Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008745.1 Hibiscus syriacus cultivar Beakdansim tig00111834_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: 1915556
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:608416 original size:38 final size:37
Alignment explanation
Indices: 608337--608517 Score: 167
Period size: 36 Copynumber: 5.0 Consensus size: 37
608327 ATATATAAAC
* * * *
608337 GTTTTCAAAAAC-ATATAATATATAAATTTTTAAAAT
1 GTTTTTAAAAACTATATATTATATATATTTTCAAAAT
608373 G-TTTTAAAAACTATATATTATATATATTTTCAAAAT
1 GTTTTTAAAAACTATATATTATATATATTTTCAAAAT
* * *
608409 GGTTTTTAAAAATTATATATTATATAAATGTTTTCATAA-
1 -GTTTTTAAAAACTATATATTATAT--ATATTTTCAAAAT
** * * * *
608448 CATTTTCAAAAGTATATA-T-TATATATTTTAAAAAC
1 GTTTTTAAAAACTATATATTATATATATTTTCAAAAT
*
608483 GTTTTCAAAAACTATATATTATATA-ATTTTCAAAA
1 GTTTTTAAAAACTATATATTATATATATTTTCAAAA
608518 AAATATATTT
Statistics
Matches: 117, Mismatches: 20, Indels: 16
0.76 0.13 0.10
Matches are distributed among these distances:
34 9 0.08
35 22 0.19
36 35 0.30
37 6 0.05
38 35 0.30
40 10 0.09
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
GTTTTTAAAAACTATATATTATATATATTTTCAAAAT
Found at i:608499 original size:26 final size:25
Alignment explanation
Indices: 608468--608534 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
608458 AGTATATATT
608468 ATATATTTTAAAAACGTTTTC-AAAAA
1 ATATATTTTAAAAA--TTTTCAAAAAA
* * *
608494 CTATATATTATATAATTTTCAAAAAA
1 ATATATTTTA-AAAATTTTCAAAAAA
*
608520 ATATATTTTCAAAAT
1 ATATATTTTAAAAAT
608535 GGTTTTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
25 9 0.28
26 20 0.62
27 3 0.09
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (25 bp):
ATATATTTTAAAAATTTTCAAAAAA
Found at i:608590 original size:36 final size:34
Alignment explanation
Indices: 608539--608703 Score: 104
Period size: 34 Copynumber: 4.7 Consensus size: 34
608529 CAAAATGGTT
* * * * *
608539 TTTTTAAAATTATATATTATAAATGTTTTCATAACG
1 TTTTCAAAAGTATATATTAT--ATATTTTAAAAACG
608575 TTTTCAAAAGTATATATTATATATTTTAAAAACG
1 TTTTCAAAAGTATATATTATATATTTTAAAAACG
**
608609 TTTTCAAAA--ACTATATTATATAATTTTCAAAAATA
1 TTTTCAAAAGTA-TATATTATAT-ATTTT-AAAAACG
** * * *
608644 TTTGAAAAACTATATAATATACATATTTTCAAAAAATG
1 TTTTCAAAAGTATAT-AT-TATATATTTT--AAAAACG
*
608682 TTTT--AAACTATATATTATATAT
1 TTTTCAAAAGTATATATTATATAT
608704 GTATTTTCAA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
32 1 0.01
33 10 0.09
34 31 0.29
35 14 0.13
36 30 0.28
37 8 0.07
38 13 0.12
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (34 bp):
TTTTCAAAAGTATATATTATATATTTTAAAAACG
Found at i:608617 original size:125 final size:124
Alignment explanation
Indices: 608394--608641 Score: 437
Period size: 125 Copynumber: 2.0 Consensus size: 124
608384 TATATATTAT
608394 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACATTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACATTTTCAAAA
608459 GTATATATTATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAA
66 GTATATATTATATATTTTAAAAACGTTTTCAAAAAC--TATATTATATAATTTTCAAAAAA
* *
608520 ATATATTTTCAAAATGGTTTTTTTAAAATTATATA-T-TATAAATGTTTTCATAACGTTTTCAAA
1 ATATATTTTCAAAATGG-TTTTTAAAAATTATATATTATATAAATGTTTTCATAACATTTTCAAA
608583 AGTATATATTATATATTTTAAAAACGTTTTCAAAAACTATATTATATAATTTTCAAAAA
65 AGTATATATTATATATTTTAAAAACGTTTTCAAAAACTATATTATATAATTTTCAAAAA
608642 TATTTGAAAA
Statistics
Matches: 119, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
123 22 0.18
125 63 0.53
126 18 0.15
127 16 0.13
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (124 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACATTTTCAAAA
GTATATATTATATATTTTAAAAACGTTTTCAAAAACTATATTATATAATTTTCAAAAAA
Found at i:608629 original size:33 final size:34
Alignment explanation
Indices: 608571--608703 Score: 107
Period size: 34 Copynumber: 3.8 Consensus size: 34
608561 ATGTTTTCAT
608571 AACGTTTTCAAAAGTA-TATATTATATATTTT-AAA
1 AACGTTTTCAAAA--ACTATATTATATATTTTCAAA
608605 AACGTTTTCAAAAACTATATTATATAATTTTCAAA
1 AACGTTTTCAAAAACTATATTATAT-ATTTTCAAA
*
608640 AA--TATTTGAAAAACTATATAATATACATATTTTCAAAA
1 AACGT-TTTCAAAAACTATAT--TAT--ATATTTTC-AAA
* *
608678 AATGTTTT-AAACTA-TATATTATATAT
1 AACGTTTTCAAA-AACTATATTATATAT
608704 GTATTTTCAA
Statistics
Matches: 85, Mismatches: 2, Indels: 24
0.77 0.02 0.22
Matches are distributed among these distances:
32 1 0.01
33 11 0.13
34 36 0.42
35 5 0.06
36 6 0.07
37 6 0.07
38 15 0.18
39 4 0.05
40 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.42
Consensus pattern (34 bp):
AACGTTTTCAAAAACTATATTATATATTTTCAAA
Found at i:608739 original size:37 final size:36
Alignment explanation
Indices: 608615--608742 Score: 120
Period size: 36 Copynumber: 3.5 Consensus size: 36
608605 AACGTTTTCA
*
608615 AAAACTATAT--TATATA-ATTTTCAAAAATATTTG
1 AAAACTATATAATATATATATTTTCAAAAAAATTTG
* *
608648 AAAAACTATATAATATACATATTTTC-AAAAAATGTTT
1 -AAAACTATATAATATATATATTTTCAAAAAAAT-TTG
* *
608685 TAAACTATATATTATATATGTATTTTCAAAAACAATTTG
1 AAAACTATATA--ATATATATATTTTCAAAAA-AATTTG
* *
608724 CAAACTACATAATATATAT
1 AAAACTATATAATATATAT
608743 GTGTATATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
34 10 0.13
36 21 0.28
37 15 0.20
38 12 0.16
39 15 0.20
40 3 0.04
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (36 bp):
AAAACTATATAATATATATATTTTCAAAAAAATTTG
Found at i:608740 original size:39 final size:38
Alignment explanation
Indices: 608631--608744 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 38
608621 ATATTATATA
* *
608631 ATTTTCAAAAATATTTGAAAAACTATATAATATACA--T
1 ATTTTCAAAAAAATTTG-AAAACTATATAATATATATGT
** *
608668 ATTTTC-AAAAAATGTTTTAAACTATATATTATATATGT
1 ATTTTCAAAAAAAT-TTGAAAACTATATAATATATATGT
* *
608706 ATTTTCAAAAACAATTTGCAAACTACATAATATATATGT
1 ATTTTCAAAAA-AATTTGAAAACTATATAATATATATGT
608745 GTATATATGT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
36 21 0.33
37 8 0.13
38 7 0.11
39 24 0.38
40 3 0.05
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (38 bp):
ATTTTCAAAAAAATTTGAAAACTATATAATATATATGT
Found at i:609506 original size:84 final size:84
Alignment explanation
Indices: 609399--610137 Score: 676
Period size: 84 Copynumber: 8.9 Consensus size: 84
609389 CCAGGGGTCT
* * * * * *
609399 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACGTTGAGCTGAGCGGAGT
1 TTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAGT
609464 CGAACTCAAAGGTCTTTTG
66 CGAACTCAAAGGTCTTTTG
* * * * * *
609483 TTGGCAAACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATG-CCTTGGAGCTGAGCATAG
1 TTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTT-GAGCTGAGCGTAG
*
609547 TCGAACTCGAAGGTCTTTTG
65 TCGAACTCAAAGGTCTTTTG
* * * * *** * *
609567 TTGGCATATAGCCCTTCTCGACTTAAGCTACATTGGAAATGATGTGCCGTTGAGCTGAGCGTAGT
1 TTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAGT
609632 CGAACTCAAAGGTCTTTTG
66 CGAACTCAAAGGTCTTTTG
* ** * * * * * * *
609651 ATCACAG-CTAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTA
1 TTGGCAGAC-AACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG-AGCTGAGCGTA
* * *
609715 ATCGAACTTAAGGGTC---T-
64 GTCGAACTCAAAGGTCTTTTG
* * * ** * *
609732 TTGGCAGATAGCCCTTCTCGACTTAAGCTACACTGGAAATGATGTGCCGTTGAGCTGAGCGTAGT
1 TTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAGT
609797 CGAACTCAAAGGTCTTTTG
66 CGAACTCAAAGGTCTTTTG
* ** * * * * * * *
609816 ATCACAG-CTAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTA
1 TTGGCAGAC-AACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG-AGCTGAGCGTA
* * *
609880 ATCGAACTTAAGGGTC---T-
64 GTCGAACTCAAAGGTCTTTTG
* * * *
609897 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTT-GAGCTGAGCGTAG
* *
609961 TCGAACTCGAAGGTCTTGTG
65 TCGAACTCAAAGGTCTTTTG
* * * *
609981 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCATAG
1 TTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTT-GAGCTGAGCGTAG
*
610045 TCGAACTCGAAGGTCTTTTG
65 TCGAACTCAAAGGTCTTTTG
* * * * *
610065 TTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG-AGCTGAGCGTAG
610130 TCGAACTC
65 TCGAACTC
610138 GGGGGTCTTT
Statistics
Matches: 516, Mismatches: 120, Indels: 37
0.77 0.18 0.05
Matches are distributed among these distances:
80 49 0.09
81 69 0.13
82 2 0.00
83 5 0.01
84 322 0.62
85 69 0.13
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (84 bp):
TTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAGT
CGAACTCAAAGGTCTTTTG
Found at i:609786 original size:165 final size:164
Alignment explanation
Indices: 609331--610137 Score: 917
Period size: 165 Copynumber: 4.9 Consensus size: 164
609321 ACAAATAGCT
* * * * * ** *
609331 CTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCC-CGAAGTTGAGTATAATCGAACCCAGGG
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATATG-CCCTTGAAGCTGAGTATAATCGAACTGAAGG
* *
609395 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACGTTGAGCTGAGCG
65 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCG
* * *
609460 GAGTCGAACTCAAAGGTCTTTTGTTGGCA-AACAACC
130 TAGTCGAACTCAAAGGTCTTTTGAT--CACAGCAACC
* * * * * * * *
609496 CTTCTAGACTTAAGTTGTACTGCAAATGATATG-CCTTGGAGCTGAGCATAGTCGAACTCGAA-G
