Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 16 of 19
Found at i:2353800 original size:24 final size:24
Alignment explanation
Indices: 2353755--2353800 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2353745 ATAATAATAA
*
2353755 TTTTAATTAAAATAATATATATTT
1 TTTTAATTAAAATAATAAATATTT
* * *
2353779 TTTTAATTTAATTATTAAATAT
1 TTTTAATTAAAATAATAAATAT
2353801 AAAAATATTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAATTAAAATAATAAATATTT
Found at i:2353815 original size:14 final size:15
Alignment explanation
Indices: 2353791--2353821 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2353781 TTAATTTAAT
2353791 TATTAAATATAAAAA
1 TATTAAATATAAAAA
2353806 TATT-AATATAAAAA
1 TATTAAATATAAAAA
2353820 TA
1 TA
2353822 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TATTAAATATAAAAA
Found at i:2354690 original size:18 final size:16
Alignment explanation
Indices: 2354650--2354703 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2354640 ATTTTATAAT
2354650 TATATA-AATTTTA-A
1 TATATATAATTTTAGA
* *
2354664 TATGT-TAATAATTTATA
1 TATATATAAT--TTTAGA
2354681 TATATATAATTTTAGA
1 TATATATAATTTTAGA
2354697 TATATAT
1 TATATAT
2354704 TCATATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 7 0.22
16 16 0.50
17 5 0.16
18 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (16 bp):
TATATATAATTTTAGA
Found at i:2354963 original size:17 final size:16
Alignment explanation
Indices: 2354943--2354996 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
2354933 CAAATGAAAA
2354943 ATAAATTAAAATATAAT
1 ATAAA-TAAAATATAAT
*
2354960 ATAAGATAAAAAATAAT
1 ATAA-ATAAAATATAAT
* *
2354977 ATGAATATAATATAAAT
1 ATAAATAAAATAT-AAT
2354994 ATA
1 ATA
2354997 TTATTACAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 7 0.23
17 22 0.73
18 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (16 bp):
ATAAATAAAATATAAT
Found at i:2355250 original size:15 final size:16
Alignment explanation
Indices: 2355223--2355287 Score: 64
Period size: 15 Copynumber: 4.2 Consensus size: 16
2355213 TCTGTTTATG
*
2355223 TTATAGTTA-TATATT
1 TTATATTTATTATATT
*
2355238 TTAT-TTTATTATA-A
1 TTATATTTATTATATT
*
2355252 TTATATTTAATATATT
1 TTATATTTATTATATT
*
2355268 TTATATTTATATAAATT
1 TTATATTTAT-TATATT
2355285 TTA
1 TTA
2355288 ATACATTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 7 0.17
15 16 0.40
16 9 0.22
17 8 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTATATTTATTATATT
Found at i:2355265 original size:9 final size:8
Alignment explanation
Indices: 2355224--2355280 Score: 50
Period size: 8 Copynumber: 7.5 Consensus size: 8
2355214 CTGTTTATGT
*
2355224 TATAGTTA
1 TATATTTA
2355232 TATATTT-
1 TATATTTA
2355239 TAT-TTTA
1 TATATTTA
*
2355246 TTATAATTA
1 -TATATTTA
*
2355255 TAT-TTAA
1 TATATTTA
2355262 TATATTT-
1 TATATTTA
2355269 TATATTTA
1 TATATTTA
2355277 TATA
1 TATA
2355281 AATTTTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
6 3 0.08
7 15 0.38
8 18 0.46
9 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (8 bp):
TATATTTA
Found at i:2355267 original size:30 final size:29
Alignment explanation
Indices: 2355223--2355281 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
2355213 TCTGTTTATG
2355223 TTATAGTTATATATTTTAT-TTTATTATAA
1 TTATAGTTATATATTTTATATTTA-TATAA
*
2355252 TTATATTTAATATATTTTATATTTATATAA
1 TTATAGTT-ATATATTTTATATTTATATAA
2355282 ATTTTAATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.26
30 16 0.59
31 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTATAGTTATATATTTTATATTTATATAA
Found at i:2355785 original size:12 final size:12
Alignment explanation
Indices: 2355768--2355794 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2355758 AATGTCATGT
2355768 TAATATTTAAAA
1 TAATATTTAAAA
2355780 TAATATTTAAAA
1 TAATATTTAAAA
2355792 TAA
1 TAA
2355795 CACGTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATATTTAAAA
Found at i:2357516 original size:13 final size:13
Alignment explanation
Indices: 2357498--2357524 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2357488 TGATCTAAGT
2357498 TACTCAAATACGA
1 TACTCAAATACGA
2357511 TACTCAAATACGA
1 TACTCAAATACGA
2357524 T
1 T
2357525 TGTGAGTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (13 bp):
TACTCAAATACGA
Found at i:2358768 original size:3 final size:3
Alignment explanation
Indices: 2358760--2358789 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2358750 ACCAGCTAAA
2358760 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2358790 AATACTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2359721 original size:24 final size:24
Alignment explanation
Indices: 2359691--2359738 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2359681 TTCAGGATTG
2359691 TTCTTTGATTCTTGGAATTTTGAC
1 TTCTTTGATTCTTGGAATTTTGAC
2359715 TTCTTTGATTCTTGGAATTTTGAC
1 TTCTTTGATTCTTGGAATTTTGAC
2359739 AAGAGAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (24 bp):
TTCTTTGATTCTTGGAATTTTGAC
Found at i:2368729 original size:11 final size:10
Alignment explanation
Indices: 2368703--2368736 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2368693 TAATAAAATA
*
2368703 AAAGAAAAAG
1 AAAGAAGAAG
2368713 AAAGAAGAAG
1 AAAGAAGAAG
2368723 AAGAGAAGAAG
1 AA-AGAAGAAG
2368734 AAA
1 AAA
2368737 AGAACCACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAGAAGAAG
Found at i:2368740 original size:11 final size:11
Alignment explanation
Indices: 2368702--2368740 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2368692 ATAATAAAAT
*
2368702 AAAAGAAAAAG
1 AAAAGAAGAAG
2368713 -AAAGAAGAAG
1 AAAAGAAGAAG
*
2368723 AAGAGAAGAAG
1 AAAAGAAGAAG
2368734 AAAAGAA
1 AAAAGAA
2368741 CCACCGCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:2368951 original size:10 final size:10
Alignment explanation
Indices: 2368935--2368989 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 10
2368925 TATTTTATTT
2368935 ATATATTTTA
1 ATATATTTTA
* *
2368945 TTATATTATA
1 ATATATTTTA
2368955 ATATA-TTTA
1 ATATATTTTA
*
2368964 AAATATTTT-
1 ATATATTTTA
*
2368973 ATAAATTTTA
1 ATATATTTTA
2368983 ATATATT
1 ATATATT
2368990 AATAATTTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
9 14 0.40
10 21 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATATTTTA
Found at i:2368994 original size:18 final size:18
Alignment explanation
Indices: 2368939--2369012 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
2368929 TTATTTATAT
*
2368939 ATTTTATTATATT-ATAA
1 ATTTTAATATATTAATAA
* *
2368956 TATATTTAAAATATTTTATAA
1 -AT-TTTAATATA-TTAATAA
2368977 ATTTTAATATATTAAT-A
1 ATTTTAATATATTAATAA
* *
2368994 ATTTAAATTATATAAATAA
1 ATTTTAA-TATATTAATAA
2369013 TAAAATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.16
18 14 0.31
19 16 0.36
20 4 0.09
21 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTAATATATTAATAA
Found at i:2369087 original size:18 final size:18
Alignment explanation
Indices: 2368919--2369088 Score: 52
Period size: 19 Copynumber: 9.2 Consensus size: 18
2368909 GAGTGTTTTT
*
2368919 TATTTATATTTTATTTATA
1 TATTTATATTATATTTA-A
2368938 TATTT-TATTATATTATAA
1 TATTTATATTATATT-TAA
**
2368956 TATATT-TAAAATATTTTATA
1 TAT-TTATATTATA-TTTA-A
* *
2368976 AATTT-TAATATA-TTAA
1 TATTTATATTATATTTAA
*
2368992 TAATTTAAATTATA--TAA
1 T-ATTTATATTATATTTAA
* ** *
2369009 -A-TAATAAAATTTTTATA
1 TATTTATATTATATTTA-A
2369026 TATTTATATTATA-TTAA
1 TATTTATATTATATTTAA
* *
2369043 TATTCATATTATTTTACTTGATCA
1 TATT--TA-TATTATA-TT--TAA
2369067 TATTTATATTATATTTAA
1 TATTTATATTATATTTAA
2369085 TATT
1 TATT
2369089 ATGAGATTTA
Statistics
Matches: 112, Mismatches: 21, Indels: 37
0.66 0.12 0.22
Matches are distributed among these distances:
14 5 0.04
15 1 0.01
