Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3615
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: 30660
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:877 original size:94 final size:91
Alignment explanation
Indices: 696--877 Score: 197
Period size: 94 Copynumber: 1.9 Consensus size: 91
686 TATTGACAAC
*
696 AAGAAATTGAAATTACCTCAACATGTCCTGAGGCTCAACTTCACCTCTCGCAATAAGAGATTGAA
1 AAGAAATTGAAATAACCTCAACATGTCCTGAGGCTCAACTTCACCTCTCGCAATAAGAGATTG--
* *
761 AAATTTTTTGATAAATATAAATTAATAAG
64 -AATTTTTTGATAAACAAAAATTAATAAG
* * * * * *
790 AAGAAATTGAAATAATCTCAACGTAGTCCTTGAGGCTCAACTTACACTTCTCGCTAGTATGAGTT
1 AAGAAATTGAAATAACCTCAACAT-GTCC-TGAGGCTCAACTT-CACCTCTCGC-AATAAGAGAT
855 TG-ATTTTTTGA-AAGACAAAAATT
62 TGAATTTTTTGATAA-ACAAAAATT
878 GAGTAAATAC
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
93 2 0.03
94 37 0.50
95 4 0.05
96 13 0.18
97 9 0.12
98 9 0.12
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.31
Consensus pattern (91 bp):
AAGAAATTGAAATAACCTCAACATGTCCTGAGGCTCAACTTCACCTCTCGCAATAAGAGATTGAA
TTTTTTGATAAACAAAAATTAATAAG
Found at i:1098 original size:96 final size:101
Alignment explanation
Indices: 998--1188 Score: 252
Period size: 96 Copynumber: 1.9 Consensus size: 101
988 GCTCAACTCA
* *
998 CTCTCGCAATATGAAGCTTGAATTTTTTTTTTG-AA-ATAAA-ATTGAAAAGCAGA-A-ATATAG
1 CTCTCGCAATATGAAGCTTGAA-TTTTTTATTGAAATATAAATATTGAAAAGCAGAGAGAAATAG
1058 -AAATTACCTCAACGTGCCTTGAGG-CTCATCCTCAAC
65 AAAATTACCTCAACGT-CCTTGAGGTCTCATCCTCAAC
* * *
1094 CTCTCGCAATATGAGGTTTGAATTTTTTATTGAAAAATATAAATATTGAAAAGCAGAGAGAAATT
1 CTCTCGCAATATGAAGCTTGAATTTTTTATTG--AAATATAAATATTGAAAAGCAGAGAGAAATA
1159 GAAAATTACCTCAACGTCCTTGAGGTCTCA
64 GAAAATTACCTCAACGTCCTTGAGGTCTCA
1189 AAAAACATCG
Statistics
Matches: 81, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
95 9 0.11
96 20 0.25
98 2 0.02
99 5 0.06
100 13 0.16
101 1 0.01
102 12 0.15
103 19 0.23
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (101 bp):
CTCTCGCAATATGAAGCTTGAATTTTTTATTGAAATATAAATATTGAAAAGCAGAGAGAAATAGA
AAATTACCTCAACGTCCTTGAGGTCTCATCCTCAAC
Found at i:1984 original size:78 final size:74
Alignment explanation
Indices: 1704--2047 Score: 384
Period size: 76 Copynumber: 4.6 Consensus size: 74
1694 AAACTAATTG
* *
1704 AACAG-AATTGAAAATACCTCAACGTGT-CTGAGGCTCAACTCAATTTCTCGCAATAGGAGTTGA
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTC-ATTTCTCGCAATATGAGTTGA
1767 TTTTTTTTTGAA
65 --TTTTTTTGAA
* * *
1779 AGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAA-TCATTTCTCGCAATAT-AGTTGA
1 A-ACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1842 -TTTTTTGAA
65 TTTTTTTGAA
* *
1851 AGACA-AAATTGAAAATACCTCA-CATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 A-ACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
*
1914 TTTTTTTTTGAC
65 --TTTTTTTGAA
* **
1926 AACAGAAATTAGAAATTACCTCAGCGTGTCCT-AGGACTCAAACTCACCTCTCGCAATATGAGTT
1 AACAGAAATT-GAAAATACCTCAGCGTGTCCTGAGG-CTC-AACTCATTTCTCGCAATATGAGTT
**
1990 GAAATTTTTGAA
63 GATTTTTTTGAA
* *
2002 AACAGAAATTGAAAATTACCTCGGCGTGTCTTGA-GCTCAA-TCATTT
1 AACAGAAATTGAAAA-TACCTCAGCGTGTCCTGAGGCTCAACTCATTT
2048 GAACAGAAAT
Statistics
Matches: 235, Mismatches: 19, Indels: 32
0.82 0.07 0.11
Matches are distributed among these distances:
70 17 0.07
71 33 0.14
72 20 0.09
73 4 0.02
74 5 0.02
75 28 0.12
76 62 0.26
77 32 0.14
78 34 0.14
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (74 bp):
AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
TTTTTTGAA
Found at i:2054 original size:47 final size:47
Alignment explanation
Indices: 2002--2094 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
1992 AATTTTTGAA
**
2002 AACAGAAA-TTGAAAATTACCTCGGCGTGTCTTGAGCTCAA-TCATTTG
1 AACAGAAATTTG-AAATTACCTCAACGTGTCTTGAGC-CAACTCATTTG
