Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009572.1 Hibiscus syriacus cultivar Beakdansim tig00116937_pilon, 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: 2529503
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 13
Found at i:931349 original size:20 final size:20
Alignment explanation
Indices: 931295--931353 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
931285 GCGATTCTCT
**
931295 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
931315 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
931335 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
931354 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:931544 original size:25 final size:24
Alignment explanation
Indices: 931490--931544 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
931480 TGTTTATTAT
* *
931490 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
931514 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
931540 TGTTT
1 TGTTT
931545 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:932696 original size:18 final size:18
Alignment explanation
Indices: 932675--932719 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
932665 TCCACTTCGG
*
932675 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
932693 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
932711 GAGCCATCA
1 GAGCCATCA
932720 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:933129 original size:19 final size:19
Alignment explanation
Indices: 933105--933144 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
933095 GCCAAACTGT
933105 TTTTTGTATTTGT-TTTTGG
1 TTTTTGT-TTTGTCTTTTGG
933124 TTTTTGTTTTGTCTTTTGG
1 TTTTTGTTTTGTCTTTTGG
933143 TT
1 TT
933145 GAAGTAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.03, C:0.03, G:0.20, T:0.75
Consensus pattern (19 bp):
TTTTTGTTTTGTCTTTTGG
Found at i:933252 original size:19 final size:20
Alignment explanation
Indices: 933198--933264 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
933188 TAGTTTACTT
* *
933198 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
933218 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
933238 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
933257 TCGCAACG
1 TCGCAACG
933265 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:933272 original size:14 final size:14
Alignment explanation
Indices: 933253--933310 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
933243 ATGCGAAATG
933253 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
933267 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
933283 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
933299 AAAATCGCAACG
1 AAAATCGCAACG
933311 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:933295 original size:32 final size:33
Alignment explanation
Indices: 933237--933327 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
933227 GGAAATGGCT
933237 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
933270 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
933302 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
933328 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:933375 original size:32 final size:33
Alignment explanation
Indices: 933339--933417 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
933329 GCGATTTGTG
* **
933339 TTTCGCGTTGCGATTTTGTCGTTGTGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTACGATTTTCA
933371 TTTCGCATTGCGATTTTGTCGTTACGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTACGATTTTCA
933404 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
933418 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 24 0.56
33 19 0.44
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTACGATTTTCA
Found at i:933437 original size:20 final size:20
Alignment explanation
Indices: 933412--933457 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
933402 CATTTCGCAT
933412 TGCGATAGCCATTTCCGCGC
1 TGCGATAGCCATTTCCGCGC
* * *
933432 TGCGATAGTCATTTTCGCGT
1 TGCGATAGCCATTTCCGCGC
933452 TGCGAT
1 TGCGAT
933458 TTTAAGTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (20 bp):
TGCGATAGCCATTTCCGCGC
Found at i:935345 original size:14 final size:14
Alignment explanation
Indices: 935326--935361 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
935316 ATTGTTTAAT
935326 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
935340 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
935354 TGATTTGT
1 TGATTTGT
935362 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:935507 original size:14 final size:14
Alignment explanation
Indices: 935488--935541 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
935478 GAAACTGACT
935488 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
935502 ATCGCAATGCAAAATGAAA
1 ATCGCAA--C--GA-GAAA
935521 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
935535 ATCGCAA
1 ATCGCAA
935542 TGCGATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 18 0.55
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.33
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:935590 original size:20 final size:20
Alignment explanation
Indices: 935565--935656 Score: 71
Period size: 20 Copynumber: 4.6 Consensus size: 20
935555 TCGCATTACG
*
935565 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
935585 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
935606 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* *
935625 ATTTTC-ACGTTGCGGTGGCC
1 ATTTTCGA-GTTGCGATAGCC
*
935645 ATTTTCGCGTTG
1 ATTTTCGAGTTG
935657 TGATTTCCCC
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
19 4 0.07
20 47 0.87
21 3 0.06
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:935651 original size:40 final size:41
Alignment explanation
Indices: 935565--935651 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 41
935555 TCGCATTACG
* * * * ***
935565 ATTTTCTAGTTGCGATAGCCATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAATTGCGATAGCCATTTTCACGTTGCGAGTGGCC
935606 A-TTTCGAATTGCGATAGCCATTTTCACGTTGCG-GTGGCC
1 ATTTTCGAATTGCGATAGCCATTTTCACGTTGCGAGTGGCC
935645 ATTTTCG
1 ATTTTCG
935652 CGTTGTGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
39 3 0.08
40 34 0.89
41 1 0.03
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (41 bp):
ATTTTCGAATTGCGATAGCCATTTTCACGTTGCGAGTGGCC
Found at i:936816 original size:24 final size:24
Alignment explanation
Indices: 936789--936842 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
936779 GTATTCAAAA
*
936789 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
936813 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
936837 TTTGAT
1 TTTGAT
936843 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:937034 original size:12 final size:12
Alignment explanation
Indices: 937017--937041 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
937007 ATATAATCCT
937017 GAAGAAGAAAAA
1 GAAGAAGAAAAA
937029 GAAGAAGAAAAA
1 GAAGAAGAAAAA
937041 G
1 G
937042 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:939287 original size:181 final size:178
Alignment explanation
Indices: 938987--939345 Score: 666
Period size: 181 Copynumber: 2.0 Consensus size: 178
938977 TGGATCACCA
938987 GTGCCATCACAATCATCTTTTCCTCTACCAAATATGGATCATCAAAATCCAAAGCTCATATGGTG
1 GTGCCATCACAATCATCTTTTCCTCTACCAAATATGGATCATCAAAATCCAAAGCTCATATGGTG
939052 TCAAGAAAAAGGCAATCAAAATCGCAATCATCTTTAAAATCCCAATCACAACTGGCTTCACCTTT
66 TCAAGAAAAAGGCAATCAAAATCGCAATCATCTTTAAAATCCCAATCACAACTGGCTTCACCTTT
*
939117 TGGGACTGTTAACTTAGGTGA-TTTTAAATGCAACCGTTGTATTATGT
131 TGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGT
939164 GTGCCATCACAATCATCTTTTCCTCTACCAAAATATGGATCATCATCAAAATCCAAAGCTCATAT
1 GTGCCATCACAATCATCTTTTCCTCTACC-AAATATGG---ATCATCAAAATCCAAAGCTCATAT
939229 GGTGTCAAGAAAAAGGCAATCAAAATCGCAATCATCTTTAAAATCCCAATCACAACTGGCTTCAC
62 GGTGTCAAGAAAAAGGCAATCAAAATCGCAATCATCTTTAAAATCCCAATCACAACTGGCTTCAC
939294 CTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGT
127 CTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGT
939346 AGATTTTATG
Statistics
Matches: 176, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
177 29 0.16
178 8 0.05
181 114 0.65
182 25 0.14
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (178 bp):
GTGCCATCACAATCATCTTTTCCTCTACCAAATATGGATCATCAAAATCCAAAGCTCATATGGTG
TCAAGAAAAAGGCAATCAAAATCGCAATCATCTTTAAAATCCCAATCACAACTGGCTTCACCTTT
TGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGT
Found at i:939528 original size:33 final size:33
Alignment explanation
Indices: 939486--939609 Score: 171
Period size: 33 Copynumber: 3.8 Consensus size: 33
939476 AATTACTATC
939486 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
**
939519 GCAATGCGAAATGAAAATCGCAAC--GCTAATT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
* * *
939550 CCGCAATGCAAAATGAAAATCGCAACGAGGGAATC
1 --GCAATGCGAAATGAAAATCGCAACGAGAGAATT
939585 GCAATGCGAAATGAAAATCGCAACG
1 GCAATGCGAAATGAAAATCGCAACG
939610 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
31 5 0.06
33 71 0.89
35 4 0.05
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATT
Found at i:939591 original size:66 final size:66
Alignment explanation
Indices: 939485--939615 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
939475 AAATTACTAT
* * *
939485 CGCAATGCGAAATGAAAATCGCAACGAGAGAATTGCAATGCGAAATGAAAATCGCAACGCTAATT
1 CGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
939550 C
66 C
*
939551 CGCAATGCAAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 CGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
939616 TAATTTCGCG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (66 bp):
CGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
C
Found at i:939660 original size:33 final size:33
Alignment explanation
Indices: 939609--939698 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
939599 AAATCGCAAC
