Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold749
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: 46862
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2139 original size:4 final size:4
Alignment explanation
Indices: 2132--2166 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2122 AAACTATATA
*
2132 TATG TATG TATG TATG TATG TATT TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
2167 CTTTTCATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.00, G:0.20, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:4103 original size:20 final size:20
Alignment explanation
Indices: 4078--4126 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
4068 AAATAGAGGC
4078 TCCCTCTTCCCTCTCAAGCA
1 TCCCTCTTCCCTCTCAAGCA
* ** *
4098 TCCCTCATCCCTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGCA
4118 TCCCTCTTC
1 TCCCTCTTC
4127 AATTCTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.49, G:0.04, T:0.37
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGCA
Found at i:7647 original size:82 final size:79
Alignment explanation
Indices: 7547--7736 Score: 213
Period size: 79 Copynumber: 2.4 Consensus size: 79
7537 GTGTTCCTTT
* * * * *
7547 GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TCAGAAGAAAAAAAAATCG
1 GAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTCAG--G-AAAAAAAACCG
7611 -GGATTGGAGTATCCCCTC
62 AGG-TTGGAGTATCCCCTC
* ** * * *
7629 GAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGAGGT
1 GAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTCAGGAAAAAAAACCGAGGT
7694 TGGAGTATCCCCTC
66 TGGAGTATCCCCTC
*
7708 GAAAGTAACGGGGTTGGAGTATCCCCGAT
1 GAAAATAACGGGGTTGGAGTATCCCCGAT
7737 GAAATAACGA
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
79 49 0.53
80 3 0.03
81 1 0.01
82 40 0.43
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (79 bp):
GAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTCAGGAAAAAAAACCGAGGT
TGGAGTATCCCCTC
Found at i:7723 original size:28 final size:27
Alignment explanation
Indices: 7688--7759 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
7678 GGAATAAAGC
7688 CGAGGTTGGAGTATCCCC-TCGAAAGTAA
1 CGAGGTTGGAGTATCCCCAT-GAAA-TAA
*
7716 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGAGGTTGGAGTATCCCC-ATGAAATAA
7744 CGAGGTTGGAGTATCC
1 CGAGGTTGGAGTATCC
7760 TCGATTGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 35 0.88
29 4 0.10
30 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (27 bp):
CGAGGTTGGAGTATCCCCATGAAATAA
Found at i:7817 original size:52 final size:51
Alignment explanation
Indices: 7748--8084 Score: 229
Period size: 52 Copynumber: 6.4 Consensus size: 51
7738 AAATAACGAG
* * *
7748 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAATCGGA
*** * * *
7800 GTTGGAGTATCCCCGATTAAAAGAAAATTAGCGTTTTGAAAATAAAACCTGG-
1 GTTGGAGTATCCCCGATTGTGA-AAAATTAGTGTTTTGGAAATAAAATC-GGA
* * *
7852 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAA-CTGGG
1 GTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAATC-GGA
* * **** * * *
7904 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGGAGTATCCCCGATGAT-TAAT-GGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TT--AGTGTTTTGGA-AATAAAATCGGA
*
7959 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTAGTG--TTTTGGAAATAAAATCGGA
* * * *
8013 GTTGGAGTATCCCCGATTATAAAAAATTAGTGTTTTGAAAATAAAATAGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGA
*
8064 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
8085 GAGAATTGAG
Statistics
Matches: 220, Mismatches: 43, Indels: 45
0.71 0.14 0.15
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 2 0.01
51 41 0.19
52 86 0.39
53 26 0.12
54 25 0.11
55 17 0.08
56 7 0.03
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGA
Found at i:7931 original size:212 final size:212
Alignment explanation
Indices: 7691--8086 Score: 640
Period size: 212 Copynumber: 1.9 Consensus size: 212
7681 ATAAAGCCGA
7691 GGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
1 GGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATG-AATAACGAGGTTGGAGT
*
7756 ATCCTCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
65 ATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
*
7819 AAAGAAAATTAGCGTTTTGAAAATAAAACCT-GG-GTTGGAGTATCCCCGATTGTGGAAAAATTA
