Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2309
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: 135274
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 2 of 2
Found at i:127206 original size:20 final size:20
Alignment explanation
Indices: 127183--127245 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
127173 CAACAGCAAT
*
127183 AAGCAAACAGCGAAAACAGC
1 AAGCAAACAGCGAAAACAAC
127203 AAGCAAAC-G-G----CAAC
1 AAGCAAACAGCGAAAACAAC
*
127217 AAGCAAACAGCAAAAACAAC
1 AAGCAAACAGCGAAAACAAC
127237 AAGCAAACA
1 AAGCAAACA
127246 CCAGCAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
18 1 0.03
19 1 0.03
20 21 0.60
ACGTcount: A:0.59, C:0.25, G:0.16, T:0.00
Consensus pattern (20 bp):
AAGCAAACAGCGAAAACAAC
Found at i:127221 original size:14 final size:14
Alignment explanation
Indices: 127202--127262 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 14
127192 GCGAAAACAG
*
127202 CAAGCAAACGGCAA
1 CAAGCAAACAGCAA
127216 CAAGCAAACAGCAA
1 CAAGCAAACAGCAA
*
127230 -AAAC-AACAAGCAAA
1 CAAGCAAAC-AGC-AA
127244 CACCAGCAAACAGCAA
1 CA--AGCAAACAGCAA
127260 CAA
1 CAA
127263 AAAAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
12 3 0.08
13 6 0.16
14 16 0.42
15 1 0.03
16 4 0.11
17 5 0.13
18 3 0.08
ACGTcount: A:0.57, C:0.30, G:0.13, T:0.00
Consensus pattern (14 bp):
CAAGCAAACAGCAA
Found at i:127223 original size:34 final size:34
Alignment explanation
Indices: 127178--127244 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
127168 GCAAACAACA
* * *
127178 GCAATAAGCAAACAGCGAAAACAGCAAGCAAACG
1 GCAACAAGCAAACAGCAAAAACAACAAGCAAACG
127212 GCAACAAGCAAACAGCAAAAACAACAAGCAAAC
1 GCAACAAGCAAACAGCAAAAACAACAAGCAAAC
127245 ACCAGCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.57, C:0.25, G:0.16, T:0.01
Consensus pattern (34 bp):
GCAACAAGCAAACAGCAAAAACAACAAGCAAACG
Found at i:127263 original size:20 final size:20
Alignment explanation
Indices: 127184--127263 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 20
127174 AACAGCAATA
* *
127184 AGCAAACAGCGA-AAACAGCA
1 AGCAAACAGCAACAAACA-CC
* * *
127204 AGCAAACGGCAACAAGCAAAC
1 AGCAAACAGCAACAAAC-ACC
*
127225 AGCAAAAACAACAAGCAAACACC
1 AGC--AAACAGCAA-CAAACACC
127248 AGCAAACAGCAACAAA
1 AGCAAACAGCAACAAA
127264 AAAAAAAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
20 14 0.31
21 14 0.31
22 1 0.02
23 12 0.27
24 4 0.09
ACGTcount: A:0.57, C:0.28, G:0.15, T:0.00
Consensus pattern (20 bp):
AGCAAACAGCAACAAACACC
Found at i:130617 original size:48 final size:49
Alignment explanation
Indices: 130501--130628 Score: 161
Period size: 49 Copynumber: 2.6 Consensus size: 49
130491 GAGAGGAGTG
* * ** *
130501 CCAATGTGCCAATTCAAGGCCAACGACATTGGGTTAAGGGAAAAGTAGA
1 CCAATGTGCTAATTCAAGGCCAGCGACATTGGGCCAAGGAAAAAGTAGA
* *
130550 CCAATGTGCTAATTTAAGGCCAGCGACATTGGGCC-AGAGAAAAAGTGGA
1 CCAATGTGCTAATTCAAGGCCAGCGACATTGGGCCAAG-GAAAAAGTAGA
*
130599 -CAATGTGCTGATTCAAGGCCAGCGACATTG
1 CCAATGTGCTAATTCAAGGCCAGCGACATTG
130629 AACTAATAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 30 0.43
49 39 0.57
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (49 bp):
CCAATGTGCTAATTCAAGGCCAGCGACATTGGGCCAAGGAAAAAGTAGA
Found at i:130789 original size:28 final size:28
Alignment explanation
Indices: 130758--131499 Score: 604
