Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2413
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: 73481
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Found at i:7750 original size:26 final size:27
Alignment explanation
Indices: 7721--7771 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
7711 TTTCTTGATT
7721 GAAA-AACGGGGTTGGAGTATCCCCTC
1 GAAAGAACGGGGTTGGAGTATCCCCTC
*
7747 GAAAGAATGGGGTTGGAGTATCCCC
1 GAAAGAACGGGGTTGGAGTATCCCC
7772 AATGATGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (27 bp):
GAAAGAACGGGGTTGGAGTATCCCCTC
Found at i:10113 original size:20 final size:20
Alignment explanation
Indices: 10066--10140 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
10056 AAAAAGACAT
*
10066 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
10085 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
10106 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
10126 AATGTATCGATACAT
1 AATGTATCGATACAT
10141 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:10134 original size:40 final size:39
Alignment explanation
Indices: 10063--10140 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
10053 GGTAAAAAGA
* *
10063 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
10102 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
10141 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:11495 original size:14 final size:15
Alignment explanation
Indices: 11465--11500 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
11455 AAATTATCTG
11465 ATATTTATTTTTAAT
1 ATATTTATTTTTAAT
*
11480 ATATTTA-TTTTGAT
1 ATATTTATTTTTAAT
11494 ATATTTA
1 ATATTTA
11501 AATATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
ATATTTATTTTTAAT
Found at i:18430 original size:21 final size:21
Alignment explanation
Indices: 18389--18433 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
18379 AAATAAATAA
* *
18389 AAAATTTTAATTTTTATATTT
1 AAAATTATAATTTATATATTT
18410 AAAATTATAATTTGATA-ATTT
1 AAAATTATAATTT-ATATATTT
18431 AAA
1 AAA
18434 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AAAATTATAATTTATATATTT
Found at i:21158 original size:28 final size:28
Alignment explanation
Indices: 21108--21166 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
21098 AATAAGGATG
* * *
21108 TCTTATTAAGATAATGCAGATAA-ATTTA
1 TCTTATTAAGACAAAGCAAATAAGA-TTA
21136 TCTTATTAAGACAAAGCAAATAAGATTA
1 TCTTATTAAGACAAAGCAAATAAGATTA
21164 TCT
1 TCT
21167 AAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (28 bp):
TCTTATTAAGACAAAGCAAATAAGATTA
Found at i:21982 original size:18 final size:17
Alignment explanation
Indices: 21959--21992 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21949 TAATAAAAGA
21959 TAGTAAAAGTTCTTAATC
1 TAGTAAAAGTT-TTAATC
*
21977 TAGTAAGAGTTTTAAT
1 TAGTAAAAGTTTTAAT
21993 AAAATTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (17 bp):
TAGTAAAAGTTTTAATC
Found at i:22469 original size:11 final size:11
Alignment explanation
Indices: 22453--22478 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22443 ATCATTCAGA
22453 TAGATCATCAT
1 TAGATCATCAT
22464 TAGATCATCAT
1 TAGATCATCAT
22475 TAGA
1 TAGA
22479 CGGAGGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (11 bp):
TAGATCATCAT
Found at i:23173 original size:3 final size:3
Alignment explanation
Indices: 23165--23209 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
23155 TTACTTTTTA
23165 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
23210 TTTTATTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:24246 original size:16 final size:17
Alignment explanation
Indices: 24225--24259 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
24215 ATATATTTTA
*
24225 ATTTTATATTTTAT-AT
1 ATTTTATAATTTATCAT
24241 ATTTTATAATTTATCAT
1 ATTTTATAATTTATCAT
24258 AT
1 AT
24260 AAAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTATAATTTATCAT
Found at i:24361 original size:38 final size:37
Alignment explanation
Indices: 24292--24366 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
24282 ATGTAAAAAT
* * **
24292 TAAAAAATATATTAAGTTATTTATATTTTAAAATTTAA
1 TAAAAAATATATTAAATTATTTAAAAATT-AAATTTAA
24330 TAAAAAATAATATTAAATTA-TTAAAAATTAAATTTAA
1 TAAAAAAT-ATATTAAATTATTTAAAAATTAAATTTAA
24367 AAATATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.25
38 14 0.44
39 10 0.31
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (37 bp):
TAAAAAATATATTAAATTATTTAAAAATTAAATTTAA
Found at i:24824 original size:14 final size:14
Alignment explanation
Indices: 24805--24841 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
24795 AGATTCTCTC
*
24805 AGAAAAAAAAAAAG
1 AGAAAAAAAAAAAA
24819 AGAAAAAAAAAAAA
1 AGAAAAAAAAAAAA
24833 AGGAAAAAA
1 A-GAAAAAA
24842 CCCATGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAAAA
Found at i:24828 original size:16 final size:15
Alignment explanation
Indices: 24807--24841 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
24797 ATTCTCTCAG
24807 AAAAAAAAAAAGAGAA
1 AAAAAAAAAAAG-GAA
24823 AAAAAAAAAAAGGAA
1 AAAAAAAAAAAGGAA
24838 AAAA
1 AAAA
24842 CCCATGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAGGAA
Found at i:30191 original size:16 final size:16
Alignment explanation
Indices: 30170--30202 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30160 GGAGACCTAT
30170 GTTATCTAGATTTAGA
1 GTTATCTAGATTTAGA
30186 GTTATCTAGATTTAGA
1 GTTATCTAGATTTAGA
30202 G
1 G
30203 GTAAGTATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (16 bp):
GTTATCTAGATTTAGA
Found at i:33504 original size:13 final size:13
Alignment explanation
Indices: 33486--33510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33476 ACAAAAAATA
33486 TGTATCGATACAT
1 TGTATCGATACAT
33499 TGTATCGATACA
1 TGTATCGATACA
33511 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:33506 original size:32 final size:33
Alignment explanation
Indices: 33465--33530 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
33455 AGTAGCTTAA
33465 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
33497 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
33530 A
1 A
33531 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:37948 original size:19 final size:18
Alignment explanation
Indices: 37905--37960 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
37895 AATTTTGATG
*
37905 TTAAGTTATAAATTTAA-
1 TTAAATTATAAATTTAAT
*
37922 ATATAATTATAATATTTAAT
1 TTA-AATTATAA-ATTTAAT
37942 TTAAATT-TAAATATTAAT
1 TTAAATTATAAAT-TTAAT
37960 T
1 T
37961 AACGATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.12
18 16 0.50
19 10 0.31
20 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAAATTATAAATTTAAT
Found at i:39661 original size:19 final size:20
Alignment explanation
Indices: 39627--39665 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
39617 TCGATATGCA
39627 TATTTATATATTTAATTTAAT
1 TATTTATATA-TTAATTTAAT
39648 TATTTATATA-TAATTTAA
1 TATTTATATATTAATTTAA
39666 AAATAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTATATATTAATTTAAT
Found at i:40116 original size:17 final size:17
Alignment explanation
Indices: 40094--40126 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40084 TTATGTCACG
40094 AAAAAAATACGAACATA
1 AAAAAAATACGAACATA
40111 AAAAAAATACGAACAT
1 AAAAAAATACGAACAT
40127 GAATGTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.12, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAAAATACGAACATA
Found at i:40384 original size:6 final size:6
Alignment explanation
Indices: 40373--40406 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
40363 GGTAAAAAAT
* *
40373 AATACG AATACG AATATG AATACG AATGCG AATA
1 AATACG AATACG AATACG AATACG AATACG AATA
40407 TGTTATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.21
Consensus pattern (6 bp):
AATACG
