Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold889
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: 68758
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1099 original size:51 final size:51
Alignment explanation
Indices: 1039--1205 Score: 145
Period size: 51 Copynumber: 3.3 Consensus size: 51
1029 AAATAACGAG
* ** *
1039 GTTGGAGTATCCTCAATTGTGAAAAATTGGTGTTTTGAAAATAAAATCAGA
1 GTTGGAGTATCCCCAATTAAGAAAAATTGGTGTTTTAAAAATAAAATCAGA
* * * * *
1090 GTTGGAGTATCCCCGATTAAGGAAAATTGGTGTTTTAAAAATAAAAACGGG
1 GTTGGAGTATCCCCAATTAAGAAAAATTGGTGTTTTAAAAATAAAATCAGA
* * * * *** * * * * *
1141 GTTAGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGTAAGG
1 GTTGGAGTATCCCCAATTAAGAAAAATTGGTGTTTTAAAAATAAAATCAGA
1192 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1206 TCGGAAATAA
Statistics
Matches: 93, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 93 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCAATTAAGAAAAATTGGTGTTTTAAAAATAAAATCAGA
Found at i:1251 original size:27 final size:28
Alignment explanation
Indices: 1189--1260 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
1179 GAATAAAGTA
**
1189 AGGGTTGGAGTATCCCCTCGGAAATAAC
1 AGGGTTGGAGTATCCCCAAGGAAATAAC
* *
1217 AGGGTTGGAGTATCCCCAATG-ATTAAC
1 AGGGTTGGAGTATCCCCAAGGAAATAAC
*
1244 GGGGTTGGAGTATCCCC
1 AGGGTTGGAGTATCCCC
1261 GATTGTGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.24
Consensus pattern (28 bp):
AGGGTTGGAGTATCCCCAAGGAAATAAC
Found at i:1327 original size:53 final size:51
Alignment explanation
Indices: 1247--1368 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 51
1237 GATTAACGGG
* * * *
1247 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAG--TGTTTTGAAAATAAAATCGGA
1300 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGAAAATAAAATCGGA
* *
1351 GATGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
1369 GCGGAGAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
51 35 0.56
52 1 0.02
53 26 0.42
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:1327 original size:210 final size:210
Alignment explanation
Indices: 925--1368 Score: 590
Period size: 210 Copynumber: 2.1 Consensus size: 210
915 CCTCGGAAAT
* * * ** **
925 AACGAGGTTGGAGTAT-CCCAATTATTAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAAGGGTTGGAGT
** * * *
989 ATCCCCTCGGAGGGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCA
66 ATCCCCTCGGA-GAATAACAGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTATCCCCA
*
1054 ATTGTGAAAAATTGGTGTTTTGAAAATAAAATCAGAGTTGGAGTATCCCCGATTAAGGAAAATTG
130 ATTGTGAAAAATTGGTGTTTTGAAAATAAAATCAGAGTTGGAGTATCCCCGATTAAGGAAAATTA
1119 GTGTTTTAAAAATAAA
195 GTGTTTTAAAAATAAA
* *
1135 AACGGGGTTAGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGTAAGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAAGGGTTGGAGT
* * *
1200 ATCCCCTCGGA-AATAACAGGGTTGGAGTATCCCCAATG-ATTAACGGGGTTGGAGTATCCCCGA
66 ATCCCCTCGGAGAATAACAGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTATCCCCAA
* * *
1263 TTGTGAAAAATTGGTATTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA-GAAAAT
131 TTGTGAAAAATTGG--TGTTTTGAAAATAAAATCAGAGTTGGAGTATCCCCGATTA-AGGAAAAT
*
1327 TAGTGTTTTGAAAATAAA
193 TAGTGTTTTAAAAATAAA
* * * *
1345 ATCGGAGATGGAATATCCCCGATT
1 AACGGGGTTGGAGTATCCCCGATT
1369 GCGGAGAATT
Statistics
Matches: 203, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
208 35 0.17
209 23 0.11
210 92 0.45
211 53 0.26
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (210 bp):
AACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAAGGGTTGGAGT
ATCCCCTCGGAGAATAACAGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTATCCCCAA
TTGTGAAAAATTGGTGTTTTGAAAATAAAATCAGAGTTGGAGTATCCCCGATTAAGGAAAATTAG
TGTTTTAAAAATAAA
Found at i:2946 original size:49 final size:49
Alignment explanation
Indices: 2874--2975 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
2864 TGAGCATAGA
2874 AAGGGACTTCTAAAATGTTAGAAATGTCCAAAACAGAAACCAAAAGATC
1 AAGGGACTTCTAAAATGTTAGAAATGTCCAAAACAGAAACCAAAAGATC
2923 AAGGGACTTCTAAAATGTTAGAAATGTCCAAAACAGAAACCAAAAGATC
1 AAGGGACTTCTAAAATGTTAGAAATGTCCAAAACAGAAACCAAAAGATC
2972 AAGG
1 AAGG
2976 TAGAGAGAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (49 bp):
AAGGGACTTCTAAAATGTTAGAAATGTCCAAAACAGAAACCAAAAGATC
Found at i:4724 original size:53 final size:50
