Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167988.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_245, whole genome shotgun sequence
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: 43863
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:2030 original size:16 final size:16
Alignment explanation
Indices: 1984--2030 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1974 GATAAAAAGA
*
1984 TTCAGGTCATTTTGAG
1 TTCAGGTCATTTTGGG
** *
2000 TTTGGGTCATCTTGGG
1 TTCAGGTCATTTTGGG
2016 TTCAGGTCATTTTGG
1 TTCAGGTCATTTTGG
2031 ATTCTGGACT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.30, T:0.45
Consensus pattern (16 bp):
TTCAGGTCATTTTGGG
Found at i:4835 original size:619 final size:621
Alignment explanation
Indices: 3175--5046 Score: 3471
Period size: 622 Copynumber: 3.0 Consensus size: 621
3165 TTATTTGCTT
3175 CTCAATAGTTTTTGGAGAAAAGTCTACACTGGAAGATCCGAAAGTTGTAGTTGTACGACGATCAA
1 CTCAATAGTTTTTGGAGAAAAG--TACACTGGAAGATCCGAAAGTTGTAGTTGTACGACGATCAA
*
3240 TTAAATGAGAAAAAAGGGTTCATAGAGCTGATTGCAATTCTGGAG-AAAAAAATTCTAATGAAAT
64 TTAAATGAGAAAAGA-GGTTCATAGAGCTGATTGCAATTCTGGAGAAAAAAAATTCTAATGAAAT
3304 TTTGAGTCTAATGAAATGGTACAAAGGAATATTTTACTACATATTTTGCATTTAATGGTACAAAG
128 TTTGAGTCTAATGAAATGGTACAAAGGAATATTTTACTACATATTTTGCATTTAATGGTACAAAG
3369 AGTACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTTAGTTGTTTCACAGCGGT
193 AGTACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTTAGTTGTTTCACAGCGGT
3434 TCAAAAGTTCTTGAACAACAACCCTGAGCCCGCCTGCCGTCGTTTCCTCGAACCAAAATCACCTC
258 TCAAAAGTTCTTGAACAACAACCCTGAGCCCGCCTGCCGTCGTTTCCTCGAACCAAAATCACCTC
3499 ATAAGAGTGACGGGACTGGAAGTTGCAGCGGCGGTGAGCATTTTCCTCCTTTCTTTTATTTGGAA
323 ATAAGAGTGACGGGACTGGAAGTTGCAGCGGCGGTGAGCATTTTCCTCCTTTCTTTT-TTTGGAA
* *
3564 GACATGTAGATGTGGTGATTTGGGTCTAGTTGTTTCCTTGGATGACCTGGGCGATACACAATCAA
387 AACACGTAGATGTGGTGATTTGGGT-TAGTTGTTTCCTTGGATGACCTGGGCGATACACAATCAA
3629 TTGAGGATAGTGGCCAAAAAAGAAAAAAATGAATGAAGAATACCGCCAAGA-ATTGCTACTTTCT
451 TTGAGGATAGTGGCCAAAAAAGAAAAAAATGAATGAAGAATACCGCCAAGACATTGCTACTTTCT
*
3693 CACTTTTGTGGGCGGAAAGGATGGTCAAACTTGGGAAGAGGCCTAGCATGGGGAACAACTGTCCT
516 CACTTTTGTGGGCAGAAAGGATGGTCAAACTTGGGAAGAGGCCTAGCATGGGGAAC-ACTGTCCT
3758 TCTCAATTGCTTCAACGCCTTCTCTTCCTCTATCTACCAATA
580 TCTCAATTGCTTCAACGCCTTCTCTTCCTCTATCTACCAATA
3800 CTCAATAGTTTTTGGAG-AAAGTACACTGGAAGATCCGAAAGTTGTAGTTGTACGACGATCAATT
1 CTCAATAGTTTTTGGAGAAAAGTACACTGGAAGATCCGAAAGTTGTAGTTGTACGACGATCAATT
3864 AAATGAGAAAAGAGGTTCATAGAGCTGATTGCAATTCTGGAGAAAAAAAATTCTAATGAAATTTT
66 AAATGAGAAAAGAGGTTCATAGAGCTGATTGCAATTCTGGAGAAAAAAAATTCTAATGAAATTTT
3929 GAGTCTAATGAAATGGTACAAAGGAATATTTTACTACATATTTTGCATTTAATGGTACAAAGAGT
