Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2427
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: 50549
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:25182 original size:87 final size:87
Alignment explanation
Indices: 24888--25278 Score: 292
Period size: 88 Copynumber: 4.5 Consensus size: 87
24878 TTATTTTAAA
** * * ** *
24888 GAAACTCCATCCCTCCTATTCT-AGGGGGTACTCCAACCTCAGTT-TAGTAAAAATTCAAAATTT
1 GAAACTCCATCCCTATTATT-TGAGGGGATACTCCAACCCCA-TTCTAACAAAAATTCAAACTTT
* * * *
24951 TCC-CATATAATTTTGTTCTTGGG
64 TCCTCACATAATTTTATCCTTAGG
* * * *
24974 GAAACTCCATCCCTATTATTTTGTGGGGATACTCCAACCTCGTTCTAACTAAAATTCAAACTCAC
1 GAAACTCCATCCCTATTA-TTTGAGGGGATACTCCAACCCCATTCTAACAAAAATTCAAACT---
**
25039 TTTTGT-AC--AATTTTATCCTTAGG
62 TTTCCTCACATAATTTTATCCTTAGG
* * *
25062 GAAACTCCATTCCTATTATTTCGAGGGGGTACTCCAACCCCATTATAACAAAAATTCAAA-TTTT
1 GAAACTCCATCCCTATTATTT-GAGGGGATACTCCAACCCCATTCTAACAAAAATTCAAACTTTT
*
25126 CCTCACATAATTTTGTCCTTAGG
65 CCTCACATAATTTTATCCTTAGG
* * * * * * * * * *
25149 GAAACTCTATCCCCACTATTCTGAGAGAATACTCTAACCGCATTCTAACAGAATTTCAAATTTTT
1 GAAACTCCATCCCTATTATT-TGAGGGGATACTCCAACCCCATTCTAACAAAAATTCAAACTTTT
* ***
25214 CTTTTTATAATTTTATCCTTAGG
65 CCTCACATAATTTTATCCTTAGG
** * * *
25237 GAAACTCCATTTCTATTATTCTAAGAGGATATTCCAACCCCA
1 GAAACTCCATCCCTATTATT-TGAGGGGATACTCCAACCCCA
25279 CCTCTCTAAC
Statistics
Matches: 240, Mismatches: 52, Indels: 24
0.76 0.16 0.08
Matches are distributed among these distances:
84 4 0.02
85 2 0.01
86 19 0.08
87 95 0.40
88 116 0.48
90 4 0.02
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (87 bp):
GAAACTCCATCCCTATTATTTGAGGGGATACTCCAACCCCATTCTAACAAAAATTCAAACTTTTC
CTCACATAATTTTATCCTTAGG
Found at i:25197 original size:175 final size:175
Alignment explanation
Indices: 24888--25256 Score: 433
Period size: 175 Copynumber: 2.1 Consensus size: 175
24878 TTATTTTAAA
* ** * * **
24888 GAAACTCCATCCCTCCTA-TTCTAGGGGGTACTCCAACCTCAGTTTAGTAAAAATTCAAAATTTT
1 GAAACTCCATTCCTATTATTTCGAGGGGGTACTCCAACCCCAGTTTAACAAAAATTCAAAATTTT
* * * * * * * * * * *
24952 CCCATATAATTTTGTTCTTGGGGAAACTCCATCCCTATTATTTTGTGGGGATACTCCAACCTCGT
66 CCCACATAATTTTGTCCTTAGGGAAACTCCATCCCCACTATTCTGAGAGAATACTCCAACCGCAT
25017 TCTAACTA-AAATTCAAA-CTCACTTTTGTACAATTTTATCCTTAGG
131 TCTAAC-AGAAATTCAAATCTCACTTTT-TACAATTTTATCCTTAGG
25062 GAAACTCCATTCCTATTATTTCGAGGGGGTACTCCAACCCCA-TTATAACAAAAATTC-AAATTT
1 GAAACTCCATTCCTATTATTTCGAGGGGGTACTCCAACCCCAGTT-TAACAAAAATTCAAAATTT
* *
25125 TCCTCACATAATTTTGTCCTTAGGGAAACTCTATCCCCACTATTCTGAGAGAATACTCTAACCGC
65 TCC-CACATAATTTTGTCCTTAGGGAAACTCCATCCCCACTATTCTGAGAGAATACTCCAACCGC
* * ** *
25190 ATTCTAACAGAATTTCAAATTTTTCTTTTTATAATTTTATCCTTAGG
129 ATTCTAACAGAAATTCAAATCTCACTTTTTACAATTTTATCCTTAGG
*
25237 GAAACTCCATTTCTATTATT
1 GAAACTCCATTCCTATTATT
25257 CTAAGAGGAT
Statistics
Matches: 164, Mismatches: 26, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
174 27 0.16
175 131 0.80
176 6 0.04
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (175 bp):
GAAACTCCATTCCTATTATTTCGAGGGGGTACTCCAACCCCAGTTTAACAAAAATTCAAAATTTT
CCCACATAATTTTGTCCTTAGGGAAACTCCATCCCCACTATTCTGAGAGAATACTCCAACCGCAT
TCTAACAGAAATTCAAATCTCACTTTTTACAATTTTATCCTTAGG
Found at i:25571 original size:45 final size:45
Alignment explanation
Indices: 25507--25597 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
25497 TGTTTGTGAT
*
25507 TGTTTGCTTGCAATAGTTTGTATTCCTTTTCATCTTACTAGCACA
1 TGTTTGCTTGCAATAGTTTGTATTCCTTTTCATCTTACTAACACA
