Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1367
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: 24157
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:3648 original size:21 final size:21
Alignment explanation
Indices: 3624--3726 Score: 101
Period size: 21 Copynumber: 5.0 Consensus size: 21
3614 GGCGTCCTCC
3624 ACAAAAAAAAAACAAAACAAA
1 ACAAAAAAAAAACAAAACAAA
3645 AC-AAAAAAAAACAAAAACAAA
1 ACAAAAAAAAAAC-AAAACAAA
*
3666 A-AACAAAAAAAC--AA-AAA
1 ACAAAAAAAAAACAAAACAAA
*
3683 ACAAAAAACAAAGCAAAA-AAA
1 ACAAAAAA-AAAACAAAACAAA
3704 TACAAAAACAAAAACAACAACAA
1 -ACAAAAA-AAAAACAA-AACAA
3727 CAAAAAGGGT
Statistics
Matches: 68, Mismatches: 4, Indels: 17
0.76 0.04 0.19
Matches are distributed among these distances:
17 4 0.06
18 7 0.10
19 4 0.06
20 10 0.15
21 25 0.37
22 13 0.19
23 3 0.04
24 2 0.03
ACGTcount: A:0.83, C:0.16, G:0.01, T:0.01
Consensus pattern (21 bp):
ACAAAAAAAAAACAAAACAAA
Found at i:3650 original size:15 final size:14
Alignment explanation
Indices: 3628--3732 Score: 108
Period size: 15 Copynumber: 7.4 Consensus size: 14
3618 TCCTCCACAA
3628 AAAAAAAACAAAAC
1 AAAAAAAACAAAAC
*
3642 AAAACAAAAAAAAAC
1 AAAA-AAAACAAAAC
*
3657 AAAAACAA-AAAAC
1 AAAAAAAACAAAAC
3670 -AAAAAAACAAAA-
1 AAAAAAAACAAAAC
*
3682 AACAAAAAACAAAGC
1 AA-AAAAAACAAAAC
3697 AAAAAAATACAAAAAC
1 AAAAAAA-AC-AAAAC
*
3713 AAAAACAACAACAAC
1 AAAAAAAACAA-AAC
3728 AAAAA
1 AAAAA
3733 GGGTCCGGAT
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.08
13 10 0.13
14 24 0.31
15 27 0.35
16 10 0.13
ACGTcount: A:0.83, C:0.15, G:0.01, T:0.01
Consensus pattern (14 bp):
AAAAAAAACAAAAC
Found at i:3654 original size:22 final size:22
Alignment explanation
Indices: 3626--3726 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
3616 CGTCCTCCAC
3626 AAAAAAAAAACAAAACAAAACA
1 AAAAAAAAAACAAAACAAAACA
*
3648 AAAAAAAACA-AAAAC-AAA-A
1 AAAAAAAAAACAAAACAAAACA
*
3667 AACAAAAAAAC--AA-AAAACA
1 AAAAAAAAAACAAAACAAAACA
* *
3686 AAAAACAAAGCAAAA-AAATACA
1 AAAAAAAAAACAAAACAAA-ACA
*
3708 AAAACAAAAACAACAACAA
1 AAAAAAAAAACAA-AACAA
3727 CAAAAAGGGT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
18 5 0.08
19 18 0.29
20 3 0.05
21 10 0.16
22 22 0.35
23 2 0.03
24 2 0.03
ACGTcount: A:0.83, C:0.15, G:0.01, T:0.01
Consensus pattern (22 bp):
AAAAAAAAAACAAAACAAAACA
Found at i:3700 original size:50 final size:51
Alignment explanation
Indices: 3627--3732 Score: 153
Period size: 50 Copynumber: 2.1 Consensus size: 51
3617 GTCCTCCACA
3627 AAAAAAAAACAAAACAAAACAAAAAAAAACAAAAACAAAAAACAA-AAAAAC
1 AAAAAAAAACAAAACAAAACAAAAAAAAACAAAAAC-AAAAACAACAAAAAC
* * * *
3678 AAAAAACAA-AAAACAAAGCAAAAAAATACAAAAACAAAAACAACAACAAC
1 AAAAAAAAACAAAACAAAACAAAAAAAAACAAAAACAAAAACAACAAAAAC
3728 AAAAA
1 AAAAA
3733 GGGTCCGGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 8 0.16
50 34 0.68
51 8 0.16
ACGTcount: A:0.83, C:0.15, G:0.01, T:0.01
Consensus pattern (51 bp):
AAAAAAAAACAAAACAAAACAAAAAAAAACAAAAACAAAAACAACAAAAAC
Found at i:3703 original size:1 final size:1
Alignment explanation
Indices: 3626--3690 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
3616 CGTCCTCCAC
* * * * * * * *
3626 AAAAAAAAAACAAAACAAAACAAAAAAAAACAAAAACAAAAAACAAAAAAACAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3691 CAAAGCAAAA
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3729 original size:6 final size:6
Alignment explanation
Indices: 3624--3726 Score: 81
Period size: 6 Copynumber: 16.7 Consensus size: 6
3614 GGCGTCCTCC
3624 ACAAAA A-AAAA AC-AAA AC-AAA AC-AAA A-AAAA ACAAAA ACAAAAA
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA AC-AAAA
*
3668 ACAAAAAA ACAAAAA ACAAAAA ACAAAGCA AAAAAA TACAAAA ACAAAA
1 AC--AAAA AC-AAAA AC-AAAA ACAAA--A ACAAAA -ACAAAA ACAAAA
*
3717 ACAACA ACAA
1 ACAAAA ACAA
3727 CAAAAAGGGT
Statistics
Matches: 86, Mismatches: 3, Indels: 16
0.82 0.03 0.15
Matches are distributed among these distances:
5 23 0.27
6 26 0.30
7 25 0.29
8 12 0.14
ACGTcount: A:0.83, C:0.16, G:0.01, T:0.01
Consensus pattern (6 bp):
