Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_pilon, 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: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1193913 original size:2 final size:2
Alignment explanation
Indices: 1193906--1193930 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1193896 TATAAGTAAT
1193906 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1193931 GCATTAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1195580 original size:14 final size:15
Alignment explanation
Indices: 1195561--1195590 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1195551 ATCTTGTATG
1195561 CCTA-TTATAATTTC
1 CCTATTTATAATTTC
1195575 CCTATTTATAATTTC
1 CCTATTTATAATTTC
1195590 C
1 C
1195591 TGTTGGTCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (15 bp):
CCTATTTATAATTTC
Found at i:1200542 original size:150 final size:149
Alignment explanation
Indices: 1200271--1200572 Score: 579
Period size: 150 Copynumber: 2.0 Consensus size: 149
1200261 TTTCTGTCCT
1200271 ATCACTTTTTCTGAGTTCAGAGGCTCATCGCAACGCCTTGCTAAAAGTTTTGAACCAACCTTTGT
1 ATCACTTTTTCTGAGTTCAGAGGCTCATCGCAACGCCTTGCTAAAAGTTTTGAACCAACCTTTGT
1200336 CCCGAAGGGGTTACCCACAGAAAAGCTAGCGCGACTATTTGCCAAGATACAAGTCGATAACATTT
66 CCCGAAGGGGTTACCCACAGAAAAGCTAGCGCGACTATTTGCCAAGATACAAGTCGATAACATTT
1200401 TATCTTTTTCAAATGATGAG
131 TATCTTTTTC-AATGATGAG
1200421 ATCACTTTTTCTGAGTTCAGAGGCTCATCGCAACGCCTTGCTAAAAGTTTTGAACCAGACCTTTG
1 ATCACTTTTTCTGAGTTCAGAGGCTCATCGCAACGCCTTGCTAAAAGTTTTGAACCA-ACCTTTG
1200486 TCCCGAAGGGGTTACCCACAGAAAAGCTAGCGCGACTA-TTGCCAAGATACAAGTCGATAACATT
65 TCCCGAAGGGGTTACCCACAGAAAAGCTAGCGCGACTATTTGCCAAGATACAAGTCGATAACATT
1200550 TTATCTTTTTCAATGATGAG
130 TTATCTTTTTCAATGATGAG
1200570 ATC
1 ATC
1200573 CCTTCGGGGA
Statistics
Matches: 151, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
149 12 0.08
150 94 0.62
151 45 0.30
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (149 bp):
ATCACTTTTTCTGAGTTCAGAGGCTCATCGCAACGCCTTGCTAAAAGTTTTGAACCAACCTTTGT
CCCGAAGGGGTTACCCACAGAAAAGCTAGCGCGACTATTTGCCAAGATACAAGTCGATAACATTT
TATCTTTTTCAATGATGAG
Found at i:1204441 original size:9 final size:9
Alignment explanation
Indices: 1204414--1204501 Score: 65
Period size: 9 Copynumber: 9.7 Consensus size: 9
1204404 GTATTTACCT
*
1204414 AAAGATGAA
1 AAAGAAGAA
* *
1204423 AATGATGAA
1 AAAGAAGAA
1204432 AAAGAAGAA
1 AAAGAAGAA
*
1204441 AAAAAAGGAA
1 AAAGAA-GAA
*
1204451 AAA-AAAAA
1 AAAGAAGAA
1204459 AAAGGAA-AA
1 AAA-GAAGAA
1204468 AAAGGAA-AA
1 AAA-GAAGAA
*
1204477 AAAGAAAAA
1 AAAGAAGAA
1204486 AAAGAAGAGA
1 AAAGAAGA-A
1204496 AAAGAA
1 AAAGAA
1204502 AAACAAAACA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
8 8 0.12
9 45 0.66
10 15 0.22
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:1204443 original size:10 final size:9
Alignment explanation
Indices: 1204429--1204504 Score: 77
Period size: 9 Copynumber: 8.7 Consensus size: 9
1204419 TGAAAATGAT
*
1204429 GAAAAAGAA
1 GAAAAAAAA
1204438 GAAAAAAAA
1 GAAAAAAAA
*
1204447 G--GAAAAA
1 GAAAAAAAA
1204454 -AAAAAAAA
1 GAAAAAAAA
*
1204462 GGAAAAAAA
1 GAAAAAAAA
*
1204471 GGAAAAAAA
1 GAAAAAAAA
1204480 GAAAAAAAA
1 GAAAAAAAA
*
1204489 GAAGAGAAAA
1 GAA-AAAAAA
1204499 GAAAAA
1 GAAAAA
1204505 CAAAACAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
7 5 0.09
8 5 0.09
9 38 0.68
10 8 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:1204458 original size:14 final size:15
Alignment explanation
Indices: 1204439--1204488 Score: 73
Period size: 15 Copynumber: 3.2 Consensus size: 15
1204429 GAAAAAGAAG
1204439 AAAAAAAAGGAAAAA
1 AAAAAAAAGGAAAAA
1204454 AAAAAAAAGGAAAAA
1 AAAAAAAAGGAAAAA
*
1204469 AAGGAAAAAAAGAAAAA
1 AA--AAAAAAGGAAAAA
1204486 AAA
1 AAA
1204489 GAAGAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 18 0.56
17 14 0.44
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGGAAAAA
Found at i:1204467 original size:24 final size:24
Alignment explanation
Indices: 1204430--1204486 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
1204420 GAAAATGATG
*
1204430 AAAAAGAAGAAAAAAAAGGAAAAA
1 AAAAAAAAGAAAAAAAAGGAAAAA
*
1204454 AAAAAAAAGGAAAAAAAGGAAAAA
1 AAAAAAAAGAAAAAAAAGGAAAAA
1204478 AAGAAAAAA
1 AA-AAAAAA
1204487 AAGAAGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAAGGAAAAA
Found at i:1204503 original size:24 final size:22
Alignment explanation
Indices: 1204430--1204503 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 22
1204420 GAAAATGATG
1204430 AAAAAGAAGAAAAAAAAG-GAAA
1 AAAAAGAA-AAAAAAAAGAGAAA
* *
1204452 AAAAA-AAAAAGGAAAAAAAGGAA
1 AAAAAGAAAAA--AAAAAGAGAAA
1204475 AAAAAGAAAAAAAAGAAGAGAAA
1 AAAAAGAAAAAAAA-AAGAGAAA
1204498 AGAAAA
1 A-AAAA
1204504 ACAAAACAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 3 0.07
21 2 0.05
22 13 0.31
23 15 0.36
24 9 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAGAAA
Found at i:1204515 original size:12 final size:11
Alignment explanation
Indices: 1204495--1204531 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1204485 AAAAGAAGAG
*
1204495 AAAAGAAAAAC
1 AAAACAAAAAC
1204506 AAAACAAAAAC
1 AAAACAAAAAC
1204517 AAAAACAAAAAC
1 -AAAACAAAAAC
1204529 AAA
1 AAA
1204532 TAAATTGGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.84, C:0.14, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAC
Found at i:1204528 original size:6 final size:6
Alignment explanation
Indices: 1204495--1204531 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1204485 AAAAGAAGAG
*
1204495 AAAAGA AAAAC- AAAACA AAAACA AAAACA AAAACA AA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AA
1204532 TAAATTGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.84, C:0.14, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:1205753 original size:53 final size:52
Alignment explanation
Indices: 1205666--1206383 Score: 842
Period size: 53 Copynumber: 13.8 Consensus size: 52
1205656 AAGCATAGAA
* * *
1205666 GATTGTTCGAGTTCTACACCCTGAAGAAAAAGAGAGCGGACCC-TAAGAAGAT
1 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGC-GACCCGTAGGAAGAT
*
1205718 TATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGAT
1 GATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGC-GACCCGTAGGAAGAT
* * *
1205772 TATTGTTCGAGTTCTACTCCTTGAAGAAA-AGGGA-CGA-CCGTAGG-A-A-
1 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGACCCGTAGGAAGAT
1205818 GA-TGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGAT
1 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGA-CCCGTAGGAAGAT
* *
1205870 TATTGTTCGAGTTCTTACT-CCTGAAGAAATAGAGAGCGGACTCGTAGGAAGAT
1 GATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGC-GACCCGTAGGAAGAT
*
1205923 TATTGTTCGAGTTTCTACTCCCTGAAGAAA-AGAGA--GACCCGTA-GAAGAT
1 GATTGTTCGAG-TTCTACTCCCTGAAGAAATAGAGAGCGACCCGTAGGAAGAT
1205972 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGAT
1 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGA-CCCGTAGGAAGAT
* * * *
1206025 TATCGTTCGAGTTCTACTCCCTGAAG-AA-AGAGAGCGAGCCCATAGGCAGAT
1 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGA-CCCGTAGGAAGAT
* * *
1206076 GATTGTTCGAGTTCTACTCCCTGAAAAAAGAGAGAGCGAGCCCGTA-GCAGAT
1 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGA-CCCGTAGGAAGAT
* * *
1206128 GATTGTTCGAGTTCTACTCCCTGAAAAAAGAGAGAGTGGACCCGTAGGAAGAT
1 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAG-CGACCCGTAGGAAGAT
* * * * * * *
1206181 TATTGATCGAGTGCTTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAAGAACAA
1 GATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGA-CCCGTAGGAAGAT
*
1206235 GATTGTTCGAGTTCTACTCCCTGAA-AAA-AGAGAGCGAGCCCGTAGGAAGAA
1 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGA-CCCGTAGGAAGAT
* * * * *
1206286 GATTTTTCGAGTTCTACTCCTTGAAGAAAGAGAGAGTGGACCCGTAGGAAGAA
1 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAG-CGACCCGTAGGAAGAT
**
1206339 GATTGTTCGAGTTCTTACTCCCTGAAGCGATAGAGAGCGAACCCG
1 GATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCG-ACCCG
1206384 ATTTTGGAGA
Statistics
Matches: 591, Mismatches: 45, Indels: 58
0.85 0.06 0.08
Matches are distributed among these distances:
45 25 0.04
46 5 0.01
47 4 0.01
48 19 0.03
49 35 0.06
50 10 0.02
51 92 0.16
52 82 0.14
53 211 0.36
54 108 0.18
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (52 bp):
GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGACCCGTAGGAAGAT
Found at i:1206111 original size:104 final size:104
Alignment explanation
Indices: 1205666--1206383 Score: 833
Period size: 104 Copynumber: 6.9 Consensus size: 104
1205656 AAGCATAGAA
* * * *
1205666 GATTGTTCGAGTTCTACACCCTGAAGAAAAAGAGAGCG-GACCC-TAAGAAGATTATTGTTCGAG
1 GATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAG-CCCGTAGGAAGATGATTGTTCGAG
1205729 TTCTTACTCCCTGAAGAAATAGAGAGCG-GACCCGTAGGAAGAT
65 TTC-TACTCCCTGAAG-AA-AGAGAGCGAG-CCCGTAGGAAGAT
* * *
1205772 TATTGTTCGAGTTCTACTCCTTGAAGAAA-AGGGA-CGA--CCGTAGG-A-A-GA-TGTTCGAGT
1 GATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGAAGATGATTGTTCGAGT
1205829 TCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGAT
66 TCTACTCCCTGAAG-AA-AGAGAGCGAGCCCGTAGGAAGAT
* * * *
1205870 TATTGTTCGAGTTCTTACT-CCTGAAGAAATAGAGAGCG-GACTCGTAGGAAGATTATTGTTCGA
1 GATTGTTCGAGTTC-TACTCCCTGAAGAAAGAGAGAGCGAG-CCCGTAGGAAGATGATTGTTCGA
*
1205933 GTTTCTACTCCCTGAAGAAA-AGAGAGA-CCCGTA-GAAGAT
64 G-TTCTACTCCCTGAAGAAAGAGAGCGAGCCCGTAGGAAGAT
* * *
1205972 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATCGTTCGAGT
1 GATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGAAGATGATTGTTCGAGT
* *
1206037 TCTACTCCCTGAAGAAAGAGAGCGAGCCCATAGGCAGAT
66 TCTACTCCCTGAAGAAAGAGAGCGAGCCCGTAGGAAGAT
* *
1206076 GATTGTTCGAGTTCTACTCCCTGAAAAAAGAGAGAGCGAGCCCGTA-GCAGATGATTGTTCGAGT
1 GATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGAAGATGATTGTTCGAGT
* * *
1206140 TCTACTCCCTGAAAAAAGAGAGAGTGGACCCGTAGGAAGAT
66 TCTACTCCCTGAAGAAAGAGAGCG-AG-CCCGTAGGAAGAT
* * * * * *
1206181 TATTGATCGAGTGCTTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAAGAACAAGATTGTTCGAG
1 GATTGTTCGAGTTC-TACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGAAGATGATTGTTCGAG
* *
1206246 TTCTACTCCCTGAAAAAAGAGAGCGAGCCCGTAGGAAGAA
65 TTCTACTCCCTGAAGAAAGAGAGCGAGCCCGTAGGAAGAT
* * * *
1206286 GATTTTTCGAGTTCTACTCCTTGAAGAAAGAGAGAGTG-GACCCGTAGGAAGAAGATTGTTCGAG
1 GATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAG-CCCGTAGGAAGATGATTGTTCGAG
* *
1206350 TTCTTACTCCCTGAAGCGATAGAGAGCGAACCCG
65 TTC-TACTCCCTGAA--GAAAGAGAGCGAGCCCG
1206384 ATTTTGGAGA
Statistics
Matches: 537, Mismatches: 48, Indels: 53
0.84 0.08 0.08
Matches are distributed among these distances:
98 60 0.11
99 20 0.04
100 3 0.01
101 23 0.04
102 75 0.14
103 54 0.10
104 106 0.20
105 61 0.11
106 68 0.13
107 67 0.12
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (104 bp):
GATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGAAGATGATTGTTCGAGT
TCTACTCCCTGAAGAAAGAGAGCGAGCCCGTAGGAAGAT
Found at i:1206245 original size:210 final size:208
Alignment explanation
Indices: 1205666--1206365 Score: 903
Period size: 210 Copynumber: 3.4 Consensus size: 208
1205656 AAGCATAGAA
* * *
1205666 GATTGTTCGAGTTCTACACCCTGAAGAAAA-AGAGAGCGGACCC-TAAGAAGATTATTGTTCGAG
1 GATTGTTCGAGTTCTACTCCCTGAA-AAAAGAGAGAGCGGACCCGTAGGAAGATGATTGTTCGAG
*