Period size: 28 Copynumber: 25.4 Consensus size: 28
130748 CACTAACTTA
* * *
130758 TGTGGGCTTTGAAAGGATACTATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
130786 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
130814 TGTGGGCTTTAAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
130842 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
130870 TGTAGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
130898 TGTGAGTTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
130926 TGTGAGCTTTAAAAAGATGCCACTAATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
130954 TGTGTAAGCTTTGAGAAGGATGCCACTGACT
1 TGTG--GGCTTTGA-AAGGATGCCACTGACT
* * * *
130985 TATGGGCTTTAAGAAGGATACCATTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
* *
131014 TATGGACTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
*
131043 TGTGGGCTATGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
131071 TGTAGACTTTGAAATGGGTTGCCACCGACTT
1 TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* *
131102 GTGTGGGCTTTGAAATGATTTGCCACCGACT
1 -TGTGGGCTTTGAAAGGA--TGCCACTGACT
* * * * **
131133 TGAGTAGCCTTTCAAATGGGTTGCCACCAACTT
1 T--GTGGGCTTTGAAA--GGATGCCACTGAC-T
*
131166 GTGTGGGCTTTAAAAAGGATGCCACTGACT
1 -TGTGGGCTTT-GAAAGGATGCCACTGACT
**
131196 TGTACGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
* *
131225 TATGGGCTTTGAGAAGGATGCCATTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
*
131254 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
131282 TATAGGCTTTGAAATGAGTTGCCACCGACTT
1 TGTGGGCTTTGAAA-G-GATGCCACTGAC-T
* * *
131313 CTCTGGGCTTTGAAATGGGTTGCCACCGACTT
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* * * *
131345 GTGTGGGCTTTCAAATTAGTTGCCACCGACTT
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* *
131377 GTGTGGGCTTTGAAATGATGCCACCGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
131406 TATGGGCTTTGAAATGATGCTACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
131434 TGTGGGGTTT-AAATGGATGCCACTGACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
* * **
131462 TGTGGGCCTTGAAATGATGCCACCAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
131490 TGTGGACTTT
1 TGTGGGCTTT
131500 AAAAAGGTGC
Statistics
Matches: 597, Mismatches: 93, Indels: 48
0.81 0.13 0.07
Matches are distributed among these distances:
27 3 0.01
28 282 0.47
29 119 0.20
30 42 0.07
31 29 0.05
32 115 0.19
33 5 0.01
34 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:130999 original size:29 final size:28
Alignment explanation
Indices: 130758--131785 Score: 537
Period size: 28 Copynumber: 35.8 Consensus size: 28
130748 CACTAACTTA
* * * *
130758 TGTGGGCTTTGAAAGGATACTATTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
130786 TGTGGGCTTTGAAAA-GATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
130814 TGTGGGCTTTAAAAAGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
130842 TGTGGGCTTTGAAAA-GATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
130870 TGTAGGCTTTGAAAA-GATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
130898 TGTGAGTTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
130926 TGTGAGCTTTAAAAAGATGCCACTAATT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
130954 TGTGTAAGCTTTGAGAAGGATGCCACTGACT
1 TGTG--GGCTTT-AAAAGGATGCCACTGACT
