Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold851
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: 185800
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13941 original size:22 final size:22
Alignment explanation
Indices: 13909--13952 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13899 TTTTGAACCA
*
13909 TTACCATTTCGTACCAAATCCC
1 TTACCAATTCGTACCAAATCCC
*
13931 TTACCAATTCGTACCAATTCCC
1 TTACCAATTCGTACCAAATCCC
13953 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.36, G:0.05, T:0.32
Consensus pattern (22 bp):
TTACCAATTCGTACCAAATCCC
Found at i:18559 original size:28 final size:30
Alignment explanation
Indices: 18508--18563 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
18498 GTGATTAAAT
18508 AAAATTGACACAAGTAGAATTTAAAAGAAA
1 AAAATTGACACAAGTAGAATTTAAAAGAAA
18538 AAAATTGACAGCAAG-A-AA-TTAAAAGA
1 AAAATTGACA-CAAGTAGAATTTAAAAGA
18564 TAAGTCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 8 0.32
29 2 0.08
30 11 0.44
31 4 0.16
ACGTcount: A:0.61, C:0.07, G:0.14, T:0.18
Consensus pattern (30 bp):
AAAATTGACACAAGTAGAATTTAAAAGAAA
Found at i:31884 original size:21 final size:21
Alignment explanation
Indices: 31839--31901 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
31829 TTTGAACCAT
* * *
31839 TACCAATTCGTACCAAATACCA
1 TACCATTTCATACC-AATTCCA
31861 TACCATTTCATACCAATTCCA
1 TACCATTTCATACCAATTCCA
31882 TACCATTTCGA-ACCAATTCC
1 TACCATTTC-ATACCAATTCC
31902 CAAATACCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (21 bp):
TACCATTTCATACCAATTCCA
Found at i:31885 original size:11 final size:11
Alignment explanation
Indices: 31839--31901 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 11
31829 TTTGAACCAT
*
31839 TACCAATT-CG
1 TACCAATTCCA
*
31849 TACCAAATACCA
1 TACC-AATTCCA
*
31861 TACC-ATTTCA
1 TACCAATTCCA
31871 TACCAATTCCA
1 TACCAATTCCA
* *
31882 TACCATTTCGA
1 TACCAATTCCA
31893 -ACCAATTCC
1 TACCAATTCC
31902 CAAATACCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
10 19 0.46
11 17 0.41
12 5 0.12
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (11 bp):
TACCAATTCCA
Found at i:32249 original size:25 final size:24
Alignment explanation
Indices: 32212--32258 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
32202 AGGAGTTCGA
*
32212 AAAAAAAATAAAATAAAAAAAATC
1 AAAAAAAATAAAAGAAAAAAAATC
*
32236 AAAAAAATTGAAAAGAAAAAAAA
1 AAAAAAAAT-AAAAGAAAAAAAA
32259 AATTACATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.11
Consensus pattern (24 bp):
AAAAAAAATAAAAGAAAAAAAATC
Found at i:37572 original size:10 final size:10
Alignment explanation
Indices: 37556--37613 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
37546 CAACTCCGAC
37556 CAGCTCAATT
1 CAGCTCAATT
* *
37566 GAGCTCATTT
1 CAGCTCAATT
37576 CAGCTCAA-T
1 CAGCTCAATT
37585 CGAGCTCAATT
1 C-AGCTCAATT
*
37596 TAGCTACAATT
1 CAGCT-CAATT
37607 CAGCTCA
1 CAGCTCA
37614 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:37579 original size:20 final size:20
Alignment explanation
Indices: 37556--37616 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
37546 CAACTCCGAC
37556 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
37576 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
37597 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
37617 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:40604 original size:21 final size:23
Alignment explanation
Indices: 40559--40605 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40549 TCACCTGCAA
* *
40559 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
40582 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
40603 TAA
1 TAA
