Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000134.1 Hibiscus syriacus cultivar Beakdansim tig00000245_pilon, whole genome shotgun sequence
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: 105876
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:720 original size:3 final size:3
Alignment explanation
Indices: 712--741 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
702 AAATAGGGTT
712 TTG TTG TTG -TG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
742 AATATAAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:930 original size:40 final size:40
Alignment explanation
Indices: 859--937 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
849 ACCACGGTGC
* *
859 TGAACACTGATACACGAATGTACCAAGCTGAACTGATAAT
1 TGAACACTGATACACGAATGTACAAAACTGAACTGATAAT
*
899 TGAACATTGATACAC-AATGTACTAAAACTGAACTGATAA
1 TGAACACTGATACACGAATGTAC-AAAACTGAACTGATAA
938 GCACTCACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 7 0.20
40 28 0.80
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (40 bp):
TGAACACTGATACACGAATGTACAAAACTGAACTGATAAT
Found at i:1086 original size:18 final size:18
Alignment explanation
Indices: 1060--1125 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
1050 GTCTTATATT
* *
1060 ATCTAATAACTGTAAATC
1 ATCTGATAACTGAAAATC
1078 ATCTGATAACTGAAAATC
1 ATCTGATAACTGAAAATC
* *
1096 ATATGATCACTGAAAATC
1 ATCTGATAACTGAAAATC
1114 ATCTGATAACTG
1 ATCTGATAACTG
1126 TAAACATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (18 bp):
ATCTGATAACTGAAAATC
Found at i:1259 original size:18 final size:19
Alignment explanation
Indices: 1222--1259 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1212 TAAAATATTC
*
1222 CATACTGAAAATTTATAAAT
1 CATACTGAAAA-TAATAAAT
1242 CATACTGAAAA-AATAAAT
1 CATACTGAAAATAATAAAT
1260 GAGATTGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (19 bp):
CATACTGAAAATAATAAAT
Found at i:2659 original size:30 final size:30
Alignment explanation
Indices: 2614--2687 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
2604 CCAAAAATTT
* * *
2614 AACTTTTGAAATTTTACATTTTTAGTC-CTT
1 AACTTTTAAAATTTTACA-CTTTAGTCTCTA
* *
2644 AAGTTTTACAATTTTACACTTTAGTCTCTA
1 AACTTTTAAAATTTTACACTTTAGTCTCTA
2674 AACTTTTAAAATTT
1 AACTTTTAAAATTT
2688 ATATTCAGTC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 7 0.19
30 29 0.81
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.50
Consensus pattern (30 bp):
AACTTTTAAAATTTTACACTTTAGTCTCTA
Found at i:9441 original size:13 final size:13
Alignment explanation
Indices: 9423--9448 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9413 AAAAATAAAA
9423 AAAAATATTTTTT
1 AAAAATATTTTTT
9436 AAAAATATTTTTT
1 AAAAATATTTTTT
9449 TTTGGAAAAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:9611 original size:19 final size:19
Alignment explanation
Indices: 9587--9624 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9577 TCTCATCTAA
* *
9587 ACATCCGTGTATTAACACC
1 ACATCCGTATATGAACACC
9606 ACATCCGTATATGAACACC
1 ACATCCGTATATGAACACC
9625 GGGGAGCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.11, T:0.24
Consensus pattern (19 bp):
ACATCCGTATATGAACACC
Found at i:9691 original size:14 final size:14
Alignment explanation
Indices: 9672--9698 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9662 TTAAGGTTTT
9672 GATTTAGGGATTTA
1 GATTTAGGGATTTA
9686 GATTTAGGGATTT
1 GATTTAGGGATTT
9699 TGGCAGCAAT
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:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (14 bp):
GATTTAGGGATTTA
Found at i:32153 original size:33 final size:33
Alignment explanation
Indices: 32092--32156 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
32082 CCTGTTATCG
* *
32092 TTTATTGACTTACTGCTATTCTCCATTATCTTA
1 TTTATTGAATTACTGCTATTATCCATTATCTTA
**
32125 TTTATTGAATTACTGCTATTATGTATTATCTT
1 TTTATTGAATTACTGCTATTATCCATTATCTT
32157 GTTGGCAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (33 bp):
TTTATTGAATTACTGCTATTATCCATTATCTTA