* * *
130985 TATGGGCTTTAAGAAGGATACCATTGACT
1 TGTGGGCTTTAA-AAGGATGCCACTGACT
* * *
131014 TATGGACTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* *
131043 TGTGGGCTATGAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * * *
131071 TGTAGACTTTGAAATGGGTTGCCACCGACTT
1 TGTGGGCTTT-AAA-AGGATGCCACTGAC-T
* * *
131102 GTGTGGGCTTTGAAATGATTTGCCACCGACT
1 -TGTGGGCTTTAAAAGGA--TGCCACTGACT
* * * * **
131133 TGAGTAGCCTTTCAAATGGGTTGCCACCAACTT
1 T--GTGGGCTTT-AAA-AGGATGCCACTGAC-T
131166 GTGTGGGCTTTAAAAAGGATGCCACTGACT
1 -TGTGGGCTTT-AAAAGGATGCCACTGACT
** *
131196 TGTACGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
131225 TATGGGCTTTGAGAAGGATGCCATTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
131254 TGTGGGCTTTGAAAA-GATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * * * *
131282 TATAGGCTTTGAAATGAGTTGCCACCGACTT
1 TGTGGGCTTT-AAAAG-GATGCCACTGAC-T
* * * *
131313 CTCTGGGCTTTGAAATGGGTTGCCACCGACTT
1 -TGTGGGCTTT-AAA-AGGATGCCACTGAC-T
* *
131345 GTGTGGGCTTTCAAATTA-GTTGCCACCGACTT
1 -TGTGGGCTTT-AAA--AGGATGCCACTGAC-T
* * *
131377 GTGTGGGCTTTGAAATGATGCCACCGACT
1 -TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
131406 TATGGGCTTTGAAATGATGCTACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
131434 TGTGGGGTTTAAATGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * **
131462 TGTGGGCCTTGAAATGATGCCACCAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
131490 TGTGGACTTTAAAAAGG-TGCTGTCACGGAGT
1 TGTGGGCTTT-AAAAGGATGC---CACTGACT
* * * *
131521 TGTTGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
** * * *
131548 TGT-GAATTTAAAAGGATGTCACAGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
*
131575 TGTGGACTTT-AAAGGATGCCAC-GA--
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
131599 AGTTGACTTT-AAAGGATGCCAC-GAAGT
1 TGTGGGCTTTAAAAGGATGCCACTG-ACT
* * * * *
131626 TGTTGACTTAAAAAGG-TGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
** * * *
131653 TGTGGATTTTAAAA-AAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGA-TGCCACTGACT
* * * *
131681 TGTGGACTTT-AAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * ** * *
131708 TGTAGAC-TTAAAATAATGCCACAGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
131735 TGTGGACTTTAAAAAGG-TGCCACGGAAT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* *
131763 TATGGACTTTAAAAGGATGCCAC
1 TGTGGGCTTTAAAAGGATGCCAC
131786 GGAATTATGT
Statistics
Matches: 818, Mismatches: 135, Indels: 94
0.78 0.13 0.09
Matches are distributed among these distances:
24 21 0.03
25 1 0.00
26 6 0.01
27 123 0.15
28 324 0.40
29 137 0.17
30 47 0.06
31 45 0.06
32 107 0.13
33 5 0.01
34 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTAAAAGGATGCCACTGACT
Found at i:131242 original size:211 final size:205
Alignment explanation
Indices: 130699--131499 Score: 828
Period size: 211 Copynumber: 3.9 Consensus size: 205
130689 AAAGTGGTGA
* * * * * *
130699 TTTGAAAAGAGTTGCCATCGACTTGTGTGAGCTTTTAAAAAAAAAG-TGCCACTAACTTATGTGG
1 TTTGAAATGA-TTGCCACCGACTTGTGT-AGC-TTT--CAAATAAGTTGCCACCAACTTGTGTGG
* * * * * * * *
130763 GCTTTGAAAGGATACTATTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTAAAA
61 GCTTTAAAAGGATGCCACTGACTTATGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTAGAA
* * *
