Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2221
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: 61651
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:4713 original size:16 final size:17
Alignment explanation
Indices: 4692--4725 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4682 GTTATTATCT
*
4692 ATTATTAA-AATAAATA
1 ATTATTAATAAAAAATA
4708 ATTATTAATAAAAAATA
1 ATTATTAATAAAAAATA
4725 A
1 A
4726 AAAATGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTATTAATAAAAAATA
Found at i:6584 original size:22 final size:22
Alignment explanation
Indices: 6557--6611 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
6547 AAAATTTTTA
6557 ATTTAAATTTAAATATAAAA-AT
1 ATTTAAATTT-AATATAAAATAT
6579 ATTTAAATATTAATATAAAATAT
1 ATTTAAAT-TTAATATAAAATAT
*
6602 ATTTTAATTT
1 ATTTAAATTT
6612 TTTATTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAAATTTAATATAAAATAT
Found at i:12007 original size:52 final size:52
Alignment explanation
Indices: 11937--12057 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
11927 GAAAATTTAT
*
11937 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
11989 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
12041 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
12058 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:12070 original size:52 final size:51
Alignment explanation
Indices: 11937--12077 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
11927 GAAAATTTAT
11937 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
11989 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
12041 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
12078 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:12084 original size:13 final size:13
Alignment explanation
Indices: 12066--12090 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12056 CAAAGATCAG
12066 TGTATCGATACAA
1 TGTATCGATACAA
12079 TGTATCGATACA
1 TGTATCGATACA
12091 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12171 original size:13 final size:13
Alignment explanation
Indices: 12153--12177 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12143 CAAAAAAACA
12153 TGTATCGATACAT
1 TGTATCGATACAT
12166 TGTATCGATACA
1 TGTATCGATACA
12178 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:13341 original size:14 final size:14
Alignment explanation
Indices: 13324--13354 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13314 AAATTTAGCT
13324 ATATAAATATAAAA
1 ATATAAATATAAAA
*
13338 ATATTAATATAAAA
1 ATATAAATATAAAA
13352 ATA
1 ATA
13355 ATTTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATAAATATAAAA
Found at i:13871 original size:18 final size:17
Alignment explanation
Indices: 13842--13899 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
13832 ATAATGTTTA
13842 AAATATTTATATTTATAT
1 AAAT-TTTATATTTATAT
13860 AAATTTTGATATATTA-AT
1 AAATTTT-ATAT-TTATAT
13878 -AA-TTTATA-TTATAT
1 AAATTTTATATTTATAT
13892 AAATTTTA
1 AAATTTTA
13900 AAAATATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 5 0.14
16 7 0.20
17 5 0.14
18 10 0.29
19 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AAATTTTATATTTATAT
Found at i:14155 original size:21 final size:21
Alignment explanation
Indices: 14142--14191 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
14132 TTGACAGAAA
14142 TTAAGACAATTTTGCCAGACT
1 TTAAGACAATTTTGCCAGACT
14163 TTAAGACAATTTTGCCAGACT
1 TTAAGACAATTTTGCCAGACT
