Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 18 of 21
Found at i:1993786 original size:30 final size:31
Alignment explanation
Indices: 1993740--1993797 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1993730 TATACATAAA
1993740 TATATTTATGATATATATAAATT-TAATTTTT
1 TATATTTATGATATATA-AAATTATAATTTTT
*
1993771 TATATTT-TTATATATAAAATTATAATT
1 TATATTTATGATATATAAAATTATAATT
1993798 CATATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 5 0.20
30 13 0.52
31 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (31 bp):
TATATTTATGATATATAAAATTATAATTTTT
Found at i:1993843 original size:16 final size:15
Alignment explanation
Indices: 1993812--1993868 Score: 71
Period size: 16 Copynumber: 3.7 Consensus size: 15
1993802 TTTTTATGTT
*
1993812 TAAATATATAAAAAA
1 TAAATATATTAAAAA
1993827 TAAATATAATTAAAAA
1 TAAATAT-ATTAAAAA
1993843 TAAATAT-TTAAAAAA
1 TAAATATATT-AAAAA
1993858 TTAAATATATT
1 -TAAATATATT
1993869 TAATATATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 2 0.05
15 12 0.32
16 21 0.57
17 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATATATTAAAAA
Found at i:1993855 original size:31 final size:32
Alignment explanation
Indices: 1993812--1993871 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
1993802 TTTTTATGTT
1993812 TAAATATATAAAAAA-TAAATATAATTAAAAA
1 TAAATATATAAAAAATTAAATATAATTAAAAA
* *
1993843 TAAATATTTAAAAAATTAAATATATTTAA
1 TAAATATATAAAAAATTAAATATAATTAA
1993872 TATATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (32 bp):
TAAATATATAAAAAATTAAATATAATTAAAAA
Found at i:1993869 original size:18 final size:18
Alignment explanation
Indices: 1993811--1993881 Score: 66
Period size: 18 Copynumber: 4.3 Consensus size: 18
1993801 ATTTTTATGT
1993811 TTAAATATA--TAAAAAA
1 TTAAATATATTTAAAAAA
*
1993827 -TAAATATAATT-AAAAA
1 TTAAATATATTTAAAAAA
1993843 -T-AA-ATATTTAAAAAA
1 TTAAATATATTTAAAAAA
* *
1993858 TTAAATATATTTAATATA
1 TTAAATATATTTAAAAAA
1993876 TTAAAT
1 TTAAAT
1993882 TTTAATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 5 0.11
15 15 0.33
16 7 0.15
17 3 0.07
18 16 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAATATATTTAAAAAA
Found at i:1993916 original size:2 final size:2
Alignment explanation
Indices: 1993911--1993950 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1993901 TTTAAAAATA
* * *
1993911 AT AT AT AT AT AT AT AT TT AT AT TT AA AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1993951 CAATACATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1994289 original size:22 final size:24
Alignment explanation
Indices: 1994264--1994325 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 24
1994254 TTTTATTTTT
1994264 AAATATAATTATAAAAAA-A-TAA
1 AAATATAATTATAAAAAATATTAA
* * *
1994286 AAATAATCATAACAAAAAATATTAA
1 AAAT-ATAATTATAAAAAATATTAA
*
1994311 AAAT-TAATTTTAAAA
1 AAATATAATTATAAAA
1994326 TATCATATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
22 4 0.13
23 18 0.60
24 1 0.03
25 7 0.23
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATATAATTATAAAAAATATTAA
Found at i:1994291 original size:20 final size:21
Alignment explanation
Indices: 1994263--1994303 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1994253 ATTTTATTTT
* *
1994263 TAAATATAATTATAA-AAAAA
1 TAAAAATAATCATAACAAAAA
1994283 TAAAAATAATCATAACAAAAA
1 TAAAAATAATCATAACAAAAA
1994304 ATATTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAAATAATCATAACAAAAA
Found at i:1995140 original size:24 final size:23
Alignment explanation
Indices: 1995103--1995159 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
1995093 ATGTTATTAT
*
1995103 TTAAAAAATATAAATATATTTTTA
1 TTAATAAATATAAATA-ATTTTTA
*
1995127 -TAATTAAATTTAAATAATTTTTA
1 TTAA-TAAATATAAATAATTTTTA
1995150 TTAATAAATA
1 TTAATAAATA
1995160 ATAATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAATAAATATAAATAATTTTTA
Found at i:1995542 original size:3 final size:3
Alignment explanation
Indices: 1995534--1995575 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1995524 ACGGCACAAA
1995534 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1995576 TCCTCAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2002516 original size:2 final size:2
Alignment explanation
Indices: 2002509--2002552 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2002499 ATTGTGGCTC
2002509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2002550 TA T
1 TA T
2002553 TGTTAACTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2006824 original size:17 final size:17
Alignment explanation
Indices: 2006804--2006850 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
2006794 ATAATTAATT
2006804 TTAAT-TTTTTATTATTA
1 TTAATATTTTT-TTATTA
2006821 TTAATATTTTTTTATT-
1 TTAATATTTTTTTATTA
* *
2006837 TAAATACTTTTTTA
1 TTAATATTTTTTTA
2006851 ATTAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 12 0.44
17 10 0.37
18 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TTAATATTTTTTTATTA
Found at i:2006847 original size:16 final size:16
Alignment explanation
Indices: 2006823--2006857 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2006813 TATTATTATT
* *
2006823 AATATTTTTTTATTTA
1 AATACTTTTTTAATTA
2006839 AATACTTTTTTAATTA
1 AATACTTTTTTAATTA
2006855 AAT
1 AAT
2006858 TAATTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
AATACTTTTTTAATTA
Found at i:2007191 original size:2 final size:2
Alignment explanation
Indices: 2007184--2007209 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2007174 CTTGCAACTG
2007184 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
2007210 ACACGAAGCT
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:2011232 original size:20 final size:22
Alignment explanation
Indices: 2011204--2011260 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
2011194 TGATAAATTT
*
2011204 TTATAAAAATTAAAAAATTATAA
1 TTAT-AAAATTAAAAAATAATAA
*
2011227 TTA-AAAA-TATAAAATAATAA
1 TTATAAAATTAAAAAATAATAA
2011247 TTATAAAATTAAAA
1 TTATAAAATTAAAA
2011261 GATGAACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 14 0.48
21 8 0.28
22 4 0.14
23 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TTATAAAATTAAAAAATAATAA
Found at i:2015024 original size:22 final size:22
Alignment explanation
Indices: 2014997--2015048 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
2014987 ATAATATAAT
*
2014997 ATTTTTAATCTT-TATTATTAG
1 ATTTTTAATCTTATATTATTAA
*
2015018 ATGTTTTAAATTTTATATTATTAA
1 AT-TTTT-AATCTTATATTATTAA
2015042 ATTTTTA
1 ATTTTTA
2015049 TTTATTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.08
22 5 0.19
23 9 0.35
24 10 0.38
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTTTAATCTTATATTATTAA
Found at i:2015041 original size:15 final size:15
Alignment explanation
Indices: 2015023--2015055 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2015013 ATTAGATGTT
2015023 TTAAA-TTTTATATTA
1 TTAAATTTTTAT-TTA
2015038 TTAAATTTTTATTTA
1 TTAAATTTTTATTTA
2015053 TTA
1 TTA
2015056 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTAAATTTTTATTTA
Found at i:2015541 original size:18 final size:17
