Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4375.1
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: 63995
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.30
Warning! 1883 characters in sequence are not A, C, G, or T
Found at i:2209 original size:98 final size:98
Alignment explanation
Indices: 2040--2236 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
2030 AAAATCCGTA
* * *
2040 CGCACGGGGATAAAGTGAGCCGACCTAGTTAATCTATCGACAACAACCCAAATCGCATCTTTCTT
1 CGCACGGGGATAAAGTGAGCCGACCTAGTCAATCTATCAACAACAACCCAAATCGCATCCTTCTT
2105 ACTTGCTGACAATGGCAGTCCGGACACAAAGTC
66 ACTTGCTGACAATGGCAGTCCGGACACAAAGTC
* *
2138 CGCACGGGGATAAAGTGAGCCGACTTAGTCAGTCTATCAACAACAACCCAAATCGCATCCTTCTT
1 CGCACGGGGATAAAGTGAGCCGACCTAGTCAATCTATCAACAACAACCCAAATCGCATCCTTCTT
2203 ACTTGCTGACAATGGCAGTCCGGACACAAAGTC
66 ACTTGCTGACAATGGCAGTCCGGACACAAAGTC
2236 C
1 C
2237 ATTGTGACTC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (98 bp):
CGCACGGGGATAAAGTGAGCCGACCTAGTCAATCTATCAACAACAACCCAAATCGCATCCTTCTT
ACTTGCTGACAATGGCAGTCCGGACACAAAGTC
Found at i:15734 original size:27 final size:27
Alignment explanation
Indices: 15677--15736 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
15667 ATACATCTCA
*
15677 TAGGGGCATATCAGTCATTTTACCATG
1 TAGGGGCATATCAGTCATTTTACAATG
*
15704 TAGGGGCATTTCAGTCATTTTATCAAT-
1 TAGGGGCATATCAGTCATTTTA-CAATG
15731 TAGGGG
1 TAGGGG
15737 GTCAAGGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (27 bp):
TAGGGGCATATCAGTCATTTTACAATG
Found at i:17903 original size:46 final size:47
Alignment explanation
Indices: 17655--18017 Score: 264
Period size: 46 Copynumber: 7.7 Consensus size: 47
17645 AGGGTGTAAT
17655 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTT-ATCCATCAA-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCAT-C-TCAAG
* * * **
17702 GTCGATCCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATCAAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TC-ATCTCAAG
* * * * * *
17751 GCCGACGCCATGTCCTAAACATGGTCTTACACTGGCTCCCACATTTC-CG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT---TCATCTCAAG
* * * *
17800 TGCCGATGCCATGTTCCAGACATGGTCTTACACTGAC-ACATCTCGTA-
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCTC-AAG
*
17847 GCCAATG-CATGTCCCAGACAT-GTCTTACACTGGCTTGCATCTCAAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATCTCAAG
* * * ** *
17893 GCCGATG-CATGTCCCTGACAT-GACTTACACTAGCTCTTGTCTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATCTCAAG
* * * * **
17939 GCAGATGCCATGTCCCAAACATGGTCTTATACTGGCTCTCATAAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCAT-CTCAAG
*
17987 GCTGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
18018 AGCGCACGAA
Statistics
Matches: 250, Mismatches: 50, Indels: 33
0.75 0.15 0.10
Matches are distributed among these distances:
44 12 0.05
45 14 0.06
46 70 0.28
47 60 0.24
48 25 0.10
49 33 0.13
50 35 0.14
51 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCTCAAG
Found at i:22473 original size:17 final size:17
Alignment explanation
Indices: 22445--22490 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
22435 AAATGTCTTC
22445 AATTTAGTAAAGAGGACT
1 AATTT-GTAAAGAGGACT
*
