Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold177
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: 788481
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.27
Warning! 150793 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:727894 original size:13 final size:13
Alignment explanation
Indices: 727876--727903 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
727866 CACCAAAGTA
727876 TGTATCGATACAT
1 TGTATCGATACAT
727889 TGTATCGATACAT
1 TGTATCGATACAT
727902 TG
1 TG
727904 GTTTGTAACG
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:732037 original size:13 final size:13
Alignment explanation
Indices: 732019--732043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
732009 CAAAGATCAG
732019 TGTATCGATACAA
1 TGTATCGATACAA
732032 TGTATCGATACA
1 TGTATCGATACA
732044 TTTGAGTTAT
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:732123 original size:13 final size:13
Alignment explanation
Indices: 732105--732162 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
732095 ACAAAACTTA
732105 TGTATCGATACAT
1 TGTATCGATACAT
732118 TGTATCGATACAACACTTT
1 TGTATCGAT---ACA---T
732137 ATGTATCGATACAT
1 -TGTATCGATACAT
732151 TGTATCGATACA
1 TGTATCGATACA
732163 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:732143 original size:20 final size:20
Alignment explanation
Indices: 732118--732183 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
732108 ATCGATACAT
732118 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
732138 TGTATCGAT---ACA---T-
1 TGTATCGATACAACACTTTA
732151 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
732171 TGTATCGATACAA
1 TGTATCGATACAA
732184 ATCATTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 22 0.56
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAACACTTTA
Found at i:732144 original size:33 final size:33
Alignment explanation
Indices: 732084--732182 Score: 182
Period size: 33 Copynumber: 3.0 Consensus size: 33
732074 AGTAGCTTAA
*
732084 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
732116 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
732149 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
732182 A
1 A
732183 AATCATTGAA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 17 0.26
33 48 0.74
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACACTTTATGTATCGATAC
Found at i:741415 original size:13 final size:13
Alignment explanation
Indices: 741397--741426 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
741387 ACAATTCTTC
741397 ATGTATCGATACA
1 ATGTATCGATACA
*
741410 ATGTATTGATACA
1 ATGTATCGATACA
741423 ATGT
1 ATGT
741427 GCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:741433 original size:33 final size:32
Alignment explanation
Indices: 741374--741443 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 32
741364 GCCGTTTGGG
741374 ACAATGTATCGATACAATTCTTCATGTATCGAT
1 ACAATGTATCGATACAATTC-TCATGTATCGAT
* *
741407 ACAATGTATTGATACAATGTGC-CATGTATCGTT
1 ACAATGTATCGATACAAT-T-CTCATGTATCGAT
741440 ACAA
1 ACAA
741444 ACAGTTGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 31 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (32 bp):
ACAATGTATCGATACAATTCTCATGTATCGAT
Found at i:741537 original size:31 final size:31
Alignment explanation
Indices: 741499--741569 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
741489 GTGCATGTAT
* *
741499 TGATACAATGAACATGTATCGGTACAATATA
1 TGATACAATGAACATGAATCGATACAATATA
*
741530 TGATACAATGAACATGAATCGATACAATGTA
1 TGATACAATGAACATGAATCGATACAATATA
741561 TCGATACAA
1 T-GATACAA
741570 ATCATAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 29 0.81