* * *
939609 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
939642 GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
* *
939675 GTGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
939699 AGTACTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
Found at i:939824 original size:14 final size:14
Alignment explanation
Indices: 939805--939841 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
939795 CATCAATTAA
939805 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
939819 ACAAATCACCTTTT
1 ACAAATCAACTTTT
939833 ACAAATCAA
1 ACAAATCAA
939842 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:941260 original size:42 final size:42
Alignment explanation
Indices: 941201--941374 Score: 165
Period size: 42 Copynumber: 4.1 Consensus size: 42
941191 GTGAATCGGG
* *
941201 CTCTTGAATGGTGGGAGGGACCTCTTCAACG-ATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGAATGACAGTGGC
* * *
941243 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGGAATGACAGTGGC
* * * * *
941285 CTCTTCAACGATAGGAGTGGACTCTTGAGGGAATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGAATGACAGTGGC
* * * *
941328 CTCTTGAATGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGGAATGACAGTGGC
941370 CTCTT
1 CTCTT
941375 CAATGATAGG
Statistics
Matches: 105, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
41 5 0.05
42 64 0.61
43 35 0.33
44 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGAATGACAGTGGC
Found at i:941267 original size:21 final size:21
Alignment explanation
Indices: 941201--941267 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
941191 GTGAATCGGG
*
941201 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
941221 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
941243 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
941264 CTCT
1 CTCT
941268 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:941343 original size:85 final size:84
Alignment explanation
Indices: 941231--941407 Score: 327
Period size: 85 Copynumber: 2.1 Consensus size: 84
941221 CCTCTTCAAC
941231 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
941296 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
* *
941315 GAATGACAGTGGCCTCTTGAATGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATG
1 G-ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACG
941380 ATAGGAGTGGACTCTTGAGG
65 ATAGGAGTGGACTCTTGAGG
941400 GATGACAG
1 GATGACAG
941408 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
84 8 0.09
85 82 0.91
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:941392 original size:42 final size:42
Alignment explanation
Indices: 941256--941404 Score: 190
Period size: 42 Copynumber: 3.5 Consensus size: 42
941246 TTGAACGGTG
*
941256 GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATA
1 GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGATA
* * * * * * *
941298 GGAGTGGACTCTTGAGGGAATGACAGTGGCCTCTTGAATGGTG
1 GGAGGGGACTCTCGA-GGAATGATAGGGGCCTCTTCAATGATA
941341 GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGATA
1 GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGATA
* * *
941383 GGAGTGGACTCTTGAGGGATGA
1 GGAGGGGACTCTCGAGGAATGA
941405 CAGGCGAGTC
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 54 0.61
43 34 0.39
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.22
Consensus pattern (42 bp):
GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGATA
Found at i:941801 original size:91 final size:90
Alignment explanation
Indices: 941626--941810 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
941616 ATTTCAAACT
*
941626 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
941691 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
941719 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
941783 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
941810 T
1 T
941811 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:943539 original size:40 final size:37
Alignment explanation
Indices: 943495--943607 Score: 117
Period size: 33 Copynumber: 3.1 Consensus size: 37
943485 TCTTTTGGTT
*
943495 GAAATAAAAATCGCAACGAGATAATGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGA-AATGA-AATCGCAACGC
**
943534 GGAAATGACTATCGCAACGAG--A-G-AATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAAATGAAATCGCAACGC
* *
943568 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAAATG-AAATCGCAACGC
943606 GA
1 GA
943608 TTTTGGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
33 17 0.28
34 11 0.18
35 1 0.02
36 2 0.03
37 1 0.02
38 12 0.20
40 17 0.28
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGAGAAATGAAATCGCAACGC
Found at i:943581 original size:19 final size:19
Alignment explanation
Indices: 943495--943607 Score: 110
Period size: 19 Copynumber: 6.1 Consensus size: 19
943485 TCTTTTGGTT
* *
943495 GAAATAAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
943514 GATAATGATAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
943534 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
943552 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
943568 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
943587 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
943606 GA
1 GA
943608 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 35 0.45
20 26 0.33
21 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:943625 original size:19 final size:19
Alignment explanation
Indices: 943603--943650 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
943593 AAAATCGCAA
*
943603 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
943622 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
943642 TGCGATTTT
1 TGCGATTTT
943651 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:944237 original size:20 final size:20
Alignment explanation
Indices: 944209--944262 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
944199 GATTTTGTAT
*
944209 TATCACATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
944229 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
*
944249 TGTCGCATTGCGAT
1 TATCGCATTGCGAT
944263 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:944373 original size:21 final size:21
Alignment explanation
Indices: 944333--944373 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
944323 ACTGTAGACC
**
944333 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
944354 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
944374 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:946224 original size:19 final size:19
Alignment explanation
Indices: 946197--946236 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
946187 ACAGGGAACC
946197 TTATCGGGGTCTTATAACT
1 TTATCGGGGTCTTATAACT
*
946216 TTATTGGGGTCTTATAACT
1 TTATCGGGGTCTTATAACT
946235 TT
1 TT
946237 GGAAAACTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (19 bp):
TTATCGGGGTCTTATAACT
Found at i:948018 original size:22 final size:22
Alignment explanation
Indices: 947993--948048 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
947983 TAAAAAATTA
*
947993 TATATATATTTTATTAAAAAAG
1 TATATATATTTTAATAAAAAAG
* * *
948015 TATATAAATTTAAAATAATAAAG
1 TATATATATTT-TAATAAAAAAG
948038 TA-ATATATTTT
1 TATATATATTTT
948049 CGATGAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (22 bp):
TATATATATTTTAATAAAAAAG
Found at i:948560 original size:7 final size:8
Alignment explanation
Indices: 948540--948573 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
948530 AATCTCAAGG
948540 TTTTTTTCC
1 TTTTTTT-C
948549 TTTTTTTC
1 TTTTTTTC
948557 TTTTTTTC
1 TTTTTTTC
948565 TTTTATTTC
1 TTTT-TTTC
948574 GATTTAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 13 0.54
9 11 0.46
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:948562 original size:17 final size:17
Alignment explanation
Indices: 948540--948573 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
948530 AATCTCAAGG
948540 TTTTTTTCCTTTT-TTTC
1 TTTTTTT-CTTTTATTTC
948557 TTTTTTTCTTTTATTTC
1 TTTTTTTCTTTTATTTC
948574 GATTTAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTTATTTC
Found at i:951191 original size:56 final size:56
Alignment explanation
Indices: 951072--951183 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
951062 ACACACCATC
951072 CACTA-TTTTTTTTATAGAAATCATATAATTTTATTTCATATTTTTACCTTATTTT
1 CACTATTTTTTTTTATAGAAATCATATAATTTTATTTCATATTTTTACCTTATTTT
951127 CACTATTTTTTTTTATAGAAATCATATAATTTTATTTCATATTTTTACCCTTATTTT
1 CACTATTTTTTTTTATAGAAATCATATAATTTTATTTCATATTTTTA-CCTTATTTT
951184 TTTATTTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 5 0.09
56 41 0.75
57 9 0.16
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.58
Consensus pattern (56 bp):
CACTATTTTTTTTTATAGAAATCATATAATTTTATTTCATATTTTTACCTTATTTT
Found at i:951235 original size:16 final size:16
Alignment explanation
Indices: 951214--951246 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
951204 TTTTGCCACA
951214 TAAGTAGAAAGTGCTT
1 TAAGTAGAAAGTGCTT
*
951230 TAAGTAGAAAGTTCTT
1 TAAGTAGAAAGTGCTT
951246 T
1 T
951247 CTGAAAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (16 bp):
TAAGTAGAAAGTGCTT
Found at i:951573 original size:26 final size:25
Alignment explanation
Indices: 951487--951573 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 25
951477 ATTTAATATT
*
951487 AATAAAATATT-TTAATATCATTTTAA
1 AATATAATATTATTAATAT--TTTTAA
*
951513 AATATTA-ATTATTAA-ATTATTTAA
1 AATATAATATTATTAATATT-TTTAA
*
951537 AATAT-AT-TTATTAATATTTCTAA
1 AATATAATATTATTAATATTTTTAA
951560 TAATATAATATTAT
1 -AATATAATATTAT
951574 ATTTTTAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
23 13 0.25
24 18 0.35
25 7 0.14
26 13 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
AATATAATATTATTAATATTTTTAA
Found at i:951575 original size:22 final size:23
Alignment explanation
Indices: 951545--951589 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
