Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold315
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: 43591
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1876 original size:40 final size:40
Alignment explanation
Indices: 1814--2089 Score: 239
Period size: 40 Copynumber: 7.2 Consensus size: 40
1804 CGGATGATAA
*
1814 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAAT-T
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCTAGT-GCTAATAT
* * *
1854 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGCTAATAT
*
1894 -CGGGCTAAGTCCCGAAGGC--TTGTGC--GAGCTATATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTA-ATAT
* *
1930 -CGGGCTAAGT-CCGAAGGCATTTGT-C--GAGCTATTAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTAATAT
* * *
1965 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGT-ATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTAATAT
* * *
2002 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGCTAATAT
*
2042 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GCTAATAT
2082 CC-GGCTAA
1 CCGGGCTAA
2090 ACTCCGAAGG
Statistics
Matches: 202, Mismatches: 18, Indels: 33
0.80 0.07 0.13
Matches are distributed among these distances:
34 2 0.01
35 12 0.06
36 45 0.22
37 21 0.10
38 21 0.10
39 33 0.16
40 65 0.32
41 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTAATAT
Found at i:1936 original size:36 final size:38
Alignment explanation
Indices: 1855--2064 Score: 265
Period size: 36 Copynumber: 5.6 Consensus size: 38
1845 TGGCTAATTC
1855 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATAT
1 CGGGCTAAGTCCCGAAGGCATT-GTGCGAGCTACTATAT
1894 CGGGCTAAGTCCCGAAGGC-TTGTGCGAGCTA-TATAT
1 CGGGCTAAGTCCCGAAGGCATTGTGCGAGCTACTATAT
1930 CGGGCTAAGT-CCGAAGGCATT-TGTCGAGCTA-T-TAT
1 CGGGCTAAGTCCCGAAGGCATTGTG-CGAGCTACTATAT
* *
1965 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAG-TATTATAC
1 -CGGGCTAAGTCCCGAAGGCA-TTGTGCGAGCTACTATAT
* * *
2003 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCA-TTGTGCGAGCTACTAT-AT
2043 CGGGCTAAGTCCCGAAGGCATT
1 CGGGCTAAGTCCCGAAGGCATT
2065 TGAGCTAGTG
Statistics
Matches: 158, Mismatches: 3, Indels: 20
0.87 0.02 0.11
Matches are distributed among these distances:
35 13 0.08
36 46 0.29
37 27 0.17
38 24 0.15
39 26 0.16
40 22 0.14
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (38 bp):
CGGGCTAAGTCCCGAAGGCATTGTGCGAGCTACTATAT
Found at i:1990 original size:73 final size:78
Alignment explanation
Indices: 1814--2066 Score: 310
Period size: 73 Copynumber: 3.3 Consensus size: 78
1804 CGGATGATAA
* * * * * *
1814 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAATTCCGGGCTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGT--ATTATACCGGGCTAAGTCCCGAAGGCATTT
1878 GTGCGAGCTACTATAT
63 GTGCGAGCTACTATAT
*
1894 -CGGGCTAAGTCCCGAAGGC--TTGTGCGAGCTA-TATATCGGGCTAAGT-CCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TATTATACCGGGCTAAGTCCCGAAGGCATTTGT
1954 -CGAGCTA-T-TAT
65 GCGAGCTACTATAT
1965 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTATTATACCGGGCTAAGTCCCGAAGGCATTTGTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTATTATACCGGGCTAAGTCCCGAAGGCATTTGTG
* * *
2029 CAAGTTACTATAA
66 CGAGCTACTATAT
2042 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
2067 AGCTAGTGGC
Statistics
Matches: 151, Mismatches: 11, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
71 11 0.07
72 13 0.09
73 30 0.20
74 27 0.18
75 17 0.11
76 1 0.01
77 20 0.13
