Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000687.1 Hibiscus syriacus cultivar Beakdansim tig00001341_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: 88193
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:832 original size:3 final size:3
Alignment explanation
Indices: 824--892 Score: 120
Period size: 3 Copynumber: 22.7 Consensus size: 3
814 ATTTAATATT
*
824 TAA TAA TAA TAA TAA TAA TGA 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
872 TAA TAA TAA TAA TAA TTAA TA
1 TAA TAA TAA TAA TAA -TAA TA
893 TGGGTAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1720 original size:113 final size:113
Alignment explanation
Indices: 1105--2100 Score: 1558
Period size: 110 Copynumber: 8.9 Consensus size: 113
1095 TGATAGAGTA
* *
1105 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * *
1170 GAACTCTAC-CTGGCAA-GTTGATCCATCAAATGATGAATTCAAGCAAAA-G
63 GAAC-CTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
* *
1219 ATGAAC-AA--GTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
1280 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAATGATGATCCATCAA-ATGATGGATTCAGGTAAAAGG
1329 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
1394 CCTTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAATGATGATCCATCAA-ATGATGGATTCAGGTAAAAGG
1443 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
1508 CTTTCTCTGGGAAATGATGATCCATCAAATGATGAATTCAGGTAAAAGG
66 CCTTCTCT-GGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
*
1557 TTGAACAAATTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1619 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
66 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
*
1667 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1732 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
66 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
*
1780 TTGAACAAA---TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1842 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
66 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
1890 TTGAACAAATT-TT-TCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTT-TCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
1951 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
66 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
1999 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
2064 CTTTCTCTGGAAATGATGATCCATCAAATGATAGATT
66 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATT
2101 TGAATCTTTG
Statistics
Matches: 837, Mismatches: 27, Indels: 37
0.93 0.03 0.04
Matches are distributed among these distances:
106 2 0.00
107 26 0.03
108 11 0.01
109 83 0.10
110 220 0.26
111 96 0.11
112 21 0.03
113 155 0.19
114 207 0.25
115 16 0.02
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
Found at i:2989 original size:83 final size:83
Alignment explanation
Indices: 2815--3621 Score: 1495
Period size: 83 Copynumber: 9.8 Consensus size: 83
2805 GTAGTTCTTA
*
2815 CCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTA
2879 AATTCAATGATTTGTTCTG
65 AATTCAATGATTTGTTCTG
2898 CCAAACCAGATCAGATAAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTA
1 CCAAACCAGATCAGAT-AACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTA
2963 AATTCAATGA-TTGTTCTG
65 AATTCAATGATTTGTTCTG
2981 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
3046 ATTCAATGATTTGTTCTG
66 ATTCAATGATTTGTTCTG
3064 CCAAACCAGATCAGATAACTC-AAGAACACTTCCAGAAGATGCTATG-ACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
3127 ATTCAATGATTTGTTCTG
66 ATTCAATGATTTGTTCTG
3145 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-A-ACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
3208 ATTCAATGATTTGTTCTG
66 ATTCAATGATTTGTTCTG
3226 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
3291 ATTCAATGATTTGTTCTG
66 ATTCAATGATTTGTTCTG
*
3309 CCAAACCAGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
3374 ATTCAATGATTTGTTCT-
66 ATTCAATGATTTGTTCTG
3391 CTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTA
1 C-CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTA
3456 AATTCAATGATTTGTTCTG
65 AATTCAATGATTTGTTCTG
3475 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
3540 ATTCAATGATTTGTTCTG
66 ATTCAATGATTTGTTCTG
*
3558 CCAAACAAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTA
3622 GTTAATGTTT
Statistics
Matches: 711, Mismatches: 4, Indels: 18
0.97 0.01 0.02
Matches are distributed among these distances:
81 136 0.19
82 111 0.16
83 406 0.57
84 58 0.08
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
ATTCAATGATTTGTTCTG
Found at i:4764 original size:15 final size:13
Alignment explanation
Indices: 4742--4794 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 13
4732 CCTTGACCCC
4742 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
4755 ACTCTTTTTCTTTTT
1 -CT-TTTTTCTTTTT
*
4770 CTTTTTTTTTCTTTT
1 C-TTTTTTCT-TTTT
4785 CTTTTTTCTT
1 CTTTTTTCTT
4795 CATTTTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 1 0.03
