Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3367
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: 107606
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4402 original size:40 final size:40
Alignment explanation
Indices: 4284--4462 Score: 165
Period size: 40 Copynumber: 4.5 Consensus size: 40
4274 TTGAATGCTG
* *
4284 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTA-AGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGA-T-ACTAAT
** * *
4323 ATCCGGACTAAGAT-CCGAAGG--TTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCCTTTGTGCGAGATACTAAT
4362 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
* * ** *
4402 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACT-AAT
4442 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
4463 ATTGAATGAG
Statistics
Matches: 119, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
37 1 0.01
38 18 0.15
39 13 0.11
40 86 0.72
41 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
Found at i:4419 original size:78 final size:80
Alignment explanation
Indices: 4284--4462 Score: 210
Period size: 78 Copynumber: 2.3 Consensus size: 80
4274 TTGAATGCTG
* * *
4284 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGG-TTT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGATTC
*
4347 GTGCGAGTTATT-AAT
66 GTGCGAGTT-TTAAAA
**
4362 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGG-
4423 ATTCGTGCGAGTTTTAAAA
62 ATTCGTGCGAGTTTTAAAA
4442 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
4463 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
77 2 0.02
78 41 0.47
79 11 0.12
80 34 0.39
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGATTC
GTGCGAGTTTTAAAA
Found at i:4463 original size:40 final size:39
Alignment explanation
Indices: 4347--4465 Score: 166
Period size: 40 Copynumber: 3.0 Consensus size: 39
4337 CCGAAGGTTT
* *
4347 GTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTT
1 GTGCGAGTT-TTAATTCCGGGTTAAGTCCCGAAGGCATTC
**
4387 GTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTC
1 GTGCGAG-TTTTAATTCCGGGTTAAGTCCCGAAGGCATTC
*
4427 GTGCGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATT
1 GTGCGAGTTTT-AATTCCGGGTTAAGTCCCGAAGGCATT
4466 GAATGAGTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.03
40 67 0.96
41 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
GTGCGAGTTTTAATTCCGGGTTAAGTCCCGAAGGCATTC
Found at i:4486 original size:39 final size:38
Alignment explanation
Indices: 4363--4512 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
4353 GTTATTAATT
* ** * *
4363 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
4403 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
4442 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
4482 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
4513 GAGCTAATCC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:11801 original size:43 final size:43
Alignment explanation
Indices: 11740--11871 Score: 228
Period size: 43 Copynumber: 3.1 Consensus size: 43
11730 TGCTCAAATT
* *
11740 ACCGGCATTAAGCCTGCTAGGCACGAAGACCCGAATACACATC
1 ACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACATC
*
11783 ACCGGCATGAATCCTGCTAGGCACGAAGGCCCGAATACACATC
1 ACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACATC
*
11826 ACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACACATC
1 ACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACATC
11869 ACC
1 ACC
11872 AAGTTTTCAT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.31, C:0.34, G:0.23, T:0.12
Consensus pattern (43 bp):
ACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACATC
Found at i:13076 original size:16 final size:16
Alignment explanation
