Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2701
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: 8249
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Found at i:1721 original size:20 final size:20
Alignment explanation
Indices: 1697--1743 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1687 TACAATGAGA
1697 AATGTATCGATACAATTTCTT
1 AATGTATCGATAC-ATTTCTT
*
1718 -ATGTATCGATACATTTTTT
1 AATGTATCGATACATTTCTT
1737 AATGTAT
1 AATGTAT
1744 TTATATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (20 bp):
AATGTATCGATACATTTCTT
Found at i:1825 original size:20 final size:21
Alignment explanation
Indices: 1798--1846 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
1788 ATTTCAGGCA
*
1798 TGTATCGATACATTTCCTTAT
1 TGTATCGATACATTGCCTTAT
1819 T-TATCGATACATTGCCTTAT
1 TGTATCGATACATTGCCTTAT
1839 TGTATCGA
1 TGTATCGA
1847 AACAAATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATTGCCTTAT
Found at i:3341 original size:53 final size:52
Alignment explanation
Indices: 2632--3389 Score: 231
Period size: 52 Copynumber: 14.7 Consensus size: 52
2622 GAGATGAAAA
* * * * * * *
2632 AATGCCAATGTGCTGA-CCTAAGGCCAGCGACGTTAGG-CTCAAAGATAATAAA
1 AATGCCAATGTGCTGATTC-AAGGCCAGCGACATT-GGACTTAAAAATGAGAAG
* * * * * *
2684 AATGCCAATATACTGATTCAAGGCTAGCGATATTGGACTCAAAGAT--GAAG
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAGAAG
** * * **
2734 TGTGCCAATGTGCTGATTCAAGGCTAACGACATTGGGTTTAAGGAAA-GTA-AAG
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAA--AAATG-AGAAG
* * * * * *
2787 -GTGCCAATATGCTGATTCAAGGCCAGCGATATCGAACTTAAAAATGATAA-
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAGAAG
* * * * * *** ** * * * *
2837 AGGTCCCAATATGTTGACTCACTACCAATGATATCGGACTTAAAGATGAGAAA
1 A-ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAGAAG
* ** * * * * * *
2890 AATGCCAATGTGCTGATCCAAGGCCAATGA-AATGGGCTTAAAGATAATAAA
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAGAAG
* * * * * * * * *
2941 AAGTGCTAATATGCTTATTCAAGGCCAACAATATTAGACTTAAAGA-CAG-AG
1 AA-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAGAAG
** * * * * **
2992 TGTGCTAATGTGCTGATTAAAGGGCAACGACATTGGGTTTAAAAAAAT-A-AAG
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT--AAAAATGAGAAG
* ** * * * *
3044 -ATACCAATACGCTGATTCAAGGCTAGTGATATCGGACTTAAAAGAT-A-AATG
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAA-ATGAGAA-G
* * * * * ** * * * *
3095 --TGCTAATATGTTGACTCACGGCCAATGATATCGGACTTAAAGATGATAA-
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAGAAG
* * * * * * * * * *
3144 ATGTGCCAATATGTTGACTCACGGCCAACGATATCGGACTTAAAGATGAGAAA
1 A-ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAGAAG
* * *
3197 AATGCCAATGTGCTGATTTAAGGCCAACGACATTGGACTTAAAAATGATAAG
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAGAAG
* * * * * *
3249 AATGCCAATGTACTAATTCAAGGCCAGTGATATTAGACTTAAAATTTGAGAAG
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAA-ATGAGAAG
* * * * * * *
3302 AATGCCAATATGCTGATTCAAGACCAGCGACAATGGACTTACAGATAACAAG
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAGAAG
* * * ** *
3354 GATTCCAACGTGCTGATTTGAGGCCAGTGACATTGG
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
3390 GTTTAGAGAA
Statistics
Matches: 536, Mismatches: 143, Indels: 54
0.73 0.20 0.07
Matches are distributed among these distances:
49 6 0.01
50 107 0.20
51 52 0.10
52 314 0.59
53 57 0.11
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (52 bp):
AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAGAAG
Found at i:3378 original size:105 final size:105
Alignment explanation
Indices: 3190--3383 Score: 235
Period size: 105 Copynumber: 1.8 Consensus size: 105
3180 GACTTAAAGA
* * * * * *
3190 TGAGAAAAATGCCAATGTGCTGATTTAAGGCCAACGACATTGGACTTAAAAATGATAAGAATGCC
1 TGAGAAAAATGCCAATATGCTGATTCAAGACCAACGACAATGGACTTAAAAATAACAAGAATGCC
*
3255 AATGTACTAATTCAAGGCCAGTGATATTAGACTTAAAATT
66 AACGTACTAATTCAAGGCCAGTGATATTAGACTTAAAATT
* * * * * *
3295 TGAGAAGAATGCCAATATGCTGATTCAAGACCAGCGACAATGGACTTACAGATAACAAGGATTCC
1 TGAGAAAAATGCCAATATGCTGATTCAAGACCAACGACAATGGACTTAAAAATAACAAGAATGCC
* * **
3360 AACGTGCTGATTTGAGGCCAGTGA
66 AACGTACTAATTCAAGGCCAGTGA
3384 CATTGGGTTT
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
105 72 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (105 bp):
TGAGAAAAATGCCAATATGCTGATTCAAGACCAACGACAATGGACTTAAAAATAACAAGAATGCC
AACGTACTAATTCAAGGCCAGTGATATTAGACTTAAAATT
Found at i:3535 original size:31 final size:32
Alignment explanation
Indices: 3503--3641 Score: 201
Period size: 31 Copynumber: 4.4 Consensus size: 32
3493 GACATTAGGC
*
3503 TTAGAAGGGGTTGCCACCGACTTGTGTGGGCT
1 TTAGAAAGGGTTGCCACCGACTTGTGTGGGCT
* * *
3535 TTAGAAA-GATTGCCATCGACTTGTGTGGCCT
1 TTAGAAAGGGTTGCCACCGACTTGTGTGGGCT
* *
3566 TTAGAAAAGAGTTACCACCGACTTGTGTGGGCT
1 TTAG-AAAGGGTTGCCACCGACTTGTGTGGGCT
3599 TTA-AAAGGGTTGCCACCGACTTGTGTGGGCT
1 TTAGAAAGGGTTGCCACCGACTTGTGTGGGCT
3630 TTAGAAAGGGTT
1 TTAGAAAGGGTT
3642 ACGATCGGGT
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
31 54 0.58
32 17 0.18