1205729 TTCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCTT
65 TTCTTACTCCCTGAAGAAA-AGAGAG-GGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCT
*
1205794 GAAGAAAAGGGA-CGA--CCGT-AG--GAAGA-TGTTCGAGTTCTACTCCCTGAAGAAATAGAGA
128 GAAGAAAAGAGAGCGAGCCCGTAAGAAGAAGATTGTTCGAGTTCTACTCCCTGAAG-AA-AGAGA
1205852 GCGAGCCCGTAGGAAGAT
191 GCGAGCCCGTAGGAAGAT
* * * * *
1205870 TATTGTTCGAGTTCTTACT-CCTGAAGAAATAGAGAGCGGACTCGTAGGAAGATTATTGTTCGAG
1 GATTGTTCGAGTTC-TACTCCCTGAAAAAAGAGAGAGCGGACCCGTAGGAAGATGATTGTTCGAG
*
1205934 TT-TCTACTCCCTGAAGAAAAGAGA--GACCCGTA-GAAGATGATTGTTCGAGTTCTACTCCCTG
65 TTCT-TACTCCCTGAAGAAAAGAGAGGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTG
* ** *
1205995 AAGAAATAGAGAGCGAGCCCGTAGGAAGATTATCGTTCGAGTTCTACTCCCTGAAGAAAGAGAGC
129 AAGAAA-AGAGAGCGAGCCCGTAAGAAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGC
* *
1206060 GAGCCCATAGGCAGAT
193 GAGCCCGTAGGAAGAT
*
1206076 GATTGTTCGAGTTCTACTCCCTGAAAAAAGAGAGAGC-GAGCCCGTA-GCAGATGATTGTTCGAG
1 GATTGTTCGAGTTCTACTCCCTGAAAAAAGAGAGAGCGGA-CCCGTAGGAAGATGATTGTTCGAG
* * *
1206139 TTC-TACTCCCTGAAAAAAGAGAGAGTGGACCCGTAGGAAGATTATTGATCGAGTGCTTACTCCC
65 TTCTTACTCCCTGAAGAAA-AGAGAG-GGACCCGTAGGAAGATTATTGTTCGAGTTC-TACTCCC
* *
1206203 TGAAGAAAGAGAGAGCGAGCCCGTAAGAACAAGATTGTTCGAGTTCTACTCCCTGAAAAAAGAGA
127 TGAAGAAA-AGAGAGCGAGCCCGTAAGAAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGA
*
1206268 GCGAGCCCGTAGGAAGAA
191 GCGAGCCCGTAGGAAGAT
* * * * *
1206286 GATTTTTCGAGTTCTACTCCTTGAAGAAAGAGAGAGTGGACCCGTAGGAAGAAGATTGTTCGAGT
1 GATTGTTCGAGTTCTACTCCCTGAAAAAAGAGAGAGCGGACCCGTAGGAAGATGATTGTTCGAGT
1206351 TCTTACTCCCTGAAG
66 TCTTACTCCCTGAAG
1206366 CGATAGAGAG
Statistics
Matches: 431, Mismatches: 41, Indels: 40
0.84 0.08 0.08
Matches are distributed among these distances:
200 33 0.08
201 12 0.03
202 3 0.01
203 3 0.01
204 55 0.13
205 68 0.16
206 55 0.13
207 5 0.01
208 30 0.07
209 17 0.04
210 119 0.28
211 20 0.05
212 11 0.03
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.23
Consensus pattern (208 bp):
GATTGTTCGAGTTCTACTCCCTGAAAAAAGAGAGAGCGGACCCGTAGGAAGATGATTGTTCGAGT
TCTTACTCCCTGAAGAAAAGAGAGGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAA
GAAAAGAGAGCGAGCCCGTAAGAAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGCGAG
CCCGTAGGAAGAT
Found at i:1213473 original size:14 final size:14
Alignment explanation
Indices: 1213454--1213493 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1213444 ATGGGAAAAT
*
1213454 TTTGAAAAACTATG
1 TTTGAAAAACAATG
1213468 TTTG-AAAACAATG
1 TTTGAAAAACAATG
*
1213481 TTTGAAAATCAAT
1 TTTGAAAAACAAT
1213494 ATATAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (14 bp):
TTTGAAAAACAATG
Found at i:1213995 original size:21 final size:22
Alignment explanation
Indices: 1213951--1213996 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1213941 AGAACTCGAA
1213951 GGGGATATCGATACCCTCAGGG
1 GGGGATATCGATACCCTCAGGG
1213973 GGGGATATCGATACCCTCAGGG
1 GGGGATATCGATACCCTCAGGG
1213995 GG
1 GG
1213997 TATCGGTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.17
Consensus pattern (22 bp):
GGGGATATCGATACCCTCAGGG
Found at i:1214023 original size:23 final size:23
Alignment explanation
Indices: 1213994--1214052 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
1213984 TACCCTCAGG
*
1213994 GGGTATCGGTACCCATTCAAAGA
1 GGGTATCGATACCCATTCAAAGA
*
1214017 GGGTATCGATACCCATTCAAAGG
1 GGGTATCGATACCCATTCAAAGA
*
1214040 GGGTATAGATACC
1 GGGTATCGATACC
1214053 TACCGTACAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (23 bp):
GGGTATCGATACCCATTCAAAGA
Found at i:1219953 original size:29 final size:29
Alignment explanation
Indices: 1219891--1219958 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1219881 AACAATTAGT
* * *
1219891 ATAATAATTCATATACTTTTTGTATTAAA
1 ATAATAATTCATATACTTTATATAATAAA
1219920 ATAATAATTCATATAC-TTATATAATAAA
1 ATAATAATTCATATACTTTATATAATAAA
1219948 ATTAATTAATT
1 A-TAA-TAATT
1219959 TTAATGATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 10 0.29
29 19 0.56
30 5 0.15
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (29 bp):
ATAATAATTCATATACTTTATATAATAAA
Found at i:1227481 original size:27 final size:27
Alignment explanation
Indices: 1227451--1227629 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
1227441 GGGAAGCCAC
* * *
1227451 CAGAGGTATGTTGATCCCAGGGATCAA
1 CAGAGGCATGCTGATCCCAGGGACCAA
* *
1227478 CAGAGGAATGCAGATCCCAGGGACCAA
1 CAGAGGCATGCTGATCCCAGGGACCAA
* * * *
1227505 CAGAGGTATGTTGATCCCAGAGATCAA
1 CAGAGGCATGCTGATCCCAGGGACCAA
* * *
1227532 CAGAGGAATGCAGATCCCAGGGACCCA
1 CAGAGGCATGCTGATCCCAGGGACCAA
* * *
1227559 CAGAGACATGCCGATCCCAGGGACCTA
1 CAGAGGCATGCTGATCCCAGGGACCAA
* *
1227586 CAGAGACATGCTGATCCTAGGGACCAA
1 CAGAGGCATGCTGATCCCAGGGACCAA
*
1227613 CAGAGGCATGTTGATCC
1 CAGAGGCATGCTGATCC
1227630 AAGAGGCCAT
Statistics
Matches: 128, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 128 1.00
ACGTcount: A:0.32, C:0.25, G:0.28, T:0.15
Consensus pattern (27 bp):
CAGAGGCATGCTGATCCCAGGGACCAA
Found at i:1227515 original size:54 final size:54
Alignment explanation
Indices: 1227451--1227629 Score: 243
Period size: 54 Copynumber: 3.3 Consensus size: 54
1227441 GGGAAGCCAC
*
1227451 CAGAGGTATGTTGATCCCAGGGATCAACAGAGGAATGCAGATCCCAGGGACCAA
1 CAGAGGCATGTTGATCCCAGGGATCAACAGAGGAATGCAGATCCCAGGGACCAA
* * *
1227505 CAGAGGTATGTTGATCCCAGAGATCAACAGAGGAATGCAGATCCCAGGGACCCA
1 CAGAGGCATGTTGATCCCAGGGATCAACAGAGGAATGCAGATCCCAGGGACCAA
* ** * * * *
1227559 CAGAGACATGCCGATCCCAGGGACCTACAGA-GACATGCTGATCCTAGGGACCAA
1 CAGAGGCATGTTGATCCCAGGGATCAACAGAGGA-ATGCAGATCCCAGGGACCAA
1227613 CAGAGGCATGTTGATCC
1 CAGAGGCATGTTGATCC
1227630 AAGAGGCCAT
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
53 2 0.02
54 107 0.98
ACGTcount: A:0.32, C:0.25, G:0.28, T:0.15
Consensus pattern (54 bp):
CAGAGGCATGTTGATCCCAGGGATCAACAGAGGAATGCAGATCCCAGGGACCAA
Found at i:1227629 original size:81 final size:81
Alignment explanation
Indices: 1227451--1227629 Score: 216
Period size: 81 Copynumber: 2.2 Consensus size: 81
1227441 GGGAAGCCAC
* * ** *
1227451 CAGAGGTATGTTGATCCCAGGGATCAACAGAGGAATGCAGATCCCAGGGACCAACAGAGGTATGT
1 CAGAGGAATGTTGATCCCAGGGACCAACAGAGGAATGCAGATCCCAGGGACCAACAGAGACATGC
*
1227516 TGATCCCAGAGATCAA
66 TGATCCCAGAGACCAA
** * * *
1227532 CAGAGGAATGCAGATCCCAGGGACCCACAGA-GACATGCCGATCCCAGGGACCTACAGAGACATG
1 CAGAGGAATGTTGATCCCAGGGACCAACAGAGGA-ATGCAGATCCCAGGGACCAACAGAGACATG
* *
1227596 CTGATCCTAGGGACCAA
65 CTGATCCCAGAGACCAA
*
1227613 CAGAGGCATGTTGATCC
1 CAGAGGAATGTTGATCC
1227630 AAGAGGCCAT
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 2 0.02
81 79 0.98
ACGTcount: A:0.32, C:0.25, G:0.28, T:0.15
Consensus pattern (81 bp):
CAGAGGAATGTTGATCCCAGGGACCAACAGAGGAATGCAGATCCCAGGGACCAACAGAGACATGC
TGATCCCAGAGACCAA
Found at i:1228230 original size:42 final size:42
Alignment explanation
Indices: 1228107--1228232 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 42
1228097 GGTGTGTCAC
* ** * *
1228107 GAGTAGATCCGAATTAATTTGGGTAAAGTGTTGGGGAAATAG
1 GAGTAGATCCGGATTAATTACGGTAAAGTGTTGGGAAAATGG
* * * * *** *
1228149 GAGTAAATCTGGATTAATTATGATAAAAAATTGGAAAAATGG
1 GAGTAGATCCGGATTAATTACGGTAAAGTGTTGGGAAAATGG
*
1228191 GAGTAGATCCGGATTAATTACGGCAAAGTGTTGGGAAAATGG
1 GAGTAGATCCGGATTAATTACGGTAAAGTGTTGGGAAAATGG
1228233 AAAGGTAATA
Statistics
Matches: 63, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.38, C:0.06, G:0.29, T:0.27
Consensus pattern (42 bp):
GAGTAGATCCGGATTAATTACGGTAAAGTGTTGGGAAAATGG
Found at i:1235359 original size:180 final size:180
Alignment explanation
Indices: 1235061--1235401 Score: 565
Period size: 180 Copynumber: 1.9 Consensus size: 180
1235051 TATTTCTTGT
1235061 CTAAAATAAGCATTTACTTAAACTTAATTATCAAGAAATCTCTAATCACTAGAATTACAATAAAA
1 CTAAAATAAGCATTTACTTAAACTTAATTATCAAGAAATCTCTAATCACTAGAATTACAATAAAA
* *
1235126 TCTAAATTAATTACCAATTAAAATTTGAGTTAATATCTAGCGATCTCCCCATTGACACAAACTTC
66 TCTAAATTAATTACCAATTAAAATTTGAGTCAATATCTAGCAATCTCCCCATTGACACAAACTTC
* *
1235191 ATGTGTGCATCAGTCTTCAAATCTTCAACAAAATTCAAAAGACTTCTAGC
131 ATGTCTGCATCAGCCTTCAAATCTTCAACAAAATTCAAAAGACTTCTAGC
*
1235241 CTAAAATAAGCATTTACTTAAATTTAATTATCAAGAAATCTCTAATCACTAGAATTACAATAAAA
1 CTAAAATAAGCATTTACTTAAACTTAATTATCAAGAAATCTCTAATCACTAGAATTACAATAAAA
* * * * **
1235306 TCTAAATTGATTACCAATTAAAATTTGAGTCAATATCTAGTAATTTTCCCATTGACACGGACTTC
66 TCTAAATTAATTACCAATTAAAATTTGAGTCAATATCTAGCAATCTCCCCATTGACACAAACTTC
* *
1235371 ATTTCTGGATCAGCCTTCAAATCTTCAACAA
131 ATGTCTGCATCAGCCTTCAAATCTTCAACAA
1235402 CTTTAGTTCT
Statistics
Matches: 148, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
180 148 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (180 bp):
CTAAAATAAGCATTTACTTAAACTTAATTATCAAGAAATCTCTAATCACTAGAATTACAATAAAA
TCTAAATTAATTACCAATTAAAATTTGAGTCAATATCTAGCAATCTCCCCATTGACACAAACTTC
ATGTCTGCATCAGCCTTCAAATCTTCAACAAAATTCAAAAGACTTCTAGC
Found at i:1237002 original size:43 final size:43
Alignment explanation
Indices: 1236941--1237072 Score: 255
Period size: 43 Copynumber: 3.1 Consensus size: 43
1236931 ATCTTCACTT
1236941 TCGACCAATTATGCTTTAGATCTCTATGAGCAAACACATTTGG
1 TCGACCAATTATGCTTTAGATCTCTATGAGCAAACACATTTGG
1236984 TCGACCAATTATGCTTTAGATCTCTATGAGCAAACACATTTGG
1 TCGACCAATTATGCTTTAGATCTCTATGAGCAAACACATTTGG
*
1237027 TCGACCAATTATGCTTTAGATCTCTATGAGCAAATACATTTGG
1 TCGACCAATTATGCTTTAGATCTCTATGAGCAAACACATTTGG
1237070 TCG
1 TCG
1237073 GTTAGTCAAA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 88 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (43 bp):
TCGACCAATTATGCTTTAGATCTCTATGAGCAAACACATTTGG
Found at i:1242170 original size:64 final size:63
Alignment explanation
Indices: 1242056--1242208 Score: 157
Period size: 64 Copynumber: 2.4 Consensus size: 63
1242046 TTCAGTGTGT
* * * * *
1242056 ATCGATGCACAGGAAGTGCATCGTTGCACCCCTTAAAAATGGAAATATCGAA-TGCAATTAGTGC
1 ATCGATGCATAGGAAGTGCATCGATACACCCCTTAAAAATGAAAACATCGAAGTGC--TTAGTGC
* * * *
1242120 ATCGATGCATAGGAAGTGCATCGATACACCCCCTT-AAGATTAAAACATCGAAGGTGCTTTGTGT
1 ATCGATGCATAGGAAGTGCATCGATACA-CCCCTTAAAAATGAAAACATCGAA-GTGCTTAGTGC
* *
1242184 ATCGATGCATGGGTAGTGCATCGAT
1 ATCGATGCATAGGAAGTGCATCGAT
1242209 GCACATGTTA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
64 66 0.88
65 6 0.08
66 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (63 bp):
ATCGATGCATAGGAAGTGCATCGATACACCCCTTAAAAATGAAAACATCGAAGTGCTTAGTGC
Found at i:1243767 original size:23 final size:23
Alignment explanation
Indices: 1243737--1243780 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1243727 ATTTTATATG
1243737 GCACTTCGGTGCAATTCTACGCA
1 GCACTTCGGTGCAATTCTACGCA
1243760 GCACTTCGGTGCAATTCTACG
1 GCACTTCGGTGCAATTCTACG
1243781 TGGCGCTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCA
Found at i:1243793 original size:23 final size:23
Alignment explanation
Indices: 1243735--1243795 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1243725 ACATTTTATA
1243735 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
**
1243758 CAGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1243781 TGGCGCTTTGGTGCA
1 TGGCACTTCGGTGCA
1243796 TTTATACGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1247182 original size:64 final size:62
Alignment explanation
Indices: 1247104--1247260 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 62
