Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3511
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: 45426
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:10716 original size:68 final size:68
Alignment explanation
Indices: 10634--10779 Score: 256
Period size: 68 Copynumber: 2.1 Consensus size: 68
10624 CACTCATGCA
* *
10634 ACCTAGCTACATTTATATCTCATGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
1 ACCTAGCTACATTTATATCCCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
*
10699 GTG
66 ATG
*
10702 ACCTAGCTACATTTATCTCCCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
1 ACCTAGCTACATTTATATCCCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
10767 ATG
66 ATG
10770 ACCTAGCTAC
1 ACCTAGCTAC
10780 TATATAGTAT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 74 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (68 bp):
ACCTAGCTACATTTATATCCCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
ATG
Found at i:10812 original size:68 final size:66
Alignment explanation
Indices: 10634--10805 Score: 229
Period size: 68 Copynumber: 2.5 Consensus size: 66
10624 CACTCATGCA
10634 ACCTAGCTACATTTATATCTCATGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
1 ACCTAGCTACATTTATATCT--TGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
*
10699 GTG
64 ATG
* **
10702 ACCTAGCTACATTTATCTCCCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
1 ACCTAGCTACATTTATAT--CTTGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
10767 ATG
64 ATG
*
10770 ACCTAGCTACTATATAGTATCTTGTAGC-CTTCTTGT
1 ACCTAGCTAC-ATTTA-TATCTTGTAGCTC-TCTTGT
10806 ACACATGATA
Statistics
Matches: 91, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
67 1 0.01
68 83 0.91
69 4 0.04
70 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.34
Consensus pattern (66 bp):
ACCTAGCTACATTTATATCTTGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACATAT
G
Found at i:12325 original size:27 final size:27
Alignment explanation
Indices: 12295--12608 Score: 385
Period size: 27 Copynumber: 11.6 Consensus size: 27
12285 TTAGTTTACC
*
12295 AAATTACAAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
12322 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
12349 AAATCACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* ** **
12376 AAATTACCAAAACACCTTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
12403 AAATTACCAAAATACCCATGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
12430 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
12457 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
12484 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
12511 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
12538 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
12565 AAATTACCAAAATTCCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
**
12592 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
12609 TCGACCTGTA
Statistics
Matches: 246, Mismatches: 41, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 246 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:12361 original size:54 final size:54
Alignment explanation
Indices: 12295--12680 Score: 425
Period size: 54 Copynumber: 7.1 Consensus size: 54
12285 TTAGTTTACC
* * *
12295 AAATTACAAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * * *
12349 AAATCACCAAAATACCCCTAGTTTGTAAAATTACCAAAACACCTTTGGTTTACA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * * *
12403 AAATTACCAAAATACCCATGGTTTGTAAAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
*
12457 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * * * *
12511 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * ** * *** *
12565 AAATTACCAAAATTCCCCT-GATTTGTGAAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCTTGGTTTATA
*** * * * * *
12619 AAATTATTGAAATA-CCCTCGACTTGTAAAATTACCAAAGTACCCTTGATTTACA
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCTTGGTTTATA
*
12673 GAATTACC
1 AAATTACC
12681 GTTTTACCCT
Statistics
Matches: 279, Mismatches: 51, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
53 5 0.02
54 274 0.98
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
Found at i:12661 original size:27 final size:27
Alignment explanation
Indices: 12295--12669 Score: 298
Period size: 27 Copynumber: 13.9 Consensus size: 27
