Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3091
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: 51640
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:1490 original size:79 final size:81
Alignment explanation
Indices: 1381--1563 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
1371 TACTCGTTCA
* *
1381 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
1444 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
1461 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
1524 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
1540 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
1564 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:1563 original size:40 final size:40
Alignment explanation
Indices: 1360--1563 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
1350 CGGAATTTAA
** *
1360 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1400 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1440 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1479 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
1519 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
1559 CCGGA
1 CCGGA
1564 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:9643 original size:79 final size:80
Alignment explanation
Indices: 9544--9726 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
9534 TACTCGTTCA
* *
9544 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
9607 ATTTAGTAAC-TCGCACC
64 ATATAGTAACTTAGCA-C
* **
9624 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
* *
9688 ATGGTCACTTAGCAC
66 ATAGTAACTTAGCAC
*
9703 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
9727 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:9659 original size:39 final size:40
Alignment explanation
Indices: 9542--9726 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
9532 GCTACTCGTT
*
9542 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
9582 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
9622 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
9661 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
9702 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9727 CATCATTCGA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 78 0.62
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:12607 original size:36 final size:36
Alignment explanation
Indices: 12562--12633 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
12552 TCTATTACTA
*
12562 TATGGAATCATAGTTTATAATGTCAGGATTCATCAC
1 TATGGAATCATAGTTTATAATGTCAAGATTCATCAC
12598 TATGGAATCATAGTTTATAATGTCAAGATTCATCAC
1 TATGGAATCATAGTTTATAATGTCAAGATTCATCAC
12634 ACTATCACAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (36 bp):
TATGGAATCATAGTTTATAATGTCAAGATTCATCAC
Found at i:14916 original size:32 final size:34
Alignment explanation
Indices: 14880--14954 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 34
14870 GGCCCTGTCG
*
14880 TGGTCTTA-CATTC-ACATGCCATAACCCAGTTA
1 TGGTCTTATCATTCGACATGCCATAACCCAGCTA
* ** *
14912 TGGTCTTATTATTCGATTTGCCATAGCCCAGCTA
1 TGGTCTTATCATTCGACATGCCATAACCCAGCTA
14946 TGGTCTTAT
1 TGGTCTTAT
14955 TCAGTATCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 8 0.22
33 4 0.11
34 24 0.67
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (34 bp):
TGGTCTTATCATTCGACATGCCATAACCCAGCTA
Found at i:19409 original size:84 final size:84
Alignment explanation
Indices: 19259--19416 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
19249 ATATCGTACA
* * * * * *
19259 ATGCCAACATCCCAGACGTGGTCTTACATGCCATCACATATTGATGCCACTGTCCCGGACAGGGT
1 ATGCCAACATCCCAGACATGGTCTTACATGCAATAACATATCGATGCCAATGTCCCAGACAGGGT
19324 CTTACACGAATCAAATTCG
66 CTTACACGAATCAAATTCG
** * *
19343 ATGCCAATGTCCCAGACATGGTCTTACATGTAATAACATATCGATGCCAATGTCCCATAC-GTGG
1 ATGCCAACATCCCAGACATGGTCTTACATGCAATAACATATCGATGCCAATGTCCCAGACAG-GG
19407 TCTTACACGA
65 TCTTACACGA
19417 GAACACATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
83 1 0.02
84 62 0.98
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (84 bp):
ATGCCAACATCCCAGACATGGTCTTACATGCAATAACATATCGATGCCAATGTCCCAGACAGGGT
CTTACACGAATCAAATTCG
Found at i:19425 original size:43 final size:42
Alignment explanation
Indices: 19259--19427 Score: 155
Period size: 43 Copynumber: 4.0 Consensus size: 42
19249 ATATCGTACA
** * * * *
19259 ATGCCAACATCCCAGACGTGGTCTTACATGCCATCACATATTG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-AAACACATATCG
* * * *
19302 ATGCCACTGTCCCGGACAG-GGTCTTACACGAATCAAAT-TCG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGAAACACATATCG
* *
19343 ATGCCAATGTCCCAGACATGGTCTTACATGTAATA-ACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-AA-ACACATATCG
*
19386 ATGCCAATGTCCCATACGTGGTCTTACACGAGAACACATATC
1 ATGCCAATGTCCCAGACGTGGTCTTACACGA-AACACATATC
19428 AGAAATCCTA
Statistics
Matches: 102, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
41 27 0.26
42 13 0.13
43 61 0.60