25552 TGTTTGCTTGCAATAGTTTGTATTCCTTTTCATCTTACTAACACA
1 TGTTTGCTTGCAATAGTTTGTATTCCTTTTCATCTTACTAACACA
25597 T
1 T
25598 TTCATTCTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.47
Consensus pattern (45 bp):
TGTTTGCTTGCAATAGTTTGTATTCCTTTTCATCTTACTAACACA
Found at i:31447 original size:13 final size:13
Alignment explanation
Indices: 31429--31453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31419 CATTGTAATT
31429 TGTATCGATACAA
1 TGTATCGATACAA
31442 TGTATCGATACA
1 TGTATCGATACA
31454 TTGCAACTTG
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:31452 original size:33 final size:33
Alignment explanation
Indices: 31407--31473 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
31397 ACTTTCACAT
* * * *
31407 AATGTATGGATACATTGTAATTTGTATCGATAC
1 AATGTATCGATACATTGCAACTTGTAACGATAC
31440 AATGTATCGATACATTGCAACTTGTAACGATAC
1 AATGTATCGATACATTGCAACTTGTAACGATAC
31473 A
1 A
31474 TCATGAAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (33 bp):
AATGTATCGATACATTGCAACTTGTAACGATAC
Found at i:32150 original size:32 final size:33
Alignment explanation
Indices: 32104--32166 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
32094 AGCCAAACTT
* **
32104 GTATTGATACACAAAGTA-TGTATCGATACAAA
1 GTATCGATACACAAAAAATTGTATCGATACAAA
32136 GTATCGATACACAAAAAATTGTATCGATACA
1 GTATCGATACACAAAAAATTGTATCGATACA
32167 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.27
Consensus pattern (33 bp):
GTATCGATACACAAAAAATTGTATCGATACAAA
Found at i:33167 original size:55 final size:52
Alignment explanation
Indices: 33043--33185 Score: 160
Period size: 55 Copynumber: 2.7 Consensus size: 52
33033 GGGACCTTCA
* * * *
33043 TCATCTTTAAAACCCAATGTTGTTGGCCTTGAATCAGCACATTGGCATTTTTC
1 TCATCTTT-AAACCTAATGTCGTTGGCCGTGAATCAGCACATTGACATTTTTC
* ** * *
33096 TCATCTTCAAGTCTAATGTCGCTGACCGTGAATCAGCACATTGACATCCTTTTTC
1 TCATCTTTAAACCTAATGTCGTTGGCCGTGAATCAGCACATTGACA---TTTTTC
*
33151 TCATCTTTAAACCTAATATCGTTGGCCGTGAATCA
1 TCATCTTTAAACCTAATGTCGTTGGCCGTGAATCA
33186 ACGTATTGGT
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
52 30 0.42
53 7 0.10
55 35 0.49
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (52 bp):
TCATCTTTAAACCTAATGTCGTTGGCCGTGAATCAGCACATTGACATTTTTC
Found at i:33867 original size:13 final size:13
Alignment explanation
Indices: 33849--33873 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33839 CATAAAGTGT
33849 TGTATCGATACAA
1 TGTATCGATACAA
33862 TGTATCGATACA
1 TGTATCGATACA
33874 TAAGTTTTGT
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:33889 original size:32 final size:33
Alignment explanation
Indices: 33829--33894 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
33819 TTCAACGATT
33829 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
33862 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
33894 T
1 T
33895 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:34929 original size:20 final size:20
Alignment explanation
Indices: 34884--34930 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
34874 GTTAACAACC
*
34884 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
34904 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
34925 CATGTT
1 CATGTT
34931 CAGCACCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:43756 original size:78 final size:79
Alignment explanation
Indices: 43661--43840 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 79
43651 TGGAGATAAC
* * * *
43661 AACGGGGCTGGAGTATCCCCAATTGTGAGAAATCAAT-ATTTGGAAATAAAGTC-GGAGTTGGAG
