Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1291
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: 54645
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:9247 original size:72 final size:72
Alignment explanation
Indices: 9041--10386 Score: 2152
Period size: 72 Copynumber: 18.7 Consensus size: 72
9031 TAAGCCTTTT
* * * ** * *
9041 AATTTATGTTTTTCAAAA-TCAATTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
*
9105 GTAATTTT
65 GTAATTTC
* * * *
9113 AATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
1 AATTTCTGTT-TT-CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
9178 GGTAATTTC
64 GGTAATTTC
* *
9187 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
9252 TATTTTC
66 TAATTTC
9259 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
9323 T-ATTTC
66 TAATTTC
9329 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
9393 TAATTTC
66 TAATTTC
9400 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
9465 TATTTTC
66 TAATTTC
*
9472 AATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
9537 GTAATTTC
65 GTAATTTC
**
9545 AATCTT-TGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAG
1 AAT-TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
9609 GTAATTTC
65 GTAATTTC
9617 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
9681 TAATTTC
66 TAATTTC
*
9688 AATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
9753 TATTTTC
66 TAATTTC
* *
9760 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
9825 TAATTTT
66 TAATTTC
* * * *
9832 AATTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTG
1 AATTTCTGTT-TT--CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTG
9897 AGGTAATTTC
63 AGGTAATTTC
* * *
9907 AATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
9972 TATTTTC
66 TAATTTC
9979 AATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
10044 GTAATTTC
65 GTAATTTC
*
10052 AATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
10117 TATTTTC
66 TAATTTC
10124 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
10189 TAATTTC
66 TAATTTC
*
10196 AATTTCCGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
10261 TAATTTC
66 TAATTTC
*
10268 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
* *
10333 TATTTTT
66 TAATTTC
* * * ** *
10340 AGTTTATGTTTT--AAATT-GACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCT
10387 TTTAATTTTT
Statistics
Matches: 1207, Mismatches: 54, Indels: 29
0.94 0.04 0.02
Matches are distributed among these distances:
69 26 0.02
70 74 0.06
71 140 0.12
72 694 0.57
73 143 0.12
74 63 0.05
75 67 0.06
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (72 bp):
AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTC
Found at i:9542 original size:145 final size:144
Alignment explanation
Indices: 9041--10656 Score: 2455
Period size: 145 Copynumber: 11.3 Consensus size: 144
9031 TAAGCCTTTT
* * * ** * *
9041 AATTTATGTTTTTCAAAA-TCAATTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
* * * *
9105 GTAATTTTAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGA
65 GTAATTTCAATTTCTGTT-TT-CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA
*
9170 CACGCTGAGGTAATTTC
128 CACGTTGAGGTAATTTC
* *
9187 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
9252 TATTTTCAATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
9316 GTTGAGGT-ATTTC
131 GTTGAGGTAATTTC
9329 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
9393 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
*
9458 GTTGAGGTATTTTC
131 GTTGAGGTAATTTC
*
9472 AATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
**
9537 GTAATTTCAATCTT-TGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
65 GTAATTTCAAT-TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
9601 ACGTTGAGGTAATTTC
129 ACGTTGAGGTAATTTC
9617 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
9681 TAATTTCAATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
*
9746 GTTGAGGTATTTTC
131 GTTGAGGTAATTTC
* *
9760 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
* * * *
9825 TAATTTTAATTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGA
66 TAATTTCAATTTCTGTT-TT--CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA
*
9890 CACGCTGAGGTAATTTC
128 CACGTTGAGGTAATTTC
* * *
9907 AATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