40606 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:42011 original size:23 final size:22
Alignment explanation
Indices: 41959--42011 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
41949 TCCTTGTCTT
*
41959 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
41981 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
42004 TTTCTTTT
1 TTTCTTTT
42012 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:42025 original size:18 final size:18
Alignment explanation
Indices: 42004--42043 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41994 CTTTCTTCAA
* * *
42004 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
42022 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
42040 TTTC
1 TTTC
42044 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.25, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:44711 original size:21 final size:21
Alignment explanation
Indices: 44672--44721 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
44662 AGAGAAAAAT
**
44672 AAAATTGAAAAAGAAGAAATTG
1 AAAA-TGAAAAAGAAGAAAAGG
**
44694 AAAATGAAAAAGGCGAAAAGG
1 AAAATGAAAAAGAAGAAAAGG
44715 AAAATGA
1 AAAATGA
44722 GAGAGAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.22, T:0.12
Consensus pattern (21 bp):
AAAATGAAAAAGAAGAAAAGG
Found at i:48012 original size:99 final size:98
Alignment explanation
Indices: 47841--48135 Score: 452
Period size: 99 Copynumber: 3.0 Consensus size: 98
47831 TACGGTTTCA
* * * * *
47841 CCATGCAATTTTTTACAAGCT-AACCTCAGCTCAATTTTAGCTCCATG-ACTTTGAATCAGCTTA
1 CCATGCAATCTTTTGCAAGTTGAA-CTCAGCTCAATTTTAGCTCCATGAAC-TCGAA-CAGCTTG
47904 AACTCAGCTTAATTTAGTTTATGCATTTATTTAGCT
63 AACTCAGCTTAATTTAGTTTATGCATTTATTTAGCT
47940 CCATGCAATCTTTTGCAAGTTGAACTCAGCTCAATTTTAGCTCCATGAACTCGAACCAGCTTGAA
1 CCATGCAATCTTTTGCAAGTTGAACTCAGCTCAATTTTAGCTCCATGAACTCGAA-CAGCTTGAA
*
48005 CTCAGCTTAATTTAGTTTATGCATTTGTTTAGCT
65 CTCAGCTTAATTTAGTTTATGCATTTATTTAGCT
48039 CCATGCAATCTTTTGCAAGTTGAACTCAGCTCAATTTTAGCTCCATGAACTCGAACAGCTTGAAC
1 CCATGCAATCTTTTGCAAGTTGAACTCAGCTCAATTTTAGCTCCATGAACTCGAACAGCTTGAAC
** *
48104 TCAGCTT-ATTTAGTTTGCGTATTTATTTAGCT
66 TCAGCTTAATTTAGTTTATGCATTTATTTAGCT
48136 ACTGGAATAA
Statistics
Matches: 183, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
97 21 0.11
98 17 0.09
99 141 0.77
100 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (98 bp):
CCATGCAATCTTTTGCAAGTTGAACTCAGCTCAATTTTAGCTCCATGAACTCGAACAGCTTGAAC
TCAGCTTAATTTAGTTTATGCATTTATTTAGCT
Found at i:48402 original size:22 final size:24
Alignment explanation
Indices: 48354--48415 Score: 92
Period size: 22 Copynumber: 2.6 Consensus size: 24
48344 AAAGTAAAGG
48354 TTTAATGTGTCTTGCTGTTGCCAGAT
1 TTTAATGTGTCTTGC--TTGCCAGAT
48380 TTTAATGTGTCTTGC-TGCC-GAT
1 TTTAATGTGTCTTGCTTGCCAGAT
48402 TTTAATGTGTCTTG
1 TTTAATGTGTCTTG
48416 ACCTGATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.47
23 4 0.11
26 15 0.42
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.48
Consensus pattern (24 bp):
TTTAATGTGTCTTGCTTGCCAGAT
Found at i:57242 original size:18 final size:18
Alignment explanation
Indices: 57197--57249 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
57187 CATTTTCATA
* *
57197 CTCTTTCTTTTCTTTACT
1 CTCTTTATTTTCTTTTCT
*
57215 CATC-TCATTTTCTTTTCT
1 C-TCTTTATTTTCTTTTCT
57233 CTCTTTATTTTTCTTTT
1 CTCTTTA-TTTTCTTTT
57250 TTTTTTTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 2 0.07
18 15 0.54
19 11 0.39
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.68
Consensus pattern (18 bp):
CTCTTTATTTTCTTTTCT
Found at i:58362 original size:12 final size:12
Alignment explanation
Indices: 58345--58389 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
58335 ACGAGATTGT
58345 AAAAAAAATTCC
1 AAAAAAAATTCC