33 22 0.24
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (32 bp):
TTAGAAAGGGTTGCCACCGACTTGTGTGGGCT
Found at i:3619 original size:64 final size:64
Alignment explanation
Indices: 3516--3636 Score: 199
Period size: 64 Copynumber: 1.9 Consensus size: 64
3506 GAAGGGGTTG
*
3516 CCACCGACTTGTGTGGGCTTTAGAAAGATTGCCATCGACTTGTGTGGCCTTTAGAAAAGAGTTA
1 CCACCGACTTGTGTGGGCTTTAGAAAGATTGCCACCGACTTGTGTGGCCTTTAGAAAAGAGTTA
* *
3580 CCACCGACTTGTGTGGGCTTTA-AAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAA
1 CCACCGACTTGTGTGGGCTTTAGAAA-GATTGCCACCGACTTGTGTGGCCTTTAGAAA
3637 GGGTTACGAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
63 3 0.06
64 50 0.94
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (64 bp):
CCACCGACTTGTGTGGGCTTTAGAAAGATTGCCACCGACTTGTGTGGCCTTTAGAAAAGAGTTA
Found at i:3754 original size:34 final size:33
Alignment explanation
Indices: 3666--3775 Score: 123
Period size: 34 Copynumber: 3.3 Consensus size: 33
3656 TGGACTTAAC
* *
3666 AAGGGGCCACAGAGTTATAGGCATAAAAAGAAA
1 AAGGTGCCACAGAGTTATGGGCATAAAAAGAAA
* * * *
3699 AAGGTACCATAGAGTTGTGGGCCTAAAAAGGAAA
1 AAGGTGCCACAGAGTTATGGGCATAAAAA-GAAA
*
3733 AAGGTGCCACCA-AGTTATGGGCTTAAAAAGAAA
1 AAGGTGCCA-CAGAGTTATGGGCATAAAAAGAAA
3766 AAGGGTGCCA
1 AA-GGTGCCA
3776 TGGATTATGG
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
33 29 0.45
34 34 0.53
35 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.28, T:0.15
Consensus pattern (33 bp):
AAGGTGCCACAGAGTTATGGGCATAAAAAGAAA
Found at i:3784 original size:33 final size:33
Alignment explanation
Indices: 3666--3785 Score: 118
Period size: 33 Copynumber: 3.6 Consensus size: 33
3656 TGGACTTAAC
* * *
3666 AAGGGGCCACAGAGTTATAGGCATAAAAAGAAA
1 AAGGTGCCATAGAGTTATGGGCATAAAAAGAAA
* * *
3699 AAGGTACCATAGAGTTGTGGGCCTAAAAAGGAAA
1 AAGGTGCCATAGAGTTATGGGCATAAAAA-GAAA
* *
3733 AAGGTGCCACCA-AGTTATGGGCTTAAAAAGAAA
1 AAGGTGCCA-TAGAGTTATGGGCATAAAAAGAAA
*
3766 AAGGGTGCCATGGA-TTATGG
1 AA-GGTGCCATAGAGTTATGG
3786 ACTTTGACGA
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
33 35 0.49
34 35 0.49
35 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.29, T:0.17
Consensus pattern (33 bp):
AAGGTGCCATAGAGTTATGGGCATAAAAAGAAA
Found at i:3867 original size:33 final size:32
Alignment explanation
Indices: 3760--4216 Score: 227
Period size: 33 Copynumber: 14.7 Consensus size: 32
3750 TGGGCTTAAA
** *
3760 AAGAAAAAGGGTGCCATGGA-TTATGGACTTT
1 AAGAAAAAGGGTGCCACAGAGTTGTGGACTTT
* * *
3791 GACGAAAAA-GGTGCCACGGAGTTGTGGACCTT
1 -AAGAAAAAGGGTGCCACAGAGTTGTGGACTTT
