Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010302.1 Corchorus capsularis cultivar CVL-1 contig10323, whole genome shotgun sequence
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: 6774
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Found at i:136 original size:31 final size:31
Alignment explanation
Indices: 90--591 Score: 529
Period size: 31 Copynumber: 16.1 Consensus size: 31
80 AAAACCCGAA
*
90 AAGGCCATCGGCAAATGCCGACGCCAAGGCC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
* * * * *
121 ATGGGCATCGTCAAATGCCAACACCAAGACC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
* **
152 AAGGGCCATCAGCAAATGCCGACGCCAAGAAC
1 AAGGG-CATCGGCAAATGCCGACGCCAAGGCC
*
184 ATGGGCATCGGCAAATGCCGACGCCAAGGCC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
* ** *
215 AAGGGCATTGGCAAATGCCGAATCCAAGTCC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
* * *
246 AAGGGCATCGGCAAATACCTACGTCAAGGCC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
*** *
277 ATTTGCATCGGCAAATGCCGACGCCAAGGCA
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
*
308 AAGGGCATCAGCAAATGCCGACGCCAAGGCC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
* *
339 AAGGGCATCGGTAAATGCCGA-GCCTAGGGCC
1 AAGGGCATCGGCAAATGCCGACGCC-AAGGCC
* *
370 AAGGGTATCGGCAAATGCCGACGTCAAGGCC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
* * * * *
401 ATGAGCATCGGCAAATGTCGACACCAAGGAC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
* * * * * *
432 TAGGACCATCGACAAATGCTGATGCCAAGACC
1 AAGG-GCATCGGCAAATGCCGACGCCAAGGCC
* * * * *
464 ATGGGCATCGTCAAATGCCGACACCAAGACT
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
*
495 AAGGGCCATCGGCAAATGCCGACGCCAAGGGC
1 AAGGG-CATCGGCAAATGCCGACGCCAAGGCC
527 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCC
* * * *
558 AAGCGCCATCGGCAATTGCCGATGCCAATGCC
1 AAG-GGCATCGGCAAATGCCGACGCCAAGGCC
590 AA
1 AA
592 AGAGGCAAGG
Statistics
Matches: 381, Mismatches: 84, Indels: 11
0.80 0.18 0.02
Matches are distributed among these distances:
30 3 0.01
31 278 0.73
32 100 0.26
ACGTcount: A:0.31, C:0.30, G:0.27, T:0.12
Consensus pattern (31 bp):
AAGGGCATCGGCAAATGCCGACGCCAAGGCC
Found at i:172 original size:63 final size:62
Alignment explanation
Indices: 90--746 Score: 561
Period size: 63 Copynumber: 10.5 Consensus size: 62
80 AAAACCCGAA
* * * * * *
90 AAGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCGTCAAATGCCAACACCAAGACC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCC
* ** *
152 AAGGGCCATCAGCAAATGCCGACGCCAAGAACATGGGCATCGGCAAATGCCGACGCCAAGGCC
1 AAGGG-CATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCC
* ** * * * *
215 AAGGGCATTGGCAAATGCCGAATCCAAGTCCAAGGGCATCGGCAAATACCTACGTCAAGGCC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCC
*** * *
277 ATTTGCATCGGCAAATGCCGACGCCAAGGCAAAGGGCATCAGCAAATGCCGACGCCAAGGCC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCC
* * * *
339 AAGGGCATCGGTAAATGCCGA-GCCTAGGGCCAAGGGTATCGGCAAATGCCGACGTCAAGGCC
1 AAGGGCATCGGCAAATGCCGACGCC-AAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCC
* * * * * * * * * * *
401 ATGAGCATCGGCAAATGTCGACACCAAGGACTAGGACCATCGACAAATGCTGATGCCAAGACC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGG-GCATCGGCAAATGCCGACGCCAAGGCC
* * * * * *
464 ATGGGCATCGTCAAATGCCGACACCAAGACTAAGGGCCATCGGCAAATGCCGACGCCAAGGGC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGG-CATCGGCAAATGCCGACGCCAAGGCC
* * * *
527 AAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGCGCCATCGGCAATTGCCGATGCCAATGCC
1 AAGGGCATCGGCAAATGCCGACGCCAAGGCCAAG-GGCATCGGCAAATGCCGACGCCAAGGCC
* * * * * ** * * ** * * **
590 AAAGAGGCA-AGGGACAT--C-A-TCAAATTCCGACGCAATCGGCAAATGCCGATGCCAATGAA
1 -AAG-GGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCC
* * * *
649 ACAGGCCATCGGCAAATGCCGACACCAAGGCCATGGGCATCGGCAAATGCCGACTCCAAGGCC
1 A-AGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCC
* * * *
712 ATGGGCCATCGGCAAATGCTGATGCCAACGCCAAG
1 AAGGG-CATCGGCAAATGCCGACGCCAAGGCCAAG
747 TGGACTAGCT
Statistics
Matches: 465, Mismatches: 115, Indels: 29
0.76 0.19 0.05
Matches are distributed among these distances:
58 4 0.01
59 31 0.07
60 6 0.01
61 5 0.01
62 178 0.38
63 228 0.49
64 9 0.02
65 4 0.01
ACGTcount: A:0.31, C:0.30, G:0.27, T:0.12
Consensus pattern (62 bp):
AAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCC
Found at i:660 original size:32 final size:30
Alignment explanation
Indices: 624--739 Score: 99
Period size: 32 Copynumber: 3.7 Consensus size: 30
614 TTCCGACGCA
624 ATCGGCAAATGCCGATGCCAATGAAACAGGCC
1 ATCGGCAAATGCCGATGCCAA-G-AACAGGCC
** ** *
656 ATCGGCAAATGCCGACACCAAGGCCATGGGC
1 ATCGGCAAATGCCGATGCCAAGAACA-GGCC
**
687 ATCGGCAAATGCCGACT-CCAAGGCCATGGGCC
1 ATCGGCAAATGCCGA-TGCCAAGAACA--GGCC
*
719 ATCGGCAAATGCTGATGCCAA
1 ATCGGCAAATGCCGATGCCAA
740 CGCCAAGTGG