Alignment explanation
Indices: 2015518--2015555 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2015508 TATAAATTTA
*
2015518 TATATATTTTAATATATT
1 TATATATTATAATA-ATT
2015536 TATATATTATAATAATT
1 TATATATTATAATAATT
2015553 TAT
1 TAT
2015556 TTTTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATATTATAATAATT
Found at i:2015563 original size:17 final size:18
Alignment explanation
Indices: 2015478--2015555 Score: 72
Period size: 17 Copynumber: 4.4 Consensus size: 18
2015468 TGTATTTTCG
*
2015478 TATTTTTATATTATAATTA
1 TATTTATATATTATAA-TA
* * *
2015497 TATTAAAAAATTATAA-A
1 TATTTATATATTATAATA
*
2015514 T-TTATATATATTTTAATA
1 TATT-TATATATTATAATA
2015532 TATTTATATATTATAATA
1 TATTTATATATTATAATA
2015550 -ATTTAT
1 TATTTAT
2015556 TTTTTATATT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
16 2 0.04
17 16 0.34
18 15 0.32
19 14 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTATATATTATAATA
Found at i:2018787 original size:5 final size:5
Alignment explanation
Indices: 2018779--2018804 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2018769 TCAACTCATA
2018779 AAACT AAACT AAACT AAACT AAACT A
1 AAACT AAACT AAACT AAACT AAACT A
2018805 TGTTACTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AAACT
Found at i:2021264 original size:21 final size:20
Alignment explanation
Indices: 2021249--2021286 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2021239 AAAATTAATA
2021249 AAAAATTAATATAAATATAT
1 AAAAATTAATATAAATATAT
*
2021269 AAAAATTTATAT-AATATA
1 AAAAATTAATATAAATATA
2021287 AATTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTAATATAAATATAT
Found at i:2024633 original size:4 final size:4
Alignment explanation
Indices: 2024620--2024656 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
2024610 TAATCAAATC
2024620 ATTT ATTTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2024657 TGCACTGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:2029990 original size:13 final size:13
Alignment explanation
Indices: 2029974--2029998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2029964 TTTATTTTTA
2029974 AATATTCATATTT
1 AATATTCATATTT
2029987 AATATTCATATT
1 AATATTCATATT
2029999 CGATATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATTCATATTT
Found at i:2037288 original size:19 final size:19
Alignment explanation
Indices: 2037260--2037327 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
2037250 TTCGGTAATT
* *
2037260 TATATTTATTTAATTTAAA
1 TATATATATTTAATATAAA
* * *
2037279 TATAAATATTAAATAT-GA
1 TATATATATTTAATATAAA
2037297 T-TATATATTTAATATAAA
1 TATATATATTTAATATAAA
*
2037315 TATTTATATTTAA
1 TATATATATTTAA
2037328 AAATATTTTG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
17 12 0.32
18 4 0.11
19 22 0.58
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (19 bp):
TATATATATTTAATATAAA
Found at i:2037391 original size:16 final size:15
Alignment explanation
Indices: 2037367--2037418 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
2037357 ATTATTTTAA
2037367 AAAATATAAAAAATT
1 AAAATATAAAAAATT
2037382 AAAATAATAAAAAA-T
1 AAAAT-ATAAAAAATT
*
2037397 -AAATATAAAATATT
1 AAAATATAAAAAATT
*
2037411 AATATATA
1 AAAATATA
2037419 CTGAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 7 0.22
14 5 0.16
15 12 0.38
16 8 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATATAAAAAATT
Found at i:2037404 original size:13 final size:13
Alignment explanation
Indices: 2037368--2037416 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
2037358 TTATTTTAAA
2037368 AAATATAAAAAATT
1 AAATATAAAAAA-T
2037382 AAAATAATAAAAAAT
1 -AAAT-ATAAAAAAT
*
2037397 AAATATAAAATAT
1 AAATATAAAAAAT
*
2037410 TAATATA
1 AAATATA
2037417 TACTGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 14 0.45
14 4 0.13
15 5 0.16
16 8 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATATAAAAAAT
Found at i:2037521 original size:2 final size:2
Alignment explanation
Indices: 2037514--2037538 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2037504 TTATAAAAAT
2037514 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
2037539 GAAATAAGAC
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:2037873 original size:10 final size:10
Alignment explanation
Indices: 2037858--2037884 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2037848 TCACCTGCTG
2037858 GCTGCTGGGT
1 GCTGCTGGGT
2037868 GCTGCTGGGT
1 GCTGCTGGGT
2037878 GCTGCTG
1 GCTGCTG
2037885 AGACCACACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.22, G:0.48, T:0.30
Consensus pattern (10 bp):
GCTGCTGGGT
Found at i:2038260 original size:12 final size:12
Alignment explanation
Indices: 2038243--2038267 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2038233 TATGTTATAA
2038243 ATAAAATTTTTT
1 ATAAAATTTTTT
2038255 ATAAAATTTTTT
1 ATAAAATTTTTT
2038267 A
1 A
2038268 AAATTATATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAAAATTTTTT
Found at i:2038985 original size:14 final size:14
Alignment explanation
Indices: 2038966--2039009 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2038956 TTTTTTTTGT
2038966 AAATAAAATTATTA
1 AAATAAAATTATTA
*
2038980 AAAT--AATCA-T-
1 AAATAAAATTATTA
2038990 AAATAAAATTATTA
1 AAATAAAATTATTA
2039004 AAATAA
1 AAATAA
2039010 TAATAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 4 0.17
11 1 0.04
12 8 0.33
13 1 0.04
14 10 0.42
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATAAAATTATTA
Found at i:2038992 original size:24 final size:24
Alignment explanation
Indices: 2038965--2039017 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2038955 ATTTTTTTTG
*
2038965 TAAATAAAATTATTAAAATAATCA
1 TAAATAAAATTATTAAAATAATAA
2038989 TAAATAAAATTATTAAAATAATAA
1 TAAATAAAATTATTAAAATAATAA
2039013 TAAAT
1 TAAAT
2039018 GTTAACGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAATAAAATTATTAAAATAATAA
Found at i:2039714 original size:2 final size:2
Alignment explanation
Indices: 2039707--2039735 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2039697 TAACTCTAAC
2039707 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2039736 CCCCCCTAAC
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2041403 original size:2 final size:2
Alignment explanation
Indices: 2041398--2041438 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2041388 ACACAAATGG
* * *
2041398 TA TA TA TA CA AA TA CA 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
2041439 TTTTTAAGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2041663 original size:20 final size:20
Alignment explanation
Indices: 2041593--2041665 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
2041583 TTAAAAAATA
*
2041593 AAATTATTTAAAA-ATAATT
1 AAATTTTTTAAAATATAATT
*
2041612 ATAATTTATATTAAAATAATATTT
1 A-AATTT-T-TTAAAAT-ATAATT
* *
2041636 ATATTTTTTAAAATTTAATT
1 AAATTTTTTAAAATATAATT
2041656 AAATTTTTTA
1 AAATTTTTTA
2041666 TTAATTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.02
20 17 0.40
21 8 0.19
22 7 0.16
23 4 0.09
24 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATTTTTTAAAATATAATT
Found at i:2041710 original size:15 final size:15
Alignment explanation
Indices: 2041678--2041758 Score: 53
Period size: 15 Copynumber: 5.4 Consensus size: 15
2041668 AATTTTTTAA
2041678 ATTT-AATTAA-TAT
1 ATTTAAATTAATTAT
*
2041691 CATTTAAATTTATTAT
1 -ATTTAAATTAATTAT
**
2041707 ATTTGTATTAATTAT
1 ATTTAAATTAATTAT
*
2041722 ATTTAAA--AATTAA
1 ATTTAAATTAATTAT
*
2041735 ATATTAAATATAAATAT
1 AT-TTAAAT-TAATTAT
2041752 ATATTAA
1 AT-TTAA
2041759 TATTTAAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
13 7 0.13
14 9 0.17
15 22 0.42
16 3 0.06
17 11 0.21
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (15 bp):
ATTTAAATTAATTAT
Found at i:2042904 original size:23 final size:23
Alignment explanation
Indices: 2042855--2042909 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
2042845 TATTAAAATG
* * *
2042855 TTATATATATATATATAATATTT
1 TTATAAATTTATATATAATATTA
2042878 TTATAAATTTATA-ATAATAATTA
1 TTATAAATTTATATATAAT-ATTA
*
2042901 TTATTAATT
1 TTATAAATT
2042910 AGTAATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTATAAATTTATATATAATATTA
Found at i:2043077 original size:20 final size:20
Alignment explanation
Indices: 2043041--2043109 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 20
2043031 TTAATTTATA
*
2043041 TTATA-ATTATATTTAAAATT
1 TTATATATT-TATATAAAATT
2043061 TTATATATTTATAT-AAATT
1 TTATATATTTATATAAAATT
*
2043080 TTGACATATATTTATATATTAATT
1 TT---ATATATTTATATA-AAATT
2043104 TTATAT
1 TTATAT
2043110 TTATATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
19 7 0.17
20 9 0.22
21 7 0.17
22 12 0.29
24 6 0.15
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (20 bp):
TTATATATTTATATAAAATT
Found at i:2043118 original size:24 final size:24
Alignment explanation
Indices: 2043033--2043118 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
2043023 TATTAGTATT
*
2043033 AATTTATATTATA-ATTATATTTAA
1 AATTTATATTATATATTA-ATTTTA
* *
2043057 AATTTTATATATTTATATAAATTTTGA
1 AA-TTTATAT-TATATATTAATTTT-A
* *
2043084 CATATAT-TTATATATTAATTTTA
1 AATTTATATTATATATTAATTTTA
*
2043107 TATTTATATTAT
1 AATTTATATTAT
2043119 TTTTTTATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
23 6 0.12
24 18 0.38
25 8 0.17
26 11 0.23
27 5 0.10
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (24 bp):
AATTTATATTATATATTAATTTTA
Found at i:2043124 original size:19 final size:20
Alignment explanation
Indices: 2043086--2043140 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
2043076 AATTTTGACA
2043086 TATATTTATA-TATTAATTT
1 TATATTTATATTATTAATTT
*
2043105 TATATTTATATTATT-TTTT
1 TATATTTATATTATTAATTT
*
2043124 TATA-ATATATTA-TAATT
1 TATATTTATATTATTAATT
2043141 ATATTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 1 0.03
18 9 0.29
19 17 0.55
20 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATATTTATATTATTAATTT
Found at i:2046864 original size:20 final size:19
Alignment explanation
Indices: 2046826--2046892 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
2046816 GTTTAAAGTT
2046826 TTATATAAATTTTTATATA
1 TTATATAAATTTTTATATA
* *
2046845 TTATATTAA--TTT-T-TG
1 TTATATAAATTTTTATATA
*
2046860 TTATATAAATTTTAATATTA
1 TTATATAAATTTTTATA-TA
2046880 TTATA-AAATTTTT
1 TTATATAAATTTTT
2046893 TCGAGTTTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
15 9 0.24
16 1 0.03
17 5 0.14
18 1 0.03
19 15 0.41
20 6 0.16
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (19 bp):
TTATATAAATTTTTATATA
Found at i:2046867 original size:34 final size:34
Alignment explanation
Indices: 2046826--2046892 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
2046816 GTTTAAAGTT
* *
2046826 TTATATAAATTTTTATA-TATTATATTAATTTTTG
1 TTATATAAATTTTAATATTATTATA-AAATTTTTG
2046860 TTATATAAATTTTAATATTATTATAAAATTTTT
1 TTATATAAATTTTAATATTATTATAAAATTTTT
2046893 TCGAGTTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 23 0.77
35 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (34 bp):
TTATATAAATTTTAATATTATTATAAAATTTTTG
Found at i:2047829 original size:20 final size:21
Alignment explanation
Indices: 2047804--2047842 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2047794 TAATTTTTTT
2047804 AATTTAAAT-TAATTTAATTC
1 AATTTAAATATAATTTAATTC
*
2047824 AATTTAAATATTATTTAAT
1 AATTTAAATATAATTTAAT
2047843 AATAAAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTAAATATAATTTAATTC
Found at i:2048140 original size:32 final size:32
Alignment explanation
Indices: 2048070--2048143 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
2048060 ATTTATTTGG
*
2048070 ATTATTATTTTATAAAATTTAATTAAATAATAAT
1 ATTA-TATTATATAAAATTTAA-TAAATAATAAT
2048104 -TTATATTATATAAAATTT-A-AAATAATTATAT
1 ATTATATTATATAAAATTTAATAAATAA-TA-AT
2048135 ATTATATTA
1 ATTATATTA
2048144 CTATTTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
29 6 0.17
30 2 0.06
31 3 0.08
32 22 0.61
33 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
ATTATATTATATAAAATTTAATAAATAATAAT
Found at i:2048142 original size:5 final size:5
Alignment explanation
Indices: 2048132--2048196 Score: 51
Period size: 5 Copynumber: 12.0 Consensus size: 5
2048122 AAAATAATTA
*
2048132 TATAT TATAT TACTATT TATAT TATAT TTTAAT TATATT TATAT TAATACT
1 TATAT TATAT TA-TA-T TATAT TATAT TAT-AT TATA-T TATAT T-ATA-T
*
2048183 TA-AT TTTAT TATAT
1 TATAT TATAT TATAT
2048197 CTATTAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
4 2 0.04
5 25 0.51
6 17 0.35
7 5 0.10
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:2048149 original size:82 final size:81
Alignment explanation
Indices: 2048046--2048196 Score: 175
Period size: 82 Copynumber: 1.9 Consensus size: 81
2048036 TGTATATATC
* *
2048046 AATTATATTTATATATTTATTTGGATTATTATTTT-ATAAAATTTA-ATTAAATA-ATAATTTAT
1 AATTATATTTATATATCTATTTAGATTA-TATTTTAATAAAATTTATATT-AATACATAATTT-T
2048108 ATTATATAAAATTTAAAAT
63 ATTATATAAAATTTAAAAT
* * * *
2048127 AATTATATATTATAT-TACTATTTATATTATATTTTAATTATATTTATATTAATACTTAATTTTA
1 AATTATAT-TTATATAT-CTATTTAGATTATATTTTAATAAAATTTATATTAATACATAATTTTA
2048191 TTATAT
64 TTATAT
2048197 CTATTAAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
81 15 0.25
82 35 0.59
83 9 0.15
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (81 bp):
AATTATATTTATATATCTATTTAGATTATATTTTAATAAAATTTATATTAATACATAATTTTATT
ATATAAAATTTAAAAT
Found at i:2048154 original size:17 final size:17
Alignment explanation
Indices: 2048132--2048177 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
2048122 AAAATAATTA
*
2048132 TATATTATATTACTATT
1 TATATTATATTACTAAT
*
2048149 TATATTATATT-TTAAT
1 TATATTATATTACTAAT
2048165 TATATTTATATTA
1 TATA-TTATATTA
2048178 ATACTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATTATATTACTAAT
Found at i:2048159 original size:11 final size:11
Alignment explanation
Indices: 2048128--2048177 Score: 66
Period size: 11 Copynumber: 4.4 Consensus size: 11
2048118 ATTTAAAATA
2048128 ATTATATATTAT
1 ATTATAT-TTAT
2048140 ATTACTATTTAT
1 ATTA-TATTTAT
2048152 ATTATATTT-T
1 ATTATATTTAT
2048162 AATTATATTTAT
1 -ATTATATTTAT
2048174 ATTA
1 ATTA
2048178 ATACTTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.03