12285 TTAGTTTACC
* *
12295 AAATTACAAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
* * * *
12322 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
12349 AAATCACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* * * * **
12376 AAATTACCAAAACACCTTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
*
12403 AAATTACCAAAATACCCAT-GGTTTGTA
1 AAATTACCAAAATACCC-TCGATTTGTA
* * *
12430 AAATTACTAAAATACCCTTTG-TTTATA
1 AAATTACCAAAATACCC-TCGATTTGTA
*
12457 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* *
12484 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
12511 AAATTATCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
*
12538 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACCAAAATACCCTC-GATTTGTA
* *
12565 AAATTACCAAAATTCCC-CTGATTTGTG
1 AAATTACCAAAATACCCTC-GATTTGTA
** **
12592 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*** *
12619 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
12646 AAATTACCAAAGTACCCTTGATTT
1 AAATTACCAAAATACCCTCGATTT
12670 ACAGAATTAC
Statistics
Matches: 284, Mismatches: 53, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
27 280 0.99
28 4 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:12715 original size:27 final size:26
Alignment explanation
Indices: 12592--12717 Score: 81
Period size: 27 Copynumber: 4.7 Consensus size: 26
12582 CTGATTTGTG
* **
12592 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTAC-GAAATACCCTCGACTTACA
* **
12619 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTA-CGAAATACCCTCGACTTACA
* * *
12646 AAATTACCAAAGTACCCTTGATTTACA
1 AAATTACGAAA-TACCCTCGACTTACA
* *** *
12673 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTA-CGAAATACCCTCGACTTACA
12700 AAATTATCGAAATACCCT
1 AAATTA-CGAAATACCCT
12718 TATAGGGTAG
Statistics
Matches: 77, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
26 3 0.04
27 73 0.95
28 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (26 bp):
AAATTACGAAATACCCTCGACTTACA
Found at i:12754 original size:27 final size:27
Alignment explanation
Indices: 12701--12976 Score: 338
Period size: 27 Copynumber: 10.3 Consensus size: 27
12691 CGATTTACAA
* * *
12701 AATTATCGAAATACCCTTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
12728 AAATACCGATATATCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
12755 AATTACTGAAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
12782 AATTAGCGAAATACCCCTGTAGGGCAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
12809 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
12836 AATTATCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
12863 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
12890 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
12917 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
12944 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
12970 AATTACC
1 AATTACC
12977 ATTTTGCCCC
Statistics
Matches: 216, Mismatches: 33, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
26 16 0.07
27 200 0.93
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:13455 original size:22 final size:22
Alignment explanation
Indices: 13403--13467 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
13393 TTAAAGCCTT
* *
13403 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
13425 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
13447 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
13468 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:13686 original size:27 final size:27
Alignment explanation
Indices: 13648--13699 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
13638 CATTATTTAT
*
13648 TCTGGTGGCTCTGCCACAATATCTGTA
1 TCTGGTGACTCTGCCACAATATCTGTA
*
13675 TCTGGTGACTCTGTCACAATATCTG
1 TCTGGTGACTCTGCCACAATATCTG
13700 ATAACTGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (27 bp):
TCTGGTGACTCTGCCACAATATCTGTA
Found at i:13869 original size:19 final size:19
Alignment explanation
Indices: 13847--13903 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
13837 TTCTGATTTT
13847 TGATTCTGTTACTTGATAC
1 TGATTCTGTTACTTGATAC
13866 TGATTCTG--A-TT--T--
1 TGATTCTGTTACTTGATAC
*
13878 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACTTGATAC
13897 TGATTCT
1 TGATTCT
13904 AATTCTGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 14