16 3 0.03
17 16 0.14
18 27 0.24
19 32 0.29
20 13 0.12
21 6 0.05
22 3 0.03
24 6 0.05
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (18 bp):
TATTTATATTATATTTAA
Found at i:2369089 original size:12 final size:11
Alignment explanation
Indices: 2368917--2369090 Score: 53
Period size: 11 Copynumber: 15.9 Consensus size: 11
2368907 TTGAGTGTTT
2368917 TTTAT-TTATA
1 TTTATATTATA
2368927 TTT-TATTTATA
1 TTTATA-TTATA
*
2368938 TATTTTATTATA
1 T-TTATATTATA
*
2368950 -TTATAATATA
1 TTTATATTATA
* *
2368960 TTTAAAATAT-
1 TTTATATTATA
*
2368970 TTTATAAATTTTA
1 TTTAT--ATTATA
*
2368983 -ATATATTAATAA
1 TTTATATT-AT-A
*
2368995 TTTAAATTATA
1 TTTATATTATA
** * *
2369006 TAAATAATAAAA
1 TTTAT-ATTATA
*
2369018 TTTTTA-TATA
1 TTTATATTATA
2369028 TTTATATTATA
1 TTTATATTATA
*
2369039 TTAATATTCATA
1 TTTATATT-ATA
2369051 -TTAT-TT-TA
1 TTTATATTATA
* * *
2369059 CTT-GATCATA
1 TTTATATTATA
2369069 TTTATATTATA
1 TTTATATTATA
2369080 TTTAATATTAT
1 TTT-ATATTAT
2369091 GAGATTTACA
Statistics
Matches: 117, Mismatches: 28, Indels: 36
0.65 0.15 0.20
Matches are distributed among these distances:
8 2 0.02
9 4 0.03
10 31 0.26
11 41 0.35
12 32 0.27
13 7 0.06
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.57
Consensus pattern (11 bp):
TTTATATTATA
Found at i:2369111 original size:41 final size:40
Alignment explanation
Indices: 2369023--2369113 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 40
2369013 TAAAATTTTT
* *
2369023 ATATATTTATATTATATTAATATTCATATTATTTTACTTG
1 ATATATTTATATTATATTAATATTCATATGATTTTACTTA
2369063 ATCATATTTATATTATATTTAATATT-ATGA-GA-TTTACATTTA
1 AT-ATATTTATATTATA-TTAATATTCAT-ATGATTTTAC--TTA
2369105 ATATATTTA
1 ATATATTTA
2369114 AAATATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
40 7 0.16
41 24 0.55
42 13 0.30
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (40 bp):
ATATATTTATATTATATTAATATTCATATGATTTTACTTA
Found at i:2369285 original size:14 final size:14
Alignment explanation
Indices: 2369266--2369305 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 14
2369256 AAAATTTTAA
2369266 TATATTTAATAATT
1 TATATTTAATAATT
2369280 TATA-TT--TAATT
1 TATATTTAATAATT
2369291 TATATTTAAATAATT
1 TATATTT-AATAATT
2369306 AATAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.41
12 2 0.09
13 2 0.09
14 4 0.18
15 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATTTAATAATT
Found at i:2369567 original size:16 final size:17
Alignment explanation
Indices: 2369541--2369574 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2369531 AATTTAACTT
2369541 TTTATTTTAAATAAAAA
1 TTTATTTTAAATAAAAA
*
2369558 TTTA-TTTAAATATAAA
1 TTTATTTTAAATAAAAA
2369574 T
1 T
2369575 AAAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTATTTTAAATAAAAA
Found at i:2369610 original size:27 final size:28
Alignment explanation
Indices: 2369549--2369612 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 28
2369539 TTTTTATTTT
*
2369549 AAATA-AAAATTTATTTAAATATAAATA
1 AAATATAAAACTTATTTAAATATAAATA
*
2369576 AAAAATAAAACTTATTTAAATAT-AATA
1 AAATATAAAACTTATTTAAATATAAATA
2369603 AAATATAAAA
1 AAATATAAAA
2369613 ATTTATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 17 0.52
28 16 0.48
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
AAATATAAAACTTATTTAAATATAAATA
Found at i:2369613 original size:28 final size:29
Alignment explanation
Indices: 2369549--2369649 Score: 113
Period size: 28 Copynumber: 3.6 Consensus size: 29
2369539 TTTTTATTTT
2369549 AAATAAAAATTTATTTAAATATAAATAAA
1 AAATAAAAATTTATTTAAATATAAATAAA
*
2369578 AAAT-AAAACTTATTTAAATAT-AATAAA
1 AAATAAAAATTTATTTAAATATAAATAAA
* *
2369605 ATATAAAAATTTATTTTTAA-A-AAATAAA
1 AAATAAAAATTTA-TTTAAATATAAATAAA
**
2369633 AAATCTAAATTT-TTTAA
1 AAATAAAAATTTATTTAA
2369650 TATTTTATCT
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
26 4 0.07
27 9 0.15
28 39 0.64
29 9 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATAAAAATTTATTTAAATATAAATAAA
Found at i:2369645 original size:23 final size:23
Alignment explanation
Indices: 2369602--2369645 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2369592 TAAATATAAT
* *
2369602 AAAATATAAAAATTTATTTTTAA
1 AAAATATAAAAATTAAATTTTAA
2369625 AAAATA-AAAAATCTAAATTTT
1 AAAATATAAAAAT-TAAATTTT
2369646 TTAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAATATAAAAATTAAATTTTAA
Found at i:2369839 original size:10 final size:10
Alignment explanation
Indices: 2369809--2369871 Score: 76
Period size: 10 Copynumber: 6.4 Consensus size: 10
2369799 TTTGATGTCG
2369809 TATT-ATTTA
1 TATTAATTTA
*
2369818 TATCAA-TTA
1 TATTAATTTA
2369827 TATTAATTTA
1 TATTAATTTA
*
2369837 TATGAATTTA
1 TATTAATTTA
2369847 TATTAATTTA
1 TATTAATTTA
*
2369857 TATATAATATA
1 TAT-TAATTTA
2369868 TATT
1 TATT
2369872 GATATAAGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
9 11 0.24
10 26 0.57
11 9 0.20
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (10 bp):
TATTAATTTA
Found at i:2369846 original size:29 final size:31
Alignment explanation
Indices: 2369813--2369870 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
2369803 ATGTCGTATT
*
2369813 ATTTATATCAA-TTATAT-TAATTTATATGA
1 ATTTATATCAATTTATATATAATATATATGA
*
2369842 ATTTATATTAATTTATATATAATATATAT
1 ATTTATATCAATTTATATATAATATATAT
2369871 TGATATAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 6 0.24
31 9 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (31 bp):
ATTTATATCAATTTATATATAATATATATGA
Found at i:2370774 original size:30 final size:30
Alignment explanation
Indices: 2370731--2370800 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
2370721 TTCTAAAAAA
2370731 AATATAA-AAAATAAAATCAATTAA-AATAT
1 AATATAATAAAATAAAATCAA-TAATAATAT
*
2370760 AATATAATAAAATAAGATCAATAATAATAT
1 AATATAATAAAATAAAATCAATAATAATAT
2370790 AA-ATATATAAA
1 AATATA-ATAAA
2370801 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 13 0.35
30 24 0.65
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (30 bp):
AATATAATAAAATAAAATCAATAATAATAT
Found at i:2370841 original size:30 final size:30
Alignment explanation
Indices: 2370779--2370857 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
2370769 AAATAAGATC
*
2370779 AATAATAATATAAATATATAAATATTTTAA
1 AATAATAATATAAATATATAAATATATTAA
* *
2370809 AATATATAATATAAAT-TATTAATCTATTAA
1 AATA-ATAATATAAATATATAAATATATTAA
2370839 AAT-A-AATATAAATATATAA
1 AATAATAATATAAATATATAA
2370858 CTTTTTATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
27 9 0.21
28 5 0.12
30 18 0.42
31 11 0.26
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (30 bp):
AATAATAATATAAATATATAAATATATTAA
Found at i:2370904 original size:11 final size:10
Alignment explanation
Indices: 2370883--2370908 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2370873 TATCACATTT
2370883 AAAATAAAAA
1 AAAATAAAAA
2370893 AAAATAAAAA
1 AAAATAAAAA
2370903 AAAATA
1 AAAATA
2370909 CAGATTACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:2372517 original size:27 final size:28
Alignment explanation
Indices: 2372401--2372515 Score: 99
Period size: 29 Copynumber: 4.0 Consensus size: 28
2372391 AACTAAAATA
*
2372401 ATAATAATTTAAAAAATAAATATATTTTT
1 ATAAAAATTT-AAAAATAAATATATTTTT
* * *
2372430 GTCAAACTTTAAAATATAAATAAATATTTTT
1 ATAAAAATTTAAAA-ATAAAT--ATATTTTT
* *
2372461 -TAAATA-TTAATAAAAAAATATATTTTTT
1 ATAAAAATTTAA-AAATAAATATA-TTTTT
*
2372489 ATAAAAATTTAAAAATAAGTATATTTT
1 ATAAAAATTTAAAAATAAATATATTTT
2372516 ATCCTATTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
27 3 0.04
28 13 0.19
29 35 0.51
30 9 0.13
31 8 0.12
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
ATAAAAATTTAAAAATAAATATATTTTT
Found at i:2375989 original size:16 final size:16