Found at i:33839 original size:69 final size:69
Alignment explanation
Indices: 33728--33870 Score: 241
Period size: 69 Copynumber: 2.1 Consensus size: 69
33718 GCTTCTGCCT
* * *
33728 TTTGATTTTGAACTGCTGGCATTCATCTGATTGATATCCTCATCAGATGAAGAGTTGTTTGTATA
1 TTTGATTTTAAACTGCTGGCATTCATCCGATTGAGATCCTCATCAGATGAAGAGTTGTTTGTATA
33793 CAAG
66 CAAG
* *
33797 TTTGATTTTAAACTGCTGGCATTCATCCGATTGAGCTCCTCATTAGATGAAGAGTTGTTTGTATA
1 TTTGATTTTAAACTGCTGGCATTCATCCGATTGAGATCCTCATCAGATGAAGAGTTGTTTGTATA
33862 CAAG
66 CAAG
33866 TTTGA
1 TTTGA
33871 CTCTTGCATT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (69 bp):
TTTGATTTTAAACTGCTGGCATTCATCCGATTGAGATCCTCATCAGATGAAGAGTTGTTTGTATA
CAAG
Found at i:35181 original size:2 final size:2
Alignment explanation
Indices: 35174--35198 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35164 ATTACCTCGT
35174 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
35199 ATGCCTTTTA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35878 original size:39 final size:39
Alignment explanation
Indices: 35819--35955 Score: 177
Period size: 39 Copynumber: 3.5 Consensus size: 39
35809 CCTATAGAGT
* * * *
35819 ACAAGTGCATTCTGCTCTTTGTATTTGATATTGTAGGGG
1 ACAATTGCATTCTGCTCTTTGTATCTCAAATTGTAGGGG
* *
35858 ACGATTGCATTCTGCTCTTTGTATCTCAAATTGCAGGGG
1 ACAATTGCATTCTGCTCTTTGTATCTCAAATTGTAGGGG
*
35897 ACAAGTT-CATTCTGTTCTTTGTATCTCAAATTGTAGGGG
1 ACAA-TTGCATTCTGCTCTTTGTATCTCAAATTGTAGGGG
**
35936 ACTCTTGCATTCTGCTCTTT
1 ACAATTGCATTCTGCTCTTT
35956 ATATGTAATA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 2 0.02
39 80 0.95
40 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (39 bp):
ACAATTGCATTCTGCTCTTTGTATCTCAAATTGTAGGGG
Found at i:40907 original size:95 final size:96
Alignment explanation
Indices: 40807--41002 Score: 333
Period size: 96 Copynumber: 2.1 Consensus size: 96
40797 TAAAAAAAAT
40807 AAAGATGTGATATAATAAAATAAAATAAAAA-CAATGAATACTGACAGCTGGTGA-CCAGTACCA
1 AAAGATGTGATATAATAAAATAAAATAAAAAGCAATGAATACTGACAGCTGGTGATCC-GTACCA
* *
40870 ATGTTTATGTCGGCATCGCTCATAAAGATAAA
65 ATGTTTATGCCGGCATCGATCATAAAGATAAA
*
40902 AAAGATGTGATATAATAAAATAAAATAAAAAGCAATGAATACTGACAGTTGGTGATCCGTACCAA
1 AAAGATGTGATATAATAAAATAAAATAAAAAGCAATGAATACTGACAGCTGGTGATCCGTACCAA
*
40967 TGTTTATGCCGGCATCGATTATAAAGATAAA
66 TGTTTATGCCGGCATCGATCATAAAGATAAA
40998 AAAGA
1 AAAGA
41003 GAGACTAATG
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
95 31 0.33
96 62 0.65
97 2 0.02
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.24
Consensus pattern (96 bp):
AAAGATGTGATATAATAAAATAAAATAAAAAGCAATGAATACTGACAGCTGGTGATCCGTACCAA
TGTTTATGCCGGCATCGATCATAAAGATAAA
Found at i:42369 original size:16 final size:16
Alignment explanation
Indices: 42337--42378 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
42327 CTTCAATATT
* *
42337 TATTAAAATTTTTATA
1 TATTAAAATTATAATA
42353 TATTAAAATTATAATA
1 TATTAAAATTATAATA
42369 T-TTGAAAATT
1 TATT-AAAATT
42379 GAAATTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TATTAAAATTATAATA
Found at i:42469 original size:16 final size:18
Alignment explanation
Indices: 42448--42488 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
42438 TATTGTACGA
42448 ATTAAAT-AATT-TTAAT
1 ATTAAATAAATTATTAAT
*
42464 ATTAAAATAAATTATTATT
1 ATT-AAATAAATTATTAAT
42483 ATTAAA
1 ATTAAA
42489 GATTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 4 0.19
18 7 0.33
19 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAAATAAATTATTAAT
Found at i:43672 original size:31 final size:33
Alignment explanation
Indices: 43609--43673 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
43599 TACAATAAAA
* *
43609 ATGATTAAGTTTGAAAGATAGAGTGATTAAATT
1 ATGAGTAAGTTTGAAAGATAGAGTAATTAAATT
*
43642 ATGAGTAA-TTTGAAAGTTA-AGTAATTAAATT
1 ATGAGTAAGTTTGAAAGATAGAGTAATTAAATT
43673 A
1 A
43674 AAAAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 12 0.41
32 10 0.34
33 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (33 bp):
ATGAGTAAGTTTGAAAGATAGAGTAATTAAATT