Alignment explanation
Indices: 4625--4725 Score: 166
Period size: 53 Copynumber: 2.0 Consensus size: 50
4615 CCATAGTTGT
*
4625 CTAGAGAATTGATTACCTTGGATAGTGATATAATCACCCTTTATATGGAA
1 CTAGAGAATTGATTACCTTGGATAGTGATATAATCACCCTTCATATGGAA
4675 CTAGAGAATTGATTACCTTGGAAGATAGTGATATAATCACCCTTCATATGG
1 CTAGAGAATTGATTACCTT-G--GATAGTGATATAATCACCCTTCATATGG
4726 TGTAAAGGTG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
50 19 0.40
51 1 0.02
53 27 0.57
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (50 bp):
CTAGAGAATTGATTACCTTGGATAGTGATATAATCACCCTTCATATGGAA
Found at i:6066 original size:16 final size:16
Alignment explanation
Indices: 5978--6120 Score: 90
Period size: 16 Copynumber: 8.8 Consensus size: 16
5968 TTAAACTTGT
* *
5978 ATAAATTAAACTTGAAA
1 ATAATTTAAAATT-AAA
*
5995 ATAATTTAAATTTAAA
1 ATAATTTAAAATTAAA
* * *
6011 ATTATTCGAAACTTAAA
1 ATAATT-TAAAATTAAA
* *
6028 AAAATTTAAACTTAAA
1 ATAATTTAAAATTAAA
*
6044 ATAATTTAAATTTAAA
1 ATAATTTAAAATTAAA
* *
6060 TTGATTTAAAATTAAA
1 ATAATTTAAAATTAAA
** *
6076 ACGA-TTCAAATATAAA
1 ATAATTTAAAAT-TAAA
* ** *
6092 ACAAAATAAATTTAAA
1 ATAATTTAAAATTAAA
6108 ATAATTTAAAATT
1 ATAATTTAAAATT
6121 TTAATATAAA
Statistics
Matches: 99, Mismatches: 24, Indels: 7
0.76 0.18 0.05
Matches are distributed among these distances:
15 6 0.06
16 66 0.67
17 27 0.27
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.36
Consensus pattern (16 bp):
ATAATTTAAAATTAAA
Found at i:6092 original size:48 final size:47
Alignment explanation
Indices: 5980--6120 Score: 133
Period size: 48 Copynumber: 2.9 Consensus size: 47
5970 AAACTTGTAT
* *
5980 AAATT-AAACTTGAAAATAATTTAAATTTAAAATTATTCGAAACTTAAAA
1 AAATTCAAACTT-AAAATAATTTAAATTT-AAATTATT-TAAAATTAAAA
*
6029 AAATTTAAACTTAAAATAATTTAAATTTAAATTGATTTAAAATTAAAA
1 AAATTCAAACTTAAAATAATTTAAATTTAAATT-ATTTAAAATTAAAA
** * ** *
6077 CGATTCAAA-TATAAAACAAAATAAATTTAAAATAATTTAAAATT
1 AAATTCAAACT-TAAAATAATTTAAATTT-AAATTATTTAAAATT
6121 TTAATATAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
47 1 0.01
48 44 0.56
49 28 0.35
50 6 0.08
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (47 bp):
AAATTCAAACTTAAAATAATTTAAATTTAAATTATTTAAAATTAAAA
Found at i:10865 original size:16 final size:16
Alignment explanation
Indices: 10837--10883 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
10827 AACCTAATTG
*
10837 ACCCGAACTCAAAATA
1 ACCCGAACCCAAAATA
* *
10853 ACCTGAACCCAAAACA
1 ACCCGAACCCAAAATA
*
10869 ACCCCAACCCAAAAT
1 ACCCGAACCCAAAAT
10884 GATCTGAACT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.38, G:0.04, T:0.09
Consensus pattern (16 bp):
ACCCGAACCCAAAATA
Found at i:10945 original size:32 final size:32
Alignment explanation
Indices: 10874--10946 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
10864 AAACAACCCC
* * *
10874 AACCCAAAATGATCTGAACTCGAAATGACCCG
1 AACCCAAAATGATCTGAACACGAAATGACACA
* *
10906 AATCCAAAGTGA-CTCGAACACGAAATGACACA
1 AACCCAAAATGATCT-GAACACGAAATGACACA
10938 AACCCAAAA
1 AACCCAAAA
10947 ATAACCCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
31 2 0.06
32 31 0.94
ACGTcount: A:0.47, C:0.27, G:0.14, T:0.12
Consensus pattern (32 bp):
AACCCAAAATGATCTGAACACGAAATGACACA
Found at i:10989 original size:15 final size:16
Alignment explanation
Indices: 10971--11008 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
10961 TTATAACCCG
10971 AAATAACT-CAATCCA
1 AAATAACTCCAATCCA
10986 AAATAA-TCCAATCCA
1 AAATAACTCCAATCCA
11001 AAACTAAC
1 AAA-TAAC
11009 CCGACCCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 16 0.80
16 3 0.15
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAACTCCAATCCA
Found at i:15259 original size:29 final size:27
Alignment explanation
Indices: 15223--15294 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 27
15213 TTGATTTATT
15223 ATTTAATTAATAAAAAATATTTTATTTAA
1 ATTTAATTAATAAAAAATA-TTT-TTTAA
*
15252 ATTTAATT-AT-AAATATATTTTTTAA
1 ATTTAATTAATAAAAAATATTTTTTAA
* *
15277 ATATATTTTAATAAAAAA
1 ATTTA-ATTAATAAAAAA
15295 ATAAATTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
25 9 0.25
26 5 0.14
27 8 0.22
28 6 0.17
29 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTAATTAATAAAAAATATTTTTTAA
Found at i:15279 original size:13 final size:13
Alignment explanation
Indices: 15261--15285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15251 AATTTAATTA
