Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1035
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: 48174
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7825 original size:122 final size:122
Alignment explanation
Indices: 7605--8070 Score: 593
Period size: 122 Copynumber: 3.8 Consensus size: 122
7595 AGGAAAATCA
** *
7605 ACTCATATCACGAGAGGTGAGTTGAGCCTTTTAATTTCTG-TTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
* *
7669 GAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTTTAGTTTATGTTTAAATG
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGTATTTTTTAGTTTATGTTTAAATG
* *
7726 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTAATTTTTGTTTTTC-AAAATCAAATCATATTG
1 ACTCATATTGCGAGAGGTGAGTTAAGCC-TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTG
* * * ** * *
7790 CTAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT-CTGTTATTTTTCAAAAAT
65 CGAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGT-ATTT---TTTAGT-TTATGTTT---AAAT
*
7854 CA
122 -G
*
7856 ACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
*
7921 GAGAAGTGAGTTGAGCCT-AGGGGCACGCCAAGGTA-TTTTTAGTTTATGTTTTAAATTG
66 GAGAAGTGAGTTGAGCCTCA-GGACACGCCAAGGTATTTTTTAGTTTATG-TTTAAA-TG
*
7979 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTC-AAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
* *
8043 TAGAGGTGAGTTGAGCCTCAGGACACGC
66 GAGAAGTGAGTTGAGCCTCAGGACACGC
8071 TGAGGTAATT
Statistics
Matches: 296, Mismatches: 32, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
121 25 0.08
122 96 0.32
123 57 0.19
124 1 0.00
125 8 0.03
126 14 0.05
128 2 0.01
129 23 0.08
130 70 0.24
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (122 bp):
ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
GAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGTATTTTTTAGTTTATGTTTAAATG
Found at i:8042 original size:252 final size:252
Alignment explanation
Indices: 7598--8137 Score: 906
Period size: 252 Copynumber: 2.1 Consensus size: 252
7588 CTTTCCAAGG
**
7598 AAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTCAAAAATCAACTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTCAAAAATCAACTCA
*
7663 TATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTTTAGTTTATGTTTAAATGAC
66 TATTGCGAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTATTTTTTAGTTTATGTTTAAATGAC
*
7728 TCATATTGCGAGAGGTGAGTTAAGCCTTTTTAATTTTTGTTTTTCAAAATCAAATCATATTGCTA
131 TCATATTGCGAGAGGTGAGTTAAGCCTTTTTAATTTATGTTTTTCAAAATCAAATCATATTGCTA
****
7793 GAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTATT-TTTCA
196 GAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTATTAAAAAA
7849 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTG-TTTTCAAAAATCAACTC
7914 ATATTGCGAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTA-TTTTTAGTTTATGTTTTAAATT
65 ATATTGCGAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTATTTTTTAGTTTATG-TTTAAA-T
*
7978 GACTCATATTGCGAGAGGTGAGTTAAGCC-TTTTAATTTATGTTTTTCAAAATCAACTCATATTG
128 GACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTAATTTATGTTTTTCAAAATCAAATCATATTG
* * *
8042 CTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAATTTCTGTTGTTAAAAAA
193 CTAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTATTAAAAAA
**
8102 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
8138 CAGGACACGC
Statistics
Matches: 271, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
251 58 0.21
252 148 0.55
253 65 0.24
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (252 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTCAAAAATCAACTCA
TATTGCGAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTATTTTTTAGTTTATGTTTAAATGAC
TCATATTGCGAGAGGTGAGTTAAGCCTTTTTAATTTATGTTTTTCAAAATCAAATCATATTGCTA
GAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTATTAAAAAA
Found at i:8294 original size:73 final size:72
Alignment explanation
Indices: 8007--8676 Score: 822