**
58357 AAAAAAAATTTGA
1 AAAAAAAA-TTCC
58370 AAAAAAAATTCC
1 AAAAAAAATTCC
58382 AAAAAAAA
1 AAAAAAAA
58390 GTTTGTATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCC
Found at i:58363 original size:13 final size:13
Alignment explanation
Indices: 58345--58389 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
58335 ACGAGATTGT
58345 AAAAAAAATTCC-
1 AAAAAAAATTCCA
**
58357 AAAAAAAATTTGA
1 AAAAAAAATTCCA
58370 AAAAAAAATTCCA
1 AAAAAAAATTCCA
58383 AAAAAAA
1 AAAAAAA
58390 GTTTGTATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAAAATTCCA
Found at i:58378 original size:25 final size:26
Alignment explanation
Indices: 58345--58394 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
58335 ACGAGATTGT
58345 AAAAAAAATTCCAAAAAAAA-TTTGA
1 AAAAAAAATTCCAAAAAAAAGTTTGA
58370 AAAAAAAATTCCAAAAAAAAGTTTG
1 AAAAAAAATTCCAAAAAAAAGTTTG
58395 TATTCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.66, C:0.08, G:0.06, T:0.20
Consensus pattern (26 bp):
AAAAAAAATTCCAAAAAAAAGTTTGA
Found at i:65944 original size:835 final size:835
Alignment explanation
Indices: 64335--65982 Score: 3278
Period size: 835 Copynumber: 2.0 Consensus size: 835
64325 TTCATCCAAC
64335 TGTTGTTGGAATTTCTTAAATATGTCACCATTATTATCACATGTAGATATTTTTTTAAAACCTGC
1 TGTTGTTGGAATTTCTTAAATATGTCACCATTATTATCACATGTAGATATTTTTTTAAAACCTGC
64400 AAAACACTCAACACTCAAAAATAAAAGTTATCAAACCTTACCGTTAATCACTCAAAAAGGAAAAT
66 AAAACACTCAACACTCAAAAATAAAAGTTATCAAACCTTACCGTTAATCACTCAAAAAGGAAAAT
64465 TTAAATTTTCAATGAGCTAGAATTCAGTCTTGTGAGTCCTTTAGGACTTTAGGAGAGTTTATATC
131 TTAAATTTTCAATGAGCTAGAATTCAGTCTTGTGAGTCCTTTAGGACTTTAGGAGAGTTTATATC
64530 AACCAATTAGATAGTGGCTGAACCGATCTACCAAAGAATCCTAATTTGCACTAGGATGCCAAAAA
196 AACCAATTAGATAGTGGCTGAACCGATCTACCAAAGAATCCTAATTTGCACTAGGATGCCAAAAA
64595 CTGACGAGACACCAACTGATTCGTGTTGCACCGAGGAAGAAGTTGTGCACACGTGTAAATCCTAC
261 CTGACGAGACACCAACTGATTCGTGTTGCACCGAGGAAGAAGTTGTGCACACGTGTAAATCCTAC
64660 TAACACAAGAAACAAGAAGGTGTTAGATAACGTAACGGAAGAATAAAGGCAAACAAATGAAAACC
326 TAACACAAGAAACAAGAAGGTGTTAGATAACGTAACGGAAGAATAAAGGCAAACAAATGAAAACC
64725 TACAGCTAAGAATCAATAAAAATTGCTGAAAACAGAAAACCCGAAAAACTGCGGAGTAACTTGCC
391 TACAGCTAAGAATCAATAAAAATTGCTGAAAACAGAAAACCCGAAAAACTGCGGAGTAACTTGCC
*
64790 AACTTCGTTCGAGGTGTTCTTGATCTCGAAAAATCACGAAATTAAATCTGGAGTGTCCTTATATA
456 AACTTCGTTCGAGGTGTTCCTGATCTCGAAAAATCACGAAATTAAATCTGGAGTGTCCTTATATA
64855 TTTAATTTTTGATCTGCAAAGTTTGGGCACCAAATTCAACCCGCTGAATCTTTTTTAAAATTTTT
521 TTTAATTTTTGATCTGCAAAGTTTGGGCACCAAATTCAACCCGCTGAATCTTTTTTAAAATTTTT
64920 ATTGAATTTCGTATTTTTTGATTTTTTTTGACTTTTTTGACTGATATTTTTGCGGGTTTAATTTT
586 ATTGAATTTCGTATTTTTTGATTTTTTTTGACTTTTTTGACTGATATTTTTGCGGGTTTAATTTT
64985 TTTTATATTCTATCACAGTGCTAAAAATATGTATGTAAAATTTTAGATCAATCAGATAACGTTTA
651 TTTTATATTCTATCACAGTGCTAAAAATATGTATGTAAAATTTTAGATCAATCAGATAACGTTTA
65050 CCCAATCAAATGAATTTTTTTCGAACAATTTTTCTGGGTATAACTGCTGTTTGTGCTTTAAAAAA
716 CCCAATCAAATGAATTTTTTTCGAACAATTTTTCTGGGTATAACTGCTGTTTGTGCTTTAAAAAA
65115 TAGAGATCAGTTTAGAAATCAACCAAGAACACCTTAAATAAAAGTTATCAAATGT
781 TAGAGATCAGTTTAGAAATCAACCAAGAACACCTTAAATAAAAGTTATCAAATGT
65170 TGTTGTTGGAATTTCTTAAATATGTCACCATTATTATCACATGTAGATATTTTTTTAAAACCTGC
1 TGTTGTTGGAATTTCTTAAATATGTCACCATTATTATCACATGTAGATATTTTTTTAAAACCTGC
65235 AAAACACTCAACACTCAAAAATAAAAGTTATCAAACCTTACCGTTAATCACTCAAAAAGGAAAAT
66 AAAACACTCAACACTCAAAAATAAAAGTTATCAAACCTTACCGTTAATCACTCAAAAAGGAAAAT
65300 TTAAATTTTCAATGAGCTAGAATTCAGTCTTGTGAGTCCTTTAGGACTTTAGGAGAGTTTATATC
131 TTAAATTTTCAATGAGCTAGAATTCAGTCTTGTGAGTCCTTTAGGACTTTAGGAGAGTTTATATC
65365 AACCAATTAGATAGTGGCTGAACCGATCTACCAAAGAATCCTAATTTGCACTAGGATGCCAAAAA
196 AACCAATTAGATAGTGGCTGAACCGATCTACCAAAGAATCCTAATTTGCACTAGGATGCCAAAAA