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTATAATCGAACT-GAAGG
* * * *
609559 GTCTTTTGTTGGCATATAGCCCTTCTCGACTTAAGCTACATTGGAAATGATGTGCCGTTGAGCTG
65 GTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTG
609624 AGCGTAGTCGAACTCAAAGGTCTTTTGATCACAGCTAACC
126 AGCGTAGTCGAACTCAAAGGTCTTTTGATCACAGC-AACC
* * *
609664 CTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGG
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTATAATCGAACTGAAGGG
* *
609729 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACACTGGAAATGATGTGCCGTTGAGCTGAGCGT
66 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGT
609794 AGTCGAACTCAAAGGTCTTTTGATCACAGCTAACC
131 AGTCGAACTCAAAGGTCTTTTGATCACAGC-AACC
* * *
609829 CTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGG
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTATAATCGAACTGAAGGG
*
609894 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC-TTGGAGCTGAGCG
66 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCG
* * * **
609958 TAGTCGAACTCGAAGGTCTTGTGTTGGCAGACAACC
130 TAGTCGAACTCAAAGGTCTTTTGATCACAG-CAACC
* * * * * * *
609994 CTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCATAGTCGAACTCGAA-G
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTATAATCGAACT-GAAGG
* * * * * *
610057 GTCTTTTGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCT
65 GTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTG-AGCT
* *
610122 GAGTGTAATCGAACTC
125 GAGCGTAGTCGAACTC
610138 GGGGGTCTTT
Statistics
Matches: 560, Mismatches: 63, Indels: 34
0.85 0.10 0.05
Matches are distributed among these distances:
163 2 0.00
164 47 0.08
165 303 0.54
166 4 0.01
167 4 0.01
168 156 0.28
169 44 0.08
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (164 bp):
CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTATAATCGAACTGAAGGG
TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGT
AGTCGAACTCAAAGGTCTTTTGATCACAGCAACC
Found at i:610185 original size:249 final size:249
Alignment explanation
Indices: 609354--610161 Score: 912
Period size: 249 Copynumber: 3.2 Consensus size: 249
609344 GCTATGTTGT
* * * *
609354 AAATGATATGACCC-CGAAGTTGAGTATAATCGAACCCAGGGGTCTTTGGCAGATAGCCCTTCTC
1 AAATGATATG-CCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTC
* *
609418 GACTTAAGCTATGCTGCAAATGATGTGACGTT-GAGCTGAGCGGAGTCGAACTCAAAGGTCTTTT
65 GACTTAAGCTATGCTGCAAATGATGTGACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTT
*
609482 GTTGGCAAACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCATAG
129 GTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCATAG
* * * *** *
609547 TCGAACTCGAAGGTCTTTTGTTGGCATATAGCCCTTCTCGACTTAAGCTACATTGG
194 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * * * * * * * *
609603 AAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGATCACAGCTAACCCTT
1 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTC-TTTG---GCAGATAGCCCTT
* * * * * * * * * * * * *
609667 CTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC-
62 CTCGACTTAAGCTATGCTGCAAATGATGTGACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCT
* * * * ** * * *
609731 -T-TTGGCAGATAGCCCTTCTCGACTTAAGCTACACTGGAAATGATGTGCCGTT-GAGCTGAGCG
127 TTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCC-TTGGAGCTGAGCA
* * ** * * * * *
609793 TAGTCGAACTCAAAGGTCTTTTGATCACAGCTAACCCTTCTAGCCTTGAGTTATGCTGT
191 TAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * *
609852 AAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCG
* *
609917 ACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGTG
66 ACTTAAGCTATGCTGCAAATGATGTGACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT-TG
*
609981 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCATAGT
130 TTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCATAGT
*
610046 CGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGC
195 CGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* **
610101 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTT
1 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTT
610162 ATGGCCTTGA
Statistics
Matches: 443, Mismatches: 103, Indels: 26
0.77 0.18 0.05
Matches are distributed among these distances:
245 27 0.06
246 32 0.07
248 25 0.06
249 275 0.62
250 26 0.06
252 36 0.08
253 22 0.05
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (249 bp):
AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATGCTGCAAATGATGTGACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGT
TGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCATAGTC
GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
Found at i:613398 original size:18 final size:19
Alignment explanation
Indices: 613357--613401 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
613347 AGTTAATGTG
*
613357 AATGCAAATAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
613376 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
613394 AATGCAAA
1 AATGCAAA
613402 ATGTCTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:615101 original size:15 final size:16
Alignment explanation
Indices: 615075--615104 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
615065 TTATTACTAA
615075 AAATATTCAAAAAAAG
1 AAATATTCAAAAAAAG
615091 AAATA-TCAAAAAAA
1 AAATATTCAAAAAAA
615105 ATGATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.07, G:0.03, T:0.17
Consensus pattern (16 bp):
AAATATTCAAAAAAAG
Found at i:616480 original size:10 final size:10
Alignment explanation
Indices: 616465--616522 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
616455 AGAAAAGAAA
616465 AAATAATAAT
1 AAATAATAAT
616475 AAATAAATAA-
1 AAAT-AATAAT
616485 AAATAAGTAAT
1 AAATAA-TAAT
616496 AAAT--TAA-
1 AAATAATAAT
616503 AAATAA-AAT
1 AAATAATAAT
616512 AAATAATAAT
1 AAATAATAAT
616522 A
1 A
616523 TTATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
7 4 0.10
8 5 0.12
9 8 0.20
10 15 0.37
11 9 0.22
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (10 bp):
AAATAATAAT
Found at i:616627 original size:38 final size:37
Alignment explanation
Indices: 616537--616718 Score: 167
Period size: 38 Copynumber: 5.0 Consensus size: 37
616527 ATATATAAAC
* * * *
616537 GTTTTCAAAAAC-ATATAATATATAAATTTTTAAAAT
1 GTTTTTAAAAACTATATATTATATATATTTTCAAAAT
*
616573 GTTTTAAAAAACTATATATTATATATATTTTCAAAAT
1 GTTTTTAAAAACTATATATTATATATATTTTCAAAAT
* * *
616610 GGTTTTTAAAAATTATATATTATATAAATGTTTTCATAA-
1 -GTTTTTAAAAACTATATATTATAT--ATATTTTCAAAAT
** * * * *
616649 CATTTTCAAAAGTATATA-T-TATATATTTTAAAAAC
1 GTTTTTAAAAACTATATATTATATATATTTTCAAAAT
*
616684 GTTTTCAAAAACTATATATTATATA-ATTTTCAAAA
1 GTTTTTAAAAACTATATATTATATATATTTTCAAAA
616719 AAAAATATTT
Statistics
Matches: 118, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
34 9 0.08
35 13 0.11
36 24 0.20
37 26 0.22
38 36 0.31
40 10 0.08
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
GTTTTTAAAAACTATATATTATATATATTTTCAAAAT
Found at i:616753 original size:128 final size:128
Alignment explanation
Indices: 616597--616849 Score: 456
Period size: 128 Copynumber: 2.0 Consensus size: 128
616587 TATATTATAT
616597 ATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACATTTTCAAAAGT
1 ATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACATTTTCAAAAGT
616662 ATATA-T-TATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAAAA
66 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAAAA
* *
616723 ATATTTTCAAAATGATTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATTTTCAAAATG--GTTTTTAAAAATTATATATTATATAAATGTTTTCATAACATTTTCAAAA
616788 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
64 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
616850 TATTTGAAAA
Statistics
Matches: 121, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
126 14 0.12
128 54 0.45
129 1 0.01
130 52 0.43
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (128 bp):
ATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACATTTTCAAAAGT
ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAAAA
Found at i:616815 original size:36 final size:37
Alignment explanation
Indices: 616741--616925 Score: 182
Period size: 36 Copynumber: 5.0 Consensus size: 37
616731 AAAATGATTT
* * *
616741 TTTTAAAAATTATATATTATATAAATGTTTTC-ATAACG
1 TTTTAAAAACTATATATTATAT--ATATTTTCAAAAACG
* *
616779 TTTTCAAAAGTATATATTATATATATTTT-AAAAACG
1 TTTTAAAAACTATATATTATATATATTTTCAAAAACG
**
616815 TTTTCAAAAACTATATATTATATA-ATTTTCAAAAATA
1 TTTT-AAAAACTATATATTATATATATTTTCAAAAACG
* * * *
616852 TTTGAAAAACTATATAATATACATATTTTCAAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTC-AAAAACG
616890 TTTT--AAACTATATATTATATATGTATTTTCAAAAAC
1 TTTTAAAAACTATATATTATATA--TATTTTCAAAAAC
616926 AATTTGCAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
36 52 0.42
37 36 0.29
38 36 0.29
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAAACG
Found at i:616904 original size:38 final size:37
Alignment explanation
Indices: 616789--616950 Score: 126
Period size: 36 Copynumber: 4.4 Consensus size: 37
616779 TTTTCAAAAG
