Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1348
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: 32500
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1240 original size:15 final size:15
Alignment explanation
Indices: 1220--1249 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1210 TATTTGTAAG
1220 GGCTCAACTAATTCA
1 GGCTCAACTAATTCA
1235 GGCTCAACTAATTCA
1 GGCTCAACTAATTCA
1250 AAGCACATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
GGCTCAACTAATTCA
Found at i:1411 original size:40 final size:40
Alignment explanation
Indices: 1374--1559 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
1364 GCTACTCGTT
* *
1374 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1414 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
1454 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
1494 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
1535 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
1560 CATCATTCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 115 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:4448 original size:44 final size:46
Alignment explanation
Indices: 4340--4448 Score: 136
Period size: 48 Copynumber: 2.4 Consensus size: 46
4330 CTATGATACA
*
4340 ATCCCATGTAAGACCATGTCTTAGACATGGACTTGGCATCGATCTATG
1 ATCCCATGTAAGACCATGTCTTAGACATGGACTTGGCATC-A-CGATG
*
4388 ATCCCATGTAAGACCATGT-TTGGGACATGG-CATTGGCAT-A-GATG
1 ATCCCATGTAAGACCATGTCTT-AGACATGGAC-TTGGCATCACGATG
4432 ATCCCATGTAAGACCAT
1 ATCCCATGTAAGACCAT
4449 ATCCGGGATA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
44 20 0.35
46 1 0.02
47 3 0.05
48 33 0.58
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (46 bp):
ATCCCATGTAAGACCATGTCTTAGACATGGACTTGGCATCACGATG
Found at i:4465 original size:44 final size:44
Alignment explanation
Indices: 4385--4470 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
4375 GCATCGATCT
* ** *
4385 ATGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATAG
1 ATGATCCCATGTAAGACCATATCCGGGACATGGCATTAGCATAG
* *
4429 ATGATCCCATGTAAGACCATATCCGGGATATTGCATTAGCAT
1 ATGATCCCATGTAAGACCATATCCGGGACATGGCATTAGCAT
4471 CCTACCATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
ATGATCCCATGTAAGACCATATCCGGGACATGGCATTAGCATAG
Found at i:6073 original size:46 final size:45
Alignment explanation
Indices: 5896--6112 Score: 133
Period size: 46 Copynumber: 4.7 Consensus size: 45
5886 TTTGTGTGCT
** *
5896 AGTGTAAGACATGTCTGGG-ACATGCATCGGCC-ACATTATCAGAGCC
1 AGTGTAAGACATGTCTGGGTACATGCATCGGCCTTGA-GAT-A-AGCC
* * * * * *
5942 AGTGTAAGACCATTTCTAGG-ACATGGAATCGGCATTGAGACAAGTGCT
1 AGTGTAAGA-CATGTCTGGGTACAT-GCATCGGCCTTGAGATAA--GCC
* *
5990 ATTGTAAGACATGTCT-GGTACATGCATTGGCCTTGAGACATAAGCC
1 AGTGTAAGACATGTCTGGGTACATGCATCGGCCTTGAG--ATAAGCC
* ** *
6036 AGTGTAAGACATGTCTGGGT-TATGCATCGG-CTATGAGATGTGTC
1 AGTGTAAGACATGTCTGGGTACATGCATCGGCCT-TGAGATAAGCC
*
6080 AGTGTAAGACCATGTCTGGG-AGATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGTACAT-GCATCGGC
6113 ACAGATATGC
Statistics
Matches: 134, Mismatches: 23, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
44 13 0.10
45 14 0.10
46 59 0.44
47 26 0.19
48 21 0.16
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGTACATGCATCGGCCTTGAGATAAGCC
Found at i:6141 original size:50 final size:50
Alignment explanation
Indices: 6032--6212 Score: 159
Period size: 50 Copynumber: 3.8 Consensus size: 50
6022 TTGAGACATA
**
6032 AGCCAGTGTAAGA-CATGTCTGGGTTAT-GCATCGG--CTATGA-GATG-T
1 AGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGGCACTA-GATGATGAT
* *
6077 -GTCAGTGTAAGACCATGTCTGGGAGATGGCATCGGCAC-AGAT-ATGCA-
1 AGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGGCACTAGATGATG-AT
* * * * *
6124 AGAACTAGTGTATGACCATGTTTGGGACATGGCATCGGC-CTCGATGATGAT
1 AG--CCAGTGTAAGACCATGTCTGGGAAATGGCATCGGCACTAGATGATGAT
*
6175 AGCCAGTGTAAGACCATGTCCGGGAAATGGCATCGGCA
1 AGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGGCA
6213 ACTTACCCCA
Statistics
Matches: 108, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
44 11 0.10
45 12 0.11
46 12 0.11
47 1 0.01
48 2 0.02
49 31 0.29
50 34 0.31
51 5 0.05
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (50 bp):
AGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGGCACTAGATGATGAT
Found at i:9724 original size:13 final size:13
Alignment explanation
Indices: 9706--9730 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9696 AGATAAGCCG
9706 TTTTGTTTTTTTT
1 TTTTGTTTTTTTT
9719 TTTTGTTTTTTT
1 TTTTGTTTTTTT
9731 AAGGAAAACA