951535 AAAATATATT
951545 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
951568 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
951590 AATAATCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:951645 original size:22 final size:22
Alignment explanation
Indices: 951615--951677 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
951605 TATAATATAT
*
951615 ATAAGATATTATATTTTATTTA
1 ATAAAATATTATATTTTATTTA
* * **
951637 ATAATATATAATAAATTA-TTA
1 ATAAAATATTATATTTTATTTA
951658 ATAAAAT-TTATATATTTATT
1 ATAAAATATTATAT-TTTATT
951678 AATTTCATAG
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 4 0.13
21 12 0.39
22 15 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAAAATATTATATTTTATTTA
Found at i:951654 original size:29 final size:29
Alignment explanation
Indices: 951539--951655 Score: 78
Period size: 29 Copynumber: 3.9 Consensus size: 29
951529 TTATTTAAAA
* * *
951539 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTAATAATA--TATAATAA-ATTATAT
* * *
951571 TATATTT-TTAATATTATAAAATAATCA-AT
1 TATATTTAATAATA-TATAATA-AATTATAT
* *
951600 TATATTATAAT-ATATATAAGATATTATAT
1 TATATT-TAATAATATATAATAAATTATAT
*
951629 TTTATTTAATAATATATAATAAATTAT
1 TATATTTAATAATATATAATAAATTAT
951656 TAATAAAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
28 7 0.10
29 35 0.50
30 13 0.19
31 8 0.11
32 7 0.10
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (29 bp):
TATATTTAATAATATATAATAAATTATAT
Found at i:951929 original size:20 final size:20
Alignment explanation
Indices: 951905--951959 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
951895 TTATTAAAAT
951905 TATAAAAATAATATTTTAATA
1 TATAAAAA-AATATTTTAATA
*
951926 -ATAAATAAATTATTTTAATA
1 TATAAA-AAAATATTTTAATA
*
951946 TTTAAAAAAATATT
1 TATAAAAAAATATT
951960 AAGTTTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAAAAAAATATTTTAATA
Found at i:952214 original size:39 final size:39
Alignment explanation
Indices: 952160--952234 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
952150 CAAACATACT
952160 CTAAAAACTCCTTCCACTTACATGACATAAAAGTGTACC
1 CTAAAAACTCCTTCCACTTACATGACATAAAAGTGTACC
*
952199 CTAAAATCTCCTTCCACTTACATGACATAAAAGTGT
1 CTAAAAACTCCTTCCACTTACATGACATAAAAGTGT
952235 GCTAAATTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.28
Consensus pattern (39 bp):
CTAAAAACTCCTTCCACTTACATGACATAAAAGTGTACC
Found at i:954235 original size:31 final size:30
Alignment explanation
Indices: 954200--954270 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
954190 GTGTCGTAAT
954200 AATAAAATATAAATTTAAAAGTTTAGA-TAAA
1 AATAAAATATAAATTTAAAA-TTTA-ATTAAA
* * *
954231 AATAAAATATATATTTTAAATTTAATTTAA
1 AATAAAATATAAATTTAAAATTTAATTAAA
954261 AATAAAATAT
1 AATAAAATAT
954271 TTTTAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.03
30 17 0.47
31 18 0.50
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (30 bp):
AATAAAATATAAATTTAAAATTTAATTAAA
Found at i:954291 original size:27 final size:27
Alignment explanation
Indices: 954231--954326 Score: 87
Period size: 26 Copynumber: 3.6 Consensus size: 27
954221 TTTAGATAAA
* *
954231 AATAA-AATATATATTTTAAATTTAATTT
1 AATAATAAAATAT-TTTTAAA-TTAAGTT
954259 AA-AATAAAATATTTTTAAATTAAGTT
1 AATAATAAAATATTTTTAAATTAAGTT
*
954285 AATAAT-AAAT-TTTATTTAA-TAAGTT
1 AATAATAAAATATTT-TTAAATTAAGTT
954310 AAT-ATAAAAATATTTTT
1 AATAAT-AAAATATTTTT
954327 TAAGTTAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
24 2 0.03
25 12 0.20
26 22 0.37
27 15 0.25
28 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
AATAATAAAATATTTTTAAATTAAGTT
Found at i:954330 original size:23 final size:24
Alignment explanation
Indices: 954278--954338 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
954268 TATTTTTAAA
* *
954278 TTAAGTTAATA-ATAAATTTTATT
1 TTAAGTTAATATAAAAATATTATT
954301 TAATAAGTTAATATAAAAATATT-TT
1 T--TAAGTTAATATAAAAATATTATT
954326 TTAAGTTAATATA
1 TTAAGTTAATATA
954339 TATAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 13 0.39
25 13 0.39
26 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (24 bp):
TTAAGTTAATATAAAAATATTATT
Found at i:955524 original size:220 final size:222
Alignment explanation
Indices: 955071--955557 Score: 700
Period size: 220 Copynumber: 2.2 Consensus size: 222
955061 CTTATTCATA
* *
955071 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATT---GT
* *
955136 CGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTC
63 CGGGTCGGGTCGGATGAAACTTTATTTTGGTCGGGTCGGATCAGGTTTTTTTAAGTGTGATATT-
* *
955201 AGGTCGGGTCGGGTTCGGGTTTGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATAT
127 --GTCGGGTCGAGTTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATAT
955266 AATTCAGGTCAGGTCGGATTAAGTCACTGTTTT
190 AATTCAGGTCAGGTCGGATTAAGTCACTGTTTT
* *
955299 TATTAAATAAAAATAATTTTTTATTATTTTGGGTTGGGTCGGGTCAGATTTCTAATTCATATA-T
1 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTC-GG---G-TTTCTAATTCATATATT
* * *
955363 -TCGGGTCGGGTCGGATGAAACTTTATTTTGTTTGGGTCGGGTCAGG-TTTTTTAAGTGTGATA-
61 GTCGGGTCGGGTCGGATGAAACTTTATTTTGGTCGGGTCGGATCAGGTTTTTTTAAGTGTGATAT
955425 T-TCGGGTCGAG-TCGGG-TCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATA
126 TGTCGGGTCGAGTTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATA
* *
955487 ATTCGGGTCGGGTCGGATTAAGTCACTGTTTT
191 ATTCAGGTCAGGTCGGATTAAGTCACTGTTTT
*
955519 TATTAAATAAAAATACTTTTTTATTATTTCGGGTCGGGT
1 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGT
955558 TTTTAAAGTG
Statistics
Matches: 238, Mismatches: 16, Indels: 18
0.88 0.06 0.07
Matches are distributed among these distances:
220 111 0.47
221 5 0.02
222 9 0.04
226 1 0.00
227 16 0.07
228 77 0.32
229 2 0.01
232 2 0.01
233 15 0.06
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (222 bp):
TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTGTCGG
GTCGGGTCGGATGAAACTTTATTTTGGTCGGGTCGGATCAGGTTTTTTTAAGTGTGATATTGTCG
GGTCGAGTTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCA
GGTCAGGTCGGATTAAGTCACTGTTTT
Found at i:955588 original size:37 final size:38
Alignment explanation
Indices: 955547--955627 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
955537 TTTTATTATT
955547 TCGGGTCGGG-TTTTTAAAGTGTGATATTCGGGTCGAG
1 TCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGAG
* *
955584 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGAG
955622 TCGGGT
1 TCGGGT
955628 TCAGGTTTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 10 0.24
38 31 0.76
ACGTcount: A:0.12, C:0.11, G:0.40, T:0.37
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGAG
Found at i:955809 original size:38 final size:38
Alignment explanation
Indices: 955744--955827 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
955734 ACTTTATTTT
*
955744 GTTCGGGTCGGGTTTTTTAAGTTTGATATTCGGGTCGA
1 GTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
*
955782 G-TCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGTCGG
1 GTTCGGGTC-GGGTTTTTTAAGTGTGATATTCGGGTCGA
955820 GTTCGGGT
1 GTTCGGGT
955828 TTAGGGTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
37 7 0.17
38 29 0.69
39 6 0.14
ACGTcount: A:0.11, C:0.11, G:0.39, T:0.39
Consensus pattern (38 bp):
GTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:956372 original size:16 final size:18
Alignment explanation
Indices: 956351--956396 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
956341 TATAGAATTG
956351 GATTTCAATTCC-T-ACA
1 GATTTCAATTCCTTCACA
956367 GATTTCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
*
956385 GATTCCAATTCC
1 GATTTCAATTCC
956397 CTCATAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 14 0.52
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:957099 original size:16 final size:16
Alignment explanation
Indices: 957080--957111 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
957070 ATAGAAAAGT
957080 TCTCAAGCATTCAAGG
1 TCTCAAGCATTCAAGG
957096 TCTCAAGCATTCAAGG
1 TCTCAAGCATTCAAGG
957112 CAACTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (16 bp):
TCTCAAGCATTCAAGG
Found at i:961095 original size:107 final size:106
Alignment explanation
Indices: 960943--961155 Score: 392
Period size: 106 Copynumber: 2.0 Consensus size: 106
960933 TTTAAGGAAG
960943 CAAATGGTGTATAACCTGTTAAAACGTATTGAATAAAAAATCGAGTTTTCGCAACCAATCTAGAC
1 CAAATGGTGTATAACCTGTTAAAACGTATTGAATAAAAAATCGAG-TTTCGCAACCAATCTAGAC
961008 ATTGACATTGTTCTTCTTATGTAGTGTGAGGATGAGGAAGTT
65 ATTGACATTGTTCTTCTTATGTAGTGTGAGGATGAGGAAGTT
*
961050 CAAATGGTGTATAA-CTGTTAAAACGTATTGAAATAAAAATTCGAGTTTCGCAACCAATCTAGAC
1 CAAATGGTGTATAACCTGTTAAAACGTATTG-AATAAAAAATCGAGTTTCGCAACCAATCTAGAC
961114 ATTGACATTGTTCTTCTTATGTAGTGTGAGGATGAGGAAGTT
65 ATTGACATTGTTCTTCTTATGTAGTGTGAGGATGAGGAAGTT
961156 GGTCAGGTCT
Statistics
Matches: 104, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
106 77 0.74
107 27 0.26
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (106 bp):
CAAATGGTGTATAACCTGTTAAAACGTATTGAATAAAAAATCGAGTTTCGCAACCAATCTAGACA
TTGACATTGTTCTTCTTATGTAGTGTGAGGATGAGGAAGTT
Found at i:961447 original size:23 final size:23
Alignment explanation
Indices: 961412--961456 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
961402 CTTTAATATT
961412 AAATTATAAATAT-TTTGAATTA
1 AAATTATAAATATATTTGAATTA
* *
961434 AAATCTATAGATATATTTTAATT
1 AAAT-TATAAATATATTTGAATT
961457 GTTGCACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
AAATTATAAATATATTTGAATTA
Found at i:961949 original size:43 final size:43
Alignment explanation
Indices: 961888--961978 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
961878 ATTTATTATT
*
961888 TCAAATGTATTTTTGTTTAGAGTGGTAAGAATTGTATAATATC
1 TCAAATGTATTTTTGTTTAGAGTGATAAGAATTGTATAATATC
961931 TCAAATGTATTTTTGTTTAGAGTGATAAGAATTGTATAATATC
1 TCAAATGTATTTTTGTTTAGAGTGATAAGAATTGTATAATATC
961974 T-AAAT
1 TCAAAT
961979 ATTTAGAGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 4 0.09
43 43 0.91
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.44