* *
616789 TATATAT-TATATATATTTT-AAAAACGT-TTTCAAAAAC
1 TATATATATATATATATTTTCAAAAA-ATATTT--GAAAC
616826 TATATAT-TATATA-ATTTTC-AAAAATATTTGAAAAAC
1 TATATATATATATATATTTTCAAAAAATATTTG--AAAC
* * *
616862 TATATA-ATATACATATTTTCAAAAAATGTTTTAAAC
1 TATATATATATATATATTTTCAAAAAATATTTGAAAC
*
616898 TATATATTATATATGTATTTTCAAAAACA-ATTTGCAAAC
1 TATATA-TATATATATATTTTCAAAAA-ATATTTG-AAAC
*
616937 TACATA-ATATATAT
1 TATATATATATATAT
616951 GTGTATATAT
Statistics
Matches: 103, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
35 1 0.01
36 37 0.36
37 26 0.25
38 29 0.28
39 10 0.10
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (37 bp):
TATATATATATATATATTTTCAAAAAATATTTGAAAC
Found at i:616974 original size:8 final size:8
Alignment explanation
Indices: 616963--616994 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
616953 GTATATATGT
616963 ATAAAAAA
1 ATAAAAAA
616971 ATAAAAAA
1 ATAAAAAA
616979 AT-AAAAA
1 ATAAAAAA
616986 ATAAAAAA
1 ATAAAAAA
616994 A
1 A
616995 AATGGACGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:616986 original size:15 final size:15
Alignment explanation
Indices: 616966--616994 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
616956 TATATGTATA
616966 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
616981 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
616995 AATGGACGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:624005 original size:21 final size:21
Alignment explanation
Indices: 623979--624023 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
623969 GCGAAAAAAT
623979 GTTGGACCAATAGACATTTCA
1 GTTGGACCAATAGACATTTCA
624000 GTTGGACCAATAGACATTTCA
1 GTTGGACCAATAGACATTTCA
624021 GTT
1 GTT
624024 CTCACAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (21 bp):
GTTGGACCAATAGACATTTCA
Found at i:628473 original size:66 final size:66
Alignment explanation
Indices: 628390--628523 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
628380 TCGGCCTCGT
*
628390 GGGGAAACACTTTGAGGACTTGGAGACCGTCCACCGCGGCTCCGTCTATCAGGACTTTCACCCCT
1 GGGGAAACACTTCGAGGACTTGGAGACCGTCCACCGCGGCTCCGTCTATCAGGACTTTCACCCCT
628455 A
66 A
* *
628456 GGGGAAACACTTCGAGGACTTGGAGACCTTCCACCGCGGCTCCGTCTATCAGGACTTTCACCCTT
1 GGGGAAACACTTCGAGGACTTGGAGACCGTCCACCGCGGCTCCGTCTATCAGGACTTTCACCCCT
628521 A
66 A
628522 GG
1 GG
628524 TGGAGATGCC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.21, C:0.31, G:0.26, T:0.22
Consensus pattern (66 bp):
GGGGAAACACTTCGAGGACTTGGAGACCGTCCACCGCGGCTCCGTCTATCAGGACTTTCACCCCT
A
Found at i:629584 original size:8 final size:9
Alignment explanation
Indices: 629567--629594 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
629557 CCAAACAAGC
629567 TTTTCTTTT
1 TTTTCTTTT
629576 TTTTCTTTT
1 TTTTCTTTT
629585 TTTTCTTTT
1 TTTTCTTTT
629594 T
1 T
629595 GAAAATAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:631481 original size:30 final size:32
Alignment explanation
Indices: 631447--631516 Score: 81
Period size: 35 Copynumber: 2.2 Consensus size: 32
631437 AAAATCGAAT
631447 TAAACAGGAAC-GGA-GAAAAACCGTTTATGC
1 TAAACAGGAACGGGAGGAAAAACCGTTTATGC
* *
631477 TAAACTGGGACGGGATGGGGAAAAACCGTTTATGC
1 TAAACAGGAACGGGA---GGAAAAACCGTTTATGC
631512 TAAAC
1 TAAAC
631517 GGGGAGGGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 9 0.27
31 3 0.09
35 21 0.64
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.19
Consensus pattern (32 bp):
TAAACAGGAACGGGAGGAAAAACCGTTTATGC
Found at i:631507 original size:35 final size:36
Alignment explanation
Indices: 631461--631533 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 36
631451 CAGGAACGGA
*
631461 GAAAAACCGTTTATGCTAAACTGGGA-CGGGATGGG
1 GAAAAACCGTTTATGCTAAACGGGGAGCGGGATGGG
*
631496 GAAAAACCGTTTATGCTAAACGGGGAGGGGGATGGG
1 GAAAAACCGTTTATGCTAAACGGGGAGCGGGATGGG
631532 GA
1 GA
631534 CGAGTTTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 25 0.71
36 10 0.29
ACGTcount: A:0.32, C:0.12, G:0.38, T:0.18
Consensus pattern (36 bp):
GAAAAACCGTTTATGCTAAACGGGGAGCGGGATGGG
Found at i:631585 original size:12 final size:12
Alignment explanation
Indices: 631570--631596 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
631560 ACCTGGCCCA
631570 ATACCCGACCCG
1 ATACCCGACCCG
631582 ATACCCGACCCG
1 ATACCCGACCCG
631594 ATA
1 ATA
631597 AATATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.44, G:0.15, T:0.11
Consensus pattern (12 bp):
ATACCCGACCCG
Found at i:631666 original size:2 final size:2
Alignment explanation
Indices: 631659--631710 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
631649 TTAAATTAAA
* * * *
631659 AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
631699 AT AT AT AT AT AT
1 AT AT AT AT AT AT
631711 CCGACCCGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:631671 original size:44 final size:42
Alignment explanation
Indices: 631622--631710 Score: 133
Period size: 44 Copynumber: 2.1 Consensus size: 42
631612 AATTATTATT
631622 TATATATATAATATTAATAAATTTAATTTAAATTAAAATATATA
1 TATATATATAATATTAATAAATTTAATTTAAA-T-AAATATATA
* * *
631666 TATATATATAATATTTATATATTTAATTTAAATATATATATA
1 TATATATATAATATTAATAAATTTAATTTAAATAAATATATA
631708 TAT
1 TAT
631711 CCGACCCGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
42 11 0.26
43 1 0.02
44 30 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
TATATATATAATATTAATAAATTTAATTTAAATAAATATATA
Found at i:631678 original size:17 final size:17
Alignment explanation
Indices: 631658--631707 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
631648 TTTAAATTAA
631658 AATATATATATATATAT
1 AATATATATATATATAT
*
631675 AATAT-T-TATATATTT
1 AATATATATATATATAT
* *
631690 AATTTAAATATATATAT
1 AATATATATATATATAT
631707 A
1 A
631708 TATCCGACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 12 0.44
16 1 0.04
17 14 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATATATATATATAT
Found at i:631678 original size:38 final size:39
Alignment explanation
Indices: 631622--631710 Score: 114
Period size: 38 Copynumber: 2.3 Consensus size: 39
631612 AATTATTATT
631622 TATATATATA-ATATTAATAAATTTA-AT-TTAAATTAAAA
1 TATATATATATATATTAAT--ATTTATATATTAAATTAAAA
* *
631660 TATATATATATATA-TAATATTTATATATTTAATTTAAA
1 TATATATATATATATTAATATTTATATATTAAATTAAAA
631698 TATATATATATAT
1 TATATATATATAT
631711 CCGACCCGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
36 5 0.11
37 2 0.04
38 36 0.78
39 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (39 bp):
TATATATATATATATTAATATTTATATATTAAATTAAAA
Found at i:632095 original size:15 final size:15
Alignment explanation
Indices: 632023--632098 Score: 75
Period size: 15 Copynumber: 5.1 Consensus size: 15
632013 ATATTCAATC
632023 ATTTAATAAATAT-AT
1 ATTTAA-AAATATAAT
*
632038 ATTTAAAATTA-AAT
1 ATTTAAAAATATAAT
* **
632052 CTTTAAAAAGCTAAT
1 ATTTAAAAATATAAT
*
632067 ATTTAAATAATATAAG
1 ATTTAAA-AATATAAT
632083 ATTTAAAAATATAAT
1 ATTTAAAAATATAAT
632098 A
1 A
632099 ACCGATCCAG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
14 13 0.27
15 23 0.48
16 12 0.25
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATTTAAAAATATAAT
Found at i:632098 original size:31 final size:29
Alignment explanation
Indices: 632023--632098 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 29
632013 ATATTCAATC
* *
632023 ATTTAATAAATAT-ATATTTAAAATTAAAT
1 ATTTAA-AAATATAATATTTAAAAATAAAG
* **
632052 CTTTAAAAAGCTAATATTTAAATAATATAAG
1 ATTTAAAAATATAATATTTAAA-AATA-AAG
632083 ATTTAAAAATATAATA
1 ATTTAAAAATATAATA
632099 ACCGATCCAG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
28 4 0.11
29 14 0.39
30 3 0.08
31 15 0.42
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (29 bp):
ATTTAAAAATATAATATTTAAAAATAAAG
Found at i:632916 original size:20 final size:20
Alignment explanation
Indices: 632891--632985 Score: 93
Period size: 20 Copynumber: 4.7 Consensus size: 20
632881 AATTGGGAAA
*
632891 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
632911 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
632932 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
632952 TTCACAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
632972 TTCGCAACGAGATA
1 ATCGCAACGCGATA
632986 ATACAGAATC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.03
20 42 0.69
21 15 0.25
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:633752 original size:24 final size:24
Alignment explanation
Indices: 633725--633778 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
633715 GTATTCGAAA
*
633725 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
633749 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
633773 TTTGAT
1 TTTGAT
633779 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:633969 original size:12 final size:12
Alignment explanation
Indices: 633952--633976 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
633942 ATATAATCCT
633952 GAAGAAGAAAAA
1 GAAGAAGAAAAA
633964 GAAGAAGAAAAA
1 GAAGAAGAAAAA
633976 G
1 G
633977 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:636268 original size:20 final size:20
Alignment explanation
