Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 98 of 103
Found at i:36171769 original size:30 final size:32
Alignment explanation
Indices: 36171735--36171805 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 32
36171725 ACTTAAAATT
** *
36171735 AGTATTT-AAAAAAA-AAAGTAACATTAAGGA
1 AGTATTTAAAAAAAAGAAAAAAACATTAAGAA
36171765 AGTATTCGTAAAAAAAAGAAAAAAACATTAAGAA
1 AGTATT--TAAAAAAAAGAAAAAAACATTAAGAA
36171799 AGTATTT
1 AGTATTT
36171806 TTCCTTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
30 6 0.18
32 2 0.06
33 7 0.21
34 19 0.56
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (32 bp):
AGTATTTAAAAAAAAGAAAAAAACATTAAGAA
Found at i:36177645 original size:23 final size:23
Alignment explanation
Indices: 36177619--36177666 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
36177609 TAAAAAAAAA
*
36177619 ATCAATAACAATGGGTGATTACC
1 ATCAATAACAATGGGTGATCACC
*
36177642 ATCAATATCAATGGGTGATCACC
1 ATCAATAACAATGGGTGATCACC
36177665 AT
1 AT
36177667 GAAGATAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (23 bp):
ATCAATAACAATGGGTGATCACC
Found at i:36190388 original size:2 final size:2
Alignment explanation
Indices: 36190381--36190410 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
36190371 ATTAAAGTGA
*
36190381 CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
36190411 GTCTAGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:36191485 original size:15 final size:15
Alignment explanation
Indices: 36191467--36191497 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36191457 ATAGACTTTC
*
36191467 ATAAATGAGAAAGAA
1 ATAAAGGAGAAAGAA
36191482 ATAAAGGAGAAAGAA
1 ATAAAGGAGAAAGAA
36191497 A
1 A
36191498 ACACGCATAT
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:0.68, C:0.00, G:0.23, T:0.10
Consensus pattern (15 bp):
ATAAAGGAGAAAGAA
Found at i:36192664 original size:13 final size:13
Alignment explanation
Indices: 36192632--36192656 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36192622 AAGATTAAAA
36192632 AATATAAAATAAT
1 AATATAAAATAAT
36192645 AATATAAAATAA
1 AATATAAAATAA
36192657 ATAAATAATA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATATAAAATAAT
Found at i:36200202 original size:15 final size:16
Alignment explanation
Indices: 36200169--36200202 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
36200159 TTATAATCTC
*
36200169 TTGATTTTTTTTTTAG
1 TTGATTTTTTCTTTAG
36200185 TTGATTTTTTCTTT-G
1 TTGATTTTTTCTTTAG
36200200 TTG
1 TTG
36200203 TTGTACCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.74
Consensus pattern (16 bp):
TTGATTTTTTCTTTAG
Found at i:36203153 original size:11 final size:10
Alignment explanation
Indices: 36203134--36203163 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
36203124 AAATCAAATC
36203134 AATAAAAAAA
1 AATAAAAAAA
*
36203144 ATTAAAAAAA
1 AATAAAAAAA
36203154 AATAAAAAAA
1 AATAAAAAAA
36203164 GTCTACTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:36204540 original size:19 final size:20
Alignment explanation
Indices: 36204516--36204562 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
36204506 AAGGAATATT
36204516 AATAAAATA-GAAA-AAATAA
1 AATAAAATATGAAATAAA-AA
36204535 AATAAAA-ATGAAATAAAAA
1 AATAAAATATGAAATAAAAA
*
36204554 AAGAAAATA
1 AATAAAATA
36204563 ATAATAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 19 0.79
20 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (20 bp):
AATAAAATATGAAATAAAAA
Found at i:36205985 original size:35 final size:35
Alignment explanation
Indices: 36205944--36206013 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
36205934 AAAGAACAAG
*
36205944 AATAAGTGAAGTACTA-TTTCACA-CAGAACAACTAA
1 AATAAGTGAAGCACTACTTT-A-AGCAGAACAACTAA
36205979 AATAAGTGAAGCACTACTTTAAGCAGAACAACTAA
1 AATAAGTGAAGCACTACTTTAAGCAGAACAACTAA
36206014 TTCAAGTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 1 0.03
35 28 0.88
36 3 0.09
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (35 bp):
AATAAGTGAAGCACTACTTTAAGCAGAACAACTAA
Found at i:36207981 original size:6 final size:6
Alignment explanation
Indices: 36207955--36208038 Score: 80
Period size: 6 Copynumber: 14.0 Consensus size: 6
36207945 ATAGTGTTCC
* * * * *
36207955 TGGTGG TGGCGG TGATGG TGGTGG TGGAGG T-GTCGA TGGTGG TGGCGG
1 TGGTGG TGGTGG TGGTGG TGGTGG TGGTGG TGGT-GG TGGTGG TGGTGG
* * *
36208003 TGGCGG TGGCGG TGGTGG TGGTGG CGGTGG TGGTGG
1 TGGTGG TGGTGG TGGTGG TGGTGG TGGTGG TGGTGG
36208039 AGAGGGCCAA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
5 1 0.02
6 61 0.95
7 2 0.03
ACGTcount: A:0.04, C:0.07, G:0.63, T:0.26
Consensus pattern (6 bp):
TGGTGG
Found at i:36208038 original size:12 final size:12
Alignment explanation
Indices: 36207955--36208035 Score: 90
Period size: 12 Copynumber: 6.8 Consensus size: 12
36207945 ATAGTGTTCC
36207955 TGGTGGTGGCGG
1 TGGTGGTGGCGG
* *
36207967 TGATGGTGGTGG
1 TGGTGGTGGCGG
* * *
36207979 TGGAGGTGTCGA
1 TGGTGGTGGCGG
36207991 TGGTGGTGGCGG
1 TGGTGGTGGCGG
*
36208003 TGGCGGTGGCGG
1 TGGTGGTGGCGG
*
36208015 TGGTGGTGGTGG
1 TGGTGGTGGCGG
*
36208027 CGGTGGTGG
1 TGGTGGTGG
36208036 TGGAGAGGGC
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 55 1.00
ACGTcount: A:0.04, C:0.07, G:0.63, T:0.26
Consensus pattern (12 bp):
TGGTGGTGGCGG
Found at i:36209882 original size:21 final size:21
Alignment explanation
Indices: 36209852--36209894 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
36209842 CATGGTGTCC
*
36209852 CAGGCCGGTGAAGCTGCTTCT
1 CAGGCCGGTGAAACTGCTTCT
*
36209873 CAGGCTGGTGAAACTGCTTCT
1 CAGGCCGGTGAAACTGCTTCT
36209894 C
1 C
36209895 GTTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (21 bp):
CAGGCCGGTGAAACTGCTTCT
Found at i:36212599 original size:16 final size:16
Alignment explanation
Indices: 36212580--36212612 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36212570 TTTAATATAC
36212580 TTATATTAT-TATTTTT
1 TTAT-TTATATATTTTT
36212596 TTATTTATATATTTTT
1 TTATTTATATATTTTT
36212612 T
1 T
36212613 ATAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTATATATTTTT
Found at i:36213935 original size:2 final size:2
Alignment explanation
Indices: 36213928--36213971 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
36213918 TTTGTAAACC
* * *
36213928 TA TA TA TA AA TA TA TA T- TA TT TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36213969 TA T
1 TA T
36213972 TATTTATGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36213967 original size:27 final size:27
Alignment explanation
Indices: 36213928--36213980 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
36213918 TTTGTAAACC
36213928 TATATATAAATATATATTATTTATGTA
1 TATATATAAATATATATTATTTATGTA
*
36213955 TATATATATATATATATTATTTATGT
1 TATATATAAATATATATTATTTATGT
36213981 TCTGAATGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (27 bp):
TATATATAAATATATATTATTTATGTA
Found at i:36228156 original size:28 final size:28
Alignment explanation
Indices: 36228116--36228171 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
36228106 AGTATGTAGT
36228116 TTGAATTATTCACAGCCTCTGCCCAGAA
1 TTGAATTATTCACAGCCTCTGCCCAGAA
36228144 TTGAATTATTCACAGCCTCTGCCCAGAA
1 TTGAATTATTCACAGCCTCTGCCCAGAA
36228172 ATACTTAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (28 bp):
TTGAATTATTCACAGCCTCTGCCCAGAA
Found at i:36233545 original size:2 final size:2
Alignment explanation
Indices: 36233538--36233573 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
36233528 TTTTGAAATN
36233538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36233574 TTTCCCACTG
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):
AT
Found at i:36239704 original size:13 final size:13
Alignment explanation
Indices: 36239686--36239710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36239676 ATTATAATCT
36239686 AGTCCTTTTATAA
1 AGTCCTTTTATAA
36239699 AGTCCTTTTATA
1 AGTCCTTTTATA
36239711 GTGTTAAATA
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
AGTCCTTTTATAA
Found at i:36244099 original size:2 final size:2
Alignment explanation
Indices: 36244092--36244132 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
36244082 TAATGTAGGA
36244092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36244133 CTAAAATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36244172 original size:2 final size:2