131 GAGTCTAATGAAATGGTACAAAGGAATATTTTACTACATATTTTGCATTTAATGGTACAAAGAGT
3994 ACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTTAGTTGTTTCACAGCGGTTCA
196 ACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTTAGTTGTTTCACAGCGGTTCA
4059 AAAGTTCTTGAACAACAACCCTGAGCCCGCCTGCCGTCGTTTCCTCGAACCAAAATCACCTCATA
261 AAAGTTCTTGAACAACAACCCTGAGCCCGCCTGCCGTCGTTTCCTCGAACCAAAATCACCTCATA
4124 AGAGTGACGGGACTGGAAGTTGCAGCGGCGGTGAGCATTTTCCTCCTTTCTTTTTTTGGAAAACA
326 AGAGTGACGGGACTGGAAGTTGCAGCGGCGGTGAGCATTTTCCTCCTTTCTTTTTTTGGAAAACA
4189 CGTAGATGTGGTGATTTGGGTTTAGTTGTTTCCTTGGATGACCTGGGCGATACACAATCAATTGA
391 CGTAGATGTGGTGATTTGGG-TTAGTTGTTTCCTTGGATGACCTGGGCGATACACAATCAATTGA
4254 GGATAGTGGCCAAAAAAG-AAAAAATGAATGAAGAATACCGCCAAGACATTGCTACTTTCTCACT
455 GGATAGTGGCCAAAAAAGAAAAAAATGAATGAAGAATACCGCCAAGACATTGCTACTTTCTCACT
4318 TTTGTGGGC-GAAAGGATGGTCAAACTTGGGAAGAGGCCTAGCATGGGGAACACTGTCCTTCTCA
520 TTTGTGGGCAGAAAGGATGGTCAAACTTGGGAAGAGGCCTAGCATGGGGAACACTGTCCTTCTCA
4382 ATTGCTTCAACG-CTTCTCTTCCTCTATCTACCAATA
585 ATTGCTTCAACGCCTTCTCTTCCTCTATCTACCAATA
4418 CTCAATAGTTTTTGGAGAAAAGTACACTGGAAGATCCGAAAGTTGTAGTTGTACGACGATCAATT
1 CTCAATAGTTTTTGGAGAAAAGTACACTGGAAGATCCGAAAGTTGTAGTTGTACGACGATCAATT
4483 AAATGAGAAAAGAGGTTCATAGAGCTGATTGCAATTCTGGAGAAAAAAAATTCTAATGAAATTTT
66 AAATGAGAAAAGAGGTTCATAGAGCTGATTGCAATTCTGGAGAAAAAAAATTCTAATGAAATTTT
4548 GAGTCTAATGAAATGGTACAAAGGAATATTTTTACTACATATTTTGCATTTAAT-GTACAAAGAG
131 GAGTCTAATGAAATGGTACAAAGGAATA-TTTTACTACATATTTTGCATTTAATGGTACAAAGAG
*
4612 TACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTAGTTGTTGTTTCACAGCGGT
195 TACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGT--TAGTTGTTTCACAGCGGT
4677 TC-AAAGTTCTTGAAC-ACAA-CCTGAGCCCGCCTGCCGTCGTTTCCTCGAACCAAAATCACCTC
258 TCAAAAGTTCTTGAACAACAACCCTGAGCCCGCCTGCCGTCGTTTCCTCGAACCAAAATCACCTC
4739 ATAAGAGTGACGGGACTGGAAGTTGCAGCGGCGGGTGAGCATTTTCCTCCTTTCTTTTCTTTGGA
323 ATAAGAGTGACGGGACTGGAAGTTGCAGCGGC-GGTGAGCATTTTCCTCCTTTCTTTT-TTTGGA
4804 AAACACGTAGATGTGGTGATTTGGGTTAGTTGTTTCCTTGGATGACCTGGGCGATACACAATCAA
386 AAACACGTAGATGTGGTGATTTGGGTTAGTTGTTTCCTTGGATGACCTGGGCGATACACAATCAA
4869 TTGAGGATAGTGGCCAAAAAAGAAAAAAATGAATGAAGAATACCGCCAAGACATTGCTACTTTCT
451 TTGAGGATAGTGGCCAAAAAAGAAAAAAATGAATGAAGAATACCGCCAAGACATTGCTACTTTCT
*
4934 CACTTTTGTGGGCAGAAAGGATGGTCAAACTT-GGAAGAGGCCTAGCATGGGGGACCACTGTCCT
516 CACTTTTGTGGGCAGAAAGGATGGTCAAACTTGGGAAGAGGCCTAGCAT-GGGGAACACTGTCCT
*
4998 TCTCAATTGCTTCAATGCCTTCT-TTCCTCTTATCTACCAATA
580 TCTCAATTGCTTCAACGCCTTCTCTTCCTC-TATCTACCAATA
5040 CTCAATA
1 CTCAATA
5047 ATTTGTACGA
Statistics
Matches: 1227, Mismatches: 6, Indels: 31
0.97 0.00 0.02
Matches are distributed among these distances:
618 116 0.09
619 311 0.25
620 210 0.17
621 218 0.18
622 351 0.29
624 4 0.00
625 17 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (621 bp):
CTCAATAGTTTTTGGAGAAAAGTACACTGGAAGATCCGAAAGTTGTAGTTGTACGACGATCAATT
AAATGAGAAAAGAGGTTCATAGAGCTGATTGCAATTCTGGAGAAAAAAAATTCTAATGAAATTTT
GAGTCTAATGAAATGGTACAAAGGAATATTTTACTACATATTTTGCATTTAATGGTACAAAGAGT
ACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTTAGTTGTTTCACAGCGGTTCA
AAAGTTCTTGAACAACAACCCTGAGCCCGCCTGCCGTCGTTTCCTCGAACCAAAATCACCTCATA
AGAGTGACGGGACTGGAAGTTGCAGCGGCGGTGAGCATTTTCCTCCTTTCTTTTTTTGGAAAACA
CGTAGATGTGGTGATTTGGGTTAGTTGTTTCCTTGGATGACCTGGGCGATACACAATCAATTGAG
GATAGTGGCCAAAAAAGAAAAAAATGAATGAAGAATACCGCCAAGACATTGCTACTTTCTCACTT
TTGTGGGCAGAAAGGATGGTCAAACTTGGGAAGAGGCCTAGCATGGGGAACACTGTCCTTCTCAA
TTGCTTCAACGCCTTCTCTTCCTCTATCTACCAATA
Found at i:5835 original size:465 final size:459
Alignment explanation
Indices: 4916--5842 Score: 1686
Period size: 465 Copynumber: 2.0 Consensus size: 459
4906 GAATACCGCC
4916 AAGACATTGCTACTTTCTCACTTTTGTGGGCAGAAAGGATGGTCAAACTTGGAAGAGGCCTAGCA
1 AAGACATTGCTACTTTCTCACTTTTGTGGGCAGAAAGGATGGTCAAACTTGGAAGAGGCCTAGCA
4981 TGGGGGACCACTGTCCTTCTCAATTGCTTCAATGCCTTCTTTCCTCTTATCTACCAATACTCAAT
66 TGGGGGACCACTGTCCTTCTCAATTGCTTCAATGCCTTCTTTCCTCTTATCTACCAATACTCAAT
5046 AATTTGTACGACGATCAAATTAAATGAGAAAAAAGGGTGCAATTCTGGAGAAAAAAAAATTCTAA
131 AATTTGTACGACGATCAAATTAAATGAGAAAAAAGGGTGCAATTCTGGAG-AAAAAAAATTCTAA
5111 TGAAATTTTGAGTCTAATGAAAATGGTACAAAGGAATATTTACTACATATTTGCATTTAATGGTA
195 TGAAATTTTGAGTCTAATGAAAATGGTACAAAGGAATATTTACTACATATTTGCATTTAATGGTA
5176 CAAAGAGTACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTTAGTTGTTTCACA
260 CAAAGAGTACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTTAGTTGTTTCACA
5241 GCGGTTCAAAAGTTCTTGAAACAACAACCCTGAGCCCGCCTGCCCTTCTTTTCCTCGAACCAAAA
325 GCGGTTCAAAAGTTCTTGAAACAACAACCCTGAGCCCGCCTGCCCTTCTTTTCCTCGAACCAAAA
5306 TCACCTCATAAGAGTGGCGGGACTGGAAGTTGCAGCGGCGGTGAGCATTTCCTCCTTTTCTTTTC
390 TCACCTCATAAGAGTGGCGGGACTGGAAGTTGCAGCGGCGGTGAGCATTTCCTCCTTTTCTTTTC
5371 TTTGG
455 TTTGG
5376 AAGACATGTGCTACTTTCTCAACTTTTGTGGGCAGAAAGGATGGTCAAACTTGGGAAGAGGCCTA
1 AAGACAT-TGCTACTTTCTC-ACTTTTGTGGGCAGAAAGGATGGTCAAACTT-GGAAGAGGCCTA
5441 GCATGGGGGACCACTGTCCCTTCTCAAATTGCTTCAATGCCTTCTCTTCCTC-TATCTACCAATA
63 GCATGGGGGACCACTGT-CCTTCTC-AATTGCTTCAATGCCTTCT-TTCCTCTTATCTACCAATA
*
5505 CTCAATAATTTGTACGACGATCAAAATTAAATGAGAAAAAAGGTTGCAATTCTGGAG-AAAAAAA
125 CTCAATAATTTGTACGACGATC-AAATTAAATGAGAAAAAAGGGTGCAATTCTGGAGAAAAAAAA
5569 TTCTAATGAAATTTTGAGTCTAATG-AAATGGTACAAAGGAATATTTTACTACATATTTTGCATT
189 TTCTAATGAAATTTTGAGTCTAATGAAAATGGTACAAAGGAATA-TTTACTACATA-TTTGCATT
5633 TAATGGTACAAAGAGTACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTTAGTT
252 TAATGGTACAAAGAGTACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTTAGTT
5698 GTTTCACAGCGGTTCAAAAGTTCTTG-AACAACAACCCTGAGCCCGCCTG-CCTTCTTTTCCTCG
317 GTTTCACAGCGGTTCAAAAGTTCTTGAAACAACAACCCTGAGCCCGCCTGCCCTTCTTTTCCTCG
5761 AACCAAAATCACCTCATAAGAGTGGCGGGACTGGAAGTTGCAGCGGCCGGTGAGCATTTTTCCTC
382 AACCAAAATCACCTCATAAGAGTGGCGGGACTGGAAGTTGCAGCGG-CGGTGAGCA--TTTCCTC
5826 C-TTTCTTTTCTTTGG
444 CTTTTCTTTTCTTTGG
5841 AA
1 AA
5843 AACACGTAGA
Statistics
Matches: 454, Mismatches: 1, Indels: 19
0.96 0.00 0.04
Matches are distributed among these distances:
460 7 0.02
461 12 0.03
462 31 0.07
463 107 0.24
464 82 0.18
465 168 0.37
466 47 0.10
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (459 bp):
AAGACATTGCTACTTTCTCACTTTTGTGGGCAGAAAGGATGGTCAAACTTGGAAGAGGCCTAGCA
TGGGGGACCACTGTCCTTCTCAATTGCTTCAATGCCTTCTTTCCTCTTATCTACCAATACTCAAT
AATTTGTACGACGATCAAATTAAATGAGAAAAAAGGGTGCAATTCTGGAGAAAAAAAATTCTAAT
GAAATTTTGAGTCTAATGAAAATGGTACAAAGGAATATTTACTACATATTTGCATTTAATGGTAC
AAAGAGTACAGAAATGAATCTGCAATGTCACAGTTAATGGGTCCAATGAGTTAGTTGTTTCACAG
CGGTTCAAAAGTTCTTGAAACAACAACCCTGAGCCCGCCTGCCCTTCTTTTCCTCGAACCAAAAT
CACCTCATAAGAGTGGCGGGACTGGAAGTTGCAGCGGCGGTGAGCATTTCCTCCTTTTCTTTTCT
TTGG
Found at i:14194 original size:21 final size:22
Alignment explanation
Indices: 14161--14203 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
14151 ATCAAAATTT
14161 TCTTTTTTCTTTTGAAAGCAAA
1 TCTTTTTTCTTTTGAAAGCAAA
*
14183 TCTTTTTT-TTTTTAAAGCAAA
1 TCTTTTTTCTTTTGAAAGCAAA
14204 ACAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (22 bp):
TCTTTTTTCTTTTGAAAGCAAA
Found at i:17203 original size:7 final size:7
Alignment explanation
Indices: 17182--17296 Score: 59
Period size: 7 Copynumber: 17.4 Consensus size: 7
17172 GGGTCTAGAG
17182 TTAGGG-
1 TTAGGGT
*
17188 TTAGAGT
1 TTAGGGT
17195 TTAGGGT
1 TTAGGGT
17202 TTAGGGT
1 TTAGGGT
* *
17209 TGA-GAT
1 TTAGGGT
17215 TTA-GGT
1 TTAGGGT
*
17221 TTA-AG-
1 TTAGGGT
17226 TTAGGGT
1 TTAGGGT
* *
17233 TTAAGGA
1 TTAGGGT
17240 TTA-GGT
1 TTAGGGT
*
17246 TT-TGGT
1 TTAGGGT
*
17252 TTAAGGT
1 TTAGGGT
**
17259 TTAGTAT
1 TTAGGGT
17266 TTAGGGT
1 TTAGGGT
17273 TTA-GGT
1 TTAGGGT
17279 TTAGACGGT
1 TTAG--GGT
17288 TTA-GGT
1 TTAGGGT
17294 TTA
1 TTA
17297 AGATTTGGAT
Statistics
Matches: 84, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
5 3 0.04
6 37 0.44
7 38 0.45
9 6 0.07
ACGTcount: A:0.22, C:0.01, G:0.33, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:17253 original size:31 final size:31
Alignment explanation
Indices: 17195--17256 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
17185 GGGTTAGAGT
