Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008269.1 Hibiscus syriacus cultivar Beakdansim tig00110926_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: 799769
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:496386 original size:22 final size:22
Alignment explanation
Indices: 496358--496458 Score: 150
Period size: 22 Copynumber: 4.6 Consensus size: 22
496348 ATATCTAAAT
496358 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
496380 TCTTCAAAGATGATAGATT-TAT
1 TCTTCAAAGATGATAGATTCT-C
*
496402 TCTTCAAAGATGATAGATTCTA
1 TCTTCAAAGATGATAGATTCTC
*
496424 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
496446 TTTTCAAAGATGA
1 TCTTCAAAGATGA
496459 AAGTTTTATT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
21 1 0.01
22 70 0.97
23 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:497216 original size:45 final size:45
Alignment explanation
Indices: 497162--497273 Score: 143
Period size: 45 Copynumber: 2.4 Consensus size: 45
497152 GGGGGCTTTT
* * *
497162 TGATATTTTCAAAGCCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGAGTCATATGTAAGCCCTACAGTGCA
* * *
497207 TGATGTTTTCAAAGCCTTTGGGTCATATGTAAGTCCTACAGTGCA
1 TGATGTTTTCAAAGCCTTCGAGTCATATGTAAGCCCTACAGTGCA
*
497252 GGATGTTTTCAAAAAGCCTTCG
1 TGATGTTTTC--AAAGCCTTCG
497274 GGAGCTTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 48 0.84
47 9 0.16
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGAGTCATATGTAAGCCCTACAGTGCA
Found at i:497281 original size:121 final size:122
Alignment explanation
Indices: 497115--497351 Score: 379
Period size: 121 Copynumber: 1.9 Consensus size: 122
497105 CCCACATCCA
*
497115 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGGGCTTTTTGATATTTTCAAAGCCTT
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTT
* * *
497180 C-GAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAGCCTTTGGGTCATATG
66 CAG-GTCATCTGTAAGCCCTACAGTCCAGGATGTTTTCAAAAGCCTTTGGGTCATATG
* *
497236 TAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTTAAAGCCTT
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTT
*
497301 CAGGTCATCTGTAAGTCCTACAGTCCAGGATGTTTTCAAAAAGCCTTTGGG
66 CAGGTCATCTGTAAGCCCTACAGTCCAGGATGTTTTC-AAAAGCCTTTGGG
497352 AGCTTTTTGA
Statistics
Matches: 106, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
121 93 0.88
122 1 0.01
123 12 0.11
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (122 bp):
TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTT
CAGGTCATCTGTAAGCCCTACAGTCCAGGATGTTTTCAAAAGCCTTTGGGTCATATG
Found at i:497343 original size:76 final size:76
Alignment explanation
Indices: 497207--497804 Score: 954
Period size: 76 Copynumber: 7.9 Consensus size: 76
497197 CTTCAGTGCA
* * *
497207 TGATGTTTTCAAAGCCTTTGGGTCATATGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
497272 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
497283 TGATATTTTTAAAGCCTTCAGGTCATCTGTAAGTCCTACAGTCCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
*
497348 TGGGAGCTTTT
66 CGGGAGCTTTT
497359 TGATA--TTCAAAGCCTTCGGGTCATCTGTAA-TACCTACAGTGCAGGATGTTTTCAAAAAGCCT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGT-CCTACAGTGCAGGATGTTTTCAAAAAGCCT
497421 TCGGGAGCTTTT
65 TCGGGAGCTTTT
* *
497433 TGATATTTTCAAAGCCTTCGAGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAACCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
497498 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
497509 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
*
497574 CAGGAGCTTTT
66 CGGGAGCTTTT
*
497585 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATATTTTCAAAAAAGCCT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTC-AAAAAGCCT
497650 TCGGGAGCTTTT
65 TCGGGAGCTTTT
*
497662 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGTAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
497727 CGGGAGCTTTT
66 CGGGAGCTTTT
* * * ** *
497738 TGATAGTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTTAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
497801 CGGG
66 CGGG
497805 TCATCCATAA
Statistics
Matches: 484, Mismatches: 33, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
73 1 0.00
74 76 0.16
75 4 0.01
76 329 0.68
77 74 0.15
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (76 bp):
TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:497591 original size:152 final size:152
Alignment explanation
Indices: 497207--497804 Score: 936
Period size: 150 Copynumber: 4.0 Consensus size: 152
497197 CTTCAGTGCA
* * * *
497207 TGATGTTTTCAAAGCCTTTGGGTCATATGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
* *
497272 CGGGAGCTTTTTGATATTTTTAAAGCCTTC-AGGTCATCTGTAAGTCCTACAGTCCAGGATGTTT
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGA-GTCATCTGTAAGTCCTACAGTGCAGGATGTTT
* *
497336 TCAAAAAGCCTTTGGGAGCTTTT
130 TCAAAAAACCTTCGGGAGCTTTT
*
497359 TGATA--TTCAAAGCCTTCGGGTCATCTGTAATACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
497422 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGAGTCATCTGTAAGTCCTACAGTGCAGGATGTTTT
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGAGTCATCTGTAAGTCCTACAGTGCAGGATGTTTT
497487 CAAAAAACCTTCGGGAGCTTTT
131 CAAAAAACCTTCGGGAGCTTTT
* *
497509 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
* * *
497574 CAGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATATTTT
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGAGTCATCTGTAAGTCCTACAGTGCAGGATGTTTT
497639 CAAAAAAGCCTTCGGGAGCTTTT
131 CAAAAAA-CCTTCGGGAGCTTTT
* *
497662 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGTAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
* * * * ** *
497727 CGGGAGCTTTTTGATAGTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTTAGTGCATGATGTTTT
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGAGTCATCTGTAAGTCCTACAGTGCAGGATGTTTT
497792 C--AAAACCTTCGGG
131 CAAAAAACCTTCGGG
497805 TCATCCATAA
Statistics
Matches: 415, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
150 148 0.36
151 5 0.01
152 128 0.31
153 134 0.32
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (152 bp):
TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTTTGATATTTTCAAAGCCTTCGAGTCATCTGTAAGTCCTACAGTGCAGGATGTTTT
CAAAAAACCTTCGGGAGCTTTT
Found at i:497726 original size:153 final size:153
Alignment explanation
Indices: 497207--497796 Score: 956
Period size: 153 Copynumber: 3.9 Consensus size: 153
497197 CTTCAGTGCA
* * *
497207 TGATGTTTTCAAAGCCTTTGGGTCATATGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
* * *
497272 CGGGAGCTTTTTGATATTTTTAAAGCCTTCAGGTCATCTGTAAGTCCTACAGTCCAGGATGTTTT
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTT
*
497337 C-AAAAAGCCTTTGGGAGCTTTT
131 CAAAAAAGCCTTCGGGAGCTTTT
497359 TGATA--TTCAAAGCCTTCGGGTCATCTGTAA-TACCTACAGTGCAGGATGTTTTCAAAAAGCCT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGT-CCTACAGTGCAGGATGTTTTCAAAAAGCCT
*
497421 TCGGGAGCTTTTTGATATTTTCAAAGCCTTCGAGTCATCTGTAAGTCCTACAGTGCAGGATGTTT
65 TCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTT
497486 TCAAAAAA-CCTTCGGGAGCTTTT
130 TCAAAAAAGCCTTCGGGAGCTTTT
* * *
497509 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
* *
497574 CAGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATATTTT
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTT
497639 CAAAAAAGCCTTCGGGAGCTTTT
131 CAAAAAAGCCTTCGGGAGCTTTT
*
497662 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGTAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
* * * ** *
497727 CGGGAGCTTTTTGATAGTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTTAGTGCATGATGTTTT
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTT
497792 CAAAA
131 CAAAA
497797 CCTTCGGGTC
Statistics
Matches: 406, Mismatches: 26, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
149 1 0.00
150 135 0.33
151 5 0.01
152 127 0.31
153 138 0.34
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (153 bp):
TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCAGGATGTTTT
CAAAAAAGCCTTCGGGAGCTTTT
Found at i:497795 original size:45 final size:45
Alignment explanation
Indices: 497744--497840 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
497734 TTTTTGATAG
* * * ** *
497744 TTTCAAAGCCTTCGGGTCATCTATAAGCCCTTTAGTGCATGATGT
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAAGATGT
497789 TTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAAGATGT
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAAGATGT
497834 TTTCAAA
1 TTTCAAA
497841 TGAGATTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAAGATGT
Found at i:498110 original size:3 final size:3
Alignment explanation
Indices: 498102--498158 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
498092 TATTTTTAAA
** *
498102 ATT ATT ATT ATT ATT ACA ATT ATT ATT ATT ATT AAT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
498149 ATT ATT ATT A
1 ATT ATT ATT A
498159 AATTAACAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:498451 original size:18 final size:19
Alignment explanation
Indices: 498412--498452 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
498402 GTCACCATTT
*
498412 TTTGGTGAGTCACCACAAG
1 TTTGGTGACTCACCACAAG
498431 TTTGGTGACTCACCA-AAG
1 TTTGGTGACTCACCACAAG
498449 TTTG
1 TTTG
498453 CTCCTTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (19 bp):
TTTGGTGACTCACCACAAG
