Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1991
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: 47235
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:8908 original size:101 final size:103
Alignment explanation
Indices: 8740--8993 Score: 374
Period size: 103 Copynumber: 2.4 Consensus size: 103
8730 GGGGTTCTGT
8740 GTGCTGATTCCCCGATTCATTGGTG-GTCTACATGTGCG-TGATCCACCATATCTTGAAATGTGA
1 GTGCTGATTCCCCGATTCATTGGTGTG-CTA-A-GTGCGAT-ATCCACCATATCTTGAAATGTGA
8803 AAAGGGGGTTGCTA-TGCTGATTCCCCCGAGGGG-TTGCTAA
62 AAAGGGGGTTGCTAGTGCTGATTCCCCCGAGGGGTTTGCTAA
*
8843 GTGCTGATTCCCCGGTTCATTGGTGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTG-AAA
1 GTGCTGATTCCCCGATTCATTGGTGTGCTAAGTGCGATATCCACCATATC-TTGAAATGTGAAAA
8907 GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTTGCTAA
65 GGGGGTTGCTA-GTGCTGATTCCCCCGAGGGGTTTGCTAA
** *
8947 GTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 GTGCTGATTCCCCGATTCATTGGT-GTGCTAAGTGCGATATCCACCA
8994 ATAACGTTAA
Statistics
Matches: 139, Mismatches: 5, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
101 31 0.22
102 12 0.09
103 46 0.33
104 29 0.21
105 21 0.15
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.30
Consensus pattern (103 bp):
GTGCTGATTCCCCGATTCATTGGTGTGCTAAGTGCGATATCCACCATATCTTGAAATGTGAAAAG
GGGGTTGCTAGTGCTGATTCCCCCGAGGGGTTTGCTAA
Found at i:8961 original size:27 final size:28
Alignment explanation
Indices: 8906--8959 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
8896 GAAATGTGAA
*
8906 AGGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGGTTGCTAAGTGCTGATTCCCCCG
*
8934 AGGGGTTTGCTAAGTGCTGATTCCCC
1 AGGGGGTTGCTAAGTGCTGATTCCCC
8960 GATTCAGCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.13, C:0.24, G:0.33, T:0.30
Consensus pattern (28 bp):
AGGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:16249 original size:104 final size:104
Alignment explanation
Indices: 16069--16335 Score: 455
Period size: 104 Copynumber: 2.6 Consensus size: 104
16059 TTGTATATAA
** *
16069 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
16133 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
16173 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
16238 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
** *
16277 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
16336 ATAACGGTTA
Statistics
Matches: 154, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
104 153 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:26533 original size:39 final size:39
Alignment explanation
Indices: 26490--26635 Score: 220
Period size: 39 Copynumber: 3.7 Consensus size: 39
26480 AACATGTTTT
*
26490 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
26529 TGAGTAGTGTGATATATACTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
26568 TGAGTATTGTGATATATGCTTAAATGTTATATGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * * *
26607 TGTGTAATGTGATATACGCTTAAAAGTTA
1 TGAGTATTGTGATATATGCTTAAATGTTA
26636 ATATCATTAC
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 97 1.00
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:26541 original size:17 final size:16
Alignment explanation
Indices: 26517--26585 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 16
26507 GCTTGAATGT
26517 TATGTGATTATATGAG
1 TATGTGATTATATGAG
*
26533 TAGTGTGATATATACTTAAATG
1 TA-TGTGAT-TATA--T-GA-G
26555 TTATGTGATTATATGAG
1 -TATGTGATTATATGAG
26572 TATTGTGA-TATATG
1 TA-TGTGATTATATG
26586 CTTAAATGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
16 10 0.23
17 12 0.28
18 5 0.12
19 1 0.02
20 1 0.02
21 5 0.12
22 7 0.16
23 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (16 bp):
TATGTGATTATATGAG
Found at i:30032 original size:26 final size:26
Alignment explanation
Indices: 29996--30047 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
29986 GGATCTAGCC
29996 TGTTTCTTAGGTCATTGAGCAGAGCT
1 TGTTTCTTAGGTCATTGAGCAGAGCT
30022 TGTTTCTTAGGTCATTGAGCAGAGCT
1 TGTTTCTTAGGTCATTGAGCAGAGCT
30048 AGAGGGCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.38
Consensus pattern (26 bp):
TGTTTCTTAGGTCATTGAGCAGAGCT
Found at i:33443 original size:17 final size:16
Alignment explanation
