Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3690
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: 57444
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3811 original size:113 final size:116
Alignment explanation
Indices: 3609--3821 Score: 292
Period size: 113 Copynumber: 1.9 Consensus size: 116
3599 ATATTCGATG
* *
3609 ATAACCGGGCTAAGTCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCATT
1 ATAACCGGGCTAAGTCCGAAGGCATTTGTGCGAGTGACTAATT-CAGGCTAAGCCCGAAGGCATT
* * *
3674 TGTGCGAGTTACTATATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
65 TGAGCGAGTTACTATATCCGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
* *
3726 ATAACCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACT-A-T-AGGCTAAGTCCGAAGGCATTG
1 ATAACCGGGCTAAGTCCGAAGGCATTTGTGCGAGTGACTAATTCAGGCTAAGCCCGAAGGCATT-
*
3788 TGAGC-AG-TAGCTATATCCGGCTAAATTCCGAAGG
65 TGAGCGAGTTA-CTATATCCGGCTAAATCCCGAAGG
3822 TACTTGGTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
112 2 0.02
113 41 0.48
114 4 0.05
115 1 0.01
116 1 0.01
117 37 0.43
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (116 bp):
ATAACCGGGCTAAGTCCGAAGGCATTTGTGCGAGTGACTAATTCAGGCTAAGCCCGAAGGCATTT
GAGCGAGTTACTATATCCGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
Found at i:3821 original size:39 final size:38
Alignment explanation
Indices: 3616--3821 Score: 244
Period size: 39 Copynumber: 5.4 Consensus size: 38
3606 ATGATAACCG
* *
3616 GGCTAAGTCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATA-TCC
* *
3654 GGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATATCG
1 -GGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATATCC
*
3693 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATATCC
3732 GGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATA---
1 -GGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATATCC
*
3768 GGCTAAGTCCGAAGGCA-TTGTGAGCAG-TAGCTATATCC
1 GGCTAAGTCCGAAGGCATTTGTGCG-AGTTA-CTATATCC
*
3806 GGCTAAATTCCGAAGG
1 GGCT-AAGTCCGAAGG
3822 TACTTGGTTT
Statistics
Matches: 149, Mismatches: 9, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
34 8 0.05
35 24 0.16
38 11 0.07
39 97 0.65
40 9 0.06
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (38 bp):
GGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:11682 original size:40 final size:39
Alignment explanation
Indices: 11573--11720 Score: 208
Period size: 40 Copynumber: 3.7 Consensus size: 39
11563 TATTCGGATG
* *
11573 ATAACCGGGCTAAGTACCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACT
* *
11613 A-ATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACT
*
11652 ATAATCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACT
11692 ATAACCGGGCTAAGTCCTGAAGGCATTTG
1 ATAACCGGGCTAAGTCC-GAAGGCATTTG
11721 AGCAAGTAGC
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
39 35 0.36
40 61 0.64
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (39 bp):
ATAACCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACT
Found at i:11743 original size:79 final size:79
Alignment explanation
Indices: 11581--11753 Score: 192
Period size: 79 Copynumber: 2.2 Consensus size: 79
11571 TGATAACCGG
* * * *
11581 GCTAAGTACCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGA
1 GCTAAGTACCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGAGCAA
**
11646 GTTACTATAATCGG
66 GTTACTATAATCCA
* *
11660 GCTAAGT-CTCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCTGAAGGCATTTGAG
1 GCTAAGTAC-CGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAG
11723 CAAG-TAGCTAT-ATCCA
63 CAAGTTA-CTATAATCCA
* *
11739 GCTAAATTCCGAAGG
1 GCTAAGTACCGAAGG
11754 TACTTGGCTT
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
78 3 0.04
79 55 0.69
80 22 0.28
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (79 bp):
GCTAAGTACCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGAGCAA
GTTACTATAATCCA
Found at i:15327 original size:50 final size:50
Alignment explanation
Indices: 15267--15482 Score: 254
Period size: 50 Copynumber: 4.3 Consensus size: 50
15257 ATCACTCATT
* * *
15267 TGGCCGAATATACAAGATCAAATATAATATCACATATATGCATACCTATG
