Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 11 of 19
Found at i:2335426 original size:16 final size:16
Alignment explanation
Indices: 2335405--2335455 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
2335395 TTGATAAATA
2335405 ATTTTAAAATAATATT
1 ATTTTAAAATAATATT
2335421 ATTTT--AATAAT-TT
1 ATTTTAAAATAATATT
*
2335434 ATTTTAAAATTAAAATT
1 ATTTTAAAA-TAATATT
2335451 ATTTT
1 ATTTT
2335456 GATTAATCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
15 2 0.07
16 8 0.27
17 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTAAAATAATATT
Found at i:2335437 original size:13 final size:13
Alignment explanation
Indices: 2335412--2335444 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2335402 ATAATTTTAA
2335412 AATAATATTATTTT
1 AATAAT-TTATTTT
2335426 AATAATTTATTTT
1 AATAATTTATTTT
2335439 AA-AATT
1 AATAATT
2335445 AAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 9 0.47
14 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATAATTTATTTT
Found at i:2335784 original size:22 final size:24
Alignment explanation
Indices: 2335746--2335793 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
2335736 AATTTACATA
*
2335746 TTATTAATAAATTAAATAAT-TTT
1 TTATTAATAAATAAAATAATGTTT
*
2335769 TTATTAA-AAATAAAATTATGTTT
1 TTATTAATAAATAAAATAATGTTT
2335792 TT
1 TT
2335794 TTATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTATTAATAAATAAAATAATGTTT
Found at i:2335992 original size:17 final size:17
Alignment explanation
Indices: 2335940--2335993 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 17
2335930 TAACTTTTAA
2335940 TAATTT-TAAAAAATTAT
1 TAATTTATAAAAAA-TAT
2335957 TAATTTGATATATAAAATAT
1 TAATTT-ATA-A-AAAATAT
2335977 TAATTTATAAAAAATAT
1 TAATTTATAAAAAATAT
2335994 AAAAAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 13 0.39
18 1 0.03
19 5 0.15
20 10 0.30
21 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAATTTATAAAAAATAT
Found at i:2336058 original size:24 final size:24
Alignment explanation
Indices: 2336026--2336079 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 24
2336016 GAATATTCTC
2336026 TAATGATATTAATTATATTAATAA-TAA
1 TAAT-ATATTAA--ATA-TAATAATTAA
2336053 TAATATATTAAATATAATAATTAA
1 TAATATATTAAATATAATAATTAA
2336077 TAA
1 TAA
2336080 ATTTATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.23
24 9 0.35
26 7 0.27
27 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATATATTAAATATAATAATTAA
Found at i:2336061 original size:17 final size:17
Alignment explanation
Indices: 2336039--2336073 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2336029 TGATATTAAT
2336039 TATATT-AATAATAATAA
1 TATATTAAAT-ATAATAA
2336056 TATATTAAATATAATAA
1 TATATTAAATATAATAA
2336073 T
1 T
2336074 TAATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATTAAATATAATAA
Found at i:2336485 original size:3 final size:3
Alignment explanation
Indices: 2336477--2336503 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2336467 CGATGGACCA
2336477 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2336504 TTCTAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2337447 original size:18 final size:19
Alignment explanation
Indices: 2337415--2337458 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
2337405 TTAAAAATAT
*
2337415 AATTATATTTTATATTTTA
1 AATTATATTTGATATTTTA
2337434 AATTA-ATTTGATATTTT-
1 AATTATATTTGATATTTTA
2337451 AATTATAT
1 AATTATAT
2337459 CATTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 13 0.57
19 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
AATTATATTTGATATTTTA
Found at i:2340601 original size:36 final size:37
Alignment explanation
Indices: 2340532--2340602 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
2340522 TTTTTATGTT
* *
2340532 AATATTTTTATATATTTTAATTAAATTTAAATAAATA
1 AATATTTTTATATATTTAAATAAAATTTAAATAAATA
2340569 AATATTTTTAT-TA-TTAAATAATAATTTAAATAAA
1 AATATTTTTATATATTTAAATAA-AATTTAAATAAA
2340603 ATCAATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 6 0.19
36 14 0.45
37 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
AATATTTTTATATATTTAAATAAAATTTAAATAAATA
Found at i:2342580 original size:2 final size:2
Alignment explanation
Indices: 2342573--2342603 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2342563 ACTTATAGCT
2342573 TC 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 TC T
2342604 TTTAATGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2343173 original size:2 final size:2
Alignment explanation
Indices: 2343166--2343191 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2343156 TTTCAAGGTA
2343166 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2343192 TACACGCACA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2347765 original size:18 final size:20
Alignment explanation
Indices: 2347737--2347773 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2347727 ACGAGCAGTG
2347737 CTCACCAATATTG-ACTTTC
1 CTCACCAATATTGCACTTTC
2347756 CTCA-CAATATTGCACTTT
1 CTCACCAATATTGCACTTT
2347774 TGCATGCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (20 bp):
CTCACCAATATTGCACTTTC
Found at i:2351095 original size:16 final size:17
Alignment explanation
Indices: 2351074--2351105 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2351064 ATTATCTATC
2351074 TATATTAA-TATTAAAT
1 TATATTAATTATTAAAT
2351090 TATATTAATTATTAAA
1 TATATTAATTATTAAA
2351106 AAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATTAATTATTAAAT
Found at i:2351127 original size:5 final size:6
Alignment explanation
Indices: 2351105--2351135 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
2351095 TAATTATTAA
2351105 AAAAATT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAA-T AAAAAT AAAAAT AAAAAT AAAAAT
2351136 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:2352064 original size:17 final size:17
Alignment explanation
Indices: 2352038--2352071 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2352028 TTAATTATGA
*
2352038 ATATTAGATATAAATAT
1 ATATTAGATAAAAATAT
*
2352055 ATATTTGATAAAAATAT
1 ATATTAGATAAAAATAT
2352072 TTTTAAAATT
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:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATATTAGATAAAAATAT
Found at i:2368005 original size:2 final size:2
Alignment explanation
Indices: 2367998--2368032 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2367988 TAACATAATG
2367998 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 A
2368033 CTTTTATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2368741 original size:19 final size:19
Alignment explanation
Indices: 2368713--2368750 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2368703 TTTAATTTAA
*
2368713 TTAATTTAT-ATAATTATTT
1 TTAATATATAATAA-TATTT
2368732 TTAATATATAATAATATTT
1 TTAATATATAATAATATTT
2368751 ATTTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAATATATAATAATATTT
Found at i:2369122 original size:2 final size:2
Alignment explanation
Indices: 2369115--2369164 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
2369105 TCAAGTAAGA
* * *
2369115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2369157 GT AT AT AT
