Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2448
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: 83734
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1324 original size:14 final size:14
Alignment explanation
Indices: 1301--1330 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1291 TAAACAGAAT
1301 TAATAAATTTAATA
1 TAATAAATTTAATA
*
1315 TAATATATTTAATA
1 TAATAAATTTAATA
1329 TA
1 TA
1331 TCTATCGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATAAATTTAATA
Found at i:1853 original size:15 final size:15
Alignment explanation
Indices: 1829--1865 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
1819 ATTATTAATA
1829 TTTTTAAAAAATTATT
1 TTTTTAAAAAA-TATT
1845 TTTTTAAAAAATATT
1 TTTTTAAAAAATATT
1860 TATTTT
1 T-TTTT
1866 TCATGAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTAAAAAATATT
Found at i:2111 original size:21 final size:21
Alignment explanation
Indices: 2078--2118 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2068 CTAAGTAAAA
2078 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
2099 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
2119 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:2183 original size:20 final size:19
Alignment explanation
Indices: 2158--2228 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
2148 ACCCTGAAAA
2158 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
2178 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
2197 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
2218 GTATCGATACA
1 GTATCGATACA
2229 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:2281 original size:53 final size:53
Alignment explanation
Indices: 2198--2334 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
2188 AAATTGCATA
*
2198 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAAATT
*
2252 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAAATT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAAATT
*
2305 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
2335 TTGGTAGTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAAATT
Found at i:2321 original size:18 final size:19
Alignment explanation
Indices: 2298--2334 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2288 TGGCAGTAGC
2298 CAAAAT-TGTATCGATACA
1 CAAAATATGTATCGATACA
2316 CAAAATATGTATCGATACA
1 CAAAATATGTATCGATACA
2335 TTGGTAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (19 bp):
CAAAATATGTATCGATACA
Found at i:2377 original size:10 final size:10
Alignment explanation
Indices: 2358--2388 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2348 AATCTCATTT
2358 TCACTGTTCA
1 TCACTGTTCA
*
2368 TCACTATTCA
1 TCACTGTTCA
2378 TCACTGTTCA
1 TCACTGTTCA
2388 T
1 T
2389 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:2414 original size:21 final size:22
Alignment explanation
Indices: 2376--2431 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
2366 CATCACTATT
2376 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
*
2398 CATCACT-TTCTTGTATCGATA
1 CATCACTGTTCATGTATCGATA
*
2419 AATCACTGTTCAT
1 CATCACTGTTCAT
2432 ACCATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:9446 original size:16 final size:16
Alignment explanation
Indices: 9425--9461 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
9415 TATATTATTC
*
9425 GAATTCAATTCATTTT
1 GAATTCAATTAATTTT
9441 GAATTCAATTAATTTT
1 GAATTCAATTAATTTT
*
9457 AAATT
1 GAATT
9462 TATTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (16 bp):
GAATTCAATTAATTTT
Found at i:9589 original size:21 final size:21
Alignment explanation
Indices: 9565--9605 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9555 TTTTACTTAT
9565 TTCAAATGAA-AATTATTCATA
1 TTCAAATGAATAATT-TTCATA
*
9586 TTCAATTGAATAATTTTCAT
1 TTCAAATGAATAATTTTCAT
9606 CTTTATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (21 bp):
TTCAAATGAATAATTTTCATA
Found at i:10232 original size:19 final size:19
Alignment explanation
Indices: 10200--10237 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
10190 GAAATTAAAT
*
10200 TAATTTTATAATTTTTTTA
1 TAATTTTATAATTTATTTA
10219 TAATATTTAT-ATTTATTTA
1 TAAT-TTTATAATTTATTTA
10238 ATTCGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATTTTATAATTTATTTA
Found at i:12245 original size:24 final size:22
Alignment explanation