Period size: 73 Copynumber: 9.2 Consensus size: 72
7997 GAGTTAAGCC
* * ** *
8007 TTTT-AATTTATGTTTTTCAAAA-TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
*
8070 CTGAGGTAA
65 TTGAGGT-A
* * *
8079 TTTT-AATTTCTGTTGTTAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGA
1 TTTTCAATTTCTGTT-TT----CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA
* *
8143 CACGCTGAGTTA
61 CACGTTGAGGTA
* * * *
8155 ATTT-AATTTCTGTTTTCAAAA-T-AACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACGC
1 TTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
8217 TGAGGTA
66 TGAGGTA
*
8224 TTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTGAAGACACG
1 TTTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
8289 TTGAGGTA
65 TTGAGGTA
* * * *
8297 ATTTCAATTTATGTTTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACAAGT
1 TTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
8362 TGAGGTA
66 TGAGGTA
8369 TTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
1 TTTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
8434 TTGAGGTA
65 TTGAGGTA
* * * *
8442 ATTTCAATTTATGTTTTCAAAATTCAACTCATATTGTGAG-AA-GAGTTGAGCCTCAAGACAAGT
1 TTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
8505 TGA-GTA
66 TGAGGTA
8511 TTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATA
1 TTTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC--A
8576 C-TT-AGGTA
63 CGTTGAGGTA
* * * * ** *
8584 TTGTCAATTTTTTGTATGTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 TTTTCAA-TTTCTG--T-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
*
8649 ATGTTGAGGTA
62 ACGTTGAGGTA
*
8660 TTTTCCATTTCTGTTTT
1 TTTTCAATTTCTGTTTT
8677 TCAATTTATG
Statistics
Matches: 532, Mismatches: 44, Indels: 44
0.86 0.07 0.07
Matches are distributed among these distances:
69 62 0.12
70 58 0.11
71 19 0.04
72 128 0.24
73 134 0.25
74 7 0.01
75 10 0.02
76 70 0.13
77 44 0.08
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (72 bp):
TTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
TGAGGTA
Found at i:8379 original size:145 final size:144
Alignment explanation
Indices: 8011--8680 Score: 876
Period size: 145 Copynumber: 4.6 Consensus size: 144
8001 TAAGCCTTTT
** * *
8011 AATTTATGTTTTTCAAAATCAACTCATATTGCT-AGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTATG-TTTTCAAAATCAACTCATATTG-TGAGAAATGAGTTGAGCCTCAGGACAAGTTGAG
* *
8075 GTAATTTT-AATTTCTG-TTGTTAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
64 GT-ATTTTCAATTTCTGCTT-TT----CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCT
* * *
8138 CAGGACACGCTGAGTTAATTT-
123 CAAGACACGTTGAGGTAATTTC
* * * * *
8159 AATTTCTGTTTTCAAAAT-AACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGT
1 AATTTATGTTTTCAAAATCAACTCATATTGTGAGAAATGAGTTGAGCCTCAGGACAAGTTGAGGT
*
8223 ATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTGAAGACAC
66 ATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
8288 GTTGAGGTAATTTC
131 GTTGAGGTAATTTC
*
8302 AATTTATGTTTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACAAGTTGAGG
1 AATTTATGTTTTCAAAA-TCAACTCATATTGTGAGAAATGAGTTGAGCCTCAGGACAAGTTGAGG
8367 TATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
65 TATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
8432 CGTTGAGGTAATTTC
130 CGTTGAGGTAATTTC
*
8447 AATTTATGTTTTCAAAATTCAACTCATATTGTGAG-AA-GAGTTGAGCCTCAAGACAAGTTGA-G
1 AATTTATGTTTTCAAAA-TCAACTCATATTGTGAGAAATGAGTTGAGCCTCAGGACAAGTTGAGG
8509 TATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
65 TATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC-
8574 TAC-TT-AGGT-ATTGTC
129 -ACGTTGAGGTAATT-TC
* * * ** *
8589 AATTTTTTGTATGTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGTT
1 AA-TTTATG--T-TTTC-AAAATCAACTCATATTGTGAGAAATGAGTTGAGCCTCAGGACAAGTT
* *
8654 GAGGTATTTTCCATTTCTGTTTTTCAA
61 GAGGTATTTTCAATTTCTGCTTTTCAA
8681 TTTATGTTTT
Statistics
Matches: 478, Mismatches: 27, Indels: 33
0.89 0.05 0.06
Matches are distributed among these distances:
141 3 0.01
142 126 0.26
143 47 0.10
144 5 0.01
145 160 0.33
146 70 0.15
147 16 0.03
148 29 0.06
149 22 0.05
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (144 bp):
AATTTATGTTTTCAAAATCAACTCATATTGTGAGAAATGAGTTGAGCCTCAGGACAAGTTGAGGT
ATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
GTTGAGGTAATTTC
Found at i:8747 original size:86 final size:86
Alignment explanation
Indices: 8598--8815 Score: 321
Period size: 86 Copynumber: 2.5 Consensus size: 86
8588 CAATTTTTTG
* * *
8598 TATG-TTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGTTGAGGTATT
1 TATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT
* **
8662 TTCCATTTCTGTTTTTCAATT
66 TTCAATTTCTACTTTTCAATT
* * *
8683 TATGTTTTCAAAAATCAATTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
1 TATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT
8748 TTCAATTTCTACTTTTCAATT
66 TTCAATTTCTACTTTTCAATT
* *
8769 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCT
1 TATG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
8816 TTTAATTTTT
Statistics
Matches: 118, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
85 4 0.03
86 75 0.64
87 39 0.33
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (86 bp):
TATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT
TTCAATTTCTACTTTTCAATT
Found at i:8952 original size:58 final size:56
Alignment explanation
Indices: 8759--8985 Score: 257
Period size: 58 Copynumber: 4.1 Consensus size: 56
8749 TCAATTTCTA
* *
8759 CTTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGC
1 CTTTTCAATTTTTG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
8814 CTTTT-AATTTTTGTTTTTCAAAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTTTG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* ******
8870 CTTTTTCTATTTTTCAAAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 C-TTTTCAATTTTT-GTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
8928 CTTTTGCAAATTCTGTTTTC--AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTTTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
8983 CTT
1 CTT
8986 GGCTCACGTG
Statistics
Matches: 145, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
54 13 0.09
55 42 0.29
56 34 0.23
57 8 0.06
58 48 0.33
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (56 bp):
CTTTTCAATTTTTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:8977 original size:55 final size:55
Alignment explanation
Indices: 8759--8985 Score: 260
Period size: 55 Copynumber: 4.1 Consensus size: 55
8749 TCAATTTCTA
*
8759 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGC
1 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
8814 CTTTT-AATTTTTGTTTTTCAAAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* ********
8870 CTTTTTCTATTTTTCAAAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 C-TTTTC-A-ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
8928 CTTTTGCAAATTCTG-TTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
8983 CTT
1 CTT
8986 GGCTCACGTG
Statistics
Matches: 141, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
54 13 0.09
55 42 0.30
56 37 0.26
57 9 0.06
58 36 0.26
59 1 0.01
60 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (55 bp):
CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:9252 original size:13 final size:14
Alignment explanation
Indices: 9227--9255 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9217 TTTAATTTTC
9227 AAAATTTTAAAAAA
1 AAAATTTTAAAAAA
9241 AAAATTTTAAAAAA
1 AAAATTTTAAAAAA
9255 A
1 A
9256 TAAAAATTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTTTAAAAAA
Found at i:9253 original size:15 final size:15
Alignment explanation
Indices: 9227--9260 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
9217 TTTAATTTTC
9227 AAAATTTTAAAAAA-
1 AAAATTTTAAAAAAT
9241 AAAATTTTAAAAAAAT
1 AAAATTTT-AAAAAAT
9257 AAAA
1 AAAA
9261 ATTGCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 6 0.33
