Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2134
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: 72709
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:733 original size:41 final size:39
Alignment explanation
Indices: 679--782 Score: 154
Period size: 39 Copynumber: 2.6 Consensus size: 39
669 AAGAGAAAGA
*
679 AGAGAGGAGGGATGATAGGAGGAGAGACAGAGAGATAGTAG
1 AGAGAGGAGGGATGATAGGAGGAGA-A-AGAGAGATAATAG
* *
720 AGATAGGAGGGATGATAGGAGGAGAAGGAGAGATAATAG
1 AGAGAGGAGGGATGATAGGAGGAGAAAGAGAGATAATAG
*
759 AGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGGAGGGATGATAGGAGGAG
783 GAGAGAAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 33 0.57
40 1 0.02
41 24 0.41
ACGTcount: A:0.41, C:0.02, G:0.47, T:0.10
Consensus pattern (39 bp):
AGAGAGGAGGGATGATAGGAGGAGAAAGAGAGATAATAG
Found at i:736 original size:21 final size:20
Alignment explanation
Indices: 712--773 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
702 GAGACAGAGA
712 GATAGTAGAGATAGGAGGGAT
1 GATAGTAGAGA-AGGAGGGAT
* *
733 GATAGGAGGAGAAGGAGAGAT
1 GATAGTA-GAGAAGGAGGGAT
*
754 AATAG-AGAG-AGGAGGGAT
1 GATAGTAGAGAAGGAGGGAT
772 GA
1 GA
774 CAGGAGGAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 9 0.26
19 3 0.09
20 1 0.03
21 18 0.51
22 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.13
Consensus pattern (20 bp):
GATAGTAGAGAAGGAGGGAT
Found at i:1393 original size:14 final size:14
Alignment explanation
Indices: 1374--1403 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1364 CATAAGATGG
*
1374 AAGGAAAGGAGTGA
1 AAGGAAAGGAGGGA
1388 AAGGAAAGGAGGGA
1 AAGGAAAGGAGGGA
1402 AA
1 AA
1404 CTTCAGCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.43, T:0.03
Consensus pattern (14 bp):
AAGGAAAGGAGGGA
Found at i:9535 original size:12 final size:11
Alignment explanation
Indices: 9513--9588 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
9503 AGAGAAAGAA
*
9513 GAGAGAGGAGG
1 GAGATAGGAGG
9524 GATGATAGGAGG
1 GA-GATAGGAGG
*
9536 AGAGACAGGA--
1 -GAGATAGGAGG
*
9546 GAGATAGTA--
1 GAGATAGGAGG
9555 GAGATAGGAGG
1 GAGATAGGAGG
9566 GATGATAGGAGG
1 GA-GATAGGAGG
*
9578 AGAGACAGGAG
1 -GAGATAGGAG
9589 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:9545 original size:24 final size:24
Alignment explanation
Indices: 9512--9597 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
9502 AAGAGAAAGA
*
9512 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
9536 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
9554 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
9578 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
9598 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:9564 original size:42 final size:42
Alignment explanation
Indices: 9503--9621 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
9493 TAGCCCTCAA
* *
9503 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
9545 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
9587 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
9622 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:20807 original size:42 final size:42
Alignment explanation
Indices: 20746--20864 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
20736 TAGCCCTCAA
* *
20746 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAAACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAAACAGG
* *
20788 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAAACAGG
* *
20830 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
