Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 17 of 28
Found at i:2600898 original size:32 final size:32
Alignment explanation
Indices: 2600853--2600914 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
2600843 TTTGAATTTA
2600853 TTTAAGTTGAAATTTATTTAAATTTAAGTTTG
1 TTTAAGTTGAAATTTATTTAAATTTAAGTTTG
* *
2600885 TTTAAGTTTAAATTTATTTAGATTTAAGTT
1 TTTAAGTTGAAATTTATTTAAATTTAAGTT
2600915 CATTCGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (32 bp):
TTTAAGTTGAAATTTATTTAAATTTAAGTTTG
Found at i:2600910 original size:16 final size:16
Alignment explanation
Indices: 2600847--2600949 Score: 68
Period size: 16 Copynumber: 6.4 Consensus size: 16
2600837 CTTCGGTTTG
*
2600847 AATTTATTTA-AGTTGA
1 AATTTATTTAGA-TTTA
*
2600863 AATTTATTTAAATTTA
1 AATTTATTTAGATTTA
* *
2600879 AGTTTGTTTA-AGTTTA
1 AATTTATTTAGA-TTTA
2600895 AATTTATTTAGATTTA
1 AATTTATTTAGATTTA
* * *
2600911 AGTTCA-TTCGAATTTA
1 AATTTATTTAG-ATTTA
* * *
2600927 GATTTATATGGATTTA
1 AATTTATTTAGATTTA
2600943 AATTTAT
1 AATTTAT
2600950 ATGAGTTTAT
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
15 4 0.06
16 60 0.88
17 4 0.06
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (16 bp):
AATTTATTTAGATTTA
Found at i:2600932 original size:32 final size:32
Alignment explanation
Indices: 2600856--2600965 Score: 89
Period size: 32 Copynumber: 3.4 Consensus size: 32
2600846 GAATTTATTT
* * ** *
2600856 AAGTTGAAATTTATTTAAATTTAAGTTTGTTT
1 AAGTTTAAATTTATTTAGATTTAAGTTCATTG
2600888 AAGTTTAAATTTATTTAGATTTAAGTTCATTCG
1 AAGTTTAAATTTATTTAGATTTAAGTTCATT-G
* * * * *
2600921 AA-TTTAGATTTATATGGATTTAAATTTATATG
1 AAGTTTAAATTTATTTAGATTTAAGTTCAT-TG
*
2600953 -AGTTTATATTTAT
1 AAGTTTAAATTTAT
2600966 ATGGGTTCGA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
31 1 0.02
32 60 0.94
33 3 0.05
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.52
Consensus pattern (32 bp):
AAGTTTAAATTTATTTAGATTTAAGTTCATTG
Found at i:2600950 original size:16 final size:16
Alignment explanation
Indices: 2600891--2600969 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
2600881 TTTGTTTAAG
* *
2600891 TTTAAATTTATTTAGA
1 TTTAAATTTATATGGA
* * *
2600907 TTTAAGTTCAT-TCGAA
1 TTTAAATTTATAT-GGA
*
2600923 TTTAGATTTATATGGA
1 TTTAAATTTATATGGA
2600939 TTTAAATTTATAT-GA
1 TTTAAATTTATATGGA
*
2600954 GTTTATATTTATATGG
1 -TTTAAATTTATATGG
2600970 GTTCGAATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
15 3 0.06
16 44 0.90
17 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.52
Consensus pattern (16 bp):
TTTAAATTTATATGGA
Found at i:2600979 original size:32 final size:32
Alignment explanation
Indices: 2600923--2600994 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
2600913 TTCATTCGAA
*
2600923 TTTAGATTTATATGGATTTAAATTTATATGAG
1 TTTAGATTTATATGGATTCAAATTTATATGAG
* * * * *
2600955 TTTATATTTATATGGGTTCGAATTTTTTTGAG
1 TTTAGATTTATATGGATTCAAATTTATATGAG
*
2600987 TTTGGATT
1 TTTAGATT
2600995 CGAATTCGAG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.01, G:0.18, T:0.54
Consensus pattern (32 bp):
TTTAGATTTATATGGATTCAAATTTATATGAG
Found at i:2603310 original size:8 final size:8
Alignment explanation
Indices: 2603299--2603342 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
2603289 TGTTTTTATC
2603299 TTTTTTTA
1 TTTTTTTA
2603307 TTTTTTTA
1 TTTTTTTA
2603315 TTTTTTTA
1 TTTTTTTA
***
2603323 TAACTTT-
1 TTTTTTTA
2603330 TTTTTTTA
1 TTTTTTTA
2603338 TTTTT
1 TTTTT
2603343 ATCATTTCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2603602 original size:8 final size:8
Alignment explanation
Indices: 2603557--2603604 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
2603547 AATATAAATA
2603557 TAATATTT
1 TAATATTT
2603565 T--TATTT
1 TAATATTT
*
2603571 AAATATTT
1 TAATATTT
2603579 TAA-ATTT
1 TAATATTT
2603586 TATATATTT
1 TA-ATATTT
2603595 TAATATTT
1 TAATATTT
2603603 TA
1 TA
2603605 TGTATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
6 5 0.15
7 6 0.18
8 17 0.50
9 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TAATATTT
Found at i:2604071 original size:20 final size:19
Alignment explanation
Indices: 2604027--2604071 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2604017 TAAGGTGATA
* *
2604027 TTTTTAATATATTTATATT
1 TTTTTAATATATTTAGAGT
2604046 TATTTTAATATATTTAAGAGT
1 T-TTTTAATATATTT-AGAGT
2604067 TTTTT
1 TTTTT
2604072 TATAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 4 0.18
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTTAATATATTTAGAGT
Found at i:2605517 original size:20 final size:20
Alignment explanation
Indices: 2605489--2605528 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2605479 CAATCTATTT
2605489 ATTTAAATATTTAAA-AAATA
1 ATTTAAATA-TTAAATAAATA
*
2605509 ATTTTAATATTAAATAAATA
1 ATTTAAATATTAAATAAATA
2605529 TTATTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTAAATATTAAATAAATA
Found at i:2607973 original size:2 final size:2
Alignment explanation
Indices: 2607966--2607990 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2607956 TGTTATCATT
2607966 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2607991 CTAAAGCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2608397 original size:20 final size:20
Alignment explanation
Indices: 2608374--2608429 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 20
2608364 TTTAAAAATT
*
2608374 ATATATTTATATAAATTTTA
1 ATATATATATATAAATTTTA
*
2608394 ATATATATA-AT-ATTTTTA
1 ATATATATATATAAATTTTA
* *
2608412 TTATATATATATATATTT
1 ATATATATATATAAATTT
2608430 GCGTCCAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 14 0.48
19 4 0.14
20 11 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATATATATAAATTTTA
Found at i:2611813 original size:2 final size:2
Alignment explanation
Indices: 2611806--2611851 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2611796 ACACGTATGC
2611806 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
2611848 TA TA
1 TA TA
2611852 CACATTATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2613594 original size:3 final size:3
Alignment explanation
Indices: 2613586--2613646 Score: 95
Period size: 3 Copynumber: 20.3 Consensus size: 3
2613576 TTATGTATTG
* * *
2613586 AAT AAT AAT ACT AAT AAT AAT AAT AAT ACT AAT AAT AAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2613634 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
2613647 TATTCAAGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2614181 original size:27 final size:27
Alignment explanation
Indices: 2614110--2614183 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
2614100 CGATACTTAA
*
2614110 ATTTAATA-ATTCATATATTCATGTCAT
1 ATTTAATATATT-ATATATTCATATCAT
*
2614137 ATTTATATATTTTATATATTGCA-ATCAT
1 ATTTA-ATATATTATATATT-CATATCAT
2614165 ATTTAATATATTATATATT
1 ATTTAATATATTATATATT
2614184 TATAAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 18 0.44
28 19 0.46
29 4 0.10
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTTAATATATTATATATTCATATCAT
Found at i:2614976 original size:13 final size:13
Alignment explanation
Indices: 2614950--2614982 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2614940 GTTATGAATT
2614950 ATTAATAAATCAC
1 ATTAATAAATCAC
2614963 A-TAATAATATCAC
1 ATTAATAA-ATCAC
2614976 ATTAATA
1 ATTAATA
2614983 TATAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 7 0.39