Indices: 12210--12285 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 22
12200 AATCATAACA
*
12210 TATTATATTTTATTTATTATAT
1 TATTTTATTTTATTTATTATAT
** *
12232 TATTTTCATATTTATCAAATATAT
1 TATTTT-AT-TTTATTTATTATAT
12256 TATATTTATTTCGTATTT-TTATAT
1 TAT-TTTATTT--TATTTATTATAT
12280 TATTTT
1 TATTTT
12286 TAAAATTATA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
22 5 0.12
23 7 0.17
24 24 0.57
25 6 0.14
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (22 bp):
TATTTTATTTTATTTATTATAT
Found at i:12906 original size:4 final size:4
Alignment explanation
Indices: 12897--12923 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12887 CAACTCCAAA
12897 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
12924 AAGATGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:13443 original size:16 final size:16
Alignment explanation
Indices: 13402--13452 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
13392 AATCGTTAAG
13402 TTTTAAA-TTAAATTA
1 TTTTAAATTTAAATTA
* * *
13417 GTTTGATTTTAAATTA
1 TTTTAAATTTAAATTA
13433 TTTTAAATTT-AATT-
1 TTTTAAATTTAAATTA
13447 TTTTAA
1 TTTTAA
13453 GTAATGTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 6 0.21
15 8 0.28
16 15 0.52
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:25407 original size:2 final size:2
Alignment explanation
Indices: 25402--25464 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
25392 TATTTTTTTG
25402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25444 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
25465 GACTTCTAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30980 original size:2 final size:2
Alignment explanation
Indices: 30973--31021 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
30963 TTAGGGCCTA
*
30973 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31015 AT AT AT A
1 AT AT AT A
31022 GAGAGAGAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32311 original size:15 final size:15
Alignment explanation
Indices: 32291--32319 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32281 AAATAATATT
32291 TTTAATTTAAATTAA
1 TTTAATTTAAATTAA
32306 TTTAATTTAAATTA
1 TTTAATTTAAATTA
32320 TTATCTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAATTTAAATTAA
Found at i:32901 original size:58 final size:59
Alignment explanation
Indices: 32816--32932 Score: 191
Period size: 58 Copynumber: 2.0 Consensus size: 59
32806 TCTCAAGTTT
*
32816 AAGAGTTCTAGTCAGAACCAAATACCTCATACATTGAA-AACTTGCTGGAGGGAAGTAA
1 AAGAGTTCTAGTCAGAACCAAACACCTCATACATTGAACAACTTGCTGGAGGGAAGTAA
* * *
32874 AAGAGTTCTAGTTAGAATCAAACACCTCATACATTGAACACCTTGCTGGAGGGAAGTAA
1 AAGAGTTCTAGTCAGAACCAAACACCTCATACATTGAACAACTTGCTGGAGGGAAGTAA
32933 CTATGGCAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
58 35 0.65
59 19 0.35
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (59 bp):
AAGAGTTCTAGTCAGAACCAAACACCTCATACATTGAACAACTTGCTGGAGGGAAGTAA
Found at i:34932 original size:44 final size:44
Alignment explanation
Indices: 34869--35001 Score: 239
Period size: 44 Copynumber: 3.0 Consensus size: 44
34859 ATCAGAAACC
* **
34869 TGTTATTTACCAATCTTTCTTGAAGATATCATTTACTATTTTCT
1 TGTTATTTCCCAATCTTTCTTGAAGGGATCATTTACTATTTTCT
34913 TGTTATTTCCCAATCTTTCTTGAAGGGATCATTTACTATTTTCT
1 TGTTATTTCCCAATCTTTCTTGAAGGGATCATTTACTATTTTCT
34957 TGTTATTTCCCAATCTTTCTTGAAGGGATCATTTACTATTTTCT
1 TGTTATTTCCCAATCTTTCTTGAAGGGATCATTTACTATTTTCT
35001 T
1 T
35002 AGTACTAGCA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 86 1.00
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.51
Consensus pattern (44 bp):
TGTTATTTCCCAATCTTTCTTGAAGGGATCATTTACTATTTTCT
Found at i:35956 original size:14 final size:14
Alignment explanation
Indices: 35933--35974 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
35923 TTTTTTATTT
35933 TTAAATAAATTAAA
1 TTAAATAAATTAAA
* *
35947 TTAAAAAAATTATA
1 TTAAATAAATTAAA
*
35961 TTAATTAAATTAAA
1 TTAAATAAATTAAA
35975 ATTATTTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAATAAATTAAA
Found at i:36043 original size:26 final size:26
Alignment explanation
Indices: 35993--36043 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
35983 ATTAAATTTG
* *
35993 ATTAATTAATTAAATTAATTTTTTAT
1 ATTAATAAATTAAATTAATATTTTAT
36019 ATTAATAAATTAAAATT-ATATTTTA
1 ATTAATAAATT-AAATTAATATTTTA
