Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2372
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: 50278
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Found at i:153 original size:45 final size:44
Alignment explanation
Indices: 47--217 Score: 176
Period size: 45 Copynumber: 3.9 Consensus size: 44
37 AGCACCGAGG
47 TGCCGATGGTGG-CGAGGCTCCCGCTACTGACCAA--GCCTAGTTT
1 TGCCGATGGTGGCCGAGGCTCCCGC-AC-GACCAAGGGCCTAGTTT
* *
90 TGCCGTTTTGGTGTCCGAGGCTCCCGCACGAACCAAGGGCCT-GATTT
1 TGCCG--ATGGTGGCCGAGGCTCCCGCACG-ACCAAGGGCCTAG-TTT
*
137 TGCCGATGGTGGCCGAGGCTCCCG-ACGACCAAGGGCTTAGTTT
1 TGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTAGTTT
* * * *
180 GGCCGATGG-GCCCGAGCCT-CTGCACGACCAAGGGCCTA
1 TGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTA
218 AGGGTTGCGA
Statistics
Matches: 109, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
41 2 0.02
42 22 0.20
43 26 0.24
44 5 0.05
45 29 0.27
46 13 0.12
47 12 0.11
ACGTcount: A:0.16, C:0.31, G:0.32, T:0.20
Consensus pattern (44 bp):
TGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTAGTTT
Found at i:939 original size:42 final size:42
Alignment explanation
Indices: 878--1128 Score: 278
Period size: 42 Copynumber: 5.9 Consensus size: 42
868 TAGCTTTGGT
878 TGGTGCTCGAAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
1 TGGTGCTCG-AGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
*
921 TGGTGCTCGAGGCTCCCGCACAT-CATAGCACCGAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCA-AGCACCAAGGTGCCGA
* ** * * *
963 TGGT-CTCCGAGGCTCCC-CACAACCAAGGGCCTAGTTTGCCGG
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAG-GTGCCGA
* *
1005 TGGTG-TCCGATGCTCCCGCACATCCATGCACCAAGGTGCCGA
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
* *
1047 TGGTGCTCGAGGCTCCCGCACATCCAAGCATCAAGGTTACCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGG-TGCCGA
* *
1090 TGGTGGCT-GAGGCTCCCACACATCCGAGCCACCAAGGTG
1 TGGT-GCTCGAGGCTCCCGCACATCCAAG-CACCAAGGTG
1129 ATGGAGGCTC
Statistics
Matches: 175, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
41 14 0.08
42 101 0.58
43 50 0.29
44 10 0.06
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.17
Consensus pattern (42 bp):
TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
Found at i:9101 original size:43 final size:43
Alignment explanation
Indices: 9031--9123 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 43
9021 TCTTCTTTAG
*
9031 CCCGCACATCCCAGGCACCAAGGTGCCGATGGGTGCCCGAGGCT
1 CCCGCACATCCCAAGCACCAAGGTGCCGAT-GGTGCCCGAGGCT
* *
9075 CCCGCACAT-CCAAGCACCAAGTTGCCGATGGTGTCCGAGGCT
1 CCCGCACATCCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCT
9117 CCCGCAC
1 CCCGCAC
9124 CTCCTAGCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 19 0.41
43 18 0.39
44 9 0.20
ACGTcount: A:0.19, C:0.40, G:0.28, T:0.13
Consensus pattern (43 bp):
CCCGCACATCCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCT
Found at i:9145 original size:25 final size:25
Alignment explanation
Indices: 9111--9159 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
9101 GATGGTGTCC
* *
9111 GAGGCTCCCGCACCTCCTAGCCACT
1 GAGGCTCCCGCACATCCGAGCCACT
9136 GAGGCTCCCGCACATCCGAGCCAC
1 GAGGCTCCCGCACATCCGAGCCAC
9160 CAAGGTGCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (25 bp):
GAGGCTCCCGCACATCCGAGCCACT
Found at i:9184 original size:43 final size:41
Alignment explanation
Indices: 9136--10171 Score: 755
Period size: 43 Copynumber: 24.6 Consensus size: 41
9126 CCTAGCCACT
* * *
9136 GAGGCTCCCGCACATCCGAGCCACCAAGGTGCCGATGGTGCCC
1 GAGGCTCCCGCACA-CCAAG-CGCCTAGGTGCCGATGGTGCCC
*
9179 GAGGCTCCCGCACGACC-A------AGG-GCCGATGGTGGCC
1 GAGGCTCCCGCAC-ACCAAGCGCCTAGGTGCCGATGGTGCCC
* * ** *
9213 GAGGCCCCCGCACGACCAAGGGCCTATTTTACCGATGGTGCCC
1 GAGGCTCCCGCAC-ACCAAGCGCCTA-GGTGCCGATGGTGCCC
* * * * *
9256 GAGCCTCTCGCATGACCAAGGGTCTAGGTTGCCGATGGTGCCC
1 GAGGCTCCCGCA-CACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * * * * *
9299 GAGGTTCCGGCACATCCAAGCACCAAGGTGTCGATGGTGCTC
1 GAGGCTCCCGCACA-CCAAGCGCCTAGGTGCCGATGGTGCCC
* * *
9341 GAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGTCC
1 GAGGCTCCCGCAC-ACCAAGCGCCTAG-GTGCCGATGGTGCCC
* * * *
9384 GAGGCTCCCGCACATCCCAGCACCTAGGAGCCGATGGTGGCC
1 GAGGCTCCCGCACA-CCAAGCGCCTAGGTGCCGATGGTGCCC
* **
9426 GAGGCTCCCGCACGACCAAGGGCCTATTTTGCCGATGGTGCCC
1 GAGGCTCCCGCAC-ACCAAGCGCCTA-GGTGCCGATGGTGCCC
* * *
9469 GAGGCTCCCGCACGACCAAGGGCTTAGTTTGCCGATGGTGCCC
1 GAGGCTCCCGCAC-ACCAAGCGCCTAG-GTGCCGATGGTGCCC
* * * * *
9512 GAGCCTCTCGCACGACCAAGGGCCTAGGTTGTCGATGGTGCGC
1 GAGGCTCCCGCAC-ACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * * * * *
9555 GAGGTTCTCGGACATCCAAGCACCAAGGTGCCGATGGTGCTC
1 GAGGCTCCCGCACA-CCAAGCGCCTAGGTGCCGATGGTGCCC
* * ** *
9597 GAGGCTCCCGCACGCCAAGGGCCTAGGTTGCCGACAGTGTCC
1 GAGGCTCCCGCACACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * * * *
9639 GAGGCTCCCGCCCATCATAGCACCGAGGTGCCGATGGTGGCC
1 GAGGCTCCCGCACACCA-AGCGCCTAGGTGCCGATGGTGCCC
* * *
9681 GAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGTCC
1 GAGGCTCCCGCAC-ACCAAGCGCCTAG-GTGCCGATGGTGCCC
* ** *
9724 GAGGCTCCCGCACGACCAAGGGCCTATTTTGCCGATGGTGGCC
1 GAGGCTCCCGCAC-ACCAAGCGCCTA-GGTGCCGATGGTGCCC
* * *
9767 GAGGCTCCCGCACGACCAAGGGCTTAGTTTGCCGATGGTGCCC
1 GAGGCTCCCGCAC-ACCAAGCGCCTAG-GTGCCGATGGTGCCC
* * * * *
9810 GAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGC
1 GAGGCTCCCGCAC-ACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * * * *
9853 GAGGTTCTCGCACATCCAAGCACCAAGGTGCCGATGGTGCTC
1 GAGGCTCCCGCACA-CCAAGCGCCTAGGTGCCGATGGTGCCC
* ** *
9895 GAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGACAGTGTCC
1 GAGGCTCCCGCAC-ACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * *
9938 GAGGCTCCCGCACATCATAGCACCGAGGTGCCGATGGTGCCC
1 GAGGCTCCCGCACACCA-AGCGCCTAGGTGCCGATGGTGCCC
* *
9980 GAGGCTACCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCC
1 GAGGCTCCCGCAC-ACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * * *
10023 GAGGCTCCCGCACATCGAAGCACCGAGGTGCCGATGGCGCCC
1 GAGGCTCCCGCACA-CCAAGCGCCTAGGTGCCGATGGTGCCC
* * * * * *
10065 GAGG--CCC-AATACCAAGGGCTTAGTTTGCCGATGGTGTCC
1 GAGGCTCCCGCACACCAAGCGCCTAG-GTGCCGATGGTGCCC
* * * *
10104 GGGGCTCCTGCACATCCTAGCACC-AGGTTGCCGATGGTGCCC
1 GAGGCTCCCGCACA-CCAAGCGCCTAGG-TGCCGATGGTGCCC
*
10146 GAGGCTCCCGCACGACCAAGGGCCTA
1 GAGGCTCCCGCAC-ACCAAGCGCCTA
10172 TGCTACCGGA
Statistics
Matches: 790, Mismatches: 160, Indels: 86
0.76 0.15 0.08
Matches are distributed among these distances:
34 28 0.04
35 4 0.01
38 7 0.01
39 17 0.02
40 3 0.00
41 13 0.02
42 263 0.33
43 454 0.57
44 1 0.00
ACGTcount: A:0.18, C:0.34, G:0.32, T:0.16
Consensus pattern (41 bp):
GAGGCTCCCGCACACCAAGCGCCTAGGTGCCGATGGTGCCC
Found at i:9206 original size:34 final size:34
Alignment explanation
Indices: 9158--9236 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
9148 CATCCGAGCC
*
9158 ACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACG
1 ACCAAGG-GCCGATGGTGCCCGAGGCCCCCGCACG
*
9193 ACCAAGGGCCGATGGTGGCCGAGGCCCCCGCACG
1 ACCAAGGGCCGATGGTGCCCGAGGCCCCCGCACG
9227 ACCAAGGGCC
1 ACCAAGGGCC
9237 TATTTTACCG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 35 0.83
35 7 0.17
ACGTcount: A:0.19, C:0.38, G:0.35, T:0.08
Consensus pattern (34 bp):
ACCAAGGGCCGATGGTGCCCGAGGCCCCCGCACG
Found at i:9386 original size:128 final size:128
Alignment explanation
Indices: 9165--10171 Score: 884
Period size: 128 Copynumber: 8.0 Consensus size: 128
9155 GCCACCAAGG
*
9165 TGCCGATGGTGCCCGAGGCTCCCG--C-A-C--G-ACCAAGG-GCCGATGGTGGC-CGAGGCCCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACCAAGGTGCCGATGGT-GCTCGAGGCTCC
* * * * * *
9221 CGCACGACCAAGGGCCTATTTTACCGATGGTGCCCGAGCCTCTCGCATGACCAAGGGTCTAGGT
65 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGT
* * *
9285 TGCCGATGGTGCCCGAGGTTCCGGCAC-ATCCAAGCACCAAGGTGTCGATGGTGCTCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCC
* * **
9349 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGTCCGAGGCTCCCGCAC-ATCCCAGCACCTAGG-
65 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGT
* * ** *** *
9412 AGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACC-AAGGTGCCGATGGTGCTCGAGGCTCC
* * *
9477 CGCACGACCAAGGGCTTAGTTTGCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGT
65 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGT
* * * * *
9541 TGTCGATGGTGCGCGAGGTTCTCGGAC-ATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCC
* ** * * * ** *
9605 CGCACG-CCAAGGGCCTAGGTTGCCGACAGTGTCCGAGGCTCCCGC-CCATCATAGCACCGAGG-
65 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCA-AGGGCCTAGGT
* ** * *
9667 TGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTG-TCCGAGGCTC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACCAAG-GTGCCGATGGTGCT-CGAGGCTC
* * * *
9731 CCGCACGACCAAGGGCCTATTTTGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCTTAGTT
64 CCGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGT
* * ** * * * * *
9796 TGCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCT
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACCAAGG-TGCCGATGGTGCTCGAGGCTCC
** * * *
9861 CGCAC-ATCCAAGCACCAAG-GTGCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGT
65 CGCACGA-CCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGT
** * * * * *
9924 TGCCGACAGTGTCCGAGGCTCCCGCAC-ATCATAGCACCGAGGTGCCGATGGTGCCCGAGGCTAC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCA-AGCACCAAGGTGCCGATGGTGCTCGAGGCTCC
* * ** *
9988 CGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCCGCAC-ATCGAAGCACCGAGG-
65 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGT
* ** ** ** * *
10051 TGCCGATGGCGCCCGAGG---CC-CAATACCAAGGGCTTAGTTTGCCGATGGTG-TCCGGGGCTC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACCAAG-GTGCCGATGGTGCT-CGAGGCTC