*
17195 TTAGGGTTTAGGGTTGAGATTTAGGTTTAAG
1 TTAGGGTTTAGGATTGAGATTTAGGTTTAAG
* *
17226 TTAGGGTTTAAGGATT-AGGTTTTGGTTTAAG
1 TTAGGGTTT-AGGATTGAGATTTAGGTTTAAG
17257 GTTTAGTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.44
Consensus pattern (31 bp):
TTAGGGTTTAGGATTGAGATTTAGGTTTAAG
Found at i:17258 original size:13 final size:13
Alignment explanation
Indices: 17193--17315 Score: 74
Period size: 13 Copynumber: 9.3 Consensus size: 13
17183 TAGGGTTAGA
*
17193 GTTTAGGGTTTAGG
1 GTTTA-GGTTTAAG
* *
17207 GTTGAGATTT-AG
1 GTTTAGGTTTAAG
* *
17219 GTTTAAG-TTAGG
1 GTTTAGGTTTAAG
*
17231 GTTTAAGGATT-AG
1 GTTT-AGGTTTAAG
*
17244 GTTTTGGTTTAAG
1 GTTTAGGTTTAAG
* *
17257 GTTTAGTATTTAGG
1 GTTTAG-GTTTAAG
17271 GTTTAGGTTTAGACG
1 GTTTAGGTTTA-A-G
17286 GTTTAGGTTTAAG
1 GTTTAGGTTTAAG
*
17299 ATTT-GGATTTAAG
1 GTTTAGG-TTTAAG
17312 GTTT
1 GTTT
17316 TGGAATGCAT
Statistics
Matches: 83, Mismatches: 18, Indels: 17
0.70 0.15 0.14
Matches are distributed among these distances:
11 2 0.02
12 16 0.19
13 35 0.42
14 18 0.22
15 12 0.14
ACGTcount: A:0.22, C:0.01, G:0.32, T:0.46
Consensus pattern (13 bp):
GTTTAGGTTTAAG
Found at i:17281 original size:6 final size:6
Alignment explanation
Indices: 17182--17296 Score: 61
Period size: 6 Copynumber: 17.5 Consensus size: 6
17172 GGGTCTAGAG
* * * *
17182 TTAGGG TTAGAGT TTAGGGT TTAGGGT TGAGAT TTAGGT TTAAG- TTAGGGT
1 TTAGGT TTAG-GT TTA-GGT TTA-GGT TTAGGT TTAGGT TTAGGT TTA-GGT
* * *
17233 TTAAGGA TTAGGT TTTGGT TTAAGGT TTAGTAT TTAGGGT TTAGGT TTAGACGGT
1 TT-AGGT TTAGGT TTAGGT TT-AGGT TTAG-GT TTA-GGT TTAGGT TT--A-GGT
17288 TTAGGT TTA
1 TTAGGT TTA
17297 AGATTTGGAT
Statistics
Matches: 85, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
5 3 0.04
6 38 0.45
7 35 0.41
8 4 0.05
9 5 0.06
ACGTcount: A:0.22, C:0.01, G:0.33, T:0.44
Consensus pattern (6 bp):
TTAGGT
Found at i:20199 original size:11 final size:10
Alignment explanation
Indices: 20149--20199 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 10
20139 TAAACTTCGG
20149 GAGAAAAAAA
1 GAGAAAAAAA
20159 -AG-AAAAAA
1 GAGAAAAAAA
20167 GAGAAGAAAAA
1 GAGAA-AAAAA
*
20178 GAAGAAGAAAA
1 G-AGAAAAAAA
20189 GAGAAATAAAA
1 GAGAAA-AAAA
20200 TAAAATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 6 0.18
9 4 0.12
10 5 0.15
11 15 0.44
12 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (10 bp):
GAGAAAAAAA
Found at i:20199 original size:22 final size:21
Alignment explanation
Indices: 20150--20193 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
20140 AAACTTCGGG
20150 AGAAAAAAAAGAAAAAAGAGA
1 AGAAAAAAAAGAAAAAAGAGA
*
20171 AGAAAAAGAAGAAGAAAAGAGA
1 AGAAAAAAAAGAA-AAAAGAGA
20193 A
1 A