65430 CTGACGAGACACCAACTGATTCGTGTTGCACCGAGGAAGAAGTTGTGCACACGTGTAAATCCTAC
261 CTGACGAGACACCAACTGATTCGTGTTGCACCGAGGAAGAAGTTGTGCACACGTGTAAATCCTAC
*
65495 TAACACAAGAAACAAGAAGGTGTTAGATAATGTAACGGAAGAATAAAGGCAAACAAATGAAAACC
326 TAACACAAGAAACAAGAAGGTGTTAGATAACGTAACGGAAGAATAAAGGCAAACAAATGAAAACC
65560 TACAGCTAAGAATCAATAAAAATTGCTGAAAACAGAAAACCCGAAAAACTGCGGAGTAACTTGCC
391 TACAGCTAAGAATCAATAAAAATTGCTGAAAACAGAAAACCCGAAAAACTGCGGAGTAACTTGCC
65625 AACTTCGTTCGAGGTGTTCCTGATCTCGAAAAATCACGAAATTAAATCTGGAGTGTCCTTATATA
456 AACTTCGTTCGAGGTGTTCCTGATCTCGAAAAATCACGAAATTAAATCTGGAGTGTCCTTATATA
65690 TTTAATTTTTGATCTGCAAAGTTTGGGCACCAAATTCAACCCGCTGAATCTTTTTTAAAATTTTT
521 TTTAATTTTTGATCTGCAAAGTTTGGGCACCAAATTCAACCCGCTGAATCTTTTTTAAAATTTTT
65755 ATTGAATTTCGTATTTTTTGATTTTTTTTGACTTTTTTGACTGATATTTTTGCGGGTTTAATTTT
586 ATTGAATTTCGTATTTTTTGATTTTTTTTGACTTTTTTGACTGATATTTTTGCGGGTTTAATTTT
65820 TTTTATATTCTATCACAGTGCTAAAAATATGTATGTAAAATTTTAGATCAATCAGATAACGTTTA
651 TTTTATATTCTATCACAGTGCTAAAAATATGTATGTAAAATTTTAGATCAATCAGATAACGTTTA
65885 CCCAATCAAATGAATTTTTTTCGAACAATTTTTCTGGGTATAACTGCTGTTTGTGCTTTAAAAAA
716 CCCAATCAAATGAATTTTTTTCGAACAATTTTTCTGGGTATAACTGCTGTTTGTGCTTTAAAAAA
65950 TAGAGATCAGTTTAGAAATCAACCAAGAACACC
781 TAGAGATCAGTTTAGAAATCAACCAAGAACACC
65983 CAAAACGCCC
Statistics
Matches: 811, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
835 811 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (835 bp):
TGTTGTTGGAATTTCTTAAATATGTCACCATTATTATCACATGTAGATATTTTTTTAAAACCTGC
AAAACACTCAACACTCAAAAATAAAAGTTATCAAACCTTACCGTTAATCACTCAAAAAGGAAAAT
TTAAATTTTCAATGAGCTAGAATTCAGTCTTGTGAGTCCTTTAGGACTTTAGGAGAGTTTATATC
AACCAATTAGATAGTGGCTGAACCGATCTACCAAAGAATCCTAATTTGCACTAGGATGCCAAAAA
CTGACGAGACACCAACTGATTCGTGTTGCACCGAGGAAGAAGTTGTGCACACGTGTAAATCCTAC
TAACACAAGAAACAAGAAGGTGTTAGATAACGTAACGGAAGAATAAAGGCAAACAAATGAAAACC
TACAGCTAAGAATCAATAAAAATTGCTGAAAACAGAAAACCCGAAAAACTGCGGAGTAACTTGCC
AACTTCGTTCGAGGTGTTCCTGATCTCGAAAAATCACGAAATTAAATCTGGAGTGTCCTTATATA
TTTAATTTTTGATCTGCAAAGTTTGGGCACCAAATTCAACCCGCTGAATCTTTTTTAAAATTTTT
ATTGAATTTCGTATTTTTTGATTTTTTTTGACTTTTTTGACTGATATTTTTGCGGGTTTAATTTT
TTTTATATTCTATCACAGTGCTAAAAATATGTATGTAAAATTTTAGATCAATCAGATAACGTTTA
CCCAATCAAATGAATTTTTTTCGAACAATTTTTCTGGGTATAACTGCTGTTTGTGCTTTAAAAAA
TAGAGATCAGTTTAGAAATCAACCAAGAACACCTTAAATAAAAGTTATCAAATGT
Found at i:73448 original size:21 final size:21
Alignment explanation
Indices: 73403--73465 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
73393 CTTTAACCAT
* *
73403 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
73425 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
73446 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
73466 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:80851 original size:19 final size:18
Alignment explanation
Indices: 80815--80854 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
80805 TTTCCACTCG
*
80815 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
80833 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
80852 TTT
1 TTT
80855 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:80985 original size:18 final size:17
Alignment explanation
Indices: 80926--80986 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
80916 GCACTCTTTC
*
80926 TTTTCTTTCTCCAATCTTT
1 TTTTCTTT-TTCAAT-TTT
*
80945 TTCTCTTTTTCAATTTT
1 TTTTCTTTTTCAATTTT
*
80962 TGTTTCTTTTTCGATTTCT
1 T-TTTCTTTTTCAATTT-T
80981 TTTTCT
1 TTTTCT
80987 CTCGTCACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 23 0.64
19 9 0.25
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTTTTTCAATTTT
Found at i:81925 original size:14 final size:13
Alignment explanation
Indices: 81906--81953 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
