Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold579
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: 36893
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:6468 original size:96 final size:96
Alignment explanation
Indices: 6286--8534 Score: 3101
Period size: 96 Copynumber: 23.3 Consensus size: 96
6276 CGCTGCGGGA
* * * * * * * *
6286 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
6349 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
6380 CTTATCACATATATACACTTTAACATTCATCACATC-GCCATTAGGCCTTATCACATATATATAA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT-A
6444 CACTTTCACATTCATCACATCGGCCATTAGGC
65 CACTTTCACATTCATCACATCGGCCATTAGGC
* *
6476 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
6541 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
6572 CTTATCACATATATACACTTTAACCATTCATCACATCGGCCATTAGGCC-TATCACATATATATA
1 CTTATCACATATATACACTTTCA-CATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
*
6636 CACCTTTCACATTCATCACATCGGCCATTAGCC
65 CA-CTTTCACATTCATCACATCGGCCATTAGGC
* *
6669 CTTATCACATATATACACTTTCACATTC-TCACAATCGGCCATTAAGCCCTATCACATATATATA
1 CTTATCACATATATACACTTTCACATTCATCAC-ATCGGCCATTAGGCCTTATCACATATATATA
6733 CACTTTCACATTCATCACATCGGCCATTAGGC
65 CACTTTCACATTCATCACATCGGCCATTAGGC
6765 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
*
6828 ACACTTTCATATTCATCACATCGGCCATTA-GC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
6860 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
*
6923 ACACTTTCACATTCATCACATCGGCCCATTAAGC
64 ACACTTTCACATTCATCACATCGG-CCATTAGGC
*
6957 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
*
7022 AACAC-TTCTCATTCATCACATCGGCCATTAGGC
64 -ACACTTTCACATTCATCACATCGGCCATTAGGC
*
7055 CTTATCACAATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
1 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
*
7120 CACTTTCACATTCATCACATCAGCCATTAGGC
65 CACTTTCACATTCATCACATCGGCCATTAGGC
* *
7152 CTGCCA-AACTATATATACACTTTCACATTCATCACATC-GCCATTAGGCCTTAT--CA-ATATA
1 CT--TATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
7212 TACACTTTCACATTCATCACATACGG-CATTA-GC
63 TACACTTTCACATTCATCACAT-CGGCCATTAGGC
*
7245 GCTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
1 -CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
* *
7310 CACTTTCACATTCATCACATCAGCCATTAGGA
65 CACTTTCACATTCATCACATCGGCCATTAGGC
7342 CTTATCACATATATACACTTTCACATTCATCACATC-GCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
7406 ACTTTCACATTCATTACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
7437 CTTATCACATATATACACTTTCA-ATACTCATCACATCGGCCATTAGG-CTTATCACATATATAT
1 CTTATCACATATATACACTTTCACAT--TCATCACATCGGCCATTAGGCCTTATCACATATATAT
* *
7500 ACACTTTCATACTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7533 CTTATCACATATATATACACTTTCACATTCATCACATTCTGCCCATTA-CCCTTATCAC--ATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACA-TC-GGCCATTAGGCCTTATCACATATAT
7595 ATACACTTTCACATTCAATCACATCGGCCATTAGGC
62 ATACACTTTCACATTC-ATCACATCGGCCATTAGGC
*
7631 CTTTATCCATATATATAACACTTTCACATTCATCACATCGGCCATTA-GCCTTATCACATATATA
1 C-TTAT-CACATATAT-ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
7695 T--ACTTTCACATTCATCACAATGACGGCCATTAGGC
63 TACACTTTCACATTCATCAC-AT--CGGCCATTAGGC
* *
7730 CTTATCACATATAATACAC-TT-ACTATTCATCACATATCACATGCCATTAGGCCTCTAATCAGA
1 CTTATCACATAT-ATACACTTTCAC-ATTCATCAC--AT--C-GGCCATTAGGCCT-T-ATCACA
*
7793 TATATATACACTTTCACATTCATCACATCAGCCATTAGGC
57 TATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7833 C-TATCACATATATATCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATA
1 CTTATCACATATATA-CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
7895 CACTTTTCAACATTCATCACATCGGCCATTAGGC
65 CAC-TTTC-ACATTCATCACATCGGCCATTAGGC
* * *
7929 CTTATCACATATATATAACTATCATTATTCATCACA-CGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATA-CACTTTCA-CATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
**
7993 ACACTTTTCACATTCATTCACATC-AACATTAGGAC
64 ACAC-TTTCACATTCA-TCACATCGGCCATTAGG-C
*
8028 TTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
8091 ACTTTCACATTCATTACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
8122 CTTATCACATATATACACTTTCA-ATACTCATCACATCGGCCCATTAGGCCTTATCACATATATA
1 CTTATCACATATATACACTTTCACAT--TCATCACATCGG-CCATTAGGCCTTATCACATATATA
* * *
8186 TACACTTTCATACTCATGACATCGGCCATTAGGC
63 TACACTTTCACATTCATCACATCGGCCATTAGGC
*