Consensus pattern (43 bp):
TCAAATGTATTTTTGTTTAGAGTGATAAGAATTGTATAATATC
Found at i:962311 original size:24 final size:25
Alignment explanation
Indices: 962284--962394 Score: 122
Period size: 24 Copynumber: 4.5 Consensus size: 25
962274 AAATTGAACG
*
962284 ACCGGTTTTTTTA-CCGGATTAAAA
1 ACCGGTTTTTTTATCCGGATAAAAA
* *
962308 ACCGGTTTTTTTCAAACCAGATAAAAA
1 ACCGGTTTTTTT--ATCCGGATAAAAA
962335 ACCGG-TTTTTTATCCGGAT-AAAA
1 ACCGGTTTTTTTATCCGGATAAAAA
* * *
962358 ACC-GATTTTTTATCCGAAAAAAAA
1 ACCGGTTTTTTTATCCGGATAAAAA
962382 ACCGGTTTTTTTA
1 ACCGGTTTTTTTA
962395 AAAAAAAATC
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
22 1 0.01
23 19 0.26
24 25 0.34
25 8 0.11
26 7 0.09
27 14 0.19
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (25 bp):
ACCGGTTTTTTTATCCGGATAAAAA
Found at i:962397 original size:20 final size:20
Alignment explanation
Indices: 962374--962412 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
962364 TTTTTATCCG
962374 AAAAAAAAACCGGTTTTTTT
1 AAAAAAAAACCGGTTTTTTT
*
962394 AAAAAAAAATCGGTTTTTT
1 AAAAAAAAACCGGTTTTTT
962413 GCAAACCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAAAAAAACCGGTTTTTTT
Found at i:964396 original size:25 final size:25
Alignment explanation
Indices: 964350--964417 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
964340 TCTATATGCT
*
964350 ATAATGCATGTATATATATCAAATAA
1 ATAATACATGT-TATATATCAAATAA
964376 ATAATACATGTTATATATCAAATAA
1 ATAATACATGTTATATATCAAATAA
964401 ATAATACATGTTATATA
1 ATAATACATGTTATATA
964418 AATCTGGACA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 31 0.76
26 10 0.24
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (25 bp):
ATAATACATGTTATATATCAAATAA
Found at i:971373 original size:30 final size:29
Alignment explanation
Indices: 971339--971403 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
971329 ACACGTTGGG
971339 ACAGCTTAGTGGAGCATTTGGAAGACATA
1 ACAGCTTAGTGGAGCATTTGGAAGACATA
* * *
971368 CACAGCCTGGTGGAGCATTTGGGAGACATA
1 -ACAGCTTAGTGGAGCATTTGGAAGACATA
971398 ACAGCT
1 ACAGCT
971404 CACACAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (29 bp):
ACAGCTTAGTGGAGCATTTGGAAGACATA
Found at i:973419 original size:113 final size:112
Alignment explanation
Indices: 973208--973433 Score: 443
Period size: 113 Copynumber: 2.0 Consensus size: 112
973198 ACCCGAAATC
973208 ATTTAGCAAAATAATGTAAAAAATATAATAAAGCGATCTGAAATCACTTTCTTCCAAATCATTCG
1 ATTTAGCAAAATAATGTAAAAAATATAATAAAGCGATCTGAAATCACTTTCTTCCAAATCATTCG
973273 AGATTGACTTATCTCAAGTCTTCCTCATAACATACTTTAATAATATA
66 AGATTGACTTATCTCAAGTCTTCCTCATAACATACTTTAATAATATA
973320 ATTTAGCAAAATAATGTAAAAAATATAATAAAGCGATCTGAAATCACTTTCTTTCCAAATCATTC
1 ATTTAGCAAAATAATGTAAAAAATATAATAAAGCGATCTGAAATCACTTTC-TTCCAAATCATTC
973385 GAGATTGACTTATCTCAAGTCTTCCTCATAACATACTTTAATAATATA
65 GAGATTGACTTATCTCAAGTCTTCCTCATAACATACTTTAATAATATA
973433 A
1 A
973434 GAAAGATGCA
Statistics
Matches: 113, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
112 51 0.45
113 62 0.55
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (112 bp):
ATTTAGCAAAATAATGTAAAAAATATAATAAAGCGATCTGAAATCACTTTCTTCCAAATCATTCG
AGATTGACTTATCTCAAGTCTTCCTCATAACATACTTTAATAATATA
Found at i:979643 original size:42 final size:43
Alignment explanation
Indices: 979558--979736 Score: 126
Period size: 43 Copynumber: 4.2 Consensus size: 43
979548 AAAAATTATT
*
979558 AAATTAGGGGCTTGAATTATAAAAGTAAAAAGTATGATTAAAA
1 AAATTAGGGCCTTGAATTATAAAAGTAAAAAGTATGATTAAAA
*
979601 AAATTAGGGACCTTG-ATTAT-AAAGTAAAAGAG-A-GGTT-AAA
1 AAATTAGGG-CCTTGAATTATAAAAGTAAAA-AGTATGATTAAAA
* * * *
979641 AAATTAGTGGCC-TCAATTTTAAAGGTAAAAA--ATGATACTGAAA
1 AAATTAG-GGCCTTGAATTATAAAAGTAAAAAGTATGAT--TAAAA
* * *
979684 AAATTAGGAGCC-TCAGTTATAAAGGTAAAAAGTGA-GATTGAAAAA
1 AAATTAGG-GCCTTGAATTATAAAAGTAAAAAGT-ATGATT--AAAA
979729 AAATTAGG
1 AAATTAGG
979737 ATCATCAATT
Statistics
Matches: 112, Mismatches: 9, Indels: 28
0.75 0.06 0.19
Matches are distributed among these distances:
39 2 0.02
40 19 0.17
41 13 0.12
42 12 0.11
43 47 0.42
44 4 0.04
45 14 0.12
46 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.26
Consensus pattern (43 bp):
AAATTAGGGCCTTGAATTATAAAAGTAAAAAGTATGATTAAAA
Found at i:979687 original size:43 final size:43
Alignment explanation
Indices: 979638--979750 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 43
979628 AAGAGAGGTT
* *
979638 AAAAAATTAGTG-GCCTCAATTTTAAAGGTAAAAAATGATACTG
1 AAAAAATTAG-GAGCCTCAATTATAAAGGTAAAAAATGAGACTG
* * *
979681 AAAAAATTAGGAGCCTCAGTTATAAAGGTAAAAAGTGAGATTG
1 AAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAATGAGACTG
* *
979724 AAAAAAAATTAGGATCATCAATTATAA
1 --AAAAAATTAGGAGCCTCAATTATAA
979751 TTATAAAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.02
43 36 0.61
45 22 0.37
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.26
Consensus pattern (43 bp):
AAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAATGAGACTG
Found at i:979749 original size:45 final size:45
Alignment explanation
Indices: 979638--979778 Score: 126
Period size: 43 Copynumber: 3.2 Consensus size: 45
979628 AAGAGAGGTT
* * * * *
979638 AAAAAATTAGTG-GCCTCAATTTTAAAGGTAAAAAATGATACTG--
1 AAAAAATTAG-GAGCATCAATTATAAAGGTAAAAAGTGAGATTGAA
* *
979681 AAAAAATTAGGAGCCTCAGTTATAAAGGTAAAAAGTGAGATTGAA
1 AAAAAATTAGGAGCATCAATTATAAAGGTAAAAAGTGAGATTGAA
* *** **
979726 AAAAAATTAGGATCATCAATTATAATTATAAAAAAGTTTGATTGAA
1 AAAAAATTAGGAGCATCAATTATAAAGGT-AAAAAGTGAGATTGAA
979772 AAAAAAT
1 AAAAAAT
979779 AAAGGCCCCC
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.01
43 36 0.44
45 23 0.28
46 21 0.26
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (45 bp):
AAAAAATTAGGAGCATCAATTATAAAGGTAAAAAGTGAGATTGAA
Found at i:982353 original size:23 final size:23
Alignment explanation
Indices: 982323--982375 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
982313 CCTGTAATTG
982323 ATTTTCCGGAAAATGTTTT-CTTC
1 ATTTTCCGGAAAATGTTTTAC-TC
982346 ATTTTCCGGAAAATGTTTTACTC
1 ATTTTCCGGAAAATGTTTTACTC
982369 ATTTTCC
1 ATTTTCC
982376 AGTGTTTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (23 bp):
ATTTTCCGGAAAATGTTTTACTC
Found at i:982731 original size:32 final size:32
Alignment explanation
Indices: 982692--982785 Score: 102
Period size: 32 Copynumber: 2.9 Consensus size: 32
982682 TTTAATAATA
982692 TAATAAATTATTAATAAA-ATTAATTTTATTAT
1 TAATAAATTATTAATAAATATTAATTTTATT-T
* *
982724 TAATAAATT-TAGAATATATATACTAATTTTATTT
1 TAATAAATTAT-TAATA-A-ATATTAATTTTATTT
* *
982758 TAATAAATAATTAATAAATTTTAATTTT
1 TAATAAATTATTAATAAATATTAATTTT
982786 GAATATAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
31 1 0.02
32 22 0.43
33 2 0.04
34 14 0.27
35 12 0.24
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (32 bp):
TAATAAATTATTAATAAATATTAATTTTATTT
Found at i:986209 original size:43 final size:43
Alignment explanation
Indices: 986160--986263 Score: 154
Period size: 43 Copynumber: 2.4 Consensus size: 43
986150 AAATATATCA
*
986160 ATATTTTAAATAATTAAAATAATACATTTTATAATAATTTATT
1 ATATTTTAAATAATTAAAATAATACATTTTATAATAACTTATT
* * * *
986203 GTATTTTAAATTATTAAAATAATATATTTTATAATAACTTGTT
1 ATATTTTAAATAATTAAAATAATACATTTTATAATAACTTATT
*
986246 ATATTTTTAATAATTAAA
1 ATATTTTAAATAATTAAA
986264 TAAAATATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (43 bp):
ATATTTTAAATAATTAAAATAATACATTTTATAATAACTTATT
Found at i:989334 original size:13 final size:13
Alignment explanation
Indices: 989316--989348 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
989306 GATTTTCTTG
*
989316 TTGAAAATCATTT
1 TTGAAAATCAATT
989329 TTG-AAATCAATT
1 TTGAAAATCAATT
989341 TTGAAAAT
1 TTGAAAAT
989349 TATTCCTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (13 bp):
TTGAAAATCAATT
Found at i:990516 original size:15 final size:15
Alignment explanation
Indices: 990496--990525 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
990486 AATTTCTCTC
990496 TCGTTATCTAAACCA
1 TCGTTATCTAAACCA
990511 TCGTTATCTAAACCA
1 TCGTTATCTAAACCA
990526 AATGTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
TCGTTATCTAAACCA
Found at i:991391 original size:21 final size:22
Alignment explanation
Indices: 991365--991441 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
991355 ACCCGTCGGG
* *
991365 TGTATCGATACAC-TCGAGGAA
1 TGTATCGGTACACATCAAGGAA
991386 TGTATCGGTACACATTCAAGGAA
1 TGTATCGGTACACA-TCAAGGAA
*
991409 AGTATCGGTACACATTCAAGG--
1 TGTATCGGTACACA-TCAAGGAA
*
991430 TGTATCGATACA
1 TGTATCGGTACA
991442 TAGCAAGGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 22 0.45
23 27 0.55
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (22 bp):
TGTATCGGTACACATCAAGGAA
Found at i:991413 original size:23 final size:23
Alignment explanation
Indices: 991381--991429 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
991371 GATACACTCG
*
991381 AGGAATGTATCGGTACACATTCA
1 AGGAAAGTATCGGTACACATTCA
991404 AGGAAAGTATCGGTACACATTCA
1 AGGAAAGTATCGGTACACATTCA
991427 AGG
1 AGG
991430 TGTATCGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (23 bp):
AGGAAAGTATCGGTACACATTCA
Found at i:993095 original size:72 final size:72
Alignment explanation
Indices: 992978--993121 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
992968 ATAACATTCT
992978 AATTACTTCCATCCTAGCTATGGGAGCATATGTTTCATCATAATCTATACCTTCTTTTTGAGTAT
1 AATTACTTCCATCCTAGCTATGGGAGCATATGTTTCATCATAATCTATACCTTCTTTTTGAGTAT
993043 AGATTTG
66 AGATTTG
993050 AATTACTTCCATCCTAGCTATGGGAGCATATGTTTCATCATAATCTATACCTTCTTTTTGAGTAT
1 AATTACTTCCATCCTAGCTATGGGAGCATATGTTTCATCATAATCTATACCTTCTTTTTGAGTAT
993115 AGATTTG
66 AGATTTG
993122 TTCGTACTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (72 bp):
AATTACTTCCATCCTAGCTATGGGAGCATATGTTTCATCATAATCTATACCTTCTTTTTGAGTAT
AGATTTG
Found at i:997950 original size:28 final size:27
Alignment explanation
Indices: 997900--997955 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
997890 TCTGAGTCGT
997900 TTATATCATTAAATTTCAATTTTATCAA
1 TTATATCATTAAATTTCAATTTTA-CAA
* *