* * ** *
10111 CTGCAC-ATCCTAGCACC-AGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTA
64 CCGCACGA-CCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTA
10172 TGCTACCGGA
Statistics
Matches: 712, Mismatches: 141, Indels: 65
0.78 0.15 0.07
Matches are distributed among these distances:
120 22 0.03
122 2 0.00
123 46 0.06
124 35 0.05
126 36 0.05
127 155 0.22
128 316 0.44
129 100 0.14
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (128 bp):
TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCC
GCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGT
Found at i:9729 original size:298 final size:298
Alignment explanation
Indices: 9370--10035 Score: 1156
Period size: 298 Copynumber: 2.2 Consensus size: 298
9360 GGGCCTAGTT
* * ** ** *
9370 TGCCGATGGTGTCCGAGGCTCCCGCAC-ATCCCAGCACCTAGGAGCCGATGGTGGCCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGTTGCCGATGGTGCCCGAGGCTCC
9434 CGCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTT
65 CGCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTT
* *
9499 GCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGTCGATGGTGCGCGAGGTTCTC
130 GCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCTC
*
9564 GGACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACG-CCAAGGGCCTAGGTTGC
195 GCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGC
*
9628 CGACAGTGTCCGAGGCTCCCGCCCATCATAGCACCGAGG
260 CGACAGTGTCCGAGGCTCCCGCACATCATAGCACCGAGG
* *
9667 TGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGTCCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAG-TTGCCGATGGTGCCCGAGGCTCC
*
9732 CGCACGACCAAGGGCCTATTTTGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCTTAGTTT
65 CGCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTT
9797 GCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCTC
130 GCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCTC
9862 GCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGC
195 GCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGC
9927 CGACAGTGTCCGAGGCTCCCGCACATCATAGCACCGAGG
260 CGACAGTGTCCGAGGCTCCCGCACATCATAGCACCGAGG
*
9966 TGCCGATGGTGCCCGAGGCTACCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTA-GTTGCCGATGGTGCCCGAGGCTCC
10031 CGCAC
65 CGCAC
10036 ATCGAAGCAC
Statistics
Matches: 350, Mismatches: 15, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
297 35 0.10
298 194 0.55
299 120 0.34
300 1 0.00
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (298 bp):
TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGTTGCCGATGGTGCCCGAGGCTCCC
GCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTTG
CCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCTCG
CACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCC
GACAGTGTCCGAGGCTCCCGCACATCATAGCACCGAGG
Found at i:10036 original size:85 final size:84
Alignment explanation
Indices: 9200--10171 Score: 863
Period size: 85 Copynumber: 11.5 Consensus size: 84
9190 ACGACCAAGG
* * ** * * *
9200 GCCGATGGTGGCCGAGGCCCCCGCACGACCAAGGGCCTATTTTACCGATGGTGCCCGAGCCTCTC
1 GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCC
* *
9265 GCATGACCAAGGGTCTAGGTT
66 GCA-CACCAAGGGCCTAGG-T
* * ** * * *
9286 GCCGATGGTGCCCGAGGTTCCGGCAC-ATCCAAGCACCAAGG-TGTCGATGGTGCTCGAGGCTCC
1 GCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCC
*
9349 CGCACGACCAAGGGCCTAGTTT
65 CGCAC-ACCAAGGGCCTAG-GT
* * ** * *
9371 GCCGATGGTGTCCGAGGCTCCCGCAC-ATCCCAGCACCTAGG-AGCCGATGGTGGCCGAGGCTCC
1 GCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCC
**
9434 CGCACGACCAAGGGCCTATTTT
65 CGCAC-ACCAAGGGCCTA-GGT
* * * *
9456 GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTTGCCGATGGTGCCCGAGCCTCTC
1 GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCC
9521 GCACGACCAAGGGCCTAGGTT
66 GCAC-ACCAAGGGCCTAGG-T
* * * * * ** * *
9542 GTCGATGGTGCGCGAGGTTCTCGGAC-ATCCAAGCACCAAGG-TGCCGATGGTGCTCGAGGCTCC
1 GCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCC
*
9605 CGCACGCCAAGGGCCTAGGTT
65 CGCACACCAAGGGCCTAGG-T
** * * * ** * *
9626 GCCGACAGTGTCCGAGGCTCCCGC-CCATCATAGCACCGAGG-TGCCGATGGTGGCCGAGGCTCC
1 GCCGATGGTGCCCGAGGCTCCCGCACGACCA-AGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCC
*
9689 CGCACGACCAAGGGCCTAGTTT
65 CGCAC-ACCAAGGGCCTAG-GT
* ** *
9711 GCCGATGGTGTCCGAGGCTCCCGCACGACCAAGGGCCTATTTTGCCGATGGTGGCCGAGGCTCCC
1 GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCC
* *
9776 GCACGACCAAGGGCTTAGTTT
66 GCAC-ACCAAGGGCCTAG-GT
* * * * * *
9797 GCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCTC
1 GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCC
** *
9862 GCACATCCAAGCACCAAGGT
66 GCACA-CCAAGGGCCTAGGT
* ** *
9882 GCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGACAGTGTCCGAGGCTCCC
1 GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCC
* ** *
9947 GCACATCATAGCACCGAGGT
66 GCACACCA-AGGGCCTAGGT
*
