Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2400
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: 53862
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:1132 original size:36 final size:36
Alignment explanation
Indices: 1083--1351 Score: 112
Period size: 36 Copynumber: 7.2 Consensus size: 36
1073 CTCAGATTAG
1083 TTGTTGATAGTAGTAATGTGAAATATGCAGAAACAT
1 TTGTTGATAGTAGTAATGTGAAATATGCAGAAACAT
* * * * * * ** *
1119 TTGTTGATTGTAGTTATCATGCAGATTATTTC-GGATTAG
1 TTGTTGATAGTAGTAAT-GTG-A-AATA-TGCAGAAACAT
* * *
1158 TTATTGATAGTAGCAATATGAAATATGCAGAAACAT
1 TTGTTGATAGTAGTAATGTGAAATATGCAGAAACAT
* * * * * ** *
1194 TTGTTGATTGTAGTTATCGTGCAGAGTATTTC-GGATTAG
1 TTGTTGATAGTAGTAAT-GTG-A-AATA-TGCAGAAACAT
* *
1233 TTATTGATAGTAGCAATGTGAAATATGCAGAAACAT
1 TTGTTGATAGTAGTAATGTGAAATATGCAGAAACAT
* * * * * ** *
1269 TTGTTGATTGTAGTTATCGTGTAGATTATTTC-GGATTAG
1 TTGTTGATAGTAGTAAT-GTG-A-AATA-TGCAGAAACAT
* * *
1308 TTATTGATAGTAGCAATGTAAAATATGCAGAAACAT
1 TTGTTGATAGTAGTAATGTGAAATATGCAGAAACAT
1344 TTGTTGAT
1 TTGTTGAT
1352 TCTAGTTATC
Statistics
Matches: 156, Mismatches: 62, Indels: 30
0.63 0.25 0.12
Matches are distributed among these distances:
35 6 0.04
36 66 0.42
37 10 0.06
38 11 0.07
39 57 0.37
40 6 0.04
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (36 bp):
TTGTTGATAGTAGTAATGTGAAATATGCAGAAACAT
Found at i:1165 original size:39 final size:39
Alignment explanation
Indices: 1122--1245 Score: 94
Period size: 39 Copynumber: 3.3 Consensus size: 39
1112 GAAACATTTG
* *
1122 TTGATTGTAGTTATCATGCAGATTATTTCGGATTAGTTA
1 TTGATAGTAGTTATCATGCAGAATATTTCGGATTAGTTA
** * * ** * *
1161 TTGATAGTAGCAAT-ATG-A-AATA-TGCAGAAACATTTG
1 TTGATAGTAGTTATCATGCAGAATATTTC-GGATTAGTTA
* * *
1197 TTGATTGTAGTTATCGTGCAGAGTATTTCGGATTAGTTA
1 TTGATAGTAGTTATCATGCAGAATATTTCGGATTAGTTA
1236 TTGATAGTAG
1 TTGATAGTAG
1246 CAATGTGAAA
Statistics
Matches: 58, Mismatches: 22, Indels: 10
0.64 0.24 0.11
Matches are distributed among these distances:
35 2 0.03
36 19 0.33
37 3 0.05
38 4 0.07
39 28 0.48
40 2 0.03
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (39 bp):
TTGATAGTAGTTATCATGCAGAATATTTCGGATTAGTTA
Found at i:1167 original size:75 final size:75
Alignment explanation
Indices: 1063--1395 Score: 549
Period size: 75 Copynumber: 4.4 Consensus size: 75
1053 ATGTGAAATA
* * * * *
1063 TGCAAATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATT
1 TGCAGATTATTTCGGATTAGTTATTGATAGTAGCAATGTGAAATATGCAGAAACATTTGTTGATT
*
1128 GTAGTTATCA
66 GTAGTTATCG
*
1138 TGCAGATTATTTCGGATTAGTTATTGATAGTAGCAATATGAAATATGCAGAAACATTTGTTGATT
1 TGCAGATTATTTCGGATTAGTTATTGATAGTAGCAATGTGAAATATGCAGAAACATTTGTTGATT
1203 GTAGTTATCG
66 GTAGTTATCG
*
1213 TGCAGAGTATTTCGGATTAGTTATTGATAGTAGCAATGTGAAATATGCAGAAACATTTGTTGATT
1 TGCAGATTATTTCGGATTAGTTATTGATAGTAGCAATGTGAAATATGCAGAAACATTTGTTGATT
1278 GTAGTTATCG
66 GTAGTTATCG
* *
1288 TGTAGATTATTTCGGATTAGTTATTGATAGTAGCAATGTAAAATATGCAGAAACATTTGTTGATT
1 TGCAGATTATTTCGGATTAGTTATTGATAGTAGCAATGTGAAATATGCAGAAACATTTGTTGATT
*
1353 CTAGTTATCG
66 GTAGTTATCG
* *
1363 TGCAGATTATCTCGGATTAGTTGTTGATAGTAG
1 TGCAGATTATTTCGGATTAGTTATTGATAGTAG
1396 TAATATGTGT
Statistics
Matches: 242, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 242 1.00
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (75 bp):
TGCAGATTATTTCGGATTAGTTATTGATAGTAGCAATGTGAAATATGCAGAAACATTTGTTGATT
GTAGTTATCG
Found at i:1908 original size:20 final size:22
Alignment explanation
Indices: 1877--1920 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
1867 GCTATATTTT
