Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2995
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: 46901
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Found at i:2650 original size:39 final size:38
Alignment explanation
Indices: 2490--2716 Score: 286
Period size: 38 Copynumber: 6.0 Consensus size: 38
2480 ATTTCGGATG
* * *
2490 ATAA-CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTG
1 ATAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
*
2527 ACTAGTTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
1 A-TA-ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
*
2567 ATTATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
1 ATAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
2605 ATTAATCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTACT
1 A-TAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT--T
*
2645 ATAATCCGGGCTAAGT-CCGAAGGCATTGGTGCGAGTT
1 ATAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
* *
2682 ACTAAT-CGGGCTATGTCCCGAA-GCA-TTGAGCGAGT
1 A-TAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
2717 AGCTATATCC
Statistics
Matches: 171, Mismatches: 11, Indels: 17
0.86 0.06 0.09
Matches are distributed among these distances:
36 8 0.05
37 15 0.09
38 66 0.39
39 49 0.29
40 33 0.19
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.26
Consensus pattern (38 bp):
ATAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
Found at i:2652 original size:78 final size:79
Alignment explanation
Indices: 2490--2728 Score: 316
Period size: 78 Copynumber: 3.1 Consensus size: 79
2480 ATTTCGGATG
* * * *
2490 ATAA-CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGC
1 ATAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATCCGGGCTAAGTCCCGAAGGC
2554 ATTTGTGCGAGT--T
65 ATTTGTGCGAGTACT
* *
2567 ATTATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAATCCGGGCTAAGT-CCGAAGGCA
1 ATAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATCCGGGCTAAGTCCCGAAGGCA
2631 TTTGTGCGAGTACT
66 TTTGTGCGAGTACT
* *
2645 ATAATCCGGGCTAAGT-CCGAAGGCATTGGTGCGAGTTACTAAT-CGGGCTATGTCCCGAA-GCA
1 ATAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATCCGGGCTAAGTCCCGAAGGCA
*
2707 -TTGAGCGAGTAGCT
66 TTTGTGCGAGTA-CT
2721 AT-ATCCGG
1 ATAATCCGG
2729 TTAAATCCAA
Statistics
Matches: 146, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
75 16 0.11
76 36 0.25
77 45 0.31
78 49 0.34
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (79 bp):
ATAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTACT
Found at i:10763 original size:40 final size:39
Alignment explanation
Indices: 10706--10936 Score: 295
Period size: 40 Copynumber: 5.8 Consensus size: 39
10696 CGGATGATAA
* * *
10706 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TT
* * *
10746 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TT
*
10786 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT--ATT
*
10827 -CGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-T
*
10866 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-T
* *
10906 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
10937 AGCTATATCA
Statistics
Matches: 171, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.01
39 9 0.05
40 158 0.92
41 1 0.01
42 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATT
Found at i:10920 original size:120 final size:119
Alignment explanation
Indices: 10707--10936 Score: 347
Period size: 120 Copynumber: 1.9 Consensus size: 119
10697 GGATGATAAC
* * *
10707 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCTGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGGT
* *
10772 GCGAGTTATTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACATT
66 GCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCA-TTGAGCGAGTTATTACATT
*
10827 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGCT-ACTA-TATCCGGGCTAAGTCCCGAAGGCATTG
1 CGGGCTAAGTCCCGAAGGCATTTGCGCGAG-TGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTG
* *
10890 GTGCGAGTTACTATATCCGGGCTATGTCCCGAAGGCATTGAGCGAGT
64 GTGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTGAGCGAGT
10937 AGCTATATCA
Statistics
Matches: 100, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
119 10 0.10
120 89 0.89
121 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.26
Consensus pattern (119 bp):
CGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGGT
GCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTGAGCGAGTTATTACATT
Found at i:13363 original size:39 final size:40
Alignment explanation
Indices: 13147--13353 Score: 314
Period size: 40 Copynumber: 5.2 Consensus size: 40
13137 TCGATTGATA
* *
13147 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
13187 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
13226 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
13266 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
13306 CTGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
13346 CC-GGCTAA
1 CCGGGCTAA
13354 ACTCCGAAGG
Statistics
Matches: 156, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
39 43 0.28
40 113 0.72
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:16471 original size:42 final size:40
Alignment explanation
Indices: 16383--16578 Score: 205
Period size: 42 Copynumber: 4.7 Consensus size: 40
16373 CTAAGATTAA
* * *
16383 GTGTAAGACCATATCTGGGATATGGAATCATTTGAGACTTT
1 GTGTAAGACCATATCT-GGATATGGCATCATATGAGACTTC
* *
16424 GTGTAAGACCATATTTGGTATGTGGCATCAATATGAGACTTC
1 GTGTAAGACCATATCTGG-ATATGGCATC-ATATGAGACTTC
16466 GTGTAAGACCATATCTGAGATATGGCATCGATATGAGACTTC
1 GTGTAAGACCATATCTG-GATATGGCATC-ATATGAGACTTC
* * * *
16508 GTGTAAGACCATAGCTGAGCTATTGGCATCGATACGAGA-TTAT
1 GTGTAAGACCATATCTG-GATA-TGGCATC-ATATGAGACTT-C
*
16551 ATGTAAGACCATATCTGGGATATGGCAT
1 GTGTAAGACCATATCT-GGATATGGCAT
16579 TGGTACGGTA
Statistics
Matches: 134, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
40 2 0.01
41 23 0.17
42 75 0.56
43 33 0.25
44 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (40 bp):
GTGTAAGACCATATCTGGATATGGCATCATATGAGACTTC
Found at i:16565 original size:85 final size:82
Alignment explanation
Indices: 16376--16578 Score: 255
Period size: 85 Copynumber: 2.4 Consensus size: 82
16366 AGGGTTACTA
* * * **
16376 AGATTAAGTGTAAGACCATATCTGGGATATGGAATCATTTGAGACTTTGTGTAAGACCATATTTG
1 AGATTAA-TGTAAGACCATATCTGGGATATGGCATCATATGAGACTTCGTGTAAGACCATAGCTG
*
16441 GTATGTGGCATCAATATG
65 GTATGTGGCATCAATACG
** *
16459 AGACTTCGTGTAAGACCATATCTGAGATATGGCATCGATATGAGACTTCGTGTAAGACCATAGCT
1 AGA-TTAATGTAAGACCATATCTGGGATATGGCATC-ATATGAGACTTCGTGTAAGACCATAGCT
*
16524 GAGCTAT-TGGCATCGATACG
64 G-G-TATGTGGCATCAATACG
16544 AGATTATATGTAAGACCATATCTGGGATATGGCAT
1 AGATTA-ATGTAAGACCATATCTGGGATATGGCAT
16579 TGGTACGGTA
Statistics
Matches: 102, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
83 29 0.28
84 29 0.28
85 41 0.40
86 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (82 bp):
AGATTAATGTAAGACCATATCTGGGATATGGCATCATATGAGACTTCGTGTAAGACCATAGCTGG
TATGTGGCATCAATACG
Found at i:17671 original size:18 final size:17
Alignment explanation
Indices: 17648--17682 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17638 GATTTATGGC
17648 ATGATAAATGTTGTATGT
1 ATGATAAATGTTG-ATGT
*
17666 ATGATAGATGTTGATGT
1 ATGATAAATGTTGATGT
17683 GGTACTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (17 bp):
ATGATAAATGTTGATGT
Found at i:23855 original size:13 final size:13
Alignment explanation
Indices: 23837--23862 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23827 TATTTTAACA
23837 TTATTTTATGTGT
1 TTATTTTATGTGT
23850 TTATTTTATGTGT
1 TTATTTTATGTGT
23863 GAATTGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (13 bp):
TTATTTTATGTGT
Found at i:25457 original size:17 final size:17
Alignment explanation
Indices: 25435--25468 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
25425 GATTCATAAT
25435 ATATATATATTTAGTTA