1 TGGCCGAATATACAAGATCAAATATAACATCACATATGTGCATACCTATA
* * * *
15317 TGGCCAAATATGCAAGATCAAATATAACATCACATATGTGCTTACTTATA
1 TGGCCGAATATACAAGATCAAATATAACATCACATATGTGCATACCTATA
** * * *
15367 TGGATGAATATACAA-ATTCAAATATAATATCACATTTGTGCATACCTTTA
1 TGGCCGAATATACAAGA-TCAAATATAACATCACATATGTGCATACCTATA
* * * * *
15417 TAGCCCAATATACAAGATCCAATATAACATCACATATGTACATACCTATG
1 TGGCCGAATATACAAGATCAAATATAACATCACATATGTGCATACCTATA
*
15467 TGGCCGAATATTCAAG
1 TGGCCGAATATACAAG
15483 GACATTTAGC
Statistics
Matches: 135, Mismatches: 29, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
49 1 0.01
50 133 0.99
51 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (50 bp):
TGGCCGAATATACAAGATCAAATATAACATCACATATGTGCATACCTATA
Found at i:15476 original size:100 final size:100
Alignment explanation
Indices: 15267--15482 Score: 281
Period size: 100 Copynumber: 2.2 Consensus size: 100
15257 ATCACTCATT
* * *
15267 TGGCCGAATATACAAGATCAAATATAATATCACATATATGCATACCTATGTGGCCAAATATGCAA
1 TGGCCGAATATACAAGATCAAATATAATATCACATATATGCATACCTATATAGCCAAATATACAA
* * *
15332 GATCAAATATAACATCACATATGTGCTTACTTATA
66 GATCAAATATAACATCACATATGTACATACCTATA
** * * * *
15367 TGGATGAATATACAA-ATTCAAATATAATATCACATTTGTGCATACCTTTATAGCCCAATATACA
1 TGGCCGAATATACAAGA-TCAAATATAATATCACATATATGCATACCTATATAGCCAAATATACA
* *
15431 AGATCCAATATAACATCACATATGTACATACCTATG
65 AGATCAAATATAACATCACATATGTACATACCTATA
*
15467 TGGCCGAATATTCAAG
1 TGGCCGAATATACAAG
15483 GACATTTAGC
Statistics
Matches: 97, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
99 1 0.01
100 96 0.99
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (100 bp):
TGGCCGAATATACAAGATCAAATATAATATCACATATATGCATACCTATATAGCCAAATATACAA
GATCAAATATAACATCACATATGTACATACCTATA
Found at i:22256 original size:31 final size:31
Alignment explanation
Indices: 22204--22289 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
22194 TCAATCTCAG
*
22204 CATAT-ACTGGGCTGAAACCTTTACATTATT
1 CATATCACTGGGCTGAAGCCTTTACATTATT
* * *
22234 CATGTCACTGAGCTGAAGCCTTTTCATTATT
1 CATATCACTGGGCTGAAGCCTTTACATTATT
*
22265 CATATCACTGGGCCGAAGCCTTTAC
1 CATATCACTGGGCTGAAGCCTTTAC
22290 TGTAAACGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 4 0.09
31 43 0.91
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (31 bp):
CATATCACTGGGCTGAAGCCTTTACATTATT
Found at i:22461 original size:24 final size:25
Alignment explanation
Indices: 22434--22541 Score: 130
Period size: 25 Copynumber: 4.4 Consensus size: 25
22424 CTGGAGGCCT
22434 AGCCTCTTTT-AAT-AACTGGGGCAA
1 AGCC-CTTTTCAATAAACTGGGGCAA
*
22458 AGCCCTTTTCGATAAACTGGGGCAA
1 AGCCCTTTTCAATAAACTGGGGCAA
** *
22483 AGCCCTTTTCGGTAAATTGGGGCAA
1 AGCCCTTTTCAATAAACTGGGGCAA
** *
22508 AGCCCTTTTCGGTAAACTAGGGCAA
1 AGCCCTTTTCAATAAACTGGGGCAA
22533 AGCCCTTTT
1 AGCCCTTTT
22542 GCACTTCCTC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
23 5 0.06
24 6 0.08
25 66 0.86
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTCAATAAACTGGGGCAA
Found at i:22475 original size:25 final size:25
Alignment explanation
Indices: 22447--22541 Score: 163
Period size: 25 Copynumber: 3.8 Consensus size: 25
22437 CTCTTTTAAT
*
22447 AACTGGGGCAAAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGGTA
22472 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
22497 AATTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
22522 AACTAGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
22542 GCACTTCCTC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:22605 original size:11 final size:11
Alignment explanation
Indices: 22589--22627 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
22579 TATATGAATT
22589 TATCATGTGCA
1 TATCATGTGCA
*
22600 TATCA--TACA
1 TATCATGTGCA
22609 TATCATGTGCA
1 TATCATGTGCA
22620 TATCATGT
1 TATCATGT
22628 TAAATCATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 8 0.33
11 16 0.67
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (11 bp):
TATCATGTGCA
Found at i:25401 original size:2 final size:2
Alignment explanation
Indices: 25394--25427 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25384 TCAATATAAT