9972 TATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
66 TAATTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
10037 CGTTGAGGTAATTTC
130 CGTTGAGGTAATTTC
*
10052 AATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
10117 TATTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
10182 GTTGAGGTAATTTC
131 GTTGAGGTAATTTC
*
10196 AATTTCCGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
10261 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
* * *
10326 ATTGAGGTATTTTT
131 GTTGAGGTAATTTC
* * * * *
10340 AGTTTATGTTTT--AAATT-GACTCATATTGCGAG--A-G-G-TGAG--TTAAG-C-C-TT---T
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
* ***
10389 TAATTT---TTGT-TTTTCAAA--A-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
66 TAATTTCAATT-TCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
10447 CGTTGAGGTAATTTC
130 CGTTGAGGTAATTTC
10462 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
* *
10527 TATTTTCAATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
66 TAATTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
10592 CGTTGAGGTAATTTC
130 CGTTGAGGTAATTTC
**
10607 AATCTT-TGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAT-TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCT
10657 TTTAATTTCT
Statistics
Matches: 1359, Mismatches: 73, Indels: 77
0.90 0.05 0.05
Matches are distributed among these distances:
122 61 0.04
123 1 0.00
124 5 0.00
125 20 0.01
126 1 0.00
127 1 0.00
128 7 0.01
129 1 0.00
130 4 0.00
131 2 0.00
132 5 0.00
133 2 0.00
134 5 0.00
135 2 0.00
136 4 0.00
137 1 0.00
138 6 0.00
139 1 0.00
140 1 0.00
141 85 0.06
142 81 0.06
143 194 0.14
144 292 0.21
145 372 0.27
146 69 0.05
147 134 0.10
148 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (144 bp):
AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
GTTGAGGTAATTTC
Found at i:10592 original size:73 final size:72
Alignment explanation
Indices: 10390--10656 Score: 448
Period size: 72 Copynumber: 3.7 Consensus size: 72
10380 TAAGCCTTTT
*
10390 AATTTTTGTTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
10454 GTAATTTC
65 GTAATTTC
10462 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
10527 TATTTTC
66 TAATTTC
*
10534 AATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
10599 GTAATTTC
65 GTAATTTC
**
10607 AATCTT-TGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAT-TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCT
10657 TTTAATTTCT
Statistics
Matches: 185, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
71 9 0.05
72 107 0.58
73 67 0.36
74 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (72 bp):
AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTC
Found at i:10684 original size:55 final size:54
Alignment explanation
Indices: 10613--10767 Score: 240
Period size: 55 Copynumber: 2.8 Consensus size: 54
10603 TTTCAATCTT
* *
10613 TGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT-AATTTC
1 TGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTCAAATTC
*
10666 TGTTTTTCAAAAAATCAACCCATATTGCGAGAGGTGAGTTGAGCCTTTTGCAAATTC
1 TG-TTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT-CAAATTC
*
10723 TGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
1 TGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
10768 GGCTCACGTG
Statistics
Matches: 93, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
53 2 0.02
54 5 0.05
55 74 0.80
56 5 0.05
57 7 0.08
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (54 bp):
TGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTCAAATTC
Found at i:11028 original size:14 final size:15
Alignment explanation
Indices: 11009--11041 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
10999 TTTAATTTTC
11009 AAAATTTCAAAAAA-
1 AAAATTTCAAAAAAT
*
11023 AAAATTTTAAAAAAT
1 AAAATTTCAAAAAAT
11038 AAAA
1 AAAA
11042 ATTGCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATTTCAAAAAAT
Found at i:11074 original size:30 final size:31
Alignment explanation
Indices: 11040--11141 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
11030 TAAAAAATAA
*
11040 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
11070 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
11100 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
11130 AAATTTCATTTT
1 AAATTTCATTTT