Alignment explanation
Indices: 2375968--2375999 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2375958 AATTATATTA
*
2375968 AAATTCTTGAATTGTT
1 AAATTCCTGAATTGTT
2375984 AAATTCCTGAATTGTT
1 AAATTCCTGAATTGTT
2376000 TACCTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (16 bp):
AAATTCCTGAATTGTT
Found at i:2376511 original size:50 final size:50
Alignment explanation
Indices: 2376436--2376537 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
2376426 AATTTAAAAC
2376436 TGTTAATAATAATAACCCAACATTTAAATTGTGATCAGTGGATATGTCTT
1 TGTTAATAATAATAACCCAACATTTAAATTGTGATCAGTGGATATGTCTT
2376486 TGTTAATAATAATAACCCAACATTTAAATTGTGATCAGTGGATATGTCTT
1 TGTTAATAATAATAACCCAACATTTAAATTGTGATCAGTGGATATGTCTT
2376536 TG
1 TG
2376538 ATATATTATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (50 bp):
TGTTAATAATAATAACCCAACATTTAAATTGTGATCAGTGGATATGTCTT
Found at i:2376634 original size:2 final size:2
Alignment explanation
Indices: 2376627--2376655 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2376617 ATATTCTTGT
2376627 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2376656 TTTCTTTTAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2378722 original size:125 final size:124
Alignment explanation
Indices: 2378541--2378788 Score: 435
Period size: 125 Copynumber: 2.0 Consensus size: 124
2378531 CCCTGCAAAC
* *
2378541 AATGATCAGATTGTTAACAGAGAATGCCAATAGGAAGAAGAAAGAAAAAAAGCTAATAGCTTGAT
1 AATGATCAGATTATTAACAGACAATGCCAATAGGAAGAAGAAAGAAAAAAAGCTAATAGCTTGAT
2378606 TTAAACACAAAACAATAAAAAAAATGAAGATGCACCTTCGCAAAAAGACAGAACGAAAAT
66 TTAAACACAAAACAAT-AAAAAAATGAAGATGCACCTTCGCAAAAAGACAGAACGAAAAT
*
2378666 AATGATCAGATTATTAACAGACAATGCCAATAGGAAGAAGAAA-AAAAAACATCTAATAGCTTGA
1 AATGATCAGATTATTAACAGACAATGCCAATAGGAAGAAGAAAGAAAAAA-AGCTAATAGCTTGA
*
2378730 TTTAAACACAAAACAATAAAAAAATGAAGATGCACTTTCGCAAAAAGACAGAACGAAAA
65 TTTAAACACAAAACAATAAAAAAATGAAGATGCACCTTCGCAAAAAGACAGAACGAAAA
2378789 CCAGAACCAA
Statistics
Matches: 118, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
124 47 0.40
125 71 0.60
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.17
Consensus pattern (124 bp):
AATGATCAGATTATTAACAGACAATGCCAATAGGAAGAAGAAAGAAAAAAAGCTAATAGCTTGAT
TTAAACACAAAACAATAAAAAAATGAAGATGCACCTTCGCAAAAAGACAGAACGAAAAT
Found at i:2382720 original size:14 final size:14
Alignment explanation
Indices: 2382678--2382714 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2382668 TCGAATTTAA
2382678 ATTTAAATTTTTTT
1 ATTTAAATTTTTTT
2382692 ATTTAAATTTTTTT
1 ATTTAAATTTTTTT
2382706 ATTTAAATT
1 ATTTAAATT
2382715 AATTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTAAATTTTTTT
Found at i:2382749 original size:19 final size:20
Alignment explanation
Indices: 2382712--2382758 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2382702 TTTTATTTAA
* *
2382712 ATTAATTTAAATTATTATTT
1 ATTAATTTAAAATAATATTT
2382732 ATTAA-TTAAAATAATA-TT
1 ATTAATTTAAAATAATATTT
2382750 -TTAATTTAA
1 ATTAATTTAA
2382759 TTTAACTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 6 0.25
19 9 0.38
20 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAATTTAAAATAATATTT
Found at i:2383506 original size:12 final size:12
Alignment explanation
Indices: 2383491--2383516 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2383481 TTTAATTAAA
2383491 TTAATTTTTATT
1 TTAATTTTTATT
2383503 TTAATTTTTATT
1 TTAATTTTTATT
2383515 TT
1 TT
2383517 TAATAGATGA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTAATTTTTATT
Found at i:2384389 original size:20 final size:22
Alignment explanation
Indices: 2384364--2384405 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
2384354 TAACATCTAT
2384364 AATATTATC-AATTTTT-TTAA
1 AATATTATCAAATTTTTATTAA
2384384 AATATTATCAAATTTTTATTAA
1 AATATTATCAAATTTTTATTAA
2384406 TAACGATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 7 0.35
22 4 0.20
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTATCAAATTTTTATTAA
Found at i:2386703 original size:31 final size:31
Alignment explanation
Indices: 2386668--2386767 Score: 98
Period size: 31 Copynumber: 3.2 Consensus size: 31
2386658 TACGTGATAA
2386668 TAATAT-TTAAAGTATTTATAATTATAAATTT
1 TAATATATTAAA-TATTTATAATTATAAATTT
*
2386699 TAATATATT-AATAATTTATATTATATAAATTT
1 TAATATATTAAAT-ATTTATAAT-TATAAATTT
* * **
2386731 TAAAATATTATTATATTTAT-ATTATATTTTT
1 TAATATATTA-AATATTTATAATTATAAATTT
2386762 TAATAT
1 TAATAT
2386768 TTTTATAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
30 1 0.02
31 28 0.49
32 20 0.35
33 6 0.11
34 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
TAATATATTAAATATTTATAATTATAAATTT
Found at i:2386708 original size:17 final size:17
Alignment explanation
Indices: 2386688--2386741 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
2386678 AGTATTTATA
2386688 ATTATAAATTTTAATAT
1 ATTATAAATTTTAATAT
2386705 ATTA-ATAA-TTT-ATAT
1 ATTATA-AATTTTAATAT
*
2386720 -TATATAAATTTTAAAAT
1 AT-TATAAATTTTAATAT
2386737 ATTAT
1 ATTAT
2386742 TATATTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
14 1 0.03
15 8 0.27
16 8 0.27
17 12 0.40
18 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTATAAATTTTAATAT
Found at i:2386754 original size:33 final size:33
Alignment explanation
Indices: 2386680--2386757 Score: 115
Period size: 32 Copynumber: 2.4 Consensus size: 33
2386670 ATATTTAAAG
* *
2386680 TATTTATAAT-TATAAATTTTAATATATTAATA
1 TATTTATATTATATAAATTTTAAAATATTAATA
*
2386712 -ATTTATATTATATAAATTTTAAAATATTATTA
1 TATTTATATTATATAAATTTTAAAATATTAATA
2386744 TATTTATATTATAT
1 TATTTATATTATAT
2386758 TTTTTAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
31 8 0.20
32 20 0.49
33 13 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TATTTATATTATATAAATTTTAAAATATTAATA
Found at i:2386779 original size:28 final size:29
Alignment explanation
Indices: 2386713--2386798 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 29
2386703 ATATTAATAA
* *
2386713 TTTATAT-TATAT-AAATTTTAAAATATT
1 TTTATATATATATGATATTTTATAATATT
* * * *
2386740 ATTATATTTATATTATATTTTTTAATATT
1 TTTATATATATATGATATTTTATAATATT
*
2386769 TTTATA-ATATATGATATTTTATATTATT
1 TTTATATATATATGATATTTTATAATATT
2386797 TT
1 TT
2386799 GGATAATGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
27 6 0.12
28 25 0.52
29 17 0.35
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (29 bp):
TTTATATATATATGATATTTTATAATATT
Found at i:2387243 original size:9 final size:9
Alignment explanation
Indices: 2387208--2387278 Score: 67
Period size: 9 Copynumber: 7.9 Consensus size: 9
2387198 AAAATTTTAA
2387208 AAATTAAAT
1 AAATTAAAT
*
2387217 AATTTTAAA-
1 AA-ATTAAAT
*
2387226 AAATTAATT
1 AAATTAAAT
2387235 AAA-TAAATT
1 AAATTAAA-T
2387244 AAATATAAAT
1 AAAT-TAAAT
2387254 AAA-TAAAT
1 AAATTAAAT
*
2387262 AATTTAAAT
1 AAATTAAAT
2387271 AAATTAAA
1 AAATTAAA
2387279 ATTATTCAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
8 14 0.28
9 23 0.46
10 9 0.18
11 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATTAAAT
Found at i:2387262 original size:14 final size:14
Alignment explanation
Indices: 2387212--2387262 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
2387202 TTTTAAAAAT
* *
2387212 TAAATAATTTTAAA
1 TAAATAAATATAAA
*
2387226 -AAATTAAT-TAAA
1 TAAATAAATATAAA
2387238 TAAATTAAATATAAA
1 TAAA-TAAATATAAA
2387253 TAAATAAATA
1 TAAATAAATA
2387263 ATTTAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 4 0.13
13 9 0.29
14 10 0.32
15 8 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAATAAATATAAA
Found at i:2387875 original size:6 final size:6
Alignment explanation
Indices: 2387834--2387967 Score: 59
Period size: 6 Copynumber: 23.0 Consensus size: 6
2387824 ATTAATTATG
* * * * * *