14184 TTAAGACA
1 TTAAGACA
14192 TGCTTGGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (21 bp):
TTAAGACAATTTTGCCAGACT
Found at i:15437 original size:24 final size:25
Alignment explanation
Indices: 15406--15463 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
15396 GTAACCACCA
*
15406 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
15430 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
15456 TTGTTGAC
1 TTGTTGAC
15464 TAGTCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:19985 original size:24 final size:25
Alignment explanation
Indices: 19954--20011 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
19944 GTAACCACCA
*
19954 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
19978 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
20004 TTGTTGAC
1 TTGTTGAC
20012 TAGCCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:20072 original size:22 final size:23
Alignment explanation
Indices: 20049--20115 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 23
20039 TTTAATTGGA
*
20049 TTTGGATTTAAGTTTATATAGAT
1 TTTGGATTTAAGTTTATATAGAG
** ** * *
20072 TTTTAATTCGATTTTA-ATTGAG
1 TTTGGATTTAAGTTTATATAGAG
*
20094 TTTGGGTTTAAGTTTATATAGA
1 TTTGGATTTAAGTTTATATAGA
20116 TTTTTAATTT
Statistics
Matches: 29, Mismatches: 14, Indels: 2
0.64 0.31 0.04
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.28, C:0.01, G:0.18, T:0.52
Consensus pattern (23 bp):
TTTGGATTTAAGTTTATATAGAG
Found at i:20104 original size:45 final size:45
Alignment explanation
Indices: 20038--20124 Score: 149
Period size: 45 Copynumber: 1.9 Consensus size: 45
20028 TTTGTTATTT
20038 TTTTAATTGGATTTGGATTTAAGTTTATATAGATTTTTAATTCGA
1 TTTTAATTGGATTTGGATTTAAGTTTATATAGATTTTTAATTCGA
*
20083 TTTTAATT-GAGTTTGGGTTTAAGTTTATATAGATTTTTAATT
1 TTTTAATTGGA-TTTGGATTTAAGTTTATATAGATTTTTAATT
20125 TGTGTTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 2 0.05
45 38 0.95
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (45 bp):
TTTTAATTGGATTTGGATTTAAGTTTATATAGATTTTTAATTCGA
Found at i:20721 original size:27 final size:27
Alignment explanation
Indices: 20659--20722 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
20649 TATTTTTTTT
*
20659 AAAATTATTTTTTATTTTTTACACTATA
1 AAAATTA-TATTTATTTTTTACACTATA
* *
20687 ATAA-TATATTTATTTTTTATA-TGATA
1 AAAATTATATTTATTTTTTACACT-ATA
20713 AAAATTATAT
1 AAAATTATAT
20723 AATATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
25 1 0.03
26 19 0.63
27 7 0.23
28 3 0.10
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (27 bp):
AAAATTATATTTATTTTTTACACTATA
Found at i:25115 original size:26 final size:26
Alignment explanation
Indices: 25086--25138 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
25076 AGTTACAATG
*
25086 AAATTTAACGTAGTTTTAATTATTTT
1 AAATTTAACATAGTTTTAATTATTTT
25112 AAATTTAACATAGTTTTAATTATTTT
1 AAATTTAACATAGTTTTAATTATTTT
25138 A
1 A
25139 TCTATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (26 bp):
AAATTTAACATAGTTTTAATTATTTT
Found at i:27158 original size:2 final size:2
Alignment explanation
Indices: 27151--27194 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
27141 AAAGTTAACT
27151 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27193 TA
1 TA
27195 ACCTAATTTT
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):
TA
Found at i:27531 original size:16 final size:15
Alignment explanation