1877 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
1898 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
1919 CA
1 CA
1921 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:2720 original size:75 final size:75
Alignment explanation
Indices: 2595--2804 Score: 330
Period size: 75 Copynumber: 2.8 Consensus size: 75
2585 ATAAGCTTTC
*
2595 AATGTGAAATATGTAGAAACATTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTAGTTGT
1 AATGTGAAATATGAAGAAACATTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTAGTTGT
2660 TGATAGTAGT
66 TGATAGTAGT
* *
2670 AATGTGAAATATGAAAAAACATTTGTTGATTGTAGTTATCGTGCAAATTATCTCGGATTAGTTGT
1 AATGTGAAATATGAAGAAACATTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTAGTTGT
*
2735 TTATAGTAGT
66 TGATAGTAGT
* ** * * *
2745 ACTGTGAAATATGCTGAAACATTTGTTGATTGTAATTATCATGCGGATTATCTCGGATTA
1 AATGTGAAATATGAAGAAACATTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTA
2805 TCATTTCATT
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 123 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (75 bp):
AATGTGAAATATGAAGAAACATTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTAGTTGT
TGATAGTAGT
Found at i:2735 original size:39 final size:39
Alignment explanation
Indices: 2617--2744 Score: 118
Period size: 39 Copynumber: 3.4 Consensus size: 39
2607 GTAGAAACAT
* *
2617 TTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTAG
1 TTGTTGATAGTAGTTATCGTGCAAATTATCTCGGATTAG
* ***** ** *
2656 TTGTTGATAGTAGTAAT-GTG-AAA-TATGAAAAAACAT
1 TTGTTGATAGTAGTTATCGTGCAAATTATCTCGGATTAG
*
2692 TTGTTGATTGTAGTTATCGTGCAAATTATCTCGGATTAG
1 TTGTTGATAGTAGTTATCGTGCAAATTATCTCGGATTAG
*
2731 TTGTTTATAGTAGT
1 TTGTTGATAGTAGT
2745 ACTGTGAAAT
Statistics
Matches: 63, Mismatches: 23, Indels: 6
0.68 0.25 0.07
Matches are distributed among these distances:
36 20 0.32
37 5 0.08
38 6 0.10
39 32 0.51
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (39 bp):
TTGTTGATAGTAGTTATCGTGCAAATTATCTCGGATTAG
Found at i:4186 original size:21 final size:21
Alignment explanation
Indices: 4142--4186 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4132 AAAAGATATA
* **
4142 TTTGGATGAAAGAATACATTT
1 TTTGGATGAAAAAATACAACT
*
4163 TTTGGATGAAAAAATATAACT
1 TTTGGATGAAAAAATACAACT
4184 TTT
1 TTT
4187 AAGACCAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (21 bp):
TTTGGATGAAAAAATACAACT
Found at i:6589 original size:2 final size:2
Alignment explanation
Indices: 6582--6618 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6572 AATCAAACTT
6582 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6619 TACTTAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9399 original size:20 final size:21
Alignment explanation
Indices: 9374--9413 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
9364 TACTTGTGTT
9374 GTGTTTGTATTATTT-TTTTC
1 GTGTTTGTATTATTTATTTTC
*
9394 GTGTTTGTTTTATTTATTTT
1 GTGTTTGTATTATTTATTTT
9414 TTTGTGTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (21 bp):
GTGTTTGTATTATTTATTTTC
Found at i:9403 original size:24 final size:24
Alignment explanation
Indices: 9367--9420 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
9357 ATTTGTGTAC
9367 TTGTGTTGTGTTTGTA-TTATTTTT
1 TTGTGTTGTGTTT-TATTTATTTTT
9391 TTCGTGTT-TGTTTTATTTATTTTT
1 TT-GTGTTGTGTTTTATTTATTTTT
9415 TTGTGT
1 TTGTGT
9421 CGTATAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.21
24 17 0.61
25 5 0.18
ACGTcount: A:0.07, C:0.02, G:0.19, T:0.72
Consensus pattern (24 bp):
TTGTGTTGTGTTTTATTTATTTTT
Found at i:11747 original size:16 final size:17
Alignment explanation