Alignment explanation
Indices: 36244165--36244197 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
36244155 ATGTAGGATA
36244165 AT AT AT AT AT AT -T AT AT A- 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
36244198 ATTCTGCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36245828 original size:11 final size:11
Alignment explanation
Indices: 36245812--36245836 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
36245802 AATAAAAATT
36245812 AAAAAAAGAAA
1 AAAAAAAGAAA
36245823 AAAAAAAGAAA
1 AAAAAAAGAAA
36245834 AAA
1 AAA
36245837 GAGAGATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:36245829 original size:29 final size:29
Alignment explanation
Indices: 36245773--36245829 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
36245763 CTATCCCCCA
* * *
36245773 AATAAAAATTAACCAAAAATAAATAAAAT
1 AATAAAAATTAACAAAAAAAAAAAAAAAT
36245802 AATAAAAATTAA-AAAAAGAAAAAAAAAA
1 AATAAAAATTAACAAAAA-AAAAAAAAAA
36245830 GAAAAAAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.16
Consensus pattern (29 bp):
AATAAAAATTAACAAAAAAAAAAAAAAAT
Found at i:36246997 original size:2 final size:2
Alignment explanation
Indices: 36246990--36247084 Score: 190
Period size: 2 Copynumber: 47.5 Consensus size: 2
36246980 AAAAGGGTAA
36246990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36247032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36247074 AT AT AT AT AT A
1 AT AT AT AT AT A
36247085 NNNNNNNNNN
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 93 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36247408 original size:21 final size:21
Alignment explanation
Indices: 36247354--36247408 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
36247344 AAATAGTAAT
* *
36247354 AAATAATAATAGATCTAGGGTAA
1 AAATAATAAT--ATATAGGATAA
36247377 AAATACA-AATATATAGGATAA
1 AAATA-ATAATATATAGGATAA
36247398 AAATAATAATA
1 AAATAATAATA
36247409 ATAAATGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 1 0.04
21 18 0.64
23 8 0.29
24 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.25
Consensus pattern (21 bp):
AAATAATAATATATAGGATAA
Found at i:36248299 original size:2 final size:2
Alignment explanation
Indices: 36248292--36248319 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36248282 GTTCGGTACA
36248292 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
36248320 GCATAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36249246 original size:15 final size:15
Alignment explanation
Indices: 36249226--36249254 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
36249216 ATCGATTTAG
36249226 AACTCCATCGAATAA
1 AACTCCATCGAATAA
36249241 AACTCCATCGAATA
1 AACTCCATCGAATA
36249255 GAACAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.28, G:0.07, T:0.21
Consensus pattern (15 bp):
AACTCCATCGAATAA
Found at i:36257070 original size:31 final size:31
Alignment explanation
Indices: 36257034--36257094 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
36257024 GAAATCCATT
* *
36257034 GGAAATTTTCAAC-GAAATTTTCGTTGGAAAA
1 GGAAA-TTCCAACGGAAAATTTCGTTGGAAAA
36257065 GGAAATTCCAACGGAAAATTTCGTTGGAAA
1 GGAAATTCCAACGGAAAATTTCGTTGGAAA
36257095 GCATATTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.28
Consensus pattern (31 bp):
GGAAATTCCAACGGAAAATTTCGTTGGAAAA
Found at i:36257105 original size:31 final size:30
Alignment explanation
Indices: 36257037--36257106 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
36257027 ATCCATTGGA
* * *
36257037 AATTTTCAACGAAATTTTCGTTGGAAAAGG
1 AATTTCCAACGAAAATTTCGTTGGAAAAGC
*
36257067 AAATTCCAACGGAAAATTTCGTTGG-AAAGC
1 AATTTCCAAC-GAAAATTTCGTTGGAAAAGC
36257097 ATATTTCCAA
1 A-ATTTCCAA
36257107 TGGATTTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (30 bp):
AATTTCCAACGAAAATTTCGTTGGAAAAGC
Found at i:36257438 original size:9 final size:8
Alignment explanation
Indices: 36257415--36257440 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
36257405 TGAAAATTAT
36257415 ATTAAAAA
1 ATTAAAAA
36257423 ATTAAAAA
1 ATTAAAAA
36257431 ATTAAAAA
1 ATTAAAAA
36257439 AT
1 AT
36257441 CTTCTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
ATTAAAAA
Found at i:36257583 original size:36 final size:35
Alignment explanation
Indices: 36257543--36257623 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
36257533 ATTTTCTTCC
* * * *
36257543 ACAAAAATATTAAAATTTAAATTTAAATTA-TAAAAA
1 ACAAATATATT-AAACTTAAAATTAAATAACT-AAAA
*
36257579 ACAAATATCTTAAACTTAAAATTAAATAACTAAAA
1 ACAAATATATTAAACTTAAAATTAAATAACTAAAA
36257614 ACAAATATAT
1 ACAAATATAT
36257624 GGGGAACAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 28 0.74
36 10 0.26
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (35 bp):
ACAAATATATTAAACTTAAAATTAAATAACTAAAA
Found at i:36260016 original size:2 final size:2
Alignment explanation
Indices: 36260011--36260046 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
36260001 TATATCTCAT
36260011 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36260047 TCAGTTATAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36260039 original size:25 final size:25
Alignment explanation
Indices: 36259998--36260046 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
36259988 AATCTTTATT
*
36259998 TAATATATCTCATTATATATATATA
1 TAATATATATCATTATATATATATA
36260023 TAATATATAT-A-TATATATATATA
1 TAATATATATCATTATATATATATA
36260046 T
1 T
36260047 TCAGTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.57
24 1 0.04
25 9 0.39
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATATATATCATTATATATATATA
Found at i:36260150 original size:2 final size:2
Alignment explanation
Indices: 36260143--36260195 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
36260133 CTTGTTTATC
36260143 TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
36260185 TA -A TA TA -A TA T
1 TA TA TA TA TA TA T
36260196 TTTTTAATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:36260177 original size:25 final size:25
Alignment explanation
Indices: 36260143--36260191 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
36260133 CTTGTTTATC
36260143 TATATATATATAT-ATATATATATAG
1 TATATATATATATAATATA-ATATAG
36260168 TATATATATATATAATATAATATA
1 TATATATATATATAATATAATATA
36260192 ATATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TATATATATATATAATATAATATAG
Found at i:36261283 original size:11 final size:11
Alignment explanation
Indices: 36261267--36261311 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
36261257 TTAATTAAAC
*
36261267 TCCGTTGAAAA
1 TCCGTTGCAAA
36261278 TCCGTTGCAAA
1 TCCGTTGCAAA
36261289 TCCGTTGCAAA
1 TCCGTTGCAAA
* *
36261300 TCTGTTGGAAA
1 TCCGTTGCAAA
36261311 T
1 T
36261312 ACAATGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (11 bp):
TCCGTTGCAAA
Found at i:36262748 original size:8 final size:8
Alignment explanation
Indices: 36262735--36262761 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
36262725 CTTGTTGCTG
36262735 TTTTTTGT
1 TTTTTTGT
36262743 TTTTTTGT
1 TTTTTTGT
36262751 TTTTTTGT
1 TTTTTTGT
36262759 TTT
1 TTT
36262762 GTTTAAAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTTGT
Found at i:36270279 original size:61 final size:62
Alignment explanation
Indices: 36270204--36270367 Score: 190
Period size: 61 Copynumber: 2.7 Consensus size: 62
36270194 CAGTGAATGC
* *
36270204 AATTTCTATCGATACATTGTCCAAATGTATCGATAGATTTGAATTGAGAAGCATTCTGGATG
1 AATTTCTATCGATACATTATCCAAATGTATCGATAGATTTGAAATGAGAAGCATTCTGGATG
* * * * * *
36270266 AATTT-TATTGATACATCATCTAAATGTATCGATAGATTTGAAAAGGGGAA-CATTTTGGATG
1 AATTTCTATCGATACATTATCCAAATGTATCGATAGATTTG-AAATGAGAAGCATTCTGGATG
* * * *
36270327 AA-ATCTATCAATACATTACCCAAATGTATCAATAGATTTGA
1 AATTTCTATCGATACATTATCCAAATGTATCGATAGATTTGA
36270368 GGTAGAAAGC
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
60 2 0.02
61 72 0.85
62 11 0.13
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (62 bp):
AATTTCTATCGATACATTATCCAAATGTATCGATAGATTTGAAATGAGAAGCATTCTGGATG
Found at i:36280348 original size:3 final size:3
Alignment explanation
Indices: 36280340--36280380 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
36280330 GAGAACCTTA
* *