* * *
3823 -AG-AAAGGGGTGCCATAGAGTTGAGGACTTT
1 AAGAAAAAGGGTGCCACAGAGTTGTGGACTTT
*
3853 GAAGAAAAAGGGTGCCACAGAGTTGTAGAC-TT
1 -AAGAAAAAGGGTGCCACAGAGTTGTGGACTTT
* * **
3885 --G-AAAAGGGTGCCAC-GAAATCGTAAACTTT
1 AAGAAAAAGGGTGCCACAG-AGTTGTGGACTTT
* *
3914 AAAAGAAAAA-GGTACCATAGAGTTGTGGAC-TT
1 --AAGAAAAAGGGTGCCACAGAGTTGTGGACTTT
*
3946 ---AAAAA-GGTGCCACGGAGTTGTGGACTTT
1 AAGAAAAAGGGTGCCACAGAGTTGTGGACTTT
* * *
3974 AAAAGAAAAA-TGTACCACAGAGTTGTGAAC-TT
1 --AAGAAAAAGGGTGCCACAGAGTTGTGGACTTT
*
4006 ---AAAAAGGGTGCCACAGAGTTATGGACTTT
1 AAGAAAAAGGGTGCCACAGAGTTGTGGACTTT
** *
4035 GAA-AGAAAACCGTGCCACGGAGTTGTGGACTTT
1 -AAGA-AAAAGGGTGCCACAGAGTTGTGGACTTT
* *
4068 GAAG-AAAA-GGTGCCATAGAGATGTGGACTTT
1 -AAGAAAAAGGGTGCCACAGAGTTGTGGACTTT
*
4099 --G--AAAGGGTGCCAC-GAAGTTGTGGACTTAA
1 AAGAAAAAGGGTGCCACAG-AGTTGTGGACTT-T
** * *
4128 AAGAAAAAGGGTGCCATGGAATTGTGGACTTAAAA
1 AAGAAAAAGGGTGCCACAGAGTTGTGGACTT---T
*
4163 AAGAAAAA-GGTGCCA-TGAAGTTGTGGACTTT
1 AAGAAAAAGGGTGCCACAG-AGTTGTGGACTTT
* ** *
4194 GAAAAAAAAAAGTGCCACGGAGT
1 -AAGAAAAAGGGTGCCACAGAGT
4217 CATGAATTTT
Statistics
Matches: 332, Mismatches: 53, Indels: 79
0.72 0.11 0.17
Matches are distributed among these distances:
27 32 0.10
28 57 0.17
29 8 0.02
30 20 0.06
31 30 0.09
32 36 0.11
33 114 0.34
34 25 0.08
35 10 0.03
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (32 bp):
AAGAAAAAGGGTGCCACAGAGTTGTGGACTTT
Found at i:3936 original size:61 final size:59
Alignment explanation
Indices: 3854--4019 Score: 197
Period size: 60 Copynumber: 2.7 Consensus size: 59
3844 GAGGACTTTG
*
3854 AAGAAAAAGGGTGCCACAGAGTTGTAGACTTGAAAAGGGTGCCACGAAATCGTAAACTTTAA
1 AAGAAAAA-GGTACCACAGAGTTGT-GACTT-AAAAGGGTGCCACGAAATCGTAAACTTTAA
* * * * * **
3916 AAGAAAAAGGTACCATAGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTTAA
1 AAGAAAAAGGTACCACAGAGTTGT-GACTTAAAAGGGTGCCACGAAATCGTAAACTTTAA
*
3976 AAGAAAAATGTACCACAGAGTTGTGAACTTAAAAAGGGTGCCAC
1 AAGAAAAAGGTACCACAGAGTTGTG-ACTT-AAAAGGGTGCCAC
4020 AGAGTTATGG
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 1 0.01
60 50 0.56
61 31 0.34
62 8 0.09
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.20
Consensus pattern (59 bp):
AAGAAAAAGGTACCACAGAGTTGTGACTTAAAAGGGTGCCACGAAATCGTAAACTTTAA
Found at i:4034 original size:121 final size:119
Alignment explanation
Indices: 3763--4103 Score: 339
Period size: 121 Copynumber: 2.8 Consensus size: 119
3753 GCTTAAAAAG
* * *
3763 AAAAAGGGTGCCATGGATTATGGACTTTGACGAAAAAGGTGCCACGGAGTTGTGGACCTTAGAAA