0.67 0.02 0.31
Matches are distributed among these distances:
12 8 0.27
14 2 0.07
15 1 0.03
16 2 0.07
17 2 0.07
19 15 0.50
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (19 bp):
TGATTCTGTTACTTGATAC
Found at i:13882 original size:31 final size:32
Alignment explanation
Indices: 13836--13903 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 32
13826 TTGCATTCAC
*
13836 ATTCTGATTTTTGATTCTGTTACTTGATACTG
1 ATTCTGATTTTTGATTCTGTTACCTGATACTG
13868 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTTGATTCTGTTACCTGATACTG
13899 ATTCT
1 ATTCT
13904 AATTCTGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 28 0.80
32 7 0.20
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (32 bp):
ATTCTGATTTTTGATTCTGTTACCTGATACTG
Found at i:24226 original size:68 final size:68
Alignment explanation
Indices: 24151--24296 Score: 283
Period size: 68 Copynumber: 2.1 Consensus size: 68
24141 CACTCATGCA
24151 ACCTAGCTACATTTATATCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
1 ACCTAGCTACATTTATATCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
24216 GTG
66 GTG
*
24219 ACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
1 ACCTAGCTACATTTATATCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
24284 GTG
66 GTG
24287 ACCTAGCTAC
1 ACCTAGCTAC
24297 TATATAGTAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 77 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (68 bp):
ACCTAGCTACATTTATATCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACAT
GTG
Found at i:27382 original size:42 final size:42
Alignment explanation
Indices: 27331--27442 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 42
27321 CAAGACTACG
*
27331 TGTAAGACCATATCTGGGATATGGCATCGATATGAGACTT-CA
1 TGTAAGACCATATCTGGGATATGGCATCGATACGAGA-TTACA
* * * *
27373 TGTAAGACCATACCTGGGCTATTAGCATCGATACGATATTACA
1 TGTAAGACCATATCTGGGATA-TGGCATCGATACGAGATTACA
* *
27416 TATAAAACCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
27443 TGGTACGGTA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
42 26 0.45
43 32 0.55
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATACGAGATTACA
Found at i:32225 original size:40 final size:40
Alignment explanation
Indices: 32167--32359 Score: 271
Period size: 40 Copynumber: 4.8 Consensus size: 40
32157 TCGGATAATA
* *
32167 ACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAT-
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATG
* * * *
32207 TCTGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATA
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATG
* * *
32247 ACCGTGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATG
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATG
*
32287 ACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATG
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATG
*
32327 ACCGGGCTAAGTCCCGAAGGCATTTGGGCGAGT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
32360 AGCTATATCC
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
39 2 0.01
40 134 0.99
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (40 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATG
Found at i:32385 original size:39 final size:40
Alignment explanation
Indices: 32167--32385 Score: 167
Period size: 40 Copynumber: 5.5 Consensus size: 40
32157 TCGGATAATA
** * * *
32167 ACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAT-
1 ACCGGGCTAAACCCCGAAGGCATTTGGGCGAGTTACT-ATG
* * ** * * *
32207 TCTGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATA
1 ACCGGGCTAAACCCCGAAGGCATTTGGGCGAGTTACTATG
* * ** * *
32247 ACCGTGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATG
1 ACCGGGCTAAACCCCGAAGGCATTTGGGCGAGTTACTATG
* ** *
32287 ACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATG
1 ACCGGGCTAAACCCCGAAGGCATTTGGGCGAGTTACTATG
**
32327 ACCGGGCTAAGTCCCGAAGGCATTTGGGCGAG-TAGCTAT-
1 ACCGGGCTAAACCCCGAAGGCATTTGGGCGAGTTA-CTATG
32366 ATCC-GGCTAAACCCCGAAGG
1 A-CCGGGCTAAACCCCGAAGG
32386 TACTTGGTTG
Statistics
Matches: 158, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 19 0.12
40 139 0.88
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
ACCGGGCTAAACCCCGAAGGCATTTGGGCGAGTTACTATG
Found at i:37376 original size:47 final size:47
Alignment explanation
Indices: 37312--37632 Score: 563
