Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1593
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: 27114
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Found at i:105 original size:28 final size:28
Alignment explanation
Indices: 1--722 Score: 806
Period size: 28 Copynumber: 25.4 Consensus size: 28
1 CTTTCAAAGCCCAC-AGTCA--GGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
26 CCTTTCAAAGCCCACCAAGTCAGTGGCACT
1 -CTTTCAAAGCCCA-CAAGTCAGTGGCACT
* *
56 CTTTTCAAAGCCCACAAATCAGTGACACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* *
85 CTTTTAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
113 CTTTCAAAGCCCACAAGTCAGTGGC-CT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
140 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
169 TTTTCAAAGCCCACAA-TCAAT-GCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
195 CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* *
224 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
252 CTTTCAGAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
280 CTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
307 CATTGCGAAGCCCACAATTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
336 CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
363 CTTTTTAAAGCCCACAAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
392 CCTTTTAAAGGTCACGCAAGTCAGTGGTAC-
1 -CTTTCAAA-G-CCCACAAGTCAGTGGCACT
*
422 CTTTTCAAAGCCC-CGAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
450 CTTTC-AAGCCCACAAGTTAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
476 CCTTTCAAAGCCCACGAGTTAGTGGCACC
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
*
505 CTTTCAAAGCCCACACAAGTCAGTGACACT
1 CTTTCAAAG-CC-CACAAGTCAGTGGCACT
*
535 CCTTTTCAAAGCCCACGAGTCAGTGGCAC-
1 -C-TTTCAAAGCCCACAAGTCAGTGGCACT
564 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
592 CTTTCAAAGCCCACGAGTCAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
619 CCTTTCAAAGCCCACGCAAGTCAGTGGCACC
1 -CTTTCAAAGCCCA--CAAGTCAGTGGCACT
* **
650 CTTTTAAAGCCCACGCAAGTCAGTAACACT
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACT
*
680 CTTTTCAAAGCCCACATGTGTCAGTGGCAACTT
1 C-TTTCAAAGCCCACA--AGTCAGTGGC-AC-T
*
713 TTTTCAAAGC
1 CTTTCAAAGC
723 TTACACAAGC
Statistics
Matches: 605, Mismatches: 54, Indels: 68
0.83 0.07 0.09
Matches are distributed among these distances:
26 25 0.04
27 81 0.13
28 315 0.52
29 36 0.06
30 92 0.15
31 36 0.06
32 19 0.03
33 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1330 original size:20 final size:20
Alignment explanation
Indices: 1302--1376 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1292 TTTTACCTTG
1302 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1322 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1342 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1362 ATGTATCGATACATT
1 ATGTATCGATACATT
1377 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1369 original size:40 final size:39
Alignment explanation
Indices: 1302--1379 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1292 TTTTACCTTG
* *
1302 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1342 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1380 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:2314 original size:22 final size:22
Alignment explanation
