Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2890
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: 47624
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:2385 original size:40 final size:40
Alignment explanation
Indices: 2301--2484 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
2291 TTGAATGCTG
* * * *
2301 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
2340 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
2381 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
2421 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
2461 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
2485 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:2438 original size:80 final size:81
Alignment explanation
Indices: 2301--2481 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
2291 TTGAATGCTG
* * *
2301 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
2365 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
2381 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
2442 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
2461 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
2482 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:2538 original size:39 final size:39
Alignment explanation
Indices: 2301--2543 Score: 122
Period size: 40 Copynumber: 6.1 Consensus size: 39
2291 TTGAATGCTG
* ** *
2301 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTGAAC-GAGTGACTATA
* * ** * *
2341 TCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTA-A
1 TCCGGGCTAAG-TCCCGAAGGCA-TTGAACGAGTGACTATA
* * **
2380 TTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGAT-ACTA-A
1 -TCCGGGCTAAGTCCCGAAGG-CATTGAACGAG-TGACTATA
* ** ** *
2420 TTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA
1 -TCCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACT-ATA
* * *
2461 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATA
*
2500 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATA
2539 TCCGG
1 TCCGG
2544 TTAAATTCCG
Statistics
Matches: 166, Mismatches: 24, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
38 20 0.12
39 27 0.16
40 110 0.66
41 9 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATA
Found at i:10160 original size:40 final size:40
Alignment explanation
Indices: 10076--10259 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
10066 TTGAATGCTG
* * * *
10076 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
10115 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
10156 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
10196 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
10236 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
10260 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:10213 original size:80 final size:81
Alignment explanation
Indices: 10076--10256 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
10066 TTGAATGCTG
* * *
10076 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
10140 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
10156 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
10217 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
10236 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
10257 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:10280 original size:39 final size:38
Alignment explanation
Indices: 10157--10306 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
10147 GTTATTAATT
* ** * *
10157 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
10197 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
10236 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
10276 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
10307 GAGCTAATCC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:14536 original size:8 final size:8
Alignment explanation
Indices: 14523--14585 Score: 54
Period size: 8 Copynumber: 7.9 Consensus size: 8
14513 ATCGGTAAAA
14523 GCCGAAAT
1 GCCGAAAT
14531 GCCGAAAT
1 GCCGAAAT
* *
14539 ACCGAAAA
1 GCCGAAAT
*
14547 GTCGAAAT
1 GCCGAAAT
14555 GCCGAAAT
1 GCCGAAAT
* * *
14563 ACCAAAAA
1 GCCGAAAT
**
14571 GTTGAAAT
1 GCCGAAAT
14579 GCCGAAA
1 GCCGAAA
14586 AGCTTAAAGT
Statistics
Matches: 39, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.13
Consensus pattern (8 bp):
GCCGAAAT
Found at i:14552 original size:24 final size:24
Alignment explanation
Indices: 14519--14585 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
14509 ATGAATCGGT
* *
14519 AAAAGCCGAAATGCCGAAATACCG
1 AAAAGTCGAAATGCCGAAATACCA
14543 AAAAGTCGAAATGCCGAAATACCA
1 AAAAGTCGAAATGCCGAAATACCA
*
14567 AAAAGTTGAAATGCCGAAA
1 AAAAGTCGAAATGCCGAAA
14586 AGCTTAAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.12
Consensus pattern (24 bp):
AAAAGTCGAAATGCCGAAATACCA
Found at i:14859 original size:29 final size:28
Alignment explanation
Indices: 14817--14898 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 28
14807 TGAATGTCAC
14817 TGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAATGGGCCATATACAGGTGA-T
**
14846 TGGGCCTAATGGGCCATATGA-ATATGAT
1 TGGGCCTAATGGGCCATAT-ACAGGTGAT
* *
14874 TGGGCTTAATGGGCCAGATACAGGT
1 TGGGCCTAATGGGCCATATACAGGT
14899 ATGTGAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.02
28 20 0.44
29 23 0.51
30 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.27
Consensus pattern (28 bp):
TGGGCCTAATGGGCCATATACAGGTGAT
Found at i:18577 original size:36 final size:36
Alignment explanation
Indices: 18530--18598 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
18520 ATGCCTTCTT
18530 GAATGTAAATATAAATAAAACTTAGACCGAAGTTTA
1 GAATGTAAATATAAATAAAACTTAGACCGAAGTTTA