2387834 ATATAA TTATAA ATATAA TTATAT TTATATC GTATAA ATAT-A ATA-AA
1 ATATAA ATATAA ATATAA ATATAA ATATA-A ATATAA ATATAA ATATAA
* * * * * *
2387881 ATATAAA AAATTA ATATTA ATATAA ATATAA A-AT-A TTTTAA ATTTAA
1 ATAT-AA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
*
2387928 TTAT-A ATAT-A ATA-AA ATATTAA A-ATATA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATA-TAA ATATA-A ATATAA ATATAA
2387968 TCTATTTTCA
Statistics
Matches: 99, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
4 1 0.01
5 25 0.25
6 58 0.59
7 15 0.15
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (6 bp):
ATATAA
Found at i:2387890 original size:9 final size:10
Alignment explanation
Indices: 2387869--2387968 Score: 66
Period size: 10 Copynumber: 9.9 Consensus size: 10
2387859 TATATCGTAT
2387869 AAATATAATA
1 AAATATAATA
2387879 AAATATAA-A
1 AAATATAATA
2387888 AAAT-TAATA
1 AAATATAATA
*
2387897 TTAATATAAATA
1 -AAATAT-AATA
* *
2387909 TAAA-ATATTTT
1 -AAATATA-ATA
*
2387920 AAATTTAATTA
1 AAATATAA-TA
*
2387931 TAATATAATA
1 AAATATAATA
2387941 AAATAT--TA
1 AAATATAATA
2387949 AAATATAATA
1 AAATATAATA
2387959 TAAATATAAT
1 -AAATATAAT
2387969 CTATTTTCAT
Statistics
Matches: 70, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
8 11 0.16
9 6 0.09
10 24 0.34
11 22 0.31
12 7 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATATAATA
Found at i:2388187 original size:31 final size:31
Alignment explanation
Indices: 2388117--2388200 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 31
2388107 AAGTTATTAC
*
2388117 ATAA-TTTAATATATTATATTTATTAATTTAT
1 ATAATTTTGATATATTATATTTATT-ATTTAT
*
2388148 ATGAATTTTTATATATTAATAATTTATT-TTTAT
1 AT-AATTTTGATATATT-AT-ATTTATTATTTAT
2388181 AT-ATTTTGATAT-TTATATTT
1 ATAATTTTGATATATTATATTT
2388201 TTAAATATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
28 4 0.09
29 2 0.04
30 2 0.04
31 11 0.23
32 2 0.04
33 17 0.36
34 2 0.04
35 7 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (31 bp):
ATAATTTTGATATATTATATTTATTATTTAT
Found at i:2388194 original size:22 final size:22
Alignment explanation
Indices: 2388152--2388237 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 22
2388142 ATTTATATGA
*
2388152 ATTTTTATATA--TTAATAATTT
1 ATTTTTATATATTTTGAT-ATTT
2388173 ATTTTTATATATTTTGATATTTAT
1 ATTTTTATATATTTTGATA-TT-T
*
2388197 ATTTTTAAATATATTT-AT-TTT
1 ATTTTTATATAT-TTTGATATTT
*
2388218 ATGTTTTACATCATTTTGAT
1 AT-TTTTATAT-ATTTTGAT
2388238 TTAATAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
21 14 0.26
22 13 0.24
23 10 0.19
24 14 0.26
25 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.63
Consensus pattern (22 bp):
ATTTTTATATATTTTGATATTT
Found at i:2388651 original size:14 final size:14
Alignment explanation
Indices: 2388632--2388661 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2388622 AATAATTTAA
*
2388632 ATTTATTAAATATT
1 ATTTATTAAAAATT
2388646 ATTTATTAAAAATT
1 ATTTATTAAAAATT
2388660 AT
1 AT
2388662 AATATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTATTAAAAATT
Found at i:2388674 original size:23 final size:21
Alignment explanation
Indices: 2388636--2388680 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
2388626 ATTTAAATTT
* *
2388636 ATTAAATATTATTTATTAAAA
1 ATTAAATATTAATTATAAAAA
2388657 ATTATAATATATAATTATAAAAA
1 ATTA-AATAT-TAATTATAAAAA
2388680 A
1 A
2388681 AATATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAAATATTAATTATAAAAA
Found at i:2397658 original size:2 final size:2
Alignment explanation
Indices: 2397653--2397690 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2397643 TGTGTGTGAG
2397653 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
2397691 AAGGAAGAAT
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:2399449 original size:13 final size:13
Alignment explanation
Indices: 2399431--2399457 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2399421 ATTCGAATTC
2399431 AAAAAATAAATAT
1 AAAAAATAAATAT
2399444 AAAAAATAAATAT
1 AAAAAATAAATAT
2399457 A
1 A
2399458 TGTTTGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAAAATAAATAT
Found at i:2401150 original size:16 final size:15
Alignment explanation
Indices: 2401125--2401167 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2401115 TATTTATCTA
*
2401125 AATATATATTTTATT
1 AATATTTATTTTATT
*
2401140 AAGTATTTATTATATTT
1 AA-TATTTATTTTA-TT
2401157 AATATTTATTT
1 AATATTTATTT
2401168 AATGTACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 2 0.09
16 17 0.74
17 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
AATATTTATTTTATT
Found at i:2401845 original size:16 final size:18
Alignment explanation
Indices: 2401816--2401848 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2401806 AAATATAGAG
2401816 ATATAATATCTTTTAAAT
1 ATATAATATCTTTTAAAT
2401834 ATATAAT-T-TTTTAAA
1 ATATAATATCTTTTAAA
2401849 AAAGATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATAATATCTTTTAAAT
Found at i:2405320 original size:16 final size:16
Alignment explanation
Indices: 2405301--2405367 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
2405291 ATATATATCT
2405301 TAAAAATTATATAATA
1 TAAAAATTATATAATA
*
2405317 TAAATTATTA-ATACAT-
1 TAAA-AATTATATA-ATA
*
2405333 TAAAATTTATATAAATA
1 TAAAAATTATAT-AATA
*
2405350 TAAAATATTTTA-AATA
1 TAAAA-ATTATATAATA
2405366 TA
1 TA
2405368 TTGTAATATG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
15 3 0.08
16 21 0.52
17 12 0.30
18 4 0.10
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAAATTATATAATA
Found at i:2405794 original size:21 final size:22
Alignment explanation
Indices: 2405765--2405805 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
2405755 TTTAAATTTA
2405765 ATTATAAAT-ATTTATAATTACT
1 ATTATAAATAATTT-TAATTACT
2405787 ATTA-AAATAATTTTAATTA
1 ATTATAAATAATTTTAATTA
2405806 ATAATATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTATAAATAATTTTAATTACT
Found at i:2406479 original size:18 final size:18
Alignment explanation
Indices: 2406453--2406488 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2406443 ACGATTTAAA
*
2406453 TTTATAATTTAAAATAAT
1 TTTAAAATTTAAAATAAT
*
2406471 TTTAAAATTTAAATTAAT
1 TTTAAAATTTAAAATAAT
2406489 CGATTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAAATTTAAAATAAT
Found at i:2407260 original size:2 final size:2
Alignment explanation
Indices: 2407253--2407278 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2407243 GGGCAGGCCT
2407253 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
2407279 GTGGAAGCCC
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):
TA
Found at i:2408957 original size:30 final size:30
Alignment explanation
Indices: 2408921--2408995 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
2408911 AAATCCTTAA
*
2408921 AATTTACATTCAAATTAA-CTCTTAACTTTT
1 AATTTACATTCAAATTAATCT-TTAACCTTT
* *
2408951 AATTTACACTCTAATTAATCTTTAACCTTT
1 AATTTACATTCAAATTAATCTTTAACCTTT
* *
2408981 AATTTATATCCAAAT
1 AATTTACATTCAAAT
2408996 AAACCTATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 35 0.95
31 2 0.05
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.45
Consensus pattern (30 bp):
AATTTACATTCAAATTAATCTTTAACCTTT
Found at i:2418460 original size:15 final size:17
Alignment explanation
Indices: 2418423--2418480 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 17
2418413 AGCATGAAAT
2418423 TTAATTATTTATATATA
1 TTAATTATTTATATATA
2418440 TATAATT-TTTATAT-TA
1 T-TAATTATTTATATATA
*
2418456 TTAA-TATATTA-ATAAA
1 TTAATTAT-TTATATATA
2418472 TTAATTATT
1 TTAATTATT
2418481 AGGTTTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 12 0.34
17 11 0.31
18 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAATTATTTATATATA
Found at i:2419493 original size:21 final size:22
Alignment explanation
Indices: 2419454--2419494 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
2419444 TTTAGATTTT
2419454 AATAATTATAAAAAAAATAATA
1 AATAATTATAAAAAAAATAATA
2419476 AATAA-TA-AAAAGAAAATAA
1 AATAATTATAAAA-AAAATAA
2419495 AATAGTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (22 bp):
AATAATTATAAAAAAAATAATA
Found at i:2419590 original size:16 final size:16
Alignment explanation
Indices: 2419569--2419616 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
2419559 TTGATCCAAC
2419569 TTAAATTTAAAATAAT
1 TTAAATTTAAAATAAT
2419585 TTAAATTTAAAATAAT
1 TTAAATTTAAAATAAT
* * *
2419601 CTGAACTTAAAATAAT
1 TTAAATTTAAAATAAT
2419617 ACAAATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (16 bp):
TTAAATTTAAAATAAT
Found at i:2419665 original size:37 final size:38
Alignment explanation
Indices: 2419570--2419706 Score: 104
Period size: 37 Copynumber: 3.6 Consensus size: 38
2419560 TGATCCAACT
*
2419570 TAAATTTAAAATAATTTAAATTTAAAATAATCTGAACTTAA
1 TAAATTT-AAATAA-TTAAATTTAAAATTATCTGAAC-TAA
* **
2419611 AATAATACAAATAATTAAATTTAAAATTATCT-AATCTAA
1 TA-AATTTAAATAATTAAATTTAAAATTATCTGAA-CTAA
*
2419650 TAAATTTAAAT-ATTAAACTT--AATTAATCTGAAACTAA
1 TAAATTTAAATAATTAAATTTAAAATT-ATCTG-AACTAA
* * *
2419687 TTAACTTAAGT-ATTAAATTT
1 TAAATTTAAATAATTAAATTT
2419707 TATTAAATTA
Statistics
Matches: 79, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
35 4 0.05
36 4 0.05
37 28 0.35
38 9 0.11
39 6 0.08
40 18 0.23
41 7 0.09
42 3 0.04
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (38 bp):
TAAATTTAAATAATTAAATTTAAAATTATCTGAACTAA
Found at i:2419739 original size:16 final size:15
Alignment explanation
Indices: 2419712--2419773 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 15
2419702 AATTTTATTA
*
2419712 AATTAAATTTAAAAT
1 AATTAAAATTAAAAT
*
2419727 GATTTAAAATTAAAAT
1 -AATTAAAATTAAAAT
2419743 AATTAAAATTAAAAAT
1 AATTAAAATT-AAAAT
*
2419759 AATATAAAAATAAAA
1 AAT-TAAAATTAAAA
2419774 ATATTTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.22
16 25 0.62
17 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
AATTAAAATTAAAAT
Found at i:2419752 original size:32 final size:33
Alignment explanation
Indices: 2419732--2419801 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
2419722 AAAATGATTT
*
2419732 AAAATTAAAATAATTAAAATTAAAAATAATATA
1 AAAATAAAAATAATTAAAATTAAAAATAATATA
*
2419765 AAAATAAAAAT-ATTTAAATGTAAAAATAA-ATA
1 AAAATAAAAATAATTAAAAT-TAAAAATAATATA
2419797 AAAAT
1 AAAAT
2419802 TTAACACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 15 0.44
33 19 0.56
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (33 bp):
AAAATAAAAATAATTAAAATTAAAAATAATATA
Found at i:2419782 original size:16 final size:16
Alignment explanation
Indices: 2419722--2419792 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
2419712 AATTAAATTT
*
2419722 AAAATGATTT-AAAATT
1 AAAAT-ATTTAAAAATA
* *
2419738 AAAATAATTAAAATTA
1 AAAATATTTAAAAATA
*
2419754 AAAATAATATAAAAATA
1 AAAAT-ATTTAAAAATA
**
2419771 AAAATATTTAAATGTA
1 AAAATATTTAAAAATA
2419787 AAAATA
1 AAAATA
2419793 AATAAAAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 3 0.07
16 28 0.64
17 13 0.30
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATATTTAAAAATA
Found at i:2419818 original size:21 final size:20
Alignment explanation
Indices: 2419763--2419835 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 20
2419753 AAAAATAATA
*
2419763 TAAAAATAAAAATATTTAAAT
1 TAAAAATAATAA-ATTTAAAT
2419784 GTAAAAATAAATAAAAATTTAACACT
1 -TAAAAAT-AAT--AAATTTAA-A-T
2419810 TAAAAATAATTAAATTTAAAT
1 TAAAAATAA-TAAATTTAAAT
2419831 TAAAA
1 TAAAA
2419836 TTAACCCAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
21 6 0.14
22 8 0.18
23 10 0.23
24 8 0.18
25 11 0.25
26 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (20 bp):
TAAAAATAATAAATTTAAAT
Found at i:2420524 original size:25 final size:24
Alignment explanation
Indices: 2420494--2420540 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
2420484 ATTTTGAGAG
2420494 TTTAAATAAAAATAAATTAAAATTT
1 TTTAAATAAAAATAAA-TAAAATTT
*
2420519 TTTAAATATAAATAAATAAAAT
1 TTTAAATAAAAATAAATAAAAT
2420541 AAATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TTTAAATAAAAATAAATAAAATTT
Found at i:2420607 original size:21 final size:20
Alignment explanation
Indices: 2420560--2420625 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
2420550 ATTTTATATA
* *
2420560 ATAAAATTATAAATAAATAAT
1 ATAAAATTATAAAT-ATTAAG
*
2420581 AAAAAATTATAAATATTAAG
1 ATAAAATTATAAATATTAAG
*
2420601 ATTAAAATTTATATATATTAA-
1 A-TAAAA-TTATAAATATTAAG
2420622 ATAA
1 ATAA
2420626 TTTAATTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 8 0.21
21 18 0.47
22 12 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAAAATTATAAATATTAAG
Found at i:2420607 original size:42 final size:42
Alignment explanation
Indices: 2420525--2420609 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
2420515 ATTTTTTAAA
* ** * *
2420525 TATAAATAAATAAAATAAATTATTTATTTTATATAATAAAAT
1 TATAAATAAATAAAAAAAATTATAAATATTATAGAATAAAAT
*
2420567 TATAAATAAATAATAAAAAATTATAAATATTA-AGATTAAAAT
1 TATAAATAAATAA-AAAAAATTATAAATATTATAGAATAAAAT
2420609 T
1 T
2420610 TATATATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
42 22 0.61
43 14 0.39
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (42 bp):
TATAAATAAATAAAAAAAATTATAAATATTATAGAATAAAAT
Found at i:2421682 original size:74 final size:73
Alignment explanation
Indices: 2421543--2421704 Score: 222
Period size: 74 Copynumber: 2.2 Consensus size: 73
2421533 ATCGATCTAA
*
2421543 TTAAATTAATTAAAATATAATTTAAAGAAAAAATAGTTTTATATTACTTAATTTTTAAATTAATT
1 TTAAATTAA--AAAATATAATATAAAGAAAAAATAGTTTTATATTACTTAATTTTTAAATTAATT
*
2421608 TGATTTAAAT
64 TAATTTAAAT
2421618 TTAAATTAAAAAATATAAAATATAAAGTAAAAAA-A-TTTTATATTA-TTGAATTTTTAAATTAA
1 TTAAATTAAAAAATAT--AATATAAAG-AAAAAATAGTTTTATATTACTT-AATTTTTAAATTAA
2421680 TTTAATTTAAAT
62 TTTAATTTAAAT
*
2421692 TTAACTTAAAAAA
1 TTAAATTAAAAAA
2421705 AATATTAGAG
Statistics
Matches: 80, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
73 9 0.11
74 47 0.59
75 18 0.22
76 6 0.08
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (73 bp):
TTAAATTAAAAAATATAATATAAAGAAAAAATAGTTTTATATTACTTAATTTTTAAATTAATTTA
ATTTAAAT
Found at i:2424758 original size:18 final size:17
Alignment explanation
Indices: 2424735--2424789 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
2424725 AGAAGATAAT
2424735 TAAAATACTAATAAAATA
1 TAAAATA-TAATAAAATA
*
2424753 TAAAATATAAATATAATA
1 TAAAATAT-AATAAAATA
*
2424771 -AAAAT-TATTAAAATA
1 TAAAATATAATAAAATA
2424786 TAAA
1 TAAA
2424790 TTATTAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 7 0.22
16 4 0.12
17 6 0.19
18 15 0.47
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAATATAATAAAATA
Found at i:2424788 original size:26 final size:24
Alignment explanation
Indices: 2424737--2424790 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
2424727 AAGATAATTA
2424737 AAATACTAATAAAATATAAAATAT
1 AAATACTAATAAAATATAAAATAT
2424761 AAATA-TAATAAAAATTATTAAAATAT
1 AAATACTAAT-AAAA-TA-TAAAATAT
2424787 AAAT
1 AAAT
2424791 TATTAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 4 0.15
24 9 0.33
25 2 0.07
26 12 0.44
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAATACTAATAAAATATAAAATAT
Found at i:2424790 original size:15 final size:15
Alignment explanation
Indices: 2424767--2424803 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2424757 ATATAAATAT
*
2424767 AATAAAAATTATTAA
1 AATATAAATTATTAA
2424782 AATATAAATTATTAA
1 AATATAAATTATTAA
*
2424797 TATATAA
1 AATATAA
