Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2060
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: 80632
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2033 original size:149 final size:144
Alignment explanation
Indices: 1522--2796 Score: 1236
Period size: 149 Copynumber: 8.5 Consensus size: 144
1512 TTATTTCTAC
* ** * * *
1522 TTTCAAAATTCAACTCATATTATGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTT-T
1 TTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGT-ATTTTCA
* * * ** * *
1586 ATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
65 ATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
1651 AATTTCAATTTCTGT
130 AATTTCAATTTCTGT
* * * * *
1666 TTTCAAAATTCAACTCAGATTGAGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAA
* *
1731 TTTCTGTTTTTCAAAAAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
66 TTTATG-TTTTC-------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
*
1796 CTGGGGTAATTTCAATTTCTGT
123 CTGAGGTAATTTCAATTTCTGT
* * * *
1818 TTTCAAAATTCAACTCATATTACGAGTA-ATGAGTTGAACCTCAAGACACGTTGAGGTATTTTCA
1 TTTCAAAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
* * *
1882 ATTTATGTTTTCAAAAATCTACTCATATTGTGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGA
65 ATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGA
* *
1946 GGTATTTTCAATTTCTAT
127 GGTAATTTCAATTTCTGT
** * * ** *
1964 CTTTCAAAAAAAAAAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTGG
1 -TTTC--AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGG---T--
* **
2029 CAATTTTTGTTTCTTAATTTATG-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCT
58 --A----T-TTTC--AATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * *
2093 CAAGACAGGTTGAGGTAATTTCAATTTCTGT
114 CAGGACACGCTGAGGTAATTTCAATTTCTGT
* * * *
2124 TTTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAA
* *
2189 TTTCTGTTTTTCAAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
66 TTTATG-TTTTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
2254 AGGTAATTTCAATTTCTGT
126 AGGTAATTTCAATTTCTGT
* * * * *
2273 TTTCAAAATTCAATTCATATTGCAAGTA-ATGAGTTGAACCTCAAGACACGTTGAGGTATTTTCA
1 TTTCAAAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
* *
2337 ATTTATGTTTTCAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGA
65 ATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGA
* *
2401 GGTATTTTCAATTTCTAT
127 GGTAATTTCAATTTCTGT
* * ** *
2419 CTTTCAAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATT
1 -TTTC----AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCT---G-A--
* **
2484 GGTAATTTTTGTTTCTTAATTTATG-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGC
55 GGT-A----T-TTTC--AATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
2548 CTCAAGACACGTTGAGGTAATTTCAATTTCTGT
112 CTCAGGACACGCTGAGGTAATTTCAATTTCTGT
* *
2581 TTTCAAAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTC
1 TTTC-AAAAA-TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTC
* *
2646 AATTTTTGTCTTTCAAAAAAATCAACTC--ATTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTG
64 AATTTATGT-TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
2709 AGGTAATTTCAATTTCTGTT
126 AGGTAATTTCAATTTCTG-T
* * *
2729 TTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCGTCAGGGCACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAA
2794 TTT
66 TTT
2797 CTACTTTCCA
Statistics
Matches: 945, Mismatches: 117, Indels: 136
0.79 0.10 0.11
Matches are distributed among these distances:
143 16 0.02
144 130 0.14
145 20 0.02
146 102 0.11
147 69 0.07
148 12 0.01
149 173 0.18
150 3 0.00
151 41 0.04
152 125 0.13
153 4 0.00
154 2 0.00
155 2 0.00
156 2 0.00
157 44 0.05
158 7 0.01
159 40 0.04
160 24 0.03
161 8 0.01
162 61 0.06
163 13 0.01
164 38 0.04
165 9 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (144 bp):
TTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAA
TTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
ATTTCAATTTCTGT
Found at i:2576 original size:85 final size:75
Alignment explanation
Indices: 1526--2796 Score: 959
Period size: 72 Copynumber: 16.9 Consensus size: 75