2049 AACAGAAATTTGAAATTACCTCAACGTGTCTTGAGCCAACTCATTT
1 AACAGAAATTTGAAATTACCTCAACGTGTCTTGAGCCAACTCATTT
2095 CTCGCAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
46 3 0.07
47 36 0.86
48 3 0.07
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (47 bp):
AACAGAAATTTGAAATTACCTCAACGTGTCTTGAGCCAACTCATTTG
Found at i:2437 original size:267 final size:266
Alignment explanation
Indices: 2164--2790 Score: 865
Period size: 267 Copynumber: 2.3 Consensus size: 266
2154 ACTCATTTCA
* **
2164 TCGCAATAGAGTTGAAATTTTTTTTGA-GAAAGACAGAAA-TGAAAATACCTCAGCATTGTGAAC
1 TCGCAATAGAGTTG-AATTTTGTTAAATGAAA-ACAGAAATTG-AAATACCT-AGC---GTG-AC
2227 C-GAGGCTCAACTCACCTCTCGCATATGATGAGCTGATTTTGAAAAAGTAGAAATTAAAA-GTTC
58 CTGAGGCTCAACTCACCTCTCGCA-AT-ATGAGCTG-TTTTGAAAAAGTAGAAATTAAAAGGTTC
2290 AA-CCACCTCTCGCAATATGAGTTGATTC-TGAACAAC-T-AAATTG-AAACAG-AATTG-AATA
120 AACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAAATTGAAAACAGAAATTGAAATA
2348 CCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAAT
185 CCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAAT
*
2413 T-AAGGGTTCAACCACTTC
250 TAAAAGGTTCAACCAC--C
*
2431 TCGCAATATAGTTG-ATTTTGTTAAATTGAAAACAGAAATTGAAATACCTAGCGTGACCTGAGGC
1 TCGCAATAGAGTTGAATTTTGTTAAA-TGAAAACAGAAATTGAAATACCTAGCGTGACCTGAGGC
2495 TCAACTCACCTCTCGCAATATGAGCTGTTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTC
65 TCAACTCACCTCTCGCAATATGAGCTGTTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTC
2560 TCGCAATATGAGTTGATTCTTGAACAACGTAAAATTGAAAACAGAAATTGAAATACCTCAGCGTG
130 TCGCAATATGAGTTGATTCTTGAACAACGTAAAATTGAAAACAGAAATTGAAATACCTCAGCGTG
*
2625 ACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAGTAGAAATTAAAAGGTTC
195 ACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTC
2690 AACCACC
260 AACCACC
2697 TCGCAATATGAGTTG-ATTCTTGAACAATGTAAATTG-AAACAGAAATTGAAATACCTCAGCGTG
1 TCGCAATA-GAGTTGAATT-TTG-----T-TAAA-TGAAAACAGAAATTGAAATACCT-AGCGTG
2760 ACCTGAGGCTCAACTCA-C-CTCGCAATATGAG
56 ACCTGAGGCTCAACTCACCTCTCGCAATATGAG
2791 TTGAAATTAA
Statistics
Matches: 331, Mismatches: 7, Indels: 39
0.88 0.02 0.10
Matches are distributed among these distances:
259 23 0.07
260 14 0.04
261 31 0.09
262 33 0.10
263 1 0.00
264 6 0.02
265 17 0.05
266 29 0.09
267 96 0.29
268 16 0.05
272 13 0.04
273 22 0.07
274 30 0.09
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (266 bp):
TCGCAATAGAGTTGAATTTTGTTAAATGAAAACAGAAATTGAAATACCTAGCGTGACCTGAGGCT
CAACTCACCTCTCGCAATATGAGCTGTTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCT
CGCAATATGAGTTGATTCTTGAACAACGTAAAATTGAAAACAGAAATTGAAATACCTCAGCGTGA
CCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCA
ACCACC
Found at i:2549 original size:128 final size:132
Alignment explanation
Indices: 2196--2790 Score: 808
Period size: 128 Copynumber: 4.4 Consensus size: 132
2186 TTTGAGAAAG
2196 ACAGAAA-TGAAAATACCTCAGCATTGTGAACC-GAGGCTCAACTCACCTCTCGCATATGATGAG
1 ACAGAAATTG-AAATACCTCAGC---GTG-ACCTGAGGCTCAACTCACCTCTCGCA-AT-ATGAG
2259 CTGATTTTGAAAAAGTAGAAATTAAAA-GTTCAACCACCTCTCGCAATATGAGTTGATTC-TGAA
59 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCACCTCTCGCAATATGAGTTGATTCTTG--
*
2322 CAACTAAATTGAA
122 --ATTAAATTGAA
2335 ACAG-AATTG-AATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
1 ACAGAAATTGAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
* *
2398 TGAAAAAGTAGAAATT-AAGGGTTCAACCACTTCTCGCAATAT-AGTTGATT-TTG-TTAAATTG
66 TGAAAAAGTAGAAATTAAAAGGTTCAACCACCTCTCGCAATATGAGTTGATTCTTGATTAAATTG
2459 AAA
131 -AA
2462 ACAGAAATTGAAATACCT-AGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTG-TTT
1 ACAGAAATTGAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
2525 TGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT
66 TGAAAAAGTAGAAATTAAAAGGTTCAA-CCACCTCTCGCAATATGAGTTGATTCTTG----A--T
*