130828 AGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTAGGCTTTGAAA--AGATGCC
126 GGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTAGACTTTGAAATGAGTTGCC
* * *
130891 ACTGAC-TTGTGAGT
191 ACCGACTTTGTGGGC
* * * * * **
130905 TTTGAAAGGA-TGCCACTGACTTGTG-AGCTTT-AAA-AAGATGCCACTAATTTGTGTAAGCTTT
1 TTTGAAATGATTGCCACCGACTTGTGTAGCTTTCAAATAAGTTGCCACCAACTTGTGTGGGCTTT
* * * * *
130966 GAGAAGGATGCCACTGACTTATGGGCTTTAAGAAGGATACCATTGACTTATGGACTTTGAGAAGG
66 -AAAAGGATGCCACTGACTTATGGGCTTTGA-AAGGATGCCACTGACTTATGGGCTTT-AGAAGG
* * *
131031 ATGCCACTGACTTGTGGGCTATGAAAGGATGCCACTGACTTGTAGACTTTGAAATGGGTTGCCAC
128 ATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTAGACTTTGAAATGAGTTGCCAC
131096 CGACTTGTGTGGGC
193 CGACTT-TGTGGGC
* **
131110 TTTGAAATGATTTGCCACCGACTTGAGTAGCCTTTCAAATGGGTTGCCACCAACTTGTGTGGGCT
1 TTTGAAATGA-TTGCCACCGACTTGTGTAG-CTTTCAAATAAGTTGCCACCAACTTGTGTGGGCT
* **
131175 TTAAAAAGGATGCCACTGACTTGTACGCTTTGAGAAGGATGCCACTGACTTATGGGCTTTGAGAA
64 TT-AAAAGGATGCCACTGACTTATGGGCTTTGA-AAGGATGCCACTGACTTATGGGCTTT-AGAA
* * *
131240 GGATGCCATTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTATAGGCTTTGAAATGAGTTGCC
126 GGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTAGACTTTGAAATGAGTTGCC
*
131305 ACCGACTTCTCTGGGC
191 ACCGACTT-TGTGGGC
* * * *
131321 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAATTAGTTGCCACCGACTTGTGTGGGCT
1 TTTGAAAT-GATTGCCACCGACTTGTGT-AGCTTTCAAATAAGTTGCCACCAACTTGTGTGGGCT
* * * * * * *
131386 TTGAAATGATGCCACCGACTTATGGGCTTTGAAATGATGCTACTGACTTGTGGGGTTTA-AATGG
64 TTAAAAGGATGCCACTGACTTATGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTAGAA-GG
* * ** *
131450 ATGCCACTGACTTGTGGGCCTTGAAATGATGCCACCAACTTGTGGACTTT
128 ATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTAGACTTT
131500 AAAAAGGTGC
Statistics
Matches: 498, Mismatches: 80, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
197 3 0.01
198 22 0.04
199 23 0.05
200 21 0.04
201 58 0.12
202 3 0.01
203 10 0.02
204 14 0.03
205 14 0.03
206 9 0.02
207 15 0.03
208 47 0.09
209 26 0.05
210 27 0.05
211 204 0.41
212 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (205 bp):
TTTGAAATGATTGCCACCGACTTGTGTAGCTTTCAAATAAGTTGCCACCAACTTGTGTGGGCTTT
AAAAGGATGCCACTGACTTATGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTAGAAGGATG
CCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTAGACTTTGAAATGAGTTGCCACCGA
CTTTGTGGGC
Found at i:131545 original size:27 final size:27
Alignment explanation
Indices: 131442--131826 Score: 298
Period size: 27 Copynumber: 14.1 Consensus size: 27
131432 CTTGTGGGGT
* * * *
131442 TTAAATGGATGCCACTGACTTGTGGGCC
1 TTAAAAGGATGCCACGGAGTTGT-GGAC
* * ** *
131470 TTGAAATGATGCCACCAACTTGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
*
131497 TTTAAAAAGG-TGCTGTCACGGAGTTGTTGAC
1 -TT-AAAAGGATGC---CACGGAGTTGTGGAC
* *
131528 TTAAAAGGATGCCACGGAGTTGTGAAT
1 TTAAAAGGATGCCACGGAGTTGTGGAC
* *
131555 TTAAAAGGATGTCACAGAGTTGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
* *
131582 TTTAAAGGATGCCACGAAG-T-T-GAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
* * *
131606 TTTAAAGGATGCCACGAAGTTGTTGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
*
131633 TTAAAAAGG-TGCCACGGAGTTGTGGATT
1 TT-AAAAGGATGCCACGGAGTTGTGGA-C
*
131661 TTAAAA-AAGTGCCACGGAGTTGTGGAC