15261 TAAATATATTTTT
1 TAAATATATTTTT
15274 TAAATATATTTT
1 TAAATATATTTT
15286 AATAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATATTTTT
Found at i:15420 original size:11 final size:11
Alignment explanation
Indices: 15406--15442 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
15396 TTTAATTTAA
15406 ATATAATGAT-T
1 ATATAAT-ATAT
15417 ATATAATATAT
1 ATATAATATAT
15428 ATAT-ATATAT
1 ATATAATATAT
15438 ATATA
1 ATATA
15443 TTCCTTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 12 0.50
11 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
ATATAATATAT
Found at i:17242 original size:13 final size:13
Alignment explanation
Indices: 17220--17254 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
17210 GATTAAAATA
17220 TTAAAGATTTTTAT
1 TTAAA-ATTTTTAT
*
17234 TTTAAATTTTTAT
1 TTAAAATTTTTAT
17247 TTAAAATT
1 TTAAAATT
17255 AAATAAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (13 bp):
TTAAAATTTTTAT
Found at i:17979 original size:30 final size:30
Alignment explanation
Indices: 17943--18020 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
17933 CATCCTAAAG
*
17943 GGATTAAATTTATATTTTGTATAATTATGC
1 GGATTAAATTAATATTTTGTATAATTATGC
*
17973 GGATTAAATTAATATTTTGTATAATTATGG
1 GGATTAAATTAATATTTTGTATAATTATGC
*
18003 GGATTAAATTCATATTTT
1 GGATTAAATTAATATTTT
18021 AATATAAGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.49
Consensus pattern (30 bp):
GGATTAAATTAATATTTTGTATAATTATGC
Found at i:20834 original size:18 final size:16
Alignment explanation
Indices: 20811--20849 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
20801 TGTATGTTTT
20811 TGTATGTGTCTGCATGTG
1 TGTATGTGTCTG--TGTG
*
20829 TGTATGTGTTTGTGTG
1 TGTATGTGTCTGTGTG
20845 TGTAT
1 TGTAT
20850 ATATAATAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.10, C:0.05, G:0.33, T:0.51
Consensus pattern (16 bp):
TGTATGTGTCTGTGTG
Found at i:24599 original size:26 final size:26
Alignment explanation
Indices: 24552--24602 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
24542 TAATATTTAT
*
24552 ATATTTTTATAATTAAATTAAAAATA
1 ATATTTTTATAAATAAATTAAAAATA
*
24578 ATATTTTTATTAAATGAA-TAAAAAT
1 ATATTTTTA-TAAATAAATTAAAAAT
24603 TTAGATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
ATATTTTTATAAATAAATTAAAAATA
Found at i:24972 original size:24 final size:24
Alignment explanation
Indices: 24921--25008 Score: 72
Period size: 24 Copynumber: 3.6 Consensus size: 24
24911 AATCTTCATT
* **
24921 TTATATATATATAT-ATATATTATT
1 TTATATATTTATATCATAT-TTAAA
24945 TTATATATTTATATCATATTTAAA
1 TTATATATTTATATCATATTTAAA
* * *
24969 TTATTTTTTTATATTCATATTT-AC
1 TTATATATTTATA-TCATATTTAAA
24993 TATATTATATTTATAT
1 T-TA-TATATTTATAT
25009 AAATTTTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
24 29 0.56
25 15 0.29
26 8 0.15
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATATATTTATATCATATTTAAA
Found at i:24998 original size:25 final size:26
Alignment explanation
Indices: 24948--25008 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
24938 TATTATTTTA
24948 TATATTTATA-TCATATTTAAATTAT
1 TATATTTATATTCATATTTAAATTAT
* *
24973 T-TTTTTATATTCATATTT-ACTATAT
1 TATATTTATATTCATATTTAAAT-TAT
24998 TATATTTATAT
1 TATATTTATAT
25009 AAATTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 9 0.30
25 13 0.43
26 8 0.27
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (26 bp):
TATATTTATATTCATATTTAAATTAT
Found at i:25299 original size:23 final size:21
Alignment explanation
Indices: 25273--25326 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 21
25263 ATTTGTTTAC
25273 TTATGTTGTTTTTATCTTATTTT
1 TTATGTTGTTTTTA--TTATTTT
*
25296 TTATTTTATGTTTTTATTATTTT
1 TTA-TGT-TGTTTTTATTATTTT
25319 TTCATGTT
1 TT-ATGTT
25327 ATATTCATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
22 1 0.04
23 14 0.54
24 3 0.12
25 8 0.31
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74
Consensus pattern (21 bp):
TTATGTTGTTTTTATTATTTT
Found at i:25328 original size:24 final size:24
Alignment explanation
Indices: 25279--25328 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 24
25269 TTACTTATGT
*
25279 TGTTTTTATCTTATTTTTTATTTTA
1 TGTTTTTA-CTTATTTTTTATGTTA
25304 TGTTTTTA-TTATTTTTTCATGTTA
1 TGTTTTTACTTATTTTTT-ATGTTA
25328 T
1 T
25329 ATTCATCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 6 0.26