Found at i:44042 original size:25 final size:25
Alignment explanation
Indices: 43993--44042 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
43983 CTTCCATTTT
*
43993 TACTTTAATTTTAATTTGGTCCTTA
1 TACTTTAATTTTAATTTAGTCCTTA
* * *
44018 TACTTTATTTTTACTTTAGTTCTTA
1 TACTTTAATTTTAATTTAGTCCTTA
44043 CTTTAAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.12, G:0.06, T:0.60
Consensus pattern (25 bp):
TACTTTAATTTTAATTTAGTCCTTA
Found at i:44569 original size:16 final size:16
Alignment explanation
Indices: 44548--44578 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
44538 CCACACACAC
44548 ACAGACAAAAAAAAAA
1 ACAGACAAAAAAAAAA
44564 ACAGACAAAAAAAAA
1 ACAGACAAAAAAAAA
44579 CTAAAGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.13, G:0.06, T:0.00
Consensus pattern (16 bp):
ACAGACAAAAAAAAAA
Found at i:47950 original size:20 final size:20
Alignment explanation
Indices: 47925--47999 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
47915 TTGCAGCCCT
*
47925 GGTGCATAGATGCACAGCAA
1 GGTGCATGGATGCACAGCAA
*
47945 GGTGCATGGATGCACAGCAG
1 GGTGCATGGATGCACAGCAA
47965 GGTGCATGGATGCACAGC-A
1 GGTGCATGGATGCACAGCAA
*
47984 GAGTGCATCGATGCAC
1 G-GTGCATGGATGCAC
48000 TAATTGCATT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.28, C:0.21, G:0.35, T:0.16
Consensus pattern (20 bp):
GGTGCATGGATGCACAGCAA
Found at i:48071 original size:21 final size:22
Alignment explanation
Indices: 48023--48081 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
48013 AATAGAATGT
*
48023 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTAGTGG-AG
48046 GTGCATGGATGCACT-GTAGG-G
1 GTGCATGGATGCACTAGT-GGAG
48067 GTGCATGGATGCACT
1 GTGCATGGATGCACT
48082 TTGACACCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.20, C:0.19, G:0.37, T:0.24
Consensus pattern (22 bp):
GTGCATGGATGCACTAGTGGAG
Found at i:48329 original size:21 final size:21
Alignment explanation
Indices: 48305--48344 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
48295 ATGTTTAATG
48305 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
48326 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
48345 CCAATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:51497 original size:20 final size:21
Alignment explanation
Indices: 51472--51520 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
51462 GGAGTTCATG
*
51472 GATGCACTACA-TGGTGCATC
1 GATGCACTACAGGGGTGCATC
*
51492 GATGCACTACAGGGGTGCATG
1 GATGCACTACAGGGGTGCATC
51513 GATGCACT
1 GATGCACT
51521 TTGACACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (21 bp):
GATGCACTACAGGGGTGCATC
Found at i:52434 original size:32 final size:34
Alignment explanation
Indices: 52371--52445 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
52361 TCGGGTCGGG
52371 TATATATA-TTTAAATTAAATATATAAATATT-A
1 TATATATATTTTAAATTAAATATATAAATATTAA
*
52403 TATATATATTTTAAATTAAAT-TA-AATTTATTAA
1 TATATATATTTTAAATTAAATATATAA-ATATTAA
52436 TATTATATAT
1 TA-TATATAT
52446 ATATATAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
31 2 0.05
32 14 0.37
33 15 0.39
34 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATATATATTTTAAATTAAATATATAAATATTAA
Found at i:52443 original size:34 final size:34
Alignment explanation
Indices: 52371--52451 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 34
52361 TCGGGTCGGG
52371 TATATATATTTAAATTAAATATATAAATATTATA
1 TATATATATTTAAATTAAATATATAAATATTATA
*
52405 TATATAT-TTTAAATTAAATTAAATTTATTAATATTATA
1 TATATATATTTAAATTAAA-T--A--TATAAATATTATA
52443 TATATATAT
1 TATATATAT
52452 AATAATTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
33 11 0.28
34 8 0.20
36 1 0.03
38 19 0.47
39 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATATATATTTAAATTAAATATATAAATATTATA
Found at i:52620 original size:29 final size:29
Alignment explanation
Indices: 52547--52622 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
52537 CCCATCCCCA
* *
52547 TCCCCGTCCCCATTTAACATAAACGGTTT
1 TCCCCGTCCCCGTTTAACATAAACGATTT