8220 CTTATCACATATATATACACTTTCACATTCATCACATCGGCC-TTA-GCCTTATCA-ACATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
8282 ACACTTTCACATTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
8315 CTTATCACATATATATACACTTTCACATTCATCACAATCGGCCATTAGG-CTTATCAC---TATA
1 CTTATCAC--ATATATACACTTTCACATTCATCAC-ATCGGCCATTAGGCCTTATCACATATATA
8376 TACACTTTCACATTCATCACATCGG-CATTA-GC
63 TACACTTTCACATTCATCACATCGGCCATTAGGC
* *
8408 CTTATCACAT-TATATACTTTCAACATTCTACCACTATCGGACTCCATTAGGCCTTATCACATAT
1 CTTATCACATATATACACTTTC-ACATTC-ATCAC-ATCGG---CCATTAGGCCTTATCACATAT
* *
8472 -TATATCACTTTCGCATTCATCACATCGTCCAATTAGG-
60 ATATA-CACTTTCACATTCATCACATCGGCC-ATTAGGC
8509 -TTATCA-ATA-ATACAC-TTCACATTCAT
1 CTTATCACATATATACACTTTCACATTCAT
8535 AATATTGTAT
Statistics
Matches: 1970, Mismatches: 88, Indels: 192
0.88 0.04 0.09
Matches are distributed among these distances:
90 10 0.01
91 8 0.00
92 37 0.02
93 45 0.02
94 111 0.06
95 330 0.17
96 469 0.24
97 417 0.21
98 253 0.13
99 168 0.09
100 29 0.01
101 18 0.01
102 18 0.01
103 24 0.01
104 14 0.01
105 2 0.00
106 17 0.01
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:6540 original size:49 final size:49
Alignment explanation
Indices: 6286--8534 Score: 3096
Period size: 49 Copynumber: 46.7 Consensus size: 49
6276 CGCTGCGGGA
* * * * *
6286 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
6333 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6380 CTTATCAC--ATATATACACTTTAACATTCATCACATC-GCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6426 CTTATCACATATATATAACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATAT-ACACTTTCACATTCATCACATCGGCCATTAGGC
*
6476 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6523 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6572 CTTATCAC--ATATATACACTTTAACCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCA-CATTCATCACATCGGCCATTAGGC
*
6620 C-TATCACATATATATACACCTTTCACATTCATCACATCGGCCATTAGCC
1 CTTATCACATATATATACA-CTTTCACATTCATCACATCGGCCATTAGGC
*
6669 CTTATCAC--ATATATACACTTTCACATTC-TCACAATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCAC-ATCGGCCATTAGGC
*
6716 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6765 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6814 CTTATCAC--ATATATACACTTTCATATTCATCACATCGGCCATTA-GC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6860 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6909 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGG-CCATTAGGC
*
6957 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7006 CTTATCACATATATATAACAC-TTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATAT-ACACTTTCACATTCATCACATCGGCCATTAGGC
*
7055 CTTATCACA-ATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7103 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
** *
7152 C-TGCCAAACTATATATACACTTTCACATTCATCACATC-GCCATTAGGC
1 CTTATCACA-TATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7200 CTTAT--CA-ATATATACACTTTCACATTCATCACATACGG-CATTA-GC
1 CTTATCACATATATATACACTTTCACATTCATCACAT-CGGCCATTAGGC
*
7245 GCTTATCAC--ATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 -CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7293 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7342 CTTATCAC--ATATATACACTTTCACATTCATCACATC-GCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7388 CTTATCACATATATATACACTTTCACATTCATTACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7437 CTTATCAC--ATATATACACTTTCA-ATACTCATCACATCGGCCATTAGG-
1 CTTATCACATATATATACACTTTCACAT--TCATCACATCGGCCATTAGGC
* *
7484 CTTATCACATATATATACACTTTCATACTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7533 CTTATCACATATATATACACTTTCACATTCATCACATTCTGCCCATTA-CC
1 CTTATCACATATATATACACTTTCACATTCATCACA-TC-GGCCATTAGGC
7583 CTTATCAC--ATATATACACTTTCACATTCAATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTC-ATCACATCGGCCATTAGGC
7631 CTTTATC-CATATATATAACACTTTCACATTCATCACATCGGCCATTA-GC
1 C-TTATCACATATATAT-ACACTTTCACATTCATCACATCGGCCATTAGGC
7680 CTTATCACATATATAT--ACTTTCACATTCATCACAATGACGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCAC-AT--CGGCCATTAGGC
*
7730 CTTATCACATATA-ATACAC-TT-ACTATTCATCACATATCACATGCCATTAGGC
1 CTTATCACATATATATACACTTTCAC-ATTCATCAC--AT--C-GGCCATTAGGC
* *
7782 CTCTAATCAGATATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CT-T-ATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7833 C-TATCACATATATAT-CACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7880 CTTATCAC--ATATATACACTTTTCAACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACAC-TTTC-ACATTCATCACATCGGCCATTAGGC