36044 AAATATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTAATAAATTAAATTAATATTTTAT
Found at i:36046 original size:13 final size:14
Alignment explanation
Indices: 36004--36063 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 14
35994 TTAATTAATT
*
36004 AAATTAAT-TTTTT
1 AAATTAATATTTTA
* **
36017 ATATTAATAAATTA
1 AAATTAATATTTTA
36031 AAATT-ATATTTTA
1 AAATTAATATTTTA
*
36044 AAATATAATATTTTT
1 AAAT-TAATATTTTA
36059 AAATT
1 AAATT
36064 TTTATAATTC
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
13 17 0.47
14 8 0.22
15 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTAATATTTTA
Found at i:36462 original size:11 final size:11
Alignment explanation
Indices: 36446--36478 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
36436 TAATTATTTG
36446 ATATAAATATA
1 ATATAAATATA
*
36457 ATATAAAAATA
1 ATATAAATATA
36468 ATATAAATATA
1 ATATAAATATA
36479 TAAATATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAATATA
Found at i:36476 original size:17 final size:16
Alignment explanation
Indices: 36451--36484 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
36441 ATTTGATATA
36451 AATATAATATAAAAAT
1 AATATAATATAAAAAT
*
36467 AATATAAATATATAAAT
1 AATAT-AATATAAAAAT
36484 A
1 A
36485 TGTTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATATAATATAAAAAT
Found at i:36641 original size:21 final size:22
Alignment explanation
Indices: 36602--36650 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
36592 TAAAAATATT
*
36602 TTATTTAAATTTAATTATAAAA
1 TTATATAAATTTAATTATAAAA
36624 -TATATAAATATTAA-TATAAAA
1 TTATATAAAT-TTAATTATAAAA
36645 TTATAT
1 TTATAT
36651 TTTAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATATAAATTTAATTATAAAA
Found at i:36844 original size:2 final size:2
Alignment explanation
Indices: 36839--36870 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36829 AATTTTTTTC
36839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36871 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38363 original size:59 final size:58
Alignment explanation
Indices: 38244--38369 Score: 189
Period size: 59 Copynumber: 2.2 Consensus size: 58
38234 TTGTATGACA
* **
38244 TATTTAAAATTTAAATTAAATCAAATCTAAAATAATTAAATGTATAATTCATTCTAAT
1 TATTTAAAATTTAAATAAAATCAAATCTAAAATAATTAAATGTATAATTCATAATAAT
* * *
38302 TATTTTAAAATTTAAATAAAATTAAATCTAAAATAATTAAATGTATGATTCATAATCAT
1 TA-TTTAAAATTTAAATAAAATCAAATCTAAAATAATTAAATGTATAATTCATAATAAT
38361 TATTTAAAA
1 TATTTAAAA
38370 CAATCTACAC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 9 0.15
59 52 0.85
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (58 bp):
TATTTAAAATTTAAATAAAATCAAATCTAAAATAATTAAATGTATAATTCATAATAAT
Found at i:40894 original size:96 final size:96
Alignment explanation
Indices: 40760--40940 Score: 326
Period size: 96 Copynumber: 1.9 Consensus size: 96
40750 CGACAAGAAG
* * *
40760 TTTGAATTTTGGGATGTTACCTAAAGGCGTGCCTATTCCTCCCTCCGGGCCTAGTAGGCGTACAT
1 TTTGAATTTTGGGATGTTACCTAAAGGAGTGCCCATTCCTCCCTCCGGACCTAGTAGGCGTACAT
40825 CGGATCCCCCACCTCCTCCATCAACAACAAA
66 CGGATCCCCCACCTCCTCCATCAACAACAAA
*
40856 TTTGAATTTTGGGATGTTGCCTAAAGGAGTGCCCATTCCTCCCTCCGGACCTAGTAGGCGTACAT
1 TTTGAATTTTGGGATGTTACCTAAAGGAGTGCCCATTCCTCCCTCCGGACCTAGTAGGCGTACAT
40921 CGGATCCCCCACCTCCTCCA
66 CGGATCCCCCACCTCCTCCA
40941 GCATTGTAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.27
Consensus pattern (96 bp):
TTTGAATTTTGGGATGTTACCTAAAGGAGTGCCCATTCCTCCCTCCGGACCTAGTAGGCGTACAT
CGGATCCCCCACCTCCTCCATCAACAACAAA
Found at i:41054 original size:2 final size:2
Alignment explanation
Indices: 41047--41077 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41037 TTAAAAACCT
41047 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41078 GCTGTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41806 original size:2 final size:2
Alignment explanation
Indices: 41799--41823 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41789 CTTTACAATG
41799 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
41824 CATAGTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48955 original size:126 final size:126
Alignment explanation
Indices: 48730--48967 Score: 379
Period size: 126 Copynumber: 1.9 Consensus size: 126
48720 AAGGCGTACC
* *
48730 TATTCTTTCATCCGGGCCTAGCAGAGGCCATTGGGATTCTCCACCTCCTCCATCAGCAATAAATT