Found at i:502815 original size:3 final size:3
Alignment explanation
Indices: 502795--502842 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
502785 GCCCGATTCC
* *
502795 ATT AAT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
502843 TCTGATGCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:504803 original size:84 final size:83
Alignment explanation
Indices: 504682--504848 Score: 230
Period size: 83 Copynumber: 2.0 Consensus size: 83
504672 AAAATAATCG
* *
504682 GATTAATAATTTAAGCATATTTAAATTTGAATTTATATATGATAAAAACATATATTATGTATATA
1 GATTAATAATTTAAACATATTTAAATTTAAATTTATATATGA-AAAAACATATATTATGTATATA
*
504747 TGATAT-ATAATCGGATTAA
65 TAAT-TGATAATCGGATTAA
* * * *
504766 GATTAATAATTTAAACATATTTAAA-TTAAATTTTATATATGAAAAAATATATATTGTTTGTATA
1 GATTAATAATTTAAACATATTTAAATTTAAA-TTTATATATGAAAAAACATATATTATGTATATA
504830 TAATTGATAATCGGATTAA
65 TAATTGATAATCGGATTAA
504849 TAATTTAGGC
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
82 1 0.01
83 38 0.51
84 35 0.47
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (83 bp):
GATTAATAATTTAAACATATTTAAATTTAAATTTATATATGAAAAAACATATATTATGTATATAT
AATTGATAATCGGATTAA
Found at i:505191 original size:20 final size:23
Alignment explanation
Indices: 505134--505241 Score: 86
Period size: 20 Copynumber: 4.7 Consensus size: 23
505124 ATTTAATGAT
505134 TATATAGTAAGAAATTATATATATATA
1 TATATA-TAA-AAATTAT-TATAT-TA
505161 TATATATAAAAATTATTA-ATTA
1 TATATATAAAAATTATTATATTA
505183 TAT-TA-AAAAATTAAAATTATACTT-
1 TATATATAAAAATT---ATTATA-TTA
*
505207 TATATATATAAATTATTA-ATTA
1 TATATATAAAAATTATTATATTA
505229 TAT-TA-AAAAATTA
1 TATATATAAAAATTA
505242 AAATTCTACT
Statistics
Matches: 71, Mismatches: 2, Indels: 23
0.74 0.02 0.24
Matches are distributed among these distances:
20 14 0.20
21 6 0.08
22 9 0.13
23 10 0.14
24 6 0.08
25 11 0.15
26 9 0.13
27 6 0.08
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (23 bp):
TATATATAAAAATTATTATATTA
Found at i:505198 original size:26 final size:26
Alignment explanation
Indices: 505169--505246 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
505159 TATATATATA
505169 AAAATTATTAATTATATTAAAAAATT
1 AAAATTATTAATTATATTAAAAAATT
* * *
505195 AAAATTA-TACTT-TA-T-ATATA-T
1 AAAATTATTAATTATATTAAAAAATT
505216 -AAATTATTAATTATATTAAAAAATT
1 AAAATTATTAATTATATTAAAAAATT
505241 AAAATT
1 AAAATT
505247 CTACTTTGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
20 6 0.15
21 5 0.12
22 5 0.12
23 2 0.05
24 5 0.12
25 5 0.12
26 12 0.30
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAATTATTAATTATATTAAAAAATT
Found at i:505222 original size:46 final size:46
Alignment explanation
Indices: 505161--505261 Score: 168
Period size: 46 Copynumber: 2.2 Consensus size: 46
505151 TATATATATA
*
505161 TATATATAAAAATTATTAATTATATTAAAAAATTAAAATTATACTT
1 TATATATATAAATTATTAATTATATTAAAAAATTAAAATTATACTT
*
505207 TATATATATAAATTATTAATTATATTAAAAAATTAAAATTCTACTT
1 TATATATATAAATTATTAATTATATTAAAAAATTAAAATTATACTT
505253 TGAT-TATAT
1 T-ATATATAT
505262 GAAAGTTACA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
46 50 0.96
47 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (46 bp):
TATATATATAAATTATTAATTATATTAAAAAATTAAAATTATACTT
Found at i:505436 original size:2 final size:2
Alignment explanation
Indices: 505429--505522 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
505419 TTATTGATTT
505429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
505471 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
505513 TA TA TA TA TA
1 TA TA TA TA TA
505523 ATCAAATATA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:507554 original size:65 final size:65
Alignment explanation
Indices: 507482--507637 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 65
507472 TACACTTGGG
* * *
507482 GTGCATCGGTACACT-AATTACATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCAAGGT
1 GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCAAGAT
507545 CT
65 -T
** * * *
507547 GTGCATCGGTACA-TAAAATGTATTCGATGTTTCAATAAAATCAGGAGTGTATCGATGCATGATT
1 GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCAAGATT
* *
507611 GTACATCGGTACAC-AAAATGCATTCGA
1 GTGCATCGGTACACTAAAATACATTCGA
507638 ATTAGGGTGT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
64 26 0.33
65 50 0.64
66 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCAAGATT
Found at i:510423 original size:20 final size:21
Alignment explanation
Indices: 510385--510423 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
510375 AAGCTTTAAG
* *
510385 ATCATCGATTTTCTTTTGATA
1 ATCATCGATTTACTCTTGATA
510406 ATCATC-ATTTACTCTTGA
1 ATCATCGATTTACTCTTGA
510424 AAGTAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.49
Consensus pattern (21 bp):
ATCATCGATTTACTCTTGATA
Found at i:512553 original size:65 final size:64
Alignment explanation
Indices: 512476--512631 Score: 163
Period size: 65 Copynumber: 2.4 Consensus size: 64
512466 TACACCTAGG
* * * *
512476 GTGCATCGGTATACT-AATTACATTCGATGTTTCAA-AAGAGCCAAGATTGCATCGATGCATGGT
1 GTGCATCAGTATA-TAAAATACATTCGATGTTTCAATAA-AACCAAGAGTGCATCGATGCATGGT
512539 CT
64 -T
* * * *
512541 GTGCATCAGTATATAAAATGCATTCGATGTTTCAATAAAATCAGGAGTGTATCGATGCATGGTT
1 GTGCATCAGTATATAAAATACATTCGATGTTTCAATAAAACCAAGAGTGCATCGATGCATGGTT
* * * *
512605 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCAGTATATAAAATACATTCGA
512632 ATTAGGGTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 26 0.33
65 50 0.64
66 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (64 bp):
GTGCATCAGTATATAAAATACATTCGATGTTTCAATAAAACCAAGAGTGCATCGATGCATGGTT
Found at i:514291 original size:7 final size:7
Alignment explanation
Indices: 514279--514306 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
514269 AGATATAAGC
514279 CATGTGA
1 CATGTGA
514286 CATGTGA
1 CATGTGA
514293 CATGTGA
1 CATGTGA
514300 CATGTGA
1 CATGTGA
514307 TATGAGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
CATGTGA
Found at i:514548 original size:18 final size:18
Alignment explanation
Indices: 514525--514580 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
514515 TATGTTCTAT
514525 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
514543 GTGGTCCTTCGGGATATA
1 GTGGTCCTTCGGGACATA
514561 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
514579 GT
1 GT
514581 TTTCATACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.16, C:0.20, G:0.34, T:0.30
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:517826 original size:18 final size:18
Alignment explanation
Indices: 517803--517846 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
517793 TGTGTTCTAT
*
517803 GTGGTCTTTCGGGACATA
1 GTGGTCCTTCGGGACATA
517821 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
517839 GTGGTCCT
1 GTGGTCCT
517847 ACGAGATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.20, G:0.34, T:0.32
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:520973 original size:16 final size:17
Alignment explanation
Indices: 520949--520981 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
520939 TCTATTTGGC
*
520949 TGATGATTTT-TTGACA
1 TGATCATTTTGTTGACA
520965 TGATCATTTTGTTGACA
1 TGATCATTTTGTTGACA
520982 GCACACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (17 bp):
TGATCATTTTGTTGACA
Found at i:523820 original size:21 final size:21
Alignment explanation
Indices: 523796--523837 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
523786 AGTATCCATA
523796 GAAGGCAATTAGATCCCCCTT
1 GAAGGCAATTAGATCCCCCTT
523817 GAAGGCAATTAGATCCCCCTT
1 GAAGGCAATTAGATCCCCCTT
523838 TCTTTTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
GAAGGCAATTAGATCCCCCTT
Found at i:527489 original size:135 final size:135
Alignment explanation
Indices: 527247--527505 Score: 385
Period size: 135 Copynumber: 1.9 Consensus size: 135
527237 GAGAAGTGAA
*
527247 GCTCTGGTTGCTGCTTGGGATATGACAAAGTTCTATACAAAAGCTTTGATTCTGAAAAACGAGCA
1 GCTCTGGTTGCTGCTGGGGATATGACAAAGTTCTATACAAAAGCTTTGATTCTGAAAAACGAGCA
* *
527312 GGAGATGGTTGTGGCTGAGAAGACCATCTCTTGCCTTCTTGAGCGTCATCTGTATCAAAGATGAA
66 GGAGATGATTGTGGCTGAGAAGACCATCTCTTGCCTTCTTGAGCATCATCTGTATCAAAGATGAA
527377 GAGAG
131 GAGAG
** * * *
527382 GCTCTGGTTGCTGCTGGGGATATGATGAAGTTCTATACAAAGGTTTTGATTCTGAAAAATGAGCA
1 GCTCTGGTTGCTGCTGGGGATATGACAAAGTTCTATACAAAAGCTTTGATTCTGAAAAACGAGCA
* * * * *
527447 -GATGATGATTGTGGTTGTGAGGACCATCTCTTGCTTTCTTGAGCATCTTCTGTATCAAA
66 GGA-GATGATTGTGGCTGAGAAGACCATCTCTTGCCTTCTTGAGCATCATCTGTATCAAA
527506 CATATGCTGA
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
134 2 0.02
135 108 0.98
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (135 bp):
GCTCTGGTTGCTGCTGGGGATATGACAAAGTTCTATACAAAAGCTTTGATTCTGAAAAACGAGCA
GGAGATGATTGTGGCTGAGAAGACCATCTCTTGCCTTCTTGAGCATCATCTGTATCAAAGATGAA
GAGAG
Found at i:530281 original size:13 final size:14
Alignment explanation
Indices: 530256--530287 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
530246 TAAATTACAG
530256 TTATAATTAAATTA
1 TTATAATTAAATTA
530270 TTATAA-TAAATTA
1 TTATAATTAAATTA
530283 -TATAA
1 TTATAA
530288 AATGAGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.28
13 7 0.39
14 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATAATTAAATTA
Found at i:537985 original size:16 final size:16
Alignment explanation
Indices: 537964--537994 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
537954 AATCCCTGAT