Indices: 11716--11750 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
11706 TTTGTTACAT
*
11716 AAATTATTTTAGATTCA
1 AAATTATTTTAAATTCA
11733 AAATT-TTTTAAATTCA
1 AAATTATTTTAAATTCA
11749 AA
1 AA
11751 TCGTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (17 bp):
AAATTATTTTAAATTCA
Found at i:11774 original size:32 final size:31
Alignment explanation
Indices: 11734--11793 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
11724 TTAGATTCAA
*
11734 AATTTTTTAAATTCAAATCGTTTTATATTTG
1 AATTTTTTAAATTCAAATCATTTTATATTTG
* *
11765 AATTGTTTTAAATTTAAATTATTTTATAT
1 AATT-TTTTAAATTCAAATCATTTTATAT
11794 ATTTAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (31 bp):
AATTTTTTAAATTCAAATCATTTTATATTTG
Found at i:11784 original size:16 final size:16
Alignment explanation
Indices: 11733--11790 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
11723 TTTAGATTCA
*
11733 AAATT-TTTTAAATTC
1 AAATTGTTTTAAATTT
* *
11748 AAATCGTTTTATATTT
1 AAATTGTTTTAAATTT
*
11764 GAATTGTTTTAAATTT
1 AAATTGTTTTAAATTT
*
11780 AAATTATTTTA
1 AAATTGTTTTA
11791 TATATTTAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
15 4 0.12
16 30 0.88
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.55
Consensus pattern (16 bp):
AAATTGTTTTAAATTT
Found at i:11974 original size:16 final size:16
Alignment explanation
Indices: 11953--11983 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11943 TTAATTTAAC
*
11953 TAATCAAATTGATTTT
1 TAATCAAATTAATTTT
11969 TAATCAAATTAATTT
1 TAATCAAATTAATTT
11984 GAATTGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (16 bp):
TAATCAAATTAATTTT
Found at i:12012 original size:17 final size:17
Alignment explanation
Indices: 11990--12038 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
11980 ATTTGAATTG
11990 AATTATTTTAAATTTTT
1 AATTATTTTAAATTTTT
**
12007 AATTATTTTAAATAATT
1 AATTATTTTAAATTTTT
*
12024 AAATATTTT-AATTTT
1 AATTATTTTAAATTTT
12039 AAATCATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTATTTTAAATTTTT
Found at i:13906 original size:28 final size:29
Alignment explanation
Indices: 13874--13939 Score: 71
Period size: 33 Copynumber: 2.2 Consensus size: 29
13864 GTTTCTACTT
13874 AATGCATGCTTT-TAGGGTTTATAAAAGA
1 AATGCATGCTTTGTAGGGTTTATAAAAGA
**
13902 AATGCCTCATTTTTTGGTAGGGTTTATAAAAGA
1 AATG---CATGCTTT-GTAGGGTTTATAAAAGA
13935 AATGC
1 AATGC
13940 CTCATTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
28 4 0.13
30 1 0.03
31 6 0.19
33 20 0.65
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
AATGCATGCTTTGTAGGGTTTATAAAAGA
Found at i:13923 original size:33 final size:33
Alignment explanation
Indices: 13886--13948 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
13876 TGCATGCTTT
13886 TAGGGTTTATAAAAGAAATGCCTCATTTTTTGG
1 TAGGGTTTATAAAAGAAATGCCTCATTTTTTGG
13919 TAGGGTTTATAAAAGAAATGCCTCATTTTT
1 TAGGGTTTATAAAAGAAATGCCTCATTTTT
13949 GGTTTACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (33 bp):
TAGGGTTTATAAAAGAAATGCCTCATTTTTTGG
Found at i:19381 original size:2 final size:2
Alignment explanation
Indices: 19374--19400 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19364 TCTTATGTAG
19374 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
19401 GCTCATCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25242 original size:18 final size:17
Alignment explanation
Indices: 25178--25243 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 17
25168 TATTTAAAAT
* *
25178 ATTTTATATTTATATAA
1 ATTTGATATATATATAA
*
25195 ATTTTGATACAT-TA-ATA
1 A-TTTGATATATATATA-A
25212 ATTT-ATA-ATATATAA
