Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2576
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: 26920
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Found at i:4261 original size:18 final size:18
Alignment explanation
Indices: 4238--4279 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
4228 TTACAGCGTG
4238 AAGAAATCAGAGTTGGCA
1 AAGAAATCAGAGTTGGCA
4256 AAGAAATCAGAGTTGGCA
1 AAGAAATCAGAGTTGGCA
4274 AAGAAA
1 AAGAAA
4280 AGCTCATGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.10, G:0.26, T:0.14
Consensus pattern (18 bp):
AAGAAATCAGAGTTGGCA
Found at i:12262 original size:10 final size:10
Alignment explanation
Indices: 12249--12293 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
12239 TGTCCTTTAC
12249 AAAAA-AAAA
1 AAAAACAAAA
*
12258 CAAAACAAAA
1 AAAAACAAAA
12268 AAAAACAAAA
1 AAAAACAAAA
12278 AAAAACCAAGAA
1 AAAAA-CAA-AA
12290 AAAA
1 AAAA
12294 TAGCCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 4 0.13
10 18 0.58
11 3 0.10
12 6 0.19
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:12267 original size:15 final size:15
Alignment explanation
Indices: 12247--12282 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
12237 GGTGTCCTTT
12247 ACAAAAAAAAACAAA
1 ACAAAAAAAAACAAA
12262 ACAAAAAAAAACAAA
1 ACAAAAAAAAACAAA
12277 A-AAAAA
1 ACAAAAA
12283 CCAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (15 bp):
ACAAAAAAAAACAAA
Found at i:12278 original size:11 final size:11
Alignment explanation
Indices: 12252--12293 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
12242 CCTTTACAAA
12252 AAAAAACAAAAC
1 AAAAAA-AAAAC
12264 -AAAAAAAAAC
1 AAAAAAAAAAC
*
12274 AAAAAAAAACC
1 AAAAAAAAAAC
12285 AAGAAAAAA
1 AA-AAAAAA
12294 TAGCCAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 5 0.19
11 16 0.59
12 6 0.22
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:13562 original size:28 final size:29
Alignment explanation
Indices: 13520--14194 Score: 879
Period size: 28 Copynumber: 23.6 Consensus size: 29
13510 AATGTTCATC
* * *
13520 CTTTTCAAAGTCCACGAGTCAGTAGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
13548 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13577 GTTTTCAAAGCCCACAAATCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
13606 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13634 CCTTTCAAAGCCCACAAGTCAATGGCTACT
1 CTTTTCAAAGCCCACAAGTCAGTGGC-ACT
* *
13664 CATTTCAAAGCCCATAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
13693 GTTTTCAAAGCCCACAAATTAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13722 ATTTTTAAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
13750 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13779 CTTTTGAAAGCCCACAAGTTAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
13807 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
13835 CCTTTCAAAACCCACAAATCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
13864 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
13892 CCTTTCAAAACCCACAAATCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
13921 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13949 CCTTTCAAAGCCTACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13978 CTTTTCAAAGCCCACAAGTTAGTAGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
14006 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
14034 CCTTTCAAAACCCACAAGTTAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
14063 CTTTTCAAAGCCTACAAGTTAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
14091 ATTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
14119 CCTTTC-AAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
**
14147 CTTTTCAAAGCCCACACGAGTTGGTGGCAACT
1 CTTTTCAAAGCCCACA--AGTCAGTGGC-ACT
*