14 5 0.28
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (13 bp):
ATTAATAAATCAC
Found at i:2616051 original size:18 final size:20
Alignment explanation
Indices: 2616012--2616051 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2616002 AATTTTTAAA
*
2616012 AATATTTTTATATTAATATT
1 AATATTTTTATATAAATATT
2616032 AATATTTTTAT-TAAAT-TT
1 AATATTTTTATATAAATATT
2616050 AA
1 AA
2616052 ATAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATTTTTATATAAATATT
Found at i:2616075 original size:21 final size:23
Alignment explanation
Indices: 2616034--2616096 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 23
2616024 TTAATATTAA
2616034 TATTTTTATTAAATTTAAATAAAT
1 TATTTTTATTAAA-TTAAATAAAT
2616058 TATTTTTATT-AA-TAAAT-AAT
1 TATTTTTATTAAATTAAATAAAT
* **
2616078 AATTTAAATTAAATTAAAT
1 TATTTTTATTAAATTAAAT
2616097 CGATTAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 10 0.29
21 7 0.21
22 5 0.15
23 2 0.06
24 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTTATTAAATTAAATAAAT
Found at i:2618804 original size:38 final size:37
Alignment explanation
Indices: 2618762--2618841 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 37
2618752 ATTATAATAA
*
2618762 ATATATATTATTTATGTC-ATGTATATTATTTTTATATT
1 ATATA-ATTATTTATATCAATGTATATTATTTTT-TATT
* * *
2618800 ATATAATTTTTTATATCATATTTTTATTATTTTTTATT
1 ATATAATTATTTATATCA-ATGTATATTATTTTTTATT
2618838 ATAT
1 ATAT
2618842 TTTACTCAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 10 0.28
38 13 0.36
39 13 0.36
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (37 bp):
ATATAATTATTTATATCAATGTATATTATTTTTTATT
Found at i:2618815 original size:12 final size:11
Alignment explanation
Indices: 2618798--2618844 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 11
2618788 TATTTTTATA
2618798 TTATATAATTTT
1 TTATAT-ATTTT
2618810 TTATATCATATTT
1 TTATAT-AT-TTT
2618823 TTAT-TATTTT
1 TTATATATTTT
2618833 TTATTATATTTT
1 TTA-TATATTTT
2618845 ACTCAGATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 6 0.19
11 3 0.10
12 15 0.48
13 7 0.23
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATATATTTT
Found at i:2619596 original size:154 final size:153
Alignment explanation
Indices: 2619280--2619565 Score: 367
Period size: 154 Copynumber: 1.9 Consensus size: 153
2619270 AATTTATTTA
*
2619280 AATTTTTTAATTTTTATTTAATTATTTTACTTAAAAAATACAATGTTATTAAATCTTTTTTAATA
1 AATTTTTTAATTTTTATTTAATTATTTTACTTAAAAAATACAACGTTATTAAATCTTTTTTAATA
* * * * * ** *
2619345 TATAATCTTTTAAAATCTGACTTAATATATAAGATTATGAAACACTAATATTATTGACATTATTA
66 TATAATCTTTTAAAATCCGACTTAATATATAAGATTATGAAACACTAATATAACTCAAAAGATCA
* * * **
2619410 AGGTTTTGAAAAACTATTTGTTAT
131 A-GTATTCAAAAACTATCTGAAAT
*
2619434 AATTTTTTAATTTTTATTTAATTATTTTA-TTAAAAAAATATAACGTTATTAAATCTTTTTTAAT
1 AATTTTTTAATTTTTATTTAATTATTTTACTT-AAAAAATACAACGTTATTAAATCTTTTTTAAT
* * * *
2619498 ATATAATTTTTTAAAATCCGGCTTAATATATAAGATTATGAAACACTGATATAAGCTCAAAAGCT
65 ATATAATCTTTTAAAATCCGACTTAATATATAAGATTATGAAACACTAATATAA-CTCAAAAGAT
2619563 CAA
129 CAA
2619566 TAATTCATAA
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
153 2 0.02
154 108 0.93
155 6 0.05
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (153 bp):
AATTTTTTAATTTTTATTTAATTATTTTACTTAAAAAATACAACGTTATTAAATCTTTTTTAATA
TATAATCTTTTAAAATCCGACTTAATATATAAGATTATGAAACACTAATATAACTCAAAAGATCA
AGTATTCAAAAACTATCTGAAAT
Found at i:2622081 original size:17 final size:15
Alignment explanation
Indices: 2622052--2622085 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
2622042 ACTCTTCATT
2622052 AATTTTTTATCTTTA
1 AATTTTTTATCTTTA
2622067 AATTTTGTTATTCTTTA
1 AATTTT-TTA-TCTTTA
2622084 AA
1 AA
2622086 AAAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (15 bp):
AATTTTTTATCTTTA
Found at i:2624208 original size:2 final size:2
Alignment explanation
Indices: 2624201--2624238 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2624191 CCAATATTCC
2624201 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
2624239 GTAAATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2625905 original size:20 final size:20
Alignment explanation
Indices: 2625880--2625919 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2625870 GTATTTAAAT
*
2625880 TTAAATAAAAATTTTAATTA
1 TTAAATAAAAATTTGAATTA
*
2625900 TTAAATAATAATTTGAATTA
1 TTAAATAAAAATTTGAATTA
2625920 AAAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TTAAATAAAAATTTGAATTA
Found at i:2626182 original size:8 final size:8
Alignment explanation
Indices: 2626169--2626194 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2626159 ATAAAATTTT
2626169 AATTATTC
1 AATTATTC
2626177 AATTATTC
1 AATTATTC
2626185 AATTATTC
1 AATTATTC
2626193 AA
1 AA
2626195 AAGTCATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (8 bp):
AATTATTC
Found at i:2627839 original size:20 final size:21
Alignment explanation
Indices: 2627796--2627917 Score: 83
Period size: 20 Copynumber: 5.7 Consensus size: 21
2627786 ATTATATACA
* * *
2627796 AATATAATAAAAATAATTTA-
1 AATATATTAAATATAAATTAT
2627816 AATATATTAAATA-AAATTAT
1 AATATATTAAATATAAATTAT
*
2627836 AATA-A-TAAATATAAATATAAA
1 AATATATTAAATATAAAT-T-AT
*
2627857 AACATATTAAACTTATTTAAATTAT
1 AATATATTAAA--TA--TAAATTAT
*
2627882 AATATTTTAAATAT-AATTAT
1 AATATATTAAATATAAATTAT
*
2627902 AATATATATATATATA
1 AATATAT-TAAATATA
2627918 TATAAACATC
Statistics
Matches: 80, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
18 6 0.08
19 10 0.12
20 28 0.35
21 11 0.14
22 1 0.01
23 6 0.08
25 12 0.15
26 1 0.01
27 5 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATATTAAATATAAATTAT
Found at i:2627844 original size:18 final size:18
Alignment explanation
Indices: 2627798--2627855 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
2627788 TATATACAAA
*
2627798 TATAATAA-AAAT-AATT
1 TATAATAATAAATAAAAT
2627814 TA-AATATATTAAATAAAAT
1 TATAATA-A-TAAATAAAAT
2627833 TATAATAATAAATATAAA-
1 TATAATAATAAATA-AAAT
2627851 TATAA
1 TATAA
2627856 AAACATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 4 0.11
16 3 0.09
18 15 0.43
19 9 0.26
20 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAATAATAAATAAAAT
Found at i:2630229 original size:24 final size:25
Alignment explanation
Indices: 2630201--2630247 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
2630191 TATTATTTAT
*
2630201 TTATTGTTAATATA-TAAATATATA
1 TTATTATTAATATATTAAATATATA
2630225 TTATTATTAATATATTAAATATA
1 TTATTATTAATATATTAAATATA
2630248 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTATTATTAATATATTAAATATATA
Found at i:2632350 original size:23 final size:23
Alignment explanation
Indices: 2632310--2632359 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2632300 TTTAAATTTA
2632310 AATTTAAATTAATAAATTTAAAT
1 AATTTAAATTAATAAATTTAAAT
* *
2632333 AATTT-AATATAATTAATTTATAT
1 AATTTAAAT-TAATAAATTTAAAT
2632356 AATT
1 AATT
2632360 ATTTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATTTAAATTAATAAATTTAAAT
Found at i:2632351 original size:37 final size:37
Alignment explanation
Indices: 2632310--2632401 Score: 93
Period size: 37 Copynumber: 2.5 Consensus size: 37
2632300 TTTAAATTTA
2632310 AATTTAAATTAA-TAAATTTAAATAATTTAAT-A-TAATT
1 AATTTAAA-TAATTAAATTTAAAT--TTTAATAATTAATT
* **
2632347 AATTTATATAATTATTTTTAAATTTTAATAATTAATT
1 AATTTAAATAATTAAATTTAAATTTTAATAATTAATT
*
2632384 AATTTAAA-ATTTAAATTT