Indices: 2288--2342 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2278 AGCCTTTGAC
*
2288 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATATTT
2310 CATGCATTTTTTTATTATATTT
1 CATGCATTTTTTTATTATATTT
2332 CATGCATTTTT
1 CATGCATTTTT
2343 AACATGTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATATTT
Found at i:13376 original size:33 final size:32
Alignment explanation
Indices: 13339--13450 Score: 115
Period size: 33 Copynumber: 3.4 Consensus size: 32
13329 CGTCCTCCAC
13339 CAAAA-AAAAAAGAAGAAAAAAAAAACAACAAAA
1 CAAAACAAAAAA-AAGAAAAAAAAAACAA-AAAA
*
13372 CAAAACAAAAAAAAGAGAAAAAAAACAAAACAA
1 CAAAACAAAAAAAAGAAAAAAAAAACAAAA-AA
13405 -AAAA-AAACAAAAA-AAAACAAACAAACAAAAAAA
1 CAAAACAAA-AAAAAGAAAA-AAA-AAAC-AAAAAA
13438 CAACAACAAAAAA
1 CAA-AACAAAAAA
13451 GGTCCGGATG
Statistics
Matches: 68, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
31 6 0.09
32 14 0.21
33 28 0.41
34 12 0.18
35 5 0.07
36 3 0.04
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (32 bp):
CAAAACAAAAAAAAGAAAAAAAAAACAAAAAA
Found at i:13382 original size:25 final size:25
Alignment explanation
Indices: 13354--13448 Score: 106
Period size: 25 Copynumber: 3.8 Consensus size: 25
13344 AAAAAAGAAG
*
13354 AAAAAAAAA-ACAACAAAACAAAAC
1 AAAAAAAAACAAAACAAAACAAAAC
*
13378 AAAAAAAAGAGAAAA-AAAACAAAAC
1 AAAAAAAA-ACAAAACAAAACAAAAC
*
13403 AAAAAAAAACAAAAAAAAAC-AAAC
1 AAAAAAAAACAAAACAAAACAAAAC
13427 AAACAAAAAAACAACAACAAAA
1 -AA-AAAAAAACAA-AACAAAA
13449 AAGGTCCGGA
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
24 17 0.27
25 26 0.42
26 13 0.21
27 6 0.10
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (25 bp):
AAAAAAAAACAAAACAAAACAAAAC
Found at i:13391 original size:35 final size:34
Alignment explanation
Indices: 13342--13448 Score: 126
Period size: 35 Copynumber: 3.0 Consensus size: 34
13332 CCTCCACCAA
13342 AAAAAAAAGAAGAAAAAAAAAACAACAAAACAAAAC
1 AAAAAAAAG-AGAAAAAAAAAA-AACAAAACAAAAC
*
13378 AAAAAAAAGAGAAAAAAAACAAAACAAAAAAAAAC
1 AAAAAAAAGAGAAAAAAAA-AAAACAAAACAAAAC
*
13413 AAAAAAAA-ACAAACAAACAAAAAAACAACAACAAAA
1 AAAAAAAAGA-GAA-AAA-AAAAAAACAA-AACAAAA
13449 AAGGTCCGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
34 1 0.02
35 32 0.51
36 21 0.33
37 9 0.14
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (34 bp):
AAAAAAAAGAGAAAAAAAAAAAACAAAACAAAAC
Found at i:13426 original size:14 final size:14
Alignment explanation
Indices: 13339--13450 Score: 99
Period size: 14 Copynumber: 7.8 Consensus size: 14
13329 CGTCCTCCAC
13339 CAAA-AAAAAAAGAA
1 CAAACAAAAAAA-AA
*
13353 GAAA-AAAAAAACAA
1 CAAACAAAAAAA-AA
13367 CAAAACAAAACAAAAA
1 C-AAACAAAA-AAAAA
*
13383 -AAAGAGAAAAAAAA
1 CAAACA-AAAAAAAA
13397 CAAAACAAAAAAAAA
1 C-AAACAAAAAAAAA
13412 CAAA-AAAAAACAAA
1 CAAACAAAAAA-AAA
13426 CAAACAAAAAAACAA
1 CAAACAAAAAAA-AA
13441 C-AACAAAAAA
1 CAAACAAAAAA
13451 GGTCCGGATG
Statistics
Matches: 84, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
13 6 0.07
14 41 0.49
15 24 0.29
16 10 0.12
17 3 0.04
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (14 bp):
CAAACAAAAAAAAA
Found at i:13450 original size:1 final size:1
Alignment explanation
Indices: 13340--13437 Score: 70
Period size: 1 Copynumber: 98.0 Consensus size: 1
13330 GTCCTCCACC
* * * * * * * * * *
13340 AAAAAAAAAAGAAGAAAAAAAAAACAACAAAACAAAACAAAAAAAAGAGAAAAAAAACAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