9967 GCCGATGGTGCCCGAGGCTACCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCC
1 GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCC
* ** *
10032 GCACATCGAAGCACCGAGGT
66 GCACA-CCAAGGGCCTAGGT
* ** * * * * *
10052 GCCGATGGCGCCCGAGG---CC-CAATACCAAGGGCTTAGTTTGCCGATGGTGTCCGGGGCTCCT
1 GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCC
* **
10113 GCACATCCTAGCACC-AGGTT
66 GCACA-CCAAGGGCCTAGG-T
10133 GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTA
1 GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTA
10172 TGCTACCGGA
Statistics
Matches: 739, Mismatches: 125, Indels: 45
0.81 0.14 0.05
Matches are distributed among these distances:
80 3 0.00
81 65 0.09
82 2 0.00
83 3 0.00
84 70 0.09
85 384 0.52
86 212 0.29
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (84 bp):
GCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCC
GCACACCAAGGGCCTAGGT
Found at i:10252 original size:24 final size:24
Alignment explanation
Indices: 10176--10254 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
10166 GGCCTATGCT
* *
10176 ACCGGAACGGTTCACCGGAGCACC
1 ACCGGGACGGTTCGCCGGAGCACC
10200 GA-CGGGACGGTTCGCCGGAGCACC
1 -ACCGGGACGGTTCGCCGGAGCACC
* *
10224 GCCGGGACGGATCGCCGGAGCACC
1 ACCGGGACGGTTCGCCGGAGCACC
10248 ACCGGGA
1 ACCGGGA
10255 ACCTAACCGG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
24 47 0.98
25 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.38, T:0.06
Consensus pattern (24 bp):
ACCGGGACGGTTCGCCGGAGCACC
Found at i:10518 original size:42 final size:42
Alignment explanation
Indices: 10463--10754 Score: 335
Period size: 42 Copynumber: 6.9 Consensus size: 42
10453 ACTTTAGCTT
* *
10463 TGGTGCT-GAAGGCTCCCGCTCATCCATGCACCAAGGTGCCGA
1 TGGTGCTCG-AGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
10505 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
*
10547 TGGTGCTCGAGGCTCCCGCACAT-CATAGCACCGAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCA-AGCACCAAGGTGCCGA
* ** * * *
10589 TGGT-CTCCGAGGCTCCC-CACAACCAAGGGCCTAGTTTGCCGG
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAG-GTGCCGA
* *
10631 TGGTG-TCCGATGCTCCCGCACATCCATGCACCAAGGTGCCGA
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
* *
10673 TGGTGCTCGAGGCTCCCGCACATCCAAGCATCAAGGTTACCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGG-TGCCGA
* *
10716 TGGTGGCT-GAGGCTCCCACACATCCGAGCCACCAAGGTG
1 TGGT-GCTCGAGGCTCCCGCACATCCAAG-CACCAAGGTG
10755 ATGGAGGCTC
Statistics
Matches: 214, Mismatches: 25, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
41 14 0.07
42 148 0.69
43 42 0.20
44 10 0.05
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.17
Consensus pattern (42 bp):
TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
Found at i:14235 original size:48 final size:48
Alignment explanation
Indices: 14153--14246 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
14143 TTTCTTGGCT
* * *
14153 TAAAAATGCCTAAGTCAGCCTAATTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAATTTCCAACAATAAAGGATTCAACCG
*
14201 TAAAAACGCCTAAGTTAG-CTCAA-TTCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AATTTC-CAACAATAAAGGATTCAAC
14247 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 5 0.12
48 35 0.88
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAATTTCCAACAATAAAGGATTCAACCG
Found at i:19263 original size:47 final size:48
Alignment explanation
Indices: 19172--19264 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 48
19162 TTTCTTGGCT
* * *
19172 TAAAAATGCCTAAGTCAGCCTAATTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAATTTCCAACAATAAAGGATTCAACCG
19220 TAAAAACGCCTAAGT-AG-CTCAA-TTCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AATTTC-CAACAATAAAGGATTCAAC
19265 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
46 5 0.12
47 21 0.52
48 14 0.35
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.23
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAATTTCCAACAATAAAGGATTCAACCG
Found at i:24356 original size:43 final size:43
Alignment explanation
Indices: 24286--24378 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 43
24276 TCTTCTTTAG
*
24286 CCCGCACATCCCAGGCACCAAGGTGCCGATGGGTGCCCGAGGCT
1 CCCGCACATCCCAAGCACCAAGGTGCCGAT-GGTGCCCGAGGCT
* *
24330 CCCGCACAT-CCAAGCACCAAGTTGCCGATGGTGTCCGAGGCT
1 CCCGCACATCCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCT
24372 CCCGCAC
1 CCCGCAC
24379 CTCCTAGCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 19 0.41
43 18 0.39
44 9 0.20
ACGTcount: A:0.19, C:0.40, G:0.28, T:0.13
Consensus pattern (43 bp):
CCCGCACATCCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCT
Found at i:24400 original size:25 final size:25
Alignment explanation
Indices: 24366--24414 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
24356 GATGGTGTCC
* *
24366 GAGGCTCCCGCACCTCCTAGCCACT
1 GAGGCTCCCGCACATCCGAGCCACT
24391 GAGGCTCCCGCACATCCGAGCCAC