Period size: 47 Copynumber: 6.8 Consensus size: 47
37302 ACTATCACAT
*
37312 ATATATACACTTCCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
37359 ATATATACACTCTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
37406 ATATATACACTTTCATATTCATC-CATCGGCCATTAGGCCTTATCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
37452 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 --ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
37501 ATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
37548 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 --ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
37597 ATATATACACTTTCACATTCATCACATCGGCCATTA
1 ATATATACACTTTCACATTCATCACATCGGCCATTA
37633 CGCCATACTA
Statistics
Matches: 262, Mismatches: 7, Indels: 10
0.94 0.03 0.04
Matches are distributed among these distances:
46 23 0.09
47 148 0.56
48 22 0.08
49 69 0.26
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (47 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:37582 original size:96 final size:96
Alignment explanation
Indices: 37312--37632 Score: 585
Period size: 96 Copynumber: 3.4 Consensus size: 96
37302 ACTATCACAT
* *
37312 ATATATACACTTCCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTCTCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
37375 ATTCATCACATCGGCCATTAGGCCTTATCAC
66 ATTCATCACATCGGCCATTAGGCCTTATCAC
*
37406 ATATATACACTTTCATATTCATC-CATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
37470 ATTCATCACATCGGCCATTAGGCCTTATCAC
66 ATTCATCACATCGGCCATTAGGCCTTATCAC
*
37501 ATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
37566 ATTCATCACATCGGCCATTAGGCCTTATCAC
66 ATTCATCACATCGGCCATTAGGCCTTATCAC
37597 ATATATACACTTTCACATTCATCACATCGGCCATTA
1 ATATATACACTTTCACATTCATCACATCGGCCATTA
37633 CGCCATACTA
Statistics
Matches: 220, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
93 23 0.10
94 21 0.10
95 69 0.31
96 107 0.49
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (96 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
ATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:41076 original size:40 final size:40
Alignment explanation
Indices: 41032--41219 Score: 238
Period size: 40 Copynumber: 4.8 Consensus size: 40
41022 AGCATGATTA
* * *
41032 CTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* * *
41072 CTCTTCGAGG-TTTAGCACGGATATATTACTAGCACGAATG
1 CTCTTCG-GGACTTAGCCCGGATATATCACTAGCACGAATG
* * * *
41112 CTCTTCGGAACTTAGCTCAGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
*
41152 CTCCTC-GGACTTAGCCCGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
*
41191 CTCCTC-GGACTTAGCCCGGATATATCACT
1 CTCTTCGGGACTTAGCCCGGATATATCACT
41220 CTCAATTCTC
Statistics
Matches: 129, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
39 59 0.46
40 68 0.53
41 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
Found at i:41166 original size:22 final size:22
Alignment explanation
Indices: 41141--41205 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
41131 GATACATCAC
41141 TAGCACGAATGCTCCTCGGACT
1 TAGCACGAATGCTCCTCGGACT
* * * *
41163 TAGCCCGGAT-AT-ATC--AC-
1 TAGCACGAATGCTCCTCGGACT
41180 TAGCACGAATGCTCCTCGGACT
1 TAGCACGAATGCTCCTCGGACT
41202 TAGC
1 TAGC
41206 CCGGATATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 8 0.27
18 3 0.10
19 2 0.07
20 2 0.07
21 3 0.10
22 12 0.40
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.23
Consensus pattern (22 bp):
TAGCACGAATGCTCCTCGGACT
Found at i:41184 original size:79 final size:79
Alignment explanation
Indices: 41039--41219 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 79
41029 TTACTCTTCG
* * * * * * ** *
41039 GGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGAGGTTTAGCACGGATATATTACTAG
1 GGACTTAGCCCAGATACATCACTAGCACGAATGCTCCTCGAGACTTAGCACGGATATATCACTAG
*
41104 CACGAATGCTCTTC
66 CACGAATGCTCCTC
* *
41118 GGAACTTAGCTCAGATACATCACTAGCACGAATGCTCCTCG-GACTTAGCCCGGATATATCACTA
1 GG-ACTTAGCCCAGATACATCACTAGCACGAATGCTCCTCGAGACTTAGCACGGATATATCACTA
41182 GCACGAATGCTCCTC
65 GCACGAATGCTCCTC
* *
41197 GGACTTAGCCCGGATATATCACT
1 GGACTTAGCCCAGATACATCACT
41220 CTCAATTCTC
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
78 18 0.21
79 37 0.43
80 31 0.36
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (79 bp):