14 16 0.47
15 17 0.50
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
CTTTTTTCTTTTT
Found at i:4791 original size:22 final size:22
Alignment explanation
Indices: 4742--4805 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 22
4732 CCTTGACCCC
**
4742 CTTTTTTC-TTTTTACTCTTTTT
1 CTTTTTTCTTTTTTTTTC-TTTT
4764 CTTTTTCT-TTT-TTTTTCTTTT
1 CTTTTT-TCTTTTTTTTTCTTTT
*
4785 CTTTTTTCTTCATTTTTTCTT
1 CTTTTTTCTT-TTTTTTTCTT
4806 CAAGCATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
20 1 0.03
21 12 0.35
22 10 0.29
23 11 0.32
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (22 bp):
CTTTTTTCTTTTTTTTTCTTTT
Found at i:15392 original size:15 final size:13
Alignment explanation
Indices: 15360--15397 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
15350 TTTGACAGAA
15360 AAAT-AAATAATG
1 AAATAAAATAATG
15372 AAATAAAATAATTG
1 AAATAAAATAA-TG
15386 CAAATAAAATAA
1 -AAATAAAATAA
15398 AACATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:15491 original size:6 final size:7
Alignment explanation
Indices: 15472--15496 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
15462 TAAATATATA
15472 AATTTTT
1 AATTTTT
15479 AATTTTT
1 AATTTTT
15486 AATTTTT
1 AATTTTT
15493 AATT
1 AATT
15497 AATAGAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:16894 original size:3 final size:3
Alignment explanation
Indices: 16886--16945 Score: 95
Period size: 3 Copynumber: 20.3 Consensus size: 3
16876 ATATTAATTA
* *
16886 ATT ATT ATT ATT ATT ATA ATT ATT ATT ATT ATT ATT ATT ATC A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16933 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
16946 AATATATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 1 0.02
3 51 0.98
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:19708 original size:32 final size:32
Alignment explanation
Indices: 19662--19724 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
19652 TGCATGTTGC
*
19662 ATCATTTAAGATAATAATGTGGTATATGTCAT
1 ATCATTTAAGATAATAATGTGATATATGTCAT
* * *
19694 ATCATTTGATATAATAATGTGATATGTGTCA
1 ATCATTTAAGATAATAATGTGATATATGTCA
19725 CAATGTCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (32 bp):
ATCATTTAAGATAATAATGTGATATATGTCAT
Found at i:19855 original size:265 final size:270
Alignment explanation
Indices: 19378--20189 Score: 926
Period size: 265 Copynumber: 3.0 Consensus size: 270
19368 ATCCAAGGTA
* * *
19378 ATGATATAGTACATGTTACGTCATCTAAAATAATTATGTGGTATGTGTCATATCATATGATATAA
1 ATGA-ATAG-ACATGTTGCGTCATCTAAGATAATAATGTGGTATGTGTCATATCATATGATATAA
* * * * * * *
19443 TAATGTAACATGTGTTACAATGTCCAAAATAAGGACATGACATATTATGGAGTACAAAAATTAAG
64 TAATGTGATATGTGTCACAATGTCCAAAATAATGACGTGACATATTATGGAGTAAAAAAATAAAG
19508 TCGAATTTGAGTATGTTTCTTGTTTGTTTAAAGATTGTAAACTATAATCAACACTTATTTATGTA
129 TCGAATTTGAGTATGTTTCTTGTTTGTTTAAAGATTGTAAACTATAATCAACACTTATTTATGTA
* * *
19573 CTCATTGAGAAGTCAAAATCGGATAAACACCTTTCATTTTTGTGCAGTGAGTGCACAATCACTTT
194 CTCATTGAGAGGTCAAAATCAGATACACACCTTTCATTTTTGTGCAG-GAGTGCACAATCACTTT
19638 GAATGA-TG-AT-
258 GAATGATTGAATG
* * * *
19648 ATG-AT-G-CATGTTGCATCATTTAAGATAATAATGTGGTATATGTCATATCATTTGATATAATA
1 ATGAATAGACATGTTGCGTCATCTAAGATAATAATGTGGTATGTGTCATATCATATGATATAATA
* * * *
19710 ATGTGATATGTGTCACAATGTCCAAAATAATAATGTGACATATTATGGAATAAAAAAATAAAGTT
66 ATGTGATATGTGTCACAATGTCCAAAATAATGACGTGACATATTATGGAGTAAAAAAATAAAGTC
* * * * * *
19775 GAATTTGAGTATGTTTATTATGTGTTTAGAGATTGCAAACTATAATCAACACTTATTTATGTGCT
131 GAATTTGAGTATGTTTCTTGTTTGTTTAAAGATTGTAAACTATAATCAACACTTATTTATGTACT
* * * * *
19840 TATTAAGAGGTCAAAACCTG-TGACACACCTTT-ATTTTTTTGTGCGGGGAGTGCACAATCACTT
196 CATTGAGAGGTCAAAATCAGAT-ACACACCTTTCA--TTTTTGTGC-AGGAGTGCACAATCACTT
19903 TGAATGATGTTTCGCTTTGAATG
257 TGAATGA---------TTGAATG
* * * *
19926 ATGATATAGTACATGTTGCGTC-TCCTAAGATAATGATGTGGTATGTGTCATCTCATCTAATATA
1 ATGA-ATAG-ACATGTTGCGTCAT-CTAAGATAATAATGTGGTATGTGTCATATCATATGATATA
* * ** *
19990 ATAATATGATATGTGTCACAATGTCCAAAATAATGACGTGGCATAAAATGGAGTACAAAAATTAA
63 ATAATGTGATATGTGTCACAATGTCCAAAATAATGACGTGACATATTATGGAGTA-AAAAAATAA
* * * * *
20055 A-TCGAATTTTAGTATGTCTCTTGTTTATTTAAAGATTGTAAACTATAATCAACCCTTATTTGTG
127 AGTCGAATTTGAGTATGTTTCTTGTTTGTTTAAAGATTGTAAACTATAATCAACACTTATTTATG
* * *
20119 TACTCATTGAGAGGTCAAAATCAGAGACACACCTTTCATTTTTGTG-TGGGGTGCACAATCACTT
192 TACTCATTGAGAGGTCAAAATCAGATACACACCTTTCATTTTTGTGCAGGAGTGCACAATCACTT
20183 TGAATGA
257 TGAATGA
20190 CGTTTCGCTC
Statistics
Matches: 452, Mismatches: 65, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
264 2 0.00
265 186 0.41
266 32 0.07
267 2 0.00
268 2 0.00
270 3 0.01
276 2 0.00
277 2 0.00
278 3 0.01
280 25 0.06
281 1 0.00
282 9 0.02
283 173 0.38
284 10 0.02
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (270 bp):
ATGAATAGACATGTTGCGTCATCTAAGATAATAATGTGGTATGTGTCATATCATATGATATAATA
ATGTGATATGTGTCACAATGTCCAAAATAATGACGTGACATATTATGGAGTAAAAAAATAAAGTC
GAATTTGAGTATGTTTCTTGTTTGTTTAAAGATTGTAAACTATAATCAACACTTATTTATGTACT
CATTGAGAGGTCAAAATCAGATACACACCTTTCATTTTTGTGCAGGAGTGCACAATCACTTTGAA
TGATTGAATG