ACAAAA
Found at i:5208 original size:30 final size:30
Alignment explanation
Indices: 5168--6013 Score: 1024
Period size: 30 Copynumber: 28.9 Consensus size: 30
5158 ACTCTTTTTT
* *
5168 AAAGCCCACAAATCAGTGGCACCCTTCTCCC
1 AAAGCCCACAAGTCAGTGGCACCCTT-TTCC
* *
5199 AAAG-CCACAAGTCAGTGGCAACC--TTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *
5226 AAAGCCCACAAATCAGTGGCACCCTTCTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTC-C
*
5257 AAAGCCCACAAGTCAGTGGCACCCTTCTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTC-C
*
5288 AAAGCCCATAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
5318 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
5347 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *
5376 AAAGCCCACAAGTCAGTGGCAACC--TTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * *
5404 AAAGCCCAAAAATCAGTGGCACCCTTCTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTC-C
*
5435 AAAGCCCACAAGTCAGTGGCAACC--TT-C
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
5462 AAAG-CCACAAGTCAGTGGCACCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
5491 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
5521 AAAG-CCACAAGTCAGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
5549 AAAGCCCACAAAGTCAGTGGCACCCTTTTCA
1 AAAGCCCAC-AAGTCAGTGGCACCCTTTTCC
* *
5580 AAAGTCCACAAGTCAGTGGTACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *
5610 AAAGCCCACAAGTTAGTGGTACCCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-CCCTTTTCC
5641 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * * *
5671 AAAGCCCACAAGTCAATGGTA-TCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
5700 AAAGCCCATAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * *
5730 AAAGCCCACAAGTCTGTGACA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
5759 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * *
5788 -AA--CCACAAGTCAGTGGTA-TCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *
5814 AAAGCCCATAAGTCAATGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * *
5844 AAAGCCCACAAGTCAGTGGTA-TCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
5873 AAAGCCCACAAGTTAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *
5903 AAAGCCCGCAAGTCAGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
5932 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * *
5962 AAAG-CCACAAGTCAATGG---CCTCTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
5988 AAAGCCCACAAGTCAGTGGCAACCTT
1 AAAGCCCACAAGTCAGTGGCACCCTT
6014 CAAAAGCACA
Statistics
Matches: 710, Mismatches: 78, Indels: 55
0.84 0.09 0.07
Matches are distributed among these distances:
26 49 0.07
27 26 0.04
28 55 0.08
29 219 0.31
30 237 0.33
31 124 0.17
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.22
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTCC
Found at i:5450 original size:59 final size:59
Alignment explanation
Indices: 5168--6013 Score: 1024
Period size: 59 Copynumber: 14.4 Consensus size: 59
5158 ACTCTTTTTT
* * *
5168 AAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAG-CCACAAGTCAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTT-TTCCAAAGCCCACAAGTCAGTGGCATCTCTTCA
* * *
5226 AAAGCCCACAAATCAGTGGCACCCTTCTCTCAAAGCCCACAAGTCAGTGGCACCCTTCTCTC-
1 AAAGCCCACAAGTCAGTGGCACCCTTTTC-CAAAGCCCACAAGTCAGTGGCA-TC-TCT-TCA
* * *
5288 AAAGCCCATAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTCTTCA
* *
5347 AAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTCAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTCTTCA
* * * *
5404 AAAGCCCAAAAATCAGTGGCACCCTTCTCTCAAAGCCCACAAGTCAGTGGCAAC-CTTC-
1 AAAGCCCACAAGTCAGTGGCACCCTTTTC-CAAAGCCCACAAGTCAGTGGCATCTCTTCA
* * * *
5462 AAAG-CCACAAGTCAGTGGCACCTTTTTCCAAAGCCCACAAGTCAGTGGCACCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATC-TCTTCA
* * *
5521 AAAG-CCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAAGTCAGTGGCACCCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCAC-AAGTCAGTGGCA-TCTCTTCA
* * * ** * *