20194 ATAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAGAAAAAAGAGA
Found at i:21524 original size:144 final size:145
Alignment explanation
Indices: 21248--21725 Score: 477
Period size: 147 Copynumber: 3.4 Consensus size: 145
21238 AATGCGTACA
* * *
21248 TAATTGCTTTGTTGAAAATTTTTAATTTAGA-CTTAATTTTTGAGAAAGCTATTTTCTA-TTT-A
1 TAATTGCTTTGTTGAAAATTTTTAATTTA-ATCTTAATTTTTTAAAAATCTATTTTCTATTTTCA
* * * * * *
21310 AAA-AAGAAAA-ATATTTTACTAATAATTTATA-T-TAA-AAAATATAAATGCT-ATGGCTTTTG
65 AAACAAAAAAATATATTTTACTAATAAATCATACTATAATAAAAAATAAATGCTAATGGTTTTTA
21369 AT-TTATAAATTAAAT
130 ATATTATAAATTAAAT
* * *
21384 TAATTTCTTTGTTGAAAATTCTT-ATTTAATCTTTA-TTTTTAAAAATCTATTTTCTATTTTACA
1 TAATTGCTTTGTTGAAAATTTTTAATTTAATCTTAATTTTTTAAAAATCTATTTTCTATTTT-CA
21447 AAACAAAAAAATATATTTTACTAATAAATCATACTATAATAAAAAATAAATGCTAATGGTTTTTA
65 AAACAAAAAAATATATTTTACTAATAAATCATACTATAATAAAAAATAAATGCTAATGGTTTTTA
21512 ATATTATAAATTAAAT
130 ATATTATAAATTAAAT
* * * * * * * * *
21528 TAATTACTTTGTTGCAATTTTTTAATTTAATTTTACTTTTTTAAAAAACTCTTTTTTTTTTTCAA
1 TAATTGCTTTGTTGAAAATTTTTAATTTAATCTTAATTTTTTAAAAATCTATTTTCTATTTTCAA
* * * ** * * * *
21593 AAGGCAAATAGATATTTTTCTAAAAAAAAATCATACTATAAT-AAAATTAAATACTAATGATTTT
66 AA--CAAAAAAATATATTT-TACTAATAAATCATACTATAATAAAAAATAAATGCTAATGGTTTT
21657 TAATATTATAAATTAAGA-
128 TAATATTATAAATTAA-AT
* * *
21675 CAATTGCTTTGTTTG--AA-TTGTAATTTAATCTTAATTTTTTAAAAATATATT
1 TAATTGCTTTG-TTGAAAATTTTTAATTTAATCTTAATTTTTTAAAAATCTATT
21726 CTACTAATAA
Statistics
Matches: 283, Mismatches: 41, Indels: 27
0.81 0.12 0.08
Matches are distributed among these distances:
134 19 0.07
135 12 0.04
136 21 0.07
137 4 0.01
138 6 0.02
139 19 0.07
140 1 0.00
141 3 0.01
142 13 0.05
143 10 0.04
144 32 0.11
145 42 0.15
146 22 0.08
147 56 0.20
148 23 0.08
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (145 bp):
TAATTGCTTTGTTGAAAATTTTTAATTTAATCTTAATTTTTTAAAAATCTATTTTCTATTTTCAA
AACAAAAAAATATATTTTACTAATAAATCATACTATAATAAAAAATAAATGCTAATGGTTTTTAA
TATTATAAATTAAAT
Found at i:31930 original size:166 final size:165
Alignment explanation
Indices: 31645--32084 Score: 589
Period size: 166 Copynumber: 2.6 Consensus size: 165
31635 CAATAATTTT
* * * **
31645 TTTCTAGAATTTGTTGGGATTAATAAATGCATCTTCTATTGTAAAATACCTTCAATATAATGCCA
1 TTTCTA-AATTTGTTGGGATTATTAAAGGCATCTTCTATTGTAAAATGCCTTCAATATAACACCA
* ** *
31710 CACAAATATTAATATGGTTAATAAAGGCGTATATTCAAGAAAACATTTTTTATTATAAATTATCT
65 CACAAATATTAACACAGTTAATAAAGGCGTATATTCAAGAAAACATCTTTTATTATAAATTATCT
31775 ACATAAATATTGAAGGCATTTCTTGATAATAAATGC
130 ACATAAATATTGAAGGCATTTCTTGATAATAAATGC
* * **
31811 TTTCTAAATTCTGTTGGGATTATTAAAGGCGTTTTCTATTGTAAAATGCCTTCAATATAACATTA