1 AATTTAAATAATTAAATTT
2632402 TATCACTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
35 6 0.13
36 11 0.24
37 28 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
AATTTAAATAATTAAATTTAAATTTTAATAATTAATT
Found at i:2632357 original size:13 final size:14
Alignment explanation
Indices: 2632332--2632360 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2632322 TAAATTTAAA
2632332 TAATTTAATATAAT
1 TAATTTAATATAAT
2632346 TAATTT-ATATAAT
1 TAATTTAATATAAT
2632359 TA
1 TA
2632361 TTTTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATTTAATATAAT
Found at i:2634631 original size:2 final size:2
Alignment explanation
Indices: 2634624--2634659 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2634614 TCATCATTAT
2634624 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
2634660 GATCTAGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2636546 original size:2 final size:2
Alignment explanation
Indices: 2636539--2636577 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2636529 GAAATCCATA
2636539 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 A
2636578 CTTTTACCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2637405 original size:6 final size:6
Alignment explanation
Indices: 2637396--2637422 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2637386 TTAAAAGTAA
2637396 AAAATT AAAATT AAAATT AAAATT AAA
1 AAAATT AAAATT AAAATT AAAATT AAA
2637423 GACAGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:2639728 original size:29 final size:30
Alignment explanation
Indices: 2639678--2639750 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
2639668 TAATTTGATT
*
2639678 ATATTAATAATTTATATTATAT-AAATTTTAA
1 ATATT-AT-ATTTATATCATATCAAATTTTAA
* *
2639709 A-ATATATATTTATATCATATCATATTTTAT
1 ATAT-TATATTTATATCATATCAAATTTTAA
2639739 ATATTATATTTA
1 ATATTATATTTA
2639751 AATAATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
29 12 0.33
30 20 0.56
31 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATTATATTTATATCATATCAAATTTTAA
Found at i:2639747 original size:14 final size:14
Alignment explanation
Indices: 2639620--2639771 Score: 59
Period size: 14 Copynumber: 10.9 Consensus size: 14
2639610 AACCTAATAA
*
2639620 TTTATATATCA-AT
1 TTTATATATTATAT
* *
2639633 TTCATAT-TCATAT
1 TTTATATATTATAT
* * *
2639646 TTAAAATATTTTAT
1 TTTATATATTATAT
*
2639660 ATT-TATATTA-AT
1 TTTATATATTATAT
* *
2639672 TTGATTATATTAATAA
1 TTTA-TATATT-ATAT
*
2639688 TTTATATTATATAAAT
1 TTTATA-TAT-TATAT
*
2639704 TTTA-AAATATATAT
1 TTTATATAT-TATAT
*
2639718 TTATATCATATCATAT
1 TT-TAT-ATATTATAT
2639734 TTTATATATTATA-
1 TTTATATATTATAT
*
2639747 TTTAAATAATTATA-
1 TTTATAT-ATTATAT
2639761 TTTA-ATATTAT
1 TTTATATATTAT
2639772 CGGATCTAAA
Statistics
Matches: 106, Mismatches: 21, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
12 11 0.10
13 26 0.25
14 37 0.35
15 9 0.08
16 19 0.18
17 4 0.04
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (14 bp):
TTTATATATTATAT
Found at i:2639950 original size:2 final size:2
Alignment explanation
Indices: 2639935--2639984 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
2639925 CCAAATTACT
* * *
2639935 TA TA TA TG TG TA TA TA CA 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
2639977 TA TA TA TA
1 TA TA TA TA
2639985 ATGGATATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2645165 original size:17 final size:17
Alignment explanation
Indices: 2645129--2645162 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2645119 TAAATAATTT
2645129 TATTTTTAATCAAATAA
1 TATTTTTAATCAAATAA
*
2645146 TATTATTTAATTAAATA
1 TATT-TTTAATCAAATA
2645163 TATAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTTTAATCAAATAA
Found at i:2645835 original size:11 final size:11
Alignment explanation
Indices: 2645799--2645847 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
2645789 ATAAAAATAA
*
2645799 TATATTTTTAT
1 TATATTTATAT
* *
2645810 ATAAATTT-TAA
1 -TATATTTATAT
2645821 TATATTTATAT
1 TATATTTATAT
2645832 TATATTTATAT
1 TATATTTATAT
2645843 TATAT
1 TATAT
2645848 CAAAATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 6 0.19
11 20 0.62
12 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2645843 original size:17 final size:17
Alignment explanation
Indices: 2645821--2645887 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 17
2645811 TAAATTTTAA
2645821 TATATTTATATTATATT
1 TATATTTATATTATATT
* *
2645838 TATA-TTATATCAAAATT
1 TATATTTATAT-TATATT
2645855 TATATTTTATATTAATAATT
1 TATA-TTTATATT-AT-ATT
*
2645875 TTTATTTCATATT
1 TATATTT-ATATT
2645888 TAATATTATC
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
16 6 0.15
17 12 0.31
19 10 0.26
20 11 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTATATTATATT
Found at i:2645880 original size:20 final size:20
Alignment explanation
Indices: 2645836--2645892 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2645826 TTATATTATA
* *
2645836 TTTATATTATATCAA-AATT
1 TTTATTTTATATTAATAATT
*
2645855 TATATTTTATATTAATAATT
1 TTTATTTTATATTAATAATT
*
2645875 TTTATTTCATATTTAATA
1 TTTATTTTATA-TTAATA
2645893 TTATCAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 12 0.39
20 13 0.42
21 6 0.19
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTATTTTATATTAATAATT
Found at i:2645894 original size:34 final size:36
Alignment explanation
Indices: 2645806--2645894 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 36
2645796 TAATATATTT
* *
2645806 TTATAT-AAATTTTAATATATTTATATTATATTTATA
1 TTATATCAAAATTTAATAT-TTTATATTATAATTATA
2645842 TTATATCAAAATTT-ATATTTTATATTAATAATT-T-
1 TTATATCAAAATTTAATATTTTATATT-ATAATTATA
* *
2645876 TTATTTC-ATATTTAATATT
1 TTATATCAAAATTTAATATT
2645895 ATCAAAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
33 5 0.11
34 11 0.24
35 9 0.20
36 15 0.33
37 6 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.58
Consensus pattern (36 bp):
TTATATCAAAATTTAATATTTTATATTATAATTATA
Found at i:2646266 original size:21 final size:22
Alignment explanation
Indices: 2646209--2646267 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
2646199 GATGCATTTT
*
2646209 ATAAATAT-CATATTATTAATAA
1 ATAAATATAAATATT-TTAATAA
2646231 ATAAATATAAA-ATTTTAA-AA
1 ATAAATATAAATATTTTAATAA
2646251 A-AAATATAAATTATTTT
1 ATAAATATAAA-TATTTT
2646268 GTTTAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 9 0.27
20 3 0.09
21 9 0.27
22 11 0.33
23 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAATATAAATATTTTAATAA
Found at i:2647567 original size:2 final size:2
Alignment explanation
Indices: 2647560--2647588 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2647550 CAAATAATTT
2647560 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2647589 TCATATCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2647873 original size:2 final size:2
Alignment explanation
Indices: 2647868--2647904 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2647858 CACACACGTG
2647868 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2647905 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2648120 original size:2 final size:2
Alignment explanation
Indices: 2648113--2648139 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2648103 ATGTTTTCTA
2648113 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
2648140 CACACACACA