1 GAGGCTCCCGCACATCCGAGCCAC
24415 CAAGGTGCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (25 bp):
GAGGCTCCCGCACATCCGAGCCACT
Found at i:24439 original size:43 final size:42
Alignment explanation
Indices: 24391--25428 Score: 849
Period size: 43 Copynumber: 24.6 Consensus size: 42
24381 CCTAGCCACT
* * *
24391 GAGGCTCCCGCAC-ATCCGAGCCACCAAGGTGCCGATGGTGCCC
1 GAGGCTCCCGCACGA-CCAAG-CGCCTAGGTGCCGATGGTGCCC
*
24434 GAGGCTCCCGCACGACC-A------AGG-GCCGATGGTGGCC
1 GAGGCTCCCGCACGACCAAGCGCCTAGGTGCCGATGGTGCCC
* * ** *
24468 GAGGCCCCCGCACGACCAAGGGCCTATTTTACCGATGGTGCCC
1 GAGGCTCCCGCACGACCAAGCGCCTA-GGTGCCGATGGTGCCC
* * * *
24511 GAGCCTCTCGCACGACCAAGGGTCTAGGTTGCCGATGGTGCCC
1 GAGGCTCCCGCACGACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * * * * *
24554 GAGGTTCCGGCAC-ATCCAAGCACCAAGGTGTCGATGGTGCTC
1 GAGGCTCCCGCACGA-CCAAGCGCCTAGGTGCCGATGGTGCCC
* * *
24596 GAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGTCC
1 GAGGCTCCCGCACGACCAAGCGCCTAG-GTGCCGATGGTGCCC
* * * *
24639 GAGGCTCCCGCAC-ATCCCAGCACCTAGGAGCCGATGGTGGCC
1 GAGGCTCCCGCACGA-CCAAGCGCCTAGGTGCCGATGGTGCCC
* **
24681 GAGGCTCCCGCACGACCAAGGGCCTATTTTGCCGATGGTGCCC
1 GAGGCTCCCGCACGACCAAGCGCCTA-GGTGCCGATGGTGCCC
* * *
24724 GAGGCTCCCGCACGACCAAGGGCTTAGTTTGCCGATGGTGCCC
1 GAGGCTCCCGCACGACCAAGCGCCTAG-GTGCCGATGGTGCCC
* * * * *
24767 GAGCCTCTCGCACGACCAAGGGCCTAGGTTGTCGATGGTGCGC
1 GAGGCTCCCGCACGACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * * * * *
24810 GAGGTTCTCGGAC-ATCCAAGCACCAAGGTGCCGATGGTGCTC
1 GAGGCTCCCGCACGA-CCAAGCGCCTAGGTGCCGATGGTGCCC
* ** *
24852 GAGGCTCCCGCACG-CCAAGGGCCTAGGTTGCCGACAGTGTCC
1 GAGGCTCCCGCACGACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * * * *
24894 GAGGCTCCCGC-CCATCATAGCACCGAGGTGCCGATGGTGGCC
1 GAGGCTCCCGCACGACCA-AGCGCCTAGGTGCCGATGGTGCCC
* * *
24936 GAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGTCC
1 GAGGCTCCCGCACGACCAAGCGCCTAG-GTGCCGATGGTGCCC
* ** *
24979 GAGGCTCCCGCACGACCAAGGGCCTATTTTGCCGATGGTGGCC
1 GAGGCTCCCGCACGACCAAGCGCCTA-GGTGCCGATGGTGCCC
* * *
25022 GAGGCTCCCGCACGACCAAGGGCTTAGTTTGCCGATGGTGCCC
1 GAGGCTCCCGCACGACCAAGCGCCTAG-GTGCCGATGGTGCCC
* * * * *
25065 GAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGC
1 GAGGCTCCCGCACGACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * * * *
25108 GAGGTTCTCGCAC-ATCCAAGCACCAAGGTGCCGATGGTGCTC
1 GAGGCTCCCGCACGA-CCAAGCGCCTAGGTGCCGATGGTGCCC
* ** *
25150 GAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGACAGTGTCC
1 GAGGCTCCCGCACGACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * *
25193 GAGGCTCCCGCAC-ATCATAGCACCGAGGTGCCGATGGTGCCC
1 GAGGCTCCCGCACGACCA-AGCGCCTAGGTGCCGATGGTGCCC
* *
25235 GAGGCTACCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCC
1 GAGGCTCCCGCACGACCAAGCGCCTAGG-TGCCGATGGTGCCC
* * * *
25278 GAGGCTCCCGCAC-ATCGAAGCACCGAGGTGCCGATGGCGCCC
1 GAGGCTCCCGCACGA-CCAAGCGCCTAGGTGCCGATGGTGCCC
* * * * *
25320 GAGGCT-CCGCA-TACCAAGGGCTTAGTTTGCCGATGGTGTCC
1 GAGGCTCCCGCACGACCAAGCGCCTAG-GTGCCGATGGTGCCC
* * * *
25361 GGGGCTCCTGCAC-ATCCTAGCACC-AGGTTGCCGATGGTGCCC
1 GAGGCTCCCGCACGA-CCAAGCGCCTAGG-TGCCGATGGTGCCC
*
25403 GAGGCTCCCGCACGACCAAGGGCCTA
1 GAGGCTCCCGCACGACCAAGCGCCTA
25429 TGCTACCGGA
Statistics
Matches: 799, Mismatches: 152, Indels: 88
0.77 0.15 0.08
Matches are distributed among these distances:
34 28 0.04
35 4 0.01
40 7 0.01
41 35 0.04
42 266 0.33
43 458 0.57
44 1 0.00
ACGTcount: A:0.18, C:0.34, G:0.32, T:0.16
Consensus pattern (42 bp):
GAGGCTCCCGCACGACCAAGCGCCTAGGTGCCGATGGTGCCC
Found at i:24461 original size:34 final size:34
Alignment explanation
Indices: 24413--24491 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
24403 CATCCGAGCC
*
24413 ACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACG
1 ACCAAGG-GCCGATGGTGCCCGAGGCCCCCGCACG
*
24448 ACCAAGGGCCGATGGTGGCCGAGGCCCCCGCACG
1 ACCAAGGGCCGATGGTGCCCGAGGCCCCCGCACG
24482 ACCAAGGGCC
1 ACCAAGGGCC
24492 TATTTTACCG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 35 0.83
35 7 0.17
ACGTcount: A:0.19, C:0.38, G:0.35, T:0.08
Consensus pattern (34 bp):
ACCAAGGGCCGATGGTGCCCGAGGCCCCCGCACG
Found at i:24615 original size:85 final size:84
Alignment explanation
Indices: 24499--25415 Score: 725
Period size: 85 Copynumber: 10.8 Consensus size: 84
24489 GCCTATTTTA
* * * * * *
24499 CCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGTCTAGGTTGCCGATGGTGCCCGAGGTTCCGG
1 CCGATGGTG-CCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCG
24564 CACATCCAAGCACCAAGGTG
65 CACATCCAAGCACCAAGGTG
* *
24584 TCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGTCCGAGGCTCCCG
1 CCGATGGTGC-CGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCG
* * *
24649 CACATCCCAGCACCTAGGAG
65 CACATCCAAGCACCAAGGTG
*
24669 CCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCCCG
1 CCGATGGT-GCCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCG
** ** *
24734 CACGA-CCAAGGGCTTAGTTTG