1 AT AT AT AT
2369165 TTTGTTGTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:2369953 original size:2 final size:2
Alignment explanation
Indices: 2369946--2369978 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2369936 CGGTAAAACA
2369946 TC TC 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 TC TC T
2369979 TATTATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2373368 original size:13 final size:13
Alignment explanation
Indices: 2373350--2373375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2373340 CATCCTGACC
2373350 ACAAAAAAAAAAA
1 ACAAAAAAAAAAA
2373363 ACAAAAAAAAAAA
1 ACAAAAAAAAAAA
2373376 TATCGAGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
ACAAAAAAAAAAA
Found at i:2373433 original size:15 final size:15
Alignment explanation
Indices: 2373413--2373443 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2373403 AACAAAAGTG
2373413 AGGACTAATATACTT
1 AGGACTAATATACTT
*
2373428 AGGACTTATATACTT
1 AGGACTAATATACTT
2373443 A
1 A
2373444 CAGATATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (15 bp):
AGGACTAATATACTT
Found at i:2374353 original size:15 final size:15
Alignment explanation
Indices: 2374326--2374374 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2374316 TTATTTTTAA
*
2374326 AAAAAT-TATATATT
1 AAAAATATAAATATT
2374340 AAAAATATAAATATT
1 AAAAATATAAATATT
* * *
2374355 AAATATAAAAATTTT
1 AAAAATATAAATATT
2374370 AAAAA
1 AAAAA
2374375 AAATAAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 6 0.21
15 23 0.79
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAATATAAATATT
Found at i:2377574 original size:23 final size:20
Alignment explanation
Indices: 2377539--2377588 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 20
2377529 TAAAATATTT
2377539 TATTTAA-ATTTAATTATAAAAA
1 TATTTAATA-TTAA-TAT-AAAA
2377561 TATATTAATATTAATATAAAA
1 TAT-TTAATATTAATATAAAA
2377582 TATTTAA
1 TATTTAA
2377589 AAGATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 4 0.15
21 7 0.27
22 6 0.23
23 8 0.31
24 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTTAATATTAATATAAAA
Found at i:2378031 original size:2 final size:2
Alignment explanation
Indices: 2378024--2378052 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2378014 TTTAATGTTC
2378024 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 A
2378053 GGCTGTCGGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2378912 original size:2 final size:2
Alignment explanation
Indices: 2378905--2378937 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2378895 ATGGAGTACT
2378905 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 T
2378938 GTAAACGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2380047 original size:20 final size:20
Alignment explanation
Indices: 2380006--2380078 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
2379996 TGGGGTATCC
*
2380006 ATATTATAATTATATTTAAT
1 ATATTATAATTATATGTAAT
*
2380026 ATATTATATATT-TATGTCAT
1 ATATTATA-ATTATATGTAAT
* * **
2380046 AT-TTTTATTTATATCAAAT
1 ATATTATAATTATATGTAAT
*
2380065 CATATTTTAATTAT
1 -ATATTATAATTAT
2380079 TTATCATGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.05
19 9 0.22
20 18 0.44
21 12 0.29
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (20 bp):
ATATTATAATTATATGTAAT
Found at i:2380762 original size:12 final size:12
Alignment explanation
Indices: 2380745--2380769 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2380735 AATTTTTTTA
2380745 ATTTTATTATTT
1 ATTTTATTATTT
2380757 ATTTTATTATTT
1 ATTTTATTATTT
2380769 A
1 A
2380770 AATAATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTATTATTT
Found at i:2380803 original size:19 final size:19
Alignment explanation
Indices: 2380781--2380819 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2380771 ATAATATTAA
*
2380781 TATATGTAA-AATTTTATTT
1 TATAT-TAATAATTATATTT
2380800 TATATTAATAATTATATTT
1 TATATTAATAATTATATTT
2380819 T
1 T
2380820 TATAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TATATTAATAATTATATTT
Found at i:2382992 original size:2 final size:2
Alignment explanation
Indices: 2382987--2383023 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2382977 ATATATATGT
2382987 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2383024 AGTATAATTG
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2387469 original size:22 final size:22
Alignment explanation
Indices: 2387441--2387489 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2387431 TATCCATCGA
*
2387441 ATTTTCAGGTTCTCGTGAATGT
1 ATTTTCAGGTTCGCGTGAATGT
*
2387463 ATTTTCAGTTTCGCGTGAATGT
1 ATTTTCAGGTTCGCGTGAATGT
2387485 ATTTT
1 ATTTT
2387490 TCTTTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.49
Consensus pattern (22 bp):
ATTTTCAGGTTCGCGTGAATGT
Found at i:2390049 original size:16 final size:16
Alignment explanation
Indices: 2390028--2390059 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2390018 TTTTGAAGGT
2390028 GAGCATAACTCTGTCA
1 GAGCATAACTCTGTCA
2390044 GAGCATAACTCTGTCA
1 GAGCATAACTCTGTCA
2390060 ACTATGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (16 bp):
GAGCATAACTCTGTCA
Found at i:2393504 original size:26 final size:28
Alignment explanation
Indices: 2393456--2393528 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
2393446 TAGAGTGATG
**
2393456 AATAAATTTAAATATAATTACAT-AATA
1 AATAAATTTAAATATAAAAACATAAATA
*
2393483 AATAAATTT-TATATAAAAACATAAATA
1 AATAAATTTAAATATAAAAACATAAATA
*
2393510 AATATATTTATACATATAA
1 AATAAATTTA-A-ATATAA
2393529 TTAATTACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
26 10 0.27
27 21 0.57
30 6 0.16
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (28 bp):
AATAAATTTAAATATAAAAACATAAATA
Found at i:2393539 original size:14 final size:14
Alignment explanation
Indices: 2393520--2393570 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
2393510 AATATATTTA
2393520 TACATATAATTAAT
1 TACATATAATTAAT
*
2393534 TACATA-AAATAATTT
1 TACATATAATTAA--T
*
2393549 TATATATAATTAAT
1 TACATATAATTAAT
2393563 TACATATA
1 TACATATA
2393571 TAGATAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 5 0.17
14 14 0.47
15 6 0.20
16 5 0.17
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (14 bp):
TACATATAATTAAT
Found at i:2393562 original size:29 final size:31
Alignment explanation
Indices: 2393509--2393568 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
2393499 AAACATAAAT
2393509 AAATATATTTATACATATAATTAATTACATA
1 AAATATATTTATACATATAATTAATTACATA
*
2393540 AAATA-ATTT-TATATATAATTAATTACATA
1 AAATATATTTATACATATAATTAATTACATA
2393569 TATAGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 19 0.68
30 4 0.14
31 5 0.18
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (31 bp):
AAATATATTTATACATATAATTAATTACATA
Found at i:2393577 original size:20 final size:19
Alignment explanation
Indices: 2393549--2393590 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2393539 AAAATAATTT
* *
2393549 TATATATAATTAATTACATA
1 TATAGATAAATAATTACA-A
2393569 TATAGATAAATAATTACAA
1 TATAGATAAATAATTACAA
2393588 TAT
1 TAT