36280340 CTC CTC CTC CTC CTC CTC CTC CTC CTC TTT CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
36280381 TCATCCAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (3 bp):
CTC
Found at i:36280816 original size:62 final size:62
Alignment explanation
Indices: 36280714--36280844 Score: 244
Period size: 62 Copynumber: 2.1 Consensus size: 62
36280704 TGTTTTCATT
36280714 GCTTCTTTGTGAGCATTTAATTAAAATTTGTTGTAAATTAAATAATAACAAGTAAGAAAAAG
1 GCTTCTTTGTGAGCATTTAATTAAAATTTGTTGTAAATTAAATAATAACAAGTAAGAAAAAG
* *
36280776 GGTTCTTTGTGAGCATTTAATTAAAATTTGTTGTAGATTAAATAATAACAAGTAAGAAAAAG
1 GCTTCTTTGTGAGCATTTAATTAAAATTTGTTGTAAATTAAATAATAACAAGTAAGAAAAAG
36280838 GCTTCTT
1 GCTTCTT
36280845 ATTTGATTCA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (62 bp):
GCTTCTTTGTGAGCATTTAATTAAAATTTGTTGTAAATTAAATAATAACAAGTAAGAAAAAG
Found at i:36285500 original size:35 final size:34
Alignment explanation
Indices: 36285461--36285588 Score: 104
Period size: 32 Copynumber: 3.8 Consensus size: 34
36285451 GATCTCACGA
*
36285461 GAAAAACCATTGTTGTAGGTTGTGGTTGAACTTTT
1 GAAAAACCATTGTTG-AGGTTATGGTTGAACTTTT
* * * ***
36285496 GAAAAACCACT-TTGA-GTTTTGGTTGAGCCCGT
1 GAAAAACCATTGTTGAGGTTATGGTTGAACTTTT
*
36285528 GAAAAACTATTG-TGAAAGGTTATGGTTGAACTTTT
1 GAAAAACCATTGTTG--AGGTTATGGTTGAACTTTT
* *
36285563 GAAAAACCACT-TTG-GGTTTTGGTTGA
1 GAAAAACCATTGTTGAGGTTATGGTTGA
36285589 TCCCGGTAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
32 34 0.47
33 1 0.01
34 4 0.06
35 33 0.46
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (34 bp):
GAAAAACCATTGTTGAGGTTATGGTTGAACTTTT
Found at i:36285531 original size:32 final size:32
Alignment explanation
Indices: 36285438--36285603 Score: 93
Period size: 32 Copynumber: 4.9 Consensus size: 32
36285428 AAGTTAGTTG
* * *
36285438 TTGAGTTTTGGTTGATCTCACGAGAAAAACCATT
1 TTGAGTTTTGGTTGAAC-C-CGTGAAAAACCACT
* ***
36285472 GTTGTAGGTTGTGGTTGAACTTTTGAAAAACCACT
1 -TTG-A-GTTTTGGTTGAACCCGTGAAAAACCACT
* *
36285507 TTGAGTTTTGGTTGAGCCCGTGAAAAACTA-T
1 TTGAGTTTTGGTTGAACCCGTGAAAAACCACT
* ***
36285538 TGTGAAAGGTTATGGTTGAACTTTTGAAAAACCACT
1 T-TG--A-GTTTTGGTTGAACCCGTGAAAAACCACT
* *
36285574 TTGGGTTTTGGTTGATCCCG-GTAAAAACCA
1 TTGAGTTTTGGTTGAACCCGTG-AAAAACCA
36285604 TTGTGAAAGG
Statistics
Matches: 98, Mismatches: 25, Indels: 19
0.69 0.18 0.13
Matches are distributed among these distances:
31 3 0.03
32 41 0.42
33 1 0.01
34 4 0.04
35 35 0.36
36 3 0.03
37 11 0.11
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (32 bp):
TTGAGTTTTGGTTGAACCCGTGAAAAACCACT
Found at i:36285548 original size:67 final size:66
Alignment explanation
Indices: 36285438--36285615 Score: 250
Period size: 67 Copynumber: 2.6 Consensus size: 66
36285428 AAGTTAGTTG
* *
36285438 TTGAGTTTTGGTTGATCTCACGAGAAAAACCATTGTTG-TAGGTTGTGGTTGAACTTTTGAAAAA
1 TTGAGTTTTGGTTGATC-C-CG-GAAAAACCATTG-TGAAAGGTTATGGTTGAACTTTTGAAAAA
36285502 CCACT
62 CCACT
* *
36285507 TTGAGTTTTGGTTGAGCCCGTGAAAAACTATTGTGAAAGGTTATGGTTGAACTTTTGAAAAACCA
1 TTGAGTTTTGGTTGATCCCG-GAAAAACCATTGTGAAAGGTTATGGTTGAACTTTTGAAAAACCA
36285572 CT
65 CT
*
36285574 TTGGGTTTTGGTTGATCCCGGTAAAAACCATTGTGAAAGGTT
1 TTGAGTTTTGGTTGATCCCGG-AAAAACCATTGTGAAAGGTT
36285616 TTAGCTAAGC
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
66 3 0.03
67 79 0.80
68 1 0.01
69 16 0.16
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (66 bp):
TTGAGTTTTGGTTGATCCCGGAAAAACCATTGTGAAAGGTTATGGTTGAACTTTTGAAAAACCAC
T
Found at i:36286774 original size:59 final size:59
Alignment explanation
Indices: 36286683--36286802 Score: 195
Period size: 59 Copynumber: 2.0 Consensus size: 59
36286673 TTCTTTTACG
* *
36286683 TGGTCTTTCCTTTCTTTGGTAAGCTTCATCTTTTGTTTGAAGTACCCTACCCTCTCTTT
1 TGGTCCTTCATTTCTTTGGTAAGCTTCATCTTTTGTTTGAAGTACCCTACCCTCTCTTT
* * *
36286742 TGGTCCTTCATTTTTTTGGTAAGCTTCGTCTTTTGTTTGAAGTACCTTACCCTCTCTTT
1 TGGTCCTTCATTTCTTTGGTAAGCTTCATCTTTTGTTTGAAGTACCCTACCCTCTCTTT
36286801 TG
1 TG
36286803 CTCGAGAGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.12, C:0.23, G:0.15, T:0.50
Consensus pattern (59 bp):
TGGTCCTTCATTTCTTTGGTAAGCTTCATCTTTTGTTTGAAGTACCCTACCCTCTCTTT
Found at i:36293038 original size:123 final size:122
Alignment explanation
Indices: 36292885--36293128 Score: 275
Period size: 123 Copynumber: 2.0 Consensus size: 122
36292875 TCAAGTATGA
* * *
36292885 AGGGATAAAAATAAAAAATTTAATATTTGAAGCA-ACGGAATT-ATAAAACTTTTAAAAA-ATAA
1 AGGGATAAAAACAAAAAATTCAATATTTGAAG-AGACGAAATTGA-AAAA-----AAAAATATAA
* * *
36292947 AAATA-AAAATATAAAATTTTGAAACAAAACAAAGAC-AAGTTATAAAATTTTGAAACTTTGGG
59 AAAGACAAAATATAAAATTTTAAAACAAAACAAAGACAAAATTATAAAATTTTGAAACTTTGGG
* *
36293009 AGGGA-AAAAACAAAATATTCAATATTTGAAGAGACGAAATTGAAAAAAAAAATTTTTAAAAAGA
1 AGGGATAAAAACAAAAAATTCAATATTTGAAGAGACGAAATTGAAAAAAAAAA--TATAAAAAGA
* *
36293073 CAAATTATAAAATTTTAAAACAAAACAAAGACAAAATTATAAATTTTTGAAACTTT
64 CAAAATATAAAATTTTAAAACAAAACAAAGACAAAATTATAAAATTTTGAAACTTT
36293129 TTGGGGTGGG
Statistics
Matches: 103, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
118 5 0.05
121 7 0.07
122 30 0.29
123 55 0.53
124 6 0.06
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (122 bp):
AGGGATAAAAACAAAAAATTCAATATTTGAAGAGACGAAATTGAAAAAAAAAATATAAAAAGACA
AAATATAAAATTTTAAAACAAAACAAAGACAAAATTATAAAATTTTGAAACTTTGGG
Found at i:36295003 original size:30 final size:30
Alignment explanation
Indices: 36294967--36295029 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
36294957 ATGTCTAAAC
36294967 AGTAAGGATATAAGAAAAGAAAAAGGAATT
1 AGTAAGGATATAAGAAAAGAAAAAGGAATT
36294997 AGTAAGGATATAAGAAAAGAAAAAGGAATT
1 AGTAAGGATATAAGAAAAGAAAAAGGAATT
36295027 AGT
1 AGT
36295030 TCCTCCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.17
Consensus pattern (30 bp):
AGTAAGGATATAAGAAAAGAAAAAGGAATT
Found at i:36298516 original size:16 final size:17
Alignment explanation
Indices: 36298481--36298519 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
36298471 TTTTTTTTCA
*
36298481 AAAATTGTTTAAAGAAAT
1 AAAA-TGTTTAAACAAAT
36298499 AAAATGTTT-AACAAAT
1 AAAATGTTTAAACAAAT
36298515 AAAAT
1 AAAAT
36298520 AATGTAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 5 0.25
18 4 0.20
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (17 bp):
AAAATGTTTAAACAAAT
Found at i:36310966 original size:143 final size:140
Alignment explanation
Indices: 36310801--36311086 Score: 545
Period size: 143 Copynumber: 2.0 Consensus size: 140
36310791 TTGTTTAATT
36310801 AAAAAACATTAACGTTTGTTTGGGTTTTTTTCTTTTCTAACTTTTCTCTGCTTTTGTCTGCTCAC
1 AAAAAACATTAACGTTTGTTTGGGTTTTTTTCTTTTCTAACTTTTCTCTGCTTTTGTCTGCTCAC
36310866 TTTCTCACTATCTAAACAAGAAACATATATAGAAAAAATTCTAGCTAGATTTTATTAAAAAAATA
66 TTTCTCACTATCTAAACAAGAAACATATATAGAAAAAATTCTAGCTAGATTTTATTAAAAAAATA
36310931 GATAAATAATAA
131 -AT-AATAATAA
36310943 AAANAAACATTAACGTTTGTTTGGGTTTTTTTCTTTTCTAACTTTTCTCTGCTTTTGTCTGCTCA
1 AAA-AAACATTAACGTTTGTTTGGGTTTTTTTCTTTTCTAACTTTTCTCTGCTTTTGTCTGCTCA
36311008 CTTTCTCACTATCTAAACAAGAAACATATATAGAAAAAATTCTAGCTAGATTTTATTAAAAAAAT
65 CTTTCTCACTATCTAAACAAGAAACATATATAGAAAAAATTCTAGCTAGATTTTATTAAAAAAAT
36311073 AATAATAATAA
130 AATAATAATAA
36311084 AAA
1 AAA
36311087 GACTGACTTT
Statistics
Matches: 143, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
141 11 0.08
142 5 0.03
143 127 0.89
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (140 bp):
AAAAAACATTAACGTTTGTTTGGGTTTTTTTCTTTTCTAACTTTTCTCTGCTTTTGTCTGCTCAC
TTTCTCACTATCTAAACAAGAAACATATATAGAAAAAATTCTAGCTAGATTTTATTAAAAAAATA
ATAATAATAA
Found at i:36313423 original size:3 final size:3
Alignment explanation
Indices: 36313415--36313459 Score: 63
Period size: 3 Copynumber: 14.0 Consensus size: 3
36313405 TAGACACCTA
36313415 AAT AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT GAAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT -AAT -AAT AAT
36313460 TTTAGATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
3 30 0.77
4 9 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:36313743 original size:21 final size:22
Alignment explanation
Indices: 36313706--36313748 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
36313696 AATTAACCCC
*
36313706 AAAAAAAAAGGGCAAGA-AAGA
1 AAAAAAAAAGAGCAAGAGAAGA
36313727 AAAAAAAAAGAAG-AAGAGAAGA
1 AAAAAAAAAG-AGCAAGAGAAGA
