Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3360
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: 91565
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2453 original size:26 final size:26
Alignment explanation
Indices: 2406--2473 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
2396 TGTACAAGCA
** * *
2406 ATAAGTGTGCGATTCGATTATGTTGC
1 ATAAGTGTGCGAAACGAATATGATGC
*
2432 ATAAGTGTGCGAAAGGAATATGATGC
1 ATAAGTGTGCGAAACGAATATGATGC
2458 AGCTAAGTGTGGCGAA
1 A--TAAGTGT-GCGAA
2474 TTGACCATGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 22 0.65
28 7 0.21
29 5 0.15
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (26 bp):
ATAAGTGTGCGAAACGAATATGATGC
Found at i:8223 original size:40 final size:39
Alignment explanation
Indices: 8172--8355 Score: 165
Period size: 40 Copynumber: 4.6 Consensus size: 39
8162 TAACTCATTC
*
8172 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-TTTAAAACTCGCACA
*** *
8212 AATGCCTTCGGGACTTAACCCGGAATTGGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAAAACTCGCACA
* *
8252 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAA-AACTCGCACA
* ** * ** *
8292 AATACCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-AAAC-TCGCACA
*
8333 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
8356 CAGCATTCAA
Statistics
Matches: 116, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
39 5 0.04
40 99 0.85
41 12 0.10
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAAAACTCGCACA
Found at i:8315 original size:80 final size:80
Alignment explanation
Indices: 8175--8355 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
8165 CTCATTCAAT
* * *
8175 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGA-ATT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATA-T
* *
8239 GGT-A-TCTCGCACAAA
65 AGTCACT-TAGCACAAA
**
8254 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAGTCCGGAT
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGGA-CTTAACCCGGAT
8317 ATAGTCACTTAGCACAAA
63 ATAGTCACTTAGCACAAA
*
8335 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
8356 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
79 7 0.08
80 70 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:16745 original size:43 final size:43
Alignment explanation
Indices: 16663--16810 Score: 133
Period size: 43 Copynumber: 3.5 Consensus size: 43
16653 TGAGATATAT
* * * *
16663 TGTAAGACCGTGTCTAGGACACAGGCCTCGAT-TGAGATTTACG
1 TGTAAGACCATGTCTGGGACACAGGCATCGATAT-TGATTTACG
16706 TGTAAGACCATGTCTGGGACATCA-GCATCG-TATCTGATTT-CG
1 TGTAAGACCATGTCTGGGACA-CAGGCATCGATAT-TGATTTACG
* * * * * *
16748 TGTAAGACCCTATCTGGGATAGAGGCATCGATATTGAATTACA
1 TGTAAGACCATGTCTGGGACACAGGCATCGATATTGATTTACG
* *
16791 TGTAAGACCACGTCCGGGAC
1 TGTAAGACCATGTCTGGGAC
16811 GTCGGCATTG
Statistics
Matches: 84, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
41 1 0.01
42 32 0.38
43 49 0.58
44 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACACAGGCATCGATATTGATTTACG
Found at i:16776 original size:42 final size:42
Alignment explanation
Indices: 16698--16800 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 42
16688 CCTCGATTGA
*
16698 GATTTACGTGTAAGACCATGTCTGGGACATCAGCATCG-TATCT
1 GATTT-CGTGTAAGACCATATCTGGGACATCAGCATCGATAT-T
* * *
16741 GATTTCGTGTAAGACCCTATCTGGGATA-GAGGCATCGATATT
1 GATTTCGTGTAAGACCATATCTGGGACATCA-GCATCGATATT
* *
16783 GAATTACATGTAAGACCA
1 G-ATTTCGTGTAAGACCA
16801 CGTCCGGGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.02
42 28 0.56
43 21 0.42
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (42 bp):
GATTTCGTGTAAGACCATATCTGGGACATCAGCATCGATATT
Found at i:27486 original size:18 final size:18
Alignment explanation
Indices: 27463--27501 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
27453 TATATGGAAA
*
27463 AAAATGACGTTTTGATCC
1 AAAATGACATTTTGATCC
*
27481 AAAATGACATTTTTATCC
1 AAAATGACATTTTGATCC
27499 AAA
1 AAA
27502 GCCAAGCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (18 bp):
AAAATGACATTTTGATCC
Found at i:39775 original size:30 final size:30
Alignment explanation
Indices: 39741--39800 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
39731 ATTTACTACG
39741 AACTTTGAAAAAATTACACTTTTGCCCCTA
1 AACTTTGAAAAAATTACACTTTTGCCCCTA
*** *
39771 AACTTTTCCATAATTACACTTTTGCCCCTA
1 AACTTTGAAAAAATTACACTTTTGCCCCTA
39801 GGCTTGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTGAAAAAATTACACTTTTGCCCCTA
Found at i:48433 original size:12 final size:12
Alignment explanation
Indices: 48416--48441 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48406 TTTAAACAAA
48416 AAATTATATATC
1 AAATTATATATC
48428 AAATTATATATC
1 AAATTATATATC
48440 AA
1 AA
48442 TAATAAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATTATATATC
Found at i:52282 original size:46 final size:45
Alignment explanation
Indices: 52229--52404 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 45
52219 TATTTGGGCA
52229 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** *