22463 AATTTGTAAAGAGGATT
1 AATTTGTAAAGAGGACT
*
22480 GATTTGTAAAG
1 AATTTGTAAAG
22491 TGCCAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (17 bp):
AATTTGTAAAGAGGACT
Found at i:23980 original size:50 final size:49
Alignment explanation
Indices: 23921--24095 Score: 183
Period size: 50 Copynumber: 3.5 Consensus size: 49
23911 AATATGCATG
* *
23921 GTAGCCTGCACTTAGTACTACACACGTGACCTCATCATTTGATACATGTA
1 GTAGCCTGCACTTAGTACTACACACGTGA-CTAATCATTTGATACACGTA
* * *
23971 GTAGCCTGCACTTAGTACTACACACGTGATCGAAGTCA-TTGAGTACGCATA
1 GTAGCCTGCACTTAGTACTACACACGTGA-CTAA-TCATTTGA-TACACGTA
* * * * *
24022 GTAGCCTGCACTTAGTACTACACATGCGACTTAA-CAGTATCATAAACGTA
1 GTAGCCTGCACTTAGTACTACACACGTGAC-TAATCA-TTTGATACACGTA
*
24072 GTAGCCTACACTTAGTACTACACA
1 GTAGCCTGCACTTAGTACTACACA
24096 TGTGTATTCA
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
49 2 0.02
50 64 0.61
51 39 0.37
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (49 bp):
GTAGCCTGCACTTAGTACTACACACGTGACTAATCATTTGATACACGTA
Found at i:27361 original size:34 final size:34
Alignment explanation
Indices: 27323--27389 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
27313 CCTCGACTCG
* *
27323 GGTTGCACTAACACTGGTGCTTTGGTCAACCGCA
1 GGTTGCACTAACACTGATGCTTCGGTCAACCGCA
27357 GGTTGCACTAACACTGATGCTTCGGTCAACCGC
1 GGTTGCACTAACACTGATGCTTCGGTCAACCGC
27390 TCTTCCAACT
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:0.21, C:0.28, G:0.25, T:0.25
Consensus pattern (34 bp):
GGTTGCACTAACACTGATGCTTCGGTCAACCGCA
Found at i:31344 original size:10 final size:9
Alignment explanation
Indices: 31326--31413 Score: 54
Period size: 9 Copynumber: 9.4 Consensus size: 9
31316 TAAAATTTAA
31326 AAAATATTT
1 AAAATATTT
31335 AAAATCATTT
1 AAAAT-ATTT
*
31345 AAAATATTA
1 AAAATATTT
*
31354 AAAATA-TA
1 AAAATATTT
31362 ATAAATCATTT
1 A-AAAT-ATTT
* *
31373 TAAATGTTTT
1 AAAAT-ATTT
* *
31383 ATAATATTA
1 AAAATATTT
31392 AAAATATATT
1 AAAATAT-TT
*
31402 -TAATATTT
1 AAAATATTT
31410 AAAA
1 AAAA
31414 AATAATTTGA
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
8 5 0.08
9 33 0.55
10 21 0.35
11 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (9 bp):
AAAATATTT
Found at i:31366 original size:19 final size:19
Alignment explanation
Indices: 31317--31366 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
31307 AATTCTATGT
* *
31317 AAAATTTAA-AAAATATTT
1 AAAATATAATAAAATATTA
*
31335 AAAATCAT-TTAAAATATTA
1 AAAAT-ATAATAAAATATTA
31354 AAAATATAATAAA
1 AAAATATAATAAA
31367 TCATTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATATAATAAAATATTA
Found at i:31430 original size:31 final size:34
Alignment explanation
Indices: 31383--31472 Score: 107
Period size: 33 Copynumber: 2.7 Consensus size: 34
31373 TAAATGTTTT
31383 ATAATATTAAAAATATA-TTTAATATTTA-AAAA
1 ATAATATTAAAAATATATTTTAATATTTATAAAA
*
31415 ATAAT-TTGAAAATATATTTTTAATATTTATAAAA
1 ATAATATTAAAAATATA-TTTTAATATTTATAAAA
*
31449 AAATATATTATAAAATAT-TTTTAA
1 ATA-ATATTA-AAAATATATTTTAA
31473 AAAATACATT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
31 10 0.20
32 5 0.10
33 11 0.22
34 6 0.12
35 8 0.16
36 2 0.04
37 7 0.14
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (34 bp):
ATAATATTAAAAATATATTTTAATATTTATAAAA
