Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold641
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: 37418
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:5049 original size:14 final size:15
Alignment explanation
Indices: 5011--5052 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
5001 AAGTAAAAAA
5011 AAATTTGTTT-ATTT
1 AAATTTGTTTAATTT
5025 -AATTTAGTTTAATTT
1 AAATTT-GTTTAATTT
5040 AAATTT-TTTAATT
1 AAATTTGTTTAATT
5053 ATATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.20
14 11 0.44
15 4 0.16
16 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (15 bp):
AAATTTGTTTAATTT
Found at i:5797 original size:9 final size:9
Alignment explanation
Indices: 5783--5808 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5773 TCCACTTTCA
5783 AATTTTAAG
1 AATTTTAAG
5792 AATTTTAAG
1 AATTTTAAG
5801 AATTTTAA
1 AATTTTAA
5809 TATTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (9 bp):
AATTTTAAG
Found at i:8841 original size:30 final size:30
Alignment explanation
Indices: 8807--8863 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
8797 TATGATCATT
*
8807 ATATTAAGATT-TTAATTTTTTTAATTATTA
1 ATATTAAGATTGAT-ATTTTTTTAATTATTA
* *
8837 ATATTTATATTGATATTTTTTTAATTA
1 ATATTAAGATTGATATTTTTTTAATTA
8864 ATTATAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 22 0.96
31 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (30 bp):
ATATTAAGATTGATATTTTTTTAATTATTA
Found at i:10276 original size:21 final size:21
Alignment explanation
Indices: 10250--10293 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
10240 GCTTATGTAA
10250 ATGAAAAATAAAAG-AGAGAAG
1 ATGAAAAAT-AAAGCAGAGAAG
10271 ATGAAAAATAAAGCAGAGAAG
1 ATGAAAAATAAAGCAGAGAAG
10292 AT
1 AT
10294 TTACATATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.64, C:0.02, G:0.23, T:0.11
Consensus pattern (21 bp):
ATGAAAAATAAAGCAGAGAAG
Found at i:11508 original size:17 final size:15
Alignment explanation
Indices: 11470--11555 Score: 61
Period size: 15 Copynumber: 5.7 Consensus size: 15
11460 TTCATAAATT
*
11470 TATATTATATTTTTA
1 TATATTATATATTTA
11485 TATTATTATCATATTTA
1 TA-TATTAT-ATATTTA
11502 TGATATTATAT-TTTA
1 T-ATATTATATATTTA
* *
11517 TAAAATTTTA-ATTTA
1 T-ATATTATATATTTA
* * *
11532 TTTTTTATGTATTTA
1 TATATTATATATTTA
11547 TAT-TTATAT
1 TATATTATAT
11556 TTTTTTTTTC
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
14 8 0.15
15 25 0.45
16 8 0.15
17 13 0.24
18 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (15 bp):
TATATTATATATTTA
Found at i:12012 original size:20 final size:20
Alignment explanation
Indices: 11987--12028 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
11977 AATTTTTAAA
11987 ATTTTTTAAATAAATAAA-AT
1 ATTTTTTAAA-AAATAAATAT
12007 ATTTTTTAAAAAATAAATAT
1 ATTTTTTAAAAAATAAATAT
12027 AT
1 AT
12029 ATTTATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTTTTAAAAAATAAATAT
Found at i:12033 original size:19 final size:20
Alignment explanation
Indices: 11983--12033 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
11973 ATATAATTTT
11983 TAAAAT-TT-TTTAAATAAA
1 TAAAATATTATTTAAATAAA
*
12001 TAAAATATTTTTTAAA-AAA
1 TAAAATATTATTTAAATAAA
12020 T-AAATATATATTTA
1 TAAAATAT-TATTTA
12034 TACTTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 12 0.41
19 11 0.38
20 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAATATTATTTAAATAAA
Found at i:12652 original size:21 final size:23
Alignment explanation
Indices: 12607--12657 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
12597 AATATTCTGT
12607 TATAATTTATTTAATGATATTAA
1 TATAATTTATTTAATGATATTAA
12630 TATAATTT-TTT-AT-ATATTTAA
1 TATAATTTATTTAATGATA-TTAA
*
12651 TAAAATT
1 TATAATT