GGACTTAGCCCAGATACATCACTAGCACGAATGCTCCTCGAGACTTAGCACGGATATATCACTAG
CACGAATGCTCCTC
Found at i:42467 original size:37 final size:35
Alignment explanation
Indices: 42417--42493 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 35
42407 TTATTACGAA
* *
42417 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATC-CC-CACGAAGTCATCGG
*
42454 GTCTTACCCGGACAAAATCCCCACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACGAAGTCATCGG
42489 GTCTT
1 GTCTT
42494 TAGAGCACGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 17 0.46
36 2 0.05
37 18 0.49
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (35 bp):
GTCTTACCCGGACAAAATCCCCACGAAGTCATCGG
Found at i:42686 original size:47 final size:47
Alignment explanation
Indices: 42608--43632 Score: 1609
Period size: 47 Copynumber: 21.9 Consensus size: 47
42598 CCCTTCGGGA
* * * * * *
42608 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42655 CCTGTCACATATATACACTTTCACATTCATCACATC-GCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42701 CTTATCAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42746 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42792 CTTATCA-ATATATATAACTTTCACA-TCATCACATCAGCCATTAGGC
1 CTTATCACATATATA-CACTTTCACATTCATCACATCGGCCATTAGGC
*
42838 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42885 CTTATCACATATTATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATA-TATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42933 C-TATCACATATATATATTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42979 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43026 CTTATCACATATATACACTTTCACATTCATCACATC-GCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43072 CTTATCAC-TATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43118 CTT-TCACATATATACACTTTCATATTCATCAACATCCGCCATTAGGG
1 CTTATCACATATATACACTTTCACATTCATC-ACATCGGCCATTAGGC
*
43165 CTTATCACATATATATACACTTTCAATATTCATCACATC-GCCATTAGGC
1 CTTATCAC--ATATATACACTTTC-ACATTCATCACATCGGCCATTAGGC
*
43214 CTTATCCATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTAT-CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43262 CTTATACACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTAT-CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43310 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43357 CTTATCACATATATACACTTTCATATTCATCACATC-G-CATT-GGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43401 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43447 CTTATCACATATATATACACTTTCACATT--TCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43494 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43541 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43590 CTTATCACAT-TATACACTTTCACATTCATGACATCGGCCATTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
43633 CGCATACTAT
Statistics
Matches: 915, Mismatches: 35, Indels: 57
0.91 0.03 0.06
Matches are distributed among these distances:
44 65 0.07
45 96 0.10
46 197 0.22
47 334 0.37
48 133 0.15
49 60 0.07
50 21 0.02
51 9 0.01
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43086 original size:233 final size:234
Alignment explanation
Indices: 42608--43632 Score: 1605
Period size: 233 Copynumber: 4.4 Consensus size: 234
42598 CCCTTCGGGA
* * * * * * * *
42608 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
42673 TTTCACATTCATCACATCGCCATTAGGCCTTATCAC--ATATACACTTTCACATTCATCACATCG
66 TTTCACATTCATCACATCGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
42736 GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTTATCA-
131 GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
42799 ATATATATAACTTTCACA-TCATCACATCAGCCATTAGGC
196 ATATATA-CACTTTCACATTCATCACATCGGCCATTAGGC
*
42838 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATTATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA-TATACA
* * *
42903 CTTTCACATTCATCATATCGGCCATTAGGCC-TATCACATATATATATTTTCACATTCATCACAT
65 CTTTCACATTCATCACATC-GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
42967 CGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
129 CGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
43032 ACATATATACACTTTCACATTCATCACATC-GCCATTAGGC
194 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43072 CTTATCAC-TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT-TCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* * *