537964 ATCCCTAAAGATAACC
1 ATCCCTAAAGATAACC
*
537980 ATCCCTGAAGATAAC
1 ATCCCTAAAGATAAC
537995 TTACAGAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (16 bp):
ATCCCTAAAGATAACC
Found at i:543680 original size:25 final size:25
Alignment explanation
Indices: 543646--543697 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
543636 TCCACAGAAG
543646 ATAGTTGAGTCAATTTATTAAACTC
1 ATAGTTGAGTCAATTTATTAAACTC
543671 ATAGTTGAGTCAATTTATTAAACTC
1 ATAGTTGAGTCAATTTATTAAACTC
543696 AT
1 AT
543698 CAATAACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (25 bp):
ATAGTTGAGTCAATTTATTAAACTC
Found at i:546399 original size:2 final size:2
Alignment explanation
Indices: 546392--546440 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
546382 CACTTCAAAA
546392 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
546434 AT AT AT A
1 AT AT AT A
546441 GTCAAGCATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:548557 original size:16 final size:16
Alignment explanation
Indices: 548536--548569 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
548526 CTACAAACTC
548536 TAGAGTTATATAAATA
1 TAGAGTTATATAAATA
548552 TAGAGTTATATAAATA
1 TAGAGTTATATAAATA
548568 TA
1 TA
548570 CCTCTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
TAGAGTTATATAAATA
Found at i:550788 original size:2 final size:2
Alignment explanation
Indices: 550781--550811 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
550771 TCAAATTAAA
550781 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
550812 ATTTTTTATA
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:551368 original size:2 final size:2
Alignment explanation
Indices: 551361--551401 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
551351 TCAATTTTAA
551361 AT AT AT AT AT 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 AT AT AT AT AT A
551402 AAATACGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:554793 original size:2 final size:2
Alignment explanation
Indices: 554786--554812 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
554776 GTCTATCGTC
554786 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 A
554813 AATTCTCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:564089 original size:18 final size:20
Alignment explanation
Indices: 564066--564105 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
564056 TTCTCAGTAA
564066 TTTTATT-TC-CTAATAATC
1 TTTTATTCTCACTAATAATC
*
564084 TTTTATTCTCACTGATAATC
1 TTTTATTCTCACTAATAATC
564104 TT
1 TT
564106 ACATTCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 10 0.53
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTATTCTCACTAATAATC
Found at i:566258 original size:21 final size:21
Alignment explanation
Indices: 566234--566277 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
566224 GAGCCGGAGG
*
566234 AGGAGGAGCACGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
* * *
566255 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAAGAACT
566276 AG
1 AG
566278 CTCCCTGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:567837 original size:23 final size:22
Alignment explanation
Indices: 567807--567888 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
567797 GCATGACCCT
*
567807 GTGCATCGATACACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
567829 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
567851 GTGTATCGATGCACATTCAAGGG
1 GTGCATCGATGCACATTCAA-GG
567874 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
567889 TGTTAAGTGC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.32
22 3 0.06
23 17 0.36
24 12 0.26
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:567903 original size:44 final size:44
Alignment explanation
Indices: 567807--567905 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
567797 GCATGACCCT
* * *
567807 GTGCATCGATACACATTCAAGGCGTGCATCGGTGCACCTTCATG
1 GTGCATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATA
* * *
567851 GTGTATCGATGCACATTCAAGGGGATGCATCGATGCA-CTGTTA-A
1 GTGCATCGATGCACATTCAAGGCG-TGCATCGATGCACCT-TCATA
567895 GTGCATCGATG
1 GTGCATCGATG
567906 ACTAAGCACA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
44 33 0.72
45 13 0.28
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (44 bp):
GTGCATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATA
Found at i:573411 original size:45 final size:45
Alignment explanation
Indices: 573362--573449 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
573352 AAAATAGCCA
*
573362 GAGTGCATCGATGCATGGCT-TGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGG-TATGTGCATCGATGCATAAAATGCACT
573407 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
1 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
573450 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 1 0.02
45 40 0.98
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCACT
Found at i:579366 original size:26 final size:27
Alignment explanation
Indices: 579328--579397 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
579318 ATAATAACAT
* **
579328 AAAATAATTATAATTTAAAAA-GGAAA
1 AAAATAATAATAATAAAAAAAGGGAAA
579354 AAAATAATAATAAATAAAAAAAGGGAAA
1 AAAATAATAAT-AATAAAAAAAGGGAAA
*
579382 ATAATAA-AATAATAAA
1 AAAATAATAATAATAAA
579398 TAATAATAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 16 0.42
27 11 0.29
28 11 0.29
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (27 bp):
AAAATAATAATAATAAAAAAAGGGAAA
Found at i:579486 original size:18 final size:18
Alignment explanation
Indices: 579443--579486 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
579433 GTTGTTTTTA
*
579443 AAATAAAAGATAAAAATT
1 AAATAAATGATAAAAATT
579461 AAATAAATGA-AAATAATT
1 AAATAAATGATAAA-AATT
579479 AAATAAAT
1 AAATAAAT
579487 AATCTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
AAATAAATGATAAAAATT
Found at i:580146 original size:71 final size:74
Alignment explanation
Indices: 580064--580252 Score: 260
Period size: 75 Copynumber: 2.6 Consensus size: 74
580054 TAAAACATGT
* * *
580064 TAAATCATAATTAAAACACTTAAAACTATTTAAACTAAAATACCT-AAAAA-ATAATAT-TTAAA
1 TAAATCATAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAAAAGATAAAATATAAAA
*
580126 ATAATATTC
66 ATAATATCC
*
580135 TAAATCCTAATTAAAATAC-TAAAACATATTTAAACTAAAATACCTAAAAAAAGATAAAATATAA
1 TAAATCATAATTAAAATACTTAAAAC-TATTTAAACTAAAATACCT-AAAAAAGATAAAATATAA
580199 AAATAATATCC
64 AAATAATATCC
* * *
580210 TAAAACTTAATTAAAATACTAAAAACTATTTAAACTAAAATAC
1 TAAATCATAATTAAAATACTTAAAACTATTTAAACTAAAATAC
580253 AAAGATAAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
70 6 0.06
71 36 0.35
73 5 0.05
74 6 0.06
75 46 0.44
76 5 0.05
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.30
Consensus pattern (74 bp):
TAAATCATAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAAAAGATAAAATATAAAA
ATAATATCC
Found at i:580277 original size:75 final size:72
Alignment explanation
Indices: 580071--580288 Score: 237
Period size: 75 Copynumber: 3.0 Consensus size: 72
580061 TGTTAAATCA
* * *
580071 TAATTAAAACACTTAAAACTATTTAAACTAAAATAC---CTAAAAAATAATATTTAAAATAATAT
1 TAATTAAAATAC-TAAAACTATTTAAACTAAAATACAAAATAAAATATAAT-TTTAAAATAATAT
* *
580133 TCTAAATCC
64 CCTAAAACC
* * *
580142 TAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAA-AAAGATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAAC-TATTTAAACTAAAATA-C-AAAATAAA-ATATAATTTTAAAATAAT
*
580206 ATCCTAAAACT
62 ATCCTAAAACC
*
580217 TAATTAAAATACTAAAAACTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATATTA
1 TAATTAAAATACT-AAAACTATTTAAACTAAAATACAAA-ATAAAATATAAT-TTTAAAATAATA
580282 TCCTAAA
63 TCCTAAA
580289 CTTGAGCTTA
Statistics
Matches: 123, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
70 6 0.05
71 27 0.22
72 1 0.01
73 3 0.02
74 8 0.07
75 68 0.55
76 10 0.08
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (72 bp):
TAATTAAAATACTAAAACTATTTAAACTAAAATACAAAATAAAATATAATTTTAAAATAATATCC
TAAAACC
Found at i:583051 original size:24 final size:26
Alignment explanation
Indices: 583003--583051 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
582993 TAGATTATCT
*
583003 AATATAGAGTTTAAATAATTTAAATA
1 AATATAGAGTTTAAATAATTAAAATA
*
583029 AATATA-AG-TTAATTAATTAAAAT
1 AATATAGAGTTTAAATAATTAAAAT
583052 TTCCTTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 2 0.10
26 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (26 bp):
AATATAGAGTTTAAATAATTAAAATA
Found at i:586950 original size:42 final size:42
Alignment explanation
Indices: 586891--586975 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
586881 AAGAATAGTT
*
586891 GCAATCAAGCGCCTGAACCCTGAATCAAGACAAGGTGTTCGA
1 GCAATCAAGCGCCTGAACCCTGAATCAACACAAGGTGTTCGA
586933 GCAATCAAGCGCCTGAACCCTGAATCAACACAAGGTGTTCGA
1 GCAATCAAGCGCCTGAACCCTGAATCAACACAAGGTGTTCGA
586975 G
1 G
586976 AGTTCATGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (42 bp):
GCAATCAAGCGCCTGAACCCTGAATCAACACAAGGTGTTCGA
Found at i:589494 original size:14 final size:14
Alignment explanation
Indices: 589472--589538 Score: 51
Period size: 14 Copynumber: 5.4 Consensus size: 14
589462 CCTCGCATAG
*
589472 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
589486 CTCGGTCGGATGG-
1 CTCGGTCGGATGGC
589499 CT---TCGGAT-G-
1 CTCGGTCGGATGGC
589508 CTC--TCGGATGGC
1 CTCGGTCGGATGGC
* *
589520 CTCAGTTGGATGGC
1 CTCGGTCGGATGGC
589534 CTCGG