Indices: 13055--13085 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13045 AAATGATGAA
13055 TCATTCCACTTACTTT
1 TCATTCCACTTACTTT
*
13071 TCATTCCATTTACTT
1 TCATTCCACTTACTT
13086 AGCATAAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.29, G:0.00, T:0.52
Consensus pattern (16 bp):
TCATTCCACTTACTTT
Found at i:13774 original size:40 final size:39
Alignment explanation
Indices: 13722--13813 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 39
13712 CACCAGAAAA
* *
13722 AAGCTCATAAGAGCTAATCCAACTGAAATACGCCAAACAG
1 AAGCTCATAAGAGCTAATCCAACTGAAACAC-ACAAACAG
* ** * *
13762 AAGCTCATAAGAGTTGGTCCACCTGAAACACACTAACAG
1 AAGCTCATAAGAGCTAATCCAACTGAAACACACAAACAG
13801 AAGCTCATAAGAG
1 AAGCTCATAAGAG
13814 TTAAAAAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 19 0.42
40 26 0.58
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.16
Consensus pattern (39 bp):
AAGCTCATAAGAGCTAATCCAACTGAAACACACAAACAG
Found at i:14951 original size:13 final size:13
Alignment explanation
Indices: 14933--14962 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
14923 CTTTTTATTA
14933 CAAAATTAACTAT
1 CAAAATTAACTAT
14946 CAAAATTAACTAT
1 CAAAATTAACTAT
14959 CAAA
1 CAAA
14963 TCAATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (13 bp):
CAAAATTAACTAT
Found at i:17969 original size:6 final size:6
Alignment explanation
Indices: 17958--17982 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17948 TAAGTCACAA
17958 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
17983 GAGTTTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:26234 original size:42 final size:42
Alignment explanation
Indices: 26180--26285 Score: 160
Period size: 42 Copynumber: 2.5 Consensus size: 42
26170 TAAGGGTTAC
*
26180 TAAGATTATGTGTAAGACTATATCTGGGATATGACATCT-ATA
1 TAAGATTTTGTGTAAGACTATATCTGGGATATGACAT-TGATA
* * *
26222 TGAGATTTTGTGTAAGACCATATCTGGGATATGGCATTGATA
1 TAAGATTTTGTGTAAGACTATATCTGGGATATGACATTGATA
26264 TAAGATTTTGTGTAAGACTATA
1 TAAGATTTTGTGTAAGACTATA
26286 GCTAGGCTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.02
42 56 0.98
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (42 bp):
TAAGATTTTGTGTAAGACTATATCTGGGATATGACATTGATA
Found at i:26334 original size:85 final size:84
Alignment explanation
Indices: 26180--26337 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 84
26170 TAAGGGTTAC
* * * *** *
26180 TAAGATTATGTGTAAGACTATATCTGGGATATGACATCTATATGAGATTTTGTGTAAGACCATAT
1 TAAGATTATGTGTAAGACTATAGCTAGGATATGACATCGATATGAGATTACATATAAGACCATAT
26245 CTGGGATATGGCATTGATA
66 CTGGGATATGGCATTGATA
* * * *
26264 TAAGATTTTGTGTAAGACTATAGCTAGGCTATTGGCATCGATATGGGATTACATATAAGACCATA
1 TAAGATTATGTGTAAGACTATAGCTAGGATA-TGACATCGATATGAGATTACATATAAGACCATA
26329 TCTGGGATA
65 TCTGGGATA
26338 AGGAATTGGT
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
84 27 0.44
85 35 0.56
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (84 bp):
TAAGATTATGTGTAAGACTATAGCTAGGATATGACATCGATATGAGATTACATATAAGACCATAT
CTGGGATATGGCATTGATA
Found at i:29157 original size:55 final size:53
Alignment explanation
Indices: 29070--29324 Score: 220
Period size: 55 Copynumber: 4.8 Consensus size: 53
29060 ATTAGGGTTT
*
29070 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAA-GTTTCTAAGGC
* * * * * * *
29125 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGAC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTT--TCTAAGGC
* * * *
29180 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTC-TAAGGC
* **
29233 AAGGATACCATGTAAGACCATGTCTTGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAGTTTCTAAGGC
* * *
29282 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAG
29325 GTACCCGCGT
Statistics
