Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold534
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: 40237
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Found at i:2270 original size:39 final size:39
Alignment explanation
Indices: 2216--2437 Score: 285
Period size: 39 Copynumber: 5.7 Consensus size: 39
2206 TTGATACCCG
*
2216 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AATCC
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA-CC
*
2255 GGCTAAGTCCCGAAGG-A-TTGTAG--AGTTACTATATCC
1 GGCTAAGTCCCGAAGGCATTTGT-GCTAGTTACTATAACC
* *
2291 GAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCACC
1 G-GCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAACC
*
2331 GGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATCACC
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAACC
* * *
2370 AGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAACG
1 -GGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAACC
*
2410 GGCTAAGT-CCGAAGGCATTTGAGCTAGT
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGT
2438 AGCTATATCG
Statistics
Matches: 163, Mismatches: 12, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
36 10 0.06
37 20 0.12
38 21 0.13
39 65 0.40
40 47 0.29
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAACC
Found at i:2392 original size:79 final size:78
Alignment explanation
Indices: 2216--2446 Score: 298
Period size: 79 Copynumber: 3.0 Consensus size: 78
2206 TTGATACCCG
* *
2216 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AATCCGGCTAAGTCCCGAAGG-A-TTGTAG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGCTAAGTCCCGAAGGCATTTGT-G
2278 --AGTTACTATATCC
64 CTAGTTACTATATCC
*
2291 GAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCACCGGCTAAGTCCCGAAGGCATTTGTGC
1 G-GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGCTAAGTCCCGAAGGCATTTGTGC
2356 TAGTTACTATCA-CC
65 TAGTTACTAT-ATCC
* * *
2370 AGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAACGGGCTAAGT-CCGAAGGCATTTGAGC
1 -GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGCTAAGTCCCGAAGGCATTTGTGC
2434 TAG-TAGCTATATC
65 TAGTTA-CTATATC
2447 GCGCTAAATC
Statistics
Matches: 139, Mismatches: 7, Indels: 17
0.85 0.04 0.10
Matches are distributed among these distances:
75 1 0.01
76 49 0.35
77 6 0.04
78 27 0.19
79 54 0.39
80 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (78 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGCTAAGTCCCGAAGGCATTTGTGCT
AGTTACTATATCC
Found at i:9637 original size:85 final size:85
Alignment explanation
Indices: 9527--9705 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
9517 GGCCGGCCAT
9527 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAC
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAC
9592 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
9612 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAC
9677 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
9697 GAGCATGGG
1 GAGCATGGG
9706 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAC
GTAAGGATTAATAAAATAAA
Found at i:10970 original size:39 final size:40
Alignment explanation
Indices: 10869--11052 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
10859 TCGAATGATG
* * *
10869 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACAATA
*
10909 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTAC-AATA
*
10949 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACAATA
* *
10987 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACAATA
* *
11027 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
11053 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
38 12 0.10
39 46 0.37
40 57 0.46
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACAATA
Found at i:11004 original size:78 final size:81
Alignment explanation
Indices: 10869--11050 Score: 232
Period size: 78 Copynumber: 2.3 Consensus size: 81
10859 TCGAATGATG
* *
10869 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
10933 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * **
10948 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTA-CAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
11009 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
11027 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
11051 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
77 1 0.01
78 46 0.51
79 26 0.29
80 17 0.19
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:13659 original size:40 final size:40
Alignment explanation
Indices: 13422--13668 Score: 342
Period size: 40 Copynumber: 6.2 Consensus size: 40
13412 GGATTGATAC
*
13422 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
*
13461 TCCGGGCTAAGT-CCGAAGGCATTTGTG-TGAGTTACTATAT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTTACTATAA
* *
13501 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
*
13541 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
* * *
13581 CCAGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
* *
13621 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTA-CTATAA
13661 CC-GGCTAA
1 CCGGGCTAA
13669 ACTCCAAGGT
Statistics
Matches: 187, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.01
39 41 0.22
40 145 0.78
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
Found at i:17829 original size:20 final size:20
Alignment explanation
Indices: 17804--17842 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17794 TGGAGCAGGA
*
17804 ATATTGATACCTTAGGAAAT
1 ATATTGATACCTTAAGAAAT
17824 ATATTGATACCTTAAGAAA
1 ATATTGATACCTTAAGAAA
17843 AGTATCGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
ATATTGATACCTTAAGAAAT
Found at i:17852 original size:20 final size:20
Alignment explanation
Indices: 17804--17853 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
17794 TGGAGCAGGA
* *
17804 ATATTGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
*
17824 ATATTGATACCTTAAGAAA-
1 ATATCGATACCTTAAGAAAT
17843 AGTATCGATAC
1 A-TATCGATAC
17854 GAGATCGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:20882 original size:83 final size:80
Alignment explanation
Indices: 20795--20983 Score: 195
Period size: 79 Copynumber: 2.3 Consensus size: 80
20785 GTGCTTGAAT
* * * * *
20795 TTTTAAAATACATAAAAAAAGGCCTTTAAATTAAAAAAAA-TAATTACACCCTGCTCTTTTTTCA
1 TTTTAAAATGCATAAAAAAAGGCCCTCAAATTAAAAAAAATTAA--AC-CCATACTC-TTTTTCA
*
20859 CTCATTTAG-GTACTTAAAC
62 CTCAATT-GTGTACTTAAAC
* * * * *
20878 TTTTAAAGTGCAT-CAAAAATGCCCTCAATTTAAAAAAAATTAAACCTATACTCTTTTTCACTCA
1 TTTTAAAATGCATAAAAAAAGGCCCTCAAATTAAAAAAAATTAAACCCATACTCTTTTTCACTCA
20942 ATTGTGTACTTAAAC
66 ATTGTGTACTTAAAC
* *
20957 TTTCAAAATGCATAAAAAAAGACCCTC
1 TTTTAAAATGCATAAAAAAAGGCCCTC
20984 TGACCATTAA
Statistics
Matches: 87, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
78 1 0.01
79 34 0.39
80 15 0.17
81 2 0.02
82 21 0.24
83 14 0.16
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (80 bp):
TTTTAAAATGCATAAAAAAAGGCCCTCAAATTAAAAAAAATTAAACCCATACTCTTTTTCACTCA
ATTGTGTACTTAAAC
Found at i:21129 original size:16 final size:16
Alignment explanation
Indices: 21108--21155 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
21098 AAATAATTTT
21108 TTTTAAAAGTAT-TAAA
1 TTTTAAAA-TATATAAA
21124 TTTTAAAATATATAAA
1 TTTTAAAATATATAAA
* *
21140 TTATAAAAAATATAAA
1 TTTTAAAATATATAAA
21156 AATCATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 3 0.10
16 26 0.90
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
TTTTAAAATATATAAA
Found at i:21151 original size:18 final size:18
Alignment explanation