1 CTCGG
589539 ATGCCCAGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
9 3 0.07
10 12 0.27
11 1 0.02
12 3 0.07
13 2 0.04
14 24 0.53
ACGTcount: A:0.09, C:0.27, G:0.37, T:0.27
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:589516 original size:34 final size:34
Alignment explanation
Indices: 589477--589542 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
589467 CATAGCTCGT
* *
589477 TCGGATGGCCTCGGTCGGATGGCTTCGGATGCTC
1 TCGGATGGCCTCAGTCGGATGGCCTCGGATGCTC
*
589511 TCGGATGGCCTCAGTTGGATGGCCTCGGATGC
1 TCGGATGGCCTCAGTCGGATGGCCTCGGATGC
589543 CCAGCGTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.11, C:0.26, G:0.38, T:0.26
Consensus pattern (34 bp):
TCGGATGGCCTCAGTCGGATGGCCTCGGATGCTC
Found at i:589618 original size:29 final size:29
Alignment explanation
Indices: 589581--589638 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
589571 GCAATCTCTT
*
589581 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
589610 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
589639 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:590108 original size:24 final size:24
Alignment explanation
Indices: 590072--590182 Score: 73
Period size: 24 Copynumber: 4.7 Consensus size: 24
590062 CATTTAAATA
* *
590072 ATAAATGAACACAAATGAACAAAC
1 ATAAACGAACACAAACGAACAAAC
* * *
590096 ATAAACGACCACAAACGAACGAAT
1 ATAAACGAACACAAACGAACAAAC
* * **
590120 GTAAACGAACACAATA-AAATGAAC
1 ATAAACGAACACAA-ACGAACAAAC
** *
590144 ATAAACGAACGTAAATGAACAAA-
1 ATAAACGAACACAAACGAACAAAC
* *
590167 ACAAACGAACATAAAC
1 ATAAACGAACACAAAC
590183 CACAACAACA
Statistics
Matches: 66, Mismatches: 19, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
23 14 0.21
24 51 0.77
25 1 0.02
ACGTcount: A:0.59, C:0.19, G:0.11, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAAACGAACAAAC
Found at i:590158 original size:34 final size:33
Alignment explanation
Indices: 590113--590182 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
590103 ACCACAAACG
* *
590113 AACGAATGTAAACGAACACAATA-AAATGAACATA
1 AACGAACGTAAACGAACA-AA-ACAAACGAACATA
*
590147 AACGAACGTAAATGAACAAAACAAACGAACATA
1 AACGAACGTAAACGAACAAAACAAACGAACATA
590180 AAC
1 AAC
590183 CACAACAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 1 0.03
33 15 0.47
34 16 0.50
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.11
Consensus pattern (33 bp):
AACGAACGTAAACGAACAAAACAAACGAACATA
Found at i:590159 original size:20 final size:19
Alignment explanation
Indices: 590136--590173 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
590126 GAACACAATA
*
590136 AAATGAACATAAACGAACGT
1 AAATGAACA-AAACAAACGT
590156 AAATGAACAAAACAAACG
1 AAATGAACAAAACAAACG
590174 AACATAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.61, C:0.16, G:0.13, T:0.11
Consensus pattern (19 bp):
AAATGAACAAAACAAACGT
Found at i:592591 original size:17 final size:17
Alignment explanation
Indices: 592569--592601 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
592559 CAAATACGAA
592569 AATTTT-AATTTATTTTG
1 AATTTTCAA-TTATTTTG
592586 AATTTTCAATTATTTT
1 AATTTTCAATTATTTT
592602 ATTCATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (17 bp):
AATTTTCAATTATTTTG
Found at i:593831 original size:15 final size:15
Alignment explanation
Indices: 593811--593843 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
593801 TTAGCCGGGT
*
593811 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
593826 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
593841 GGG
1 GGG
593844 TAATGTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:595365 original size:34 final size:34
Alignment explanation
Indices: 595321--595389 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
595311 AAATTAATTG
* * *
595321 TAGCATCAAAACAACTAATCTCCCTGATATAAGC
1 TAGCAGCAAAACAACCAATCTCCCAGATATAAGC
595355 TAGCAGCAAAACAACCAATCTCCCAGATATAAGC
1 TAGCAGCAAAACAACCAATCTCCCAGATATAAGC
595389 T
1 T
595390 TCATTAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (34 bp):
TAGCAGCAAAACAACCAATCTCCCAGATATAAGC
Found at i:604313 original size:12 final size:12
Alignment explanation
Indices: 604296--604320 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
604286 GTATCGATGC
604296 ACTGCTATAGTA
1 ACTGCTATAGTA
604308 ACTGCTATAGTA
1 ACTGCTATAGTA
604320 A
1 A
604321 TTTATGAAAA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ACTGCTATAGTA
Found at i:604836 original size:44 final size:45
Alignment explanation
Indices: 604720--604861 Score: 232
Period size: 45 Copynumber: 3.2 Consensus size: 45
604710 ATAAATAAAT
* * *
604720 TTACCATTTATCCCATAAGCTTGTAAGCTTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
604765 TTACCATTTATTCCATAAGCTCTTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
604810 TTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
604854 TTGCCATT
1 TTACCATT
604862 AACCTCATTT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 42 0.47
45 48 0.53
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:605059 original size:59 final size:59
Alignment explanation
Indices: 604996--605107 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
604986 CTTCCCCTTT
* *
604996 CATTTTACCACACGAAGTTCCCTAT-TCAAAAATCCATACCATTAGTATAATTTTGTTAC
1 CATTTTACCACACGAAATGCCCTATGT-AAAAATCCATACCATTAGTATAATTTTGTTAC
* * * *
605055 CATTTTAGCACATGAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTT
1 CATTTTACCACACGAAATGCCCTATGTAAAAATCCATACCATTAGTATAATTT
605108 CCTTATCTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (59 bp):
CATTTTACCACACGAAATGCCCTATGTAAAAATCCATACCATTAGTATAATTTTGTTAC
Found at i:605148 original size:118 final size:114
Alignment explanation
Indices: 605025--605360 Score: 336
Period size: 118 Copynumber: 2.9 Consensus size: 114
605015 CCCTATTCAA
* * **
605025 AAATCCATAC-CATTAGTATAATTTTGTTACCATTTTAGCACATGAAATGCCCTATGTGAAAATC
1 AAATCCATACAC-TCAGTATGATTTCCTTACCATTTTAGCACAT-AAATGCCCTATGTG-AAATC
* * ** *
605089 CATACCATTAGTATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGG
63 CATA-CATTAGTATGATTTCCTTATCTTT-TAGCACACTCAGTGCTCCATATGG
* * * *
605143 AAATCCATACACTCAGTATGATTCCCTTACCTTTTTAGAACATAAAATGCCCTATTTGGAAATCC
1 AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACAT-AAATGCCCTATGT-GAAATCC
** * *
605208 ATATTTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGG
64 ATACATT-AGTATGATTTCCTTATCTTTTAGCACACTCAGTGCTCCATATGG
* * *
605260 AAATCTATACACTCAGTATGATTTCCTTATCA-TTTAGCACACTCAATGCTCCATATG-GAAATC
1 AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACA-TAAATGC-CC-TATGTGAAATC
* *
605323 TATACACTCAGTATGATTTCCTTATCATTTTAGCACAC
63 CATACA-TTAGTATGATTTCCTTATC-TTTTAGCACAC
605361 AAAGTGTCAT
Statistics
Matches: 179, Mismatches: 31, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
116 38 0.21
117 63 0.35
118 76 0.42
119 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (114 bp):
AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACATAAATGCCCTATGTGAAATCCAT
ACATTAGTATGATTTCCTTATCTTTTAGCACACTCAGTGCTCCATATGG
Found at i:605280 original size:58 final size:58
Alignment explanation
Indices: 605084--605360 Score: 290
Period size: 58 Copynumber: 4.7 Consensus size: 58
605074 CCCTATGTGA
* * * * * ** *
605084 AAATCCATAC-CATTAGTATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGG
1 AAATCCATACAC-TCAGTATGATTTCCTTATCATT-TAGCACACTCAATGCTCCATATGG
* * * * * *
605143 AAATCCATACACTCAGTATGATTCCCTTACCTTTTTAGAACA-TAAAATGC-CCTATTTGG
1 AAATCCATACACTCAGTATGATTTCCTTATC-ATTTAGCACACT-CAATGCTCC-ATATGG
*** * *
605202 AAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGG
1 AAATCCATACACTCAGTATGATTTCCTTATCATTTAGCACACTCAATGCTCCATATGG
*
605260 AAATCTATACACTCAGTATGATTTCCTTATCATTTAGCACACTCAATGCTCCATATGG
1 AAATCCATACACTCAGTATGATTTCCTTATCATTTAGCACACTCAATGCTCCATATGG
*
605318 AAATCTATACACTCAGTATGATTTCCTTATCATTTTAGCACAC
1 AAATCCATACACTCAGTATGATTTCCTTATCA-TTTAGCACAC
605361 AAAGTGTCAT
Statistics
Matches: 184, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
58 102 0.55
59 78 0.42
60 4 0.02
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (58 bp):
AAATCCATACACTCAGTATGATTTCCTTATCATTTAGCACACTCAATGCTCCATATGG
Found at i:605355 original size:117 final size:118
Alignment explanation
Indices: 605058--605360 Score: 330
Period size: 117 Copynumber: 2.6 Consensus size: 118
605048 TTGTTACCAT
* * * * *
605058 TTTAGCACATGAAATGCCCTATGTGAAAATCCATAC-CATTAGTATGATTTCCTTATC-TTTGTA
1 TTTAGAACATAAAATGCCCTATATGGAAATCCATACAC-TCAGTATGATTTCCTTATCATTT-TA
* * ** * *
605121 GCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCCTTACCTT
64 GCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCTTACCTA
* *** *
605176 TTTAGAACATAAAATGCCCTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGC
1 TTTAGAACATAAAATGCCCTATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGC
* * *
605240 ACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCCTTATC-A
66 ACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCTTACCTA
* * *
605292 TTTAGCACACT-CAATGCTCC-ATATGGAAATCTATACACTCAGTATGATTTCCTTATCATTTTA
1 TTTAGAACA-TAAAATGC-CCTATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTA
605355 GCACAC
64 GCACAC
605361 AAAGTGTCAT
Statistics
Matches: 155, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
116 45 0.29
117 60 0.39
118 50 0.32
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (118 bp):
TTTAGAACATAAAATGCCCTATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGC
ACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCTTACCTA
Found at i:613897 original size:21 final size:21
Alignment explanation
Indices: 613871--613954 Score: 57
Period size: 21 Copynumber: 3.9 Consensus size: 21
613861 TTTTGGTGCA
613871 GAGGGAATCGATCCCCCCCAT
1 GAGGGAATCGATCCCCCCCAT
* **
613892 GAGGGAA-CTGATTCCCCCTTT
1 GAGGGAATC-GATCCCCCCCAT
*
613913 GAATGGGAACCGATTCCCCCCACA-
1 G-A-GGGAATCGA-TCCCCCC-CAT
*
613937 G-GGGAATCGATACCCCCC
1 GAGGGAATCGATCCCCCCC
613955 TAGGGTTCTG
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
19 1 0.02
20 7 0.14
21 25 0.51
22 1 0.02
23 7 0.14
24 8 0.16
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.17
Consensus pattern (21 bp):
GAGGGAATCGATCCCCCCCAT
Found at i:621012 original size:44 final size:45
Alignment explanation
Indices: 620901--621038 Score: 233
Period size: 45 Copynumber: 3.1 Consensus size: 45
620891 ATAAAGTTAT
* *
620901 CATTTATCCCATAAGCTCGTAAGCTTATTTTACCAACATACTTAC
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
*
620946 CATTTATTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTAC
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
*
620991 CA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGC
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
621035 CATT
1 CATT
621039 AACCTCATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
44 42 0.48
45 45 0.52
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
Found at i:621039 original size:44 final size:44
Alignment explanation
Indices: 620904--621039 Score: 227
Period size: 44 Copynumber: 3.1 Consensus size: 44
620894 AAGTTATCAT
* *
620904 TTATCCCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA
*
620948 TTTATTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTACCA
1 -TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA
*
620993 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA
621037 TTA
1 TTA
621040 ACCTCATTTA
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
44 45 0.52
45 41 0.48
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (44 bp):
TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA
Found at i:621336 original size:116 final size:117
Alignment explanation
Indices: 621202--621472 Score: 298
Period size: 116 Copynumber: 2.3 Consensus size: 117
621192 CCCTATTCAA
* ** * *
621202 AAATCCATAC-CATTAGTATGATTTTGTTACCATTTTAGCACATGAAATGCCTTATGTGAAAATC
1 AAATCCATACAC-TCAGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATGTGAAAATC
* * * ** *
621266 CATACCATT-AGTATGATTTCC-TATCTTTGTAGCAC-CTTAGTGCTTTATCTGG
65 CATA-CATTCAATATGATTTCCTTATCATT-TAGCACACTCAGTGCTCCATATGG
* * * *
621318 AAATCCATACACTCAGTATGATTCCCTTACCTTTTTAGCACATAAAATGCCCTATTTGGAAATCC
1 AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATGTGAAAATCC
**
621383 ATATTTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGG
66 ATACATTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGG
* * * *
621435 AAATCTATACACTCAGTACGATTTCCTTATCGTTTTAG
1 AAATCCATACACTCAGTATGATTTCCTTACCATTTTAG
621473 TACACAAAGT
Statistics
Matches: 129, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
115 2 0.02
116 74 0.57
117 53 0.41
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (117 bp):
AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATGTGAAAATCC
ATACATTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGG
Found at i:621384 original size:59 final size:57
Alignment explanation
Indices: 621175--621472 Score: 197
Period size: 59 Copynumber: 5.1 Consensus size: 57
621165 TCCCCTTTCA
* *** * ** * *
621175 TTTTAGCATATGAAGTGCCCTATTCAAAAATCCATACCATTAGTATGATTTTGTTACCA
1 TTTTAGCACAT-AAGTGCCCTATTTGGAAATCCATACC-TCAGTATGATTTCCTTATCT
* * * * *
621234 TTTTAGCACATGAAATGCCTTATGTGAAAATCCATACCATTAGTATGATTTCC-TATCT
1 TTTTAGCACAT-AAGTGCCCTATTTGGAAATCCATACC-TCAGTATGATTTCCTTATCT
* * * ** * * *
621292 TTGTAGCACCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCCTTACCT
1 TTTTAGCACATAAGTGCCCTATTTGGAAATCCATAC-CTCAGTATGATTTCCTTATCT
* ** *
621350 TTTTAGCACATAAAATGCCCTATTTGGAAATCCATATTTTCAATATGATTTCCTTATC-
1 TTTTAGCACAT-AAGTGCCCTATTTGGAAATCCATA-CCTCAGTATGATTTCCTTATCT
* * * * * *
621408 ATTTAGCACACTCAGTGCTCC-ATATGGAAATCTATACACTCAGTACGATTTCCTTATCG
1 TTTTAGCACA-TAAGTGC-CCTATTTGGAAATCCATAC-CTCAGTATGATTTCCTTATCT
621467 TTTTAG
1 TTTTAG
621473 TACACAAAGT
Statistics
Matches: 189, Mismatches: 42, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
57 32 0.17
58 69 0.37
59 88 0.47
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (57 bp):
TTTTAGCACATAAGTGCCCTATTTGGAAATCCATACCTCAGTATGATTTCCTTATCT
Found at i:626040 original size:15 final size:16
Alignment explanation
Indices: 626020--626050 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
626010 TAACCAGTAC
626020 TAATACAATA-ACATA
1 TAATACAATACACATA
626035 TAATACAATACACATA
1 TAATACAATACACATA
626051 CTTTCATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (16 bp):
TAATACAATACACATA
Found at i:631840 original size:24 final size:26
Alignment explanation
Indices: 631792--631840 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
631782 TAGATTATCT
*
631792 AATATAGAGTTTAAATAATTTAAATA
1 AATATAGAGTTTAAATAATTAAAATA
*
631818 AATATA-AG-TTAATTAATTAAAAT
1 AATATAGAGTTTAAATAATTAAAAT
631841 TTACTTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 2 0.10
26 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (26 bp):
AATATAGAGTTTAAATAATTAAAATA
Found at i:632252 original size:26 final size:26
Alignment explanation
Indices: 632220--632271 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
632210 CATCCGATAG
632220 TGCAAAAGCCTTGCCATCCGTATACC
1 TGCAAAAGCCTTGCCATCCGTATACC
632246 TGCAAAAGCCTTGCCATCCGTATACC
1 TGCAAAAGCCTTGCCATCCGTATACC
632272 AAGTGTCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (26 bp):
TGCAAAAGCCTTGCCATCCGTATACC
Found at i:634428 original size:27 final size:27
Alignment explanation
Indices: 634396--634462 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
634386 GTTAATGGCT
* *
634396 CTGAATCATTCAGAATGTACTTCTTTG
1 CTGAATCATTCAAAATGTACTTCTGTG
* *
634423 CTGAATCATTCAAAATTTATTTCTGTG
1 CTGAATCATTCAAAATGTACTTCTGTG
*
634450 TTGAATCATTCAA
1 CTGAATCATTCAA
634463 CACTGTTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (27 bp):
CTGAATCATTCAAAATGTACTTCTGTG
Found at i:634477 original size:23 final size:23
Alignment explanation
Indices: 634451--634513 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
634441 ATTTCTGTGT
* *
634451 TGAATCATTCAACACTGTTTTGC
1 TGAATCAGTCAGCACTGTTTTGC
634474 TGAATCAGTCAGCACTGTTTTGC
1 TGAATCAGTCAGCACTGTTTTGC
*
634497 TAAATCAGTCAGCACTG
1 TGAATCAGTCAGCACTG
634514 AATCATTTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAATCAGTCAGCACTGTTTTGC
Found at i:643482 original size:20 final size:20
Alignment explanation
Indices: 643457--643507 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
643447 ACTTGATATT
*
643457 CGACTCGAAAAGCTCGTGAG
1 CGACTCGAAAAGCTCGTCAG
*
643477 CGACTCGAAAAGTTCGTCAG
1 CGACTCGAAAAGCTCGTCAG
*
643497 CAACTCGAAAA
1 CGACTCGAAAA
643508 CATAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (20 bp):
CGACTCGAAAAGCTCGTCAG
Found at i:644695 original size:16 final size:16
Alignment explanation
Indices: 644671--644735 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
644661 TAATAAAAAA
644671 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
644687 ACTAACATAAACGAAC
1 ACGAACATAAACGAAC
*
644703 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
644719 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
644735 A
1 A
644736 TAAAAATTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:645702 original size:14 final size:14
Alignment explanation
Indices: 645670--645696 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
645660 GAATGAACAT
645670 AAACGAACATAACC
1 AAACGAACATAACC
645684 AAACGAACATAAC
1 AAACGAACATAAC
645697 TGAACGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.26, G:0.07, T:0.07
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:646741 original size:3 final size:3
Alignment explanation
Indices: 646735--646817 Score: 130
Period size: 3 Copynumber: 27.7 Consensus size: 3
646725 ATAATATAAA
* *
646735 TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT TAT TAT AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
646783 TAT TAT TAT TAT TAT CAT TAT CAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
646818 AATATATTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:646753 original size:21 final size:21
Alignment explanation
Indices: 646729--646826 Score: 128
Period size: 21 Copynumber: 4.7 Consensus size: 21
646719 TTACCAATAA
646729 TATAAATATTATTATTATTAT
1 TATAAATATTATTATTATTAT
*
646750 TATAATTATTATTATTATTAT
1 TATAAATATTATTATTATTAT
*
646771 TATAATTATTATTATTATTAT
1 TATAAATATTATTATTATTAT
* *
646792 TAT-TATCATTATCATTATTAT
1 TATAAAT-ATTATTATTATTAT
646813 TATTAAATA-TATTA
1 TA-TAAATATTATTA
646827 AATACATATA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.01
21 63 0.93
22 2 0.03
23 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATAAATATTATTATTATTAT
Found at i:648162 original size:16 final size:15
Alignment explanation