Indices: 27510--27581 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 15
27500 TAGATCAAAC
27510 AATTTAATTAAATTTA
1 AATTTAATTAAA-TTA
*
27526 AATTTAAATTTAATTA
1 AATTT-AATTAAATTA
* *
27542 ATATATAATTAAAATA
1 A-ATTTAATTAAATTA
27558 ATATTTAA-TAAATTTA
1 A-ATTTAATTAAA-TTA
27574 TAATTTAA
1 -AATTTAA
27582 ATTTTAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.09
16 32 0.70
17 10 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAATTAAATTA
Found at i:27553 original size:27 final size:29
Alignment explanation
Indices: 27520--27594 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 29
27510 AATTTAATTA
*
27520 AATTTAAATTTAA-ATTTAATTAATATAT
1 AATTTAAATTTAATATTTAATAAATATAT
* *
27548 AA-TTAAA-ATAATATTTAATAAATTTAT
1 AATTTAAATTTAATATTTAATAAATATAT
27575 AATTTAAATTTTAATATTTA
1 AATTTAAA-TTTAATATTTA
27595 TAATTTATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 3 0.08
27 20 0.51
28 7 0.18
30 9 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATTTAAATTTAATATTTAATAAATATAT
Found at i:29441 original size:37 final size:37
Alignment explanation
Indices: 29391--29467 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
29381 GTTGGACAAG
29391 ACACCATATAAGTTGCAAAAAGGTTAAAAACCTTCTT
1 ACACCATATAAGTTGCAAAAAGGTTAAAAACCTTCTT
* *
29428 ACACCATATAAGTTGTAAAAAGGTTAAATACCTTCTT
1 ACACCATATAAGTTGCAAAAAGGTTAAAAACCTTCTT
29465 ACA
1 ACA
29468 AATATATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (37 bp):
ACACCATATAAGTTGCAAAAAGGTTAAAAACCTTCTT
Found at i:31601 original size:21 final size:19
Alignment explanation
Indices: 31577--31630 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
31567 TTTCAACAAT
31577 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAA-AGT-A
* *
31598 TTGTATCGATACATAAGTG
1 TTGTATCGATACAAAAGTA
31617 TTGTATCGATACAA
1 TTGTATCGATACAA
31631 TGTATCGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACAAAAGTA
Found at i:31622 original size:19 final size:19
Alignment explanation
Indices: 31577--31659 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
31567 TTTCAACAAT
* *
31577 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-G
31598 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
31617 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
31631 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
31649 TTCTATCGATA
1 TTGTATCGATA
31660 TAATGTATCG
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
13 11 0.21
15 2 0.04
17 2 0.04
19 21 0.40
20 3 0.06
21 14 0.26
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:31636 original size:13 final size:13
Alignment explanation
Indices: 31618--31642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31608 ACATAAGTGT
31618 TGTATCGATACAA
1 TGTATCGATACAA
31631 TGTATCGATACA
1 TGTATCGATACA
31643 TAAGTGTTCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:31640 original size:32 final size:32
Alignment explanation
Indices: 31599--31669 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
31589 AAACAGTAAT
*
31599 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTCTATCGATACAA
*
31631 TGTATCGATACATAAGTGTTCTATCGATATAA
1 TGTATCGATACATAAGTGTTCTATCGATACAA
31663 TGTATCG
1 TGTATCG
31670 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTCTATCGATACAA
Found at i:35986 original size:2 final size:2
Alignment explanation
Indices: 35979--36023 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
35969 TTTTAAATGC
35979 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