16 4 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTTAAAAAAT
Found at i:9299 original size:30 final size:30
Alignment explanation
Indices: 9259--9359 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 30
9249 AAAAAAATAA
* *
9259 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
9289 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* * *
9319 AAATTTCACTTAGA-CCCTAAACCTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
9348 AAATTTCATTTT
1 AAATTTCATTTT
9360 AATCCTAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
29 26 0.43
30 34 0.57
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:9366 original size:29 final size:29
Alignment explanation
Indices: 9288--9368 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
9278 AAACTTTTCC
* * *
9288 TAAATTTCATTTTGACCCTTAAACTTTCTT
1 TAAATTTCATTTTAACCC-TAAACCTTCAT
*
9318 TAAATTTCA-CTTAGACCCTAAACCTTCAT
1 TAAATTTCATTTTA-ACCCTAAACCTTCAT
*
9347 TAAATTTCATTTTAATCCTAAA
1 TAAATTTCATTTTAACCCTAAA
9369 TTTTTAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 27 0.63
30 16 0.37
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.43
Consensus pattern (29 bp):
TAAATTTCATTTTAACCCTAAACCTTCAT
Found at i:9805 original size:14 final size:15
Alignment explanation
Indices: 9779--9818 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
9769 ATCAAATAAA
9779 GAAAAGAGAAGAGAG
1 GAAAAGAGAAGAGAG
*
9794 GAAAAG-GAAGAGTG
1 GAAAAGAGAAGAGAG
9808 G--AAGAGAAGAG
1 GAAAAGAGAAGAG
9819 CCCGTCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 3 0.13
13 6 0.26
14 8 0.35
15 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (15 bp):
GAAAAGAGAAGAGAG
Found at i:9927 original size:23 final size:23
Alignment explanation
Indices: 9895--9977 Score: 100
Period size: 23 Copynumber: 3.6 Consensus size: 23
9885 CGGCCCGAAG
9895 AAGAGGAAGAAAAAGAAAGGAAAA
1 AAGA-GAAGAAAAAGAAAGGAAAA
9919 AAGAGAAGAAAAGAGAGAA-G-AAA
1 AAGAGAAGAAAA-AGA-AAGGAAAA
*
9942 AAGAGAAGAAAAAGAAAGAAAAA
1 AAGAGAAGAAAAAGAAAGGAAAA
9965 AAG-GAGAGAAAAA
1 AAGAGA-AGAAAAA
9978 ATAGAAAAGG
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
21 2 0.04
22 5 0.09
23 36 0.68
24 8 0.15
25 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (23 bp):
AAGAGAAGAAAAAGAAAGGAAAA
Found at i:9930 original size:10 final size:11
Alignment explanation
Indices: 9895--9964 Score: 90
Period size: 12 Copynumber: 6.2 Consensus size: 11
9885 CGGCCCGAAG
9895 AAGAGGAAGAAA
1 AAGA-GAAGAAA
9907 AAGA-AAGGAAAA
1 AAGAGAA-G-AAA
9919 AAGAGAAGAAA
1 AAGAGAAGAAA
9930 AGAGAGAAGAAA
1 A-AGAGAAGAAA
9942 AAGAGAAGAAA
1 AAGAGAAGAAA
9953 AAGA-AAGAAA
1 AAGAGAAGAAA
9963 AA
1 AA
9965 AAGGAGAGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.19
11 19 0.35
12 23 0.43
13 2 0.04
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (11 bp):
AAGAGAAGAAA
Found at i:9965 original size:11 final size:12
Alignment explanation
Indices: 9895--9983 Score: 82
Period size: 12 Copynumber: 7.6 Consensus size: 12
9885 CGGCCCGAAG
9895 AAGAGGAAG-AAA
1 AAGA-GAAGAAAA
9907 AAGA-AAGGAAAA
1 AAGAGAA-GAAAA
9919 AAGAGAAGAAAA
1 AAGAGAAGAAAA
*
9931 GAGAGAAG-AAA
1 AAGAGAAGAAAA
9942 AAGAGAAG-AAA
1 AAGAGAAGAAAA
9953 AAGA-AAGAAAA
1 AAGAGAAGAAAA
9964 AA-AGGAGAGAAAA
1 AAGA-GA-AGAAAA
*
9977 AATAGAA
1 AAGAGAA
9984 AAGGAAAGAA
Statistics
Matches: 67, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
10 6 0.09
11 23 0.34
12 25 0.37
13 12 0.18
14 1 0.01
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (12 bp):
AAGAGAAGAAAA
Found at i:9978 original size:13 final size:12
Alignment explanation
Indices: 9915--9978 Score: 69
Period size: 13 Copynumber: 5.3 Consensus size: 12
9905 AAAAGAAAGG
9915 AAAAA-AGAGAA
1 AAAAAGAGAGAA
*
9926 GAAAAGAGAGAA
1 AAAAAGAGAGAA
*
9938 GAAAAAGAGA-AG
1 -AAAAAGAGAGAA
*
9950 AAAAAGAAAGAA
1 AAAAAGAGAGAA
9962 AAAAAGGAGAGAA
1 AAAAA-GAGAGAA
9975 AAAA
1 AAAA
9979 TAGAAAAGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