1247094 TTCAGTGTGT
* * *
1247104 ATCGATGCACAGGAAGTGCATCGATGCACCCCTTAAAAATGGAAATATCGAA-TGCAATTAGTGC
1 ATCGATGCATAGGAAGTGCATCGATGCACCCCTT-AAAATGAAAACATCGAAGTGC--TTAGTGC
* * * * * *
1247168 ATCGATGCATAGGAAGCGCATCGATACACCCCCTTAAGATTAAAACATCGAAGGTGCTTTGTGT
1 ATCGATGCATAGGAAGTGCATCGATGCA-CCCCTTAAAATGAAAACATCGAA-GTGCTTAGTGC
* *
1247232 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
1247261 ATGTTAAGGG
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
63 1 0.01
64 67 0.87
65 6 0.08
66 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (62 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGTGCTTAGTGC
Found at i:1248809 original size:23 final size:23
Alignment explanation
Indices: 1248779--1248838 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1248769 CATTTTATAT
*
1248779 GGCACTTCGGTGTAATTCTACAC
1 GGCACTTCGGTGCAATTCTACAC
*
1248802 GGCACTTCGGTGCAATTCTACAT
1 GGCACTTCGGTGCAATTCTACAC
* *
1248825 AGCACTTTGGTGCA
1 GGCACTTCGGTGCA
1248839 TTTATACGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACAC
Found at i:1253826 original size:23 final size:23
Alignment explanation
Indices: 1253782--1253843 Score: 97
Period size: 23 Copynumber: 2.6 Consensus size: 23
1253772 CATTTTATAT
1253782 GGCACTTCGGTGTCCAATTCTACAC
1 GGCACTTCGGTG--CAATTCTACAC
*
1253807 GGCACTTCGGTGCAATTCTACAT
1 GGCACTTCGGTGCAATTCTACAC
1253830 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1253844 TTTATACGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 24 0.67
25 12 0.33
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACAC
Found at i:1260236 original size:74 final size:74
Alignment explanation
Indices: 1260115--1260262 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
1260105 ATATCATTCA
1260115 GTGAATTGACGATGGCTGCACAAAAAGAATGTTGAGGGGGGAATCTAGTTTGATATTATATCCAA
1 GTGAATTGACGATGGCTGCACAAAAAGAATGTTGAGGGGGGAATCTAGTTTGATATTATATCCAA
1260180 CAAACATAG
66 CAAACATAG
1260189 GTGAATTGACGATGGCTGCACAAAAAGAATGTTGAGGGGGGAATCTAGTTTGATATTATATCCAA
1 GTGAATTGACGATGGCTGCACAAAAAGAATGTTGAGGGGGGAATCTAGTTTGATATTATATCCAA
1260254 CAAACATAG
66 CAAACATAG
1260263 ATAAATATTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (74 bp):
GTGAATTGACGATGGCTGCACAAAAAGAATGTTGAGGGGGGAATCTAGTTTGATATTATATCCAA
CAAACATAG
Found at i:1260440 original size:21 final size:20
Alignment explanation
Indices: 1260354--1260511 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1260344 AAATGACCAA
**
1260354 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1260373 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1260393 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1260413 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1260434 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1260455 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1260475 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1260496 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1260512 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1260540 original size:20 final size:20
Alignment explanation
Indices: 1260478--1260767 Score: 284
Period size: 20 Copynumber: 14.5 Consensus size: 20
1260468 CGATTTTCCA
* ** *
1260478 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1260498 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1260518 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1260538 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1260558 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1260578 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1260598 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1260618 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1260638 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1260658 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
1260678 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1260698 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1260718 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1260738 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1260758 AAATCACAAC
1 AAATCGCAAC
1260768 ACTGAAATTT
Statistics
Matches: 230, Mismatches: 32, Indels: 16
0.83 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 226 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1260564 original size:60 final size:60
Alignment explanation
Indices: 1260498--1260767 Score: 321
Period size: 60 Copynumber: 4.5 Consensus size: 60
1260488 GCGAATATGA
* * * * *
1260498 AAATCGCAACGCGAA-CACATAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAACGAGAATCCGTAAATCGCAACGAT-AATCCGT
* * * * * * * *
1260558 ATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTATATCGCAACGCGT-ATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* *
1260618 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
1260678 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
1260738 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
1260768 ACTGAAATTT
Statistics
Matches: 188, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
59 1 0.01
60 185 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:1261486 original size:24 final size:23
Alignment explanation
Indices: 1261447--1261492 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1261437 AAATTTGGTC
1261447 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
1261471 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
1261493 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:1263971 original size:33 final size:34
Alignment explanation
Indices: 1263920--1264084 Score: 183
Period size: 33 Copynumber: 4.7 Consensus size: 34
1263910 CGGAAATTAC
* *
1263920 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
1263953 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
1263987 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
1264025 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
1264058 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
1264085 CGAGAGAATC
Statistics
Matches: 113, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 50 0.44
34 16 0.14
35 1 0.01
36 2 0.02
37 1 0.01
38 26 0.23
39 16 0.14
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:1264003 original size:19 final size:19
Alignment explanation
Indices: 1263934--1264122 Score: 219
Period size: 19 Copynumber: 10.7 Consensus size: 19
1263924 GCAACGAGAG
1263934 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1263953 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1263967 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1263987 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1264006 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1264025 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1264039 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1264058 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1264077 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1264091 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1264110 AATCGCATTGCGA
1 AATCGCAATGCGA
1264123 TTCTCCCGTT
Statistics
Matches: 146, Mismatches: 8, Indels: 32
0.78 0.04 0.17
Matches are distributed among these distances:
14 32 0.22
15 2 0.01
16 5 0.03
17 5 0.03
18 2 0.01
19 84 0.58
20 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1264061 original size:52 final size:52
Alignment explanation
Indices: 1263920--1264122 Score: 281
Period size: 52 Copynumber: 3.9 Consensus size: 52
1263910 CGGAAATTAC
*
1263920 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1263967 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1264025 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
1264077 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1264123 TTCTCCCGTT
Statistics
Matches: 140, Mismatches: 5, Indels: 17
0.86 0.03 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 85 0.61
53 29 0.21
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1264171 original size:19 final size:19
Alignment explanation
Indices: 1264131--1264280 Score: 203
Period size: 19 Copynumber: 8.4 Consensus size: 19
1264121 GATTCTCCCG
1264131 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1264151 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1264170 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1264184 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1264203 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1264222 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1264236 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1264255 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1264274 TTGCGAT
1 TTGCGAT
1264281 AGTCAATTTT
Statistics
Matches: 116, Mismatches: 4, Indels: 21
0.82 0.03 0.15
Matches are distributed among these distances:
14 12 0.10
16 14 0.12
17 14 0.12
19 61 0.53
20 15 0.13
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1264225 original size:52 final size:52
Alignment explanation
Indices: 1264112--1264280 Score: 320
Period size: 52 Copynumber: 3.2 Consensus size: 52
1264102 GAAATTAAAA
*
1264112 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1264165 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1264217 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1264269 TCGCATTGCGAT
1 TCGCATTGCGAT
1264281 AGTCAATTTT
Statistics
Matches: 115, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 82 0.71
53 33 0.29
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:1264240 original size:33 final size:33
Alignment explanation
Indices: 1264112--1264262 Score: 137
Period size: 33 Copynumber: 4.4 Consensus size: 33
1264102 GAAATTAAAA
*
1264112 TCGCATTGCGATTCTCCCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
1264145 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 T-CGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TCATT
* * * *
1264186 GCG-ATTTTC-ATT-TCGCATTGCGATTTTCATT
1 TCGCA-TTGCGATTCTCTCGTTGCGATTTTCATT
1264217 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1264250 TCGCATTGCGATT
1 TCGCATTGCGATT
1264263 TTCATTTCGC
Statistics
Matches: 93, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
31 9 0.10
32 5 0.05
33 39 0.42
34 10 0.11
35 2 0.02
36 3 0.03
37 5 0.05
39 10 0.11
40 6 0.06
41 4 0.04
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1264406 original size:14 final size:14
Alignment explanation
Indices: 1264387--1264423 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1264377 CATCAATTAC
1264387 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1264401 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1264415 ACAAATCAA
1 ACAAATCAA
1264424 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1264503 original size:12 final size:12
Alignment explanation
Indices: 1264488--1264523 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1264478 TCACTTTACA
1264488 AATCAATTAAAC
1 AATCAATTAAAC
**
1264500 AATCAAAAAAAC
1 AATCAATTAAAC
1264512 AATCAATTAAAC
1 AATCAATTAAAC
1264524 TATTTAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:1265850 original size:21 final size:21
Alignment explanation