Indices: 636243--636300 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
636233 ATTCATTTGA
636243 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
636263 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
636283 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
636301 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:636360 original size:19 final size:19
Alignment explanation
Indices: 636338--636383 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
636328 GATTTTCTCG
636338 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
636357 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
636376 TTGCGATT
1 TTGCGATT
636384 CTCTCGTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:636542 original size:14 final size:14
Alignment explanation
Indices: 636523--636559 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
636513 CATCAATTAA
636523 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
636537 ACAAATCATCTTTT
1 ACAAATCAACATTT
636551 ACAAATCAA
1 ACAAATCAA
636560 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:638772 original size:21 final size:21
Alignment explanation
Indices: 638746--638790 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
638736 GATTTCTGGG
* *
638746 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
638767 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
638788 CAA
1 CAA
638791 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:640502 original size:22 final size:22
Alignment explanation
Indices: 640428--640494 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
640418 TTATGGACAT
640428 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
640450 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
640472 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
640494 A
1 A
640495 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:641563 original size:20 final size:20
Alignment explanation
Indices: 641508--641563 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
641498 GAAACTTAAA
*
641508 ATCGCAACGCGAAAACGACT
1 ATCGCAACGCGAAAATGACT
641528 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
641548 ATCGTAACGCGGAAAT
1 ATCGCAACGCGAAAAT
641564 AATGCGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:641590 original size:19 final size:19
Alignment explanation
Indices: 641566--641695 Score: 82
Period size: 19 Copynumber: 7.3 Consensus size: 19
641556 GCGGAAATAA
641566 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
641585 TGCGA-TTT--TGT--CGT
1 TGCGATTTTCATTTCGCGT
*
641599 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
*
641618 TGCGA-TTT--TGT--CGT
1 TGCGATTTTCATTTCGCGT
*
641632 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
***
641651 TGCGATAGCCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
** *
641671 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
641691 TGCGA
1 TGCGA
641696 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
14 15 0.17
15 6 0.07
16 4 0.05
17 4 0.05
18 6 0.07
19 25 0.29
20 23 0.27
21 3 0.03
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.44
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:641601 original size:14 final size:14
Alignment explanation
Indices: 641582--641640 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
641572 TTTCATTTCG
641582 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
641596 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
641613 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
641629 CGTTGCGATTTT
1 CGTTGCGATTTT
641641 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:641608 original size:33 final size:33
Alignment explanation
Indices: 641566--641656 Score: 173
Period size: 33 Copynumber: 2.8 Consensus size: 33
641556 GCGGAAATAA
*
641566 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
641599 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
641632 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
641657 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
Found at i:641675 original size:20 final size:19
Alignment explanation
Indices: 641641--641695 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
641631 TTGCGATTTT
*
641641 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
641660 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
641680 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
641696 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:642235 original size:18 final size:18
Alignment explanation
Indices: 642212--642277 Score: 123
Period size: 18 Copynumber: 3.7 Consensus size: 18
642202 CGGGTCGATC
642212 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
642230 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
642248 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
642266 AGGTGATGGCTC
1 AGGTGATGGCTC
642278 CCAAAGTGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.14, C:0.12, G:0.47, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:643644 original size:20 final size:20
Alignment explanation
Indices: 643596--643654 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
643586 AATAGTTTCT
** *
643596 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
643616 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
643636 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
643655 AGAGAATCGC
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:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:643949 original size:22 final size:22
Alignment explanation
Indices: 643922--643963 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
643912 GATGGAGATA
643922 GACGGATTTCGCCGGAGATGTG
1 GACGGATTTCGCCGGAGATGTG
*
643944 GACGGATTTCGTCGGAGATG
1 GACGGATTTCGCCGGAGATG
643964 GGTGAGAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.17, G:0.40, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGTG
Found at i:644205 original size:20 final size:20
Alignment explanation
Indices: 644145--644208 Score: 119
Period size: 20 Copynumber: 3.2 Consensus size: 20
644135 GATTATGTAT
644145 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
644165 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
644185 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
644205 TATC
1 TATC
644209 TCATTACGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:644251 original size:20 final size:20
Alignment explanation
Indices: 644145--644256 Score: 109
Period size: 20 Copynumber: 5.5 Consensus size: 20
644135 GATTATGTAT
*
644145 TATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGAAAGTCAG
* *
644165 AATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGAAAGTCAG
*
644185 TATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGAAAGTCAG
* * ** *
644205 TATCTCATTACGATTTTGT-AT
1 TATCGCATTGCGA--AAGTCAG
*
644226 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGAAAGTCAG
644246 TATCGCATTGC
1 TATCGCATTGC
644257 AATTTTCCCA
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 60 0.78
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGAAAGTCAG
Found at i:644262 original size:41 final size:41
Alignment explanation
Indices: 644125--644262 Score: 138
Period size: 41 Copynumber: 3.4 Consensus size: 41
644115 CGCTTTGAAA
* * *
644125 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCAATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * *
644166 ATCGCGTTGCGAA---AGTCAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGC-AATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
644206 ATCTCATTACGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCAATTTTGTATTATCGCGTTGCGAAAGTCAGT
644247 ATCGCATTGCAATTTT
1 ATCGCATTGCAATTTT
644263 CCCAATTCGC
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
39 3 0.04
40 28 0.37
41 42 0.55
42 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCAATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:644278 original size:41 final size:41
Alignment explanation
Indices: 644185--644280 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
644175 CGAAAGTCAG
* * * ** *
644185 TATCGCGTTGCGAAAGTCAGTATCTCATTACGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTACAATTTTCCAA
* *
644226 TATCGCATTGCGATAGTCAGTATCGCATTGCAATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTACAATTTT-CCAA
644268 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
644281 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTACAATTTTCCAA
Found at i:655965 original size:21 final size:21
Alignment explanation
Indices: 655941--655980 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
655931 TTATAAAATT
*
655941 TAAT-TAAAAGATTATATTATA
1 TAATATAAAA-ATAATATTATA
655962 TAATATAAAAATAATATTA
1 TAATATAAAAATAATATTA
655981 ACATAACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TAATATAAAAATAATATTATA
Found at i:667178 original size:24 final size:24
Alignment explanation
Indices: 667151--667204 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