1 AAAAAGGGTGCCA-CGATTATGGACTTTAAAGAAAAAGGTGCCACGGAGTTGTGGA-CTTAGAAA
* * * *
3828 GGGGTGCCATAGAGTTGAGGACTTTGAAGAAAAAGGGTGCCACAGAGTTGTAGACTT
64 -AGGTGCCATAGAGTTGTGGACTTTAAAGAAAAAGGGTACCACAGAGTTGTAGACTT
* * * * **
3885 GAAAAGGGTGCCACGA-AATCGTAAACTTTAAAAGAAAAAGGTACCATAGAGTTGTGGACTTA-A
1 AAAAAGGGTGCCACGATTAT-G--GACTTT-AAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGA
** *
3948 AAAGGTGCCACGGAGTTGTGGACTTTAAAAGAAAAA-TGTACCACAGAGTTGT-GAACTT
62 AAAGGTGCCATAGAGTTGTGGACTTT-AAAGAAAAAGGGTACCACAGAGTTGTAG-ACTT
**
4006 AAAAAGGGTGCCACAGAGTTATGGACTTTGAAAGAAAACCGTGCCACGGAGTTGTGGACTTTGAA
1 AAAAAGGGTGCCAC-GA-TTATGGACTTT-AAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT--A
*
4071 GAAAAGGTGCCATAGAGATGTGGACTTTGAAAG
60 GAAAAGGTGCCATAGAGTTGTGGACTTT-AAAG
4104 GGTGCCACGA
Statistics
Matches: 177, Mismatches: 29, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
120 3 0.02
121 83 0.47
122 27 0.15
123 10 0.06
124 26 0.15
125 28 0.16
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.22
Consensus pattern (119 bp):
AAAAAGGGTGCCACGATTATGGACTTTAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAAAG
GTGCCATAGAGTTGTGGACTTTAAAGAAAAAGGGTACCACAGAGTTGTAGACTT
Found at i:4043 original size:61 final size:61
Alignment explanation
Indices: 3763--4103 Score: 282
Period size: 61 Copynumber: 5.6 Consensus size: 61
3753 GCTTAAAAAG
** * * *
3763 AAAAAGGGTGCCATGGA-TTATGGACTTTG-ACGAAAAAGGTGCCACGGAGTTGTGGACCTT
1 AAAAAGGGTGCCACAGAGTTATGGACTTTGAAAGAAAAAGGTGCCACAGAGTTGT-GAACTT
* *
3823 AGAAAGGGGTGCCATAGAGTTGA-GGACTTTG-AAGAAAAAGGGTGCCACAGAGTTGT-AGACTT
1 A-AAAAGGGTGCCACAGAGTT-ATGGACTTTGAAAGAAAAA-GGTGCCACAGAGTTGTGA-ACTT
* * ** ** * * * *
3885 GAAAAGGGTGCCAC-GAAATCGTAAACTTTAAAAGAAAAAGGTACCATAGAGTTGTGGACTT
1 AAAAAGGGTGCCACAG-AGTTATGGACTTTGAAAGAAAAAGGTGCCACAGAGTTGTGAACTT
* * * * *
3946 AAAAA-GGTGCCACGGAGTTGTGGACTTTAAAAGAAAAATGTACCACAGAGTTGTGAACTT
1 AAAAAGGGTGCCACAGAGTTATGGACTTTGAAAGAAAAAGGTGCCACAGAGTTGTGAACTT
** * *
4006 AAAAAGGGTGCCACAGAGTTATGGACTTTGAAAGAAAACCGTGCCACGGAGTTGTGGACTTT
1 AAAAAGGGTGCCACAGAGTTATGGACTTTGAAAGAAAAAGGTGCCACAGAGTTGTGAAC-TT
* * * *
4068 GAAGAAAAGGTGCCATAGAGATGTGGACTTTGAAAG
1 -AA-AAAGGGTGCCACAGAGTTATGGACTTTGAAAG
4104 GGTGCCACGA
Statistics
Matches: 230, Mismatches: 37, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
60 53 0.23
61 101 0.44
62 30 0.13
63 18 0.08
64 28 0.12
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.22
Consensus pattern (61 bp):
AAAAAGGGTGCCACAGAGTTATGGACTTTGAAAGAAAAAGGTGCCACAGAGTTGTGAACTT