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:2648144 original size:2 final size:2
Alignment explanation
Indices: 2648139--2648166 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2648129 ATATATATAT
2648139 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2648167 CACCACCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2649259 original size:14 final size:14
Alignment explanation
Indices: 2649242--2649275 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2649232 CAAGTGCGTG
2649242 TATATACAAACATA
1 TATATACAAACATA
* *
2649256 TATATATATACATA
1 TATATACAAACATA
2649270 TATATA
1 TATATA
2649276 TATATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (14 bp):
TATATACAAACATA
Found at i:2649303 original size:2 final size:2
Alignment explanation
Indices: 2649253--2649284 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2649243 ATATACAAAC
*
2649253 AT AT AT AT AT AT AC 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
2649285 TCAAATTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2649612 original size:2 final size:2
Alignment explanation
Indices: 2649607--2649632 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2649597 CCCGCGCGCG
2649607 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
2649633 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2650162 original size:2 final size:2
Alignment explanation
Indices: 2650157--2650208 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2650147 AATCTTATAT
2650157 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2650199 AC AC AC AC AC
1 AC AC AC AC AC
2650209 TAACTGTAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2650821 original size:23 final size:20
Alignment explanation
Indices: 2650794--2650846 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
2650784 AATTCGGTTA
2650794 AAATTAAATTAATTGATTAAATT
1 AAATTAAATT-ATTGATT-AA-T
2650817 AAATT-AATT-TTGATTAAT
1 AAATTAAATTATTGATTAAT
*
2650835 AAATTATATTAT
1 AAATTAAATTAT
2650847 AAAATTATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 6 0.22
19 5 0.19
20 7 0.26
22 4 0.15
23 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
AAATTAAATTATTGATTAAT
Found at i:2650927 original size:16 final size:16
Alignment explanation
Indices: 2650901--2650937 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2650891 ATTTGATTTA
2650901 AAATTTAAAAATAATC
1 AAATTTAAAAATAATC
* *
2650917 GAATTTGAAAATAATC
1 AAATTTAAAAATAATC
2650933 AAATT
1 AAATT
2650938 ATCTGGATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (16 bp):
AAATTTAAAAATAATC
Found at i:2656460 original size:20 final size:21
Alignment explanation
Indices: 2656409--2656461 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
2656399 AAATTTATTT
2656409 TAAATTATTAAAATTTTAAAA
1 TAAATTATTAAAATTTTAAAA
*
2656430 TAAAATA-TAAAA-TTTAAGAA
1 TAAATTATTAAAATTTTAA-AA
2656450 -AAATTATTAAAA
1 TAAATTATTAAAA
2656462 AAATATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 10 0.36
20 12 0.43
21 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAATTATTAAAATTTTAAAA
Found at i:2656467 original size:30 final size:30
Alignment explanation
Indices: 2656418--2656481 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
2656408 TTAAATTATT
*
2656418 AAAATTTTAAAATAAAATATAAAATTTAAGA
1 AAAATTTTAAAATAAAATATAAAATATAA-A
2656449 AAAATTATT-AAA-AAAATATAAAATATAAA
1 AAAATT-TTAAAATAAAATATAAAATATAAA
2656478 AAAA
1 AAAA
2656482 CAATTTTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 5 0.16
30 15 0.48
31 9 0.29
32 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (30 bp):
AAAATTTTAAAATAAAATATAAAATATAAA
Found at i:2657077 original size:28 final size:30
Alignment explanation
Indices: 2657041--2657102 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 30
2657031 GACTTTAATA
*
2657041 AATATTAATCAAAAA-ATAAA-ATTAATTT-
1 AATAATAAT-AAAAATATAAAGATTAATTTC
*
2657069 AATAATAATAAAAATATAAAGATTTATTTC
1 AATAATAATAAAAATATAAAGATTAATTTC
2657099 AATA
1 AATA
2657103 TAACAGACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 13 0.45
29 7 0.24
30 4 0.14
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (30 bp):
AATAATAATAAAAATATAAAGATTAATTTC
Found at i:2657619 original size:26 final size:26
Alignment explanation
Indices: 2657569--2657619 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2657559 TTAATTAAGG
* *
2657569 TTTTTATTTTTAATTAGAATGTAAAA
1 TTTTTAATTTTAATTAAAATGTAAAA
2657595 TTTTTAATTTTAATTTAAAAT-TAAA
1 TTTTTAATTTTAA-TTAAAATGTAAA
2657620 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTTTAATTTTAATTAAAATGTAAAA
Found at i:2657929 original size:17 final size:17
Alignment explanation
Indices: 2657877--2657931 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
2657867 ATACATATAT
2657877 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
*
2657893 T-GAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
2657908 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
2657926 TAAAAT
1 TAAAAT
2657932 ATTTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 5 0.16
16 2 0.06
17 8 0.26
18 7 0.23
19 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:2658369 original size:23 final size:23
Alignment explanation
Indices: 2658341--2658386 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2658331 AAAATTATCG
**
2658341 ATTATTATATTTAATATAATAAT
1 ATTATTATAAATAATATAATAAT
*
2658364 ATTATTATAAATAATATATTAAT
1 ATTATTATAAATAATATAATAAT
2658387 TAATCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATTATAAATAATATAATAAT
Found at i:2659000 original size:13 final size:13
Alignment explanation
Indices: 2658984--2659013 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2658974 TAATATTTTT
*
2658984 TAATAATTATAAA
1 TAATAAATATAAA
2658997 TAATAAATATAAA
1 TAATAAATATAAA
2659010 TAAT
1 TAAT
2659014 TAAAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAATAAATATAAA
Found at i:2660693 original size:34 final size:32
Alignment explanation
Indices: 2660655--2660768 Score: 99
Period size: 34 Copynumber: 3.4 Consensus size: 32
2660645 CCAAATCACC
2660655 CATTTAATCAACAATGTTAAACTACTAAATTTCT
1 CATTTAATCAACAATG-TAAACTACTAAA-TTCT
* * *
2660689 CATTTAGTCAACAATAGCAAA-TCACCAAA-TCAT
1 CATTTAATCAACAAT-GTAAACT-ACTAAATTC-T
*
2660722 CTATTTAATCAATAATGATAAACTACTAAA-TCAT
1 C-ATTTAATCAACAATG-TAAACTACTAAATTC-T
2660756 CATTTAATCAACA
1 CATTTAATCAACA
2660769 CCCTTCACTA
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
32 2 0.03
33 15 0.23
34 47 0.71
35 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (32 bp):
CATTTAATCAACAATGTAAACTACTAAATTCT
Found at i:2660728 original size:68 final size:67
Alignment explanation
Indices: 2660643--2660768 Score: 182
Period size: 68 Copynumber: 1.9 Consensus size: 67
2660633 AATGGTAAGC
* *
2660643 CACCAAATCACCCATTTAATCAACAATGTTAAACTACTAAATTTC-TCATTTAGTCAACAATAGC
1 CACCAAATCACCCATTTAATCAACAATGATAAACTACTAAA--TCATCATTTAATCAACAATAGC
2660707 AAAT
64 AAAT
* * *
2660711 CACCAAATCATCTATTTAATCAATAATGATAAACTACTAAATCATCATTTAATCAACA
1 CACCAAATCACCCATTTAATCAACAATGATAAACTACTAAATCATCATTTAATCAACA
2660769 CCCTTCACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
66 2 0.04
67 13 0.25
68 37 0.71
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.30
Consensus pattern (67 bp):
CACCAAATCACCCATTTAATCAACAATGATAAACTACTAAATCATCATTTAATCAACAATAGCAA
AT