13405 AAAAAAACAAAAAAAAACAAACAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13438 CAACAACAAA
Statistics
Matches: 69, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:14866 original size:30 final size:29
Alignment explanation
Indices: 14830--14995 Score: 212
Period size: 28 Copynumber: 5.7 Consensus size: 29
14820 CATCATTTCC
*
14830 AAAGCCCACAAGTCAGTGGCACCCTCTTCA
1 AAAGCCCACAAGTCAGTGGCA-ACTCTTCA
* * *
14860 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACTCTTCA
14889 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTCAGTGGCAACTCTTCA
* *
14917 AAAGCCCACAAGTCAGTGGCACCCTTTTTC-
1 AAAGCCCACAAGTCAGTGGCA-AC-TCTTCA
*
14947 AAAGCCCACAAATCAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTCAGTGGCAACTCTTCA
*
14975 AAAGCCCACAAGTCCGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
14996 TCTTTTTCCT
Statistics
Matches: 119, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
27 3 0.03
28 43 0.36
29 29 0.24
30 41 0.34
31 3 0.03
ACGTcount: A:0.32, C:0.33, G:0.17, T:0.17
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCAACTCTTCA
Found at i:14963 original size:87 final size:86
Alignment explanation
Indices: 14830--14995 Score: 253
Period size: 87 Copynumber: 1.9 Consensus size: 86
14820 CATCATTTCC
* * * *
14830 AAAGCCCACAAGTCAGTGGCACCCTCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCC
1 AAAGCCCACAAGTCAGTGGCACCCTCTTCAAAAGCCCACAAATCAGTGGCAAC-CTTCAAAAGCC
14895 CACAAGTCAGTGGCAACCTTCA
65 CACAAGTCAGTGGCAACCTTCA
*
14917 AAAGCCCACAAGTCAGTGGCACCCTTTTTC-AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCC
1 AAAGCCCACAAGTCAGTGGCACCC-TCTTCAAAAGCCCACAAATCAGTGGCAACCTTCAAAAGCC
*
14981 CACAAGTCCGTGGCA
65 CACAAGTCAGTGGCA
14996 TCTTTTTCCT
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
86 23 0.32
87 45 0.62
88 4 0.06
ACGTcount: A:0.32, C:0.33, G:0.17, T:0.17
Consensus pattern (86 bp):
AAAGCCCACAAGTCAGTGGCACCCTCTTCAAAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCC
ACAAGTCAGTGGCAACCTTCA
Found at i:14968 original size:58 final size:57
Alignment explanation
Indices: 14816--15003 Score: 286
Period size: 58 Copynumber: 3.2 Consensus size: 57
14806 TTCGTTGGTT
* * *
14816 GTGGCATCATTTCCAAAGCCCACAAGTCAGTGGCACCCTCTTCAAAAGCCCACAAGTCA
1 GTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCA-AC-CTTCAAAAGCCCACAAGTCA
*
14875 GTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCA
1 GTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCA
* * *
14932 GTGGCACCCTTTTTCAAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCC
1 GTGGCA-TCTTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCA
14990 GTGGCATCTTTTTC
1 GTGGCATCTTTTTC
15004 CTTTTAAGCC
Statistics
Matches: 121, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
57 33 0.27
58 54 0.45
59 34 0.28
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.21
Consensus pattern (57 bp):
GTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCA
Found at i:15041 original size:32 final size:32
Alignment explanation
Indices: 14976--15065 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
14966 CAACCTTCAA
* *
14976 AAGCCCACAAGTCCGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCA-CCTTTTCCTTTT
*
15009 AAGCCCACAACTCCGTGGCACCTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
*
15041 AAGTCCACAACTCCGTGGCACCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