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
30 2 0.03
31 29 0.41
32 40 0.56
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.13
Consensus pattern (30 bp):
ATCGGCAAATGCCGATGCCAAGAACAGGCC
Found at i:662 original size:280 final size:277
Alignment explanation
Indices: 87--739 Score: 701
Period size: 280 Copynumber: 2.3 Consensus size: 277
77 ATCAAAACCC
* *
87 GAAA-AGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCGTCAAATGCCAACACCAA-GA
1 GAAACAGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACACCAAGGA
* * * *
150 CCAAGGGCCATC-AGCAAATGCCGACGCCAAGAACATGGGCATCGGCAAATGCCGACGCCAAGGC
66 -CAAGGGCCATCGA-CAAATGCTGATGCCAAGAACATGGGCATCGGCAAATGCCGACACCAAGAC
* * * * * *
214 CAAGGGCATTGGCAAATGCCGAATCCAAGTCCAAGGGCATCGGCAAATACCTACGTCAAGGCCAT
129 CAAGGGCATCGGCAAATGCCGAAGCCAAGGCCAAGGGCATCGGCAAATACCGACGCCAAGGCCAA
** * * *
279 TTGCATCGGCAAATGCCGACGCCAAGGCAAAGGGCATCAGCAAATGCCGACGCCAAGGCCAAGGG
194 GCGCATCGGCAAATGCCGACGCCAAGCCAAAGGGCA-CAGCAAAT-CCGACGCAAAGGCCAAGCG
* *
344 CATCGGTAAATGCCGAGCCTA
257 CATCGGCAAATGCCGAGCCAA
*** ** * * *
365 GGGCCAAGGGTATCGGCAAATGCCGACGTCAAGGCCATGAGCATCGGCAAATGTCGACACCAAGG
1 GAAAC-AGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACACCAAGG
* * * * *
430 ACTAGGACCATCGACAAATGCTGATGCCAAGACCATGGGCATCGTCAAATGCCGACACCAAGACT
65 ACAAGGGCCATCGACAAATGCTGATGCCAAGAACATGGGCATCGGCAAATGCCGACACCAAGACC
* * *
495 AAGGGCCATCGGCAAATGCCGACGCCAAGGGCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAA
130 AAGGG-CATCGGCAAATGCCGAAGCCAAGGCCAAGGGCATCGGCAAATACCGACGCCAAGGCCAA
* * * * * ** *
560 GCGCCATCGGCAATTGCCGATGCCAATGCCAAAGAGGCA-AGGGACAT-C-A-TCAAATTCCGA-
194 GCG-CATCGGCAAATGCCGACGCCAA-GCCAAAG-GGCACA-GCAAATCCGACGCAAAGGCCAAG
620 CGCAATCGGCAAATGCCGATGCCAA
255 CGC-ATCGGCAAATGCCGA-GCCAA
* *
645 TGAAACAGGCCATCGGCAAATGCCGACACCAAGGCCATGGGCATCGGCAAATGCCGACTCCAAGG
1 -GAAACAGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACACCAAGG
* * *
710 CCATGGGCCATCGGCAAATGCTGATGCCAA
65 ACAAGGGCCATCGACAAATGCTGATGCCAA
740 CGCCAAGTGG
Statistics
Matches: 305, Mismatches: 58, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
278 3 0.01
279 20 0.07
280 190 0.62
281 57 0.19
282 21 0.07
283 10 0.03
284 4 0.01
ACGTcount: A:0.31, C:0.30, G:0.27, T:0.12
Consensus pattern (277 bp):
GAAACAGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACACCAAGGA
CAAGGGCCATCGACAAATGCTGATGCCAAGAACATGGGCATCGGCAAATGCCGACACCAAGACCA
AGGGCATCGGCAAATGCCGAAGCCAAGGCCAAGGGCATCGGCAAATACCGACGCCAAGGCCAAGC
GCATCGGCAAATGCCGACGCCAAGCCAAAGGGCACAGCAAATCCGACGCAAAGGCCAAGCGCATC
GGCAAATGCCGAGCCAA
Found at i:677 original size:154 final size:153
Alignment explanation
Indices: 498--824 Score: 440
Period size: 154 Copynumber: 2.1 Consensus size: 153
488 CAAGACTAAG
* *
498 GGCCATCGGCAAATGCCGACGCCAAGGGCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGCG
1 GGCCATCGGCAAATGCCGACACCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGCG
* * * *
563 CCATCGGCAATTGCCGATGCCAATGCCAAAGAGG-CAAGGGACATCATCAAATTCCGACGCAATC
66 CCATCGGCAAATGCCGATGCCAACGCC-AAGAGGACAAGCGACATCATCAAATTCAGACGCAATC
* * *
627 GGCAAATGCCGATGCCAATGAAAC
130 GGCAAATACCGACGCCAAGGAAAC
* * * *
651 AGGCCATCGGCAAATGCCGACACCAAGGCCATGGGCATCGGCAAATGCCGACTCCAAGGCCATGG
1 -GGCCATCGGCAAATGCCGACACCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGC
* * * *
716 GCCATCGGCAAATGCTGATGCCAACGCCAAGTGGACTAGCTACATCATCAAATTCAGACGCAATC
65 GCCATCGGCAAATGCCGATGCCAACGCCAAGAGGACAAGCGACATCATCAAATTCAGACGCAATC
**
781 GGCAAATACCGACGCCAAGGCCAC
130 GGCAAATACCGACGCCAAGGAAAC
*
805 GTGCCATCAGCAAATGCCGA
1 G-GCCATCGGCAAATGCCGA
825 TGCCAATGCC
Statistics
Matches: 151, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
153 6 0.04
154 145 0.96
ACGTcount: A:0.31, C:0.31, G:0.26, T:0.12
Consensus pattern (153 bp):
GGCCATCGGCAAATGCCGACACCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGCG
CCATCGGCAAATGCCGATGCCAACGCCAAGAGGACAAGCGACATCATCAAATTCAGACGCAATCG
GCAAATACCGACGCCAAGGAAAC
Found at i:693 original size:31 final size:32
Alignment explanation
Indices: 652--730 Score: 142
Period size: 31 Copynumber: 2.5 Consensus size: 32
642 CAATGAAACA
652 GGCCATCGGCAAATGCCGACACCAAGGCCATG
1 GGCCATCGGCAAATGCCGACACCAAGGCCATG
*
684 GG-CATCGGCAAATGCCGACTCCAAGGCCATG
1 GGCCATCGGCAAATGCCGACACCAAGGCCATG
715 GGCCATCGGCAAATGC
1 GGCCATCGGCAAATGC
731 TGATGCCAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 30 0.67
32 15 0.33
ACGTcount: A:0.27, C:0.33, G:0.29, T:0.11
Consensus pattern (32 bp):
GGCCATCGGCAAATGCCGACACCAAGGCCATG
Found at i:799 original size:91 final size:92
Alignment explanation
Indices: 687--918 Score: 297
Period size: 91 Copynumber: 2.5 Consensus size: 92
677 GGCCATGGGC
* *
687 ATCGGCAAATGCCGACTCCAAGGCCATGGGCCATCGGCAAATGCTGATGCCAACGCCAA-GTGGA
1 ATCGGCAAATGCCGACGCCAAGGCCATGGGCCATCGGCAAATGCCGATGCCAACGCCAACGT-GA
* * *
751 CTAGCTACATCATCAAATTCAGAC-GCA