1516 TTCTACTTTC
* ** * ** *
1526 AAAATTCAACTCATATTATGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTTTATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
* *
1591 T-ATTTT--C
66 TGTTTTTAAA
* * *
1598 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
*
1663 TG-TTTT--C
66 TGTTTTTAAA
* * * * * *
1670 AAAATTCAACTCAGATTGAGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
1735 TGTTTTTCAAAAAAA
66 TGTTTTT-----AAA
* ** * * *
1750 AAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGGGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
*
1815 TG-TTTT--C
66 TGTTTTTAAA
* * * * * * *
1822 AAAATTCAACTCATATTACGAGTAATGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATTTA
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
*
1887 TG-TTTT--C
66 TGTTTTTAAA
* * ** * * *
1894 AAAAATCTACTCATATTGTGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG---ACACGCTGAGGTAATTTCAAT
* * *
1958 TTCTATCTTTCAAA
63 TTTTGT-TTTTAAA
* * ** ** * *
1972 AAAAA-AAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGT-ATTGGCAATTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATT-TCAATTT
2035 TTGTTTCTTAATTTA
65 TTGTTT-TTAA---A
* * *
2050 TGTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAGGTTGAGGTAATTTC
1 ------AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTC
* *
2115 AATTTCTG-TTTT--C
60 AATTTTTGTTTTTAAA
* * * * *
2128 AAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
2193 TGTTTTTCAAAA
66 TGTTTTT--AAA
* ** * *
2205 AAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
*
2270 TG-TTTT--C
66 TGTTTTTAAA
* * * * * * * *
2277 AAAATTCAATTCATATTGCAAGTAATGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATTTA
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
*
2342 TG-TTTT--C
66 TGTTTTTAAA
* ** * * *
2349 AAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG---ACACGCTGAGGTAATTTCAAT
* **
2413 TTCTATCTTTCAAAA
63 TT-T-TGTTTTTAAA
* ** ** *
2428 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGT-ATTGGT-AATT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATT--TCAATT
2491 TTTGTTTCTTAATTTA
64 TTTGTTT-TTAA---A
* *
2507 TGTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
1 ------AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTC
* *
2572 AATTTCTG-TTTTCAA
60 AATTTTTGTTTTTAAA
* * *
2587 AAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
* *
2652 TGTCTTTCAA
66 TGTTTTTAAA
** * * *
2662 AAAAATCAACTC--ATTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
*
2725 TGTTTTT--C
66 TGTTTTTAAA
* * * * *
2733 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCGTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
2797 CTACTTTCCA
Statistics
Matches: 985, Mismatches: 153, Indels: 121
0.78 0.12 0.10
Matches are distributed among these distances:
71 14 0.01
72 372 0.38
73 103 0.10
74 109 0.11
75 42 0.04
76 13 0.01
77 104 0.11
78 9 0.01
79 41 0.04
80 60 0.06
83 5 0.01
84 9 0.01
85 98 0.10
86 6 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTT
TGTTTTTAAA
Found at i:2619 original size:74 final size:73
Alignment explanation
Indices: 2501--2798 Score: 390
Period size: 73 Copynumber: 4.1 Consensus size: 73
2491 TTTGTTTCTT
* * *
2501 AATTTATG-TTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
2564 GTAATTTC
66 GTAATTTC
*
2572 AATTTCTGTTTTCAAAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGA
1 AATTTCTGTTTTCAAAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGA
*
2637 GGTATTTTC
65 GGTAATTTC
* ** * *
2646 AATTTTTGTCTTTCAAAAAAATCAACTC--ATTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTG
1 AATTTCTGT-TTTC-AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTG
2709 AGGTAATTTC
64 AGGTAATTTC
* * * *
2719 AATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCGTCAGGGCACGCTGA
1 AATTTCTG-TTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGA
*
2783 GGTATTTTC
65 GGTAATTTC
2792 AATTTCT
1 AATTTCT
2799 ACTTTCCAAT
Statistics
Matches: 201, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
71 19 0.09
72 4 0.02
73 101 0.50
74 60 0.30
75 11 0.05