32 7 0.19
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (31 bp):
TGATACAATGAACATGAATCGATACAATATA
Found at i:746200 original size:27 final size:26
Alignment explanation
Indices: 746148--746203 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
746138 TTAAAATTCA
*
746148 AAATTTAAATTTAAGACAATATTTTT
1 AAATTTAAATTTAAGACAATAATTTT
*
746174 AAATTTCAAATTT-AGATAACTAATTTT
1 AAATTT-AAATTTAAGACAA-TAATTTT
746201 AAA
1 AAA
746204 AATCAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (26 bp):
AAATTTAAATTTAAGACAATAATTTT
Found at i:753412 original size:58 final size:57
Alignment explanation
Indices: 753241--753558 Score: 206
Period size: 57 Copynumber: 5.5 Consensus size: 57
753231 TCGATGCATT
* * * * * *
753241 TTTATGTCA-TTTTCTATAACTT-AGG-TTTTTATGTCATTTCATGTATTTTTATGTCA
1 TTTAGGTCATTTTTC-ATAACTTAAGGACTTTTAT-ACATTTCATGAATGTTGATGTCA
* * * * * * * * *
753297 TCTTA-GTCATTGTTCGTGACTTAGGGA-TTTTATGACATTTTATTCATTCTTGTTGTCA
1 T-TTAGGTCATTTTTCATAACTTAAGGACTTTTAT-ACATTTCA-TGAATGTTGATGTCA
753355 GTTTA-GTCATTTTTCATAACTTAAGGACTTTTATATCATTTCATGAATGTTGATGTCA
1 -TTTAGGTCATTTTTCATAACTTAAGGACTTTTATA-CATTTCATGAATGTTGATGTCA
* * ** *
753413 TTTAGGTCATTTTCCATAA-TCTAGGGACTTGGATGCAATTT-ATGAATGTTGATGTCA
1 TTTAGGTCATTTTTCATAACT-TAAGGACTTTTATAC-ATTTCATGAATGTTGATGTCA
* * * * *
753470 TTTAGGTCATTTTT-ATGA-TCTAAGGACTTTGATACAATTTTATGAGTATTGATGTCA
1 TTTAGGTCATTTTTCATAACT-TAAGGACTTTTATAC-ATTTCATGAATGTTGATGTCA
* * *
753527 TTTAGGTCATTTTTTTATAATTTAAAGACTTT
1 TTTAGGTCA-TTTTTCATAACTTAAGGACTTT
753559 CATGTAATTT
Statistics
Matches: 212, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
56 32 0.15
57 80 0.38
58 74 0.35
59 25 0.12
60 1 0.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (57 bp):
TTTAGGTCATTTTTCATAACTTAAGGACTTTTATACATTTCATGAATGTTGATGTCA
Found at i:753540 original size:57 final size:56
Alignment explanation
Indices: 753350--753540 Score: 217
Period size: 57 Copynumber: 3.3 Consensus size: 56
753340 TCATTCTTGT
* * *
753350 TGTCAGTTTA-GTCATTTTTCATAACTTAAGGACTTTTATATC-ATTTCATGAATGTTGA
1 TGTCA-TTTAGGTCATTTTT-ATATC-TAAGGACTTTGATA-CAATTTTATGAATGTTGA
* * * *
753408 TGTCATTTAGGTCATTTTCCATAATCTAGGGACTTGGATGCAA-TTTATGAATGTTGA
1 TGTCATTTAGGTCATTTT-TAT-ATCTAAGGACTTTGATACAATTTTATGAATGTTGA
* *
753465 TGTCATTTAGGTCATTTTTATGATCTAAGGACTTTGATACAATTTTATGAGTATTGA
1 TGTCATTTAGGTCATTTTTAT-ATCTAAGGACTTTGATACAATTTTATGAATGTTGA
753522 TGTCATTTAGGTCATTTTT
1 TGTCATTTAGGTCATTTTT
753541 TTATAATTTA
Statistics
Matches: 114, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
56 19 0.17
57 67 0.59
58 26 0.23
59 2 0.02
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (56 bp):
TGTCATTTAGGTCATTTTTATATCTAAGGACTTTGATACAATTTTATGAATGTTGA
Found at i:755289 original size:26 final size:27
Alignment explanation
Indices: 755242--755300 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
755232 CCAAATGAAA
*
755242 TTTAAATTTAAAAATAAGATAAC-ATT
1 TTTAAATTTAAAAATAAGATAACTAAT
* *
755268 TTTAAATTTCAAATTCAA-ATAACTAAT
1 TTTAAATTTAAAAAT-AAGATAACTAAT
755295 TTTAAA
1 TTTAAA
755301 AATTAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.41
Consensus pattern (27 bp):
TTTAAATTTAAAAATAAGATAACTAAT
Found at i:757044 original size:14 final size:15
Alignment explanation
Indices: 757027--757068 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
757017 ATACTTAGAG
757027 ATATAAATTTA-AAA
1 ATATAAATTTATAAA
*
757041 ATATAACTTTATAAA
1 ATATAAATTTATAAA
* *
757056 AAATATATTTATA
1 ATATAAATTTATA
757069 TTCGATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATAAATTTATAAA
Found at i:760337 original size:27 final size:26
Alignment explanation