Indices: 1265820--1265882 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1265810 GTGAATCGGG
1265820 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
* * **
1265841 CTCTTCAATGATGACAGTGG-C
1 CTCTTGAATGGTGGGAG-GGAC
*
1265862 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
1265883 TCTCGAGGAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGAC
Found at i:1266412 original size:14 final size:14
Alignment explanation
Indices: 1266393--1266449 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1266383 GCGAAATGAA
*
1266393 AATCGCAACGACAG
1 AATCGCAACGAAAG
1266407 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1266424 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1266440 AATCGCAACG
1 AATCGCAACG
1266450 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1266420 original size:33 final size:33
Alignment explanation
Indices: 1266374--1266466 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1266364 GCGAAACCAA
*
1266374 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1266407 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1266440 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1266467 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1266431 original size:19 final size:19
Alignment explanation
Indices: 1266337--1266471 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1266327 TAGTTTACTT
* *
1266337 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1266357 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1266376 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1266395 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1266409 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1266428 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1266442 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1266461 TCGCAATGCGA
1 TCGCAACGCGA
1266472 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1266489 original size:19 final size:19
Alignment explanation
Indices: 1266467--1266595 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1266457 AAAATCGCAA
1266467 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1266486 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1266500 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1266519 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1266533 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1266552 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1266571 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1266591 TGCGA
1 TGCGA
1266596 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1266509 original size:33 final size:33
Alignment explanation
Indices: 1266467--1266558 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1266457 AAAATCGCAA
1266467 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1266500 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1266533 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1266559 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1266767 original size:93 final size:92
Alignment explanation
Indices: 1266643--1266964 Score: 503
Period size: 93 Copynumber: 3.6 Consensus size: 92
1266633 ATGGATTGCA
1266643 TTAC-TTCAACC-AAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1266705 TAGCAGAATTGGCAGCAACCGAACAAAT
65 TAGCAGAATTGGCAGCAACCGAACAAAT
1266733 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1266798 TAGCAGAATTGGCAGCAACCGAACAAAT
65 TAGCAGAATTGGCAGCAACCGAACAAAT
**
1266826 TTACTTTCAACCAAAAGACAAAACAAAGACAATACTATTTCACAGTGTTAAAGTTTA-A-AG---
1 TTACTTTCAACCAAAAGACAAAACAAAGACAATACTATTTCACAGTGTTAAAGAATACACAGTTT
1266886 AGCA-AA-----AGCAACCGAACAAAT
66 AGCAGAATTGGCAGCAACCGAACAAAT
1266907 TTACTTTCAACCAAAAGACAAAACAAAGAC-ATACTATTTCACAGTGTTAAAGAATACA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAATACTATTTCACAGTGTTAAAGAATACA
1266965 GAATTGGCAG
Statistics
Matches: 224, Mismatches: 4, Indels: 17
0.91 0.02 0.07
Matches are distributed among these distances:
80 24 0.11
81 46 0.21
86 2 0.01
87 4 0.02
90 6 0.03
91 8 0.04
92 31 0.14
93 103 0.46
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (92 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAATACTATTTCACAGTGTTAAAGAATACACAGTTT
AGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1266977 original size:81 final size:82
Alignment explanation
Indices: 1266801--1266992 Score: 289
Period size: 81 Copynumber: 2.4 Consensus size: 82
1266791 CACAGTTTAG
1266801 CAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAATACTATTT
1 CAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAATACTATTT
**
1266866 CACAGTGTTAAAGTTTA
66 CACAGTGTTAAAGAATA
* *****
1266883 AAG-AGCAAAAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-ATACTATTT
1 CAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAATACTATTT
1266946 CACAGTGTTAAAGAATA
66 CACAGTGTTAAAGAATA
*
1266963 CAGAATTGGCAGCAACCGAATAAATTTACT
1 CAGAATTGGCAGCAACCGAACAAATTTACT
1266993 AAGCAATCTA
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
80 26 0.28
81 66 0.70
82 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (82 bp):
CAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAATACTATTT
CACAGTGTTAAAGAATA
Found at i:1268699 original size:14 final size:14
Alignment explanation
Indices: 1268680--1268749 Score: 86
Period size: 14 Copynumber: 4.6 Consensus size: 14
1268670 TTGAAATGAA
1268680 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1268694 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1268708 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1268727 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1268741 AATCGCAAC
1 AATCGCAAC
1268750 ACGAAATGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
14 33 0.67
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 10 0.20
ACGTcount: A:0.44, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1268732 original size:19 final size:19
Alignment explanation
Indices: 1268708--1268772 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
1268698 GCAACGAGAG
1268708 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1268727 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
1268741 AATCGCAACACGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1268760 AATCGCAATGCGA
1 AATCGCAACGCGA
1268773 TTTTGGTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 10 0.27
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 21 0.57
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1268736 original size:33 final size:33
Alignment explanation
Indices: 1268694--1268767 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
1268684 GCAACGAGAG
*
1268694 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAACACGAAATGAA
1268727 AATCGCAACGAGAGAATCGCAACACGAAATGAA
1 AATCGCAACGAGAGAATCGCAACACGAAATGAA
1268760 AATCGCAA
1 AATCGCAA
1268768 TGCGATTTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAACACGAAATGAA
Found at i:1268790 original size:19 final size:19
Alignment explanation
Indices: 1268768--1268882 Score: 105
Period size: 19 Copynumber: 6.3 Consensus size: 19
1268758 AAAATCGCAA
**
1268768 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
1268787 TGCGA--TTC-TCTCG--T
1 TGCGATTTTCATTTCGCGT
1268801 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
1268820 TGCGATTGTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*** *
1268839 TGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATT-TCGCGT
*
1268859 TGCGATTTTCATTTCTCGT
1 TGCGATTTTCATTTCGCGT
1268878 TGCGA
1 TGCGA
1268883 CTCTTCTGCA
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 6 0.08
19 46 0.57
20 15 0.19
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1268871 original size:39 final size:38
Alignment explanation
Indices: 1268809--1268883 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 38
1268799 GTTGCGATTT
1268809 TCATTTCGCGTTGCGATTGTCATTTCGCGTTGCGACAG
1 TCATTTCGCGTTGCGATTGTCATTTCGCGTTGCGACAG
* * *
1268847 TCATTCTCTCGTTGCGATTTTCATTTCTCGTTGCGAC
1 TCATT-TCGCGTTGCGATTGTCATTTCGCGTTGCGAC
1268884 TCTTCTGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 5 0.15
39 28 0.85
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.41
Consensus pattern (38 bp):
TCATTTCGCGTTGCGATTGTCATTTCGCGTTGCGACAG
Found at i:1269000 original size:31 final size:32
Alignment explanation
Indices: 1268965--1269032 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
1268955 ACTAACTTGA
*
1268965 AAATCGCAACGAGAGAATAGCAACGCG-AATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
* *
1268996 AAATCGCAACGACAGAATCGTAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
1269028 AAATC
1 AAATC
1269033 TAAGTGAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 24 0.73
32 9 0.27
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.12
Consensus pattern (32 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATG
Found at i:1269432 original size:20 final size:20
Alignment explanation
Indices: 1269407--1269521 Score: 151
Period size: 20 Copynumber: 5.7 Consensus size: 20
1269397 CTTTAAATAT
1269407 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1269427 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1269449 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1269468 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1269488 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1269508 CGCGTTACGATTTA
1 CGCGTTGCGATTTA
1269522 TGTGTTCGCG
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 63 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1269534 original size:40 final size:40
Alignment explanation
Indices: 1269406--1269538 Score: 169
Period size: 40 Copynumber: 3.3 Consensus size: 40
1269396 GCTTTAAATA
*
1269406 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
1269447 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* * *
1269487 ACACGTTGCGATTTACGGATACGCGTTACGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1269527 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1269539 ATTCGCGTTG
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
40 47 0.61
41 30 0.39
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:1269545 original size:14 final size:14
Alignment explanation
Indices: 1269526--1269552 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1269516 GATTTATGTG
1269526 TTCGCGTTGCGATA
1 TTCGCGTTGCGATA
1269540 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1269553 TTTGGAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.22, G:0.30, T:0.37
Consensus pattern (14 bp):
TTCGCGTTGCGATA
Found at i:1269571 original size:21 final size:21
Alignment explanation
Indices: 1269541--1269623 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1269531 GTTGCGATAT
*
1269541 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1269562 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1269583 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1269604 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1269624 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1273640 original size:2 final size:2
Alignment explanation
Indices: 1273633--1273662 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1273623 GTTCCTTTAA
