Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1969
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: 23840
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Found at i:915 original size:295 final size:295
Alignment explanation
Indices: 1--6560 Score: 12401
Period size: 295 Copynumber: 22.3 Consensus size: 295
*
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCAAGGCTCAAGCGCGATCA-GGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
65 ATAAATAGAATGCGCAAGAATTGAACGGGTGCGATCATACCAGCACCCTAATGCACCGGATCCCA
66 ATAAATAGAATGCGCAAGAATTG-ACGGGTGCGATCATACCAGCA--CTAATGCACCGGATCCCA
*
130 TTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAG
128 TCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAG
195 TCCTCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTTATATCTCA
193 TCCTCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTA-TTTTTTTATATCTCA
260 TCGTTTAACTAATTAGTTATTTACGGAA-AAATCACTCG
257 TCGTTTAACTAATTAGTTATTTACGGAATAAATCACTCG
298 AAACGTTATTTGGTCGTA-TTAAATTCAAATTCGAGGCTCAA-CGCGATCAGGGGTAGCCTTTAA
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTT-A
*
361 TATATAATAGAATGCGCAAAGAAAATTGAC-GGTGCGATCATATCAGCACTAATGCACCGGATCC
65 TATA-AATAGAATGCGC-AAG--AATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCC
*
425 CATCAGAACTCCGTAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGA
126 CATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGA
490 AGTCCTCGTG-TGCA-CCCTCCAATTTTATATCTCATATTAAATTTTTTTCTATTTTTTTATATC
191 AGTCCTCGTGTTGCACCCCTCCAATTTTATATCTC--ATTAAATTTTTTTCTATTTTTTTATATC
553 TCATCG-TTAACTAATTAGTTATTTACGGAATAAATCACTCG
254 TCATCGTTTAACTAATTAGTTATTTACGGAATAAATCACTCG
594 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
659 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
724 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
789 TCGTGTTGCA-CCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTTATATCTCATCG
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTA-TTTTTTTATATCTCATCG
853 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
260 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
889 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
954 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
1019 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
1084 TCGTGTTGCA-CCCTCCAATTTTATATCTCATTAAATTTTTTTTCTATTTTTTTATATCTCATCG
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAA-TTTTTTTCTATTTTTTTATATCTCATCG
1148 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
260 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
1184 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCA-GGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1248 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
1313 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
1378 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTTATATCTCATCG
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTA-TTTTTTTATATCTCATCG
1443 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
260 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
1479 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
*
1544 ATAAATAGAATGCGC--GACA---A---GTGCGATCATACCAGCACTAATGCACCGAATCCCATC
66 ATAAATAGAATGCGCAAGA-ATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATC
1601 AGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
130 AGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
1666 CTCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTTCTATTTTTTTTATATCTCAT
195 CTCGTGTTGCACCCCTCCAATTTTATATCTCATTAAA-TTTTTTTCTA-TTTTTTTATATCTCAT
1731 CGTTTAACTAATTAGTTATTTACGGAATAAATCACTCG
258 CGTTTAACTAATTAGTTATTTACGGAATAAATCACTCG
1769 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1834 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
*
1899 GAACTCTGCAGTTAAGCGTGCTCT-GGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
131 GAACTCCGCAGTTAAGCGTGCT-TGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
1963 CTCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTA-TTTTTTATATCTCATCG
195 CTCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCG
*
2027 TATAACTAATTAGTTATTTACGGAATAAATCACTCG
260 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
2063 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
2128 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
2193 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
2258 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
2323 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
261 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
2358 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
2423 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
2488 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
2553 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
2618 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
261 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
2653 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
2718 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
2783 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
2848 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
2913 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