1 ATTTGATATATATATAA
25227 ATTTCGATATATATATA
1 ATTT-GATATATATATA
25244 TATATATCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
14 2 0.05
15 10 0.26
16 5 0.13
17 8 0.21
18 14 0.36
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTGATATATATATAA
Found at i:26585 original size:19 final size:19
Alignment explanation
Indices: 26554--26625 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
26544 TATAATTAAC
26554 TTTAAAT-AA-AAATATTA
1 TTTAAATAAATAAATATTA
*
26571 TTTTAATAAATAAATATTAA
1 TTTAAATAAATAAATATT-A
26591 TTTAAATTAAATTAAAT-TTA
1 TTTAAA-TAAA-TAAATATTA
26611 -TTAAATCAAATAAAT
1 TTTAAAT-AAATAAAT
26626 TATTTTACTT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
17 6 0.13
18 8 0.17
19 15 0.32
20 7 0.15
21 6 0.13
22 5 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAAATAAATAAATATTA
Found at i:27255 original size:19 final size:21
Alignment explanation
Indices: 27210--27259 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
27200 TTTATATTGA
27210 TTTAATTATAAAATATATAAAT
1 TTTAA-TATAAAATATATAAAT
*
27232 ATTAATATAAAA-ATA-AAAT
1 TTTAATATAAAATATATAAAT
27251 TTTAATATA
1 TTTAATATA
27260 TTCTAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 12 0.46
20 3 0.12
21 7 0.27
22 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAATATAAAATATATAAAT
Found at i:27260 original size:27 final size:27
Alignment explanation
Indices: 27181--27261 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
27171 AAAATAATAC
*
27181 TAATATAAAAAATAATATTTT--TATAT
1 TAATAT-AAAAATAAAATTTTAATATAT
* * ** *
27207 TGATTTAATTATAAAATATATAA-ATAT
1 TAATATAAAAATAAAAT-TTTAATATAT
27234 TAATATAAAAATAAAATTTTAATATAT
1 TAATATAAAAATAAAATTTTAATATAT
27261 T
1 T
27262 CTAAATATTT
Statistics
Matches: 40, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
25 8 0.20
26 10 0.25
27 22 0.55
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
TAATATAAAAATAAAATTTTAATATAT
Found at i:27879 original size:15 final size:15
Alignment explanation
Indices: 27859--27891 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
27849 TTATTTACAA
27859 AAATAATATAA-ATTT
1 AAATAATA-AATATTT
27874 AAATAATAAATATTT
1 AAATAATAAATATTT
27889 AAA
1 AAA
27892 ATTTCATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATAATAAATATTT
Found at i:27916 original size:11 final size:11
Alignment explanation
Indices: 27894--27928 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
27884 TATTTAAAAT
27894 TTCATATTTAAA
1 TTCAT-TTTAAA
27906 TTCATTTTAAA
1 TTCATTTTAAA
*
27917 TTTATTTTAAA
1 TTCATTTTAAA
27928 T
1 T
27929 AATAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (11 bp):
TTCATTTTAAA
Found at i:28399 original size:17 final size:18
Alignment explanation
Indices: 28378--28422 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
28368 AATAATTTTT
*
28378 TATTTTAATTAATTACAA
1 TATTTTAATAAATTACAA
* *
28396 -ATTTTAAAAAATTATAA
1 TATTTTAATAAATTACAA
28413 TATTTTAATA
1 TATTTTAATA
28423 TAAAAAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTTAATAAATTACAA
Found at i:28912 original size:19 final size:19
Alignment explanation
Indices: 28888--28924 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28878 ATTTTTATTT
28888 AAATTTAATTATAAATATA
1 AAATTTAATTATAAATATA
* *
28907 AAATTTATTTTTAAATAT
1 AAATTTAATTATAAATAT
28925 TTTAATATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTAATTATAAATATA
Found at i:29111 original size:3 final size:3
Alignment explanation
Indices: 29103--29149 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
29093 AAATCAAACA