43135 TTTCATATTCATCAACATCCGCCATTAGGGCTTATCACATATATATACACTTTCAATATTCATCA
66 TTTCACATTCATC-ACAT-CGCCATTAGGCCTTATCAC--ATATATACACTTTC-ACATTCATCA
*
43200 CATC-GCCATTAGGCCTTATCCATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
126 CATCGGCCATTAGGCCTTAT-CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
43264 TATACACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
190 TAT-CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43310 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
43375 TTTCATATTCATCACATCG-CATT-GGCCTTATCACATATATACACTTTCATATTCATCACATCG
66 TTTCACATTCATCACATCGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
43438 GCCATTAGG-CTTATCACATATATATACACTTTCACATT--TCACATCGGCCATTAGGCCTTATC
131 GCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
43500 ACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
194 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43541 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT-TATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
43605 ACTTTCACATTCATGACATCGGCCATTA
64 ACTTTCACATTCATCACATC-GCCATTA
43633 CGCATACTAT
Statistics
Matches: 743, Mismatches: 26, Indels: 47
0.91 0.03 0.06
Matches are distributed among these distances:
230 49 0.07
231 98 0.13
232 79 0.11
233 196 0.26
234 81 0.11
235 44 0.06
236 69 0.09
237 35 0.05
238 20 0.03
239 45 0.06
240 27 0.04
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (234 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43106 original size:280 final size:281
Alignment explanation
Indices: 42608--43632 Score: 1643
Period size: 280 Copynumber: 3.7 Consensus size: 281
42598 CCCTTCGGGA
* * * * * * *
42608 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
42671 ACTTTCACATTCATCACATC-GCCATTAGGCCTTATCAC--ATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
42733 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTTAT
131 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
* * *
42797 CAATATATATAACTTTCACA-TCATCACATCAGCCATTAGGCCTTATTACATATATACACTTTCA
196 CACTATATA-CACTTTCACATTCATCACATC-GCCATTAGGCCTTATCACATATATACACTTTCA
*
42861 CATTCATCACATCGGCCATTAGG
259 TATTCATCACATCGGCCATTAGG
*
42884 CCTTATCACATAT-TATACACTTTCACATTCATCATATCGGCCATTAGGCC-TATCACATATATA
1 -CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
* *
42947 TATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
65 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
43012 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC-GCCATTAGGCCTTA
130 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
43076 TCACTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT-TCACATATATACACTTTCA
195 TCACTATATACACTTTCACATTCATCACATC-GCCATTAGGCCTTATCACATATATACACTTTCA
*
43140 TATTCATCAACATCCGCCATTAGGG
259 TATTCATC-ACATCGGCCATTA-GG
* *
43165 CTTATCACATATATATACACTTTCAATATTCATCACATC-GCCATTAGGCCTTATCCATATATAT
1 CTTATCACATATATATACACTTTC-ACATTCATCACATCGGCCATTAGGCCTTAT-CACATATAT
43229 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATACACATATATACACTTTCACATTCATC
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-CACATATATACACTTTCACATTCATC
43294 ACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
128 ACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
*
43359 TATCACATATATACACTTTCATATTCATCACATCG-CATT-GGCCTTATCACATATATACACTTT
193 TATCAC-TATATACACTTTCACATTCATCACATCGCCATTAGGCCTTATCACATATATACACTTT
43422 CATATTCATCACATCGGCCATTAGG
257 CATATTCATCACATCGGCCATTAGG
43447 CTTATCACATATATATACACTTTCACATT--TCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
43510 ACTTTCATATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
*
43575 CATCGGCCATTAGGCCTTATCACAT-TATACACTTTCACATTCATGACATCGGCCATTA
129 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
43633 CGCATACTAT
Statistics
Matches: 703, Mismatches: 26, Indels: 36
0.92 0.03 0.05
Matches are distributed among these distances:
277 41 0.06
278 53 0.08
279 125 0.18
280 199 0.28
281 28 0.04
282 41 0.06
283 62 0.09
284 109 0.16
285 19 0.03
286 26 0.04
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (281 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
CACTATATACACTTTCACATTCATCACATCGCCATTAGGCCTTATCACATATATACACTTTCATA
TTCATCACATCGGCCATTAGG
Done.