11142 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:11679 original size:14 final size:14
Alignment explanation
Indices: 11658--11701 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
11648 CAGGCCAGCC
*
11658 CAAAAAAAAACAAAG
1 CAAAAAAAAA-GAAG
*
11673 CAAAAAAAAAGCAG
1 CAAAAAAAAAGAAG
11687 CAAAAAAAGAAGAAG
1 CAAAAAAA-AAGAAG
11702 AAAGAAGCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.75, C:0.11, G:0.14, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAGAAG
Found at i:11691 original size:24 final size:25
Alignment explanation
Indices: 11681--11736 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 25
11671 AGCAAAAAAA
11681 AAGCAGCAAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAAGAAGAAGAAAG
*
11706 AAGCAG-AAAAAAAGAATAAGAAAG
1 AAGCAGCAAAAAAAGAAGAAGAAAG
11730 AAGCAGC
1 AAGCAGC
11737 CCACTTTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 23 0.79
25 6 0.21
ACGTcount: A:0.66, C:0.09, G:0.23, T:0.02
Consensus pattern (25 bp):
AAGCAGCAAAAAAAGAAGAAGAAAG
Found at i:12364 original size:17 final size:17
Alignment explanation
Indices: 12321--12368 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
12311 AGAAAAAAAT
12321 CGTGTTTCAAAAATTTTCA
1 CGTGTTTC-AAAA-TTTCA
12340 --TGTCTTCAAAATTTCA
1 CGTGT-TTCAAAATTTCA
12356 CGTGTTTCAAAAT
1 CGTGTTTCAAAAT
12369 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAATTTCA
Found at i:12444 original size:17 final size:16
Alignment explanation
Indices: 12417--12471 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 16
12407 TTCGTGTTTC
12417 TTTCTAAAAATATCGTGT
1 TTTC-AAAAAT-TCGTGT
12435 TTTCAAAAATTTCCGTG-
1 TTTCAAAAA-TT-CGTGT
12452 TTTCAAAAATTCGTGT
1 TTTCAAAAATTCGTGT
12468 TTTC
1 TTTC
12472 GTGTTTTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.12
16 6 0.18
17 15 0.44
18 9 0.26
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (16 bp):
TTTCAAAAATTCGTGT
Found at i:12508 original size:20 final size:20
Alignment explanation
Indices: 12470--12506 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
12460 ATTCGTGTTT
12470 TCGTGTTTTCAAAAAAAATC
1 TCGTGTTTTCAAAAAAAATC
12490 TCGTG-TTTCAAAAAAAA
1 TCGTGTTTTCAAAAAAAA
12507 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (20 bp):
TCGTGTTTTCAAAAAAAATC
Found at i:12521 original size:8 final size:8
Alignment explanation
Indices: 12501--12532 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
12491 CGTGTTTCAA
12501 AAAAAAAT
1 AAAAAAAT
12509 AAAAATAAT
1 AAAAA-AAT
12518 AAAAAAAT
1 AAAAAAAT
12526 AAAAAAA
1 AAAAAAA
12533 ATTCTCGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:12533 original size:9 final size:9
Alignment explanation
Indices: 12500--12534 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
12490 TCGTGTTTCA
12500 AAAAAAAAT
1 AAAAAAAAT
*
12509 AAAAATAAT
1 AAAAAAAAT
12518 -AAAAAAAT
1 AAAAAAAAT
12526 AAAAAAAAT
1 AAAAAAAAT
12535 TCTCGTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:12620 original size:18 final size:18
Alignment explanation
Indices: 12597--13028 Score: 209
Period size: 17 Copynumber: 25.0 Consensus size: 18
12587 AAATTTAGTG
12597 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
12615 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
12633 TCTTT-GTGTTTTCAAAAA
1 T-TTTCGTGTTTTCAAAAA
* * *
12651 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
12668 TTTTCGTGTTTAAAAAAAAA
1 TTTTCGTGTTT--TCAAAAA
* *
12688 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
12706 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
12723 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
12741 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
12757 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
12775 TTCTCGCG-TTTAAAAAA
1 TTTTCGTGTTTTCAAAAA
**
12792 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
12810 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
12824 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
12839 ---TCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
12853 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
12870 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
12887 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
12904 TTCCCGTG-TTTCAGAAAAAA
1 TTTTCGTGTTTTC---AAAAA
* *
12924 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* * *