Found at i:20150 original size:283 final size:280
Alignment explanation
Indices: 19634--20198 Score: 724
Period size: 283 Copynumber: 2.0 Consensus size: 280
19624 TGCACAATCA
* *
19634 CTTTGAATGATGATATGATGCATGTTGCATCATTTAAGATAATAATGTGGTATATGTCATATCAT
1 CTTTGAATGATGATATGATACATGTTGCATCATCTAAGATAATAATGTGGTATATGTCATATCAT
* * * * **
19699 TTGATATAATAATGTGATATGTGTCACAATGTCCAAAATAATAATGTGACATATTATGGAATAAA
66 CTAATATAATAATATGATATGTGTCACAATGTCCAAAATAATAACGTGACATAAAATGGAATAAA
* * * *
19764 AAAATAAAGTTGAATTTGAGTATGTTTATTATGTGTTTAGAGATTGCAAACTATAATCAACACTT
131 AAAATAAAGTCGAATTTGAGTATGTCTATTATGTATTTAAAGATTGCAAACTATAATCAACACTT
* * * *
19829 ATTTATGTGCTTATTAAGAGGTCAAAACCTGTGACACACCTTT-ATTTTTTTGTGCGGGGAGTGC
196 ATTTATGTACTCATTAAGAGGTCAAAACCAGAGACACACCTTTCA--TTTTTGTG-GGGG-GTGC
*
19893 ACAATCACTTTGAATGATGTTTCG
257 ACAATCACTTTGAATGACGTTTCG
* * * *
19917 CTTTGAATGATGATAT-AGTACATGTTGCGTC-TCCTAAGATAATGATGTGGTATGTGTCATCTC
1 CTTTGAATGATGATATGA-TACATGTTGCATCAT-CTAAGATAATAATGTGGTATATGTCATATC
* * *
19980 ATCTAATATAATAATATGATATGTGTCACAATGTCCAAAATAATGACGTGGCATAAAATGGAGTA
64 ATCTAATATAATAATATGATATGTGTCACAATGTCCAAAATAATAACGTGACATAAAATGGAATA
* * * * * * *
20045 CAAAAATTAAA-TCGAATTTTAGTATGTCTCTTGTTTATTTAAAGATTGTAAACTATAATCAACC
129 -AAAAAATAAAGTCGAATTTGAGTATGTCTATTATGTATTTAAAGATTGCAAACTATAATCAACA
* * * *
20109 CTTATTTGTGTACTCATTGAGAGGTCAAAATCAGAGACACACCTTTCATTTTTGTGTGGGGTGCA
193 CTTATTTATGTACTCATTAAGAGGTCAAAACCAGAGACACACCTTTCATTTTTGTGGGGGGTGCA
20174 CAATCACTTTGAATGACGTTTCG
258 CAATCACTTTGAATGACGTTTCG
20197 CT
1 CT
20199 CTAGTTAGAA
Statistics
Matches: 243, Mismatches: 35, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
280 29 0.12
281 3 0.01
282 10 0.04
283 191 0.79
284 10 0.04
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (280 bp):
CTTTGAATGATGATATGATACATGTTGCATCATCTAAGATAATAATGTGGTATATGTCATATCAT
CTAATATAATAATATGATATGTGTCACAATGTCCAAAATAATAACGTGACATAAAATGGAATAAA
AAAATAAAGTCGAATTTGAGTATGTCTATTATGTATTTAAAGATTGCAAACTATAATCAACACTT
ATTTATGTACTCATTAAGAGGTCAAAACCAGAGACACACCTTTCATTTTTGTGGGGGGTGCACAA
TCACTTTGAATGACGTTTCG
Found at i:20983 original size:19 final size:18
Alignment explanation
Indices: 20946--20985 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20936 CTTTTTTTTA
*
20946 TTTTTATTATAGTATTAT
1 TTTTTATTATAGTACTAT
*
20964 TTTTTATTATATTTACTAT
1 TTTTTATTATA-GTACTAT
20983 TTT
1 TTT
20986 AATAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTTATTATAGTACTAT
Found at i:23361 original size:2 final size:2
Alignment explanation
Indices: 23349--23380 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
23339 TTGTTTGGGT
23349 TA TA T- TA 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 TA TA TA TA T
23381 TTCTTTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:23409 original size:3 final size:3
Alignment explanation
Indices: 23401--23442 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
23391 ATTTGTTTAT
* *
23401 TTA TTA TTA TTA TTA TTA TTA ATA TT- TTT TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23443 TTTTCAGGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:23415 original size:9 final size:8
Alignment explanation
Indices: 23400--23444 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
23390 TATTTGTTTA
23400 TTTATTAT
1 TTTATTAT
23408 TATTATTAT
1 T-TTATTAT
*
23417 TATTAATAT
1 T-TTATTAT
*
23426 TTTTTTAT
1 TTTATTAT
23434 TTTATTAT
1 TTTATTAT
23442 TTT
1 TTT
23445 TTCAGGCCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 16 0.50
9 16 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTATTAT
Found at i:23444 original size:15 final size:15
Alignment explanation
Indices: 23389--23446 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 15
23379 ATTTCTTTGT
23389 TTATTTGTTTA-TTTA
1 TTATTT-TTTATTTTA
23404 TTATTATTATTATTATTA
1 TTATT-TT-TTATT-TTA
*
23422 ATATTTTTTTATTTTA
1 TTA-TTTTTTATTTTA
23438 TTATTTTTT
1 TTATTTTTT
23447 CAGGCCCCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
15 12 0.33
16 9 0.25
17 6 0.17
18 7 0.19
19 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (15 bp):
TTATTTTTTATTTTA
Found at i:26550 original size:110 final size:110
Alignment explanation
Indices: 26406--27156 Score: 1047
Period size: 110 Copynumber: 6.9 Consensus size: 110
26396 GTGGTTGCTT
** * *
26406 AACTTCACAGCGAAGGGGCGACTGAAGGTCAACAAATAACTTTTTAGTTTCATTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
* * * *
26471 TCAACTTCACATCAAAGGATATTAGACTCTAGACAACACAAGCTC
66 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
* * * * *
26516 AACTTCACTGTGAAGGGGCCACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAATCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
*
26581 TCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTC
66 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
* * * *
26626 AACTTCACAGTGAAGGGGCGACTGACTGTCAACAAACAACTTTTTAGTTTCATTTAGAGCCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
26691 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