44 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAAACACATATCG
Found at i:24026 original size:93 final size:93
Alignment explanation
Indices: 23898--24069 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
23888 GCCCATAAGT
* *
23898 GAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCAATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCAATAAGTGAACTCGGACTCAACTCAA
23963 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
23991 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCAATAAGTGAACTCGGACTCAACTCAA
*
24056 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
24070 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCAATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:24065 original size:46 final size:46
Alignment explanation
Indices: 23890--24065 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
23880 TGTAACCCGC
* * *
23890 CCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
23936 CAATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
23982 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
24029 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
24066 TGCCCAAATA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 67 0.62
47 32 0.30
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:24084 original size:46 final size:44
Alignment explanation
Indices: 23941--24084 Score: 116
Period size: 46 Copynumber: 3.1 Consensus size: 44
23931 CGCATCAATA
* *
23941 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * *
23990 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
24033 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
24080 AGTGA
1 AGTGA
24085 CATGTCACTT
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 4 0.05
46 33 0.43
47 28 0.36
48 4 0.05
49 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:30265 original size:46 final size:45
Alignment explanation
Indices: 30212--30385 Score: 158
Period size: 46 Copynumber: 3.8 Consensus size: 45
30202 GTAACTCGCC
*
30212 CATAAGTGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCAT
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
30257 CAATAAGTGAACTCAGACTCAACTCAATGAGCTCGGATGCCTAGTT-ACAT
1 C-ATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * * *
30307 C-T--CTCGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
30350 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 -CATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
30386 ATGCCCAAAT
Statistics
Matches: 103, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 59 0.57
47 25 0.24
48 2 0.02
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:30347 original size:93 final size:93
Alignment explanation
Indices: 30219--30390 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
30209 GCCCATAAGT
* * *
30219 GAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCAATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCAGACATTCGCATCAATAAGTGAACTCAGACTCAACTCAA
*
30284 TGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * * *
30312 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCAGACATTCGCATCAATAAGTGAACTCAGACTCAACTCAA
*
30377 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
30391 CAAATATCCT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCAGACATTCGCATCAATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:31765 original size:19 final size:19
Alignment explanation
Indices: 31705--31768 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
31695 AAATCATTCG
*
31705 ATAACAGTAACTCATCTGT
1 ATAACAGTAATTCATCTGT
* * **
31724 TTAAACAGTACTTCATCCAT
1 AT-AACAGTAATTCATCTGT
*
31744 ATAATAGTAATTCATCTGT
1 ATAACAGTAATTCATCTGT
31763 ATAACA
1 ATAACA
31769 CATAACTTTT
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (19 bp):
ATAACAGTAATTCATCTGT
Found at i:31990 original size:24 final size:23
Alignment explanation
Indices: 31927--32032 Score: 79
Period size: 24 Copynumber: 4.3 Consensus size: 23
31917 AGCTCCTCCT
*
31927 GAGCTGATGAACAATAAGCTCTATG
1 GAGCTGA-GAACAATAAGCTCTA-C
* *
31952 GAGTTGA-AACAGTAAGCTCTGAC
1 GAGCTGAGAACAATAAGCTCT-AC
* *
31975 GAGCTGAGAACAGTAATCTCTTAC
1 GAGCTGAGAACAATAAGCTC-TAC
* *
31999 GAGTTGATATATCAATAAGCTCATAC
1 GAGCTGAGA-A-CAATAAGCTC-TAC
32025 GAGCTGAG
1 GAGCTGAG
32033 GTGAGTCCAC
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
23 18 0.28
24 21 0.33
25 8 0.12
26 17 0.27
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.25
Consensus pattern (23 bp):
GAGCTGAGAACAATAAGCTCTAC
Found at i:38356 original size:48 final size:48
Alignment explanation
Indices: 38284--38410 Score: 168
Period size: 48 Copynumber: 2.6 Consensus size: 48
38274 TTAATGAGAT
* *
38284 CCAGTGTAAGACCATGTCTAGGACATGGCATTGACGT-TGATATGTGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATTCA-GTATGATATGTGTG
38332 CCAGTGTAAGACCATGTCTGGGACATGGCA-TCAGTGATGATATGTGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATTCAGT-ATGATATGTGTG
** * *
38380 GTAGTGTAAGACCATATCTGGAACATGGCAT