81896 TAGCTTCTTC
81906 TTTTTTTCACGAAT
1 TTTTTTTCAC-AAT
81920 TTTTTTTCACAAT
1 TTTTTTTCACAAT
*
81933 TTTTTTTCA-ATT
1 TTTTTTTCACAAT
81945 TTTTTTTCA
1 TTTTTTTCA
81954 ACTTGATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
12 11 0.33
13 12 0.36
14 10 0.30
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (13 bp):
TTTTTTTCACAAT
Found at i:81950 original size:12 final size:12
Alignment explanation
Indices: 81906--81954 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 12
81896 TAGCTTCTTC
81906 TTTTTTTCACGAAT
1 TTTTTTTCA--AAT
81920 TTTTTTTCACAAT
1 TTTTTTTCA-AAT
*
81933 TTTTTTTCAATT
1 TTTTTTTCAAAT
81945 TTTTTTTCAA
1 TTTTTTTCAA
81955 CTTGATATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 12 0.36
13 12 0.36
14 9 0.27
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.65
Consensus pattern (12 bp):
TTTTTTTCAAAT
Found at i:82007 original size:11 final size:11
Alignment explanation
Indices: 81991--82033 Score: 61
Period size: 10 Copynumber: 3.9 Consensus size: 11
81981 ATGGAAACCA
81991 AATTTTTTTTG
1 AATTTTTTTTG
82002 AA-TTTTTTTG
1 AATTTTTTTTG
82012 AATTTTTTTTCG
1 AATTTTTTTT-G
*
82024 AGTTTTTTTT
1 AATTTTTTTT
82034 CAAGAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.34
11 9 0.31
12 10 0.34
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.72
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:82034 original size:12 final size:12
Alignment explanation
Indices: 81991--82034 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
81981 ATGGAAACCA
81991 AATTTTTTTT-G
1 AATTTTTTTTCG
82002 AA-TTTTTTT-G
1 AATTTTTTTTCG
82012 AATTTTTTTTCG
1 AATTTTTTTTCG
*
82024 AGTTTTTTTTC
1 AATTTTTTTTC
82035 AAGAAACTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.33
11 9 0.30
12 11 0.37
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (12 bp):
AATTTTTTTTCG
Found at i:93797 original size:56 final size:55
Alignment explanation
Indices: 93681--93798 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
93671 TGCATGCTTT
* * * *
93681 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
93735 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
93791 CATTAAAT
1 CATTAAAT
93799 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:94447 original size:20 final size:20
Alignment explanation
Indices: 94422--94476 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
94412 ACGAGTTAAA
* *
94422 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
94442 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
94462 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
94477 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:97946 original size:18 final size:18
Alignment explanation
Indices: 97925--97959 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
97915 TTTTTCTTTT
97925 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
97943 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
97960 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:110119 original size:12 final size:11
Alignment explanation
Indices: 110100--110132 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
110090 TTAAATTAAG
110100 TAAAAAATAAA
1 TAAAAAATAAA
110111 TAAATAAATAAA
1 TAAA-AAATAAA
110123 T-AAAAATAAA
1 TAAAAAATAAA
110133 ACTTTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 6 0.29
12 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:112856 original size:22 final size:22
Alignment explanation
Indices: 112826--112869 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
112816 TTTGGTATTT
112826 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
112848 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