Found at i:2665084 original size:13 final size:13
Alignment explanation
Indices: 2665015--2665092 Score: 56
Period size: 13 Copynumber: 5.9 Consensus size: 13
2665005 AATATAAATT
*
2665015 TTTAAATATATTA
1 TTTAAATTTATTA
2665028 TTTAAATTTATTTTGA
1 TTTAAATTTA--TT-A
*
2665044 TTTTAATTTGATTA
1 TTTAAATTT-ATTA
*
2665058 -GT--A-TTATATA
1 TTTAAATTTAT-TA
2665068 TTTAAATTTATTA
1 TTTAAATTTATTA
2665081 TTTAAATTTATT
1 TTTAAATTTATT
2665093 TTCTTTATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
9 2 0.04
10 4 0.08
11 2 0.04
13 25 0.48
14 5 0.10
15 4 0.08
16 9 0.17
17 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (13 bp):
TTTAAATTTATTA
Found at i:2666345 original size:22 final size:23
Alignment explanation
Indices: 2666294--2666345 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2666284 AGAAATGTGA
2666294 TAAAAAATTTAAAAAAATTTTAT
1 TAAAAAATTTAAAAAAATTTTAT
** *
2666317 T-TTAAATTTAATAAAATTTT-T
1 TAAAAAATTTAAAAAAATTTTAT
2666338 TAAAAAAT
1 TAAAAAAT
2666346 AATTTTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 2 0.09
22 20 0.87
23 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAAAATTTAAAAAAATTTTAT
Found at i:2666351 original size:13 final size:13
Alignment explanation
Indices: 2666335--2666380 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
2666325 TAATAAAATT
2666335 TTTTAAAAAATAA
1 TTTTAAAAAATAA
2666348 TTTTAAAAAATAA
1 TTTTAAAAAATAA
2666361 TTATTATAAATAAT-A
1 TT-TTA-AAA-AATAA
2666376 TTTTA
1 TTTTA
2666381 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 15 0.50
14 6 0.20
15 6 0.20
16 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTTAAAAAATAA
Found at i:2666375 original size:16 final size:15
Alignment explanation
Indices: 2666326--2666381 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
2666316 TTTTAAATTT
*
2666326 AATAA-AATTTTTTA
1 AATAATAATTTTATA
*
2666340 AAAAATAATTTTA-A
1 AATAATAATTTTATA
2666354 AA-AATAATTATTATA
1 AATAATAATT-TTATA
2666369 AATAAT-ATTTTAT
1 AATAATAATTTTAT
2666382 TTTTTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
13 7 0.19
14 14 0.39
15 12 0.33
16 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATAATTTTATA
Found at i:2667470 original size:22 final size:21
Alignment explanation
Indices: 2667443--2667487 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2667433 TTAAATAATT
*
2667443 ATTTAATAATAAATATATTTAA
1 ATTTAATAATAAA-ATATATAA
*
2667465 ATTTAATTATAAAATATATAA
1 ATTTAATAATAAAATATATAA
2667486 AT
1 AT
2667488 ATTAGTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTAATAATAAAATATATAA
Found at i:2669044 original size:20 final size:19
Alignment explanation
Indices: 2669003--2669083 Score: 61
Period size: 22 Copynumber: 4.5 Consensus size: 19
2668993 ATTTACATTG
2669003 TATTATAT-AATTATTATTATA
1 TATTATATAAATT-TTA--ATA
2669024 TATTTATATAAATTTTAATA
1 TA-TTATATAAATTTTAATA
2669044 TATTA-AT-AA-TTT-A-A
1 TATTATATAAATTTTAATA
*
2669058 -ATTATATAAATTTTAAAA
1 TATTATATAAATTTTAATA
2669076 TATT-TATA
1 TATTATATA
2669084 TTATTTTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 19
0.73 0.00 0.27
Matches are distributed among these distances:
13 4 0.08
14 3 0.06
15 3 0.06
16 6 0.12
17 3 0.06
18 7 0.13
19 6 0.12
20 5 0.10
21 2 0.04
22 9 0.17
23 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTATATAAATTTTAATA
Found at i:2669072 original size:16 final size:16
Alignment explanation
Indices: 2669027--2669074 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
2669017 TATTATATAT
2669027 TTATATAAATTTT-AA
1 TTATATAAATTTTAAA
*
2669042 -TATATTAATAATTTAAA
1 TTATA-TAA-ATTTTAAA
2669059 TTATATAAATTTTAAA
1 TTATATAAATTTTAAA
2669075 ATATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 4 0.15
15 3 0.11
16 11 0.41
17 5 0.19
18 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATATAAATTTTAAA
Found at i:2669083 original size:18 final size:18
Alignment explanation
Indices: 2669030--2669083 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
2669020 TATATATTTA
*
2669030 TATAAATTTTAATATATT
1 TATAAATTTTAAAATATT
* *
2669048 AAT-AA-TTT-AAAT-TA
1 TATAAATTTTAAAATATT
2669062 TATAAATTTTAAAATATT
1 TATAAATTTTAAAATATT
2669080 TATA
1 TATA
2669084 TTATTTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
14 3 0.11
15 5 0.19
16 6 0.22
17 6 0.22
18 7 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAATTTTAAAATATT
Found at i:2669439 original size:20 final size:20
Alignment explanation
Indices: 2669414--2669483 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
2669404 AAAATTATAA
2669414 TTAAAATTTTATTTTAAATT
1 TTAAAATTTTATTTTAAATT
* *
2669434 TTAAAATATTA-ATTAAATT
1 TTAAAATTTTATTTTAAATT
* * *
2669453 ATTAAAA-TATATTTAAAATA
1 -TTAAAATTTTATTTTAAATT
*
2669473 ATAAAATTTTA
1 TTAAAATTTTA
2669484 AAGTAATGAT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 14 0.37
20 24 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAAATTTTATTTTAAATT
Found at i:2669468 original size:19 final size:20
Alignment explanation
Indices: 2669413--2669479 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 20
2669403 AAAAATTATA
*
2669413 ATTAAAATTTTATTTTAAATT
1 ATTAAAATATTA-TTTAAATT
*
2669434 -TTAAAATATTAATTAAATT
1 ATTAAAATATTATTTAAATT
*
2669453 ATTAAAATA-TATTTAAAAT
1 ATTAAAATATTATTTAAATT
*
2669472 AATAAAAT
1 ATTAAAAT
2669480 TTTAAAGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 22 0.55
20 18 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTAAAATATTATTTAAATT
Found at i:2670369 original size:29 final size:29
Alignment explanation
Indices: 2670337--2670427 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
2670327 TTATTTTTAA
*
2670337 AAAATAAAAAAATTATTTTTAAAAATTTT
1 AAAATAAAAATATTATTTTTAAAAATTTT
*
2670366 AAAA-ATAAAATATTATTTTTAATAATTATT
1 AAAATA-AAAATATTATTTTTAAAAATT-TT
***
2670396 -TTTTAAAAATA-TATTTTTAAAAAATTTT
1 AAAATAAAAATATTATTTTT-AAAAATTTT
2670424 AAAA
1 AAAA
2670428 ATAACATTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
28 10 0.21
29 35 0.73
30 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAATAAAAATATTATTTTTAAAAATTTT
Found at i:2670420 original size:15 final size:14
Alignment explanation
Indices: 2670372--2670418 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
2670362 TTTTAAAAAT
2670372 AAAATATTATTTTTA
1 AAAATA-TATTTTTA
*
2670387 ATAAT-TATTTTTTA
1 AAAATATA-TTTTTA
2670401 AAAATATATTTTTA
1 AAAATATATTTTTA
2670415 AAAA
1 AAAA
2670419 ATTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 20 0.71
15 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AAAATATATTTTTA
Found at i:2670459 original size:57 final size:56
Alignment explanation
Indices: 2670344--2670459 Score: 128
Period size: 57 Copynumber: 2.1 Consensus size: 56
2670334 TAAAAAATAA
* * * ***
2670344 AAAAATTATTTTTAAAAATTTTAAAAATAAAATATTATTTTTAATAATTATTTTTT
1 AAAAATTATTTTTAAAAATTTTAAAAATAAAATATCATTCTTAATAATAATAAATT
*
2670400 AAAAATATATTTTTAAAAAATTTTAAAAATAACAT-TCATTCTTAAT-ATAACTAAATT
1 AAAAAT-TATTTTT-AAAAATTTTAAAAATAAAATATCATTCTTAATAATAA-TAAATT
2670457 AAA
1 AAA
2670460 GGTGATGTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
56 9 0.18
57 22 0.44
58 19 0.38
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (56 bp):
AAAAATTATTTTTAAAAATTTTAAAAATAAAATATCATTCTTAATAATAATAAATT
Found at i:2670595 original size:23 final size:19
Alignment explanation