Indices: 21128--21177 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
21118 ATTAAATTTT
* *
21128 AAAATATATAAATTATAA
1 AAAATATAAAAATCATAA
21146 AAAATATAAAAATCATAAA
1 AAAATATAAAAATCAT-AA
21165 AAAATTATAAAAA
1 AAAA-TATAAAAA
21178 AAAATTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 14 0.50
19 6 0.21
20 8 0.29
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATATAAAAATCATAA
Found at i:21177 original size:9 final size:9
Alignment explanation
Indices: 21128--21219 Score: 52
Period size: 9 Copynumber: 10.3 Consensus size: 9
21118 ATTAAATTTT
21128 AAAA-TATA
1 AAAATTATA
*
21136 TAAATTATA
1 AAAATTATA
*
21145 AAAAATATA
1 AAAATTATA
*
21154 AAAATCATAAA
1 AAAAT--TATA
21165 AAAATTAT-
1 AAAATTATA
21173 -AAA--A-A
1 AAAATTATA
*
21178 AAAATTGTA
1 AAAATTATA
21187 AAAATTTATAAA
1 AAAA-TTAT--A
*
21199 AAAATTAAA
1 AAAATTATA
21208 AAAATTATA
1 AAAATTATA
21217 AAA
1 AAA
21220 GGCATTTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
5 1 0.02
6 3 0.05
7 3 0.05
8 3 0.05
9 34 0.54
10 3 0.05
11 11 0.17
12 5 0.08
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (9 bp):
AAAATTATA
Found at i:21189 original size:11 final size:11
Alignment explanation
Indices: 21137--21219 Score: 72
Period size: 11 Copynumber: 8.0 Consensus size: 11
21127 TAAAATATAT
21137 AAATTAT-AAA
1 AAATTATAAAA
21147 AAA-TAT--AA
1 AAATTATAAAA
*
21155 AAATCATAAAA
1 AAATTATAAAA
21166 AAATTATAAAAAA
1 AAATTAT--AAAA
*
21179 AAATTGT-AAA
1 AAATTATAAAA
*
21189 AATTTATAAAA
1 AAATTATAAAA
21200 AAA-T-TAAAA
1 AAATTATAAAA
21209 AAATTATAAAA
1 AAATTATAAAA
21220 GGCATTTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
8 5 0.08
9 13 0.22
10 13 0.22
11 18 0.31
13 10 0.17
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (11 bp):
AAATTATAAAA
Found at i:21201 original size:20 final size:20
Alignment explanation
Indices: 21137--21219 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 20
21127 TAAAATATAT
21137 AAATTATAAAAAA-TATAAAA
1 AAATTA-AAAAAATTATAAAA
*
21157 ATCA-TAAAAAAATTATAAAAAA
1 A-AATTAAAAAAATTAT--AAAA
* *
21179 AAATTGTAAAAATTTATAAAA
1 AAATT-AAAAAAATTATAAAA
21200 AAATTAAAAAAATTATAAAA
1 AAATTAAAAAAATTATAAAA
21220 GGCATTTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
19 6 0.12
20 19 0.37
21 11 0.22
22 6 0.12
23 9 0.18
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (20 bp):
AAATTAAAAAAATTATAAAA
Found at i:21417 original size:9 final size:9
Alignment explanation
Indices: 21403--21530 Score: 57
Period size: 9 Copynumber: 13.2 Consensus size: 9
21393 TTTTGGTAGA
21403 ATAATTTTT
1 ATAATTTTT
21412 ATAATTTTT
1 ATAATTTTT
*
21421 TTACATTTTTTTT
1 ATA-A---TTTTT
21434 ATAATTTTCTT
1 ATAA-TTT-TT
* *
21445 ACGAATTTAT
1 A-TAATTTTT
*
21455 A-AAATTTT
1 ATAATTTTT
21463 ATAATTCTTT
1 ATAATT-TTT
21473 -TAGGATTTTT
1 ATA--ATTTTT
21483 ATAATTTTT
1 ATAATTTTT
*
21492 TTAAATTTTT
1 AT-AATTTTT
*
21502 AATAAATTTT
1 -ATAATTTTT
21512 A-AATTTTT
1 ATAATTTTT
21520 -TAAATTTTT
1 AT-AATTTTT
21529 AT
1 AT
21531 TAAAATTTAA
Statistics
Matches: 92, Mismatches: 11, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
8 12 0.13
9 31 0.34
10 27 0.29
11 12 0.13
12 3 0.03
13 7 0.08
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:21423 original size:11 final size:11
Alignment explanation
Indices: 21407--21441 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
21397 GGTAGAATAA
21407 TTTTTATAATT
1 TTTTTATAATT
* *
21418 TTTTTACATTT
1 TTTTTATAATT
21429 TTTTTATAATT
1 TTTTTATAATT
21440 TT
1 TT
21442 CTTACGAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:21441 original size:10 final size:10
Alignment explanation
Indices: 21403--21528 Score: 56
Period size: 10 Copynumber: 12.9 Consensus size: 10
21393 TTTTGGTAGA
21403 ATAA-TTTTT
1 ATAATTTTTT
21412 ATAATTTTTT
1 ATAATTTTTT