1 CCAGTGTAAGACCATGTCTGGGACATGGCAT
38411 CGGCACTGAT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
46 2 0.03
47 2 0.03
48 66 0.94
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (48 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATTCAGTATGATATGTGTG
Found at i:39018 original size:58 final size:58
Alignment explanation
Indices: 38928--39043 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
38918 CAGCCACTTA
38928 TATTCCTTGCAAGTAAGTGATTTAGATGGCCTTTCTTGATGATTTTTGCATTTTTCGG
1 TATTCCTTGCAAGTAAGTGATTTAGATGGCCTTTCTTGATGATTTTTGCATTTTTCGG
38986 TATTCCTTGCAAGTAAGTGATTTAGATGGCCTTTCTTGATGATTTTTGCATTTTTCGG
1 TATTCCTTGCAAGTAAGTGATTTAGATGGCCTTTCTTGATGATTTTTGCATTTTTCGG
39044 ACCCTTGTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.47
Consensus pattern (58 bp):
TATTCCTTGCAAGTAAGTGATTTAGATGGCCTTTCTTGATGATTTTTGCATTTTTCGG
Found at i:40004 original size:49 final size:47
Alignment explanation
Indices: 39867--40042 Score: 138
Period size: 49 Copynumber: 3.6 Consensus size: 47
39857 GATGTGTGTT
* * * * **
39867 AGTGTAAGACCTGTCTGGGACATGGCATCGACATAGATAAGCGGGAG-C
1 AGTGTAAGACCTGTTTGGGACATGGCGTCGACCTAGAT--GTGAAAGTC
* * * * *
39915 TGGTGTAAGACTTGTTTGGGACATGGCATCGGCCTGGATGTATGAAAGTC
1 -AGTGTAAGACCTGTTTGGGACATGGCGTCGACCTAGATG--TGAAAGTC
* * *
39965 AGTGTAAGACCTATTTGGGACATGGCGTCGACTTAGATGTGAGAGTC
1 AGTGTAAGACCTGTTTGGGACATGGCGTCGACCTAGATGTGAAAGTC
* * *
40012 AGTGTAAAACCATGTTTGGAACTTGGCGTCG
1 AGTGTAAGACC-TGTTTGGGACATGGCGTCG
40043 GCATCGTACC
Statistics
Matches: 102, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
47 18 0.18
48 16 0.16
49 67 0.66
50 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (47 bp):
AGTGTAAGACCTGTTTGGGACATGGCGTCGACCTAGATGTGAAAGTC
Found at i:41243 original size:27 final size:26
Alignment explanation
Indices: 41195--41246 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
41185 GCGAGGCTGC
*
41195 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
41221 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
41247 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42007 original size:81 final size:81
Alignment explanation
Indices: 41888--42220 Score: 549
Period size: 81 Copynumber: 4.1 Consensus size: 81
41878 TACCCCACGA
* * *
41888 GGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAA
1 GGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAA
41953 TAATTCTACCCTACAG
66 TAATTCTACCCTACAG
*
41969 GGGTATTTCGGTATTTCTACCGTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAA
1 GGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAA
42034 TAATTCTACCCTACAG
66 TAATTCTACCCTACAG
* * *
42050 GGGTATTTCGGTATTTCTACCCTATAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCAG
1 GGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAA
42115 TAATTCTACCCTACAG
66 TAATTCTACCCTACAG
* * * * **
42131 GGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTATTTCTACCTTATAAGGGTATTTCGG
1 GGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAA
42196 TAATTCTACCCTACAG
66 TAATTCTACCCTACAG
42212 GGGTATTTC
1 GGGTATTTC
42221 AATAATTTTG
Statistics
Matches: 237, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 237 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (81 bp):
GGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAA
TAATTCTACCCTACAG
Found at i:42227 original size:27 final size:27
Alignment explanation
Indices: 41870--42220 Score: 497
Period size: 27 Copynumber: 13.0 Consensus size: 27
41860 CGGGCAAAAT
* * *
41870 GGTAATTTTACCCCAC-GAGGGTATCTC
1 GGTAATTCTACCCTACAG-GGGTATTTC
41897 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
41924 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
41951 AATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
41978 GGTATTTCTACCGTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
42005 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
42032 AATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
42059 GGTATTTCTACCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42086 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42113 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42140 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
42167 GGTATTTCTACCTTATAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
42194 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
42221 AATAATTTTG
Statistics
Matches: 288, Mismatches: 35, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
27 287 1.00
28 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:42242 original size:27 final size:27
Alignment explanation
Indices: 42212--42363 Score: 112
Period size: 27 Copynumber: 5.7 Consensus size: 27
42202 TACCCTACAG
42212 GGGTATTTCAATAATTTTGTAAATCGA
1 GGGTATTTCAATAATTTTGTAAATCGA
*** ** *
42239 GGGTAAAACGGTAATTCTGTAAATCG-
1 GGGTATTTCAATAATTTTGTAAATCGA
* ** *
42265 GGGTACTTT-GATAATTTTACAAGTCGA
1 GGGTA-TTTCAATAATTTTGTAAATCGA
* * * *