52275 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GAA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
52322 TCC-AAGCTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
52368 CCCGAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52405 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 1 0.01
46 66 0.61
47 30 0.28
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:53198 original size:48 final size:50
Alignment explanation
Indices: 53142--53242 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 50
53132 GAATTGAAGA
53142 ATTATGAGTCTA-TTTCATATGGATGGAACAAAACAGGTA-ATGAGTTAT
1 ATTATGAGTCTATTTTCATATGGATGGAACAAAACAGGTATATGAGTTAT
53190 ATTATGAGTCTATTTTCATATGGATGGAACAAAACAGGTATATGAGTTAT
1 ATTATGAGTCTATTTTCATATGGATGGAACAAAACAGGTATATGAGTTAT
53240 ATT
1 ATT
53243 TTATGAGATG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 12 0.24
49 27 0.53
50 12 0.24
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.36
Consensus pattern (50 bp):
ATTATGAGTCTATTTTCATATGGATGGAACAAAACAGGTATATGAGTTAT
Found at i:55386 original size:14 final size:15
Alignment explanation
Indices: 55359--55406 Score: 66
Period size: 14 Copynumber: 3.4 Consensus size: 15
55349 ATCGTTTTGG
55359 TTTCTTTA-TCTGGA
1 TTTCTTTATTCTGGA
55373 -TTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
55387 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
55401 TTTCTT
1 TTTCTT
55407 GTTATCTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 7 0.23
14 14 0.45
15 10 0.32
ACGTcount: A:0.10, C:0.15, G:0.12, T:0.62
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:57825 original size:45 final size:45
Alignment explanation
Indices: 57776--57949 Score: 194
Period size: 45 Copynumber: 3.8 Consensus size: 45
57766 ATGTTTGGCA
57776 TCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
57821 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
57868 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
57914 CCCGAGCTC-TTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
57950 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 49 0.45
46 19 0.17
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:57929 original size:92 final size:92
Alignment explanation
Indices: 57772--57941 Score: 288
Period size: 92 Copynumber: 1.8 Consensus size: 92
57762 TAGGATGTTT
* *
57772 GGCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GGCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
57837 TGAGTCCGAGTTCGAGAGATGTAACTA
66 TGAGTCCGAGTTCGAGAGATGTAACTA
* *
57864 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTC-TTGAG
1 GGCATCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
57928 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
57942 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 43 0.59
93 30 0.41
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (92 bp):
GGCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:59590 original size:54 final size:54
Alignment explanation
Indices: 59430--59598 Score: 232
Period size: 55 Copynumber: 3.1 Consensus size: 54
59420 GTTACGTACG
* * *
59430 TGGTATCCTTGACTTAT-GAACTCACCAATGCCATGCCTTGGCATGGTCTTACA
1 TGGTATCATTGCCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACA
* * * * *
59483 TGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACA
1 TGGTATCATTGCCTTATAG-AACTCATCAATGCCATGCCTTGGCATGGTCTTACA
*
59538 TGGTATCATTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACA
1 TGGTATCATTGCCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACA
*
59592 TGATATC
1 TGGTATC
59599 TTTATCTTAC
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
53 13 0.13
54 39 0.39
55 48 0.48
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (54 bp):
TGGTATCATTGCCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACA
Found at i:59635 original size:47 final size:47
Alignment explanation
Indices: 59580--59700 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
59570 CATGCCTTGG
* *
59580 CATGGTCTTACATGATATCTTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
*
59627 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
** *
59674 CATAATCTTACATGGTATCCTTGTCTT
1 CATGGTCTTACATGGTATCCTTATCTT
59701 GGTGCCAATG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
Found at i:62413 original size:37 final size:37
Alignment explanation
Indices: 62363--62441 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
62353 TTATTACGAA
* * *
62363 GTCTTACCCGGACATAATCTCAACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCAACACGAAGTCATCGG
* *
62400 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCAACACGAAGTCATCGG
62437 GTCTT
1 GTCTT
62442 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCAACACGAAGTCATCGG
Found at i:62638 original size:47 final size:47
Alignment explanation
Indices: 62560--63066 Score: 847
Period size: 47 Copynumber: 10.7 Consensus size: 47
62550 CCCTTCGGGA
* * * * *
62560 CTTATCACA-ATTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATA-TATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