12658 ATAATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 12 0.46
22 3 0.12
23 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATAATTTATTTAATGATATTAA
Found at i:13150 original size:19 final size:19
Alignment explanation
Indices: 13124--13160 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
13114 ATAAAATATT
13124 ATAATTATAAT-TTTTAAA
1 ATAATTATAATATTTTAAA
13142 ATAATTTATAATATTTTAA
1 ATAA-TTATAATATTTTAA
13161 TATTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATTATAATATTTTAAA
Found at i:13285 original size:88 final size:87
Alignment explanation
Indices: 13199--13360 Score: 231
Period size: 88 Copynumber: 1.9 Consensus size: 87
13189 AAGTAAAATT
* * *
13199 TTAATATATAT-TATACGT-TCATAACTTTAATTGTTATAAATAATTAATTATAT-ATTTCTTAA
1 TTAATATATATATATAC-TATCATAAATTTAATTATTATAAATAATTAATTATATAAATT-TTAA
13261 TTACTTATTAATAAATAATTAAAA
64 TTACTTATTAATAAATAATTAAAA
* *
13285 TTAATATATATAATTTACTATCATAAATTTTATTATTATAAATAATTAATTATATAAATTTTAAT
1 TTAATATATAT-ATATACTATCATAAATTTAATTATTATAAATAATTAATTATATAAATTTTAAT
13350 TACTTATTAAT
65 TACTTATTAAT
13361 TATATATTAC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
86 11 0.16
87 1 0.01
88 52 0.78
89 3 0.04
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (87 bp):
TTAATATATATATATACTATCATAAATTTAATTATTATAAATAATTAATTATATAAATTTTAATT
ACTTATTAATAAATAATTAAAA
Found at i:14376 original size:18 final size:18
Alignment explanation
Indices: 14335--14378 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
14325 AAAATATTAG
*
14335 ATTAAAATATGTATATAT
1 ATTAAAATATGTATAAAT
*
14353 AATAAAATAT-TATAAAAT
1 ATTAAAATATGTAT-AAAT
14371 ATTAAAAT
1 ATTAAAAT
14379 TACATTCATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATTAAAATATGTATAAAT
Found at i:14428 original size:33 final size:34
Alignment explanation
Indices: 14356--14428 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 34
14346 TATATATAAT
*
14356 AAAATATTATAAAATATTAAAATTACATTCATGTT
1 AAAA-ATTATAAAATATTAAAATTACATTCATGTC
*
14391 AAAAATTAT-AATTATTAAAATTACATT-ATTGTC
1 AAAAATTATAAAATATTAAAATTACATTCA-TGTC
14424 AAAAA
1 AAAAA
14429 ATAATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 1 0.03
33 25 0.71
34 5 0.14
35 4 0.11
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAAATTATAAAATATTAAAATTACATTCATGTC
Found at i:16220 original size:33 final size:33
Alignment explanation
Indices: 16183--16246 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
16173 ATGACCTGAA
16183 AATTCTAAGTTCCCATGAATCCAGCAAGAAAAC
1 AATTCTAAGTTCCCATGAATCCAGCAAGAAAAC
16216 AATTCTAAGTTCCCATGAATCCAGCAAGAAA
1 AATTCTAAGTTCCCATGAATCCAGCAAGAAA
16247 CTAGCAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.22
Consensus pattern (33 bp):
AATTCTAAGTTCCCATGAATCCAGCAAGAAAAC
Found at i:17645 original size:12 final size:12
Alignment explanation
Indices: 17628--17655 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17618 TGTTTTAGGG
17628 ATTTTCATTTTT
1 ATTTTCATTTTT
17640 ATTTTCATTTTT
1 ATTTTCATTTTT
17652 ATTT
1 ATTT
17656 GATATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (12 bp):
ATTTTCATTTTT
Found at i:17676 original size:13 final size:12
Alignment explanation
Indices: 17634--17675 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
17624 AGGGATTTTC
17634 ATTTTTATTT-T
1 ATTTTTATTTAT
17645 CATTTTTATTTGAT
1 -ATTTTTATTT-AT
17659 ATTTATTATTTAT
1 ATTT-TTATTTAT
17672 ATTT
1 ATTT
17676 AAAATTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.37
13 10 0.37
14 7 0.26
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (12 bp):
ATTTTTATTTAT
Found at i:19011 original size:15 final size:15
Alignment explanation
Indices: 18961--19027 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