1 TTTCTAAATT-TGTTGGGATTATTAAAGGCATCTTCTATTGTAAAATGCCTTCAATATAACACCA
* *
31876 CACAAATATTAACACAGTTAATAAAGGTGTATATTTAAGAAAACATCTTTTATTATAAATTATCT
65 CACAAATATTAACACAGTTAATAAAGGCGTATATTCAAGAAAACATCTTTTATTATAAATTATCT
31941 ACATAAATATTGAAGGCATTTCTTGATAATAAATGC
130 ACATAAATATTGAAGGCATTTCTTGATAATAAATGC
* * * *
31977 CTTCTAAATTTTGTTGGGATTATTAAAGGCATCTTCTACTATAAAACGCCTTCAATATATAGCA-
1 TTTCTAAA-TTTGTTGGGATTATTAAAGGCATCTTCTATTGTAAAATGCCTTCAATATA-A-CAC
* * * * *
32041 -ACGCAAATTTTAACA-TGGTAATTGAAGGCGTATATTCAAGAAAA
63 CACACAAATATTAACACAGTTAA-TAAAGGCGTATATTCAAGAAAA
32085 ACACCTTTAA
Statistics
Matches: 241, Mismatches: 28, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
165 8 0.03
166 228 0.95
167 3 0.01
168 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (165 bp):
TTTCTAAATTTGTTGGGATTATTAAAGGCATCTTCTATTGTAAAATGCCTTCAATATAACACCAC
ACAAATATTAACACAGTTAATAAAGGCGTATATTCAAGAAAACATCTTTTATTATAAATTATCTA
CATAAATATTGAAGGCATTTCTTGATAATAAATGC
Found at i:33292 original size:80 final size:80
Alignment explanation
Indices: 33080--33302 Score: 266
Period size: 80 Copynumber: 2.8 Consensus size: 80
33070 GTCTAATTTT
* * * *
33080 TTTTGCTGAATGATATTGTATGATATTAGGGGGCTGAATCATATGCTGAATGATTTACTGAACCT
1 TTTTGCTAAATGATATTGTATGATATTAGGGGGCTGAATCATATGCTGAATGGTTTGCTGAATCT
*
33145 TGTTATATGATATTG
66 TATTATATGATATTG
* * * * * * *
33160 TATTACCAAATGGTATTGTATGATATTGGGGGGCTGAATCATATGCTAAATGGTTTGTTGAATCT
1 TTTTGCTAAATGATATTGTATGATATTAGGGGGCTGAATCATATGCTGAATGGTTTGCTGAATCT
* *
33225 TATTGTCTGATATTG
66 TATTATATGATATTG
* * * * * *
33240 TTTTGCTAAATGATTTTGTATGATATTAGGAGGCTAAATCGTATGTTGAATGGATTGCTGAAT
1 TTTTGCTAAATGATATTGTATGATATTAGGGGGCTGAATCATATGCTGAATGGTTTGCTGAAT
33303 GATGTTTCTG
Statistics
Matches: 116, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
80 116 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.41
Consensus pattern (80 bp):
TTTTGCTAAATGATATTGTATGATATTAGGGGGCTGAATCATATGCTGAATGGTTTGCTGAATCT
TATTATATGATATTG
Found at i:37244 original size:304 final size:303
Alignment explanation
Indices: 36689--37292 Score: 838
Period size: 304 Copynumber: 2.0 Consensus size: 303
36679 ATTTTGAAGG
*
36689 CGTTTTTAACCAAAATCGCCTTTAACAATCACCACAAAAATCAATTGTGTGAAATATTAAAGGTG
1 CGTTTTTAACCAAAATCGCCTTTAACAATCACCACAAAAATCAATTGTGTGAAATATTAAAGGCG
* * * * **
36754 TTTTGGGAAAAAAATGCCTTCAAGAATCCGTCACGTCTTTTTTGTATGGATTATTGAAGGCGTTT
66 TTTTGGGAAAAAAACGCATTCAAGAATCCATCACATCTTTTTTGTATAAATTATTGAAGGCGTTT
* * * * *
36819 TAAAAAAATGCCTTCAATAATACCAACTCAAAATTAATCGAATGATTTATGAATGGTATTTTCCT
131 TAAAAAAACGCCTTCAATAATACCAACTAAAAATTAATCGAATGATTTATAAAGGGCATTTTCCT
* * * *
36884 ACAGGTAACGCCTTGAATAATTCCTAACAAAATGTTATTGAAGACGTTTCTGGATATAACAGCCT