* *
7929 CTTATCACATATATATA-ACTATCATTATTCATCACA-CGGCCATTAGGC
1 CTTATCACATATATATACACTTTCA-CATTCATCACATCGGCCATTAGGC
**
7977 CTTATCACATATATATACACTTTTCACATTCATTCACATC-AACATTAGGAC
1 CTTATCACATATATATACAC-TTTCACATTCA-TCACATCGGCCATTAGG-C
*
8028 TTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8075 CTTATCAC--ATATATACACTTTCACATTCATTACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8122 CTTATCAC--ATATATACACTTTCA-ATACTCATCACATCGGCCCATTAGGC
1 CTTATCACATATATATACACTTTCACAT--TCATCACATCGG-CCATTAGGC
* * *
8171 CTTATCACATATATATACACTTTCATACTCATGACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8220 CTTATCACATATATATACACTTTCACATTCATCACATCGGCC-TTA-GC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8267 CTTATCA-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8315 CTTATCACATATATATACACTTTCACATTCATCACAATCGGCCATTAGG-
1 CTTATCACATATATATACACTTTCACATTCATCAC-ATCGGCCATTAGGC
8364 CTTATCAC---TATATACACTTTCACATTCATCACATCGG-CATTA-GC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8408 CTTATCACAT-TATAT--ACTTTCAACATTCTACCACTATCGGACTCCATTAGGC
1 CTTATCACATATATATACACTTTC-ACATTC-ATCAC-ATCGG---CCATTAGGC
* *
8460 CTTATCACATAT-TATATCACTTTCGCATTCATCACATCGTCCAATTAGG-
1 CTTATCACATATATATA-CACTTTCACATTCATCACATCGGCC-ATTAGGC
8509 -TTAT--CA-ATA-ATACAC-TTCACATTCAT
1 CTTATCACATATATATACACTTTCACATTCAT
8535 AATATTGTAT
Statistics
Matches: 2008, Mismatches: 85, Indels: 222
0.87 0.04 0.10
Matches are distributed among these distances:
43 11 0.01
44 22 0.01
45 45 0.02
46 159 0.08
47 457 0.23
48 348 0.17
49 637 0.32
50 175 0.09
51 74 0.04
52 33 0.02
53 6 0.00
54 16 0.01
55 12 0.01
56 11 0.01
57 2 0.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:8954 original size:15 final size:15
Alignment explanation
Indices: 8922--8950 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
8912 ATTTTCAATG
8922 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
8937 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
8951 ATTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:14758 original size:26 final size:27
Alignment explanation
Indices: 14722--14774 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
14712 TGTCAGCTAG
* *
14722 TGAAATTTTAA-TGTTCGAATGTATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
*
14748 TGAATTTTTAAGTGTCCGAATGCATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
14775 CAGAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (27 bp):
TGAAATTTTAAGTGTCCGAATGCATGC
Found at i:16107 original size:48 final size:48
Alignment explanation
Indices: 16043--16190 Score: 206
Period size: 48 Copynumber: 3.1 Consensus size: 48
16033 TTGATGTACA
*
16043 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTAAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* * *
16091 AGATATATATATGTGGTAAAGTCGAAAGGCTAATGCGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
** ** * *
16139 AGCCATGCATATGTGGTAAAGGCAAATGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
16187 AGAT
1 AGAT
16191 GTGTATATAT
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 86 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (48 bp):
AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:18156 original size:40 final size:40
Alignment explanation
Indices: 18103--18376 Score: 487
Period size: 40 Copynumber: 6.9 Consensus size: 40
18093 CAGTATGTTA
*
18103 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
18143 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
18183 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
*
18223 TATTCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
*
18263 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
* *
18303 TATCCGGGCTAAGTCCTGAAGAGTATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
*
18343 TATCCGGGCTAAGCCCCGAAG-GCATTCGTGCTGG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGG
18377 GACAAAATCT
Statistics
Matches: 224, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
39 12 0.05
40 212 0.95
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.26
Consensus pattern (40 bp):
TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
Found at i:21131 original size:26 final size:27
Alignment explanation
Indices: 21095--21147 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
21085 TGTCAGCTAG
* *
