Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3185
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: 114188
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1546 original size:17 final size:16
Alignment explanation
Indices: 1524--1566 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1514 TGGACTGAAT
*
1524 ATAAAAATTTAAACTAA
1 ATAAAAATATAAA-TAA
*
1541 ATAAAATAAATAAATAA
1 ATAAAA-ATATAAATAA
1558 ATAAAAATA
1 ATAAAAATA
1567 AAACTTTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAATATAAATAA
Found at i:1564 original size:18 final size:18
Alignment explanation
Indices: 1533--1568 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1523 TATAAAAATT
1533 TAAACTAAATAAAATAAA
1 TAAACTAAATAAAATAAA
1551 TAAA-TAAATAAAAATAAA
1 TAAACTAAAT-AAAATAAA
1569 ACTTTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAACTAAATAAAATAAA
Found at i:14740 original size:20 final size:20
Alignment explanation
Indices: 14694--14740 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
14684 AGCTCGTTTC
*
14694 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
14714 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
14734 CAGCTCA
1 CAGCTCA
14741 ATCTTAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:19736 original size:13 final size:13
Alignment explanation
Indices: 19718--19743 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19708 ACCTGAAAGC
19718 AATTTAATTCATA
1 AATTTAATTCATA
19731 AATTTAATTCATA
1 AATTTAATTCATA
19744 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:21457 original size:18 final size:16
Alignment explanation
Indices: 21413--21468 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 16
21403 TCTTCACTCA
*
21413 TTTTCTTTTCAAACTC
1 TTTTCTTTTCAATCTC
21429 TCTTTCTTTTTCAATCTC
1 T-TTTC-TTTTCAATCTC
*
21447 ATTTTGCTTTTCACTCTC
1 -TTTT-CTTTTCAATCTC
21465 TTTT
1 TTTT
21469 GTGATACGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 1 0.03
17 8 0.24
18 23 0.68
19 2 0.06
ACGTcount: A:0.12, C:0.25, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTTCTTTTCAATCTC
Found at i:21746 original size:152 final size:151
Alignment explanation
Indices: 21470--21772 Score: 525
Period size: 152 Copynumber: 2.0 Consensus size: 151
21460 CTCTCTTTTG
* *
21470 TGATACGAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCACATTGCCACAAGGCC
1 TGATACAAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGGCC
* * * *
21535 TAATAACGAGATCAAAGGCCCGAAAAATGTGGTCCAAACTAAATGGGACCGTTCAAGAGCTTGTT
66 CAATAACAAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTT
21600 AGCAAGGCCTTAGATGCATACA
131 -GCAAGGCCTTAGATGCATACA
21622 TGATACAAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGGCC
1 TGATACAAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGGCC
* *
21687 CAATAACAAGATCAAAGGCCCGACAAATGCGGTCCAAACTAAGTGGGACCATTCAAGAGCTTGTT
66 CAATAACAAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTT
21752 GCAAGGCCTTAGATGCATACA
131 GCAAGGCCTTAGATGCATACA
21773 CGAGAGAACA
Statistics
Matches: 143, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
151 21 0.15
152 122 0.85
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.19
Consensus pattern (151 bp):
TGATACAAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGGCC
CAATAACAAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTT
GCAAGGCCTTAGATGCATACA
Found at i:24528 original size:16 final size:16
Alignment explanation
Indices: 24507--24538 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
24497 TAATGTGTTT
24507 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
24523 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
24539 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:26060 original size:12 final size:12
Alignment explanation
Indices: 26043--26070 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
26033 AGGAAATTTG
26043 AAAAAAAAATTC
1 AAAAAAAAATTC
26055 AAAAAAAAATTC
1 AAAAAAAAATTC
26067 AAAA
1 AAAA
26071 TTTTTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:27057 original size:18 final size:18