2590 AAAATTGAAA
124 TAAATTG-AA
*
2600 ACAGAAATTGAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 ACAGAAATTGAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
2665 TGAAAAAGTAGAAATTAAAAGGTTCAACCA-C-CTCGCAATATGAGTTGATTCTTGAACAATGTA
66 TGAAAAAGTAGAAATTAAAAGGTTCAACCACCTCTCGCAATATGAGTTGATTCTTG----AT-TA
2728 AATTGAA
126 AATTGAA
2735 ACAGAAATTGAAATACCTCAGCGTGACCTGAGGCTCAACTCA-C-CTCGCAATATGAG
1 ACAGAAATTGAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
2791 TTGAAATTAA
Statistics
Matches: 427, Mismatches: 8, Indels: 48
0.88 0.02 0.10
Matches are distributed among these distances:
126 7 0.02
127 25 0.06
128 56 0.13
129 22 0.05
130 8 0.02
131 15 0.04
132 49 0.11
133 18 0.04
134 26 0.06
135 45 0.11
136 6 0.01
137 39 0.09
138 31 0.07
139 50 0.12
140 30 0.07
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (132 bp):
ACAGAAATTGAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
TGAAAAAGTAGAAATTAAAAGGTTCAACCACCTCTCGCAATATGAGTTGATTCTTGATTAAATTG
AA
Found at i:2835 original size:67 final size:68
Alignment explanation
Indices: 2727--2881 Score: 206
Period size: 67 Copynumber: 2.2 Consensus size: 68
2717 TGAACAATGT
* * *
2727 AAATTGAAACAGAAATTGAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTC-GCAATATGAG
1 AAATTAAAACAAAAATTGAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCAGCAATATGAG
2791 TTG
66 TTG
*
2794 AAATTAAAACAAAAATTGAAAATACCTCAGCGT-CCCCGAGGCTCAACTCACCTCTAGCAATATG
1 AAATTAAAACAAAAATTG-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTC-AGCAATATG
2858 AGTTG
64 AGTTG
**
2863 ATTTTGAAAAACAAAAATT
1 AAATT--AAAACAAAAATT
2882 AAAGGCTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
67 35 0.45
68 14 0.18
69 16 0.21
71 12 0.16
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.23
Consensus pattern (68 bp):
AAATTAAAACAAAAATTGAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCAGCAATATGAG
TTG
Found at i:2976 original size:119 final size:118
Alignment explanation
Indices: 2765--3002 Score: 340
Period size: 119 Copynumber: 2.0 Consensus size: 118
2755 GCGTGACCTG
*
2765 AGGCTCAACTCACCTCGCAATATGAGTTGAAATTAAAACAAAAATTGAAAATACCTCAGCGTCCC
1 AGGCTCAACTCACCTCGCAATATGAGTTGAAATTAAAACAAAAACTGAAAATACCTCAGCGTCCC
2830 CGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAA
66 CGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTG--AAACAAAAATTAA
* * * *
2884 AGGCTTAACTCACCTCTCGCAATATGAG-T-CATTTAAAACATAAACT-AAAATACCTCAGCGTG
1 AGGCTCAACTCA-C-CTCGCAATATGAGTTGAAATTAAAACAAAAACTGAAAATACCTCAGCGT-
* *
2946 CCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACAAAAATTAA
63 CCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAACAAAAATTAA
3002 A
1 A
3003 ATACCTCAAC
Statistics
Matches: 108, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
118 29 0.27
119 59 0.55
120 7 0.06
121 13 0.12
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (118 bp):
AGGCTCAACTCACCTCGCAATATGAGTTGAAATTAAAACAAAAACTGAAAATACCTCAGCGTCCC
CGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAACAAAAATTAA
Found at i:3024 original size:70 final size:70
Alignment explanation
Indices: 2884--3055 Score: 217
Period size: 70 Copynumber: 2.5 Consensus size: 70
2874 CAAAAATTAA
* * * * *
2884 AGGCTTAACTCACCTCTCGCAATATGAG-TCA--TTTAAAACATAAACTAAAATACCTCAGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAAACTAAAATACCTCAACGTG
2946 CCCCG
66 CCCCG
* *
2951 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACAAAAATTAAAATACCTCAACGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAAACTAAAATACCTCAACGTG
* **
3016 TCTTG
66 CCCCG
3021 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTT
3056 CCTTGAAAAG
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
67 26 0.29
68 2 0.02
69 1 0.01
70 62 0.68