25394 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
25428 TATATATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:30318 original size:39 final size:39
Alignment explanation
Indices: 30265--30677 Score: 650
Period size: 39 Copynumber: 10.5 Consensus size: 39
30255 ACAAAGCATG
* * *
30265 CGGGACTTTAAGCCCGAATATAATACCAGCACGAAAGCCTT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
30306 CAGGG-CTTAGCCCGGATATAACACCAGCATGAATGCCTT
1 C-GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
30345 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* * * *
30384 TGGGGCTTAGCCCGGATATAAGACCAGCACGAAAGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
30423 CAGGG-CGTAGCCCGGATATAACACCAGCACGAATGCCTT
1 C-GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
30462 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
30501 TGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
30540 CGGGACTTAGCCCGGATATAACACCAGCATGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
30579 CGGGACTTAGCCCAGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
30618 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCTTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
30657 CGGGACTTAGCCCGGATATAA
1 CGGGACTTAGCCCGGATATAA
30678 TTCTCCATTA
Statistics
Matches: 345, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
38 6 0.02
39 329 0.95
40 5 0.01
41 2 0.01
42 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:31694 original size:2 final size:2
Alignment explanation
Indices: 31687--31712 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31677 TCAATATAAT
31687 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
31713 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:36968 original size:47 final size:47
Alignment explanation
Indices: 36861--37388 Score: 849
Period size: 47 Copynumber: 11.1 Consensus size: 47
36851 GAAATGATAG
36861 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
36910 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
36957 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT-GTGA
*
37005 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
37052 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
37101 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
37148 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
37195 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
37242 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* *
37291 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
37338 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
37385 TAAG
1 TAAG
37389 TCCCGAAGGG
Statistics
Matches: 450, Mismatches: 24, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
47 280 0.62
48 45 0.10
49 125 0.28
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:37166 original size:96 final size:96
Alignment explanation
Indices: 36861--37388 Score: 913
Period size: 96 Copynumber: 5.6 Consensus size: 96
36851 GAAATGATAG
36861 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
36926 ATGTGATGAATGTGAAAGTGTATATACGTGA
66 ATGTGATGAATGTGAAAGTGTATATACGTGA
36957 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAT-TGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
37021 ATGTGATGAATGTGAAAGTGTATATACGTGA
66 ATGTGATGAATGTGAAAGTGTATATACGTGA
*
37052 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
*
37117 ATGTGATGAATGTGAAAGTGTATATATGTGA
66 ATGTGATGAATGTGAAAGTGTATATACGTGA
37148 TAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
37211 ATGTGATGAATGTGAAAGTGTATATACGTGA
66 ATGTGATGAATGTGAAAGTGTATATACGTGA
*
37242 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
* *
37307 ATGTGATGAATGTGAAAGTATATATATGTGA
66 ATGTGATGAATGTGAAAGTGTATATACGTGA
* * * * * * *
37338 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
37389 TCCCGAAGGG
Statistics
Matches: 414, Mismatches: 15, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
94 101 0.24
95 96 0.23
96 217 0.52
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (96 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATACGTGA
Found at i:37293 original size:190 final size:190