15066 AAGCCCAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 34 0.64
33 19 0.36
ACGTcount: A:0.20, C:0.33, G:0.14, T:0.32
Consensus pattern (32 bp):
AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:15144 original size:35 final size:35
Alignment explanation
Indices: 15104--15231 Score: 161
Period size: 35 Copynumber: 3.7 Consensus size: 35
15094 CATATTGGCA
15104 CCTTTTCTTTTTTAAGTCCACAACTCCGTGGCACT
1 CCTTTTCTTTTTTAAGTCCACAACTCCGTGGCACT
15139 CCTTTTCTTTTTTAAGTCCACAACTCCGTGGCACT
1 CCTTTTCTTTTTTAAGTCCACAACTCCGTGGCACT
** * *
15174 TATTTTCTTTTGTAAG-CTCACAACTCTGTGGCACCT
1 CCTTTTCTTTTTTAAGTC-CACAACTCCGTGGCA-CT
** *
15210 GTTTTTC-TTTTTAAGCCCACAA
1 CCTTTTCTTTTTTAAGTCCACAA
15232 GTCAGTGACA
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
34 1 0.01
35 74 0.89
36 8 0.10
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (35 bp):
CCTTTTCTTTTTTAAGTCCACAACTCCGTGGCACT
Found at i:15244 original size:35 final size:34
Alignment explanation
Indices: 15106--15249 Score: 155
Period size: 35 Copynumber: 4.1 Consensus size: 34
15096 TATTGGCACC
* *
15106 TTTTCTTTTTTAAGTCCACAACTCCGTGGCACTCC
1 TTTTCTTTTTTAAGCCCACAACTCCGTGGCACT-T
*
15141 TTTTCTTTTTTAAGTCCACAACTCCGTGGCACTT
1 TTTTCTTTTTTAAGCCCACAACTCCGTGGCACTT
* * *
15175 ATTTTCTTTTGTAAGCTCACAACTCTGTGGCACCTGT
1 -TTTTCTTTTTTAAGCCCACAACTCCGTGGCA-CT-T
* * * *
15212 TTTTC-TTTTTAAGCCCACAAGTCAGTGACACCT
1 TTTTCTTTTTTAAGCCCACAACTCCGTGGCACTT
15245 TTTTC
1 TTTTC
15250 AAAAGCCCAC
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
33 6 0.06
34 1 0.01
35 80 0.84
36 7 0.07
37 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (34 bp):
TTTTCTTTTTTAAGCCCACAACTCCGTGGCACTT
Found at i:15366 original size:49 final size:49
Alignment explanation
Indices: 15306--15684 Score: 374
Period size: 49 Copynumber: 8.0 Consensus size: 49
15296 GGCGTCTTTT
* * *
15306 TTTAAGTCCAATATCGTTGACCTTGAATTAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * * * *
15355 TTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* *
15404 TTTAAGTCCAATATCACTGGTCC-TAAATCAGCATATTGGCACC---ATC
1 TTTAAGTCCAATATCGCTGG-CCTTGAATCAGCATATTGGCACCTTTATC
* * * * *
15450 TCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA---TAATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* *
15496 -------CCAATATCACTGGCCTTGAATCAGCATATTGGCACC-TTGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
15537 TTTAAGACCAATGTCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTTATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TTATC
* * *
15589 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
15638 TTTAAGTCCAATATTGTTGGCCTTGAATCAGCATATTGGCATCTTTA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
15685 ACATTCCTAA
Statistics
Matches: 272, Mismatches: 41, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
39 31 0.11
41 3 0.01
45 2 0.01
46 38 0.14
48 33 0.12
49 118 0.43
50 3 0.01
52 44 0.16
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (49 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
Found at i:15575 original size:87 final size:85
Alignment explanation
Indices: 15411--15577 Score: 255
Period size: 87 Copynumber: 1.9 Consensus size: 85
15401 ATCTTTAAGT
15411 CCAATATCACTGGTCCTAAATCAGCATATTGGCACCATCTCTAAGACCAATGTCGCTGGCCTTGA
1 CCAATATCACTGGTCCTAAATCAGCATATTGGCACCATCTCTAAGACCAATGTCGCTGGCCTTGA