36313749 GAGAGGTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAGAGCAAGAGAAGA
Found at i:36316318 original size:20 final size:20
Alignment explanation
Indices: 36316295--36316336 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
36316285 TTTTATTATT
* *
36316295 ATATATATATATATAATTTG
1 ATATACATATATATAATATG
36316315 ATATACATATATATAATATG
1 ATATACATATATATAATATG
36316335 AT
1 AT
36316337 TATTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
ATATACATATATATAATATG
Found at i:36317947 original size:29 final size:28
Alignment explanation
Indices: 36317897--36317979 Score: 87
Period size: 30 Copynumber: 2.9 Consensus size: 28
36317887 TTAGAAAAAT
* * *
36317897 TTAAATAAGTTTTAAT-TTTTTATTGCA
1 TTAAATAAATTTTTATATTTTTATTGAA
*
36317924 TTAAATTAAATTTTTATATTTTTATTTTAA
1 TTAAA-TAAATTTTTATATTTTTA-TTGAA
*
36317954 GTAAAATAAATTTTTATATTTTTATT
1 -TTAAATAAATTTTTATATTTTTATT
36317980 TTGAGTCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
27 5 0.11
28 9 0.19
29 8 0.17
30 21 0.45
31 4 0.09
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (28 bp):
TTAAATAAATTTTTATATTTTTATTGAA
Found at i:36317964 original size:30 final size:30
Alignment explanation
Indices: 36317925--36317990 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
36317915 TTTATTGCAT
*
36317925 TAAATTAAATTTTTATATTTTTATTTTAAG
1 TAAAATAAATTTTTATATTTTTATTTTAAG
*
36317955 TAAAATAAATTTTTATATTTTTATTTTGAG
1 TAAAATAAATTTTTATATTTTTATTTTAAG
*
36317985 TCAAAT
1 TAAAAT
36317991 TAATCATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (30 bp):
TAAAATAAATTTTTATATTTTTATTTTAAG
Found at i:36328923 original size:2 final size:2
Alignment explanation
Indices: 36328918--36328951 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
36328908 TTGAAAAAAA
36328918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36328952 TTGGGTGTAT
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):
AT
Found at i:36366603 original size:2 final size:2
Alignment explanation
Indices: 36366596--36366638 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
36366586 TTTAGTGTTC
36366596 CT CT CT CT CT 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 CT CT CT CT CT
36366638 C
1 C
36366639 CTTTCTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:36368610 original size:2 final size:2
Alignment explanation
Indices: 36368603--36368636 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
36368593 CAAAGAGAAA
* *
36368603 AG AG AG AG AA AG AG GG 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
36368637 TTTGTATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36385773 original size:3 final size:3
Alignment explanation
Indices: 36385765--36385791 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
36385755 ATACAAGTAT
36385765 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
36385792 CTACTCTGTC
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):
TAA
Found at i:36403183 original size:2 final size:2
Alignment explanation
Indices: 36403176--36403203 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36403166 ATCTCAGTTA
36403176 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
36403204 AACCAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:36412443 original size:29 final size:29
Alignment explanation
Indices: 36412401--36412459 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
36412391 ATTTCTGCCA
36412401 CAGTTAATTGCAGTTTTAATCTAAAAGAG
1 CAGTTAATTGCAGTTTTAATCTAAAAGAG
36412430 CAGTTAATTGCAGTTTTAATCTAAAAGAG
1 CAGTTAATTGCAGTTTTAATCTAAAAGAG
36412459 C
1 C
36412460 TTACATCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (29 bp):
CAGTTAATTGCAGTTTTAATCTAAAAGAG
Found at i:36412469 original size:16 final size:16
Alignment explanation
Indices: 36412448--36412479 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
36412438 TGCAGTTTTA
36412448 ATCTAAAAGAGCTTAC
1 ATCTAAAAGAGCTTAC
36412464 ATCTAAAAGAGCTTAC
1 ATCTAAAAGAGCTTAC
36412480 TTACTTTCCT
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:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
ATCTAAAAGAGCTTAC
Found at i:36418820 original size:2 final size:2
Alignment explanation
Indices: 36418813--36418856 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
36418803 AACCTTTTTA
36418813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36418855 AT
1 AT
36418857 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36425778 original size:2 final size:2
Alignment explanation
Indices: 36425771--36425796 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36425761 TCTTTGAAAG
36425771 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
36425797 AATGCTTAAT
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:36427819 original size:2 final size:2
Alignment explanation
Indices: 36427812--36427853 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
36427802 GAACCCATGG
36427812 CT CT CT CT CT 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 CT CT CT CT CT
36427854 AACATTAAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:36429134 original size:18 final size:18
Alignment explanation
Indices: 36429113--36429169 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
36429103 ATTTCTTTTT
*
36429113 ATTTTTTTCTTTTTTTTC
1 ATTTTTTTCTTTTTTCTC
36429131 A-TTTTTTCATTTTTTCCTC
1 ATTTTTTTC-TTTTTT-CTC
36429150 ATTTTCTTT-TTTTTTCTC
1 ATTTT-TTTCTTTTTTCTC
36429168 AT
1 AT
36429170 ATGTCAGCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 7 0.21
18 12 0.35
19 9 0.26
20 3 0.09
21 3 0.09
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTTTTCTTTTTTCTC
Found at i:36429135 original size:17 final size:17
Alignment explanation
Indices: 36429115--36429165 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
36429105 TTCTTTTTAT
36429115 TTTTTTCTTTTTTTTCA
1 TTTTTTCTTTTTTTTCA
*
36429132 TTTTTTCATTTTTTCCTCA
1 TTTTTTC-TTTTTT-TTCA
*
36429151 TTTTCT-TTTTTTTTC
1 TTTTTTCTTTTTTTTC
36429166 TCATATGTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 2 0.07
17 13 0.45
18 6 0.21
19 8 0.28
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTCA
Found at i:36429144 original size:19 final size:16
Alignment explanation
Indices: 36429104--36429165 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 16
36429094 TTAATTGTAA
*
36429104 TTTCTTTTTATTT--T
1 TTTCTTTTTTTTTCAT
36429118 TTTC-TTTTTTTTCAT
1 TTTCTTTTTTTTTCAT
36429133 TTT-TTCATTTTTTCCTCAT
1 TTTCTT--TTTTTT--TCAT
36429152 TTTCTTTTTTTTTC
1 TTTCTTTTTTTTTC
36429166 TCATATGTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 7 0.18
14 4 0.10
15 5 0.13
16 2 0.05
17 6 0.15
18 6 0.15
19 7 0.18
20 2 0.05
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTTTTTCAT
Found at i:36432129 original size:18 final size:16
Alignment explanation
Indices: 36432091--36432121 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36432081 AAGTGAAAAA
36432091 TATCACATGATTATAT
1 TATCACATGATTATAT
36432107 TATCACATG-TTATAT
1 TATCACATGATTATAT
36432122 CATTATCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (16 bp):
TATCACATGATTATAT
Found at i:36432287 original size:31 final size:30
Alignment explanation
Indices: 36432252--36432349 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 30
36432242 TTATAGTGGT
*
36432252 TTATTTGACTCAAAATAAAAAGTATAAAGAC
1 TTATTTAACTCAAAATAAAAA-TATAAAGAC
* * * *
36432283 TTATTTAATTTAAAATAAAAATATTAAGAT
1 TTATTTAACTCAAAATAAAAATATAAAGAC
* * ** * *
36432313 TTAATTAA-ACGTAATAAAAGTATAAAAAC
1 TTATTTAACTCAAAATAAAAATATAAAGAC
36432342 TTATTTAA
1 TTATTTAA
36432350 ATTTTTTTAA
Statistics
Matches: 52, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 20 0.38
30 14 0.27
31 18 0.35
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (30 bp):
TTATTTAACTCAAAATAAAAATATAAAGAC
Found at i:36432930 original size:21 final size:21
Alignment explanation
Indices: 36432906--36432949 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
36432896 TTTAAAAAAA
36432906 TTAAATAAAATTTTT-TATTAT
1 TTAAATAAAATTTTTATATT-T
*
36432927 TT-AATTAAATTTTTATATTT
1 TTAAATAAAATTTTTATATTT
36432947 TTA
1 TTA
36432950 TTTTGAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAAATAAAATTTTTATATTT
Found at i:36440581 original size:16 final size:16