29103 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29150 ATGGTGTATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29283 original size:3 final size:3
Alignment explanation
Indices: 29277--29305 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29267 ATAATAATAA
29277 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29306 ATTTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29572 original size:16 final size:16
Alignment explanation
Indices: 29553--29602 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
29543 AATAAATTAT
29553 TTTTTTGATTATTTAA
1 TTTTTTGATTATTTAA
* *
29569 TTTTTTGA-GATTT-T
1 TTTTTTGATTATTTAA
29583 TTTATTTGATTATTTAA
1 TTT-TTTGATTATTTAA
29600 TTT
1 TTT
29603 AAAAACTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 3 0.11
15 9 0.33
16 12 0.44
17 3 0.11
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (16 bp):
TTTTTTGATTATTTAA
Found at i:30733 original size:22 final size:22
Alignment explanation
Indices: 30708--30750 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30698 TTAAAATTAT
*
30708 TTTAT-ATTAATATTTATATATC
1 TTTATAATTAA-ATTTAAATATC
30730 TTTATAATTAAATTTAAATAT
1 TTTATAATTAAATTTAAATAT
30751 TAAAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATAATTAAATTTAAATATC
Found at i:31037 original size:32 final size:32
Alignment explanation
Indices: 31000--31099 Score: 128
Period size: 32 Copynumber: 3.0 Consensus size: 32
30990 AAATAGAAGG
31000 TGCCATTTTAAACACGAATAAAATTATTATAT
1 TGCCATTTTAAACACGAATAAAATTATTATAT
31032 TGCCATTTTAAACACGAATAAAATTATTATATATAT
1 TGCCATTTTAAACACGAAT-AAA--ATTAT-TATAT
*** *
31068 TATAATTTTAAATACGAATAAAATTATTATAT
1 TGCCATTTTAAACACGAATAAAATTATTATAT
31100 ATATTATAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
32 24 0.40
33 8 0.13
35 8 0.13
36 20 0.33
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (32 bp):
TGCCATTTTAAACACGAATAAAATTATTATAT
Found at i:31076 original size:36 final size:36
Alignment explanation
Indices: 31004--31126 Score: 175
Period size: 36 Copynumber: 3.6 Consensus size: 36
30994 AGAAGGTGCC
***
31004 ATTTTAAACACGAAT-AAA--ATTAT-TATATTGCC
1 ATTTTAAACACGAATAAAATTATTATATATATTATA
31036 ATTTTAAACACGAATAAAATTATTATATATATTATA
1 ATTTTAAACACGAATAAAATTATTATATATATTATA
*
31072 ATTTTAAATACGAATAAAATTATTATATATATTATA
1 ATTTTAAACACGAATAAAATTATTATATATATTATA
31108 ATTTTAAACAC-AATAAAAT
1 ATTTTAAACACGAATAAAAT
31127 ATATGTTAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
32 15 0.18
33 3 0.04
35 13 0.16
36 51 0.62
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (36 bp):
ATTTTAAACACGAATAAAATTATTATATATATTATA
Found at i:31092 original size:18 final size:18
Alignment explanation
Indices: 31036--31092 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
31026 TTATATTGCC
*
31036 ATTTTAAACACGAATAAA
1 ATTTTAAATACGAATAAA
* * * *
31054 ATTATTATATA-TATTATA
1 ATT-TTAAATACGAATAAA
31072 ATTTTAAATACGAATAAA
1 ATTTTAAATACGAATAAA
31090 ATT
1 ATT
31093 ATTATATATA
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
17 6 0.21
18 17 0.61
19 5 0.18
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (18 bp):
ATTTTAAATACGAATAAA
Found at i:32395 original size:2 final size:2
Alignment explanation
Indices: 32388--32418 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
32378 CTATATTAGC
*
32388 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32419 AGAGGTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32879 original size:2 final size:2
Alignment explanation
Indices: 32872--32919 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