Indices: 2670558--2670610 Score: 52
Period size: 24 Copynumber: 2.5 Consensus size: 19
2670548 ATACTGGATG
2670558 TTATTAATATGTTATAATATATA
1 TTATTAA-AT-TTAT-ATAT-TA
2670581 TTTATATAAATTTATATATTA
1 -TTAT-TAAATTTATATATTA
2670602 TTATTAAAT
1 TTATTAAAT
2670611 CGAATGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 5 0.18
20 4 0.14
21 2 0.07
22 4 0.14
23 4 0.14
24 6 0.21
25 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTATTAAATTTATATATTA
Found at i:2673305 original size:2 final size:2
Alignment explanation
Indices: 2673256--2673290 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2673246 TGTGGGATGC
*
2673256 AT AT AT AT AT AT AT AT GT 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 A
2673291 ATTTTACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2674287 original size:20 final size:22
Alignment explanation
Indices: 2674245--2674288 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2674235 AACACTAAAT
*
2674245 TTTAAATAATAATAATTAATTAA
1 TTTAAATAAAAATAATT-ATTAA
2674268 TTTAAATAAAAAT-ATT-TTAA
1 TTTAAATAAAAATAATTATTAA
2674288 T
1 T
2674289 AAATTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAATAAAAATAATTATTAA
Found at i:2674555 original size:48 final size:48
Alignment explanation
Indices: 2674503--2674600 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
2674493 AAGAATATAT
2674503 TTATCTTTTCATTTAAAATTAACTTAAGAATAATAACTTGGGGGTAAA
1 TTATCTTTTCATTTAAAATTAACTTAAGAATAATAACTTGGGGGTAAA
* *
2674551 TTATCTTTTCATTTAAAATTAATTTAAGAATAATAATTTGGGGGTAAA
1 TTATCTTTTCATTTAAAATTAACTTAAGAATAATAACTTGGGGGTAAA
2674599 TT
1 TT
2674601 TATTTTTAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (48 bp):
TTATCTTTTCATTTAAAATTAACTTAAGAATAATAACTTGGGGGTAAA
Found at i:2674687 original size:29 final size:30
Alignment explanation
Indices: 2674626--2674689 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2674616 CTTAAGAGGA
* *
2674626 TAAATAATAATTTTTTAAATATTAAGGGTG
1 TAAATAATAATTTTTTAAAGATAAAGGGTG
*
2674656 TAAAT-ATATTTTTTATAAAGATAAAGGG-G
1 TAAATAATAATTTTT-TAAAGATAAAGGGTG
2674685 TAAAT
1 TAAAT
2674690 GTCTTTTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (30 bp):
TAAATAATAATTTTTTAAAGATAAAGGGTG
Found at i:2675580 original size:20 final size:22
Alignment explanation
Indices: 2675538--2675582 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
2675528 TTGGAAAAGA
*
2675538 AAGAAAAAAAAAAAGAGTGAGAG
1 AAGAAAAAAAAAAAGAG-CAGAG
2675561 AAGAAAAAAAAAAA-A-CAGAG
1 AAGAAAAAAAAAAAGAGCAGAG
2675581 AA
1 AA
2675583 AGAATAGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (22 bp):
AAGAAAAAAAAAAAGAGCAGAG
Found at i:2675586 original size:24 final size:24
Alignment explanation
Indices: 2675533--2675586 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2675523 TGTTGTTGGA
* *
2675533 AAAGAAAGAAAAAAAAAAAGAGTG
1 AAAGAAAGAAAAAAAAAAACAGAG
*
2675557 AGAG-AAGAAAAAAAAAAAACAGAG
1 AAAGAAAG-AAAAAAAAAAACAGAG
2675581 AAAGAA
1 AAAGAA
2675587 TAGAGGGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.12
24 20 0.83
25 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (24 bp):
AAAGAAAGAAAAAAAAAAACAGAG
Found at i:2676692 original size:2 final size:2
Alignment explanation
Indices: 2676685--2676710 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2676675 GATGCGTTAC
2676685 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
2676711 GCGGTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2676932 original size:2 final size:2
Alignment explanation
Indices: 2676925--2676949 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2676915 AGCAATGATC
2676925 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2676950 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2677212 original size:2 final size:2
Alignment explanation
Indices: 2677205--2677244 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2677195 TTGTTATCTC
*
2677205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2677245 TTATGTACTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2679335 original size:17 final size:17
Alignment explanation
Indices: 2679292--2679338 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
2679282 TTTATATAAA
2679292 ATTTTAATA-TATTAAT
1 ATTTTAATATTATTAAT
*
2679308 AATTT-ATATTA-TATAT
1 ATTTTAATATTATTA-AT
2679324 ATTTTAATATTATTA
1 ATTTTAATATTATTA
2679339 TTCTCGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 5 0.20
16 12 0.48
17 6 0.24
18 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTAATATTATTAAT
Found at i:2679349 original size:77 final size:76
Alignment explanation
Indices: 2679220--2679361 Score: 171
Period size: 77 Copynumber: 1.9 Consensus size: 76
2679210 ACTTATTTGA
* * *
2679220 TAATATAATAATTTTTATATTTTTATTATGTTAATATTATTTATTTTATGTTAAGTTATAAATTT
1 TAATATAATAATATTTATATTTATATTATGTTAATATTATTTATTTCATGTTAAGTTATAAATTT
2679285 ATATAAAATTT
66 ATATAAAATTT
* * * * *
2679296 TAATATATTAATAATTTATA-TTATATATATTTTAATATTA-TTATTCTCGTGTTATGTTCTAAA
1 TAATATAATAAT-ATTTATATTTATAT-TATGTTAATATTATTTATT-TCATGTTAAGTTATAAA
2679359 TTT
63 TTT
2679362 CTTTCCGTGT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
76 21 0.38
77 34 0.62
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (76 bp):
TAATATAATAATATTTATATTTATATTATGTTAATATTATTTATTTCATGTTAAGTTATAAATTT
ATATAAAATTT
Found at i:2680898 original size:18 final size:17
Alignment explanation
Indices: 2680865--2680908 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
2680855 TAATAATGTT
2680865 ATTTTATT-AAATAATA
1 ATTTTATTAAAATAATA
*
2680881 TTTTTATTAAAATAAATA
1 ATTTTATTAAAAT-AATA
*
2680899 ATTTAATTAA
1 ATTTTATTAA
2680909 TAATTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTATTAAAATAATA
Found at i:2684030 original size:14 final size:13
Alignment explanation
Indices: 2684007--2684036 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
2683997 GTCACTAATA
2684007 TAAGACCGGATAT
1 TAAGACCGGATAT
2684020 TAAGAACCGGATAT
1 TAAG-ACCGGATAT
2684034 TAA
1 TAA
2684037 ACATGACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.23
Consensus pattern (13 bp):
TAAGACCGGATAT
Found at i:2684304 original size:35 final size:35
Alignment explanation
Indices: 2684237--2684306 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
2684227 AGAATAATAT
* **
2684237 TTATAAATTAAAATAATATATTTATTTAAATATAA
1 TTATAAAATAAAATAATATATAAATTTAAATATAA
*
2684272 TTATAAAATATAATAATATATAAATATT-AATATAA
1 TTATAAAATAAAATAATATATAAAT-TTAAATATAA
2684307 AAATAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 28 0.93
36 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (35 bp):
TTATAAAATAAAATAATATATAAATTTAAATATAA
Found at i:2686189 original size:14 final size:14
Alignment explanation
Indices: 2686170--2686217 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
2686160 AAGTTGGTTA
2686170 AATTTAATTTATTT
1 AATTTAATTTATTT
*
2686184 AATTTAATTGATTT
1 AATTTAATTTATTT
*
2686198 GATTTTAATTTTATTT
1 -AATTTAA-TTTATTT
2686214 AATT
1 AATT
2686218 AAATAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 13 0.46
15 9 0.32
16 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (14 bp):
AATTTAATTTATTT
Found at i:2686244 original size:14 final size:13
Alignment explanation
Indices: 2686172--2686255 Score: 53
Period size: 13 Copynumber: 6.0 Consensus size: 13
2686162 GTTGGTTAAA
*
2686172 TTTAATTTATTTAA