11 18 0.51
12 13 0.37
13 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:2048168 original size:28 final size:26
Alignment explanation
Indices: 2048134--2048196 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 26
2048124 AATAATTATA
*
2048134 TATTATATTACTATTTATA-TTATATTT
1 TATTATATTA-TATTAATACTTA-ATTT
2048161 TAATTATATTTATATTAATACTTAATTT
1 T-ATTATA-TTATATTAATACTTAATTT
2048189 TATTATAT
1 TATTATAT
2048197 CTATTAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 1 0.03
27 7 0.22
28 18 0.56
29 6 0.19
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTATATTATATTAATACTTAATTT
Found at i:2048185 original size:22 final size:22
Alignment explanation
Indices: 2048128--2048196 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
2048118 ATTTAAAATA
*
2048128 ATTATATATTATATTACTATTTAT
1 ATTATATCTTA-ATTA-TATTTAT
*
2048152 ATTATATTTTAATTATATTTAT
1 ATTATATCTTAATTATATTTAT
*
2048174 ATTA-ATACTTAATTTTA-TTAT
1 ATTATAT-CTTAATTATATTTAT
2048195 AT
1 AT
2048197 CTATTAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.20
22 19 0.46
23 4 0.10
24 10 0.24
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTATATCTTAATTATATTTAT
Found at i:2048978 original size:15 final size:16
Alignment explanation
Indices: 2048955--2048989 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2048945 ATGTATTTAA
*
2048955 AATTTAATTTATA-TT
1 AATTAAATTTATATTT
2048970 AATTAAATTTATATTT
1 AATTAAATTTATATTT
2048986 AATT
1 AATT
2048990 TATATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTAAATTTATATTT
Found at i:2050165 original size:2 final size:2
Alignment explanation
Indices: 2050158--2050190 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2050148 TAACAACTAC
2050158 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 A
2050191 AAATAGCTGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2053213 original size:12 final size:12
Alignment explanation
Indices: 2053196--2053233 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2053186 ATTATTATTT
2053196 ATATTAAAGTATA
1 ATATTAAA-TATA
2053209 A-ATTAAATATA
1 ATATTAAATATA
2053220 ATATTAAATATA
1 ATATTAAATATA
2053232 AT
1 AT
2053234 TGTTTGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 5 0.21
12 18 0.75
13 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
ATATTAAATATA
Found at i:2054031 original size:23 final size:24
Alignment explanation
Indices: 2054005--2054058 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
2053995 TTAAATTATT
2054005 ATTTAAAATAATATTAAAAATT-A
1 ATTTAAAATAATATTAAAAATTAA
** * * *
2054028 ATTTTTATTAATATTTATAATTAA
1 ATTTAAAATAATATTAAAAATTAA
2054052 ATTTAAA
1 ATTTAAA
2054059 TAAAGATAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTAAAATAATATTAAAAATTAA
Found at i:2055205 original size:17 final size:17
Alignment explanation
Indices: 2055157--2055205 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 17
2055147 ATATTAAAAA
* *
2055157 TATTT-ATATAAATATA
1 TATTTAATATTAATATT
*
2055173 TATTTAGTA-TAA-ATT
1 TATTTAATATTAATATT
2055188 TATTTAATATTAATATT
1 TATTTAATATTAATATT
2055205 T
1 T
2055206 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 10 0.38
16 10 0.38
17 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TATTTAATATTAATATT
Found at i:2056181 original size:18 final size:18
Alignment explanation
Indices: 2056158--2056192 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2056148 TGTCTTATTT
2056158 ATGATAAAGACAATGATA
1 ATGATAAAGACAATGATA
* *
2056176 ATGATAATGAGAATGAT
1 ATGATAAAGACAATGAT
2056193 GGTGATGTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.20, T:0.26
Consensus pattern (18 bp):
ATGATAAAGACAATGATA
Found at i:2058597 original size:4 final size:4
Alignment explanation
Indices: 2058588--2058615 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2058578 AAACTGTCCA
2058588 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2058616 TCCAAGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:2060601 original size:3 final size:3
Alignment explanation
Indices: 2060593--2060617 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2060583 GTCGGCTTTT
2060593 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
2060618 GTAAATTGCC
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2060653 original size:18 final size:18
Alignment explanation
Indices: 2060635--2060668 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2060625 GCCCGACATA
2060635 AATA-AAAATAAAAATAT
1 AATATAAAATAAAAATAT
*
2060652 AATATAATATAAAAATA
1 AATATAAAATAAAAATA
2060669 ATATAAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATAAAATAAAAATAT
Found at i:2060669 original size:16 final size:16
Alignment explanation
Indices: 2060641--2060674 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2060631 CATAAATAAA
2060641 AATAAAAATATAATAT
1 AATAAAAATATAATAT
2060657 AATATAAAA-ATAATAT
1 AATA-AAAATATAATAT
2060673 AA
1 AA
2060675 ATACAGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAAAATATAATAT
Found at i:2061112 original size:21 final size:18
Alignment explanation
Indices: 2061071--2061113 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 18
2061061 AATAAATATT
*
2061071 TTTTATTAAAATAGGTAA
1 TTTTATTAAAAAAGGTAA
2061089 TTTTATTAAAAGAATGGATAA
1 TTTTATTAAAA-AA-GG-TAA
2061110 TTTT
1 TTTT
2061114 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 11 0.52
19 1 0.05
20 2 0.10
21 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (18 bp):
TTTTATTAAAAAAGGTAA
Found at i:2061846 original size:23 final size:21
Alignment explanation
Indices: 2061803--2061859 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
2061793 AATATTTCTA
2061803 ATTTCTAATTATTTATATAAATCT
1 ATTT-TAATTATTTATATAAA--T
* * *
2061827 TTTTTAATTATTTTTTTAAAT
1 ATTTTAATTATTTATATAAAT
2061848 ATTTTAATTATT
1 ATTTTAATTATT
2061860 AATTTCCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 12 0.41
23 14 0.48
24 3 0.10
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTAATTATTTATATAAAT
Found at i:2065156 original size:25 final size:24
Alignment explanation
Indices: 2065114--2065176 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
2065104 TACGGCTCAA
*
2065114 TTTTTTTAAATGGGTTATATATATATT
1 TTTTTTTAAAT---TTATATATATAAT
* *
2065141 TTTTGTTTAAATTTATTTTTATAAT
1 TTTT-TTTAAATTTATATATATAAT
2065166 TTTTTTTAAAT
1 TTTTTTTAAAT
2065177 ATTGAGCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 7 0.22
25 14 0.44
27 4 0.12
28 7 0.22
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
TTTTTTTAAATTTATATATATAAT
Found at i:2065512 original size:24 final size:24
Alignment explanation
Indices: 2065485--2065559 Score: 87
Period size: 26 Copynumber: 3.0 Consensus size: 24
2065475 TTATGCTTTC
2065485 AAAAATTATATAATATAAGTTTTTAA
1 AAAAATTATATAATATAA-TTTTT-A
*
2065511 AAAAATTATATAATATAATTTATA
1 AAAAATTATATAATATAATTTTTA
* *
2065535 ATATATATATATATATATAATTTTT
1 AAAAAT-TATATA-ATATAATTTTT
2065560 CGAATGATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.12
25 10 0.23
26 28 0.65
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (24 bp):