1 TTAAAAGGA-TGCCACGGAGTTGTGGAC
* * *
131688 TTTAAAGGGTGCCACGGAGTTGTAGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
** *
131715 TTAAAATAATGCCACAGAGTTGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
* *
131742 TTTAAAAAGG-TGCCACGGAATTATGGAC
1 -TT-AAAAGGATGCCACGGAGTTGTGGAC
* * *
131770 TTTAAAAGGATGCCACGGAATTATGTAC
1 -TTAAAAGGATGCCACGGAGTTGTGGAC
* * *
131798 TTAAAAGGATACCACGGAATCGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
131825 TT
1 TT
131827 TGAAAAAAAA
Statistics
Matches: 291, Mismatches: 49, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
24 22 0.08
25 2 0.01
26 2 0.01
27 151 0.52
28 84 0.29
29 14 0.05
30 5 0.02
31 11 0.04
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (27 bp):
TTAAAAGGATGCCACGGAGTTGTGGAC
Found at i:131689 original size:55 final size:55
Alignment explanation
Indices: 131489--131834 Score: 291
Period size: 55 Copynumber: 6.3 Consensus size: 55
131479 TGCCACCAAC
* *
131489 TTGTGGACTTTAAAAAGGTGCTGTCACGGAGTTGTTGACTTAAAAGGATGCCACGGAG
1 TTGTGGACTTTAAAAAAGTGC---CACGGAGTTGTGGACTTAAAAGGATGCCACGGAG
* * * * * *
131547 TTGT-GAATTT-AAAAGGATGTCACAGAGTTGTGGACTTTAAAGGATGCCACGAAG
1 TTGTGGACTTTAAAAAAG-TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAG
** * *
131601 -T-T-GACTTTAAAGGA-TGCCACGAAGTTGTTGACTTAAAAAGG-TGCCACGGAG
1 TTGTGGACTTTAAAAAAGTGCCACGGAGTTGTGGACTT-AAAAGGATGCCACGGAG
* * *
131652 TTGTGGATTTTAAAAAAGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAG
1 TTGTGGACTTTAAAAAAGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAG
* * *
131707 TTGTAGAC-TTAAAATAA-TGCCACAGAGTTGTGGACTTTAAAAAGG-TGCCACGGAA
1 TTGTGGACTTTAAAA-AAGTGCCACGGAGTTGTGGAC-TT-AAAAGGATGCCACGGAG
* * * * * * *
131762 TTATGGACTTT-AAAAGGATGCCACGGAATTATGTACTTAAAAGGATACCACGGAA
1 TTGTGGACTTTAAAAAAG-TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAG
*
131817 TCGTGGACTTTGAAAAAA
1 TTGTGGACTTT-AAAAAA
131835 AATGCCACTG
Statistics
Matches: 233, Mismatches: 38, Indels: 35
0.76 0.12 0.11
Matches are distributed among these distances:
51 25 0.11
52 12 0.05
53 4 0.02
54 74 0.32
55 76 0.33
56 27 0.12
57 11 0.05
58 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (55 bp):
TTGTGGACTTTAAAAAAGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAG
Found at i:131709 original size:82 final size:82
Alignment explanation
Indices: 131489--131788 Score: 342
Period size: 82 Copynumber: 3.7 Consensus size: 82
131479 TGCCACCAAC
* * *
131489 TTGTGGACTTTAAAAAGGTGCTGTCACGGAGTTGTTGACTTAAAAGGATGCCACGGAGTTG-TGA
1 TTGTGGACTTTAAAAAAGTGC---CACGGAGTTGTGGACTTTAAAGGATGCCACGGAGTTGTTGA
* * *
131553 ATTTAAAAGGATGTCACAGAG
63 CTTAAAAAGG-TGCCACAGAG
** * *
131574 TTGTGGACTTTAAAGGA-TGCCACGAAG-T-T-GACTTTAAAGGATGCCACGAAGTTGTTGACTT
1 TTGTGGACTTTAAAAAAGTGCCACGGAGTTGTGGACTTTAAAGGATGCCACGGAGTTGTTGACTT
*
131635 AAAAAGGTGCCACGGAG
66 AAAAAGGTGCCACAGAG
* * *
131652 TTGTGGATTTTAAAAAAGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTAGACTT
1 TTGTGGACTTTAAAAAAGTGCCACGGAGTTGTGGACTTTAAAGGATGCCACGGAGTTGTTGACTT
*
131717 AAAATA-ATGCCACAGAG
66 AAAA-AGGTGCCACAGAG
* * *
131734 TTGTGGACTTTAAAAAGGTGCCACGGAATTATGGACTTTAAAAGGATGCCACGGA
1 TTGTGGACTTTAAAAAAGTGCCACGGAGTTGTGGACTTT-AAAGGATGCCACGGA
131789 ATTATGTACT
Statistics