Alignment explanation
Indices: 27001--27060 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
26991 AGTGCGAGCG
27001 AGAAAAAGAAATCAAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
27022 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
27040 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
27058 AGA
1 AGA
27061 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:28786 original size:22 final size:18
Alignment explanation
Indices: 28735--28776 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
28725 AACATTTCTT
28735 GGCTCGACTCACGAGCGA
1 GGCTCGACTCACGAGCGA
28753 GGCTCGACTCACGAGCGA
1 GGCTCGACTCACGAGCGA
28771 GGCTCG
1 GGCTCG
28777 TTATTCTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.33, G:0.36, T:0.12
Consensus pattern (18 bp):
GGCTCGACTCACGAGCGA
Found at i:29133 original size:16 final size:16
Alignment explanation
Indices: 29112--29143 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29102 TAATGTGTTT
29112 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
29128 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
29144 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:29469 original size:72 final size:73
Alignment explanation
Indices: 29330--29477 Score: 183
Period size: 72 Copynumber: 2.0 Consensus size: 73
29320 GCAGGTACAT
* * *
29330 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTATTGAGTGCAT
1 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCAT
29395 GGGACTTG
66 GGGACTTG
* * * * * * *
29403 GGACGGCATTTAAAGCGAAA-GTTGCTGTTGTA-TTTTCCCAACCAGCCGAATTTAGTGTGTGTA
1 GGACGGCATTTAAAG-AAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCA
29466 TGGGACTTG
65 TGGGACTTG
29475 GGA
1 GGA
29478 TAGCATTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 37 0.58
73 24 0.38
74 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (73 bp):
GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCAT
GGGACTTG
Found at i:30831 original size:10 final size:10
Alignment explanation
Indices: 30816--30853 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
30806 TTGGGTTAAG
30816 ATTGAGCTGA
1 ATTGAGCTGA
30826 ATTGAGCTCGA
1 ATTGAGCT-GA
30837 A-TGAGCTGA
1 ATTGAGCTGA
*
30846 CTTGAGCT
1 ATTGAGCT
30854 TGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:30841 original size:20 final size:20
Alignment explanation
Indices: 30818--30864 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
30808 GGGTTAAGAT
30818 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
30838 TGAGCTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAA
30858 TGAGCTG
1 TGAGCTG
30865 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:32131 original size:19 final size:19
Alignment explanation
Indices: 32109--32146 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
32099 AACTAGCCAA
32109 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
32128 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
32147 TTCTAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
GGACAACTCAAGAGTCATT
Found at i:33973 original size:12 final size:12
Alignment explanation
Indices: 33956--33980 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33946 TTTCACTCTT
33956 CTCTTTTTCAAA
1 CTCTTTTTCAAA
33968 CTCTTTTTCAAA
1 CTCTTTTTCAAA
33980 C
1 C
33981 CCTCTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:35008 original size:32 final size:30
Alignment explanation
Indices: 34948--35012 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
34938 TATAACTTGA
*
34948 TTTTTTTTGCTCACCTTTTTTTTTCTTTTCTT
1 TTTTTTTTGCTCA-CTTTTTTTTACTTTT-TT
34980 TTTTTTTTGCTCGA-TTTTTTTTCACTTTTTT
1 TTTTTTTTGCTC-ACTTTTTTTT-ACTTTTTT
35011 TT
1 TT
35013 GAATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 12 0.40
32 17 0.57
33 1 0.03
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (30 bp):
TTTTTTTTGCTCACTTTTTTTTACTTTTTT
Found at i:35045 original size:12 final size:12
Alignment explanation