78 14 0.09
79 16 0.11
80 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTATTATACCGGGCTAAGTCCCGAAGGCATTTGTG
CGAGCTACTATAT
Found at i:9963 original size:40 final size:39
Alignment explanation
Indices: 9901--10227 Score: 374
Period size: 40 Copynumber: 8.2 Consensus size: 39
9891 CGGATGATAA
* * *
9901 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGT-ACTATA-T
*
9941 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
*
9981 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
*
10021 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* *
10061 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* * * * *
10101 CTGGGCTAATTCCTGAAGGCGTTTGTGCGAGCTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* *
10140 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* * *
10180 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATAT
10220 CC-GGCTAA
1 CCGGGCTAA
10228 ACTCCGAAGG
Statistics
Matches: 261, Mismatches: 21, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
39 39 0.15
40 218 0.84
41 4 0.02
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
Found at i:10034 original size:80 final size:80
Alignment explanation
Indices: 9901--10202 Score: 414
Period size: 80 Copynumber: 3.8 Consensus size: 80
9891 CGGATGATAA
* * *
9901 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAG-TGGCTA-ATTCCGGGCTAAGTCCCGAAGGCAT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGCT-ACTATA-TCCGGGCTAAGTCCCGAAGGCAT
9963 TCGTGCGAGCTACTATAT
63 TCGTGCGAGCTACTATAT
*
9981 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTCG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTCG
10046 TGCGAGCTACTATAT
66 TGCGAGCTACTATAT
* * * * * * *
10061 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTATTATATCTGGGCTAATTCCTGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTCG
*
10126 TGCGAGCTATTATA-
66 TGCGAGCTACTATAT
* * *
10140 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATT
10203 TGAGCTAGTG
Statistics
Matches: 197, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
79 54 0.27
80 139 0.71
81 4 0.02
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGCTACTATAT
Found at i:18590 original size:37 final size:37
Alignment explanation
Indices: 18540--18618 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
18530 TTATTACGAA
* * *
18540 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
18577 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
18614 GTCTT
1 GTCTT
18619 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:18881 original size:47 final size:47
Alignment explanation
Indices: 18737--19397 Score: 1063
Period size: 47 Copynumber: 14.1 Consensus size: 47
18727 CCCTTCGGGA
* * * * * * *
18737 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
18784 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
18830 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
18877 CTTATTATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18924 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
18971 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19018 CTTATCACCTATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
19065 CTTATCACATATATACTCTTTCACATTCATCACATCGGCTATTAGCC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19112 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