12942 ATTTCGTTTTTTCTAAACA
1 TTTTCGTGTTTTC-AAAAA
*
12961 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
12978 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
12994 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
13012 TTCTCGTATTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
13029 AAACTTTCGT
Statistics
Matches: 316, Mismatches: 63, Indels: 71
0.70 0.14 0.16
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 9 0.03
15 3 0.01
16 21 0.07
17 123 0.39
18 112 0.35
19 11 0.03
20 27 0.09
21 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:12740 original size:55 final size:53
Alignment explanation
Indices: 12597--12993 Score: 177
Period size: 55 Copynumber: 7.6 Consensus size: 53
12587 AAATTTAGTG
**
12597 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAAAATTTGTGTTTTCAAAAA
* * * ** *
12651 TTCTGGCGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTTACGTGTTTTCACAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTT--GTGTTTTCAAAAA
* * * ** *
12706 TTTTCGTGTTTCACAAATTCTCGTGTTTTC-AAAAACTCCAGTG-TTTC-AAAG
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAAT-TTGTGTTTTCAAAAA
* * * * * *
12757 TTTCCATGTTTTCAAAAATTCTCGCG-TTTAAAAAAAATTCGTG-TTTCAAAATA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAAAATTTGTGTTTTCAAAA-A
* ** ** *
12810 TTCTCGCATTTC---AATTTT--TGTTTT---TTAAA-TCGTG-TTTCAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTGTGTTTTCAAAAA
* * * * *
12853 ATGTCGTGTTTTAAAAATTTTCGTG-TTTC--TAAAATTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTT--GTGTTTTCAAAAA
** * * * * *
12904 TTCCCGTGTTTCAGAAAAAAATGTCGTGTTTT-AAGAAAATTTCGTTTTTTCTAAACA
1 TTTTCGTGTTTC---AAAAATTTTCGTGTTTTCAAAAAAATTT-GTGTTTTC-AAAAA
* *
12961 TTTTCGTGTTTCTAAAATTTTCGTGTTTACAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAA
12994 TTCTCGTGTT
Statistics
Matches: 253, Mismatches: 63, Indels: 53
0.69 0.17 0.14
Matches are distributed among these distances:
43 8 0.03
44 13 0.05
45 3 0.01
46 6 0.02
47 4 0.02
48 9 0.04
49 6 0.02
51 33 0.13
52 35 0.14
53 34 0.13
54 35 0.14
55 46 0.18
56 7 0.03
57 14 0.06
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (53 bp):
TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTGTGTTTTCAAAAA
Found at i:12750 original size:73 final size:73
Alignment explanation
Indices: 12610--12751 Score: 173
Period size: 73 Copynumber: 1.9 Consensus size: 73
12600 TCGTGTTTTC
* * * *
12610 AAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTTCAAAAATTTTCGT
1 AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCGTTTCAAAAATCTCCGT
12675 GTTTAAAA
66 GTTTAAAA
* * *
12683 AAAAATTTACGTGTTTTCACAAAT-TTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAAA-CTCC
1 AAAAATTTACGTGTTTTCAAAAATCTTT-GTGTTTTCAAAAATTCTCGCG-TTTCAAAAATCTCC
12745 AGTGTTT
64 -GTGTTT
12752 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:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (73 bp):
AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCGTTTCAAAAATCTCCGT
GTTTAAAA
Found at i:13029 original size:18 final size:18
Alignment explanation
Indices: 12991--13029 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12981 TCGTGTTTAC
* *
12991 AAATTCTCGTGTTTTCAA
1 AAATTCTCGTATTTTAAA
13009 AAATTCTCGTATTTTAAA
1 AAATTCTCGTATTTTAAA
13027 AAA
1 AAA
13030 AACTTTCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (18 bp):
AAATTCTCGTATTTTAAA
Found at i:16076 original size:597 final size:596
Alignment explanation
Indices: 14966--16879 Score: 3226
Period size: 597 Copynumber: 3.2 Consensus size: 596
14956 AACCCAGGTT
* * * * *
14966 AAGCCCTTCAAGCTTGGGAAGATGCTGACACATATCATTAGGCAAACTACCAGATAGACTATTGC
1 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
* * * * *
15031 TAGAGAGATCAATGGCCTTCAGAGAAGAAACGTTGAAGATTGAAGTTGGAATCTGACTTGTAAGG
66 TGGAGAGATCAATGGTCTTCAGAGAAGAAATGTTGAAGATGGAAGTTGGAATCTGACCTGTAAGG
* * * *
15096 CCTTTAATTGCTGTAATACTAAGCATTTCCAAACCAAAAAGATTACCGATTTCCTTAGGAATTTG
131 CCTTTAATTTC-GTAATACTAAGCAGTTCCAAACCAAGAAGATTACCGATTTCCTCAGGAATTTG
15161 ACCTGCACACA-GAGTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAGA
195 ACCTGCACACATG-GTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAGA
* * * *
15225 GGTTTTCTTTTCTGTTCTACAGTAATTTGGAAACGCTAGATCTTCATATATTTCAGCATATGTTT
