Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3818
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: 47682
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4099 original size:46 final size:46
Alignment explanation
Indices: 4049--4205 Score: 169
Period size: 46 Copynumber: 3.4 Consensus size: 46
4039 TGGTTGAGCA
4049 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
4095 TCCGAACTCATTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
**
4140 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
4188 CCCGAGCTCGTTGAGTTG
1 TCCGAACTCGTTGAGTTG
4206 TGTACCCCCG
Statistics
Matches: 90, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.06
45 3 0.03
46 44 0.49
47 28 0.31
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5904 original size:47 final size:47
Alignment explanation
Indices: 5741--6487 Score: 575
Period size: 47 Copynumber: 15.4 Consensus size: 47
5731 CCTTCGAGAA
* * * * * * *
5741 CTTATCAACATTTATGCACTTTCACA-TCATTACGTTGGCCACTCGGC
1 CTTATC-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5788 CCTGTCACATATATAC-CTTT-ACCATTCAAT-ACATCGGCCCATTAGG-
1 CTTATCACATATATACACTTTCA-CATTC-ATCACATCGG-CCATTAGGC
*
5834 CTTATCACATATATACACTTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACAC-TTTCACATTCATCACATCGGCCATTAGGC
*
5882 CTTATCACATAT-TACCACTTTCACATTCATCACATCGGGCATTTAGG-
1 CTTATCACATATATA-CACTTTCACATTCATCACATCGGCCA-TTAGGC
* *
5929 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
5976 CTTATTCACACATAATACAC-TTGACATTCATCAC-GCGGCTATTAGGC
1 CTTA-TCACATAT-ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
6023 CTTATCACACATATACACTTT-ACA-TCATCACATCGGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATC-GGCCATTAGGC
* * *
6069 CTTATTAAATATATACAACACTTTCACATTCATCACATCGGACTATTAGGCCC
1 CTTATCACATATAT---ACACTTTCACATTCATCACATCGG-CCATTAGG--C
* * * * *
6122 CTTATCAAACATATACACTTTCACATTCATGCA-GTCCGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCAT-CACATCGGCCATTAGGC
* * *
6169 CTTATCACACATAAATACACTTTCACATTCATCACGTCGGCTATTAGG-
1 CTTAT--CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
6217 CTTATTACATCTATCATATACTTTCAC-TTCATCACATC-GCCATTAGGC
1 CTTATCACA--TAT-ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
6265 CTTATCAGCAATATATAAATACACTTTCA-ATTCAT-ACAT-GG-CGTTTGG-
1 CTTATCA-C---ATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
6313 CTTATTACATATGTACATATACTTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATA--T--ATACACTTT-CACATTCATCACATCGGCCATTAGGC
* *
6365 CTTAATCACATATATACTAGAAAAAACACTTCACATTCATCACATCGGCCCCTTAGGC
1 CTT-ATCACATATATAC--------AC-TTTCACATTCATCACATCGG-CCATTAGGC
*
6423 CTTATCACATATACTACAC-TTCTCATTCATCACATCGG-CATTAGGC
1 CTTATCACATATA-TACACTTTCACATTCATCACATCGGCCATTAGGC
*
6469 CTTATTACATATATACACT
1 CTTATCACATATATACACT
6488 CTCTTGCTGA
Statistics
Matches: 584, Mismatches: 54, Indels: 125
0.77 0.07 0.16
Matches are distributed among these distances:
44 11 0.02
45 21 0.04
46 98 0.17
47 118 0.20
48 110 0.19
49 80 0.14
50 36 0.06
51 41 0.07
52 4 0.01
53 20 0.03
57 29 0.05
58 16 0.03
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:6250 original size:242 final size:234
Alignment explanation
Indices: 5792--6487 Score: 550
Period size: 242 Copynumber: 2.9 Consensus size: 234
5782 CTCGGCCCTG
* *
5792 TCACATATATACCTTTACCATTCAATACATCGGCCCATTAGGCTTATCACATATATACACTTTTC
1 TCACA-ATATACCTTTACCATTCAATACATCGGCCCATTAGGCTTATCAAATATATACACCTTTC
* *
5857 ACATTCATCGCATCGGCCATTAGGCCTTATCACATATTACCACTTTCACATTCATCACATCGGGC
65 ACATTCATCACATCGGCCATTAGGCCTTATCACATATTACCACTTTCACATTCATCACATCGCGC
* *
5922 ATTTAGGCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATTCACAC
130 ATTTAGGCTTATCACATAAATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATTCACAC
* *
5987 ATAATACACTTGACATTCATCAC-GCGGCTATTAGGCCTTA
195 ATAATACACTTCACATTCATCACAGC-GCCATTAGGCCTTA
* * *
6027 TCACACATATACACTTTA-CA-TC-ATCACATCGGGCTATTAGGCCTTATTAAATATATACAACA
1 TCACA-ATATAC-CTTTACCATTCAAT-ACATCGGCCCATTAGG-CTTATCAAATATATAC-AC-
*
6089 CTTTCACATTCATCACATCGGACTATTAGGCCCCTTATCAAACATA-TA-CACTTTCACATTCAT
60 CTTTCACATTCATCACATCGG-CCATTAGG--CCTTATC--ACATATTACCACTTTCACATTCAT
* *
6152 GCA-GTC-CGC-TATTAGGCCTTATCACACATAAATACACTTTCACATTCATCACGTCGGCTATT
120 -CACATCGCGCAT-TTAGG-CTTAT--CACATAAATACACTTTCACATTCATCACATCGGCTATT
* * *
6214 AGG-CTTATT-ACATCTATCATATACTTTCAC-TTCATCACATCGCCATTAGGCCTTA
180 AGGCCTTATTCACA-C-ATAATACAC-TTCACATTCATCACAGCGCCATTAGGCCTTA
**** * * * * * * *
6269 TCAGCAATATATAAATACACTTTCAATTCATACATGG--CGTTTGGCTTATTACATATGTACATA
1 TCA-CAATATACCTTTAC-CATTCAATACAT-C--GGCCCATTAGGCTTATCAAATATATAC--A
*
6332 TACTTTCCACATTCATCACATCGGCCATTAGGCCTTAATCACATATATACTAGAAAAAACAC-TT
59 -CCTTT-CACATTCATCACATCGGCCATTAGGCCTT-ATCACATAT-TAC---------CACTTT
** * *
6396 CACATTCATCACATCG-GCCCCTTAGGCCTTATCACATATACTACAC-TTCTCATTCATCACATC
111 CACATTCATCACATCGCG-CATTTAGG-CTTATCACATA-AATACACTTTCACATTCATCACATC
*
6459 GGC-ATTAGGCCTTATT-ACATAT-ATACACT
173 GGCTATTAGGCCTTATTCACACATAATACACT
6488 CTCTTGCTGA
Statistics
Matches: 373, Mismatches: 39, Indels: 85
0.75 0.08 0.17
Matches are distributed among these distances:
233 2 0.01
234 16 0.04
235 27 0.07
236 7 0.02
237 19 0.05
238 8 0.02
239 7 0.02
240 32 0.09
241 13 0.03
242 84 0.23
243 12 0.03
244 24 0.06
245 19 0.05
246 17 0.05
247 2 0.01
248 1 0.00
249 5 0.01
250 2 0.01
251 6 0.02
252 35 0.09
253 20 0.05
254 15 0.04
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (234 bp):
TCACAATATACCTTTACCATTCAATACATCGGCCCATTAGGCTTATCAAATATATACACCTTTCA
CATTCATCACATCGGCCATTAGGCCTTATCACATATTACCACTTTCACATTCATCACATCGCGCA
TTTAGGCTTATCACATAAATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATTCACACA
TAATACACTTCACATTCATCACAGCGCCATTAGGCCTTA
Found at i:6506 original size:48 final size:46
Alignment explanation
Indices: 6390--6487 Score: 144
Period size: 48 Copynumber: 2.1 Consensus size: 46
6380 ACTAGAAAAA
* *
6390 ACACTTCACATTCATCACATCGGCCCCTTAGGCCTTATCACATATACT
1 ACACTTCTCATTCATCACATCGG--CATTAGGCCTTATCACATATACT
*
6438 ACACTTCTCATTCATCACATCGGCATTAGGCCTTATTACATATA-T
1 ACACTTCTCATTCATCACATCGGCATTAGGCCTTATCACATATACT
6483 ACACT
1 ACACT
6488 CTCTTGCTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
45 6 0.13
46 19 0.40
48 22 0.47
ACGTcount: A:0.29, C:0.32, G:0.08, T:0.32
Consensus pattern (46 bp):
ACACTTCTCATTCATCACATCGGCATTAGGCCTTATCACATATACT
Found at i:10687 original size:93 final size:93
Alignment explanation
Indices: 10574--10745 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
10564 CGCCCATAAG
* *
10574 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
10639 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
10667 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
10732 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
10746 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:10742 original size:46 final size:46
Alignment explanation
Indices: 10567--10742 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
10557 TGTAACCCGC
* * *
10567 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
10613 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
10663 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
10706 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
10743 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:17167 original size:42 final size:44
Alignment explanation