2393591 TATAAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAGATAAATAATTACAA
Found at i:2395733 original size:19 final size:19
Alignment explanation
Indices: 2395683--2395751 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
2395673 ATAGCTCGAC
* * *
2395683 TTATTTATTAAA-TAAATT
1 TTATTTTTTAAATTTAATA
*
2395701 TTATTTTTT-TATTTAATA
1 TTATTTTTTAAATTTAATA
2395719 TTATTTTTTAAATTTAATA
1 TTATTTTTTAAATTTAATA
2395738 TT-TTTATTTAAATT
1 TTATTT-TTTAAATT
2395752 CTTATTTCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.02
18 24 0.56
19 18 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTTTTAAATTTAATA
Found at i:2399095 original size:141 final size:141
Alignment explanation
Indices: 2398835--2399113 Score: 450
Period size: 141 Copynumber: 2.0 Consensus size: 141
2398825 TATTTTGCTT
* * * *
2398835 ACTTAAAACACAATGTTTATAGAAAGGTAGATTTGTTGTTTTGAGTCTAAGAAGCAATCCACTAT
1 ACTTAAAACACAATGCTTACAAAAAGGTAGATTTGTTGTTTTGAGTCCAAGAAGCAATCCACTAT
* * * *
2398900 TAGATAAAATCTTTATACCTCGTTCTAACATATGACCTAATCTACAATGTCACATCATTGTTGAT
66 CAGATAAAATCTATATACCTCATTCTAACATATGACCTAATCTACAATGCCACATCATTGTTGAT
2398965 TCTTCATCTGA
131 TCTTCATCTGA
*
2398976 ACTTAAAACACAATGCTTACAAAAAGGTAGATTTGTTGTTTTGAGTCCAATAAGCAATCCACTAT
1 ACTTAAAACACAATGCTTACAAAAAGGTAGATTTGTTGTTTTGAGTCCAAGAAGCAATCCACTAT
* * *
2399041 CAGATAAAATCTATATACCTTATTCTGACATATGACCTAATCTACGATGCCACATCATTGTTGAT
66 CAGATAAAATCTATATACCTCATTCTAACATATGACCTAATCTACAATGCCACATCATTGTTGAT
2399106 TCTTCATC
131 TCTTCATC
2399114 CGAATTGGTT
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
141 126 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (141 bp):
ACTTAAAACACAATGCTTACAAAAAGGTAGATTTGTTGTTTTGAGTCCAAGAAGCAATCCACTAT
CAGATAAAATCTATATACCTCATTCTAACATATGACCTAATCTACAATGCCACATCATTGTTGAT
TCTTCATCTGA
Found at i:2400766 original size:50 final size:50
Alignment explanation
Indices: 2400705--2400873 Score: 173
Period size: 50 Copynumber: 3.4 Consensus size: 50
2400695 AGATGCTTAG
* * *
2400705 AATCAACAATTATGGTCACCTT-TCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AATCAACAATTATGATCA-CTTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
* * * * *
2400755 AATCAATAATTA-CAACTACTTCTCTCGATTATCAAAGGTTTGTG-AGAAAT
1 AATCAACAATTATGATC-ACTTCTCTCGATTGTCAAAGGTTAGTGAAG-AAT
* * * *
2400805 AGTCAACAATTACGACCACTTCTCTCGATTGTAAAAGGTTAGTGAAGAAT
1 AATCAACAATTATGATCACTTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
*
2400855 AATCAATAATTATGATCAC
1 AATCAACAATTATGATCAC
2400874 CTCTTTTGTA
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
49 6 0.06
50 86 0.90
51 4 0.04
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (50 bp):
AATCAACAATTATGATCACTTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
Found at i:2403295 original size:31 final size:33
Alignment explanation
Indices: 2403259--2403322 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
2403249 TGTAGTGATT
*
2403259 AAAATTTAT-TTAATT-ATTATTTTTTTTAAAA
1 AAAATTTATATTAATTAATTATTTTTATTAAAA
*
2403290 AAAATTTATAATTAATTAATTGTTTTTATTAAA
1 AAAATTTAT-ATTAATTAATTATTTTTATTAAA
2403323 TTAAAAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 9 0.32
33 6 0.21
34 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (33 bp):
AAAATTTATATTAATTAATTATTTTTATTAAAA
Found at i:2404430 original size:2 final size:2
Alignment explanation
Indices: 2404423--2404452 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2404413 CCTGGATTTC
2404423 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
2404453 TGTCCGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2406405 original size:51 final size:50
Alignment explanation
Indices: 2406318--2406424 Score: 173
Period size: 51 Copynumber: 2.1 Consensus size: 50
2406308 ATTAAAAAAA
2406318 TAATTTATAATTTAAATTTAAATTATAAAATATTAATATAAAATA-TTTT
1 TAATTTATAATTTAAATTTAAATTATAAAATATTAATATAAAATATTTTT
2406367 TAATTTA-AATTTAAATTATAAAATTATAAAAATATTAATATAAAATATTTTT
1 TAATTTATAATTTAAATT-T-AAATTAT-AAAATATTAATATAAAATATTTTT
2406419 TAATTT
1 TAATTT
2406425 TTATTATTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
48 10 0.19
49 8 0.15
50 7 0.13
51 19 0.35
52 10 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (50 bp):
TAATTTATAATTTAAATTTAAATTATAAAATATTAATATAAAATATTTTT
Found at i:2406413 original size:13 final size:13
Alignment explanation
Indices: 2406341--2406415 Score: 54
Period size: 13 Copynumber: 5.8 Consensus size: 13
2406331 AAATTTAAAT
2406341 TATAAAATATTAA
1 TATAAAATATTAA
2406354 TATAAAATATTTTTAA
1 TATAAAATA---TTAA
*
2406370 T-TTAAAT-TTAA
1 TATAAAATATTAA
2406381 -ATTATAAA-ATT-A
1 TA-TA-AAATATTAA
2406393 TA-AAAATATTAA
1 TATAAAATATTAA
2406405 TATAAAATATT
1 TATAAAATATT
2406416 TTTTAATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 22
0.67 0.03 0.30
Matches are distributed among these distances:
10 3 0.06
11 8 0.16
12 5 0.10
13 23 0.47
15 5 0.10
16 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATAAAATATTAA
Found at i:2406776 original size:6 final size:6
Alignment explanation
Indices: 2406765--2406804 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
2406755 GCGTGCCCTT
*
2406765 GTCCTA GTCCTA GTCCTA GTCCTA GTCCTA GTCATA GTCC
1 GTCCTA GTCCTA GTCCTA GTCCTA GTCCTA GTCCTA GTCC
2406805 AATTCTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (6 bp):
GTCCTA
Found at i:2407357 original size:21 final size:21
Alignment explanation
Indices: 2407328--2407380 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
2407318 ATGTAATATA
* *
2407328 ATAAGATATTTAAAATAA-AAT
1 ATAAAATATATAAAA-AATAAT
2407349 ATAAAATATATAAAAAATTAAT
1 ATAAAATATATAAAAAA-TAAT
2407371 AT-AAATATAT
1 ATAAAATATAT
2407381 GAATATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 21 0.75
22 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
ATAAAATATATAAAAAATAAT
Found at i:2407369 original size:29 final size:29
Alignment explanation
Indices: 2407337--2407393 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2407327 AATAAGATAT
2407337 TTAAAATAAA-ATATAAAATATATAAAAAA
1 TTAAAATAAATATAT-AAATATATAAAAAA
* * *
2407366 TTAATATAAATATATGAATATATTAAAA
1 TTAAAATAAATATATAAATATATAAAAA
2407394 TTTATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
TTAAAATAAATATATAAATATATAAAAAA
Found at i:2407425 original size:31 final size:33
Alignment explanation
Indices: 2407354--2407454 Score: 92
Period size: 29 Copynumber: 3.2 Consensus size: 33
2407344 AAAATATAAA
*
2407354 ATATATAAAAAATTAATATAAATATATGA-A---T
1 ATATAT-AAAAATT-ATATAAATATATAATATTTT
*
2407385 ATAT-TAAAATTTATAT-AATATA-AAT-TTTT
1 ATATATAAAAATTATATAAATATATAATATTTT
*
2407414 ATATATAAAAATTATTTAAATATATAATATTTT
1 ATATATAAAAATTATATAAATATATAATATTTT
*
2407447 AAATATAA
1 ATATATAA
2407455 TTTGAATGTG
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
26 1 0.02
27 6 0.11
28 4 0.07
29 11 0.19
30 11 0.19
31 10 0.18
32 3 0.05
33 11 0.19
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (33 bp):
ATATATAAAAATTATATAAATATATAATATTTT
Found at i:2407431 original size:17 final size:17
Alignment explanation
Indices: 2407393--2407437 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2407383 ATATATTAAA