2424804 TATTTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAAATTATTAA
Found at i:2426086 original size:5 final size:5
Alignment explanation
Indices: 2426076--2426100 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2426066 CGTGATGCTG
2426076 CTCAT CTCAT CTCAT CTCAT CTCAT
1 CTCAT CTCAT CTCAT CTCAT CTCAT
2426101 GCATGCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (5 bp):
CTCAT
Found at i:2426340 original size:27 final size:25
Alignment explanation
Indices: 2426307--2426374 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
2426297 ATTCAATTTT
* * *
2426307 TTTAAAATATTTATATTATTAATATA
1 TTTAAAA-ATATATATAATAAATATA
2426333 TTTAAAAATATATATAATAAATATA
1 TTTAAAAATATATATAATAAATATA
*
2426358 TTTAAAAAT-TAAATAAT
1 TTTAAAAATATATATAAT
2426375 TTATTGATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 7 0.18
25 24 0.63
26 7 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTAAAAATATATATAATAAATATA
Found at i:2426344 original size:12 final size:12
Alignment explanation
Indices: 2426327--2426366 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
2426317 TTATATTATT
2426327 AATATATTTAAA
1 AATATATTTAAA
*
2426339 AATATATATAATA
1 AATATATTTAA-A
2426352 AATATATTTAAA
1 AATATATTTAAA
2426364 AAT
1 AAT
2426367 TAAATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATATATTTAAA
Found at i:2427049 original size:18 final size:19
Alignment explanation
Indices: 2427012--2427056 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
2427002 TTGATATATT
2427012 AATAATA-T-ATAAATTTA
1 AATAATATTAATAAATTTA
*
2427029 AATATTATTAATAAA-TTA
1 AATAATATTAATAAATTTA
2427047 AATAATATTA
1 AATAATATTA
2427057 CTTTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 13 0.54
19 5 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAATATTAATAAATTTA
Found at i:2431947 original size:29 final size:28
Alignment explanation
Indices: 2431914--2431990 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
2431904 AAATTTAAAA
2431914 TTTATTATTAATAAATAATAAAAATAATT
1 TTTATTATTAA-AAATAATAAAAATAATT
* * * *
2431943 TTTA-TAATAAAATTTAAATAAAATTATTT
1 TTTATTATTAAAA-AT-AATAAAAATAATT
2431972 TTTATTATTAAATAATAAT
1 TTTATTATTAAA-AATAAT
2431991 TTAAATTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
27 2 0.05
28 6 0.16
29 22 0.58
30 7 0.18
31 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTATTATTAAAAATAATAAAAATAATT
Found at i:2432279 original size:13 final size:13
Alignment explanation
Indices: 2432263--2432301 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2432253 TTTAAAATAT
2432263 TTTTTTATATTAA
1 TTTTTTATATTAA
2432276 TTTTATTATATTAA
1 TTTT-TTATATTAA
**
2432290 TAATTTATATTA
1 TTTTTTATATTA
2432302 TAAAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTATATTAA
Found at i:2432284 original size:14 final size:14
Alignment explanation
Indices: 2432261--2432290 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2432251 TATTTAAAAT
*
2432261 ATTTTTTTATATTA
1 ATTTTATTATATTA
2432275 ATTTTATTATATTA
1 ATTTTATTATATTA
2432289 AT
1 AT
2432291 AATTTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTATTATATTA
Found at i:2432367 original size:67 final size:66
Alignment explanation
Indices: 2432239--2432391 Score: 154
Period size: 67 Copynumber: 2.3 Consensus size: 66
2432229 TGGTATATTT
* *
2432239 ATTTTATAATTA-TATTTAAAATATTTTTTTATATTAATTTTATTATATTAATAATTTATATTAT
1 ATTTTA-AATTATTATTTAAAATATTATTTTATATTAATTTTATCATATTAATAATTTATATT-T
2432303 AAAA
64 -AAA
* *
2432307 ATTTTAAATTATGTATTTAAATTA-TATTTTA-A-TAATTTTATACATATT-ATATTTTCATATT
1 ATTTTAAATTAT-TATTTAAAATATTATTTTATATTAATTTTAT-CATATTAATAATTT-ATATT
2432368 TAAA
63 TAAA
2432372 ATTATTAAATTTATCTATTT
1 ATT-TTAAA-TTAT-TATTT
2432392 GCCCTCCAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
65 6 0.08
66 21 0.28
67 25 0.34
68 12 0.16
69 10 0.14
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.57
Consensus pattern (66 bp):
ATTTTAAATTATTATTTAAAATATTATTTTATATTAATTTTATCATATTAATAATTTATATTTAA
A
Found at i:2432593 original size:17 final size:17
Alignment explanation
Indices: 2432526--2432593 Score: 65
Period size: 17 Copynumber: 4.1 Consensus size: 17
2432516 AAAAAATAAA
2432526 AAAATATTATTAAATATT
1 AAAAT-TTATTAAATATT
2432544 AAAATTTAATT-AATA--
1 AAAATTT-ATTAAATATT
2432559 AAAA-TTATTAATATATT
1 AAAATTTATTAA-ATATT
2432576 AAAATTTATATAAA-ATT
1 AAAATTTAT-TAAATATT
2432593 A
1 A
2432594 TAATATTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.07
14 3 0.07
15 7 0.16
17 14 0.33
18 13 0.30
19 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTTATTAAATATT
Found at i:2432597 original size:27 final size:32
Alignment explanation
Indices: 2432526--2432605 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
2432516 AAAAAATAAA
2432526 AAAATATTATTAA-ATATTAAAATTTAATTAAT
1 AAAA-ATTATTAATATATTAAAATTTAATTAAT
2432558 AAAAATTATTAATATATTAAAATTT-A-T-AT
1 AAAAATTATTAATATATTAAAATTTAATTAAT
*
2432587 -AAAATTA-TAATATTTTAAA
1 AAAAATTATTAATATATTAAA
2432606 CACAATAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
27 11 0.24
28 7 0.15
29 2 0.04
30 1 0.02
31 9 0.20
32 16 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
AAAAATTATTAATATATTAAAATTTAATTAAT
Found at i:2437249 original size:42 final size:42
Alignment explanation
Indices: 2437169--2437281 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 42
2437159 GGGTACATGC
*
2437169 ATTAGCATTTAAAGCAATATATA--CATATAATTAAATATGA
1 ATTAGCATTTAAAGCAATATATATTTATATAATTAAATATGA
* * * *
2437209 ATTAACATTTAAAGTAATATATATTTATATAATTATATATGG
1 ATTAGCATTTAAAGCAATATATATTTATATAATTAAATATGA
** * *
2437251 ATTAGCATACAAAGCAATCTACATTTATATA
1 ATTAGCATTTAAAGCAATATATATTTATATA
2437282 TAATTTTATA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 21 0.35
42 39 0.65
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (42 bp):
ATTAGCATTTAAAGCAATATATATTTATATAATTAAATATGA
Found at i:2437478 original size:19 final size:17
Alignment explanation
Indices: 2437443--2437521 Score: 71
Period size: 16 Copynumber: 4.8 Consensus size: 17
2437433 AATCAAAGAA
*
2437443 AAATTAACAA-ATATAC
1 AAATTAAAAATATATAC
2437459 AAATTAAAAATGAGTATAC
1 AAATTAAAAAT-A-TATAC
2437478 AAA-T-AAAA-ATATAC
1 AAATTAAAAATATATAC
2437492 AAATTAAAAAT-TA-AC
1 AAATTAAAAATATATAC
*
2437507 AAATATACAAATATA
1 AAAT-TAAAAATATA
2437522 ATTTTTGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
14 8 0.15
15 8 0.15
16 21 0.40
17 6 0.11
18 2 0.04
19 8 0.15
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.25
Consensus pattern (17 bp):
AAATTAAAAATATATAC
Found at i:2437492 original size:14 final size:14
Alignment explanation
Indices: 2437473--2437521 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 14
2437463 TAAAAATGAG
2437473 TATACAAATAAAAA
1 TATACAAATAAAAA
2437487 TATACAAATTAAAAA
1 TATACAAA-TAAAAA
2437502 T-TAACAAATATACAAA
1 TAT-ACAAATA-A-AAA
2437518 TATA
1 TATA
2437522 ATTTTTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 11 0.37
15 13 0.43
16 5 0.17
17 1 0.03
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (14 bp):
TATACAAATAAAAA
Found at i:2437747 original size:2 final size:2
Alignment explanation
Indices: 2437742--2437776 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2437732 TAAAAAAAGT
*
2437742 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2437777 GTACATAAAA
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2439622 original size:2 final size:2
Alignment explanation
Indices: 2439615--2439646 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2439605 AATAAGTTAA
2439615 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2439647 ATCATATCTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2440980 original size:21 final size:23