20865 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.44, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAAACAGG
Found at i:30140 original size:12 final size:12
Alignment explanation
Indices: 30125--30159 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
30115 TCTATTATCT
30125 CTCCTATCTCTC
1 CTCCTATCTCTC
30137 CTCCTATCATC-C
1 CTCCTATC-TCTC
30149 CTCCTATCTCT
1 CTCCTATCTCT
30160 TCTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:32103 original size:29 final size:29
Alignment explanation
Indices: 32070--32130 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
32060 TAGGAAATTT
*
32070 ATTGTGGT-TTACTTTGATATACAACAAAA
1 ATTGTGGTATT-CTTTAATATACAACAAAA
* *
32099 ATTGTTGTATTTTTTAATATACAACAAAA
1 ATTGTGGTATTCTTTAATATACAACAAAA
32128 ATT
1 ATT
32131 TGGATGATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (29 bp):
ATTGTGGTATTCTTTAATATACAACAAAA
Found at i:34687 original size:12 final size:11
Alignment explanation
Indices: 34665--34740 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
34655 AGAGAAAGAA
*
34665 GAGAGAGGAGG
1 GAGATAGGAGG
34676 GATGATAGGAGG
1 GA-GATAGGAGG
*
34688 AGAGACAGGA--
1 -GAGATAGGAGG
*
34698 GAGATAGTA--
1 GAGATAGGAGG
34707 GAGATAGGAGG
1 GAGATAGGAGG
34718 GATGATAGGAGG
1 GA-GATAGGAGG
*
34730 AGAGACAGGAG
1 -GAGATAGGAG
34741 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:34716 original size:42 final size:42
Alignment explanation
Indices: 34655--34773 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
34645 TAGCCCTCAA
* *
34655 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
34697 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
34739 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
34774 GAGAGAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:34757 original size:18 final size:18
Alignment explanation
Indices: 34730--34779 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
34720 TGATAGGAGG
*
34730 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
34748 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
34766 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
34780 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:47242 original size:24 final size:24
Alignment explanation
Indices: 47215--47273 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
47205 TTTATTATCT
* *
47215 CTCCGATCTCTCTTCCTATCATCC
1 CTCCCATCTCTCCTCCTATCATCC
* *
47239 CTCCTATCTCTCCTCCTTTCATCC
1 CTCCCATCTCTCCTCCTATCATCC
47263 CTCCCATCTCT
1 CTCCCATCTCT
47274 TCTTTCTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.10, C:0.49, G:0.02, T:0.39
Consensus pattern (24 bp):
CTCCCATCTCTCCTCCTATCATCC
Found at i:47245 original size:12 final size:12
Alignment explanation
Indices: 47228--47266 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
47218 CGATCTCTCT
47228 TCCTATCATCCC
1 TCCTATCATCCC
47240 TCCTATC-TCTCC
1 TCCTATCATC-CC
*
47252 TCCTTTCATCCC
1 TCCTATCATCCC
47264 TCC
1 TCC
47267 CATCTCTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.10, C:0.51, G:0.00, T:0.38
Consensus pattern (12 bp):
TCCTATCATCCC
Found at i:50545 original size:28 final size:29
Alignment explanation
Indices: 50502--50583 Score: 107
Period size: 28 Copynumber: 2.9 Consensus size: 29
50492 ATTAATAAAT
*
50502 AAGAAAGATC-AAGGAAGTGAAATCAA-C
1 AAGAAATATCAAAGGAAGTGAAATCAAGC
* *
50529 AAGAAATATGAAAGGAAATGAAAT-AAGC
1 AAGAAATATCAAAGGAAGTGAAATCAAGC
*
50557 AAGAAATATCAAAGGAAGAGAAATCAA
1 AAGAAATATCAAAGGAAGTGAAATCAA
50584 TGGAGAGGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.22
