATAAGTATTGTATCGATACA
1 TTGTATCGATACATAAGTATTGTATCAATACA
30233 T
1 T
30234 AATTAGCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (32 bp):
TTGTATCGATACATAAGTATTGTATCAATACA
Found at i:30293 original size:13 final size:13
Alignment explanation
Indices: 30275--30300 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30265 CATTTTTCTG
30275 TGTATCGATACAT
1 TGTATCGATACAT
30288 TGTATCGATACAT
1 TGTATCGATACAT
30301 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:30297 original size:33 final size:33
Alignment explanation
Indices: 30255--30321 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
30245 GCCAAGGAAA
***
30255 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
30288 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
30321 T
1 T
30322 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:32880 original size:79 final size:78
Alignment explanation
Indices: 32785--32988 Score: 248
Period size: 79 Copynumber: 2.6 Consensus size: 78
32775 CGTTAATCAT
*
32785 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGGCTTTATTCCCAA-AATA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAATAAT-
* *
32849 CTGATTTCTCATAAT
65 C-GATTTCTCACAAC
* * * * * * * *
32864 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTCTAATCATC
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAATAATC
32929 GATTTCTCACAAC
66 GATTTCTCACAAC
* * * *
32942 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCTAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCG
32989 TTATTATCTC
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
78 51 0.48
79 53 0.50
80 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAATAATC
GATTTCTCACAAC
Found at i:36749 original size:20 final size:19
Alignment explanation
Indices: 36712--36802 Score: 121
Period size: 20 Copynumber: 4.6 Consensus size: 19
36702 AAAATGCTTG
36712 AATGTATCGATAAATGAGC
1 AATGTATCGATAAATGAGC
36731 AATGTATCGATAGAATGAGC
1 AATGTATCGATA-AATGAGC
*
36751 AATGTATCGATACAAGGAGC
1 AATGTATCGATA-AATGAGC
*
36771 AATGTATCGATATAATGCA-A
1 AATGTATCGATA-AATG-AGC
36791 AATGTATCGATA
1 AATGTATCGATA
36803 CATCTAGGTA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.18
20 52 0.80
21 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (19 bp):
AATGTATCGATAAATGAGC
Found at i:36778 original size:40 final size:40
Alignment explanation
Indices: 36712--36804 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
36702 AAAATGCTTG
* *
36712 AATGTATCGATA-AATGAGCAATGTATCGATAGAATG-AGC
1 AATGTATCGATACAAGGAGCAATGTATCGATAGAATGCA-A
*
36751 AATGTATCGATACAAGGAGCAATGTATCGATATAATGCAA
1 AATGTATCGATACAAGGAGCAATGTATCGATAGAATGCAA
36791 AATGTATCGATACA
1 AATGTATCGATACA
36805 TCTAGGTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
39 12 0.24
40 36 0.73
41 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (40 bp):
AATGTATCGATACAAGGAGCAATGTATCGATAGAATGCAA
Found at i:37617 original size:37 final size:36
Alignment explanation
Indices: 37529--37620 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
37519 TCGAGGATAA
* * *
37529 AGGAAAAAAGGAAAACGAAATGCGTCCTGCTCTTTG
1 AGGAAAAAAGGAAAAAGAAATACGTCATGCTCTTTG
*
37565 AGGAAAAAAAAGAAAAAGAAATACGTCATGCTCTTTG
1 AGG-AAAAAAGGAAAAAGAAATACGTCATGCTCTTTG
* *
37602 AGGACAAAAGGGAAAAGAA
1 AGGAAAAAAGGAAAAAGAA
37621 TGGAATGAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 16 0.33
37 32 0.67
ACGTcount: A:0.49, C:0.12, G:0.24, T:0.15
Consensus pattern (36 bp):
AGGAAAAAAGGAAAAAGAAATACGTCATGCTCTTTG
Found at i:37761 original size:61 final size:60
Alignment explanation
Indices: 37658--37845 Score: 254
Period size: 61 Copynumber: 3.1 Consensus size: 60
37648 GGACAAAGGA
** * * *
37658 GAAAATGAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCATCAACTCGTGTGAGCTTT
1 GAAAA-GAAAAGGCATCCTGCTCTTTGAGGACT-GGAAGTGCCACCAACTTGTGTGGGCTTT
37720 GAAAAGAAAAGGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
1 GAAAAGAAAAGGCATCCTGCTCTTTGAGGACTGGAA-GTGCCACCAACTTGTGTGGGCTTT
* * *
37781 GCAAAGAGAAA-GCATCCTGCTCTTTGAAGACGGGAAGTGCCACCAACTTGTGTGGGCTTT
1 GAAAAGA-AAAGGCATCCTGCTCTTTGAGGACTGGAAGTGCCACCAACTTGTGTGGGCTTT
37841 -AAAAG
1 GAAAAG
37846 GCGTCTCTTT
Statistics
Matches: 115, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
59 4 0.03
60 26 0.23
61 77 0.67
62 8 0.07