997928 TTATATTATTAAACTTT-ATTTTTACAA
1 TTATATCATTAAA-TTTCAATTTTACAA
997955 T
1 T
997956 CAATTATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 18 0.72
29 3 0.12
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.54
Consensus pattern (27 bp):
TTATATCATTAAATTTCAATTTTACAA
Found at i:999097 original size:16 final size:17
Alignment explanation
Indices: 999066--999103 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
999056 TTATTAATAG
999066 AAAATATATAAAAAAATTT
1 AAAATATA-AAAAAAA-TT
999085 AAAATAT-AAAAAAATT
1 AAAATATAAAAAAAATT
999101 AAA
1 AAA
999104 TTTAGGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 7 0.37
19 7 0.37
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATATAAAAAAAATT
Found at i:999790 original size:23 final size:24
Alignment explanation
Indices: 999745--999792 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
999735 TTCAAAGATT
*
999745 AAAAGAGATAAAATTAATTAATAA
1 AAAAGAGATAAAATTAATAAATAA
*
999769 AAAAGAGATAAACTTAA-AAATAA
1 AAAAGAGATAAAATTAATAAATAA
999792 A
1 A
999793 CTATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.21
Consensus pattern (24 bp):
AAAAGAGATAAAATTAATAAATAA
Found at i:1002021 original size:19 final size:19
Alignment explanation
Indices: 1001993--1002029 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1001983 CAAAGTGTGT
*
1001993 TAATAATTATTTACTATTC
1 TAATAATTATTTAATATTC
*
1002012 TAATACTTATTTAATATT
1 TAATAATTATTTAATATT
1002030 ATTTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATAATTATTTAATATTC
Found at i:1004296 original size:60 final size:60
Alignment explanation
Indices: 1004142--1004306 Score: 199
Period size: 59 Copynumber: 2.8 Consensus size: 60
1004132 TGAGATGTTT
* * * **
1004142 AAAAGTTTGGGGACTAATTTAGAATAAGGGTCATAGTTTGAGGATGCATTTGGAATATTC
1 AAAAGTTTAGGGACTAATTTAGAATAAGAGTCATAGTTTGAGGATGCAATTAAAATATTC
* * * *
1004202 -AAAGTTTAGGGACCAATTTAGAATGAGATTCATAGTTT-ATGGATGGAATTAAAATATTC
1 AAAAGTTTAGGGACTAATTTAGAATAAGAGTCATAGTTTGA-GGATGCAATTAAAATATTC
* * *
1004261 AAAAATTTAGGGACTAATTTAGAATAAGAGACATAGTTTCAGGATG
1 AAAAGTTTAGGGACTAATTTAGAATAAGAGTCATAGTTTGAGGATG
1004307 TACGTTGAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.01
59 48 0.55
60 38 0.43
61 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (60 bp):
AAAAGTTTAGGGACTAATTTAGAATAAGAGTCATAGTTTGAGGATGCAATTAAAATATTC
Found at i:1005881 original size:18 final size:18
Alignment explanation
Indices: 1005858--1005904 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
1005848 ATGCAAAATA
1005858 GGTACCGATACCCAAAGG
1 GGTACCGATACCCAAAGG
1005876 GGTACCGATACCCAAAGG
1 GGTACCGATACCCAAAGG
1005894 GGTACCGATAC
1 GGTACCGATAC
1005905 TACTTTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.32, C:0.28, G:0.28, T:0.13
Consensus pattern (18 bp):
GGTACCGATACCCAAAGG
Found at i:1006030 original size:21 final size:22
Alignment explanation
Indices: 1005995--1006038 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1005985 TAAATATAAC
1005995 AAAGGAAGTACCGATACTCATT
1 AAAGGAAGTACCGATACTCATT
*
1006017 AAAGG-AGTATCGATACTCATT
1 AAAGGAAGTACCGATACTCATT
1006038 A
1 A
1006039 TCCTGGGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (22 bp):
AAAGGAAGTACCGATACTCATT
Found at i:1007278 original size:20 final size:20
Alignment explanation
Indices: 1007253--1007295 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1007243 TTTTCTCTTT
* *
1007253 AAAGCAAAATTAGATTTTGG
1 AAAGCAAAATGAAATTTTGG
1007273 AAAGCAAAATGAAATTTTGG
1 AAAGCAAAATGAAATTTTGG
1007293 AAA
1 AAA
1007296 ATGATTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.26
Consensus pattern (20 bp):
AAAGCAAAATGAAATTTTGG
Found at i:1012084 original size:19 final size:19
Alignment explanation
Indices: 1012060--1012111 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1012050 GAATGCAATT
1012060 TTGGTATCGATACCCAGGC
1 TTGGTATCGATACCCAGGC
*
1012079 TTGGTATCGATACCTAGGC
1 TTGGTATCGATACCCAGGC
1012098 TTGGTATCGATACC
1 TTGGTATCGATACC
1012112 ATAGCTAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (19 bp):
TTGGTATCGATACCCAGGC
Found at i:1012729 original size:22 final size:22
Alignment explanation
Indices: 1012701--1012743 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1012691 CGAGGGTTTC
1012701 ATAGGTCCTTCAGGACATATTT
1 ATAGGTCCTTCAGGACATATTT
*
1012723 ATAGGTCCTTCGGGACATATT
1 ATAGGTCCTTCAGGACATATT
1012744 CCACATGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (22 bp):
ATAGGTCCTTCAGGACATATTT
Found at i:1014117 original size:42 final size:42
Alignment explanation
Indices: 1014037--1014119 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1014027 CTCAACAAGT
* **
1014037 ATTACCTTATGATTATACATTAATATTATTGTCAAATTATAA
1 ATTACCTTATGATTATACATTAAAATTACCGTCAAATTATAA
* *
1014079 ATTAGCTTATGATTATACGTTAAAATTACCGTTC-AATTATA
1 ATTACCTTATGATTATACATTAAAATTACCG-TCAAATTATA
1014120 TTTTTTACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (42 bp):
ATTACCTTATGATTATACATTAAAATTACCGTCAAATTATAA
Found at i:1020672 original size:90 final size:90
Alignment explanation
Indices: 1020551--1020728 Score: 295
Period size: 90 Copynumber: 2.0 Consensus size: 90
1020541 TAATCCCGAA
*
1020551 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCCCAATATGA
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAT-CCCAATATGA
1020615 TTAGGGTAACTTAGATATAAAAGGAT
65 TTAGGGTAACTTAGATATAAAAGGAT
* *
1020641 TATTAAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAAATCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCCAATATGAT
* *
1020706 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTAGATATAAAAGG
1020729 GTGTGTTAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 77 0.94
91 5 0.06
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCCAATATGAT
TAGGGTAACTTAGATATAAAAGGAT
Found at i:1030268 original size:24 final size:24
Alignment explanation
Indices: 1030241--1030287 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1030231 TTTCATTTAT
1030241 AATTAGAGTTTGAATTTAAATTTC
1 AATTAGAGTTTGAATTTAAATTTC
* * *
1030265 AATTTGAGTTTGAGTTTGAATTT
1 AATTAGAGTTTGAATTTAAATTT
1030288 AAATGTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (24 bp):
AATTAGAGTTTGAATTTAAATTTC
Found at i:1030820 original size:200 final size:200
Alignment explanation
Indices: 1030474--1031644 Score: 1837
Period size: 200 Copynumber: 5.8 Consensus size: 200
1030464 TTATTCATTC
* * * * ** * *
1030474 GTGTCGATACATGTTGTCCATAATGTA-TTTCCAAACCAAGTGTACGAAAAAAGTGTCGATACAT
1 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCAC-AACAAAGTGTCGATACAT
* * * *
1030538 TTATAACAAGTGTCGATACTAAAAACATCGAAACACATAGA-TATAATGTAATAGGTAAAATAAC
65 TTATAACAAGTGTCGATCCGAAAAACATCGAAACCCATA-ATTATAATGTAATAGGTAAATTAAC
* *
1030602 AATGTAACCGGCCTAAATATACCGGTTTTTGAGAAAACATGTATACATAAAGTATCGACACAAAT
129 AATGTAACCGGCCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAAT
*
1030667 ACAATAA
194 ACAACAA
*
1030674 GTGTCGATACTTTTTGTCCAGCGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
* * *
1030739 TATAATAAGTGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
66 TATAACAAGTGTCGATCCGAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
* *
1030804 TGTAACCGGTCTAAATATACCGGTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATGA
131 TGTAACCGGCCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAAT-A
1030869 -AACAA
195 CAACAA
* * *
1030874 GTGTCGATACTTTTTGTACAGAGTGTATTTTAAAAACCAAGTGCACAACAAAATGTCGATACAAT
1 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1030939 TATAACAAGTGTCGATCCGAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
66 TATAACAAGTGTCGATCCGAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
* *
1031004 TGTAACCGGTCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCAACACAAATGA
131 TGTAACCGGCCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAAT-A
1031069 -AACAA
195 CAACAA
*
1031074 TTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
* *
1031139 TATAACAAGTGTCGATCCGAAAAATATCGAAACCCATAATTATAATATAATAGGTAAATTAACAA
66 TATAACAAGTGTCGATCCGAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
* * *
1031204 TGTAACCAGCCTAAATATACTGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATCC
131 TGTAACCGGCCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATAC
1031269 AACAA
196 AACAA
* * *
1031274 ATGTCGATACTTTTTGTTCAAAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
*
1031339 TATAACAAGTGTCGATCCGAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTAACAA
66 TATAACAAGTGTCGATCCGAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
* * * * * *
1031404 TGTAACTGACCTAAATATATCGGTTTATGAGAAAACAAGTATACATAAAGTATTGACACAAATCC
131 TGTAACCGGCCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATAC
1031469 AACAA
196 AACAA
*
1031474 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTTTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
*
1031539 TATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
66 TATAACAAGTGTCGATCCGAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
** * *
1031604 TGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGT
131 TGTAACCGGCCTAAATATACCGG-TTTATGAGAAAACAGGT
1031645 CTAACTAATG
Statistics
Matches: 899, Mismatches: 67, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
199 1 0.00
200 867 0.96
201 31 0.03
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (200 bp):
GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
TATAACAAGTGTCGATCCGAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
TGTAACCGGCCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATAC
AACAA
Found at i:1031768 original size:200 final size:199
Alignment explanation
Indices: 1030474--1031860 Score: 1768
Period size: 200 Copynumber: 6.9 Consensus size: 199
1030464 TTATTCATTC
* * * ** * *
1030474 GTGTCGATACATGTTGTCCATAATGTA-TTTCCAAACCAAGTGTACGAAAAAAGTGTCGATACAT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTAAAAACCAAGTGCAC-AACAAAGTGTCGATACAT