261 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
2948 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
3013 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
3078 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
3143 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTTCTATTTTTTTATATCTCATCG
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAA-TTTTTTTCTATTTTTTTATATCTCATCG
3208 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
260 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
3244 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
3309 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
3374 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
3439 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTTCTATTTTTTTATATCTCATCG
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAA-TTTTTTTCTATTTTTTTATATCTCATCG
3504 -TTAACTAATTAGTTATTTACGGAATAAATCACTCG
260 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
3539 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAA-CGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
3603 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
3668 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
3733 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
3798 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
261 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
3833 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
3898 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
3963 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
4028 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
4093 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
261 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
4128 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
4193 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
4258 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
*
4323 TCGTGTTGCACCCCCCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
4388 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
261 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
4423 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAA-CGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
4487 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
4552 GAACTCCGCAGTTAAGCGTGCTT-GGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
4616 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTTCT-TTTTTTTATATCTCATCG
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAA-TTTTTTTCTATTTTTTTATATCTCATCG
4680 -TTAACTAATTAGTTATTTACGGAATAAATCACTCG
260 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
4715 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
4780 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
4845 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
4910 TCGTGTTGCACCCCTCCAATTATCTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATC
196 TCGTGTTGCACCCCTCCAATT-T-TATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATC
4975 GTTTAACTAATTAGTTATTTACGGAATAAATCACTCG
259 GTTTAACTAATTAGTTATTTACGGAATAAATCACTCG
5012 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
5077 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
5142 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
5207 TCGTGTTGCA-CCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
5271 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
261 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
5306 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
* *
5371 ATAAATAGAATGCGCAAGAATTAAGGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
5436 GAACTCCGCAGTTAAGCGTGCTT-GG-GAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
*
5499 TCGTGTTGCACCCCTCCAATTTTATATCTTATTAAATTTTTTTTCTATTTTTTTATATCTCATCG
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAA-TTTTTTTCTATTTTTTTATATCTCATCG
5564 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
260 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
* *
5600 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAACCGCGATCAGGCGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
* *
5665 ATCAATAGAATGCGCAAGAATTGACGGGTGCGATCATATCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
*
5730 GAACTTCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCT--TGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
5793 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
5858 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
261 TTAACTAATTAGTTATTTACGGAATAAATCACTCG
*
5893 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGTTCAAGCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
* *
5958 ATAAATAGAATGCGCAAGAATTAAGGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
6023 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
*
6088 TCGTGTTGCACCCCTCCAATTTTATATCTTATTAAATTTTTTTTCTATTTTTTTATATCTCATCG
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAA-TTTTTTTCTATTTTTTTATATCTCATCG
6153 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
260 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
* *
6189 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAACCGCGATCAGGCGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
*
6254 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATATCAGCACTAATGCACCGGATCCCATCA