32862 AAATTATAGT
* * *
32872 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA AA 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
32914 TA TA TA
1 TA TA TA
32920 CCTTGAAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36240 original size:12 final size:12
Alignment explanation
Indices: 36223--36259 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
36213 CTGCTGTTTA
36223 TTTTATTTAATT
1 TTTTATTTAATT
*
36235 TTTTATTCAATT
1 TTTTATTTAATT
36247 TTTTATTTAATT
1 TTTTATTTAATT
36259 T
1 T
36260 ATGTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATTTAATT
Found at i:36413 original size:20 final size:20
Alignment explanation
Indices: 36388--36425 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36378 AATTATAATT
*
36388 TTTTTTAATTATCGACTTAG
1 TTTTTTAATTATCAACTTAG
36408 TTTTTTAATTATCAACTT
1 TTTTTTAATTATCAACTT
36426 GTAATTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTTTAATTATCAACTTAG
Found at i:39189 original size:2 final size:2
Alignment explanation
Indices: 39182--39212 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39172 GAGAAATTAA
39182 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 A
39213 ACATACCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42884 original size:16 final size:16
Alignment explanation
Indices: 42863--42897 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
42853 TCCGGATGCG
42863 TCGAACATGGGTGACA
1 TCGAACATGGGTGACA
42879 TCGAACATGGGTGACA
1 TCGAACATGGGTGACA
42895 TCG
1 TCG
42898 GATACTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (16 bp):
TCGAACATGGGTGACA
Found at i:45366 original size:2 final size:2
Alignment explanation
Indices: 45359--45387 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45349 ATGACTCATT
45359 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45388 GGGTTGACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45897 original size:25 final size:25
Alignment explanation
Indices: 45869--45917 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
45859 TCAAGAAAGG
*
45869 AAATTCTTACGGGAATGAAAATTTA
1 AAATTCTTACGAGAATGAAAATTTA
* *
45894 AAATTTTTATGAGAATGAAAATTT
1 AAATTCTTACGAGAATGAAAATTT
45918 TTATAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.37
Consensus pattern (25 bp):
AAATTCTTACGAGAATGAAAATTTA
Found at i:46892 original size:23 final size:22
Alignment explanation
Indices: 46866--46911 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
46856 TTAAATGACT
46866 TAAACCCAAATGATCAAACCTAA
1 TAAACCCAAAT-ATCAAACCTAA
* * *
46889 TAAACTCAAGTATCAAATCTAA
1 TAAACCCAAATATCAAACCTAA
46911 T
1 T
46912 TGATCCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (22 bp):
TAAACCCAAATATCAAACCTAA
Found at i:48152 original size:20 final size:21
Alignment explanation
Indices: 48105--48152 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
48095 ATTTTAAACT
*
48105 TAATTTTTATATTAATATTGA
1 TAATTTTTATATTAATATTAA
48126 TATATTTTTATTATTAA-A-TAA
1 TA-ATTTTTA-TATTAATATTAA
48147 TAATTT
1 TAATTT
48153 GAATTGATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 6 0.25
22 8 0.33
23 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATTTTTATATTAATATTAA
Found at i:51582 original size:22 final size:22
Alignment explanation
Indices: 51557--51623 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
51547 TACAACACGT
51557 TTAATTATTTATTATATTTATA
1 TTAATTATTTATTATATTTATA
* *
51579 TTAATAATTT-TTA-ATATAT-
1 TTAATTATTTATTATATTTATA
* *
51598 TTAATAATATATATTATAATTATA
1 TTAAT--TATTTATTATATTTATA
51622 TT
1 TT