259 GGTTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTCATATATTTCAGCATATGTTT
* *
15290 TTCATCAAATGAAATAAAAAGTTTTTCCTTTTGTTATCTATTACAAATCAAACTTTTTTA-TAAA
324 TTCATCAAATGAAATAAAAACTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATTAAA
* * * *
15354 CAAATTACTTAAAATTTAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTAAACCCCAAATA
389 -AAAATACTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATA
* *
15419 TAATTCTCTGAGTTGTGTCAGATTTCCAATACTTCTTGGAATAATCCCCGTCAATTGATTCAAGG
453 TAATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAATGATCCCCGTCAATTGATTCAAGG
*
15484 ACAAGGACAAATTTTTAAGGTTGCTGCATTTACCCATACTTGACGGAATGTTACCAGATAACTCA
518 ACAAGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCA
*
15549 TTGCTATACAAGTA
583 TTGCTATGCAAGTA
15563 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
1 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
**
15628 TGGAGAGATCAATGGTCTTCAGAGAAGAAATGTTGAAGATCAAAGTTGGAATCTGACCTGTAAGG
66 TGGAGAGATCAATGGTCTTCAGAGAAGAAATGTTGAAGATGGAAGTTGGAATCTGACCTGTAAGG
* *
15693 CCTTTAATTTCAGTAATACTAAGCAGTTCTAAACCAAGAAGATTATCGATTTCCTCAGGAATTTG
131 CCTTTAATTTC-GTAATACTAAGCAGTTCCAAACCAAGAAGATTACCGATTTCCTCAGGAATTTG
15758 ACCTGCACACATGGTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAGAG
195 ACCTGCACACATGGTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAGAG
*
15823 GTTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTCATATATTTCGGCATATGTTTT
260 GTTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTCATATATTTCAGCATATGTTTT
15888 TCATCAAATGAAATAAAAACTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATTAAAA
325 TCATCAAATGAAATAAAAACTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATTAAAA
15953 AAATACTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATATA
390 AAATACTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATATA
* * *
16018 ATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAAGGATCCCCGTCAGTTGATTCAAGGAA
455 ATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAATGATCCCCGTCAATTGATTCAAGGAC
*
16083 AAGGACAAACTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCATT
520 AAGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCATT
16148 GCTATGCAAGTA
585 GCTATGCAAGTA
*
16160 AAGCACTTCAAGCTTGGGAAGATGTTGACAAATATCATTAGGCAAACTACCTGATAGGCTATTGT
1 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
*
16225 TGGAGAGA-CTAATGGTCTTCAGAGAAGAAATGTTGAAGATGGAACTTGGAATCTGACCTGTAAG
66 TGGAGAGATC-AATGGTCTTCAGAGAAGAAATGTTGAAGATGGAAGTTGGAATCTGACCTGTAAG
*
16289 GCCTTTAATTGCTCG-AATATTAAGCAGTTCCAAACCAAGAAGATTACCGATTTCCTCAGGAATT
130 GCCTTTAATT--TCGTAATACTAAGCAGTTCCAAACCAAGAAGATTACCGATTTCCTCAGGAATT
* *
16353 TGACCTGCACACATAGTCGAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAG
193 TGACCTGCACACATGGTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAG
**
16418 AGGTTTTCTTTTCTGTTCTATGGTAATTTGGAGATGTTAGATTTTCATATATTTCAGCATATGTT
258 AGGTTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTCATATATTTCAGCATATGTT
* * * *
16483 TTTCATCAAATGAAATAAAAACTTTTTCCATTTGTTATCTCTTACAAATCAAACCCTTTTATGAA
323 TTTCATCAAATGAAATAAAAACTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATTAA
*
16548 AAAAATCCTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATA
388 AAAAATACTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATA
16613 TAATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAATGATCCCCGTCAATTGATTCAAGG
453 TAATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAATGATCCCCGTCAATTGATTCAAGG
16678 ACAAGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCA
518 ACAAGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCA
16743 TTGCTATGCAAGTA
583 TTGCTATGCAAGTA
16757 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
1 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
** * * * *
16822 TGGAGAGAAT-AATAATCTTCAGAGAAGATATTTTGAAGATGGAAGATGGAACCTGACC
66 TGGAGAG-ATCAATGGTCTTCAGAGAAGAAATGTTGAAGATGGAAGTTGGAATCTGACC
16880 AGATAATTGA
Statistics
Matches: 1244, Mismatches: 66, Indels: 14
0.94 0.05 0.01
Matches are distributed among these distances:
596 1 0.00
597 1234 0.99
598 7 0.01
599 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (596 bp):
AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
TGGAGAGATCAATGGTCTTCAGAGAAGAAATGTTGAAGATGGAAGTTGGAATCTGACCTGTAAGG