11 12 0.28
12 13 0.30
13 18 0.42
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAGAA
Found at i:9997 original size:37 final size:35
Alignment explanation
Indices: 9895--10004 Score: 118
Period size: 37 Copynumber: 3.1 Consensus size: 35
9885 CGGCCCGAAG
*
9895 AAGAG-GAAGAAAAAG-AAAGGAAAAAAGAGAAGAA
1 AAGAGAGAAGAAAAAGAAAAGGAAAAAA-AGAAAAA
* *
9929 AAGAGAGAAGAAAAAGAGAAGAAAAAGAAAGAAAAA
1 AAGAGAGAAGAAAAAGAAAAGGAAAA-AAAGAAAAA
9965 AAGGAGAGAA-AAAATAGAAAAGGAAAGAAAAGAAATAA
1 AA-GAGAGAAGAAAA-AGAAAAGGAAA-AAAAGAAA-AA
10003 AA
1 AA
10005 AAATAAAAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
34 5 0.08
35 10 0.16
36 19 0.30
37 25 0.39
38 5 0.08
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (35 bp):
AAGAGAGAAGAAAAAGAAAAGGAAAAAAAGAAAAA
Found at i:9998 original size:24 final size:24
Alignment explanation
Indices: 9904--10005 Score: 68
Period size: 24 Copynumber: 4.2 Consensus size: 24
9894 GAAGAGGAAG
9904 AAAAAG-AAAGGAAA-AAAGAGAAGA
1 AAAAAGAAAAGGAAAGAAA-AGAA-A
* * * *
9928 AAAGAGAGAAGAAAAAGAGAAGAAA
1 AAAAAGAAAAG-GAAAGAAAAGAAA
* *
9953 AAGAAAGAAAA--AAAGGAGAGAAA
1 AA-AAAGAAAAGGAAAGAAAAGAAA
*
9976 AAATAGAAAAGGAAAGAAAAGAAA
1 AAAAAGAAAAGGAAAGAAAAGAAA
10000 TAAAAA
1 -AAAAA
10006 AATAAAAAGA
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
22 7 0.12
23 11 0.19
24 15 0.26
25 10 0.17
26 13 0.22
27 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (24 bp):
AAAAAGAAAAGGAAAGAAAAGAAA
Found at i:10004 original size:19 final size:18
Alignment explanation
Indices: 9905--10004 Score: 57
Period size: 19 Copynumber: 5.4 Consensus size: 18
9895 AAGAGGAAGA
9905 AAAAGAAAGGAAA-AAAGAG
1 AAAA-AAAGGAAAGAAA-AG
*
9924 AAGAAAAGAGAGAAGAAAAAG
1 AAAAAAAG-GA-AAG-AAAAG
* *
9945 AGAAGAA--AAAG-AAAG
1 AAAAAAAGGAAAGAAAAG
*
9960 AAAAAAAGGAGAGAAAA-
1 AAAAAAAGGAAAGAAAAG
9977 AATAGAAAAGGAAAGAAAAG
1 AA-A-AAAAGGAAAGAAAAG
9997 AAATAAAA
1 AAA-AAAA
10005 AAATAAAAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
15 9 0.15
17 8 0.13
18 9 0.15
19 23 0.37
20 4 0.06
21 6 0.10
22 3 0.05
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (18 bp):
AAAAAAAGGAAAGAAAAG
Found at i:10135 original size:23 final size:23
Alignment explanation
Indices: 10109--10155 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
10099 CCAGCCCAAA
10109 AAAAAAAAGCAA-AAAAAAGAAGC
1 AAAAAAAAG-AAGAAAAAAGAAGC
*
10132 AAAAAAAAGAAGAAGAAAGAAGC
1 AAAAAAAAGAAGAAAAAAGAAGC
10155 A
1 A
10156 GCAGGCCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAAAAGAAGAAAAAAGAAGC
Found at i:10140 original size:13 final size:13
Alignment explanation
Indices: 10105--10143 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
10095 CAGGCCAGCC
*
10105 CAAAAAAAAAAAG
1 CAAAAAAAAGAAG
10118 CAAAAAAAAGAAG
1 CAAAAAAAAGAAG
10131 CAAAAAAAAGAAG
1 CAAAAAAAAGAAG
10144 AAGAAAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAGAAG
Found at i:10313 original size:15 final size:15
Alignment explanation
Indices: 10293--10327 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
10283 AACATCCAGC
10293 AAAAAAAAAA-GAAA
1 AAAAAAAAAAGGAAA
10307 GAAAAAAAAAAGGAAA
1 -AAAAAAAAAAGGAAA
10323 AAAAA
1 AAAAA
10328 GGCCCATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGGAAA
Found at i:10928 original size:16 final size:16
Alignment explanation
Indices: 10880--10928 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
10870 TTTCTTTCTA
*
10880 AAAAAATCGTGTTTTC
1 AAAAATTCGTGTTTTC
10896 AAAAATTTCCGTG-TTTC
1 AAAAA-TT-CGTGTTTTC
10913 AAAAATTCGTGTTTTC
1 AAAAATTCGTGTTTTC
10929 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 10 0.34
18 4 0.14
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (16 bp):
AAAAATTCGTGTTTTC
Found at i:10957 original size:19 final size:20
Alignment explanation
Indices: 10927--10964 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
10917 ATTCGTGTTT
10927 TCGTGTTTTCAAAAAAAATC
1 TCGTGTTTTCAAAAAAAATC