5580 AAAGTCCACAAGTCAGTGGTACCCTTTTCCAAAGCCCACAAGTTAGTGGTACCCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGG--CATCTCTTCA
* * *
5641 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAATGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTCTTCA
* * * * *
5700 AAAGCCCATAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCTGTGACATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTCTTCA
* * *
5759 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC-AA--CCACAAGTCAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTCTTCA
* * * *
5814 AAAGCCCATAAGTCAATGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTCTTCA
* * * *
5873 AAAGCCCACAAGTTAGTGGCACCCTTTTCCAAAGCCCGCAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTCTTCA
*
5932 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAG-CCACAAGTCAATGGC--CTCTTCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTCTTCA
*
5988 AAAGCCCACAAGTCAGTGGCAACCTT
1 AAAGCCCACAAGTCAGTGGCACCCTT
6014 CAAAAGCACA
Statistics
Matches: 700, Mismatches: 66, Indels: 46
0.86 0.08 0.06
Matches are distributed among these distances:
55 39 0.06
56 60 0.09
57 47 0.07
58 109 0.16
59 296 0.42
60 28 0.04
61 90 0.13
62 29 0.04
63 2 0.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.22
Consensus pattern (59 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTCTTCA
Found at i:6186 original size:43 final size:43
Alignment explanation
Indices: 6121--6394 Score: 323
Period size: 43 Copynumber: 6.1 Consensus size: 43
6111 GCACCTTCAT
* *
6121 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGTAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
6164 CTTTAAGTCCAATATAGTTGGCCTTGAGTCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
6211 ATCTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
6256 CTTTAAGGCCAATATAGCTTGCCTTGAATCAGCATATTAGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
*
6303 TTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
6348 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
6391 CTTT
1 CTTT
6395 TCCATCTTTA
Statistics
Matches: 197, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
43 119 0.60
45 2 0.01
47 2 0.01
49 74 0.38
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:6229 original size:92 final size:92
Alignment explanation
Indices: 6072--6447 Score: 608
Period size: 92 Copynumber: 4.0 Consensus size: 92
6062 GTGGCATCTT
* *
6072 CTTTAAGTCCAATATAGCTGGCCTTGAGTTAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
6137 GCTGGCCTTGAATCAGCACATTGGTAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
6164 CTTTAAGTCCAATATAGTTGGCCTTGAGTCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
6229 GCTAGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * *
6256 CTTTAAGGCCAATATAGCTTGCCTTGAATCAGCATATTAGCACCTTCTTCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
6321 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
6348 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAAT
*
6413 GTAGCTGGCCTTGAATCAGCACATTGACATC
63 GTAGCTGGCCTTGAATCAGCACATTGGCA-C
6444 CTTT
1 CTTT
6448 TTCTCATCTT
Statistics
Matches: 263, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
92 214 0.81
94 2 0.01
95 42 0.16
96 5 0.02
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:6426 original size:52 final size:55
Alignment explanation
Indices: 6348--6469 Score: 169
Period size: 52 Copynumber: 2.3 Consensus size: 55
6338 ACATTGGCAC
* *
6348 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* *
6400 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
**
6455 CTTTAAACCCAATAT
1 CTTTAAGTCCAATAT
6470 CGTTGGCTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
52 38 0.64
53 2 0.03
54 5 0.08
55 14 0.24
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:7140 original size:32 final size:33
Alignment explanation
Indices: 7077--7145 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
7067 TTCAATAATT
7077 TGTATCGATACATAAAGTGTTGTATCAATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