36021 AT A
1 AT A
36024 ATCATTTGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40468 original size:21 final size:22
Alignment explanation
Indices: 40443--40484 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
40433 ATTTTCAACT
*
40443 AAAATAAAATATA-TTTAGTTA
1 AAAATAAAATAAATTTTAGTTA
*
40464 AAAATAATATAAATTTTAGTT
1 AAAATAAAATAAATTTTAGTT
40485 TTATTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
AAAATAAAATAAATTTTAGTTA
Found at i:40829 original size:2 final size:2
Alignment explanation
Indices: 40822--40847 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40812 TAATTTTTAG
40822 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
40848 TTCTTAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41686 original size:21 final size:22
Alignment explanation
Indices: 41657--41698 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
41647 AAATTAATAA
*
41657 AACTAAAATTTATATTATTTTT
1 AACTAAAATATATATTATTTTT
*
41679 AACT-AAATATATTTTATTTT
1 AACTAAAATATATATTATTTT
41699 AGCTGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
AACTAAAATATATATTATTTTT
Found at i:48176 original size:2 final size:2
Alignment explanation
Indices: 48169--48208 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
48159 CAATACGTAA
48169 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
48209 GCTTTATGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:48405 original size:2 final size:2
Alignment explanation
Indices: 48398--48429 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
48388 TACCATTAAC
48398 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48430 CGTTTGGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49546 original size:14 final size:14
Alignment explanation
Indices: 49523--49552 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49513 TGAGAAGTAT
49523 TAATTAAATAATAA
1 TAATTAAATAATAA
*
49537 TAATTTAATAATAA
1 TAATTAAATAATAA
49551 TA
1 TA
49553 TTCCCACCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTAAATAATAA
Found at i:49939 original size:21 final size:21
Alignment explanation
Indices: 49913--49956 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
49903 ATTTTTAAAT
*
49913 TTTTAT-TTAAATTTATTTTTA
1 TTTTATCTT-AATTTATTTATA
49934 TTTTATCTTAATTTATTTATA
1 TTTTATCTTAATTTATTTATA
49955 TT
1 TT
49957 ATTCATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATCTTAATTTATTTATA
Found at i:50465 original size:2 final size:2
Alignment explanation
Indices: 50458--50505 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
50448 GGGTAATGAG
50458 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
50500 AT AT AT
1 AT AT AT
50506 CACTATGGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52240 original size:7 final size:6
Alignment explanation
Indices: 52211--52244 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
52201 ATAACGGCAA
*
52211 CCTTTT CCTTTT CCTTTT TCTTTT CCCTTTT CCT
1 CCTTTT CCTTTT CCTTTT CCTTTT -CCTTTT CCT
52245 ACCCACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (6 bp):
CCTTTT
Found at i:52408 original size:2 final size:2
Alignment explanation
Indices: 52401--52432 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52391 CAAATAAACA
52401 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
52433 TAGCACTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52680 original size:11 final size:11
Alignment explanation