Matches: 164, Mismatches: 29, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
49 38 0.23
52 7 0.04
53 37 0.23
54 12 0.07
55 66 0.40
56 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTCTAAGGC
Found at i:29276 original size:108 final size:110
Alignment explanation
Indices: 29077--29277 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
29067 TTTAAGGATA
*
29077 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
29142 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGACAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGACAAAGGTC
* * *
29187 CCATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
** *
29249 ACCATGTCTTGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
29278 TCAAAAGGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.56
109 7 0.09
110 26 0.32
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGACAAAGGTC
Found at i:29430 original size:23 final size:24
Alignment explanation
Indices: 29393--29440 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
29383 AAGGTAAGGT
**
29393 AAGGTAAGATGAGTT-ATACTAAA
1 AAGGTAAGACAAGTTCATACTAAA
*
29416 AAGGTAAGACAAGTTCATGCTAAA
1 AAGGTAAGACAAGTTCATACTAAA
29440 A
1 A
29441 GAGCAAAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (24 bp):
AAGGTAAGACAAGTTCATACTAAA
Found at i:29537 original size:16 final size:16
Alignment explanation
Indices: 29516--29546 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29506 ATAAATTTGA
29516 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
29532 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
29547 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:32536 original size:20 final size:21
Alignment explanation
Indices: 32511--32549 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
32501 CTCTTGAAGT
32511 AGGGC-ACACGCCCGTGTGAA
1 AGGGCAACACGCCCGTGTGAA
32531 AGGGCAACACGCCCGTGTG
1 AGGGCAACACGCCCGTGTG
32550 GTCATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.31, G:0.36, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGAA
Found at i:33923 original size:49 final size:49
Alignment explanation
Indices: 33812--33931 Score: 136
Period size: 49 Copynumber: 2.4 Consensus size: 49
33802 GAGGCTGACA
* * * * *
33812 CCATGTCCTAGACATGGTCTTACATTAGCTTTCACATATTCGTGCCGCTG
1 CCATGTCCCAGACATGGTCTTACATGAGCCTT-ACATATCCGTGCCGATG
*
33862 CCATGTCTCAGACATGGTCTTACACTGA-CACTT-CATATCCGTGCCGATG
1 CCATGTCCCAGACATGGTCTTACA-TGAGC-CTTACATATCCGTGCCGATG
*
33911 CCATGTCCCAGACATGTTCTT
1 CCATGTCCCAGACATGGTCTT
33932 GCCGATGCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
49 33 0.55
50 23 0.38
51 4 0.07
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (49 bp):
CCATGTCCCAGACATGGTCTTACATGAGCCTTACATATCCGTGCCGATG
Found at i:34032 original size:48 final size:49
Alignment explanation
Indices: 33931--34047 Score: 124
Period size: 47 Copynumber: 2.5 Consensus size: 49
33921 GACATGTTCT
33931 TGCCGATG-CATGTCCCAGACAT-GTCTTACGATAGCTCTCATCTCAATG
1 TGCCGATGTCATGTCCCAGACATGGTCTTACGATAGCTCTCA-CTCAATG
*
33979 T--CGATGTCATGTCCCAGACATGGTCTTAC-ACTGGCTCTCA-T-AATG
1 TGCCGATGTCATGTCCCAGACATGGTCTTACGA-TAGCTCTCACTCAATG
**
34024 TGGCCGATGT-ATGTCTTAGACATG
1 T-GCCGATGTCATGTCCCAGACATG
34048 TTTTGCACTA
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
45 5 0.08
46 6 0.10
47 27 0.45
48 22 0.37
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (49 bp):
TGCCGATGTCATGTCCCAGACATGGTCTTACGATAGCTCTCACTCAATG
Found at i:38451 original size:48 final size:49
Alignment explanation
Indices: 38385--38624 Score: 285
Period size: 48 Copynumber: 4.9 Consensus size: 49
38375 ATACTAGGGT
* * *
38385 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTG-A
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGAA
* **
38433 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATTGCATCGGCAT-TTA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGAA
* * * * *
38481 TATGAGAGCTAGTGTAAGCCCATGTCTAGG-ACATGCCATCGACCTCGACA
1 TATGAGAGCTAGTGTAAGACCATGT-TTGGAACATGGCATCGGCATCGA-A
*
38531 TATG-G-GCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCACCGATA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGA-A
*
38579 TATGAGAGCCAGTGTAAGACCATGTTT-GAGACATGGCATCGGCATC
1 TATGAGAGCTAGTGTAAGACCATGTTTGGA-ACATGGCATCGGCATC
38625 TTACCCTTTT
Statistics
Matches: 163, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
47 3 0.02
48 114 0.70
49 7 0.04
50 39 0.24
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (49 bp):
TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGAA
Found at i:54467 original size:26 final size:26
Alignment explanation
Indices: 54428--54516 Score: 106
Period size: 26 Copynumber: 3.3 Consensus size: 26
54418 GTGCGACCTT
* *
54428 AAGGCATTTATTTCATATTGCGCCACA
1 AAGGC-TTTCTTTCATATTACGCCACA
*
54455 AAAGCTTTCTTTCATATTACGCCACA
1 AAGGCTTTCTTTCATATTACGCCACA
* *
54481 AAGGCTTTTTTTTTCATATTACACCACA
1 AAGGC--TTTCTTTCATATTACGCCACA
54509 AAGGCTTT
1 AAGGCTTT
54517 TCCTTCCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 26 0.48
27 4 0.07
28 24 0.44
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.37
Consensus pattern (26 bp):
AAGGCTTTCTTTCATATTACGCCACA
Found at i:54507 original size:28 final size:28
Alignment explanation
Indices: 54438--54517 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 28
54428 AAGGCATTTA
* *
54438 TTTCATATTGCGCCACAAAAGC--TTTC
1 TTTCATATTACGCCACAAAGGCTTTTTC
*
54464 TTTCATATTACGCCACAAAGGCTTTTTT
1 TTTCATATTACGCCACAAAGGCTTTTTC
*
54492 TTTCATATTACACCACAAAGGCTTTT
1 TTTCATATTACGCCACAAAGGCTTTT
54518 CCTTCCTAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 20 0.42
28 28 0.58
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.39
Consensus pattern (28 bp):
TTTCATATTACGCCACAAAGGCTTTTTC
Found at i:58089 original size:19 final size:18
Alignment explanation
Indices: 58065--58105 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
58055 GTTGTGATTA
* *
58065 AATTATATTTGAATTGATG
1 AATTATATGTGAAAT-ATG
58084 AATTATATGTGAAATATG
1 AATTATATGTGAAATATG
58102 AATT
1 AATT
58106 TAAAAGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (18 bp):
AATTATATGTGAAATATG
Found at i:58323 original size:22 final size:22
Alignment explanation
Indices: 58298--58342 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
58288 ACTATGTGTC
*
58298 AAACCGTGCATGATTCAAAATA
1 AAACCATGCATGATTCAAAATA
58320 AAACCATGCATGATTCAAAATA
1 AAACCATGCATGATTCAAAATA
58342 A
1 A
58343 GGTCACAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.22
Consensus pattern (22 bp):
AAACCATGCATGATTCAAAATA
Found at i:65633 original size:47 final size:47
Alignment explanation
Indices: 65564--65657 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
65554 TTGAGTAGAA
*
65564 GATTGGTTCAAAATGGATGGAAAAACTTTTCACGAACTTTTAGTTGT
1 GATTGGTTCAAAATGGATGGAAAAACTTTTCACGAACCTTTAGTTGT
*
65611 GATTGGTTCACAATGGATGGAAAAACTTTTCACGAACCTTTAGTTGT
1 GATTGGTTCAAAATGGATGGAAAAACTTTTCACGAACCTTTAGTTGT
65658 AACTTTCACA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (47 bp):
GATTGGTTCAAAATGGATGGAAAAACTTTTCACGAACCTTTAGTTGT
Found at i:74717 original size:15 final size:15
Alignment explanation
Indices: 74699--74728 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
74689 TATGAACATG
74699 ATAAAAATGAATTAA
1 ATAAAAATGAATTAA
74714 ATAAAAATGAATTAA
1 ATAAAAATGAATTAA
74729 GTCAATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
ATAAAAATGAATTAA
Found at i:77728 original size:36 final size:35