CCTTTAATTTCGTAATACTAAGCAGTTCCAAACCAAGAAGATTACCGATTTCCTCAGGAATTTGA
CCTGCACACATGGTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAGAGG
TTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTCATATATTTCAGCATATGTTTTT
CATCAAATGAAATAAAAACTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATTAAAAA
AATACTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATATAA
TTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAATGATCCCCGTCAATTGATTCAAGGACA
AGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCATTG
CTATGCAAGTA
Found at i:22464 original size:13 final size:14
Alignment explanation
Indices: 22447--22483 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
22437 ATACACCTTT
22447 TTTATATTTACTAA
1 TTTATATTTACTAA
22461 TTATATATTTACTAA
1 TT-TATATTTACTAA
22476 -TTATATTT
1 TTTATATTT
22484 GAGTATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 3 0.14
15 12 0.55
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATATTTACTAA
Found at i:22469 original size:15 final size:15
Alignment explanation
Indices: 22449--22481 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
22439 ACACCTTTTT
22449 TATATTTACTAATTA
1 TATATTTACTAATTA
22464 TATATTTACTAATTA
1 TATATTTACTAATTA
22479 TAT
1 TAT
22482 TTGAGTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTTACTAATTA
Found at i:23246 original size:26 final size:27
Alignment explanation
Indices: 23202--23257 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
23192 TAATGGAGTT
23202 AACATTTAGTGTTTAAAAAATATCTTA
1 AACATTTAGTGTTTAAAAAATATCTTA
23229 AACATTTAGTGTTTAAAAAATATCTTA
1 AACATTTAGTGTTTAAAAAATATCTTA
23256 AA
1 AA
23258 AATTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (27 bp):
AACATTTAGTGTTTAAAAAATATCTTA
Found at i:24800 original size:13 final size:13
Alignment explanation
Indices: 24768--24800 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
24758 AATTATACGC
*
24768 CAAATTTTCAAGT
1 CAAATTTTCAACT
24781 C-AATTTTCAACT
1 CAAATTTTCAACT
24793 CAAATTTT
1 CAAATTTT
24801 GTATGTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (13 bp):
CAAATTTTCAACT
Found at i:27595 original size:28 final size:28
Alignment explanation
Indices: 27558--27611 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
27548 TTGTAAGCCT
*
27558 TAAAACAATCAACAAAATATATTTTTGTC
1 TAAAACAATCAACAAAA-ATATGTTTGTC
*
27587 TAAAA-AATCAATAAAAATATGTTTG
1 TAAAACAATCAACAAAAATATGTTTG
27612 AAATTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 10 0.43
29 5 0.22
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (28 bp):
TAAAACAATCAACAAAAATATGTTTGTC
Found at i:28513 original size:28 final size:28
Alignment explanation
Indices: 28477--28550 Score: 132
Period size: 28 Copynumber: 2.6 Consensus size: 28
28467 CAGTAACAGT
28477 ACAGTGTGGGCCTTAG-CTCGATATAGTA
1 ACAGTGTGGGCCTTAGCCT-GATATAGTA
28505 ACAGTGTGGGCCTTAGCCTGATATAGTA
1 ACAGTGTGGGCCTTAGCCTGATATAGTA
28533 ACAGTGTGGGCCTTAGCC
1 ACAGTGTGGGCCTTAGCC
28551 CAATACAGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 43 0.96
29 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCTGATATAGTA
Found at i:28560 original size:28 final size:28
Alignment explanation
Indices: 28472--28560 Score: 126
Period size: 28 Copynumber: 3.2 Consensus size: 28
28462 CTATGCAGTA
*
28472 ACAGT-ACAGTGTGGGCCTTAGCTCGAT
1 ACAGTAACAGTGTGGGCCTTAGCCCGAT
* *
28499 ATAGTAACAGTGTGGGCCTTAGCCTGAT
1 ACAGTAACAGTGTGGGCCTTAGCCCGAT
* *
28527 ATAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCGAT
28555 ACAGTA
1 ACAGTA
28561 TTAGTACAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
27 4 0.07
28 51 0.93
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCGAT
Found at i:28935 original size:27 final size:27
Alignment explanation
Indices: 28905--29288 Score: 275
Period size: 27 Copynumber: 14.3 Consensus size: 27
28895 GGGTAGAACA
*
28905 GTCATTTTACCCTAAGAGGGTATTTTG
1 GTCATTTTACCCTAAGAGGGTATTTCG
28932 GTCATTTTACCCTTAAG-GGGTATTTCG
1 GTCATTTTACCC-TAAGAGGGTATTTCG
* * *
28959 ATTATTTTACCCTTCA-AGGGTATTTCG
1 GTCATTTTACCC-TAAGAGGGTATTTCG
* * * **
28986 ATCATTTTACTCTTCA-AGGGTATTTTA
1 GTCATTTTAC-CCTAAGAGGGTATTTCG
* *
29013 GTCATTTTACCCTTCA-AGTGTATTTCG
1 GTCATTTTACCC-TAAGAGGGTATTTCG
** * *
29040 GTCATTTTACCCTTCGGGGGTAATTCG
1 GTCATTTTACCCTAAGAGGGTATTTCG
* * ***
29067 GTTATTTTATCCTTTTAGGGTATTTCG
1 GTCATTTTACCCTAAGAGGGTATTTCG
* * ** *