Indices: 760282--760337 Score: 60
Period size: 25 Copynumber: 2.1 Consensus size: 26
760272 AAGTGTTTAG
* *
760282 AAAATAAATTATTTATATTATTATAT
1 AAAATAAATTATATATATTATAATAT
*
760308 AAAA-AAATTATATATAATATATAATGT
1 AAAATAAATTATATAT-AT-TATAATAT
760335 AAA
1 AAA
760338 TAACATATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 10 0.40
26 6 0.24
27 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
AAAATAAATTATATATATTATAATAT
Found at i:762528 original size:24 final size:25
Alignment explanation
Indices: 762447--762581 Score: 62
Period size: 24 Copynumber: 5.3 Consensus size: 25
762437 GAGATATTAT
* **
762447 ATTAAAGTGTATATA-TAAAATAAATT
1 ATTAAA-T-TATATATTATAATAAAAA
* *
762473 ATTAAACTTATAT-TTATATTAAAGA
1 ATTAAA-TTATATATTATAATAAAAA
* * *
762498 CTAAAATTATATATTA-AATAAACA
1 ATTAAATTATATATTATAATAAAAA
* *
762522 ATTAAA-TATTTATTATAACAAAAA
1 ATTAAATTATATATTATAATAAAAA
* **
762546 AGTAAATTAATGAAATAAAATAATAAAAA
1 ATTAAATT-AT---ATATTATAATAAAAA
762575 ATTAAAT
1 ATTAAAT
762582 GATTTAAAAA
Statistics
Matches: 81, Mismatches: 20, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
23 8 0.10
24 27 0.33
25 20 0.25
26 9 0.11
29 17 0.21
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (25 bp):
ATTAAATTATATATTATAATAAAAA
Found at i:763216 original size:19 final size:19
Alignment explanation
Indices: 763166--763225 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
763156 ATTAGTTATT
763166 ATATTTAAAT-TTTATTT-A
1 ATATTTAAATATTT-TTTAA
*
763184 ATATTAAAATTATTTTTTAA
1 ATATTTAAA-TATTTTTTAA
763204 ATATTTAAATATTTTTTAA
1 ATATTTAAATATTTTTTAA
763223 ATA
1 ATA
763226 AATCAATCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.22
19 17 0.46
20 12 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTAAATATTTTTTAA
Found at i:769900 original size:13 final size:13
Alignment explanation
Indices: 769879--769916 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
769869 GAAAAATGGT
*
769879 ACAATGATGTTTA
1 ACAAGGATGTTTA
769892 ACAAGGATG-TTA
1 ACAAGGATGTTTA
769904 ACAAGGATGTTTA
1 ACAAGGATGTTTA
769917 TAATATAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (13 bp):
ACAAGGATGTTTA
Found at i:772143 original size:17 final size:16
Alignment explanation
Indices: 772121--772159 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
772111 AATATAGTAA
*
772121 AAAAATCAAAAAAATAT
1 AAAAATCAAAAAAA-AG
772138 AAAAAT-AAAAAAAAG
1 AAAAATCAAAAAAAAG
772153 AAAAATC
1 AAAAATC
772160 GTGAAAGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 7 0.35
16 7 0.35
17 6 0.30
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAATCAAAAAAAAG
Found at i:772677 original size:22 final size:24
Alignment explanation
Indices: 772634--772686 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 24
772624 AAACAGCAAG
*
772634 ATAAAAG-GAAGAAGAACGAACA-
1 ATAAAAGAGAAGAAGAAAGAACAC
772656 A-AAAAGAGAAG-AGAAAGCAACAC
1 ATAAAAGAGAAGAAGAAAG-AACAC
772679 ATAAAAGA
1 ATAAAAGA
772687 AAAAAGCAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 10 0.38
22 9 0.35
23 1 0.04
24 6 0.23
ACGTcount: A:0.66, C:0.09, G:0.21, T:0.04
Consensus pattern (24 bp):
ATAAAAGAGAAGAAGAAAGAACAC
Found at i:776120 original size:20 final size:20
Alignment explanation
Indices: 776086--776160 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
776076 GTAAAAAGAC
**
776086 AGAATGTATTAATACATTGA
1 AGAATGTATCGATACATTGA
*
776106 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* * *
776126 TA-CATGTATTGATAAATTGA
1 -AGAATGTATCGATACATTGA
* *
776146 AAAATATATCGATAC
1 AGAATGTATCGATAC
776161 CTTGCCTCCA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:776725 original size:28 final size:30