Indices: 34993--35051 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
34983 TTTTTGCTCG
34993 ATTTTTTTTC-A
1 ATTTTTTTTCGA
*
35004 CTTTTTTTT-GA
1 ATTTTTTTTCGA
*
35015 ATTTTTTTTTCAATCA
1 A-TTTTTTTTC---GA
35031 ATTTTTTTTCGA
1 ATTTTTTTTCGA
35043 ATTTTTTTT
1 ATTTTTTTT
35052 TTGATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
11 9 0.24
12 18 0.47
15 9 0.24
16 2 0.05
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.71
Consensus pattern (12 bp):
ATTTTTTTTCGA
Found at i:35058 original size:12 final size:13
Alignment explanation
Indices: 35005--35062 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 13
34995 TTTTTTTCAC
35005 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
35017 TTTTTTTTC-AAT
1 TTTTTTTTCGAAT
35029 CAATTTTTTTTCGAAT
1 ---TTTTTTTTCGAAT
*
35045 TTTTTTTTTG-AT
1 TTTTTTTTCGAAT
35057 TTTTTT
1 TTTTTT
35063 GTTACTCCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 19 0.47
13 9 0.22
15 9 0.22
16 3 0.08
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:37410 original size:10 final size:10
Alignment explanation
Indices: 37395--37456 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
37385 TTTGAACCAT
*
37395 TACCAATTCG
1 TACCAATTCA
*
37405 TACCAAATACCA
1 TACC-AAT-TCA
*
37417 TACCATTTCA
1 TACCAATTCA
37427 TACCAATTCCA
1 TACCAATT-CA
* *
37438 TACCATTTCG
1 TACCAATTCA
37448 TACCAATTC
1 TACCAATTC
37457 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:37440 original size:21 final size:21
Alignment explanation
Indices: 37395--37457 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37385 TTTGAACCAT
* *
37395 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
37417 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
37438 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
37458 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:41720 original size:11 final size:11
Alignment explanation
Indices: 41704--41742 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
41694 TAGTTTCTTT
41704 AAAAAAAATTC
1 AAAAAAAATTC
*
41715 AAAAAAAAAT-
1 AAAAAAAATTC
41725 -AAAAAAATTC
1 AAAAAAAATTC
41735 AAAAAAAA
1 AAAAAAAA
41743 AATTTGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 8 0.33
11 16 0.67
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:41721 original size:12 final size:12
Alignment explanation
Indices: 41704--41743 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
41694 TAGTTTCTTT
41704 AAAAAAAATTCA
1 AAAAAAAATTCA
41716 AAAAAAAA-T--
1 AAAAAAAATTCA
41725 -AAAAAAATTCA
1 AAAAAAAATTCA
41736 AAAAAAAA
1 AAAAAAAA
41744 ATTTGGTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
8 7 0.29
9 1 0.04
11 1 0.04
12 15 0.62
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:41745 original size:21 final size:20
Alignment explanation
Indices: 41705--41743 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
41695 AGTTTCTTTA
41705 AAAAAAATTCAAAAAAAAAT
1 AAAAAAATTCAAAAAAAAAT
41725 AAAAAAATTCAAAAAAAAA
1 AAAAAAATTCAAAAAAAAA
41744 ATTTGGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAAAAATTCAAAAAAAAAT
Found at i:41806 original size:14 final size:14
Alignment explanation
Indices: 41787--41838 Score: 86
Period size: 14 Copynumber: 3.6 Consensus size: 14
41777 ATCAAGTTGA
41787 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
41801 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
41815 AAAAAAAATTTTCGTG
1 AAAAAAAA--TTCGTG
41831 AAAAAAAA
1 AAAAAAAA
41839 AGAAGAAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
14 22 0.61
16 14 0.39
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (14 bp):
AAAAAAAATTCGTG
Found at i:41807 original size:16 final size:16
Alignment explanation
Indices: 41786--41839 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
41776 TATCAAGTTG
41786 AAAAAAAAATTCGTG-
1 AAAAAAAAATTCGTGA
41801 -AAAAAAAATTCGTGA
1 AAAAAAAAATTCGTGA
**
41816 AAAAAAATTTTCGTGA
1 AAAAAAAAATTCGTGA
41832 AAAAAAAA
1 AAAAAAAA
41840 GAAGAAGCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.41
16 20 0.59