29094 ATCATTTTACCATTTGAGGGTATTTTG
1 GTCATTTTACCCTAAGAGGGTATTTCG
*
29121 GTCATTTTACCCTATA-AAGGTATTTCG
1 GTCATTTTACCCTA-AGAGGGTATTTCG
** *
29148 GTCATTTTACCCATTGGA-GGTATTTTG
1 GTCATTTTACCC-TAAGAGGGTATTTCG
*
29175 GTCATTTTACCC-ATCGAGGGTATTTCG
1 GTCATTTTACCCTA-AGAGGGTATTTCG
* *
29202 GTCATTTTACCC-ATCGAGGGTATTTTG
1 GTCATTTTACCCTA-AGAGGGTATTTCG
* * *
29229 GTCATTTTACCAT-CGGGGGTATTTCG
1 GTCATTTTACCCTAAGAGGGTATTTCG
* * *
29255 ATCATTTTACCC-ATTGAGGGTATTTTG
1 GTCATTTTACCCTA-AGAGGGTATTTCG
29282 GTCATTT
1 GTCATTT
29289 GCCCACGAAT
Statistics
Matches: 292, Mismatches: 52, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
26 25 0.09
27 260 0.89
28 7 0.02
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTAAGAGGGTATTTCG
Found at i:28979 original size:54 final size:53
Alignment explanation
Indices: 28905--29288 Score: 346
Period size: 54 Copynumber: 7.1 Consensus size: 53
28895 GGGTAGAACA
* *
28905 GTCATTTTACCC-TAAGAGGGTATTTTGGTCATTTTACCCTTAAGGGGTATTTCG
1 GTCATTTTACCCTTCA-AGGGTATTTCGGTCATTTTACCCTT-AGGGGTATTTCG
* * * * * **
28959 ATTATTTTACCCTTCAAGGGTATTTCGATCATTTTACTCTTCAAGGGTATTTTA
1 GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTT-AGGGGTATTTCG
* * *
29013 GTCATTTTACCCTTCAAGTGTATTTCGGTCATTTTACCCTTCGGGGGTAATTCG
1 GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTT-AGGGGTATTTCG
* * ** * * * *
29067 GTTATTTTATCCTTTTAGGGTATTTCGATCATTTTACCATTTGAGGGTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTTAG-GGGTATTTCG
* *
29121 GTCATTTTACCCTAT-AAAGGTATTTCGGTCATTTTACCCATT-GGAGGTATTTTG
1 GTCATTTTACCCT-TCAAGGGTATTTCGGTCATTTTACCC-TTAGG-GGTATTTCG
* * * * *
29175 GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTTAG-GGGTATTTCG
* ** * *
29229 GTCATTTTA-CCATCGGGGGTATTTCGATCATTTTACCCATT-GAGGGTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCC-TTAG-GGGTATTTCG
29282 GTCATTT
1 GTCATTT
29289 GCCCACGAAT
Statistics
Matches: 278, Mismatches: 43, Indels: 19
0.82 0.13 0.06
Matches are distributed among these distances:
53 50 0.18
54 222 0.80
55 6 0.02
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (53 bp):
GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTTAGGGGTATTTCG
Found at i:29036 original size:81 final size:81
Alignment explanation
Indices: 28921--29288 Score: 352
Period size: 81 Copynumber: 4.6 Consensus size: 81
28911 TTACCCTAAG
* *
28921 AGGGTATTTTGGTCATTTTACCCTT-AAGGGGTATTTCGATTATTTTACCCTTCAAGGGTATTTC
1 AGGGTATTTTGGTCATTTTACCCTTCAA-GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTC
*
28985 GATCATTTTACTCTTCA
65 GGTCATTTTACTCTTCA
* * ** *
29002 AGGGTATTTTAGTCATTTTACCCTTCAAGTGTATTTCGGTCATTTTACCCTTCGGGGGTAATTCG
1 AGGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCG
* **
29067 GTTATTTTA-TCCTTTT
66 GTCATTTTACT-CTTCA
* * * ** * *
29083 AGGGTATTTCGATCATTTTACCATTTGAGGGTATTTTGGTCATTTTACCCTAT-AAAGGTATTTC
1 AGGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCT-TCAAGGGTATTTC
* **
29147 GGTCATTTTACCCATTGG
65 GGTCATTTTACTC-TTCA
* * * * *
29165 A-GGTATTTTGGTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTTG
1 AGGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCG
* *
29229 GTCATTTTAC-CATCG
66 GTCATTTTACTCTTCA
* * * * *
29244 GGGGTATTTCGATCATTTTACCCATT-GAGGGTATTTTGGTCATTT
1 AGGGTATTTTGGTCATTTTACCC-TTCAAGGGTATTTCGGTCATTT
29289 GCCCACGAAT
Statistics
Matches: 235, Mismatches: 44, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
79 2 0.01
80 40 0.17
81 187 0.80
82 6 0.03
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.44
Consensus pattern (81 bp):
AGGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCG
GTCATTTTACTCTTCA
Found at i:29087 original size:108 final size:106
Alignment explanation
Indices: 28904--29288 Score: 416
Period size: 108 Copynumber: 3.6 Consensus size: 106
28894 CGGGTAGAAC
* * *
28904 AGTCATTTTACCC-TAAGAGGGTATTTTGGTCATTTTACCCTTAAGGGGTATTTCGATTATTTTA
1 AGTCATTTTACCCTTAA-AGGGTATTTCGGTCATTTTACCCTT-GGGGGTATTTCGGTTATTTTA
*
28968 CCCTTCAAGGGTATTTCGATCATTTTACTCTTCAAGGGTATTTT
64 CCCTTCAAGGGTATTTCGATCATTTTAC-CTTCGAGGGTATTTT
* * * *
29012 AGTCATTTTACCCTTCAAGTGTATTTCGGTCATTTTACCCTTCGGGGGTAATTCGGTTATTTTAT
1 AGTCATTTTACCCTTAAAGGGTATTTCGGTCATTTTACCCTT-GGGGGTATTTCGGTTATTTTAC
** *
29077 CCTTTTAGGGTATTTCGATCATTTTACCATTTGAGGGTATTTT
65 CCTTCAAGGGTATTTCGATCATTTTACC-TTCGAGGGTATTTT