Matches: 184, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
78 45 0.24
79 21 0.11
80 2 0.01
81 7 0.04
82 77 0.42
83 15 0.08
84 3 0.02
85 14 0.08
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (82 bp):
TTGTGGACTTTAAAAAAGTGCCACGGAGTTGTGGACTTTAAAGGATGCCACGGAGTTGTTGACTT
AAAAAGGTGCCACAGAG
Found at i:131789 original size:28 final size:28
Alignment explanation
Indices: 131378--131832 Score: 326
Period size: 28 Copynumber: 16.5 Consensus size: 28
131368 CACCGACTTG
* * * * *
131378 TGTGGGCTTTGAAATGATGCCACCGACT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* * * * * * *
131406 TATGGGCTTTGAAATGATGCTACTGACT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
** * * *
131434 TGTGGGGTTTAAATGGATGCCACTGACT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* * * * ** *
131462 TGTGGGCCTTGAAATGATGCCACCAACT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
131490 TGTGGACTTTAAAAAGG-TGCTGTCACGGAGT
1 TGTGGACTTT-AAAAGGATGC---CACGGAGT
*
131521 TGTTGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* * *
131548 TGT-GAATTTAAAAGGATGTCACAGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
131575 TGTGGACTTT-AAAGGATGCCACGAAG-
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
131601 T-T-GACTTT-AAAGGATGCCACGAAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* *
131626 TGTTGACTTAAAAAGG-TGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* *
131653 TGTGGATTTTAAAA-AAGTGCCACGGAGT
1 TGTGGACTTTAAAAGGA-TGCCACGGAGT
*
131681 TGTGGACTTT-AAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* ** *
131708 TGTAGAC-TTAAAATAATGCCACAGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
131735 TGTGGACTTTAAAAAGG-TGCCACGGAAT
1 TGTGGACTTT-AAAAGGATGCCACGGAGT
* *
131763 TATGGACTTTAAAAGGATGCCACGGAAT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* * * *
131791 TATGTAC-TTAAAAGGATACCACGGAAT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
131818 CGTGGACTTTGAAAA
1 TGTGGACTTT-AAAA
131833 AAAATGCCAC
Statistics
Matches: 351, Mismatches: 56, Indels: 39
0.79 0.13 0.09
Matches are distributed among these distances:
24 22 0.06
25 2 0.01
26 6 0.02
27 139 0.40
28 148 0.42
29 18 0.05
30 5 0.01
31 11 0.03
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (28 bp):
TGTGGACTTTAAAAGGATGCCACGGAGT
Found at i:131848 original size:30 final size:30
Alignment explanation
Indices: 131809--131890 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
131799 TAAAAGGATA
*
131809 CCACGGAATCGTGGACTTTGAAAAAAAATG
1 CCACTGAATCGTGGACTTTGAAAAAAAATG
* *
131839 CCACTGAATCGTGAACTTTGAAAAGAAATG
1 CCACTGAATCGTGGACTTTGAAAAAAAATG
*
131869 CCACTAAATCGTGGACTTTGAA
1 CCACTGAATCGTGGACTTTGAA
131891 GAGGTCACAG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (30 bp):
CCACTGAATCGTGGACTTTGAAAAAAAATG
Found at i:133187 original size:25 final size:25
Alignment explanation
Indices: 133148--133196 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
133138 TGTTGTTCTC
133148 TTTTTATTTTGCTTTTGCACATTTTT
1 TTTTTATTTTGCTTTT-CACATTTTT
* *
133174 TTTTTGTTTT-CTTTTCATATTTT
1 TTTTTATTTTGCTTTTCACATTTT
133197 GTACTTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 5 0.24
26 9 0.43
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.73
Consensus pattern (25 bp):
TTTTTATTTTGCTTTTCACATTTTT
Done.