Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold399
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: 323073
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 5237 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:235388 original size:27 final size:27
Alignment explanation
Indices: 235358--235482 Score: 205
Period size: 27 Copynumber: 4.6 Consensus size: 27
235348 TACCCTCATA
235358 GGTAAAATGACCGTAATACCCCTGTAG
1 GGTAAAATGACCGTAATACCCCTGTAG
*
235385 GGTAAAATGACCGTAATACCCCTGTAT
1 GGTAAAATGACCGTAATACCCCTGTAG
* *
235412 GGTAAAATGATCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATACCCCTGTAG
* *
235439 GGTAAAATGATCGTAATACCCCTGTAT
1 GGTAAAATGACCGTAATACCCCTGTAG
235466 GGTAAAATGACCGTAAT
1 GGTAAAATGACCGTAAT
235483 GCTCTGGTGG
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 91 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (27 bp):
GGTAAAATGACCGTAATACCCCTGTAG
Found at i:235483 original size:54 final size:54
Alignment explanation
Indices: 235358--235484 Score: 227
Period size: 54 Copynumber: 2.4 Consensus size: 54
235348 TACCCTCATA
*
235358 GGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAT
1 GGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAT
* *
235412 GGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATGATCGTAATACCCCTGTAT
1 GGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAT
235466 GGTAAAATGACCGTAATGC
1 GGTAAAATGACCGTAATGC
235485 TCTGGTGGGT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (54 bp):
GGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAT
Found at i:235579 original size:24 final size:24
Alignment explanation
Indices: 235546--235604 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
235536 TCTATGGTTA
235546 AATGACTGATTTGTCTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
* *
235570 TATGACTGATTTGTCTTTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
235594 AATGACTGATT
1 AATGACTGATT
235605 CTGAGCATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.47
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:235706 original size:27 final size:27
Alignment explanation
Indices: 235669--235732 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
235659 TGGAGGAATA
235669 ACTG-TACTGGTGGCTCT-GCCACA-AT
1 ACTGTTACTGGTGGCT-TGGCCACATAT
235694 CACTGTTACTGGTGGCTTGGCCACATAT
1 -ACTGTTACTGGTGGCTTGGCCACATAT
*
235722 ACTATTACTGG
1 ACTGTTACTGG
235733 CAGCTTTGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 5 0.15
27 27 0.79
28 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.31
Consensus pattern (27 bp):
ACTGTTACTGGTGGCTTGGCCACATAT
Found at i:235738 original size:27 final size:27
Alignment explanation
Indices: 235686--235738 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
235676 TGGTGGCTCT
* **
235686 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTATTACTGGCAGCTTG
235713 GCCACATAT-ACTATTACTGGCAGCTT
1 GCCACA-ATCACTATTACTGGCAGCTT
235739 TGCTGCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTATTACTGGCAGCTTG
Found at i:235758 original size:26 final size:26
Alignment explanation
Indices: 235720--235773 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
235710 TTGGCCACAT
235720 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* *
235746 ATACTGTTGCTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
235772 AT
1 AT