19159 CTTATTATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19206 CTTATCACCTATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19253 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
19300 CTTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19347 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19394 CTTA
1 CTTA
19398 CTATCATTTC
Statistics
Matches: 570, Mismatches: 43, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 0.07
47 531 0.93
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:22894 original size:48 final size:46
Alignment explanation
Indices: 22820--23178 Score: 251
Period size: 48 Copynumber: 7.7 Consensus size: 46
22810 TGAATTGTCA
* **
22820 ATGCCATGTCACAGACATGGTCTTACACTGGCTCACATGTTGAGGCTG
1 ATGCCATGTC-CA-ACATGGTCTTACACTGGCTCACATATCAAGGCTG
* * * ** * *
22868 ATGCCATGTCCCAGACATGGTTTTACACTAGCCCTTATAT-AGTGGCCG
1 ATGCCATGT-CCA-ACATGGTCTTACACTGGCTCACATATCA-AGGCTG
* * *
22916 ACGCCATGTCACAAACATGGTCTTACACTGGCTCACA-ATCAATGTTG
1 ATGCCATGTC-C-AACATGGTCTTACACTGGCTCACATATCAAGGCTG
** *** * * * *
22963 ATGAAATGTTTGACATGGTCCTACACTGGCTCTCATAATCAACGCCG
1 ATGCCATGTCCAACATGGTCTTACACTGGCTCACAT-ATCAAGGCTG
* * ***
23010 ATGCCACGTCCAACATGGTCTTACACTGGCTCTCATATGGTGGCTG
1 ATGCCATGTCCAACATGGTCTTACACTGGCTCACATATCAAGGCTG
* * * *
23056 ATGCCATGTTCAACATGGTCTTGCACTGGCTCACA-GTCAACGCTG
1 ATGCCATGTCCAACATGGTCTTACACTGGCTCACATATCAAGGCTG
* * * **
23101 ATGCCATGTCCAACATGGTCTTACACTAGCT-ATCATAACATA-ACCA
1 ATGCCATGTCCAACATGGTCTTACACTGGCTCA-CATATCA-AGGCTG
23147 ATGCCATGTTCCCAACATGGTCTTACACTGGC
1 ATGCCATG-T-CCAACATGGTCTTACACTGGC
23179 ATACGAAATG
Statistics
Matches: 239, Mismatches: 60, Indels: 24
0.74 0.19 0.07
Matches are distributed among these distances:
44 1 0.00
45 56 0.23
46 47 0.20
47 49 0.21
48 84 0.35
49 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (46 bp):
ATGCCATGTCCAACATGGTCTTACACTGGCTCACATATCAAGGCTG
Found at i:23103 original size:138 final size:140
Alignment explanation
Indices: 22867--23231 Score: 357
Period size: 138 Copynumber: 2.6 Consensus size: 140
22857 TGTTGAGGCT
* * *
22867 GATGCCATGTCCCAGACATGGTTTTACACTAGCCCTTATATAGTGGCCGACGCCATGTCACAAAC
1 GATGCCATGTCCCA-ACATGGTCTTACACTGGCCCTCATATAGTGGCCGACGCCATGTCACAAAC
* * *** * *
22932 ATGGTCTTACACTGGCTCACAATCAATGTTGATGAAATGTTTGACATGGTCCTACACTGGCTCTC
65 ATGGTCTTACACTGGCTCACAATCAACGCTGATGAAATGTCCAACATGGTCCTACACTAGCTATC
*
22997 ATAATCA-ACGCC
130 ATAA-CATA-ACC
* * * * * *
23009 GATGCCACGT-CCAACATGGTCTTACACTGGCTCTCATATGGTGGCTGATGCCATGT-TC-AACA
1 GATGCCATGTCCCAACATGGTCTTACACTGGCCCTCATATAGTGGCCGACGCCATGTCACAAACA
* * ** *
23071 TGGTCTTGCACTGGCTCACAGTCAACGCTGATGCCATGTCCAACATGGTCTTACACTAGCTATCA
66 TGGTCTTACACTGGCTCACAATCAACGCTGATGAAATGTCCAACATGGTCCTACACTAGCTATCA
23136 TAACATAACC
131 TAACATAACC
* * * * *
23146 AATGCCATGTTCCCAACATGGTCTTACACTGG-CATACGAAAT-GTGGCCAATGCCATGTC-CAA
1 GATGCCATG-TCCCAACATGGTCTTACACTGGCCCT-C-ATATAGTGGCCGACGCCATGTCACAA
* *
23208 GACATGGTTTTACACTAGCTCACA
63 -ACATGGTCTTACACTGGCTCACA
23232 TGTCACCCCA
Statistics
Matches: 183, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
137 11 0.06
138 63 0.34
139 37 0.20
140 40 0.22
141 23 0.13
142 9 0.05
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (140 bp):
GATGCCATGTCCCAACATGGTCTTACACTGGCCCTCATATAGTGGCCGACGCCATGTCACAAACA
TGGTCTTACACTGGCTCACAATCAACGCTGATGAAATGTCCAACATGGTCCTACACTAGCTATCA
TAACATAACC
Found at i:23151 original size:91 final size:92
Alignment explanation
Indices: 22975--23178 Score: 239
Period size: 91 Copynumber: 2.2 Consensus size: 92