Indices: 17063--17168 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
17053 GAGATGTCGG
* * *
17063 GTAAGACCGTGTCTGGGACATAGGCCTTTATTTGAGATTTACGT
1 GTAAGACCATGTCTGGGACATAGGCATATATTTGAGATTTACGT
17107 GTAAGACCATGTCTGGGACATAGGCATCATATTTG-G-TTT-CGT
1 GTAAGACCATGTCTGGGACATAGGCAT-ATATTTGAGATTTACGT
* *
17149 GTAAGACCCTGTCAGGGACA
1 GTAAGACCATGTCTGGGACA
17169 GAGGTATCGA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 21 0.38
43 3 0.05
44 26 0.46
45 6 0.11
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (44 bp):
GTAAGACCATGTCTGGGACATAGGCATATATTTGAGATTTACGT
Found at i:18924 original size:68 final size:64
Alignment explanation
Indices: 18814--19067 Score: 221
Period size: 68 Copynumber: 3.9 Consensus size: 64
18804 ATACAAATAG
* ** * * *
18814 TATGTAGCTAGGTCACATGTATGGTGCTGA-GTGTACATCATGT-GTACAAGAGAGCTACAAGAC
1 TATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGCTAC--GAG
18877 ATTA
62 A-TA
* *
18881 TGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATA
1 T-ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
* * * * *
18946 TATGTAGTTAGGTCGCATGCGTGGTTCTAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 TATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
19011 TA
63 TA
* * * *
19013 AAT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGCT
1 TATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGCT
19068 GAACTATATG
Statistics
Matches: 155, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 20 0.13
64 25 0.16
65 3 0.02
66 23 0.15
67 35 0.23
68 47 0.30
69 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (64 bp):
TATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
Found at i:23384 original size:93 final size:93
Alignment explanation
Indices: 23224--23393 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 93
23214 GCCCATAAGC
* * *
23224 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTAAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTAAA
23289 CGAGTTCGGATGCCTAGTTACATCTCAT
66 CGAGTTCGGATGCCTAGTTACATCTCAT
* * * *
23317 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTGAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTAAA
23382 CGAGTTCGGATG
66 CGAGTTCGGATG
23394 GTCAACCATC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTAAA
CGAGTTCGGATGCCTAGTTACATCTCAT
Found at i:23391 original size:46 final size:46
Alignment explanation
Indices: 23216--23391 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
23206 TGTAACCCGC
* * * * *
23216 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * * *
23262 CCATGAGTGAACTCGGACTCAACTAAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
*
23312 -C-TCA-TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
*
23355 CCATAAGTGAACTCGGACTGAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
23392 TGGTCAACCA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:25797 original size:15 final size:15
Alignment explanation
Indices: 25768--25817 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
25758 CAAAGATAAC
*
25768 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
25782 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
25797 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
25812 AAGAAA
1 AAGAAA
25818 CCCAAGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.60, C:0.12, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:25826 original size:15 final size:15
Alignment explanation
Indices: 25779--25826 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
25769 AGAAAACCGA
25779 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
25793 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
25809 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