65 CAC-ATCCAAGCACCAAG-GTG
* * * * * * *
24755 CCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGTCGATGGTGCGCGAGGTTCTCG
1 CCGATGGTG-CCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCG
*
24820 GACATCCAAGCACCAAGGTG
65 CACATCCAAGCACCAAGGTG
* ** *
24840 CCGATGGTGCTCGAGGCTCCCGCACG-CCAAGGGCCTAGGTTGCCGACAGTGTCCGAGGCTCCCG
1 CCGATGGTGC-CGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCG
* *
24904 CCCAT-CATAGCACCGAGGTG
65 CACATCCA-AGCACCAAGGTG
*
24924 CCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGTCCGAGGCTCCCG
1 CCGATGGT-GCCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCG
** ***
24989 CACGA-CCAAGGGCCTATTTTG
65 CAC-ATCCAAGCACC-AAGGTG
* * *
25010 CCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCTTAGTTTGCCGATGGTGCCCGAGCCTCTCG
1 CCGATGGT-GCCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCG
** *
25075 CACGA-CCAAGGGCCTAGGTTG
65 CAC-ATCCAAGCACCAAGG-TG
* * * ** * * *
25096 CCGATGGTACGCGAGGTTCTCGCAC-ATCCAAGCACCAAG-GTGCCGATGGTGCTCGAGGCTCCC
1 CCGATGGTGC-CGAGGCTCCCGCACGA-CCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCC
** *
25159 GCACGA-CCAAGGGCCTAGGTTG
64 GCAC-ATCCAAGCACCAAGG-TG
** * ** * * *
25181 CCGACAGTGTCCGAGGCTCCCGCAC-ATCATAGCACCGAG-GTGCCGATGGTGCCCGAGGCTACC
1 CCGATGGTG-CCGAGGCTCCCGCACGACCA-AGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCC
** *
25244 GCACGA-CCAAGGGCCTAGGTTG
64 GCAC-ATCCAAGCACCAAGG-TG
* ** * * *
25266 CCGATGGTGCCCGAGGCTCCCGCAC-ATCGAAGCACCGAG-GTGCCGATGGCGCCCGAGGCT-CC
1 CCGATGGTG-CCGAGGCTCCCGCACGA-CCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCC
* ** ** *
25328 GCATA-CCAAGGGCTTAGTTTG
64 GCACATCCAAGCACCAAG-GTG
* * * ** *
25349 CCGATGGTGTCCGGGGCTCCTGCAC-ATCCTAGCACC-AGGTTGCCGATGGTGCCCGAGGCTCCC
1 CCGATGGTG-CCGAGGCTCCCGCACGA-CCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCC
25412 GCAC
64 GCAC
25416 GACCAAGGGC
Statistics
Matches: 709, Mismatches: 101, Indels: 45
0.83 0.12 0.05
Matches are distributed among these distances:
82 2 0.00
83 66 0.09
84 82 0.12
85 378 0.53
86 181 0.26
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (84 bp):
CCGATGGTGCCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGC
ACATCCAAGCACCAAGGTG
Found at i:24619 original size:128 final size:128
Alignment explanation
Indices: 24420--25428 Score: 920
Period size: 128 Copynumber: 8.0 Consensus size: 128
24410 GCCACCAAGG
*
24420 TGCCGATGGTGCCCGAGGCTCCCG--C-A-C--G-ACCAAGG-GCCGATGGTGGC-CGAGGCCCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACCAAGGTGCCGATGGT-GCTCGAGGCTCC
* * * * *
24476 CGCACGACCAAGGGCCTATTTTACCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGTCTAGGT
65 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGT
* * *
24540 TGCCGATGGTGCCCGAGGTTCCGGCAC-ATCCAAGCACCAAGGTGTCGATGGTGCTCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCC
* * **
24604 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGTCCGAGGCTCCCGCAC-ATCCCAGCACCTAGG-
65 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGT
* * ** *** *
24667 AGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACC-AAGGTGCCGATGGTGCTCGAGGCTCC
* * *
24732 CGCACGACCAAGGGCTTAGTTTGCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGT
65 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGT
* * * * *
24796 TGTCGATGGTGCGCGAGGTTCTCGGAC-ATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCC
* ** * * * ** *
24860 CGCACG-CCAAGGGCCTAGGTTGCCGACAGTGTCCGAGGCTCCCGC-CCATCATAGCACCGAGG-
65 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCA-AGGGCCTAGGT
* ** * *
24922 TGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTG-TCCGAGGCTC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACCAAG-GTGCCGATGGTGCT-CGAGGCTC
* * * *
24986 CCGCACGACCAAGGGCCTATTTTGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCTTAGTT
64 CCGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGT
* * ** * * * * *
25051 TGCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCT
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACCAAGG-TGCCGATGGTGCTCGAGGCTCC
** * * *
25116 CGCAC-ATCCAAGCACCAAG-GTGCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGT
65 CGCACGA-CCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGT
** * * * * *
25179 TGCCGACAGTGTCCGAGGCTCCCGCAC-ATCATAGCACCGAGGTGCCGATGGTGCCCGAGGCTAC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCA-AGCACCAAGGTGCCGATGGTGCTCGAGGCTCC
* * ** *
25243 CGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCCCGCAC-ATCGAAGCACCGAGG-
65 CGCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGT
* * ** ** * *
25306 TGCCGATGGCGCCCGAGGCT-CCGCA-TACCAAGGGCTTAGTTTGCCGATGGTG-TCCGGGGCTC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACCAAG-GTGCCGATGGTGCT-CGAGGCTC
* * ** *
25368 CTGCAC-ATCCTAGCACC-AGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTA
64 CCGCACGA-CCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTA
25429 TGCTACCGGA
Statistics
Matches: 716, Mismatches: 139, Indels: 63
0.78 0.15 0.07
Matches are distributed among these distances:
120 22 0.03
122 2 0.00
124 1 0.00
125 44 0.06
126 73 0.10
127 157 0.22
128 317 0.44
129 100 0.14
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (128 bp):
TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCC
GCACGACCAAGGGCCTAGTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGT
Found at i:24984 original size:298 final size:298
Alignment explanation
Indices: 24625--25357 Score: 1181
Period size: 298 Copynumber: 2.5 Consensus size: 298
24615 GGGCCTAGTT
* * ** ** *
24625 TGCCGATGGTGTCCGAGGCTCCCGCAC-ATCCCAGCACCTAGGAGCCGATGGTGGCCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGTTGCCGATGGTGCCCGAGGCTCC
24689 CGCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTT
65 CGCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTT
* *
24754 GCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGTCGATGGTGCGCGAGGTTCTC
130 GCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCTC
*
24819 GGACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACG-CCAAGGGCCTAGGTTGC
195 GCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGC
*
24883 CGACAGTGTCCGAGGCTCCCGCCCATCATAGCACCGAGG
260 CGACAGTGTCCGAGGCTCCCGCACATCATAGCACCGAGG
* *
24922 TGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCCTAGTTTGCCGATGGTGTCCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAG-TTGCCGATGGTGCCCGAGGCTCC
*
24987 CGCACGACCAAGGGCCTATTTTGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGCTTAGTTT
65 CGCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTT
25052 GCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCTC
130 GCCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCTC
25117 GCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGC
195 GCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGC
25182 CGACAGTGTCCGAGGCTCCCGCACATCATAGCACCGAGG
260 CGACAGTGTCCGAGGCTCCCGCACATCATAGCACCGAGG
*
25221 TGCCGATGGTGCCCGAGGCTACCGCACGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTA-GTTGCCGATGGTGCCCGAGGCTCC
* ** * ** * *
25286 CGCAC-ATCGAAGCACCGA-GGTGCCGATGGCGCCCGAGGCT-CCGCA-TACCAAGGGCTTAGTT
65 CGCACGA-CCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTT
25347 TGCCGATGGTG
129 TGCCGATGGTG
25358 TCCGGGGCTC
Statistics
Matches: 407, Mismatches: 24, Indels: 11
0.92 0.05 0.02
Matches are distributed among these distances:
296 26 0.06
297 40 0.10
298 213 0.52
299 127 0.31
300 1 0.00
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (298 bp):
TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGTTGCCGATGGTGCCCGAGGCTCCC
GCACGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTTG
CCGATGGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTACGCGAGGTTCTCG
CACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCC
GACAGTGTCCGAGGCTCCCGCACATCATAGCACCGAGG
Found at i:25509 original size:24 final size:24
Alignment explanation
Indices: 25433--25511 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
25423 GGCCTATGCT
* *
25433 ACCGGAACGGTTCACCGGAGCACC
1 ACCGGGACGGTTCGCCGGAGCACC
25457 GA-CGGGACGGTTCGCCGGAGCACC
1 -ACCGGGACGGTTCGCCGGAGCACC
* *
25481 GCCGGGACGGATCGCCGGAGCACC
1 ACCGGGACGGTTCGCCGGAGCACC
25505 ACCGGGA
1 ACCGGGA
25512 ACCTAACCGG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
24 47 0.98
25 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.38, T:0.06
Consensus pattern (24 bp):
ACCGGGACGGTTCGCCGGAGCACC
Found at i:25775 original size:42 final size:42
Alignment explanation
Indices: 25720--26011 Score: 335
Period size: 42 Copynumber: 6.9 Consensus size: 42
25710 ACTTTAGCTT
* *
25720 TGGTGCT-GAAGGCTCCCGCTCATCCATGCACCAAGGTGCCGA
1 TGGTGCTCG-AGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
25762 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
*
25804 TGGTGCTCGAGGCTCCCGCACAT-CATAGCACCGAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCA-AGCACCAAGGTGCCGA
* ** * * *
25846 TGGT-CTCCGAGGCTCCC-CACAACCAAGGGCCTAGTTTGCCGG
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAG-GTGCCGA
* *
25888 TGGTG-TCCGATGCTCCCGCACATCCATGCACCAAGGTGCCGA
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
* *
25930 TGGTGCTCGAGGCTCCCGCACATCCAAGCATCAAGGTTACCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGG-TGCCGA
* *
25973 TGGTGGCT-GAGGCTCCCACACATCCGAGCCACCAAGGTG
1 TGGT-GCTCGAGGCTCCCGCACATCCAAG-CACCAAGGTG
26012 ATGGAGGCTC
Statistics
Matches: 214, Mismatches: 25, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
41 14 0.07
42 148 0.69
43 42 0.20
44 10 0.05
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.17
Consensus pattern (42 bp):
TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
Found at i:38254 original size:18 final size:17
Alignment explanation