130 AAA-AAAATTAGCGTTTTGAAAATAAAA--TAGGAGTTGGAATATCCCCGATTGTGGAAAAATTA
7882 GTGTTTTAGCAATAAAACTGG
192 GTGTTTTAGCAATAAAACTGG
* * *
7903 GGTTGGAGTATCCCCTCGGAAA-TAACGGGGTTGGAGTATCCCCGATGATTAATGGGGTTGGAGT
1 GGTTGGAGTATCCCCTC-GAAAGTAACGGGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAGT
*
7967 ATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
65 ATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
* *
8032 TAAAAAATTAGTGTTTTGAAAATAAAATAGGAGTTGGAATATCCCCGATTGTGGA
130 AAAAAAATTAGCGTTTTGAAAATAAAATAGGAGTTGGAATATCCCCGATTGTGGA
8087 GAATTGAGAA
Statistics
Matches: 171, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
210 1 0.01
211 30 0.18
212 95 0.56
213 45 0.26
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (212 bp):
GGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAGTA
TCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
AAAAAATTAGCGTTTTGAAAATAAAATAGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGT
TTTAGCAATAAAACTGG
Found at i:7967 original size:27 final size:28
Alignment explanation
Indices: 7900--7975 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
7890 GCAATAAAAC
***
7900 TGGGGTTGGAGTATCCCCTCGGAAATAA
1 TGGGGTTGGAGTATCCCCGATGAAATAA
* *
7928 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 TGGGGTTGGAGTATCCCCGATGAAATAA
7955 TGGGGTTGGAGTATCCCCGAT
1 TGGGGTTGGAGTATCCCCGAT
7976 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.26
Consensus pattern (28 bp):
TGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:10464 original size:33 final size:33
Alignment explanation
Indices: 10422--10486 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
10412 AAAATTTTCA
***
10422 AATGTATCGATACAAAGATCCATGTATCGATAT
1 AATGTATCGATACAAAGAAAAATGTATCGATAT
*
10455 AATGTATCGATACACAGAAAAATGTATCGATA
1 AATGTATCGATACAAAGAAAAATGTATCGATA
10487 CATTTCCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAT
Found at i:10649 original size:76 final size:76
Alignment explanation
Indices: 10538--10686 Score: 298
Period size: 76 Copynumber: 2.0 Consensus size: 76
10528 TATGTATCGA
10538 TACAAATTGTTGAATTTCAAAATTTTTGACCGTTGGGACCCTGTATCGATACATTTGTAGAATGT
1 TACAAATTGTTGAATTTCAAAATTTTTGACCGTTGGGACCCTGTATCGATACATTTGTAGAATGT
10603 ATCGATACATT
66 ATCGATACATT
10614 TACAAATTGTTGAATTTCAAAATTTTTGACCGTTGGGACCCTGTATCGATACATTTGTAGAATGT
1 TACAAATTGTTGAATTTCAAAATTTTTGACCGTTGGGACCCTGTATCGATACATTTGTAGAATGT
10679 ATCGATAC
66 ATCGATAC
10687 TTTCCACAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (76 bp):
TACAAATTGTTGAATTTCAAAATTTTTGACCGTTGGGACCCTGTATCGATACATTTGTAGAATGT
ATCGATACATT
Found at i:10681 original size:21 final size:22
Alignment explanation
Indices: 10655--10753 Score: 125
Period size: 21 Copynumber: 4.7 Consensus size: 22
10645 GTTGGGACCC
** *
10655 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTCCACAAA
10676 TGTATCGATAC-TTTCCACAAA
1 TGTATCGATACATTTCCACAAA
10697 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTCCACAAA
*
10718 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTCCACAAA
*
10739 TGTATCGATATATTT
1 TGTATCGATACATTT
10754 GGATAATTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
20 4 0.06
21 64 0.91
22 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATTTCCACAAA
Found at i:10966 original size:21 final size:22
Alignment explanation
Indices: 10937--10982 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
10927 TGTTCAGACA
** *
10937 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
10959 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
10980 AGT
1 AGT
10983 TTCAACAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:12923 original size:28 final size:28
Alignment explanation
Indices: 12864--12933 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
12854 CCACCCATTT
*
12864 ATTTGTCAAAAATGATGGTTATTTTGTG
1 ATTTGTCAAAAATGGTGGTTATTTTGTG
12892 -TTTGTCAAAAATGGTGGTT-TCCTTTG-G
1 ATTTGTCAAAAATGGTGGTTAT--TTTGTG
*
12919 ATTTGTCAAATATGG
1 ATTTGTCAAAAATGG
12934 AGGCTTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
26 1 0.03
27 19 0.51
28 17 0.46
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGGTTATTTTGTG
Found at i:13035 original size:20 final size:20
Alignment explanation