21422 -TACATTTTTTTT
1 ATA-A--TTTTTT
21434 ATAATTTTCTT
1 ATAATTTT-TT
*
21445 ACGAA---TTT
1 A-TAATTTTTT
**
21453 ATAAAATTTT
1 ATAATTTTTT
21463 ATAATTCTTTT
1 ATAATT-TTTT
**
21474 AGGA-TTTTT
1 ATAATTTTTT
21483 ATAATTTTTT
1 ATAATTTTTT
*
21493 -TAAATTTTTA
1 AT-AATTTTTT
*
21503 ATAA-ATTTT
1 ATAATTTTTT
21512 A-AATTTTTT
1 ATAATTTTTT
21521 A-AATTTTT
1 ATAATTTTT
21529 ATTAAAATTT
Statistics
Matches: 90, Mismatches: 12, Indels: 30
0.68 0.09 0.23
Matches are distributed among these distances:
7 2 0.02
8 5 0.06
9 30 0.33
10 32 0.36
11 10 0.11
12 9 0.10
13 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:21501 original size:20 final size:20
Alignment explanation
Indices: 21403--21534 Score: 71
Period size: 20 Copynumber: 6.7 Consensus size: 20
21393 TTTTGGTAGA
* *
21403 ATAATTTTTATAATTTTTTT
1 ATAATTTTTTTAAATTTTTT
* *
21423 ACATTTTTTTTATAATTTTCTT
1 ATAATTTTTTTA-AATTTT-TT
* * *
21445 ACGAA--TTTATAAA-ATTTT
1 A-TAATTTTTTTAAATTTTTT
* *
21463 ATAATTCTTTTAGGA-TTTTT
1 ATAATTTTTTTA-AATTTTTT
*
21483 ATAATTTTTTTAAATTTTTA
1 ATAATTTTTTTAAATTTTTT
*
21503 ATAA--ATTTTAAATTTTTT
1 ATAATTTTTTTAAATTTTTT
21521 A-AATTTTTATTAAA
1 ATAATTTTT-TTAAA
21535 ATTTAATCAT
Statistics
Matches: 83, Mismatches: 19, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
17 4 0.05
18 16 0.19
19 9 0.11
20 40 0.48
21 10 0.12
22 3 0.04
23 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (20 bp):
ATAATTTTTTTAAATTTTTT
Found at i:21507 original size:11 final size:10
Alignment explanation
Indices: 21450--21530 Score: 59
Period size: 9 Copynumber: 8.5 Consensus size: 10
21440 TTCTTACGAA
*
21450 TTTATAAAAT
1 TTTATAAATT
21460 TTTAT-AATT
1 TTTATAAATT
*
21469 CTTT-TAGGATT
1 -TTTATA-AATT
21480 TTTAT-AATT
1 TTTATAAATT
*
21489 TTTTTAAATT
1 TTTATAAATT
21499 TTTAATAAA--
1 TTT-ATAAATT
21508 TTT-TAAATT
1 TTTATAAATT
21517 TTT-TAAATT
1 TTTATAAATT
21526 TTTAT
1 TTTAT
21531 TAAAATTTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
7 4 0.07
9 26 0.46
10 19 0.33
11 8 0.14
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTATAAATT
Found at i:21518 original size:27 final size:28
Alignment explanation
Indices: 21479--21540 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
21469 CTTTTAGGAT
21479 TTTTATAATTTTTTTAAATTTTTAATAAA
1 TTTTA-AATTTTTTTAAATTTTTAATAAA
*
21508 TTTTAAA-TTTTTTAAATTTTTATTAAA
1 TTTTAAATTTTTTTAAATTTTTAATAAA
*
21535 ATTTAA
1 TTTTAA
21541 TCATTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.77
28 2 0.06
29 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAAATTTTTTTAAATTTTTAATAAA
Found at i:24394 original size:22 final size:22
Alignment explanation
Indices: 24369--24418 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
24359 CATTTATGTG
*
24369 TTTAAATTTCTATT-TTAATTAT
1 TTTAAATTT-TATTATTAATTAA
*
24391 TTTATATTTTATTATTAATTAA
1 TTTAAATTTTATTATTAATTAA
24413 TTTAAA
1 TTTAAA
24419 ATAATAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAAATTTTATTATTAATTAA
Found at i:26048 original size:3 final size:3
Alignment explanation
Indices: 26040--26071 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
26030 CATAAATCAA
26040 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
26072 AAGACAAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:29959 original size:40 final size:40
Alignment explanation
Indices: 29904--30048 Score: 240
Period size: 40 Copynumber: 3.6 Consensus size: 40
29894 ATTTGAATGA
29904 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
29944 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
* *
29984 GATCCGGGCTAAGTCCC-AAGGCATTTGTGCGAGTTGATAT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTT
*
30024 -ATCCGGGCTAAGACCCGAAGGCATT
1 GATCCGGGCTAAGTCCCGAAGGCATT
30049 CGTGTGAGTT
Statistics