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTGTTTTTTTT
Found at i:9761 original size:17 final size:17
Alignment explanation
Indices: 9735--9772 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
9725 TTTTTTAAGG
9735 AAAACAAATGAATCTTA
1 AAAACAAATGAATCTTA
*
9752 AAAACGAATGAATCTTA
1 AAAACAAATGAATCTTA
9769 AAAA
1 AAAA
9773 TAAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAACAAATGAATCTTA
Found at i:14061 original size:37 final size:37
Alignment explanation
Indices: 14011--14155 Score: 245
Period size: 37 Copynumber: 3.9 Consensus size: 37
14001 ACCTTTAGCT
* * *
14011 CGGACGTAATCTCCACACGAAGTTATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
*
14048 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
14085 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
*
14122 CGGACATAATCTCCACACGTAGTCATCGAGTCTT
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTT
14156 TAGAGCTCGG
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 102 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
Found at i:14361 original size:47 final size:47
Alignment explanation
Indices: 14274--14782 Score: 822
Period size: 47 Copynumber: 10.7 Consensus size: 47
14264 CCCTTCGGGA
* * * * * *
14274 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
14321 CCTGTAACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14368 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
14415 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14462 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
14509 CTTATCACATATATACACTTTCACATTCATCACCTCGGCAATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
14556 CTTATCACATATATACACTTTCACATTCATCACGTCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14603 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14652 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14701 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
14748 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
14783 AGAATCCTAA
Statistics
Matches: 437, Mismatches: 22, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
46 1 0.00
47 341 0.78
49 95 0.22
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:18669 original size:40 final size:39
Alignment explanation
Indices: 18637--19028 Score: 487
Period size: 40 Copynumber: 9.8 Consensus size: 39
18627 CCAGCATGAT
* * * *
18637 TGCTCTTCAGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
** * * *
18677 TGCTCTTCGAGGTTTAGCACGGATATATCTCTAGCACGAA
1 TGCTCTTCG-GACTTAGCCCGGATACATCACTAGCACGAA
* *
18717 TGCTCTTCGGAACTTAGTCCAGATACATCACTAGCACGAA
1 TGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAA
*
18757 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAA
* * *
18797 TGCTCTTCGAGATTTATCCCGGATATATCACTAGCACGAA
1 TGCTCTTCG-GACTTAGCCCGGATACATCACTAGCACGAA
* *
18837 TGCTCTTCGAAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCG-GACTTAGCCCGGATACATCACTAGCACGAA
* * *
18877 TGCTCTTCGGGATTTATCCCGGATATATCACTAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
*
18917 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAA
*
18957 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAA
*
18997 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTC-GGACTTAGCCCGGATACATCACT
19029 CTCAATTCTC
Statistics
Matches: 311, Mismatches: 35, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.01
40 303 0.97
41 4 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (39 bp):
TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:18851 original size:120 final size:120
Alignment explanation
Indices: 18637--19028 Score: 599
Period size: 120 Copynumber: 3.3 Consensus size: 120
18627 CCAGCATGAT
* * * * * * *
18637 TGCTCTTCAGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGAGGTTTAGCACGGATA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGAGATTTATCCCGGATA
* *
18702 TATCTCTAGCACGAATGCTCTTCGGAACTTAGTCCAGATACATCACTAGCACGAA
66 TATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * *
18757 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGAGATTTATCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGAGATTTATCCCGGATA
*
18822 TATCACTAGCACGAATGCTCTTCGAAACTTAGTCCGGATACATCACTAGCACGAA
66 TATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * *
18877 TGCTCTTCGGGATTTATCCCGGATATATCACTAGCACGAATGCTCTTCG-GAACTTAGT-CCGGA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGAG-ATTTA-TCCCGGA
*
18940 TACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
64 TATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