196 ACAGGCAACACCTTGAATAATCCCTAACAAAATGTTATTGAAGACATTTCTGGATATAACAGCCT
*
36949 TCAATAATCTGA-CTATTAAAATTTATCGTATGGAATATTAATGA
261 TCAATAATCTGATC-A-TAAAATTTATCGTATGAAATATTAATGA
* * * * **
36993 CGTTTTTTACCAAAATCGCTTTTAATAATC-CTACCAAAAATTTATTGTGTGAAATATTAAAGGC
1 CGTTTTTAACCAAAATCGCCTTTAACAATCACCA-CAAAAATCAATTGTGTGAAATATTAAAGGC
* * *
37057 GTTTTGGGCAAAAAACGCATTCAAGAATTCATCGCATCTTTTTTGTATAAATTATTGAAGGCGTT
65 GTTTTGGGAAAAAAACGCATTCAAGAATCCATCACATCTTTTTTGTATAAATTATTGAAGGCGTT
*
37122 TTACGAAAAACGCCTTCAATAATACCAACTAAAAATTAATCGAATGGA-TTATAAAGGGCATTTT
130 TTA-AAAAAACGCCTTCAATAATACCAACTAAAAATTAATCGAAT-GATTTATAAAGGGCATTTT
* * * * *
37186 TCTA-GGGCAACACCTTGAATAATCCCTAACAAAATGTTATTGAAGGCATTTTTGGATATAACTG
193 CCTACAGGCAACACCTTGAATAATCCCTAACAAAATGTTATTGAAGACATTTCTGGATATAACAG
*
37250 CCTTCAATAATCTGATCATAAAATTTATCGTCTGAAATATTAA
258 CCTTCAATAATCTGATCATAAAATTTATCGTATGAAATATTAA
37293 AAGCTTTTTG
Statistics
Matches: 263, Mismatches: 33, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
303 25 0.10
304 181 0.69
305 55 0.21
306 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (303 bp):
CGTTTTTAACCAAAATCGCCTTTAACAATCACCACAAAAATCAATTGTGTGAAATATTAAAGGCG
TTTTGGGAAAAAAACGCATTCAAGAATCCATCACATCTTTTTTGTATAAATTATTGAAGGCGTTT
TAAAAAAACGCCTTCAATAATACCAACTAAAAATTAATCGAATGATTTATAAAGGGCATTTTCCT
ACAGGCAACACCTTGAATAATCCCTAACAAAATGTTATTGAAGACATTTCTGGATATAACAGCCT
TCAATAATCTGATCATAAAATTTATCGTATGAAATATTAATGA
Found at i:40339 original size:21 final size:21
Alignment explanation
Indices: 40313--40353 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40303 ATACATTTGT
*
40313 GGTAAATGATACATTTGAGGA
1 GGTAAAAGATACATTTGAGGA
40334 GGTAAAAGATACATTTGAGG
1 GGTAAAAGATACATTTGAGG
40354 TGGATAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.27
Consensus pattern (21 bp):
GGTAAAAGATACATTTGAGGA
Found at i:40380 original size:21 final size:21
Alignment explanation
Indices: 40350--40403 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
40340 AGATACATTT
* * *
40350 GAGGTGGATAACAACTATATG
1 GAGGTAGATAACAACCATATA
*
40371 GAGGTAGATAATAACCATATA
1 GAGGTAGATAACAACCATATA
40392 GAGGTAGATAAC
1 GAGGTAGATAAC
40404 CATGAGGAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.22
Consensus pattern (21 bp):
GAGGTAGATAACAACCATATA
Found at i:40731 original size:6 final size:6
Alignment explanation
Indices: 40720--40757 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
40710 ACTAAAATCG
*
40720 CACCAT CACCAT CACCAT CACCAT CTCCAT CACCAT CA
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CA
40758 TCTGGACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CACCAT
Done.