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAAACTAAAATACCTCAACGTG
CCCCG
Found at i:11335 original size:12 final size:12
Alignment explanation
Indices: 11315--11350 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
11305 TGGGATATGC
*
11315 AATGTATGAATG
1 AATGCATGAATG
11327 AATGCATGAATG
1 AATGCATGAATG
11339 AATGCATGAATG
1 AATGCATGAATG
11351 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:15692 original size:17 final size:17
Alignment explanation
Indices: 15670--15704 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15660 TTAGATCTAA
* *
15670 AAATAAGTTTAGGTTTT
1 AAATAAGTATAAGTTTT
15687 AAATAAGTATAAGTTTT
1 AAATAAGTATAAGTTTT
15704 A
1 A
15705 TGAAGTTGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (17 bp):
AAATAAGTATAAGTTTT
Found at i:17205 original size:20 final size:23
Alignment explanation
Indices: 17182--17228 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 23
17172 TATAAATATG
17182 TATAATT-ATTATT-TAACAT-A
1 TATAATTAATTATTATAACATAA
*
17202 TATAATTAATTTTTATAACATAA
1 TATAATTAATTATTATAACATAA
17225 TATA
1 TATA
17229 TTCGGGCTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 5 0.22
22 6 0.26
23 5 0.22
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TATAATTAATTATTATAACATAA
Found at i:17630 original size:13 final size:14
Alignment explanation
Indices: 17606--17634 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17596 AAGATTTGAT
17606 TTTTATTTTTATTA
1 TTTTATTTTTATTA
17620 TTTTA-TTTTATTA
1 TTTTATTTTTATTA
17633 TT
1 TT
17635 AAATTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTTTTATTA
Found at i:18330 original size:3 final size:3
Alignment explanation
Indices: 18285--18460 Score: 132
Period size: 3 Copynumber: 59.3 Consensus size: 3
18275 ACATTGTTAG
* * *
18285 TAT TAC TAT TAG TAT T-T T-T TAT T-T TAC TAT TAT T-T ATATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT
* * * * * * *
18328 TAT TAT TAT TAT TAC TAT CAT TAT TAT TTT TAC TAT TAC AAT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
18376 CTAT AAT TAT TAT TAT TAT TAT TA- TATT TAT TAT TAT TAT TAT TAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * *
18422 TAT TAT T-T TCAT TA- TAG TAC TAT TAT TAT TAC TAT TAT T
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18461 TTTGTTTCCT
Statistics
Matches: 136, Mismatches: 26, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
2 13 0.10
3 114 0.84
4 8 0.06
5 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:18995 original size:125 final size:126
Alignment explanation
Indices: 18830--19059 Score: 300
Period size: 125 Copynumber: 1.8 Consensus size: 126
18820 ATTTTTTCCC
* * * * *
18830 AAAATAGAGGTAATATTTCGTGTTTGGAAGTTCGAGAAATCGTGCCCTACCGTGCTGAGTTTCGA
1 AAAATAGAGGCAATATTTCGTATTTGGAAATTCAAGAAATCGTGCCCAACCGTGCTGAGTTTCGA
** * * * * *
18895 TTTTTCGTTTGACCGAATAACTAAATATCGTTTTGAAATTCCGTCCATGTTTTCTTAAATT
66 TTTACCGTATGACCAAATAACCAAATATCCTTTTAAAATTCCGTCCATGTTTTCTTAAATT
* ** *
18956 AAAAT-GAGGCAATATTTCGTATTTGGAAATTCAATAAATCGTGCCCAATTGTGCTGGGTTTCGA
1 AAAATAGAGGCAATATTTCGTATTTGGAAATTCAAGAAATCGTGCCCAACCGTGCTGAGTTTCGA
*
19020 TTTACCGTATGACCAAATAGCCAAATATCCTTTTAAAATT
66 TTTACCGTATGACCAAATAACCAAATATCCTTTTAAAATT
19060 TCAAATGTAT
Statistics
Matches: 87, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
125 82 0.94
126 5 0.06
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (126 bp):
AAAATAGAGGCAATATTTCGTATTTGGAAATTCAAGAAATCGTGCCCAACCGTGCTGAGTTTCGA
TTTACCGTATGACCAAATAACCAAATATCCTTTTAAAATTCCGTCCATGTTTTCTTAAATT
Found at i:23136 original size:25 final size:23
Alignment explanation
Indices: 23084--23138 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
23074 TATAAATAGT
23084 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
23107 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