65 CAAGCGACATCATCAAAATCAGACAGCA
* * * * *
778 ATCGGCAAATACCGACGCCAAGGCCACGTGCCATCAGCAAATGCCGATGCCAATGCCAACGTGAC
1 ATCGGCAAATGCCGACGCCAAGGCCATGGGCCATCGGCAAATGCCGATGCCAACGCCAACGTGAC
* * *
843 AAGGGACATCATCAAAATCCGACAAGGCC
66 AAGCGACATCATCAAAATCAGAC-A-GCA
*
872 ATCGGCAAATGCCGACGACAAGGCCATGGGCCATCGGCAAATGCCGA
1 ATCGGCAAATGCCGACGCCAAGGCCATGGGCCATCGGCAAATGCCGA
919 CGACAAGGCA
Statistics
Matches: 119, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
91 73 0.61
92 2 0.02
94 44 0.37
ACGTcount: A:0.32, C:0.31, G:0.24, T:0.13
Consensus pattern (92 bp):
ATCGGCAAATGCCGACGCCAAGGCCATGGGCCATCGGCAAATGCCGATGCCAACGCCAACGTGAC
AAGCGACATCATCAAAATCAGACAGCA
Found at i:909 original size:32 final size:32
Alignment explanation
Indices: 868--949 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
858 AATCCGACAA
*
868 GGCCATCGGCAAATGCCGACGACAAGGCCATG
1 GGCCATCGGCAAATGCCGACGACAAGGCAATG
*
900 GGCCATCGGCAAATGCCGACGACAAGGCAATT
1 GGCCATCGGCAAATGCCGACGACAAGGCAATG
*
932 GGCCATC-GCAAATACCGA
1 GGCCATCGGCAAATGCCGA
950 TGCCACATCG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 10 0.21
32 37 0.79
ACGTcount: A:0.30, C:0.30, G:0.28, T:0.11
Consensus pattern (32 bp):
GGCCATCGGCAAATGCCGACGACAAGGCAATG
Found at i:1735 original size:31 final size:31
Alignment explanation
Indices: 1564--2119 Score: 619
Period size: 31 Copynumber: 17.7 Consensus size: 31
1554 TGCCAAGAAA
* * *
1564 CATCGGCAAATGCCGACGACAAGGACAAGGCTT
1 CATCGGCAAATGCCGACGCCAAGGCCAAGG--G
* *
1597 CATCGGCAAATGCCAACGCCAAGGCCTAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG
*
1628 CCATCGGCAAATGCCGACGCCAAGGCAAAGGG
1 -CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* * *
1660 CCATCGGCAAATGACGACGACAAGGCCATGGG
1 -CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* *
1692 CCATCGGCAAATGCCGACGCCAAGGCCATGCG
1 -CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* *
1724 CATTGGCAAATGCCGACGCAAAGGCCAAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* *
1755 CATCGGCAAATGCCGAAGCCAAGGCTAAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* * * *
1786 CATCGGCAAATACCGACGTCAAGGCCATGGA
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* * *
1817 CATCGGCAAATGCCGACGACGAGGCAAAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG
*
1848 CATCGGCAAATGACGACGCCAAGGCCAAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* * *
1879 CATCGGTAAATGCCGAAGCC-AGGACAAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* * *
1909 TATCGGCAAATGCCGACGTCAAGGCCATGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* **
1940 CATCGGCAAAGGCCGTTGCCAAGGCCAAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* *
1971 CCATCGGCAAATGCCGACGACAAGGCCACGGG
1 -CATCGGCAAATGCCGACGCCAAGGCCAAGGG
* * * * *
2003 CATCGTCAGATGCCGACACCAAGACTAAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG
*
2034 CCATCGGCAAATGCCGACGCCAAGGGCAAGGG
1 -CATCGGCAAATGCCGACGCCAAGGCCAAGGG
** *
2066 CATCGGCAAATGCCGACGGTAAGGCCAAGCGC
1 CATCGGCAAATGCCGACGCCAAGGCCAAG-GG
** *
2098 CATCGGTTAATGCCGATGCCAA
1 CATCGGCAAATGCCGACGCCAA
2120 TATCAAGGAG
Statistics
Matches: 436, Mismatches: 82, Indels: 11
0.82 0.16 0.02
Matches are distributed among these distances:
30 25 0.06
31 231 0.53
32 154 0.35
33 26 0.06
ACGTcount: A:0.30, C:0.29, G:0.31, T:0.10
Consensus pattern (31 bp):
CATCGGCAAATGCCGACGCCAAGGCCAAGGG
Found at i:1989 original size:63 final size:62
Alignment explanation
Indices: 1564--2119 Score: 612
Period size: 63 Copynumber: 8.9 Consensus size: 62
1554 TGCCAAGAAA
* * * *
1564 CATCGGCAAATGCCGACGACAAGGACAAGGCTTCATCGGCAAATGCCAACGCCAAGGCC-TAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGG--GCATCGGCAAATGCCGACGCCAAGGCCAT-GGG
* * *
1628 CCATCGGCAAATGCCGACGCCAAGGCAAAGGGCCATCGGCAAATGACGACGACAAGGCCATGGG
1 -CATCGGCAAATGCCGACGCCAAGGCCAAGGG-CATCGGCAAATGCCGACGCCAAGGCCATGGG
* * * * *
1692 CCATCGGCAAATGCCGACGCCAAGGCCATGCGCATTGGCAAATGCCGACGCAAAGGCCAAGGG
1 -CATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCATGGG
* * * * *
1755 CATCGGCAAATGCCGAAGCCAAGGCTAAGGGCATCGGCAAATACCGACGTCAAGGCCATGGA
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCATGGG
* * * * *
1817 CATCGGCAAATGCCGACGACGAGGCAAAGGGCATCGGCAAATGACGACGCCAAGGCCAAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCATGGG
* * * * *
1879 CATCGGTAAATGCCGAAGCC-AGGACAAGGGTATCGGCAAATGCCGACGTCAAGGCCATGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCATGGG
* ** * *
1940 CATCGGCAAAGGCCGTTGCCAAGGCCAAGGGCCATCGGCAAATGCCGACGACAAGGCCACGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG-CATCGGCAAATGCCGACGCCAAGGCCATGGG
* * * * * * *
2003 CATCGTCAGATGCCGACACCAAGACTAAGGGCCATCGGCAAATGCCGACGCCAAGGGCAAGGG
1 CATCGGCAAATGCCGACGCCAAGGCCAAGGG-CATCGGCAAATGCCGACGCCAAGGCCATGGG
** * ** *
2066 CATCGGCAAATGCCGACGGTAAGGCCAAGCGCCATCGGTTAATGCCGATGCCAA
1 CATCGGCAAATGCCGACGCCAAGGCCAAG-GGCATCGGCAAATGCCGACGCCAA