Matches: 100, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
39 30 0.30
40 70 0.70
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (40 bp):
GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
Found at i:30058 original size:40 final size:40
Alignment explanation
Indices: 29904--30094 Score: 237
Period size: 40 Copynumber: 4.8 Consensus size: 40
29894 ATTTGAATGA
*
29904 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATAT
*
29944 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATAT
*
29984 GATCCGGGCTAAGTCCC-AAGGCATTTGTGCGAGTTGATAT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATAT
* * *
30024 -ATCCGGGCTAAGACCCGAAGGCATTCGTG-TGAGTTGCTAT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AG-TGATAT
* * * *
30064 G-CCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCT
30095 TGTGGTAATA
Statistics
Matches: 136, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
39 30 0.22
40 105 0.77
41 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (40 bp):
GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATAT
Found at i:30070 original size:79 final size:80
Alignment explanation
Indices: 29907--30093 Score: 229
Period size: 79 Copynumber: 2.4 Consensus size: 80
29897 TGAATGAGAT
* * * *
29907 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGATATGATCCGGGCTAAGACCCGAAGGCATTCG
* *
29972 TGCTAGTGATTTGAT
66 TGCTAGTGATATGAC
29987 CCGGGCTAAGTCCC-AAGGCATTTGTGCGAGTTGATAT-ATCCGGGCTAAGACCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGATATGATCCGGGCTAAGACCCGAAGGCATTC
*
30050 GTG-TGAGTTGCTATG-C
65 GTGCT-AG-TGATATGAC
* * *
30066 CCGGGTTAAGACCCGAAGGCAATTGTGC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC
30094 TTGTGGTAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.60
80 36 0.39
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGATATGATCCGGGCTAAGACCCGAAGGCATTCG
TGCTAGTGATATGAC
Found at i:38296 original size:40 final size:41
Alignment explanation
Indices: 38241--38431 Score: 248
Period size: 40 Copynumber: 4.8 Consensus size: 41
38231 ATTTGAATGA
*
38241 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGATAT
*
38281 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGATAT
*
38321 GATCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTGATAT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGATAT
* * * *
38361 -ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGATAT
* * * *
38401 G-CCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCT
38432 TGTGGTAATA
Statistics
Matches: 138, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
39 30 0.22
40 108 0.78
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.26
Consensus pattern (41 bp):
GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGATAT
Found at i:38365 original size:79 final size:80
Alignment explanation
Indices: 38241--38430 Score: 242
Period size: 79 Copynumber: 2.4 Consensus size: 80
38231 ATTTGAATGA
* * *
38241 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGTCCCGAAGGCAT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGATATGATCCGGGCTAAGACCCGAAGGCAT
*
38306 TTGTGCTAGTGATTT
66 TCGTGCTAGTGATTT
38321 GATCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTGATAT-ATCCGGGCTAAGACCCGAAGGCA
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGATATGATCCGGGCTAAGACCCGAAGGCA
* * *
38384 TTCGTGCGAGTTGCTAT
65 TTCGTGCTAG-TGATTT
* * * *
38401 G-CCCGGGTTAAGACCCGAAGGCAATTGTGC
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGC
38431 TTGTGGTAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
79 57 0.59
80 39 0.41
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.26
Consensus pattern (80 bp):
GATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGATATGATCCGGGCTAAGACCCGAAGGCAT
TCGTGCTAGTGATTT
Done.