1 ATATATATATTTAGTTA
25452 ATATATATATTTAGTTA
1 ATATATATATTTAGTTA
25469 TGTAATGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATATATATATTTAGTTA
Found at i:25878 original size:40 final size:41
Alignment explanation
Indices: 25826--26008 Score: 129
Period size: 41 Copynumber: 4.5 Consensus size: 41
25816 GTAAAAATTG
* *
25826 TAAAACACAGAGCAATAGCGACGTTTTA-CCAAAAACGCCGC
1 TAAAA-ACAGAGCAATAGCGACGTTTTAGCAAAAAACGCCAC
* * * *
25867 TAAAAATAGAGCAATAGCGGCGTTTTAGTAAAAAATGCCAC
1 TAAAAACAGAGCAATAGCGACGTTTTAGCAAAAAACGCCAC
* * * * ** *
25908 TAAAAACAGAGCATTAGCGGCGCTTTCGGTAAAAA-GCCGC
1 TAAAAACAGAGCAATAGCGACGTTTTAGCAAAAAACGCCAC
* * * * ** *
25948 TAAAAACCAGAGCATTAGCGGCGCTTTCGGTAAAAA-GCCGC
1 TAAAAA-CAGAGCAATAGCGACGTTTTAGCAAAAAACGCCAC
*
25989 TAAAAACCAGAGCATTAGCG
1 TAAAAA-CAGAGCAATAGCG
26009 GCGCTTTTGG
Statistics
Matches: 127, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 30 0.24
41 97 0.76
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.17
Consensus pattern (41 bp):
TAAAAACAGAGCAATAGCGACGTTTTAGCAAAAAACGCCAC
Found at i:25901 original size:41 final size:41
Alignment explanation
Indices: 25856--26034 Score: 247
Period size: 41 Copynumber: 4.4 Consensus size: 41
25846 ACGTTTTACC
* * *
25856 AAAAACGCCGCTAAAAA-TAGAGCAATAGCGGCG-TTTTAGT
1 AAAAA-GCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* *
25896 AAAAAATGCCACTAAAAA-CAGAGCATTAGCGGCGCTTTCGGT
1 -AAAAA-GCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
25938 AAAAAGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
1 AAAAAGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
25979 AAAAAGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAAAGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
26020 AAAACGCCGCTAAAA
1 AAAAAGCCGCTAAAA
26035 GTCATATAAC
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 10 0.08
41 112 0.88
42 5 0.04
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAAAGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:26212 original size:7 final size:7
Alignment explanation
Indices: 26191--26288 Score: 52
Period size: 7 Copynumber: 13.4 Consensus size: 7
26181 TTAATTATCA
*
26191 TTATAGT
1 TTATGGT
*
26198 TTAAGGT
1 TTATGGT
26205 TTATGGT
1 TTATGGT
* *
26212 TTAAGAT
1 TTATGGT
*
26219 ATATGGT
1 TTATGGT
*
26226 TTAGGGT
1 TTATGGT
*
26233 TTAAGGT
1 TTATGGT
26240 TTATGAGT
1 TTATG-GT
26248 TAACTATGGT
1 T---TATGGT
* *
26258 TTAAGAT
1 TTATGGT
*
26265 ATATGGT
1 TTATGGT
*
26272 TTAGGGT
1 TTATGGT
*
26279 TTAAGGT
1 TTATGGT
26286 TTA
1 TTA
26289 GGAGTTAACT
Statistics
Matches: 67, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
7 57 0.85
8 3 0.04
10 3 0.04
11 4 0.06
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.46
Consensus pattern (7 bp):
TTATGGT
Found at i:26213 original size:14 final size:14
Alignment explanation
Indices: 26191--26288 Score: 70
Period size: 14 Copynumber: 6.7 Consensus size: 14
26181 TTAATTATCA
*
26191 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
26205 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
* *
26219 ATATGGTTTAGGGT
1 TTATGGTTTAAGGT
* *
26233 TTAAGGTTTATGAGT
1 TTATGGTTTAAG-GT
*
26248 TAACTATGGTTTAAGAT
1 T---TATGGTTTAAGGT
* *
26265 ATATGGTTTAGGGT
1 TTATGGTTTAAGGT
*
26279 TTAAGGTTTA
1 TTATGGTTTA
26289 GGAGTTAACT
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
14 51 0.80
15 3 0.05
17 1 0.02
18 9 0.14
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.46
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:26226 original size:21 final size:21
Alignment explanation
Indices: 26202--26283 Score: 92
Period size: 21 Copynumber: 3.7 Consensus size: 21
26192 TATAGTTTAA
*
26202 GGTTTATGGTTTAAGATATAT
1 GGTTTAGGGTTTAAGATATAT
* *
26223 GGTTTAGGGTTTAAGGTTTAT
1 GGTTTAGGGTTTAAGATATAT
*
26244 GAGTTAACTATGGTTTAAGATATAT
1 G-GTT---TAGGGTTTAAGATATAT
26269 GGTTTAGGGTTTAAG
1 GGTTTAGGGTTTAAG
26284 GTTTAGGAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 29 0.58