2120 TATCAAGGAG
Statistics
Matches: 413, Mismatches: 73, Indels: 12
0.83 0.15 0.02
Matches are distributed among these distances:
61 51 0.12
62 131 0.32
63 147 0.36
64 56 0.14
65 28 0.07
ACGTcount: A:0.30, C:0.29, G:0.31, T:0.10
Consensus pattern (62 bp):
CATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCATGGG
Found at i:2199 original size:32 final size:31
Alignment explanation
Indices: 2158--2246 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 31
2148 TTCCGACGCA
*
2158 ATCGGCAAATGCCGATGCCAATGCAACA-GGCC
1 ATCGGCAAATGCCGATGCCAAGGC--CATGGCC
** *
2190 ATCGGCAAATGCCGACACCAAGGCCATGGGC
1 ATCGGCAAATGCCGATGCCAAGGCCATGGCC
* *
2221 ATCGGCAAATGCTGATGCCAACGCCA
1 ATCGGCAAATGCCGATGCCAAGGCCA
2247 AGTGGACTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 2 0.04
31 25 0.52
32 21 0.44
ACGTcount: A:0.30, C:0.31, G:0.26, T:0.12
Consensus pattern (31 bp):
ATCGGCAAATGCCGATGCCAAGGCCATGGCC
Found at i:2224 original size:122 final size:122
Alignment explanation
Indices: 2036--2326 Score: 311
Period size: 122 Copynumber: 2.4 Consensus size: 122
2026 ACTAAGGGCC
* ***
2036 ATCGGCAAATGCCGACGCCAAGGGCA-AGGGCATCGGCAAATGCCGACGGTAAGGCCAAGCGCCA
1 ATCGGCAAATGCCGACGCCAA-GGCACAGGCCATCGGCAAATGCCGACACCAAGGCCAAGCGCCA
** * * * *
2100 TCGGTTAATGCCGATGCCAATATCAAG-GAGACAAGGGACATCATCAAATTCCGACGCA
65 TCGGCAAATGCCGATGCCAACACCAAGTG-GACAAGCGACATCATCAAATTCAGACGCA
* * * *
2158 ATCGGCAAATGCCGATGCCAATGCAACAGGCCATCGGCAAATGCCGACACCAAGGCCATG-GGCA
1 ATCGGCAAATGCCGACGCCAAGGC-ACAGGCCATCGGCAAATGCCGACACCAAGGCCAAGCGCCA
* * * * *
2222 TCGGCAAATGCTGATGCCAACGCCAAGTGGACTAGCTACATCATCAAATTTAGACGCA
65 TCGGCAAATGCCGATGCCAACACCAAGTGGACAAGCGACATCATCAAATTCAGACGCA
* * *
2280 ATCGGCACATACCGACGCCAAGGC-CACGTGCCATCGGCAAGTGCCGA
1 ATCGGCAAATGCCGACGCCAAGGCACA-G-GCCATCGGCAAATGCCGA
2327 TGCCAATGCC
Statistics
Matches: 140, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
120 2 0.01
121 3 0.02
122 106 0.76
123 29 0.21
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14
Consensus pattern (122 bp):
ATCGGCAAATGCCGACGCCAAGGCACAGGCCATCGGCAAATGCCGACACCAAGGCCAAGCGCCAT
CGGCAAATGCCGATGCCAACACCAAGTGGACAAGCGACATCATCAAATTCAGACGCA
Found at i:2227 original size:31 final size:31
Alignment explanation
Indices: 2158--2232 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
2148 TTCCGACGCA
** *
2158 ATCGGCAAATGCCGATGCCAATGCAACAGGCC
1 ATCGGCAAATGCCGACACCAAGGC-ACAGGCC
*
2190 ATCGGCAAATGCCGACACCAAGGC-CATGGGC
1 ATCGGCAAATGCCGACACCAAGGCACA-GGCC
2221 ATCGGCAAATGC
1 ATCGGCAAATGC
2233 TGATGCCAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 2 0.05
31 15 0.39
32 21 0.55
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.12
Consensus pattern (31 bp):
ATCGGCAAATGCCGACACCAAGGCACAGGCC
Found at i:2409 original size:94 final size:93
Alignment explanation
Indices: 2183--2425 Score: 280
Period size: 94 Copynumber: 2.6 Consensus size: 93
2173 TGCCAATGCA
*
2183 ACAGGCCATCGGCAAATGCCGAC-ACCAAGGCCATGGG-CATCGGCAAATGCTGATGCCAACGCC
1 ACAGGCCATCGGCAAATGCCGACGA-CAAGGCCATGGGCCATCGGCAAATGCCGATGCCAACGCC
* * * *
2246 AAGTGGACTAGCTACATCATCAAATTTAG
65 AAGTGGACAAGCGACATCATCAAAATCAG
* * * * * * * *
2275 AC--GCAATCGGCACATACCGACGCCAAGGCCACGTGCCATCGGCAAGTGCCGATGCCAATGCCA
1 ACAGGCCATCGGCAAATGCCGACGACAAGGCCATGGGCCATCGGCAAATGCCGATGCCAACGCCA
* *
2338 ACGT-GACAAGGGACATCATCAAAATCCG
66 A-GTGGACAAGCGACATCATCAAAATCAG
*
2366 ACAAGGCCATCGGCAAATGCCGACGACAAGGCCATGGGCCATCGGCAAATACCGATGCCA
1 AC-AGGCCATCGGCAAATGCCGACGACAAGGCCATGGGCCATCGGCAAATGCCGATGCCA
2426 CATCAGGACT
Statistics
Matches: 122, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
90 26 0.21
91 45 0.37
92 4 0.03
94 47 0.39
ACGTcount: A:0.31, C:0.31, G:0.25, T:0.13
Consensus pattern (93 bp):
ACAGGCCATCGGCAAATGCCGACGACAAGGCCATGGGCCATCGGCAAATGCCGATGCCAACGCCA
AGTGGACAAGCGACATCATCAAAATCAG
Found at i:2869 original size:33 final size:32
Alignment explanation
Indices: 2825--3004 Score: 163
Period size: 32 Copynumber: 5.6 Consensus size: 32
2815 ACGTCGGTGC
* *
2825 CAAGGGACATCGACAAATGCCGACGA-CAAGGA
1 CAAGGCACATCGGCAAATGCCGAC-ACCAAGGA
*
2857 CAAGGCATCATCGGCAAATGCCGACACCAAGGC
1 CAAGGCA-CATCGGCAAATGCCGACACCAAGGA
* *
2890 CAAGGGACATCGGCAAATGCCGACACCAA-AA
1 CAAGGCACATCGGCAAATGCCGACACCAAGGA
* * *
2921 CCAAGGGC-CATCGGCAAATGCCGACGCCAGGGC
1 -CAA-GGCACATCGGCAAATGCCGACACCAAGGA
* * * *
2954 CATGG-GCATCGGCAAATGCCGACTCCAAGGC
1 CAAGGCACATCGGCAAATGCCGACACCAAGGA
*
2985 CATGGGC-CATCGGCAAATGC
1 CA-AGGCACATCGGCAAATGC
3005 TGATGCCAAC
Statistics
Matches: 125, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
31 27 0.22
32 69 0.55
33 29 0.23
ACGTcount: A:0.32, C:0.31, G:0.28, T:0.09
Consensus pattern (32 bp):
CAAGGCACATCGGCAAATGCCGACACCAAGGA
Found at i:2992 original size:63 final size:64
Alignment explanation
Indices: 2823--3004 Score: 219
Period size: 63 Copynumber: 2.8 Consensus size: 64