42292 GAGTATTTCAGTAATTTTATAAATTGA
1 GGGTATTTCAATAATTTTGTAAATCGA
*
42319 GGGTATTTCAATAATTTTG-AAAACTGA
1 GGGTATTTCAATAATTTTGTAAATC-GA
**
42346 GGGTATTTCGGTAATTTT
1 GGGTATTTCAATAATTTT
42364 ACAAATCAAG
Statistics
Matches: 94, Mismatches: 27, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
26 23 0.24
27 71 0.76
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGTATTTCAATAATTTTGTAAATCGA
Found at i:42251 original size:81 final size:81
Alignment explanation
Indices: 41923--42256 Score: 294
Period size: 81 Copynumber: 4.1 Consensus size: 81
41913 AGGGGTATTT
* * * * **
41923 CGGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCGGTATTTCTA
1 CGGTAATTCTACCTTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAATATTTCTA
** ***
41988 CCGTACAAGGGTATTT
66 CAATACAAGGGTAAAA
* * * * **
42004 CGGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCGGTATTTCTA
1 CGGTAATTCTACCTTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAATATTTCTA
** * ***
42069 CCCTATAAGGGTATTT
66 CAATACAAGGGTAAAA
* * * * **
42085 CGATAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTA
1 CGGTAATTCTACCTTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAATATTTCTA
** ***
42150 CCCTACAAGGGTATTT
66 CAATACAAGGGTAAAA
* * *
42166 CGGTATTTCTACCTTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAATAATTTTG
1 CGGTAATTCTACCTTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAAT-A-TTTC
*
42231 TA-AAT-CGAGGGTAAAA
64 TACAATACAAGGGTAAAA
42247 CGGTAATTCT
1 CGGTAATTCT
42257 GTAAATCGGG
Statistics
Matches: 230, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
81 223 0.97
82 2 0.01
83 5 0.02
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (81 bp):
CGGTAATTCTACCTTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAATATTTCTA
CAATACAAGGGTAAAA
Found at i:42352 original size:54 final size:53
Alignment explanation
Indices: 42211--42370 Score: 155
Period size: 53 Copynumber: 3.0 Consensus size: 53
42201 CTACCCTACA
* *** * *
42211 GGGGTATTTCAATAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATC
1 GGGGTATTTCAATAATTTTGAAAATCGAGGGTATTTCGGTAATTTTATAAATC
* * * * *
42264 GGGGTACTTT-GATAATTTT-ACAAGTCGAGAGTATTTCAGTAATTTTATAAATT
1 GGGGTA-TTTCAATAATTTTGA-AAATCGAGGGTATTTCGGTAATTTTATAAATC
*
42317 GAGGGTATTTCAATAATTTTGAAAA-CTGAGGGTATTTCGGTAATTTTACAAATC
1 G-GGGTATTTCAATAATTTTGAAAATC-GAGGGTATTTCGGTAATTTTATAAATC
42371 AAGGATATTT
Statistics
Matches: 84, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
53 42 0.50
54 41 0.49
55 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (53 bp):
GGGGTATTTCAATAATTTTGAAAATCGAGGGTATTTCGGTAATTTTATAAATC
Found at i:47854 original size:80 final size:79
Alignment explanation
Indices: 47717--47941 Score: 256
Period size: 80 Copynumber: 2.8 Consensus size: 79
47707 TTGAATGCTG
* * * * * *
47717 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT
47781 TGTGCGAGATA-CAAA
64 TGTGCGAGATATCAAA
* *
47796 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATT
* * *
47861 CGTGCGAGTTATTAAA
64 TGTGCGAGATATCAAA
* * * * *
47877 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
47942 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
79 39 0.32
80 70 0.57
81 14 0.11
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:47921 original size:39 final size:39
Alignment explanation
Indices: 47717--47939 Score: 225
Period size: 40 Copynumber: 5.6 Consensus size: 39
47707 TTGAATGCTG
* * * * * *
47717 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** *
47757 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAAA
* * *
47796 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
47837 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
47877 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
47916 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
47940 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
39 39 0.25
40 105 0.68
41 11 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:47959 original size:79 final size:80
Alignment explanation
Indices: 47797--47974 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
47787 AGATACAAAT
* * * *
47797 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
47862 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
47877 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
47941 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
* *
47956 TCC-GGTTAAATCCCAAAGG
1 TCCGGGTTAAGTCCCGAAGG
47975 TACGTGATTT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
78 15 0.18
79 48 0.59
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:49481 original size:13 final size:13
Alignment explanation
Indices: 49463--49489 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49453 ATCAGCCATA
49463 AAACGAGCACGCC
1 AAACGAGCACGCC
49476 AAACGAGCACGCC
1 AAACGAGCACGCC
49489 A
1 A
49490 TAAAGTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.37, G:0.22, T:0.00
Consensus pattern (13 bp):
AAACGAGCACGCC
Done.