14179 CTTTTTAAAGCCCACA
1 CTTTTCAAAGCCCACA
14195 CAAGTTGGTG
Statistics
Matches: 568, Mismatches: 64, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
27 21 0.04
28 261 0.46
29 237 0.42
30 23 0.04
31 8 0.01
32 18 0.03
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (29 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:13640 original size:57 final size:58
Alignment explanation
Indices: 13520--14194 Score: 888
Period size: 57 Copynumber: 11.8 Consensus size: 58
13510 AATGTTCATC
* * *
13520 CTTTTCAAAGTCCACGAGTCAGTAGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
13577 GTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
13634 CCTTTCAAAGCCCACAAGTCAATGGCTACTCATTTCAAAGCCCATAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * ** *
13693 GTTTTCAAAGCCCACAAATTAGTGGCACTATTTTTAAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
13750 CTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTGAAAGCCCACAAGTTAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
13807 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAACCCACAAATCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13864 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAACCCACAAATCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
*
13921 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCTACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13978 CTTTTCAAAGCCCACAAGTTAGTAGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * * *
14034 CCTTTCAAAACCCACAAGTTAGTGGCACTCTTTTCAAAGCCTACAAGTTAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
*
14091 ATTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC-AAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
** * *
14147 CTTTTCAAAGCCCACACGAGTTGGTGGCAACTCTTTTTAAAGCCCACA
1 CTTTTCAAAGCCCACA--AGTCAGTGGC-ACTCCTTTCAAAGCCCACA
14195 CAAGTTGGTG
Statistics
Matches: 547, Mismatches: 58, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
55 19 0.03
56 66 0.12
57 335 0.61
58 91 0.17
59 23 0.04
60 4 0.01
61 9 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (58 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:13857 original size:85 final size:86
Alignment explanation
Indices: 13520--14194 Score: 864
Period size: 85 Copynumber: 7.8 Consensus size: 86
13510 AATGTTCATC
* * * *
13520 CTTTTCAAAGTCCACGAGTCAGTAGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTGTTTTCA
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCA
*
13584 AAGCCCACAAATCAGTGGCACT
65 AAGCCCACAAGTCAGTGGCACT
* *
13606 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAATGGCTACTCATTTC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGC-AC-CTTTTC
*
13670 AAAGCCCATAAGTCAGTGGCACT
64 AAAGCCCACAAGTCAGTGGCACT
* * * ** *
13693 GTTTTCAAAGCCCACAAATTAGTGGCACTATTTTTAAAGCCCACAAGTCAGTGGCACCTTTTCAA
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAA
13758 AGCCCACAAGTCAGTGGCACT
66 AGCCCACAAGTCAGTGGCACT
* * *
13779 CTTTTGAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAA
* *
13843 AACCCACAAATCAGTGGCACT
66 AGCCCACAAGTCAGTGGCACT
* *
13864 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAACCCACAAATCAGTGGCACTCTTTTCA
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCA
13928 AAGCCCACAAGTCAGTGGCAC-
65 AAGCCCACAAGTCAGTGGCACT
* * * * *
13949 CCTTTCAAAGCCTACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTAGCATCC-TTTCA
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCA
14013 AAGCCCACAAGTCAGTGGCAC-
65 AAGCCCACAAGTCAGTGGCACT
* * * * * * *
14034 CCTTTCAAAACCCACAAGTTAGTGGCACTCTTTTCAAAGCCTACAAGTTAGTGGCACATTTTCAA
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAA
14099 AGCCCACAAGTCAGTGGCAC-
66 AGCCCACAAGTCAGTGGCACT
* * **