* * *
1030538 TTATAACAAGTGTCGATACTAAAAACATCGAAACACATAGA-TATAATGTAATAGGTAAAATAAC
65 TTATAACAAGTGTCGAT-CCAAAAACATCGAAACCCATA-ATTATAATGTAATAGGTAAATTAAC
* * *
1030602 AATGTAACCGGCCTAAATATACCGGTTTTTGAGAAAACATGTATACATAAAGTATCGACACAAAT
128 AATGTAACCGGTCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAAT
1030667 AC-AATAA
193 -CTAATAA
**
1030674 GTGTCGATACTTTTTGTCCAGCGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
* *
1030739 TATAATAAGTGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
66 TATAACAAGTGTCGAT-CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
* **
1030804 TGTAACCGGTCTAAATATACCGGTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATGA
130 TGTAACCGGTCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATCT
*
1030869 AACAA
195 AATAA
* * * *
1030874 GTGTCGATACTTTTTGTACAGAGTGTATTTTAAAAACCAAGTGCACAACAAAATGTCGATACAAT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1030939 TATAACAAGTGTCGATCCGAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
66 TATAACAAGTGTCGATCC-AAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
* **
1031004 TGTAACCGGTCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCAACACAAATGA
130 TGTAACCGGTCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATCT
*
1031069 AACAA
195 AATAA
* *
1031074 TTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
* *
1031139 TATAACAAGTGTCGATCCGAAAAATATCGAAACCCATAATTATAATATAATAGGTAAATTAACAA
66 TATAACAAGTGTCGATCC-AAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
* * * *
1031204 TGTAACCAGCCTAAATATACTGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATCC
130 TGTAACCGGTCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATCT
*
1031269 AACAA
195 AATAA
* *
1031274 ATGTCGATACTTTTTGTTCA-AAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACAT
1 GTGTCGATACTTTTTGTCCAGAA-TGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACAT
*
1031338 TTATAACAAGTGTCGATCCGAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTAACA
65 TTATAACAAGTGTCGATCC-AAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACA
* ** * * *
1031403 ATGTAACTGACCTAAATATATCGGTTTATGAGAAAACAAGTATACATAAAGTATTGACACAAATC
129 ATGTAACCGGTCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATC
* *
1031468 CAACAA
194 TAATAA
* *
1031474 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTTTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1031539 TATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
66 TATAACAAGTGTCGAT-CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAA
* * * * * * **
1031604 TGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTA-ACTAATGTATCAACACTTTA
130 TGTAACCGGTCTAAATATACCGG-TTTATGAGAAAACAGGTATACA-TAAAGTATCGACAC-AAA
* **
1031668 T-TTATTT
192 TCTAATAA
* * * *** * * *
1031675 GTGTCGATACTTTTTATCCATAATG-AATTCCCAAACTATGTGCAC-GCTTAAAGTGTCGATACA
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTAAAAACCAAGTGCACAAC--AAAGTGTCGATACA
* * ** * ** * *
1031738 TTTATTAA-AAGTATCGA-CCAAAATACATCGAGACTGAAAATTATAATGTAATAGGCCACTTTA
64 TTTA-TAACAAGTGTCGATCCAAAA-ACATCGAAACCCATAATTATAATGTAATAGGTAAATTAA
* * * * * *
1031801 CAATGTAACCGGTTTAAATTTACCGGTTTTATGAGCAAATAGGTCTACATAATGTATCGA
127 CAATGTAACCGGTCTAAATATACCGG-TTTATGAGAAAACAGGTATACATAAAGTATCGA
1031861 TACTTTTTAC
Statistics
Matches: 1072, Mismatches: 100, Indels: 30
0.89 0.08 0.02
Matches are distributed among these distances:
199 11 0.01
200 961 0.90
201 95 0.09
202 5 0.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (199 bp):
GTGTCGATACTTTTTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
TATAACAAGTGTCGATCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAACAAT
GTAACCGGTCTAAATATACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATCTA
ATAA
Found at i:1031877 original size:200 final size:200
Alignment explanation
Indices: 1031523--1032088 Score: 671
Period size: 200 Copynumber: 2.8 Consensus size: 200
1031513 AGTGCACAAC
* * ** *
1031523 AAAGTTTCGATACATTTA-TAACAAGTGTCGATCCCAAAA-ACATCGAAACCCATAATTATAATG
1 AAAGTTTCGATACATTTATTAA-AAGTATCGA-CCCAAAATACATCGAGACTGAAAATTATAATG
* *
1031586 TAATAGGTAAATTAACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTA-AC
64 TAATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACA-
* * * *
1031650 TAATGTATCAACACTTTATT-TATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTAT
128 TAATGTATCGACACTTT-TTAAATTTGTGTCGATACTTTTTATACATAATGAA-TCCCAAACGAT
* *
1031714 GTGCACGCTT
191 GTCCACGCAT
*
1031724 AAAGTGTCGATACATTTATTAAAAGTATCGA-CCAAAATACATCGAGACTGAAAATTATAATGTA
1 AAAGTTTCGATACATTTATTAAAAGTATCGACCCAAAATACATCGAGACTGAAAATTATAATGTA
* * *
1031788 ATAGGCCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGCAAATAGGTCTACATAA
66 ATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACATAA
* * * * * * * *
1031853 TGTATCGATACTTTTTACATTTGTGTCGATACTTTATGTACATAATTAATGCCTACCGATGTCCA
131 TGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTATACATAATGAATCCCAAACGATGTCCA
1031918 CGCAT
196 CGCAT
* * * * *
1031923 AAAGTTTC-A-ATATTTATAAAAAGTATCAACCCCAAATACATCGAGACTGGAAATTATAATGTA
1 AAAGTTTCGATACATTTATTAAAAGTATCGACCCAAAATACATCGAGACTGAAAATTATAATGTA
* * * ** *
1031986 ATAGGTCAATTTACAATGTAACAGGTTGAAATTTACCGATGTAAAT-AGAAAATAGGTCAACATA
66 ATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGT-TTTATGAGAAAATAGGTCTACATA
* * *
1032050 ATGTGTCGACACTTTTTAAATTCGTGTCGACACTTTTTA
130 ATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTA
1032089 AAATTACGCG
Statistics
Matches: 313, Mismatches: 46, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
197 17 0.05
198 115 0.37
199 33 0.11
200 119 0.38
201 26 0.08
202 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (200 bp):
AAAGTTTCGATACATTTATTAAAAGTATCGACCCAAAATACATCGAGACTGAAAATTATAATGTA
ATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACATAA
TGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTATACATAATGAATCCCAAACGATGTCCA
CGCAT
Found at i:1032041 original size:198 final size:200
Alignment explanation
Indices: 1030723--1032085 Score: 655
Period size: 200 Copynumber: 6.8 Consensus size: 200
1030713 AGTGCACAAC
* * * ** *
1030723 AAAGTGTCGATACATTTATAATAAGTGTCAATCCCAAAA-ACATCGAAACCCATAATTATAATGT
1 AAAGTGTCGATACATTTATAAAAAGTATCAA--CCAAAATACATCGAGACTGAAAATTATAATGT
* * * * *
1030787 AATAGGTAAATTAACAATGTAACCGGTCTAAATATACCGG-TTTATGAGAAAATAGGTATACATA
64 AATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACATA
* *** * *** * * * * * *** * *
1030851 AAGTATCGACACAAATGAAACAAGTGTCGATACTTTTTGTACAGAGTGTATTTTAAAAACCAAGT
129 ATGTATCGACACTTTTTAAATTTGTGTCGATACTTTATATACATAATG-AATTCCCAAACGATGT
* *
1030916 GCACAACA-
193 CCAC-GCAT
* * * * * ** *
1030924 AAA-TGTCGATACAATTATAACAAGTGTCGATCCGAAAA-ACATCGAAACCCATAATTATAATGT
1 AAAGTGTCGATACATTTATAAAAAGTATC-AACC-AAAATACATCGAGACTGAAAATTATAATGT
* * * * * *
1030987 AATAGGTAAATTAACAATGTAACCGGTCTAAATATACCGG-TTTATGAGAAAACAGGTATACATA
64 AATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACATA
* * *** * ** * * * * * * *** * *
1031051 AAGTATCAACACAAATGAAACAAT-TGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAG
129 ATGTATCGACACTTTTTAAA-TTTGTGTCGATACTTTATATACATAATG-AATTCCCAAACGATG
* * *
1031115 TGCAC-AAC
192 TCCACGCAT
* * * * * ** * *
1031123 AAAGTGTCGATACATTTATAACAAGTGTCGATCCGAAAA-ATATCGAAACCCATAATTATAATAT
1 AAAGTGTCGATACATTTATAAAAAGTATC-AACC-AAAATACATCGAGACTGAAAATTATAATGT
* * * ** * * * *
1031187 AATAGGTAAATTAACAATGTAACCAGCCTAAATATACTGG-TTTATGAGAAAACAGGTATACATA
64 AATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACATA
* *** ** **** * * * * *** * *
1031251 AAGTATCGACACAAATCCAACAAATGTCGATACTTTTTGTTCA-AAGTGTATTTTAAAAACCAAG
129 ATGTATCGACACTTTTTAAATTTGTGTCGATACTTTATATACATAA-TG-AATTCCCAAACGATG
* * *
1031315 TGCAC-AAC
192 TCCACGCAT
* * * * * ** *
1031323 AAAGTGTCGATACATTTATAACAAGTGTCGATCCGAAAA-ACATCAAAACCCATAATTATAATGT
1 AAAGTGTCGATACATTTATAAAAAGTATC-AACC-AAAATACATCGAGACTGAAAATTATAATGT
* * * *** * * * * *
1031387 AATAGGTAAATTAACAATGTAACTGACCTAAATATATCGG-TTTATGAGAAAACAAGTATACATA
64 AATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACATA
* * *** ** *** * * * * * * *** * *
1031451 AAGTATTGACACAAATCCAACAAGTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGT
129 ATGTATCGACACTTTTTAAATTTGTGTCGATACTTTATATACATAATG-AATTCCCAAACGATGT
* * *
1031516 GCAC-AAC
193 CCACGCAT
* * * * * ** *
1031523 AAAGTTTCGATACATTTATAACAAGTGTCGATCCCAAAA-ACATCGAAACCCATAATTATAATGT
1 AAAGTGTCGATACATTTATAAAAAGTATC-A-ACCAAAATACATCGAGACTGAAAATTATAATGT
* *
1031587 AATAGGTAAATTAACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTA-ACT
64 AATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACA-T
* * * * *
1031651 AATGTATCAACACTTTATT-TATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTATG
128 AATGTATCGACACTTT-TTAAATTTGTGTCGATACTTTATATACATAATGAATTCCCAAACGATG
* *
1031715 TGCACGCTT
192 TCCACGCAT
* *
1031724 AAAGTGTCGATACATTTATTAAAAGTATCGACCAAAATACATCGAGACTGAAAATTATAATGTAA
1 AAAGTGTCGATACATTTATAAAAAGTATCAACCAAAATACATCGAGACTGAAAATTATAATGTAA
* * *
1031789 TAGGCCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGCAAATAGGTCTACATAAT
66 TAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACATAAT
* * * * * * *
1031854 GTATCGATACTTTTTACATTTGTGTCGATACTTTATGTACATAATTAA-TGCCTACCGATGTCCA
131 GTATCGACACTTTTTAAATTTGTGTCGATACTTTATATACATAATGAATTCCCAAACGATGTCCA
1031918 CGCAT
196 CGCAT
* * * *
1031923 AAAGTTTC-A-ATATTTATAAAAAGTATCAACCCCAAATACATCGAGACTGGAAATTATAATGTA
1 AAAGTGTCGATACATTTATAAAAAGTATCAA-CCAAAATACATCGAGACTGAAAATTATAATGTA
* * * ** *
1031986 ATAGGTCAATTTACAATGTAACAGGTTGAAATTTACCGATGTAAAT-AGAAAATAGGTCAACATA
65 ATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGT-TTTATGAGAAAATAGGTCTACATA
* * *
1032050 ATGTGTCGACACTTTTTAAATTCGTGTCGACACTTT
129 ATGTATCGACACTTTTTAAATTTGTGTCGATACTTT
1032086 TTAAAATTAC
Statistics
Matches: 1026, Mismatches: 118, Indels: 39
0.87 0.10 0.03
Matches are distributed among these distances:
197 17 0.02
198 115 0.11
199 40 0.04
200 768 0.75
201 85 0.08
202 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (200 bp):
AAAGTGTCGATACATTTATAAAAAGTATCAACCAAAATACATCGAGACTGAAAATTATAATGTAA
TAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACATAAT
GTATCGACACTTTTTAAATTTGTGTCGATACTTTATATACATAATGAATTCCCAAACGATGTCCA
CGCAT
Found at i:1036214 original size:87 final size:87
Alignment explanation
Indices: 1036112--1036274 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
1036102 AAATAGGTCA
*
1036112 ATATAAGCGCTACCTATTACATTATATAAGCGCTTCCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1036177 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* * *
1036199 ATATAAGTGCTACCTATTACATTATATAAGTGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1036264 CCGGTTAAATG
66 CCGGTTAAATG
1036275 ATATAATATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:1036246 original size:23 final size:23
Alignment explanation
Indices: 1036196--1036240 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1036186 TGCCTATTTT
*
1036196 ATTATATAAGTGCTACCTATTAC
1 ATTATATAAGTGCTACCTAATAC
1036219 ATTATATAAGTGCTACCTAATA
1 ATTATATAAGTGCTACCTAATA
1036241 TGTTATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGTGCTACCTAATAC
Found at i:1041997 original size:45 final size:45
Alignment explanation
Indices: 1041933--1042031 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
1041923 ATTCCAGAAG
* * *
1041933 CTCCACATTACAAATTTCAGCCGCTTCCAGCACTGCCAGCAGTCC
1 CTCCACGTTACAAATTTCAGCAGCTTCCAACACTGCCAGCAGTCC
* * *
1041978 CTCCACGTTGCAAATTTCAGTAGCTTCCAACACTGCCAGTAGTCC
1 CTCCACGTTACAAATTTCAGCAGCTTCCAACACTGCCAGCAGTCC
*
1042023 CCCCACGTT
1 CTCCACGTT
1042032 TCAGCTCCAG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.23, C:0.38, G:0.14, T:0.24
Consensus pattern (45 bp):
CTCCACGTTACAAATTTCAGCAGCTTCCAACACTGCCAGCAGTCC
Found at i:1042970 original size:21 final size:22
Alignment explanation
Indices: 1042946--1042988 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1042936 TTTTTGTTTT
1042946 ATTAT-ATTTT-TTCACTATTTA
1 ATTATAATTTTGTT-ACTATTTA
1042967 ATTATAATTTTGTTACTATTTA
1 ATTATAATTTTGTTACTATTTA
1042989 TCTCATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 13 0.65
23 2 0.10
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTATAATTTTGTTACTATTTA
Found at i:1048057 original size:7 final size:7
Alignment explanation
Indices: 1048024--1048050 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1048014 TTCATCAGGA
1048024 AAAAAAG
1 AAAAAAG
1048031 AAAAAAG
1 AAAAAAG
1048038 AAAAAAG
1 AAAAAAG
1048045 AAAAAA
1 AAAAAA
1048051 AGGAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1052611 original size:22 final size:22
Alignment explanation
Indices: 1052586--1052706 Score: 188
Period size: 22 Copynumber: 5.5 Consensus size: 22
1052576 ATCTACATTC
1052586 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1052608 TTCAAAGATGATAGATTCTATT
1 TTCAAAGATGATAGATTCTCTT
* *
1052630 TCCAAAGATAATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
1052652 TTCAAAGATAATAAATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1052674 TTCAAAGATGATAGATTCTTTT
1 TTCAAAGATGATAGATTCTCTT
1052696 TTCAAAGATGA
1 TTCAAAGATGA
1052707 AAGCTTTATT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 90 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1053541 original size:74 final size:73
Alignment explanation
Indices: 1053399--1053608 Score: 339
Period size: 74 Copynumber: 2.9 Consensus size: 73
1053389 TTCAAATAGT
* * *
1053399 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGCGTCTCGCTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACCC
1053464 GAAACAAC
66 GAAACAAC
* *
1053472 AATTTATCTCACTTGAGATTGTTTTTCTTAAAAACAAAATTTGTCTCGCTTGAGACAATTTCACC
1 AATTTATCTCACTTGAGATTGTTTTTCTT-AAAACAAAATTCGTCTCGCTTGAGACAGTTTCACC
1053537 CGAAACAAC
65 CGAAACAAC
* * *
1053546 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAGATTCGTCTCGCTTTAGACAGTTTCAC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCAC
1053609 TAGAAACAGA
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
73 59 0.47
74 67 0.53
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACCC
GAAACAAC
Found at i:1053580 original size:37 final size:36
Alignment explanation
Indices: 1053399--1053581 Score: 134
Period size: 37 Copynumber: 5.0 Consensus size: 36
1053389 TTCAAATAGT
*
1053399 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAA
* *** * * ** **
1053435 ACTGCGTCTCGCTTGAGA-CAGTTTCACTCGAAACAA
1 AATTTATCTCACTTGAGATTA-TTTTTCTTAAAACAA
*
1053471 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAAACAA
1 -AATTTATCTCACTTGAGATTATTTTTCTT-AAAACAA
* * ** ** ***
1053509 AATTTGTCTCGCTTGAGACAATTTCACCCGAAACAA
1 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAA
1053545 CAATTTATCTCACTTGAGATTATTTTTCTTAAAACAA
1 -AATTTATCTCACTTGAGATTATTTTTCTTAAAACAA
1053582 GATTCGTCTC
Statistics
Matches: 101, Mismatches: 41, Indels: 9
0.67 0.27 0.06
Matches are distributed among these distances:
36 30 0.30
37 65 0.64
38 6 0.06
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (36 bp):
AATTTATCTCACTTGAGATTATTTTTCTTAAAACAA
Found at i:1054037 original size:45 final size:45
Alignment explanation
Indices: 1053973--1054071 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
1053963 GTTCCAACAG
* *
1053973 CTCCACATTACAAATTCCAGTAGCTTCCAGCACTGCCAGCAGTCC
1 CTCCACGTTACAAATTCCAGTAGCTTCCAGCAATGCCAGCAGTCC
* * *
1054018 CTCCACGTTGCAAATTCCAGTAGCTTCCAGCAATTCCAGTAGTCC
1 CTCCACGTTACAAATTCCAGTAGCTTCCAGCAATGCCAGCAGTCC
*
1054063 CCCCACGTT
1 CTCCACGTT
1054072 TTAGCTCCAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.24, C:0.37, G:0.14, T:0.24
Consensus pattern (45 bp):
CTCCACGTTACAAATTCCAGTAGCTTCCAGCAATGCCAGCAGTCC
Found at i:1055021 original size:22 final size:21
Alignment explanation
Indices: 1054979--1055021 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1054969 TTTTTGTTTT
*
1054979 ATTATATTTTTTCACTGTTTA
1 ATTATATTTTTTCACTATTTA
1055000 ATTATAATTTTGTT-ACTATTTA
1 ATTAT-ATTTT-TTCACTATTTA
1055022 TCTCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 12 0.63
23 2 0.11
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTATATTTTTTCACTATTTA
Found at i:1055096 original size:2 final size:2
Alignment explanation
Indices: 1055089--1055131 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1055079 AGTCACATTA
1055089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1055131 A
1 A
1055132 AGATGATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1058774 original size:14 final size:14
Alignment explanation
Indices: 1058755--1058783 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1058745 GTCTTTTATT
1058755 TTTTGTATTTAAGA
1 TTTTGTATTTAAGA
1058769 TTTTGTATTTAAGA
1 TTTTGTATTTAAGA
1058783 T
1 T
1058784 ATATCTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTTTGTATTTAAGA
Found at i:1060651 original size:81 final size:82
Alignment explanation
Indices: 1060516--1060675 Score: 286
Period size: 81 Copynumber: 2.0 Consensus size: 82
1060506 GGAATTAAGA
* *
1060516 ATGTTATAGTCTAAAATATTAAATCCACCATTAATTGAATTGATATGTTAGGTTTAAATACTCAT
1 ATGTTATAGCCTAAAATATTAAATCCACCATTAATTGAATTGATATGTTAGGTTTAAATACTAAT
1060581 TAGA-TTTATTGATAGT
66 TAGATTTTATTGATAGT
*
1060597 ATGTTATAGCCTAAAATATTAAATCCACCATTAATTGAATTGATATGTTGGGTTTAAATACTAAT
1 ATGTTATAGCCTAAAATATTAAATCCACCATTAATTGAATTGATATGTTAGGTTTAAATACTAAT
1060662 TAGATTTTATTGAT
66 TAGATTTTATTGAT
1060676 CGTGACTATT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 66 0.88
82 9 0.12
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (82 bp):
ATGTTATAGCCTAAAATATTAAATCCACCATTAATTGAATTGATATGTTAGGTTTAAATACTAAT
TAGATTTTATTGATAGT
Found at i:1061230 original size:64 final size:60
Alignment explanation
Indices: 1061148--1061274 Score: 164
Period size: 60 Copynumber: 2.0 Consensus size: 60
1061138 GAACATATGA
* * *
1061148 ATAGTTGAATGATCATTTTATTTATAACTTTTAATACTCGGGAAACTCAACAAAATAATGTCCT
1 ATAGTCGAATGATCA--TT-TTT-TAACTTTTAATACTCAGAAAACTCAACAAAATAATGTCCT
* * *
1061212 ATAGTCGAATGATTATTTTTTAACTTTTAATAGTCAGAAAACTCAACAAAATAATGTTCT
1 ATAGTCGAATGATCATTTTTTAACTTTTAATACTCAGAAAACTCAACAAAATAATGTCCT
1061272 ATA
1 ATA
1061275 ACCGATGAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 39 0.68
61 3 0.05
62 2 0.04
64 13 0.23
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (60 bp):
ATAGTCGAATGATCATTTTTTAACTTTTAATACTCAGAAAACTCAACAAAATAATGTCCT
Found at i:1061298 original size:60 final size:60
Alignment explanation
Indices: 1061165--1061298 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 60
1061155 AATGATCATT
* * **
1061165 TTATTTATA-ACTTTTAATACTCGGGAAACTCAACAAAATAATGTCCTATAGTCGAATGA
1 TTATTTATATACTTTTAATACTCAGAAAACTCAACAAAATAATGTCCTATAACCGAATGA
* * *
1061224 TTATTT-TTTAACTTTTAATAGTCAGAAAACTCAACAAAATAATGTTCTATAACCG-ATGAA
1 TTATTTATAT-ACTTTTAATACTCAGAAAACTCAACAAAATAATGTCCTATAACCGAATG-A
1061284 TTATTTATATACTTT
1 TTATTTATATACTTT
1061299 ACCTTAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
58 1 0.02
59 9 0.14
60 51 0.81
61 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (60 bp):
TTATTTATATACTTTTAATACTCAGAAAACTCAACAAAATAATGTCCTATAACCGAATGA
Found at i:1065585 original size:3 final size:3
Alignment explanation
Indices: 1065577--1065641 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
1065567 TCAATTTTTA
1065577 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1065624 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
1065642 GAATGAAGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1067075 original size:3 final size:3
Alignment explanation
Indices: 1067067--1067093 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1067057 ATGCAAAATC
1067067 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1067094 AGACACTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1071464 original size:21 final size:21