667141 ATTCTTTTGC
667151 TTCAATTGAGCTCAAATTTTAGGA
1 TTCAATTGAGCTCAAATTTTAGGA
*
667175 TTCAATTGAGCTCAAATTTTAGGC
1 TTCAATTGAGCTCAAATTTTAGGA
667199 TTCAAT
1 TTCAAT
667205 CGAACTTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (24 bp):
TTCAATTGAGCTCAAATTTTAGGA
Found at i:667474 original size:21 final size:21
Alignment explanation
Indices: 667450--667497 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
667440 GATTTTGCCA
* *
667450 GTTTTCAGCCGGTTCACCTCG
1 GTTTTCAACCGGTTCACCCCG
667471 GTTTTCAACCGGTTCACCCCG
1 GTTTTCAACCGGTTCACCCCG
*
667492 ATTTTC
1 GTTTTC
667498 TCGGTTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.19, T:0.35
Consensus pattern (21 bp):
GTTTTCAACCGGTTCACCCCG
Found at i:668344 original size:22 final size:22
Alignment explanation
Indices: 668286--668344 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
668276 CTTTCTGCTC
668286 AAACACTCATAAAAAATCAACCA
1 AAACA-TCATAAAAAATCAACCA
* *
668309 AAA-ATAATTCAAAAATCCAACCA
1 AAACATCA-TAAAAAAT-CAACCA
668332 AAACATCATAAAA
1 AAACATCATAAAA
668345 CGATCGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 2 0.07
22 8 0.28
23 16 0.55
24 3 0.10
ACGTcount: A:0.63, C:0.22, G:0.00, T:0.15
Consensus pattern (22 bp):
AAACATCATAAAAAATCAACCA
Found at i:669303 original size:39 final size:41
Alignment explanation
Indices: 669260--669355 Score: 94
Period size: 39 Copynumber: 2.5 Consensus size: 41
669250 CATAATCCTC
* *
669260 AAATTATTTGAC-TC-TAACATTTTAAAACCCTAATTTCTT
1 AAATTATTTAACATCATAACATTCTAAAACCCTAATTTCTT
* ** *
669299 AAA-T-TTTAACATCATAACGTTCTAAATTCTTAATTTCTT
1 AAATTATTTAACATCATAACATTCTAAAACCCTAATTTCTT
*
669338 AAATTATTTCACAT-ATAA
1 AAATTATTTAACATCATAA
669356 ATTATTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
37 5 0.11
38 3 0.07
39 26 0.57
40 5 0.11
41 7 0.15
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.44
Consensus pattern (41 bp):
AAATTATTTAACATCATAACATTCTAAAACCCTAATTTCTT
Found at i:669516 original size:15 final size:15
Alignment explanation
Indices: 669481--669514 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
669471 GATTATATAT
669481 ATTTTAGAATTTTAA
1 ATTTTAGAATTTTAA
*
669496 ATTTTAG-ATTTTAG
1 ATTTTAGAATTTTAA
669510 ATTTT
1 ATTTT
669515 TATATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (15 bp):
ATTTTAGAATTTTAA
Found at i:669634 original size:21 final size:22
Alignment explanation
Indices: 669610--669668 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
669600 TATACTAATA
669610 TATATTAACTTAAAATAT-TTT
1 TATATTAACTTAAAATATATTT
*
669631 TATATTAACTTGTTAAATATATTT
1 TATATTAAC-T-TAAAATATATTT
669655 TACTATTAACTTAA
1 TA-TATTAACTTAA
669669 TTTAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 9 0.28
22 1 0.03
23 9 0.28
24 6 0.19
25 7 0.22
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:669652 original size:25 final size:24
Alignment explanation
Indices: 669619--669666 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
669609 ATATATTAAC
669619 TTAAAATATTTTTA-TATTAACTTG
1 TTAAAATA-TTTTACTATTAACTTG
669643 TTAAATATATTTTACTATTAACTT
1 TTAAA-ATATTTTACTATTAACTT
669667 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (24 bp):
TTAAAATATTTTACTATTAACTTG
Found at i:670858 original size:23 final size:23
Alignment explanation
Indices: 670801--670860 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
670791 ACTTTGATGT
* *
670801 TGAATCATTCAACATTGTTTTGC
1 TGAATCAGTCAGCATTGTTTTGC
670824 TGAATCAGTCAGCATTGTTTTGC
1 TGAATCAGTCAGCATTGTTTTGC
670847 TGAATCAGTCAGCA
1 TGAATCAGTCAGCA
670861 CTGAATCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (23 bp):
TGAATCAGTCAGCATTGTTTTGC
Found at i:683208 original size:29 final size:30
Alignment explanation
Indices: 683176--683253 Score: 72
Period size: 31 Copynumber: 2.6 Consensus size: 30
683166 AAGTCTATCA
683176 ACTATTAAAAGTTATAAAGT-AGTCAT-TCG
1 ACTATTAAAAGTTATAAAGTAAGT-ATCTCG
* ** *
683205 ACTA-TAGAAAATTACTTTATTAAGTATCTCG
1 ACTATTA-AAAGTTA-TAAAGTAAGTATCTCG
683236 ACTATTAAAAGTTATAAA
1 ACTATTAAAAGTTATAAA
683254 ATGGTCACAC
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
28 2 0.05
29 10 0.27
30 7 0.19
31 16 0.43
32 2 0.05
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (30 bp):
ACTATTAAAAGTTATAAAGTAAGTATCTCG
Found at i:683210 original size:60 final size:59
Alignment explanation
Indices: 683135--683253 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 59
683125 AGTTCACAAA
* *
683135 TAGTCTTCCGACTATAGAATACTGTA-TTATTAAGTCTATCAACTATTAAAAGTTATAAAG
1 TAGTCTTCCGACTATAGAA-AAT-TACTTATTAAGTATATCAACTATTAAAAGTTATAAAG
* *
683195 TAGTCATT-CGACTATAGAAAATTACTTTATTAAGTATCTCGACTATTAAAAGTTATAAA
1 TAGTC-TTCCGACTATAGAAAATTAC-TTATTAAGTATATCAACTATTAAAAGTTATAAA
683254 ATGGTCACAC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
58 2 0.04
59 2 0.04
60 46 0.88
61 2 0.04
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (59 bp):
TAGTCTTCCGACTATAGAAAATTACTTATTAAGTATATCAACTATTAAAAGTTATAAAG
Found at i:684099 original size:2 final size:2
Alignment explanation
Indices: 684092--684121 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
684082 TGCTTTTGTA
684092 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
684122 TATTTTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:684922 original size:13 final size:13
Alignment explanation
Indices: 684904--684935 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
684894 TTCAGTTTAG
684904 ATTGTTTCATCAT
1 ATTGTTTCATCAT
684917 ATTGTTTCATCAT
1 ATTGTTTCATCAT
684930 A-TGTTT
1 ATTGTTT
684936 ATATAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.56
Consensus pattern (13 bp):
ATTGTTTCATCAT
Found at i:687038 original size:2 final size:2
Alignment explanation
Indices: 687031--687060 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
687021 GACAAGAACA
687031 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
687061 CTTAGTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:687233 original size:20 final size:20
Alignment explanation
Indices: 687208--687245 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
687198 AACCTCATTT
*
687208 CTCTTAAGAATCTAATTTTC
1 CTCTTAAGAATATAATTTTC
687228 CTCTTAAGAATATAATTT
1 CTCTTAAGAATATAATTT
687246 GATATATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (20 bp):
CTCTTAAGAATATAATTTTC
Found at i:687721 original size:13 final size:14
Alignment explanation
Indices: 687703--687734 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
687693 TCTCGGTCGA
687703 CGGGTCAA-CGGGT
1 CGGGTCAACCGGGT
687716 CGGGTCAACCGGGT
1 CGGGTCAACCGGGT
687730 CGGGT
1 CGGGT
687735 AATTTTGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (14 bp):
CGGGTCAACCGGGT
Found at i:701828 original size:122 final size:121
Alignment explanation
Indices: 701606--701842 Score: 350
Period size: 122 Copynumber: 2.0 Consensus size: 121
701596 TAAGAGATTC
* *
701606 TACCTCTCTAAGTAAATATATGAGGTAAAATTCACTCTCACCTATAAAAAAATTAATTTTGTATT
1 TACCTCTCTAAATAAATAAATGAGGTAAAATTCACTCTCACCTATAAAAAAATTAATTTTGTATT
* * *
701671 TTTTTAATTATTGAACAAGTGAGAATGAATGATTGAGATTAACAGTAAAATTTTTT
66 TTTTTAATGATTGAACAAGTGAGAATGAATGATTGAAACTAACAGTAAAATTTTTT
* * **
701727 TACCTCTCTAAATAAATAAATGAGGTAAAATTTAC-CATCATCTATAAAAATTTTAAATTTTGTA
1 TACCTCTCTAAATAAATAAATGAGGTAAAATTCACTC-TCACCTATAAAAAAATT-AATTTTGTA
* *
701791 TTTTTTTAATGATTGAACAAGTGAGGATGAATGATTGAAACTAACGGTAAAA
64 TTTTTTTAATGATTGAACAAGTGAGAATGAATGATTGAAACTAACAGTAAAA
701843 ATAAAAATAA
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
120 1 0.01
121 46 0.45
122 56 0.54
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (121 bp):
TACCTCTCTAAATAAATAAATGAGGTAAAATTCACTCTCACCTATAAAAAAATTAATTTTGTATT
TTTTTAATGATTGAACAAGTGAGAATGAATGATTGAAACTAACAGTAAAATTTTTT
Found at i:710024 original size:34 final size:34
Alignment explanation
Indices: 709984--710061 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
709974 CGTTCGGTAA
709984 TATGTTCGTTTATATTCATTCATTTATGCTCGTT
1 TATGTTCGTTTATATTCATTCATTTATGCTCGTT
* * * * *
710018 TATGTTCGCTTATTTTCATTCGTTTATGTTTGTT
1 TATGTTCGTTTATATTCATTCATTTATGCTCGTT
*
710052 TATGTGCGTT
1 TATGTTCGTT
710062 CATTTATGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.14, C:0.13, G:0.15, T:0.58
Consensus pattern (34 bp):
TATGTTCGTTTATATTCATTCATTTATGCTCGTT
Found at i:710054 original size:24 final size:24
Alignment explanation
Indices: 710013--710072 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
710003 TCATTTATGC
* * *
710013 TCGTTTATGTTCGCTTATTTTCAT
1 TCGTTTATGTTTGCTTATGTGCAT
* *
710037 TCGTTTATGTTTGTTTATGTGCGT
1 TCGTTTATGTTTGCTTATGTGCAT
*
710061 TCATTTATGTTT
1 TCGTTTATGTTT
710073 AACACAGTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.60
Consensus pattern (24 bp):
TCGTTTATGTTTGCTTATGTGCAT
Found at i:710293 original size:23 final size:23
Alignment explanation
Indices: 710262--710370 Score: 130
Period size: 24 Copynumber: 4.7 Consensus size: 23
710252 TTTACGATCA
*
710262 TTTATGTTCATTTATTGTGTTCG
1 TTTATGTTCGTTTATTGTGTTCG
* *
710285 TTTAAGTTCGTTCACTTGTGTTCG
1 TTTATGTTCGTTTA-TTGTGTTCG