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.20
Consensus pattern (16 bp):
AAAAAAAAATTCGTGA
Found at i:57943 original size:12 final size:12
Alignment explanation
Indices: 57926--57984 Score: 97
Period size: 12 Copynumber: 5.2 Consensus size: 12
57916 TAATAGTTTC
57926 TTCAAAAAAAAA
1 TTCAAAAAAAAA
57938 TTCAAAAAAAAA
1 TTCAAAAAAAAA
57950 TTC--AAAAAAA
1 TTCAAAAAAAAA
57960 TTC-AAAAAAAA
1 TTCAAAAAAAAA
57971 TTCAAAAAAAAA
1 TTCAAAAAAAAA
57983 TT
1 TT
57985 GGTTTCCATT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.22
11 10 0.22
12 25 0.56
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.20
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:57946 original size:11 final size:11
Alignment explanation
Indices: 57930--57981 Score: 88
Period size: 11 Copynumber: 4.7 Consensus size: 11
57920 AGTTTCTTCA
57930 AAAAAAAATTC
1 AAAAAAAATTC
57941 AAAAAAAAATTC
1 -AAAAAAAATTC
57953 -AAAAAAATTC
1 AAAAAAAATTC
57963 AAAAAAAATTC
1 AAAAAAAATTC
57974 AAAAAAAA
1 AAAAAAAA
57982 ATTGGTTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.26
11 18 0.46
12 11 0.28
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:57959 original size:22 final size:21
Alignment explanation
Indices: 57931--57980 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 21
57921 GTTTCTTCAA
57931 AAAAAAATTCAAAAAAAAATTC
1 AAAAAAATTC-AAAAAAAATTC
57953 AAAAAAATTCAAAAAAAATTC
1 AAAAAAATTCAAAAAAAATTC
57974 AAAAAAA
1 AAAAAAA
57981 AATTGGTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (21 bp):
AAAAAAATTCAAAAAAAATTC
Found at i:58041 original size:15 final size:16
Alignment explanation
Indices: 58021--58060 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
58011 GATATCAAGT
58021 TGAAAAAAAAA-TTCG
1 TGAAAAAAAAATTTCG
58036 TGAAAAAAAAATTTCG
1 TGAAAAAAAAATTTCG
58052 TGAAAAAAA
1 TGAAAAAAA
58061 GAAGAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:64868 original size:12 final size:12
Alignment explanation
Indices: 64851--64875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64841 TTTCACTCTT
64851 CTCTTTTTCAAA
1 CTCTTTTTCAAA
64863 CTCTTTTTCAAA
1 CTCTTTTTCAAA
64875 C
1 C
64876 CCTCTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:67050 original size:11 final size:11
Alignment explanation
Indices: 67000--67066 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 11
66990 TTGGAGTAAC
67000 AAAAAAA-TCA
1 AAAAAAATTCA
67010 AAAAAAATTCGAA
1 AAAAAAATTC--A
*
67023 AAAAAATTGATTGA
1 AAAAAA---ATTCA
67037 AAAAAAATTCA
1 AAAAAAATTCA
* *
67048 AAAAAAAGTGA
1 AAAAAAATTCA
67059 AAAAAAAT
1 AAAAAAAT
67067 CGAGCAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
10 7 0.15
11 22 0.48
13 7 0.15
14 7 0.15
16 3 0.07
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.16
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:67077 original size:37 final size:37
Alignment explanation
Indices: 67000--67090 Score: 105
Period size: 38 Copynumber: 2.5 Consensus size: 37
66990 TTGGAGTAAC
* *
67000 AAAAAAATCAAAAAAAATTCGAAAAAAAATTGATTG-AA
1 AAAAAAATCAAAAAAAAGTCGAAAAAAAATCGA--GCAA
*
67038 AAAAAATTCAAAAAAAAGT-GAAAAAAAATCGAGCAA
1 AAAAAAATCAAAAAAAAGTCGAAAAAAAATCGAGCAA
**
67074 AAAAAAAAGAAAAAAAA
1 AAAAAAATCAAAAAAAA
67091 AGGGTGAGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 1 0.02
36 16 0.35
37 12 0.26
38 17 0.37
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (37 bp):
AAAAAAATCAAAAAAAAGTCGAAAAAAAATCGAGCAA
Found at i:67125 original size:28 final size:27
Alignment explanation
Indices: 67047--67125 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
67037 AAAAAAATTC
*
67047 AAAAAAAAGTGAAAAAAAA-TCGAGCAA
1 AAAAAAAAGTAAAAAAAAAGT-GAGCAA
67074 AAAAAAAAG-AAAAAAAAAGGGTGAGCAA
1 AAAAAAAAGTAAAAAAAAA--GTGAGCAA
* *
67102 AAAAATCAAGTTAAAAAAAAGTGA
1 AAAAA-AAAGTAAAAAAAAAGTGA
67126 AAAGTCTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
26 8 0.18
27 9 0.20
28 15 0.34
29 4 0.09
30 8 0.18
ACGTcount: A:0.70, C:0.05, G:0.16, T:0.09
Consensus pattern (27 bp):
AAAAAAAAGTAAAAAAAAAGTGAGCAA