235774 GCTACTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:235785 original size:26 final size:26
Alignment explanation
Indices: 235730--235785 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
235720 ATACTATTAC
** *
235730 TGGCAGCTTTGCTGCGATACTGTTGC
1 TGGCAGCTTTGCTGCGATACTACTGA
*
235756 TGGCAGCTTTGCTGCGATGCTACTGA
1 TGGCAGCTTTGCTGCGATACTACTGA
235782 TGGC
1 TGGC
235786 TTTGTGTCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.12, C:0.23, G:0.32, T:0.32
Consensus pattern (26 bp):
TGGCAGCTTTGCTGCGATACTACTGA
Found at i:235817 original size:32 final size:31
Alignment explanation
Indices: 235776--236021 Score: 201
Period size: 32 Copynumber: 7.7 Consensus size: 31
235766 GCTGCGATGC
* * *
235776 TACTGATGGCTTTGTGTCGGTCATAGTACCAT
1 TACTGATGGCTTTGTGCCGATCATA-TACCGT
235808 TACTGATGGCTTTGTGCCGATCATATTACC-T
1 TACTGATGGCTTTGTGCCGATCATA-TACCGT
* * * *
235839 TATTGATGG-TTGTGTGCCAATCATTTCCCTGT
1 TACTGATGGCTT-TGTGCCGATCATATACC-GT
* * *
235871 TACTGATGG-TTGTGTGCCGGTCATATCACTGC
1 TACTGATGGCTT-TGTGCCGATCATAT-ACCGT
* *
235903 TACTGACGGCTTTGTGCCGATCATGTTACCGT
1 TACTGATGGCTTTGTGCCGATCAT-ATACCGT
* * ***
235935 TACTGATGGCTGTGTGTCGATCATATCACTAC
1 TACTGATGGCTTTGTGCCGATCATAT-ACCGT
* * *
235967 TACTGATGGCTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATAT-ACCGT
*
235999 TACTGATGGCTTTGTGCCAATCA
1 TACTGATGGCTTTGTGCCGATCA
236022 CATTACTGTA
Statistics
Matches: 177, Mismatches: 30, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
30 5 0.03
31 21 0.12
32 147 0.83
33 4 0.02
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (31 bp):
TACTGATGGCTTTGTGCCGATCATATACCGT
Found at i:235942 original size:64 final size:64
Alignment explanation
Indices: 235773--236021 Score: 249
Period size: 64 Copynumber: 3.9 Consensus size: 64
235763 TTTGCTGCGA
* * * *
235773 TGCTACTGATGGCTTTGTGTCGGTCATAG-TACCATTACTGATGGCTTTGTGCCGATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCAT-GTTACCGTTACTGATGGCTTTGTGCCGATCATATCAC
* * * *
235837 --CTTATTGATGG-TTGTGTGCCAATCAT-TTCCCTGTTACTGATGG-TTGTGTGCCGGTCATAT
1 TGC-TACTGATGGCTT-TGTGCCGATCATGTTACC-GTTACTGATGGCTT-TGTGCCGATCATAT
235897 CAC
62 CAC
* * *
235900 TGCTACTGACGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTGTGTGTCGATCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTTTGTGCCGATCATATCAC
* * * * * * *
235964 TACTACTGATGGCTGTGTGCCGATCATATCACTGCTACTGATGGCTTTGTGCCAATCA
1 TGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTTTGTGCCGATCA
236022 CATTACTGTA
Statistics
Matches: 150, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
62 8 0.05
63 42 0.28
64 92 0.61
65 8 0.05
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTTTGTGCCGATCATATCAC
Found at i:235991 original size:96 final size:95
Alignment explanation
Indices: 235808--236027 Score: 305
Period size: 96 Copynumber: 2.3 Consensus size: 95
235798 ATAGTACCAT
* * * * **
235808 TACTGATGGCTTTGTGCCGATCATATTACCTTATTGATGGTTGTGTGCCAATCATTTCCCTGTTA
1 TACTGATGGCTTTGTGCCGATCATATTACCTTACTGATGGCTGTGTGCCAATCATATCACTACTA
* *
235873 CTGATGGTTGTGTGCCGGTCATATCACTGC
66 CTGATGGCTGTGTGCCGATCATATCACTGC
* * * *
235903 TACTGACGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTGTGTGTCGATCATATCACTACT
1 TACTGATGGCTTTGTGCCGATCATATTACC-TTACTGATGGCTGTGTGCCAATCATATCACTACT
235968 ACTGATGGCTGTGTGCCGATCATATCACTGC
65 ACTGATGGCTGTGTGCCGATCATATCACTGC
* *
235999 TACTGATGGCTTTGTGCCAATCACATTAC