14119 CCTTTC-AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTGGTGGCAACTCTTT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA--AGTCAGTGGC-AC-CTTT
*
14183 TTAAAGCCCACA
62 TCAAAGCCCACA
14195 CAAGTTGGTG
Statistics
Matches: 526, Mismatches: 52, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
84 36 0.07
85 238 0.45
86 158 0.30
87 58 0.11
88 36 0.07
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (86 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAA
AGCCCACAAGTCAGTGGCACT
Found at i:14216 original size:32 final size:32
Alignment explanation
Indices: 14130--14207 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
14120 CTTTCAAGCC
** *
14130 CACAAGTCAGTGGC-ACTCTTTTCAAAGCCCA
1 CACAAGTTGGTGGCAACTCTTTTTAAAGCCCA
*
14161 CACGAGTTGGTGGCAACTCTTTTTAAAGCCCA
1 CACAAGTTGGTGGCAACTCTTTTTAAAGCCCA
14193 CACAAGTTGGTGGCA
1 CACAAGTTGGTGGCA
14208 CCATTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 11 0.27
32 30 0.73
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (32 bp):
CACAAGTTGGTGGCAACTCTTTTTAAAGCCCA
Found at i:14802 original size:20 final size:20
Alignment explanation
Indices: 14771--14845 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
14761 TTTTACCCAG
*
14771 ATGTATCAATACATTTTTAA
1 ATGTATCGATACATTTTTAA
* * * *
14791 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTAA
* * * *
14811 ATGTATTGATATATTCTTCA
1 ATGTATCGATACATTTTTAA
14831 ATGTATCGATACATT
1 ATGTATCGATACATT
14846 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTAA
Found at i:16195 original size:79 final size:78
Alignment explanation
Indices: 16062--16259 Score: 236
Period size: 79 Copynumber: 2.5 Consensus size: 78
16052 AAGAACGGGG
** ** * *
16062 TTGGAGTATCCCCTTAAAAATAACGGGGTTGGAGTATCTCCGGTTATGAAAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATC-CCAATTACGAAAAATCAAT-ATTTAG
*
16126 GAAATAAAATCGAGA
64 GAAATAAAACCGAGA
* *
16141 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCTAATTACGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC-AATTACGAAAAATCAATATTTAGG
* * *
16206 AAATAAAGCCGGGG
65 AAATAAAACCGAGA
* *
16220 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCC
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
16260 CGACAAAATA
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
78 3 0.03
79 100 0.97
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (78 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCAATTACGAAAAATCAATATTTAGGA
AATAAAACCGAGA
Found at i:16255 original size:28 final size:28
Alignment explanation
Indices: 16215--16286 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
16205 GAAATAAAGC
* * *
16215 CGGGGTTGGAGTATCCCC-TCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAC-AAAATAA
16243 CGGGGTTGGAGTATCCCCGACAAAATAA
1 CGGGGTTGGAGTATCCCCGACAAAATAA
*
16271 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
16287 TCGATTGCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGACAAAATAA
Found at i:16345 original size:52 final size:51
Alignment explanation
Indices: 16269--16657 Score: 241
Period size: 51 Copynumber: 7.5 Consensus size: 51
16259 CCGACAAAAT
* * * *
16269 AACGAGGTTGGAGTATCCTCGATTGCGAAAAATTGGTGTTTTTGGAAATAAA
1 AACGGGGTTGGAGTATCCCCGATTGAGGAAAATTGGTG-TTTTGGAAATAAA
* ** * *
16321 ATCGAAGTTGGAGTATCCCTGATTGAAGGAAAATTGGTGTTTTGAAAATAAA
1 AACGGGGTTGGAGTATCCCCGATTG-AGGAAAATTGGTGTTTTGGAAATAAA
* **
16373 ACCGGGGTTGGAGTATCCCCGATT-ATGGAAAATCAGTGTTTTGGAAATAAA
1 AACGGGGTTGGAGTATCCCCGATTGA-GGAAAATTGGTGTTTTGGAAATAAA
* * *** *
16424 AACGGGGTTGGATTATCCCCGATTG-TGAGAAATCAATATTTTGGAAA-AAA
1 AACGGGGTTGGAGTATCCCCGATTGAGGA-AAATTGGTGTTTTGGAAATAAA
* * ** * * *****
16474 AGGCGGGGTTGGAGTATCCCC--TCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAA
1 A-ACGGGGTTGGAGTATCCCCGAT-TGAGG-AA---AATTGGTGTTTTGGAAAT-AAA