76 6 0.03
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (73 bp):
AATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
GTAATTTC
Found at i:2680 original size:455 final size:453
Alignment explanation
Indices: 1594--2796 Score: 2061
Period size: 455 Copynumber: 2.6 Consensus size: 453
1584 TTATTTCTAT
1594 TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
1 TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
*
1659 TTTCTGTTTTCAAAATTCAACTCAGATTGAGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTA
66 TTTCTGTTTTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTA
1724 TTTTCAATTTCTGTTTTTCAAAAAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCA
131 TTTTCAATTTCTGTTTTTC----AAAAAAAATCGACTCA-ATTGCGAGAGGTGAGTTGAGCCTCA
* *
1789 GGACACGCTGGGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTACGAGTAATGAGTTG
191 GGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGTAATGAGTTG
* *
1854 AACCTCAAGACACGTTGAGGTATTTTCAATTTATGTTTTCAAAAATCTACTCATATTGTGAGAGG
256 AACCTCAAGACACGTTGAGGTATTTTCAATTTATGTTTTCAAAAATCAACTCATATTGAGAGAGG
1919 TGAGTTGAGCCTCGGTTCACATGCTGAGGTATTTTCAATTTCTATCTTTCAAAAAAAAAAACTCA
321 TGAGTTGAGCCTCGGTTCACATGCTGAGGTATTTTCAATTTCTATCTTTCAAAAAAAAAAACTCA
1984 TAATGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTGGCAATTTTTGTTTCTTAATTT
386 TAATGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTGGCAATTTTTGTTTCTTAATTT
2049 ATG
451 ATG
*
2052 TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAGGTTGAGGTAATTTCAA
1 TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
2117 TTTCTGTTTTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTA
66 TTTCTGTTTTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTA
2182 TTTTCAATTTCTGTTTTTCAAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
131 TTTTCAATTTCTGTTTTTC-AAAAAAAATCGACTCA-ATTGCGAGAGGTGAGTTGAGCCTCAGGA
* *
2247 CACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAATTCATATTGCAAGTAATGAGTTGAAC
194 CACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGTAATGAGTTGAAC
2312 CTCAAGACACGTTGAGGTATTTTCAATTTATGTTTTCAAAAATCAACTCATATTGAGAGAGGTGA
259 CTCAAGACACGTTGAGGTATTTTCAATTTATGTTTTCAAAAATCAACTCATATTGAGAGAGGTGA
2377 GTTGAGCCTCGGTTCACATGCTGAGGTATTTTCAATTTCTATCTTTCAAAAAAAAATCAACTCAT
324 GTTGAGCCTCGGTTCACATGCTGAGGTATTTTCAATTTCTATCTTTCAAAAAAAAA--AACTCAT
* * *
2442 AATGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGGTAATTTTTGTTTCTTAATTTA
387 AATGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTGGCAATTTTTGTTTCTTAATTTA
2507 TG
452 TG
2509 TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
1 TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
* *
2574 TTTCTGTTTTCAAAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGG
66 TTTCTGTTTTC--AAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGG
* * *
2639 TATTTTCAATTTTTGTCTTTC-AAAAAAATCAACTC-ATTGCGAGAGGTGAGTTGAGCCTCAGGA
129 TATTTTCAATTTCTGTTTTTCAAAAAAAATCGACTCAATTGCGAGAGGTGAGTTGAGCCTCAGGA
* *
2702 CGCGCTGAGGTAATTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAG-AGATGAGTTGA
194 CACGCTGAGGTAATTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGTA-ATGAGTTGA
* * * * *
2766 GCGTCAGGGCACGCTGAGGTATTTTCAATTT
257 ACCTCAAGACACGTTGAGGTATTTTCAATTT
2797 CTACTTTCCA
Statistics
Matches: 713, Mismatches: 26, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
455 279 0.39
456 59 0.08
457 159 0.22
458 147 0.21
459 69 0.10
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (453 bp):
TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
TTTCTGTTTTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTA
TTTTCAATTTCTGTTTTTCAAAAAAAATCGACTCAATTGCGAGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGTAATGAGTTGAACCT
CAAGACACGTTGAGGTATTTTCAATTTATGTTTTCAAAAATCAACTCATATTGAGAGAGGTGAGT
TGAGCCTCGGTTCACATGCTGAGGTATTTTCAATTTCTATCTTTCAAAAAAAAAAACTCATAATG
CGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTGGCAATTTTTGTTTCTTAATTTATG
Found at i:3005 original size:177 final size:173
Alignment explanation
Indices: 2663--3007 Score: 444
Period size: 177 Copynumber: 1.9 Consensus size: 173