28 34 0.74
29 2 0.04
ACGTcount: A:0.60, C:0.07, G:0.21, T:0.12
Consensus pattern (29 bp):
AAGAAATATCAAAGGAAGTGAAATCAAGC
Found at i:53161 original size:12 final size:11
Alignment explanation
Indices: 53139--53214 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
53129 AGAGAAAGAA
*
53139 GAGAGAGGAGG
1 GAGATAGGAGG
53150 GATGATAGGAGG
1 GA-GATAGGAGG
*
53162 AGAGACAGGA--
1 -GAGATAGGAGG
*
53172 GAGATAGTA--
1 GAGATAGGAGG
53181 GAGATAGGAGG
1 GAGATAGGAGG
53192 GATGATAGGAGG
1 GA-GATAGGAGG
*
53204 AGAGACAGGAG
1 -GAGATAGGAG
53215 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:53171 original size:24 final size:24
Alignment explanation
Indices: 53138--53223 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
53128 AAGAGAAAGA
*
53138 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
53162 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
53180 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
53204 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
53224 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:53190 original size:42 final size:42
Alignment explanation
Indices: 53129--53247 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
53119 TAGCCCTCAA
* *
53129 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
53171 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
53213 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
53248 GAGAGAAGAG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:60708 original size:52 final size:52
Alignment explanation
Indices: 60435--60754 Score: 170
Period size: 52 Copynumber: 6.0 Consensus size: 52
60425 AACATTAATT
* * * *
60435 TTAAAGATGAT-ATGGGTGCCAATGTGCTGATTAAAGGCTAGCGACATTAGAC
1 TTAAAGATGATGA-GAGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGAA
* * * * * * * *
60487 TTAGAAGGA-GATAAGGGTGCCAA-GTTGTTGATTCAA-GTTCGGTGACGTTGGAC
1 TTA-AA-GATGATGAGAGTGCCAATG-TGCTGATTCAAGGCT-AGCGACATTGGAA
* ** * * * *
60540 TTAAAGACGAAAAGATTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
1 TTAAAGATGATGAGAGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGAA
* * * * **
60592 TTAGAAGGA-GATTTTTGACAAATATGCCAATGTG-TCGATTCAAGGCCTA-CGACACTAGCT
1 TTA-AA-GATGA----TG--AGA-GTGCCAATGTGCT-GATTCAAGG-CTAGCGACATTGGAA
* *
60652 TTAAAGATGATGA-AGGTGCCAATGTGCTGATTCAAGGCTAGTGATATTGGAA
1 TTAAAGATGATGAGA-GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGAA
* *
60704 TTAAAGATGATGAGAGTGCCAATGTGGTGATTCAAGGGTAGCGACATTGGA
1 TTAAAGATGATGAGAGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGA
60755 CTTGAGAAAG
Statistics
Matches: 206, Mismatches: 39, Indels: 46
0.71 0.13 0.16
Matches are distributed among these distances:
51 5 0.02
52 111 0.54
53 44 0.21
54 5 0.02
55 2 0.01
58 2 0.01
59 7 0.03
60 28 0.14
61 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.27
Consensus pattern (52 bp):
TTAAAGATGATGAGAGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGAA
Found at i:60844 original size:31 final size:32
Alignment explanation
Indices: 60809--60878 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
60799 CCAATGACAT
* *
60809 TGGGCTTAAAAG-GGGATGCCACTAATTTGTG
1 TGGGCTTAAAAGAGGGATGCCACCAACTTGTG
** *
60840 TGGGCTTTTAAGAGGGTTGCCACCAACTTGTG
1 TGGGCTTAAAAGAGGGATGCCACCAACTTGTG
60872 TGGGCTT
1 TGGGCTT
60879 TGAAAATGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (32 bp):
TGGGCTTAAAAGAGGGATGCCACCAACTTGTG
Found at i:60871 original size:32 final size:33
Alignment explanation
Indices: 60825--60973 Score: 137