Found at i:40396 original size:18 final size:18
Alignment explanation
Indices: 40373--40408 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40363 GGTAAAAAAT
40373 AATACGAATACGAATATG
1 AATACGAATACGAATATG
*
40391 AATACGAATGCGAATATG
1 AATACGAATACGAATATG
40409 TTATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.22
Consensus pattern (18 bp):
AATACGAATACGAATATG
Found at i:49647 original size:18 final size:18
Alignment explanation
Indices: 49626--49661 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
49616 TCTCAGCCAT
49626 TATTCTAATGAAAATTGA
1 TATTCTAATGAAAATTGA
*
49644 TATTCTAATTAAAATTGA
1 TATTCTAATGAAAATTGA
49662 CTTTACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (18 bp):
TATTCTAATGAAAATTGA
Found at i:56158 original size:27 final size:25
Alignment explanation
Indices: 56128--56184 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
56118 CATATCATTA
*
56128 TTTATTTACGAAAATAATATTTTTAAT
1 TTTAATTA-GAAAATAAT-TTTTTAAT
* *
56155 TTTAATTATAAAATTATTTTTTAAT
1 TTTAATTAGAAAATAATTTTTTAAT
*
56180 ATTAA
1 TTTAA
56185 AATAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 12 0.46
26 7 0.27
27 7 0.27
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTAATTAGAAAATAATTTTTTAAT
Found at i:56178 original size:19 final size:19
Alignment explanation
Indices: 56154--56193 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
56144 ATATTTTTAA
*
56154 TTTTAAT-TATAAAATTATT
1 TTTTAATAT-TAAAATAATT
56173 TTTTAATATTAAAATAATT
1 TTTTAATATTAAAATAATT
56192 TT
1 TT
56194 ATTAGTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTAATATTAAAATAATT
Found at i:56373 original size:17 final size:17
Alignment explanation
Indices: 56351--56384 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
56341 TATTTATGAA
56351 TAAAATATAAAAATAAT
1 TAAAATATAAAAATAAT
*
56368 TAAAATATAAATATAAT
1 TAAAATATAAAAATAAT
56385 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATATAAAAATAAT
Found at i:56605 original size:22 final size:19
Alignment explanation
Indices: 56574--56615 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
56564 TATTTTTATT
56574 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
56595 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
56615 T
1 T
56616 GTTTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:56744 original size:6 final size:6
Alignment explanation
Indices: 56733--56786 Score: 90
Period size: 6 Copynumber: 9.0 Consensus size: 6
56723 AGTGACGCGA
* *
56733 ATTTTT ATTTTT ATTTTT ATGTTT ATTTTT GTTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
56781 ATTTTT
1 ATTTTT
56787 GTTGTGAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:58692 original size:87 final size:87
Alignment explanation
Indices: 58598--58764 Score: 253
Period size: 87 Copynumber: 1.9 Consensus size: 87
58588 GATAAAAGAT
* * * **
58598 ATATTTTTTATTTCCCTTTGTGTGTTTGGTAGCAAAGAAAGAAATGTGAAAAGCTAAAAAATAAT
1 ATATTTTTTATTTCCATTGGTGTGTTTGGTAGCAAAGAAAGAAAAGTGAAAAGAAAAAAAATAAT
58663 TTTCTTTCAACCAATACAAAAC
66 TTTCTTTCAACCAATACAAAAC
** *
58685 ATATTTTTTATTTTTATTGGTGTGTTTGGTAGGAAAGAAAGAAAAGTGAAAAGAAAAAAAATAAT
1 ATATTTTTTATTTCCATTGGTGTGTTTGGTAGCAAAGAAAGAAAAGTGAAAAGAAAAAAAATAAT
*
58750 TTTCTTTCTACCAAT
66 TTTCTTTCAACCAAT
58765 TACTTGGTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (87 bp):
ATATTTTTTATTTCCATTGGTGTGTTTGGTAGCAAAGAAAGAAAAGTGAAAAGAAAAAAAATAAT
TTTCTTTCAACCAATACAAAAC
Found at i:59016 original size:15 final size:16
Alignment explanation
Indices: 58993--59049 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 16
58983 TAAAATTATT
58993 AATAAATATAAA-TTA
1 AATAAATATAAACTTA
*
59008 AATACATATAAACTTAAA
1 AATAAATATAAACTT--A
*
59026 AATAAATAAATAAACATA
1 AATAAAT--ATAAACTTA
59044 AATAAA
1 AATAAA
59050 AATCTGTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 11 0.32
16 2 0.06
18 14 0.41
20 7 0.21