25 8 0.35
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.74
Consensus pattern (24 bp):
TGTTTTTACTTATTTTTTATGTTA
Found at i:25543 original size:117 final size:116
Alignment explanation
Indices: 25338--25557 Score: 287
Period size: 117 Copynumber: 1.9 Consensus size: 116
25328 TATTCATCTT
* * *
25338 GTTTAATTATGTCATTTTTGAAATTACCAAAATCCAATTATACTATTTAAATAACTCTCAATTTT
1 GTTTAATCATGTCATGTTTAAAATTACCAAAATCCAATTATACTATTTAAATAACTCTCAATTTT
* *
25403 ATATTTCATATCATCGTGCTAGTGTTATTTTACTTTTTCATTATTTATATC
66 ATATTTCATATCATCATACTAGTGTTATTTTACTTTTTCATTATTTATATC
* * ** *
25454 GTTTAATCATGTTATGTTTAAAATTATCAAAATTTAATTGATACTATTTAAATAACTTTCAATTT
1 GTTTAATCATGTCATGTTTAAAATTACCAAAATCCAATT-ATACTATTTAAATAACTCTCAATTT
* * * * * *
25519 TATGTTTCATGTTATCATATTAGTGTTGTTTTATTTTTT
65 TATATTTCATATCATCATACTAGTGTTATTTTACTTTTT
25558 TATATCATAT
Statistics
Matches: 87, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
116 32 0.37
117 55 0.63
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.51
Consensus pattern (116 bp):
GTTTAATCATGTCATGTTTAAAATTACCAAAATCCAATTATACTATTTAAATAACTCTCAATTTT
ATATTTCATATCATCATACTAGTGTTATTTTACTTTTTCATTATTTATATC
Found at i:25957 original size:44 final size:44
Alignment explanation
Indices: 25909--26023 Score: 124
Period size: 47 Copynumber: 2.5 Consensus size: 44
25899 TTGGGGGTAG
25909 TTTTGTAATTAAAATCAAATTGAGATAATATCAAATG-TGGGCAA
1 TTTTGTAA-TAAAATCAAATTGAGATAATATCAAATGATGGGCAA
* * * *
25953 TTTTGTAATAAAATCTACATTGAAGGATAATGTTAATTGATGGGCAA
1 TTTTGTAATAAAATC-AAATTG-A-GATAATATCAAATGATGGGCAA
* *
26000 TTTGGTAATAAAACCCAAATTGAG
1 TTTTGTAATAAAA-TCAAATTGAG
26024 GCTGAAAGGA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
43 7 0.12
44 13 0.22
45 2 0.03
46 12 0.20
47 24 0.41
48 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (44 bp):
TTTTGTAATAAAATCAAATTGAGATAATATCAAATGATGGGCAA
Found at i:26578 original size:19 final size:19
Alignment explanation
Indices: 26536--26578 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
26526 CATGGTATTG
26536 ATAAATTATTGATAAAAAT
1 ATAAATTATTGATAAAAAT
* *
26555 TTAAA-TATTGAATAATAAT
1 ATAAATTATTG-ATAAAAAT
26574 ATAAA
1 ATAAA
26579 ATGAATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
ATAAATTATTGATAAAAAT
Found at i:26983 original size:21 final size:21
Alignment explanation
Indices: 26934--26986 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
26924 ATATAATCTA
26934 AATAAA-TTAATTTTTTATAT
1 AATAAATTTAATTTTTTATAT
*
26954 --T-TATCTTAATTTTTTATAT
1 AATAAAT-TTAATTTTTTATAT
26973 AATAAATTTAATTT
1 AATAAATTTAATTT
26987 ATATATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
17 1 0.04
18 1 0.04
19 14 0.54
21 8 0.31
22 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
AATAAATTTAATTTTTTATAT
Found at i:27004 original size:11 final size:11
Alignment explanation
Indices: 26988--27034 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
26978 ATTTAATTTA
*
26988 TATATTTATGT
1 TATATTTATAT
26999 TATATTTATAT
1 TATATTTATAT
27010 TAT-TTTATATT
1 TATATTTATA-T
*
27021 TATAATT-TAT
1 TATATTTATAT
27031 TATA
1 TATA
27035 AAAGTTATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 11 0.34
11 19 0.59
12 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:27017 original size:16 final size:17
Alignment explanation
Indices: 26988--27030 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
26978 ATTTAATTTA
26988 TATATTTATGTTATATT
1 TATATTTATGTTATATT
*
27005 TATA-TTATTTTATATT
1 TATATTTATGTTATATT
27021 TATAATTTAT
1 TAT-ATTTAT
27031 TATAAAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 14 0.61
17 5 0.22
18 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TATATTTATGTTATATT
Found at i:27028 original size:7 final size:6
Alignment explanation
Indices: 26978--27030 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
26968 TATATAATAA
26978 ATTTA- ATTTAT ATATT-T ATGTTAT ATTTAT A-TTAT -TTTAT ATTTAT
1 ATTTAT ATTTAT AT-TTAT AT-TTAT ATTTAT ATTTAT ATTTAT ATTTAT
27024 AATTTAT
1 -ATTTAT
27031 TATAAAAGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
5 13 0.32
6 17 0.41
7 11 0.27
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:27033 original size:16 final size:16
Alignment explanation
Indices: 26983--27034 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