1273633 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1273663 AAACAAACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1274106 original size:19 final size:19
Alignment explanation
Indices: 1274082--1274139 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 19
1274072 AAATAACCAA
* *
1274082 CTAAATCGTAATGCGATCT
1 CTAAATCGCAACGCGATCT
*
1274101 CTAAATCGCAACGTGATCT
1 CTAAATCGCAACGCGATCT
*
1274120 CTAAATTGCAACGCGATCT
1 CTAAATCGCAACGCGATCT
1274139 C
1 C
1274140 CAGTATCGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (19 bp):
CTAAATCGCAACGCGATCT
Found at i:1274269 original size:21 final size:21
Alignment explanation
Indices: 1274243--1274312 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
1274233 AGTCTAAATT
*
1274243 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
** *
1274264 CGTTGCGATTTTCCAAATT--
1 CGTTGCGATAGTCCAAGTTCG
* * *
1274283 CGTTGTGATAGACTAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
1274304 CGTTGCGAT
1 CGTTGCGAT
1274313 TTTGGAAAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
19 13 0.36
21 23 0.64
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:1274293 original size:40 final size:40
Alignment explanation
Indices: 1274238--1274315 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
1274228 ACGTTAGTCT
*
1274238 AAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCC
1 AAATTCGTTGCGATAGACGAAGTTCGCGTTGCGATTTTCC
* *
1274278 AAATTCGTTGTGATAGACTAAGTTCGCGTTGCGATTTT
1 AAATTCGTTGCGATAGACGAAGTTCGCGTTGCGATTTT
1274316 GGAAAATCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (40 bp):
AAATTCGTTGCGATAGACGAAGTTCGCGTTGCGATTTTCC
Found at i:1274750 original size:19 final size:19
Alignment explanation
Indices: 1274726--1274813 Score: 79
Period size: 19 Copynumber: 4.4 Consensus size: 19
1274716 TTATTTTGGA
1274726 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
1274745 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
* *
1274767 GTGTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
1274789 ATTTTAACTATCGCAACA-
1 TTTTTCACTATCGCAACAC
1274807 TTTTTCA
1 TTTTTCA
1274814 AAATCGCGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
18 5 0.09
19 24 0.44
21 3 0.05
22 12 0.22
23 5 0.09
25 6 0.11
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:1276422 original size:45 final size:41
Alignment explanation
Indices: 1276373--1276471 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 41
1276363 ATAATATCAA
* *
1276373 TAGGTTGGTGGTTGGTAGTTAATAATTATCTATTAATAACTCGGG
1 TAGGTTGGTGGTTGGTA--T--TAATTATCCATTAATAACCCGGG
*
1276418 TAGGTTGGTGG-T--TATTAATTATCCATTAATATCCCGGG
1 TAGGTTGGTGGTTGGTATTAATTATCCATTAATAACCCGGG
1276456 TAGGTTGGTGGTTGGT
1 TAGGTTGGTGGTTGGT
1276472 GGTTGCATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
38 31 0.65
39 1 0.02
40 1 0.02
41 1 0.02
42 2 0.04
44 1 0.02
45 11 0.23
ACGTcount: A:0.22, C:0.08, G:0.29, T:0.40
Consensus pattern (41 bp):
TAGGTTGGTGGTTGGTATTAATTATCCATTAATAACCCGGG
Found at i:1276465 original size:38 final size:38
Alignment explanation
Indices: 1276382--1276468 Score: 129
Period size: 38 Copynumber: 2.3 Consensus size: 38
1276372 ATAGGTTGGT
* * *
1276382 GGTTGGTAGTTAATAATTATCTATTAATAACTCGGGTA
1 GGTTGGTGGTTAATAATTATCCATTAATAACCCGGGTA
* *
1276420 GGTTGGTGGTTATTAATTATCCATTAATATCCCGGGTA
1 GGTTGGTGGTTAATAATTATCCATTAATAACCCGGGTA
1276458 GGTTGGTGGTT
1 GGTTGGTGGTT
1276469 GGTGGTTGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.40
Consensus pattern (38 bp):
GGTTGGTGGTTAATAATTATCCATTAATAACCCGGGTA
Found at i:1277931 original size:27 final size:27
Alignment explanation
Indices: 1277897--1278140 Score: 177
Period size: 27 Copynumber: 8.7 Consensus size: 27
1277887 CATATGATGG
1277897 ATAATATCAATAGTTGAATGAATGTGA
1 ATAATATCAATAGTTGAATGAATGTGA
1277924 ATAATATCAATAGTTGAATGAATGTGA
1 ATAATATCAATAGTTGAATGAATGTGA
* *
1277951 ATAATATCAATAGTTGAATTAATGCGA
1 ATAATATCAATAGTTGAATGAATGTGA
* * * *
1277978 TTAATATCAATAATTGAATTAATATGATGG
1 ATAATATCAATAGTTGAA-TGA-ATG-TGA
* * * * *
1278008 ATATTTGTTGACGATATATTTTAATGAATATGA
1 ATA-AT-AT--C-A-ATAGTTGAATGAATGTGA
* ** *
1278041 TTAATATCAATAG-AAAAAGAAATGTGA
1 ATAATATCAATAGTTGAATG-AATGTGA
*
1278068 ATAATATCAATAGTTGAATTAATGTGA
1 ATAATATCAATAGTTGAATGAATGTGA
* * * *
1278095 TTAATATCAATATTTGAATTAATATG-
1 ATAATATCAATAGTTGAATGAATGTGA
* *
1278121 ATGGATATTAATAGTTGAAT
1 AT-AATATCAATAGTTGAAT
1278141 TATGGATATA
Statistics
Matches: 170, Mismatches: 35, Indels: 24
0.74 0.15 0.10
Matches are distributed among these distances:
26 4 0.02
27 133 0.78
28 5 0.03
29 4 0.02
30 3 0.02
31 2 0.01
32 2 0.01
33 4 0.02
34 3 0.02
35 3 0.02
36 7 0.04
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.37
Consensus pattern (27 bp):
ATAATATCAATAGTTGAATGAATGTGA
Found at i:1278088 original size:117 final size:117
Alignment explanation
Indices: 1277913--1278129 Score: 355
Period size: 117 Copynumber: 1.9 Consensus size: 117
1277903 TCAATAGTTG
* ** *
1277913 AATGAATGTGAATAATATCAATAGTTGAATGAATGTGAATAATATCAATAGTTGAATTAATGCGA
1 AATGAATATGAATAATATCAATAGTAAAAAGAATGTGAATAATATCAATAGTTGAATTAATGCGA
1277978 TTAATATCAATAATTGAATTAATATGATGGATATTTGTTGACGATATATTTT
66 TTAATATCAATAATTGAATTAATATGATGGATATTTGTTGACGATATATTTT
* *
1278030 AATGAATATGATTAATATCAATAG-AAAAAGAAATGTGAATAATATCAATAGTTGAATTAATGTG
1 AATGAATATGAATAATATCAATAGTAAAAAG-AATGTGAATAATATCAATAGTTGAATTAATGCG
*
1278094 ATTAATATCAATATTTGAATTAATATGATGGATATT
65 ATTAATATCAATAATTGAATTAATATGATGGATATT
1278130 AATAGTTGAA
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
116 3 0.03
117 89 0.97
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.37
Consensus pattern (117 bp):
AATGAATATGAATAATATCAATAGTAAAAAGAATGTGAATAATATCAATAGTTGAATTAATGCGA
TTAATATCAATAATTGAATTAATATGATGGATATTTGTTGACGATATATTTT
Found at i:1279426 original size:17 final size:18
Alignment explanation
Indices: 1279400--1279437 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1279390 ATTAATTTAA
* *
1279400 CATCGAATGCATTTTATG
1 CATCGAATGCACTTAATG
1279418 CATCG-ATGCACTTAATG
1 CATCGAATGCACTTAATG
1279435 CAT
1 CAT
1279438 TTGATGCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (18 bp):
CATCGAATGCACTTAATG
Found at i:1279435 original size:26 final size:26
Alignment explanation
Indices: 1279405--1279454 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1279395 TTTAACATCG
*
1279405 AATGCATTTTATGCATCGATGCACTT
1 AATGCATTTGATGCATCGATGCACTT
1279431 AATGCATTTGATGCATCGATGCAC
1 AATGCATTTGATGCATCGATGCAC
1279455 AAGACCATGC
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:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (26 bp):
AATGCATTTGATGCATCGATGCACTT
Found at i:1279916 original size:14 final size:14
Alignment explanation
Indices: 1279897--1279930 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1279887 AAACAATCTA
1279897 CCTTGTGAGGATTT
1 CCTTGTGAGGATTT
1279911 CCTTGTGAGGATTT
1 CCTTGTGAGGATTT
1279925 CCTTGT
1 CCTTGT
1279931 AAGTTTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.18, G:0.26, T:0.44
Consensus pattern (14 bp):
CCTTGTGAGGATTT
Found at i:1288000 original size:22 final size:22
Alignment explanation
Indices: 1287972--1288023 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
1287962 TTTCAAAGTG
*
1287972 ATGCATCGATACTGCAC-ATACC
1 ATGCATCGATA-TGCACAAGACC
1287994 ATGCATCG--ATGCACAAGACC
1 ATGCATCGATATGCACAAGACC
1288014 ATGCATCGAT
1 ATGCATCGAT
1288024 GCACTCAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.19
20 13 0.50
22 8 0.31
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (22 bp):
ATGCATCGATATGCACAAGACC
Found at i:1290779 original size:63 final size:64
Alignment explanation
Indices: 1290725--1290886 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 64
1290715 CGGTGCACCA
*
1290725 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAA-ATAGCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAT-GCAGAGTGCATCGATGCATGG
** * *
1290788 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATGCAGAGTGCATCGATGCATGG
* *
1290853 AGAGTGCATC-AGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGA-TGCATGAAATGCATTCGATGTT
1290887 CAATTAATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 29 0.34
64 13 0.15
65 43 0.51
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCAGAGTGCATCGATGCATGG
Found at i:1290858 original size:19 final size:19
Alignment explanation
Indices: 1290834--1290884 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1290824 GAAAATATTC
1290834 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
1290853 AGAGTGCATC-AGTGCATGG
1 AGAGTGCATCGA-TGCATGG
1290872 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1290885 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1291118 original size:20 final size:21
Alignment explanation
Indices: 1291095--1291134 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1291085 GAATCGAATA
1291095 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1291115 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1291135 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1291944 original size:21 final size:21
Alignment explanation
Indices: 1291920--1291963 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1291910 CTGAAGGAAG
*
1291920 AGGAGGAGCACGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
*
1291941 AGGAGCAGCTCGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
1291962 AG
1 AG
1291964 CTCCCGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.36, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:1292818 original size:21 final size:21
Alignment explanation
Indices: 1292762--1292822 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1292752 TCAATAAGCC
* *
1292762 ATTAGGA-GCTTGAGGATCAGG
1 ATTAGGATG-TTGAGGAACGGG
* **
1292783 ATTAGGTTGAGGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
1292804 ATTAGGATGTTGAGGAACG
1 ATTAGGATGTTGAGGAACG
1292823 AGAGGACGGT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.41, T:0.23
Consensus pattern (21 bp):
ATTAGGATGTTGAGGAACGGG
Found at i:1297445 original size:22 final size:21
Alignment explanation
Indices: 1297403--1297442 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1297393 GAGTTTGTTT
*
1297403 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1297424 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1297443 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1299423 original size:64 final size:64
Alignment explanation
Indices: 1299370--1299532 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
1299360 CGGTGCACCA
*
1299370 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
1299434 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
1299499 AGAATGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
1299533 CAATTAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 39 0.46
65 45 0.54
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:1299522 original size:17 final size:19
Alignment explanation
Indices: 1299484--1299530 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1299474 ATATTCAGAG
1299484 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
1299503 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