23132 AATAGTG
1 AATAGTG
23139 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:23219 original size:22 final size:22
Alignment explanation
Indices: 23194--23268 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
23184 TATGAAATAG
*
23194 ATATAAAAAAAATATGTACATA
1 ATATAAAAAAAATATATACATA
* *
23216 ATATAGTGTAAAAAATACATACATA
1 ATATA---AAAAAAATATATACATA
**
23241 ATATAATTAAAATATATACATA
1 ATATAAAAAAAATATATACATA
*
23263 AGATAA
1 ATATAA
23269 CATGTAGAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 23 0.55
25 19 0.45
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
ATATAAAAAAAATATATACATA
Found at i:23238 original size:25 final size:25
Alignment explanation
Indices: 23200--23347 Score: 90
Period size: 25 Copynumber: 5.9 Consensus size: 25
23190 ATAGATATAA
*
23200 AAAAAATATGTACATAATATAGTGT
1 AAAAAATATATACATAATATAGTGT
* *
23225 AAAAAATACATACATAATATAAT-T
1 AAAAAATATATACATAATATAGTGT
* *
23249 --AAAATATATACATAAGATAACATGTAGAA
1 AAAAAATATATACAT-A-AT-ATA-GT-G-T
* *
23278 AAAAAATATATAAATAATATAGTAT
1 AAAAAATATATACATAATATAGTGT
* * *
23303 TAAAGATATATACATAAAATA--GT
1 AAAAAATATATACATAATATAGTGT
* * *
23326 ATAATATATATACGTAATATAG
1 AAAAAATATATACATAATATAG
23348 AATTTAGAAT
Statistics
Matches: 92, Mismatches: 21, Indels: 21
0.69 0.16 0.16
Matches are distributed among these distances:
22 12 0.13
23 18 0.20
24 3 0.03
25 39 0.42
26 1 0.01
27 2 0.02
28 2 0.02
29 2 0.02
30 1 0.01
31 12 0.13
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (25 bp):
AAAAAATATATACATAATATAGTGT
Found at i:23279 original size:27 final size:28
Alignment explanation
Indices: 23249--23320 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 28
23239 TAATATAATT
23249 AAAATATATACATAAGATAACAT-GTA-G
1 AAAATATATACATAA-ATAACATAGTATG
* * * * *
23276 AAAAAAAATATATAAATAATATAGTATT
1 AAAATATATACATAAATAACATAGTATG
23304 AAAGATATATACATAAA
1 AAA-ATATATACATAAA
23321 ATAGTATAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
26 6 0.18
27 15 0.44
28 3 0.09
29 10 0.29
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (28 bp):
AAAATATATACATAAATAACATAGTATG
Found at i:23732 original size:16 final size:16
Alignment explanation
Indices: 23694--23732 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
23684 CTCCAAAAAA
*
23694 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
23710 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
23726 AATAACT
1 AAAAACT
23733 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:23957 original size:30 final size:30
Alignment explanation
Indices: 23889--23957 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
23879 TAGGTATAAG
*
23889 TGGTGGTGAAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
23919 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
23949 TGGTGGTGG
1 TGGTGGTGG
23958 CAAAGGCTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.16, C:0.06, G:0.51, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:24766 original size:86 final size:86
Alignment explanation
Indices: 24572--24798 Score: 244
Period size: 86 Copynumber: 2.6 Consensus size: 86
24562 TTATTCTTTA
* * * * *
24572 CTCGGCATGTGATCCTGA-GCTTAACTCATTTCTCGCAATATGAATTGACTCTTTAAAACTAAAC
1 CTCGGCATGTGA-CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTAAAAC-AAAC
*
24636 ATTAAAAACAGAAATTGAAAATAG
63 ATTAAAAACAGAAATTGAAAATAC
* * * *
24660 CTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAA-AAA-ATT
1 CTCGGCATGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAACA-T
* **
24723 TGTAAAACAGATTTTGAAAATAC
65 T-AAAAACAGAAATTGAAAATAC
* * *
24746 CTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT
1 CTCGGCATGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
24799 GCAAAGCATA
Statistics