26973 AATAAATTTA
26983 ATTTATATATTTATGTTAT
1 ATTTATA-ATTTA--TTAT
*
27002 ATTTAT-ATTATTTTAT
1 ATTTATAATT-TATTAT
27018 ATTTATAATTTATTAT
1 ATTTATAATTTATTAT
27034 A
1 A
27035 AAAGTTATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 16 0.55
17 6 0.21
18 1 0.03
19 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
ATTTATAATTTATTAT
Found at i:27942 original size:30 final size:29
Alignment explanation
Indices: 27877--27986 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 29
27867 TATCAATTTA
*
27877 TATTCATATTAATTTATATTATGT-ATTGGG
1 TATTCATATTAATTTATATTATGTGA-T-AG
* * *
27907 CATTCACATTAATTTATATTATATGATAAG
1 TATTCATATTAATTTATATTATGTGAT-AG
* *
27937 TATTCATATTAATATATAATT-TGTGATTG
1 TATTCATATTAATTTAT-ATTATGTGATAG
27966 ATATTCATATTAATTTATATT
1 -TATTCATATTAATTTATATT
27987 TAATGGGTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
29 4 0.06
30 58 0.88
31 4 0.06
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (29 bp):
TATTCATATTAATTTATATTATGTGATAG
Found at i:28518 original size:20 final size:20
Alignment explanation
Indices: 28495--28639 Score: 119
Period size: 20 Copynumber: 6.7 Consensus size: 20
28485 AAGTACCCAG
28495 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
28515 ATGTATCGATACATATATAA
1 ATGTATCGATACATTTTTCA
* * *
28535 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
28555 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
28575 ATGTATCAATACATTCTATCTTTTTACCCA
1 ATGTATCGAT--A--C-A--TTTTT---CA
28605 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
28626 ATGTATCGATACAT
1 ATGTATCGATACAT
28640 CTAGTTAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
20 74 0.73
21 2 0.02
22 1 0.01
24 6 0.06
25 1 0.01
26 1 0.01
27 5 0.05
29 1 0.01
30 2 0.02
31 9 0.09
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:39210 original size:8 final size:8
Alignment explanation
Indices: 39195--39249 Score: 67
Period size: 8 Copynumber: 6.9 Consensus size: 8
39185 CGTCTTTCAT
39195 ACAAAAAA
1 ACAAAAAA
*
39203 ATAAAAAA
1 ACAAAAAA
39211 ACAAAAAA
1 ACAAAAAA
*
39219 ACAAAGAA
1 ACAAAAAA
*
39227 A-AAAATA
1 ACAAAAAA
39234 ACAAAAAA
1 ACAAAAAA
39242 ACAGAAAA
1 ACA-AAAA
39250 GGGGTCTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
7 5 0.13
8 30 0.77
9 4 0.10
ACGTcount: A:0.84, C:0.09, G:0.04, T:0.04
Consensus pattern (8 bp):
ACAAAAAA
Found at i:39236 original size:23 final size:24
Alignment explanation
Indices: 39195--39249 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
39185 CGTCTTTCAT
39195 ACAAAAAAATAAAAAAACAAAAAA
1 ACAAAAAAATAAAAAAACAAAAAA
* *
39219 ACAAAGAAA-AAAATAACAAAAAA
1 ACAAAAAAATAAAAAAACAAAAAA
*
39242 ACAGAAAA
1 ACAAAAAA
39250 GGGGTCTAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.84, C:0.09, G:0.04, T:0.04
Consensus pattern (24 bp):
ACAAAAAAATAAAAAAACAAAAAA
Found at i:40504 original size:28 final size:28
Alignment explanation
Indices: 40461--41132 Score: 844
Period size: 28 Copynumber: 23.4 Consensus size: 28
40451 CGTTCATCTC
*
40461 TTCAAAGCCTACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
40489 TTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
40517 TTCAAAGCCCACAAG-CTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTC-AGTGG-CAC-CCT
* *
40547 TTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
40575 TTCAAAGACCACAAGCCAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGG-CAC-CCT
*
40605 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
40633 TTCAAAGACCACAAGCCAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGG-CAC-CCT
*
40663 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
40691 TTCAAAGCCCACAAGTCAGTGACACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
40719 TTCAAAGCCCACAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
40747 TTCAAAGCCCACGAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
40775 TTCAAAGCCAACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
40804 TTCAAAGCCCACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
40832 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
40860 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
40888 TTCAAAGCCCACAAG-CTAGTGGCATCCT
1 TTCAAAGCCCACAAGTC-AGTGGCACCCT
40916 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
40944 TTCAAAACCCACAAGCCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