1299520 TGCATTCGATG
1 TGCA-TCGATG
1299531 TTCAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:1299772 original size:20 final size:21
Alignment explanation
Indices: 1299749--1299788 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1299739 GAATCGAATA
1299749 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1299769 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1299789 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1300774 original size:10 final size:10
Alignment explanation
Indices: 1300739--1300841 Score: 117
Period size: 10 Copynumber: 10.6 Consensus size: 10
1300729 GCTGTTGGAA
1300739 ACCGG-TTTG
1 ACCGGTTTTG
*
1300748 ACCGGTTTTCA
1 ACCGGTTTT-G
1300759 ACCGGTTTTG
1 ACCGGTTTTG
1300769 ACCGG-TTTG
1 ACCGGTTTTG
1300778 ACCGGTTTTG
1 ACCGGTTTTG
*
1300788 ACTGG-TTTG
1 ACCGGTTTTG
1300797 ACCGGTTTTG
1 ACCGGTTTTG
*
1300807 ACTGGTTTTG
1 ACCGGTTTTG
*
1300817 ACCGG-TTCG
1 ACCGGTTTTG
1300826 AACC-GTTTTG
1 -ACCGGTTTTG
1300836 ACCGGT
1 ACCGGT
1300842 CTGACCCGAC
Statistics
Matches: 79, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
9 29 0.37
10 41 0.52
11 9 0.11
ACGTcount: A:0.13, C:0.21, G:0.29, T:0.37
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1300783 original size:19 final size:19
Alignment explanation
Indices: 1300739--1300841 Score: 111
Period size: 19 Copynumber: 5.3 Consensus size: 19
1300729 GCTGTTGGAA
*
1300739 ACCGG-TTTGACCGGTTTTCA
1 ACCGGTTTTGACCGG-TTT-G
1300759 ACCGGTTTTGACCGGTTTG
1 ACCGGTTTTGACCGGTTTG
*
1300778 ACCGGTTTTGACTGGTTTG
1 ACCGGTTTTGACCGGTTTG
*
1300797 ACCGGTTTTGACTGGTTTTG
1 ACCGGTTTTGACCGG-TTTG
* *
1300817 ACCGG-TTCGAACCGTTTTG
1 ACCGGTTTTG-ACCGGTTTG
1300836 ACCGGT
1 ACCGGT
1300842 CTGACCCGAC
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
19 45 0.61
20 20 0.27
21 9 0.12
ACGTcount: A:0.13, C:0.21, G:0.29, T:0.37
Consensus pattern (19 bp):
ACCGGTTTTGACCGGTTTG
Found at i:1308070 original size:9 final size:9
Alignment explanation
Indices: 1308056--1308125 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
1308046 GCTGCTGGAA
1308056 ACCGGTTTG
1 ACCGGTTTG
1308065 ACCGGTTTTCG
1 ACCGG-TTT-G
*
1308076 ACCGATTTTG
1 ACCG-GTTTG
* *
1308086 ATCGGTTCG
1 ACCGGTTTG
*
1308095 AACCGTTTTG
1 -ACCGGTTTG
*
1308105 ACCGGTTTA
1 ACCGGTTTG
*
1308114 ACCGGTCTG
1 ACCGGTTTG
1308123 ACC
1 ACC
1308126 CGACCCGACC
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
9 25 0.54
10 13 0.28
11 8 0.17
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1308103 original size:19 final size:19
Alignment explanation
Indices: 1308061--1308111 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1308051 TGGAAACCGG
1308061 TTTGACCGGTTTTCGACCGAT
1 TTTGACCGG--TTCGACCGAT
*
1308082 TTTGATCGGTTCGAACCG-T
1 TTTGACCGGTTCG-ACCGAT
1308101 TTTGACCGGTT
1 TTTGACCGGTT
1308112 TAACCGGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 15 0.56
20 4 0.15
21 8 0.30
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (19 bp):
TTTGACCGGTTCGACCGAT
Found at i:1308165 original size:17 final size:17
Alignment explanation
Indices: 1308143--1308176 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1308133 ACCCGACCAG
1308143 TCCGACCCGACCGTTGA
1 TCCGACCCGACCGTTGA
1308160 TCCGACCCGACCGTTGA
1 TCCGACCCGACCGTTGA
1308177 CCGTTGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.24, T:0.18
Consensus pattern (17 bp):
TCCGACCCGACCGTTGA
Found at i:1314241 original size:195 final size:195
Alignment explanation
Indices: 1313883--1314242 Score: 477
Period size: 195 Copynumber: 1.8 Consensus size: 195
1313873 GTGTTTTGCT
* * *
1313883 ACAATATCTCTTTCATCACATATAAGTTGATTTTAATGCATTATTTGTGACAATACAAATGATCA
1 ACAATATCTCTTTCATAACATATAAGTTGATTTTAATGCATTATCTGTGACAATACAAATAATCA
* ** * *
1313948 ATAATGAAATATTATTTAATTTAGTGACGTAAACAACTGTCATAGAATATAAATTATAAAGTGAT
66 ATAACGAAATATTACATAATTTAGTGACATAAACAACTGTCATAGAATATAAATTATAAAGTGAC
* * *
1314013 GTTATGCATAAACGTCATTCATAATATTATTAGGTAACATTTATATTATGTCACTAAAAAATATG
131 GTTATACATAAACGTCATCCATAATACTATTAGGTAACATTTATATTATGTCACTAAAAAATATG
* * * * *
1314078 ACAATATCTCTTTCGTAACATATAGGTTGATTTTAATGTATTATCTGTGACGATATAAATAATCA
1 ACAATATCTCTTTCATAACATATAAGTTGATTTTAATGCATTATCTGTGACAATACAAATAATCA
* ** ** * * *
1314143 ATAACGAAATTTTACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAATTATATAGTGAC
66 ATAACGAAATATTACATAATTTAGTGACATAAACAACTGTCATAGAATATAAATTATAAAGTGAC
* * *
1314208 GTTATATATAAATGTCATCCATGATACTATTAGGT
131 GTTATACATAAACGTCATCCATAATACTATTAGGT
1314243 GACGATATAT
Statistics
Matches: 138, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
195 138 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (195 bp):
ACAATATCTCTTTCATAACATATAAGTTGATTTTAATGCATTATCTGTGACAATACAAATAATCA
ATAACGAAATATTACATAATTTAGTGACATAAACAACTGTCATAGAATATAAATTATAAAGTGAC
GTTATACATAAACGTCATCCATAATACTATTAGGTAACATTTATATTATGTCACTAAAAAATATG
Found at i:1315827 original size:67 final size:67
Alignment explanation
Indices: 1315748--1315879 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
1315738 CAGACAGATT
* * *
1315748 TTATTTATGTGTTAAATACCCTTTTTAAAAATATTACCGATTTAGTATCTTTTCTCGAAATACGC
1 TTATTTATGTGTTAAATACCCCTTTTAAAAATATTACCGATCTAGTATCTTTTCCCGAAATACGC
1315813 AG
66 AG
*
1315815 TTATTTATGTGTTAAATACCCCTTTTAAAAATGTTACCGATCTAGTATCTTTTCCCGAAATACGC
1 TTATTTATGTGTTAAATACCCCTTTTAAAAATATTACCGATCTAGTATCTTTTCCCGAAATACGC
1315880 GGCTCATCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (67 bp):
TTATTTATGTGTTAAATACCCCTTTTAAAAATATTACCGATCTAGTATCTTTTCCCGAAATACGC
AG
Found at i:1319328 original size:23 final size:23
Alignment explanation
Indices: 1319302--1319364 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1319292 ATATAACCAC
1319302 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1319325 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1319348 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1319365 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1319755 original size:23 final size:23
Alignment explanation
Indices: 1319729--1319791 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1319719 ATATAACCAC
1319729 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1319752 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1319775 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1319792 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1320201 original size:42 final size:42
Alignment explanation
Indices: 1320151--1320258 Score: 216
Period size: 42 Copynumber: 2.6 Consensus size: 42
1320141 TACCTAAATA
1320151 TGTAGTTATTGTACATACCTAAATTTAATGATAATATATACT
1 TGTAGTTATTGTACATACCTAAATTTAATGATAATATATACT
1320193 TGTAGTTATTGTACATACCTAAATTTAATGATAATATATACT
1 TGTAGTTATTGTACATACCTAAATTTAATGATAATATATACT
1320235 TGTAGTTATTGTACATACCTAAAT
1 TGTAGTTATTGTACATACCTAAAT
1320259 ATGTACTGCG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (42 bp):
TGTAGTTATTGTACATACCTAAATTTAATGATAATATATACT
Found at i:1322983 original size:183 final size:183
Alignment explanation
Indices: 1322675--1323166 Score: 878
Period size: 183 Copynumber: 2.7 Consensus size: 183
1322665 TTAAAATTAC
*
1322675 CGACACTTTTTTCAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1322740 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
1322805 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGAAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGAAAATGT
*
1322858 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATTAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1322923 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
* * * *
1322988 ATATTACAAAATTATCTATTACATTATAATTCTGGGTTTCGATGTGTAACTGT
131 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGAAAATGT
* *
1323041 CGACACGTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
* *
1323105 TATTAAAAAGTGTCGATATAAGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACC
65 TATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACC
1323167 AATAGCATTG
Statistics
Matches: 297, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
183 294 0.99
184 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGAAAATGT
Found at i:1325021 original size:3 final size:3
Alignment explanation
Indices: 1325013--1325105 Score: 60
Period size: 3 Copynumber: 31.0 Consensus size: 3
1325003 ACTTGTTTGG
* * * * * * *
1325013 ATC ATC ATC ATC ATC ATC ATC ATC GTC GTC GTC GTC GTC GTC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * * *
1325061 ATC TTC ATC GTC AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1325106 GTCAGCTTCA
Statistics
Matches: 74, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:1325030 original size:12 final size:12
Alignment explanation
Indices: 1325014--1325109 Score: 81
Period size: 12 Copynumber: 8.2 Consensus size: 12
1325004 CTTGTTTGGA
*
1325014 TCATCATCATCA
1 TCATCATCATCG
1325026 TCATCATCATCG
1 TCATCATCATCG
* * *
1325038 TCGTCGTCGTCG
1 TCATCATCATCG
* *
1325050 TCGTCGTCA---
1 TCATCATCATCG
*
1325059 TCATCTTCATCG
1 TCATCATCATCG
* *
1325071 TCAGCTTCATCG
1 TCATCATCATCG
1325083 TCATCATCATCG
1 TCATCATCATCG
*
1325095 TCATCTTCATCG
1 TCATCATCATCG
1325107 TCA
1 TCA
1325110 GCTTCATCTT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.10
12 63 0.90
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.35
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:1325114 original size:12 final size:12
Alignment explanation
Indices: 1325063--1325117 Score: 83
Period size: 12 Copynumber: 4.6 Consensus size: 12
1325053 TCGTCATCAT
1325063 CTTCATCGTCAG
1 CTTCATCGTCAG
*
1325075 CTTCATCGTCAT
1 CTTCATCGTCAG
* *
1325087 CATCATCGTCAT
1 CTTCATCGTCAG
1325099 CTTCATCGTCAG
1 CTTCATCGTCAG
1325111 CTTCATC
1 CTTCATC
1325118 TTCATTGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.18, C:0.35, G:0.11, T:0.36
Consensus pattern (12 bp):
CTTCATCGTCAG
Found at i:1325120 original size:6 final size:6
Alignment explanation
Indices: 1325059--1325122 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
1325049 GTCGTCGTCA
* * * * * *
1325059 TCATCT TCATCG TCAGCT TCATCG TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
1325107 TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCAT
1325123 TGACCGCTTG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:1326840 original size:109 final size:109
Alignment explanation
Indices: 1326649--1326859 Score: 395
Period size: 109 Copynumber: 1.9 Consensus size: 109
1326639 ATAAAACCGG
*
1326649 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
1 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACAATATACTTTTGGGTTTCGATGTTTTT
1326714 GGGATCGACACTTTTTATATATGGATCGACACATTATTTATCGA
66 GGGATCGACACTTTTTATATATGGATCGACACATTATTTATCGA
1326758 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACAATATACTTTTGGGTTTCGATGTTTTT
1 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACAATATACTTTTGGGTTTCGATGTTTTT
* *
1326823 GGGATCGATACTTTTTATATATGGATCGACACTTTAT
66 GGGATCGACACTTTTTATATATGGATCGACACATTAT
1326860 GGTTGCACCC
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 99 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (109 bp):
TATACTTGTACCGGTTAGATTGAAAAATTACATATTACAATATACTTTTGGGTTTCGATGTTTTT
GGGATCGACACTTTTTATATATGGATCGACACATTATTTATCGA