Indices: 52664--52703 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
52654 ATAAATTTAA
*
52664 AATATAATTAT
1 AATATAAATAT
52675 AATATAAATAT
1 AATATAAATAT
*
52686 AATATAAATTT
1 AATATAAATAT
52697 AAT-TAAA
1 AATATAAA
52704 AGAATTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATAAATAT
Found at i:52927 original size:2 final size:2
Alignment explanation
Indices: 52920--52958 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
52910 TGTCTCAATT
52920 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
52959 TTCAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:54591 original size:17 final size:18
Alignment explanation
Indices: 54565--54605 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
54555 AATTTGAATC
*
54565 AATT-TTATTTGATT-TA
1 AATTATTATTTAATTATA
54581 AATTATTATTTAATTATA
1 AATTATTATTTAATTATA
54599 AA-TATTA
1 AATTATTA
54606 ATATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
AATTATTATTTAATTATA
Found at i:56120 original size:20 final size:21
Alignment explanation
Indices: 56095--56138 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
56085 AGGCGTGGTT
*
56095 TAAAAG-AA-AATATAAAAGAG
1 TAAAAGCAATAATAGAAAAG-G
56115 TAAAAGCAATAATAGAAAAGG
1 TAAAAGCAATAATAGAAAAGG
56136 TAA
1 TAA
56139 TGAGTAGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 6 0.29
22 9 0.43
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (21 bp):
TAAAAGCAATAATAGAAAAGG
Found at i:57015 original size:22 final size:21
Alignment explanation
Indices: 56990--57047 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
56980 CTATTTATTG
**
56990 ATATAATTTTGATAGTTTTTTA
1 ATATAATTTTGATAG-GATTTA
*
57012 ATATAATGTTGATAGGATTTA
1 ATATAATTTTGATAGGATTTA
*
57033 ACATAATTTTGATAG
1 ATATAATTTTGATAG
57048 CCTTTTGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (21 bp):
ATATAATTTTGATAGGATTTA
Found at i:57145 original size:21 final size:19
Alignment explanation
Indices: 57060--57147 Score: 59
Period size: 20 Copynumber: 4.3 Consensus size: 19
57050 TTTTGTAATT
57060 ATTTTCATAATTTTTGATATA
1 ATTTT-ATAATTTTT-ATATA
** * * *
57081 ATGTTGGTAATCTTTGTAAA
1 AT-TTTATAATTTTTATATA
*
57101 ATTTTAATAATTTTTATATG
1 ATTTT-ATAATTTTTATATA
*
57121 ATTTTATTATTCTTTAATATA
1 ATTTTATAATT-TTT-ATATA
57142 ATTTTA
1 ATTTTA
57148 ACAAGCTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
19 7 0.14
20 22 0.44
21 19 0.38
22 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (19 bp):
ATTTTATAATTTTTATATA
Found at i:57190 original size:21 final size:21
Alignment explanation
Indices: 57101--57203 Score: 73
Period size: 21 Copynumber: 4.9 Consensus size: 21
57091 TCTTTGTAAA
* *
57101 ATTTTAAT-AATTTTTATATG
1 ATTTTAATAAACTTTGATATG
* ** * *
57121 ATTTTATTATTCTTTAATATA
1 ATTTTAATAAACTTTGATATG
* * * * *
57142 ATTTTAACAAGCTTTAGGTGTA
1 ATTTTAATAAACTTT-GATATG
*
57164 ATTTTAATAAATTTTGATATG
1 ATTTTAATAAACTTTGATATG
57185 ATTTTAATAAACTTTGATA
1 ATTTTAATAAACTTTGATA
57204 AATTTCAATA
Statistics
Matches: 61, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 7 0.11
21 39 0.64
22 15 0.25
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (21 bp):
ATTTTAATAAACTTTGATATG
Found at i:57232 original size:52 final size:51
Alignment explanation
Indices: 57165--57299 Score: 150
Period size: 52 Copynumber: 2.6 Consensus size: 51
57155 TTAGGTGTAA
57165 TTTTAATA-AATTTTGATATGATTTTAATAA-ACTTTGATAAATTTCAAT-AC
1 TTTTAATATAATTTTGATAT-ATTTTAATAACACTTTG-TAAATTTCAATAAC