66 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
* *
26736 AACTTCACAGCGAAGGGGC-AGCTGGCTGTCAACAAACAACTTTCCAG--T--TTCAGAGTCAAT
1 AACTTCACAGCGAAGGGGCGA-CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAAT
* *
26796 TTCAACTTCA-AGGCGAAGGATATTGGCCTCGAAACAACACAAGCTC
65 TTCAACTTCACA-GCGAAGGATATTGGACTCGAGACAACACAAGCTC
* *
26842 AACTTCACAGCGAAGGGACAACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
* * *
26907 TCAACTTCACAACGAATGATATTGGACTCGAGACAACACACGCTC
66 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
* * * *
26952 AACTTCACAGCAAAAGGGCGACTGACGGTCAACAAACAACTTTTCAGTTTCATTCAGAGCCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
**
27017 TCAACTTCACAATGAAGGATATTATTGGACTCGAGACAACACAAGCTC
66 TCAACTTCACAGCGAAGG--A-TATTGGACTCGAGACAACACAAGCTC
* *
27065 AACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTCCA--TT--TTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
*
27126 TCAACTTCAC-GACGAAGGATATTGGCCTCGA
66 TCAACTTCACAG-CGAAGGATATTGGACTCGA
27157 AATAGCACAA
Statistics
Matches: 573, Mismatches: 56, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
105 1 0.00
106 105 0.18
107 2 0.00
108 2 0.00
109 28 0.05
110 365 0.64
111 3 0.01
112 1 0.00
113 66 0.12
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (110 bp):
AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
Found at i:26908 original size:216 final size:218
Alignment explanation
Indices: 26406--27156 Score: 1018
Period size: 216 Copynumber: 3.4 Consensus size: 218
26396 GTGGTTGCTT
** * *
26406 AACTTCACAGCGAAGGGGCGACTGAAGGTCAACAAATAACTTTTTAGTTTCATTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
* * * * * *
26471 TCAACTTCACATCAAAGGATATTAGACTCTAGACAACACAAGCTCAACTTCACTGTGAAGGGGCC
66 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGG-C
* *
26536 A-CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAATCAATTTCAACTTCACAGCGAAGGA
130 AGCTGACTGTCAACAAACAACTTTTCAG-TT-ATTCAGAGTCAATTTCAACTTCACAGCGAAGGA
*
26600 TATTGAACTCGAGACAACACAAGCTC
193 TATTGGACTCGAGACAACACAAGCTC
* * * *
26626 AACTTCACAGTGAAGGGGCGACTGACTGTCAACAAACAACTTTTTAGTTTCATTTAGAGCCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
26691 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCA
66 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCA
* *
26756 GCTGGCTGTCAACAAACAACTTTCCAG-T-TTCAGAGTCAATTTCAACTTCA-AGGCGAAGGATA
131 GCTGACTGTCAACAAACAACTTTTCAGTTATTCAGAGTCAATTTCAACTTCACA-GCGAAGGATA
* *
26818 TTGGCCTCGAAACAACACAAGCTC
195 TTGGACTCGAGACAACACAAGCTC
* *
26842 AACTTCACAGCGAAGGGACAACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
* * * * *
26907 TCAACTTCACAACGAATGATATTGGACTCGAGACAACACACGCTCAACTTCACAGCAAAAGGGC-
66 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCA
* * **
26971 GACTGACGGTCAACAAACAACTTTTCAGTTTCATTCAGAGCCAATTTCAACTTCACAATGAAGGA
131 G-CTGACTGTCAACAAACAACTTTTCAG-TT-ATTCAGAGTCAATTTCAACTTCACAGCGAAGG-
27036 TATTATTGGACTCGAGACAACACAAGCTC
192 -A-TATTGGACTCGAGACAACACAAGCTC
* *
27065 AACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTCCA--TT--TTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
*
27126 TCAACTTCAC-GACGAAGGATATTGGCCTCGA
66 TCAACTTCACAG-CGAAGGATATTGGACTCGA
27157 AATAGCACAA
Statistics
Matches: 474, Mismatches: 45, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
215 2 0.00
216 192 0.41
218 2 0.00
219 42 0.09
220 166 0.35
221 3 0.01
222 1 0.00
223 66 0.14
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (218 bp):
AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCA
GCTGACTGTCAACAAACAACTTTTCAGTTATTCAGAGTCAATTTCAACTTCACAGCGAAGGATAT
TGGACTCGAGACAACACAAGCTC
Found at i:27520 original size:84 final size:84
Alignment explanation
Indices: 27273--28041 Score: 600
Period size: 84 Copynumber: 9.2 Consensus size: 84
27263 AATCGTGCCC
* * *
27273 ACCAAATG-CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
1 ACCAAA-GACCTTCGAGTTCGACTACACTCACCTCCAAGGCACATCATTTGCAGTATAACTTAAG
* **
27337 TCAAGAAGGGTTATCTGCCA
65 TCGAGAAGGGTTATCTGCTG
* * * * * * *
27357 ACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACACTCA-CCTCCAAGGCACATCATTTGCAGTATAACTTAAG
* *
27422 GCTAGAAGGGTTATCTG-TG
65 TCGAGAAGGGTTATCTGCTG
* * * * *
27441 ACCAAAAGACCTTTGAGTTTGACTACACTCACCTCCAAGTCATATCATTTGCAGCATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACACTCACCTCCAAGGCACATCATTTGCAGTATAACTTAAG
**
27506 TCGAGAAGGGTTATCTGCCA
65 TCGAGAAGGGTTATCTGCTG
* * * * * * *
27526 ACCAAAGACATTCGAGTTCGATTACGCTCAGCTCCAAGGCATATCATTTACAGTATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACACTCACCTCCAAGGCACATCATTTGCAGTATAACTTAAGT
*
27591 CGAGAAGGGCTA--T-CTG
66 CGAGAAGGGTTATCTGCTG
* * * * * * * *
27607 -CCAAAGATCC-TCGAGTTCGATTGCACTCAACTTCGAGGGCACATCATTTACAATATAACTCAA
1 ACCAAAGA-CCTTCGAGTTCGACTACACTC-ACCTCCAAGGCACATCATTTGCAGTATAACTTAA
* * *
27670 GGCTAGAAGGGTTATC-GTTG
64 GTCGAGAAGGGTTATCTGCTG
* * * * *
27690 ACCAAAAAAACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAA
1 ACC--AAAGACCTTCGAGTTCGACTACACTCACCTCCAAGGCACATCATTTGCAGTATAACTTAA