1 AACGGGGTTGGAGTATCCCCAATTGTGAAAAATCAATGATTAGGAAATAAAATCGGGA-TTGGAG
*
43724 TATCCCCTTGAAAAT
65 TATCCCCTCGAAAAT
** *
43739 AACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGATTAGGAAATAAAATCGGGATTGGAGT
1 AACGGGGTTGGAGTATCCCCAATTGTGAAAAATCAATGATTAGGAAATAAAATCGGGATTGGAGT
* * **
43804 ATCTCCTCGGAGGT
66 ATCCCCTCGAAAAT
*
43818 AACGGGGTTGAAGTATCCCCAAT
1 AACGGGGTTGGAGTATCCCCAAT
43841 GAAATAACGA
Statistics
Matches: 85, Mismatches: 15, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
78 32 0.38
79 50 0.59
80 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (79 bp):
AACGGGGTTGGAGTATCCCCAATTGTGAAAAATCAATGATTAGGAAATAAAATCGGGATTGGAGT
ATCCCCTCGAAAAT
Found at i:44003 original size:51 final size:49
Alignment explanation
Indices: 43851--44245 Score: 207
Period size: 52 Copynumber: 7.6 Consensus size: 49
43841 GAAATAACGA
* ** *
43851 GGTTGAAGTATCCTTGATTGTGAAAAATTGATGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTG-TG-TTTT-GAAATAAAACCGG
* **
43903 AGTTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTTGAAGATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATT-GTGTTTTGAA-ATAAAACCGG
* *
43955 GGTTGGAGCATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATT-GTGTTTT-GAAATAAAACCGG
* * * ** * * *
44006 GGTTGGAGTATCCTCGATTATGAGAAATCAATATTTTGGAAATAAAGCTGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAT-TGTGTTTT-GAAATAAAACCGG
* ** *** * * **** ** *
44057 GGTGGGAGTATCCCCTCGAAGGT-AATGGGGTTGGAGTATCCCGATGAAATAATGA
1 GGTTGGAGTAT-CCC-CGATTGTGAA--AAATT-GTGTTTTGAAAT-AAA-ACCGG
* *
44112 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATT-GTG-TTTT-GAAATAAAACCGG
* *** *
44164 AGTTGGAGTATCCCCGATTAAAAGAAAATTGGTGTTTTGAAAATAAAACCAG
1 GGTTGGAGTATCCCCGATTGTGA-AAAATT-GTGTTTTG-AAATAAAACCGG
* *
44216 GGTTGGAGTATCCCCGATTATGAACAATTG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTG
44246 AGAAACTTAA
Statistics
Matches: 252, Mismatches: 74, Indels: 36
0.70 0.20 0.10
Matches are distributed among these distances:
50 1 0.00
51 82 0.33
52 109 0.43
53 35 0.14
54 13 0.05
55 12 0.05
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (49 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGTGTTTTGAAATAAAACCGG
Found at i:44212 original size:261 final size:262
Alignment explanation
Indices: 43741--44234 Score: 737
Period size: 261 Copynumber: 1.9 Consensus size: 262
43731 TTGAAAATAA
* * * *
43741 CGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGATTAGGAAATAAAATCGGGATTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATGATTAGGAAATAAAATCGGGATGGGAGTAT
* * *
43806 CTCCTCGGAGGTAACGGGGTTGAAGTATCCCCAATGAAATAACGAGGTTGAAGTATCCTTGATTG
66 CCCCTCGAAGGTAACGGGGTTGAAGTATCCCCAATGAAATAACGAGGTTGAAGTATCCTCGATTG
43871 TGAAAAATTGATGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAATTGGT
131 TGAAAAATTGATGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAATTGGT
* *
43936 GTTTTGAAGATAAAACCGGGGTTGGAGCATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAA
196 GTTTTGAAAATAAAACCAGGGTTGGAGCATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAA
44001 AC
261 AC
* * * * *
44003 CGGGGTTGGAGTATCCTCGATTATGAGAAATCAAT-ATTTTGGAAAT-AAAGCTGGGGTGGGAGT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATGA-TTAGGAAATAAAATC-GGGATGGGAGT
* * * * *
44066 ATCCCCTCGAAGGTAATGGGGTTGGAGTAT-CCCGATGAAATAATGAGGTTGGAGTATCCTCGAT
64 ATCCCCTCGAAGGTAACGGGGTTGAAGTATCCCCAATGAAATAACGAGGTTGAAGTATCCTCGAT