Indices: 648141--648173 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
648131 AATATTTTTG
*
648141 ATATATAT-TCATAA
1 ATATATATATAATAA
648155 ATATATATATAATAA
1 ATATATATATAATAA
648170 ATAT
1 ATAT
648174 TAACTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATATATAATAA
Found at i:648873 original size:18 final size:18
Alignment explanation
Indices: 648827--648874 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
648817 TCTTTTCAAA
648827 TTTTA-TTTATTTATTAT
1 TTTTATTTTATTTATTAT
**
648844 TTTTATAATATTTA-TAT
1 TTTTATTTTATTTATTAT
648861 GTTTTATTTTATTT
1 -TTTTATTTTATTT
648875 GCAAGTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTATTTTATTTATTAT
Found at i:648896 original size:13 final size:15
Alignment explanation
Indices: 648865--648901 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
648855 TTATATGTTT
648865 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
648880 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
648893 TA-TTTATTT
1 TATTTTATTT
648902 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:659476 original size:9 final size:9
Alignment explanation
Indices: 659445--659538 Score: 54
Period size: 10 Copynumber: 10.1 Consensus size: 9
659435 TATTATGCTT
659445 GAAGAAAAA
1 GAAGAAAAA
659454 -AA-AAAAA
1 GAAGAAAAA
659461 GAAAAGAAAAA
1 G--AAGAAAAA
659472 GAAGAGAAAGA
1 GAAGA-AAA-A
*
659483 AAAGAAAAA
1 GAAGAAAAA
*
659492 AAAGAAAAAA
1 GAAG-AAAAA
*
659502 AAAGAAAGGAA
1 GAAGAAA--AA
659513 -AAGAAGAAA
1 GAAGAA-AAA
659522 -AAGAAAAA
1 GAAGAAAAA
659530 GAA-AAAAA
1 GAAGAAAAA
659538 G
1 G
659539 GGGTCAAAGT
Statistics
Matches: 73, Mismatches: 1, Indels: 23
0.75 0.01 0.24
Matches are distributed among these distances:
7 5 0.07
8 11 0.15
9 21 0.29
10 22 0.30
11 14 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:659485 original size:29 final size:29
Alignment explanation
Indices: 659446--659538 Score: 111
Period size: 29 Copynumber: 3.2 Consensus size: 29
659436 ATTATGCTTG
*
659446 AAGAAAAAAAAAAAAGAAAAGAAAAAGAA
1 AAGAAAGAAAAAAAAGAAAAGAAAAAGAA
*
659475 GAGAAAGAAAAGAAAA-AAAAGAAAAA-AA
1 AAGAAAGAAAA-AAAAGAAAAGAAAAAGAA
* *
659503 AAGAAAGGAAAAGAAGAAAAAGAAAAAGAA
1 AAGAAAGAAAAAAAAG-AAAAGAAAAAGAA
659533 AA-AAAG
1 AAGAAAG
659539 GGGTCAAAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
27 3 0.05
28 11 0.20
29 33 0.60
30 8 0.15
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (29 bp):
AAGAAAGAAAAAAAAGAAAAGAAAAAGAA
Found at i:659515 original size:43 final size:45
Alignment explanation
Indices: 659452--659537 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 45
659442 CTTGAAGAAA
*
659452 AAAAAAAAAGAAAAGAAAAAGAAGAGAAAG-AAAAGAAAAAAAAG
1 AAAAAAAAAGAAAAGAAAAAGAAGAAAAAGAAAAAGAAAAAAAAG
*
659496 AAAAAAAAAG-AAAGGAAAAGAAGAAAAAGAAAAAGAAAAAAA
1 AAAAAAAAAGAAAAGAAAAAGAAGAAAAAGAAAAAGAAAAAAA
659538 GGGGTCAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 17 0.44
44 22 0.56
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (45 bp):
AAAAAAAAAGAAAAGAAAAAGAAGAAAAAGAAAAAGAAAAAAAAG
Found at i:659901 original size:18 final size:18
Alignment explanation
Indices: 659865--659909 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
659855 CTATTTCAAG
*
659865 TTCAATTTA--TTTGAGA
1 TTCAATTTATTTTTGAAA
659881 TTCAATTTATTTTTGAAA
1 TTCAATTTATTTTTGAAA
659899 TTCAATTTATT
1 TTCAATTTATT
659910 CTTTTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 9 0.35
18 17 0.65
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (18 bp):
TTCAATTTATTTTTGAAA
Found at i:660561 original size:52 final size:52
Alignment explanation
Indices: 660478--661214 Score: 1235
Period size: 52 Copynumber: 14.1 Consensus size: 52
660468 TATGTGCTCA
* * * *
660478 ATAGTATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGTTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
660530 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
660582 ATACCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
660634 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
660686 ATACCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
660738 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
660790 ATACCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
660842 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
660894 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
660946 ATACCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
660998 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
661050 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
661102 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * * * *
661154 ATAGCATTTTCTGGAAGTGTTTTTTTTGAGATATCTGATCTGATTAGACAGAATC
1 ATAGCATCTTCTGGAAGTG--TTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
661209 A-AGCAT
1 ATAGCAT
661215 TGAGTTTAGA
Statistics
Matches: 648, Mismatches: 32, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
51 5 0.01
52 603 0.93
53 5 0.01
54 33 0.05
55 2 0.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:662068 original size:40 final size:41
Alignment explanation
Indices: 661987--662091 Score: 160
Period size: 40 Copynumber: 2.5 Consensus size: 41
661977 ATTTCCAGAG
661987 GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 GAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAA
662029 GAAGAGGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAA
1 GAAGA-GTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAA
*
662069 GAAGAAATTCATAATGAGAAGAA
1 GAAG-AGTTCATAATGAGAAGAA
662092 TTTGTTCAAC
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
40 36 0.60
41 2 0.03
42 5 0.08
43 17 0.28
ACGTcount: A:0.47, C:0.10, G:0.26, T:0.18
Consensus pattern (41 bp):
GAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAA
Found at i:662164 original size:113 final size:113
Alignment explanation
Indices: 662035--662431 Score: 652
Period size: 113 Copynumber: 3.5 Consensus size: 113
662025 GGAAGAAGAG
662035 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
* *
662100 ACCTTTTACCTGAATTCATCATTTGATGGATCAACATTGCCAGAGAAG
66 ACCTTTTACCTGAATTCATCATTTGATGGATCAACATTTCCAGAGAAA
662148 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
* * * * * *
662213 ACCTTTTACCTGAATCCATCATTTGGTGAATCATCTTTTCCAGAAAAA
66 ACCTTTTACCTGAATTCATCATTTGATGGATCAACATTTCCAGAGAAA
*
662261 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
* *
662326 ACCTTTTGCTTGAATTCATCATTTGATGGATCAACAATTTCCAGAGAAA
66 ACCTTTTACCTGAATTCATCATTTGATGGATCAAC-ATTTCCAGAGAAA
* *
662375 GTTCGTAATGAGAAGAACTCATCTGAAGAAGGAAGAA-AAAGTTCATAATGAGGAGAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCATAATGAGAAGAA
662432 CTCATCAAGA
Statistics
Matches: 262, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
113 200 0.76
114 62 0.24
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (113 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
ACCTTTTACCTGAATTCATCATTTGATGGATCAACATTTCCAGAGAAA
Found at i:662695 original size:3 final size:3
Alignment explanation
Indices: 662689--662762 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
662679 ATAATATAAA
*
662689 TAT TAT TAT TAT TAT TAT AAT TAT 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
* *
662737 TAT TAT CAT TAT CAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
662763 AATATATTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:683574 original size:3 final size:3
Alignment explanation
Indices: 683566--683614 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
683556 AAAGACGTAC
683566 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
683614 G
1 G
683615 GTGGATGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:691544 original size:31 final size:31
Alignment explanation
Indices: 691486--691546 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
691476 ATTACTAGTT
* *
691486 AGGTTTGTATTCAGATAATGCACAGTATGTC
1 AGGTTTGCATTCAGATAATACACAGTATGTC
* **
691517 AGGTTTGCATTTAGATAATACGTAGTATGT
1 AGGTTTGCATTCAGATAATACACAGTATGT
691547 TCAATTGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (31 bp):
AGGTTTGCATTCAGATAATACACAGTATGTC
Found at i:695170 original size:29 final size:28
Alignment explanation
Indices: 695123--695229 Score: 106
Period size: 29 Copynumber: 3.8 Consensus size: 28
695113 GGATCTCAAA
* * * *
695123 CAGAATCATGATGGAGATATAATCCCACG
1 CAGAATCAGGACGGGGA-ATAATCCCATG
* *
695152 CAGAATCTGGACGGGGATATAATCTCATG
1 CAGAATCAGGACGGGGA-ATAATCCCATG
* * * *
695181 CAAAATCAGGACGGGGACTAAGCCCTTG
1 CAGAATCAGGACGGGGAATAATCCCATG
695209 CAGAATCAGGACGGGGAATAA
1 CAGAATCAGGACGGGGAATAA
695230 ATTCGACGTA
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 26 0.41
29 38 0.59
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.18
Consensus pattern (28 bp):
CAGAATCAGGACGGGGAATAATCCCATG
Found at i:695909 original size:9 final size:9
Alignment explanation
Indices: 695887--695915 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
695877 TACTAGAGGG
695887 AAAGAAAG-
1 AAAGAAAGA
695895 AAAGAAAGA
1 AAAGAAAGA
695904 AAAGAAAGA
1 AAAGAAAGA
695913 AAA
1 AAA
695916 AGTGGGAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAGAAAGA
Found at i:696482 original size:12 final size:12
Alignment explanation
Indices: 696465--696510 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
696455 CGAGTGTTAT
696465 TATATATTATTA
1 TATATATTATTA
696477 TATATATTA--A
1 TATATATTATTA