*
52576 TCCCCCGTCCCTGTTTAGA-ATAAACGATTT
1 T-CCCCGTCCCCGTTTA-ACATAAACGATTT
*
52606 TCCCCATCCCCGTTTAA
1 TCCCCGTCCCCGTTTAA
52623 TTCGGTTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 14 0.35
30 24 0.60
31 1 0.03
ACGTcount: A:0.22, C:0.36, G:0.11, T:0.32
Consensus pattern (29 bp):
TCCCCGTCCCCGTTTAACATAAACGATTT
Found at i:54131 original size:3 final size:3
Alignment explanation
Indices: 54125--54225 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
54115 TTTTTATCCA
* ** *
54125 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
54173 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54221 TAT TA
1 TAT TA
54226 AATATATTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:54157 original size:27 final size:27
Alignment explanation
Indices: 54126--54225 Score: 173
Period size: 27 Copynumber: 3.7 Consensus size: 27
54116 TTTTATCCAT
54126 ATTATTATTATTAATATTATTATTATC
1 ATTATTATTATTAATATTATTATTATC
*
54153 CTTATTATTATTAATATTATTATTATC
1 ATTATTATTATTAATATTATTATTATC
*
54180 ATTATTATTATTATTATTATTATTATC
1 ATTATTATTATTAATATTATTATTATC
*
54207 ATTATTATTATTATTATTA
1 ATTATTATTATTAATATTA
54226 AATATATTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTATTATTATTAATATTATTATTATC
Found at i:55587 original size:19 final size:19
Alignment explanation
Indices: 55549--55586 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
55539 TGTAATTTAG
55549 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
55568 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
55586 T
1 T
55587 TAAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:56357 original size:18 final size:17
Alignment explanation
Indices: 56334--56383 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
56324 CTTTTCATTC
56334 TTTTTATTTATTTATTAT
1 TTTTTATTTATTTA-TAT
*
56352 TTTTTATAATATTTATAT
1 TTTTTAT-TTATTTATAT
*
56370 GTTTTATTTTATTT
1 TTTTTA-TTTATTT
56384 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTTATTTATTTATAT
Found at i:56405 original size:13 final size:15
Alignment explanation
Indices: 56374--56410 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
56364 TTATATGTTT
56374 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
56389 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
56402 TA-TTTATTT
1 TATTTTATTT
56411 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:67038 original size:12 final size:10
Alignment explanation
Indices: 66998--67072 Score: 73
Period size: 10 Copynumber: 7.1 Consensus size: 10
66988 GCTTGAAGAG
66998 AAAAAAG-AA
1 AAAAAAGAAA
67007 AAAAAAGAAA
1 AAAAAAGAAA
67017 AAAAATAGAAA
1 AAAAA-AGAAA
67028 ATGAAAAAGAAA
1 A--AAAAAGAAA
67040 AAAAAAGAGAA
1 AAAAAAGA-AA
*
67051 GAAAAAA-AAGG
1 -AAAAAAGAA-A
67062 AAAAAAGAAA
1 AAAAAAGAAA
67072 A
1 A
67073 GGGGGTCAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
9 7 0.12
10 22 0.39
11 11 0.20
12 12 0.21
13 4 0.07
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:67041 original size:24 final size:23
Alignment explanation
Indices: 67002--67067 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
66992 GAAGAGAAAA
*
67002 AAGAAAAAAAAGAAAAAAAATAG
1 AAGAAAAAAAAGAAAAAAAAGAG
*
67025 AA-AATGAAAAAGAAAAAAAAAGAG
1 AAGAA-AAAAAAG-AAAAAAAAGAG
*
67049 AAGAAAAAAAAGGAAAAAA
1 AAGAAAAAAAAGAAAAAAA
67068 GAAAAGGGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 2 0.06
23 14 0.39
24 18 0.50
25 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (23 bp):
AAGAAAAAAAAGAAAAAAAAGAG
Found at i:67072 original size:13 final size:12
Alignment explanation
Indices: 67005--67074 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 12
66995 GAGAAAAAAG
67005 AAAAAAAA-GAA
1 AAAAAAAAGGAA
*
67016 AAAAAATA-GAA
1 AAAAAAAAGGAA
*
67027 AATGAAAAA-G-A
1 AA-AAAAAAGGAA
67038 AAAAAAAAGAGAA
1 AAAAAAAAG-GAA
67051 GAAAAAAAAGGAA
1 -AAAAAAAAGGAA
67064 AAAAGAAAAGG
1 AAAA-AAAAGG
67075 GGGTCAAGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
10 5 0.10
11 15 0.31
12 10 0.20
13 10 0.20
14 9 0.18