18951 GACAATAATC
18961 ATTAT-TTTTTTTATT
1 ATTATATTTTTTT-TT
* * *
18976 AAATATATTTTTATAT
1 -ATTATATTTTTTTTT
18992 ATTATATTTTTTTTT
1 ATTATATTTTTTTTT
* *
19007 GTTATGTTTTTTTTT
1 ATTATATTTTTTTTT
*
19022 AATATA
1 ATTATA
19028 CTAGGTTTAC
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
15 28 0.72
16 5 0.13
17 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
ATTATATTTTTTTTT
Found at i:19960 original size:8 final size:8
Alignment explanation
Indices: 19947--19975 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
19937 ATAATATAAT
19947 TATTTTAA
1 TATTTTAA
19955 TATTTTAA
1 TATTTTAA
19963 TATTTTAA
1 TATTTTAA
19971 TATTT
1 TATTT
19976 ATTTTTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATTTTAA
Found at i:20140 original size:21 final size:23
Alignment explanation
Indices: 20114--20159 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
20104 GACAAACGAG
*
20114 TTGCTTACAAGA-G-ATTTTTTA
1 TTGCTTACAAAAGGTATTTTTTA
*
20135 TTGCTTATAAAAGGTATTTTTTA
1 TTGCTTACAAAAGGTATTTTTTA
20158 TT
1 TT
20160 TTACTAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 10 0.48
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (23 bp):
TTGCTTACAAAAGGTATTTTTTA
Found at i:22320 original size:19 final size:19
Alignment explanation
Indices: 22296--22332 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22286 ATTAACATAA
*
22296 AATTGATTTTTATAGATTG
1 AATTGATATTTATAGATTG
*
22315 AATTGATATTTATTGATT
1 AATTGATATTTATAGATT
22333 CATTGAAAAT
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:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (19 bp):
AATTGATATTTATAGATTG
Found at i:22791 original size:16 final size:16
Alignment explanation
Indices: 22770--22802 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22760 AAACCATATT
22770 ATTTAATTAATAAATA
1 ATTTAATTAATAAATA
*
22786 ATTTAATTATTAAATA
1 ATTTAATTAATAAATA
22802 A
1 A
22803 GTAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAATTAATAAATA
Found at i:23104 original size:20 final size:20
Alignment explanation
Indices: 23076--23116 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
23066 TTTTTTCAAT
*
23076 AATTCTTAAAATAAATATAA
1 AATTATTAAAATAAATATAA
*
23096 AATTATTAAAATCAATATAA
1 AATTATTAAAATAAATATAA
23116 A
1 A
23117 CTTCTACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTATTAAAATAAATATAA
Found at i:23371 original size:2 final size:2
Alignment explanation
Indices: 23364--23388 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23354 ATTTTAGTAT
23364 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 T
23389 GTTAATCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24095 original size:19 final size:19
Alignment explanation
Indices: 24069--24111 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
24059 ATAATATATA
*
24069 AAATTATTAT-ACTTACAT
1 AAATTATTATAAATTACAT
24087 AAATATATTATAAATTACAT
1 AAAT-TATTATAAATTACAT
24107 AAATT
1 AAATT
24112 TATATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 7 0.32
20 11 0.50
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTATTATAAATTACAT
Found at i:26706 original size:15 final size:15
Alignment explanation
Indices: 26686--26715 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26676 TGCAATTGCG
26686 GATGTAAGGAATCTT
1 GATGTAAGGAATCTT
*
26701 GATGTAATGAATCTT
1 GATGTAAGGAATCTT
26716 ATCAAGGTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (15 bp):
GATGTAAGGAATCTT
Found at i:30874 original size:7 final size:7
Alignment explanation
Indices: 30862--30891 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
30852 AAAAGAAGAG
30862 GTTTTTT
1 GTTTTTT
30869 GTTTTTT
1 GTTTTTT
30876 GTTTTTT
1 GTTTTTT
30883 -TTTTTT