Period size: 32 Copynumber: 4.7 Consensus size: 33
60815 TAAAAGGGGA
*
60825 TGCCACTAATTTGTGTGGGCTTTTAAGAG-GGT
1 TGCCACTAACTTGTGTGGGCTTTTAAGAGTGGT
* * *
60857 TGCCACCAACTTGTGTGGGCTTTGAA-AAT-GT
1 TGCCACTAACTTGTGTGGGCTTTTAAGAGTGGT
* * * ** *
60888 TGCAACTGACTGGTGCAGGC-TTTGAGAGTGGT
1 TGCCACTAACTTGTGTGGGCTTTTAAGAGTGGT
* * *
60920 TGCCACTGACTTGTGCGGGC-TTTGAGAGTGGT
1 TGCCACTAACTTGTGTGGGCTTTTAAGAGTGGT
*
60952 TGCCACCAACTTGTGTGGGCTT
1 TGCCACTAACTTGTGTGGGCTT
60974 AAAAAAAGGT
Statistics
Matches: 94, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
30 3 0.03
31 19 0.20
32 71 0.76
33 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.32, T:0.32
Consensus pattern (33 bp):
TGCCACTAACTTGTGTGGGCTTTTAAGAGTGGT
Found at i:60997 original size:31 final size:32
Alignment explanation
Indices: 60959--61029 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
60949 GGTTGCCACC
* *
60959 AACTTGTGTGGGCTT-AAAAAAAGGTGTCAAT
1 AACTTGTGTAGGCTTAAAAAAAAGGTGGCAAT
*
60990 AACTTGTGTAGGCTTAAAAAAAAGGTGGCACT
1 AACTTGTGTAGGCTTAAAAAAAAGGTGGCAAT
61022 AACTTGTG
1 AACTTGTG
61030 AGCTTTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 14 0.39
32 22 0.61
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (32 bp):
AACTTGTGTAGGCTTAAAAAAAAGGTGGCAAT
Found at i:61003 original size:95 final size:95
Alignment explanation
Indices: 60825--61004 Score: 229
Period size: 95 Copynumber: 1.9 Consensus size: 95
60815 TAAAAGGGGA
* * ** * *
60825 TGCCACTAATTTGTGTGGGCTTTTAAGAGGGTTGCCACCAACTTGTGTGGGCTTTGAAAATGTTG
1 TGCCACTAACTTGTGCGGGCTTTTAAGAGGGTTGCCACCAACTTGTGTGGGCTTAAAAAAAGGTG
*
60890 CAACTGACTGGTGCAGGCTTTGAGAGTGGT
66 CAACTAACTGGTGCAGGCTTTGAGAGTGGT
* *
60920 TGCCACTGACTTGTGCGGGC-TTTGAGAGTGGTTGCCACCAACTTGTGTGGGCTTAAAAAAAGGT
1 TGCCACTAACTTGTGCGGGCTTTTAAGAG-GGTTGCCACCAACTTGTGTGGGCTTAAAAAAAGGT
* *
60984 GTCAA-TAACTTGTGTAGGCTT
65 G-CAACTAACTGGTGCAGGCTT
61005 AAAAAAAAGG
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
94 7 0.10
95 62 0.86
96 3 0.04
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.32
Consensus pattern (95 bp):
TGCCACTAACTTGTGCGGGCTTTTAAGAGGGTTGCCACCAACTTGTGTGGGCTTAAAAAAAGGTG
CAACTAACTGGTGCAGGCTTTGAGAGTGGT
Found at i:61082 original size:28 final size:28
Alignment explanation
Indices: 61051--61322 Score: 208
Period size: 29 Copynumber: 9.1 Consensus size: 28
61041 GGTGCTATTA
61051 ACTTATGGGCTTTGAAAGATTGCCACTG
1 ACTTATGGGCTTTGAAAGATTGCCACTG
*
61079 ACTTATGGGCTTTGAAAGATTGCCATTG
1 ACTTATGGGCTTTGAAAGATTGCCACTG
* * *
61107 ACTTATGGGCTTTAAGAAGGA-TGTCATTG
1 ACTTATGGGCTTT--GAAAGATTGCCACTG
* * * *
61136 ACTTGTGGGCTTTGAAAAAGGTGCCACTA
1 ACTTATGGGCTTTGAAAGA-TTGCCACTG
* *
61165 ACCTATGGGCTTTGAAAGGGTGTGCCACTG
1 ACTTATGGGCTTTGAAA-GAT-TGCCACTG
*
61195 ACTTGTGGGCTTTGAAAAGGA-TGCCACTG
1 ACTTATGGGCTTTG-AAA-GATTGCCACTG
61224 ACTTATGGGCTTTGAAAGAGGTTTGCCA-TCG
1 ACTTATGGGCTTTGAAAGA---TTGCCACT-G
* * *
61255 ACTTGTGTGGGCTTTTGAGAGGGTTGCCACTG
1 AC-T-TATGGGC-TTTGA-AAGATTGCCACTG
* *
61287 ACTTATATGGGCATTGAAAGGGGTTGCCACTG
1 AC-T-TATGGGCTTTGAAA--GATTGCCACTG
61319 ACTT
1 ACTT
61323 GTGTGGGCTT
Statistics
Matches: 199, Mismatches: 26, Indels: 36
0.76 0.10 0.14
Matches are distributed among these distances:
27 6 0.03
28 43 0.22
29 60 0.30
30 27 0.14
31 18 0.09
32 31 0.16
33 7 0.04
34 5 0.03
35 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (28 bp):
ACTTATGGGCTTTGAAAGATTGCCACTG
Found at i:61346 original size:97 final size:94
Alignment explanation
Indices: 61051--61404 Score: 305
Period size: 97 Copynumber: 3.9 Consensus size: 94
61041 GGTGCTATTA