44130 TGTGAAAAATT-AGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-AGAAAAT
129 TGTGAAAAATTGA-TGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGA-AAAAT
*
44193 TGGTGTTTTGAAAATAAAACCAGGGTTGGAGTATCCCCGATT
192 TGGTGTTTTGAAAATAAAACCAGGGTTGGAGCATCCCCGATT
44235 ATGAACAATT
Statistics
Matches: 208, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
260 2 0.01
261 133 0.64
262 73 0.35
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (262 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATGATTAGGAAATAAAATCGGGATGGGAGTAT
CCCCTCGAAGGTAACGGGGTTGAAGTATCCCCAATGAAATAACGAGGTTGAAGTATCCTCGATTG
TGAAAAATTGATGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAATTGGT
GTTTTGAAAATAAAACCAGGGTTGGAGCATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAA
AC
Found at i:46627 original size:13 final size:13
Alignment explanation
Indices: 46609--46634 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46599 ACAAAGATCG
46609 ATGTATCGATACA
1 ATGTATCGATACA
46622 ATGTATCGATACA
1 ATGTATCGATACA
46635 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:46645 original size:21 final size:21
Alignment explanation
Indices: 46621--46663 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
46611 GTATCGATAC
*
46621 AATGTATCGATACATTTCCTT
1 AATGTATCAATACATTTCCTT
*
46642 AATGTATCAATACATTTTCTT
1 AATGTATCAATACATTTCCTT
46663 A
1 A
46664 GCAGTAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (21 bp):
AATGTATCAATACATTTCCTT
Found at i:46697 original size:13 final size:13
Alignment explanation
Indices: 46679--46730 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
46669 AGCTTCATAG
46679 CGATACATTGTAT
1 CGATACATTGTAT
46692 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
46711 CGATACATTGTAT
1 CGATACATTGTAT
46724 CGATACA
1 CGATACA
46731 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:46711 original size:19 final size:18
Alignment explanation
Indices: 46687--46749 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
46677 AGCGATACAT
46687 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
46706 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
46719 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
46738 TGTATCGATACA
1 TGTATCGATACA
46750 TTTTCTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:46720 original size:32 final size:32
Alignment explanation
Indices: 46679--46751 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
46669 AGCTTCATAG
46679 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
46711 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
46743 CGATACATT
1 CGATACATT
46752 TTCTGTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:46778 original size:19 final size:19
Alignment explanation
Indices: 46718--46779 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
46708 TATCGATACA
46718 TTGTATCGATACAACACT-T
1 TTGTATCGATACAA-ACTGT
* **
46737 ATGTATCGATACATTTTCTGT
1 TTGTATCGATACA--AACTGT
46758 TTGTATCGATACAAACTGT
1 TTGTATCGATACAAACTGT
46777 TTG
1 TTG
46780 AAGTTCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACAAACTGT
Found at i:47542 original size:25 final size:26
Alignment explanation
Indices: 47507--47555 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
47497 CTACTATAGT
* *
47507 TATTTCATTCTATTTCAATTCTATTC
1 TATTTCATTCTATTACAACTCTATTC
47533 TATTT-ATTCTATTACAACTCTAT
1 TATTTCATTCTATTACAACTCTAT
47556 CCATCTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTTCATTCTATTACAACTCTATTC
Done.