1 GTTTTTT
30889 GTT
1 GTT
30892 CTTAATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
GTTTTTT
Found at i:30886 original size:13 final size:14
Alignment explanation
Indices: 30862--30891 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
30852 AAAAGAAGAG
30862 GTTTTTTGTTTTTT
1 GTTTTTTGTTTTTT
30876 GTTTTTT-TTTTTT
1 GTTTTTTGTTTTTT
30889 GTT
1 GTT
30892 CTTAATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (14 bp):
GTTTTTTGTTTTTT
Found at i:31076 original size:20 final size:20
Alignment explanation
Indices: 31047--31093 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
31037 TTTTTTTTTT
31047 GGAATATCATGTTTGGTTTC
1 GGAATATCATGTTTGGTTTC
*
31067 GGAATTTCATGTTTGGTTTC
1 GGAATATCATGTTTGGTTTC
31087 GAGAATA
1 G-GAATA
31094 AAAGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.43
Consensus pattern (20 bp):
GGAATATCATGTTTGGTTTC
Found at i:32067 original size:128 final size:126
Alignment explanation
Indices: 31837--32085 Score: 374
Period size: 128 Copynumber: 2.0 Consensus size: 126
31827 GCAAGTGAGC
31837 TGTTTCTGAAGGAAATAGAAGAGAAAGTCATGCCCTGATTTTTCAGAAAAGTTGAGCCTAGTTAA
1 TGTTTCTGAAGGAAATAGAAGAGAAAGTCATGCCCTGATTTTTCAGAAAAGTTGAGCCTAGTTAA
* *
31902 TAATCAGTGTTGAATTCGATCTTGGATTTAGAGCAAGAGTGCTGGAAAATCATTTTTCAGAAA
66 TAATCAGTGTTGAATTCGATCTTGGATTTAGAACAAGAATG-TGGAAAATC-TTTTTCAGAAA
* * * * *
31965 TGTTTCTGGAGGAAATAGAAGAGAGAA-TGATGTCCTGATTTTTCAGAAAGGTTGAGCCTAGTTG
1 TGTTTCTGAAGGAAATAGAAGAGA-AAGTCATGCCCTGATTTTTCAGAAAAGTTGAGCCTAGTTA
* * *
32029 ATGATGAGTGTTGAATTCGTTCTTGGATTTAGAACAAGAATGTGGAAAATCTTTTTC
65 ATAATCAGTGTTGAATTCGATCTTGGATTTAGAACAAGAATGTGGAAAATCTTTTTC
32086 CTTGTCTGCC
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
126 6 0.05
127 9 0.08
128 93 0.85
129 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.33
Consensus pattern (126 bp):
TGTTTCTGAAGGAAATAGAAGAGAAAGTCATGCCCTGATTTTTCAGAAAAGTTGAGCCTAGTTAA
TAATCAGTGTTGAATTCGATCTTGGATTTAGAACAAGAATGTGGAAAATCTTTTTCAGAAA
Found at i:32857 original size:2 final size:2
Alignment explanation
Indices: 32850--32880 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32840 CCATTTATTT
32850 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 T
32881 TTCTTTTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36434 original size:2 final size:2
Alignment explanation
Indices: 36427--36452 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36417 TCATGTAAGT
36427 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
36453 ATTGTGATTG
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):
TA
Found at i:36760 original size:48 final size:49
Alignment explanation
Indices: 36706--36802 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 49
36696 AAAAAACAAG
* * *
36706 TAGATATTGTTGTAACTCGTAAGTTACC-GATCTGTCTTATAATATTAA
1 TAGATATTGTTGTAACTCGTAAGTTACCAAAACTGTCTAATAATATTAA
* *
36754 TAGATATTGTTGTAACTTGTAAGTTGCCAAAACTGTCTAATAATATTAA
1 TAGATATTGTTGTAACTCGTAAGTTACCAAAACTGTCTAATAATATTAA
36803 AACTGTCTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 26 0.60
49 17 0.40
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (49 bp):
TAGATATTGTTGTAACTCGTAAGTTACCAAAACTGTCTAATAATATTAA
Found at i:37335 original size:34 final size:34
Alignment explanation
Indices: 37291--37355 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
37281 TAAAAAATAA
37291 AAAATAATTTG-AAAAACCATGCTTTGCTTCTTAT
1 AAAATAATTTGAAAAAACC-TGCTTTGCTTCTTAT
* *
37325 AAAATCATTTGAAAAAATCTGCTTTGCTTCT
1 AAAATAATTTGAAAAAACCTGCTTTGCTTCT
37356 GTTTGGGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 22 0.79
35 6 0.21
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (34 bp):
AAAATAATTTGAAAAAACCTGCTTTGCTTCTTAT
Done.