* * * *
61051 ACTTATGGGCTTTGAAAGA---TTGCCACTGAC-T-TATGGGCTTTGAAA-GATTGCCATTGAC-
1 ACTTATGGGCTTTAAAAGAGGTTTGCCACTGACTTGTGTGGGCTTTGAAAGGGTTGCCACTGACT
* *
61109 T-TATGGGCTTT--AAGAAGGATGTCATTG
66 TATATGGGCTTTGAAAG-AGGATGCCACTG
* * * *
61136 ACTTGTGGGCTTTGAAAA-AGG--TGCCACTAAC--CTATGGGCTTTGAAAGGGTGTGCCACTGA
1 ACTTATGGGCTTT-AAAAGAGGTTTGCCACTGACTTGTGTGGGCTTTGAAAGGGT-TGCCACTGA
*
61196 C-T-TGTGGGCTTTGAAA-AGGATGCCACTG
64 CTTATATGGGCTTTGAAAGAGGATGCCACTG
* *
61224 ACTTATGGGCTTTGAAAGAGGTTTGCCA-TCGACTTGTGTGGGCTTTTGAGAGGGTTGCCACTGA
1 ACTTATGGGCTTTAAAAGAGGTTTGCCACT-GACTTGTGTGGGC-TTTGAAAGGGTTGCCACTGA
* * *
61288 CTTATATGGGCATTGAAAGGGGTTGCCACTG
64 CTTATATGGGCTTTGAAAGAGGATGCCACTG
* * ** **
61319 ACTTGTGTGGGCTTTAAAAGAGGTTTGCCACTGATTTGTGTGCACTTTGAAAGGGGTTGCCACCA
1 AC-T-TATGGGCTTTAAAAGAGGTTTGCCACTGACTTGTGTGGGCTTTGAAA-GGGTTGCCACTG
61384 ACTTATATGGGCTTTGAAAGA
63 ACTTATATGGGCTTTGAAAGA
61405 AGGGTGCCGC
Statistics
Matches: 219, Mismatches: 28, Indels: 32
0.78 0.10 0.11
Matches are distributed among these distances:
85 13 0.06
86 26 0.12
87 5 0.02
88 44 0.20
89 1 0.00
90 9 0.04
92 16 0.07
93 11 0.05
94 12 0.05
95 12 0.05
96 7 0.03
97 62 0.28
98 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (94 bp):
ACTTATGGGCTTTAAAAGAGGTTTGCCACTGACTTGTGTGGGCTTTGAAAGGGTTGCCACTGACT
TATATGGGCTTTGAAAGAGGATGCCACTG
Found at i:61347 original size:65 final size:63
Alignment explanation
Indices: 61053--61404 Score: 260
Period size: 65 Copynumber: 5.8 Consensus size: 63
61043 TGCTATTAAC
* * * *
61053 TTATGGGCTTTGAAA--GATTGCCACTGAC-T-TATGGGCTTTGAAAGA--TTGCCATTGAC-
1 TTATGGGCATTGAAAGGGGTTGCCACTGACTTGTGTGGGCTTTGAAAGAGGTTGCCACTGACT
* * * * * * *
61109 TTATGGGC-TT-TAAGAAGGATGTCATTGAC-T-TGTGGGCTTTGAAAAAGG-TGCCACTAAC-
1 TTATGGGCATTGAAAG-GGGTTGCCACTGACTTGTGTGGGCTTTGAAAGAGGTTGCCACTGACT
* * *
61167 CTATGGGCTTTGAAA-GGGTGTGCCACTGAC-T-TGTGGGCTTTGAAA-AGGATGCCACTGAC-
1 TTATGGGCATTGAAAGGGGT-TGCCACTGACTTGTGTGGGCTTTGAAAGAGGTTGCCACTGACT
* * *
61226 TTATGGGCTTTGAAAGAGGTTTGCCA-TCGACTTGTGTGGGCTTTTGAGAG-GGTTGCCACTGAC
1 TTATGGGCATTGAAAG-GGGTTGCCACT-GACTTGTGTGGGC-TTTGAAAGAGGTTGCCACTGAC
61289 T
63 T
*
61290 TATATGGGCATTGAAAGGGGTTGCCACTGACTTGTGTGGGCTTTAAAAGAGGTTTGCCACTGA-T
1 T-TATGGGCATTGAAAGGGGTTGCCACTGACTTGTGTGGGCTTTGAAAGAGG-TTGCCACTGACT
* * ** * *
61354 TTGTGTGCACTTTGAAAGGGGTTGCCACCAACTTATATGGGCTTTGAAAGA
1 TTATGGGCA--TTGAAAGGGGTTGCCACTGACTTGTGTGGGCTTTGAAAGA
61405 AGGGTGCCGC
Statistics
Matches: 242, Mismatches: 31, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
54 2 0.01
55 2 0.01
56 8 0.03
57 24 0.10
58 20 0.08
59 49 0.20
60 10 0.04
61 4 0.02
62 7 0.03
63 30 0.12
64 26 0.11
65 60 0.25
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (63 bp):
TTATGGGCATTGAAAGGGGTTGCCACTGACTTGTGTGGGCTTTGAAAGAGGTTGCCACTGACT
Found at i:61399 original size:32 final size:32
Alignment explanation
Indices: 61054--61403 Score: 233
Period size: 32 Copynumber: 11.5 Consensus size: 32
61044 GCTATTAACT
*
61054 TATGGGCTTTGAAA--GATTGCCACTGAC-T-
1 TATGGGCTTTGAAAGGGGTTGCCACTGACTTG
* *
61082 TATGGGCTTTGAAA--GATTGCCATTGAC-T-
1 TATGGGCTTTGAAAGGGGTTGCCACTGACTTG
* * * *
61110 TATGGGCTTT--AAGAAGGATGTCATTGACTTG
1 TATGGGCTTTGAAAG-GGGTTGCCACTGACTTG
** * *
61141 --TGGGCTTTGAAAAAGG-TGCCACTAAC--C
1 TATGGGCTTTGAAAGGGGTTGCCACTGACTTG
61168 TATGGGCTTTGAAA-GGGTGTGCCACTGACTTG
1 TATGGGCTTTGAAAGGGGT-TGCCACTGACTTG
* *
61200 --TGGGCTTTGAAA-AGGATGCCACTGAC-T-
1 TATGGGCTTTGAAAGGGGTTGCCACTGACTTG
*
61227 TATGGGCTTTGAAAGAGGTTTGCCA-TCGACTTG
1 TATGGGCTTTGAAAG-GGGTTGCCACT-GACTTG