* * * *
57215 TTTTTAATATAATTTTGATAACATTTTAATAACATTTTGTAATTTTTAATAAC
1 -TTTTAATATAATTTTGAT-ATATTTTAATAACACTTTGTAAATTTCAATAAC
*
57268 TTTTAATATAATTTTAATAATATTTTATATAA
1 TTTTAATATAATTTTGAT-ATATTTTA-ATAA
57300 TTTTAATAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
51 8 0.11
52 53 0.73
53 12 0.16
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (51 bp):
TTTTAATATAATTTTGATATATTTTAATAACACTTTGTAAATTTCAATAAC
Found at i:57271 original size:11 final size:10
Alignment explanation
Indices: 57163--57308 Score: 116
Period size: 10 Copynumber: 14.1 Consensus size: 10
57153 CTTTAGGTGT
57163 AATTTTAATA
1 AATTTTAATA
*
57173 AATTTTGATA
1 AATTTTAATA
*
57183 TGATTTTAATA
1 -AATTTTAATA
* *
57194 AACTTTGATA
1 AATTTTAATA
*
57204 AATTTCAATA
1 AATTTTAATA
**
57214 CTTTTTAATA
1 AATTTTAATA
*
57224 TAATTTTGATA
1 -AATTTTAATA
57235 ACATTTTAATA
1 A-ATTTTAATA
*
57246 ACATTTT-GTA
1 A-ATTTTAATA
*
57256 ATTTTTAATA
1 AATTTTAATA
*
57266 ACTTTTAATA
1 AATTTTAATA
57276 TAATTTTAATA
1 -AATTTTAATA
57287 ATATTTT-ATA
1 A-ATTTTAATA
57297 TAATTTTAATA
1 -AATTTTAATA
57308 A
1 A
57309 TCTTTGTAAT
Statistics
Matches: 107, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
9 4 0.04
10 55 0.51
11 48 0.45
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.51
Consensus pattern (10 bp):
AATTTTAATA
Found at i:57284 original size:21 final size:21
Alignment explanation
Indices: 57237--57330 Score: 81
Period size: 21 Copynumber: 4.5 Consensus size: 21
57227 TTTTGATAAC
*
57237 ATTTTAATAACATTTT-GTA-A
1 ATTTTAATAAC-TTTTAATATA
*
57257 TTTTTAATAACTTTTAATATA
1 ATTTTAATAACTTTTAATATA
*
57278 ATTTTAATAA-TATTTTATATA
1 ATTTTAATAACT-TTTAATATA
57299 ATTTTAATAATCTTTGTAAT-T-
1 ATTTTAATAA-CTTT-TAATATA
*
57320 ATTTTGATAAC
1 ATTTTAATAAC
57331 CTCTGATTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.06
20 14 0.23
21 37 0.60
22 3 0.05
23 4 0.06
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (21 bp):
ATTTTAATAACTTTTAATATA
Found at i:57466 original size:21 final size:20
Alignment explanation
Indices: 57407--57776 Score: 98
Period size: 21 Copynumber: 18.1 Consensus size: 20
57397 ATGATTTATC
* * *
57407 ATTTTTATAACTTTTACACA
1 ATTTTGATAACTTTTATATA
57427 ATTTTGATAAC--TTATATA
1 ATTTTGATAACTTTTATATA
57445 ATTTTGATAACTTTTGATATA
1 ATTTTGATAACTTTT-ATATA
* *
57466 ATTTAGATAACCTTTAATATA
1 ATTTTGATAA-CTTTTATATA
* *
57487 A--TTGATAATCTTTGATATG
1 ATTTTGATAA-CTTTTATATA
* * *
57506 ATTTTTATAACATTTAATATT
1 ATTTTGATAAC-TTTTATATA
* * *
57527 ATTTTAATATCTTCTT-TGTA
1 ATTTTGATAACTT-TTATATA
*
57547 ATATTTGATATA-TATTTAGT-CA
1 AT-TTTGATA-ACT-TTTA-TATA
* * *
57569 GTTTTGATGA-TTTTGGATAAA
1 ATTTTGATAACTTTT--ATATA
*
57590 ATTTTGATAACATTTGATATA
1 ATTTTGATAAC-TTTTATATA
* * * *
57611 ATTTTAATAGCATTTCATGTA
1 ATTTTGATAAC-TTTTATATA
* *
57632 ATTTT-AGTAGCATTTAATATA
1 ATTTTGA-TAAC-TTTTATATA
* *
57653 ATTTTAATAATCTTTGTA-ACA
1 ATTTTGATAA-CTTT-TATATA
* ** * *
57674 A-TTTGATAGTCTTAAACACA
1 ATTTTGATA-ACTTTTATATA
* * *
57694 ATTTTGATAACCTATGATATT
1 ATTTTGATAA-CTTTTATATA
** *
57715 ATTTCAATAACTTTTATGTA
1 ATTTTGATAACTTTTATATA
** *
57735 ATTTTGCATAACCCTTATGTA
1 ATTTTG-ATAACTTTTATATA
*
57756 ATTGTT-ATAATTTTTATATA
1 ATT-TTGATAACTTTTATATA
57776 A
1 A
57777 ATATCATTAA
Statistics
Matches: 261, Mismatches: 61, Indels: 56
0.69 0.16 0.15
Matches are distributed among these distances:
18 16 0.06
19 19 0.07
20 57 0.22
21 153 0.59
22 12 0.05
23 4 0.02