1 TTTAA-TTATTTAT
2686186 TTTAATTGATTTGAT
1 TTTAATT-ATTT-AT
*
2686201 TTTAATTTTATTTAA
1 TTTAA--TTATTTAT
* * *
2686216 TTAAATAATTAAT
1 TTTAATTATTTAT
2686229 TTTAATGTATTTAT
1 TTTAAT-TATTTAT
2686243 TTT-ATTAGTTTAT
1 TTTAATTA-TTTAT
2686256 ATTTTTATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
12 2 0.04
13 19 0.35
14 17 0.31
15 11 0.20
16 4 0.07
17 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (13 bp):
TTTAATTATTTAT
Found at i:2689770 original size:22 final size:21
Alignment explanation
Indices: 2689745--2689794 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2689735 GGTTCAAAAA
* * *
2689745 ATAAAATTATTTATATTATTAT
1 ATAAAATTAATTACA-TAATAT
*
2689767 ATAAAAATAATTACATAATAT
1 ATAAAATTAATTACATAATAT
2689788 ATAAAAT
1 ATAAAAT
2689795 AAAAGATATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAATTAATTACATAATAT
Found at i:2689836 original size:27 final size:25
Alignment explanation
Indices: 2689800--2689870 Score: 65
Period size: 27 Copynumber: 2.8 Consensus size: 25
2689790 AAAATAAAAG
2689800 ATATATTAAATTATATAAGTTTAAATT
1 ATATA-TAAATTATATAA-TTTAAATT
* * *
2689827 ATTATATAAATATATTTTATTTATATT
1 A-TATATAAAT-TATATAATTTAAATT
2689854 ATATATAAA--ATATAATT
1 ATATATAAATTATATAATT
2689871 AAAAATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
23 6 0.16
26 8 0.22
27 14 0.38
28 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
ATATATAAATTATATAATTTAAATT
Found at i:2694236 original size:17 final size:17
Alignment explanation
Indices: 2694210--2694243 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2694200 AAAATTAAGT
2694210 ATATTCATATTAAATAC
1 ATATTCATATTAAATAC
* *
2694227 ATATTTATATTTAATAC
1 ATATTCATATTAAATAC
2694244 TTAATCTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTCATATTAAATAC
Found at i:2694616 original size:27 final size:25
Alignment explanation
Indices: 2694560--2694681 Score: 75
Period size: 26 Copynumber: 4.6 Consensus size: 25
2694550 ATTATACAAG
* *
2694560 TAAAATAATTAAAATAATATAATTA
1 TAAAATAAATAAAATAATATAAATA
*
2694585 AAAAATAACATAAATATAATATAAATA
1 TAAAATAA-ATAAA-ATAATATAAATA
* * ** * *
2694612 TAAAAATATATTAAATTCTTTGACATA
1 T-AAAATAAATAAAATAATAT-AAATA
*
2694639 TTAAATAAATTAAAAATAATAT-AATA
1 TAAAATAAA-T-AAAATAATATAAATA
2694665 TAAAATAATATACAAAT
1 TAAAATAA-ATA-AAAT
2694682 TATGCTAAAA
Statistics
Matches: 71, Mismatches: 18, Indels: 15
0.68 0.17 0.14
Matches are distributed among these distances:
25 8 0.11
26 29 0.41
27 22 0.31
28 12 0.17
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (25 bp):
TAAAATAAATAAAATAATATAAATA
Found at i:2695057 original size:21 final size:21
Alignment explanation
Indices: 2695032--2695073 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2695022 CTTGTCATTC
*
2695032 TTTAAA-ATTAAATATGATAAT
1 TTTAAATATAAAATAT-ATAAT
2695053 TTTAAATATAAAATATATAAT
1 TTTAAATATAAAATATATAAT
2695074 ATAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTAAATATAAAATATATAAT
Found at i:2695094 original size:36 final size:38
Alignment explanation
Indices: 2695040--2695115 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 38
2695030 TCTTTAAAAT
*
2695040 TAAATATGATAAT-TTTAAA-TATA-AAATATATAATA
1 TAAATATGATAATATTAAAATTATATAAATATATAATA
*
2695075 TAAATTATTATAATATTAAAATTTATATAAATATATAATA
1 TAAA-TATGATAATATTAAAA-TTATATAAATATATAATA
2695115 T
1 T
2695116 TTTAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 4 0.12
36 8 0.24
37 5 0.15
39 4 0.12
40 13 0.38
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (38 bp):
TAAATATGATAATATTAAAATTATATAAATATATAATA
Found at i:2695100 original size:15 final size:14
Alignment explanation
Indices: 2695053--2695101 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
2695043 ATATGATAAT
2695053 TTTA-AATATAAAA
1 TTTATAATATAAAA
* *
2695066 TATATAATATAAAT
1 TTTATAATATAAAA
2695080 TATTATAATATTAAAA
1 T-TTATAATA-TAAAA
2695096 TTTATA
1 TTTATA
2695102 TAAATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 3 0.10
14 9 0.31
15 12 0.41
16 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTATAATATAAAA
Found at i:2695103 original size:17 final size:14
Alignment explanation
Indices: 2695057--2695115 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
2695047 GATAATTTTA
*
2695057 AATATAAAATATAT
1 AATATAAATTATAT
2695071 AATATAAATTATTAT
1 AATATAAATTA-TAT
2695086 AATATTAAA--AT-T
1 AATA-TAAATTATAT
*
2695098 TATATAAA-TATAT
1 AATATAAATTATAT
2695111 AATAT
1 AATAT
2695116 TTTAAATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.11
12 6 0.16
13 6 0.16
14 11 0.29
15 7 0.18
16 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATAAATTATAT
Found at i:2695123 original size:16 final size:18
Alignment explanation
Indices: 2695067--2695139 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 18
2695057 AATATAAAAT
*
2695067 ATATAATATAAATTATTATA
1 ATATAATA-ATATTATTA-A
2695087 ATATTAA-AAT-TTATATAA
1 ATA-TAATAATATTAT-TAA
2695105 ATAT-ATAATATT-TTAA
1 ATATAATAATATTATTAA
*
2695121 ATATAATTATATTATTAA
1 ATATAATAATATTATTAA
2695139 A
1 A
2695140 AATCTTTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
16 8 0.18
17 12 0.27
18 15 0.33
19 3 0.07
20 4 0.09
21 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATAATAATATTATTAA
Found at i:2695449 original size:17 final size:18
Alignment explanation
Indices: 2695418--2695491 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 18
2695408 TTAATATAAA
2695418 TTTTATATC-ATTT-TAAT
1 TTTTATATCTATTTAT-AT
2695435 TTTTATATCTATTTATAT
1 TTTTATATCTATTTATAT
**
2695453 TAAATATATCTATTTATAT
1 T-TTTATATCTATTTATAT
** *
2695472 TAAATATATCAATTTATAT
1 T-TTTATATCTATTTATAT
2695491 T
1 T
2695492 AATTAATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
17 9 0.18
18 7 0.14
19 35 0.69
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATATCTATTTATAT
Found at i:2695462 original size:19 final size:19
Alignment explanation
Indices: 2695438--2695493 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
2695428 TTTTAATTTT
2695438 TATATCTATTTATATTAAA
1 TATATCTATTTATATTAAA
2695457 TATATCTATTTATATTAAA
1 TATATCTATTTATATTAAA
*
2695476 TATATCAATTTATATTAA
1 TATATCTATTTATATTAA
2695494 TTAATATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TATATCTATTTATATTAAA
Found at i:2695495 original size:10 final size:10
Alignment explanation
Indices: 2695436--2695511 Score: 61
Period size: 10 Copynumber: 7.8 Consensus size: 10
2695426 CATTTTAATT
2695436 TTTATATCT-A
1 TTTATAT-TAA
2695446 TTTATATTAA
1 TTTATATTAA
*
2695456 -ATATATCT-A
1 TTTATAT-TAA
2695465 TTTATATTAA
1 TTTATATTAA
* *
2695475 -ATATATCAA
1 TTTATATTAA
2695484 TTTATATTAA
1 TTTATATTAA
*
2695494 TTAATATTAA
1 TTTATATTAA
*
2695504 TATATATT
1 TTTATATT
2695512 GATTCGTATC
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
9 15 0.29
10 37 0.71
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTATATTAA
Found at i:2695509 original size:20 final size:19
Alignment explanation
Indices: 2695438--2695511 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
2695428 TTTTAATTTT
* *
2695438 TATATCTATTTATATTAAA
1 TATATCAATATATATTAAA
* *
2695457 TATATCTATTTATATTAAA
1 TATATCAATATATATTAAA
* *
2695476 TATATCAATTTATATTAAT
1 TATATCAATATATATTAAA
*
2695495 TAATATTAATATATATT
1 T-ATATCAATATATATT
2695512 GATTCGTATC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 37 0.74