* *
7110 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
7142 TGTA
1 TGTA
7146 AGCTACTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 21 0.62
33 13 0.38
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCAATACAA
Found at i:7198 original size:13 final size:13
Alignment explanation
Indices: 7182--7206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7172 ATTACTCAAA
7182 TGTATCGATACAT
1 TGTATCGATACAT
7195 TGTATCGATACA
1 TGTATCGATACA
7207 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7258 original size:52 final size:52
Alignment explanation
Indices: 7215--7395 Score: 326
Period size: 52 Copynumber: 3.5 Consensus size: 52
7205 CACTGATCTT
* *
7215 TGTATCGATACATGCAGGCAAGTTTGCCCAGATGTATTGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
7267 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
7319 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
7371 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
7396 TCATATTTCG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:15870 original size:20 final size:20
Alignment explanation
Indices: 15845--15899 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
15835 AATTTTTCAA
15845 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
15865 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
15885 AATGTATCGATACAT
1 AATGTATCGATACAT
15900 CTAGAAAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAT
Found at i:15954 original size:13 final size:13
Alignment explanation
Indices: 15936--15984 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
15926 ATGTTCTAAG
15936 TATCGATAAATTA
1 TATCGATAAATTA
* *
15949 TATCGATACACTA
1 TATCGATAAATTA
* *
15962 TATCGATACATTG
1 TATCGATAAATTA
15975 TATCGATAAA
1 TATCGATAAA
15985 AGGGGTACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (13 bp):
TATCGATAAATTA
Found at i:18580 original size:33 final size:33
Alignment explanation
Indices: 18525--18587 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
18515 ATATCCAGAA
* * *
18525 GTATCGATACATACTGCTTTGTATGGATACGTT
1 GTATCGATACACACTGCATTGTATCGATACGTT
18558 GTATCGATACACACT-CAATTGTATCGATAC
1 GTATCGATACACACTGC-ATTGTATCGATAC
18588 ATGAAACTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (33 bp):
GTATCGATACACACTGCATTGTATCGATACGTT
Found at i:18658 original size:13 final size:13
Alignment explanation
Indices: 18640--18664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18630 CATGGGACAT
18640 TGTATCGATACAA
1 TGTATCGATACAA
18653 TGTATCGATACA
1 TGTATCGATACA
18665 TGATAAAATG
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:18669 original size:20 final size:20
Alignment explanation
Indices: 18646--18685 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
18636 ACATTGTATC
*
18646 GATACAATGTATCGATACAT
1 GATAAAATGTATCGATACAT
*
18666 GATAAAATGTATCGGTACAT
1 GATAAAATGTATCGATACAT
18686 TGTGCCCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
GATAAAATGTATCGATACAT
Found at i:23106 original size:24 final size:24
Alignment explanation
Indices: 23079--23124 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
23069 CTTGCATGTA
*
23079 AAATTTAAGGTTTCTTAAAACCTT
1 AAATTTAAGGTTTCCTAAAACCTT
23103 AAATTTAAGGTTTCCTAAAACC
1 AAATTTAAGGTTTCCTAAAACC
23125 CTAATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (24 bp):
AAATTTAAGGTTTCCTAAAACCTT
Found at i:23902 original size:32 final size:32
Alignment explanation
Indices: 23855--23944 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
23845 AATTTCTTGC
* *
23855 AATTCTGTATCTATTATTGAATAAATTATTGT
1 AATTTTGTATTTATTATTGAATAAATTATTGT
* *
23887 AATTTTGTATTTATTATCGAATAAATTCTTGT
1 AATTTTGTATTTATTATTGAATAAATTATTGT
23919 AATTTTGTATTTATTTATTGAATAAA
1 AATTTTGTATTTA-TTATTGAATAAA
23945 AATTCTAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
32 41 0.79
33 11 0.21
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.52
Consensus pattern (32 bp):
AATTTTGTATTTATTATTGAATAAATTATTGT
Done.