*
696487 TATATA-AATTA
1 TATATATTATTA
*
696498 TAAATATTATTA
1 TATATATTATTA
696510 T
1 T
696511 TTACAAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.25
11 6 0.21
12 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATTATTA
Found at i:697872 original size:7 final size:7
Alignment explanation
Indices: 697860--697885 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
697850 ATTATTTTAC
697860 ATAATTT
1 ATAATTT
697867 ATAATTT
1 ATAATTT
697874 ATAATTT
1 ATAATTT
697881 ATAAT
1 ATAAT
697886 AATATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
ATAATTT
Found at i:705012 original size:12 final size:12
Alignment explanation
Indices: 704995--705040 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
704985 CGAGTGATAT
704995 TATATATTATTA
1 TATATATTATTA
705007 TATATATTA--A
1 TATATATTATTA
*
705017 TATATA-AATTA
1 TATATATTATTA
*
705028 TAAATATTATTA
1 TATATATTATTA
705040 T
1 T
705041 TTACAAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.25
11 6 0.21
12 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATTATTA
Found at i:706156 original size:13 final size:13
Alignment explanation
Indices: 706138--706162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
706128 ATGTTTTTAC
706138 GTTTTTTAATTTG
1 GTTTTTTAATTTG
706151 GTTTTTTAATTT
1 GTTTTTTAATTT
706163 TATATAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (13 bp):
GTTTTTTAATTTG
Found at i:706374 original size:32 final size:31
Alignment explanation
Indices: 706323--706382 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
706313 TCAAATAAGG
* *
706323 ATTAATTAATTTTATTATTTTATGTTTTAATC
1 ATTAATTAATTTTAGTA-TTTATGCTTTAATC
706355 ATTAATT-ATTATTAGTATTTATGCTTTA
1 ATTAATTAATT-TTAGTATTTATGCTTTA
706383 GGGTTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (31 bp):
ATTAATTAATTTTAGTATTTATGCTTTAATC
Found at i:707025 original size:2 final size:2
Alignment explanation
Indices: 707018--707044 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
707008 TTATCTTTAG
707018 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 A
707045 ATACTTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:707182 original size:15 final size:14
Alignment explanation
Indices: 707156--707187 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
707146 ATAATAAAAA
707156 ATTATAAATATATT
1 ATTATAAATATATT
707170 ATTATACAATATATT
1 ATTATA-AATATATT
707185 ATT
1 ATT
707188 TTAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:708136 original size:29 final size:30
Alignment explanation
Indices: 708088--708147 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
708078 ACCTAAATGA
* *
708088 GTAACGAAATGAAACGTTAGGTACCAAACT
1 GTAAAGAAATGAAACGTTAGGCACCAAACT
*
708118 GTAAAGAAAT-AAACGTTAGGCACTAAACT
1 GTAAAGAAATGAAACGTTAGGCACCAAACT
708147 G
1 G
708148 AAATAATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (30 bp):
GTAAAGAAATGAAACGTTAGGCACCAAACT
Found at i:716481 original size:25 final size:25
Alignment explanation
Indices: 716440--716510 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 25
716430 CATTAGGGGA
* * *
716440 TTAGGG-TTAAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTATT
716464 TTAGGGTTTGAAACCCTAATCTATT
1 TTAGGGTTTGAAACCCTAATCTATT
716489 TTAGGGTTTGAAACCCTAATCT
1 TTAGGGTTTGAAACCCTAATCT
716511 GATGGGTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
24 6 0.14
25 37 0.86
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTATT
Found at i:716606 original size:3 final size:3
Alignment explanation
Indices: 716600--716660 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
716590 AAAAAAATTG
* **
716600 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
716644 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
716661 CGAAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:716924 original size:42 final size:42
Alignment explanation
Indices: 716864--717097 Score: 171
Period size: 40 Copynumber: 5.6 Consensus size: 42
716854 AAAGGTGATA
* * *
716864 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGGTG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAGGGTG
* * * **
716906 ACACGGCTCATACTTGATGAAGAGATCTGG---TCGGAGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATC-TAGGGTG
** * *
716946 ACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCT--AGG-G-TG
* * *
716992 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGGTG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAGGGTG
* *
717034 ACACGGCTCATACGTGATGAAGAGATCTGG---TC-GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGG--TG
717074 ACACGGCTCATACGTGATGAAGAG
1 ACACGGCTCATACGTGATGAAGAG
717098 TTCTGGCCAT
Statistics
Matches: 154, Mismatches: 25, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
38 3 0.02
39 4 0.03
40 58 0.38
41 2 0.01
42 48 0.31
43 3 0.02
44 5 0.03
46 30 0.19
47 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (42 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGGTG
Found at i:717045 original size:128 final size:128
Alignment explanation
Indices: 716825--717159 Score: 625
Period size: 128 Copynumber: 2.6 Consensus size: 128
716815 ACGACACTGT
716825 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
1 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
*
716890 CTGGTTATCTAGGGTGACACGGCTCATACTTGATGAAGAGATCTGGTCGGAGAATGACACGGC
66 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGAGAATGACACGGC
*
716953 TCATACGTGATGAAGAGTTCTGGTCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
1 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
*
717018 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGC
66 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGAGAATGACACGGC
* *
717081 TCATACGTGATGAAGAGTTCTGGCCATCTACAGGTGATAACACGGTTCCTACATGATGAGGACGG
1 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
717146 CTGGTTATCTAGGG
66 CTGGTTATCTAGGG
717160 ATAATGGTTT
Statistics
Matches: 201, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 201 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (128 bp):
TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGAGAATGACACGGC
Found at i:717977 original size:63 final size:63
Alignment explanation
Indices: 717884--718143 Score: 200
Period size: 63 Copynumber: 4.2 Consensus size: 63
717874 CACAGATGTC
* *
717884 TTTTTTTCAAAAGAAGTTGTCTCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA
1 TTTTTTTCAAAAGAAGTTGTCTCGAGAGACAAAACTTTGTTTCAAAAGAAACAAACTCAAAGA
* * * * *
717947 TTTTTTTCACAA-AA-TTGTCTCAAGAGAGACAAAACTTTGTTTTAAAATAAATAGACTCAAAGA
1 TTTTTTTCAAAAGAAGTTGTCTC--GAGAGACAAAACTTTGTTTCAAAAGAAACAAACTCAAAGA
**** * * * * *
718010 -TTTTTTCAAAAGAA-ACAACTC-A-A-A-GATA-TTT-ATTCAAAAGGAACAAACTCCAAGA
1 TTTTTTTCAAAAGAAGTTGTCTCGAGAGACAAAACTTTGTTTCAAAAGAAACAAACTCAAAGA
* ** * * * *
718065 TTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTAAAATAAATAGACTCAAAGA
1 TTTTTTTCAAAAGAAGTTGTCTC--GAGAGACAAAACTTTGTTTCAAAAGAAACAAACTCAAAGA
718130 -TTTTTTCAAAAGAA
1 TTTTTTTCAAAAGAA
718144 ACAACTCAAA
Statistics
Matches: 148, Mismatches: 36, Indels: 25
0.71 0.17 0.12
Matches are distributed among these distances:
55 17 0.11
56 16 0.11
57 5 0.03
58 1 0.01
59 1 0.01
60 2 0.01
61 8 0.05
62 13 0.09
63 52 0.35
64 16 0.11
65 17 0.11
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (63 bp):
TTTTTTTCAAAAGAAGTTGTCTCGAGAGACAAAACTTTGTTTCAAAAGAAACAAACTCAAAGA
Found at i:718015 original size:26 final size:26
Alignment explanation
Indices: 718001--718229 Score: 134
Period size: 29 Copynumber: 8.0 Consensus size: 26
717991 AAATAAATAG
718001 ACTCAAAGATTTTTTCAAAAGAAACA
1 ACTCAAAGATTTTTTCAAAAGAAACA
*
718027 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGAAAC-A
* * *
718056 ACTCCAAGATTTTTTTCAAGAGAAACTG
1 ACTCAAAGA-TTTTTTCAAAAGAAAC-A
* * * * * *
718084 TCTCAAGAGAGACAAAACTTTGTTTTAAAATAAATA
1 ACTC-A-A-AG-----ATTTTTT--CAAAAGAAACA
718120 GACTCAAAGATTTTTTCAAAAGAAACA
1 -ACTCAAAGATTTTTTCAAAAGAAACA
*
718147 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGAAAC-A
* *
718176 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTT-TTCAAAAGAAAC-A
*
718205 ACTCAAAGATTTTTTCAAGAGAAAC
1 ACTCAAAGATTTTTTCAAAAGAAAC
718230 TGTCTCAAGA
Statistics
Matches: 158, Mismatches: 26, Indels: 37
0.71 0.12 0.17
Matches are distributed among these distances:
26 20 0.13
27 24 0.15
28 39 0.25
29 52 0.33
30 3 0.02
31 2 0.01
34 2 0.01
35 5 0.03
36 2 0.01
37 9 0.06
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.28
Consensus pattern (26 bp):
ACTCAAAGATTTTTTCAAAAGAAACA
Found at i:718047 original size:28 final size:27
Alignment explanation
Indices: 718001--718081 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 27
717991 AAATAAATAG
718001 ACTCAAAGATTTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTCAAAAGAAACAA
*
718027 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGAAACAA
* *
718056 ACTCCAAGATTTTTTTCAAGAGAAAC
1 ACTCAAAGA-TTTTTTCAAAAGAAAC
718082 TGTCTCAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.21
27 3 0.06
28 21 0.45
29 12 0.26
30 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGAAACAA
Found at i:718109 original size:120 final size:119
Alignment explanation
Indices: 717927--718195 Score: 477
Period size: 120 Copynumber: 2.2 Consensus size: 119
717917 ATTTTGTTTC
* *