2653 GTCTTTCAAA
* *
2663 AAAATCAACTCATTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTGAGGTAATTTCAATTTCTGT
1 AAAATCAACTCATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTCCTGT
* * *
2728 TTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCGTCAGGGCACGCTGAGGTATTTTCA
66 TTGTCAAAAATCAACTCATATTGCGAGAGATGAGCTGAGCCTCAGGGCACGCTGAGGTATTTTCA
** * *
2793 ATTTCTACTTTCCAATTTCTGCCTTTTAAAAAAAAAGAAAGAAAG
131 AAGTATACTTTCCAATTTAT--CTTTTAAAAAAAAAGAAAGAAAG
2838 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTCCT
1 AAAATCAACTC--ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTCCT
* *
2903 GTTTGTC-AAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTC-GAGTCACATG-TCGAGGTA
64 GTTTGTCAAAAATCAACTCATATTGCGAGAGATGAGCTGAGCCTCAG-GGCAC--GCT-GAGGTA
* * *
2965 TTTTCAAAGTATGCTTTTTCAATTTATTTTTGTCAAAAAAAAA
125 TTTTCAAAGTATAC-TTTCCAATTTATCTTT-T-AAAAAAAAA
3008 AATCAACTCA
Statistics
Matches: 147, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
175 12 0.08
176 38 0.26
177 60 0.41
178 18 0.12
179 19 0.13
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (173 bp):
AAAATCAACTCATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTCCTGT
TTGTCAAAAATCAACTCATATTGCGAGAGATGAGCTGAGCCTCAGGGCACGCTGAGGTATTTTCA
AAGTATACTTTCCAATTTATCTTTTAAAAAAAAAGAAAGAAAG
Found at i:5010 original size:13 final size:13
Alignment explanation
Indices: 4982--5018 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
4972 TGAATTTCTA
4982 TATTA-TATTA-T
1 TATTATTATTACT
*
4993 TATTATTGTTACT
1 TATTATTATTACT
5006 TATTATTATTACT
1 TATTATTATTACT
5019 GTTATGTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 5 0.23
12 4 0.18
13 13 0.59
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (13 bp):
TATTATTATTACT
Found at i:5017 original size:161 final size:170
Alignment explanation
Indices: 4770--5113 Score: 537
Period size: 161 Copynumber: 2.1 Consensus size: 170
4760 TTTTTTAAAT
* * *
4770 TATTTTATTTTAATATTATTATATTATGTTTAGTTTTTTTTGAATTTCTATATTATTATTATTAT
1 TATTTTATTTTAATATCATTATATTATGTTTAGCTTTTATTGAATTTCTATATTATTATTATTAT
*
4835 TATTGTTACTTATTATTATTACTGTTA-GTTACTTATTATTTATACTATACTTAAT-AT-TATTA
66 TATTGTTACTTATTATTATTACTGTTATG-TACATATTATTTATACTATACTTAATAATATATTA
4897 TTA-TATT-T-A-A-TATTATTATTTATAAATATTAGTGTA
130 TTATTATTATAATACTATTATTATTTATAAATATTAGTGTA
4933 TATTTTATTTTAATATCATTATATTATGTTTA-CTTTTATTGAATTTCTATATTA-TATTATTAT
1 TATTTTATTTTAATATCATTATATTATGTTTAGCTTTTATTGAATTTCTATATTATTATTATTAT
4996 TATTGTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATAATAATATTA
66 TATTGTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATAAT-ATATTA
5061 TTATTATTATACATTTACTATTATTATTTATAAATATTAGTGTA
130 TTATTATTATA-A--TACTATTATTATTTATAAATATTAGTGTA
5105 TATTTTATT
1 TATTTTATT
5114 ATCTATGTTT
Statistics
Matches: 165, Mismatches: 4, Indels: 15
0.90 0.02 0.08
Matches are distributed among these distances:
161 61 0.37
162 23 0.14
163 31 0.19
164 8 0.05
165 4 0.02
166 1 0.01
168 1 0.01
171 1 0.01
172 35 0.21
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (170 bp):
TATTTTATTTTAATATCATTATATTATGTTTAGCTTTTATTGAATTTCTATATTATTATTATTAT
TATTGTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATAATATATTAT
TATTATTATAATACTATTATTATTTATAAATATTAGTGTA
Found at i:5035 original size:3 final size:3
Alignment explanation
Indices: 4820--5016 Score: 76
Period size: 3 Copynumber: 64.7 Consensus size: 3
4810 TGAATTTCTA
* * *
4820 TAT TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TAC TGT TAGT TACT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TA-T
* * *
4868 TAT TAT T-T ATAC TA- TACT TAA TAT TAT TAT TA- TATT TAA TAT TAT
1 TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * *
4913 TATT TAT AAA TAT TAGT GTA- TAT T-T TAT T-T TAA TAT CAT TA- TAT
1 TA-T TAT TAT TAT TA-T -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4957 TAT GT-T TACT T-T TAT TGAAT T-T CTA- TAT TA- TAT TAT TAT TAT
1 TAT -TAT TA-T TAT TAT T--AT TAT -TAT TAT TAT TAT TAT TAT TAT
*
4999 TGT TACT TAT TAT TAT TA
1 TAT TA-T TAT TAT TAT TA
5017 CTGTTATGTA
Statistics
Matches: 146, Mismatches: 22, Indels: 52