*
710309 TTTACGTTCGTTTATTGTGTTCG
1 TTTATGTTCGTTTATTGTGTTCG
*
710332 TTTATGTTCGTTTA-TGTTCGTTCA
1 TTTATGTTCGTTTATTG-T-GTTCG
*
710356 TTTGTGTTCGTTTAT
1 TTTATGTTCGTTTAT
710371 CATTTAAATG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
22 2 0.03
23 34 0.46
24 38 0.51
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58
Consensus pattern (23 bp):
TTTATGTTCGTTTATTGTGTTCG
Found at i:710307 original size:24 final size:23
Alignment explanation
Indices: 710275--710343 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
710265 ATGTTCATTT
710275 ATTGTGTTCGTTTAAGTTCGTTC
1 ATTGTGTTCGTTTAAGTTCGTTC
* *
710298 ACTTGTGTTCGTTTACGTTCGTTT
1 A-TTGTGTTCGTTTAAGTTCGTTC
*
710322 ATTGTGTTCGTTTATGTTCGTT
1 ATTGTGTTCGTTTAAGTTCGTT
710344 TATGTTCGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
23 21 0.50
24 21 0.50
ACGTcount: A:0.10, C:0.13, G:0.22, T:0.55
Consensus pattern (23 bp):
ATTGTGTTCGTTTAAGTTCGTTC
Found at i:710317 original size:10 final size:10
Alignment explanation
Indices: 710303--710353 Score: 66
Period size: 10 Copynumber: 4.8 Consensus size: 10
710293 CGTTCACTTG
710303 TGTTCGTTTA
1 TGTTCGTTTA
*
710313 CGTTCGTTTA
1 TGTTCGTTTA
710323 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
710336 TGTTCGTTTA
1 TGTTCGTTTA
710346 TGTTCGTT
1 TGTTCGTT
710354 CATTTGTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 27 0.75
13 9 0.25
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:710344 original size:33 final size:34
Alignment explanation
Indices: 710303--710370 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 34
710293 CGTTCACTTG
*
710303 TGTTCGTTTACGTTCGTTTA-TTGTGTTCGTTTA
1 TGTTCGTTTACGTTCGTTCATTTGTGTTCGTTTA
*
710336 TGTTCGTTTATGTTCGTTCATTTGTGTTCGTTTA
1 TGTTCGTTTACGTTCGTTCATTTGTGTTCGTTTA
710370 T
1 T
710371 CATTTAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 18 0.56
34 14 0.44
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.59
Consensus pattern (34 bp):
TGTTCGTTTACGTTCGTTCATTTGTGTTCGTTTA
Found at i:714338 original size:20 final size:20
Alignment explanation
Indices: 714309--714346 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
714299 AGAACCCCAG
*
714309 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
714329 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
714347 TCAAAGGAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:714379 original size:21 final size:21
Alignment explanation
Indices: 714329--714390 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
714319 ATTCCCCTGT
714329 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
* *
714352 GGAGGAATCGGTTCCCTCAAG
1 GGGGGAATCGGTTCCCTCAAA
*
714373 GGGGGAATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
714391 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 20 0.57
22 3 0.09
23 12 0.34
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:722503 original size:160 final size:159
Alignment explanation
Indices: 722152--722575 Score: 575
Period size: 157 Copynumber: 2.7 Consensus size: 159
722142 AAAACTCGAA
* * * *
722152 AATACATGTTTACTTTCAATTCATCTTTTTGATAATAAATTTTTATTTTTCAATTTAGTTCTTCA
1 AATACATGTGTACATTCAATTCCTCTTTTTGATAA-AAATTTTTATTTTTCAATTTAGTCCTTCA
* * *
722217 ATTTTTCATAATCTCCTTATTTATTTAATTCGTCATTTA-TTTAAG--ACTGTTTTTTTACCAAA
65 ATTTTTCATAATCTCCTTATTTCTTCAATTTGTCATTTATTTTAAGTTACTGTTTTTTTACCAAA
*
722279 TTTGAGTCACATGATCCTAAACTATAGTAG
130 TTTGAGTCACATGATCCTAAACCATAGTAG
722309 AATACATGTGTA-ATATCAATTCCT-TTTCTTGATAACAAATTTTTATTTTTCAATTTAGTCCTT
1 AATACATGTGTACAT-TCAATTCCTCTTT-TTGATAA-AAATTTTTATTTTTCAATTTAGTCCTT
* * *
722372 CAATTTTT-ATAGTCTCCTTATTTCTTCAATTTGTCATTTATTTTAAGTTTA-TTTTTTTATTAT
63 CAATTTTTCATAATCTCCTTATTTCTTCAATTTGTCATTTATTTTAAG-TTACTGTTTTT-TTAC
**
722435 CAAATTTGAGTCACATTCTCCTAAACCATAGTAG
126 CAAATTTGAGTCACATGATCCTAAACCATAGTAG
*
722469 AATACATGTGTACCTTCAATTCCTCTTTTTGAT---AA-TTTT-TTTTTCAATTTAGTCCTTCAA
1 AATACATGTGTACATTCAATTCCTCTTTTTGATAAAAATTTTTATTTTTCAATTTAGTCCTTCAA
*
722529 TTTTTCATAATCTCCTTATTCCTTCAATTTGTCATTTATTTTAAGTT
66 TTTTTCATAATCTCCTTATTTCTTCAATTTGTCATTTATTTTAAGTT
722576 CAATTTTTAC
Statistics
Matches: 240, Mismatches: 17, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
154 28 0.12
155 41 0.17
156 34 0.14
157 66 0.28
159 6 0.03
160 61 0.25
161 4 0.02
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (159 bp):
AATACATGTGTACATTCAATTCCTCTTTTTGATAAAAATTTTTATTTTTCAATTTAGTCCTTCAA
TTTTTCATAATCTCCTTATTTCTTCAATTTGTCATTTATTTTAAGTTACTGTTTTTTTACCAAAT
TTGAGTCACATGATCCTAAACCATAGTAG
Found at i:728453 original size:15 final size:16
Alignment explanation
Indices: 728427--728462 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
728417 TACTTCATCT
728427 ATGAATAGTATGCAAG
1 ATGAATAGTATGCAAG
728443 ATGAA-AGTATGCAAG
1 ATGAATAGTATGCAAG
728458 ATGAA
1 ATGAA
728463 GAAGGTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (16 bp):
ATGAATAGTATGCAAG
Found at i:730566 original size:26 final size:26
Alignment explanation
Indices: 730530--730582 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
730520 ACTGCTGTAG
730530 AAGGTATGAATTTACAAATGAATGAA
1 AAGGTATGAATTTACAAATGAATGAA
730556 AAGGTATGAATTTACAAATGAATGAA
1 AAGGTATGAATTTACAAATGAATGAA
730582 A
1 A
730583 GCAGTAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.26
Consensus pattern (26 bp):
AAGGTATGAATTTACAAATGAATGAA
Found at i:736574 original size:15 final size:16
Alignment explanation
Indices: 736556--736586 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
736546 TGAGTTTATA
736556 AAAATCGAG-TAGAGT
1 AAAATCGAGTTAGAGT
736571 AAAATCGAGTTAGAGT
1 AAAATCGAGTTAGAGT
736587 TGTTAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
AAAATCGAGTTAGAGT
Found at i:739777 original size:31 final size:31
Alignment explanation
Indices: 739739--739800 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
739729 AAAATGTAAG
*
739739 AACAATCATCAGAATTCTATAAACCAGTTTC
1 AACAATCATCAGAATTCTATAAAACAGTTTC
739770 AACAATCATCAGAATTCTATAAAACAGTTTC
1 AACAATCATCAGAATTCTATAAAACAGTTTC
739801 CTTTCAGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (31 bp):
AACAATCATCAGAATTCTATAAAACAGTTTC
Found at i:740317 original size:31 final size:31
Alignment explanation
Indices: 740279--740340 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
740269 CATGGCGCAT
*
740279 GCAAAGCTTGATCCTCTCGTCACAGCTCGTA
1 GCAAAGCTTGATCCTCTCGCCACAGCTCGTA
*
740310 GCAAAGCTTTATCCTCTCGCCACAGCTCGTA
1 GCAAAGCTTGATCCTCTCGCCACAGCTCGTA
740341 TAGAACACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.26
Consensus pattern (31 bp):
GCAAAGCTTGATCCTCTCGCCACAGCTCGTA
Found at i:743759 original size:15 final size:16
Alignment explanation
Indices: 743739--743768 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
743729 TTAGGGGTAC
743739 TTTTTA-CATTATGCA
1 TTTTTATCATTATGCA
743754 TTTTTATCATTATGC
1 TTTTTATCATTATGC
743769 TTACTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (16 bp):
TTTTTATCATTATGCA
Found at i:744994 original size:30 final size:30
Alignment explanation
Indices: 744958--745015 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
744948 GTGCTCGTCG
*
744958 GAAGACGCCAGGAACACAATGCGTTTTCGA
1 GAAGACGCCACGAACACAATGCGTTTTCGA
* * *
744988 GAAGACGCGACGACCACAGTGCGTTTTC
1 GAAGACGCCACGAACACAATGCGTTTTC
745016 TGCTTTGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.17
Consensus pattern (30 bp):
GAAGACGCCACGAACACAATGCGTTTTCGA
Found at i:747200 original size:22 final size:22
Alignment explanation
Indices: 747174--747218 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
747164 AAAGAATAAA
747174 TTACTATAAGAAATTAGAAAAT
1 TTACTATAAGAAATTAGAAAAT
747196 TTACTATAAGAAATTAGAAAAT
1 TTACTATAAGAAATTAGAAAAT
747218 T
1 T
747219 CTCACAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (22 bp):
TTACTATAAGAAATTAGAAAAT
Found at i:756159 original size:33 final size:31
Alignment explanation
Indices: 756082--756171 Score: 128
Period size: 31 Copynumber: 2.8 Consensus size: 31
756072 ATACCTAATG
756082 TTTACTTTTTGTTTCATTTTAGTACCCGACA
1 TTTACTTTTTGTTTCATTTTAGTACCCGACA
* *
756113 TTTACTTTTTGTTTCGTTTTAGTACCC-CCA
1 TTTACTTTTTGTTTCATTTTAGTACCCGACA
756143 TTGTTAGCTTTTTGTTTCATTTTAGTACC
1 -T-TTA-CTTTTTGTTTCATTTTAGTACC
756172 TAATTTTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 2 0.04
31 27 0.51
32 3 0.06
33 21 0.40
ACGTcount: A:0.16, C:0.19, G:0.11, T:0.54
Consensus pattern (31 bp):
TTTACTTTTTGTTTCATTTTAGTACCCGACA
Found at i:760356 original size:14 final size:14
Alignment explanation
Indices: 760337--760364 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
760327 ATCAAGTGAC
760337 TCTTAAGCTTAAGG
1 TCTTAAGCTTAAGG
760351 TCTTAAGCTTAAGG
1 TCTTAAGCTTAAGG
760365 AAAGCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
TCTTAAGCTTAAGG
Found at i:760859 original size:102 final size:102
Alignment explanation
Indices: 760681--760884 Score: 381
Period size: 102 Copynumber: 2.0 Consensus size: 102
760671 GTTGAGCTAA
*
760681 AAAGAAAGTGAATTTCATGCTTTAACTGGAATTTCTGGGTTGTGTGCATCGATGCACATTCAATG