22 3 0.06
24 3 0.06
25 15 0.30
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.44
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGATATAT
Found at i:26256 original size:46 final size:46
Alignment explanation
Indices: 26206--26299 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
26196 GTTTAAGGTT
*
26206 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAAC
1 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
26252 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
1 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
26298 TA
1 TA
26300 GTATTTGAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.43
Consensus pattern (46 bp):
TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
Found at i:28344 original size:26 final size:27
Alignment explanation
Indices: 28277--28347 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 27
28267 TAGGTAAAGG
*
28277 TGTCTCTTTTTATCTATTCCATAGTAT
1 TGTCTGTTTTTATCTATTCCATAGTAT
28304 TAGTCATTAGGTTTTTATCTATTCCATAGTAT
1 T-GTC--T--GTTTTTATCTATTCCATAGTAT
28336 TGTCT-TTTTTAT
1 TGTCTGTTTTTAT
28348 GCACTGCTCG
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
26 7 0.18
27 1 0.03
28 3 0.08
29 1 0.03
30 1 0.03
31 3 0.08
32 22 0.58
ACGTcount: A:0.20, C:0.14, G:0.10, T:0.56
Consensus pattern (27 bp):
TGTCTGTTTTTATCTATTCCATAGTAT
Found at i:32418 original size:19 final size:19
Alignment explanation
Indices: 32396--32436 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
32386 TTTATTGATA
32396 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
32414 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
32433 TTTT
1 TTTT
32437 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:33900 original size:10 final size:10
Alignment explanation
Indices: 33887--33920 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
33877 ATATGTGGCT
33887 ATATATATAA
1 ATATATATAA
33897 ATATATATAA
1 ATATATATAA
* *
33907 ACATATATAC
1 ATATATATAA
33917 ATAT
1 ATAT
33921 TTGTTAAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (10 bp):
ATATATATAA
Found at i:38450 original size:26 final size:26
Alignment explanation
Indices: 38414--38523 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
38404 TGATACAAAT
38414 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
38440 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
38466 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
38492 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
38518 TGATAA
1 TGATAA
38524 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:40036 original size:26 final size:26
Alignment explanation
Indices: 40007--40059 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
39997 TTTACAGTTT
40007 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
40033 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
40059 T
1 T
40060 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:44249 original size:24 final size:26
Alignment explanation
Indices: 44167--44272 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
44157 TGATACAAAT
44167 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
44193 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
44219 TGATAATGGGTTAGGTAAAT-TT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
44243 TGATAAT-GGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
44267 TGATAA
1 TGATAA
44273 GAATTTCATG
Statistics
Matches: 78, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
23 12 0.15
24 19 0.24
25 2 0.03
26 45 0.58
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:45779 original size:25 final size:26
Alignment explanation
Indices: 45751--45802 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
45741 TTTACAGTTT
45751 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
45776 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
45802 T
1 T
45803 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Done.