* **
27755 GTCGATAAGGGTTATCTGCCA
64 GTCGAGAAGGGTTATCTGCTG
** * * * * *
27776 ACCAAAGACCTTCGAGTTCGACTATGCTCAACTCTAAGACACATCATTTGTAGTATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACACTCACCTCCAAGGCACATCATTTGCAGTATAACTTAAGT
* *
27841 CGAGAAGGGCTA--T-ATG
66 CGAGAAGGGTTATCTGCTG
* * * * * * * * * *
27857 -CCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGAACATCATTTACGGCATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACACTC-ACCTCCAAGGCACATCATTTGCAGTATAACTTAAG
* * * *
27921 GCTAGAAGGGTTATATG-TC
65 TCGAGAAGGGTTATCTGCTG
* * * * * * *
27940 AACAAAGACCTTGGAGTTCGACTCCACTCAGCTCAAAGGCACCATCATTTGCAGTATAGCTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACACTCACCTCCAAGGCA-CATCATTTGCAGTATAACTTAAG
* *
28005 GCAAGAAGGGTTA--T-CTG
65 TCGAGAAGGGTTATCTGCTG
*
28022 -CCAAAGAACTTCGAGTTCGA
1 ACCAAAGACCTTCGAGTTCGA
28042 TTCCATTCGG
Statistics
Matches: 534, Mismatches: 130, Indels: 45
0.75 0.18 0.06
Matches are distributed among these distances:
80 47 0.09
81 89 0.17
82 4 0.01
83 12 0.02
84 251 0.47
85 108 0.20
86 23 0.04
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (84 bp):
ACCAAAGACCTTCGAGTTCGACTACACTCACCTCCAAGGCACATCATTTGCAGTATAACTTAAGT
CGAGAAGGGTTATCTGCTG
Found at i:27824 original size:250 final size:249
Alignment explanation
Indices: 27268--28025 Score: 1047
Period size: 250 Copynumber: 3.0 Consensus size: 249
27258 AAGGGAATCG
* * *
27268 TGCCCACCAAATG-CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
1 TGCCAACCAAA-GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGC
* * *
27332 TTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGG
65 TTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGG
* *
27397 CACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAAGACCTTTGAGTTT
126 CACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCT-TGACCAAAAAGACCTTCGAGTTC
* *
27461 GACTACACTCACCTCCAAGTCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
190 GACTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* * * *
27521 TGCCAACCAAAGACATTCGAGTTCGATTACGCTCAGCTCCAAGGCATATCATTTACAGTATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCT
* *
27586 TAAGTCGAGAAGGGCTATCTGCCAAAGATCCTCGAGTTCGATTGCACTCAACTTCGAGGGCACAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACAT
* *
27651 CATTTACAATATAACTCAAGGCTAGAAGGGTTATCGTTGACCAAAAAAACCTTCGAGTTCGACTA
131 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATC-TTGACCAAAAAGACCTTCGAGTTCGACTA
* *
27716 CGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGATAAGGGTTATC
195 CACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* * * * *
27771 TGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAACTCTAAGACACATCATTTGTAGTATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCT
* *
27836 TAAGTCGAGAAGGGCTATATGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGAACAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACAT
* * * * * *
27901 CATTTACGGCATAACTCAAGGCTAGAAGGGTTAT-ATG-TCAACAAAGACCTTGGAGTTCGACTC
131 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTTGACCAA-AAAGACCTTCGAGTTCGACTA
* * * * * * *
27964 CACTCAGCTCAAAGGCACCATCATTTGCAGTATAGCTCAAGGCAAGAAGGGTTATC
195 CACTCAGCTCCAAGGCA-TATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
28020 TGCCAA
1 TGCCAA
28026 AGAACTTCGA
Statistics
Matches: 450, Mismatches: 50, Indels: 14
0.88 0.10 0.03
Matches are distributed among these distances:
247 3 0.01
248 35 0.08
249 117 0.26
250 219 0.49
252 1 0.00
253 75 0.17
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (249 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCT
TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACAT
CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTTGACCAAAAAGACCTTCGAGTTCGACTAC
ACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
Found at i:27959 original size:334 final size:328
Alignment explanation
Indices: 27284--28041 Score: 772
Period size: 334 Copynumber: 2.3 Consensus size: 328
27274 CCAAATGCCT
* * * * * * *
27284 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTT
1 TCGAGTTCGACTCCACTCAACTCAAAGGCACATCATTTGCAGTATAACTCAAGGCAAGAAGGGTT
* * * * * *
27349 ATCTGCCAACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGTAT
66 ATCTGCCAA--AAAAACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTACAGCAT
* ** * * *
27414 AACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTTGACTACACTCACCTCCAA
129 AACTCAAGGCGAGAAGGGTTATCTGCAACCAAAAGACCTTCGAGTTCGACTACACTCAACTCCAA
* * * * *
27479 GTCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACATTCGAGTT
194 GACACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATATG---ACCAAAGACACTCGAGTT
* * * * * * * * *
27544 CGATTACGCTCAGCTCCAAGGCATATCATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTGCC
256 CGATTACACTCAACTCCAAGGAACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGCC
27609 AAAGATCC
321 AAAGATCC
* * * * * * *
27617 TCGAGTTCGATTGCACTCAACTTCGAGGGCACATCATTTACAATATAACTCAAGGCTAGAAGGGT