Indices: 13010--13058 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
13000 AAATAGAGGC
13010 TCCCTCTTCCCTCTCAAGCA
1 TCCCTCTTCCCTCTCAAGCA
* ** *
13030 TCCCTCATCCCTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGCA
13050 TCCCTCTTC
1 TCCCTCTTC
13059 AATTCTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.49, G:0.04, T:0.37
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGCA
Found at i:13569 original size:11 final size:12
Alignment explanation
Indices: 13549--13577 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
13539 ATCTATTTAA
13549 ATATTTAATTAT
1 ATATTTAATTAT
13561 -TATTTAATTAT
1 ATATTTAATTAT
13572 ATATTT
1 ATATTT
13578 TTTAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTTAATTAT
Found at i:14052 original size:23 final size:23
Alignment explanation
Indices: 14006--14063 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
13996 TAAAGGCATG
*
14006 AATA-TTTGTTTTTAATTTTAAA
1 AATATTTTATTTTTAATTTTAAA
14028 AATATTTTATTTTGTAATTTTAAA
1 AATATTTTATTTT-TAATTTTAAA
14052 AAT-TTTTATTTT
1 AATATTTTATTTT
14064 AAATATTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 4 0.12
23 16 0.48
24 13 0.39
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (23 bp):
AATATTTTATTTTTAATTTTAAA
Found at i:14075 original size:24 final size:24
Alignment explanation
Indices: 14019--14076 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
14009 ATTTGTTTTT
*
14019 AATTTTAAAAATATTTTATTTTGT
1 AATTTTAAAAATATTTTATTTTGA
14043 AATTTTAAAAAT-TTTTATTTT-A
1 AATTTTAAAAATATTTTATTTTGA
*
14065 AATATTATAAAA
1 AATTTTA-AAAA
14077 CAAACTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 6 0.19
23 13 0.42
24 12 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
AATTTTAAAAATATTTTATTTTGA
Found at i:14331 original size:16 final size:17
Alignment explanation
Indices: 14312--14351 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
14302 TATACTTTAT
14312 ATATATTTAATAAT-AA
1 ATATATTTAATAATAAA
* *
14328 ATATTTTTAGTAATAAA
1 ATATATTTAATAATAAA
14345 ATATATT
1 ATATATT
14352 ACTATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATATTTAATAATAAA
Found at i:15201 original size:2 final size:2
Alignment explanation
Indices: 15194--15218 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15184 AAAATCAAAT
15194 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
15219 CTATTTTTGT
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:16045 original size:2 final size:2
Alignment explanation
Indices: 16038--16067 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
16028 GTTATCGGTC
*
16038 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16068 GCATCATAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21636 original size:37 final size:37
Alignment explanation
Indices: 21595--21670 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
21585 ATGATGAAAG
21595 AAAGCCATTTCTCATTTTTATCACCGCCTTGTGAACT
1 AAAGCCATTTCTCATTTTTATCACCGCCTTGTGAACT
21632 AAAGCCATTTCTCATTTTTATCACCGCCTTGTGAACT
1 AAAGCCATTTCTCATTTTTATCACCGCCTTGTGAACT
21669 AA
1 AA
21671 GAAACTATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (37 bp):
AAAGCCATTTCTCATTTTTATCACCGCCTTGTGAACT
Found at i:28964 original size:22 final size:22
Alignment explanation
Indices: 28931--28997 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
28921 TAATCATAAA
28931 TAAATAAAATAAATATAAAATAT
1 TAAA-AAAATAAATATAAAATAT
28954 TAAAAAAATAAATATAAAA-AT
1 TAAAAAAATAAATATAAAATAT
* *
28975 TATAAGAA-AAATATATAAATAT
1 TAAAAAAATAAATATA-AAATAT
28997 T
1 T
28998 TTAGACATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.17
21 11 0.28
22 18 0.45
23 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (22 bp):
TAAAAAAATAAATATAAAATAT
Found at i:28991 original size:13 final size:12
Alignment explanation
Indices: 28947--28993 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
28937 AAATAAATAT
28947 AAAATAT-TAAA
1 AAAATATATAAA
* *
28958 AAAATAAATATA
1 AAAATATATAAA
28970 AAAAT-TATAAGA
1 AAAATATATAA-A
28982 AAAATATATAAA
1 AAAATATATAAA
28994 TATTTTAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 9 0.31
12 15 0.52
13 5 0.17
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
AAAATATATAAA
Found at i:29635 original size:20 final size:20
Alignment explanation