62607 CCTGTCACATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62654 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
62701 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
62748 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62795 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62842 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62891 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62938 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62985 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
63032 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
63067 AGAATCCTAA
Statistics
Matches: 438, Mismatches: 18, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 389 0.89
48 1 0.00
49 47 0.11
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:62937 original size:190 final size:190
Alignment explanation
Indices: 62560--63045 Score: 843
Period size: 190 Copynumber: 2.6 Consensus size: 190
62550 CCCTTCGGGA
* * * * * * *
62560 CTTATCACA-ATTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACA
1 CTTATCACATA-TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
*
62624 CTTCCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCAC
65 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCAC
*
62687 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
130 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
62748 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGACTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
62813 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
62878 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62938 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
63003 TTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATAT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
63046 GCATGTTCAC
Statistics
Matches: 283, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
188 91 0.32
189 1 0.00
190 191 0.67
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (190 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:63106 original size:237 final size:235
Alignment explanation
Indices: 62615--63066 Score: 789
Period size: 237 Copynumber: 1.9 Consensus size: 235
62605 GCCCTGTCAC
*
62615 ATATATACACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
*
62680 TCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTA
66 TCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
62745 GGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGACTTATCACATATATA
131 GGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGACTTATCACATATATA
* * * *
62810 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
196 CACTTTCACATCCATCACATCAG-CA-TAGGCCTAATCAAAT
62852 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
62917 TCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
66 TCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
* * *
62982 GGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATG
131 GGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGACTTATCACATATATA
63047 CA-TGTTCACATCCATCACAT
196 CACT-TTCACATCCATCACAT
63067 AGAATCCTAA
Statistics
Matches: 208, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
236 1 0.00
237 207 1.00
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (235 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
TCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
GGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGACTTATCACATATATA
CACTTTCACATCCATCACATCAGCATAGGCCTAATCAAAT
Found at i:83498 original size:47 final size:47
Alignment explanation
Indices: 83446--84233 Score: 1216
Period size: 47 Copynumber: 16.6 Consensus size: 47
83436 GATAATTGTG
* *
83446 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
83493 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
83540 GTGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
83589 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
83636 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
83683 GTGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
83732 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGACCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
83779 GTGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
83828 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAGGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
83877 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
83924 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
83971 GTGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
84020 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
84067 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATATGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
84114 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
84161 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
84208 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