** ** * *
16530 TAACAAGGTTGGAGTATCCTTGATTGTGAAAAATTGGTGTTTTTGGAAATAAA
1 -AACGGGGTTGGAGTATCCCCGATTGAGGAAAATTGGTG-TTTTGGAAATAAA
* * * * *
16583 ATCGGAGTTGGAGTAT-CCCGATTAAAGGAAAATTTGTGTTTTGAAAATAAA
1 AACGGGGTTGGAGTATCCCCGATT-GAGGAAAATTGGTGTTTTGGAAATAAA
*
16634 ATCGGGGTTGGAGTATCCCCGATT
1 AACGGGGTTGGAGTATCCCCGATT
16658 ATGAAAAATT
Statistics
Matches: 253, Mismatches: 65, Indels: 38
0.71 0.18 0.11
Matches are distributed among these distances:
49 1 0.00
50 8 0.03
51 111 0.44
52 83 0.33
53 19 0.08
54 8 0.03
56 19 0.08
57 3 0.01
58 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.29
Consensus pattern (51 bp):
AACGGGGTTGGAGTATCCCCGATTGAGGAAAATTGGTGTTTTGGAAATAAA
Found at i:16533 original size:28 final size:28
Alignment explanation
Indices: 16477--16548 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
16467 GAAAAAAAGG
** **
16477 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
16505 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
16533 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
16549 TTGATTGTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:19021 original size:20 final size:20
Alignment explanation
Indices: 18996--19049 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
18986 AACTTCCTAG
18996 ATGTATCGATACATAGAAAA
1 ATGTATCGATACATAGAAAA
*
19016 ATGTATCGATACACAGAAAA
1 ATGTATCGATACATAGAAAA
19036 ATGTATCGATACAT
1 ATGTATCGATACAT
19050 TTCTTTGGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (20 bp):
ATGTATCGATACATAGAAAA
Found at i:19090 original size:13 final size:13
Alignment explanation
Indices: 19072--19123 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
19062 AGCTTCCTAG
19072 CGATACATTGTAT
1 CGATACATTGTAT
19085 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
19104 CGATACATTGTAT
1 CGATACATTGTAT
19117 CGATACA
1 CGATACA
19124 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:19104 original size:19 final size:19
Alignment explanation
Indices: 19080--19165 Score: 76
Period size: 19 Copynumber: 4.7 Consensus size: 19
19070 AGCGATACAT
19080 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
19099 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
19112 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
19131 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACT-TA
19152 TGTATCGATACAAA
1 TGTATCGATACAAA
19166 TTATTGGAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 11 0.20
14 1 0.02
16 2 0.04
18 1 0.02
19 23 0.43
20 3 0.06
21 13 0.24
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:19113 original size:32 final size:32
Alignment explanation
Indices: 19072--19144 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
19062 AGCTTCCTAG
19072 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
19104 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
19136 CGATACATT
1 CGATACATT
19145 TACTGAATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:22572 original size:79 final size:79
Alignment explanation
Indices: 22466--22656 Score: 247
Period size: 79 Copynumber: 2.4 Consensus size: 79
22456 AAAATCAATG
* *
22466 TTTTGGAAGTAAAATCGGAGTTGGAGTATCCTCTCAAAAATAACAGGGTTGGAATATCCCTAATT
1 TTTTGAAAATAAAATCGGAGTTGGAGTATCCTCTCAAAAATAACAGGGTTGGAATATCCCTAATT
22531 ATAGAAAATCGGTA
66 ATAGAAAATCGGTA
* * * ** * * *
22545 TTTTGAAACTAAAATCGGCGTTGGAGTATCCCCTCGGAAATAATAGGGTTGGAGTATCCCTGATT
1 TTTTGAAAATAAAATCGGAGTTGGAGTATCCTCTCAAAAATAACAGGGTTGGAATATCCCTAATT
* *
22610 ATAGAAAATTGGTG
66 ATAGAAAATCGGTA
* **
22624 CTTTGAAAATAAAATCAAAGTTGGAGTATCCTC
1 TTTTGAAAATAAAATCGGAGTTGGAGTATCCTC
22657 GATTGTGAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 95 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (79 bp):