25824 ATA
1 ATA
25827 CGATACTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:28906 original size:46 final size:46
Alignment explanation
Indices: 28727--28906 Score: 227
Period size: 46 Copynumber: 3.8 Consensus size: 46
28717 TGTAACCCGC
* * * *
28727 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* *
28773 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
28823 CTC-GAACTCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
28870 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28907 TGCTCAACCA
Statistics
Matches: 115, Mismatches: 12, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
46 65 0.57
47 10 0.09
48 1 0.01
49 1 0.01
50 8 0.07
51 30 0.26
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:34491 original size:36 final size:37
Alignment explanation
Indices: 34419--34496 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
34409 TTATTACGAA
* *
34419 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACATAATCCCCACACGAAGTCATCGG
*
34456 GTCTTACCCGGACA-AATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCCCCACACGAAGTCATCGG
34492 GTCTT
1 GTCTT
34497 TAGAGCTCAG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 24 0.63
37 14 0.37
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCCCCACACGAAGTCATCGG
Found at i:34774 original size:47 final size:47
Alignment explanation
Indices: 34614--34935 Score: 545
Period size: 47 Copynumber: 6.7 Consensus size: 47
34604 GCCCTTCGGG
*
34614 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
34664 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
34713 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
34760 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* *
34807 GCTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
34854 GCTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
34901 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
34936 CTATCATTTC
Statistics
Matches: 265, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
47 178 0.67
49 83 0.31
50 4 0.02
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:38369 original size:39 final size:39
Alignment explanation
Indices: 38307--38410 Score: 172
Period size: 39 Copynumber: 2.7 Consensus size: 39
38297 CCAACACAAC
*
38307 TGCCTTCGGGACTTAGCCTAGATATAACACCAGCACGAA
1 TGCCTTCGGGACTTAGCCCAGATATAACACCAGCACGAA
* * *
38346 TGCCTTCGGGACTTGGCCCAGATATATCATCAGCACGAA
1 TGCCTTCGGGACTTAGCCCAGATATAACACCAGCACGAA
38385 TGCCTTCGGGACTTAGCCCAGATATA
1 TGCCTTCGGGACTTAGCCCAGATATA
38411 CATCAAGCGA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (39 bp):
TGCCTTCGGGACTTAGCCCAGATATAACACCAGCACGAA
Found at i:42036 original size:39 final size:39
Alignment explanation
Indices: 41868--42057 Score: 191
Period size: 40 Copynumber: 4.9 Consensus size: 39
41858 TTGAATGATG
* * * *
41868 TCCGGGCTAAGTC-CGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGG-TAAGTCTCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
41907 TCCGGACTAAGATC-CGAAGGCATTTGTGCGAGATACTAAT
1 TCCGG-GTAAG-TCTCGAAGGCATTTGTGCGAGTTACTAAA
*
41947 TCCGGGCTAAG-C-CGAAGGCATTGGTGCGAGTT--TAAA
1 TCCGGG-TAAGTCTCGAAGGCATTTGTGCGAGTTACTAAA
41983 T-CGGGTAAGTCTCGAAGGCATTTGT-CGAGTTACTAAA
1 TCCGGGTAAGTCTCGAAGGCATTTGTGCGAGTTACTAAA
42020 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTA
1 TCCGGG-TAAGTCTCGAAGGCATTTGTGCGAGTTACTA
42058 TAACGGGCTA
Statistics
Matches: 128, Mismatches: 12, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
34 4 0.03
35 11 0.09
36 16 0.12
37 5 0.04
38 23 0.18
39 29 0.23
40 33 0.26
41 7 0.05
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTAAGTCTCGAAGGCATTTGTGCGAGTTACTAAA
Done.