40972 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
41000 TTCAAAGCCCACAAGCCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
41029 TTCAAAGCTCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
41057 TTCAAAGCCCACACGAGTCAGTGGCAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCT
*
41089 TTCAAAGCCCACACGAGTCAGTGGCAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCT
41121 TTCAAAGCCCAC
1 TTCAAAGCCCAC
41133 TCAAGTCGAT
Statistics
Matches: 564, Mismatches: 64, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
27 2 0.00
28 382 0.68
29 56 0.10
30 75 0.13
31 2 0.00
32 47 0.08
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:42022 original size:20 final size:20
Alignment explanation
Indices: 41999--42052 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
41989 AAGTACCCAG
* * *
41999 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATAA
*
42019 ATGTATCAATACATGTATAA
1 ATGTATCGATACATGTATAA
42039 ATGTATCGATACAT
1 ATGTATCGATACAT
42053 CTAGTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATGTATAA
Found at i:45802 original size:22 final size:22
Alignment explanation
Indices: 45777--45904 Score: 114
Period size: 22 Copynumber: 5.8 Consensus size: 22
45767 ATAAAAGTAA
*
45777 ACATTCTATTATAGTGATATGT
1 ACATACTATTATAGTGATATGT
* *
45799 ACATACGT-TTGTAGTTATATGT
1 ACATAC-TATTATAGTGATATGT
**
45821 ACATACTATTGCAGTGATATGT
1 ACATACTATTATAGTGATATGT
* * * *
45843 ATATACAATTATAGTCATATAT
1 ACATACTATTATAGTGATATGT
* * *
45865 ACATAATGTTATAGTGATGTGT
1 ACATACTATTATAGTGATATGT
* *
45887 ATATATTATTATAGTGAT
1 ACATACTATTATAGTGAT
45905 TCTTTGTGAA
Statistics
Matches: 83, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
21 1 0.01
22 81 0.98
23 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (22 bp):
ACATACTATTATAGTGATATGT
Found at i:46008 original size:20 final size:21
Alignment explanation
Indices: 45983--46053 Score: 83
Period size: 20 Copynumber: 3.4 Consensus size: 21
45973 GCAAAAATGT
45983 GTTGGTTCCCTTTGT-AAAGG
1 GTTGGTTCCCTTTGTGAAAGG
* *
46003 GTTGGTTCTCTTAGTGAAAGG
1 GTTGGTTCCCTTTGTGAAAGG
*
46024 ATTGGTT-CCTTTAGTGAAAAGG
1 GTTGGTTCCCTTT-GTG-AAAGG
46046 GTTGGTTC
1 GTTGGTTC
46054 ATTTATAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 16 0.39
21 14 0.34
22 11 0.27
ACGTcount: A:0.18, C:0.11, G:0.31, T:0.39
Consensus pattern (21 bp):
GTTGGTTCCCTTTGTGAAAGG
Found at i:46028 original size:21 final size:20
Alignment explanation
Indices: 45983--46053 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 20
45973 GCAAAAATGT
*
45983 GTTGGTTCCCTTTGT-AAAGG
1 GTTGGTT-CCTTAGTGAAAGG
46003 GTTGGTTCTCTTAGTGAAAGG
1 GTTGGTTC-CTTAGTGAAAGG
*
46024 ATTGGTTCCTTTAGTGAAAAGG
1 GTTGGTTCC-TTAGTG-AAAGG
46046 GTTGGTTC
1 GTTGGTTC
46054 ATTTATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.02
20 13 0.30
21 18 0.41
22 12 0.27
ACGTcount: A:0.18, C:0.11, G:0.31, T:0.39
Consensus pattern (20 bp):
GTTGGTTCCTTAGTGAAAGG
Found at i:46050 original size:22 final size:21
Alignment explanation
Indices: 45983--46058 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 21
45973 GCAAAAATGT
45983 GTTGGTTCCCTTT-GT-AAAGG
1 GTTGGTT-CCTTTAGTGAAAGG
46003 GTTGGTT-CTCTTAGTGAAAGG
1 GTTGGTTCCT-TTAGTGAAAGG
*
46024 ATTGGTTCCTTTAGTGAAAAGG
1 GTTGGTTCCTTTAGTG-AAAGG
*
46046 GTTGGTTCATTTA
1 GTTGGTTCCTTTA
46059 TAATTATATG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.04
19 2 0.04
20 9 0.19
21 17 0.35
22 18 0.38
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.41
Consensus pattern (21 bp):
GTTGGTTCCTTTAGTGAAAGG
Found at i:46273 original size:22 final size:21
Alignment explanation
Indices: 46208--46281 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 21
46198 TGTGAAAAAG
* *
46208 TTGGTTCTTTTTGTG--GGAA
1 TTGGTTCTTTTAGTGAAGGGA
* * *
46227 TTAGTTCTCTTAGTGAAGGGG
1 TTGGTTCTTTTAGTGAAGGGA
46248 TTGGTTCTTTTAGTGGAAGGGA
1 TTGGTTCTTTTAGT-GAAGGGA
*
46270 TTGGTTCATTTA
1 TTGGTTCTTTTA
46282 TAGTTATACG
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
19 12 0.28
21 14 0.33
22 17 0.40
ACGTcount: A:0.16, C:0.07, G:0.31, T:0.46
Consensus pattern (21 bp):
TTGGTTCTTTTAGTGAAGGGA
Found at i:46416 original size:20 final size:21
Alignment explanation
Indices: 46367--46417 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
