Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1984
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: 90121
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:3408 original size:39 final size:40
Alignment explanation
Indices: 3164--3426 Score: 291
Period size: 40 Copynumber: 6.6 Consensus size: 40
3154 TTGAATGCTG
* * * * * *
3164 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
** * * * *
3204 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAA-A
3244 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
3284 TCCCGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
3324 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
3364 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
3403 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
3427 TGAACGAGGA
Statistics
Matches: 196, Mismatches: 22, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
39 36 0.18
40 150 0.77
41 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:3446 original size:79 final size:80
Alignment explanation
Indices: 3217--3461 Score: 219
Period size: 80 Copynumber: 3.1 Consensus size: 80
3207 GGACTAAGAT
* * ** * ** * *
3217 CCGAAGGCATTTGTGCGAGATAC-AAGTTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-T
1 CCGAAGGCATTCGTGCGAGTTACTAA-AACCGGGCTAAGTCCCGAAGGCATTCGAACGAG-GAGC
*
3280 TAAATCCCGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
3297 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
3362 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
3377 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
3441 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
*
3455 CAGAAGG
1 CCGAAGG
3462 TACGTGATTT
Statistics
Matches: 141, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
78 13 0.09
79 47 0.33
80 79 0.56
81 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:8321 original size:22 final size:22
Alignment explanation
Indices: 8293--8346 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
8283 TGCAAATATG
8293 CAACACACCACTCTATACCAAC
1 CAACACACCACTCTATACCAAC
*
8315 CAACACACCACTCTGTACCAAC
1 CAACACACCACTCTATACCAAC
8337 CAACACACCA
1 CAACACACCA
8347 TGTGGGGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.41, C:0.46, G:0.02, T:0.11
Consensus pattern (22 bp):
CAACACACCACTCTATACCAAC
Found at i:8466 original size:33 final size:27
Alignment explanation
Indices: 8392--8492 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
8382 CAATATCGCA
**
8392 GCAAAGCTGCCAGTAACAGTATATGTG
1 GCAAAGCCACCAGTAACAGTATATGTG
*
8419 GCAAAGCCACCAGTATCAGTATATGTG
1 GCAAAGCCACCAGTAACAGTATATGTG
*
8446 GCAAAGCCACCGGTAACAGTA-ATTGTG
1 GCAAAGCCACCAGTAACAGTATA-TGTG
*
8473 GCAGAGCCACCAGT-ACAGTA
1 GCAAAGCCACCAGTAACAGTA
8493 CTTCCTCCAA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
26 7 0.11
27 59 0.89
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.19
Consensus pattern (27 bp):
GCAAAGCCACCAGTAACAGTATATGTG
Found at i:30547 original size:79 final size:81
Alignment explanation
Indices: 30411--30595 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
30401 TTGAATGATG
* *
30411 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
30475 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
30490 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
30552 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
30570 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
30596 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:30609 original size:40 final size:40
Alignment explanation
Indices: 30412--30595 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
30402 TGAATGATGT
* * * *
30412 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
30452 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
30492 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
30530 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
30571 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
30596 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
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:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:30617 original size:79 final size:79
Alignment explanation
Indices: 30464--30628 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
30454 GGACTAAGAT
* * **
30464 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
30529 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
30543 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
30606 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