1 TATTCTTTCATCCGGGCCTAGCAGAGGCCATTCGGATTCTCCACCTCCTCCATCAACAATAAATT
* *
48795 TGAATCTCGGGATGTTACCTAAAGACGGGCCTATTCCTCCATCCGGGTCTAATGGTGTGCG
66 TGAATCTCGGAATGTTACCTAAAGACGGGCCTATTCATCCATCCGGGTCTAATGGTGTGCG
* *
48856 TATTCTTTCATCCGGGCCTAGCCCG-GGCCTTTCGGATTCTCCACCTCCTCCATCAACAATAAAT
1 TATTCTTTCATCCGGGCCTAG-CAGAGGCCATTCGGATTCTCCACCTCCTCCATCAACAATAAAT
* * *
48920 TTGAATTTTGGAATGTTACCTAAAGACGTGCCTATTCATCCATCCGGG
65 TTGAATCTCGGAATGTTACCTAAAGACGGGCCTATTCATCCATCCGGG
48968 CCTAGTAGTC
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
126 100 0.98
127 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.30
Consensus pattern (126 bp):
TATTCTTTCATCCGGGCCTAGCAGAGGCCATTCGGATTCTCCACCTCCTCCATCAACAATAAATT
TGAATCTCGGAATGTTACCTAAAGACGGGCCTATTCATCCATCCGGGTCTAATGGTGTGCG
Found at i:49004 original size:24 final size:21
Alignment explanation
Indices: 48960--49001 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
48950 CCTATTCATC
*
48960 CATCCGGGCCTAGTAGTCGTA
1 CATCCGGGCCTAATAGTCGTA
48981 CATCCGGGCCTAATAGT-GTA
1 CATCCGGGCCTAATAGTCGTA
49001 C
1 C
49002 GTATTCTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (21 bp):
CATCCGGGCCTAATAGTCGTA
Found at i:49106 original size:147 final size:146
Alignment explanation
Indices: 48834--49348 Score: 805
Period size: 147 Copynumber: 3.5 Consensus size: 146
48824 CCTATTCCTC
* *
48834 CATCCGGGTCTAATGGTGTGCGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
1 CATCCGGGCCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
*
48899 CCTCCTCCATCAACAATAAATTTGAATTTTGGAATGTTACCTAAAGACGTGCCTATTCATCCATC
66 CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGACGTGCCTA-TCATCCATC
48964 CGGGCCTAGTAGTCGTA
130 CGGGCCTAGTAGTCGTA
*
48981 CATCCGGGCCTAATAGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
1 CATCCGGGCCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
49046 CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGACGTGCCTAGTCATCCATC
66 CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGACGTGCCTA-TCATCCATC
* *
49111 CGGGCCCAGTAGTCATA
130 CGGGCCTAGTAGTCGTA
*
49128 CATCCGGGTCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
1 CATCCGGGCCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
* * *
49193 CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGATGTGCTTATCCCTCCATC
66 CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGACGTGCCTAT-CATCCATC
*
49258 CGGACCTAGTAGTCGTA
130 CGGGCCTAGTAGTCGTA
* ** * * * ** * * *
49275 CATCCGAGCCTAATGGCATACCTATTCTTTCATCCGGACCAAGCAGGGGCCATTGGGATTCCCCA
1 CATCCGGGCCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
49340 CCTCCTCCA
66 CCTCCTCCA
49349 GCACTGTGAT
Statistics
Matches: 340, Mismatches: 27, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
146 1 0.00
147 339 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.29
Consensus pattern (146 bp):
CATCCGGGCCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGACGTGCCTATCATCCATCC
GGGCCTAGTAGTCGTA
Found at i:51033 original size:18 final size:18
Alignment explanation
Indices: 51012--51059 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
51002 TTTTAATAAA
51012 ATATTAAA-AATTATTTTT
1 ATATTAAATAA-TATTTTT
51030 ATATTAATATTAATATTTTT
1 ATATTAA-A-TAATATTTTT
51050 ATAATTAAAT
1 AT-ATTAAAT
51060 TTAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 7 0.27
19 2 0.08
20 10 0.38
21 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTAAATAATATTTTT
Found at i:52489 original size:17 final size:18
Alignment explanation
Indices: 52464--52497 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52454 TAATATCATC
*
52464 ATACTAAAATATTAAAAA
1 ATACTAAAAAATTAAAAA
52482 ATAC-AAAAAATTAAAA
1 ATACTAAAAAATTAAAA
52498 TACAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
ATACTAAAAAATTAAAAA
Found at i:53863 original size:111 final size:111
Alignment explanation
Indices: 53665--54655 Score: 1543
Period size: 111 Copynumber: 8.9 Consensus size: 111
53655 TCCATCATTG
* * *
53665 TCATCCTTACCAGCAAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* *
53730 AGGGCCTGAACCTGGTACAAATTCACCGCCGCCGCCATCACTATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
*
53776 TTATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* * * *
53841 AGGGCCTGACCCTGGTATAAATTCACCACCACCACCATCACAATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* * *
53887 TCATCTTCACCAAGGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCCAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* * *
53952 AGGGCCTGAACCTGGTACAAATTCACCACCACCGCCATCACAATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* *
53998 TCATCTTCACCAAGGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* *
54063 AGGGCCTGACCCTGGTACAAATTCACCACCACCGCCATCACAATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* *
54109 TCATCTTCACCAAGGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* *
54174 AGGGCCTGACCCTGGTACAAATTCACCACCACCGCCATCACAATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* *
54220 TCATCTTCACCAAGGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* * *
54285 AGGGCCTGAACCTGGTACAAATTCACCGCCGCCACCATCACCATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* * * * *
54331 TCATCCTCACCGACGAAGAGTTTGAATTTTAGGATGTTGCCTAAAGGGGAGCCTACTCCACCATC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
*
54396 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACCATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* ** * *
54442 TCATCCTCACCAACGAAGAGTTTGAATTTTAGGATGTTGCCTAAAGGTAAGCCTACTCCACCATC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* * *
54507 AGGGCCTGAACCTCGTACAAATTCACCGCCGCCGCCATCACCATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* * *
54553 TCATCCTCACCAACGAAGAGTTTGAATTTTAGGACT-TTGCCTAAAGACGAGCCTACTCCACCGT
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGA-TGTTGCCTAAAGGCGAGCCTACTCCGCCGT
*
54617 CAGGGCCTGACCCTGGTACAAATTCACCGCCGCCACCAT
65 CAGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCAT
54656 TTCGTCTTCA
Statistics
Matches: 834, Mismatches: 45, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
111 833 1.00
112 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (111 bp):
TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
Found at i:55750 original size:12 final size:13
Alignment explanation
Indices: 55701--55750 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
55691 AATAATTTTA
*
55701 ATTTTTTAA-ATT
1 ATTTTATAATATT
55713 ATTTTATAATATT
1 ATTTTATAATATT
55726 ATATATTGATAATATT
1 AT-T-TT-ATAATATT
55742 ATTTT-TAAT
1 ATTTTATAAT
55751 TAATATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 12 0.36
13 5 0.15
14 3 0.09
15 3 0.09
16 10 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
ATTTTATAATATT
Found at i:57744 original size:16 final size:16
Alignment explanation
Indices: 57723--57783 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
57713 ATATTTATAT
57723 TATATTTAAAAAATTA
1 TATATTTAAAAAATTA
*
57739 TATATTTATATAAATTAAAA
1 TATATTTA-AAAAATT---A
* *
57759 TTATTTTTAAATAATTA
1 -TATATTTAAAAAATTA
57776 TATATTTA
1 TATATTTA
57784 TGTAACTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
16 15 0.43
17 7 0.20
20 6 0.17
21 7 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATTTAAAAAATTA
Found at i:57744 original size:21 final size:21
Alignment explanation
Indices: 57718--57781 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
57708 TTAATATATT
57718 TATATTATATTTAAAAAATTA
1 TATATTATATTTAAAAAATTA
*
57739 TATATT-TA--T-ATAAATTA
1 TATATTATATTTAAAAAATTA
* * *
57756 -AAATTATTTTTAAATAATTA
1 TATATTATATTTAAAAAATTA
57776 TATATT
1 TATATT
57782 TATGTAACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 4 0.12
17 8 0.25
18 1 0.03
19 1 0.03
20 8 0.25
21 10 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATTATATTTAAAAAATTA
Found at i:57756 original size:25 final size:28
Alignment explanation
Indices: 57706--57758 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
57696 TTTATGTTAT
*
57706 AATTAATATATTTATATTATATTTAAAA
1 AATTAATATATTTATATTATAATTAAAA
57734 AATT-ATATATTTATA-TA-AATTAAAA
1 AATTAATATATTTATATTATAATTAAAA
57759 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 2 0.08
27 11 0.46
28 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTAATATATTTATATTATAATTAAAA
Found at i:57762 original size:37 final size:38
Alignment explanation
Indices: 57719--57803 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 38
57709 TAATATATTT
57719 ATATTATATTTAAAAAATTATATATTTATATAAATTAA
1 ATATTATATTTAAAAAATTATATATTTATATAAATTAA
* * * *
57757 A-ATTATTTTTAAATAATTATATATTTATGTAACTTAA
1 ATATTATATTTAAAAAATTATATATTTATATAAATTAA
*
57794 ATTTTATATT