717927 AAAGGAAACAAACTCAAAGATTTTTTTC-ACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTTA
1 AAAGG-AACAAACTCCAAGATTTTTTTCAACAAAACTGTCTCAAGAGAGACAAAACTTTGTTTTA
717991 AAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCA
65 AAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCA
*
718046 AAAGGAACAAACTCCAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTA
1 AAAGGAACAAACTCCAAGATTTTTTTCAACA-AAACTGTCTCAAGAGAGACAAAACTTTGTTTTA
718111 AAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCA
65 AAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCA
718166 AAAGGAACAAACTCCAAGATTTTTATTCAA
1 AAAGGAACAAACTCCAAGATTTTT-TTCAA
718196 AAGGAACAAA
Statistics
Matches: 144, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
118 21 0.15
119 7 0.05
120 111 0.77
121 5 0.03
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (119 bp):
AAAGGAACAAACTCCAAGATTTTTTTCAACAAAACTGTCTCAAGAGAGACAAAACTTTGTTTTAA
AATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCA
Found at i:718165 original size:28 final size:27
Alignment explanation
Indices: 718121--718229 Score: 139
Period size: 29 Copynumber: 3.9 Consensus size: 27
718111 AAATAAATAG
718121 ACTCAAAGATTTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTCAAAAGAAACAA
*
718147 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGAAACAA
* *
718176 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTT-TTCAAAAGAAACAA
*
718205 ACTCAAAGATTTTTTCAAGAGAAAC
1 ACTCAAAGATTTTTTCAAAAGAAAC
718230 TGTCTCAAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
26 10 0.14
27 13 0.18
28 15 0.20
29 35 0.47
30 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.27
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGAAACAA
Found at i:718190 original size:29 final size:29
Alignment explanation
Indices: 718121--718218 Score: 148
Period size: 29 Copynumber: 3.5 Consensus size: 29
718111 AAATAAATAG
*
718121 ACTCAAAGA-TTTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
718147 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
718176 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
718205 ACTCAAAGATTTTT
1 ACTCAAAGATTTTT
718219 TCAAGAGAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.14
27 3 0.05
28 11 0.17
29 41 0.64
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:718587 original size:35 final size:35
Alignment explanation
Indices: 718459--718575 Score: 112
Period size: 35 Copynumber: 3.4 Consensus size: 35
718449 GAGAAAAGAT
* ** * * *
718459 GTCTCAAGCGAGATGAAATTTGCTTTA-AGATATA
1 GTCTCAAGTGAGACAAAATTTGTTTTAGAGAAATC
* *
718493 GTCTCAAATGAGACAAAATTTGTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTAGAGAAATC
* * *
718528 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA-C
1 GTCTCAAGTGAGACAAAATTTGTTTTAGAGAAATC
718562 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
718576 TCAACTTTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
34 23 0.34
35 45 0.66
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (35 bp):
GTCTCAAGTGAGACAAAATTTGTTTTAGAGAAATC
Found at i:718705 original size:104 final size:102
Alignment explanation
Indices: 718528--718747 Score: 270
Period size: 104 Copynumber: 2.1 Consensus size: 102
718518 TAGAGAAATT
*
718528 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACGATCTCAAGTGAGATCAACTTTGTTTAATGT
1 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
* *
718593 GAAACAAATTCGAAATTTGGATCTCAAAGG-GAAAAG
66 GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAG
* *
718629 GTCTCAAGCGAGACAAA-TTTG-TTTTGAAAGAAACAA-CAATCTAAGGTGAGATTAATTTTGTT
1 GTCTCAAGCGAGACAAAGTTTGTTTTTG--AGAAACAATC--TC-AA-GTGAGATCAACTTTG-T
* * *
718691 TTAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAAT
59 TTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAG
718734 GTCTCAAGCGAGAC
1 GTCTCAAGCGAGAC
718748 GCACTTGTTT
Statistics
Matches: 103, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
99 5 0.05
100 5 0.05
101 24 0.23
102 2 0.02
103 2 0.02
104 42 0.41
105 23 0.22
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (102 bp):
GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAG
Found at i:719229 original size:4 final size:4
Alignment explanation
Indices: 719220--719265 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
719210 TGTATCATGG
* *
719220 ATGT ATGT ATGT ATGT ATGT ATGT ATGT GTGT GTGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
719266 ATACTTTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:720904 original size:20 final size:20
Alignment explanation
Indices: 720881--720921 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
720871 GGATAAATGC
720881 AATGCTTCAAGGTCGCAAAG
1 AATGCTTCAAGGTCGCAAAG
* *
720901 AATGTTTCAAGGTCTCAAAG
1 AATGCTTCAAGGTCGCAAAG
720921 A
1 A
720922 TAGGGAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (20 bp):
AATGCTTCAAGGTCGCAAAG
Found at i:723210 original size:31 final size:32
Alignment explanation
Indices: 723154--723215 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
723144 TGACAAAATG
723154 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
723186 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
723216 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:726880 original size:25 final size:25
Alignment explanation
Indices: 726839--726910 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
726829 CATTAGGGGA
* *
726839 TTAGGG-TTAAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
726863 TTAGGGTTTGAAACCCTAATCTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
726888 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
726911 ATGGGTTGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 6 0.13
25 39 0.87
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGTT
Found at i:727005 original size:3 final size:3
Alignment explanation
Indices: 726999--727059 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
726989 AAAAAAATTG
* **
726999 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
727043 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
727060 CGAAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:727248 original size:23 final size:23
Alignment explanation
Indices: 727221--727298 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
727211 CATGACGATG
727221 AAAATGATGATCAAGATGACAAC
1 AAAATGATGATCAAGATGACAAC
* * **
727244 AAAATGATGGT-AGTGATGATGAC
1 AAAATGATGATCA-AGATGACAAC
*
727267 GAAATGATGATCAAGATGACAAC
1 AAAATGATGATCAAGATGACAAC
727290 AAAAATGAT
1 -AAAATGAT
727299 AGTCATGATG
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
22 1 0.02
23 33 0.79
24 8 0.19
ACGTcount: A:0.49, C:0.09, G:0.22, T:0.21
Consensus pattern (23 bp):
AAAATGATGATCAAGATGACAAC
Found at i:727282 original size:46 final size:47
Alignment explanation
Indices: 727222--727312 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 47
727212 ATGACGATGA
*
727222 AAATGATGATCAAGATGACAAC-AAAATGATGGT-AGTGATGATGACG
1 AAATGATGATCAAGATGACAACAAAAATGATAGTCA-TGATGATGACG
727268 AAATGATGATCAAGATGACAACAAAAATGATAGTCATGATGATGA
1 AAATGATGATCAAGATGACAACAAAAATGATAGTCATGATGATGA
727313 TGATGAGGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
46 22 0.52
47 19 0.45
48 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.22
Consensus pattern (47 bp):
AAATGATGATCAAGATGACAACAAAAATGATAGTCATGATGATGACG
Found at i:727988 original size:24 final size:24
Alignment explanation
Indices: 727960--728010 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
727950 TACAAGAGAA
727960 GAAGAGTAATCAAAGAAAATAGAG
1 GAAGAGTAATCAAAGAAAATAGAG
*
727984 GAAGAGTAATCGAAGAAAATAGAG
1 GAAGAGTAATCAAAGAAAATAGAG
728008 GAA
1 GAA
728011 ATAGAGATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.04, G:0.27, T:0.12
Consensus pattern (24 bp):
GAAGAGTAATCAAAGAAAATAGAG
Found at i:736702 original size:23 final size:23
Alignment explanation
Indices: 736676--736723 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
736666 ATAAAGTACA
*
736676 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
736699 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
736722 AT
1 AT
736724 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:737130 original size:21 final size:22
Alignment explanation
Indices: 737105--737156 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
737095 ACACTTTACA
*
737105 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
737128 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
737151 ATATAA
1 ATATAA
737157 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:737141 original size:23 final size:23
Alignment explanation
Indices: 737115--737177 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
737105 ATATAACCAC
737115 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
737138 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
737161 TACCTATTACATCATAT
1 TACCTATTACATTATAT
737178 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:737635 original size:39 final size:39
Alignment explanation
Indices: 737581--737667 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
737571 TCAAGTTGTA
*
737581 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
737620 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
737659 GATTTTGAT
1 GATTTTGAT
737668 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Done.