Found at i:4187 original size:34 final size:33
Alignment explanation
Indices: 3689--4210 Score: 163
Period size: 33 Copynumber: 16.6 Consensus size: 33
3679 GTTATAGGCA
* * *
3689 TAAAAAGAAAAAGGTACCAT-AGAGTTGTGGGCC
1 TAAAAAGAAAAAGGTGCCATGA-AGTTGTGGACT
** * *
3722 TAAAAAGGAAAAAGGTGCCACCAAGTTATGGGCT
1 TAAAAA-GAAAAAGGTGCCATGAAGTTGTGGACT
* *
3756 TAAAAAGAAAAAGGGTGCCATGGA-TTATGGACT
1 TAAAAAGAAAAA-GGTGCCATGAAGTTGTGGACT
** * * *
3789 T-TGACGAAAAAGGTGCCACGGAGTTGTGGACCT
1 TAAAAAGAAAAAGGTGCCATGAAGTTGTGGA-CT
** *
3822 T----AGAAAGGGGTGCCAT-AGAGTTGAGGACT
1 TAAAAAGAAAAAGGTGCCATGA-AGTTGTGGACT
** * *
3851 T-TGAAGAAAAAGGGTGCCA-CAGAGTTGTAGACT
1 TAAAAAGAAAAA-GGTGCCATGA-AGTTGTGGACT
* * * * **
3884 T-----GAAAAGGGTGCCACGAAATCGTAAACT
1 TAAAAAGAAAAAGGTGCCATGAAGTTGTGGACT
* *
3912 TTAAAAGAAAAAGGTACCAT-AGAGTTGTGGACT
1 TAAAAAGAAAAAGGTGCCATGA-AGTTGTGGACT
* *
3945 T------AAAAAGGTGCCACGGAGTTGTGGACT
1 TAAAAAGAAAAAGGTGCCATGAAGTTGTGGACT
* * * * *
3972 TTAAAAGAAAAATGTACCA-CAGAGTTGTGAACT
1 TAAAAAGAAAAAGGTGCCATGA-AGTTGTGGACT
* *
4005 TAAAAAG-----GGTGCCA-CAGAGTTATGGACT
1 TAAAAAGAAAAAGGTGCCATGA-AGTTGTGGACT
** ** * *
4033 TTGAAAGAAAACCGTGCCACGGAGTTGTGGACT
1 TAAAAAGAAAAAGGTGCCATGAAGTTGTGGACT
** *
4066 T-TGAAG-AAAAGGTGCCAT-AGAGATGTGGACT
1 TAAAAAGAAAAAGGTGCCATGA-AGTTGTGGACT
* * *
4097 T----TG-AAAGGGTGCCACGAAGTTGTGGACT
1 TAAAAAGAAAAAGGTGCCATGAAGTTGTGGACT
4125 T-AAAAGAAAAAGGGTGCCATGGAA-TTGTGGACT
1 TAAAAAGAAAAA-GGTGCCAT-GAAGTTGTGGACT
4158 TAAAAAAGAAAAAGGTGCCATGAAGTTGTGGACTT
1 T-AAAAAGAAAAAGGTGCCATGAAGTTGTGGAC-T
4193 TGAAAAA-AAAAA-GTGCCA
1 T-AAAAAGAAAAAGGTGCCA
4211 CGGAGTCATG
Statistics
Matches: 376, Mismatches: 69, Indels: 88
0.71 0.13 0.17
Matches are distributed among these distances:
27 23 0.06
28 60 0.16
29 10 0.03
30 19 0.05
31 31 0.08
32 25 0.07
33 131 0.35
34 59 0.16
35 18 0.05
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.21
Consensus pattern (33 bp):
TAAAAAGAAAAAGGTGCCATGAAGTTGTGGACT
Found at i:5696 original size:23 final size:24
Alignment explanation
Indices: 5620--5696 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 24
5610 TGTCTTTATT
*
5620 TTTTGATTTTTGTTCTTTTTTTT-A
1 TTTTGATTTTTCTT-TTTTTTTTCA
* * * *
5644 TTTTGCTTTTGCACTTTTTTTTGTCC
1 TTTTGATTTT--TCTTTTTTTTTTCA
5670 TTTTG-TTTTTCTTTTTTTTTTCA
1 TTTTGATTTTTCTTTTTTTTTTCA
5693 TTTT
1 TTTT
5697 CGTGCTTTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
23 15 0.36
24 9 0.21
25 11 0.26
26 7 0.17
ACGTcount: A:0.05, C:0.10, G:0.08, T:0.77
Consensus pattern (24 bp):
TTTTGATTTTTCTTTTTTTTTTCA
Done.