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
AAAAAAAAGGAA
Found at i:67072 original size:38 final size:39
Alignment explanation
Indices: 66996--67072 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
66986 ATGCTTGAAG
* *
66996 AGAAAAAAGAAAAAAAAGAAAAAAAATAGAAAATGAAAA
1 AGAAAAAAGAAAAAAAAGAAAAAAAAGAGAAAAAGAAAA
* *
67035 AGAAAAAA-AAAGAGAAGAAAAAAAAG-GAAAAAAGAAAA
1 AGAAAAAAGAAAAAAAAGAAAAAAAAGAG-AAAAAGAAAA
67073 GGGGGTCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 1 0.03
38 24 0.73
39 8 0.24
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (39 bp):
AGAAAAAAGAAAAAAAAGAAAAAAAAGAGAAAAAGAAAA
Found at i:68307 original size:83 final size:83
Alignment explanation
Indices: 68168--68842 Score: 1097
Period size: 83 Copynumber: 8.2 Consensus size: 83
68158 AAACATTAAA
68168 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
68233 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
*
68251 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
* * **
68316 AG-TCCAAGCATTGAAAA
66 AGAACCAATCATTGAATT
68333 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
68398 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
*
68416 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
* *
68481 AG-TCCAAGCATTGAATT
66 AGAACCAATCATTGAATT
* * * *
68498 TAGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTTAAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
68563 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
68581 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
68646 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
* * * *
68664 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCT-GATTATA
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTA-A
* * *
68728 TAGAATCAAGCATTGAATT
65 CAGAACCAATCATTGAATT
* ** **
68747 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTGGAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
68812 AGAA-CAATCATTGAATT
66 AGAACCAATCATTGAATT
68829 TGGAAGATGAATTT
1 TGGAAGATGAATTT
68843 GCTCATAGTA
Statistics
Matches: 550, Mismatches: 38, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
82 182 0.33
83 366 0.67
84 2 0.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (83 bp):
TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
AGAACCAATCATTGAATT
Found at i:68437 original size:165 final size:165
Alignment explanation
Indices: 68152--68800 Score: 1079
Period size: 165 Copynumber: 3.9 Consensus size: 165
68142 TGTGATATCC
*
68152 CAGTCCAAACATT--AAATGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGTCCAAGCATTGAAAATGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
68215 TATCTGACCTGGTTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTC
66 TATCTGACCTGGTTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTC
68280 TGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG
131 TGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG
68315 CAGTCCAAGCATTGAAAATGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGTCCAAGCATTGAAAATGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
68380 TATCTGACCTGGTTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTC
66 TATCTGACCTGGTTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTC
68445 TGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG
131 TGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG
** *
68480 CAGTCCAAGCATTGAATTTAGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGTCCAAGCATTGAAAATGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
* * *
68545 TATTTGATCTGATTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTC
66 TATCTGACCTGGTTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTC
*
68610 TGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAA
131 TGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG
* * ** *
68645 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
1 CAG-TCCAAGCATTGAAAATGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAG
* * * * * * *
68710 TTATTTGATCT-GATTATATAGAATCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCT
65 TTATCTGACCTGGTTTA-ACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCT
68774 TCTGGAAGTGTTCTTTGAGTTATCTGA
129 TCTGGAAGTGTTCTTTGAGTTATCTGA
68801 TTTGGTTGGA
Statistics
Matches: 464, Mismatches: 18, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
163 12 0.03
165 314 0.68
166 138 0.30
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (165 bp):
CAGTCCAAGCATTGAAAATGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGACCTGGTTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTC
TGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG
Found at i:68606 original size:248 final size:248
Alignment explanation
Indices: 68168--68842 Score: 1097
Period size: 248 Copynumber: 2.7 Consensus size: 248
68158 AAACATTAAA
*
68168 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
* *
68233 AGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
66 AG-TCCAAGCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
* * * * **
68298 TATCTGACCTGGTTTAGCAG-TCCAAGCATTGAAAATGGAAGATGAATTTACCAATAGCATCTTC
130 TATCTGATCTGGTTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTC
68362 TGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAACAGAACCAATCATTGAATT
195 TGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAACAGAACCAATCATTGAATT
68416 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
*
68481 AGTCCAAGCATTGAATTTAGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
66 AGTCCAAGCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
* *
68546 ATTTGATCTGATTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCT
131 ATCTGATCTGGTTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCT
68611 GGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAACAGAACCAATCATTGAATT
196 GGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAACAGAACCAATCATTGAATT
* * * *
68664 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTATAT
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTG-GT-T-T
* *
68729 AG-AAT-CAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGA
63 AGCAGTCCAAGCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGA
* **
68792 GTTATCTGATTTGGTTGGACAGAA-CAATCATTGAATTTGGAAGATGAATTT
128 GTTATCTGATCTGGTTTAACAGAACCAATCATTGAATTTGGAAGATGAATTT
68843 GCTCATAGTA
Statistics
Matches: 399, Mismatches: 24, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
247 75 0.19
248 242 0.61
249 76 0.19
250 3 0.01
251 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (248 bp):
TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
AGTCCAAGCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
ATCTGATCTGGTTTAACAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCT
GGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAACAGAACCAATCATTGAATT
Found at i:69663 original size:113 final size:113
Alignment explanation
Indices: 69465--70451 Score: 1605
Period size: 113 Copynumber: 8.8 Consensus size: 113
69455 GATTCAAATC
* *
69465 CATCATTTGATGGATCATCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
69529 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCCTTTTACCTGAATT
65 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
*
69578 CATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
69643 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
*
69691 CATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
69756 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
*
69804 CATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
69869 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
*
69917 CATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
69982 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
70030 CATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
70095 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
* *** *
70143 CATCATTTGATGGATCAACATTGCCATAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