1 TCGAGTTCGACTCCACTCAAC-TCAAAGGCACATCATTTGCAGTATAACTCAAGGCAAGAAGGGT
* * *
27682 TATCGTTGACCAAAAAAACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGC
65 TATC--TG-CCAAAAAAACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTACAGC
* * * **
27746 ATAACTTAAGTCGATAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTATGCTCAACTC
127 ATAACTCAAGGCGAGAAGGGTTATCTG-CAACCAAAAGACCTTCGAGTTCGACTACACTCAACTC
* * * * *
27810 TAAGACACATCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATATG-CCAAAGACCCTCGAGTT
191 CAAGACACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATATGACCAAAGACACTCGAGTT
* * * * *
27874 CGATTACACTCAACTTCGAGGGAACATCATTTACGGCATAACTCAAGGCTAGAAGGGTTATATGT
256 CGATTACACTCAAC-TCCAAGGAACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATATG-
27939 CAACAAAGA-CC
319 C--CAAAGATCC
* * *
27950 TTGGAGTTCGACTCCACTCAGCTCAAAGGCACCATCATTTGCAGTATAGCTCAAGGCAAGAAGGG
1 -TCGAGTTCGACTCCACTCAACTCAAAGGCA-CATCATTTGCAGTATAACTCAAGGCAAGAAGGG
*
28015 TTATCTGCC-AAAGAA-CTTCGAGTTCGA
64 TTATCTGCCAAAAAAACCTTCGAGTTCGA
28042 TTCCATTCGG
Statistics
Matches: 347, Mismatches: 67, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
329 12 0.03
330 32 0.09
331 39 0.11
332 3 0.01
333 26 0.07
334 201 0.58
335 28 0.08
336 2 0.01
337 4 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (328 bp):
TCGAGTTCGACTCCACTCAACTCAAAGGCACATCATTTGCAGTATAACTCAAGGCAAGAAGGGTT
ATCTGCCAAAAAAACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTACAGCATAA
CTCAAGGCGAGAAGGGTTATCTGCAACCAAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGA
CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATATGACCAAAGACACTCGAGTTCGATT
ACACTCAACTCCAAGGAACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGCCAAAGA
TCC
Found at i:28405 original size:16 final size:15
Alignment explanation
Indices: 28386--28455 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
28376 ATAAAAACAT
28386 TTTATTATATTATATA
1 TTTATTATATTAT-TA
28402 TTTATT-TA-T-TTA
1 TTTATTATATTATTA
28414 TTTATT-TATTATTA
1 TTTATTATATTATTA
*
28428 -TTATTATTAATATT-
1 TTTATTA-TATTATTA
*
28442 TTTATTTTATTATT
1 TTTATTATATTATT
28456 TTGTGGGCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 10 0.22
13 7 0.15
14 10 0.22
15 13 0.28
16 6 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTATATTATTA
Found at i:28406 original size:8 final size:7
Alignment explanation
Indices: 28386--28456 Score: 56
Period size: 8 Copynumber: 9.4 Consensus size: 7
28376 ATAAAAACAT
28386 TTTATTA
1 TTTATTA
28393 TATTATATA
1 T-TTAT-TA
28402 TTTATTTA
1 TTTA-TTA
28410 TTTATTTA
1 TTTA-TTA
28418 TTTATTA
1 TTTATTA
28425 -TTATTA
1 TTTATTA
28431 -TTATTAA
1 TTTATT-A
*
28438 TATTTTTA
1 T-TTATTA
28446 TTTTATTA
1 -TTTATTA
28454 TTT
1 TTT
28457 TGTGGGCCTC
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
6 11 0.20
7 8 0.15
8 27 0.49
9 9 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTATTA
Found at i:28409 original size:4 final size:4
Alignment explanation
Indices: 28386--28423 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
28376 ATAAAAACAT
*
28386 TTTA -TTA TATTA TATA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TT
28424 ATTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:28427 original size:3 final size:3
Alignment explanation
Indices: 28387--28455 Score: 52
Period size: 3 Copynumber: 21.7 Consensus size: 3
28377 TAAAAACATT
28387 TTA TTA -TA TTA TATA TTTA TTTA TTTA TTTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA -TTA -TTA -TTA -TTA -TTA TTA TTA TTA TTA
* *
28434 TTA ATA TTT TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
28456 TTGTGGGCCT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.07
3 33 0.57
4 20 0.34
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:28546 original size:33 final size:33
Alignment explanation
Indices: 28504--28572 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
28494 TTCAGAAAAT
*
28504 AAACCAACGTATTTGAGTCCTATTGAAACACTA
1 AAACCAACGTATTTGAGTCCTATTAAAACACTA
28537 AAACCAACGTATTTGAGTCCTATTAAAACACTA
1 AAACCAACGTATTTGAGTCCTATTAAAACACTA
28570 AAA
1 AAA
28573 TCGAAGCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.26
Consensus pattern (33 bp):
AAACCAACGTATTTGAGTCCTATTAAAACACTA
Found at i:36640 original size:2 final size:2
Alignment explanation
Indices: 36633--36661 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36623 TGAACTAAAT
36633 TA TA 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 TA TA T
36662 TCACTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38433 original size:13 final size:13
Alignment explanation
Indices: 38400--38444 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
38390 GTAGAAATTA
38400 AATTAAT-ATAAT
1 AATTAATAATAAT
38412 AAATATAATAATAAT
1 -AAT-TAATAATAAT
*
38427 AATTAATAATATT
1 AATTAATAATAAT
38440 AATTA
1 AATTA
38445 TTAAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 17 0.59
14 7 0.24
15 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:38460 original size:14 final size:14