1 TACTGATGGCTTTGTGCCGATCATATTAC
236028 TGTACTTATG
Statistics
Matches: 108, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
95 28 0.26
96 80 0.74
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (95 bp):
TACTGATGGCTTTGTGCCGATCATATTACCTTACTGATGGCTGTGTGCCAATCATATCACTACTA
CTGATGGCTGTGTGCCGATCATATCACTGC
Found at i:255451 original size:37 final size:38
Alignment explanation
Indices: 255409--255484 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
255399 ACTCCCTGAA
* *
255409 CAACAGTGGAATA-GTGGAAAACTATATGTCCTATCTC
1 CAACAGTGGAATAGGTAGAAAACTATATGTCCTAGCTC
* *
255446 CAACAGTGGAATAGGTAGAAAATTGTATGTCCTAGCTC
1 CAACAGTGGAATAGGTAGAAAACTATATGTCCTAGCTC
255484 C
1 C
255485 CTGAACAGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
37 13 0.38
38 21 0.62
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (38 bp):
CAACAGTGGAATAGGTAGAAAACTATATGTCCTAGCTC
Found at i:255750 original size:44 final size:44
Alignment explanation
Indices: 255261--255736 Score: 610
Period size: 44 Copynumber: 11.0 Consensus size: 44
255251 GAAACTATAA
* * * *
255261 GTCCTATCTTCCTGAACAGTAGTGGAATAGGTGAAAGATTGTAT
1 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
* * * *
255305 GTCCTAGCTCCCTAAATAGCAGTGGAATAGGAGGAAGATTGCAT
1 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
*
255349 GTCCTAGCTCCATGAACAGCAGTGGAATAGGTGGAAGATTGTAT
1 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
* * * * *
255393 GTCCTAACTCCCTGAACAACAGTGGAATA-GTGGAAAACTATAT
1 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
* * *
255436 GTCCTATCT-CC---A-A-CAGTGGAATAGGTAGAAAATTGTAT
1 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
*
255474 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCAT
1 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
*
255518 GTCCTAGCTCCCTGAACAGTAGTGGAATAGGTGGAAGATTGTAT
1 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
*
255562 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAATATTGTAT
1 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
* * *
255606 GTCCTAGCTCCCAGAACAGCAGTGGAATAGGTGGAATATTGCAT
1 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
* * *
255650 GTCCTATCTCCTTGAACAGCGGTGGAATAGGTGGAAGATTGTA-
1 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
* * *
255693 GAT-CTTGTCACCCTGAACAACAGTGGAATAGGTGGAAGATTGTA
1 G-TCCTAG-CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTA
255737 GATCCTGTCA
Statistics
Matches: 378, Mismatches: 45, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
37 10 0.03
38 20 0.05
39 3 0.01
42 3 0.01
43 23 0.06
44 319 0.84
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (44 bp):
GTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAT
Found at i:255775 original size:44 final size:44
Alignment explanation
Indices: 255681--255776 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 44
255671 GTGGAATAGG
* * * *
255681 TGGAAGATTGTAGATCTTGTCACCCTGAACAACAGTGGAATAGG
1 TGGAAGATTGTAGATCCTGTCACCCTGAACAACAGTAGAACAGA
** *
255725 TGGAAGATTGTAGATCCTGTCACCCT-AAGCAGTAGTAGAGCAGA
1 TGGAAGATTGTAGATCCTGTCACCCTGAA-CAACAGTAGAACAGA
*
255769 TTGAAGAT
1 TGGAAGAT
255777 ACTAGCCTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 2 0.05
44 41 0.95
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (44 bp):
TGGAAGATTGTAGATCCTGTCACCCTGAACAACAGTAGAACAGA
Found at i:259842 original size:42 final size:42
Alignment explanation