84234 TCCCGAAGGG
Statistics
Matches: 683, Mismatches: 50, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
47 461 0.67
49 222 0.33
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:83553 original size:96 final size:94
Alignment explanation
Indices: 83446--84233 Score: 1216
Period size: 96 Copynumber: 8.3 Consensus size: 94
83436 GATAATTGTG
* * *
83446 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
* *
83511 GTGATAAGGCCGAATGGCCAATGTGATGA
66 GTGATAAGGCCTAATGGCCGATGTGATGA
* *
83540 GTGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
83605 ATGTGATAAGGCCTAATGGCCGATGTGATGA
64 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
83636 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TATAT
*
83701 ATGTGATAAGGCCTAATAGCCGATGTGATGA
64 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
83732 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGACCAATGTGATGAGTGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TATAT
83797 ATGTGATAAGGCCTAATGGCCGATGTGATGA
64 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
83828 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAGGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
83893 ATGTGATAAGGCCTAATGGCCGATGTGATGA
64 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
83924 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TATAT
83989 ATGTGATAAGGCCTAATGGCCGATGTGATGA
64 ATGTGATAAGGCCTAATGGCCGATGTGATGA
*
84020 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
* *
84085 GTGATAAGGCCTAATAGCCGATATGATGA
66 GTGATAAGGCCTAATGGCCGATGTGATGA
* *
84114 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
* * * * * * *
84179 GTGACAGGGCCGAGTGGCCAACGTGATGG
66 GTGATAAGGCCTAATGGCCGATGTGATGA
*
84208 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
84234 TCCCGAAGGG
Statistics
Matches: 646, Mismatches: 40, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
94 235 0.36
96 369 0.57
98 42 0.07
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (94 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:83593 original size:143 final size:143
Alignment explanation
Indices: 83446--84233 Score: 1301
Period size: 143 Copynumber: 5.5 Consensus size: 143
83436 GATAATTGTG
* * *
83446 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
83511 GTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATATATGTGATAAGGCCTAATG
66 GTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATATATGTGATAAGGCCTAATG
83576 GCCGATGTGATGA
131 GCCGATGTGATGA
*
83589 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
*
83654 GTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATATATGTGATAAGGCCTAATA
66 GTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATATATGTGATAAGGCCTAATG
83719 GCCGATGTGATGA
131 GCCGATGTGATGA
* * *
83732 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGACCAATGTGATGAGTGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TATAT
* * *
83797 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAA
64 ATGTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATATATGTGATAAGGCCTAA
*
83862 TGGCCGAGGTGATGA
129 TGGCCGATGTGATGA
*
83877 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
83942 GTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATATATGTGATAAGGCCTAATG
66 GTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATATATGTGATAAGGCCTAATG
84007 GCCGATGTGATGA
131 GCCGATGTGATGA
*
84020 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
* * * * * *
84085 GTGATAAGGCCTAATAGCCGATATGATGAATGTGAAAGTG--TATATATGTGATGAGGCCTAATG
66 GTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATATATGTGATAAGGCCTAATG
84148 GCCGATGTGATGA
131 GCCGATGTGATGA
* * * * * * *
84161 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
84226 GTGATAAG
66 GTGATAAG
84234 TCCCGAAGGG
Statistics
Matches: 607, Mismatches: 36, Indels: 6
0.94 0.06 0.01
Matches are distributed among these distances:
141 100 0.16
143 373 0.61
145 134 0.22
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (143 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCGAATGGCCAATGTGATGAGTGTGAAAGTGTATATATATGTGATAAGGCCTAATG
GCCGATGTGATGA
Found at i:86189 original size:27 final size:27
Alignment explanation
Indices: 86159--86363 Score: 250
Period size: 27 Copynumber: 7.6 Consensus size: 27
86149 ATATTGAGTC
* * * *
86159 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
86186 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
86213 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
86241 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
86268 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
* *
86295 CACACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
86322 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
86349 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
86364 GTACAATTTA
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 131 0.85
28 24 0.15
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Done.