10947 TCGTG-TTTCAAAAAAAAT
1 TCGTGTTTTCAAAAAAAAT
10965 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (20 bp):
TCGTGTTTTCAAAAAAAATC
Found at i:10970 original size:9 final size:9
Alignment explanation
Indices: 10956--11007 Score: 65
Period size: 9 Copynumber: 6.0 Consensus size: 9
10946 CTCGTGTTTC
10956 AAAAAAAAT
1 AAAAAAAAT
10965 AAAAAAAA-
1 AAAAAAAAT
10973 ATAAAAAAAT
1 A-AAAAAAAT
*
10983 AAAAATAAT
1 AAAAAAAAT
10992 --AAAAAAT
1 AAAAAAAAT
10999 AAAAAAAAT
1 AAAAAAAAT
11008 TCTCGTGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 6 0.16
8 1 0.03
9 29 0.78
10 1 0.03
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:10971 original size:10 final size:10
Alignment explanation
Indices: 10956--11006 Score: 57
Period size: 10 Copynumber: 4.7 Consensus size: 10
10946 CTCGTGTTTC
10956 AAAAAAAATA
1 AAAAAAAATA
10966 AAAAAAAATAAAA
1 AAAAAAAAT---A
10979 AAATAAAAATA
1 AAA-AAAAATA
*
10990 ATAAAAAATA
1 AAAAAAAATA
11000 AAAAAAA
1 AAAAAAA
11007 TTCTCGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 22 0.63
11 3 0.09
13 4 0.11
14 6 0.17
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:10986 original size:24 final size:24
Alignment explanation
Indices: 10959--11005 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
10949 GTGTTTCAAA
10959 AAAAATAAAAAAAAATAAAAAAAT
1 AAAAATAAAAAAAAATAAAAAAAT
*
10983 AAAAATAATAAAAAATAAAAAAA
1 AAAAATAAAAAAAAATAAAAAAA
11006 ATTCTCGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (24 bp):
AAAAATAAAAAAAAATAAAAAAAT
Found at i:11092 original size:18 final size:18
Alignment explanation
Indices: 11071--11503 Score: 213
Period size: 18 Copynumber: 25.0 Consensus size: 18
11061 AAATTTTGTG
11071 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
11089 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
11107 TCTTT-GTGTTTTCAGAAA
1 T-TTTCGTGTTTTCAAAAA
* * *
11125 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
11142 TTTTCGTGTTTAAAAAAAAA
1 TTTTCGTGTTT--TCAAAAA
* *
11162 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
11180 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
11197 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
11215 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
11231 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * **
11249 TTCTCGCGTTTAAAAAAA
1 TTTTCGTGTTTTCAAAAA
**
11267 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
11285 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
11299 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
11314 ---TCGTG-TTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
11329 ATATCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
11346 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
11363 TTTCTC-TGTTTT-AAAAA
1 TTT-TCGTGTTTTCAAAAA
**
11380 TTCCCGTG-TTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
* *
11399 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* *
11417 ATTTCGTTTTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
11436 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
11453 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
11469 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
11487 TTCTT-GTGTTTT-AAAAA
1 TT-TTCGTGTTTTCAAAAA
11504 AAAAAACTTT
Statistics
Matches: 314, Mismatches: 63, Indels: 77
0.69 0.14 0.17
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 6 0.02
15 6 0.02
16 22 0.07
17 102 0.32
18 125 0.40
19 26 0.08
20 20 0.06
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:11152 original size:17 final size:17
Alignment explanation
Indices: 11071--11503 Score: 201
Period size: 17 Copynumber: 25.0 Consensus size: 17
11061 AAATTTTGTG
11071 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
11089 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
*
11107 TCTTT-GTGTTTTCAGAAA
1 T-TTTCGTG-TTTCAAAAA
* * *
11125 TTCTGGCGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