Alignment explanation
Indices: 2440942--2440990 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
2440932 TTAGTTTTTA
*
2440942 TTTTATTTTAAAATTGG-ATAGT
1 TTTTATTATAAAATTGGAATAGT
2440964 TTTTATTATAAAA-TGGAATAGT
1 TTTTATTATAAAATTGGAATAGT
2440986 TTTTA
1 TTTTA
2440991 CATCTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (23 bp):
TTTTATTATAAAATTGGAATAGT
Found at i:2441436 original size:2 final size:2
Alignment explanation
Indices: 2441420--2441462 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2441410 CCATCACCTT
* *
2441420 TA TA TA CA TA CA 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
2441462 T
1 T
2441463 TAGTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2442126 original size:19 final size:19
Alignment explanation
Indices: 2442077--2442134 Score: 93
Period size: 19 Copynumber: 3.1 Consensus size: 19
2442067 ATTTATTTTA
2442077 ATTATTATTTAATATAAAT
1 ATTATTATTTAATATAAAT
2442096 A-TA-TATTTTAATATAAAT
1 ATTATTA-TTTAATATAAAT
2442114 ATTATTATTTAATATAAAT
1 ATTATTATTTAATATAAAT
2442133 AT
1 AT
2442135 AAAATTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.06
18 15 0.42
19 17 0.47
20 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTATTATTTAATATAAAT
Found at i:2442147 original size:18 final size:18
Alignment explanation
Indices: 2442083--2442147 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
2442073 TTTAATTATT
2442083 ATTTAATATAAATATATA
1 ATTTAATATAAATATATA
* *
2442101 TTTTAATATAAATATTATT
1 ATTTAATATAAATA-TATA
*
2442120 ATTTAATATAAATATAAA
1 ATTTAATATAAATATATA
*
2442138 ATTTATTATA
1 ATTTAATATA
2442148 TTAACGTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
18 24 0.60
19 16 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTAATATAAATATATA
Found at i:2442265 original size:26 final size:25
Alignment explanation
Indices: 2442198--2442265 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 25
2442188 TTTCAACTTA
*
2442198 AAAT-TATTATTATAATA-AAATTT
1 AAATATATTATTATAATATTAATTT
* *
2442221 AAATATA-TATTTTATTATTAATTT
1 AAATATATTATTATAATATTAATTT
* *
2442245 TAATCATATTATTGTAATATT
1 AAAT-ATATTATTATAATATT
2442266 TAATCTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 12 0.34
24 10 0.29
25 3 0.09
26 10 0.29
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
AAATATATTATTATAATATTAATTT
Found at i:2442267 original size:21 final size:21
Alignment explanation
Indices: 2442234--2442284 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2442224 TATATATTTT
*
2442234 ATTATTAAT-TTTAATCATATT
1 ATTA-TAATATTTAATCATATA
* *
2442255 ATTGTAATATTTAATCTTATA
1 ATTATAATATTTAATCATATA
2442276 ATTATAATA
1 ATTATAATA
2442285 ACGTCAATCC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTATAATATTTAATCATATA
Found at i:2442562 original size:29 final size:29
Alignment explanation
Indices: 2442504--2442602 Score: 93
Period size: 29 Copynumber: 3.4 Consensus size: 29
2442494 GTTGGTTTCT
2442504 TATTTAAATATTTTA-T-TACGT-TAATTTTA
1 TATTTAAATATTTTATTATAC-TATAA--TTA
2442533 TATTTAAATATTTTATTATACTATAATTA
1 TATTTAAATATTTTATTATACTATAATTA
*
2442562 TATTTAAAATATTTTATAATTA-TATAA--A
1 TATTT-AAATATTTTATTA-TACTATAATTA
*
2442590 TATTAAAATATTT
1 TATTTAAATATTT
2442603 ATGATGTATT
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
27 8 0.13
28 5 0.08
29 23 0.37
30 19 0.30
31 8 0.13
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (29 bp):
TATTTAAATATTTTATTATACTATAATTA
Found at i:2442574 original size:30 final size:30
Alignment explanation
Indices: 2442530--2442652 Score: 107
Period size: 30 Copynumber: 4.2 Consensus size: 30
2442520 TACGTTAATT
*
2442530 TTATATTT-AAATATTTTATTA-TACTATAA
1 TTATATTTAAAATATTTTATAATTA-TATAA
2442559 TTATATTTAAAATATTTTATAATTATATAA
1 TTATATTTAAAATATTTTATAATTATATAA
* *
2442589 --ATA-TTAAAATA-TTTATGATGTATTTATA
1 TTATATTTAAAATATTTTATAAT-TATATA-A
* * *
2442617 TTTTATTTTAATTAATTTTAT-ATTATATAA
1 TTATATTTAAAAT-ATTTTATAATTATATAA
2442647 TTATAT
1 TTATAT
2442653 AGTGTTAAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
26 7 0.09
27 13 0.17
28 4 0.05
29 8 0.10
30 25 0.32
31 12 0.16
32 3 0.04
33 5 0.06
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (30 bp):
TTATATTTAAAATATTTTATAATTATATAA
Found at i:2443007 original size:12 final size:13
Alignment explanation
Indices: 2442984--2443038 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 13
2442974 TTAAAAAAAT
*
2442984 TTTAATATTTAAG
1 TTTAATATTTAAA
2442997 TTTAA-ATTTAAA
1 TTTAATATTTAAA
2443009 TTTAACTTGATTT-AA
1 TTTAA--T-ATTTAAA
2443024 TTTAATAATTTAAA
1 TTTAAT-ATTTAAA
2443038 T
1 T
2443039 AATTATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
12 11 0.31
13 10 0.29
14 3 0.09
15 7 0.20
16 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (13 bp):
TTTAATATTTAAA
Found at i:2443079 original size:17 final size:16
Alignment explanation
Indices: 2443047--2443094 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2443037 ATAATTATTT
2443047 AAAATATATTTAAATA
1 AAAATATATTTAAATA
*
2443063 AAAATATTATTTTAATA
1 AAAATA-TATTTAAATA
*
2443080 AATAT-TAATTTAAAT
1 AAAATAT-ATTTAAAT
2443095 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 13 0.48
17 13 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATATATTTAAATA
Found at i:2443093 original size:29 final size:28
Alignment explanation
Indices: 2443029--2443093 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 28
2443019 TTTAATTTAA
*
2443029 TAATTTAAATAATTATTTAAAATATATT
1 TAATTTAAAAAATTATTTAAAATATATT
*
2443057 TAA-ATAAAAATATTATTTTAATAA-ATA-T
1 TAATTTAAAAA-ATTA-TTTAA-AATATATT
2443085 TAATTTAAA
1 TAATTTAAA
2443094 TCAATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
27 5 0.17
28 11 0.37
29 12 0.40
30 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATTTAAAAAATTATTTAAAATATATT
Found at i:2443185 original size:22 final size:23
Alignment explanation
Indices: 2443157--2443200 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2443147 TATTGATCGA
2443157 ACCTAAAT-GAATTAGACAAACT
1 ACCTAAATCGAATTAGACAAACT
* *
2443179 ACCTAAATCTAATTATACAAAC
1 ACCTAAATCGAATTAGACAAAC
2443201 CTCATATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (23 bp):
ACCTAAATCGAATTAGACAAACT
Found at i:2443551 original size:20 final size:21
Alignment explanation
Indices: 2443528--2443590 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
2443518 TTTTAAAAAT
2443528 ATATATTATATAAATTAT-TA
1 ATATATTATATAAATTATATA
*
2443548 ATATATTA-A-AATTTATATA
1 ATATATTATATAAATTATATA
*
2443567 A-ATATGATATAAA-TATATA
1 ATATATTATATAAATTATATA
*
2443586 TTATA
1 ATATA
2443591 ATATTTATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 11 0.31
19 11 0.31
20 13 0.37
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATATTATATAAATTATATA
Found at i:2443784 original size:26 final size:26
Alignment explanation
Indices: 2443745--2443799 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
2443735 ATAATATATT
2443745 AATTTGAAATCAAT-TTTTAAGAAAAA
1 AATTTGAAATCAATATTTTAA-AAAAA
*
2443771 AATTT-AAATACAATATTTTAAAATAA
1 AATTTGAAAT-CAATATTTTAAAAAAA
2443797 AAT
1 AAT
2443800 CTATTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 4 0.15
26 16 0.62
27 6 0.23
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (26 bp):
AATTTGAAATCAATATTTTAAAAAAA
Found at i:2444712 original size:9 final size:9
Alignment explanation
Indices: 2444700--2444729 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2444690 TTAAAATTTA
2444700 AATTAAATT
1 AATTAAATT
2444709 AATTAAATT
1 AATTAAATT
2444718 AAATTAAATT
1 -AATTAAATT
2444728 AA
1 AA