Alignment explanation
Indices: 36440544--36440575 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36440534 GCACTTTCTC
*
36440544 TGGACAATTGAAGAGA
1 TGGAAAATTGAAGAGA
36440560 TGGAAAATTGAAGAGA
1 TGGAAAATTGAAGAGA
36440576 GAGAAAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.31, T:0.19
Consensus pattern (16 bp):
TGGAAAATTGAAGAGA
Found at i:36440986 original size:16 final size:16
Alignment explanation
Indices: 36440947--36440979 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
36440937 ATCTTAAATC
*
36440947 AACTAAAATTAATAAA
1 AACTAAATTTAATAAA
36440963 AACTAAATTTAATAAA
1 AACTAAATTTAATAAA
36440979 A
1 A
36440980 TATAAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
AACTAAATTTAATAAA
Found at i:36444174 original size:66 final size:66
Alignment explanation
Indices: 36444079--36444202 Score: 212
Period size: 66 Copynumber: 1.9 Consensus size: 66
36444069 AGTTCAACTT
* *
36444079 ACTGCTCTCTTTTGATTCTTCAACAGAAGGCGCAACAACATTTGATGGAGAAACATCAACTTCCC
1 ACTGCTCTCTTTTAATCCTTCAACAGAAGGCGCAACAACATTTGATGGAGAAACATCAACTTCCC
36444144 C
66 C
* *
36444145 ACTGCTCTCTTTTAATCCTTCAACAGAAGGTGCGACAACATTTGATGGAGAAACATCA
1 ACTGCTCTCTTTTAATCCTTCAACAGAAGGCGCAACAACATTTGATGGAGAAACATCA
36444203 TCAATGGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (66 bp):
ACTGCTCTCTTTTAATCCTTCAACAGAAGGCGCAACAACATTTGATGGAGAAACATCAACTTCCC
C
Found at i:36447459 original size:13 final size:13
Alignment explanation
Indices: 36447441--36447466 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36447431 TTCTTAAGAA
36447441 AGAAATAGTAATG
1 AGAAATAGTAATG
36447454 AGAAATAGTAATG
1 AGAAATAGTAATG
36447467 GAGGATCAAT
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:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (13 bp):
AGAAATAGTAATG
Found at i:36453886 original size:17 final size:17
Alignment explanation
Indices: 36453853--36453885 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
36453843 AAAGTCTTTA
36453853 CTTTCTGTTTTTTTTTT
1 CTTTCTGTTTTTTTTTT
36453870 CTTTCT-TTTTTTTTTT
1 CTTTCTGTTTTTTTTTT
36453886 TTGTTTTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (17 bp):
CTTTCTGTTTTTTTTTT
Found at i:36461328 original size:3 final size:3
Alignment explanation
Indices: 36461278--36461309 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
36461268 CATTAGAACC
*
36461278 TGG TGG AGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
36461310 ATGCTGATTG
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:0.03, C:0.00, G:0.66, T:0.31
Consensus pattern (3 bp):
TGG
Found at i:36482556 original size:3 final size:3
Alignment explanation
Indices: 36482509--36482536 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
36482499 ATTGTTTAGA
36482509 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
36482537 TGAAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:36486130 original size:3 final size:3
Alignment explanation
Indices: 36486122--36486147 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36486112 TTCAAAAGCA
36486122 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
36486148 GGAAAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:36489326 original size:22 final size:22
Alignment explanation
Indices: 36489300--36489353 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
36489290 TGTCAAATAT
36489300 TGAATTTTATCAAGTATCAAAG
1 TGAATTTTATCAAGTATCAAAG
36489322 TGAATTTTATCAAGTATCAAAG
1 TGAATTTTATCAAGTATCAAAG
36489344 TGAATTTTAT
1 TGAATTTTAT
36489354 TAAATTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (22 bp):
TGAATTTTATCAAGTATCAAAG
Found at i:36512625 original size:12 final size:12
Alignment explanation
Indices: 36512597--36512632 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
36512587 CCGGTCACCT
36512597 TTCTTTCCTTCTTC
1 TTCTTT-CTT-TTC
36512611 TTCTTTCTTTTC
1 TTCTTTCTTTTC
36512623 TTCTTTCTTT
1 TTCTTTCTTT
36512633 GGCCGGCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.59
13 3 0.14
14 6 0.27
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
TTCTTTCTTTTC
Found at i:36512715 original size:24 final size:23
Alignment explanation
Indices: 36512654--36512719 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
36512644 CTCTAGATTT
36512654 TTTTTCCTTCTTTTATCTCTCTC
1 TTTTTCCTTCTTTTATCTCTCTC
* * *
36512677 TTTTTCATCTATTTTATTTCTCT-
1 TTTTTCCT-TCTTTTATCTCTCTC
36512700 TTCCTTTCCTTCTTTT-TCTC
1 TT--TTTCCTTCTTTTATCTC
36512720 ATCCTTTGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
23 12 0.35
24 17 0.50
25 5 0.15
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTCCTTCTTTTATCTCTCTC
Found at i:36513005 original size:22 final size:23
Alignment explanation
Indices: 36512975--36513021 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
36512965 ATTATTCATC
36512975 TTTTCTTTATTCATTTCATT-TTA
1 TTTTCTTTATTCATTT-ATTGTTA
36512998 TTTT-TTTATTCATTTATTGTTA
1 TTTTCTTTATTCATTTATTGTTA
36513020 TT
1 TT
36513022 ATTATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.13
22 16 0.70
23 4 0.17
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTCTTTATTCATTTATTGTTA
Found at i:36513023 original size:17 final size:17
Alignment explanation
Indices: 36512965--36513024 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
36512955 CTACCCTTTC
36512965 ATTATTCATCTTT-TCTTT
1 ATTATTCAT-TTTAT-TTT
36512983 ATTCATTTCATTTTATTTT
1 ATT-A-TTCATTTTATTTT
*
36513002 TTTATTCA-TTTATTGTT
1 ATTATTCATTTTATT-TT
36513019 ATTATT
1 ATTATT
36513025 ATTAATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 6 0.17
17 11 0.31
18 4 0.11
19 9 0.25
20 6 0.17
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.68
Consensus pattern (17 bp):
ATTATTCATTTTATTTT
Found at i:36513620 original size:22 final size:22
Alignment explanation
Indices: 36513595--36513671 Score: 66
Period size: 27 Copynumber: 3.3 Consensus size: 22
36513585 TTATTTTTAT
36513595 TTTATTTTTTAAATATTAATAA
1 TTTATTTTTTAAATATTAATAA
36513617 TTTATAATTTATTTAAAATATTAATAA
1 -TT-T-ATTT-TTT-AAATATTAATAA
** **
36513644 TTGGTAATTTAAATATTAAT-A
1 TTTATTTTTTAAATATTAATAA
36513665 TTTATTT
1 TTTATTT
36513672 ATAATTTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
21 4 0.10
22 10 0.24
23 5 0.12
24 2 0.05
25 4 0.10
26 5 0.12
27 12 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTATTTTTTAAATATTAATAA
Found at i:36513651 original size:27 final size:26
Alignment explanation
Indices: 36513598--36513654 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
36513588 TTTTTATTTT
*
36513598 ATTT-TTTAAATATTAATAATTTATA
1 ATTTATTTAAATATTAATAATTGATA
*
36513623 ATTTATTTAAAATATTAATAATTGGTA
1 ATTTATTT-AAATATTAATAATTGATA
36513650 ATTTA
1 ATTTA
36513655 AATATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 3 0.11
27 21 0.75
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTTATTTAAATATTAATAATTGATA
Found at i:36513699 original size:41 final size:41
Alignment explanation
Indices: 36513623--36513719 Score: 101
Period size: 41 Copynumber: 2.3 Consensus size: 41
36513613 ATAATTTATA
* * *
36513623 ATTTATTTAAAATATTAATAATTGGTAATTTAAATATTA-AT
1 ATTTATTTATAAT-TTAATAATTAGTAATTTAAATACTACAT
*
36513664 ATTTATTTATAATTTAATCATTAGT-ATTATAAAATACTACCAT
1 ATTTATTTATAATTTAATAATTAGTAATT-T-AAATACTA-CAT
36513707 -TTTATTTATAATT
1 ATTTATTTATAATT
36513720 AATTTATANT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
39 3 0.06
40 11 0.23
41 19 0.40
42 13 0.27
43 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (41 bp):
ATTTATTTATAATTTAATAATTAGTAATTTAAATACTACAT
Found at i:36513752 original size:20 final size:19
Alignment explanation
Indices: 36513712--36513773 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
36513702 ACCATTTTAT
36513712 TTATAA-TTAATTTATANTTA
1 TTATAATTTAATTT-TA-TTA
36513732 TTATAATTTAATTGTTATTA
1 TTATAATTTAATT-TTATTA
* * *
36513752 TGATTATTTATTTTTATT-
1 TTATAATTTAATTTTATTA
36513770 TTAT
1 TTAT
36513774 TTTATTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 3 0.08
19 5 0.14
20 19 0.53
21 8 0.22
22 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTATAATTTAATTTTATTA
Found at i:36513829 original size:27 final size:25
Alignment explanation
Indices: 36513799--36514052 Score: 128
Period size: 26 Copynumber: 10.1 Consensus size: 25