112870 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:118980 original size:12 final size:12
Alignment explanation
Indices: 118960--119020 Score: 104
Period size: 12 Copynumber: 5.1 Consensus size: 12
118950 TAGTAGTTTC
*
118960 TCAAAAAAAAAC
1 TCAAAAAAAAAT
*
118972 TCGAAAAAAAAT
1 TCAAAAAAAAAT
118984 TCAAAAAAAAAT
1 TCAAAAAAAAAT
118996 TCAAAAAAAAAT
1 TCAAAAAAAAAT
119008 TCAAAAAAAAAT
1 TCAAAAAAAAAT
119020 T
1 T
119021 TGGTTTCCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.72, C:0.10, G:0.02, T:0.16
Consensus pattern (12 bp):
TCAAAAAAAAAT
Found at i:138502 original size:10 final size:10
Alignment explanation
Indices: 138486--138543 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
138476 CAACTCCGAC
138486 CAGCTCAATT
1 CAGCTCAATT
* *
138496 GAGCTCATTT
1 CAGCTCAATT
138506 CAGCTCAA-T
1 CAGCTCAATT
138515 CGAGCTCAATT
1 C-AGCTCAATT
*
138526 TAGCTACAATT
1 CAGCT-CAATT
138537 CAGCTCA
1 CAGCTCA
138544 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:138509 original size:20 final size:20
Alignment explanation
Indices: 138486--138546 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
138476 CAACTCCGAC
138486 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
138506 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
138527 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
138547 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:139921 original size:13 final size:13
Alignment explanation
Indices: 139905--139951 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
139895 AAAAAAATAT
139905 AAAAAAATTCAAA
1 AAAAAAATTCAAA
*
139918 AAAAAATTGATTGAAA
1 AAAAAA---ATTCAAA
139934 AAAAAAATTCAAA
1 AAAAAAATTCAAA
139947 AAAAA
1 AAAAA
139952 GTGAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 17 0.59
16 12 0.41
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:139973 original size:15 final size:15
Alignment explanation
Indices: 139944--139993 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
139934 AAAAAAATTC
139944 AAAAAAAAGT--G-A
1 AAAAAAAAGTGAGCA
139956 AAAAAAAA-TCGAGCA
1 AAAAAAAAGT-GAGCA
139971 AAAAAAAAGGTGAGCA
1 AAAAAAAA-GTGAGCA
139987 AAAAAAA
1 AAAAAAA
139994 TCAAGTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 1 0.03
12 8 0.25
14 1 0.03
15 9 0.28
16 12 0.38
17 1 0.03
ACGTcount: A:0.72, C:0.06, G:0.16, T:0.06
Consensus pattern (15 bp):
AAAAAAAAGTGAGCA
Found at i:139990 original size:30 final size:28
Alignment explanation
Indices: 139944--140015 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 28
139934 AAAAAAATTC
*
139944 AAAAAAAA-GTGAAAAAAAAATCGAGCA
1 AAAAAAAAGGTGAAAAAAAAATCAAGCA
**
139971 AAAAAAAAGGTGAGCAAAAAAAATCAAGTT
1 AAAAAAAAGGTGA--AAAAAAAATCAAGCA
140001 AAAAAAAA-GTGAAAA
1 AAAAAAAAGGTGAAAA
140016 GTCTTGCGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 11 0.28
28 4 0.10
29 4 0.10
30 20 0.51
ACGTcount: A:0.69, C:0.06, G:0.15, T:0.10
Consensus pattern (28 bp):
AAAAAAAAGGTGAAAAAAAAATCAAGCA
Found at i:140905 original size:18 final size:18
Alignment explanation
Indices: 140884--140918 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
140874 AGAAAAGAAA
140884 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
140902 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
140919 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:143005 original size:10 final size:10
Alignment explanation
Indices: 142989--143046 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
142979 CAACTCCGAC
142989 CAGCTCAATT
1 CAGCTCAATT
* *
142999 GAGCTCATTT
1 CAGCTCAATT
143009 CAGCTCAA-T
1 CAGCTCAATT
143018 CGAGCTCAATT
1 C-AGCTCAATT
*
143029 TAGCTACAATT
1 CAGCT-CAATT
143040 CAGCTCA
1 CAGCTCA