Alignment explanation
Indices: 1071422--1071464 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1071412 TTTTTGGGCT
*
1071422 AGGGGAATCAGTACCCATTCA
1 AGGGGAATCAGTACCCACTCA
*
1071443 AGGGGAATC-GATACCCCCTCA
1 AGGGGAATCAG-TACCCACTCA
1071464 A
1 A
1071465 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCAGTACCCACTCA
Found at i:1071537 original size:23 final size:22
Alignment explanation
Indices: 1071493--1071537 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1071483 AATCTCATAG
*
1071493 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
1071515 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
1071538 AAATTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:1073014 original size:99 final size:102
Alignment explanation
Indices: 1072832--1073040 Score: 361
Period size: 99 Copynumber: 2.1 Consensus size: 102
1072822 GGGTCTACGC
1072832 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACA-GTGTGAAGTCTGGTGAGACACATACTTGAT
* *
1072897 CCTTGGCATATGTATATGATT-TTAAGGAATGATATGT
65 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
1072934 GGTCCTTC-GGACATATATGTATTCTTTGGAACA-TGTGAAGTCTGGTGAGACACATACTTGATC
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACAGTGTGAAGTCTGGTGAGACACATACTTGATC
*
1072997 CCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCTAGCATATGTATATGATTCTTAAGGAATGATATGT
1073034 GGTCCTT
1 GGTCCTT
1073041 ATGGACATTA
Statistics
Matches: 103, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
99 47 0.46
100 23 0.22
101 25 0.24
102 8 0.08
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (102 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACAGTGTGAAGTCTGGTGAGACACATACTTGATC
CCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:1081687 original size:3 final size:3
Alignment explanation
Indices: 1081679--1081749 Score: 103
Period size: 3 Copynumber: 24.3 Consensus size: 3
1081669 ATCAATTTTA
*
1081679 TAT TAT TA- TAT TAT TAT TAT TGT TA- TAT ATAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
1081722 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1081750 TATGAATGAA
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 6 0.10
3 53 0.85
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1081720 original size:32 final size:32
Alignment explanation
Indices: 1081679--1081749 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
1081669 ATCAATTTTA
*
1081679 TATTATTATATTATTATTATTGTTA-TATATAT
1 TATTATTATATTATTATTATTATTATTAT-TAT
1081711 TATTATTATATTATTATTATTATTATTATTAT
1 TATTATTATATTATTATTATTATTATTATTAT
1081743 TATTATT
1 TATTATT
1081750 TATGAATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
32 34 0.92
33 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (32 bp):
TATTATTATATTATTATTATTATTATTATTAT
Found at i:1081722 original size:29 final size:28
Alignment explanation
Indices: 1081676--1081752 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
1081666 CTAATCAATT
*
1081676 TTATATTATTA-TATTATTATTATTGTTA
1 TTATATTATTATTA-TATTATTATTATTA
1081704 TATATATTATTATTATATTATTATTATTA
1 T-TATATTATTATTATATTATTATTATTA
1081733 TTATTATTATTATTAT-TTAT
1 TTA-TATTATTATTATATTAT
1081753 GAATGAAGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
28 7 0.16
29 36 0.80
30 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (28 bp):
TTATATTATTATTATATTATTATTATTA
Found at i:1083630 original size:75 final size:75
Alignment explanation
Indices: 1083507--1083655 Score: 298
Period size: 75 Copynumber: 2.0 Consensus size: 75
1083497 TTTGCCGGTG
1083507 CTGGAGAAAATAATGACACCAACTTCAGCATCGCACAAAATGGATAACTCTCTTGCTTTCTTCAA
1 CTGGAGAAAATAATGACACCAACTTCAGCATCGCACAAAATGGATAACTCTCTTGCTTTCTTCAA
1083572 CAACCCATTT
66 CAACCCATTT
1083582 CTGGAGAAAATAATGACACCAACTTCAGCATCGCACAAAATGGATAACTCTCTTGCTTTCTTCAA
1 CTGGAGAAAATAATGACACCAACTTCAGCATCGCACAAAATGGATAACTCTCTTGCTTTCTTCAA
1083647 CAACCCATT
66 CAACCCATT
1083656 CTTCGTTTAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (75 bp):
CTGGAGAAAATAATGACACCAACTTCAGCATCGCACAAAATGGATAACTCTCTTGCTTTCTTCAA
CAACCCATTT
Found at i:1084556 original size:125 final size:120
Alignment explanation
Indices: 1084361--1084605 Score: 429
Period size: 125 Copynumber: 2.0 Consensus size: 120
1084351 GTAGGAGAGG
1084361 GAGGTTAGGTTTTCCATTGGTTTTGTGCTTTTGTTGGATAAGTGGGAAAGGAAATAAAAAGAGAG
1 GAGGTTAGGTTTTCCATTGGTTTTGTGCTTTTGTTGGATAAGTGGGAAAGGAAATAAAAAGAGAG
1084426 ATTTTTTTATTAGTCTCAAAGATTATAAGGTAGTATATGTTCAAAAAAAATTTAATCATT
66 -TTTTTTTATTAGTCTCAAAGATTAT-A---AGTATATGTTCAAAAAAAATTTAATCATT
1084486 GAGGTTAGGTTTTCCATTGGTTTTGTGCTTTTGTTGGATAAGTAGGGAAAGGAAATAAAAAGAGA
1 GAGGTTAGGTTTTCCATTGGTTTTGTGCTTTTGTTGGATAAGT-GGGAAAGGAAATAAAAAGAGA
1084551 -TTTTTTTATTAGTCTCAAAGATTATAAGTATATGTTCAAAAAAAATTTAATCATT
65 GTTTTTTTATTAGTCTCAAAGATTATAAGTATATGTTCAAAAAAAATTTAATCATT
1084606 TGATAATAAA
Statistics
Matches: 119, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
120 29 0.24
123 1 0.01
124 25 0.21
125 43 0.36
126 21 0.18
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.39
Consensus pattern (120 bp):
GAGGTTAGGTTTTCCATTGGTTTTGTGCTTTTGTTGGATAAGTGGGAAAGGAAATAAAAAGAGAG
TTTTTTTATTAGTCTCAAAGATTATAAGTATATGTTCAAAAAAAATTTAATCATT
Found at i:1089715 original size:22 final size:21
Alignment explanation
Indices: 1089687--1089742 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
1089677 CTCCTAAAAA
* *
1089687 TATTAAAATTTTATTTATTTTT
1 TATTAAAATTTT-TCTATTTCT
1089709 TATTAAAAATTATTTCTATTTCT
1 TATT-AAAATT-TTTCTATTTCT
1089732 T-TTAAAATTTT
1 TATTAAAATTTT
1089743 GTAAATCTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 6 0.20
22 6 0.20
23 14 0.47
24 2 0.07
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTAAAATTTTTCTATTTCT
Found at i:1093652 original size:169 final size:170
Alignment explanation
Indices: 1093352--1093690 Score: 662
Period size: 169 Copynumber: 2.0 Consensus size: 170
1093342 GAAACTTTTT
1093352 TTCCTGGAAGATAGATGAGTTCAAATTCCCATCAAGAATCTAATGGAACAGTTTCACAGGAAAGT
1 TTCCTGGAAGATAGATGAGTTCAAATTCCCATCAAGAATCTAATGGAACAGTTTCACAGGAAAGT
1093417 TTATGAATAGCTGCTGAGACACTAACTTATCCACCTGTATTTCTAATTGAAGTATGACATTGTGC
66 TTATGAATAGCTGCTGAGACACTAACTTATCCACCTGTATTTCTAATTGAAGTATGACATTGTGC
1093482 AGACCTTCAAGTTGTTTGGCAAGTTCTAGGCAGAATACAA
131 AGACCTTCAAGTTGTTTGGCAAGTTCTAGGCAGAATACAA
1093522 TTCCTGGAAGATAGATGAGTTCAAATTCCCATCAAGAATCTAATGGAACAGTTTCACAGGAAAG-
1 TTCCTGGAAGATAGATGAGTTCAAATTCCCATCAAGAATCTAATGGAACAGTTTCACAGGAAAGT
*
1093586 TTATGAATAGCTGCTGAGACACTAACTTATCCACTTGTATTTCTAATTGAAGTATGACATTGTGC
66 TTATGAATAGCTGCTGAGACACTAACTTATCCACCTGTATTTCTAATTGAAGTATGACATTGTGC
1093651 AGACCTTCAAGTTGTTTGGCAAGTTCTAGGCAGAATACAA
131 AGACCTTCAAGTTGTTTGGCAAGTTCTAGGCAGAATACAA
1093691 ACTACTAAAT
Statistics
Matches: 168, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
169 104 0.62
170 64 0.38
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (170 bp):
TTCCTGGAAGATAGATGAGTTCAAATTCCCATCAAGAATCTAATGGAACAGTTTCACAGGAAAGT
TTATGAATAGCTGCTGAGACACTAACTTATCCACCTGTATTTCTAATTGAAGTATGACATTGTGC
AGACCTTCAAGTTGTTTGGCAAGTTCTAGGCAGAATACAA
Found at i:1101127 original size:18 final size:18
Alignment explanation
Indices: 1101100--1101134 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1101090 CCATTATAAA
*
1101100 ATGTCTCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
1101118 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
1101135 GTAGAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:1101497 original size:19 final size:17
Alignment explanation
Indices: 1101463--1101505 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1101453 ACTCATTTAT
* *
1101463 ATCATATATCATATACCA
1 ATCATATAACACATA-CA
1101481 ATACATATAACACATACA
1 AT-CATATAACACATACA
1101499 ATCATAT
1 ATCATAT
1101506 CAATACATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 11 0.50
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (17 bp):
ATCATATAACACATACA
Found at i:1105522 original size:19 final size:17
Alignment explanation
Indices: 1105488--1105538 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
1105478 ACTCATTTAT
* *
1105488 ATCATATATCATATACCA
1 ATCATATAACACATA-CA
1105506 ATACATATAACACATACA
1 AT-CATATAACACATACA
1105524 ATCATATCAACACAT
1 ATCATAT-AACACAT
1105539 GCCTATATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.17
18 13 0.45
19 11 0.38
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (17 bp):
ATCATATAACACATACA
Found at i:1107523 original size:20 final size:21
Alignment explanation
Indices: 1107493--1107533 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
1107483 AGCCGTTGGA
1107493 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
1107514 GCCT-ATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
1107534 TATGTTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:1108331 original size:19 final size:19
Alignment explanation
Indices: 1108291--1108339 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1108281 AATAATTTTC
* *
1108291 TTTTGAAAGAAAAATTGGA-
1 TTTTGAAA-AAAAAATGAAT
1108310 TTTTGAAAAACAAAATGAAT
1 TTTTGAAAAA-AAAATGAAT
1108330 TTTTGAAAAA
1 TTTTGAAAAA
1108340 TGAGTTAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (19 bp):
TTTTGAAAAAAAAATGAAT
Found at i:1110523 original size:2 final size:2
Alignment explanation
Indices: 1110516--1110546 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1110506 AAATCCCAAC
1110516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1110547 CATACTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1111731 original size:21 final size:21
Alignment explanation
Indices: 1111707--1111753 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1111697 AGTAAATTAC
1111707 GTTTTAATACCTAAACTATCA
1 GTTTTAATACCTAAACTATCA
* * *
1111728 GTTTTAGTATCTAAACTTTCA
1 GTTTTAATACCTAAACTATCA
*
1111749 TTTTT
1 GTTTT
1111754 TTCATAACCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (21 bp):
GTTTTAATACCTAAACTATCA
Done.