* * *
61260 TGTGGGCTTTTGAGA-GGGTTGCCACTGACTTA
1 TATGGGC-TTTGAAAGGGGTTGCCACTGACTTG
*
61292 TATGGGCATTGAAAGGGGTTGCCACTGACTTG
1 TATGGGCTTTGAAAGGGGTTGCCACTGACTTG
* * * *
61324 TGTGGGCTTTAAAAGAGGTTTGCCACTGATTTG
1 TATGGGCTTTGAAAG-GGGTTGCCACTGACTTG
* ** ** *
61357 TGTGCACTTTGAAAGGGGTTGCCACCAACTTA
1 TATGGGCTTTGAAAGGGGTTGCCACTGACTTG
61389 TATGGGCTTTGAAAG
1 TATGGGCTTTGAAAG
61404 AAGGGTGCCG
Statistics
Matches: 257, Mismatches: 41, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
26 2 0.01
28 40 0.16
29 59 0.23
30 28 0.11
31 16 0.06
32 72 0.28
33 34 0.13
34 6 0.02
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (32 bp):
TATGGGCTTTGAAAGGGGTTGCCACTGACTTG
Found at i:61423 original size:65 final size:63
Alignment explanation
Indices: 61300--61443 Score: 157
Period size: 65 Copynumber: 2.3 Consensus size: 63
61290 TATATGGGCA
** * * * * *
61300 TTGAAAGGGGTTGCCACTGACTTGTGTGGGCTTTAAAAGAGGTTTGCCACTGATTTGTGTGCACT
1 TTGAAAGGGGTTGCCACCAACTTATATGGGCTTTAAAAGAGGTGTGCCACGGAGTTGTG-G-ACT
* *
61365 TTGAAAGGGGTTGCCACCAACTTATATGGGCTTTGAAAGAAGG-GTGCCGCGGAGTTGTGGACT
1 TTGAAAGGGGTTGCCACCAACTTATATGGGCTTTAAAAG-AGGTGTGCCACGGAGTTGTGGACT
*
61428 TTGAAAAGGG-TGCCAC
1 TTGAAAGGGGTTGCCAC
61444 AGAGTTGTGG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
62 6 0.09
63 12 0.18
64 1 0.01
65 46 0.68
66 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (63 bp):
TTGAAAGGGGTTGCCACCAACTTATATGGGCTTTAAAAGAGGTGTGCCACGGAGTTGTGGACT
Found at i:61435 original size:97 final size:96
Alignment explanation
Indices: 61233--61462 Score: 219
Period size: 97 Copynumber: 2.4 Consensus size: 96
61223 GACTTATGGG
* * **
61233 CTTTG-AAAGAGGTTTGCCA-TCGACTTGTGTGGGCTTTTGAGAGGGTTGCCACTGACTTATATG
1 CTTTGAAAAGAGGTTTGCCACT-GACTTGTGT-GAC-TTTGAAAGGGTTGCCACCAACTTATATG
* * *
61296 GGCATTGAAAGGGGTTGCCACTGACTTGTGTGGG
63 GGCATTGAAAGGGGTTGCCACGGACGTGTGTGGA
*
61330 CTTT-AAAAGAGGTTTGCCACTGATTTGTGTGCACTTTGAAAGGGGTTGCCACCAACTTATATGG
1 CTTTGAAAAGAGGTTTGCCACTGACTTGTGTG-ACTTTGAAA-GGGTTGCCACCAACTTATATGG
* *
61394 GCTTTGAAAGAAGGG-TGCCGCGGA-GT-TGTGGA
64 GCATTGAAAG--GGGTTGCCACGGACGTGTGTGGA
* *
61426 CTTTGAAAAG-GG--TGCCACAGAGTTGTG-GACTTTGAAA
1 CTTTGAAAAGAGGTTTGCCACTGACTTGTGTGACTTTGAAA
61463 ATAGTGCCAC
Statistics
Matches: 114, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
92 9 0.08
93 1 0.01
94 13 0.11
96 18 0.16
97 62 0.54
98 8 0.07
99 3 0.03
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (96 bp):
CTTTGAAAAGAGGTTTGCCACTGACTTGTGTGACTTTGAAAGGGTTGCCACCAACTTATATGGGC
ATTGAAAGGGGTTGCCACGGACGTGTGTGGA
Found at i:61476 original size:58 final size:58
Alignment explanation
Indices: 61395--61752 Score: 348
Period size: 58 Copynumber: 6.1 Consensus size: 58
61385 CTTATATGGG
* *
61395 CTTTGAAAGAAGGGTGCCGCGGAGTTGTGGACTTTGAAAAGGGTGCCACAGAGTTGTGGA
1 CTTTG-AA-AAGGGTGCCACGGAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
** * ** * * *
61455 CTTTGAAAATAGTGCCACGGAGTTATGGACTTTGAAAAGGGGTTTCACAGAGTTATGGG
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAA-GGGTGCCACGGAGTTGTGGA
* * * * * *
61514 CTTT-AAAAGGGTGCTACAGAGTTGTGGACTTTAAAAAAAGGTACCTCGGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGACTTT-GAAAAGGGTGCCACGGAGTTGTGGA
* *
61572 CTTTGAAAAGGGTGCCATGGAGTTGTGGACTTT-AAAAGGGTGCCATGGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * * * *
61629 CTTT-AAAAGGGTACCACAGAGTTGTGGA-TATT-ATAGGGGTGCCATGGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGACT-TTGAAAAGGGTGCCACGGAGTTGTGGA
* * ** * **
61685 CTTTGAAGAAGGGTGTCACTGAGCCGTGGACTTTGAAGAAAGGTGCCATTGAGTTGTGGA