1 ATATTATATT
57804 AATATTATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
37 33 0.82
38 7 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (38 bp):
ATATTATATTTAAAAAATTATATATTTATATAAATTAA
Found at i:57839 original size:28 final size:28
Alignment explanation
Indices: 57772--57863 Score: 86
Period size: 27 Copynumber: 3.4 Consensus size: 28
57762 TTTTTAAATA
*
57772 ATTATATATTTATGTAACTTAA-ATTTTAT
1 ATTATAT-TTTAT-TAAATTAATATTTTAT
* *
57801 ATTA-ATATTATTAAATTAATAATTTAT
1 ATTATATTTTATTAAATTAATATTTTAT
*
57828 ATTATATTTTA-TATAATAAATATTTTA-
1 ATTATATTTTATTA-AATTAATATTTTAT
57855 ATTAT-TTTT
1 ATTATATTTT
57864 GTAATATATT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
26 11 0.20
27 21 0.39
28 18 0.33
29 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTATATTTTATTAAATTAATATTTTAT
Found at i:57913 original size:27 final size:27
Alignment explanation
Indices: 57815--57913 Score: 92
Period size: 27 Copynumber: 3.6 Consensus size: 27
57805 ATATTATTAA
*
57815 ATTA-ATAATTTATATTATATTTTATAT
1 ATTATATAATTTA-ATTATATTTTAAAT
* * * *
57842 AATAAATATTTTAATTATTTTTGTAATAT
1 ATTATATAATTTAATTATATTT-TAA-AT
**
57871 ATTATATAATCAAATTATATTTTAAAT
1 ATTATATAATTTAATTATATTTTAAAT
*
57898 ATTATTTAATTTAATT
1 ATTATATAATTTAATT
57914 TTTAAGCTAT
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
27 26 0.46
28 12 0.21
29 18 0.32
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (27 bp):
ATTATATAATTTAATTATATTTTAAAT
Found at i:58364 original size:33 final size:34
Alignment explanation
Indices: 58322--58390 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
58312 TTTCGGTGTG
58322 TAAGTTTATTTTTAA-TAAGTAATGAATGAAATT
1 TAAGTTTATTTTTAAGTAAGTAATGAATGAAATT
*
58355 TAAGTTTATTTTTAAGTAAGTATTGAATGAAATT
1 TAAGTTTATTTTTAAGTAAGTAATGAATGAAATT
58389 TA
1 TA
58391 TTTATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 15 0.44
34 19 0.56
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (34 bp):
TAAGTTTATTTTTAAGTAAGTAATGAATGAAATT
Found at i:59622 original size:11 final size:11
Alignment explanation
Indices: 59606--59701 Score: 51
Period size: 10 Copynumber: 9.1 Consensus size: 11
59596 AATGAAATGG
59606 ATATAAATATA
1 ATATAAATATA
*
59617 ATATAAAAATA
1 ATATAAATATA
*
59628 ATAAAAATA-A
1 ATATAAATATA
* *
59638 AAATAAATTTA
1 ATATAAATATA
* * *
59649 TTA-AAATTTT
1 ATATAAATATA
59659 ATAT-AATATA
1 ATATAAATATA
*
59669 A-AT-TAT-TA
1 ATATAAATATA
*
59677 ATATAAATTTA
1 ATATAAATATA
59688 ATTATAACATATA
1 A-TATAA-ATATA
59701 A
1 A
59702 AATGTAAAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
8 3 0.05
9 6 0.10
10 22 0.35
11 22 0.35
12 5 0.08
13 5 0.08
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAAATATA
Found at i:59680 original size:13 final size:14
Alignment explanation
Indices: 59657--59685 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
59647 TATTAAAATT
59657 TTATATAATATAAA
1 TTATATAATATAAA
59671 TTAT-TAATATAAA
1 TTATATAATATAAA
59684 TT
1 TT
59686 TAATTATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:61060 original size:15 final size:15
Alignment explanation
Indices: 61015--61060 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
61005 TTTAAATATA
61015 AAAAAATAATA--AT
1 AAAAAATAATATGAT
* *
61028 AAAATATAATTTGAT
1 AAAAAATAATATGAT
*
61043 AAAAAATAATATGCT
1 AAAAAATAATATGAT
61058 AAA
1 AAA
61061 TCTAAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 9 0.35
15 17 0.65
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (15 bp):
AAAAAATAATATGAT
Found at i:61380 original size:27 final size:28
Alignment explanation
Indices: 61348--61417 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
61338 AACTATAACT
* *
61348 AATAAAAATAATAAA-CATATAAAATTA
1 AATAAAAATAATAAATAATAAAAAATTA
* *
61375 CATAAATAT-ATAAATAATAAAAAATTA
1 AATAAAAATAATAAATAATAAAAAATTA
*
61402 AATAAAATAAAATAAA
1 AATAAAA-ATAATAAA
61418 ATTATTTTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
26 5 0.15
27 22 0.67
28 1 0.03
29 5 0.15
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (28 bp):
AATAAAAATAATAAATAATAAAAAATTA
Found at i:61385 original size:18 final size:17
Alignment explanation
Indices: 61349--61394 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
61339 ACTATAACTA
61349 ATAAAAATAATAAACAT
1 ATAAAAATAATAAACAT
* *
61366 ATAAAATTACATAAATAT