Found at i:31457 original size:25 final size:26
Alignment explanation
Indices: 31423--31476 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
31413 AAATAATTTG
**
31423 AAAATATATT-TTTAATATTTATAAA
1 AAAATATATTATAAAATATTTATAAA
*
31448 AAAATATATTATAAAATATTTTTAAA
1 AAAATATATTATAAAATATTTATAAA
31474 AAA
1 AAA
31477 TACATTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAAATATATTATAAAATATTTATAAA
Found at i:34948 original size:30 final size:30
Alignment explanation
Indices: 34912--35034 Score: 174
Period size: 30 Copynumber: 4.1 Consensus size: 30
34902 GGTCAAATAG
* * * *
34912 ACTCGAACCGCCTATATCCAGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
34942 ACTCGAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
*
34972 ACTTGAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
* * *
35002 ACTCGAACTACCTATGTCCGGGTTATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
35032 ACT
1 ACT
35035 GCTCTGGGAC
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 84 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (30 bp):
ACTCGAACCACCCATGTCCGGGTGATATGA
Found at i:38361 original size:21 final size:21
Alignment explanation
Indices: 38336--38423 Score: 63
Period size: 21 Copynumber: 4.0 Consensus size: 21
38326 TAAAAAATAT
38336 TTTTAAAAATAATAATTAAAA
1 TTTTAAAAATAATAATTAAAA
* *
38357 TTTTAAAAACAATATTATAAAACA
1 TTTTAAAAATAATA--ATTAAA-A
*
38381 TTTTAAATAT-AT-ATTACAAA
1 TTTTAAAAATAATAATTA-AAA
*
38401 TTTTTTAAAATTAATAATATAAA
1 --TTTTAAAAATAATAAT-TAAA
38424 TTAAATAAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
20 4 0.08
21 15 0.29
22 8 0.16
23 9 0.18
24 13 0.25
25 2 0.04
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTAAAAATAATAATTAAAA
Found at i:38424 original size:23 final size:23
Alignment explanation
Indices: 38330--38425 Score: 72
Period size: 23 Copynumber: 4.2 Consensus size: 23
38320 TAAAGTTAAA
38330 AAATATTTTTAAAAATAATAAT-T
1 AAAT-TTTTTAAAAATAATAATAT
* * *
38353 AAA-ATTTTAAAAACAATATTAT
1 AAATTTTTTAAAAATAATAATAT
** * * *
38375 AAAACATTTTAAATAT-ATATTAC
1 -AAATTTTTTAAAAATAATAATAT
*
38398 AAATTTTTTAAAATTAATAATAT
1 AAATTTTTTAAAAATAATAATAT
38421 AAATT
1 AAATT
38426 AAATAAGCAA
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
21 14 0.25
22 12 0.21
23 22 0.39
24 9 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTTTTTAAAAATAATAATAT
Found at i:38453 original size:36 final size:37
Alignment explanation
Indices: 38413--38486 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
38403 TTTTAAAATT
*
38413 AATAATAT-AAA-TTAAATAAGCAAAATAAAT-TAAGAA
1 AATAATATAAAACTTAAAAAAG-AAAA-AAATCTAAGAA
38449 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
1 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
38486 A
1 A
38487 GAGACAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 12 0.35
37 14 0.41
38 8 0.24
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (37 bp):
AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
Found at i:38458 original size:18 final size:18
Alignment explanation
Indices: 38408--38459 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
38398 AAATTTTTTA
*