0.66 0.10 0.24
Matches are distributed among these distances:
2 21 0.14
3 97 0.66
4 23 0.16
5 5 0.03
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:5271 original size:9 final size:10
Alignment explanation
Indices: 5241--5289 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 10
5231 CTTTCTTTTG
*
5241 TATT-TTTAC
1 TATTATTTAT
5250 TATTATTGCTAT
1 TATTATT--TAT
5262 TATTA-TTAT
1 TATTATTTAT
5271 TATTATTTAT
1 TATTATTTAT
5281 TA-TATTTAT
1 TATTATTTAT
5290 ATAATATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
9 19 0.54
10 8 0.23
11 1 0.03
12 7 0.20
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (10 bp):
TATTATTTAT
Found at i:7510 original size:22 final size:22
Alignment explanation
Indices: 7485--7551 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 22
7475 AATGAAATAT
*
7485 TTTTAGGTATTTTTAGAATTTG
1 TTTTAGGTATTTTTAGAATTTC
** *
7507 TTTTCA-AAATTTTT-GGATTTC
1 TTTT-AGGTATTTTTAGAATTTC
*
7528 TTTTTGGTATTTTTAGAAATTTC
1 TTTTAGGTATTTTTAG-AATTTC
7551 T
1 T
7552 CTTTGATTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
21 15 0.45
22 11 0.33
23 7 0.21
ACGTcount: A:0.22, C:0.04, G:0.13, T:0.60
Consensus pattern (22 bp):
TTTTAGGTATTTTTAGAATTTC
Found at i:17295 original size:90 final size:92
Alignment explanation
Indices: 17117--17308 Score: 284
Period size: 90 Copynumber: 2.1 Consensus size: 92
17107 TTGATTTTAG
* *
17117 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATATAATTAT
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATATAATTAT
* *
17182 ATTTAATATTAATTATTTTAAATTGTA
66 ATGTAATATTAATTATTTTAAATTATA
*
17209 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTA-T-TA-AATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATATAATTA
17271 TATGTAATAATT-ATTATTTTAAATTATA
65 TATGTAAT-ATTAATTATTTTAAATTATA
*
17299 CAAATTCATA
1 TAAATTCATA
17309 AACTATAATC
Statistics
Matches: 92, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
90 36 0.39
91 5 0.05
92 18 0.20
93 33 0.36
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATATAATTAT
ATGTAATATTAATTATTTTAAATTATA
Found at i:17356 original size:48 final size:52
Alignment explanation
Indices: 17286--17384 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
17276 AATAATTATT
17286 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
17334 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
17385 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:17366 original size:17 final size:17
Alignment explanation
Indices: 17341--17374 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17331 ATAATTTTAA
*
17341 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
17358 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
17375 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:17391 original size:17 final size:16
Alignment explanation
Indices: 17346--17393 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
17336 TTTAAATTTT
17346 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
17363 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
17377 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
17394 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:17465 original size:18 final size:17
Alignment explanation
Indices: 17434--17468 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17424 ATTATTAAGA
17434 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
17451 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
17469 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:17507 original size:120 final size:119
Alignment explanation
Indices: 17383--17604 Score: 408
Period size: 120 Copynumber: 1.9 Consensus size: 119
17373 ATTAGTTATA
17383 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA-TTTATTAAATTA
* *
17448 TATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGT
65 TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
*
17503 ATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTATTAAATTAT
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTATTAAATTAT
17568 ATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 ATATTTTAATTAAAATATATTTAATAATAATTATGTT
17605 TAAATATGAT
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
119 48 0.48
120 51 0.52
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (119 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTATTAAATTAT
ATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
Found at i:17714 original size:144 final size:146
Alignment explanation
Indices: 17542--17812 Score: 476
Period size: 144 Copynumber: 1.9 Consensus size: 146
17532 ATAAGAATAT
*
17542 TAATTATTAAGAATTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 TAATTATTAAGAATTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTA
17607 AATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTAC
66 AATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTAC
17669 CAAAACAAATTTATGC
131 CAAAACAAATTTATGC
17685 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAA-TTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
17750 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
65 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
17813 CAATAATCAT
Statistics
Matches: 120, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
143 13 0.11
144 77 0.64
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (146 bp):
TAATTATTAAGAATTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTA
AATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTAC
CAAAACAAATTTATGC
Found at i:17725 original size:18 final size:17
Alignment explanation
Indices: 17697--17731 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17687 ATTATTAAGA
*
17697 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17714 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17732 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17942 original size:44 final size:45
Alignment explanation
Indices: 17893--17987 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
17883 TTACACCTCT
* *
17893 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
17937 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
17982 ATTACA
1 ATTACA
17988 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:17987 original size:16 final size:16
Alignment explanation
Indices: 17966--17998 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17956 TTGATTTGCT
*
17966 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
17982 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
17998 A
1 A
17999 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:18008 original size:21 final size:21
Alignment explanation
Indices: 17979--18021 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
17969 ACACCTCTAT
*
17979 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
18000 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
18021 T
1 T
18022 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:19709 original size:41 final size:40
Alignment explanation
Indices: 19652--19922 Score: 192
Period size: 41 Copynumber: 6.6 Consensus size: 40
19642 TCTGAAGTCT
* **
19652 AACAGGAGTACGTATGTGCAATTCAGGAGTACTGAAGTACA
1 AACAGG-GCACGTATGTGCAATTCAGGAGTACCAAAGTACA
* * * **
19693 AACAGTGGCATGTATGTGTAATTCA-AAGGTACCAAAGTATT
1 AACAG-GGCACGTATGTGCAATTCAGGA-GTACCAAAGTACA
* *** *
19734 AACAGGGGCACGTATGTGTAATTCAAGG-GTATTGAAGAACAA
1 AACA-GGGCACGTATGTGCAATTC-AGGAGTACCAAAGTAC-A
* * *
19776 AAAAGGGCACGTATGTGCAAATT-AGG-GCTACTAAAGTAGA
1 AACAGGGCACGTATGTGC-AATTCAGGAG-TACCAAAGTACA
* * * * *
19816 AATAGGAGCACGTACGTGCAATTCAAGATTACCGAAGTACA
1 AACAGG-GCACGTATGTGCAATTCAGGAGTACCAAAGTACA
* *
19857 AACAAGGGCTCGTATGTGCAATTCA-AAGGTACCAAAGTACA
1 AAC-AGGGCACGTATGTGCAATTCAGGA-GTACCAAAGTACA
19898 AACAGAGGCACGTATGTGCAATTCA
1 AACAG-GGCACGTATGTGCAATTCA
19923 TAATATTCTT
Statistics
Matches: 180, Mismatches: 36, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
40 18 0.10
41 149 0.83
42 13 0.07
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (40 bp):
AACAGGGCACGTATGTGCAATTCAGGAGTACCAAAGTACA
Found at i:19790 original size:82 final size:82
Alignment explanation
Indices: 19652--19922 Score: 273