30622 CCGAAGG
1 CCGAAGG
30629 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:35668 original size:30 final size:30
Alignment explanation
Indices: 35622--35682 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
35612 TTCCCGAGCC
*
35622 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * *
35652 TAGGGGAAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
35682 T
1 T
35683 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Found at i:36461 original size:68 final size:66
Alignment explanation
Indices: 36389--36560 Score: 179
Period size: 67 Copynumber: 2.6 Consensus size: 66
36379 CATCATGTGT
* * *
36389 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATATG-T-ACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAAATGATGACACCA
36452 TGTAG
62 TGTAG
** * *
36457 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAATGAATGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAAATG-ATGACACCATGT
36522 AG
65 AG
* * * *
36524 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
36561 GGTGGTACTG
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
64 27 0.30
65 3 0.03
66 16 0.18
67 31 0.34
68 13 0.14
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.23
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAAATGATGACACCATGTA
G
Found at i:36530 original size:67 final size:64
Alignment explanation
Indices: 36413--36596 Score: 201
Period size: 67 Copynumber: 2.8 Consensus size: 64
36403 AGACATTATG
* * * * *
36413 ATGTAGCTAGGTCGCATGGGTGATACTATATGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACCAAATGTACACCATGTAGACAAGAGAGCTACGAGATAA
* *
36477 ATGTAGCTAGGTCGCATGCGTGGTTCCAAATGAATGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACCAAATG--T-ACACCATGTAGACAAGAGAGCTACGAGAT
36542 AA
63 AA
* * ** * *
36544 AT-TGGCTAGGTCACATGGGTGGTACTGAGTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACCAAATGTACACCATGTAG-ACAAGAGAGC
36597 CGAACTATAT
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
62 1 0.01
63 18 0.18
64 28 0.28
66 23 0.23
67 31 0.31
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACCAAATGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:44493 original size:43 final size:42
Alignment explanation
Indices: 44445--44582 Score: 145
Period size: 43 Copynumber: 3.3 Consensus size: 42
44435 TGTGATTTCA
44445 TGTAAGACCATGTCTGGGACATTGGCATCGATATGA-GATTAT
1 TGTAAGACCATGTCTGGGACATTGGCATCGATAT-ATGATTAT
* *
44487 GTGTAAGACCATGTCTAGGACATTGGCATC-ATATATGATTCT
1 -TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTAT
* * ** * * * *
44529 TATAAGACCCTGTCTGGGACAGAGGCATCGAAATAGGATAACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTA-T
44572 TGTAAGACCAT
1 TGTAAGACCAT
44583 ATCTACGATA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
41 25 0.32
42 16 0.21
43 37 0.47
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTAT
Found at i:48408 original size:36 final size:36
Alignment explanation
Indices: 48361--48435 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
48351 AAAATGCATT
48361 TAGAAATCTTTGTGTTATTATGGTCCGAATTGGGCA
1 TAGAAATCTTTGTGTTATTATGGTCCGAATTGGGCA
48397 TAGAAATCTTTGTGTTATTATGGTCCGAATTGGGCA
1 TAGAAATCTTTGTGTTATTATGGTCCGAATTGGGCA
48433 TAG
1 TAG
48436 TTTGGATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (36 bp):
TAGAAATCTTTGTGTTATTATGGTCCGAATTGGGCA
Found at i:49895 original size:79 final size:80
Alignment explanation
Indices: 49796--50016 Score: 202
Period size: 80 Copynumber: 2.8 Consensus size: 80
49786 CTCGTTCAAG
* * ** * *
49796 TGCCTTCGGGACATAGCCCGGTCA-TAGTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGG-AATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
49859 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
49875 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
49940 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
49955 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
50017 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 37 0.31
80 74 0.63
81 6 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:49947 original size:80 final size:80
Alignment explanation
Indices: 49836--50016 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
49826 CTCATTCAAT
* * *
49836 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
49899 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
49915 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
49979 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
49996 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