36513789 TTTATAATTT
*
36513799 ATAATTTATAATTTATTTAAAATATTA
1 ATAATTGAT-ATTTATTT-AAATATTA
36513826 ATAATTGATA---ATTTAAATATTA
1 ATAATTGATATTTATTTAAATATTA
** *
36513848 ATGTTTTAT-TTATAATTTAAATATTA
1 ATAATTGATATT-T-ATTTAAATATTA
*
36513874 GT-A-TGATTATTTATTTTTAAATATTA
1 ATAATTGA-TATTTA--TTTAAATATTA
36513900 ATAACTT-ATAATTTATTTAAAATATTA
1 ATAA-TTGAT-ATTTATTT-AAATATTA
36513927 ATAATTGATA---ATTTAAATATTA
1 ATAATTGATATTTATTTAAATATTA
** * *
36513949 ATGTTTTAT-TTATAATTTAAATATTC
1 ATAATTGATATT-T-ATTTAAATATTA
*
36513975 GT-A-TGATTATTTATTTTTAAATATTA
1 ATAATTGA-TATTTA--TTTAAATATTA
36514001 ATAACTT-ATAATTTATTTAAAATATTA
1 ATAA-TTGAT-ATTTATTT-AAATATTA
*
36514028 ATAATTGATA---ATTAAAATATTA
1 ATAATTGATATTTATTTAAATATTA
36514050 ATA
1 ATA
36514053 CTTTATTATA
Statistics
Matches: 179, Mismatches: 18, Indels: 65
0.68 0.07 0.25
Matches are distributed among these distances:
22 39 0.22
23 11 0.06
24 6 0.03
25 4 0.02
26 65 0.36
27 40 0.22
28 12 0.07
29 2 0.01
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (25 bp):
ATAATTGATATTTATTTAAATATTA
Found at i:36513866 original size:7 final size:7
Alignment explanation
Indices: 36513789--36513814 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
36513779 TTTTAAAATT
36513789 TTTATAA
1 TTTATAA
36513796 TTTATAA
1 TTTATAA
36513803 TTTATAA
1 TTTATAA
36513810 TTTAT
1 TTTAT
36513815 TTAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTATAA
Found at i:36513926 original size:101 final size:101
Alignment explanation
Indices: 36513786--36514074 Score: 483
Period size: 101 Copynumber: 2.8 Consensus size: 101
36513776 TATTTTTAAA
*
36513786 ATTTTTATAAT-TT-ATAATTTATAATTTATTTAAAATATTAATAATTGATAATTTAAATATTAA
1 ATTTTTA-AATATTAATAACTTATAATTTATTTAAAATATTAATAATTGATAATTTAAATATTAA
36513849 TGTTTTATTTATAATTTAAATATTAGTATGATTATTT
65 TGTTTTATTTATAATTTAAATATTAGTATGATTATTT
36513886 ATTTTTAAATATTAATAACTTATAATTTATTTAAAATATTAATAATTGATAATTTAAATATTAAT
1 ATTTTTAAATATTAATAACTTATAATTTATTTAAAATATTAATAATTGATAATTTAAATATTAAT
*
36513951 GTTTTATTTATAATTTAAATATTCGTATGATTATTT
66 GTTTTATTTATAATTTAAATATTAGTATGATTATTT
*
36513987 ATTTTTAAATATTAATAACTTATAATTTATTTAAAATATTAATAATTGATAATTAAAATATTAAT
1 ATTTTTAAATATTAATAACTTATAATTTATTTAAAATATTAATAATTGATAATTTAAATATTAAT
**
36514052 ACTTTATTATATTAATTATAAAT
66 GTTTTATT-TA-TAATT-TAAAT
36514075 TTTTTAAAAA
Statistics
Matches: 179, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
99 3 0.02
100 9 0.05
101 155 0.87
102 2 0.01
103 5 0.03
104 5 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (101 bp):
ATTTTTAAATATTAATAACTTATAATTTATTTAAAATATTAATAATTGATAATTTAAATATTAAT
GTTTTATTTATAATTTAAATATTAGTATGATTATTT
Found at i:36513958 original size:74 final size:74
Alignment explanation
Indices: 36513857--36514015 Score: 182
Period size: 74 Copynumber: 2.1 Consensus size: 74
36513847 AATGTTTTAT
* *
36513857 TTATAATTTAAATATTAGTATGATTATTTAT-TTTTAAATATTAATAACTTATAATTTA-TTTAA
1 TTATAATTTAAATATTAG-ATGATTATTTATAATTTAAATATTAAT-A-TGATAATTTATTTTAA
36513920 AATATTAATAA-
63 AATATTAATAAC
* ** * *
36513931 TTGATAATTTAAATATTA-ATGTTTTATTTATAATTTAAATATTCGTATGATTATTTATTTTTAA
1 TT-ATAATTTAAATATTAGATG-ATTATTTATAATTTAAATATTAATATGATAATTTATTTTAAA
36513995 ATATTAATAAC
64 ATATTAATAAC
36514006 TTATAATTTA
1 TTATAATTTA
36514016 TTTAAAATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
73 11 0.15
74 34 0.47
75 28 0.38
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (74 bp):
TTATAATTTAAATATTAGATGATTATTTATAATTTAAATATTAATATGATAATTTATTTTAAAAT
ATTAATAAC
Found at i:36514104 original size:141 final size:133
Alignment explanation
Indices: 36513941--36514201 Score: 342
Period size: 141 Copynumber: 1.9 Consensus size: 133
36513931 TTGATAATTT
* * * * *
36513941 AAATATTAATGTTTTATTTATAATTTAAATATTCGTATGATTATTTATTTTTAAATATTAATAAC
1 AAATATTAATATTTTATTTATAAGTTAAATATTAGTATGATTATTAATATTTAAATATTAATAA-
36514006 TTATAATTTATTTAAAATATTAATAATTGATAATTAAAATATTAATACTTTATTATATTAATTAT
65 TT-T-ATTTA---AAAATATTAATAATTGATAATTAAAATATTAATACTTTATT-TA-TAATTAT
36514071 AAATTTTTTAA
123 AAATTTTTTAA
*
36514082 AAATATTAATATTTTATTTATAAGTTAAATATTATTATGATTATTAATATTTAAATATTAATAAT
1 AAATATTAATATTTTATTTATAAGTTAAATATTAGTATGATTATTAATATTTAAATATTAATAAT
* ** * * *
36514147 TTATTTAGAGTTATTAATAATTGATCATTTAAATATTAATATTTTATTTATAATT
66 TTATTTAAAAATATTAATAATTGATAATTAAAATATTAATACTTTATTTATAATT
36514202 TAATCATTAA
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
133 5 0.05
134 2 0.02
135 35 0.32
138 5 0.05
139 1 0.01
140 2 0.02
141 58 0.54
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (133 bp):
AAATATTAATATTTTATTTATAAGTTAAATATTAGTATGATTATTAATATTTAAATATTAATAAT
TTATTTAAAAATATTAATAATTGATAATTAAAATATTAATACTTTATTTATAATTATAAATTTTT
TAA
Found at i:36516711 original size:15 final size:15
Alignment explanation
Indices: 36516691--36516741 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 15
36516681 TAATCTCAGC
36516691 CTTTTTATTTTTGCT
1 CTTTTTATTTTTGCT
36516706 CTTTTTATTTTTACATTGCT
1 CTTTTTA--TTT---TTGCT
36516726 CTTTTTATTTTTGCT
1 CTTTTTATTTTTGCT
36516741 C
1 C
36516742 AGCCTTGCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 13 0.42
17 3 0.10
18 3 0.10
20 12 0.39
ACGTcount: A:0.10, C:0.16, G:0.06, T:0.69
Consensus pattern (15 bp):
CTTTTTATTTTTGCT
Found at i:36525490 original size:27 final size:27
Alignment explanation
Indices: 36525430--36525491 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
36525420 ATATACCTTG
* * *
36525430 GTGTGTAATAAAGTAATTCATGCCTTG
1 GTGTGTAATAAAATAATTCATGCCGTA
**
36525457 GCATGTAATAAAATAATTCATGCCGTA
1 GTGTGTAATAAAATAATTCATGCCGTA
36525484 GTGTGTAA
1 GTGTGTAA
36525492 CATCAGTAGG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (27 bp):
GTGTGTAATAAAATAATTCATGCCGTA
Found at i:36525577 original size:34 final size:34
Alignment explanation
Indices: 36525514--36525611 Score: 106
Period size: 34 Copynumber: 2.9 Consensus size: 34
36525504 GGAGAAAACT
* * * * *
36525514 TTGGTGTGTGACATCTGGTGTTGAAGCTTTGGTC
1 TTGGCGTGTAACATTTGGTATTGAAGCTTTGGCC
*
36525548 TTGGCGTGTAATATTTGGTATTGAAGCTTTGGCC
1 TTGGCGTGTAACATTTGGTATTGAAGCTTTGGCC
* ** *
36525582 TTGGCTTGTAACATTTACTACTGAAGCTTT
1 TTGGCGTGTAACATTTGGTATTGAAGCTTT
36525612 AGTATATAAC
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.17, C:0.13, G:0.28, T:0.42
Consensus pattern (34 bp):
TTGGCGTGTAACATTTGGTATTGAAGCTTTGGCC
Found at i:36527845 original size:22 final size:22
Alignment explanation
Indices: 36527815--36527883 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
36527805 TATATATATA
*
36527815 TATATAACTTGGATTTATTTTC
1 TATAAAACTTGGATTTATTTTC
* * *
36527837 TATAAAACTTTGAAAATT-TTGTC
1 TATAAAAC-TTG-GATTTATTTTC
36527860 TATAAAACTTGGATTTATTTTC
1 TATAAAACTTGGATTTATTTTC
36527882 TA
1 TA
36527884 ATTTTTGTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
21 3 0.08
22 16 0.43
23 15 0.41
24 3 0.08
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (22 bp):
TATAAAACTTGGATTTATTTTC
Found at i:36528116 original size:2 final size:2
Alignment explanation
Indices: 36528109--36528146 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
36528099 AGCACAAATA
36528109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36528147 TCTGTGTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36528784 original size:25 final size:23
Alignment explanation
Indices: 36528731--36528776 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
36528721 ATTTTTTTTG
*
36528731 TATTTTTTTCTGTATATATTGGT
1 TATTTTTCTCTGTATATATTGGT
36528754 TATTTTTCTCTGTATATATTGGT
1 TATTTTTCTCTGTATATATTGGT
36528777 GATATTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.07, G:0.13, T:0.63
Consensus pattern (23 bp):
TATTTTTCTCTGTATATATTGGT
Found at i:36532963 original size:14 final size:14
Alignment explanation
Indices: 36532944--36532970 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36532934 CAAAATTAAT
36532944 TAATTAACTAAAAC
1 TAATTAACTAAAAC
36532958 TAATTAACTAAAA
1 TAATTAACTAAAA
36532971 TTAAAATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:36535475 original size:14 final size:13
Alignment explanation
Indices: 36535453--36535486 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
36535443 ATTTTTCTAA
36535453 AAAAATAAATAAT