20 13 0.26
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATCAATATATATTAAA
Found at i:2695772 original size:17 final size:17
Alignment explanation
Indices: 2695733--2695764 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2695723 CGTTTAAAAA
2695733 TTTTTATTTTTAAATTC
1 TTTTTATTTTTAAATTC
2695750 TTTTTA-TTTTAAATT
1 TTTTTATTTTTAAATT
2695765 TATATTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATTTTTAAATTC
Found at i:2696654 original size:12 final size:12
Alignment explanation
Indices: 2696637--2696662 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2696627 AAAATTAATA
2696637 AAAATAATAAAT
1 AAAATAATAAAT
2696649 AAAATAATAAAT
1 AAAATAATAAAT
2696661 AA
1 AA
2696663 TTATATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:2696697 original size:16 final size:17
Alignment explanation
Indices: 2696653--2696707 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 17
2696643 ATAAATAAAA
2696653 TAATAAATAATTATATT
1 TAATAAATAATTATATT
*
2696670 TAATAAAAAATTAT-TT
1 TAATAAATAATTATATT
*
2696686 TTATAAATAATT-TATT
1 TAATAAATAATTATATT
*
2696702 AAATAA
1 TAATAA
2696708 CATTAAAGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 1 0.03
16 18 0.56
17 13 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATAAATAATTATATT
Found at i:2699895 original size:24 final size:24
Alignment explanation
Indices: 2699851--2699897 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
2699841 AATGACATAT
*
2699851 TTTTTATTTTTTATATTTTATAAAA
1 TTTTCATTTTTTATA-TTTATAAAA
2699876 TTTTCATTATTTTATA-TTATAA
1 TTTTCATT-TTTTATATTTATAA
2699898 TTATATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 7 0.35
26 7 0.35
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTCATTTTTTATATTTATAAAA
Found at i:2699971 original size:2 final size:2
Alignment explanation
Indices: 2699964--2699995 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2699954 TAAACCATAA
2699964 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
2699996 GGTAGCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2703369 original size:24 final size:24
Alignment explanation
Indices: 2703317--2703372 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
2703307 AAGCAACCCT
*
2703317 ATTATATTCATATTTTTTATCATA
1 ATTATATTCATATTTTTTATAATA
*
2703341 TTTATATT-AT-TTTTATATATAATA
1 ATTATATTCATATTTT-T-TATAATA
2703365 ATTATATT
1 ATTATATT
2703373 TAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 3 0.11
24 20 0.74
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTATATTCATATTTTTTATAATA
Found at i:2703384 original size:14 final size:15
Alignment explanation
Indices: 2703365--2703397 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2703355 ATATATAATA
2703365 ATTATAT-TTAAAAT
1 ATTATATGTTAAAAT
2703379 ATTATATGTTAAAAT
1 ATTATATGTTAAAAT
2703394 -TTAT
1 ATTAT
2703398 GTTATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTATATGTTAAAAT
Found at i:2704632 original size:29 final size:29
Alignment explanation
Indices: 2704600--2704656 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2704590 TTAAAATATT
* *
2704600 ATATATTTATACATGTTAT-TTATATTTTG
1 ATATATCTATACAT-TTATATCATATTTTG
*
2704629 ATATATCTATATATTTATATCATATTTT
1 ATATATCTATACATTTATATCATATTTT
2704657 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (29 bp):
ATATATCTATACATTTATATCATATTTTG
Found at i:2704679 original size:37 final size:37
Alignment explanation
Indices: 2704566--2704679 Score: 85
Period size: 37 Copynumber: 3.1 Consensus size: 37
2704556 GTATTCATAT
* *
2704566 TATTTTTACATATTA-TAATTATATTT-A-AAATATTATA
1 TATTTATACATATTATTAA-TAT-TTTGATATATATT-TA
* * * *
2704603 TATTTATACATGTTATTTATATTTTGATATATCTATA
1 TATTTATACATATTATTAATATTTTGATATATATTTA
*
2704640 TATTTATATCATATT-TTAAT-TTTTTATATCATATTTA
1 TATTTATA-CATATTATTAATATTTTGATAT-ATATTTA
2704677 TAT
1 TAT
2704680 CAATATAATT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
36 11 0.18
37 39 0.64
38 11 0.18
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (37 bp):
TATTTATACATATTATTAATATTTTGATATATATTTA
Found at i:2705362 original size:32 final size:33
Alignment explanation
Indices: 2705301--2705370 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
2705291 ATTTTAGATA
*
2705301 TAATAAAAAAATATAAAATAAATATGATATTTT
1 TAATAAAAAAATATAAAATAAATATGATATATT
*
2705334 TAATAATAAAAA-ATAATAT-AATATGATATATT
1 TAATAA-AAAAATATAAAATAAATATGATATATT
2705366 TAATA
1 TAATA
2705371 TTTTTATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 17 0.50
33 12 0.35
34 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (33 bp):
TAATAAAAAAATATAAAATAAATATGATATATT
Found at i:2706177 original size:25 final size:24
Alignment explanation
Indices: 2706149--2706200 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
2706139 ATTACATTAT
* *
2706149 TATATGTAAATTTTTAAATTTTTTA
1 TATATGTAAAATATTAAATT-TTTA
* *
2706174 TATATTTAAAATATTATATTTTTA
1 TATATGTAAAATATTAAATTTTTA
2706198 TAT
1 TAT
2706201 TATTTATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TATATGTAAAATATTAAATTTTTA
Found at i:2706465 original size:2 final size:2
Alignment explanation
Indices: 2706446--2706484 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2706436 CAACCAAGTT
* *
2706446 TA TA TG TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2706485 TTGAATGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2707491 original size:14 final size:15
Alignment explanation
Indices: 2707455--2707498 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2707445 TTAAAAAATA
*
2707455 AAATTTAATAATTTT
1 AAATTTTATAATTTT
2707470 AAATTTTA-AATTTT
1 AAATTTTATAATTTT
2707484 -AATATTTATAATTTT
1 AAAT-TTTATAATTTT
2707499 TTTTATTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 3 0.12
14 10 0.38
15 13 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATTTTATAATTTT
Found at i:2707754 original size:31 final size:31
Alignment explanation
Indices: 2707682--2707754 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
2707672 TAAATTGTGA
* *
2707682 ATAAATTAAAAATATTTAATTATTTATTTAT
1 ATAAATTAAAAATATCTAATTATTTATTAAT
*
2707713 ACAAATTAAAAATATCTAATTATTTATTAAAT
1 ATAAATTAAAAATATCTAATTATTTATT-AAT
2707745 ATAAA-TAAAA
1 ATAAATTAAAA
2707755 GTAAAAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 31 0.84
32 6 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (31 bp):
ATAAATTAAAAATATCTAATTATTTATTAAT
Found at i:2708554 original size:2 final size:2
Alignment explanation
Indices: 2708547--2708573 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2708537 TGGTGATAGC
2708547 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2708574 TTGCTTTTGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2710394 original size:41 final size:41
Alignment explanation
Indices: 2710327--2710425 Score: 171
Period size: 41 Copynumber: 2.4 Consensus size: 41
2710317 CATTTTCTTG
2710327 TTTTATGCAAAAAAAAAAAAAGAAATTTCAAACTTCATATATA
1 TTTTATGC--AAAAAAAAAAAGAAATTTCAAACTTCATATATA
*
2710370 TTTTATGCAAAAAAAAAAAGAAATTTCAAACTTCATATATG
1 TTTTATGCAAAAAAAAAAAGAAATTTCAAACTTCATATATA
2710411 TTTTATGCAAAAAAA
1 TTTTATGCAAAAAAA
2710426 GACAAATTTG
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
41 47 0.85
43 8 0.15
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (41 bp):
TTTTATGCAAAAAAAAAAAGAAATTTCAAACTTCATATATA
Done.