50017 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:49976 original size:40 final size:40
Alignment explanation
Indices: 49833--50016 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
49823 TAACTCATTC
* *
49833 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
49873 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
49913 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
49953 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
49994 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
50017 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:56129 original size:43 final size:42
Alignment explanation
Indices: 56081--56194 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 42
56071 TGTGATTTCA
56081 TGTAAGACCATGTCTGGGACATTGGCATCGATATGA-GATTAT
1 TGTAAGACCATGTCTGGGACATTGGCATCGATAT-ATGATTAT
* *
56123 GTGTAAGACCATGTCTAGGACATTGGCATC-ATATATGATTCT
1 -TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTAT
* * **
56165 TATAAGACCCT-TCTGGGACAGAGGCATCGA
1 TGTAAGACCATGTCTGGGACATTGGCATCGA
56195 AATAGGATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
40 14 0.23
41 11 0.18
42 9 0.15
43 28 0.45
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTAT
Found at i:59764 original size:41 final size:40
Alignment explanation
Indices: 59677--59806 Score: 160
Period size: 41 Copynumber: 3.3 Consensus size: 40
59667 TAACTCATTC
* *
59677 AATGCCTTC-GGACTTAACCCGG-ATT-TTAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGAATTAGT-AACTCGCACA
*
59715 AATGCCTTCGGGACTTAACCCGGAGATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGA-ATTAGTAACTCGCACA
*
59756 AAGGCCTTCGGGACTTAACCCGGAA-TAGATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAG-TAACTCGCACA
*
59796 AATACCTTCGG
1 AATGCCTTCGG
59807 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
38 9 0.11
39 16 0.20
40 20 0.25
41 34 0.43
42 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACA
Found at i:72711 original size:27 final size:27
Alignment explanation
Indices: 72670--72770 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
72660 TTGGAGGAAG
*
72670 TACTG-TACTGGTGGCTCTGCCACA-A
1 TACTGTTACTGGTGGCTTTGCCACATA
*
72695 TTACTGTTACCGGTGGCTTTGCCACATA
1 -TACTGTTACTGGTGGCTTTGCCACATA
*
72723 TACTGATACTGGTGGCTTTGCCACATA
1 TACTGTTACTGGTGGCTTTGCCACATA
**
72750 TACTGTTACTGGCAGCTTTGC
1 TACTGTTACTGGTGGCTTTGC
72771 TGCGATATTG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
26 5 0.08
27 60 0.91
28 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.34
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTTGCCACATA
Found at i:72841 original size:22 final size:22
Alignment explanation
Indices: 72816--72869 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
72806 TATCCCCACA
72816 TGGTGTGTTGGTTGGTACAGAG
1 TGGTGTGTTGGTTGGTACAGAG
*
72838 TGGTGTGTTGGTTGGTATAGAG
1 TGGTGTGTTGGTTGGTACAGAG
72860 TGGTGTGTTG
1 TGGTGTGTTG
72870 CATATTTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.11, C:0.02, G:0.46, T:0.41
Consensus pattern (22 bp):
TGGTGTGTTGGTTGGTACAGAG
Found at i:82639 original size:17 final size:19
Alignment explanation
Indices: 82617--82660 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
82607 GTGTAAGTAG
82617 GCCGTGTGG-TC-GGACAC
1 GCCGTGTGGCTCGGGACAC
82634 GCCGTGTGGCTCGGGACAC
1 GCCGTGTGGCTCGGGACAC
82653 GCCCGTGT
1 G-CCGTGT
82661 CCTCAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.38
18 2 0.08
19 7 0.29
20 6 0.25
ACGTcount: A:0.09, C:0.32, G:0.41, T:0.18
Consensus pattern (19 bp):
GCCGTGTGGCTCGGGACAC
Found at i:84154 original size:45 final size:45
Alignment explanation
Indices: 84104--84194 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
84094 CCAAAACATG
* * *
84104 TGTTACATACATCTTGAACTTAGACCACAACTCCATGAGCTCAGA
1 TGTTACATACATCATGAACTCAGACCACAACTCAATGAGCTCAGA
* * * *
84149 TGTTACATATATCATGAACTCAGACCATAACTTAATGAGTTCAGA
1 TGTTACATACATCATGAACTCAGACCACAACTCAATGAGCTCAGA
84194 T
1 T
84195 CACATAGTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (45 bp):
TGTTACATACATCATGAACTCAGACCACAACTCAATGAGCTCAGA
Found at i:88712 original size:30 final size:29
Alignment explanation
Indices: 88678--88737 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
88668 ATGGATCGGA
*
88678 AGCTTTGGCACTAACTGTGCGATTTACACT
1 AGCTTTGGCACTAACTGTGCAATTTA-ACT
*
88708 AGCTTTGGCACTAAGTGTGCAATTTAACT
1 AGCTTTGGCACTAACTGTGCAATTTAACT
88737 A
1 A
88738 ATTTCGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (29 bp):
AGCTTTGGCACTAACTGTGCAATTTAACT
Done.