Indices: 33408--33460 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
33398 TTTAATTAAT
* *
33408 TTTTTTAAAAATGTGA
1 TTTTTTAAAAATATTA
33424 TTTTTTAATAAATATTA
1 TTTTTTAA-AAATATTA
* *
33441 -TTTATAAAATTATTA
1 TTTTTTAAAAATATTA
33456 TTTTT
1 TTTTT
33461 CACTCGTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 7 0.23
16 17 0.57
17 6 0.20
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
TTTTTTAAAAATATTA
Found at i:35689 original size:39 final size:39
Alignment explanation
Indices: 35646--35782 Score: 134
Period size: 39 Copynumber: 3.5 Consensus size: 39
35636 TATTACAGTT
35646 TATAACAAGATCTAGCATTTGTTGTAGATCCTTAGGTAA
1 TATAACAAGATCTAGCATTTGTTGTAGATCCTTAGGTAA
* * * * *
35685 TATAACGAA-ATGTAACATTTGCTGCAGATCC-TCGAGTAA
1 TATAAC-AAGATCTAGCATTTGTTGTAGATCCTTAG-GTAA
* * * **
35724 TATAATAAGATCTAGCATTTGTTGTAAATCATCGGGTAA
1 TATAACAAGATCTAGCATTTGTTGTAGATCCTTAGGTAA
**
35763 TATAATGAGATCTAGCATTT
1 TATAACAAGATCTAGCATTT
35783 TTCACAGATT
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 4 0.05
39 72 0.91
40 3 0.04
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (39 bp):
TATAACAAGATCTAGCATTTGTTGTAGATCCTTAGGTAA
Found at i:35791 original size:78 final size:78
Alignment explanation
Indices: 35646--35805 Score: 178
Period size: 78 Copynumber: 2.1 Consensus size: 78
35636 TATTACAGTT
* * * * *
35646 TATAACAAGATCTAGCATTTGTTGTAGATCCTTAGGTAATATAACGAAATGTAACATTTGCTGCA
1 TATAACAAGATCTAGCATTTGTTGTAAATCATCAGGTAATATAACGAAATCTAACATTTGCTACA
*
35711 GATCCTCGAGTAA
66 GATCCTCGAGCAA
* * * * * *
35724 TATAATAAGATCTAGCATTTGTTGTAAATCATCGGGTAATATAATGAGATCTAGCATTT-TTCAC
1 TATAACAAGATCTAGCATTTGTTGTAAATCATCAGGTAATATAACGAAATCTAACATTTGCT-AC
* *
35788 AGATTCTTGAGCAA
65 AGATCCTCGAGCAA
35802 TATA
1 TATA
35806 TGATATAGGT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
77 1 0.01
78 66 0.99
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (78 bp):
TATAACAAGATCTAGCATTTGTTGTAAATCATCAGGTAATATAACGAAATCTAACATTTGCTACA
GATCCTCGAGCAA
Found at i:37142 original size:37 final size:37
Alignment explanation
Indices: 37092--37170 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
37082 TTATTACGAA
* * *
37092 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
37129 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
37166 GTCTT
1 GTCTT
37171 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:37367 original size:47 final size:47
Alignment explanation
Indices: 37289--37950 Score: 1137
Period size: 47 Copynumber: 13.9 Consensus size: 47
37279 CCCTTCGGGA
* * * * * *
37289 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
37336 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
37382 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
37429 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
37476 CTTATCACATATATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
37525 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
37572 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
37621 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
37668 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
37715 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
37762 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
37811 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
37858 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
37907 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
37951 CGCCATACTA
Statistics
Matches: 588, Mismatches: 18, Indels: 18
0.94 0.03 0.03
Matches are distributed among these distances:
46 44 0.07
47 360 0.61
49 184 0.31
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:37528 original size:96 final size:96
Alignment explanation
Indices: 37289--37950 Score: 1176
Period size: 96 Copynumber: 7.0 Consensus size: 96
37279 CCCTTCGGGA
* * * * * * *
37289 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
37352 ACTTTCACATTCATCACATCGGCCATTAGG-
66 ACTTTCACATTCATCACATCGGCCATTAGGC
37382 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
37445 ACTTTCATATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
37476 CTTATCACATATATATATACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
37541 ACTTTCATATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