Alignment explanation
Indices: 776671--776726 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
776661 AAACAGCAAC
* *
776671 ATGAAGAAGAGAGCAACGGAAGTAGCTGTA
1 ATGAAGAAGAGAGAAACGGAAGAAGCTGTA
*
776701 ATGAA-AAGA-AGAAACTGAAGAAGCTG
1 ATGAAGAAGAGAGAAACGGAAGAAGCTG
776727 CAACAAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.61
29 4 0.17
30 5 0.22
ACGTcount: A:0.48, C:0.09, G:0.30, T:0.12
Consensus pattern (30 bp):
ATGAAGAAGAGAGAAACGGAAGAAGCTGTA
Found at i:777148 original size:59 final size:59
Alignment explanation
Indices: 777037--777149 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
777027 CAAACACCAG
* *
777037 CAAAACCAGACCAGCAGCAAGCACCAATAACAGCAGCAGCAAGCACCAGCAACCAGCAA
1 CAAAACCAAACCAGCAGCAAGCAACAATAACAGCAGCAGCAAGCACCAGCAACCAGCAA
* * * * *
777096 CAAAACCAAACCAGTAGCAAGCAATAGTAATAGCAGCAGTAAGCACCAGCAACC
1 CAAAACCAAACCAGCAGCAAGCAACAATAACAGCAGCAGCAAGCACCAGCAACC
777150 TACAGCTACA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.46, C:0.32, G:0.17, T:0.05
Consensus pattern (59 bp):
CAAAACCAAACCAGCAGCAAGCAACAATAACAGCAGCAGCAAGCACCAGCAACCAGCAA
Found at i:782124 original size:33 final size:33
Alignment explanation
Indices: 782082--782146 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
782072 CAACGATTTG
782082 TATCGATACATAAAGTGTTGTATCGATACAATA
1 TATCGATACATAAAGTGTTGTATCGATACAATA
*** *
782115 TATCGATACATATTTTTTTGTATCGATACAAT
1 TATCGATACATAAAGTGTTGTATCGATACAAT
782147 TTAAGCTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (33 bp):
TATCGATACATAAAGTGTTGTATCGATACAATA
Found at i:782249 original size:52 final size:52
Alignment explanation
Indices: 782207--782331 Score: 232
Period size: 52 Copynumber: 2.4 Consensus size: 52
782197 CATTGATCTT
782207 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
782259 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
782311 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
782332 CTTTTCATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:783441 original size:20 final size:20
Alignment explanation
Indices: 783396--783468 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
783386 CTGCCAAGAA
***
783396 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
783417 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* * *
783437 ATGTATCAATACTTTGAATT
1 ATGTATCGATACATTGAATC
783457 ATGTATCGATAC
1 ATGTATCGATAC
783469 TTTTAAGGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.05
20 27 0.63
21 14 0.33
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:783469 original size:20 final size:20
Alignment explanation
Indices: 783416--783471 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
783406 ACATCTTTTT
*
783416 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
*
783436 CATGTATCAATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
783455 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
783472 TAAGGGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:785918 original size:13 final size:13
Alignment explanation
Indices: 785900--785925 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
785890 ATAATCACCC
785900 TGTATCGATACAA
1 TGTATCGATACAA
785913 TGTATCGATACAA
1 TGTATCGATACAA
785926 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:788023 original size:15 final size:15
Alignment explanation
Indices: 788003--788033 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
787993 ATTTCGTTTG
*
788003 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
788018 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
788033 G
1 G
788034 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Done.