1 AAAAATAAATAAT
*
36535466 AAATAATAAATAGT
1 AAA-AATAAATAAT
36535480 AAAAATA
1 AAAAATA
36535487 TTAAGAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AAAAATAAATAAT
Found at i:36543509 original size:235 final size:237
Alignment explanation
Indices: 36542988--36543537 Score: 816
Period size: 235 Copynumber: 2.3 Consensus size: 237
36542978 AATTAATTAC
* * *
36542988 CAATGCATAGATTGATATATGTATATATAATCAGTTTAAGGAATTAAATATAGTGTAAGGTCTAA
1 CAATACATAAATTAATATATGTATATATAATCAGTTTAAGGAATTAAATATAGTGTAAGGTCTAA
* * * * *
36543053 ATATTAGCTATTTGCTGACTGTTTTCGCCCTTTAGTATGATTAGTTGTGAAGTACATAATATCAA
66 ATATTAGCAATTTGCTGACAGTTTTCACACTTTAGTATGATTAGTTGTGAAGTACAAAATATCAA
36543118 TATTAATTAGTATTATATATCTTATATATTGACTAATCAAGCTGGGAACATGAATATCACCATCA
131 TATTAATTAGTATTATATATCTTATATATTGACTAATCAAGCTGGGAACATGAATATCACCATCA
* *
36543183 CTGAATTAATATATTTGACTAACCAACTCACTGACGCAGATG
196 CTGAATTAATATATTTAACTAACCAACTCACAGACGCAGATG
* * ** *
36543225 CAATATATAAATTAGTATACATATATATAATCAGTTTAAGGAGTTAAATATAGTGTAAGGTCTAA
1 CAATACATAAATTAATATATGTATATATAATCAGTTTAAGGAATTAAATATAGTGTAAGGTCTAA
* * * * *
36543290 ATATTAGCAATTTGCTGACAGTTTTCACACTTTATTATGGTTAGTTGTGAATTGCAAAATGTCAA
66 ATATTAGCAATTTGCTGACAGTTTTCACACTTTAGTATGATTAGTTGTGAAGTACAAAATATCAA
* * *
36543355 TATTGATTAGTATTATATATC-T-TATATTGACTAATCAGGCTGGGAACATGAATATCACTATCA
131 TATTAATTAGTATTATATATCTTATATATTGACTAATCAAGCTGGGAACATGAATATCACCATCA
* * * *
36543418 TTGAATTGATATATTTAATTAACCAAGTCACAGACGCAGATG
196 CTGAATTAATATATTTAACTAACCAACTCACAGACGCAGATG
* * *
36543460 CGATACATATATTAATATATGTATATGTAATCAGTTTAAGGAATTAAATATAGTGTAAGGTCTAA
1 CAATACATAAATTAATATATGTATATATAATCAGTTTAAGGAATTAAATATAGTGTAAGGTCTAA
36543525 ATATTAGCAATTT
66 ATATTAGCAATTT
36543538 CAACATATCA
Statistics
Matches: 278, Mismatches: 35, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
235 145 0.52
236 1 0.00
237 132 0.47
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (237 bp):
CAATACATAAATTAATATATGTATATATAATCAGTTTAAGGAATTAAATATAGTGTAAGGTCTAA
ATATTAGCAATTTGCTGACAGTTTTCACACTTTAGTATGATTAGTTGTGAAGTACAAAATATCAA
TATTAATTAGTATTATATATCTTATATATTGACTAATCAAGCTGGGAACATGAATATCACCATCA
CTGAATTAATATATTTAACTAACCAACTCACAGACGCAGATG
Found at i:36548023 original size:34 final size:34
Alignment explanation
Indices: 36547980--36548047 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
36547970 TGCTCCAGTC
* *
36547980 ATAAACTACTTTTGGAATGCGATAACTCTAATGT
1 ATAAACTACTCTTAGAATGCGATAACTCTAATGT
36548014 ATAAACTACTCTTAGAATGCGATAACTCTAATGT
1 ATAAACTACTCTTAGAATGCGATAACTCTAATGT
36548048 TGTTAAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (34 bp):
ATAAACTACTCTTAGAATGCGATAACTCTAATGT
Found at i:36550828 original size:24 final size:21
Alignment explanation
Indices: 36550801--36550866 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
36550791 ATTTCCTTGG
*
36550801 AAGAGGACCCACTTCCCATGA
1 AAGAAGACCCACTTCCCATGA
*
36550822 AAGAAGACGCACTTCCCATGA
1 AAGAAGACCCACTTCCCATGA
*
36550843 AAGAAGACCCACTTCCCTTGA
1 AAGAAGACCCACTTCCCATGA
36550864 AAG
1 AAG
36550867 GTGCCTGGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.15
Consensus pattern (21 bp):
AAGAAGACCCACTTCCCATGA
Found at i:36552015 original size:9 final size:9
Alignment explanation
Indices: 36551993--36552049 Score: 53
Period size: 9 Copynumber: 5.9 Consensus size: 9
36551983 CTGTTCCCTC
36551993 TTTTTTTT-
1 TTTTTTTTA
36552001 TCTTTTTTTA
1 T-TTTTTTTA
36552011 TTTTTATTATA
1 TTTTT-TT-TA
*
36552022 TTTTTTTAA
1 TTTTTTTTA
36552031 TTATTTTATTA
1 TT-TTTT-TTA
36552042 TTTTTTTT
1 TTTTTTTT
36552050 GTTAATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 1 0.02
9 16 0.39
10 13 0.32
11 11 0.27
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:36552037 original size:22 final size:24
Alignment explanation
Indices: 36552010--36552073 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
36552000 TTCTTTTTTT
36552010 ATTTTTATTATATTTTTTTAATT-
1 ATTTTTATTATATTTTTTTAATTA
*
36552033 A-TTTTATTAT-TTTTTTT-GTTA
1 ATTTTTATTATATTTTTTTAATTA
*
36552054 ATTTTTATTATATATTTTTA
1 ATTTTTATTATATTTTTTTA
36552074 TTTGGGGGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 2 0.06
21 8 0.23
22 18 0.51
23 7 0.20
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (24 bp):
ATTTTTATTATATTTTTTTAATTA
Found at i:36552073 original size:13 final size:13
Alignment explanation
Indices: 36552009--36552075 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 13
36551999 TTTCTTTTTT
36552009 TATTTTTATTATA
1 TATTTTTATTATA
*
36552022 T-TTTTT-TAAT-
1 TATTTTTATTATA
36552032 TA-TTTTATTAT-
1 TATTTTTATTATA
36552043 T-TTTTT-TGT-TA
1 TATTTTTAT-TATA
36552054 -ATTTTTATTATA
1 TATTTTTATTATA
36552066 TATTTTTATT
1 TATTTTTATT
36552076 TGGGGGATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
10 7 0.16
11 18 0.42
12 8 0.19
13 10 0.23
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (13 bp):
TATTTTTATTATA
Found at i:36553363 original size:19 final size:19
Alignment explanation
Indices: 36553330--36553382 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
36553320 TTAAAAAAGA
* *
36553330 AAGAGAAAAACAAGAAAAAT
1 AAGATAAAAA-AAGAAAAAC
* *
36553350 AGGATAAAAAAAGAGAAAC
1 AAGATAAAAAAAGAAAAAC
36553369 AAGATAATAAAAAG
1 AAGATAA-AAAAAG
36553383 GAAGAAGAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.08
Consensus pattern (19 bp):
AAGATAAAAAAAGAAAAAC
Found at i:36557188 original size:45 final size:45
Alignment explanation
Indices: 36557138--36557226 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
36557128 AAGATCCAAC
*
36557138 TGCTATGTGTTACAATGTTTGTGATTTTACTAGTGAGGCATTGTT
1 TGCTATGTGTTACAATGTTTGTGATTTTACCAGTGAGGCATTGTT
* *
36557183 TGCTATGTGTTATAATGTTTGTGATTTTACCAGTGAGGCGTTGT
1 TGCTATGTGTTACAATGTTTGTGATTTTACCAGTGAGGCATTGT
36557227 CAGCAATTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.19, C:0.09, G:0.26, T:0.46
Consensus pattern (45 bp):
TGCTATGTGTTACAATGTTTGTGATTTTACCAGTGAGGCATTGTT
Found at i:36558151 original size:398 final size:398
Alignment explanation
Indices: 36557415--36558198 Score: 1340
Period size: 398 Copynumber: 2.0 Consensus size: 398
36557405 TACTTGTCAA
* *
36557415 TGGCTCGACCACATCAAAATTTCCTAGGACGCATGGGCTTCAACAGGGACTAGGAGACTACTTTC
1 TGGCTCGACCACATCAAAATTTCCTAGGACGCATGGGCTTCAACAGGGACTAGGAGACCACTCTC
*
36557480 ACCTTTCTTGTTTATCTTGTCGGTGGAAGCACTCCATCTTCTACTCCTACAGGTGGAAAATCTCA
66 ACCTTTCTTATTTATCTTGTCGGTGGAAGCACTCCATCTTCTACTCCTACAGGTGGAAAATCTCA
36557545 ACTTACCATTTCAAAGAAGAACACACCCAACGACATGACGCAACTTGTCATTCTCTTGAAACAAT
131 ACTTACCATTTCAAAGAAGAACACACCCAACGACATGACGCAACTTGTCATTCTCTTGAAACAAT
* *
36557610 CTCCACAACTTTCAATGTCTCTTATAACTATTTAGCACCCAGTGTATCTATAGCAACACTTGAAT
196 CTCCACAACTTCCAATGTCTCTTATAACTATTTAGCACCCAGAGTATCTATAGCAACACTTGAAT
* *
36557675 ATGATTCAATGATTAGCAATTTTTTCCCAAACCACACAGAATTGTAAAATAATTCTAAAACCACC
261 AGGATTCAATGATTAGCAATTTTTTCCCAAACCACACAGAAGTGTAAAATAATTCTAAAACCACC
*
36557740 TTGTCAACCAATTGCTTGTCCTTTTCAAGTCTATCAATGAAAACTCACAAATGATCTAAAACAAT
326 TTGTCAACCAATTGCTTGTCCTTTTCAAGTCTATCAATGAAAACTCACAAATGATCCAAAACAAT
36557805 GGTGAGTG
391 GGTGAGTG
* *
36557813 TGGCTCGCCCACATCAAAATTTCCTATGACGCATGGGCTTCAACAGGGACT-GAGAGACCACTCT
1 TGGCTCGACCACATCAAAATTTCCTAGGACGCATGGGCTTCAACAGGGACTAG-GAGACCACTCT
* *
36557877 CACCTTTCTTATTTATCTTGTTGGTGGAAGCTCTCCATCTTCTACTCCTACAGGTGGAAAATCTC
65 CACCTTTCTTATTTATCTTGTCGGTGGAAGCACTCCATCTTCTACTCCTACAGGTGGAAAATCTC
* * * *
36557942 AACTTATCATTTCGAAAG-GGAACACACCCAATGACATGACGCAACTTGTCATTCTGTTGAAACA
130 AACTTACCATTTC-AAAGAAGAACACACCCAACGACATGACGCAACTTGTCATTCTCTTGAAACA
36558006 ATCTCCACAACTTCCAATGTCTCTTATAACTATTTAGCACCCAGAGTATAC-ATAGCAACACTTG
194 ATCTCCACAACTTCCAATGTCTCTTATAACTATTTAGCACCCAGAGTAT-CTATAGCAACACTTG
*
36558070 AATAGGATTCAATGATTAGCAATTTTTTCCCAAACCACACAGAAGTGTAAAATAATTCTAATACC
258 AATAGGATTCAATGATTAGCAATTTTTTCCCAAACCACACAGAAGTGTAAAATAATTCTAAAACC
* * *
36558135 ACCTTTTTAACCAATTGTTTGTCCTTTTCAAGTCTATCAATGAAAACTCACAAATGATCCAAAA
323 ACCTTGTCAACCAATTGCTTGTCCTTTTCAAGTCTATCAATGAAAACTCACAAATGATCCAAAA
36558199 AAAAACGGTG
Statistics
Matches: 363, Mismatches: 20, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
397 1 0.00
398 357 0.98
399 5 0.01
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (398 bp):