18566 GAATGTAAATATAAATAAAACTTAGACCGAAGT
1 GAATGTAAATATAAATAAAACTTAGACCGAAGT
18599 ATTATAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (36 bp):
GAATGTAAATATAAATAAAACTTAGACCGAAGTTTA
Found at i:22973 original size:40 final size:40
Alignment explanation
Indices: 22897--23078 Score: 262
Period size: 40 Copynumber: 4.6 Consensus size: 40
22887 AACCCAAGTA
*
22897 CCTTCGGGATTTAG-CCGGATATAG-CAACTCAG-ACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-T-AGCACAAATG
* *
22936 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
22976 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
23016 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATT
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
23056 CCTTCGTGACTTAGCCTGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
23079 CATTCGAATA
Statistics
Matches: 130, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 14 0.11
40 113 0.87
41 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:29046 original size:40 final size:40
Alignment explanation
Indices: 28972--29153 Score: 287
Period size: 40 Copynumber: 4.6 Consensus size: 40
28962 AACCTAAGTA
* *
28972 CCTTCGGGATTTAG-CCGGATATAGT-AACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
29011 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
29051 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
29091 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
29131 CCTTCGGGACTTAGCCCGAATAT
1 CCTTCGGGACTTAGCCCGGATAT
29154 CATTCGAATA
Statistics
Matches: 132, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 12 0.09
40 118 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:35398 original size:32 final size:33
Alignment explanation
Indices: 35328--35398 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
35318 AGTAAACAAC
*
35328 ACAGTATCAGTACAGTCTGGGCCAAAGCCCTAT
1 ACAGTAACAGTACAGTCTGGGCCAAAGCCCTAT
* * **
35361 TCAGTAACAGTATAGTCT-GGCCTTAGCCCTAT
1 ACAGTAACAGTACAGTCTGGGCCAAAGCCCTAT
35393 ACAGTA
1 ACAGTA
35399 GCATTGTGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (33 bp):
ACAGTAACAGTACAGTCTGGGCCAAAGCCCTAT
Found at i:37857 original size:16 final size:16
Alignment explanation
Indices: 37836--37868 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
37826 TCTTCCTCAA
*
37836 TACCTTAACATGACGC
1 TACCTTAACATCACGC
37852 TACCTTAACATCACGC
1 TACCTTAACATCACGC
37868 T
1 T
37869 CCAATATCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.27
Consensus pattern (16 bp):
TACCTTAACATCACGC
Found at i:45357 original size:47 final size:47
Alignment explanation
Indices: 45305--45417 Score: 190
Period size: 47 Copynumber: 2.4 Consensus size: 47
45295 GATAATTGTG
* *
45305 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
45352 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
45399 ATGTGAAAGTGTATATATG
1 ATGTGAAAGTGTATATATG
45418 ATAAGTATGT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 62 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:45393 original size:79 final size:79
Alignment explanation
Indices: 45343--45588 Score: 285
Period size: 79 Copynumber: 2.9 Consensus size: 79
45333 CTAATGGCCG
45343 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAA--GTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
* *
45408 TGTATATATGATAAGT
64 TGCATATATGAGAAGT
* *
45424 ATGTGATGAATGTGAAAGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 ATGTGATGAATGTGAAAGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* *
45489 TATATATGTGATAAGGCCT
66 CATATA--TGAGAA-G--T
45508 AATAGCCGATGTGATGAATGTGAAAGGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAAT
1 -AT----G-T--GATGAATGTGAAA-GTATATATGTGATAAGGCCGAATGGCCAATGTGATGAAT
*
45573 GTGAAAGTGTATATAT
57 GTGAAAGTGCATATAT
45589 ATGTGATAAG
Statistics
Matches: 147, Mismatches: 4, Indels: 18
0.87 0.02 0.11
Matches are distributed among these distances:
79 52 0.35
81 23 0.16
82 1 0.01
84 1 0.01
85 2 0.01
89 1 0.01
90 1 0.01
91 1 0.01
92 13 0.09
93 52 0.35
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (79 bp):
ATGTGATGAATGTGAAAGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
CATATATGAGAAGT
Found at i:45430 original size:34 final size:34
Alignment explanation
Indices: 45390--45456 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
45380 CGAATGGCCA
*
45390 ATGTGATGAATGTGAAAGTGTATATATGATAAGT
1 ATGTGATGAATGTGAAAGTATATATATGATAAGT
*
45424 ATGTGATGAATGTGAAAGTATATATGTGATAAG
1 ATGTGATGAATGTGAAAGTATATATATGATAAG
45457 GCCTAATGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (34 bp):
ATGTGATGAATGTGAAAGTATATATATGATAAGT
Found at i:45510 original size:47 final size:47
Alignment explanation
Indices: 45424--45938 Score: 874
Period size: 47 Copynumber: 10.9 Consensus size: 47
45414 TATGATAAGT
45424 ATGTGATGAATGTGAAA--GTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
45469 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
45516 ATGTGATGAATGTGAAAG-GTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
45562 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
45611 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
45658 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
45705 ATGTGATGAATGGGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
45754 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
45801 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
45848 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
45897 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
45939 AGCTGTATAT
Statistics
Matches: 443, Mismatches: 18, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
45 17 0.04
46 43 0.10
47 249 0.56
49 134 0.30