Alignment explanation
Indices: 36861--37388 Score: 923
Period size: 190 Copynumber: 2.8 Consensus size: 190
36851 GAAATGATAG
*
36861 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
*
36926 ATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA-
36991 TGTATATATAT-TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
130 -GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
37052 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
37117 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
37182 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
131 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
37242 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
* * * * * * * *
37307 ATGTGATGAATGTGAAAGTATATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAG
66 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* *
37372 TGTATAAATGTGATAAG
131 TATATATATGTGATAAG
37389 TCCCGAAGGG
Statistics
Matches: 324, Mismatches: 12, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
189 10 0.03
190 187 0.58
191 127 0.39
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (190 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
Found at i:37563 original size:37 final size:37
Alignment explanation
Indices: 37507--37585 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
37497 CCGAGCTCTA
* * * *
37507 AAGACCCGATGACTACGTGTGGGGATTTTGTCCTGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
37544 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
37581 AAGAC
1 AAGAC
37586 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40918 original size:62 final size:62
Alignment explanation
Indices: 40816--40935 Score: 186
Period size: 62 Copynumber: 1.9 Consensus size: 62
40806 GGACTTTAAG
* *
40816 CCCGAATATAATACCAGCACGAAAGCCTTCAGGGCTTAGCCTGGATATAACACCAGCACGAA
1 CCCGAATATAACACCAGCACGAAAGCCTTCAGGGCTTAGCCCGGATATAACACCAGCACGAA
* * **
40878 CCCGGATATAACACCAGCACGAATGCCTTTGGGGCTTAGCCCGGATATAACACCAGCA
1 CCCGAATATAACACCAGCACGAAAGCCTTCAGGGCTTAGCCCGGATATAACACCAGCA
40936 TGAATGCCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.17
Consensus pattern (62 bp):
CCCGAATATAACACCAGCACGAAAGCCTTCAGGGCTTAGCCCGGATATAACACCAGCACGAA
Found at i:40932 original size:39 final size:39
Alignment explanation
Indices: 40878--41043 Score: 262
Period size: 39 Copynumber: 4.3 Consensus size: 39
40868 CCAGCACGAA
* *
40878 CCCGGATATAACACCAGCACGAATGCCTTTGGGGCTTAG
1 CCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAG
*
40917 CCCGGATATAACACCAGCATGAATGCCTTCGTGG-CTTAG
1 CCCGGATATAACACCAGCACGAATGCCTTCG-GGACTTAG
*
40956 CCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAG
1 CCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAG
*
40995 CCCGGATATAACACCAGCACGAATGCCTTCAGGACTTAG
1 CCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAG
*
41034 CCCAGATATA
1 CCCGGATATA
41044 TATATATCAT
Statistics
Matches: 118, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
38 2 0.02
39 114 0.97
40 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.20
Consensus pattern (39 bp):
CCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAG
Found at i:45101 original size:29 final size:29
Alignment explanation
Indices: 45066--45139 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
45056 GTTGTGAGAT
* *
45066 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
45095 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
45124 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
45140 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:53400 original size:28 final size:29
Alignment explanation
Indices: 53369--53441 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 29
53359 GTTGTGAGAT
* *
53369 TGGCACTAAGTGTGCGGGCTGAAA-TGCA
1 TGGCACTAAGTGTGCGAGCTGAAAGTACA
* *
53397 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGCTGAAAGTACA
53426 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
53442 TGTGGTTGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 21 0.52
29 19 0.47
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTGAAAGTACA
Done.