37572 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
37637 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
37668 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
37731 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
37762 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
37827 ACTTTCATATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
37858 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
37923 ACTTTCACATTCATCACATCGGCCATTA
66 ACTTTCACATTCATCACATCGGCCATTA
37951 CGCCATACTA
Statistics
Matches: 549, Mismatches: 13, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
92 1 0.00
93 82 0.15
94 102 0.19
96 364 0.66
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:37569 original size:143 final size:141
Alignment explanation
Indices: 37289--37950 Score: 1137
Period size: 143 Copynumber: 4.6 Consensus size: 141
37279 CCCTTCGGGA
* * * * * * * *
37289 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
37354 TTTCACATTCATCACATCGGCCATTAGG-CTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
37418 GGCCATTAGGC
131 GGCCATTAGGC
* *
37429 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATCACATATATATAT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
37494 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCATATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
37559 TCGGCCATTAGGC
129 TCGGCCATTAGGC
37572 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
37637 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
37702 TCGGCCATTAGGC
129 TCGGCCATTAGGC
37715 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
37780 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCATATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
37845 TCGGCCATTAGGC
129 TCGGCCATTAGGC
37858 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
37923 ACTTTCACATTCATCACATCGGCCATTA
64 ACTTTCACATTCATCACATCGGCCATTA
37951 CGCCATACTA
Statistics
Matches: 498, Mismatches: 15, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
140 46 0.09
141 47 0.09
142 37 0.07
143 275 0.55
145 93 0.19
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:42676 original size:46 final size:46
Alignment explanation
Indices: 42623--42798 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 46
42613 TATTTGGGCA
* *
42623 TCCGAACTCGTTGAATTGAGTCTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
42669 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--ATG
* * *
42714 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
42762 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42799 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
42 1 0.01
43 7 0.06
44 1 0.01
45 4 0.04
46 58 0.54
47 27 0.25
48 2 0.02
49 1 0.01
50 6 0.06
51 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:42778 original size:93 final size:93
Alignment explanation
Indices: 42619--42791 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 93
42609 AGGATATTTG
* *
42619 GGCATCCGAACTCGTTGAATTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTCATGGATGCAAATGTCCGAACTCGTTGAG
42684 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
42712 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAATG-CCTGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTCATGGATGCAAATGTCC-GAACTCGTTGA
42776 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
42792 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTCATGGATGCAAATGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:44214 original size:46 final size:46
Alignment explanation
Indices: 44160--44288 Score: 145
Period size: 46 Copynumber: 2.8 Consensus size: 46
44150 TACATCTCGA
* * *
44160 GGCCGATGCACGTCCCAAACATGTCTTACACTAGCTCTCGTCTCA-AT
1 GGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTC--CTAATAT
* * *
44207 -GCTGATGCTATGTCTCAGATATGGTCTTACACTAGCTCTCCTAATAT
1 GGCCGATGC-ATGTCCCAGACAT-GTCTTACACTAGCTCTCCTAATAT
*
44254 GGCCAATGCATGTCCCAGACATGTCTTACACTAGC
1 GGCCGATGCATGTCCCAGACATGTCTTACACTAGC
44289 ACACAAATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
46 23 0.34
47 22 0.32
48 23 0.34
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
GGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCCTAATAT
Done.