143047 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:143012 original size:20 final size:20
Alignment explanation
Indices: 142989--143049 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
142979 CAACTCCGAC
142989 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
143009 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
143030 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
143050 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:148950 original size:6 final size:6
Alignment explanation
Indices: 148921--149050 Score: 66
Period size: 6 Copynumber: 21.5 Consensus size: 6
148911 TCCATTGAGC
* * ** ** *
148921 AAGAAA AGGAAA AAGAGA TTGAAA AAGAAA TTG-AA -AGAAA ACGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
** * ** ** *
148967 AAGAAA AAGAAA TTGCAA AAGAAA AAGAAA TCGAAA AAGTGA GAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
149015 AAGAAA ATGAAGAA AAGAAA ATTGAAA AAGAAA AAG
1 AAGAAA AAG-A-AA AAGAAA A-AGAAA AAGAAA AAG
149051 CGAAAAAAGA
Statistics
Matches: 86, Mismatches: 33, Indels: 10
0.67 0.26 0.08
Matches are distributed among these distances:
4 1 0.01
5 4 0.05
6 70 0.81
7 7 0.08
8 4 0.05
ACGTcount: A:0.68, C:0.02, G:0.21, T:0.08
Consensus pattern (6 bp):
AAGAAA
Found at i:148950 original size:18 final size:18
Alignment explanation
Indices: 148923--149005 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
148913 CATTGAGCAA
* * *
148923 GAAAAGGAAAAAGAGATT
1 GAAAAAGAAAAAGAAATC
*
148941 GAAAAAGAAATTGAAAGAAAAC
1 GAAAAAGAAA----AAGAAATC
*
148963 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATC
*
148981 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATC
148999 GAAAAAG
1 GAAAAAG
149006 TGAGAGAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
18 37 0.71
22 15 0.29
ACGTcount: A:0.67, C:0.04, G:0.20, T:0.08
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATC
Found at i:149032 original size:14 final size:13
Alignment explanation
Indices: 149011--149048 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
149001 AAAAGTGAGA
149011 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
149023 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
149038 GAAAAAGAAAA
1 GAAAAAGAAAA
149049 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:149062 original size:21 final size:21
Alignment explanation
Indices: 149012--149062 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
149002 AAAGTGAGAG
*
149012 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
149033 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
149054 AAAAAGAAA
1 AAAAAGAAA
149063 TTGAAAGAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:149418 original size:4 final size:4
Alignment explanation
Indices: 149389--149440 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
149379 TTATGACAAG
*
149389 TAAA -AAA TAAA CTAAG TAAA -AAA TAAA TAAA TAAA T-AA -AAA TAAA
1 TAAA TAAA TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
149434 -AAA TAAA
1 TAAA TAAA
149441 ACTTTACAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
3 13 0.32
4 24 0.60
5 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (4 bp):
TAAA
Found at i:154702 original size:105 final size:105
Alignment explanation
Indices: 154520--154728 Score: 418
Period size: 105 Copynumber: 2.0 Consensus size: 105
154510 CAAAAATTAA
154520 AGGATAAGTCCTAAAGATCCTTGAAATCCCGAAAGATTTCACAAATCTCTTCAAACGGCTCTAAT
1 AGGATAAGTCCTAAAGATCCTTGAAATCCCGAAAGATTTCACAAATCTCTTCAAACGGCTCTAAT
154585 CTCCCCTCCAAAGAATGGCGATGGCAAGAAGAAGGTTGAG
66 CTCCCCTCCAAAGAATGGCGATGGCAAGAAGAAGGTTGAG
154625 AGGATAAGTCCTAAAGATCCTTGAAATCCCGAAAGATTTCACAAATCTCTTCAAACGGCTCTAAT