TGGCTCGACCACATCAAAATTTCCTAGGACGCATGGGCTTCAACAGGGACTAGGAGACCACTCTC
ACCTTTCTTATTTATCTTGTCGGTGGAAGCACTCCATCTTCTACTCCTACAGGTGGAAAATCTCA
ACTTACCATTTCAAAGAAGAACACACCCAACGACATGACGCAACTTGTCATTCTCTTGAAACAAT
CTCCACAACTTCCAATGTCTCTTATAACTATTTAGCACCCAGAGTATCTATAGCAACACTTGAAT
AGGATTCAATGATTAGCAATTTTTTCCCAAACCACACAGAAGTGTAAAATAATTCTAAAACCACC
TTGTCAACCAATTGCTTGTCCTTTTCAAGTCTATCAATGAAAACTCACAAATGATCCAAAACAAT
GGTGAGTG
Found at i:36578630 original size:8 final size:8
Alignment explanation
Indices: 36578608--36578641 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
36578598 CCTTCTCGAC
36578608 TTTCCTTT
1 TTTCCTTT
36578616 TTCTCCTTT
1 TT-TCCTTT
36578625 TTTCCTTT
1 TTTCCTTT
*
36578633 TTTTCTTT
1 TTTCCTTT
36578641 T
1 T
36578642 CCTTTTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTCCTTT
Found at i:36579131 original size:30 final size:30
Alignment explanation
Indices: 36579095--36579153 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
36579085 TCTTTTTTTC
*
36579095 TTTTTTT-ATTATATATTTATTATTTATTTA
1 TTTTTTTGATTA-ATATTTATTATATATTTA
* *
36579125 TTTTTTTGGTTAATTTTTATTATATATTT
1 TTTTTTTGATTAATATTTATTATATATTT
36579154 TTATTTGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (30 bp):
TTTTTTTGATTAATATTTATTATATATTTA
Found at i:36580446 original size:19 final size:19
Alignment explanation
Indices: 36580413--36580465 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
36580403 TTAAAAAAGA
* *
36580413 AAGAGAAAAACAAGAAAAAT
1 AAGATAAAAA-AAGAAAAAC
* *
36580433 AGGATAAAAAAAGAGAAAC
1 AAGATAAAAAAAGAAAAAC
36580452 AAGATAATAAAAAG
1 AAGATAA-AAAAAG
36580466 GAAGAAGAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.08
Consensus pattern (19 bp):
AAGATAAAAAAAGAAAAAC
Found at i:36584278 original size:45 final size:45
Alignment explanation
Indices: 36584190--36584280 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
36584180 AAAGATTCAA
* * **
36584190 CTGCTATGTGTTACAATGTTTGTGATTTTACCAGTGAGTCATTGT
1 CTGCTATGTGCTACAATGTCTGTGATTTTACCAGAAAGTCATTGT
* *
36584235 CTGCTATGTGCTATAATGTCTGTGATTTTACTAGAAAAG-CATTGT
1 CTGCTATGTGCTACAATGTCTGTGATTTTACCAG-AAAGTCATTGT
36584280 C
1 C
36584281 AGCAGTTCGG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 37 0.95
46 2 0.05
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (45 bp):
CTGCTATGTGCTACAATGTCTGTGATTTTACCAGAAAGTCATTGT
Found at i:36594236 original size:39 final size:39
Alignment explanation
Indices: 36594192--36594272 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
36594182 TATAGTCCAA
36594192 GCAGAGAATGTAATAAAGTAAGAAGAAAAGGTTCTTTAT
1 GCAGAGAATGTAATAAAGTAAGAAGAAAAGGTTCTTTAT
36594231 GCAGAGAATGTAATAAAGTAAGAAGAAAAGGTTCTTTAT
1 GCAGAGAATGTAATAAAGTAAGAAGAAAAGGTTCTTTAT
36594270 GCA
1 GCA
36594273 AAGCCAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (39 bp):
GCAGAGAATGTAATAAAGTAAGAAGAAAAGGTTCTTTAT
Found at i:36609078 original size:42 final size:42
Alignment explanation
Indices: 36609019--36609102 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
36609009 AGACAGGCCT
* **
36609019 GTTGAGAGTTGTTCCTGCCTTAGCTTTGAAGTCGTTCACAGC
1 GTTGAGAGTGGTTCCTGCCACAGCTTTGAAGTCGTTCACAGC
36609061 GTTGAGAGTGGTTCCTGCCACAGCTTTGAAGTCGTTCACAGC
1 GTTGAGAGTGGTTCCTGCCACAGCTTTGAAGTCGTTCACAGC
36609103 ATCAACAGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (42 bp):
GTTGAGAGTGGTTCCTGCCACAGCTTTGAAGTCGTTCACAGC
Found at i:36609102 original size:18 final size:18
Alignment explanation
Indices: 36609040--36609102 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
36609030 TTCCTGCCTT
36609040 AGCTTTGAAGTCGTTCAC
1 AGCTTTGAAGTCGTTCAC
* *
36609058 AGCGTTGAGAGTGGTTCCTGCCAC
1 AGCTTTGA-AGTCG-T--T--CAC
36609082 AGCTTTGAAGTCGTTCAC
1 AGCTTTGAAGTCGTTCAC
36609100 AGC
1 AGC
36609103 ATCAACAGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
18 13 0.37
19 4 0.11
20 2 0.06
22 2 0.06
23 4 0.11
24 10 0.29
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.29
Consensus pattern (18 bp):
AGCTTTGAAGTCGTTCAC
Found at i:36609113 original size:42 final size:42
Alignment explanation
Indices: 36609029--36609113 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
36609019 GTTGAGAGTT
** * ** *
36609029 GTTCCTGCCTTAGCTTTGAAGTCGTTCACAGCGTTGAGAGTG
1 GTTCCTGCCACAGCTTTGAAGTCGTTCACAGCATCAACAGTG
36609071 GTTCCTGCCACAGCTTTGAAGTCGTTCACAGCATCAACAGTG
1 GTTCCTGCCACAGCTTTGAAGTCGTTCACAGCATCAACAGTG
36609113 G
1 G
36609114 AGCTTTGCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (42 bp):
GTTCCTGCCACAGCTTTGAAGTCGTTCACAGCATCAACAGTG
Found at i:36613162 original size:8 final size:7
Alignment explanation
Indices: 36613139--36613194 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
36613129 AATTTCAGAA
36613139 TTTTTCT
1 TTTTTCT
**
36613146 TTTCCCT
1 TTTTTCT
36613153 TTTTTACT
1 TTTTT-CT
36613161 TTTTTC-
1 TTTTTCT
*
36613167 TTTTCCT
1 TTTTTCT
36613174 TTTTTACAT
1 TTTTT-C-T
36613183 TTTTTCT
1 TTTTTCT
36613190 TTTTT
1 TTTTT
36613195 TGTGCACTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
6 5 0.13
7 19 0.49
8 9 0.23
9 6 0.15
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCT
Found at i:36613174 original size:21 final size:23
Alignment explanation
Indices: 36613073--36613192 Score: 95
Period size: 22 Copynumber: 5.2 Consensus size: 23
36613063 TTTAGAATTT
*
36613073 TTTTCCCTTCTTT--ATTTCTTTC
1 TTTTCCCTTTTTTACATTT-TTTC
* *
36613095 TTTTCCCTTTTTTACTTTTTTTTTTG
1 TTTTCCCTTTTTTAC---ATTTTTTC
** * * *
36613121 TTTTCCCAAATTTCAGAATTTTTC
1 TTTTCCC-TTTTTTACATTTTTTC
36613145 TTTTCCCTTTTTTAC-TTTTTTC
1 TTTTCCCTTTTTTACATTTTTTC
36613167 TTTT-CCTTTTTTACATTTTTTC
1 TTTTCCCTTTTTTACATTTTTTC
36613189 TTTT
1 TTTT
36613193 TTTGTGCACT
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
21 10 0.13
22 33 0.43
23 4 0.05
24 12 0.16
26 10 0.13
27 7 0.09
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTCCCTTTTTTACATTTTTTC
Found at i:36615129 original size:84 final size:84
Alignment explanation
Indices: 36614988--36615144 Score: 217
Period size: 84 Copynumber: 1.9 Consensus size: 84
36614978 TAGAAATTTA
* * *
36614988 GAGAGAGTCAGAGGAAGGTGACTTGGATAGGGAGATCAGGGACAGCACAAGATAGAAGTCTGG-A
1 GAGAGAGTCAGAGGAAGGTAACTTGGATACGGAGATCAGAGACAGCACAAGATAGAAGTCTGGAA
36615052 GAGAGCTAAAAGAAGTCGAC
66 G-GAGCTAAAAGAAGTCGAC
* * ** * *
36615072 GAGAGAGTTAGAGGAAGGTAACTTGGATACGGAGATCAGAGACTGCGTAGGATAGAAGTTTGGAA
1 GAGAGAGTCAGAGGAAGGTAACTTGGATACGGAGATCAGAGACAGCACAAGATAGAAGTCTGGAA
36615137 GGAGCTAA
66 GGAGCTAA
36615145 GAGGAAGGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 61 0.97
85 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.37, T:0.16
Consensus pattern (84 bp):
GAGAGAGTCAGAGGAAGGTAACTTGGATACGGAGATCAGAGACAGCACAAGATAGAAGTCTGGAA
GGAGCTAAAAGAAGTCGAC
Found at i:36621783 original size:109 final size:109
Alignment explanation
Indices: 36621592--36621810 Score: 429
Period size: 109 Copynumber: 2.0 Consensus size: 109
36621582 CCATAACTTT
36621592 AGCACCGTTAGACTCAAGTACTTAAAACTAGTTAGGCCAGCTTCCCTCGTGATTTCTAGCCAAAC
1 AGCACCGTTAGACTCAAGTACTTAAAACTAGTTAGGCCAGCTTCCCTCGTGATTTCTAGCCAAAC
36621657 CAATCATCAAAACAAGAGAAAAAGGTGTTTTGGTCCGGGCTGCG
66 CAATCATCAAAACAAGAGAAAAAGGTGTTTTGGTCCGGGCTGCG
*
36621701 AGCACCGTTAGACTCAAGTACTTAAAACTAGTTAGGCCAGCTTCCCTCGTGATTTTTAGCCAAAC
1 AGCACCGTTAGACTCAAGTACTTAAAACTAGTTAGGCCAGCTTCCCTCGTGATTTCTAGCCAAAC
36621766 CAATCATCAAAACAAGAGAAAAAGGTGTTTTGGTCCGGGCTGCG
66 CAATCATCAAAACAAGAGAAAAAGGTGTTTTGGTCCGGGCTGCG
36621810 A
1 A
36621811 ATGAGAAAAC
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (109 bp):
AGCACCGTTAGACTCAAGTACTTAAAACTAGTTAGGCCAGCTTCCCTCGTGATTTCTAGCCAAAC
CAATCATCAAAACAAGAGAAAAAGGTGTTTTGGTCCGGGCTGCG
Found at i:36623471 original size:30 final size:29
Alignment explanation
Indices: 36623437--36623511 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
36623427 TTACCGTTAG
*
36623437 TTATAAAGACTTATTTGATTCAAAATAAAA
1 TTATAAAGACTTATTTGAAT-AAAATAAAA
*
36623467 TTATATAAG-CTTAATTGAATAAAATAAAA
1 TTATA-AAGACTTATTTGAATAAAATAAAA
** *
36623496 AAATAAAAACTTATTT
1 TTATAAAGACTTATTT
36623512 AAATTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
28 2 0.05
29 18 0.49
30 14 0.38
31 3 0.08
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (29 bp):
TTATAAAGACTTATTTGAATAAAATAAAA
Done.