Indices: 259794--259879 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
259784 TTTTAAAATC
259794 ACATTTGACTCATAAATATTAAATAATAATATTTACGAACTT
1 ACATTTGACTCATAAATATTAAATAATAATATTTACGAACTT
259836 ACATTTGACTCATAAATATTAAATAATAATATTTACGAACTT
1 ACATTTGACTCATAAATATTAAATAATAATATTTACGAACTT
259878 AC
1 AC
259880 TCGTTAGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (42 bp):
ACATTTGACTCATAAATATTAAATAATAATATTTACGAACTT
Found at i:262021 original size:27 final size:26
Alignment explanation
Indices: 262001--262282 Score: 330
Period size: 27 Copynumber: 10.4 Consensus size: 26
261991 GGGTATAATA
262001 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
*
262028 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
* **
262055 GTCATTTTACCTTATTAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
*
262082 GTCATTTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
262109 ATCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* * *
262136 GTCATTTTAACCTATGAGGGTACTTCG
1 GTCATTTTACCCTATGGGGGTA-TTTG
* *
262163 ATCATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTA-TTTG
*
262190 GTCATTTTACCCTATTAGGGGTATTTCG
1 GTCATTTTACCCTA-TGGGGGTATTT-G
* *
262218 ATCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
262245 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
262272 GTCATTTTACC
1 GTCATTTTACC
262283 TTATTTTGGG
Statistics
Matches: 219, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
26 6 0.03
27 185 0.84
28 28 0.13
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGGTATTTG
Found at i:262059 original size:54 final size:54
Alignment explanation
Indices: 262002--262282 Score: 400
Period size: 54 Copynumber: 5.2 Consensus size: 54
261992 GGTATAATAG
* *
262002 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGA
* ** * *
262056 TCATTTTACCTTATTAGGGTATTTCGGTCATTTTATCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGA
* * *
262110 TCATTTTACCCTATAGGGGTATTTCGGTCATTTTAACCTATGAGGGTACTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGA
** *
262164 TCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATTAGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGA-GGGTATTTCGA
* * * *
262219 TCATTTTACCCTATGAGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGA
262273 TCATTTTACC
1 TCATTTTACC
262283 TTATTTTGGG
Statistics
Matches: 202, Mismatches: 24, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
54 153 0.76
55 49 0.24
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (54 bp):
TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGA
Found at i:262114 original size:81 final size:80
Alignment explanation
Indices: 262001--262282 Score: 406
Period size: 81 Copynumber: 3.5 Consensus size: 80
261991 GGGTATAATA
* *
262001 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT-GAGGGTATTTTGGTCATTTTAC
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAG-GGGTATTTCGGTCATTTTAC
*
262065 CTTATTAGGGTATTTCG
65 C-TATGAGGGTATTTCG
*
262082 GTCATTTTATCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTTTAAC
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTTT-AC
*
262147 CTATGAGGGTACTTCG
65 CTATGAGGGTATTTCG
* * *
262163 ATCATTTTACCCTATGGGGGTATTT-TAGTCATTTTACCCTATTAGGGGTATTTCGATCATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCCTA-TAGGGGTATTTCGGTCATTTTA
*
262227 CCCTATGAGGGTATTTTG
64 -CCTATGAGGGTATTTCG
*