18997 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
19029 CTCAATTCTC
Statistics
Matches: 247, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
119 1 0.00
120 245 0.99
121 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (120 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGAGATTTATCCCGGATA
TATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:20343 original size:37 final size:37
Alignment explanation
Indices: 20293--20437 Score: 245
Period size: 37 Copynumber: 3.9 Consensus size: 37
20283 ACCTTTAGCT
* * *
20293 CGGACGTAATCTCCACACGAAGTTATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
*
20330 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
20367 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
*
20404 CGGACATAATCTCCACACGTAGTCATCGAGTCTT
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTT
20438 TAGAGCTCGG
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 102 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
Found at i:20634 original size:47 final size:47
Alignment explanation
Indices: 20556--21017 Score: 710
Period size: 47 Copynumber: 9.7 Consensus size: 47
20546 CCCTTCGGGA
* * * * * *
20556 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
20603 CCTGTCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20650 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20697 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20744 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20791 CTTATCACATATATACACTTTCACATTCATCACGTCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20838 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20887 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
20936 CTTATCACATATATACACTTTCACATTTATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
20983 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
21018 AGAATCCTAA
Statistics
Matches: 390, Mismatches: 22, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
46 1 0.00
47 294 0.75
49 95 0.24
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20635 original size:25 final size:25
Alignment explanation
Indices: 20607--20684 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
20597 CTCGGCCCTG
20607 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
*** *** *
20632 TCACAT-TGGCCA-TTAGGCCTT-A
1 TCACATATATACACTTTCACATTCA
*
20654 TCACATATATACCCTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
20679 TCACAT
1 TCACAT
20685 CGGCCATTAG
Statistics
Matches: 35, Mismatches: 15, Indels: 6
0.62 0.27 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 8 0.23
25 13 0.37
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (25 bp):
TCACATATATACACTTTCACATTCA
Found at i:30409 original size:46 final size:46
Alignment explanation
Indices: 30353--30522 Score: 145
Period size: 46 Copynumber: 3.7 Consensus size: 46
30343 TGGTTGAGCA
30353 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* * * *
30399 TCCGAACTCGTTGAGTGGTGTCCGAGTT---C-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCGAA-T--G
* *
30444 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* * * *
30492 -CCTGAGCTCATTAAGTTGAGCCCGAGTTCAC
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCAC
30523 TTAGGGGCGG
Statistics
Matches: 98, Mismatches: 14, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
45 3 0.03
46 50 0.51
47 26 0.27
48 1 0.01
50 4 0.04
51 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
Found at i:30517 original size:93 final size:93
Alignment explanation
Indices: 30350--30520 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 93
30340 GGATGGTTGA
* * *
30350 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCGAACTCATTAAGT
* *
30415 GGTGTCCGAGTTCGTGAGATGTAACTAG
66 GGAGCCCGAGTTCGTGAGATGTAACTAG
* *
30443 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCATTAAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCC-GAACTCATTAAG
*
30507 TTGAGCCCGAGTTC
65 TGGAGCCCGAGTTC
30521 ACTTAGGGGC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCGAACTCATTAAGT
GGAGCCCGAGTTCGTGAGATGTAACTAG
Found at i:31429 original size:20 final size:20
Alignment explanation
Indices: 31392--31434 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
31382 CTGTTCTAAC
* *
31392 TTTAAAAATTCATAATAAAT
1 TTTAAAAAATAATAATAAAT
* *
31412 TTTAAAAAATAATTATAAGT
1 TTTAAAAAATAATAATAAAT
31432 TTT
1 TTT
31435 TCTTTACATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTAAAAAATAATAATAAAT
Done.