AAAAATTATATAATATAATTTTTA
Found at i:2068880 original size:2 final size:2
Alignment explanation
Indices: 2068873--2068904 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2068863 AAGGGCTTCA
2068873 CT CT CT 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 CT CT CT
2068905 TTGTGTCTGT
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):
CT
Found at i:2070295 original size:33 final size:31
Alignment explanation
Indices: 2070248--2070315 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
2070238 TTAATTTAAA
* *
2070248 AGATTTAGATAAAAATATTAAGTTTAAAAAAT
1 AGATTTAAATAAAAAGATT-AGTTTAAAAAAT
* *
2070280 AGATTTAAATAAAAAAGATTTGTTTTAAAAAT
1 AGATTTAAAT-AAAAAGATTAGTTTAAAAAAT
2070312 AGAT
1 AGAT
2070316 CATATTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 23 0.74
33 8 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.35
Consensus pattern (31 bp):
AGATTTAAATAAAAAGATTAGTTTAAAAAAT
Found at i:2071030 original size:4 final size:4
Alignment explanation
Indices: 2071021--2071079 Score: 100
Period size: 4 Copynumber: 14.5 Consensus size: 4
2071011 TGGTGAAAAC
*
2071021 AGAA AGAA AGAA AGAA AGAAA AAAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
2071070 AGAA AGAA AG
1 AGAA AGAA AG
2071080 GAGAAAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
4 49 0.94
5 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2071096 original size:8 final size:8
Alignment explanation
Indices: 2071016--2071106 Score: 74
Period size: 8 Copynumber: 10.6 Consensus size: 8
2071006 ACGTTTGGTG
*
2071016 AAAACAGA
1 AAAAAAGA
*
2071024 AAGAAAGA
1 AAAAAAGA
*
2071032 AAGAAAGAA
1 AAAAAAG-A
2071041 AAAAAAGA
1 AAAAAAGA
*
2071049 AAGAAAGA
1 AAAAAAGA
*
2071057 AAGAAAGA
1 AAAAAAGA
*
2071065 AAGAAAGA
1 AAAAAAGA
2071073 AAGAAAGGAGAA
1 AA-AAA--AG-A
2071085 AAAAAAGGA
1 AAAAAA-GA
2071094 AAAAAAGA
1 AAAAAAGA
2071102 AAAAA
1 AAAAA
2071107 TATTTATATA
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
8 46 0.64
9 17 0.24
10 1 0.01
11 5 0.07
12 3 0.04
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:2071586 original size:23 final size:23
Alignment explanation
Indices: 2071560--2071618 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
2071550 TTCATTTCAT
2071560 TTATTTTTTATATTATATTT-TAA
1 TTATTTTTTATATTATATTTGT-A
* *
2071583 TTATTTTTTATGTCATATTTGTA
1 TTATTTTTTATATTATATTTGTA
*
2071606 -TATTTTGTATATT
1 TTATTTTTTATATT
2071619 TAAAGTAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 10 0.33
23 19 0.63
24 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (23 bp):
TTATTTTTTATATTATATTTGTA
Found at i:2071591 original size:11 final size:12
Alignment explanation
Indices: 2071560--2071593 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2071550 TTCATTTCAT
2071560 TTATTTTTTATA
1 TTATTTTTTATA
*
2071572 TTATATTTTA-A
1 TTATTTTTTATA
2071583 TTATTTTTTAT
1 TTATTTTTTAT
2071594 GTCATATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTTTTTATA
Found at i:2072015 original size:10 final size:10
Alignment explanation
Indices: 2071986--2072024 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 10
2071976 TTTATTTGAT
2071986 AAAAAAAAAG
1 AAAAAAAAAG
2071996 AAAAAGAAAAG
1 AAAAA-AAAAG
2072007 ACAAAAAAAGAG
1 A-AAAAAAA-AG
2072019 AAAAAA
1 AAAAAA
2072025 TTTATGCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.19
11 14 0.54
12 7 0.27
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:2072141 original size:18 final size:20
Alignment explanation
Indices: 2072101--2072141 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
2072091 CATATTAATA
*
2072101 ATTTATTATATTTCATGTAT
1 ATTTATTATATGTCATGTAT
*
2072121 ATTT-TTATATGT-ATGTGT
1 ATTTATTATATGTCATGTAT
2072139 ATT
1 ATT
2072142 CGTATCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (20 bp):
ATTTATTATATGTCATGTAT
Found at i:2072552 original size:16 final size:16
Alignment explanation
Indices: 2072525--2072567 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2072515 ATTTTAAAAT
2072525 AAATTTTA-TTAATTA
1 AAATTTTATTTAATTA
*
2072540 TAATTTTATTTAATTA
1 AAATTTTATTTAATTA
2072556 AAATTTT-TTTAA
1 AAATTTTATTTAA
2072568 ATATTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTTATTTAATTA
Found at i:2072825 original size:2 final size:2
Alignment explanation
Indices: 2072820--2072857 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2072810 GTGTAAGTGA
*
2072820 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2072858 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2077153 original size:34 final size:33
Alignment explanation
Indices: 2077105--2077339 Score: 267
Period size: 34 Copynumber: 7.0 Consensus size: 33
2077095 TAGTAAAAAC
*
2077105 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
2077138 CTACAATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
2077172 CACCATTTAATCAATAATGGTAAGCTATCAAATT
1 CACCATTTAATCAACAATGGTAACCTACCAAA-T
*** *
2077206 TTTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* * *
2077239 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
2077273 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
*
2077307 CACCATTTAATCAACAATGGTAAACTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
2077340 GTATATTCTT
Statistics
Matches: 171, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
32 1 0.01
33 60 0.35
34 105 0.61
35 5 0.03
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:2077314 original size:101 final size:101
Alignment explanation
Indices: 2077105--2077339 Score: 337
Period size: 101 Copynumber: 2.3 Consensus size: 101
2077095 TAGTAAAAAC
* * * *
2077105 CACCATTTAATCAACAATGGCAACCTACCAAATCTACAATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGTAAACTACCAAATCTACAATTTAGTCAACAATGGCAAACCACCAA
* * *
2077170 ATCACCATTTAATCAATAATGGTAAGCTATCAAATT
66 ATCACCATTTAATCAACAATGGTAAACTACCAAATT
*** * * *
2077206 TTTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGGTAAACTACCAAATCTACAATTTAGTCAACAATGGCAAACCACCAA
2077271 ATCACCCATTTAATCAACAATGGTAAACTACCAAA-T
66 ATCA-CCATTTAATCAACAATGGTAAACTACCAAATT
2077307 CACCATTTAATCAACAATGGTAAACTACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
2077340 GTATATTCTT
Statistics
Matches: 117, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
101 90 0.77
102 27 0.23
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGTAAACTACCAAATCTACAATTTAGTCAACAATGGCAAACCACCAA
ATCACCATTTAATCAACAATGGTAAACTACCAAATT
Found at i:2081426 original size:2 final size:2
Alignment explanation
Indices: 2081414--2081449 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2081404 AAAGGTTAGT
2081414 TC TC TC T- 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 TC TC T
2081450 TTGTTGAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:2082803 original size:48 final size:48
Alignment explanation
Indices: 2082747--2082842 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
2082737 TTTAAAAAGA
* *
2082747 CCATCAATAAATGGTGTTATATGTGAGAATTCATACTAAATCCATATT
1 CCATCAATAAATGGTGTTATATGTGAAAATCCATACTAAATCCATATT
*