262245 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACC
262283 TTATTTTGGG
Statistics
Matches: 181, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
80 1 0.01
81 107 0.59
82 73 0.40
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (80 bp):
GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTTTACC
TATGAGGGTATTTCG
Found at i:263423 original size:24 final size:24
Alignment explanation
Indices: 263398--263444 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
263388 CCCAAATCCC
263398 AATATCCTCTCCTCAAATCTCTCCA
1 AATATCC-CTCCTCAAATCTCTCCA
*
263423 AATATCCCTCCTCAATTCTCTC
1 AATATCCCTCCTCAAATCTCTC
263445 TATGACCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.26, C:0.40, G:0.00, T:0.34
Consensus pattern (24 bp):
AATATCCCTCCTCAAATCTCTCCA
Found at i:303824 original size:27 final size:27
Alignment explanation
Indices: 303804--304136 Score: 346
Period size: 27 Copynumber: 12.6 Consensus size: 27
303794 GGGTATAACA
303804 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
303831 GTCATTTTATCCTAT-AGGGGTGTTTTG
1 GTCATTTTACCCTATGA-GGGTATTTCG
303858 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
303885 GTCATTTTATCCTATG-GGAGTATTT--
1 GTCATTTTACCCTATGAGG-GTATTTCG
* *
303910 -TGA---T-CCCTATG-GGAG-ATTTTG
1 GTCATTTTACCCTATGAGG-GTATTTCG
*
303931 ATCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
303958 ATCATTTTACCCTATTGGGGGTATTTCA
1 GTCATTTTACCCTA-TGAGGGTATTTCG
*
303986 ATCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
304013 GTCATTTTACTCTATTAGGGGTATTGCG
1 GTCATTTTACCCTATGA-GGGTATTTCG
* * * *
304041 ATCATTTTACCTTATGGGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
304068 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
304095 GTCTTTTTACCCTATCAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
304122 ATCATTTTACCCTAT
1 GTCATTTTACCCTAT
304137 TTTAGGGTCT
Statistics
Matches: 258, Mismatches: 34, Indels: 28
0.81 0.11 0.09
Matches are distributed among these distances:
19 4 0.02
20 10 0.04
21 1 0.00
22 2 0.01
24 2 0.01
25 1 0.00
26 11 0.04
27 180 0.70
28 47 0.18
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:303928 original size:19 final size:20
Alignment explanation
Indices: 303895--303933 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
303885 GTCATTTTAT
303895 CCTATGGGAGTATTTTGATC
1 CCTATGGGAGTATTTTGATC
303915 CCTATGGGAG-ATTTTGATC
1 CCTATGGGAGTATTTTGATC
303934 ATTTTACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (20 bp):
CCTATGGGAGTATTTTGATC
Found at i:303991 original size:55 final size:55
Alignment explanation
Indices: 303925--304137 Score: 302
Period size: 55 Copynumber: 3.9 Consensus size: 55
303915 CCTATGGGAG
*
303925 ATTTTGATCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATTGGGGGT
1 ATTTCGATCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATTGGGGGT
* * * *
303980 ATTTCAATCATTTTACCCTATGAGGGTATTTCGGTCATTTTACTCTATTAGGGGT
1 ATTTCGATCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATTGGGGGT
* * * * *
304035 ATTGCGATCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTA-TGGGGGT
1 ATTTCGATCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATTGGGGGT
* * *
304089 ATTTCGGTCTTTTTACCCTATCAGGGTATTTCGATCATTTTACCCTATT
1 ATTTCGATCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATT
304138 TTAGGGTCTC
Statistics
Matches: 137, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