2813 GCACGTCGGT
* *
2823 GCCAAGGGACATCGACAAATGCCGACGA-CAAGGA-CAA-GGCATCATCGGCAAATGCCGACACC
1 GCCAAGGGACATCGGCAAATGCCGAC-ACCAA-AACCAAGGGC--CATCGGCAAATGCCGACACC
2885 AAG
62 AAG
* *
2888 GCCAAGGGACATCGGCAAATGCCGACACCAAAACCAAGGGCCATCGGCAAATGCCGACGCCAGG
1 GCCAAGGGACATCGGCAAATGCCGACACCAAAACCAAGGGCCATCGGCAAATGCCGACACCAAG
* * ** *
2952 GCCATGGG-CATCGGCAAATGCCGACTCCAAGGCCATGGGCCATCGGCAAATGC
1 GCCAAGGGACATCGGCAAATGCCGACACCAAAACCAAGGGCCATCGGCAAATGC
3005 TGATGCCAAC
Statistics
Matches: 105, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
63 41 0.39
64 30 0.29
65 31 0.30
66 3 0.03
ACGTcount: A:0.32, C:0.31, G:0.28, T:0.09
Consensus pattern (64 bp):
GCCAAGGGACATCGGCAAATGCCGACACCAAAACCAAGGGCCATCGGCAAATGCCGACACCAAG
Found at i:3337 original size:25 final size:25
Alignment explanation
Indices: 3303--3416 Score: 120
Period size: 25 Copynumber: 4.3 Consensus size: 25
3293 GGCAAGGCTT
*
3303 CATCGGCAAATGCCGACGCCAATGG
1 CATCGGCAAATGCCGACGCCAAGGG
* *
3328 CATCGGCAAATGCGGAAGCCAAGGG
1 CATCGGCAAATGCCGACGCCAAGGG
*
3353 CATCGGCAAATACCAGCATCAAGGCCAAGGG
1 CATCGGCAAATGCC-G-A-C---GCCAAGGG
*
3384 CATCGGCAAATGCCGACGCCAAGGC
1 CATCGGCAAATGCCGACGCCAAGGG
*
3409 CATGGGCA
1 CATCGGCA
3417 TCGACAAATG
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
25 48 0.65
26 1 0.01
27 1 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 21 0.28
ACGTcount: A:0.31, C:0.30, G:0.30, T:0.10
Consensus pattern (25 bp):
CATCGGCAAATGCCGACGCCAAGGG
Found at i:3383 original size:31 final size:30
Alignment explanation
Indices: 2823--3605 Score: 449
Period size: 31 Copynumber: 25.4 Consensus size: 30
2813 GCACGTCGGT
* *
2823 GCCAAGGGACATCGACAAATGCCGACGACAAG
1 GCCAAGGG-CATCGGCAAATGCCGA-GCCAAG
* * *
2855 GACAAGGCATCATCGGCAAATGCCGACACCAAG
1 GCCAAGG--GCATCGGCAAATGCCGA-GCCAAG
* *
2888 GCCAAGGGACATCGGCAAATGCCGACACCAAA
1 GCCAAGGG-CATCGGCAAATGCCGA-GCCAAG
* *
2920 ACCAAGGGCCATCGGCAAATGCCGACGCCAGG
1 GCCAAGGG-CATCGGCAAATGCCGA-GCCAAG
* *
2952 GCCATGGGCATCGGCAAATGCCGACTCCAAG
1 GCCAAGGGCATCGGCAAATGCCGA-GCCAAG
* * *
2983 GCCATGGGCCATCGGCAAATGCTGATGCCAAC
1 GCCAAGGG-CATCGGCAAATGCCGA-GCCAAG
* *
3015 GCCAAGTGG-ACTAGGTGAAAT-CCGA--CAAG
1 GCCAAG-GGCA-TCGG-CAAATGCCGAGCCAAG
** *** ** * *
3044 GCCATCGGCAAATGCGGACGCCAAGACCAAG
1 GCCAAGGGCATCGGCAAATGCCGAG-CCAAG
* * *
3075 GGCAAGGGCGATCGGCAAATGCAGATGCCAAT
1 GCCAAGGGC-ATCGGCAAATGCCGA-GCCAAG
* * * * * *
3107 GCCAAGGGGACA-AGGGACAT--C-ATCAAAT
1 GCCAA-GGG-CATCGGCAAATGCCGAGCCAAG
* * * *
3135 TCCGA-CGCAATCGGCAAATGCCGATGCCATG
1 GCCAAGGGC-ATCGGCAAATGCCGA-GCCAAG
* *
3166 G-CAACGGGCCATCAGCAAATGCCGACGCTAAG
1 GCCAA-GGG-CATCGGCAAATGCCGA-GCCAAG
* ** *
3198 GCCATGGGCATCGTAAAATGCCGACTCCAAG
1 GCCAAGGGCATCGGCAAATGCCGA-GCCAAG
* * *
3229 GCCATGGGCCATCGGCAAATGCTGATGCCAAC
1 GCCAAGGG-CATCGGCAAATGCCGA-GCCAAG
* * *
3261 GCCAAGTGTCATCGACAAATGCCGATGACAAG
1 GCCAAG-GGCATCGGCAAATGCCGA-GCCAAG
* *
3293 GGCAAGGCTTCATCGGCAAATGCCGA--C---
1 GCCAAGG--GCATCGGCAAATGCCGAGCCAAG
*
3320 GCCAATGGCATCGGCAAATG-CG-G--AA-
1 GCCAAGGGCATCGGCAAATGCCGAGCCAAG
*
3345 GCCAAGGGCATCGGCAAATACC-AGCATCAAG
1 GCCAAGGGCATCGGCAAATGCCGAGC--CAAG
3376 GCCAAGGGCATCGGCAAATGCCGACGCCAAG
1 GCCAAGGGCATCGGCAAATGCCGA-GCCAAG
* *
3407 GCCATGGGCATCGACAAATGCCGATGCCAAG
1 GCCAAGGGCATCGGCAAATGCCGA-GCCAAG
* * *
3438 GCAAAGGGCATCGACAAATGCCGAAGCCAGG
1 GCCAAGGGCATCGGCAAATGCCG-AGCCAAG
* *
3469 GCCAAGGGCATAGGCAAATGCCGAAGCCAGG
1 GCCAAGGGCATCGGCAAATGCCG-AGCCAAG
*
3500 GCC-AGTGGCATCGGCAAATGCCGACGTCAAG
1 GCCAAG-GGCATCGGCAAATGCCGA-GCCAAG
* *
3531 GCCATGGGCATCGGCAAATTCCGACGCCAAG
1 GCCAAGGGCATCGGCAAATGCCGA-GCCAAG
*
3562 GACAAGGGCATCGGCAAATGCCGACGCCAAG
1 GCCAAGGGCATCGGCAAATGCCGA-GCCAAG
3593 GCCAAGGGCATCG
1 GCCAAGGGCATCG
3606 AACCAAATCT
Statistics
Matches: 589, Mismatches: 116, Indels: 93
0.74 0.15 0.12
Matches are distributed among these distances:
24 2 0.00
25 31 0.05
26 4 0.01
27 11 0.02
28 14 0.02
29 10 0.02
30 9 0.02
31 265 0.45
32 183 0.31
33 59 0.10
34 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.29, T:0.11
Consensus pattern (30 bp):
GCCAAGGGCATCGGCAAATGCCGAGCCAAG
Found at i:3447 original size:62 final size:61
Alignment explanation
Indices: 2823--3605 Score: 498
Period size: 62 Copynumber: 12.7 Consensus size: 61
2813 GCACGTCGGT
* * * * *
2823 GCCAAGGGACATCGACAAATGCCGACGACAAGGACAAGGCATCATCGGCAAATGCCGACACCAAG
1 GCCAAGGG-CATCGGCAAATGCCGACGCCAAGGCCAAGG--GCATCGGCAAATGCCGA-GCCAAG
* ** *
2888 GCCAAGGGACATCGGCAAATGCCGACACCAAAACCAAGGGCCATCGGCAAATGCCGACGCCAGG
1 GCCAAGGG-CATCGGCAAATGCCGACGCCAAGGCCAAGGG-CATCGGCAAATGCCGA-GCCAAG
* * * * *
2952 GCCATGGGCATCGGCAAATGCCGACTCCAAGGCCATGGGCCATCGGCAAATGCTGATGCCAAC
1 GCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGG-CATCGGCAAATGCCGA-GCCAAG
* * ** *** ** * *
3015 GCCAAGTGG-ACTAGGTGAAAT-CCGA---CAAGGCCATCGGCAAATGCGGACGCCAAGACCAAG