66 ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
* * *
6319 GAACTCCGTAGTTAAGCGTGCTTGTGTGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
131 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
6384 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTGTCTATTTTTTTATATCTCATCG
196 TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTT-TCTATTTTTTTATATCTCATCG
*
6449 TATAACTAATTAGTTATTTACGGAATAAATCACTCG
260 TTTAACTAATTAGTTATTTACGGAATAAATCACTCG
* *
6485 AAACGTTATTTGGTCGTATTTAAATTCAAATTCAAGGCTCAATCGCGATCAGGGGTAGCCTTTAT
1 AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
6550 ATAAATAGAAT
66 ATAAATAGAAT
6561 TGGCCGTGGT
Statistics
Matches: 6165, Mismatches: 48, Indels: 101
0.98 0.01 0.02
Matches are distributed among these distances:
289 138 0.02
290 145 0.02
291 1 0.00
292 128 0.02
293 521 0.08
294 1511 0.25
295 2180 0.35
296 950 0.15
297 531 0.09
298 33 0.01
299 20 0.00
300 2 0.00
301 5 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (295 bp):
AAACGTTATTTGGTCGTATTTAAATTCAAATTCGAGGCTCAAGCGCGATCAGGGGTAGCCTTTAT
ATAAATAGAATGCGCAAGAATTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
TCGTGTTGCACCCCTCCAATTTTATATCTCATTAAATTTTTTTCTATTTTTTTATATCTCATCGT
TTAACTAATTAGTTATTTACGGAATAAATCACTCG
Found at i:7681 original size:42 final size:42
Alignment explanation
Indices: 7586--7735 Score: 128
Period size: 43 Copynumber: 3.5 Consensus size: 42
7576 CCAACGTCCC
* * * * *
7586 AGACGTGGTCTTACATGTAATCA-AACATCGATGCCACTGCCCT
1 AGACATGGTCTTACACGAAATCAGAA-ATCGATGCCAAT-TCCT
* **
7629 AGA-ATGGGTCTTACACGAAATCAGATAT-GATGCTGATGTCCT
1 AGACAT-GGTCTTACACGAAATCAGAAATCGATGCCAAT-TCCT
*
7671 AGACATGGTCTTACACGTAAAAT-AGAAATCGATGCCAATTCCC
1 AGACATGGTCTTACACG--AAATCAGAAATCGATGCCAATTCCT
*
7714 AGACGTGGTCTTACACGAAATC
1 AGACATGGTCTTACACGAAATC
7736 CTATGTCATG
Statistics
Matches: 87, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
41 4 0.05
42 25 0.29
43 46 0.53
44 12 0.14
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (42 bp):
AGACATGGTCTTACACGAAATCAGAAATCGATGCCAATTCCT
Found at i:9881 original size:42 final size:44
Alignment explanation
Indices: 9816--9944 Score: 122
Period size: 44 Copynumber: 3.0 Consensus size: 44
9806 TCCTACATGT
* * *
9816 AATCAAATATCGATGTCATTGTCCCAAATAGGGTCTTACAC-AA
1 AATCAAATATCGATGCCAATGTCCCAAACAGGGTCTTACACGAA
* * * *
9859 AATCATATA-CGATGCCAATGTCCCAGACATGGTCTTACACGTA
1 AATCAAATATCGATGCCAATGTCCCAAACAGGGTCTTACACGAA
* * *
9902 AATCACAA-ATCGATGCCAACGTCCCAGAC-GTGGTCTTAAACGA
1 AATCA-AATATCGATGCCAATGTCCCAAACAG-GGTCTTACACGA
9945 TAACACATAT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
42 26 0.37
43 15 0.21
44 29 0.41
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (44 bp):
AATCAAATATCGATGCCAATGTCCCAAACAGGGTCTTACACGAA
Found at i:9926 original size:44 final size:43
Alignment explanation
Indices: 9785--9939 Score: 127
Period size: 42 Copynumber: 3.6 Consensus size: 43
9775 ATCTCGTACA
* * * * *
9785 ATGCCAACATCCTAGACGTGGTCCTACATGT-AATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAA-ATCG
* ** * * * * *
9828 ATGTCATTGTCCCAAATAGGGTCTTACAC-AAAATC-ATATACG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAAAT-CG
*
9870 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCACAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCA-AAATCG
*
9914 ATGCCAACGTCCCAGACGTGGTCTTA
1 ATGCCAACGTCCCAGACATGGTCTTA
9940 AACGATAACA
Statistics
Matches: 85, Mismatches: 22, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
41 2 0.02
42 27 0.32
43 27 0.32
44 26 0.31
45 3 0.04
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAAATCG
Found at i:13598 original size:31 final size:31
Alignment explanation
Indices: 13557--13620 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
13547 CCTTTTCATA
*
13557 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
13588 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
13619 TT
1 TT
13621 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:13860 original size:24 final size:24
Alignment explanation
Indices: 13833--13979 Score: 199
Period size: 24 Copynumber: 6.2 Consensus size: 24
13823 GGCCTTGCCT
* * *
13833 CTTTTAATAATTGGGGCAAAATCC
1 CTTTTAATAACTGGGGCATAAGCC
*
13857 CTTTTTATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
*
13881 C-TTTAATAACTGGGGCGTAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
* *
13904 CTGTTGATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
*
13928 CTTTTGATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
*
13952 C-TTTAATAACTGGAGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
13975 CTTTT
1 CTTTT
13980 TCACTTCCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
23 42 0.39
24 67 0.61
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (24 bp):
CTTTTAATAACTGGGGCATAAGCC
Found at i:13930 original size:71 final size:71
Alignment explanation
Indices: 13839--13976 Score: 222
Period size: 71 Copynumber: 1.9 Consensus size: 71
13829 GCCTCTTTTA
* * * * *
13839 ATAATTGGGGCAAAATCCCTTTTTATAACTGGGGCATAAGCCCTTTAATAACTGGGGCGTAAGCC
1 ATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGAGCATAAGCC
13904 CTGTTG
66 CTGTTG
*
13910 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGAGCATAAGCC
1 ATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGAGCATAAGCC
13975 CT
66 CT
13977 TTTTCACTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (71 bp):
ATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGAGCATAAGCC
CTGTTG
Found at i:13979 original size:47 final size:47
Alignment explanation
Indices: 13833--13979 Score: 197
Period size: 47 Copynumber: 3.1 Consensus size: 47
13823 GGCCTTGCCT
* * * *
13833 CTTTTAATAATTGGGGCAAAATCCCTTTTTATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCC
* *
13881 C-TTTAATAACTGGGGCGTAAGCCCTGTTGATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCCCT-TTAATAACTGGGGCATAAGCC
* *
13928 CTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGAGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
13975 CTTTT
1 CTTTT
13980 TCACTTCCTC
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
46 1 0.01
47 64 0.73
48 23 0.26
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (47 bp):
CTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
Found at i:14054 original size:20 final size:20
Alignment explanation
Indices: 14029--14095 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
14019 TTATGAATAC
14029 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
14049 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
14069 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
14089 ACCATGT
1 ATCATGT
14096 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:14060 original size:11 final size:11
Alignment explanation
Indices: 14029--14084 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
14019 TTATGAATAC
14029 ATCATGTGCAT
1 ATCATGTGCAT
*
14040 ATCA--TACAT
1 ATCATGTGCAT
14049 ATCATGTGCAT
1 ATCATGTGCAT
*
14060 ATCA--TACAT
1 ATCATGTGCAT
*
14069 GTCATGTGCAT
1 ATCATGTGCAT
14080 ATCAT
1 ATCAT
14085 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:14175 original size:25 final size:25
Alignment explanation
Indices: 14132--14179 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
14122 ATACATAAAC
* **
14132 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGTAAAACAGTCATTTTTA
14157 CCTAGGGGTAAAACAGTCATTTT
1 CCTAGGGGTAAAACAGTCATTTT
14180 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGTAAAACAGTCATTTTTA
Found at i:21679 original size:30 final size:31
Alignment explanation
Indices: 21639--21701 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
21629 CCTTTTCATA
21639 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
21670 TTTCA-ATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
21700 TT
1 TT
21702 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:21947 original size:24 final size:24
Alignment explanation
Indices: 21895--21989 Score: 131
Period size: 24 Copynumber: 4.0 Consensus size: 24
21885 GCTTTATCAT
*
21895 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
21920 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
21944 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
21967 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
21990 CACTTCCTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.35
24 29 0.46
25 12 0.19
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:21971 original size:47 final size:49
Alignment explanation
Indices: 21894--21989 Score: 144
Period size: 47 Copynumber: 2.0 Consensus size: 49
21884 TGCTTTATCA
*
21894 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
*
21943 TATAACTGG-GGCATAAGCC-C-TTTAATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
21990 CACTTCCTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 26 0.59
48 5 0.11
49 13 0.30
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (49 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
Found at i:21974 original size:23 final size:23
Alignment explanation
Indices: 21916--21988 Score: 119
Period size: 23 Copynumber: 3.1 Consensus size: 23
21906 CCTAGCCTCT
*
21916 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
21939 TTTTTATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
21963 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
21986 TTT
1 TTT
21989 TCACTTCCTC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 25 0.54
24 21 0.46
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:22061 original size:20 final size:20
Alignment explanation
Indices: 22038--22076 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
22028 TATGAATACA
22038 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
22058 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
22077 ACCATGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:22082 original size:20 final size:20
Alignment explanation
Indices: 22039--22083 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
22029 ATGAATACAT
**
22039 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAC
22059 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAC
22079 CATGT
1 CATGT
22084 TTATCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTGCATATCATACATAC
Found at i:22152 original size:25 final size:25
Alignment explanation
Indices: 22120--22167 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
22110 ATACATAAAC
* * *
22120 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
22145 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
22168 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Done.