1 AGGATAAGTCCTAAAGATCCTTGAAATCCCGAAAGATTTCACAAATCTCTTCAAACGGCTCTAAT
154690 CTCCCCTCCAAAGAATGGCGATGGCAAGAAGAAGGTTGA
66 CTCCCCTCCAAAGAATGGCGATGGCAAGAAGAAGGTTGA
154729 AGATGGCTCC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (105 bp):
AGGATAAGTCCTAAAGATCCTTGAAATCCCGAAAGATTTCACAAATCTCTTCAAACGGCTCTAAT
CTCCCCTCCAAAGAATGGCGATGGCAAGAAGAAGGTTGAG
Found at i:155074 original size:4 final size:4
Alignment explanation
Indices: 155065--155096 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
155055 AAGTTTTATT
155065 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
155097 CTTAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:165017 original size:104 final size:105
Alignment explanation
Indices: 164863--165070 Score: 400
Period size: 104 Copynumber: 2.0 Consensus size: 105
164853 CAAAAATTAA
*
164863 AGGATAAGTCCTAAAGATCCTTGAAATCCCGAAAGATTTCACAAATCTCTTCAAATGGCTCTAAT
1 AGGATAAGTCCTAAAGATCCTTGAAATCCCGAAAGATTTCACAAATCTCTTCAAACGGCTCTAAT
164928 CTCCCCTCCAAAGAATGGCGATGGCAAGAAGAAGGTTGAG
66 CTCCCCTCCAAAGAATGGCGATGGCAAGAAGAAGGTTGAG
164968 AGGATAAGTCCTAAAGATCCTTGAAAT-CCGAAAGATTTCACAAATCTCTTCAAACGGCTCTAAT
1 AGGATAAGTCCTAAAGATCCTTGAAATCCCGAAAGATTTCACAAATCTCTTCAAACGGCTCTAAT
165032 CTCCCCTCCAAAGAATGGCGATGGCAAGAAGAAGGTTGA
66 CTCCCCTCCAAAGAATGGCGATGGCAAGAAGAAGGTTGA
165071 AGATGGCTCC
Statistics
Matches: 102, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 75 0.74
105 27 0.26
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (105 bp):
AGGATAAGTCCTAAAGATCCTTGAAATCCCGAAAGATTTCACAAATCTCTTCAAACGGCTCTAAT
CTCCCCTCCAAAGAATGGCGATGGCAAGAAGAAGGTTGAG
Found at i:165414 original size:4 final size:4
Alignment explanation
Indices: 165400--165448 Score: 73
Period size: 4 Copynumber: 12.2 Consensus size: 4
165390 AGTTGTAAAG
*
165400 TTTA TTTTA TTTA -TTA TTTA TTTA TTTA TTTA TTTA CTTA TTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
165448 T
1 T
165449 ATTAGTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
3 3 0.07
4 34 0.83
5 4 0.10
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:169222 original size:12 final size:13
Alignment explanation
Indices: 169205--169233 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
169195 TTTTTTTATT
169205 TTTATTTATTTA-
1 TTTATTTATTTAG
169217 TTTATTTATTTAG
1 TTTATTTATTTAG
169230 TTTA
1 TTTA
169234 AATTTTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTATTTATTTAG
Found at i:183138 original size:18 final size:17
Alignment explanation
Indices: 183115--183150 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
183105 AGCATTTTCG
*
183115 AAAAAAAATTCAAAAAA
1 AAAAAAAAATCAAAAAA
183132 AAAAAAAAATCAAAAAA
1 AAAAAAAAATCAAAAAA
183149 AA
1 AA
183151 GTTTCTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.86, C:0.06, G:0.00, T:0.08
Consensus pattern (17 bp):
AAAAAAAAATCAAAAAA
Found at i:183208 original size:15 final size:15
Alignment explanation
Indices: 183186--183224 Score: 71
Period size: 14 Copynumber: 2.7 Consensus size: 15
183176 GATATCAAGT
183186 TGAAAAAAAATTT-G
1 TGAAAAAAAATTTCG
183200 TGAAAAAAAATTTCG
1 TGAAAAAAAATTTCG
183215 TGAAAAAAAA
1 TGAAAAAAAA
183225 AGAAGAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.23
Consensus pattern (15 bp):
TGAAAAAAAATTTCG
Found at i:184168 original size:18 final size:17
Alignment explanation
Indices: 184147--184191 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
184137 GAGTGACGAG
184147 AGAAAAATAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
184165 AGAAATAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
184183 AGAGAAAAA
1 AGA-AAAAA
184192 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.11
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Done.