15476 ATCAGCACATTGGCATAATC
66 ATCAGCACATTGGCATAATC
* * * *
15496 CCAATATCACTGG-CCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGTTGGCCT
1 CCAATATCACTGGTCC-TAAATCAGCATATTGGCACC--ATCTCTAAGACCAATGTCGCTGGCCT
*
15560 TGAATCAGCATATTGGCA
63 TGAATCAGCACATTGGCA
15578 CCTTTGTTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
84 2 0.03
85 32 0.43
87 40 0.54
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (85 bp):
CCAATATCACTGGTCCTAAATCAGCATATTGGCACCATCTCTAAGACCAATGTCGCTGGCCTTGA
ATCAGCACATTGGCATAATC
Found at i:15626 original size:139 final size:134
Alignment explanation
Indices: 15374--15629 Score: 345
Period size: 139 Copynumber: 1.9 Consensus size: 134
15364 AATGTCGCTA
* *
15374 GCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCACTGGTCCTAAATCAGCATA
1 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCACTGGTCCTAAATCAGCATA
15439 TTGGCACCATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAATCCCAATATC
66 TTGGCACCATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAATCCCAATATC
15504 ACTG
131 ACTG
* * * ** *
15508 GCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTCGTTGG-CCTTGAATCAGCAT
1 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCACTGGTCC-TAAATCAGCAT
* *
15571 ATTGGCACCTTTGTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
65 ATTGGCACC------ATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
15630 CCTTCATCTT
Statistics
Matches: 105, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
132 2 0.02
133 37 0.35
134 24 0.23
139 42 0.40
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (134 bp):
GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCACTGGTCCTAAATCAGCATA
TTGGCACCATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAATCCCAATATC
ACTG
Found at i:15701 original size:101 final size:101
Alignment explanation
Indices: 15495--15769 Score: 306
Period size: 101 Copynumber: 2.8 Consensus size: 101
15485 TTGGCATAAT
* * * * *
15495 CCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTCGTTGGCC
1 CCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCC
*** *
15559 TTGAATCAGCATATTGGCACCTTTGTTATCTTTAAG
66 TTGAATCAGCATATTGGCACCTTTAACATCTCTAAG
* * *
15595 TCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATTGTTGGCC
1 CCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCC
*
15660 TTGAATCAGCATATTGGCATCTTTAACAT-TCCTAAG
66 TTGAATCAGCATATTGGCACCTTTAACATCT-CTAAG
* * ** * * * * *
15696 CCCAATGTCATTAGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAATCTAATATCGCTGGCC
1 CCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCC
*
15759 ATGAATCAGCA
66 TTGAATCAGCA
15770 CATTATCATT
Statistics
Matches: 147, Mismatches: 26, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
99 32 0.22
100 36 0.24
101 79 0.54
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (101 bp):
CCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCC
TTGAATCAGCATATTGGCACCTTTAACATCTCTAAG
Found at i:16538 original size:13 final size:13
Alignment explanation
Indices: 16520--16544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16510 AAACTGTAAC
16520 TGTATCGATACAA
1 TGTATCGATACAA
16533 TGTATCGATACA
1 TGTATCGATACA
16545 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:16634 original size:13 final size:13
Alignment explanation