1 CTTTGAA-AAGGGTGCCACGGAGTTGTGGACTTTGAA-AAGGGTGCCACGGAGTTGTGGA
61745 CTTTGAAA
1 CTTTGAAA
61753 GTTATTTTAC
Statistics
Matches: 247, Mismatches: 42, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
55 1 0.00
56 49 0.20
57 26 0.11
58 86 0.35
59 54 0.22
60 31 0.13
ACGTcount: A:0.27, C:0.12, G:0.34, T:0.27
Consensus pattern (58 bp):
CTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
Found at i:61525 original size:87 final size:86
Alignment explanation
Indices: 61389--61752 Score: 322
Period size: 87 Copynumber: 4.2 Consensus size: 86
61379 CACCAACTTA
* * *
61389 TATGGGCTTTGAAAGAAGGGTGCCGCGGAGTTGTGGACTTTGAAAAGGGTGCCACAGAGTTGTGG
1 TATGGACTTTG-AA-AAGGGTGCCACAGAGTTGTGGACTTT-AAAAGGGTGCCACAGAGTTGTGG
* *
61454 ACTTTGAAAATA-GTGCCACGGAGT
63 ACTTT-AAAAAAGGTACCACGGAGT
** * * *
61478 TATGGACTTTGAAAAGGGGTTTCACAGAGTTATGGGCTTTAAAAGGGTGCTACAGAGTTGTGGAC
1 TATGGACTTTGAAAA-GGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGAC
*
61543 TTTAAAAAAAGGTACCTCGGAGT
65 TTT-AAAAAAGGTACCACGGAGT
* ** **
61566 TGTGGACTTTGAAAAGGGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCATGGAGTTGTGGACT
1 TATGGACTTTGAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACT
* *
61631 TT-AAAAGGGTACCACAGAGT
66 TTAAAAAAGGTACCACGGAGT
* * * ** * * **
61651 TGTGGA-TATT-ATAGGGGTGCCATGGAGTTGTGGACTTTGAAGAAGGGTGTCACTGAGCCGTGG
1 TATGGACT-TTGAAAAGGGTGCCACAGAGTTGTGGACTTT-AA-AAGGGTGCCACAGAGTTGTGG
* * **
61714 ACTTTGAAGAAAGGTGCCATTGAGT
63 ACTTT-AAAAAAGGTACCACGGAGT
*
61739 TGTGGACTTTGAAA
1 TATGGACTTTGAAA
61753 GTTATTTTAC
Statistics
Matches: 228, Mismatches: 38, Indels: 18
0.80 0.13 0.06
Matches are distributed among these distances:
84 27 0.12
85 25 0.11
86 21 0.09
87 77 0.34
88 65 0.29
89 13 0.06
ACGTcount: A:0.27, C:0.12, G:0.34, T:0.27
Consensus pattern (86 bp):
TATGGACTTTGAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACT
TTAAAAAAGGTACCACGGAGT
Found at i:61533 original size:28 final size:29
Alignment explanation
Indices: 61395--61752 Score: 348
Period size: 28 Copynumber: 12.3 Consensus size: 29
61385 CTTATATGGG
*
61395 CTTTGAAAGAAGGGTGCCGCGGAGTTGTGGA
1 CTTTG-AA-AAGGGTGCCACGGAGTTGTGGA
*
61426 CTTTGAAAAGGGTGCCACAGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
** *
61455 CTTTGAAAATAGTGCCACGGAGTTATGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
** * * *
61484 CTTTGAAAAGGGGTTTCACAGAGTTATGGG
1 CTTTGAAAA-GGGTGCCACGGAGTTGTGGA
* *
61514 CTTT-AAAAGGGTGCTACAGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * * *
61542 CTTTAAAAAAAGGTACCTCGGAGTTGTGGA
1 CTTT-GAAAAGGGTGCCACGGAGTTGTGGA
*
61572 CTTTGAAAAGGGTGCCATGGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
*
61601 CTTT-AAAAGGGTGCCATGGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* *
61629 CTTT-AAAAGGGTACCACAGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * *
61657 -TATT-ATAGGGGTGCCATGGAGTTGTGGA
1 CT-TTGAAAAGGGTGCCACGGAGTTGTGGA
* * **
61685 CTTTGAAGAAGGGTGTCACTGAGCCGTGGA
1 CTTTGAA-AAGGGTGCCACGGAGTTGTGGA
* **
61715 CTTTGAAGAAAGGTGCCATTGAGTTGTGGA
1 CTTTGAA-AAGGGTGCCACGGAGTTGTGGA
61745 CTTTGAAA
1 CTTTGAAA
61753 GTTATTTTAC
Statistics
Matches: 273, Mismatches: 47, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
27 1 0.00
28 91 0.33
29 85 0.31
30 91 0.33
31 5 0.02
ACGTcount: A:0.27, C:0.12, G:0.34, T:0.27
Consensus pattern (29 bp):
CTTTGAAAAGGGTGCCACGGAGTTGTGGA
Found at i:70106 original size:42 final size:42
Alignment explanation
Indices: 70048--70127 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