1 GCCAAG-GGCA-TCGG-CAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGAG-CCAAG
* * * * * * * * * *
3075 GGCAAGGGCGATCGGCAAATGCAGATGCCAATGCCAAGGGGACA-AGGGACAT--C-ATCAAAT
1 GCCAAGGGC-ATCGGCAAATGCCGACGCCAAGGCCAA-GGG-CATCGGCAAATGCCGAGCCAAG
* * * * * * *
3135 TCCGA-CGCAATCGGCAAATGCCGATGCCATGG-CAACGGGCCATCAGCAAATGCCGACGCTAAG
1 GCCAAGGGC-ATCGGCAAATGCCGACGCCAAGGCCAA-GGG-CATCGGCAAATGCCGA-GCCAAG
* ** * * * *
3198 GCCATGGGCATCGTAAAATGCCGACTCCAAGGCCATGGGCCATCGGCAAATGCTGATGCCAAC
1 GCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGG-CATCGGCAAATGCCGA-GCCAAG
* * * * * *
3261 GCCAAGTGTCATCGACAAATGCCGATGACAAGGGCAAGGCTTCATCGGCAAATGCCGA--C---
1 GCCAAG-GGCATCGGCAAATGCCGACGCCAAGGCCAAGG--GCATCGGCAAATGCCGAGCCAAG
* *
3320 GCCAATGGCATCGGCAAATG-CG--G--AA-GCCAAGGGCATCGGCAAATACC-AGCATCAAG
1 GCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGAGC--CAAG
* *
3376 GCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCGACAAATGCCGATGCCAAG
1 GCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGA-GCCAAG
* * * * * *
3438 GCAAAGGGCATCGACAAATGCCGAAGCCAGGGCCAAGGGCATAGGCAAATGCCGAAGCCAGG
1 GCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCG-AGCCAAG
* * *
3500 GCC-AGTGGCATCGGCAAATGCCGACGTCAAGGCCATGGGCATCGGCAAATTCCGACGCCAAG
1 GCCAAG-GGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGA-GCCAAG
*
3562 GACAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCG
1 GCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCG
3606 AACCAAATCT
Statistics
Matches: 557, Mismatches: 119, Indels: 87
0.73 0.16 0.11
Matches are distributed among these distances:
49 1 0.00
50 13 0.02
52 6 0.01
53 3 0.01
55 1 0.00
56 19 0.03
57 4 0.01
58 20 0.04
59 39 0.07
60 28 0.05
61 19 0.03
62 164 0.29
63 114 0.20
64 72 0.13
65 54 0.10
ACGTcount: A:0.31, C:0.29, G:0.29, T:0.11
Consensus pattern (61 bp):
GCCAAGGGCATCGGCAAATGCCGACGCCAAGGCCAAGGGCATCGGCAAATGCCGAGCCAAG
Found at i:5101 original size:322 final size:322
Alignment explanation
Indices: 3602--6035 Score: 3323
Period size: 322 Copynumber: 7.5 Consensus size: 322
3592 GGCCAAGGGC
* * **
3602 ATCGAACCAAATCTCAACCACATTGGAT-TTACAGATTTATTTTTTTGAGCATCTGAA-TTTGAT
1 ATCGAACCAAATCTCAACCACATTGAATATTA-AGATTTCTTTTTACGAGCATCTGAATTTTG-T
* * * *
3665 ATCCG-TTTAATTAG-AATTAATTCGGAAAAAAAAATGGGTATACGATATTAGAAGCGTGAAAAA
64 -TTCGATTTAATTAGAAATTAATTCTG--AAAAAAATGGGTAAACGATATTAGAAGCGTTAAAAA
* * * *
3728 CCTTTCAAATTTTTTGACATTGAATTATATATTTTTTTCTGTGTATTTTGGCGAAAAATTTGAGA
126 CCTTTCAATTTTTTTGGCATTGAATTATATA-TTTTTTCTGAGTATTTTGGCGAAAAAATTGAGA
* *
3793 AAAAGATTTTCGGGTCAATTTTTTGCCGAAATCGTGTACTAACACCATCACGGGTTTTTGCTAAA
190 AAAAAATTTTCGGGTCAATTTTTTGCCGAAATCGTGTA-TTA-ACCATCAC-GGTTTTTGCTAAA
* *
3858 AACGCAGTCCGATGCCCCGACTCAGTTTTGCCTGAA-TTTTGGCGTAAAGACTCCTTGAGATATC
252 AACGCAGTCCGATGCCCCGGCTCAGTTTTGCCT-AATTTTTTGCGTAAAGACTCCTTGAGATATC
3922 TATATTT
316 TATATTT
*
3929 ATCGAACCAAATCTCAACCACATTGGAT-TTAGAGATTTCTTTTTACGAGCATCTGAATTTTGTT
1 ATCGAACCAAATCTCAACCACATTGAATATTA-AGATTTCTTTTTACGAGCATCTGAATTTTGTT
* *
3993 TCGATTTAATTAAAAATTAATTCTGAAAAAAATGGGTAAACGATATT---A--GTGAAAAACCTT
65 TCGATTTAATTAGAAATTAATTCTGAAAAAAATGGGTAAACGATATTAGAAGCGTTAAAAACCTT
* *
4053 TCAATTTTTTTTGGCATTGAATTATATATTTTTTCTTAGCATTTTGGCG-AAAAATTGAGAAAAA
130 TCAA-TTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTGGCGAAAAAATTGAG-AAAA
* * * * * * * * * *
4117 ATAATTTTGGGGTTAGTATTATGTCGAAATCATGTACTAACCATCACGGGGTTTTGCTAACAACG
193 A-AATTTTCGGGTCAATTTTTTGCCGAAATCGTGTATTAACCATCAC-GGTTTTTGCTAAAAACG
* * * * * *
4182 CAGTCCGATGCCCCGAG-TCAGTTTTGTCTGATTTTTGGCCTAAAAACTCCTTGAAATATCTATA
256 CAGTCCGATGCCCCG-GCTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATATCTATA
4246 TTT
320 TTT
* *
4249 ATCGAACCAAATCTCAACCACATTGGAT-TTAAAGATTTATTTTTATC-AGCATCTGAATTTTGT
1 ATCGAACCAAATCTCAACCACATTGAATATT-AAGATTTCTTTTTA-CGAGCATCTGAATTTTGT
* * * *
4312 TTCGGTTTAATTAGAAATTAATTCAG-AAATAATGGGTAAACGATATTAGAAGCGTGAAAAAACC
64 TTCGATTTAATTAGAAATTAATTCTGAAAAAAATGGGTAAACGATATTAGAAGCGT-TAAAAACC
*
4376 TTTCAATTTTTTTGGCATTGAATTATATATTTTTTCTTAGTATTTTGGCG-AAAAATTGAG-AAA
128 TTTCAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTGGCGAAAAAATTGAGAAAA
* * * *
4439 AAATTTTCGGGTCAATTTTTTACCGAAATCTTGTATTAACTAGCACAGGTTTTTGCTAAAAACGC
193 AAATTTTCGGGTCAATTTTTTGCCGAAATCGTGTATTAACCATCAC-GGTTTTTGCTAAAAACGC
* * * *
4504 AGTCCGATGCCCCGACTCAGTTTTGCCTAATTTTTTGCGTAAATACTCCTGGAGACATCTATATT
257 AGTCCGATGCCCCGGCTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATATCTATATT
4569 T
322 T
* * * *
4570 ATCTAACTAAATCTCAACCACATTGAATATTAAGATTTCTATTTACAAGCATCTGAATTTTGTTT
1 ATCGAACCAAATCTCAACCACATTGAATATTAAGATTTCTTTTTACGAGCATCTGAATTTTGTTT
* ** *
4635 CGATTTAATTAGAAATTAATTCGGAAAAAAATGTTTAAATGATATTAGAAGCGTTAAAAACCTTT
66 CGATTTAATTAGAAATTAATTCTGAAAAAAATGGGTAAACGATATTAGAAGCGTTAAAAACCTTT
* ** *
4700 CAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTGGTGAAAATTTTGTGAAAAAAA