* * * *
29120 GGTCATTTTACCCTATAAA-GGTATTTCGGTCATTTTACCCATTGGAGGTATTTTGGTCATTTTA
1 AGTCATTTTACCCT-TAAAGGGTATTTCGGTCATTTTACCC-TTGGGGGTATTTCGGTTATTTTA
* * * *
29184 CCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTT
64 CCCTTCAAGGGTATTTCGATCATTTTA-CCTTCGAGGGTATTTT
* * *** * * * *
29228 GGTCATTTTA-CCATCGGGGGTATTTCGATCATTTTACCCATTGAGGGTATTTTGGTCATTT
1 AGTCATTTTACCCTTAAAGGGTATTTCGGTCATTTTACCC-TTGGGGGTATTTCGGTTATTT
29289 GCCCACGAAT
Statistics
Matches: 238, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
106 1 0.00
107 43 0.18
108 185 0.78
109 9 0.04
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.43
Consensus pattern (106 bp):
AGTCATTTTACCCTTAAAGGGTATTTCGGTCATTTTACCCTTGGGGGTATTTCGGTTATTTTACC
CTTCAAGGGTATTTCGATCATTTTACCTTCGAGGGTATTTT
Found at i:33891 original size:28 final size:28
Alignment explanation
Indices: 33855--33911 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
33845 TATATATGGG
33855 AAAGAATCCATTTACATGATATAAAACT
1 AAAGAATCCATTTACATGATATAAAACT
33883 AAAGAATCCATTTACATGATATAAAACT
1 AAAGAATCCATTTACATGATATAAAACT
33911 A
1 A
33912 GTGTATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (28 bp):
AAAGAATCCATTTACATGATATAAAACT
Found at i:36137 original size:4 final size:4
Alignment explanation
Indices: 36128--36175 Score: 69
Period size: 4 Copynumber: 12.0 Consensus size: 4
36118 CTTACATTAG
* * *
36128 TATT TATT TATT TATC CATC TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
36176 GGCTTGTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:40749 original size:15 final size:15
Alignment explanation
Indices: 40726--40756 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40716 TACAACAATG
*
40726 GTTTGAAGTGAAGAT
1 GTTTCAAGTGAAGAT
40741 GTTTCAAGTGAAGAT
1 GTTTCAAGTGAAGAT
40756 G
1 G
40757 AATACTCTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (15 bp):
GTTTCAAGTGAAGAT
Found at i:45273 original size:30 final size:29
Alignment explanation
Indices: 45239--45303 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
45229 TAATCCACCA
45239 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
45269 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
45299 CCCAA
1 CCCAA
45304 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:45277 original size:31 final size:30
Alignment explanation
Indices: 45246--45303 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
45236 CCACCCAACT
45246 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
45276 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
45304 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:52171 original size:26 final size:26
Alignment explanation
Indices: 52141--52190 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
52131 CCACTTAATC
*
52141 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACATAGCAACCCCTT
52167 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
52191 CTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.32, G:0.24, T:0.14
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTT
Found at i:52273 original size:26 final size:26
Alignment explanation
Indices: 52243--52292 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
52233 CCAATGAACT
*
52243 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACATAGCAACCCCTC
52269 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
52293 CTTTCACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.34, G:0.24, T:0.12
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTC
Found at i:52284 original size:102 final size:103
Alignment explanation
Indices: 52108--52370 Score: 413
Period size: 102 Copynumber: 2.6 Consensus size: 103
52098 AACCGTTATT
* * * *
52108 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGAA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
** *
52173 TCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
52210 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGA
52274 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
52313 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
52371 TTATTACAAC
Statistics
Matches: 148, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
101 1 0.01
102 81 0.55
103 65 0.44
104 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (103 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Done.