Alignment explanation
Indices: 77657--77728 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
77647 AACATTTATA
* *
77657 TATTTTAAAAAAATTTGAGAAATTTTATAATTTTT
1 TATTTTAAAAAAAATTGAGAAATTTTATAAGTTTT
* * *
77692 TATTTTAATAAAAAATTGAGATATTTTGTGAGTTTT
1 TATTTTAA-AAAAAATTGAGAAATTTTATAAGTTTT
77728 T
1 T
77729 GAAATTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 8 0.26
36 23 0.74
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (35 bp):
TATTTTAAAAAAAATTGAGAAATTTTATAAGTTTT
Found at i:94828 original size:39 final size:40
Alignment explanation
Indices: 94724--94908 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
94714 TTGAATGATG
* * *
94724 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
94763 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
94804 TCCGGGCTAAG-CCCAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
94843 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
94882 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
94909 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:94862 original size:79 final size:81
Alignment explanation
Indices: 94724--94908 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
94714 TTGAATGATG
*
94724 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
94788 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * * **
94803 TTCCGGGCTAAG-CCCAAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
94865 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
94883 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
94909 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 32 0.36
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:94930 original size:79 final size:79
Alignment explanation
Indices: 94777--94931 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
94767 GGACTAAGAT
* **
94777 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCAAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTTGAACGAGTTACTAA
94842 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
94856 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTTGAACGAGTTA-C
*
94919 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
94932 ATTCCAAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 40 0.61
80 24 0.36
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:98347 original size:45 final size:45
Alignment explanation
Indices: 98297--98406 Score: 132
Period size: 45 Copynumber: 2.4 Consensus size: 45
98287 TTTAAGCTCA
* ** *
98297 TTGAGTTGGTCTGAGTTTGTGATATATGTG-AGAAATCCGAACTTG
1 TTGAGTTGGTCCGAGTTCATGATATATGTGAAG-AATCCGAACTCG
* * * *
98342 TTGAGTTGGTCCAAGTTCATGATATATGTGAAGCATCTGAGCTCG
1 TTGAGTTGGTCCGAGTTCATGATATATGTGAAGAATCCGAACTCG
98387 TTGAGTTGGTCCGAGTTCAT
1 TTGAGTTGGTCCGAGTTCAT
98407 TATGGATACG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 53 0.96
46 2 0.04
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (45 bp):
TTGAGTTGGTCCGAGTTCATGATATATGTGAAGAATCCGAACTCG
Found at i:98436 original size:44 final size:48
Alignment explanation
Indices: 98381--98507 Score: 154
Period size: 52 Copynumber: 2.6 Consensus size: 48
98371 GAAGCATCTG
*
98381 AGCTCGTTGAGTTGGTCCGAGTTCATTATGGAT-A-C-GAG-CATCCA
1 AGCTCGTTGAGTTGGTCTGAGTTCATTATGGATGAGCAGAGACATCCA
* * *
98425 AGCTCGTTGAGTTGGTCTGAGTTTATTATGGATGCGATGCATGTGACATCCG
1 AGCTCGTTGAGTTGGTCTGAGTTCATTATGGAT--GA-GCA-GAGACATCCA
98477 AGCTCGTTGAGTTGGTCTGAGTTCATTATGG
1 AGCTCGTTGAGTTGGTCTGAGTTCATTATGG
98508 TTGTATACAT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
44 31 0.44
47 1 0.01
49 1 0.01
51 2 0.03
52 35 0.50
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.34
Consensus pattern (48 bp):
AGCTCGTTGAGTTGGTCTGAGTTCATTATGGATGAGCAGAGACATCCA
Done.