*
2407393 ATTTATATAATATAAATT
1 ATTTATAT-ATAAAAATT
2407411 -TTTATATATAAAAATT
1 ATTTATATATAAAAATT
*
2407427 ATTTAAATATA
1 ATTTATATATA
2407438 TAATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTATATATAAAAATT
Found at i:2411081 original size:2 final size:2
Alignment explanation
Indices: 2411069--2411101 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2411059 GATGTAAGTT
*
2411069 TA TA CA 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 T
2411102 GACTTAATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2411485 original size:5 final size:5
Alignment explanation
Indices: 2411475--2411508 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
2411465 AAAAAGGATT
2411475 GCCAA GCCAA GCCAA GCCAA GCCAA GCCAA GCCA
1 GCCAA GCCAA GCCAA GCCAA GCCAA GCCAA GCCA
2411509 GGAGCTGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.38, C:0.41, G:0.21, T:0.00
Consensus pattern (5 bp):
GCCAA
Found at i:2414534 original size:2 final size:2
Alignment explanation
Indices: 2414529--2414562 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2414519 GTGTGTGTGT
*
2414529 GA GA GA GT GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2414563 AGGGGGGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:2416527 original size:2 final size:2
Alignment explanation
Indices: 2416520--2416545 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2416510 ATCTAAATTT
2416520 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
2416546 CATTCAATAA
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:2423228 original size:12 final size:13
Alignment explanation
Indices: 2423206--2423234 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2423196 AAACATCTGG
2423206 ATTTCATTTATTT
1 ATTTCATTTATTT
2423219 ATTT-ATTTATTT
1 ATTTCATTTATTT
2423231 ATTT
1 ATTT
2423235 TAGATCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTCATTTATTT
Found at i:2431028 original size:16 final size:17
Alignment explanation
Indices: 2430990--2431044 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
2430980 AAATAATTTA
2430990 AATATAATA-AAAATAT
1 AATATAATATAAAATAT
*
2431006 AAAATAATATAAAAT-T
1 AATATAATATAAAATAT
* * *
2431022 TATATAAAATAAATTAT
1 AATATAATATAAAATAT
2431039 AATATA
1 AATATA
2431045 TTTGTTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATATAATATAAAATAT
Found at i:2431803 original size:17 final size:16
Alignment explanation
Indices: 2431754--2431805 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2431744 TGAATATATC
*
2431754 ATAATTTAATATAA-A
1 ATAATTAAATATAATA
*
2431769 ATATTTTAAATATAATA
1 ATA-ATTAAATATAATA
*
2431786 ATAATTAAATCTATATA
1 ATAATTAAATATA-ATA
2431803 ATA
1 ATA
2431806 TCATGGTAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 3 0.10
16 17 0.57
17 10 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATTAAATATAATA
Found at i:2433697 original size:30 final size:29
Alignment explanation
Indices: 2433629--2433697 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
2433619 CATGTTTAAG
* *
2433629 ATTTAATTTATTTTTTAAATAATTTTTTA
1 ATTTAAATTATTTTTTAAATAATTTTGTA
*
2433658 ATTTAAAATTATTTTTTAACTCAATATTTGT-
1 ATTT-AAATTATTTTTTAAAT-AAT-TTTGTA
2433689 ATTTAAATT
1 ATTTAAATT
2433698 CTCATAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 4 0.12
30 19 0.56
31 7 0.21
32 4 0.12
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (29 bp):
ATTTAAATTATTTTTTAAATAATTTTGTA
Found at i:2440327 original size:33 final size:33
Alignment explanation
Indices: 2440285--2440350 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2440275 GATATAAACA
2440285 AGTCATTCTCAATTAGCAACTCATTAACTCAGC
1 AGTCATTCTCAATTAGCAACTCATTAACTCAGC
2440318 AGTCATTCTCAATTAGCAACTCATTAACTCAGC
1 AGTCATTCTCAATTAGCAACTCATTAACTCAGC
2440351 CTTCATAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.30
Consensus pattern (33 bp):
AGTCATTCTCAATTAGCAACTCATTAACTCAGC
Found at i:2444077 original size:18 final size:18
Alignment explanation
Indices: 2444028--2444095 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
2444018 TTGTTCATTG
* *
2444028 TTTAATTAAAAATATAATA
1 TTTAAATAAAAAAATAA-A
* **
2444047 TTAAAATTTAAAAATAAA
1 TTTAAATAAAAAAATAAA
*
2444065 TTTAAATAAAAAATTAAA
1 TTTAAATAAAAAAATAAA
* *
2444083 TCTGAATAAAAAA
1 TTTAAATAAAAAA
2444096 TAGTCAAACT
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
18 26 0.68
19 12 0.32
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (18 bp):
TTTAAATAAAAAAATAAA
Found at i:2444096 original size:18 final size:18
Alignment explanation
Indices: 2444056--2444096 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2444046 ATTAAAATTT
*
2444056 AAAAA-TAAATTTAAATA
1 AAAAATTAAATCTAAATA
*
2444073 AAAAATTAAATCTGAATA
1 AAAAATTAAATCTAAATA
2444091 AAAAAT
1 AAAAAT
2444097 AGTCAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAATTAAATCTAAATA
Found at i:2446517 original size:11 final size:11
Alignment explanation
Indices: 2446503--2446633 Score: 83
Period size: 11 Copynumber: 12.1 Consensus size: 11
2446493 CTATAATTTT
2446503 AAATATAATAA
1 AAATATAATAA
2446514 AAATATAATATA
1 AAATATAATA-A
*
2446526 AAA-ATTAATTA
1 AAATA-TAATAA
2446537 AAATATAAT-A
1 AAATATAATAA
*
2446547 TAATATAATAA
1 AAATATAATAA
*
2446558 AAA-ATAATAT
1 AAATATAATAA
2446568 AAATAT-ATAA
1 AAATATAATAA
* * * *
2446578 TATTTTAAATAT
1 AAATAT-AATAA
* *
2446590 AACTATAATTA
1 AAATATAATAA
*
2446601 AAA-ATAATAT
1 AAATATAATAA
* *
2446611 AAATTTAATAT
1 AAATATAATAA
*
2446622 AAATATGATAA
1 AAATATAATAA
2446633 A
1 A
2446634 TTACATTAAT
Statistics
Matches: 91, Mismatches: 21, Indels: 16
0.71 0.16 0.12
Matches are distributed among these distances:
10 32 0.35
11 44 0.48
12 15 0.16
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (11 bp):
AAATATAATAA
Found at i:2446522 original size:23 final size:22
Alignment explanation
Indices: 2446502--2446627 Score: 125
Period size: 21 Copynumber: 5.8 Consensus size: 22
2446492 CCTATAATTT
2446502 TAAATATAATAAAAATATAATA
1 TAAATATAATAAAAATATAATA
* *
2446524 TAAAAATTAATTAAAATATAATA
1 TAAATA-TAATAAAAATATAATA
2446547 T-AATATAATAAAAA-ATAATA
1 TAAATATAATAAAAATATAATA
* * *
2446567 TAAATAT-ATAATATTTTAAATA
1 TAAATATAATAAAAATAT-AATA
* *
2446589 TAACTATAATTAAAA-ATAATA
1 TAAATATAATAAAAATATAATA
* *
2446610 TAAATTTAATATAAATAT
1 TAAATATAATAAAAATAT
2446628 GATAAATTAC
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
20 12 0.15
21 29 0.35
22 21 0.26
23 20 0.24
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATATAATAAAAATATAATA
Found at i:2446523 original size:5 final size:5
Alignment explanation
Indices: 2446504--2446623 Score: 74
Period size: 5 Copynumber: 24.4 Consensus size: 5
2446494 TATAATTTTA
* *
2446504 AATAT AATAAA AATAT AATAT AA-A- AAT-T AATTAA AATAT AATAT AATAT
1 AATAT AAT-AT AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT
* * **
2446553 AATAA AAAAT AATAT AA-AT -ATAT AATAT TTTA- AATAT AACTAT AAT-T
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA-TAT AATAT
* *
2446600 AAAAAT AATAT AAATTT AATAT AA
1 -AATAT AATAT -AATAT AATAT AA