Found at i:1328023 original size:200 final size:200
Alignment explanation
Indices: 1327699--1328655 Score: 1760
Period size: 200 Copynumber: 4.8 Consensus size: 200
1327689 AAATATCGAC
*
1327699 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCAGTTAGAT
1 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
**
1327764 TTAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
66 TGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
*
1327829 ATGGATCGACACTTTATGGTTGTACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAA
131 ATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAA
1327894 ACTAA
196 ACTAA
*
1327899 AAACGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1327964 TGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
66 TGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
*
1328029 ATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTTATTCTGGAC-AAAAATATCGACACAA
131 ATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAA
1328093 ACT-A
196 ACTAA
*
1328097 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACTGGTTAGAT
1 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1328162 TGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
66 TGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
1328227 ATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAA
131 ATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAA
1328292 ACTAA
196 ACTAA
* *
1328297 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGATATATTTGTACCGGTTAGAT
1 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
*
1328362 TGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGTATCGACACTTTTTATAT
66 TGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
* *
1328427 ATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTAATTCTGGAC-AAAAATATCGATACAA
131 ATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAA
1328491 ACTAA
196 ACTAA
1328496 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACC-GTTAGAT
1 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1328560 TGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
66 TGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
* *
1328625 ATGGTTCGACACTTTATTGTTGCACCCTGTT
131 ATGGATCGACACTTTATGGTTGCACCCTGTT
1328656 GGTCATATTG
Statistics
Matches: 735, Mismatches: 20, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
198 276 0.38
199 113 0.15
200 346 0.47
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (200 bp):
AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
TGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
ATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAA
ACTAA
Found at i:1328292 original size:398 final size:399
Alignment explanation
Indices: 1326758--1328655 Score: 3450
Period size: 398 Copynumber: 4.8 Consensus size: 399
1326748 TATTTATCGA
* *
1326758 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACAATATACTTTTGGGTTTCGATGTTTTT
1 TATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
*
1326823 GGGATCGATACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
66 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
*
1326888 GACAAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTATCATAAA
131 GACAAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
1326953 ACCGGTATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATG
196 ACCGGTATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATG
*
1327018 TTTTTGGGATTGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCA
261 TTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCA
*
1327083 TTCTGAACAAAAAAATCGACACAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCA
326 TTCTGGACAAAAAAATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCA
1327147 TAAAACCGG
391 TAAAACCGG
*
1327156 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
1 TATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
1327221 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
66 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
1327286 GACAAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
131 GACAAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
*
1327351 ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTTCGATG
196 ACCGGTATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATG
1327415 TTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCA
261 TTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCA
1327480 TTCTGGAC-AAAAAATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCA
326 TTCTGGACAAAAAAATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCA
1327544 TAAAACCGG
391 TAAAACCGG
1327553 TATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
1 TATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
* *
1327618 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCTATTCATTCTG
66 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
1327683 GACAAAAAATATCG------AC---AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
131 GACAAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
* **
1327739 ACCGGTATACTTGTACCAGTTAGATTTAAAAATTACATATTACATTATACTTTTGGGTTTCGATG
196 ACCGGTATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATG
*
1327804 TTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGTACCCTGTTTTCCATTCA
261 TTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCA
*
1327869 TTCTGGACAAAAAATATCGACACAAACTAAAAACGTGTCGACACATTATTTAGACATATTCTCTC
326 TTCTGGACAAAAAA-ATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTC
1327934 ATAAAACCGG
390 ATAAAACCGG
1327944 TATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
1 TATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
*
1328009 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTTATTCTG
66 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
1328074 GAC-AAAAATATCGACACAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
131 GACAAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
*
1328137 ACCGGTATACTTGTACTGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATG
196 ACCGGTATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATG
1328202 TTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCA
261 TTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCA
1328267 TTCTGGACAAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTC
326 TTCTGGACAAAAAA-ATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTC
*
1328332 ATAAAACCGA
390 ATAAAACCGG
*
1328342 TATATTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
1 TATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
* *
1328407 GGTATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTAATTCTG
66 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
*
1328472 GAC-AAAAATATCGATACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
131 GACAAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
1328536 ACCGGTATACTTGTACC-GTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATG
196 ACCGGTATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATG
* *
1328600 TTTTTGGGATCGACACTTTTTATATATGGTTCGACACTTTATTGTTGCACCCTGTT
261 TTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
1328656 GGTCATATTG
Statistics
Matches: 1457, Mismatches: 30, Indels: 26
0.96 0.02 0.02
Matches are distributed among these distances:
388 88 0.06
389 86 0.06
390 15 0.01
391 191 0.13
396 20 0.01
397 272 0.19
398 728 0.50
399 57 0.04
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (399 bp):
TATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
GACAAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
ACCGGTATACTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATG
TTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCA
TTCTGGACAAAAAAATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCA
TAAAACCGG
Found at i:1328820 original size:19 final size:19
Alignment explanation
Indices: 1328774--1328822 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1328764 TTATATTCAC
*
1328774 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1328793 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1328812 ATACAAAATTA
1 ATACAAAATTA
1328823 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1330651 original size:33 final size:33
Alignment explanation
Indices: 1330614--1330679 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1330604 CATCTTAATA
*
1330614 TCACCCCTTAACACAC-CAACTTCTTTCACCACT
1 TCACCCCTCAACAC-CTCAACTTCTTTCACCACT
*
1330647 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
1330680 CCATCTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:1330738 original size:21 final size:21
Alignment explanation
Indices: 1330713--1330777 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1330703 CCCCTTATGC
* *
1330713 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1330734 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1330755 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1330776 CT
1 CT
1330778 TGATTGTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1332815 original size:24 final size:24
Alignment explanation
Indices: 1332778--1332830 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1332768 CCGTTCTATC
1332778 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
1332802 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
1332826 TATTT
1 TATTT
1332831 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:1332992 original size:17 final size:18
Alignment explanation
Indices: 1332970--1333012 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1332960 ATATATCCGG
1332970 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1332987 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1333007 TATCAT
1 TATCAT
1333013 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1333021 original size:20 final size:19
Alignment explanation
Indices: 1332975--1333035 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
1332965 TCCGGTATCA
1332975 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1332994 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
* * *
1333015 TTTTACCTGTTATATCGTT
1 TTTTACCGGTTTTATCATT
1333034 TT
1 TT
1333036 GGATCGATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.14
20 27 0.77
21 3 0.09
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1333263 original size:161 final size:162
Alignment explanation
Indices: 1332998--1333335 Score: 534
Period size: 161 Copynumber: 2.1 Consensus size: 162
1332988 ATCATTTTGA
* * *
1332998 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTTAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTTAAAGTATCG
*
1333063 ACACATTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAG
66 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
* * * *
1333127 TATCGACACTTTCAATATATCCGGTAACGTTT
131 TACCAACACTTTAAATATATCCGGTAACGCTT
1333159 TACCGGTTTTATCATATTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTTAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTTAAAGTATCG
* ** *
1333224 ACACTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAG
66 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
* *
1333289 TACCAACACTTTAAATGTATCCGGTAGCGCTT