2082795 CCATCAATAAATGGTGTTATATGTGAAAATCCATACTAAATCCGTATT
1 CCATCAATAAATGGTGTTATATGTGAAAATCCATACTAAATCCATATT
2082843 AATCTTTAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (48 bp):
CCATCAATAAATGGTGTTATATGTGAAAATCCATACTAAATCCATATT
Found at i:2085565 original size:3 final size:3
Alignment explanation
Indices: 2085559--2085590 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2085549 CATCATCATC
*
2085559 ATA ATA ATA ATA ATA ATA ATA ATA ATC ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2085591 TAACATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2085969 original size:6 final size:7
Alignment explanation
Indices: 2085929--2085974 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
2085919 ATTAAATATA
2085929 TATTTAT
1 TATTTAT
2085936 TATTTAT
1 TATTTAT
*
2085943 TAATTA-
1 TATTTAT
*
2085949 TATTTAA
1 TATTTAT
2085956 TATTTAT
1 TATTTAT
2085963 T-TTTAT
1 TATTTAT
2085969 TATTTA
1 TATTTA
2085975 AATATTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 11 0.32
7 23 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTTAT
Found at i:2085972 original size:13 final size:13
Alignment explanation
Indices: 2085929--2085974 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2085919 ATTAAATATA
2085929 TATTTATTATTTAT
1 TATTTATT-TTTAT
* * *
2085943 TAATTATATTTAA
1 TATTTATTTTTAT
2085956 TATTTATTTTTAT
1 TATTTATTTTTAT
2085969 TATTTA
1 TATTTA
2085975 AATATTAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTATTTTTAT
Found at i:2089036 original size:24 final size:24
Alignment explanation
Indices: 2089009--2089055 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2088999 TATTAAAATA
*
2089009 AAAGGA-AAGAAAAGGAGTAAATTG
1 AAAGGAGAAGAAAA-GAATAAATTG
*
2089033 AAAGGAGATGAAAAGAATAAATT
1 AAAGGAGAAGAAAAGAATAAATT
2089056 AGTTCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.15
Consensus pattern (24 bp):
AAAGGAGAAGAAAAGAATAAATTG
Found at i:2090244 original size:19 final size:20
Alignment explanation
Indices: 2090201--2090254 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2090191 TTTAAATTTT
2090201 AATATTTA-TAATTTATTCTC
1 AATATTTACT-ATTTATTCTC
*
2090221 TATATTTACTATTTA-TCTC
1 AATATTTACTATTTATTCTC
*
2090240 AATATTTACAATTTA
1 AATATTTACTATTTA
2090255 ATCATGACGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.57
20 12 0.40
21 1 0.03
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATTTACTATTTATTCTC
Found at i:2097664 original size:17 final size:18
Alignment explanation
Indices: 2097642--2097676 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2097632 CATTTATAAA
2097642 AATAAAA-AAAAAATTAG
1 AATAAAAGAAAAAATTAG
2097659 AATAAAATGAAAAAATTA
1 AATAAAA-GAAAAAATTA
2097677 TAACAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
AATAAAAGAAAAAATTAG
Found at i:2098348 original size:21 final size:21
Alignment explanation
Indices: 2098322--2098362 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2098312 TATCAAAATT
*
2098322 TTAAAAAATATATATTTATAA
1 TTAAAAAATATATATATATAA
*
2098343 TTAAAATATATATATATATA
1 TTAAAAAATATATATATATA
2098363 TGAATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAAAAATATATATATATAA
Found at i:2098429 original size:29 final size:30
Alignment explanation
Indices: 2098366--2098445 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
2098356 ATATATATGA
*
2098366 ATAAATTAAAATAAATTT-AAAGTATCATCT
1 ATAAATT-AAATAAATTTAAAAGTATAATCT
*
2098396 ATAAATATAAATAATTTTAAAAGTATAAT-T
1 ATAAAT-TAAATAAATTTAAAAGTATAATCT
2098426 -TAAATTAAATTAAATTTAAA
1 ATAAATTAAA-TAAATTTAAA
2098446 TAAATATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 4 0.09
29 14 0.32
30 16 0.36
31 10 0.23
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (30 bp):
ATAAATTAAATAAATTTAAAAGTATAATCT
Found at i:2100314 original size:5 final size:6
Alignment explanation
Indices: 2100288--2100321 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
2100278 TAGATGTGGG
2100288 TTTTAT TTGTT-T TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TT-TTAT TTTTAT TTTTAT TTTTAT TTTT
2100322 GAGGCTCTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 2 0.08
6 22 0.85
7 2 0.08
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:2103634 original size:25 final size:26
Alignment explanation
Indices: 2103602--2103652 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
2103592 ATTTGGTTAC
2103602 AAAATTATA-ATA-ATTTCACAATAAA
1 AAAATTATATATATATTTCA-AATAAA
2103627 AAAATTATATATATTATTTCAAATAA
1 AAAATTATATATA-TATTTCAAATAA
2103653 TAAATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.39
26 3 0.13
27 5 0.22
28 6 0.26
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAATTATATATATATTTCAAATAAA
Found at i:2104291 original size:20 final size:20
Alignment explanation
Indices: 2104249--2104291 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2104239 AAAAAATTTA
*
2104249 ATAATAAATAAGTAATTAAT
1 ATAATAAATAACTAATTAAT
*
2104269 ATAATAAAT-ACTTATTAAGT
1 ATAATAAATAACTAATTAA-T
2104289 ATA
1 ATA
2104292 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (20 bp):
ATAATAAATAACTAATTAAT
Found at i:2106739 original size:2 final size:2
Alignment explanation
Indices: 2106729--2106764 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2106719 GATGTGTGCG
*
2106729 TA 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
2106765 AAGAATTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2107445 original size:13 final size:13
Alignment explanation
Indices: 2107398--2107453 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
2107388 AAAAAGGTAT
* *
2107398 AAAATATATGTATT
1 AAAATATA-ATATA
*
2107412 AAAATTTAA-ATA
1 AAAATATAATATA
2107424 AATATATATAATATA
1 AA-A-ATATAATATA
2107439 AAAATATAATATA
1 AAAATATAATATA
2107452 AA
1 AA
2107454 TGCCGTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
12 4 0.11
13 13 0.37
14 13 0.37
15 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
AAAATATAATATA
Found at i:2107884 original size:11 final size:11
Alignment explanation
Indices: 2107868--2107912 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
2107858 ATTCTAAAAA
2107868 TATATTTATAT
1 TATATTTATAT
*
2107879 TATATTTTTAT
1 TATATTTATAT
*
2107890 TATTATATATAT
1 TA-TATTTATAT
*
2107902 CATATTTATAT
1 TATATTTATAT
2107913 AAATATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 20 0.71
12 8 0.29
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2107912 original size:15 final size:15
Alignment explanation
Indices: 2107892--2107934 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2107882 ATTTTTATTA
2107892 TTATATATATCATAT
1 TTATATATATCATAT
*
2107907 TTATATAAAT-ATAT
1 TTATATATATCATAT
2107921 TTA-ATATTATCATA
1 TTATATA-TATCATA
2107935 CATAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 3 0.12
14 9 0.38
15 12 0.50
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATATATATCATAT
Found at i:2107919 original size:23 final size:23
Alignment explanation
Indices: 2107869--2107920 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
2107859 TTCTAAAAAT
* * * *