131 CAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTGGCGAAAAAATTGAGAAAAAAA
* * *
4765 ATTTCGGGTCAATTTTTTGCCGAAATCGTGTAATAACCATCACGGTTTTTTGCTAAAAATGCAGT
196 TTTTCGGGTCAATTTTTTGCCGAAATCGTGTATTAACCATCACGG-TTTTTGCTAAAAACGCAGT
*
4830 CCGATGCCCCGGCTCAATTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTT
260 CCGATGCCCCGGCTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTT
* * * * *
4893 ATTGAATCAAGTCTAAACCACATTGAATATTAAGATTT-TTTTTACGAGCATCTTAATTTTGTTT
1 ATCGAACCAAATCTCAACCACATTGAATATTAAGATTTCTTTTTACGAGCATCTGAATTTTGTTT
* * *
4957 CGATTTAATTAGAAATTATTTCTTAAAAAAATGGGTAAACGATATTAGAAGCATTAAAAACCTTT
66 CGATTTAATTAGAAATTAATTCTGAAAAAAATGGGTAAACGATATTAGAAGCGTTAAAAACCTTT
*
5022 CAATTTTTTTGGCATTAAAATTATATATTTTTTCTGAGTATTTTGGCGAAAAAATTGAG-AAAAA
131 CAATTTTTTTGGCATT-GAATTATATATTTTTTCTGAGTATTTTGGCGAAAAAATTGAGAAAAAA
*** * *
5086 ATTTTCGGGTCAATTTTTTATTGAAATCTTGTATTAACTATCACAGGTTTTTGCTAAAAACGCAG
195 ATTTTCGGGTCAATTTTTTGCCGAAATCGTGTATTAACCATCAC-GGTTTTTGCTAAAAACGCAG
* *
5151 TCCGATGCGCCGACTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTT
259 TCCGATGCCCCGGCTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTT
* * *
5215 ATCGAACTAAATCTCAACCACATTGAAAATTAAGATTTCTTTTTTCGAGCATCTGAATTTTGTTT
1 ATCGAACCAAATCTCAACCACATTGAATATTAAGATTTCTTTTTACGAGCATCTGAATTTTGTTT
* * *
5280 CGATTTAATTAGAAATTAATTC-GGAAAAAATGGTTAAATGATATTAGAAGCGTTAAAAACCTTT
66 CGATTTAATTAGAAATTAATTCTGAAAAAAATGGGTAAACGATATTAGAAGCGTTAAAAACCTTT
* *
5344 CAATTTTTTTGGTATTGAATTATATATTTTTTCTGAGTATTTTGGCGAAAAATTTGAGAAAAAAA
131 CAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTGGCGAAAAAATTGAGAAAAAAA
* *
5409 TTTTTGGGTCAATTTTTTGCCGAAATCGTGTATTAACCATCACGGGTTTTTGCTAAAAACGTAGT
196 TTTTCGGGTCAATTTTTTGCCGAAATCGTGTATTAACCATCAC-GGTTTTTGCTAAAAACGCAGT
*
5474 CCAATGCCCCGGCTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTT
260 CCGATGCCCCGGCTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTT
* * * *
5537 ATCGAACCAAATATCAACCACATTAAATATTAAGATTTGTTTTTACGAGCATCTTAATTTTGTTT
1 ATCGAACCAAATCTCAACCACATTGAATATTAAGATTTCTTTTTACGAGCATCTGAATTTTGTTT
* *
5602 CGATTTAATTAGAAATTATTTCTGAAAAAAATGGGTAAATGATATTAGAAGCGTTAAAAACCTTT
66 CGATTTAATTAGAAATTAATTCTGAAAAAAATGGGTAAACGATATTAGAAGCGTTAAAAACCTTT
* * * *
5667 CAATATTTTGGGCATTGAATTATATATTTTTTCTGAGTACTTTGGCAAAAAAAATTGAGAAAAAA
131 CAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTGGC-GAAAAAATTGAGAAAAAA
* * * ** *
5732 ATTTTCTGGTTAATTTTTTCCCGAAATCGTGTATTAACCATCACAGGTTTTTAATAAAATCGCAG
195 ATTTTCGGGTCAATTTTTTGCCGAAATCGTGTATTAACCATCAC-GGTTTTTGCTAAAAACGCAG
* * *
5797 TCCGATGCCCCGGCTCAGTTTTGCC-ATATTTTTGGCGTAAAGACTCTTTGAGATGTCTATATTT
259 TCCGATGCCCCGGCTCAGTTTTGCCTA-ATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTT
* ** *
5861 A-CTGAACCAAATCTCAACCACATTGAAT-TTATAGATTTATTTTTTTGAGCATCTGAATTTGGT
1 ATC-GAACCAAATCTCAACCACATTGAATATTA-AGATTTCTTTTTACGAGCATCTGAATTTTGT
* * * *
5924 TTCGGTTTAATTAGAAATTAATTCGGAAAAAAATGGGTAAACGATATTAAAAGCGTGAAAAACCT
64 TTCGATTTAATTAGAAATTAATTCTGAAAAAAATGGGTAAACGATATTAGAAGCGTTAAAAACCT
* *
5989 TTCAATTTTTTTGACATTGAATTATATATTTTTTCTGTGTATTTTGG
129 TTCAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTGG
6036 AAAAAAAAAT
Statistics
Matches: 1877, Mismatches: 198, Indels: 67
0.88 0.09 0.03
Matches are distributed among these distances:
319 21 0.01
320 173 0.09
321 320 0.17
322 591 0.31
323 323 0.17
324 336 0.18
325 13 0.01
326 24 0.01
327 62 0.03
328 14 0.01
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (322 bp):
ATCGAACCAAATCTCAACCACATTGAATATTAAGATTTCTTTTTACGAGCATCTGAATTTTGTTT
CGATTTAATTAGAAATTAATTCTGAAAAAAATGGGTAAACGATATTAGAAGCGTTAAAAACCTTT
CAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTGGCGAAAAAATTGAGAAAAAAA
TTTTCGGGTCAATTTTTTGCCGAAATCGTGTATTAACCATCACGGTTTTTGCTAAAAACGCAGTC
CGATGCCCCGGCTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTT
Found at i:6524 original size:479 final size:475
Alignment explanation
Indices: 5579--6504 Score: 1269
Period size: 479 Copynumber: 1.9 Consensus size: 475
5569 AGATTTGTTT
* * * *
5579 TTACGAGCATCTTAATTTTGTTTCGATTTAATTAGAAATTATTTCTGAAAAAAATGGGTAAATGA
1 TTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATTAATTCTGAAAAAAATGGGTAAACGA
* *
5644 TATTAGAAGCGTTAAAAACCTTTCAATATTTTGGGCATTGAATTATATATTTTTTCTGAGTACTT
66 TATT--AA-CGTGAAAAACCTTTCAATATTTTGGGCATTGAATTATATATTTTTTCTGAGCACTT
* * *
5709 TGGCAAAAAAAATTGAGAAAAAAATTTTCTGGTTAATTTTTTCCCGAAATCGTGTATTAACCATC
128 TGG-AAAAAAAATTGAGAAAAAAATTTTCGGGTTAATTTTTTCCCGAAATCGTGTACTAACAATC
** *
5774 ACAGGTTTTTAATAAAATCGCAGTCCGATGCCCCGGCTCAGTTTTGCCATATTTTTGGCGTAAAG
192 ACAGGGATTTAATAAAATCGCAGTCCGATGCCCCGACTCAGTTTTGCCATATTTTTGGCGTAAAG
* * * * *
5839 ACTCTTTGAGATGTCTATATTTACTGAACCAAATCTCAACCACATTGAATTTATAGATTTATTTT
257 ACTCCTTGAAATATCTATATTTACTGAACCAAATCCCAACCACATTGAATTTAAAGATTTATTTT
*
5904 TTTGAGCATCTGAATTTGGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAAATGGGTAAACGAT
322 TATGAGCATCTGAATTTGGTTTCGGTTTAATTAGAAATTAATTCGG-AAAAAA---GT--A-GAT
* *
5969 ATTAAAAGCGTGAAAAACCTTTCAATTTTTTTGACATTGAATTATATATTTTTTCTGTGTATTTT
380 ATTAAAAGCGTGAAAAACCTTTCAATTTTTTTGACATTGAATTATATATTTTTTATGCGTATTTT
6034 GGAAAAAAAAATGGGGTCTGAATTTTGTGTA
445 GGAAAAAAAAATGGGGTCTGAATTTTGTGTA
6065 TTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATTAATTCTGAAAAAAATGGGTAAACGA
1 TTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATTAATTCTGAAAAAAATGGGTAAACGA
* ** * *
6130 TATT-A-GTGAAAAACCTTTCAATTTTTTTTGCA-TGAATTATATATTTTTTCTTAGCATTTTGG
66 TATTAACGTGAAAAACCTTTCAATATTTTGGGCATTGAATTATATATTTTTTCTGAGCACTTTGG
** * * ** *
6192 -TGAAAAATTGAGAAAAATAATTTTGGGGTTAGTTTTTTGTCGAAATCGTGTACTAACAATCACG
131 AAAAAAAATTGAGAAAAA-AATTTTCGGGTTAATTTTTTCCCGAAATCGTGTACTAACAATCACA
** * * * *
6256 GGGATTTGCTAGCAA-CGCAGTCCGATGCCCTGACTCAGTTTTGTC-TGATTTTTGGCTTAAAGA
195 GGGATTTAATA-AAATCGCAGTCCGATGCCCCGACTCAGTTTTGCCAT-ATTTTTGGCGTAAAGA
*
6319 CTCCTTGAAATATCTATATTTA-TCGAACCAAATCCCAACCACATTGGATTTAAAGATTTATTTT
258 CTCCTTGAAATATCTATATTTACT-GAACCAAATCCCAACCACATTGAATTTAAAGATTTATTTT
* *
6383 TATGAGCATCTGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGG-AAAAA-T-GATATTAGAA
322 TATGAGCATCTGAATTTGGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAAGTAGATATTAAAA
*
6445 GCGTGAAAAACCTTTCAATTTTTTTGATATTGAATTATATATTTTTTATGCGTATTTTGG
387 GCGTGAAAAACCTTTCAATTTTTTTGACATTGAATTATATATTTTTTATGCGTATTTTGG
6505 CGAAAAATTA
Statistics
Matches: 394, Mismatches: 42, Indels: 25
0.85 0.09 0.05
Matches are distributed among these distances:
469 66 0.17
473 1 0.00
477 5 0.01
478 17 0.04
479 187 0.47
480 29 0.07
481 23 0.06
483 1 0.00
486 65 0.16
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (475 bp):
TTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATTAATTCTGAAAAAAATGGGTAAACGA
TATTAACGTGAAAAACCTTTCAATATTTTGGGCATTGAATTATATATTTTTTCTGAGCACTTTGG
AAAAAAAATTGAGAAAAAAATTTTCGGGTTAATTTTTTCCCGAAATCGTGTACTAACAATCACAG
GGATTTAATAAAATCGCAGTCCGATGCCCCGACTCAGTTTTGCCATATTTTTGGCGTAAAGACTC
CTTGAAATATCTATATTTACTGAACCAAATCCCAACCACATTGAATTTAAAGATTTATTTTTATG
AGCATCTGAATTTGGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAAGTAGATATTAAAAGCGT
GAAAAACCTTTCAATTTTTTTGACATTGAATTATATATTTTTTATGCGTATTTTGGAAAAAAAAA
TGGGGTCTGAATTTTGTGTA
Found at i:6735 original size:313 final size:315
Alignment explanation
Indices: 6065--6746 Score: 846
Period size: 314 Copynumber: 2.2 Consensus size: 315
6055 ATTTTGTGTA
* * *
6065 TTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATTAATTCTGAAAAAAATGGGTAAACGA
1 TTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTC-G-GAAAAATGGATAAACGA
* * * *
6130 TATTAGTGAAAAACCTTTCAATTTTTTTTGCATGAATTATATATTTTTTCTTAGCATTTTGGTGA
64 TATGAGTGAAAAACCTTTCAATTTTTTTTGCATGAATTATATATTTTTTATGAGCATTTTGGCGA
* * * ** * *
6195 AAAATTGAGAAAAATAATTTTGGGGTTAGTTTTTTGTCGAAATCGTGTACTAACAATCACGGGGA
129 AAAATTAAGAAAAATAATTTTCGGGTCAGTTTTTTCCCAAAATCGTGTACTAACAATCACGGAGA
** * * * *
6260 TTTGCTAGCAACGCAGTCCGATGCCCTGACTCAGTTTTGTCTGATTTTTGGCTTAAAGACTCCTT
194 TTTGCTAAAAACGCAGTCCGATGCCCCGACTCAGTTTTGTCTAATTTTTGGCATAAAAACTCCTT
**
6325 GAAATATCTATATTTATCGAACCAAATCCCAACCACATTGGATTTAAAGATTTATTT
259 GAAATATCTATATTTATCGAACCAAATCCCAACCACATTAAATTTAAAGATTTATTT
* * *
6382 TTATGAGCATCTGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAT-GATATTA-GA-
1 TTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATGGATA-AACGAT
* * * *
6444 A-GCGTGAAAAACCTTTCAA-TTTTTTTGATATTGAATTATATATTTTTTATGCGTATTTTGGCG
65 ATGAGTGAAAAACCTTTCAATTTTTTTTG-CA-TGAATTATATATTTTTTATGAGCATTTTGGCG
* *
6507 AAAAATTAAGAAAAA-AATTTTCGGGTCGGTTTTTTCCCAAAATCGTGTACGTTAACCATCACGG
128 AAAAATTAAGAAAAATAATTTTCGGGTCAGTTTTTTCCCAAAATCGTGTAC--TAACAATCACGG
** * *
6571 ATTTTTGCTAAAAACGCAGTCCTATGCCCCGGCTCAGTTTT-TCCTAATATTTT-GCATAAAAAC
191 AGATTTGCTAAAAACGCAGTCCGATGCCCCGACTCAGTTTTGT-CTAAT-TTTTGGCATAAAAAC
* **
6634 TCCTTGAGATATCTATATTTATCG-ACTCAAATCTTAACCACATTAAATATT-AAGATTT-TTT
254 TCCTTGAAATATCTATATTTATCGAAC-CAAATCCCAACCACATTAAAT-TTAAAGATTTATTT
6695 TTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
1 TTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
6747 AATGGGTAAA
Statistics
Matches: 316, Mismatches: 40, Indels: 22
0.84 0.11 0.06
Matches are distributed among these distances:
311 8 0.03
312 46 0.15
313 98 0.31
314 108 0.34
315 13 0.04
316 1 0.00
317 42 0.13
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (315 bp):
TTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATGGATAAACGATA
TGAGTGAAAAACCTTTCAATTTTTTTTGCATGAATTATATATTTTTTATGAGCATTTTGGCGAAA
AATTAAGAAAAATAATTTTCGGGTCAGTTTTTTCCCAAAATCGTGTACTAACAATCACGGAGATT
TGCTAAAAACGCAGTCCGATGCCCCGACTCAGTTTTGTCTAATTTTTGGCATAAAAACTCCTTGA
AATATCTATATTTATCGAACCAAATCCCAACCACATTAAATTTAAAGATTTATTT
Done.