131 TACCAACACTTTAAATATATCCGGTAACGCTT
*
1333321 TATCGGTTTTATCAT
1 TACCGGTTTTATCAT
1333336 TTCTATACCG
Statistics
Matches: 161, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
161 116 0.72
162 45 0.28
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (162 bp):
TACCGGTTTTATCATATTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTTAAAGTATCG
ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
TACCAACACTTTAAATATATCCGGTAACGCTT
Found at i:1336314 original size:22 final size:22
Alignment explanation
Indices: 1336286--1336327 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1336276 GTTTTTCTGC
1336286 TTTCGAATA-GAAAAGTAATAGT
1 TTTCGAATAGGAAAA-TAATAGT
1336308 TTTCGAATAGGAAAATAATA
1 TTTCGAATAGGAAAATAATA
1336328 CCTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (22 bp):
TTTCGAATAGGAAAATAATAGT
Found at i:1339374 original size:59 final size:59
Alignment explanation
Indices: 1339262--1339376 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 59
1339252 TAGTCATGTG
* * * *
1339262 ACCATTTGTAACTTTTAACAGTTGAAAGACTCAACAAATCAATACTCTCTAGTCAATGA
1 ACCATTTATAACTTTTAACAGTTGAAAGACTCAACAAATCAACACCCTATAGTCAATGA
**
1339321 ACCATTTTATAACTTTTAATGGTTG-AAGACTCAACAAAAT-AACACCCTATAGTCAA
1 ACCA-TTTATAACTTTTAACAGTTGAAAGACTCAAC-AAATCAACACCCTATAGTCAA
1339377 GGGGCTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 27 0.56
60 21 0.44
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (59 bp):
ACCATTTATAACTTTTAACAGTTGAAAGACTCAACAAATCAACACCCTATAGTCAATGA
Found at i:1340928 original size:136 final size:138
Alignment explanation
Indices: 1340768--1341041 Score: 509
Period size: 137 Copynumber: 2.0 Consensus size: 138
1340758 AAATAAATAA
*
1340768 AAATAAATTAGATTAATTTTTTTTAATATTTGATTCAAGAGTTGATCTATT-ATAAATTAATTAC
1 AAATAAATTAGATTAATTTTTTTTAATATTTGATTCAAGAGTTAATCTATTAATAAATTAATTAC
1340832 TGCTGATTATAACAAATATTTTTTAAATATTATTCATCAAAAATATTAAAAAATAAAAATAAA-T
66 TGCTGATTATAACAAATATTTTTTAAATATTATTCATCAAAAATATTAAAAAATAAAAATAAATT
1340896 TTAAAAGC
131 TTAAAAGC
1340904 AAATAAATTAGAATTAA-TTTTTTTAATATTTGATTCAAGAGTTAATCTATTAATAAATTAATTA
1 AAATAAATTAG-ATTAATTTTTTTTAATATTTGATTCAAGAGTTAATCTATTAATAAATTAATTA
1340968 CTGCTGATTATAACAAATATTTTTTAAATATTATTCATCAAAAATATTAAAAAATAAAAATAAAT
65 CTGCTGATTATAACAAATATTTTTTAAATATTATTCATCAAAAATATTAAAAAATAAAAATAAAT
1341033 TTTAAAAGC
130 TTTAAAAGC
1341042 TTTTAAATTT
Statistics
Matches: 134, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
136 44 0.33
137 81 0.60
138 9 0.07
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (138 bp):
AAATAAATTAGATTAATTTTTTTTAATATTTGATTCAAGAGTTAATCTATTAATAAATTAATTAC
TGCTGATTATAACAAATATTTTTTAAATATTATTCATCAAAAATATTAAAAAATAAAAATAAATT
TTAAAAGC
Found at i:1358248 original size:20 final size:19
Alignment explanation
Indices: 1358225--1358269 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1358215 TATTTTTTAT
* *
1358225 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
1358245 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
1358264 TATTTA
1 TATTTA
1358270 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:1358259 original size:26 final size:30
Alignment explanation
Indices: 1358220--1358275 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1358210 AATTATATTT
*
1358220 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1358247 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1358276 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:1358276 original size:3 final size:3
Alignment explanation
Indices: 1358268--1358370 Score: 154
Period size: 3 Copynumber: 34.0 Consensus size: 3
1358258 TTAATATATT
*
1358268 TAA TAA TAA TAG TAA TAA TAA T-A TAA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* *
1358313 TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
1358359 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1358371 ATGGATAAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.02
3 83 0.91
4 6 0.07
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1358818 original size:113 final size:113
Alignment explanation
Indices: 1358623--1359458 Score: 1407
Period size: 113 Copynumber: 7.4 Consensus size: 113
1358613 TCTTGATGAG
*
1358623 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG---TTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
* * * * * * *
1358684 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
1358733 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
* * * * * * *
1358797 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
1358846 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1358911 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
* *
1358959 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
1359024 GAAAAGCTGTTCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
1359072 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGGGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1359137 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
1359185 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1359250 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
1359298 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1359363 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
1359411 TTCTTCTCATTATGAA-TT-TTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1359459 GAACCTTCTC
Statistics
Matches: 701, Mismatches: 21, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
110 39 0.06
111 30 0.04
112 3 0.00
113 629 0.90
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
Found at i:1360250 original size:82 final size:81
Alignment explanation
Indices: 1360113--1360537 Score: 631
Period size: 82 Copynumber: 5.2 Consensus size: 81
1360103 TTTACTATGA
* * *
1360113 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTCT-AAACCAGGTCAGATAACTCAAAGAACACT
1360178 TCCAGAAGATGCTATTG
65 TCCAGAAGATGCTATTG
* * * * *
1360195 GCAAATTCATCTTCC-AATTCAATGCTTGATTCTATATAATCAGATCAAATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTG-TTCTCTA-AACCAGGTCAGATAACTCAAAGAACAC
1360259 TTCCAGAAGATGCTATTG
64 TTCCAGAAGATGCTATTG
* *
1360277 GCAAATTCATC-TCTAAATTCAATGATTGTTCTGCTAAACTAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCT-CTAAACCAGGTCAGATAACTCAAAGAACACT
1360341 TCCAGAAGATGCTATTG
65 TCCAGAAGATGCTATTG
* *
1360358 GTAAATTCATCTTCCAAATTCAATGACTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCT-CTAAACCAGGTCAGATAACTCAAAGAACACT
1360423 TCCAGAAGATGCTATTG
65 TCCAGAAGATGCTATTG
* *
1360440 GTAAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCT-CTAAACCAGGTCAGATAACTCAAAGAACAC
1360505 TTCCAGAAGATGCTATTG
64 TTCCAGAAGATGCTATTG
*
1360523 G-TAATTCATCTTCCA
1 GCAAATTCATCTTCCA
1360538 TTTAATGTTT
Statistics
Matches: 318, Mismatches: 19, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
81 69 0.22
82 195 0.61
83 54 0.17
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (81 bp):
GCAAATTCATCTTCCAAATTCAATGATTGTTCTCTAAACCAGGTCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATTG
Found at i:1360412 original size:163 final size:164
Alignment explanation
Indices: 1360113--1360537 Score: 664
Period size: 163 Copynumber: 2.6 Consensus size: 164
1360103 TTTACTATGA
* *
1360113 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGT-AAACCAGGTCAGATAACTCAAAGAACACT
* *
1360178 TCCAGAAGATGCTATTGGCAAATTCATCTTCC-AATTCAATGCTTGATTCTATATAATCAGATCA
65 TCCAGAAGATGCTATTGGTAAATTCATCTTCCAAATTCAATGCTTGATTCTATATAACCAGATCA
1360242 AATAACTCAAAGAACACTTCCAGAAGATGCTATTG
130 AATAACTCAAAGAACACTTCCAGAAGATGCTATTG
* *
1360277 GCAAATTCATC-TCTAAATTCAATGATTGTTCTGCTAAACTAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTG-TAAACCAGGTCAGATAACTCAAAGAACACT
* *
1360341 TCCAGAAGATGCTATTGGTAAATTCATCTTCCAAATTCAATGAC-TG-TTCTGCTA-AACCAGGT
65 TCCAGAAGATGCTATTGGTAAATTCATCTTCCAAATTCAATG-CTTGATTCT-ATATAACCAGAT
*
1360403 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
128 CAAATAACTCAAAGAACACTTCCAGAAGATGCTATTG
*
1360440 GTAAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCTG-TAAACCAGGTCAGATAACTCAAAGAACAC
1360505 TTCCAGAAGATGCTATTGGT-AATTCATCTTCCA
64 TTCCAGAAGATGCTATTGGTAAATTCATCTTCCA
1360538 TTTAATGTTT
Statistics
Matches: 242, Mismatches: 13, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
163 134 0.55
164 53 0.22
165 55 0.23
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (164 bp):
GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTAAACCAGGTCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATTGGTAAATTCATCTTCCAAATTCAATGCTTGATTCTATATAACCAGATCAA
ATAACTCAAAGAACACTTCCAGAAGATGCTATTG
Found at i:1368983 original size:20 final size:19
Alignment explanation
Indices: 1368960--1369004 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1368950 TATTTTTTAT
* *
1368960 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
1368980 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
1368999 TATTTA
1 TATTTA
1369005 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:1368994 original size:26 final size:30
Alignment explanation
Indices: 1368955--1369010 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1368945 AATTATATTT
*
1368955 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1368982 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1369011 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:1369011 original size:3 final size:3
Alignment explanation
Indices: 1369003--1369106 Score: 172
Period size: 3 Copynumber: 34.7 Consensus size: 3
1368993 TTAATATATT
*
1369003 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1369051 TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1369099 TAA TAA TA
1 TAA TAA TA
1369107 TGGATAAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1369773 original size:130 final size:132
Alignment explanation
Indices: 1369378--1369775 Score: 743
Period size: 131 Copynumber: 3.0 Consensus size: 132
1369368 ACTATACATT
1369378 AAAAATCTTCTCTTTCTCTCTCTTTTTGCTTCAAAAAGAAAAAAT-TACTAAAAAAA-ACTTGCT
1 AAAAATCTTCTCTTTCTCTCTCTTTTTGCTTCAAAAAG-AAAAATGTACTAAAAAAACACTTGCT
1369441 TTTTCTATGAAAGAAGCCAAAACTAATGTCAATGATCACTTTTACTTTATCGTTTCTTCATGAAG
65 TTTTCTATGAAAGAAGCCAAAACTAATGTCAATGATCACTTTTACTTTATCGTTTCTTCATGAAG
1369506 TAA
130 TAA
1369509 AAAAATCTTCTCTTTCTCTCTCTTTTTGCTTCAAAAAGAAAAATGTACT-AAAAAACACTTGCTT
1 AAAAATCTTCTCTTTCTCTCTCTTTTTGCTTCAAAAAGAAAAATGTACTAAAAAAACACTTGCTT
1369573 TTTCTATGAAAGAAGCCAAAACTAATGTCAATGATCACTTTTACTTTATCGTTTCTTCATGAAGT
66 TTTCTATGAAAGAAGCCAAAACTAATGTCAATGATCACTTTTACTTTATCGTTTCTTCATGAAGT
1369638 AA
131 AA
1369640 AAAAATCTTCTCTTTCTCTCTC-TTTTGCTTCAAAAAGAAAAATGTACTAAAAAAACACTTGC-T
1 AAAAATCTTCTCTTTCTCTCTCTTTTTGCTTCAAAAAGAAAAATGTACTAAAAAAACACTTGCTT
1369703 TTTCTATGAAAGAAGCCAAAACTAATGTCAATGGATCACTTTTACTTTATCGTTTCTTCATGAAG
66 TTTCTATGAAAGAAGCCAAAACTAATGTCAAT-GATCACTTTTACTTTATCGTTTCTTCATGAAG
1369768 TAA
130 TAA
1369771 AAAAA
1 AAAAA
1369776 AAAAAAAGGA
Statistics
Matches: 263, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
130 71 0.27
131 192 0.73
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (132 bp):
AAAAATCTTCTCTTTCTCTCTCTTTTTGCTTCAAAAAGAAAAATGTACTAAAAAAACACTTGCTT
TTTCTATGAAAGAAGCCAAAACTAATGTCAATGATCACTTTTACTTTATCGTTTCTTCATGAAGT
AA
Done.