1 ATAAAAATA-ATAAACAT
61384 ATAAATAATAA
1 ATAAA-AATAA
61395 AAAATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.33
18 13 0.54
19 3 0.12
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAATAATAAACAT
Found at i:61819 original size:17 final size:19
Alignment explanation
Indices: 61791--61843 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 19
61781 TATAAATGTG
*
61791 AAATAAATTAAATATAA-A
1 AAATATATTAAATATAATA
*
61809 AAA-ATATTAAAAATAATA
1 AAATATATTAAATATAATA
61827 AAATATATTAAAATATA
1 AAATATATT-AAATATA
61844 TTATATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 11 0.38
18 7 0.24
19 5 0.17
20 6 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATATATTAAATATAATA
Found at i:61822 original size:19 final size:19
Alignment explanation
Indices: 61800--61844 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
61790 GAAATAAATT
61800 AAATATA-AAAAAATATTA
1 AAATATATAAAAAATATTA
*
61818 AAA-ATAATAAAATATATTA
1 AAATAT-ATAAAAAATATTA
61837 AAATATAT
1 AAATATAT
61845 TATATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 4 0.17
19 15 0.65
20 2 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATATATAAAAAATATTA
Found at i:61838 original size:10 final size:10
Alignment explanation
Indices: 61791--61846 Score: 57
Period size: 10 Copynumber: 6.0 Consensus size: 10
61781 TATAAATGTG
*
61791 AAATAAATT-
1 AAATATATTA
61800 AAATATA--A
1 AAATATATTA
*
61808 AAAAATATTA
1 AAATATATTA
*
61818 AAA-ATAATA
1 AAATATATTA
61827 AAATATATTA
1 AAATATATTA
61837 AAATATATTA
1 AAATATATTA
61847 TATTTATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 6 0.15
9 14 0.36
10 19 0.49
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATATATTA
Found at i:62156 original size:22 final size:20
Alignment explanation
Indices: 62131--62184 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
62121 ATTTTTACTC
62131 ATTAAAATATAAAATTAAATAA
1 ATTAAAATATAAAATT-AAT-A
*
62153 ATTAAAATAATCAAATTAATA
1 ATTAAAAT-ATAAAATTAATA
*
62174 TTTAAAATATA
1 ATTAAAATATA
62185 TTTAATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.07
21 8 0.29
22 11 0.39
23 7 0.25
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTAAAATATAAAATTAATA
Found at i:62202 original size:19 final size:20
Alignment explanation
Indices: 62178--62217 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
62168 TTAATATTTA
62178 AAATATATTTAAT-AAATAT
1 AAATATATTTAATAAAATAT
62197 AAATATATTTAATAAAATAT
1 AAATATATTTAATAAAATAT
62217 A
1 A
62218 TTTAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATATATTTAATAAAATAT
Found at i:62216 original size:14 final size:15
Alignment explanation
Indices: 62192--62228 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
62182 ATATTTAATA
62192 AATATAAATATATTT
1 AATATAAATATATTT
62207 AATA-AAATATATTT
1 AATATAAATATATTT
*
62221 AAAATAAA
1 AATATAAA
62229 AAAATAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAAATATATTT
Found at i:62337 original size:27 final size:26
Alignment explanation
Indices: 62302--62361 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
62292 AATATCAATC
* *
62302 AATTCAATTAA-TTTTAATATTAAATTT
1 AATTAAATTAATTTTTAAT-TTAAA-TA
62329 AATTAAATTAATTTTTAATTTAAATA
1 AATTAAATTAATTTTTAATTTAAATA
62355 AATTAAA
1 AATTAAA
62362 CTCTCATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 8 0.27
27 15 0.50
28 7 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATTAAATTAATTTTTAATTTAAATA
Found at i:62345 original size:16 final size:17
Alignment explanation
Indices: 62326--62358 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62316 TAATATTAAA
*
62326 TTTAA-TTAAATTAATT
1 TTTAATTTAAATAAATT
62342 TTTAATTTAAATAAATT
1 TTTAATTTAAATAAATT
62359 AAACTCTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTTAAATAAATT
Found at i:62348 original size:21 final size:21
Alignment explanation
Indices: 62315--62360 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
62305 TCAATTAATT
*
62315 TTAATATTAAATTTAATTAAA
1 TTAATATTAAATTTAAATAAA
* *
62336 TTAATTTTTAATTTAAATAAA
1 TTAATATTAAATTTAAATAAA
62357 TTAA
1 TTAA
62361 ACTCTCATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATATTAAATTTAAATAAA
Found at i:70742 original size:24 final size:24
Alignment explanation
Indices: 70706--70751 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