1 AAAGAAAGTGAATTTCATGCTCTAACTGGAATTTCTGGGTTGTGTGCATCGATGCACATTCAATG
*
760746 TGTACCGATGCACTCTCAAACAAATAAACATCGAATG
66 TGTACCAATGCACTCTCAAACAAATAAACATCGAATG
760783 AAAGAAAGTGAATTTCATGCTCTAACTGGAATTTCTGGGTTGTGTGCATCGATGCACATTCAATG
1 AAAGAAAGTGAATTTCATGCTCTAACTGGAATTTCTGGGTTGTGTGCATCGATGCACATTCAATG
*
760848 TGTATCAATGCACTCTCAAACAAATAAACATCGAATG
66 TGTACCAATGCACTCTCAAACAAATAAACATCGAATG
760885 CAATTAGTGC
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (102 bp):
AAAGAAAGTGAATTTCATGCTCTAACTGGAATTTCTGGGTTGTGTGCATCGATGCACATTCAATG
TGTACCAATGCACTCTCAAACAAATAAACATCGAATG
Found at i:760985 original size:19 final size:19
Alignment explanation
Indices: 760961--761004 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 19
760951 AATTGTGTAC
760961 CGATGCATAGATAGTGCAT
1 CGATGCATAGATAGTGCAT
760980 CGATGC----ATAGTGCAT
1 CGATGCATAGATAGTGCAT
760995 CGATGCATAG
1 CGATGCATAG
761005 TGCATCGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
15 15 0.71
19 6 0.29
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (19 bp):
CGATGCATAGATAGTGCAT
Found at i:760991 original size:15 final size:15
Alignment explanation
Indices: 760971--761016 Score: 92
Period size: 15 Copynumber: 3.1 Consensus size: 15
760961 CGATGCATAG
760971 ATAGTGCATCGATGC
1 ATAGTGCATCGATGC
760986 ATAGTGCATCGATGC
1 ATAGTGCATCGATGC
761001 ATAGTGCATCGATGC
1 ATAGTGCATCGATGC
761016 A
1 A
761017 CTCGTTAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (15 bp):
ATAGTGCATCGATGC
Found at i:761001 original size:8 final size:8
Alignment explanation
Indices: 760975--761016 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
760965 GCATAGATAG
760975 TGCATCGA
1 TGCATCGA
*
760983 TGCATAG-
1 TGCATCGA
760990 TGCATCGA
1 TGCATCGA
*
760998 TGCATAG-
1 TGCATCGA
761005 TGCATCGA
1 TGCATCGA
761013 TGCA
1 TGCA
761017 CTCGTTAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.43
8 16 0.57
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (8 bp):
TGCATCGA
Found at i:761902 original size:31 final size:31
Alignment explanation
Indices: 761864--761956 Score: 125
Period size: 31 Copynumber: 3.0 Consensus size: 31
761854 AGAGTCGAGG
761864 GTTTACCTATG-TCTTTCGGGACATATGGACA
1 GTTTACCTATGTTC-TTCGGGACATATGGACA
* *
761895 GTTTACCTATGTTCTACGGGACATATGGATA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
* * *
761926 GTTTACCTAGGTTCTTCGAGACCTATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
761957 ATTGTCGATG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 52 0.96
32 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACA
Found at i:766278 original size:42 final size:42
Alignment explanation
Indices: 766219--766304 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
766209 CATCACACTA
* *
766219 TAATTAAGGCATTATTTTATTATTTTTAATAGTTCAAAGACT
1 TAATTAAGGCATCATTTTATAATTTTTAATAGTTCAAAGACT
* *
766261 TAATTAAGAG-ATCATTTTATAATTTTTAATAGTTTAAGGACT
1 TAATTAAG-GCATCATTTTATAATTTTTAATAGTTCAAAGACT
766303 TA
1 TA
766305 TAGAGTATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (42 bp):
TAATTAAGGCATCATTTTATAATTTTTAATAGTTCAAAGACT
Found at i:767181 original size:3 final size:3
Alignment explanation
Indices: 767169--767214 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
767159 AAAAAGAACG
*
767169 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
767215 CATTTAGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:771731 original size:35 final size:33
Alignment explanation
Indices: 771692--771781 Score: 94
Period size: 33 Copynumber: 2.7 Consensus size: 33
771682 ATTGAAAAAG
*
771692 AATATAAAAAGAAGATATTGTAGTAATTATCTT-TA
1 AATATAAAAAGAAGA-ATTATA-TAATTAT-TTCTA
* * *
771727 AATATATAAACAAGAATTATATAATTGTTTCTA
1 AATATAAAAAGAAGAATTATATAATTATTTCTA
771760 AATATATAAAAGAA-AATTATAT
1 AATATA-AAAAGAAGAATTATAT
771782 TACTATTCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
32 2 0.04
33 22 0.47
34 10 0.21
35 13 0.28
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (33 bp):
AATATAAAAAGAAGAATTATATAATTATTTCTA
Found at i:774667 original size:18 final size:18
Alignment explanation
Indices: 774644--774721 Score: 85
Period size: 18 Copynumber: 4.5 Consensus size: 18
774634 AAAATATTAT
*
774644 ATATATAATTACTATAAA
1 ATATATAATTAATATAAA
774662 ATATATAA--AATATAAA
1 ATATATAATTAATATAAA
774678 ATATATAATTAATATAAA
1 ATATATAATTAATATAAA
*
774696 A-ATATTATATT-ATAT-AT
1 ATATA-TA-ATTAATATAAA
774713 ATATATAAT
1 ATATATAAT
774722 CGGGGTGGGG
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
16 17 0.32
17 7 0.13
18 26 0.49
19 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATATAATTAATATAAA
Found at i:774668 original size:9 final size:9
Alignment explanation
Indices: 774642--774700 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 9
774632 CAAAAATATT
774642 ATATATATAA
1 ATATATA-AA
*
774652 TTACTATAAA
1 ATA-TATAAA
774662 ATATAT-AA
1 ATATATAAA
774670 A-ATATAAA
1 ATATATAAA
774678 ATATATAATTA
1 ATATATAA--A
774689 ATATA-AAA
1 ATATATAAA
774697 ATAT
1 ATAT
774701 TATATTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 4 0.10
8 11 0.26
9 9 0.21
10 8 0.19
11 10 0.24
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
ATATATAAA
Found at i:774672 original size:34 final size:33
Alignment explanation
Indices: 774634--774715 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 33
774624 CCCGAACTCA
*
774634 AAAATATTATATATATAATTACTATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAA-ATAT
* *
774668 AAAATATAAAATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
*
774701 --TATATTATATATATA
1 AAAATATTATATATATA
774716 TATAATCGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 12 0.29
33 4 0.10
34 26 0.62
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAAAATAT
Found at i:776674 original size:30 final size:31
Alignment explanation
Indices: 776619--776694 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
776609 TAAAAAATAT
* *
776619 AACGGTAGACACCTAAAAATGTAACGGAGAA
1 AACGTTAGACACCTAAAAATGTAACGGAAAA
**
776650 AACGTTAGACACC-AAAGGTGTAACGGAAAA
1 AACGTTAGACACCTAAAAATGTAACGGAAAA
776680 AACGTTA-AGCACCTA
1 AACGTTAGA-CACCTA
776695 TTGTTAGCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 1 0.03
30 25 0.64
31 13 0.33
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (31 bp):
AACGTTAGACACCTAAAAATGTAACGGAAAA
Found at i:778321 original size:19 final size:20
Alignment explanation
Indices: 778283--778321 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
778273 TAAGGAGGAT
*
778283 GAACTAAAATTTCAAGGGGG
1 GAACTAAAATTACAAGGGGG
*
778303 GAACTAAAA-TACTAGGGGG
1 GAACTAAAATTACAAGGGGG
778322 CGAAACAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.41, C:0.10, G:0.31, T:0.18
Consensus pattern (20 bp):
GAACTAAAATTACAAGGGGG
Found at i:781274 original size:36 final size:36
Alignment explanation
Indices: 781224--781315 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 36
781214 ATGAAGTTCA
* * *
781224 TTTATTT-ATTAAATGAATATTAACAATATTTTATG
1 TTTATTTAATTAAATGAACATGAACAAAATTTTATG
781259 TTTATTTAATTAAATGAACGAACATGAACAAAATTTTATG
1 TTTATTTAATTAAAT----GAACATGAACAAAATTTTATG
*
781299 TTCATTTAATTAAATGA
1 TTTATTTAATTAAATGA
781316 GCGAACATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
35 7 0.15
36 9 0.19
40 32 0.67
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (36 bp):
TTTATTTAATTAAATGAACATGAACAAAATTTTATG
Found at i:781295 original size:40 final size:40
Alignment explanation
Indices: 781245--781330 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
781235 AATGAATATT
* *
781245 AACAATATTTTATGTTTATTTAATTAAATGAACGAACATG
1 AACAAAATTTTATGTTCATTTAATTAAATGAACGAACATG
*
781285 AACAAAATTTTATGTTCATTTAATTAAATGAGCGAACATG
1 AACAAAATTTTATGTTCATTTAATTAAATGAACGAACATG
781325 AACAAA
1 AACAAA
781331 TGACTCGTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.35
Consensus pattern (40 bp):
AACAAAATTTTATGTTCATTTAATTAAATGAACGAACATG
Found at i:781464 original size:23 final size:23
Alignment explanation
Indices: 781438--781481 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
781428 CATTTGAATA
*
781438 TTAAGACCTAATAA-ATTTTAACC
1 TTAAAACC-AATAATATTTTAACC
*
781461 TTAAAACCATTAATATTTTAA
1 TTAAAACCAATAATATTTTAA
781482 AATCTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (23 bp):
TTAAAACCAATAATATTTTAACC
Found at i:781644 original size:14 final size:14
Alignment explanation
Indices: 781586--781652 Score: 61
Period size: 14 Copynumber: 5.1 Consensus size: 14
781576 TAAACTCAAA
*
781586 TCATTTATGTTTGT
1 TCATTTATGTTCGT
*
781600 TTATTTATGTTCGT
1 TCATTTATGTTCGT
**
781614 TTGTTTAT-TT--T
1 TCATTTATGTTCGT
*
781625 T-GTTTATGTTCGT
1 TCATTTATGTTCGT
781638 TCATTTATGTTCGT
1 TCATTTATGTTCGT
781652 T
1 T
781653 TATCATTTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 6 0.13
11 4 0.09
13 4 0.09
14 31 0.69
ACGTcount: A:0.12, C:0.07, G:0.15, T:0.66
Consensus pattern (14 bp):
TCATTTATGTTCGT
Found at i:781644 original size:24 final size:24
Alignment explanation
Indices: 781603--781655 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