2446624 ATATGATAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 24
0.69 0.13 0.19
Matches are distributed among these distances:
3 3 0.03
4 10 0.11
5 58 0.67
6 16 0.18
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:2446552 original size:33 final size:32
Alignment explanation
Indices: 2446503--2446624 Score: 124
Period size: 33 Copynumber: 3.8 Consensus size: 32
2446493 CTATAATTTT
*
2446503 AAATATAATAAAAATATAATATAAAAATTAATTA
1 AAATATAAT-ATAATATAATATAAAAA-TAATTA
2446537 AAATATAATATAATATAATA-AAAAATAATATA
1 AAATATAATATAATATAATATAAAAATAAT-TA
** **
2446569 AATATATAATATTTTA-AATATAACTATAATTA
1 AA-ATATAATATAATATAATATAAAAATAATTA
*
2446601 AAA-ATAATATAAATTTAATATAAA
1 AAATATAATAT-AATATAATATAAA
2446625 TATGATAAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
30 7 0.09
31 6 0.08
32 24 0.32
33 28 0.38
34 9 0.12
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (32 bp):
AAATATAATATAATATAATATAAAAATAATTA
Found at i:2446597 original size:43 final size:42
Alignment explanation
Indices: 2446504--2446623 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 42
2446494 TATAATTTTA
* *
2446504 AATATAATAAAAATATAATATAAAAATTAATTAAAATATAATAT
1 AATATAATAAAAA-ATAATATAAATATTAA-TATAATATAATAT
**
2446548 AATATAATAAAAAATAATATAAATATATAATATTTTA-AATAT
1 AATATAATAAAAAATAATATAAATAT-TAATATAATATAATAT
*
2446590 AACTATAATTAAAAATAATATAAAT-TTAATATAA
1 AA-TATAATAAAAAATAATATAAATATTAATATAA
2446624 ATATGATAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
41 6 0.09
42 8 0.12
43 37 0.55
44 16 0.24
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (42 bp):
AATATAATAAAAAATAATATAAATATTAATATAATATAATAT
Found at i:2446601 original size:16 final size:15
Alignment explanation
Indices: 2446504--2446623 Score: 74
Period size: 16 Copynumber: 8.1 Consensus size: 15
2446494 TATAATTTTA
*
2446504 AATATAATAAAAATAT
1 AATATAAT-TAAATAT
2446520 AATATAA--AAAT-T
1 AATATAATTAAATAT
*
2446532 AAT-TAAAATATAATAT
1 AATAT-AATTA-AATAT
* *
2446548 AATATAATAAAAAAT
1 AATATAATTAAATAT
*
2446563 AATATAA--ATATAT
1 AATATAATTAAATAT
*
2446576 AATAT-TTTAAATAT
1 AATATAATTAAATAT
*
2446590 AACTATAATTAAAAAT
1 AA-TATAATTAAATAT
*
2446606 AATATAAATTTAATAT
1 AATAT-AATTAAATAT
2446622 AA
1 AA
2446624 ATATGATAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
11 1 0.01
12 6 0.07
13 13 0.16
14 8 0.10
15 20 0.24
16 33 0.40
17 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATAATTAAATAT
Found at i:2449396 original size:2 final size:2
Alignment explanation
Indices: 2449389--2449418 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2449379 TATTTTAACA
2449389 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
2449419 GAAGCATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2456625 original size:2 final size:2
Alignment explanation
Indices: 2456620--2456655 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2456610 TGAAAAGAAG
* *
2456620 TA TA TA TA TA AA TA AA 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
2456656 ACTTTAATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2460456 original size:2 final size:2
Alignment explanation
Indices: 2460451--2460485 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2460441 TAATAATAGA
2460451 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 A
2460486 AGTAATAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2461112 original size:3 final size:3
Alignment explanation
Indices: 2461104--2461130 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2461094 AACAAATATC
2461104 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
2461131 TATTATACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2462984 original size:3 final size:3
Alignment explanation
Indices: 2462976--2463007 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2462966 TAATTTTTTA
2462976 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2463008 GATACATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2463083 original size:17 final size:17
Alignment explanation
Indices: 2463039--2463091 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
2463029 TCATATTTAA
* *
2463039 ATTTAAATTTTTAATAT
1 ATTTAAATTTATATTAT
*
2463056 TTTTAATAATTTATATTAT
1 ATTT-A-AATTTATATTAT
2463075 ATTTAAATTTATATTAT
1 ATTTAAATTTATATTAT
2463092 TCATATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 15 0.50
18 2 0.07
19 13 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTAAATTTATATTAT
Found at i:2464329 original size:2 final size:2
Alignment explanation
Indices: 2464322--2464355 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2464312 TATTTTATTT
2464322 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
2464356 AGATTTTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2464951 original size:24 final size:23
Alignment explanation
Indices: 2464911--2464955 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
2464901 ATGTAGATAA
2464911 ATTTTAATAAAATTTAAGACTTAT
1 ATTTTAATAAAATTTAA-ACTTAT
*
2464935 ATTTTAATTTAAA-TTAAACTT
1 ATTTTAA-TAAAATTTAAACTT
2464956 GAACAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 11 0.58
25 4 0.21
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTTAATAAAATTTAAACTTAT
Found at i:2465731 original size:19 final size:17
Alignment explanation
Indices: 2465687--2465722 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
2465677 AATTTAATAA
2465687 ATTTATATATTTTATTAT
1 ATTTATAT-TTTTATTAT
2465705 ATTT-TATTTTTATTAT
1 ATTTATATTTTTATTAT
2465721 AT
1 AT
2465723 AATTATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 3 0.17
18 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTATATTTTTATTAT
Found at i:2467646 original size:3 final size:3
Alignment explanation
Indices: 2467624--2467686 Score: 64
Period size: 3 Copynumber: 21.7 Consensus size: 3
2467614 CATATAATTA
2467624 AAT AA- AAT AAAT AA- AAT AAT AAT AA- ATAT AA- AAT -AT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
2467666 AATT AAT AAT AAT AAT AAT AA
1 AA-T AAT AAT AAT AAT AAT AA
2467687 ATATTAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
2 9 0.17
3 36 0.69
4 7 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2467663 original size:16 final size:17
Alignment explanation
Indices: 2467623--2467698 Score: 77
Period size: 19 Copynumber: 4.4 Consensus size: 17
2467613 TCATATAATT
2467623 AAATAA-AAT-AA-ATA
1 AAATAATAATAAATATA
2467637 AAATAATAATAAATATAA
1 AAATAATAATAAATAT-A
*
2467655 AATATAATAATAATTAATA
1 AA-ATAATAATAAAT-ATA
2467674 ATAATAATAATAAATATTA
1 A-AATAATAATAAATA-TA
2467693 AAATAA
1 AAATAA
2467699 AGATCGAACA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 2 0.04
17 2 0.04
18 9 0.17
19 27 0.52
20 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAATAATAAATATA
Found at i:2468414 original size:4 final size:4
Alignment explanation
Indices: 2468405--2468438 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2468395 GTAACAGAAT
2468405 TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
2468439 AAATACCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:2469727 original size:24 final size:27