TTTTGAAAATAAAATCGGAGTTGGAGTATCCTCTCAAAAATAACAGGGTTGGAATATCCCTAATT
ATAGAAAATCGGTA
Found at i:22786 original size:107 final size:107
Alignment explanation
Indices: 22643--22921 Score: 312
Period size: 107 Copynumber: 2.6 Consensus size: 107
22633 TAAAATCAAA
* * * *
22643 GTTGGAGTA-TCCTCGATTGTGAAAAATTGATATTTTAGAAAAAAAATTGGGGTTGGAGTATCCC
1 GTTGGAGTACCCCT-GATTGTGAAAAATTGATGTTTTAGAAATAAAATAGGGGTTGGAGTATCCC
* *
22707 CTCGAAAATAACGCGATTGGAATATC-CTCGATGACATAACGGG
65 CTCAAAAATAACGCGATTGGAATATCTC-CGATGAAATAACGGG
* * * **
22750 GTTGGAGTACCCCTGATTATGAAAAATTAATGTTTTAGATATAAAGCAGGGGTTGGAGTATCCCC
1 GTTGGAGTACCCCTGATTGTGAAAAATTGATGTTTTAGAAATAAAATAGGGGTTGGAGTATCCCC
* * * *
22815 TCAAAAATAATGGGGTTGGAGTATCTCCGATGAAATAACGGG
66 TCAAAAATAACGCGATTGGAATATCTCCGATGAAATAACGGG
* * * * * **
22857 GTTTGAGTATCCCC-AATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGAAGTTGGAGTATCCC
1 GTTGGAGTA-CCCCTGATTGTGAAAAATTGATGTTTTAGAAATAAAATAGGGGTTGGAGTATCCC
22921 C
65 C
22922 GATTAAGAAA
Statistics
Matches: 142, Mismatches: 27, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
107 134 0.94
108 8 0.06
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (107 bp):
GTTGGAGTACCCCTGATTGTGAAAAATTGATGTTTTAGAAATAAAATAGGGGTTGGAGTATCCCC
TCAAAAATAACGCGATTGGAATATCTCCGATGAAATAACGGG
Found at i:22838 original size:28 final size:28
Alignment explanation
Indices: 22798--22870 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
22788 ATATAAAGCA
*
22798 GGGGTTGGAGTATCCCCTCA-AAAATAAT
1 GGGGTTGGAGTATCCCC-CATAAAATAAC
* * *
22826 GGGGTTGGAGTATCTCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCCATAAAATAAC
*
22854 GGGGTTTGAGTATCCCC
1 GGGGTTGGAGTATCCCC
22871 AATTGTGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCCATAAAATAAC
Found at i:25309 original size:20 final size:20
Alignment explanation
Indices: 25286--25373 Score: 118
Period size: 20 Copynumber: 4.8 Consensus size: 20
25276 TATATTGTAA
25286 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGC
25306 AATGTATCG-----AT-A-C
1 AATGTATCGATACAATGAGC
25319 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGC
*
25339 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAGC
25359 AATGTATCGATACAA
1 AATGTATCGATACAA
25374 ATTGTGAAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
13 10 0.17
14 1 0.02
15 2 0.03
18 2 0.03
19 1 0.02
20 44 0.73
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGAGC
Found at i:25328 original size:33 final size:33
Alignment explanation
Indices: 25286--25355 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
25276 TATATTGTAA
25286 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
25319 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
25352 AATG
1 AATG
25356 AACAATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:25328 original size:53 final size:53
Alignment explanation
Indices: 25266--25373 Score: 164
Period size: 53 Copynumber: 2.0 Consensus size: 53
25256 AAAATGCCTG
* * *
25266 AATGTATCGATATATTGTA-AAATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATG-AGAAATGTATCGATACAATGAACAATGTATCGATAC
*
25319 AATGTATCGATACAATGAGCAATGTATCGATACAATGAACAATGTATCGATAC
1 AATGTATCGATACAATGAGAAATGTATCGATACAATGAACAATGTATCGATAC
25372 AA
1 AA
25374 ATTGTGAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.02
53 49 0.98
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.29
Consensus pattern (53 bp):
AATGTATCGATACAATGAGAAATGTATCGATACAATGAACAATGTATCGATAC
Found at i:25354 original size:13 final size:13
Alignment explanation
Indices: 25305--25335 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
25295 ATACAATGAG
25305 CAATGTATCGATA
1 CAATGTATCGATA
25318 CAATGTATCGATA
1 CAATGTATCGATA
25331 CAATG
1 CAATG
25336 AGCAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Done.