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (20 bp):
ATTTTGATAACTTTTATATA
Found at i:57501 original size:40 final size:40
Alignment explanation
Indices: 57448--57525 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
57438 TTATATAATT
*
57448 TTGATAACTTTTGATATAATTTAGATAACCTTTAATATAA
1 TTGATAACTTTTGATATAATTTAGATAACATTTAATATAA
* **
57488 TTGATAA-TCTTTGATATGATTTTTATAACATTTAATAT
1 TTGATAACT-TTTGATATAATTTAGATAACATTTAATAT
57526 TATTTTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.03
40 32 0.97
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (40 bp):
TTGATAACTTTTGATATAATTTAGATAACATTTAATATAA
Found at i:58060 original size:21 final size:21
Alignment explanation
Indices: 57888--58066 Score: 119
Period size: 21 Copynumber: 8.5 Consensus size: 21
57878 GATATATATA
* **
57888 TATATAATTTTGATAATAATCG
1 TATATAATTTTGATAAT-TTTT
*
57910 TA-ATAAATTTGATAATTTTT
1 TATATAATTTTGATAATTTTT
* *
57930 TATATAGTTTTAATAACTTTTT
1 TATATAATTTTGATAA-TTTTT
* * *
57952 TATAT-ATGTTAATGATTTTT
1 TATATAATTTTGATAATTTTT
* **
57972 TATATAATTTTAATAATACTT
1 TATATAATTTTGATAATTTTT
* * *
57993 GATATGATTTTGATAATCTTT
1 TATATAATTTTGATAATTTTT
* * *** *
58014 AATAAAATTTTGATAGCCTTC
1 TATATAATTTTGATAATTTTT
* *
58035 GATATAGTTTTGATAATTTTT
1 TATATAATTTTGATAATTTTT
58056 TATATAATTTT
1 TATATAATTTT
58067 ATTTACATTG
Statistics
Matches: 120, Mismatches: 34, Indels: 7
0.75 0.21 0.04
Matches are distributed among these distances:
20 13 0.11
21 95 0.79
22 12 0.10
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (21 bp):
TATATAATTTTGATAATTTTT
Found at i:58194 original size:9 final size:8
Alignment explanation
Indices: 58172--58234 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 8
58162 TAACTCTCAA
58172 TATAATTT
1 TATAATTT
58180 TAATAACTTT
1 T-ATAA-TTT
58190 TATAATTT
1 TATAATTT
58198 TAATAATTT
1 T-ATAATTT
58207 TGATATTATTT
1 T-ATA--ATTT
58218 TAATAATTT
1 T-ATAATTT
58227 TAATAATT
1 T-ATAATT
58235 ATTAATATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
8 5 0.10
9 31 0.65
10 4 0.08
11 8 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (8 bp):
TATAATTT
Found at i:58195 original size:18 final size:18
Alignment explanation
Indices: 58173--58241 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
58163 AACTCTCAAT
58173 ATAATTTTAATAACTTTT-
1 ATAATTTTAATAA-TTTTA
58191 ATAATTTTAATAATTTTGA
1 ATAATTTTAATAATTTT-A
*
58210 TATTATTTTAATAATTTTA
1 -ATAATTTTAATAATTTTA
58229 ATAATTATTAATA
1 ATAATT-TTAATA
58242 TAATTAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
17 4 0.09
18 18 0.40
19 7 0.16
20 16 0.36
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (18 bp):
ATAATTTTAATAATTTTA
Found at i:59301 original size:26 final size:26
Alignment explanation
Indices: 59270--59321 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
59260 AGTCATTTAG
*
59270 GCCCAATAA-TTTTAAATGTTCTAAAA
1 GCCCAA-AACTTTTAAATGTTATAAAA
59296 GCCCAAAACTTTTAAATGTTATAAAA
1 GCCCAAAACTTTTAAATGTTATAAAA
59322 CTTTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (26 bp):
GCCCAAAACTTTTAAATGTTATAAAA
Found at i:59323 original size:18 final size:17
Alignment explanation
Indices: 59300--59334 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
59290 CTAAAAGCCC
59300 AAAACTTTTAAATGTTAT
1 AAAACTTTTAAAT-TTAT
59318 AAAACTTTTAAATTTAT
1 AAAACTTTTAAATTTAT
59335 TTAAGCCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (17 bp):
AAAACTTTTAAATTTAT
Done.