70208 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
* * *
70256 CATCATTTGGTGGATCATCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * *
70320 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
65 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
* *** *
70369 CATCATTTGATGGATCAACATTGCC-----A-GTTCATAATAAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
70428 AGAA-AAAGTTCATAATGAGAAGAA
66 AGAAGAAA-TTCATAATGAGAAGAA
70452 CTCATCAAGA
Statistics
Matches: 834, Mismatches: 36, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
106 2 0.00
107 52 0.06
108 1 0.00
112 6 0.01
113 771 0.92
114 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (113 bp):
CATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
Found at i:70710 original size:3 final size:3
Alignment explanation
Indices: 70704--70798 Score: 136
Period size: 3 Copynumber: 31.7 Consensus size: 3
70694 TTTTTATCCA
* ** *
70704 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
70752 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
70799 AATATATTAA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:70736 original size:27 final size:27
Alignment explanation
Indices: 70705--70807 Score: 154
Period size: 27 Copynumber: 3.8 Consensus size: 27
70695 TTTTATCCAT
70705 ATTATTATTATTAATATTATTATTATC
1 ATTATTATTATTAATATTATTATTATC
*
70732 CTTATTATTATTAATATTATTATTATC
1 ATTATTATTATTAATATTATTATTATC
* * *
70759 ATTATTATTATTATTATTATTATCATT
1 ATTATTATTATTAATATTATTATTATC
70786 ATTATTATTATTAA-ATATATTA
1 ATTATTATTATTAATAT-TATTA
70808 AAAAAATAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
26 2 0.03
27 67 0.97
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTATTATTATTAATATTATTATTATC
Found at i:72164 original size:19 final size:19
Alignment explanation
Indices: 72126--72163 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
72116 TGTAATTTAG
72126 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
72145 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
72163 T
1 T
72164 TAAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:89628 original size:16 final size:15
Alignment explanation
Indices: 89595--89637 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
89585 AAATGGATGA
*
89595 AAATATGAAATA-TG
1 AAATATGAAAAAGTG
89609 AAATATGAAAAAGTTG
1 AAATATGAAAAAG-TG
*
89625 AAATATAAAAAAG
1 AAATATGAAAAAG
89638 ACGAGGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.44
16 14 0.56
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (15 bp):
AAATATGAAAAAGTG
Found at i:90080 original size:3 final size:3
Alignment explanation
Indices: 90072--90118 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
90062 GCCTTTAAAT
90072 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
90119 CATATATTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:94609 original size:29 final size:30
Alignment explanation
Indices: 94567--94646 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 30
94557 CACCTAACTA
*
94567 AATTGATGTAAGCAATGCA-ATCTTCATCT
1 AATTGATGTAAGCAATGAACATCTTCATCT
94596 AATTGATGTAAGCAAT-AACATCTTCATCT
1 AATTGATGTAAGCAATGAACATCTTCATCT
94625 AATTGATGTAAGCAATG-ACATC
1 AATTGATGTAAGCAATGAACATC
94647 AATTTAGTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
28 1 0.02
29 47 0.98
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (30 bp):
AATTGATGTAAGCAATGAACATCTTCATCT
Found at i:99336 original size:29 final size:30
Alignment explanation
Indices: 99292--99371 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 30
99282 CTCCTAACTA
*
99292 AATTGATGTAAGCAATGCA-ATCTTCATCT
1 AATTGATGTAAGCAATGAACATCTTCATCT
*
99321 AATTGATGTAAACAAT-AACATCTTCATCT
1 AATTGATGTAAGCAATGAACATCTTCATCT
99350 AATTGATGTAAGCAATG-ACATC
1 AATTGATGTAAGCAATGAACATC
99372 AATTTAGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 1 0.02
29 45 0.98
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (30 bp):
AATTGATGTAAGCAATGAACATCTTCATCT
Done.