Indices: 29604--29678 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
29594 TCATACCCTG
*
29604 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
29624 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
29644 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
29664 ATGTATCGATACATT
1 ATGTATCGATACATT
29679 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:29671 original size:40 final size:39
Alignment explanation
Indices: 29604--29681 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
29594 TCATACCCTG
* *
29604 ATGTATCAATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCAATACATTCTACAATATATCGATACAT-TATGA
* * *
29644 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCAATACATTCTACAATATATCGATACATTATG
29682 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (39 bp):
ATGTATCAATACATTCTACAATATATCGATACATTATGA
Found at i:30590 original size:24 final size:24
Alignment explanation
Indices: 30558--30614 Score: 91
Period size: 22 Copynumber: 2.5 Consensus size: 24
30548 AGCCTTTGAC
*
30558 CATGCATTTTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGCTT
30582 CATGCA--TTTTTTTATTATGCTT
1 CATGCATTTTTTTTTATTATGCTT
30604 CATGCATTTTT
1 CATGCATTTTT
30615 AACATGTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 21 0.70
24 9 0.30
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (24 bp):
CATGCATTTTTTTTTATTATGCTT
Found at i:38193 original size:55 final size:55
Alignment explanation
Indices: 38116--38390 Score: 432
Period size: 55 Copynumber: 5.0 Consensus size: 55
38106 TGGCATTTCT
* *
38116 TTTTGAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCTGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCC
*
38172 TTTTAAA-TCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACTC
1 TTTTAAAGTCCACAACTCCGTGGCAC-CTTTTAAAGTCCACAACTCCGTGGCACCC
*
38227 TTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACTC
1 TTTTAAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCC
38282 TTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCC
*
38337 -TTCAAAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACC
1 TTTTAAAGTCCACAACTCCGTGGCAC-CTTTTAAAGTCCACAACTCCGTGGCACC
38391 ATTCCAAAGC
Statistics
Matches: 209, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
53 1 0.00
54 29 0.14
55 150 0.72
56 28 0.13
57 1 0.00
ACGTcount: A:0.24, C:0.34, G:0.15, T:0.27
Consensus pattern (55 bp):
TTTTAAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACAACTCCGTGGCACCC
Found at i:38217 original size:83 final size:82
Alignment explanation
Indices: 38116--38390 Score: 464
Period size: 83 Copynumber: 3.3 Consensus size: 82
38106 TGGCATTTCT
* *
38116 TTTTGAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAATC
1 TTTTAAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAATC
38181 CACAACTCCGTGGCACTC
65 CACAACTCCGTGGCACTC
*
38199 TTTTAAAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 TTTTAAAGTCCACAACTCCGTGGCAC-CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAATC
38264 CACAACTCCGTGGCACTC
65 CACAACTCCGTGGCACTC
*
38282 TTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCC-TTCAAAGT
1 TTTTAAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA-T
38345 CCACAACTCCGTGGCACTC
64 CCACAACTCCGTGGCACTC
38364 TTTTAAAGTCCACAACTCCGTGGCACC
1 TTTTAAAGTCCACAACTCCGTGGCACC
38391 ATTCCAAAGC
Statistics
Matches: 184, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
81 6 0.03
82 69 0.38
83 108 0.59
84 1 0.01
ACGTcount: A:0.24, C:0.34, G:0.15, T:0.27
Consensus pattern (82 bp):
TTTTAAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAATCC
ACAACTCCGTGGCACTC
Found at i:38405 original size:28 final size:27
Alignment explanation
Indices: 38116--38390 Score: 421
Period size: 28 Copynumber: 10.0 Consensus size: 27
38106 TGGCATTTCT
*
38116 TTTTGAAGTCCACAACTCCGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCA-CC
*
38144 TTTTAAAGTCCACAACTCTGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCA-CC
38172 TTTTAAA-TCCACAACTCCGTGGCACTC
1 TTTTAAAGTCCACAACTCCGTGGCAC-C
38199 TTTTAAAGTCCACAACTCCGTGGCACTC
1 TTTTAAAGTCCACAACTCCGTGGCAC-C
38227 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCA-CC
38255 TTTT-AAGTCCACAACTCCGTGGCACTC
1 TTTTAAAGTCCACAACTCCGTGGCAC-C