Matches: 116, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
84 1 0.01
85 5 0.04
86 63 0.54
87 10 0.09
88 37 0.32
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (86 bp):
CTCGGCATGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAACATT
AAAAACAGAAATTGAAAATAC
Found at i:24842 original size:102 final size:103
Alignment explanation
Indices: 24736--24925 Score: 303
Period size: 102 Copynumber: 1.8 Consensus size: 103
24726 AAAACAGATT
* *
24736 TTGAAAATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTTTTG
1 TTGAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG
24800 -CAAAGCATAAATTGAAAAAAAATAAAAATAAAAATCAA
66 ACAAA-CATAAATTGAAAAAAAATAAAAATAAAAATCAA
* * *
24838 TTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 TTGAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTT
24903 GACAAACATAAATTGAAAAAAAA
65 GACAAACATAAATTGAAAAAAAA
24926 AGAAATTGAA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
102 53 0.66
104 23 0.29
105 4 0.05
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (103 bp):
TTGAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG
ACAAACATAAATTGAAAAAAAATAAAAATAAAAATCAA
Found at i:24974 original size:91 final size:90
Alignment explanation
Indices: 24836--25191 Score: 418
Period size: 91 Copynumber: 3.9 Consensus size: 90
24826 AATAAAAATC
* * *
24836 AATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AATTGAAAATACCTCAGCGTGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTT
* *
24901 TTGACAA-ACATAAATTGAAAAAAAAAGA
65 TTGA-AACACAGAAATTG--AAAAACAGA
* * *
24929 AATTGAAAATATCTCAGCGTGT-CCTGAGGCTGAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AATTGAAAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTT
* *
24993 GGAAAAACA-AAATTTGAAAAACAGA
66 TGAAACACAGAAA-TTGAAAAACAGA
* ** * *
25018 ATTTGAAAATACCTCAGCGTGTGAGTCAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTT
1 AATTGAAAATACCTCAGCGTGTGCCT-GAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTT
*
25083 TTGAAACACAGAAATTGAAGAACAGA
65 TTGAAACACAGAAATTGAAAAACAGA
* * * *
25109 AATGGAAAACACCTCAGC--GT-CTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTT
1 AATTGAAAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA-TTTTT
*
25171 TTGAAAGACAGAAATTGAAAA
65 TTGAAACACAGAAATTGAAAA
25192 TACCTCAACG
Statistics
Matches: 230, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
87 30 0.13
88 25 0.11
89 30 0.13
90 6 0.03
91 116 0.50
92 3 0.01
93 20 0.09
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (90 bp):
AATTGAAAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTT
TGAAACACAGAAATTGAAAAACAGA
Found at i:25026 original size:13 final size:14
Alignment explanation
Indices: 24994--25026 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
24984 TGATTTTTTG
24994 GAAAAACAAAATTT
1 GAAAAACAAAATTT
*
25008 GAAAAACAGAATTT
1 GAAAAACAAAATTT
25022 GAAAA
1 GAAAA
25027 TACCTCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
GAAAAACAAAATTT
Found at i:25067 original size:182 final size:178
Alignment explanation
Indices: 24838--25170 Score: 472
Period size: 182 Copynumber: 1.8 Consensus size: 178
24828 TAAAAATCAA
* * * *
24838 TTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 TTGAAAATACCTCAGCGTGTGATCTAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTT
* * * * *
24903 GACAA-ACATAAATTGAAAAAAAAAGAAATTGAAAATATCTCAGCGTGTCCTGAGGCTGAACTCA
66 GA-AACACAGAAATTG--AAAAAAAGAAATGGAAAACACCTCAGC--GTCCTGAGGCTCAACTCA
*
24967 CCTCTCGCAATATGAGTTGATTTTTTGGAAAAACAAAATTTGAAAAACAGAAT
126 CCTCTCGCAATATGAGCTGATTTTTTGGAAAAACAAAATTTGAAAAACAGAAT
25020 TTGAAAATACCTCAGCGTGTGAGTC-AAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTT
1 TTGAAAATACCTCAGCGTGTGA-TCTAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTT
* * * *
25084 TGAAACACAGAAATTGAAGAACAGAAATGGAAAACACCTCAGCGTCTTGAGGTTCAACTCACCTC
65 TGAAACACAGAAATTGAAAAAAAGAAATGGAAAACACCTCAGCGTCCTGAGGCTCAACTCACCTC
25149 TCGCAATATGAGCTGATTTTTT
130 TCGCAATATGAGCTGATTTTTT
25171 TTGAAAGACA
Statistics
Matches: 135, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
178 40 0.30
180 22 0.16
181 2 0.01
182 69 0.51
183 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (178 bp):
TTGAAAATACCTCAGCGTGTGATCTAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTT
GAAACACAGAAATTGAAAAAAAGAAATGGAAAACACCTCAGCGTCCTGAGGCTCAACTCACCTCT
CGCAATATGAGCTGATTTTTTGGAAAAACAAAATTTGAAAAACAGAAT
Found at i:25318 original size:73 final size:75
Alignment explanation
Indices: 25103--25701 Score: 723
Period size: 73 Copynumber: 8.2 Consensus size: 75
25093 GAAATTGAAG
* * * * *
25103 AACAGAAATGGAAAACACCTC-A-GCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGAT
1 AACAAAAATTGAAAATACCTCAACGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
25166 TTTTTTTGA-A
65 TTTTTTTGACA
* *
25176 AGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 A-ACAAAAATTGAAAATACCTCAACGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
25241 --TTTTTGACA
65 TTTTTTTGACA
* * *
25250 AACAAAAATTGAAATTACCTC-A-GCGTCTTGAGGTTCAACTCACCTATCGCAATATGAGTTGAT
1 AACAAAAATTGAAAATACCTCAACGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
25313 TTTTTTGAAA
66 TTTTTTGACA
* * * *
25323 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGAT
1 AACAAAAATTGAAAATACCTCAACGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
25388 TTTTTT-A-A
66 TTTTTTGACA
* *
25396 AGAC----ATTG-AAATACCTCAACGTGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGA
1 A-ACAAAAATTGAAAATACCTCAACGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
25456 --TTTTTGACA
65 TTTTTTTGACA
* * * * *
25465 AACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGAT
1 AACAAAAATTGAAAATACCTCAACGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
25530 TTTTTTGAAA
66 TTTTTTGACA
* * *
25540 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-
1 AACAAAAATTGAAAATACCTCAACGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
25604 -GTTTTGACA
66 TTTTTTGACA
* * * * *
25613 AACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
1 AACAAAAATTGAAAATACCTCAACGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
25678 TTTTTT-AGA
66 TTTTTTGACA
* *
25687 AACATAAATTAAAAA
1 AACAAAAATTGAAAA
25702 AACGAAAATT
Statistics
Matches: 462, Mismatches: 44, Indels: 39
0.85 0.08 0.07
Matches are distributed among these distances:
67 5 0.01
68 3 0.01
69 51 0.11
70 4 0.01
71 37 0.08
72 5 0.01
73 167 0.36
74 38 0.08
75 115 0.25
76 37 0.08
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (75 bp):
AACAAAAATTGAAAATACCTCAACGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTTGACA
Found at i:25609 original size:148 final size:149
Alignment explanation
Indices: 25097--25768 Score: 789
Period size: 148 Copynumber: 4.5 Consensus size: 149
25087 AACACAGAAA
* * * * *
25097 TTGAAGAACAGAAATGGAAAACACCTC-A-GCGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
* * *
25160 GCTGATTTTTTTTGA-AAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCT
66 GTTGA--TTTTTTGACAA-ACAAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCT
25224 CTCGCAATATGAGTTGA--TTT
128 CTCGCAATATGAGTTGATTTTT
* * * * * *
25244 TTGACAAACAAAAATTGAAATTACCTC-A-GCGTCTTGAGGTTCAACTCACCTATCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
* * * *
25307 GTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCT
66 GTTGA-TTTTTTGACAAACAAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
*
25372 CGCAATATGAGCTGATTTTT
130 CGCAATATGAGTTGATTTTT
* *
25392 TT----AA-AGACATTG-AAATACCTCAACGTGTCTTGAGGCTCAACTCACTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