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATATAAACTTA
Found at i:59598 original size:94 final size:93
Alignment explanation
Indices: 59486--59662 Score: 205
Period size: 94 Copynumber: 1.9 Consensus size: 93
59476 TTAAAAAATA
* * * *
59486 ATATTTATTAAGTTTAAAATTTAAATATTAAAAATTATAATTTC-TTTCTTTATCTTCAGACTAA
1 ATATTTAGTAAGTCTAAAATTCAAATATTAAAAATTATAATTTCTTTTC-GTATCTTCAGACTAA
59550 AATCTT-CTTTGTATAAAAAAAATATAAGTG
65 AAT-TTCCTTT-TATAAAAAAAATATAAGTG
* * * * * * *
59580 ATATTTAGTATGTCTAAAATTCGAATCTTAATATTTGTAATTTCTTTTCGTATCTTTAGACTAAA
1 ATATTTAGTAAGTCTAAAATTCAAATATTAAAAATTATAATTTCTTTTCGTATCTTCAGACTAAA
*
59645 GTTTCCTTTTATAAAAAA
66 ATTTCCTTTTATAAAAAA
59663 TCTAGATAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
93 11 0.16
94 54 0.78
95 4 0.06
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (93 bp):
ATATTTAGTAAGTCTAAAATTCAAATATTAAAAATTATAATTTCTTTTCGTATCTTCAGACTAAA
ATTTCCTTTTATAAAAAAAATATAAGTG
Found at i:60703 original size:2 final size:2
Alignment explanation
Indices: 60698--60728 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
60688 TTACACACAC
*
60698 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60729 AGGAAAAAAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:60973 original size:22 final size:21
Alignment explanation
Indices: 60921--60975 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
60911 ATTTAAATTG
*
60921 TATTTATATTT-T-TTTATAA
1 TATTTATATTTATATTTAAAA
*
60940 TA-TTATAATTATATTTAAAA
1 TATTTATATTTATATTTAAAA
60960 TATTTTATATTTATAT
1 TA-TTTATATTTATAT
60976 AAATTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 7 0.24
19 3 0.10
20 8 0.28
22 11 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTATATTTATATTTAAAA
Found at i:60978 original size:20 final size:20
Alignment explanation
Indices: 60923--60978 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
60913 TTAAATTGTA
* *
60923 TTTATATTTTTTTATAATAT
1 TTTATATTTATTTAAAATAT
*
60943 TATA-ATTATATTTAAAATAT
1 TTTATATT-TATTTAAAATAT
*
60963 TTTATATTTATATAAA
1 TTTATATTTATTTAAA
60979 TTTTAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.10
20 23 0.79
21 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATTTATTTAAAATAT
Found at i:61126 original size:2 final size:2
Alignment explanation
Indices: 61080--61112 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
61070 AGTTTATAAT
61080 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
61113 AAAAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:64453 original size:31 final size:31
Alignment explanation
Indices: 64417--64483 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
64407 ACATTACTTT
* *
64417 TAGTAATGTTATTTGGCACAACACTTTTTGG
1 TAGTAATGTTAGTTGGCACAACACTTTTTGA
* *
64448 TAGTAATGTTAGTTGGCATAATACTTTTTGA
1 TAGTAATGTTAGTTGGCACAACACTTTTTGA
64479 TAGTA
1 TAGTA
64484 GAGCTACTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (31 bp):
TAGTAATGTTAGTTGGCACAACACTTTTTGA
Found at i:64495 original size:31 final size:31
Alignment explanation
Indices: 64417--64498 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
64407 ACATTACTTT
* * *
64417 TAGTAATGTTATTTGGCACAACACTTTTTGG
1 TAGTAATGCTACTTGGCACAACACTTTTTGA
* * * *
64448 TAGTAATGTTAGTTGGCATAATACTTTTTGA
1 TAGTAATGCTACTTGGCACAACACTTTTTGA
64479 TAGTAGA-GCTACTTGGCACA
1 TAGTA-ATGCTACTTGGCACA
64499 TCTCTTATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (31 bp):
TAGTAATGCTACTTGGCACAACACTTTTTGA
Found at i:72299 original size:21 final size:21
Alignment explanation
Indices: 72231--72287 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
72221 AGTTGAATTT
72231 TTTCATTCAAAAAATGCATTC
1 TTTCATTCAAAAAATGCATTC
72252 TTTCATTCAAAAAATGCATTC
1 TTTCATTCAAAAAATGCATTC
72273 TTTCATTCAAAAAAT
1 TTTCATTCAAAAAAT
72288 ACACATTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.39
Consensus pattern (21 bp):
TTTCATTCAAAAAATGCATTC
Done.