Alignment explanation
Indices: 2469654--2469724 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
2469644 AAACAAGCCT
* *
2469654 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
*
2469682 CCATTTTTTACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
2469709 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
2469725 AATGGGTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:2474287 original size:27 final size:28
Alignment explanation
Indices: 2474227--2474297 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 28
2474217 AAACAAGCCT
* * *
2474227 CCATATTTGATAAATACAAAGAAAACTA
1 CCATTTTTTATAAACACAAAGAAAACTA
*
2474255 CCATTTTTTATAAACACAAA-ATAACTA
1 CCATTTTTTATAAACACAAAGAAAACTA
* *
2474282 CTATTTTTTACAAACA
1 CCATTTTTTATAAACA
2474298 AATAGATAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (28 bp):
CCATTTTTTATAAACACAAAGAAAACTA
Found at i:2481139 original size:2 final size:2
Alignment explanation
Indices: 2481132--2481182 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2481122 AAAGGAAATT
2481132 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2481174 AG AG AG AG A
1 AG AG AG AG A
2481183 CTCAATGACC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2494697 original size:2 final size:2
Alignment explanation
Indices: 2494690--2494715 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2494680 ACCTTCATTT
2494690 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
2494716 AATAAAAAGT
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:2494792 original size:17 final size:16
Alignment explanation
Indices: 2494761--2494796 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2494751 AGTTGATATT
*
2494761 TAAATTTTAAATTTAA
1 TAAATATTAAATTTAA
2494777 TAAATATTATAATTTAA
1 TAAATATTA-AATTTAA
2494794 TAA
1 TAA
2494797 TGATTGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATATTAAATTTAA
Found at i:2495027 original size:23 final size:19
Alignment explanation
Indices: 2494996--2495044 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 19
2494986 AATTTAATAA
2494996 AAAATTTAATTATAAAAATAT
1 AAAATTTAA-TATAAAAA-AT
2495017 ATAAATATTAATATAAAAAAT
1 A-AAAT-TTAATATAAAAAAT
2495038 AAAATTT
1 AAAATTT
2495045 TTAATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.08
20 4 0.15
21 4 0.15
22 12 0.46
23 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTTAATATAAAAAAT
Found at i:2495198 original size:2 final size:2
Alignment explanation
Indices: 2495191--2495215 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2495181 CATTCATCAT
2495191 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
2495216 CAAAGGTGGC
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:2500729 original size:16 final size:17
Alignment explanation
Indices: 2500704--2500737 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2500694 TAAAAAATTA
2500704 ATTTATATTAAAATTTT
1 ATTTATATTAAAATTTT
*
2500721 ATTTA-ATTATAATTTT
1 ATTTATATTAAAATTTT
2500737 A
1 A
2500738 GAATTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTATATTAAAATTTT
Found at i:2501136 original size:23 final size:23
Alignment explanation
Indices: 2501088--2501139 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
2501078 TGGGTCAGAT
*
2501088 TTATTTTTACTATATTTTAATCTA
1 TTATTTTTAATATATTTTAA-CTA
2501112 TTATTTTTAAATATATTTTAA-TA
1 TTATTTTT-AATATATTTTAACTA
2501135 TTATT
1 TTATT
2501140 GTGATGCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 7 0.27
24 8 0.31
25 11 0.42
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
TTATTTTTAATATATTTTAACTA
Found at i:2502005 original size:20 final size:21
Alignment explanation
Indices: 2501982--2502037 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
2501972 AAAAATATTT
2501982 TAAATA-AAATTATGATAAAA
1 TAAATATAAATTATGATAAAA
*
2502002 TAAAATATATAATTATGATATAA
1 T-AAATATA-AATTATGATAAAA
2502025 -AAATATAAATTAT
1 TAAATATAAATTAT
2502038 TAAATATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 7 0.22
21 12 0.38
22 1 0.03
23 12 0.38
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
TAAATATAAATTATGATAAAA
Found at i:2502039 original size:23 final size:23
Alignment explanation
Indices: 2501989--2502039 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2501979 TTTTAAATAA
*
2501989 AATTATGATAAAATAAAATATAT
1 AATTATGATAAAATAAAATAAAT
*
2502012 AATTATGATATAAA-AATATAAAT
1 AATTATGATA-AAATAAAATAAAT
*
2502035 TATTA
1 AATTA
2502040 AATATAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTATGATAAAATAAAATAAAT
Found at i:2502052 original size:28 final size:27
Alignment explanation
Indices: 2501985--2502053 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 27
2501975 AATATTTTAA
*
2501985 ATAAA-ATTATGAT-AAAATAAAATAT
1 ATAAATATAATGATAAAAATAAAATAT
* *
2502010 ATAATTATGAT-ATAAAAATATAAAT-T
1 ATAAATATAATGATAAAAATA-AAATAT
2502036 ATTAAATATAATGATAAA
1 A-TAAATATAATGATAAA
2502054 GTTGAAGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
25 6 0.17
26 12 0.34
27 12 0.34
28 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
ATAAATATAATGATAAAAATAAAATAT
Found at i:2502847 original size:25 final size:26
Alignment explanation
Indices: 2502814--2502865 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
2502804 TGTAAATTTA
2502814 AAATATTAAATAATTTAT-TTTATAT
1 AAATATTAAATAATTTATATTTATAT
* * *
2502839 AAATTTTAATTAATTTATATTTTTAT
1 AAATATTAAATAATTTATATTTATAT
2502865 A
1 A
2502866 TTATATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
AAATATTAAATAATTTATATTTATAT
Found at i:2502873 original size:29 final size:28
Alignment explanation
Indices: 2502831--2502894 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
2502821 AAATAATTTA
2502831 TTTTATATAAATTTTAATTAATTTATAT
1 TTTTATATAAATTTTAATTAATTTATAT
*
2502859 TTTTATATTATATTTTAATT-ATTT-T-T
1 TTTTATA-TAAATTTTAATTAATTTATAT
*
2502885 TATTATATAA
1 TTTTATATAA
2502895 TATCATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 2 0.06
26 7 0.22
27 1 0.03
28 11 0.34
29 11 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTTATATAAATTTTAATTAATTTATAT
Found at i:2502893 original size:28 final size:27
Alignment explanation
Indices: 2502827--2502893 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
2502817 TATTAAATAA
2502827 TTTATTTTATATAAATTTTAATTAATT
1 TTTATTTTATATAAATTTTAATTAATT
* * *
2502854 TATATTTTTATATTATATTTTAATTATTT
1 TTTA-TTTTATA-TAAATTTTAATTAATT
*
2502883 TTTATTATATA
1 TTTATTTTATA
2502894 ATATCATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 3 0.09
28 13 0.39
29 17 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTATTTTATATAAATTTTAATTAATT
Found at i:2508960 original size:24 final size:26
Alignment explanation
Indices: 2508912--2508961 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2508902 TATATTTGAT
2508912 ATATTTTTAAATATAAATATTAAAATA
1 ATATTTTTAAATATAAATA-TAAAATA
*
2508939 ATATTTTT-TATATAAATA-AAAAT
1 ATATTTTTAAATATAAATATAAAAT
2508962 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
26 9 0.41
27 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTTTTAAATATAAATATAAAATA
Found at i:2510993 original size:23 final size:23
Alignment explanation
Indices: 2510966--2511011 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2510956 AAGATTGCCT
2510966 GAGAGACCCTTATGGCAAGTTCC
1 GAGAGACCCTTATGGCAAGTTCC
2510989 GAGAGACCCTTATGGCAAGTTCC
1 GAGAGACCCTTATGGCAAGTTCC
2511012 ATATAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (23 bp):
GAGAGACCCTTATGGCAAGTTCC
Found at i:2514741 original size:22 final size:24
Alignment explanation
Indices: 2514698--2514741 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
2514688 CATACATAAA
*
2514698 ATATTAAATAAATTTATATTTAAT
1 ATATTAAATAAATATATATTTAAT
*
2514722 ATATT-AAT-AATATATTTTTA
1 ATATTAAATAAATATATATTTA
2514742 TATTTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 3 0.17
24 5 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTAAATAAATATATATTTAAT
Found at i:2516380 original size:29 final size:27
Alignment explanation
Indices: 2516325--2516380 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
2516315 AATATAAATA
* * *
2516325 TAAATATATAATTTTTTAAATTTTTTT
1 TAAATATATAATATTTTAAAATATTTT
2516352 TAAATATATAAAATATTTTAAAATATTTT
1 TAAATATAT--AATATTTTAAAATATTTT
2516381 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.38
29 15 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TAAATATATAATATTTTAAAATATTTT
Found at i:2526816 original size:20 final size:20
Alignment explanation
Indices: 2526793--2526863 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
2526783 TTAAAAATTA
2526793 TTTTAAAAAATATGAATAGT
1 TTTTAAAAAATATGAATAGT
*
2526813 TTTT-AAAAATATTTAATTTTA-T
1 TTTTAAAAAATA-TGAA---TAGT
*
2526835 TTTTAAAAAATATGAGTAGT
1 TTTTAAAAAATATGAATAGT
2526855 TTTTAAAAA
1 TTTTAAAAA
2526864 TATTTAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
19 9 0.21
20 17 0.40
22 7 0.17
23 9 0.21
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (20 bp):
TTTTAAAAAATATGAATAGT
Found at i:2526820 original size:19 final size:19
Alignment explanation
Indices: 2526793--2526866 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
2526783 TTAAAAATTA
*
2526793 TTTTAAAAAATATGAATAG
1 TTTTTAAAAATATGAATAG
*
2526812 TTTTTAAAAATATTTAATTTTA-
1 TTTTTAAAAATA-TGAA---TAG
*
2526834 TTTTTAAAAAATATGAGTAG
1 TTTTT-AAAAATATGAATAG
2526854 TTTTTAAAAATAT
1 TTTTTAAAAATAT
2526867 TTAATTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
19 21 0.47
20 8 0.18
22 7 0.16
23 9 0.20
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (19 bp):
TTTTTAAAAATATGAATAG
Found at i:2526841 original size:42 final size:42
Alignment explanation
Indices: 2526793--2526888 Score: 183
Period size: 42 Copynumber: 2.3 Consensus size: 42
2526783 TTAAAAATTA
2526793 TTTTAAAAAATATGAATAGTTTTTAAAAATATTTAATTTTAT
1 TTTTAAAAAATATGAATAGTTTTTAAAAATATTTAATTTTAT
*
2526835 TTTTAAAAAATATGAGTAGTTTTTAAAAATATTTAATTTTAT
1 TTTTAAAAAATATGAATAGTTTTTAAAAATATTTAATTTTAT
2526877 TTTTAAAAAATA
1 TTTTAAAAAATA
2526889 ACATAATATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (42 bp):
TTTTAAAAAATATGAATAGTTTTTAAAAATATTTAATTTTAT
Found at i:2526888 original size:23 final size:22
Alignment explanation
Indices: 2526812--2526885 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
2526802 ATATGAATAG
2526812 TTTTTAAAAATATTTAATTTTA
1 TTTTTAAAAATATTTAATTTTA
* * *
2526834 TTTTTAAAAA-ATATGA--GTA
1 TTTTTAAAAATATTTAATTTTA
2526853 GTTTTTAAAAATATTTAATTTTA
1 -TTTTTAAAAATATTTAATTTTA
2526876 TTTTTAAAAA
1 TTTTTAAAAA
2526886 ATAACATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.05
20 10 0.24
21 8 0.19
22 20 0.48
23 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTTTAAAAATATTTAATTTTA
Found at i:2527222 original size:31 final size:35
Alignment explanation
Indices: 2527161--2527224 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
2527151 TTTGACACAT
2527161 AAATAAAAAAATTAATTTGATTTTTAAAATAAATAA
1 AAATAAAAAAATTAATTT-ATTTTTAAAATAAATAA
2527197 AAAT-AAAAAATTAA-TT-TTTTT-AAATAAA
1 AAATAAAAAAATTAATTTATTTTTAAAATAAA
2527225 ATGTTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 7 0.25
32 5 0.18
34 2 0.07
35 10 0.36
36 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (35 bp):
AAATAAAAAAATTAATTTATTTTTAAAATAAATAA
Found at i:2527716 original size:106 final size:106
Alignment explanation
Indices: 2527577--2527776 Score: 273
Period size: 106 Copynumber: 1.9 Consensus size: 106
2527567 TATTTTTATT
* * *
2527577 TTAAAGAAAAAAAAAAGAATTAATGAGAAGAAATTTCAC-TTTTTAATTGTTAAAAAATGAAAAG
1 TTAAAGAAAAAAAAAAGAATTAATGAAAAGAAATTTCACGTTTTAAATT-TAAAAAAATGAAAAG
2527641 AAAATATAC-CAAGAATTAAACCAAAAAATTCCAAAAAAATTA
65 AAAATATACTCAA-AATTAAACCAAAAAATTCCAAAAAAATTA
* *
2527683 TTAAA-AAATAAAGAAAGAATTAAT-AAAAGGAAATTTCACGTTTTAAATTTAAAAAAATGGAAA
1 TTAAAGAAA-AAAAAAAGAATTAATGAAAA-GAAATTTCACGTTTTAAATTTAAAAAAATGAAAA
* *
2527746 GAAAATATACTTAAAATTAAATCAAAAAATT
64 GAAAATATACTCAAAATTAAACCAAAAAATT
2527777 TTGAAAAAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
105 6 0.07
106 67 0.81
107 10 0.12
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (106 bp):
TTAAAGAAAAAAAAAAGAATTAATGAAAAGAAATTTCACGTTTTAAATTTAAAAAAATGAAAAGA
AAATATACTCAAAATTAAACCAAAAAATTCCAAAAAAATTA
Found at i:2533072 original size:25 final size:24
Alignment explanation
Indices: 2533044--2533117 Score: 58
Period size: 27 Copynumber: 2.8 Consensus size: 24
2533034 AATATATTAA
**
2533044 AATTTAAATATTTTTAATTTATTTT
1 AATTTAAATATTTTTAATTTA-AAT
2533069 AATTTTTAAATAATTTATTTAATTTAAAT
1 AA--TTTAAAT-A-TT-TTTAATTTAAAT
*
2533098 AATTTAAATTATGTTTAATT
1 AATTTAAA-TATTTTTAATT
2533118 GTGAATATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
25 9 0.22
26 1 0.03
27 14 0.35
28 2 0.05
29 5 0.12
30 9 0.22
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (24 bp):
AATTTAAATATTTTTAATTTAAAT
Found at i:2533094 original size:18 final size:20
Alignment explanation
Indices: 2533058--2533103 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
2533048 TAAATATTTT
2533058 TAATTTATTTTAATTTTTAAA
1 TAATTTATTTTAA-TTTTAAA
2533079 TAATTTA-TTTAA-TTTAAA
1 TAATTTATTTTAATTTTAAA
2533097 TAATTTA
1 TAATTTA
2533104 AATTATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.52
20 5 0.20
21 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATTTATTTTAATTTTAAA
Found at i:2533100 original size:9 final size:9
Alignment explanation
Indices: 2533073--2533106 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2533063 TATTTTAATT
2533073 TTTAAATAA
1 TTTAAATAA
**
2533082 TTTATTTAA
1 TTTAAATAA
2533091 TTTAAATAA
1 TTTAAATAA
2533100 TTTAAAT
1 TTTAAAT
2533107 TATGTTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTAAATAA
Found at i:2533115 original size:45 final size:46
Alignment explanation
Indices: 2533029--2533117 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 46
2533019 AAAATATAAA
* *
2533029 TAAATAATATATTAAAATTTAAATATTTTTAATTTATTTTAATTTT
1 TAAATAATATATTAAAATTTAAATATATTTAAATTATTTTAATTTT
* *
2533075 TAAATAATTTATT-TAATTTAAATA-ATTTAAATTATGTTTAATT
1 TAAATAATATATTAAAATTTAAATATATTTAAATTAT-TTTAATT
2533118 GTGAATATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 9 0.24
45 17 0.45
46 12 0.32