38408 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
** *
38426 AAATAAGCAAAATAAATT
1 AAATAAATAATATAAATT
38444 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
38460 ACTTAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:38523 original size:18 final size:19
Alignment explanation
Indices: 38502--38545 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
38492 AAAATATAAG
*
38502 AAAAAAAAGT-TAAAAAGT
1 AAAAAAAAGTAAAAAAAGT
38520 -AAAAAAAGTAAAAAAAGT
1 AAAAAAAAGTAAAAAAAGT
38538 AAAAAAAA
1 AAAAAAAA
38546 ATATAAGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
18 7 0.30
19 7 0.30
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (19 bp):
AAAAAAAAGTAAAAAAAGT
Found at i:38525 original size:9 final size:9
Alignment explanation
Indices: 38503--38544 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
38493 AAATATAAGA
38503 AAAAAAAGT
1 AAAAAAAGT
*
38512 -TAAAAAGT
1 AAAAAAAGT
38520 AAAAAAAGT
1 AAAAAAAGT
38529 AAAAAAAGT
1 AAAAAAAGT
38538 AAAAAAA
1 AAAAAAA
38545 AATATAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:39979 original size:49 final size:48
Alignment explanation
Indices: 39907--40182 Score: 304
Period size: 51 Copynumber: 5.5 Consensus size: 48
39897 CTGATATGCA
*
39907 TAGTAGCATGCACTTAGTACTACACATGCGATCAACAATTCGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGATCAACAATT-GATACACG
* * * *
39956 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTC-ATTGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGATC-AA--CAATTGA-TACACG
*
40007 TAGCAGCCTGCACTTAGTACTACACATGCGATCAACAATTCGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGATCAACAATT-GATACACG
* * * *
40056 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTC-ATTGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGATC-AA--CAATTGA-TACACG
* * *
40107 TAGCAGCCTGCACTTAGTACTACACATGCGACTTAACAGTATGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-TCAACAAT-TGATACACG
*
40157 TAGTAGCCTACACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
40183 CGTGTATTCA
Statistics
Matches: 190, Mismatches: 24, Indels: 25
0.79 0.10 0.10
Matches are distributed among these distances:
48 1 0.01
49 68 0.36
50 41 0.22
51 77 0.41
52 3 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGATCAACAATTGATACACG
Found at i:40061 original size:100 final size:100
Alignment explanation
Indices: 39904--40186 Score: 496
Period size: 100 Copynumber: 2.8 Consensus size: 100
39894 AATCTGATAT
* *
39904 GCATAGTAGCATGCACTTAGTACTACACATGCGATCAACAATTCGATACACGTAGTAGCCTGCAC
1 GCATAGCAGCCTGCACTTAGTACTACACATGCGATCAACAATTCGATACACGTAGTAGCCTGCAC
39969 TTAGTACTACACACGTGATCGAAGTCATTGAGTAC
66 TTAGTACTACACACGTGATCGAAGTCATTGAGTAC
40004 GCATAGCAGCCTGCACTTAGTACTACACATGCGATCAACAATTCGATACACGTAGTAGCCTGCAC
1 GCATAGCAGCCTGCACTTAGTACTACACATGCGATCAACAATTCGATACACGTAGTAGCCTGCAC
40069 TTAGTACTACACACGTGATCGAAGTCATTGAGTAC
66 TTAGTACTACACACGTGATCGAAGTCATTGAGTAC
* * *
40104 GCATAGCAGCCTGCACTTAGTACTACACATGCGACTTAACAGTAT-GATACACGTAGTAGCCTAC
1 GCATAGCAGCCTGCACTTAGTACTACACATGCGA-TCAACAAT-TCGATACACGTAGTAGCCTGC
40168 ACTTAGTACTACACACGTG
64 ACTTAGTACTACACACGTG
40187 TATTCACAAT
Statistics
Matches: 176, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