46357 AAATTGTTAA
*
46367 TTCTCTTTGTGAAGGGATTGG
1 TTCTCTTAGTGAAGGGATTGG
46388 TTC-CTTTAGTGAA-GGATAT-G
1 TTCTC-TTAGTGAAGGGAT-TGG
46408 TTCTCTTAGT
1 TTCTCTTAGT
46418 AAAAAGTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.45
Consensus pattern (21 bp):
TTCTCTTAGTGAAGGGATTGG
Found at i:47232 original size:22 final size:22
Alignment explanation
Indices: 47188--47265 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
47178 GATATATATG
* * * *
47188 TACTATTATAATCATATGTACA
1 TACTATTATAGTGAAATGCACA
*
47210 TGCTATTATAGTGAAATGCACA
1 TACTATTATAGTGAAATGCACA
**
47232 TACTATTATAGTGAAATATACA
1 TACTATTATAGTGAAATGCACA
47254 TAC-AGTTATAGT
1 TACTA-TTATAGT
47266 CATATGTGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 1 0.02
22 46 0.98
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (22 bp):
TACTATTATAGTGAAATGCACA
Found at i:47398 original size:20 final size:21
Alignment explanation
Indices: 47342--47416 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
47332 TTTCCTAGTG
*
47342 AAGGGGTTAATTCTTTAACGA
1 AAGGGGTTAGTTCTTTAACGA
* * *
47363 AA-GGGCTAGTTCCTTTTA-TA
1 AAGGGGTTAGTT-CTTTAACGA
*
47383 AAGGGGTTAGTTCTTTCAATGA
1 AAGGGGTTAGTTCTTT-AACGA
*
47405 AA-GAGTTAGTTC
1 AAGGGGTTAGTTC
47417 CCTTAATGAG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
20 14 0.33
21 25 0.60
22 3 0.07
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (21 bp):
AAGGGGTTAGTTCTTTAACGA
Found at i:47558 original size:44 final size:44
Alignment explanation
Indices: 47528--47624 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 44
47518 AGTCAATTTC
* *
47528 AGTTATAGTTATATATACATTATGTTATAGTGATAAGTATATAT
1 AGTTATAGTTATATATACATAACGTTATAGTGATAAGTATATAT
*
47572 AGTTATAGTTATATATACATAACGTTATAGTGATAAGTACATACT
1 AGTTATAGTTATATATACATAACGTTATAGTGATAAGTATATA-T
47617 A-TTATAGT
1 AGTTATAGT
47625 GATTTTTTGT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
44 47 0.96
45 2 0.04
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (44 bp):
AGTTATAGTTATATATACATAACGTTATAGTGATAAGTATATAT
Found at i:47612 original size:22 final size:22
Alignment explanation
Indices: 47529--47627 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
47519 GTCAATTTCA
* * *
47529 GTTATAGTTATATATACATTAT
1 GTTATAGTGATATATACATAAC
*
47551 GTTATAGTGATA-AGTATATATA-
1 GTTATAGTGATATA-TACATA-AC
*
47573 GTTATAGTTATATATACATAAC
1 GTTATAGTGATATATACATAAC
47595 GTTATAGTGATA-AGTACAT-AC
1 GTTATAGTGATATA-TACATAAC
*
47616 TATTATAGTGAT
1 -GTTATAGTGAT
47628 TTTTTGTGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
21 5 0.08
22 57 0.89
23 2 0.03
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.42
Consensus pattern (22 bp):
GTTATAGTGATATATACATAAC
Found at i:47857 original size:63 final size:61
Alignment explanation
Indices: 47753--47921 Score: 187
Period size: 63 Copynumber: 2.7 Consensus size: 61
47743 AGGGATTGAG
*
47753 AAAAATGCAGAAGTTTTAAGAGATGAACCGACCCTTGAGCATAAAAAAATCAACTCC-TATGGA
1 AAAAATGCAAAAG-TTTAAGAGATGAACCGA-CCTT-AGCATAAAAAAATCAACTCCTTATGGA
* * *
47816 AAAAATGTAAAAGTTTCAAGAGATGAACCGACTCTCTAGCATAAAAGAATCGACTCCTTATGGA
1 AAAAATGCAAAAGTTT-AAGAGATGAACCGAC-CT-TAGCATAAAAAAATCAACTCCTTATGGA
* * * *
47880 CAAATTGCATAAGTTTAAGAAGATGAACTGACCTTTAGCATA
1 AAAAATGCAAAAGTTTAAG-AGATGAACCGACC-TTAGCATA
47922 GATTTTTTAC
Statistics
Matches: 91, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
62 4 0.04
63 56 0.62
64 31 0.34
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAAATGCAAAAGTTTAAGAGATGAACCGACCTTAGCATAAAAAAATCAACTCCTTATGGA
Found at i:48499 original size:24 final size:22
Alignment explanation
Indices: 48467--48531 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 22
48457 TAAGTTAAAC
48467 ATAACTTATATGTATATATAG-CT
1 ATAA-TTATATGTATATAT-GCCT
*
48490 ATAAAATTATATGTACATATGCCT
1 AT--AATTATATGTATATATGCCT
*
48514 ATAATAATATGTATATAT
1 ATAATTATATGTATATAT
48532 CATAATAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 14 0.39
23 3 0.08
24 17 0.47
25 2 0.06
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (22 bp):
ATAATTATATGTATATATGCCT
Found at i:48539 original size:22 final size:23
Alignment explanation
Indices: 48474--48539 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 23
48464 AACATAACTT
*
48474 ATATGTATATATAGCTATAA-AATT
1 ATATGTATATAT-GC-ATAATAATA
* *
48498 ATATGTACATATGCCT-ATAATA