2107869 ATATTTATATTATATTTTTATTA
1 ATATATATATCATATTTATATAA
*
2107892 TTATATATATCATATTTATATAA
1 ATATATATATCATATTTATATAA
2107915 ATATAT
1 ATATAT
2107921 TTAATATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATATATATCATATTTATATAA
Found at i:2108258 original size:23 final size:21
Alignment explanation
Indices: 2108222--2108285 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
2108212 TATATATATA
*
2108222 TATATATAACTATTTAATATATT
1 TATATA-AAATATTTAATA-ATT
2108245 TATAGTAAAATATTT--TAATT
1 TATA-TAAAATATTTAATAATT
*
2108265 T-TATAAAATATATAATAATT
1 TATATAAAATATTTAATAATT
2108285 T
1 T
2108286 TAAAATTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 9 0.25
19 2 0.06
20 10 0.28
21 2 0.06
23 11 0.31
24 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TATATAAAATATTTAATAATT
Found at i:2108970 original size:23 final size:25
Alignment explanation
Indices: 2108944--2108989 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
2108934 TTAAAAACAT
*
2108944 AAATTATT-TATATTT-TTATATAA
1 AAATGATTATATATTTATTATATAA
2108967 AAATGATTATATATTTATTATAT
1 AAATGATTATATATTTATTATAT
2108990 TTATATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 7 0.35
25 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
AAATGATTATATATTTATTATATAA
Found at i:2109030 original size:19 final size:18
Alignment explanation
Indices: 2108974--2109031 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
2108964 TAAAAATGAT
*
2108974 TATATATTTATTATATTTA
1 TATATTTTTATTATA-TTA
* *
2108993 TATAATTTTA-AATTATTA
1 TATATTTTTATTA-TATTA
2109011 TATATTTTTATTTATATTA
1 TATATTTTTA-TTATATTA
2109030 TA
1 TA
2109032 ATTAAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 13 0.42
19 17 0.55
20 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTTTATTATATTA
Found at i:2109032 original size:35 final size:35
Alignment explanation
Indices: 2108967--2109034 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
2108957 TTTTATATAA
2108967 AAATGATTATATATTTATTATATTTATATAATTTT
1 AAATGATTATATATTTATTATATTTATATAATTTT
*
2109002 AAATTATTATATATTT-TTAT-TTATATTATAATT
1 AAATGATTATATATTTATTATATT-TA-TATAATT
2109035 AAAAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 2 0.07
34 6 0.20
35 22 0.73
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
AAATGATTATATATTTATTATATTTATATAATTTT
Found at i:2110232 original size:19 final size:18
Alignment explanation
Indices: 2110191--2110235 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
2110181 TTATTTGTAT
2110191 TATTATA-TA-AAAATAA
1 TATTATATTATAAAATAA
2110207 T-TTATATTATAAAATATA
1 TATTATATTATAAAATA-A
2110225 TATTATATTAT
1 TATTATATTAT
2110236 TTTAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.20
16 3 0.12
17 6 0.24
18 2 0.08
19 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTATATTATAAAATAA
Found at i:2110789 original size:20 final size:20
Alignment explanation
Indices: 2110766--2110803 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2110756 ATTATGAATT
2110766 TTTATATTT-TCAAATTAATA
1 TTTAT-TTTATCAAATTAATA
2110786 TTTATTTTATCAAATTAA
1 TTTATTTTATCAAATTAA
2110804 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATTTTATCAAATTAATA
Found at i:2111201 original size:20 final size:19
Alignment explanation
Indices: 2111165--2111203 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2111155 ATTTTCAAAA
**
2111165 ATTAATGATTATTAACTAC
1 ATTAATGATTAGAAACTAC
2111184 ATTAAGTGATTAGAAACTAC
1 ATTAA-TGATTAGAAACTAC
2111204 GAATAATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (19 bp):
ATTAATGATTAGAAACTAC
Found at i:2113042 original size:17 final size:17
Alignment explanation
Indices: 2113008--2113051 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2112998 ATTATGAGTG
* *
2113008 ATAATATTATTTTAGTA
1 ATAAAATTATTTCAGTA
*
2113025 ATAAAATTATTTCGGTA
1 ATAAAATTATTTCAGTA
*
2113042 ATTAAATTAT
1 ATAAAATTAT
2113052 CATTGTGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (17 bp):
ATAAAATTATTTCAGTA
Found at i:2114539 original size:72 final size:73
Alignment explanation
Indices: 2114422--2114558 Score: 206
Period size: 72 Copynumber: 1.9 Consensus size: 73
2114412 CATTTAAAAA
* *
2114422 GTGATAAAATATTTTTAAAGTTTATAAATTTTAAAAGGATAACAATTGATATCGTGGTGTGACAT
1 GTGATAAAATATTTTCAAAGTTTATAAATTTAAAAAGGATAACAATTGATATCGTGGTGTGACAT
2114487 TAAATCCT
66 TAAATCCT
* * *
2114495 GTGAT-AAA-ATTTTCAGAGTTTATAAGTTTCAAAAAGGATAACAATTGATATTGTGGTGTGACA
1 GTGATAAAATATTTTCAAAGTTTATAAATTT-AAAAAGGATAACAATTGATATCGTGGTGTGACA
2114558 T
65 T
2114559 CAAACCTTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 18 0.31
72 35 0.60
73 5 0.09
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.37
Consensus pattern (73 bp):
GTGATAAAATATTTTCAAAGTTTATAAATTTAAAAAGGATAACAATTGATATCGTGGTGTGACAT
TAAATCCT
Found at i:2114809 original size:16 final size:14
Alignment explanation
Indices: 2114789--2114830 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 14
2114779 TTTAAAGTTT
2114789 AATTTATTTTTAAA
1 AATTTATTTTTAAA
2114803 TATATTTATTTTTTAAA
1 -A-ATTTA-TTTTTAAA
2114820 AATTTATTTTT
1 AATTTATTTTT
2114831 TAAGTTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.20
15 6 0.24
16 6 0.24
17 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTTATTTTTAAA
Found at i:2114824 original size:15 final size:16
Alignment explanation
Indices: 2114788--2114833 Score: 69
Period size: 15 Copynumber: 2.9 Consensus size: 16
2114778 ATTTAAAGTT
2114788 TAATTTA-TTTTTAAA
1 TAATTTATTTTTTAAA
2114803 TATATTTATTTTTTAAA
1 TA-ATTTATTTTTTAAA
2114820 -AATTTATTTTTTAA
1 TAATTTATTTTTTAA
2114834 GTTCAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.52
16 6 0.21
17 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTATTTTTTAAA
Found at i:2115537 original size:220 final size:223
Alignment explanation
Indices: 2115240--2115683 Score: 768
Period size: 220 Copynumber: 2.0 Consensus size: 223
2115230 TATTTTCATT
2115240 AATTTTCCTTGATAAACCAAAAATATTTTTCTTTAAAAATAATCTAAAGATAATTTATTACCTGA
1 AATTTTCCTTGATAAACCAAAAATATTTTTCTTTAAAAATAATCTAAAGATAATTTATTACCTGA
* *
2115305 TTATATTAATAAGATAATATAAAAAGAAAATTTATCCAATAAAAAACAACCAAGTTTCTTGAATA
66 TTATATTAATAAGATAATACAAAAAGAAAATTTATCCAATAAAAAACAACCAACTTTCTTGAATA
2115370 AATAAAAATTTGCATTTAT-AAAAAAAAGACAAATTATGCAAACTTTTAC-ATTTT-AAAAAAAA
131 AATAAAAATTTGCATTTATAAAAAAAAAGACAAATTATGCAAACTTTTACTATTTTAAAAAAAAA
**
2115432 TTTTGACTTTTGATTTATTATTTAATAG
196 AGTTGACTTTTGATTTATTATTTAATAG
* * *
2115460 AATTTTCGTTGATAAACCAAAAATATTTTTCTTTAAAATTAATCTAAAGATAATTTATTACTTGA
1 AATTTTCCTTGATAAACCAAAAATATTTTTCTTTAAAAATAATCTAAAGATAATTTATTACCTGA
*
2115525 TTATATTAATAAGATAATACAAAAAGAAAATTTATCCAATAAAAAACAACCATCTTTCTTGAATA
66 TTATATTAATAAGATAATACAAAAAGAAAATTTATCCAATAAAAAACAACCAACTTTCTTGAATA
*
2115590 AATAAAAATTTGCATTTATAAAAAAAAAAGACAAATTATGCAAACTTTTACTTTTTTTAAAAAAA
131 AATAAAAATTTGCATTTAT-AAAAAAAAAGACAAATTATGCAAACTTTTAC-TATTTTAAAAAAA
2115655 AAAGTTGACTTTTGATTTATTATTTAATA
194 AAAGTTGACTTTTGATTTATTATTTAATA
2115684 ACAATTAAAC
Statistics
Matches: 210, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
220 143 0.68