Found at i:71862 original size:11 final size:11
Alignment explanation
Indices: 71847--71881 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
71837 TTTTTGCTCG
71847 ATTTTTTTTCA
1 ATTTTTTTTCA
* *
71858 CTTTTTTTTGA
1 ATTTTTTTTCA
71869 ATTTTTTTTCA
1 ATTTTTTTTCA
71880 AT
1 AT
71882 CAATTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:71862 original size:30 final size:28
Alignment explanation
Indices: 71785--71866 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 28
71775 GCAAGACTTT
**
71785 TCACTTTTTTTTAACTTGATTTTTTTTGC
1 TCACTTTTTTTT-ACTTTTTTTTTTTTGC
*
71814 TCACCTTTTTTTTTCTTTTCTTTTTTTTGC
1 TCA-CTTTTTTTTACTTTT-TTTTTTTTGC
71844 TCGA-TTTTTTTTCACTTTTTTTT
1 TC-ACTTTTTTTT-ACTTTTTTTT
71867 GAATTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 18 0.40
30 26 0.58
31 1 0.02
ACGTcount: A:0.09, C:0.16, G:0.05, T:0.71
Consensus pattern (28 bp):
TCACTTTTTTTTACTTTTTTTTTTTTGC
Found at i:71875 original size:13 final size:13
Alignment explanation
Indices: 71859--71905 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
71849 TTTTTTTCAC
71859 TTTTTTTTGAATT
1 TTTTTTTTGAATT
* *
71872 TTTTTTCAATCAATT
1 TTTTTT--TTGAATT
71887 TTTTTTTTGAATT
1 TTTTTTTTGAATT
71900 TTTTTT
1 TTTTTT
71906 GATTTTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 17 0.61
15 11 0.39
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:73394 original size:10 final size:10
Alignment explanation
Indices: 73379--73416 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
73369 TTGGGTTAAG
73379 ATTGAGCTGA
1 ATTGAGCTGA
73389 ATTGAGCTCGA
1 ATTGAGCT-GA
73400 A-TGAGCTGA
1 ATTGAGCTGA
*
73409 CTTGAGCT
1 ATTGAGCT
73417 TGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:73404 original size:20 final size:20
Alignment explanation
Indices: 73381--73437 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
73371 GGGTTAAGAT
73381 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
73401 TGAGCTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAA
*
73421 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
73438 AAACGGAGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 23 0.74
21 8 0.26
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:82236 original size:960 final size:958
Alignment explanation
Indices: 79719--82574 Score: 5304
Period size: 954 Copynumber: 3.0 Consensus size: 958
79709 GGCCCAATTT
* * * ** * *
79719 GTAAACATTTTAGTTGTTTAAGTTAATTTTTTAAGT-TTTAGGAATATCACATGTTAAATTCGGC
1 GTAAACATCTTACTTGTTTAATTTAATTTTTTAA-TCTTTAGGAGCATTACATGTAAAATTCGGC
* * * * *
79783 CCAAAACAACCCA-ATAGGATGCATGGCCGAATTTTCCTT-TGT-TTTT-TTAATTAAGTTTAAT
65 CCAAAACAGCCCATATAAG-TGCATGGCCGAATTTACCTTGT-TATTTTATTAAATAGGTTTAAT
* ** *
79844 TTTTTA--AGTTTTCTAATTAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACC
128 TTTTTATTAG-TTACTTGTGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACC
79907 CTTTGTAAACATCTTATTATTATTTTTCTATCAAATTTTAGATTTGTTGAGTGCAGAATTTTCTT
192 CTTTGTAAACATCTTATTATTATTTTTCTATCAAATTTTAGATTTGTTGAGTGCAGAATTTTCTT
* *
79972 TGGGGTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTGATT
257 TCGGGTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTGGATT
* *
80037 GTGGGAGCCATCTTCAACCTTCTTCTTGCCATCGATATTCTTTGGAGGGGAGATTAGAGCCGTTT
322 GTGGGAACCATCTTCAACCTTCTTCTTGCCATCGATATTCGTTGGAGGGGAGATTAGAGCCGTTT
80102 GAAGAGATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTTGCTG
387 GAAGAGATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTTGCTG
80167 TTCATTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTTGTTTATTCTTCTTG
452 TTCATTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTTGTTTATTCTTCTTG
80232 TGAATTTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAAATTC
517 TGAATTTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAAATTC
* *
80297 GACTAAACTTATCTTTTCCAATTAATCTTGTCAAATTCTTCTTGTCAAAACTGACTATTTTAGGT
582 GACTAAACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTTAGGT
80362 TGCTGGAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTTCTTG
647 TGCTGGAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTTCTTG
*
80427 GACAGATTCAGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAAAACA
712 GACAGATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAAAACA
80492 TCTATTCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTTTTGGGGATCTTAATTTCCAGATC
777 TCTATTCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTTTTGGGGATCTTAATTTCCAGATC
80557 TGATTTGTTTTTAATCTTATTCTTTGTTTTAATTTTTAGATCTGTTCAATTAGAGCTTTTGTAGG
842 TGATTTGTTTTTAATCTTATTCTTTGTTTTAATTTTTAGATCTGTTCAATTAGAGCTTTTGTAGG
80622 AGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCGCCTCCGTACCA
907 AGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCGCCTCCGTACCA
80674 GTAAACATCTTACTTGTTTAATTTAA-TTTTTAATCTTTAGGAGCATTACATGTAAAATTCGGCC
1 GTAAACATCTTACTTGTTTAATTTAATTTTTTAATCTTTAGGAGCATTACATGTAAAATTCGGCC
80738 CAAAA-AG-CCATATAAGTGCATGGCCGAATTTACCTTGTTATTTTATTAAATAGGTTTAATTTT
66 CAAAACAGCCCATATAAGTGCATGGCCGAATTTACCTTGTTATTTTATTAAATAGGTTTAATTTT
80801 TTATTAGTTACTTGTGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTT
131 TTATTAGTTACTTGTGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTT
*
80866 GTAAACATCTTATTATTA-TTTTCTATCAAATTTTAGATTTGTTGAGTGTAGAATTTTCTTTCGG
196 GTAAACATCTTATTATTATTTTTCTATCAAATTTTAGATTTGTTGAGTGCAGAATTTTCTTTCGG
80930 GTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTGGATTGTGG
261 GTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTGGATTGTGG
80995 GAACCATCTTCAACCTTCTTCTTGCCATCGATATTCGTTGGAGGGGAGATTAGAGCCGTTTGAAG
326 GAACCATCTTCAACCTTCTTCTTGCCATCGATATTCGTTGGAGGGGAGATTAGAGCCGTTTGAAG
81060 AGATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTTGCTGTTCA
391 AGATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTTGCTGTTCA
81125 TTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTTGTTTATTCTTCTTGTGAA
456 TTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTTGTTTATTCTTCTTGTGAA
81190 TTTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAAATTCGACT
521 TTTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAAATTCGACT
81255 AAACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTTAGGTTGCT
586 AAACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTTAGGTTGCT
81320 GGAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTTCTTGGACA
651 GGAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTTCTTGGACA
81385 GATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAAAACATCTA
716 GATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAAAACATCTA
81450 TTCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTTTTGGGGATCTTAATTTCCAGATCTGAT
781 TTCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTTTTGGGGATCTTAATTTCCAGATCTGAT
*
81515 TTTTTTTTAATCTTATTCTTTGTTTTAATTTTTAGATCTGTTCAATTAGAGCTTTTGTAGGAGTT
846 TTGTTTTTAATCTTATTCTTTGTTTTAATTTTTAGATCTGTTCAATTAGAGCTTTTGTAGGAGTT
81580 TCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCGCCTCCGTACCA
911 TCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCGCCTCCGTACCA
81628 GTAAACATCTTACTTGTTTAATTTAATTTTTTAATCTTTAGGAGCATTACATGTAAAATTCGGCC
1 GTAAACATCTTACTTGTTTAATTTAATTTTTTAATCTTTAGGAGCATTACATGTAAAATTCGGCC
81693 CAAAACAGCCCATATAAGTGCATGGCCGAATTTACCTTGTTATTTTATTAAATAGGTTTAATTTT
66 CAAAACAGCCCATATAAGTGCATGGCCGAATTTACCTTGTTATTTTATTAAATAGGTTTAATTTT
81758 TTATTAGTTACTTGTGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTT
131 TTATTAGTTACTTGTGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTT
81823 GTAAACACATCTTATTATTATTTTTCTATCAAATTTTAGATTTGTTGAGTGCAGAATTTTCTTTC
196 GT-AA-ACATCTTATTATTATTTTTCTATCAAATTTTAGATTTGTTGAGTGCAGAATTTTCTTTC
81888 GGGTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTGGATTGT
259 GGGTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTGGATTGT
81953 GGGAACCATCTTCAACCTTCTTCTTGCCATCGATATTCGTTGGAGGGGAGATTAGAGCCGTTTGA
324 GGGAACCATCTTCAACCTTCTTCTTGCCATCGATATTCGTTGGAGGGGAGATTAGAGCCGTTTGA
*
82018 AGAGATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTTACTGTT
389 AGAGATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTTGCTGTT
*
82083 CATTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTTGTTTGTTCTTCTTGTG
454 CATTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTTGTTTATTCTTCTTGTG
82148 AATTTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAAATTCGA
519 AATTTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAAATTCGA
82213 CTAAACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTTAGGTTG
584 CTAAACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTTAGGTTG
82278 CTGGAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTTCTTGGA
649 CTGGAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTTCTTGGA
82343 CAGATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAAAACATC
714 CAGATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAAAACATC
82408 TATTCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTTTTGGGGATCTTAATTTCCAGATCTG
779 TATTCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTTTTGGGGATCTTAATTTCCAGATCTG
* * *
82473 ATTTGTTTTTAATCTTATTCTTTGTTTTGA-TTTCAGATCTGTTCGATTAGAGCTTTTGTAGGAG
844 ATTTGTTTTTAATCTTATTCTTTGTTTTAATTTTTAGATCTGTTCAATTAGAGCTTTTGTAGGAG
82537 TTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGC
909 TTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGC
82575 AACCCCCATA
Statistics
Matches: 1856, Mismatches: 32, Indels: 22
0.97 0.02 0.01
Matches are distributed among these distances:
952 23 0.01
953 11 0.01
954 817 0.44
955 138 0.07
956 4 0.00
957 123 0.07
958 2 0.00
959 84 0.05
960 654 0.35
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (958 bp):
GTAAACATCTTACTTGTTTAATTTAATTTTTTAATCTTTAGGAGCATTACATGTAAAATTCGGCC
CAAAACAGCCCATATAAGTGCATGGCCGAATTTACCTTGTTATTTTATTAAATAGGTTTAATTTT
TTATTAGTTACTTGTGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTT
GTAAACATCTTATTATTATTTTTCTATCAAATTTTAGATTTGTTGAGTGCAGAATTTTCTTTCGG
GTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTGGATTGTGG
GAACCATCTTCAACCTTCTTCTTGCCATCGATATTCGTTGGAGGGGAGATTAGAGCCGTTTGAAG
AGATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTTGCTGTTCA
TTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTTGTTTATTCTTCTTGTGAA
TTTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAAATTCGACT
AAACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTTAGGTTGCT
GGAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTTCTTGGACA
GATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAAAACATCTA
TTCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTTTTGGGGATCTTAATTTCCAGATCTGAT
TTGTTTTTAATCTTATTCTTTGTTTTAATTTTTAGATCTGTTCAATTAGAGCTTTTGTAGGAGTT
TCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCGCCTCCGTACCA
Found at i:82624 original size:6 final size:6
Alignment explanation
Indices: 82615--82707 Score: 62
Period size: 6 Copynumber: 15.0 Consensus size: 6
82605 CATTTTCATA
* * * **
82615 TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC TTTTTC
1 TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
* * **
82666 GTTTTC TTTTT- TGTTTTC TTTTTC TTCTTC ACTTTC TTTTTC
1 TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
82708 AAATTCATTA
Statistics
Matches: 64, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
5 1 0.02
6 50 0.78
7 10 0.16
8 3 0.05
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.72
Consensus pattern (6 bp):
TTTTTC
Found at i:83674 original size:10 final size:9
Alignment explanation
Indices: 83658--83705 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 9
83648 CCATCCACGA
83658 ATTTTTTTT
1 ATTTTTTTT
83667 ACTTTTTTTT
1 A-TTTTTTTT
**
83677 ATTTTTTCG
1 ATTTTTTTT
83686 ATTTTTTTT
1 ATTTTTTTT
*
83695 AAATTTTTTT
1 -ATTTTTTTT
83705 A
1 A
83706 ATCACTTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 15 0.47
10 17 0.53
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:84832 original size:13 final size:13
Alignment explanation
Indices: 84814--84839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
84804 ACCTGAAAGC
84814 AATTTAATTCATA
1 AATTTAATTCATA