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (60 bp):
GAAAAGAAAAGGCATCCTGCTCTTTGAGGACTGGAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:37875 original size:51 final size:54
Alignment explanation
Indices: 37817--37922 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 54
37807 AAGACGGGAA
*
37817 GTGCCACCAACTTGTGTGGGCTTTAAA-A-GGCGT-CTCTTTGAGGACTGAAGG
1 GTGCCACCAACTTGTGTGGGCTTTAAAGACGGCGTGCTCTTTGAGGACTAAAGG
* *
37868 GTGCCACCAACTTGTGTGGGCTTTAAAGACGTCTTGCTCTTTGAGGACTAAAGG
1 GTGCCACCAACTTGTGTGGGCTTTAAAGACGGCGTGCTCTTTGAGGACTAAAGG
37922 G
1 G
37923 CGAAAAGAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
51 27 0.55
52 1 0.02
53 3 0.06
54 18 0.37
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (54 bp):
GTGCCACCAACTTGTGTGGGCTTTAAAGACGGCGTGCTCTTTGAGGACTAAAGG
Found at i:38085 original size:55 final size:54
Alignment explanation
Indices: 38024--38132 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
38014 ACTAAAAAAA
* * *
38024 TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCTTGCTTTTTAAGGACTGAAGGG
1 TGCCACCAACTTGTGTGGGCTTT-AAAAGCGTCTTGCTCTTTAAGGACTAAAGGG
*
38079 TGCCACCAACTTGTGTGGGCTTTAAAAGCGTCTTGCTCTTTGAGGACTAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGCGTCTTGCTCTTTAAGGACTAAAGGG
38133 CGAAAGGAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 27 0.54
55 23 0.46
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (54 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGCGTCTTGCTCTTTAAGGACTAAAGGG
Found at i:38130 original size:210 final size:203
Alignment explanation
Indices: 37734--38260 Score: 792
Period size: 210 Copynumber: 2.6 Consensus size: 203
37724 AGAAAAGGCA
* *
37734 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAA-GAGAAAGCATCC
1 TCCTGCTCTTTGAGGACTAGAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAAGCATCC
* ** * * *
37798 TGCTCTTTGAAGAC-GGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCTCTTTGAGGAC
64 T-CTTTTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCTCTTTAAGGAC
37862 TGAAGGGTGCCACCAACTTGTGTGGGCTTTAAAGACGTCTTGCTCTTTGAGGACTAAAGGGCGAA
128 TGAAGGGTGCCACCAACTTGTGTGGGCTTTAAAGACGTCTTGCTCTTTGAGGACTAAAGGGCGAA
37927 AAGAGAGAGCG
193 AAGAGAGAGCG
37938 TCCTGCTCTTTGAGGACTAAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCATCCT
1 TCCTGCTCTTTGAGGACT-AGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCATCCT
* *
38003 ACTTTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCTTGCTTTTTAA
65 -CTTTTTGAAGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC-T-C--TTTAA
38068 GGACTGAAGGGTGCCACCAACTTGTGTGGGCTTTAAA-AGCGTCTTGCTCTTTGAGGACTAAAGG
124 GGACTGAAGGGTGCCACCAACTTGTGTGGGCTTTAAAGA-CGTCTTGCTCTTTGAGGACTAAAGG
*
38132 GCGAAAGGAGAGAGCG
188 GCGAAAAGAGAGAGCG
38148 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCATCCT
1 TCCTGCTCTTTGAGGACTAG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCATCCT
* *
38213 GTTCTTTGACGACTGAAAAA-GCCACCAACTTGTGTGGGCTTTGAAAGG
65 CTT-TTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
38261 AAAAGGCAAC
Statistics
Matches: 297, Mismatches: 15, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
203 3 0.01
204 65 0.22
205 3 0.01
206 34 0.11
207 1 0.00
208 29 0.10
209 10 0.03
210 152 0.51
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (203 bp):
TCCTGCTCTTTGAGGACTAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCATCCTC
TTTTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCTCTTTAAGGACTGA
AGGGTGCCACCAACTTGTGTGGGCTTTAAAGACGTCTTGCTCTTTGAGGACTAAAGGGCGAAAAG
AGAGAGCG
Found at i:38252 original size:60 final size:61
Alignment explanation
Indices: 38135--38292 Score: 194
Period size: 60 Copynumber: 2.6 Consensus size: 61
38125 CTAAAGGGCG
* * * **
38135 AAAGGAGAGAGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGAGAAAGCATCCTGCTCTTTGACGACTAGAAAAAGCCACCAACTTGTGTGGGCTTTA
* *
38196 AAAGGAGAAAGCATCCTGTTCTTTGACGACT-GAAAAAGCCACCAACTTGTGTGGGCTTTG
1 AAAGGAGAAAGCATCCTGCTCTTTGACGACTAGAAAAAGCCACCAACTTGTGTGGGCTTTA
* * * *
38256 AAAGGA-AAAGGCAACCTGCTTTTTGAGGACAAGAAAA
1 AAAGGAGAAA-GCATCCTGCTCTTTGACGACTAGAAAA
38293 GTGAAAGGAG
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 3 0.04
60 48 0.58
61 32 0.39
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (61 bp):
AAAGGAGAAAGCATCCTGCTCTTTGACGACTAGAAAAAGCCACCAACTTGTGTGGGCTTTA
Done.