Indices: 16616--16643 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16606 ATTACTCAAA
16616 TGTATCGATACAT
1 TGTATCGATACAT
16629 TGTATCGATACAT
1 TGTATCGATACAT
16642 TG
1 TG
16644 ACCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20784 original size:26 final size:28
Alignment explanation
Indices: 20727--20785 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
20717 TTAATGAAAG
* * *
20727 TTTTGTATATAAATAATTGAATAAAGAG
1 TTTTTTATATAAATAATTGAATAAAAAA
*
20755 TTTTTTATTTAAATAA-TG-ATAAAAAA
1 TTTTTTATATAAATAATTGAATAAAAAA
20781 TTTTT
1 TTTTT
20786 AATTCCTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 11 0.41
27 2 0.07
28 14 0.52
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (28 bp):
TTTTTTATATAAATAATTGAATAAAAAA
Found at i:21156 original size:128 final size:128
Alignment explanation
Indices: 20888--21157 Score: 295
Period size: 128 Copynumber: 2.1 Consensus size: 128
20878 ACTTTTTATT
*
20888 TTTATAAAAACATAATAATTAATATTTTAATATGTTAATGTAATTTTTTTTAAACTTAATTAAAT
1 TTTATAAAAA-ATAATAATTAATATTTTAATATGTTAATGTAAATTTTTTTAAACTTAATTAAAT
* * * * * *
20953 ATTATTTTCAATTTTATTAAAAAATAATAATATAAACCCTTTTTTATTTTTTATTTAAGTTTTTT
65 ATTA-TTT--ATGTTATTAAAAAATAATAATATAAACACTTTTTTATTATTTATATAAATTTATT
*
21018 TA
127 AA
*
21020 TTT-T-AAAAA-AATAATTAATATTTTAATTTGTTAATGTAAATTTTTTTAAACTTAATTAAATA
1 TTTATAAAAAATAATAATTAATATTTTAATATGTTAATGTAAATTTTTTTAAACTTAATTAAATA
* *
21082 TTA-TT-TGTTATT-AAAAATAATAAT-TAATATATTATTATTTATTAGATTTA-ATAAATTTAA
66 TTATTTATGTTATTAAAAAATAATAATATAA-ACACT-TT-TTTATT--ATTTATATAAATTT-A
21142 TTAA
125 TTAA
21146 TTTATAAAAAAT
1 TTTATAAAAAAT
21158 TAAACACTTG
Statistics
Matches: 118, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
121 3 0.03
122 14 0.12
123 8 0.07
124 6 0.05
125 6 0.05
126 12 0.10
127 1 0.01
128 59 0.50
129 1 0.01
130 4 0.03
131 1 0.01
132 3 0.03
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (128 bp):
TTTATAAAAAATAATAATTAATATTTTAATATGTTAATGTAAATTTTTTTAAACTTAATTAAATA
TTATTTATGTTATTAAAAAATAATAATATAAACACTTTTTTATTATTTATATAAATTTATTAA
Found at i:22712 original size:29 final size:29
Alignment explanation
Indices: 22680--22740 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
22670 AACCTACTTA
*
22680 AGCCTTAAAAGT-AAAGAGGTTACTATCTT
1 AGCCTT-AAAGTGAAAGAAGTTACTATCTT
**
22709 AGCCTTAAAGTGTGAGAAGTTACTATCTT
1 AGCCTTAAAGTGAAAGAAGTTACTATCTT
22738 AGC
1 AGC
22741 ATAAGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (29 bp):
AGCCTTAAAGTGAAAGAAGTTACTATCTT
Found at i:23875 original size:14 final size:14
Alignment explanation
Indices: 23858--23888 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
23848 GATGGATATA
23858 TATCGTATAATTCT
1 TATCGTATAATTCT
23872 TATCGTATAATTCT
1 TATCGTATAATTCT
23886 TAT
1 TAT
23889 ATATATTGTA
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:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Found at i:27050 original size:20 final size:20
Alignment explanation
Indices: 27004--27060 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
26994 ATTCTATGAT
* *
27004 ATGTATCGATACAACAAGTCA
1 ATGTATTGATAC-ATAAGTCA
* *
27025 ACGTATTGATACATAAGTGA
1 ATGTATTGATACATAAGTCA
27045 ATGTATTGATAC-TAAG
1 ATGTATTGATACATAAG
27061 GCTTATTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 4 0.13
20 17 0.55
21 10 0.32
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
ATGTATTGATACATAAGTCA
Done.