70696 TTAAGAAAAC
*
70706 TAATTTAAATAAATATTTAAATTA
1 TAATTTAAATAAATATATAAATTA
* *
70730 TAATTTTATTAAATATATAAAT
1 TAATTTAAATAAATATATAAAT
70752 ATTTATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTTAAATAAATATATAAATTA
Found at i:70854 original size:17 final size:16
Alignment explanation
Indices: 70823--70867 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
70813 TTATATTATT
70823 AAAT-TTTAAAATTTA
1 AAATATTTAAAATTTA
70838 AAATATTTAAAAGTTTA
1 AAATATTTAAAA-TTTA
*
70855 AATAAATTTAAAA
1 AA-ATATTTAAAA
70868 ATATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 7 0.27
17 6 0.23
18 9 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATATTTAAAATTTA
Found at i:70869 original size:8 final size:8
Alignment explanation
Indices: 70823--70883 Score: 50
Period size: 8 Copynumber: 6.9 Consensus size: 8
70813 TTATATTATT
*
70823 AAATTTTA
1 AAATTTAA
70831 AAATTTAA
1 AAATTTAA
70839 AATATTTAA
1 AA-ATTTAA
*
70848 AAGTTTAAA
1 AAATTT-AA
70857 TAAATTTAA
1 -AAATTTAA
70866 AAATATATAAA
1 AAAT-T-T-AA
70877 AAATTTA
1 AAATTTA
70884 TTAAAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
8 17 0.39
9 14 0.32
10 7 0.16
11 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
AAATTTAA
Found at i:70888 original size:28 final size:26
Alignment explanation
Indices: 70823--70888 Score: 62
Period size: 28 Copynumber: 2.5 Consensus size: 26
70813 TTATATTATT
* *
70823 AAATTT-TAAAATTTAAAATATTTAA
1 AAATTTATTAAATTTAAAATATTAAA
* *
70848 AAGTTTAAATAAATTTAAAAATATATAAA
1 AAATTT-ATTAAATTT-AAAATAT-TAAA
70877 AAATTTATTAAA
1 AAATTTATTAAA
70889 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
25 5 0.16
27 6 0.19
28 12 0.39
29 8 0.26
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AAATTTATTAAATTTAAAATATTAAA
Found at i:70890 original size:22 final size:22
Alignment explanation
Indices: 70862--70921 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
70852 TTAAATAAAT
70862 TTAAAAATATATAAAAAATT-TA
1 TTAAAAA-ATATAAAAAATTATA
70884 TTAAAAAA-ATAAAAAATTATA
1 TTAAAAAATATAAAAAATTATA
*
70905 TATAAAAAATTTAAAAA
1 T-TAAAAAATATAAAAA
70922 TAAAATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.29
21 4 0.12
22 14 0.41
23 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TTAAAAAATATAAAAAATTATA
Found at i:70921 original size:9 final size:9
Alignment explanation
Indices: 70830--70883 Score: 56
Period size: 10 Copynumber: 5.9 Consensus size: 9
70820 ATTAAATTTT
70830 AAAATTTAA
1 AAAATTTAA
*
70839 AATATTT-A
1 AAAATTTAA
*
70847 AAAGTTTAA
1 AAAATTTAA
70856 ATAAATTTAA
1 A-AAATTTAA
*
70866 AAATATATAA
1 AAA-ATTTAA
70876 AAAATTTA
1 AAAATTTA
70884 TTAAAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 6 0.17
9 14 0.39
10 16 0.44
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAATTTAA
Found at i:70929 original size:20 final size:19
Alignment explanation
Indices: 70853--70939 Score: 62
Period size: 19 Copynumber: 4.8 Consensus size: 19
70843 TTTAAAAGTT
*
70853 TAAATAAATTTAAAAATATA
1 TAAA-AAATTTAAAAATAAA
70873 TAAAAAATTTATTAAAA-AAA
1 TAAAAAATTTA--AAAATAAA
*
70893 TAAAAAA-TT----ATATA
1 TAAAAAATTTAAAAATAAA
70907 TAAAAAATTTAAAAATAAA
1 TAAAAAATTTAAAAATAAA
* *
70926 -ATAAATTTTAAAAA
1 TAAAAAATTTAAAAA
70940 ACCTTAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
13 1 0.02
14 9 0.17
15 2 0.04
18 12 0.22
19 13 0.24
20 13 0.24
21 4 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAAATTTAAAAATAAA
Found at i:71340 original size:28 final size:31
Alignment explanation
Indices: 71282--71342 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 31
71272 TGATATATAT
71282 TTTATGAGTATTTAAATTATATATGTAATTA
1 TTTATGAGTATTTAAATTATATATGTAATTA
* *
71313 TTTATGA-TA-TTATATTAT-TATGTCATTA
1 TTTATGAGTATTTAAATTATATATGTAATTA
71341 TT
1 TT
71343 AAAAATCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 11 0.39
29 8 0.29
30 2 0.07
31 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (31 bp):
TTTATGAGTATTTAAATTATATATGTAATTA
Found at i:75869 original size:19 final size:19
Alignment explanation
Indices: 75833--75869 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
75823 TATAAATCTC
*
75833 TAGTCTAATTTATATAAAT
1 TAGTCTAATCTATATAAAT
*
75852 TAGTCTAATCTATTTAAA
1 TAGTCTAATCTATATAAA
75870 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (19 bp):
TAGTCTAATCTATATAAAT
Done.