54 45 0.33
55 92 0.67
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (55 bp):
ATTTCGATCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATTGGGGGT
Found at i:304073 original size:82 final size:82
Alignment explanation
Indices: 303932--304137 Score: 306
Period size: 82 Copynumber: 2.5 Consensus size: 82
303922 GAGATTTTGA
*
303932 TCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATTGGGGGTATTTCAATCATTTTACC
1 TCATTTTACCCTATCAGGGTATTTCGATCATTTTACCCTATTGGGGGTATTTCAATCATTTTACC
303997 CTATGAGGGTATTTCGG
66 CTATGAGGGTATTTCGG
* * * * ***
304014 TCATTTTACTCTATTAGGGGTATTGCGATCATTTTACCTTA-TGGGGGTATTTTGGTCATTTTAC
1 TCATTTTACCCTATCA-GGGTATTTCGATCATTTTACCCTATTGGGGGTATTTCAATCATTTTAC
*
304078 CCTATGGGGGTATTTCGG
65 CCTATGAGGGTATTTCGG
*
304096 TCTTTTTACCCTATCAGGGTATTTCGATCATTTTACCCTATT
1 TCATTTTACCCTATCAGGGTATTTCGATCATTTTACCCTATT
304138 TTAGGGTCTC
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
81 22 0.20
82 65 0.60
83 22 0.20
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (82 bp):
TCATTTTACCCTATCAGGGTATTTCGATCATTTTACCCTATTGGGGGTATTTCAATCATTTTACC
CTATGAGGGTATTTCGG
Found at i:304706 original size:23 final size:23
Alignment explanation
Indices: 304683--304859 Score: 160
Period size: 23 Copynumber: 7.5 Consensus size: 23
304673 ACACCAAAAT
*
304683 TTGGACAGCATATATACAACAAT
1 TTGGACAGCATATATACAACAAA
*
304706 TTGGGCAGCATATATACAACAAAA
1 TTGGACAGCATATATACAAC-AAA
* * *
304730 TT-GAGCAGCATTTTTACACCAAAAA
1 TTGGA-CAGCATATATACA--ACAAA
304755 TTGGACAGCATATATACAACAAA
1 TTGGACAGCATATATACAACAAA
* * *
304778 TTGGGCAGCATATATATACCAAA
1 TTGGACAGCATATATACAACAAA
* * * * *
304801 TTGAACAACATTTTTACATCAAAA
1 TTGGACAGCATATATACAAC-AAA
*
304825 TTGGACAGCATATATACAACAAT
1 TTGGACAGCATATATACAACAAA
304848 TTAGG-CAGCATA
1 TT-GGACAGCATA
304860 NNNNNNNNNN
Statistics
Matches: 122, Mismatches: 25, Indels: 14
0.76 0.16 0.09
Matches are distributed among these distances:
23 68 0.56
24 35 0.29
25 16 0.13
26 3 0.02
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.26
Consensus pattern (23 bp):
TTGGACAGCATATATACAACAAA
Found at i:304762 original size:72 final size:70
Alignment explanation
Indices: 304626--304859 Score: 299
Period size: 72 Copynumber: 3.3 Consensus size: 70
304616 ACAGCCCTTG
* * * * * * * *
304626 TACATCAATTTGGACAGCATTTATATACCAAACTAGACAACATTTTCACACCAAAATTTGGACAG
1 TACAACAATTTGGGCAGCATATATA-AACAAAATTGACAACATTTTTACACCAAAAATTGGACAG
304691 CATATA
65 CATATA
*
304697 TACAACAATTTGGGCAGCATATATACAACAAAATTGAGCAGCATTTTTACACCAAAAATTGGACA
1 TACAACAATTTGGGCAGCATATATA-AACAAAATTGA-CAACATTTTTACACCAAAAATTGGACA
304762 GCATATA
64 GCATATA
* * * *
304769 TACAACAAATTGGGCAGCATATATATACCAAATTGAACAACATTTTTACATC-AAAATTGGACAG
1 TACAACAATTTGGGCAGCATATATAAACAAAATTG-ACAACATTTTTACACCAAAAATTGGACAG
304833 CATATA
65 CATATA
*
304839 TACAACAATTTAGGCAGCATA
1 TACAACAATTTGGGCAGCATA
304860 NNNNNNNNNN
Statistics
Matches: 144, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
70 37 0.26
71 51 0.35
72 56 0.39
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (70 bp):
TACAACAATTTGGGCAGCATATATAAACAAAATTGACAACATTTTTACACCAAAAATTGGACAGC
ATATA
Found at i:310336 original size:22 final size:24
Alignment explanation
Indices: 310294--310337 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
310284 TAACTAAGCT
310294 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