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:45682 original size:96 final size:94
Alignment explanation
Indices: 45424--45938 Score: 874
Period size: 96 Copynumber: 5.4 Consensus size: 94
45414 TATGATAAGT
45424 ATGTGATGAATGTGAAA--GTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
45487 TGTATATATGTGATAAGGCCTAATAGCCG
66 TGTATATATGTGATAAGGCCTAATGGCCG
* *
45516 ATGTGATGAATGTGAAAG-GTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
45580 TGTATATATATGTGATAAGGCCTAATGGCCG
66 TG--TATATATGTGATAAGGCCTAATGGCCG
*
45611 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* *
45676 TGTATATATGTGATAAGGCCGAATGGCCA
66 TGTATATATGTGATAAGGCCTAATGGCCG
*
45705 ATGTGATGAATGGGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
45770 AGTGTATATATGTGATAAGGCCTAATGGCCG
64 AGTGTATATATGTGATAAGGCCTAATGGCCG
* *
45801 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
45866 TGTATATATATGTGATAAGGCCTAATGGCCG
66 TG--TATATATGTGATAAGGCCTAATGGCCG
45897 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
45939 AGCTGTATAT
Statistics
Matches: 399, Mismatches: 16, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
92 17 0.04
93 46 0.12
94 89 0.22
95 44 0.11
96 203 0.51
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (94 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATGGCCG
Found at i:45769 original size:143 final size:143
Alignment explanation
Indices: 45424--45941 Score: 983
Period size: 143 Copynumber: 3.7 Consensus size: 143
45414 TATGATAAGT
45424 ATGTGATGAATGTGAAA--G--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
45485 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG-GTATATATGTGATAA
66 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
45549 GGCCGAATGGCCA
131 GGCCGAATGGCCA
45562 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
45627 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
66 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
45692 GGCCGAATGGCCA
131 GGCCGAATGGCCA
*
45705 ATGTGATGAATGGGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
45770 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
66 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
45835 GGCCGAATGGCCA
131 GGCCGAATGGCCA
45848 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
45913 AGTGTATATATGTGATAAGGCCTAATAGC
66 AGTGTATATATGTGATAAGGCCTAATAGC
45942 TGTATATATG
Statistics
Matches: 371, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
138 17 0.05
140 1 0.00
142 92 0.25
143 261 0.70
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (143 bp):
ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
GGCCGAATGGCCA
Found at i:45960 original size:24 final size:25
Alignment explanation
Indices: 45919--45965 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
45909 TGAAAGTGTA
*
45919 TATATGTGATAAGGCCTAATAGCTG
1 TATATATGATAAGGCCTAATAGCTG
45944 TATATATG-TAAGGCCTAATAGC
1 TATATATGATAAGGCCTAATAGC
45966 CGATGTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (25 bp):
TATATATGATAAGGCCTAATAGCTG
Found at i:45960 original size:71 final size:72
Alignment explanation
Indices: 45872--46009 Score: 242
Period size: 71 Copynumber: 1.9 Consensus size: 72
45862 AAAGTGTATA
* *
45872 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
1 TATATATGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
45937 ATAGCTG
66 ATAGCTG
*
45944 TATATATG-TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTA
1 TATATATGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
46008 AT
66 AT
46010 GGCCGATGTG
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 56 0.89
72 7 0.11
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (72 bp):
TATATATGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
ATAGCTG
Found at i:46015 original size:47 final size:45
Alignment explanation
Indices: 45942--46091 Score: 203
Period size: 47 Copynumber: 3.3 Consensus size: 45
45932 GCCTAATAGC
*
45942 TGTATATATGT-AAGGCCTAATAGCCGATGTGATGAATGTGAAAG
1 TGTATATATGTGAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
45986 TGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 TGTATATATGTGA--AGGCCTAATGGCCGATGTGATGAATGTGAAAG
* * * * *
46033 TGTATATATGTGACAGGCCGAGTGGCCAACGTGATGGATGTGAAAG
1 TGTATATATGTGA-AGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
46079 TGTATAAATGTGA
1 TGTATATATGTGA
46092 TAAGTCCCGA
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 11 0.12
45 1 0.01
46 39 0.41
47 44 0.46
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (45 bp):
TGTATATATGTGAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
Found at i:46015 original size:118 final size:120
Alignment explanation
Indices: 45823--46045 Score: 378
Period size: 118 Copynumber: 1.9 Consensus size: 120
45813 TGAAAGTGTA
* *
45823 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TATATATGATAAGGCCGAATAGCCAATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCC
45888 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCTG
65 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCTG
* * *
45944 TATATATG-TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATGAGGCCT
1 TATATATGATAAGGCCGAATAGCCAATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCT
46007 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
66 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
46046 CAGGCCGAGT
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
118 57 0.59
120 33 0.34
121 7 0.07
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (120 bp):
TATATATGATAAGGCCGAATAGCCAATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCT
AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCTG
Done.