84827 AATTTAATTCATA
1 AATTTAATTCATA
84840 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:86538 original size:17 final size:17
Alignment explanation
Indices: 86496--86543 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
86486 TTTTTTTTCT
*
86496 TTCTTCTTTTTTTTTAAC
1 TTCTT-TTTTTTTGTAAC
*
86514 -TCGATTTTTTTTGTAAC
1 TTC-TTTTTTTTTGTAAC
86531 TTCTTTTTTTTTG
1 TTCTTTTTTTTTG
86544 AATTTTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.10, C:0.12, G:0.06, T:0.71
Consensus pattern (17 bp):
TTCTTTTTTTTTGTAAC
Found at i:88742 original size:22 final size:22
Alignment explanation
Indices: 88712--88755 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
88702 TTTGGTATTT
88712 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
88734 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
88756 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:90198 original size:14 final size:12
Alignment explanation
Indices: 90176--90213 Score: 58
Period size: 12 Copynumber: 3.0 Consensus size: 12
90166 TAGTAGTTTC
90176 TTCAAAAAAAAA
1 TTCAAAAAAAAA
90188 TTTCGAAAAAAAAA
1 -TTC-AAAAAAAAA
90202 TTCAAAAAAAAA
1 TTCAAAAAAAAA
90214 AATTGGTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 9 0.38
13 6 0.25
14 9 0.38
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:90217 original size:14 final size:13
Alignment explanation
Indices: 90176--90214 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
90166 TAGTAGTTTC
*
90176 TTCAAAAAAAAAT
1 TTCAAAAAAAAAA
*
90189 TTCGAAAAAAAAA
1 TTCAAAAAAAAAA
90202 TTCAAAAAAAAAA
1 TTCAAAAAAAAAA
90215 ATTGGTTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (13 bp):
TTCAAAAAAAAAA
Found at i:90275 original size:16 final size:16
Alignment explanation
Indices: 90254--90310 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
90244 GATATCAAGT
90254 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
90270 TG-AAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
*
90285 TGAAAAAAAAATTTCG
1 TGAAAAAAAAAATTCG
90301 TGAAAAAAAA
1 TGAAAAAAAA
90311 GAAGCTAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
15 15 0.38
16 24 0.62
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.19
Consensus pattern (16 bp):
TGAAAAAAAAAATTCG
Found at i:90277 original size:15 final size:15
Alignment explanation
Indices: 90257--90310 Score: 99
Period size: 15 Copynumber: 3.5 Consensus size: 15
90247 ATCAAGTTGA
90257 AAAAAAAAATTCGTG
1 AAAAAAAAATTCGTG
90272 AAAAAAAAATTCGTG
1 AAAAAAAAATTCGTG
90287 AAAAAAAAATTTCGTG
1 AAAAAAAAA-TTCGTG
90303 AAAAAAAA
1 AAAAAAAA
90311 GAAGCTAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 24 0.63
16 14 0.37
ACGTcount: A:0.65, C:0.06, G:0.11, T:0.19
Consensus pattern (15 bp):
AAAAAAAAATTCGTG
Found at i:97287 original size:24 final size:24
Alignment explanation
Indices: 97255--97303 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
97245 GAATTTTTAC
97255 ATAGAATTTAATTCATAAAGTCTA
1 ATAGAATTTAATTCATAAAGTCTA
97279 ATAGAATTTAATTCATAAAGTCTA
1 ATAGAATTTAATTCATAAAGTCTA
97303 A
1 A
97304 AATGTAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (24 bp):
ATAGAATTTAATTCATAAAGTCTA
Found at i:110195 original size:48 final size:49
Alignment explanation
Indices: 110085--110237 Score: 221
Period size: 46 Copynumber: 3.2 Consensus size: 49
110075 GCCCTTCGGG
*
110085 ACTTATCACATTCATCACATCGGCCATTAGGCCCTAT-ACATATATACAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
110134 ACTTT-ACA-TCATCACATCGGCCATTA-GCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
*
110180 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATAT-TAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
*
110226 ACTTTTACATTC
1 ACTTTCACATTC
110238 TCAAAGTAAG
Statistics
Matches: 97, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
45 7 0.07
46 48 0.49
47 10 0.10
48 19 0.20
49 13 0.13
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.32
Consensus pattern (49 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
Done.