* * *
25451 GTTGA-TTTTTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTATC
66 GTTGATTTTTTGACAAACAAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTC
25515 GCAATATGAGTTGATTTTT
131 GCAATATGAGTTGATTTTT
*
25534 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
* * * *
25599 GTTGA-GTTTTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTC
66 GTTGATTTTTTGACAAACAAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTC
25663 GCAATATGAGTTGATTTTT
131 GCAATATGAGTTGATTTTT
* * *
25682 TTAGAAACATAAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC
1 TT-G-----------AAAAACA-G-AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCAC
25747 CTCTCGCAATATGAGTTGATTT
52 CTCTCGCAATATGAGTTGATTT
25769 GAAAAGCAGA
Statistics
Matches: 463, Mismatches: 36, Indels: 36
0.87 0.07 0.07
Matches are distributed among these distances:
142 80 0.17
143 7 0.02
144 38 0.08
146 72 0.16
147 69 0.15
148 132 0.29
149 1 0.00
160 6 0.01
161 1 0.00
162 56 0.12
163 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (149 bp):
TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTGACAAACAAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTC
GCAATATGAGTTGATTTTT
Found at i:25895 original size:99 final size:96
Alignment explanation
Indices: 25699--26056 Score: 427
Period size: 99 Copynumber: 3.8 Consensus size: 96
25689 CATAAATTAA
*
25699 AAAAAC-GAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAAACAG-AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* *
25763 TGA--TTTGAAAAGCAGAATTTGTAAGGCAAAAATTG
65 TGATTTTTGAAAA--A-AA-TT-AAAAGCAAAAATTG
25798 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
25863 GATTTTTGAAAAAAAAAATTAAAAGCAGAAATTG
66 GATTTTTG---AAAAAAATTAAAAGCAAAAATTG
* * *
25897 AAAAACAGAAATTAAAAATACCTCGGCGTGCCC-GAGGCTCAGCTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
25961 GATTTTTG---------AAAAGCATAAATTG
66 GATTTTTGAAAAAAATTAAAAGCAAAAATTG
* * *
25983 AAAAAAAGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC--GTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAG
26048 TTGATTTTT
64 TTGATTTTT
26057 TTGAAAGATA
Statistics
Matches: 236, Mismatches: 14, Indels: 28
0.85 0.05 0.10
Matches are distributed among these distances:
86 37 0.16
88 5 0.02
89 36 0.15
98 38 0.16
99 106 0.45
100 3 0.01
101 6 0.03
102 1 0.00
104 4 0.02
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (96 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAAAAATTAAAAGCAAAAATTG
Found at i:25913 original size:13 final size:13
Alignment explanation
Indices: 25878--25914 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
25868 TTGAAAAAAA
*
25878 AAATTAAAAGCAG
1 AAATTAAAAACAG
25891 AAATTGAAAAACAG
1 AAATT-AAAAACAG
25905 AAATTAAAAA
1 AAATTAAAAA
25915 TACCTCGGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (13 bp):
AAATTAAAAACAG
Found at i:26076 original size:89 final size:86
Alignment explanation
Indices: 25883--26056 Score: 240
Period size: 89 Copynumber: 2.0 Consensus size: 86
25873 AAAAAAAATT
* * * * *
25883 AAAAGCAGAAATTGAAAAACAGAAATTAAAAATACCTCGGCGTGCCCGAGGCTCAGCTCACCTCT
1 AAAAGCATAAAATGAAAAAAAGAAATTAAAAATACCTCGGCGTGCCCGAGGCCCAACTCACCTCT
25948 CGCAATATGAGTTGATTTTTG
66 CGCAATATGAGTTGATTTTTG
* * * *
25969 AAAAGCATAAATTGAAAAAAAGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCACC
1 AAAAGCATAAAATGAAAAAAAGAAATTAAAAATACCTC-G-GCGTG-CCCGAGGCCCAACTCACC
26034 TCTCGCAATATGAGTTGATTTTT
63 TCTCGCAATATGAGTTGATTTTT
26057 TTGAAAGATA
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
86 35 0.45
87 1 0.01
88 4 0.05
89 38 0.49
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (86 bp):
AAAAGCATAAAATGAAAAAAAGAAATTAAAAATACCTCGGCGTGCCCGAGGCCCAACTCACCTCT
CGCAATATGAGTTGATTTTTG
Done.