100 132 0.75
101 43 0.24
102 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (100 bp):
GCATAGCAGCCTGCACTTAGTACTACACATGCGATCAACAATTCGATACACGTAGTAGCCTGCAC
TTAGTACTACACACGTGATCGAAGTCATTGAGTAC
Found at i:50042 original size:54 final size:52
Alignment explanation
Indices: 49858--50169 Score: 330
Period size: 53 Copynumber: 5.9 Consensus size: 52
49848 TATCATACCA
* * * * *
49858 ATGCCATATCCCGGATATGGTC-T-TACATGAAAACACTTATCACATTTCTTCG
1 ATGCCATAGCCCAGCTATGGTCTTATACA-GAAATCACTTATCAC-TTTTTTCG
* *
49910 ATGCCATAGCCTAGCTATGGTCTTATAC-G-GATCACTTGTATCACTTTATTTCG
1 ATGCCATAGCCCAGCTATGGTCTTATACAGAAATCAC-T-TATCACTTT-TTTCG
* *
49963 AAGCCATAGCCCTGCTATGGTCTTATACAGAAATCACTTATCACTTGTTTTCTG
1 ATGCCATAGCCCAGCTATGGTCTTATACAGAAATCACTTATCACTT-TTTTC-G
*
50017 ATGCCATAGCCCAGCTATGGTCTTATAC-G-GATCACTTGTATCACTTTATTTCG
1 ATGCCATAGCCCAGCTATGGTCTTATACAGAAATCAC-T-TATCACTTT-TTTCG
* *
50070 AAGCCATAGCCCTGCTATGGTCTTATACAGAAATCACTTATCACTTGTTTTCTG
1 ATGCCATAGCCCAGCTATGGTCTTATACAGAAATCACTTATCACTT-TTTTC-G
* ** *
50124 ATGCCATAGCCCAGCTATGGTCTTATACGGGTATCACTCATCACTT
1 ATGCCATAGCCCAGCTATGGTCTTATACAGAAATCACTTATCACTT
50170 GTTGCCCTGG
Statistics
Matches: 221, Mismatches: 23, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
51 4 0.02
52 28 0.13
53 90 0.41
54 89 0.40
55 10 0.05
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (52 bp):
ATGCCATAGCCCAGCTATGGTCTTATACAGAAATCACTTATCACTTTTTTCG
Found at i:50169 original size:107 final size:107
Alignment explanation
Indices: 49873--50153 Score: 489
Period size: 107 Copynumber: 2.6 Consensus size: 107
49863 ATATCCCGGA
* * *
49873 TATGGTC-T-TACATGAAAACACTTATCACATT-TCTTC-GATGCCATAGCCTAGCTATGGTCTT
1 TATGGTCTTATACA-GAAATCACTTATCAC-TTGTTTTCTGATGCCATAGCCCAGCTATGGTCTT
49934 ATACGGATCACTTGTATCACTTTATTTCGAAGCCATAGCCCTGC
64 ATACGGATCACTTGTATCACTTTATTTCGAAGCCATAGCCCTGC
49978 TATGGTCTTATACAGAAATCACTTATCACTTGTTTTCTGATGCCATAGCCCAGCTATGGTCTTAT
1 TATGGTCTTATACAGAAATCACTTATCACTTGTTTTCTGATGCCATAGCCCAGCTATGGTCTTAT
50043 ACGGATCACTTGTATCACTTTATTTCGAAGCCATAGCCCTGC
66 ACGGATCACTTGTATCACTTTATTTCGAAGCCATAGCCCTGC
50085 TATGGTCTTATACAGAAATCACTTATCACTTGTTTTCTGATGCCATAGCCCAGCTATGGTCTTAT
1 TATGGTCTTATACAGAAATCACTTATCACTTGTTTTCTGATGCCATAGCCCAGCTATGGTCTTAT
50150 ACGG
66 ACGG
50154 GTATCACTCA
Statistics
Matches: 169, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
105 9 0.05
106 19 0.11
107 141 0.83
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (107 bp):
TATGGTCTTATACAGAAATCACTTATCACTTGTTTTCTGATGCCATAGCCCAGCTATGGTCTTAT
ACGGATCACTTGTATCACTTTATTTCGAAGCCATAGCCCTGC
Found at i:57142 original size:29 final size:29
Alignment explanation
Indices: 57109--57225 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
57099 TCGCCCATCT
* * *
57109 CATTCATATTGCCCATTAGGCTCAATTCA
1 CATTCATATGGCCCATTAGGCCCAAATCA
* * * *
57138 CATTCATATGGCCCATCAAGCCTAATTCA
1 CATTCATATGGCCCATTAGGCCCAAATCA
* *
57167 TATTCATATGGCCTATTAGGCCCAAATCA
1 CATTCATATGGCCCATTAGGCCCAAATCA
* * *
57196 CCTTTATATGGCCCGTTAGGCCCAAATCA
1 CATTCATATGGCCCATTAGGCCCAAATCA
57225 C
1 C
57226 CTTATATTCA
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (29 bp):
CATTCATATGGCCCATTAGGCCCAAATCA
Done.