51624 TTAAATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 5 0.15
20 5 0.15
21 6 0.18
22 12 0.35
23 4 0.12
24 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTATTTATTATATTTATA
Found at i:51607 original size:12 final size:11
Alignment explanation
Indices: 51558--51624 Score: 50
Period size: 12 Copynumber: 5.9 Consensus size: 11
51548 ACAACACGTT
51558 TAAT-TATTTA
1 TAATATATTTA
51568 T--TATATTTA
1 TAATATATTTA
* *
51577 TATTAATAATTTT
1 TAAT-AT-ATTTA
51590 TAATATATTTAA
1 TAATATATTT-A
51602 TAATATATATTA
1 TAATATAT-TTA
51614 TAATTATATTT
1 TAA-TATATTT
51625 TAAATAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
8 1 0.02
9 7 0.15
10 1 0.02
11 5 0.11
12 18 0.39
13 14 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TAATATATTTA
Found at i:51615 original size:19 final size:18
Alignment explanation
Indices: 51569--51615 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
51559 AATTATTTAT
51569 TATAT-TTATATTAATAA
1 TATATATTATATTAATAA
* * *
51586 TTTTTAATATATTTAATAA
1 TATATATTATA-TTAATAA
51605 TATATATTATA
1 TATATATTATA
51616 ATTATATTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
17 3 0.14
18 4 0.18
19 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATATTATATTAATAA
Found at i:52050 original size:19 final size:18
Alignment explanation
Indices: 52022--52062 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
52012 TTAGATTCAA
*
52022 ATTT-AATTTAATTCATT
1 ATTTAAATTTAAATCATT
52039 CATTTAAATTTAAATCATT
1 -ATTTAAATTTAAATCATT
52058 ATTTA
1 ATTTA
52063 TCTTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAAATTTAAATCATT
Found at i:52140 original size:22 final size:23
Alignment explanation
Indices: 52114--52156 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
52104 TAAAATTAAA
52114 TTTAA-AT-AAAATATATATTTAT
1 TTTAATATAAAAATAT-TATTTAT
52136 TTTAATATAAAAATATTATTT
1 TTTAATATAAAAATATTATTT
52157 TAAGTCACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTAATATAAAAATATTATTTAT
Found at i:52756 original size:18 final size:18
Alignment explanation
Indices: 52733--52770 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
52723 GATTTGATTT
**
52733 ATATTAAATTATTTAAAA
1 ATATTAAAAAATTTAAAA
52751 ATATTAAAAAATTTAAAA
1 ATATTAAAAAATTTAAAA
52769 AT
1 AT
52771 TATTTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTAAAAAATTTAAAA
Found at i:52784 original size:18 final size:21
Alignment explanation
Indices: 52763--52806 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
52753 ATTAAAAAAT
52763 TTAAAA-AT-TATTTTTAT-A
1 TTAAAATATATATTTTTATAA
*
52781 TTAAAATTTATATTTTTATAA
1 TTAAAATATATATTTTTATAA
52802 TTAAA
1 TTAAA
52807 TTTAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 1 0.05
20 9 0.41
21 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAAAATATATATTTTTATAA
Found at i:52796 original size:20 final size:20
Alignment explanation
Indices: 52771--52810 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
52761 ATTTAAAAAT
52771 TATTTTTAT-ATTAAAATTTA
1 TATTTTTATAATT-AAATTTA
52791 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
52811 AATAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTATAATTAAATTTA
Found at i:53223 original size:26 final size:26
Alignment explanation
Indices: 53155--53206 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
53145 TTAATTTTAA
*
53155 AGTGATCTTTTAATTTAATGATGATT
1 AGTGATCTTATAATTTAATGATGATT
53181 AGTGATCTTATAATTTAATGATGATT
1 AGTGATCTTATAATTTAATGATGATT
53207 TTGATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (26 bp):
AGTGATCTTATAATTTAATGATGATT
Done.