310318 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
310338 TCTTGTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:316076 original size:29 final size:29
Alignment explanation
Indices: 316035--316092 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
316025 ATATGCTTCC
316035 TATTTTTACAATTTAAT-ATTTTATTTTT
1 TATTTTTACAATTTAATCATTTTATTTTT
* *
316063 TATTTTTAAGAATTTAATCTTTTTATTTTT
1 TATTTTT-ACAATTTAATCATTTTATTTTT
316093 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 7 0.27
29 9 0.35
30 10 0.38
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (29 bp):
TATTTTTACAATTTAATCATTTTATTTTT
Found at i:316101 original size:23 final size:22
Alignment explanation
Indices: 316046--316102 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
316036 ATTTTTACAA
*
316046 TTTAATATTTT-ATTTTTTATT
1 TTTAAAATTTTAATTTTTTATT
316067 TTTAAGAA-TTTAATCTTTTTATT
1 TTTAA-AATTTTAAT-TTTTTATT
316090 TTTAAAATTTTAA
1 TTTAAAATTTTAA
316103 AAATTAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 8 0.26
22 5 0.16
23 18 0.58
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTAAAATTTTAATTTTTTATT
Found at i:316113 original size:31 final size:30
Alignment explanation
Indices: 316053--316113 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
316043 CAATTTAATA
* * * *
316053 TTTTATTTTTTATTTTTAAGAATTTAATCT
1 TTTTATTTTTAAATTTTAAAAATTAAATCT
316083 TTTTATTTTTAAAATTTTAAAAATTAAATCT
1 TTTTATTTTT-AAATTTTAAAAATTAAATCT
316114 AATTCTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTTATTTTTAAATTTTAAAAATTAAATCT
Found at i:318196 original size:107 final size:108
Alignment explanation
Indices: 318041--318253 Score: 365
Period size: 107 Copynumber: 2.0 Consensus size: 108
318031 CATCCCTACT
* * *
318041 TAAACAAAATTAATGAAAAGAGAAGAAAATTCTACCCATTTTTGATAAAGTTGTAGTTAAGAGTT
1 TAAACAAAATTAATGAAAAGAGAAGAAAATTCTACCCATCTTTAATAAAGTTGTAGTTAAGAATT
318106 GATATTTATCATAATACTTGTATATTATACAAAATTGTCAACC
66 GATATTTATCATAATACTTGTATATTATACAAAATTGTCAACC
318149 TAAACAAAATTAATGAAAAGA-AAGAAAATTCTACCCATCTTTAATAAAGTTGTAGTTAAGAATT
1 TAAACAAAATTAATGAAAAGAGAAGAAAATTCTACCCATCTTTAATAAAGTTGTAGTTAAGAATT
* * *
318213 TATGTTTATTATAATACTTGTATATTATACAAAATTGTCAA
66 GATATTTATCATAATACTTGTATATTATACAAAATTGTCAA
318254 ATACCAAATA
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
107 78 0.79
108 21 0.21
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (108 bp):
TAAACAAAATTAATGAAAAGAGAAGAAAATTCTACCCATCTTTAATAAAGTTGTAGTTAAGAATT
GATATTTATCATAATACTTGTATATTATACAAAATTGTCAACC
Found at i:318395 original size:33 final size:33
Alignment explanation
Indices: 318358--318420 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
318348 TGAAGAACAT
*
318358 CAAAAAAAAAAATTATACAAAATTTTCAAATAC
1 CAAAAAAAAAAATTATACAAAATTGTCAAATAC
*
318391 CAAAAAAAAAATTTATACAAAATTGTCAAA
1 CAAAAAAAAAAATTATACAAAATTGTCAAA
318421 ATTTTGCATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (33 bp):
CAAAAAAAAAAATTATACAAAATTGTCAAATAC
Found at i:319862 original size:30 final size:31
Alignment explanation
Indices: 319827--319884 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
319817 GTAAGTACTC
* **
319827 AAAATTTGAGGGATTAA-AGTGTAAATACGA
1 AAAATTTGAAGGACCAATAGTGTAAATACGA
319857 AAAATTTGAAGGACCAATAGTGTAAATA
1 AAAATTTGAAGGACCAATAGTGTAAATA
319885 TTTTAAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (31 bp):
AAAATTTGAAGGACCAATAGTGTAAATACGA
Done.