1 ATATGTATATATGCATAATAATA
48520 ATATGTATATAT-CATAATAA
1 ATATGTATATATGCATAATAA
48540 CTAAGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 3 0.09
22 19 0.54
23 2 0.06
24 11 0.31
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (23 bp):
ATATGTATATATGCATAATAATA
Found at i:48613 original size:21 final size:22
Alignment explanation
Indices: 48560--48614 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
48550 CAACTATTTT
*
48560 ACAATGAGAACCAACCCCTTTTC
1 ACAAAGAGAACCAACCCC-TTTC
*
48583 ACTAAA-AGAACCAACTCC-TTC
1 AC-AAAGAGAACCAACCCCTTTC
48604 ACAAAGAGAAC
1 ACAAAGAGAAC
48615 TAATCTCCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 10 0.36
23 13 0.46
24 2 0.07
ACGTcount: A:0.44, C:0.31, G:0.09, T:0.16
Consensus pattern (22 bp):
ACAAAGAGAACCAACCCCTTTC
Found at i:49589 original size:29 final size:29
Alignment explanation
Indices: 49556--49693 Score: 82
Period size: 29 Copynumber: 4.8 Consensus size: 29
49546 AAACTCATTA
* *
49556 AATACAAATTAATATGAATATCAATCACC
1 AATACAAATTAATATGAATACCAATCAAC
* * * * * *
49585 AATACACATTAACATAAATGCCTATCAAT
1 AATACAAATTAATATGAATACCAATCAAC
* * * *
49614 AATACAAATTAATGTGAATGCCTATCATAT
1 AATACAAATTAATATGAATACCAATCA-AC
* * ** *
49644 AATACAAATCAATATTG-ATACAAATTGAT
1 AATACAAATTAATA-TGAATACCAATCAAC
*
49673 AATACATA-TAATATGAATACC
1 AATACAAATTAATATGAATACC
49694 CCTGAGAAAA
Statistics
Matches: 84, Mismatches: 22, Indels: 7
0.74 0.19 0.06
Matches are distributed among these distances:
27 2 0.02
28 8 0.10
29 53 0.63
30 19 0.23
31 2 0.02
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (29 bp):
AATACAAATTAATATGAATACCAATCAAC
Found at i:50056 original size:30 final size:27
Alignment explanation
Indices: 50012--50068 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 27
50002 CTTTTTATGA
*
50012 ACTTTTTTTTAAAATATAATCTCTCATT
1 ACTTTTTTTTAAAATAAAATCTC-CATT
50040 ACTTCTTTTTTAAAAATAAAATCTCCATT
1 ACTT-TTTTTT-AAAATAAAATCTCCATT
50069 TCCCTCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 10 0.38
30 12 0.46
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (27 bp):
ACTTTTTTTTAAAATAAAATCTCCATT
Found at i:50691 original size:15 final size:16
Alignment explanation
Indices: 50660--50694 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
50650 AGCCGTAGTC
50660 TAAA-AATTTAAATTT
1 TAAATAATTTAAATTT
50675 TAAATAATTTAAA-TT
1 TAAATAATTTAAATTT
50690 TAAAT
1 TAAAT
50695 TACTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATAATTTAAATTT
Found at i:53467 original size:51 final size:52
Alignment explanation
Indices: 53380--53495 Score: 164
Period size: 51 Copynumber: 2.2 Consensus size: 52
53370 AGCTTGTATG
* *
53380 TATCGATACATTTAGGTCAAAAACCCATAATGTATCGATACAATGAAAAAT-
1 TATCGATACATTTAGGTCAAAAACCCAAAATATATCGATACAATGAAAAATA
* *
53431 TAATCGATACATTTGGGT-TAAAACCCAAAATATATCGATACAATGAAAAATA
1 T-ATCGATACATTTAGGTCAAAAACCCAAAATATATCGATACAATGAAAAATA
*
53483 TATCGATATATTT
1 TATCGATACATTT
53496 TCTTTCCATA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
51 42 0.72
52 16 0.28
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (52 bp):
TATCGATACATTTAGGTCAAAAACCCAAAATATATCGATACAATGAAAAATA
Found at i:53577 original size:19 final size:20
Alignment explanation
Indices: 53553--53604 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
53543 ATTTCAAACA
53553 TGTATCGATACATTCAC-TT
1 TGTATCGATACATTCACGTT
*
53572 TGTATCAATACATTCACTGTT
1 TGTATCGATACATTCAC-GTT
53593 TGTATCGATACA
1 TGTATCGATACA
53605 AATTGTAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTCACGTT
Found at i:57240 original size:23 final size:23
Alignment explanation
Indices: 57214--57257 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
57204 TTAAAATTTC
57214 TTTTTT-ATAATTTTTTATTTTTA
1 TTTTTTGAT-ATTTTTTATTTTTA
*
57237 TTTTTTGATTTTTTTTATTTT
1 TTTTTTGATATTTTTTATTTT
57258 CTCTACAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (23 bp):
TTTTTTGATATTTTTTATTTTTA
Found at i:68659 original size:21 final size:21
Alignment explanation
Indices: 68635--68675 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
68625 TCACCTTCTA
68635 GGTTACCGAGATATATTTTAG
1 GGTTACCGAGATATATTTTAG
*
68656 GGTTACCGAGATATTTTTTA
1 GGTTACCGAGATATATTTTA
68676 CATCGAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (21 bp):
GGTTACCGAGATATATTTTAG
Done.