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (46 bp):
TAAATAATATATTAAAATTTAAATATATTTAAATTATTTTAATTTT
Found at i:2537545 original size:61 final size:62
Alignment explanation
Indices: 2537476--2537599 Score: 214
Period size: 61 Copynumber: 2.0 Consensus size: 62
2537466 AACAATTCAA
* *
2537476 ACACTCTTTTTATTTTTGCTCTTTTGCCTTTTATAAATCTTAATCTTTAC-TTTTTTAACTT
1 ACACTCTTTTTATTTTTGCTCTTTTGCCTTTTACAAATCTTAATCTTCACTTTTTTTAACTT
*
2537537 ACACTCTTTTTATTTTTGTTCTTTTGCCTTTTACAAATCTTAATCTTCACTTTTTTTAACTT
1 ACACTCTTTTTATTTTTGCTCTTTTGCCTTTTACAAATCTTAATCTTCACTTTTTTTAACTT
2537599 A
1 A
2537600 AGTATCGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
61 47 0.80
62 12 0.20
ACGTcount: A:0.20, C:0.19, G:0.03, T:0.58
Consensus pattern (62 bp):
ACACTCTTTTTATTTTTGCTCTTTTGCCTTTTACAAATCTTAATCTTCACTTTTTTTAACTT
Found at i:2538564 original size:20 final size:20
Alignment explanation
Indices: 2538520--2538575 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2538510 ATATTTGAAT
*
2538520 TTAAATTTAAATTAAAAAT-T
1 TTAAATTT-AATTAAAAATAA
*
2538540 TTTAATATTAATTAAAAATAA
1 TTAAAT-TTAATTAAAAATAA
2538561 TTAAATTTAATTAAA
1 TTAAATTTAATTAAA
2538576 TTTATAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 24 0.77
21 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATTTAATTAAAAATAA
Found at i:2539456 original size:3 final size:3
Alignment explanation
Indices: 2539448--2539474 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2539438 GGCTAAGACT
2539448 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
2539475 AAAACGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2540027 original size:2 final size:2
Alignment explanation
Indices: 2540020--2540051 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2540010 TTCTTTAGCA
2540020 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
2540052 GATAACATGA
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:2541270 original size:26 final size:27
Alignment explanation
Indices: 2541216--2541282 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 27
2541206 TTTATCCGAT
*
2541216 TAAATTTTTATATTTTTATTATATTTAAA
1 TAAATTTTAATATTTTTA-T-TATTTAAA
2541245 TAAATTTTAATATTTTTA-TATTTAAA
1 TAAATTTTAATATTTTTATTATTTAAA
2541271 TAAATTTATAAT
1 TAAATTT-TAAT
2541283 TATAAATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 15 0.42
27 4 0.11
29 17 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TAAATTTTAATATTTTTATTATTTAAA
Found at i:2541362 original size:17 final size:17
Alignment explanation
Indices: 2541313--2541362 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
2541303 AACTTAAAAT
*
2541313 TTAATTTATT-TTTAAA
1 TTAATTTTTTATTTAAA
*
2541329 -TAATTTTTTATCATAAA
1 TTAATTTTTTAT-TTAAA
2541346 TTAATTTTTTATTTAAA
1 TTAATTTTTTATTTAAA
2541363 AAAAATTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 8 0.29
16 1 0.04
17 8 0.29
18 11 0.39
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAATTTTTTATTTAAA
Found at i:2541922 original size:29 final size:30
Alignment explanation
Indices: 2541889--2541955 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
2541879 TACTCACATT
* *
2541889 ATATTTATTTT-TAATTAAATTATTTAAAA
1 ATATTTATTTTAAAATTAAATAATTTAAAA
* *
2541918 ATATTT-TTTTAAAATTAAGTAATTTAATA
1 ATATTTATTTTAAAATTAAATAATTTAAAA
*
2541947 ATTTTTATT
1 ATATTTATT
2541956 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.13
29 25 0.81
30 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
ATATTTATTTTAAAATTAAATAATTTAAAA
Found at i:2542164 original size:18 final size:19
Alignment explanation
Indices: 2542143--2542186 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2542133 AAATTTAATT
2542143 TTTTTTATCTTTT-TTT-AA
1 TTTTTTAT-TTTTATTTAAA
*
2542161 TTTTATATTTTTATTTAAA
1 TTTTTTATTTTTATTTAAA
2542180 TTTTTTA
1 TTTTTTA
2542187 AATATTAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 10 0.45
19 8 0.36
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTTATTTTTATTTAAA
Found at i:2551868 original size:23 final size:23
Alignment explanation
Indices: 2551839--2551897 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
2551829 TGTTAAAATT
2551839 TTAAATGTTAAATATCAATAATA
1 TTAAATGTTAAATATCAATAATA
*
2551862 -TATAATGTTAAATATCAATAATG
1 TTA-AATGTTAAATATCAATAATA
2551885 TTAAATGTTAAAT
1 TTAAATGTTAAAT
2551898 GTTAAAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 2 0.06
23 29 0.88
24 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (23 bp):
TTAAATGTTAAATATCAATAATA
Found at i:2554907 original size:14 final size:14
Alignment explanation
Indices: 2554888--2554917 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2554878 ACATAGTGCT
*
2554888 CTTAATGTAGGTAG
1 CTTAATGTAGGCAG
2554902 CTTAATGTAGGCAG
1 CTTAATGTAGGCAG
2554916 CT
1 CT
2554918 AAGGTAACTG
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:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (14 bp):
CTTAATGTAGGCAG
Found at i:2555843 original size:2 final size:2
Alignment explanation
Indices: 2555836--2555871 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2555826 TATTTCTGCT
2555836 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
2555872 ATTTCAGGAT
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:2556559 original size:21 final size:21
Alignment explanation
Indices: 2556517--2556563 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2556507 TCGATAAATA
* *
2556517 TATTATATTTATGAGAATTTT
1 TATTATATTTATAAGAAATTT
2556538 TATT-TATTTATAAGTAAATTT
1 TATTATATTTATAAG-AAATTT
2556559 TATTA
1 TATTA
2556564 ACAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (21 bp):
TATTATATTTATAAGAAATTT
Found at i:2557964 original size:3 final size:3
Alignment explanation
Indices: 2557956--2557988 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2557946 TGACCAACGG
2557956 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2557989 TTAGGATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2560372 original size:35 final size:33
Alignment explanation
Indices: 2560333--2560415 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
2560323 GGTAACATGA
2560333 AAATT-TTAAGTAAAAATATTAA-ATTTATATAATAT
1 AAATTATTAA-TAAAAATA-TAATATTT-TA-AATAT
*
2560368 AAATTATTAATAAATATATAATATTTTAAATAT
1 AAATTATTAATAAAAATATAATATTTTAAATAT
2560401 -AATTATTATATAAAA
1 AAATTATTA-ATAAAA
2560416 TACACAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 8 0.19
33 10 0.23
34 5 0.12
35 16 0.37
36 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
AAATTATTAATAAAAATATAATATTTTAAATAT
Found at i:2560383 original size:33 final size:33
Alignment explanation
Indices: 2560346--2560414 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
2560336 TTTTAAGTAA
2560346 AAATAT-TAA-ATTTATATAATATAAATTATTA-AT
1 AAATATATAATATTT-TA-AATAT-AATTATTATAT
2560379 AAATATATAATATTTTAAATATAATTATTATAT
1 AAATATATAATATTTTAAATATAATTATTATAT
2560412 AAA
1 AAA
2560415 ATACACAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
32 8 0.24
33 16 0.48
34 5 0.15
35 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AAATATATAATATTTTAAATATAATTATTATAT
Done.