21095 TGAAATTTTAA-TGTTCGAATGTATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
*
21121 TGAATTTTTAAGTGTCCGAATGCATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
21148 CAGAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (27 bp):
TGAAATTTTAAGTGTCCGAATGCATGC
Found at i:22482 original size:48 final size:48
Alignment explanation
Indices: 22418--22565 Score: 215
Period size: 48 Copynumber: 3.1 Consensus size: 48
22408 TTGATGTACA
*
22418 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTAAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
22466 AGATATATATATGTGGTAAAGTCGAAAGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
** ** * *
22514 AGCCATGCATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
22562 AGAT
1 AGAT
22566 GTGTATATAT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 87 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (48 bp):
AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:25229 original size:20 final size:20
Alignment explanation
Indices: 25204--25244 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
25194 GACTACTATG
25204 GGCCATTGTCTGCGGCTTTT
1 GGCCATTGTCTGCGGCTTTT
25224 GGCCATTGTCTGCGGCTTTT
1 GGCCATTGTCTGCGGCTTTT
25244 G
1 G
25245 TATAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.24, G:0.32, T:0.39
Consensus pattern (20 bp):
GGCCATTGTCTGCGGCTTTT
Found at i:28974 original size:79 final size:80
Alignment explanation
Indices: 28872--29041 Score: 231
Period size: 79 Copynumber: 2.1 Consensus size: 80
28862 ACTAAGATCT
*
28872 GAAGGCATTTGTGCGAGATACTAAATTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-
1 GAAGGCATTTGTGCGAGATACTAAATCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGATACTAT
*
28935 ATTCCGGGCTAA-G-CCC
65 A-ACCGGGC-AATGTCCC
* ** *
28951 GAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 GAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
29016 ACCGGGCAATGTCCC
66 ACCGGGCAATGTCCC
29031 GAAGGCATTTG
1 GAAGGCATTTG
29042 AACGAGGAGC
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
78 3 0.04
79 63 0.78
80 15 0.19
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
GAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
ACCGGGCAATGTCCC
Found at i:29005 original size:40 final size:40
Alignment explanation
Indices: 28817--29041 Score: 255
Period size: 40 Copynumber: 5.7 Consensus size: 40
28807 TTGAATGATG
* * * *
28817 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28857 TCCGGACTAAGAT-CTGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * * *
28897 TTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
28937 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28976 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
29017 -CCGGGC-AATGTCCCGAAGGCATTTG
1 TCCGGGCTAA-GTCCCGAAGGCATTTG
29042 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
39 37 0.23
40 116 0.71
41 10 0.06
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29060 original size:119 final size:120
Alignment explanation
Indices: 28817--29047 Score: 267
Period size: 119 Copynumber: 1.9 Consensus size: 120
28807 TTGAATGATG
* *
28817 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCTGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
28882 GTGCGAGATACTAAATTCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
66 GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGATACTAAT
* * * **
28937 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* *
28999 TTGTGCGAGTTACTATAA-CCGGGC-AATG-TCCCGAAGGCATTTGAACGAG
64 TTGTGCGAGATACTA-AATCCGGACTAA-GAT-CCGAAGGCATTTGAACGAG
29048 GAGCTATATC
Statistics
Matches: 94, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
118 4 0.04
119 70 0.74
120 20 0.21
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGATACTAAT
Found at i:29063 original size:79 final size:79
Alignment explanation
Indices: 28910--29064 Score: 192
Period size: 79 Copynumber: 2.0 Consensus size: 79
28900 GGACTAAGAT
* ** *
28910 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
28975 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
*
28989 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGC-AATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAA-G-CCCGAAGGCATTTGAACGAGTGA-
*
29051 CTATATCC-GGTTAA
62 CTAAATCCGGGTTAA
29065 ATTCTGAAGG
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
78 4 0.06
79 37 0.56
80 25 0.38
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAGTC
Done.