Alignment explanation
Indices: 38443--38486 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
38433 TAATATTAAT
38443 TATTAAATAAAATA
1 TATTAAATAAAATA
38457 TATTGAAATATAAATA
1 TATT-AAATA-AAATA
* *
38473 TAGTAATTAAAATA
1 TATTAAATAAAATA
38487 GGTGTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 9 0.35
15 9 0.35
16 8 0.31
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (14 bp):
TATTAAATAAAATA
Found at i:40558 original size:3 final size:3
Alignment explanation
Indices: 40552--40642 Score: 141
Period size: 3 Copynumber: 31.0 Consensus size: 3
40542 AAAATTTAAT
40552 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
40600 TTC TTC TTC TTC TTC TTC TTC -TC CTC ATC -CC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
40643 CTCATCCCAA
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
2 3 0.04
3 80 0.96
ACGTcount: A:0.01, C:0.36, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:40656 original size:19 final size:19
Alignment explanation
Indices: 40615--40656 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
40605 CTTCTTCTTC
**
40615 TTCTTCTCCTCATCCCTTC
1 TTCTTCTCCTCATCCCTAA
40634 TTCTTCTTCCTCATCCC-AA
1 TTCTTC-TCCTCATCCCTAA
40653 TTCT
1 TTCT
40657 CTGTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.48
Consensus pattern (19 bp):
TTCTTCTCCTCATCCCTAA
Found at i:58330 original size:31 final size:31
Alignment explanation
Indices: 58258--58330 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
58248 GTTAACCTTC
* * *
58258 AGTGCTCACATTTTAATTAAAACGAAACGAA
1 AGTGATCAAATTTTAATTAAAACAAAACGAA
* * * *
58289 ACTGACCAAATTTTAATTAAAATAAAATGAA
1 AGTGATCAAATTTTAATTAAAACAAAACGAA
58320 AGTGATCAAAT
1 AGTGATCAAAT
58331 ATTATATTTT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.27
Consensus pattern (31 bp):
AGTGATCAAATTTTAATTAAAACAAAACGAA
Found at i:61476 original size:20 final size:19
Alignment explanation
Indices: 61437--61478 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
61427 TTTATTCGAT
61437 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
61456 ATTAAAACAATTAATACATA
1 ATTAAAA-AATAAATAAATA
61476 ATT
1 ATT
61479 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:61589 original size:120 final size:119
Alignment explanation
Indices: 61357--61582 Score: 296
Period size: 120 Copynumber: 1.9 Consensus size: 119
61347 ATTTATATAT
* * *
61357 ATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCTTAAGACA
1 ATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCTTAAGACA
*
61422 GCTCTTTTATTCGATATTAAAAAATAAATAAATAATTAAAACAATTAATACATA
66 GCTCTTTTATTCAATATTAAAAAATAAATAAATAATTAAAACAATTAATACATA
** * * **
61476 ATTTATAAAATAGGATATTTATTTATTTAAAAATATTAGAAAATGGACATCCAGTTGTTTTAAGA
1 ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTGCCTTAAGA
* * *
61541 CTGCTC-TTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAACA
64 CAGCTCTTTTATTCAATATTAAAAAATAAATAAATAATTAAAACA
61583 GGATTAAAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
118 9 0.10
119 25 0.27
120 37 0.40
121 21 0.23
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (119 bp):
ATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCTTAAGACA
GCTCTTTTATTCAATATTAAAAAATAAATAAATAATTAAAACAATTAATACATA
Found at i:62971 original size:3 final size:3
Alignment explanation
Indices: 62963--63040 Score: 104
Period size: 3 Copynumber: 25.7 Consensus size: 3
62953 ATATTTATTA
*
62963 AAT AAT AAT AAT AAT -AT ATAT AAT ATAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT
**
63009 AAT TTT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
63041 AATGAAATGA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 58 0.88
4 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:63251 original size:76 final size:76
Alignment explanation
Indices: 63159--63332 Score: 312
Period size: 76 Copynumber: 2.3 Consensus size: 76
63149 TCTTTTGAGT
* * *
63159 TGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGTTTTT
1 TGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
63224 TGGAAACATCA
66 TGGAAACATCA
*
63235 TGCACTGTAGGACTTACAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
1 TGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
63300 TGGAAACATCA
66 TGGAAACATCA
63311 TGCACTGTAGGACTTACAGATG
1 TGCACTGTAGGACTTACAGATG
63333 TGGGAAATAG
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 93 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (76 bp):
TGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
TGGAAACATCA
Found at i:63583 original size:76 final size:76
Alignment explanation
Indices: 63457--63667 Score: 388
Period size: 76 Copynumber: 2.8 Consensus size: 76
63447 TCAAAATAAC
63457 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
*
63522 AAGGCTTTGAA
66 AAGACTTTGAA
* *
63533 AACATCAAAAAGCTCCCGAAGGCTTTTTGGATACATCTTGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
63598 AAGACTTTGAA
66 AAGACTTTGAA
63609 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTA-GACTTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