Period size: 82 Copynumber: 3.3 Consensus size: 82
19642 TCTGAAGTCT
* * * *
19652 AACAGGAGTACGTATGTGCAATTC-AGGAGTACTGAAGTAC-AAACAGTGGCATGTATGTGTAAT
1 AACAGGAGCACGTATGTGCAATTCAAGG-GTACTGAAGTACAAAAAAG-GGCACGTATGTGAAAT
**
19715 TCAAAGGTACCAAAGTATT
64 TCAAAGGTACCAAAGTACA
* * * *
19734 AACAGGGGCACGTATGTGTAATTCAAGGGTATTGAAGAACAAAAAAGGGCACGTATGTGCAAATT
1 AACAGGAGCACGTATGTGCAATTCAAGGGTACTGAAGTACAAAAAAGGGCACGTATGTG-AAATT
* * *
19799 --AGGGCTACTAAAGTAGA
65 CAAAGG-TACCAAAGTACA
* * ** * * * *
19816 AATAGGAGCACGTACGTGCAATTCAAGATTACCGAAGTACAAACAAGGGCTCGTATGTGCAATTC
1 AACAGGAGCACGTATGTGCAATTCAAGGGTACTGAAGTACAAAAAAGGGCACGTATGTGAAATTC
19881 AAAGGTACCAAAGTACA
66 AAAGGTACCAAAGTACA
19898 AACA-GAGGCACGTATGTGCAATTCA
1 AACAGGA-GCACGTATGTGCAATTCA
19923 TAATATTCTT
Statistics
Matches: 153, Mismatches: 29, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
81 9 0.06
82 129 0.84
83 15 0.10
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (82 bp):
AACAGGAGCACGTATGTGCAATTCAAGGGTACTGAAGTACAAAAAAGGGCACGTATGTGAAATTC
AAAGGTACCAAAGTACA
Found at i:22209 original size:28 final size:27
Alignment explanation
Indices: 22162--22217 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
22152 ATTTTAACCA
* *
22162 AATTAAAATTAAGTTGTTTAAATTATTT
1 AATTAAAATTAAATTATTT-AATTATTT
* *
22190 AATTAAGATTAAATTATTTATTTATTT
1 AATTAAAATTAAATTATTTAATTATTT
22217 A
1 A
22218 TTTGGAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (27 bp):
AATTAAAATTAAATTATTTAATTATTT
Found at i:23578 original size:46 final size:46
Alignment explanation
Indices: 23528--23645 Score: 139
Period size: 46 Copynumber: 2.6 Consensus size: 46
23518 TACTGCATGT
23528 GTTGCGGACTTAAGAATACAAGAATAGGTTCCGAGC-TCATGCATAA
1 GTTGCGGACTTAAGAATACAAGAATAGGTTCCGAGCTTC-TGCATAA
* * ** *
23574 GTTGCAGACTTAAGAATACAGGTTTAGGTTCCGAGCTTCTGCATAT
1 GTTGCGGACTTAAGAATACAAGAATAGGTTCCGAGCTTCTGCATAA
* ** *
23620 GTTACGGACTCGAGAATACATGAATA
1 GTTGCGGACTTAAGAATACAAGAATA
23646 TTAAGCCCTG
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 57 0.97
47 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (46 bp):
GTTGCGGACTTAAGAATACAAGAATAGGTTCCGAGCTTCTGCATAA
Found at i:41938 original size:16 final size:16
Alignment explanation
Indices: 41917--41949 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41907 ATTCCAATGA
41917 ACCTTCATTGAGACAG
1 ACCTTCATTGAGACAG
41933 ACCTTCATTGAGACAG
1 ACCTTCATTGAGACAG
41949 A
1 A
41950 AGAGCTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (16 bp):
ACCTTCATTGAGACAG
Found at i:48923 original size:30 final size:30
Alignment explanation
Indices: 48883--48964 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
48873 CCCTAGTCAT
*
48883 CTTGCTTCCCACTTGCACCTACTCCACCAC
1 CTTGCCTCCCACTTGCACCTACTCCACCAC
48913 CTTGCCTCCCACTTGCACCTACTCCACCAC
1 CTTGCCTCCCACTTGCACCTACTCCACCAC
* * *
48943 ATTGTCTTCCACTTGCACCTAC
1 CTTGCCTCCCACTTGCACCTAC
48965 ACCATCAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.17, C:0.48, G:0.07, T:0.28
Consensus pattern (30 bp):
CTTGCCTCCCACTTGCACCTACTCCACCAC
Found at i:49397 original size:15 final size:16
Alignment explanation
Indices: 49379--49411 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
49369 GAGTTGAGAG
*
49379 TTTTGTTTTATT-TTT
1 TTTTATTTTATTATTT
49394 TTTTATTTTATTATTT
1 TTTTATTTTATTATTT
49410 TT
1 TT
49412 ACTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (16 bp):
TTTTATTTTATTATTT
Found at i:49453 original size:21 final size:18
Alignment explanation
Indices: 49400--49586 Score: 80
Period size: 18 Copynumber: 10.1 Consensus size: 18
49390 TTTTTTTTAT
* *
49400 TTTATTATTTTTACTATTA
1 TTTA-TATTATTATTATTA
49419 TTTATATTATTATTATTA
1 TTTATATTATTATTATTA
*
49437 TTTCTCATGTATATATTATTA
1 TTTAT-AT-TAT-TATTATTA
*
49458 TTTATATTA-TATATATCCTC
1 TTTATATTATTAT-TAT--TA
**
49478 TCCATATTTATT-TATATTA
1 TTTATA-TTATTAT-TATTA
* *
49497 -TTACTATCATTATTGTTA
1 TTTA-TATTATTATTATTA
* *
49515 CTTCTATTATT-TT-TTA
1 TTTATATTATTATTATTA
* * *
49531 TTTCTGACTACTATTATTA
1 TTTAT-ATTATTATTATTA
* *
49550 TATATA-TATGTATTATTG
1 TTTATATTAT-TATTATTA
*
49568 TTTGTATTATTATTATTA
1 TTTATATTATTATTATTA