70038 TTCTTCTCTC
* *
70048 CTCCTACTGTCATCCCTCCTCTCTCAATTATCTCTCCTATCT
1 CTCCTACTGTCATCCCTCCTATCTCAACTATCTCTCCTATCT
*
70090 CTCCT-CTGATCATCCCTCCTATCTCTACTATCTCTCCT
1 CTCCTACTG-TCATCCCTCCTATCTCAACTATCTCTCCT
70128 CCTATCATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 3 0.09
42 31 0.91
ACGTcount: A:0.14, C:0.44, G:0.03, T:0.40
Consensus pattern (42 bp):
CTCCTACTGTCATCCCTCCTATCTCAACTATCTCTCCTATCT
Found at i:70113 original size:33 final size:33
Alignment explanation
Indices: 70076--70145 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 33
70066 CTCTCTCAAT
*
70076 TATCTCTCCTATCTCTCCT-CTGATCATCCCTCC
1 TATCTCTACTATCTCTCCTCCT-ATCATCCCTCC
70109 TATCTCTACTATCTCTCCTCCTATCATCCCTCC
1 TATCTCTACTATCTCTCCTCCTATCATCCCTCC
70142 TATC
1 TATC
70146 CCTTCTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.94
34 2 0.06
ACGTcount: A:0.14, C:0.44, G:0.01, T:0.40
Consensus pattern (33 bp):
TATCTCTACTATCTCTCCTCCTATCATCCCTCC
Found at i:70140 original size:12 final size:11
Alignment explanation
Indices: 70081--70145 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 11
70071 TCAATTATCT
70081 CTCCTATCTCTC
1 CTCCTATCTC-C
70093 CT-CTGATCATCC
1 CTCCT-ATC-TCC
70105 CTCCTATCT--
1 CTCCTATCTCC
*
70114 CTACTATCTCTC
1 CTCCTATCTC-C
70126 CTCCTATCATCC
1 CTCCTATC-TCC
70138 CTCCTATC
1 CTCCTATC
70146 CCTTCTTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
9 8 0.18
11 3 0.07
12 27 0.61
13 6 0.14
ACGTcount: A:0.14, C:0.46, G:0.02, T:0.38
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:70157 original size:33 final size:33
Alignment explanation
Indices: 70084--70157 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
70074 ATTATCTCTC
*
70084 CTATCTCTCCTCTGATCATCCCTCCTATCTCTA
1 CTATCTCTCCTCTGATCATCCCTCCTATCCCTA
*
70117 CTATCTCTCCTCCT-ATCATCCCTCCTATCCCTT
1 CTATCTCTCCT-CTGATCATCCCTCCTATCCCTA
*
70150 CTTTCTCT
1 CTATCTCT
70158 TTGAGGGCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.95
34 2 0.05
ACGTcount: A:0.12, C:0.45, G:0.01, T:0.42
Consensus pattern (33 bp):
CTATCTCTCCTCTGATCATCCCTCCTATCCCTA
Found at i:71465 original size:20 final size:20
Alignment explanation
Indices: 71440--71489 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
71430 GCTGCACGTG
71440 TCGATACATTGAAGAATATA
1 TCGATACATTGAAGAATATA
* *
71460 TCGATACAATGAAGAATGTA
1 TCGATACATTGAAGAATATA
71480 TCGATACATT
1 TCGATACATT
71490 TGGGTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
TCGATACATTGAAGAATATA
Found at i:71530 original size:52 final size:52
Alignment explanation
Indices: 71452--71594 Score: 205
Period size: 52 Copynumber: 2.8 Consensus size: 52
71442 GATACATTGA
* *
71452 AGAATATATCGATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCT
1 AGAATATATCGATATAATGAAGAATGTATCGATACATTTGGGTCAAAAAACT
* * * *
71504 AGAATCTATCGATATAATGAAGAATGTATTGGTACATGTGGGTCAAAAAACT
1 AGAATATATCGATATAATGAAGAATGTATCGATACATTTGGGTCAAAAAACT
* * *
71556 AGAATGTATCAATATAATGAAAAATGTATCGATACATTT
1 AGAATATATCGATATAATGAAGAATGTATCGATACATTT
71595 TTATTCCAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.29
Consensus pattern (52 bp):
AGAATATATCGATATAATGAAGAATGTATCGATACATTTGGGTCAAAAAACT
Found at i:72165 original size:16 final size:16
Alignment explanation
Indices: 72144--72175 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
72134 TTGATTAAAC
72144 CAATATCTCGATATAT
1 CAATATCTCGATATAT
*
72160 CAATATCTTGATATAT
1 CAATATCTCGATATAT
72176 GTATCCACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (16 bp):
CAATATCTCGATATAT
Done.