38282 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCA-CC
38310 TTTT-AAGTCCACAACTCCGTGGCACC
1 TTTTAAAGTCCACAACTCCGTGGCACC
* *
38336 CTTCAAAGTCCACAACTCCGTGGCACTC
1 TTTTAAAGTCCACAACTCCGTGGCAC-C
38364 TTTTAAAGTCCACAACTCCGTGGCACC
1 TTTTAAAGTCCACAACTCCGTGGCACC
38391 ATTCCAAAGC
Statistics
Matches: 231, Mismatches: 8, Indels: 17
0.90 0.03 0.07
Matches are distributed among these distances:
26 6 0.03
27 91 0.39
28 132 0.57
29 2 0.01
ACGTcount: A:0.24, C:0.34, G:0.15, T:0.27
Consensus pattern (27 bp):
TTTTAAAGTCCACAACTCCGTGGCACC
Found at i:38430 original size:32 final size:32
Alignment explanation
Indices: 38389--38646 Score: 408
Period size: 32 Copynumber: 8.1 Consensus size: 32
38379 CTCCGTGGCA
*
38389 CCATTCCAAAGCTCACACAAGTCGGTGGCAAC
1 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
38421 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
1 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
*
38453 CCATTCCAAAGCCTACACAAGTCGGTGGCAAC
1 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
38485 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
1 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
*
38517 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
* *
38549 CCATTTCAAAACCCACACAAGTCGGTGGCAAC
1 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
* *
38581 CCATTTCAAAGCCCACACAAATCGGTGGCAAC
1 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
** ** *
38613 CCATTTAAAAGCCCATGCAAGTCAGTGGCAAC
1 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
38645 CC
1 CC
38647 TTTTCAAATC
Statistics
Matches: 214, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 214 1.00
ACGTcount: A:0.32, C:0.35, G:0.18, T:0.15
Consensus pattern (32 bp):
CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
Found at i:39210 original size:20 final size:20
Alignment explanation
Indices: 39182--39256 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
39172 TCATACCCTG
*
39182 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
* * * *
39202 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
39222 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
39242 ATGTATCGATACATT
1 ATGTATCGATACATT
39257 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:39249 original size:40 final size:39
Alignment explanation
Indices: 39182--39259 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
39172 TCATACCCTG
* **
39182 ATGTATCGATACATTTTTTAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
39222 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
39260 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:40168 original size:24 final size:24
Alignment explanation
Indices: 40136--40192 Score: 91
Period size: 22 Copynumber: 2.5 Consensus size: 24
40126 AGCCTTTGAC
*
40136 CATGCATTTTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGCTT
40160 CATGCA--TTTTTTTATTATGCTT
1 CATGCATTTTTTTTTATTATGCTT
40182 CATGCATTTTT
1 CATGCATTTTT
40193 AACATGCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 21 0.70
24 9 0.30
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (24 bp):
CATGCATTTTTTTTTATTATGCTT
Found at i:42608 original size:21 final size:21
Alignment explanation
Indices: 42584--42628 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
42574 GGTAATCAAT
42584 TGTTCTCTACTGGCTGATTTG
1 TGTTCTCTACTGGCTGATTTG
42605 TGTTCTCTACTGGCTGATTTG
1 TGTTCTCTACTGGCTGATTTG
42626 TGT
1 TGT
42629 CGGCATAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.24, T:0.49
Consensus pattern (21 bp):
TGTTCTCTACTGGCTGATTTG
Found at i:44461 original size:17 final size:18
Alignment explanation
Indices: 44439--44477 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
44429 ATATACTGAA
44439 TTGTTCAT-TTGCTGGAC
1 TTGTTCATGTTGCTGGAC
*
44456 TTGTTCATGTTGCTTGAC
1 TTGTTCATGTTGCTGGAC
44474 TTGT
1 TTGT
44478 CTAATTACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.51
Consensus pattern (18 bp):
TTGTTCATGTTGCTGGAC
Found at i:45260 original size:12 final size:12
Alignment explanation
Indices: 45243--45267 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45233 TCGTGTTCAG
45243 ATTTATATATAT
1 ATTTATATATAT
45255 ATTTATATATAT
1 ATTTATATATAT
45267 A
1 A
45268 GATCATTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATATAT
Done.