*
11142 TTTTCGTGTTTAAAAAAAAA
1 TTTTCGTGTTT---CAAAAA
* *
11162 TTTACGTGTTTTCACAAA
1 TTTTCGTG-TTTCAAAAA
*
11180 TTTTCGTGTTTCACAAA
1 TTTTCGTGTTTCAAAAA
*
11197 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
11215 -CTCCAGTGTTTC-AAAG
1 TTTTC-GTGTTTCAAAAA
* *
11231 TTTCCATGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
11249 TTCTCGCGTTTAAAAAAA
1 TTTTCGTGTTT-CAAAAA
**
11267 AATTCGTGTTTCAAAATA
1 TTTTCGTGTTTCAAAA-A
* **
11285 TTCTCGCATTTC---AA
1 TTTTCGTGTTTCAAAAA
***
11299 TTTT--TGTTTTTTAAA
1 TTTTCGTGTTTCAAAAA
11314 ---TCGTGTTTCAAAAAA
1 TTTTCGTGTTTC-AAAAA
* * *
11329 ATATCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
*
11346 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
*
11363 TTTCTC-TGTTTTAAAAA
1 TTT-TCGTGTTTCAAAAA
**
11380 TTCCCGTGTTTCAAAAAAA
1 TTTTCGTGTTTC--AAAAA
* * *
11399 ATGTCGTGTTTTAAGAAA
1 TTTTCGTGTTTCAA-AAA
* *
11417 ATTTCGTTTTTTCTAAAAA
1 TTTTCG-TGTTTC-AAAAA
*
11436 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
*
11453 TTTTCGTGTTT-ACAAA
1 TTTTCGTGTTTCAAAAA
*
11469 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
*
11487 TTCTT-GTGTTTTAAAAA
1 TT-TTCGTGTTTCAAAAA
11504 AAAAAACTTT
Statistics
Matches: 314, Mismatches: 69, Indels: 65
0.70 0.15 0.15
Matches are distributed among these distances:
12 4 0.01
14 9 0.03
15 6 0.02
16 16 0.05
17 118 0.38
18 115 0.37
19 29 0.09
20 14 0.04
21 3 0.01
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTTCGTGTTTCAAAAA
Found at i:11191 original size:55 final size:53
Alignment explanation
Indices: 11071--11277 Score: 159
Period size: 53 Copynumber: 3.9 Consensus size: 53
11061 AAATTTTGTG
** ** *
11071 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAGAAA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTAAAAAAAAATTTGTGTTTTCACAAA
* * *
11125 TTCTGGCGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTTACGTGTTTTCACAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTT--GTGTTTTCACAAA
* * ** * ** *
11180 TTTTCGTGTTTCACAAATTCTCGTGTTT-TCAAAAACTCCAGTG-TTTCA-AAG
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAAT-TTGTGTTTTCACAAA
* * * * *
11231 TTTCCATGTTTTCAAAAATTCTCGCGTTTAAAAAAAAATTCGTGTTT
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTAAAAAAAAATTTGTGTTT
11278 CAAAATATTC
Statistics
Matches: 119, Mismatches: 28, Indels: 13
0.74 0.17 0.08
Matches are distributed among these distances:
51 8 0.07
52 26 0.22
53 39 0.33
54 11 0.09
55 35 0.29
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (53 bp):
TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTTGTGTTTTCACAAA
Found at i:11224 original size:73 final size:73
Alignment explanation
Indices: 11084--11225 Score: 173
Period size: 73 Copynumber: 1.9 Consensus size: 73
11074 TCGTGTTTTC
* * * * *
11084 AAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAGAAATTCTGGCGTTTCAAAAATTTTCGT
1 AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCACAAATTCTCGCGTTTCAAAAATCTCCGT
11149 GTTTAAAA
66 GTTTAAAA
* *
11157 AAAAATTTACGTGTTTTCACAAAT-TTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAAA-CTCC
1 AAAAATTTACGTGTTTTCAAAAATCTTT-GTGTTTTCACAAATTCTCGCG-TTTCAAAAATCTCC
11219 AGTGTTT
64 -GTGTTT
11226 CAAAGTTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
72 19 0.32
73 40 0.68
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (73 bp):
AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCACAAATTCTCGCGTTTCAAAAATCTCCGT
GTTTAAAA
Found at i:11444 original size:90 final size:88
Alignment explanation
Indices: 11314--11486 Score: 242
Period size: 90 Copynumber: 1.9 Consensus size: 88
11304 GTTTTTTAAA
11314 TCGTGTTTCAAAAAAATATCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCTC-TGTTTTAAA
1 TCGTGTTTCAAAAAAATATCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTT-TCGTG-TTTAAA
11378 AATTCCCGTG-TTTCAAAAAAAATG
64 AATTCCCGTGTTTTCAAAAAAAATG
* * * * *
11402 TCGTGTTTTAAGAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTTCGTGTTTACA
1 TCGTGTTTCAAAAAAATATCG-TGTTT-TAAAAATTTTCGTGTTTCTAAAATTTTCGTGTTTAAA
*
11467 AATTCTCGTGTTTTCAAAAA
64 AATTCCCGTGTTTTCAAAAA
11487 TTCTTGTGTT
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
88 18 0.24
89 20 0.27
90 37 0.49
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (88 bp):
TCGTGTTTCAAAAAAATATCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTTCGTGTTTAAAAA
TTCCCGTGTTTTCAAAAAAAATG
Found at i:12232 original size:29 final size:29
Alignment explanation
Indices: 12171--12232 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
12161 TTTTAACGTT
* *
12171 TTTTTCCATTCTCTTCTTTTCTCCCTTTG
1 TTTTTCCATTCTCTTCTTTTCTCCCTCTC
12200 TTTTTCCATTCTCTTCTTTTCTCCCTCTC
1 TTTTTCCATTCTCTTCTTTTCTCCCTCTC
12229 TTTT
1 TTTT
12233 AATTTAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.03, C:0.32, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTTCCATTCTCTTCTTTTCTCCCTCTC
Found at i:20794 original size:23 final size:21
Alignment explanation
Indices: 20741--20798 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
20731 ATATAATTAC
* *
20741 TTAAAATTTTTAAATATTTTT
1 TTAATATTTTCAAATATTTTT
*
20762 TTACTAATTTTCAATATATATTTT
1 TTAAT-ATTTTCAA-ATAT-TTTT
20786 TTAATATTTTCAA
1 TTAATATTTTCAA
20799 GTACTAACGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.10
22 7 0.23
23 12 0.40
24 8 0.27
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAATATTTTCAAATATTTTT
Found at i:22413 original size:8 final size:8
Alignment explanation
Indices: 22400--22436 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
22390 GTCAAAAATA
22400 ATTTTAAT
1 ATTTTAAT
22408 ATTTTAAT
1 ATTTTAAT
22416 A-TTTAAT
1 ATTTTAAT
22423 -TTTATAAT
1 ATTT-TAAT
22431 ATTTTA
1 ATTTTA
22437 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 8 0.31
8 15 0.58
9 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTAAT
Found at i:22422 original size:15 final size:15
Alignment explanation
Indices: 22397--22440 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
22387 AAAGTCAAAA
22397 ATAAT-TTTAATATTT
1 ATAATATTTAAT-TTT
22412 -TAATATTTAATTTT
1 ATAATATTTAATTTT
*
22426 ATAATATTTTATTTT
1 ATAATATTTAATTTT
22441 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATAATATTTAATTTT
Found at i:26086 original size:20 final size:20
Alignment explanation
Indices: 26061--26100 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
26051 CGTAAAATGA
*
26061 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
26081 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
26101 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:26090 original size:34 final size:35
Alignment explanation
Indices: 26046--26112 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
26036 GAGTAAAATA
*
26046 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
26080 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
26113 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:26116 original size:14 final size:15
Alignment explanation
Indices: 26040--26116 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
26030 GATTGAGAGT
* *
26040 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
26054 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
26068 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
26088 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
26103 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
26117 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:32560 original size:23 final size:24
Alignment explanation
Indices: 32514--32560 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
32504 TTGGATACAT
*
32514 ATATATATATTTAATAATTTTTAAA
1 ATATATATATTTAATAA-TGTTAAA
*
32539 ATATATATATTTGATAA-GTTAA
1 ATATATATATTTAATAATGTTAA
32561 TAGATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
25 16 0.80
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATATATATTTAATAATGTTAAA
Done.