22965 GAAATGTTTG
* * * *
22975 ACATGGTCCTACACTGGCTCTCATAATCAACGCCGATGCCACGTCCAACATGGTCTTACACTGGC
1 ACATGGTCTTACACTGG--CTCACAGTCAACGCCGATGCCACGTCCAACATGGTCTTACACTAGC
* *** ** **
23040 TCTCATATGGTGGCTGATGCCATGTT-CA
64 TATCATAACATAACCAATGCCATGTTCCA
* * *
23068 ACATGGTCTTGCACTGGCTCACAGTCAACGCTGATGCCATGTCCAACATGGTCTTACACTAGCTA
1 ACATGGTCTTACACTGGCTCACAGTCAACGCCGATGCCACGTCCAACATGGTCTTACACTAGCTA
23133 TCATAACATAACCAATGCCATGTTCCCA
66 TCATAACATAACCAATGCCATGTT-CCA
23161 ACATGGTCTTACACTGGC
1 ACATGGTCTTACACTGGC
23179 ATACGAAATG
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
91 59 0.63
93 34 0.37
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (92 bp):
ACATGGTCTTACACTGGCTCACAGTCAACGCCGATGCCACGTCCAACATGGTCTTACACTAGCTA
TCATAACATAACCAATGCCATGTTCCA
Found at i:27943 original size:75 final size:75
Alignment explanation
Indices: 27827--27972 Score: 256
Period size: 75 Copynumber: 1.9 Consensus size: 75
27817 TTGACACGCC
* * *
27827 CGTGTCCTCAGGCCATGTAACTCTCTAGCTATGATGTCAGCGAATAATTTGAAATACATGGCCAA
1 CGTGTCCTCAAGCCATGTAACTCTCTAGCTATGACGTCAGCGAATAATTTGAAACACATGGCCAA
27892 GCCACACGTT
66 GCCACACGTT
*
27902 CGTGTCCTCAAGCCATGTAACTCTCTGGCTATGACGTCAGCGAATAATTTGAAACACATGGCCAA
1 CGTGTCCTCAAGCCATGTAACTCTCTAGCTATGACGTCAGCGAATAATTTGAAACACATGGCCAA
27967 GCCACA
66 GCCACA
27973 TGCCCGTATG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.25
Consensus pattern (75 bp):
CGTGTCCTCAAGCCATGTAACTCTCTAGCTATGACGTCAGCGAATAATTTGAAACACATGGCCAA
GCCACACGTT
Found at i:29746 original size:48 final size:48
Alignment explanation
Indices: 29675--29956 Score: 209
Period size: 48 Copynumber: 5.8 Consensus size: 48
29665 TGAATTGCCA
* *
29675 ATGCCATGTCGCAGACATGGTCTTACACTAGCTCACATGTTGAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTTGAGGCCG
* * * ** *
29723 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTTGAGGCCG
* * * * * * *
29771 AGGCCATGT-CCA-ACGTGGTCTTACATTGGCTCTCATATGGTGGCCGACGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG--CTCACAT-GT---TGAGGCCG
* * **
29823 ATGCCATGT-CCA-ACATGGTCTTACACTGGCTCTCATAACAT-A-GCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT--GTTGAGGCCG
* * *** *
29869 ATGCCATGTTCCAAACATGGTCTTACACTAGCAT-ACAAAATGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGC-TCACATGTTGAGGCCG
29917 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGT
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGT
29957 CACCCAAAAT
Statistics
Matches: 184, Mismatches: 37, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
46 29 0.16
47 8 0.04
48 108 0.59
49 2 0.01
50 5 0.03
52 32 0.17
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTTGAGGCCG
Found at i:29869 original size:52 final size:52
Alignment explanation
Indices: 29767--29897 Score: 146
Period size: 52 Copynumber: 2.6 Consensus size: 52
29757 TCGTCTCAAT
* * * *** *
29767 GCCGAGGCCATGTCCAACGTGGTCTTACATTGGCTCTCATATGGTGGCCGAC
1 GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACATAGCCGAC
*
29819 GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACATAGCCGAT
1 GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACATAGCCGAC
29871 GCC-ATG---T-TCCAAACATGGTCTTACACT
1 GCCGATGCCATGTCC-AACATGGTCTTACACT
29898 AGCATACAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
47 3 0.04
48 17 0.24
51 3 0.04
52 47 0.67
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (52 bp):
GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACATAGCCGAC
Done.