222 30 0.14
224 4 0.02
225 33 0.16
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.38
Consensus pattern (223 bp):
AATTTTCCTTGATAAACCAAAAATATTTTTCTTTAAAAATAATCTAAAGATAATTTATTACCTGA
TTATATTAATAAGATAATACAAAAAGAAAATTTATCCAATAAAAAACAACCAACTTTCTTGAATA
AATAAAAATTTGCATTTATAAAAAAAAAGACAAATTATGCAAACTTTTACTATTTTAAAAAAAAA
AGTTGACTTTTGATTTATTATTTAATAG
Found at i:2116110 original size:2 final size:2
Alignment explanation
Indices: 2116103--2116135 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2116093 ATCTACAAGG
2116103 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 A
2116136 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2116140 original size:2 final size:2
Alignment explanation
Indices: 2116135--2116166 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2116125 ATATATATAT
2116135 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
2116167 TTAAACCAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2119914 original size:18 final size:17
Alignment explanation
Indices: 2119869--2119914 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2119859 AAAAGTTACG
2119869 AGTGATAAAATTACTTT
1 AGTGATAAAATTACTTT
*
2119886 AGTAATAAAATTATCTTT
1 AGTGATAAAATTA-CTTT
2119904 -GTGATATAAAT
1 AGTGATA-AAAT
2119915 ATGCCAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.41
Consensus pattern (17 bp):
AGTGATAAAATTACTTT
Found at i:2122815 original size:28 final size:28
Alignment explanation
Indices: 2122784--2122842 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
2122774 ATTTAAAAAT
*
2122784 TAATATTTTTAAATATA-AATATATATTA
1 TAATATTTTTAAATATATAAAATAT-TTA
*
2122812 TAATTTTTTTAAATATATAAAATATTTA
1 TAATATTTTTAAATATATAAAATATTTA
2122840 TAA
1 TAA
2122843 AAAATTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TAATATTTTTAAATATATAAAATATTTA
Found at i:2123497 original size:3 final size:3
Alignment explanation
Indices: 2123489--2123518 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
2123479 TAAATTACAA
2123489 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA
2123519 ATAAATAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2127368 original size:18 final size:18
Alignment explanation
Indices: 2127342--2127384 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2127332 CTAGATGATG
*
2127342 GTTGTTGTTG-TTGTTGCT
1 GTTGCTGTTGATT-TTGCT
2127360 GTTGCTGTTGATTTTGCT
1 GTTGCTGTTGATTTTGCT
*
2127378 GCTGCTG
1 GTTGCTG
2127385 GTACAAGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.02, C:0.12, G:0.33, T:0.53
Consensus pattern (18 bp):
GTTGCTGTTGATTTTGCT
Found at i:2131028 original size:13 final size:12
Alignment explanation
Indices: 2131007--2131044 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
2130997 TTTTCTAGGG
*
2131007 TTTTGTTTTCAGT
1 TTTTTTTTTC-GT
2131020 TTTTTTTTTC-T
1 TTTTTTTTTCGT
2131031 TTTTTTTTTCGT
1 TTTTTTTTTCGT
2131043 TT
1 TT
2131045 ATCTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 11 0.48
12 3 0.13
13 9 0.39
ACGTcount: A:0.03, C:0.08, G:0.08, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTCGT
Found at i:2131408 original size:24 final size:25
Alignment explanation
Indices: 2131363--2131413 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
2131353 CAAATATTAT
*
2131363 TTATTTAAATTAATTTGATTTATAA
1 TTATTTAAAATAATTTGATTTATAA
**
2131388 TTATTTAAAAT-ATTTTTTTTATAA
1 TTATTTAAAATAATTTGATTTATAA
2131412 TT
1 TT
2131414 TTTTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATTTAAAATAATTTGATTTATAA
Found at i:2131684 original size:2 final size:2
Alignment explanation
Indices: 2131672--2131730 Score: 77
Period size: 2 Copynumber: 29.5 Consensus size: 2
2131662 AGAATTATTC
*
2131672 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT CA- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
2131714 AT CA- AT AT AT AT AT AT A
1 AT -AT AT AT AT AT AT AT A
2131731 CACAGATACA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2137483 original size:3 final size:3
Alignment explanation
Indices: 2137475--2137508 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2137465 CCCGTGGTTG
2137475 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2137509 GAAATGTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2144666 original size:25 final size:26
Alignment explanation
Indices: 2144638--2144698 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
2144628 GTAATAAAAA
*
2144638 TTAATATTAATTTTTTTATTT-TATT
1 TTAATATTAATTATTTTATTTATATT
2144663 TTAA-ATTTAATTATTTTATTTATATT
1 TTAATA-TTAATTATTTTATTTATATT
* *
2144689 TAAATTTTAA
1 TTAATATTAA
2144699 AATAAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 1 0.03
25 18 0.60
26 11 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTAATATTAATTATTTTATTTATATT
Found at i:2145547 original size:21 final size:20
Alignment explanation
Indices: 2145513--2145551 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2145503 TGACTCTCTT
2145513 ATAAATATATAATTTAAATA
1 ATAAATATATAATTTAAATA
*
2145533 ATAAATTTGATAATTTAAA
1 ATAAATAT-ATAATTTAAA
2145552 ATATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
ATAAATATATAATTTAAATA
Found at i:2154427 original size:3 final size:3
Alignment explanation
Indices: 2154419--2154455 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
2154409 TGAAAAGAAT
* *
2154419 AGA AGA AGA AGA AGA AGA AGA AGA TGA AGA TGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2154456 ACTAATCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.32, T:0.05
Consensus pattern (3 bp):
AGA
Found at i:2156876 original size:6 final size:6
Alignment explanation
Indices: 2156833--2156867 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2156823 TCATCCTCGT
* *
2156833 CACCAG CACCAG CACCAG CACCAT CACCAT CACCA
1 CACCAG CACCAG CACCAG CACCAG CACCAG CACCA
2156868 CCAACACCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.51, G:0.09, T:0.06
Consensus pattern (6 bp):
CACCAG
Found at i:2156884 original size:51 final size:51
Alignment explanation
Indices: 2156827--2156936 Score: 121
Period size: 51 Copynumber: 2.2 Consensus size: 51
2156817 TCATCTTCAT
* * * ** *
2156827 CCTCGTCACCAGCACCAGCACCAGCACCATCACCATCACCACCAACACCAC
1 CCTCGTCACCAACACCAGCACCACCACCACCACCAGAAACACCAACACCAC
* * * *
2156878 CCTCGTCAGCAACATCATCACCACCACCACCAGCAGAAACACCAACACCAC
1 CCTCGTCACCAACACCAGCACCACCACCACCACCAGAAACACCAACACCAC
*
2156929 CCTGGTCA
1 CCTCGTCA
2156937 TCATCAACGC
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.33, C:0.49, G:0.09, T:0.09
Consensus pattern (51 bp):
CCTCGTCACCAACACCAGCACCACCACCACCACCAGAAACACCAACACCAC
Found at i:2163699 original size:21 final size:21
Alignment explanation
Indices: 2163661--2163704 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2163651 TATATTAAAT
2163661 ATTAAAAAATTTAGTTAATTCA
1 ATTAAAAAATTTAGTTAA-TCA
* *
2163683 ATTAATAATTTTA-TTAATCA
1 ATTAAAAAATTTAGTTAATCA
2163703 AT
1 AT
2163705 AACTGATCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 4 0.20
22 11 0.55
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTAAAAAATTTAGTTAATCA
Done.