781593 TGTTTGTTTA
** * *
781603 TTTATGTTCGTTTGTTTATTTTTG
1 TTTATGTTCGTTCATTTATGTTCG
781627 TTTATGTTCGTTCATTTATGTTCG
1 TTTATGTTCGTTCATTTATGTTCG
781651 TTTAT
1 TTTAT
781656 CATTTCAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.11, C:0.08, G:0.15, T:0.66
Consensus pattern (24 bp):
TTTATGTTCGTTCATTTATGTTCG
Found at i:789430 original size:16 final size:16
Alignment explanation
Indices: 789409--789449 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
789399 AGGATTAGTA
*
789409 TTCTAACTTCCGATAT
1 TTCTAACTACCGATAT
789425 TTCTAACTACCGATAT
1 TTCTAACTACCGATAT
789441 TTCTAACTA
1 TTCTAACTA
789450 ATCCTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (16 bp):
TTCTAACTACCGATAT
Found at i:793002 original size:13 final size:13
Alignment explanation
Indices: 792984--793010 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
792974 TTCTATTTGT
792984 TTATCCATGAACA
1 TTATCCATGAACA
792997 TTATCCATGAACA
1 TTATCCATGAACA
793010 T
1 T
793011 GTATTCATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (13 bp):
TTATCCATGAACA
Found at i:793559 original size:18 final size:18
Alignment explanation
Indices: 793536--793590 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
793526 AAAAAAATAC
*
793536 AAATATTTTTATATAAAT
1 AAATATATTTATATAAAT
*
793554 AAATATATTTATAAAAAT
1 AAATATATTTATATAAAT
*
793572 AAAAATATTTA-ATAAAT
1 AAATATATTTATATAAAT
793589 AA
1 AA
793591 CTGTGGGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
17 7 0.21
18 26 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATATTTATATAAAT
Found at i:793561 original size:20 final size:20
Alignment explanation
Indices: 793528--793581 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 20
793518 AGCAACAAAA
*
793528 AAAAATACAAATATTTTTAT
1 AAAAATAAAAATATTTTTAT
* *
793548 ATAAAT--AAATATATTTAT
1 AAAAATAAAAATATTTTTAT
793566 AAAAATAAAAATATTT
1 AAAAATAAAAATATTT
793582 AATAAATAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 16 0.57
20 12 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATAAAAATATTTTTAT
Found at i:794314 original size:32 final size:30
Alignment explanation
Indices: 794272--794330 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
794262 ATGTTTATTT
*
794272 ATGTTGTATATTAATGTAAACTTAAATTCTTA
1 ATGTTGTATA-T-ATCTAAACTTAAATTCTTA
* *
794304 ATGTTTTATATATCTTAACTTAAATTC
1 ATGTTGTATATATCTAAACTTAAATTC
794331 ATATATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.58
31 1 0.04
32 9 0.38
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (30 bp):
ATGTTGTATATATCTAAACTTAAATTCTTA
Found at i:796952 original size:60 final size:60
Alignment explanation
Indices: 796819--796952 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
796809 ACTCGGGTGA
* * **
796819 CATTTTTTAACTTTTAATAGTCGAGGAACTCAACAAAGCAACGTCCTATAGTCAATTGAC
1 CATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAGCAACGACCTATAGTCAAAGGAC
* **
796879 CATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCTTC-ACCTTATAGTCAAAGGAC
1 CATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAGCAACGACC-TATAGTCAAAGGAC
*
796939 TATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
796953 ACCATAAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 2 0.03
60 59 0.92
61 3 0.05
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAGCAACGACCTATAGTCAAAGGAC
Found at i:798006 original size:31 final size:31
Alignment explanation
Indices: 797950--798036 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
797940 AGTTTCAAAA
* *
797950 GTAATAAATTGGTCACTAACGTTATTGAATT
1 GTAATAAATCGGTCACTAACATTATTGAATT
* * *
797981 GTAACAAATCGGTCGCTAACATTATTGATTT
1 GTAATAAATCGGTCACTAACATTATTGAATT
* *
798012 GTAATAAATTGATCACTTAACATTA
1 GTAATAAATCGGTCAC-TAACATTA
798037 ACAACCGTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 38 0.83
32 8 0.17
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (31 bp):
GTAATAAATCGGTCACTAACATTATTGAATT
Found at i:805862 original size:4 final size:4
Alignment explanation
Indices: 805853--805895 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
805843 ACTCCCGAGA
* * *
805853 TATG TATG TATG TATG TATG CATG CATG TATT TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
805896 ATGTAATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:811327 original size:35 final size:35
Alignment explanation
Indices: 811288--811361 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
811278 TTCTCTGCTC
*
811288 ATCGTCTTCTCGACAACTATAAATGATCAAACCGT
1 ATCGTCTTCTCGACAACTACAAATGATCAAACCGT
811323 ATCGTCTTCTCGACAACTACAAATGATCAAACCGT
1 ATCGTCTTCTCGACAACTACAAATGATCAAACCGT
811358 ATCG
1 ATCG
811362 GATCGTGGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (35 bp):
ATCGTCTTCTCGACAACTACAAATGATCAAACCGT
Found at i:811801 original size:18 final size:17
Alignment explanation
Indices: 811768--811803 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
811758 TTAAAAATAT
*
811768 ATATATATTTTTAATTA
1 ATATAAATTTTTAATTA
811785 ATATAAATTTATTAATTA
1 ATATAAATTT-TTAATTA
811803 A
1 A
811804 GTTATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATAAATTTTTAATTA
Found at i:819524 original size:178 final size:176
Alignment explanation
Indices: 819179--819533 Score: 459
Period size: 178 Copynumber: 2.0 Consensus size: 176
819169 CTGTTCCACC
819179 TGTTTTATAGGGTTTTCTCCATTCCTTGATTTTTTTTTCTTATTGGGTTATTTGGTATTGTTTTC
1 TGTTTTATAGGGTTTTCTCCATTCCTTGATTTTTTTTTCTTA-TGGGTTATTTGGTATTGTTTTC
* **** * *
819244 ATTTTGATACGTTGCCAAATTATATAGTTTTTTGAACTGAGCTTGATATATGGTAGTTTCTTATC
65 ATTCTGATACGTTGCCAAATTATATAGTTTAAAAAAATGAGCTTGATATAGGGTAGTTTCTTATC
* *
819309 CTTCTGTGATTGTTTCATGTTTGAGCTTGTTATTGGAACATTTCATT
130 CTTCTGTGATTATTTCATGTTTGAGCTTGTAATTGGAACATTTCATT
*
819356 TGTTTTATAGGGTTTTCTTCATTCCTTGATTTTTTTTATC-TA-GGGTTATTTGGTATTGTTTTC
1 TGTTTTATAGGGTTTTCTCCATTCCTTGATTTTTTTT-TCTTATGGGTTATTTGGTATTGTTTTC
* * * * *
819419 ATTCTGATACTTTGTCGAATTATCTAGGTTTAAAAAAAAAATGAGCTTGCTAT-GGAGTAGTTTT
65 ATTCTGATACGTTGCCAAATTATATA-GTTT---AAAAAAATGAGCTTGATATAGG-GTAG-TTT
*
819483 CTTATCC-T-TGTGATTATTTCATGTTTGAGCTTGTAATTGGAACGTTTCATT
124 CTTATCCTTCTGTGATTATTTCATGTTTGAGCTTGTAATTGGAACATTTCATT
819534 GTTATACAAT
Statistics
Matches: 155, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
175 42 0.27
176 4 0.03
177 38 0.25
178 43 0.28
179 18 0.12
180 10 0.06
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.51
Consensus pattern (176 bp):
TGTTTTATAGGGTTTTCTCCATTCCTTGATTTTTTTTTCTTATGGGTTATTTGGTATTGTTTTCA
TTCTGATACGTTGCCAAATTATATAGTTTAAAAAAATGAGCTTGATATAGGGTAGTTTCTTATCC
TTCTGTGATTATTTCATGTTTGAGCTTGTAATTGGAACATTTCATT
Found at i:824227 original size:24 final size:24
Alignment explanation
Indices: 824187--824244 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
824177 TTAGTATTTC
*
824187 TCTTT-AATATATTTTTACATAT-CA
1 TCTTTAAATA-ATATTTA-ATATACA
*
824211 TCTTTAAATAATATTTAATTTACA
1 TCTTTAAATAATATTTAATATACA
824235 T-TTTAAATAA
1 TCTTTAAATAA
824245 GGGTAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 12 0.40
24 14 0.47
25 4 0.13
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.52
Consensus pattern (24 bp):
TCTTTAAATAATATTTAATATACA
Found at i:833072 original size:36 final size:35
Alignment explanation
Indices: 833020--833216 Score: 279
Period size: 36 Copynumber: 5.5 Consensus size: 35
833010 ACGAAAGAAT
833020 GCATCGCACTTCCGATTCAAGTCGAACGGAAGGAA
1 GCATCGCACTTCCGATTCAAGTCGAACGGAAGGAA
833055 GCATCGACACTTCCGATTCAAGTCGAACGG-AGGAAA
1 GCATCG-CACTTCCGATTCAAGTCGAACGGAAGG-AA
* * *
833091 GCGTCGGCACTCCCGATTCAAGTCGAACGGAGGGAA
1 GCATC-GCACTTCCGATTCAAGTCGAACGGAAGGAA
833127 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAA
1 GCATC-GCACTTCCGATTCAAGTCGAACGGAAGGAA
* *
833163 GCATCAGCACTTCCGATTCAAGTTGAACGGAAGGAT
1 GCATC-GCACTTCCGATTCAAGTCGAACGGAAGGAA
* *
833199 GTATCGCACTTTCGATTC
1 GCATCGCACTTCCGATTC
833217 GAGTGTTCAT
Statistics
Matches: 147, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
35 21 0.14
36 123 0.84
37 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.19
Consensus pattern (35 bp):
GCATCGCACTTCCGATTCAAGTCGAACGGAAGGAA
Found at i:836661 original size:31 final size:31
Alignment explanation
Indices: 836624--836695 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
836614 ACTTTTTTAC
*
836624 TTTTAGTACCCGCAGTTAACTTTTTGTTTCA
1 TTTTAGTACCCACAGTTAACTTTTTGTTTCA
** *
836655 TTTTAGTATTCACTGTTAACTTTTTGTTTCA
1 TTTTAGTACCCACAGTTAACTTTTTGTTTCA
836686 TTTTAGTACC
1 TTTTAGTACC
836696 TATATTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (31 bp):
TTTTAGTACCCACAGTTAACTTTTTGTTTCA
Found at i:838286 original size:30 final size:30
Alignment explanation
Indices: 838245--838310 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
838235 GTTAACATCG
* * *
838245 AGTGACGATTTTGTAACAAACGATAACGTT
1 AGTGACCATTTTATAACAAACGATAACATT
*
838275 AGTGACCATTTTATAACAAACGATAATATT
1 AGTGACCATTTTATAACAAACGATAACATT
838305 AGTGAC
1 AGTGAC
838311 GAATTTGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (30 bp):
AGTGACCATTTTATAACAAACGATAACATT
Done.