2444730 AATTTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:2444738 original size:19 final size:19
Alignment explanation
Indices: 2444674--2444745 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
2444664 ATTAATTAAT
*
2444674 AAATATTTTAAA-TAGATTA
1 AAAT-TTTTAAATTAAATTA
2444693 AAA--TTTAAATTAAATT-
1 AAATTTTTAAATTAAATTA
*
2444709 -AATTAAATTAAATTAAATTA
1 AAATT--TTTAAATTAAATTA
2444729 AAATTTTT-AATTAAATT
1 AAATTTTTAAATTAAATT
2444746 TTTTTGCTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
15 2 0.05
16 6 0.14
17 5 0.12
18 9 0.21
19 17 0.40
21 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (19 bp):
AAATTTTTAAATTAAATTA
Found at i:2444745 original size:5 final size:5
Alignment explanation
Indices: 2444697--2444730 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
2444687 AGATTAAAAT
2444697 TTAAA TTAAA TT-AA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
2444731 ATTTTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TTAAA
Found at i:2445716 original size:3 final size:3
Alignment explanation
Indices: 2445708--2445732 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2445698 CTTCATTTCC
2445708 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
2445733 ATTCTGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2445923 original size:28 final size:30
Alignment explanation
Indices: 2445871--2445942 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 30
2445861 TTTCTTTCAC
2445871 TAAAAAATAAT-TAAATCATATTATAAT-A
1 TAAAAAATAATATAAATCATATTATAATAA
2445899 TAAAAAATAATATAAAT-AT-TATATAATAA
1 TAAAAAATAATATAAATCATAT-TATAATAA
2445928 TAATAATAATAATAT
1 TAA-AA-AATAATAT
2445943 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
27 1 0.03
28 19 0.49
29 9 0.23
30 2 0.05
31 8 0.21
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (30 bp):
TAAAAAATAATATAAATCATATTATAATAA
Found at i:2445941 original size:25 final size:23
Alignment explanation
Indices: 2445896--2445943 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
2445886 TCATATTATA
2445896 ATATAAAAAATAATATAAATATT
1 ATATAAAAAATAATATAAATATT
2445919 ATATAATAATAATAATA-ATAATATT
1 ATATAA-AA-AATAATATA-AATATT
2445944 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.27
24 3 0.14
25 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATAAAAAATAATATAAATATT
Found at i:2447015 original size:22 final size:22
Alignment explanation
Indices: 2446969--2447028 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
2446959 CGACTATCTA
*
2446969 TTTTATTATTTAAATTT-T-TAT
1 TTTTA-TAATTAAATTTATATAT
2446990 TTTTAT-ATTAATATTTATATAT
1 TTTTATAATTAA-ATTTATATAT
2447012 TTTTATAATTAAATTTA
1 TTTTATAATTAAATTTA
2447029 AATCAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 6 0.18
22 14 0.41
23 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTATAATTAAATTTATATAT
Found at i:2448010 original size:24 final size:21
Alignment explanation
Indices: 2447968--2448010 Score: 50
Period size: 21 Copynumber: 1.9 Consensus size: 21
2447958 TACATTACTT
*
2447968 AAAATTTTTATTTTTTATTAA
1 AAAATTTTTATTTTATATTAA
2447989 AAAATTATTTATATTTCATATT
1 AAAATT-TTTAT-TTT-ATATT
2448011 TATTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 3 0.17
24 4 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
AAAATTTTTATTTTATATTAA
Found at i:2448524 original size:2 final size:2
Alignment explanation
Indices: 2448513--2448552 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2448503 TCTATGTGCC
2448513 TA TA -A 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 TA TA T
2448553 GGAATCCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2449195 original size:10 final size:10
Alignment explanation
Indices: 2449180--2449204 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2449170 TACGAGTATA
2449180 TTAAAATTTT
1 TTAAAATTTT
2449190 TTAAAATTTT
1 TTAAAATTTT
2449200 TTAAA
1 TTAAA
2449205 GTTTCTCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAAAATTTT
Found at i:2450823 original size:84 final size:84
Alignment explanation
Indices: 2450682--2450846 Score: 321
Period size: 84 Copynumber: 2.0 Consensus size: 84
2450672 GAGGGGCAAG
2450682 CACCTGCCTTCCAAATTCAGCACTCAAACATTACTACAGAAAATATATAAAAGAGTTTCCCTTGT
1 CACCTGCCTTCCAAATTCAGCACTCAAACATTACTACAGAAAATATATAAAAGAGTTTCCCTTGT
2450747 ACACTTCCATTTTAAGGAC
66 ACACTTCCATTTTAAGGAC
*
2450766 CACCTGCCTTCCAAATTCGGCACTCAAACATTACTACAGAAAATATATAAAAGAGTTTCCCTTGT
1 CACCTGCCTTCCAAATTCAGCACTCAAACATTACTACAGAAAATATATAAAAGAGTTTCCCTTGT
2450831 ACACTTCCATTTTAAG
66 ACACTTCCATTTTAAG
2450847 CACCCAAACT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (84 bp):
CACCTGCCTTCCAAATTCAGCACTCAAACATTACTACAGAAAATATATAAAAGAGTTTCCCTTGT
ACACTTCCATTTTAAGGAC
Found at i:2452548 original size:10 final size:10
Alignment explanation
Indices: 2452510--2452568 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 10
2452500 AAATATAATT
2452510 ATAAAATATAAA
1 ATAAAATAT--A
2452522 ATAAAATAATA
1 ATAAAAT-ATA
*
2452533 CTTAAAATATA
1 -ATAAAATATA
2452544 ATAAAATATA
1 ATAAAATATA
2452554 AT-AAATATAA
1 ATAAAATAT-A
2452564 ATAAA
1 ATAAA
2452569 TTTACAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
9 6 0.15
10 14 0.34
11 6 0.15
12 13 0.32
13 2 0.05
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAAAATATA
Found at i:2453509 original size:16 final size:16
Alignment explanation
Indices: 2453447--2453518 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
2453437 TTGGATTAAA
2453447 TAAA-TTAAATTAATT
1 TAAATTTAAATTAATT
*
2453462 TAAATTTAATTTAATT
1 TAAATTTAAATTAATT
* *
2453478 CATATTTTAAA--AATTT
1 TA-AATTTAAATTAA-TT
*
2453494 TAAATTTAAATTATTT
1 TAAATTTAAATTAATT
*
2453510 TAATTTTAA
1 TAAATTTAA
2453519 GCCACGAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
15 13 0.30
16 24 0.55
17 7 0.16
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTTAAATTAATT
Found at i:2455354 original size:3 final size:3
Alignment explanation
Indices: 2455346--2455386 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2455336 ATATATACAA
2455346 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2455387 AAAATATACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2459339 original size:17 final size:19
Alignment explanation
Indices: 2459311--2459346 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2459301 AGTTAATTTG
2459311 ATTTTAATTAAAAT-TATT
1 ATTTTAATTAAAATATATT
2459329 ATTTTAA-TAAAATATATT
1 ATTTTAATTAAAATATATT
2459347 TTTATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATTAAAATATATT
Found at i:2459348 original size:15 final size:18
Alignment explanation
Indices: 2459311--2459358 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 18
2459301 AGTTAATTTG
2459311 ATTTTAATTAAAATTATT
1 ATTTTAATTAAAATTATT
2459329 ATTTTAA-TAAAA-TA-T
1 ATTTTAATTAAAATTATT
* *
2459344 ATTTTTATTTAAATT
1 ATTTTAATTAAAATT
2459359 TAATTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.27
16 6 0.23
17 6 0.23
18 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTAATTAAAATTATT
Found at i:2459373 original size:22 final size:22
Alignment explanation
Indices: 2459348--2459391 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2459338 AAATATATTT
*
2459348 TTATTTAAAT-TTAATTATAAAA
1 TTATATAAATATTAA-TATAAAA
2459370 TTATATAAATATTAATATAAAA
1 TTATATAAATATTAATATAAAA
2459392 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATATAAATATTAATATAAAA
Found at i:2463769 original size:4 final size:4
Alignment explanation
Indices: 2463762--2463792 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2463752 ATATATATAT
2463762 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2463793 TATTAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Done.