49586 T
1 T
49587 CACCCCTATT
Statistics
Matches: 128, Mismatches: 24, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
16 7 0.05
17 11 0.09
18 56 0.44
19 23 0.18
20 10 0.08
21 20 0.16
22 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTATATTATTATTATTA
Found at i:49467 original size:9 final size:10
Alignment explanation
Indices: 49386--49467 Score: 64
Period size: 9 Copynumber: 8.4 Consensus size: 10
49376 GAGTTTTGTT
* *
49386 TTATTTTTTT
1 TTATTTATTA
49396 TTATTTTATTA
1 TTA-TTTATTA
*
49407 TT-TTTACTA
1 TTATTTATTA
49416 TTATTTA-TA
1 TTATTTATTA
49425 TTA-TTATTA
1 TTATTTATTA
* *
49434 TTATTTCTCA
1 TTATTTATTA
*
49444 TGTATATATTA
1 T-TATTTATTA
49455 TTATTTA-TA
1 TTATTTATTA
49464 TTAT
1 TTAT
49468 ATATATCCTC
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
8 3 0.05
9 24 0.41
10 17 0.29
11 14 0.24
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (10 bp):
TTATTTATTA
Found at i:50866 original size:14 final size:15
Alignment explanation
Indices: 50838--50866 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
50828 TTAAGAATTT
50838 CTCCCTTTTTATCGA
1 CTCCCTTTTTATCGA
50853 CTCCCTTTTT-TCGA
1 CTCCCTTTTTATCGA
50867 GATTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.10, C:0.34, G:0.07, T:0.48
Consensus pattern (15 bp):
CTCCCTTTTTATCGA
Found at i:58238 original size:46 final size:45
Alignment explanation
Indices: 58182--58357 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 45
58172 TATTTGGGCA
58182 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACG
* * * *
58228 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAC---G
*
58273 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGGGAACG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-GGAACG
* * *
58321 CCCGAGCTCGTTGAGTTGAGTTCGAGTTCGCTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58358 GTGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 61 0.56
47 27 0.25
48 3 0.03
50 3 0.03
51 4 0.04
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (45 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACG
Found at i:58337 original size:93 final size:93
Alignment explanation
Indices: 58178--58350 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
58168 CGGATATTTG
*
58178 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
58243 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
58271 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGGGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
58336 TTGAGTTCGAGTTCG
66 TTGAGTCCGAGTTCG
58351 CTTATGGGTG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.28
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:60493 original size:30 final size:30
Alignment explanation
Indices: 60457--60514 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
60447 AAATAGTGAG
*
60457 TTACACGGCCTAGACACACTCCTGTGTGGC
1 TTACACGGCCTAGACACACTCCTATGTGGC
*
60487 TTACACGGCCTGGACACACTCCTATGTG
1 TTACACGGCCTAGACACACTCCTATGTG
60515 CTTGGCATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.33, G:0.22, T:0.24
Consensus pattern (30 bp):
TTACACGGCCTAGACACACTCCTATGTGGC
Found at i:65335 original size:42 final size:42
Alignment explanation
Indices: 65289--65377 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
65279 ATGTTATAGT
* *
65289 ATATCGATGCCAATAG-CCCAG-CTATGGTCTTACACGAATCTC
1 ATATCGATGACAAT-GTCCCAGAC-ATGGTCTTACACAAATCTC
* *
65331 ATATCGATGACAATGTCTCGGACATGGTCTTACACAAATCTC
1 ATATCGATGACAATGTCCCAGACATGGTCTTACACAAATCTC
65373 ATATC
1 ATATC
65378 CCGATAATCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 1 0.02
42 39 0.95
43 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (42 bp):
ATATCGATGACAATGTCCCAGACATGGTCTTACACAAATCTC
Found at i:75098 original size:21 final size:21
Alignment explanation
Indices: 75072--75112 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
75062 TATTTTTGAA
75072 TTATTAATATCATTAATATTG
1 TTATTAATATCATTAATATTG
* *
75093 TTATTATTATCATTATTATT
1 TTATTAATATCATTAATATT
75113 ATATGTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATTAATATCATTAATATTG
Done.