Indices: 38231--38264 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38221 TATTTCAATT
38231 TTTTAATAAAATGTAATC
1 TTTTAA-AAAATGTAATC
*
38249 TTTTAAACAATGTAAT
1 TTTTAAAAAATGTAAT
38265 GTGATTGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (17 bp):
TTTTAAAAAATGTAATC
Found at i:40049 original size:132 final size:132
Alignment explanation
Indices: 39811--40066 Score: 422
Period size: 132 Copynumber: 1.9 Consensus size: 132
39801 CGGTCTTACC
* * * *
39811 AAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTTGATCTGTTCCACTACTTTT
1 AAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTATTTGATCTATTCCACTACTGTT
* **
39876 TAAGAAGACATGATCTACAATCTTCAACCTATTCCATTGCTGTTTAGGGAGATAGGACTGGTGGC
66 TAAGAAGACATGATCTACAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTGGTGGC
39941 TT
131 TT
*
39943 AAATCTGCTTCCCTATTACCTTGGAAAGATAAGATTCACCGTATTTGATCTATTCCACTACTGTT
1 AAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTATTTGATCTATTCCACTACTGTT
* *
40008 TAGGGAGACATGATCTACAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACT
66 TAAGAAGACATGATCTACAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACT
40067 TACAATCTTT
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 114 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (132 bp):
AAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTATTTGATCTATTCCACTACTGTT
TAAGAAGACATGATCTACAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTGGTGGC
TT
Found at i:40057 original size:44 final size:44
Alignment explanation
Indices: 39992--40175 Score: 271
Period size: 44 Copynumber: 4.2 Consensus size: 44
39982 CGTATTTGAT
** * *
39992 CTATTCCACTACTGTTTAGGGAGACATGA-TCTACAATCTTCAAC
1 CTATTCCACTACTGTCCAGGGAGATAGGACT-TACAATCTTCAAC
* * **
40036 CTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTTAGT
1 CTATTCCACTACTGTCCAGGGAGATAGGACTTACAATCTTCAAC
40080 CTATTCCACTACTGTCCAGGGAGATAGGACTTACAATCTTCAAC
1 CTATTCCACTACTGTCCAGGGAGATAGGACTTACAATCTTCAAC
*
40124 CTATTCCACTACTGTCCCGGGAGATAGGACTTACAATCTTCAAC
1 CTATTCCACTACTGTCCAGGGAGATAGGACTTACAATCTTCAAC
40168 CTATTCCA
1 CTATTCCA
40176 ATGCGGTAGG
Statistics
Matches: 126, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
44 125 0.99
45 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (44 bp):
CTATTCCACTACTGTCCAGGGAGATAGGACTTACAATCTTCAAC
Found at i:42796 original size:72 final size:71
Alignment explanation
Indices: 42679--42821 Score: 241
Period size: 72 Copynumber: 2.0 Consensus size: 71
42669 TCTTTTCAAA
* * *
42679 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGATCTC
1 CTCAAGTTCTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTCGGCATGATC-C
42744 TTTTTTT
65 TTTTTTT
*
42751 CTCAAGTTCTAAACGATCTCGGGAATTAAGAAAAGATGGTGTCCTAACTTACTCGGCATGATCCT
1 CTCAAGTTCTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTCGGCATGATCCT
42816 TTTTTT
66 TTTTTT
42822 AAATCCGGGA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 8 0.12
72 59 0.88
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (71 bp):
CTCAAGTTCTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTCGGCATGATCCT
TTTTTT
Found at i:46518 original size:23 final size:24
Alignment explanation
Indices: 46463--46539 Score: 111
Period size: 24 Copynumber: 3.2 Consensus size: 24
46453 GCCTATGCTA
* *
46463 CCGGAACGGTTCACCGGAGCACCG
1 CCGGGACGGTTCGCCGGAGCACCG
*
46487 ACGGGACGGTTCGCCGGAGCA-CG
1 CCGGGACGGTTCGCCGGAGCACCG
*
46510 CCGGGACGGATCGCCGGAGCACCG
1 CCGGGACGGTTCGCCGGAGCACCG
46534 CCGGGA
1 CCGGGA
46540 ACCTAACCGG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 21 0.45
24 26 0.55
ACGTcount: A:0.18, C:0.35, G:0.40, T:0.06
Consensus pattern (24 bp):
CCGGGACGGTTCGCCGGAGCACCG
Found at i:46796 original size:42 final size:42
Alignment explanation
Indices: 46747--47038 Score: 342
Period size: 42 Copynumber: 6.9 Consensus size: 42
46737 ACTTTAGCTT
* * *
46747 TGGTGCTCAAGGCTCCCGCTCATCCATGCACCAAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
46789 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
*
46831 TGGTGCTCGAGGCTCCCGCACAT-CATAGCACCGAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCA-AGCACCAAGGTGCCGA
* ** * * *
46873 TGGT-CTCCGAGGCTCCC-CACAACCAAGGGCCTAGTTTGCCGG
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAG-GTGCCGA
* *
46915 TGGTG-TCCGATGCTCCCGCACATCCATGCACCAAGGTGCCGA
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
* *
46957 TGGTGCTCGAGGCTCCCGCACATCCAAGCATCAAGGTTACCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGG-TGCCGA
* *
47000 TGGTGGCT-GAGGCTCCCACACATCCGAGCCACCAAGGTG
1 TGGT-GCTCGAGGCTCCCGCACATCCAAG-CACCAAGGTG
47039 ATGGAGGCTC
Statistics
Matches: 214, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
41 14 0.07
42 149 0.70
43 41 0.19
44 10 0.05
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (42 bp):
TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
Done.