63668 TGGGAAATAG
Statistics
Matches: 130, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
75 12 0.09
76 118 0.91
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGACTTTGAA
Found at i:64438 original size:22 final size:22
Alignment explanation
Indices: 64361--64435 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
64351 TAAAGCTTTT
64361 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
*
64383 ATCTTTAAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
*
64405 ATCTTTGAAGAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
64427 ATCTTTGAA
1 ATCTTTGAA
64436 GAGTGTAGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:64932 original size:54 final size:53
Alignment explanation
Indices: 64802--64956 Score: 201
Period size: 54 Copynumber: 3.0 Consensus size: 53
64792 AGAATAACTG
* * * *
64802 GTTCGTAAAACATTTGACAACACATGCAT-CATCTCATGTGGTTTCTGCTCAGA
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTC-TGTGGTTTCTACTCAGA
*
64855 --T-GTAAAACACTTGACAACACATTCATCCTTTTCTGTGGTTTCTACTCAGA
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTACTCAGA
* *
64905 TGTTCGTAAAGCATTTGACAACACATTCATCCTTTTCTGTGGCTTCTACTCA
1 -GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTACTCA
64957 AATTTCTCAA
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
50 39 0.44
51 5 0.06
53 1 0.01
54 44 0.49
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.35
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTACTCAGA
Found at i:67226 original size:114 final size:114
Alignment explanation
Indices: 67026--67246 Score: 334
Period size: 114 Copynumber: 1.9 Consensus size: 114
67016 GATCATGCAG
* * * * *
67026 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAAA
1 TTCATCTTTCAAATCCAATGATTAGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAAA
*
67091 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATAAGCAAA
66 ACACCTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATAAGCAAA
* * *
67140 TTCATCTTTCAAATCCAATGATTAGTTTTAGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTAGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAAA
* * *
67205 ACACCTCTAGAAGATGTTATTGGGTCTCCTTATTTCTACTAT
66 ACACCTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTAT
67247 GAGAACGTGG
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 95 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTAGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAAA
ACACCTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATAAGCAAA
Found at i:69412 original size:7 final size:7
Alignment explanation
Indices: 69400--69507 Score: 76
Period size: 7 Copynumber: 14.4 Consensus size: 7
69390 CAATTCTCCT
69400 TTTTTTC
1 TTTTTTC
69407 TTTTTTTCC
1 -TTTTTT-C
69416 TTTTTT-
1 TTTTTTC
*
69422 TCTTTT-
1 TTTTTTC
69428 TTTTTTC
1 TTTTTTC
*
69435 ATTTTTCC
1 -TTTTTTC
*
69443 TTTTTCATA
1 TTTTT--TC
69452 TTTTTTC
1 TTTTTTC
*
69459 TTTTCTC
1 TTTTTTC
69466 TTTTTCTC
1 TTTTT-TC
*
69474 ATTTTTC
1 TTTTTTC
69481 TTTTTTCATC
1 -TTTTT--TC
69491 TTTTTTC
1 TTTTTTC
69498 TTTTTTC
1 TTTTTTC
69505 TTT
1 TTT
69508 CTTTGTTGGA
Statistics
Matches: 81, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
6 10 0.12
7 30 0.37
8 28 0.35
9 11 0.14
10 2 0.02
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:69439 original size:17 final size:16
Alignment explanation
Indices: 69398--69507 Score: 77
Period size: 17 Copynumber: 6.8 Consensus size: 16
69388 TTCAATTCTC
69398 CTTTTTTTCTTTTTTT
1 CTTTTTTTCTTTTTTT
69414 CCTTTTTTTCTTTTTTT
1 -CTTTTTTTCTTTTTTT
* *
69431 TTTCATTTTTC-CTTTTT
1 CTT--TTTTTCTTTTTTT
*
69448 CATATTTTTTC-TTTTCT
1 C-T-TTTTTTCTTTTTTT
* *
69465 CTTTTTCTC-ATTTTT
1 CTTTTTTTCTTTTTTT
69480 C-TTTTTTCATCTTTTTT
1 CTTTTTTTC-T-TTTTTT
69497 C-TTTTTTCTTT
1 CTTTTTTTCTTT
69508 CTTTGTTGGA
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
14 6 0.08
15 13 0.17
16 4 0.05
17 45 0.59
18 7 0.09
19 1 0.01
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTTTTTTCTTTTTTT
Found at i:69455 original size:27 final size:27
Alignment explanation
Indices: 69399--69507 Score: 91
Period size: 28 Copynumber: 4.0 Consensus size: 27
69389 TCAATTCTCC
*
69399 TTTTTTTCTTTTTTTCCTTTTTTTCTTT
1 TTTTTTTCTATTTTTCC-TTTTTTCTTT
*
69427 TTTTTTTC-ATTTTTCCTTTTTCATATTT
1 TTTTTTTCTATTTTTCCTTTTT--TCTTT
* *
69455 TTTCTTTTCTCTTTTTCTCATTTTTC-TT
1 TTT-TTTTCTATTTTTC-CTTTTTTCTTT
**
69483 TTTTCATCT-TTTTT-CTTTTTTCTTT
1 TTTTTTTCTATTTTTCCTTTTTTCTTT
69508 CTTTGTTGGA
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
24 7 0.10
25 2 0.03
26 10 0.15
27 11 0.16
28 20 0.30
29 6 0.09
30 6 0.09
31 5 0.07
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTTTTCTATTTTTCCTTTTTTCTTT
Found at i:69486 original size:39 final size:36
Alignment explanation
Indices: 69401--69507 Score: 128
Period size: 39 Copynumber: 2.9 Consensus size: 36
69391 AATTCTCCTT
*
69401 TTTTTCTTTTTTTCCTTTTTTTC-TTTT-TTTTTTCA
1 TTTTTC-TTTTTTCATTTTTTTCTTTTTCTTTTTTCA
*
69436 TTTTTCCTTTTTCATATTTTTTCTTTTCTCTTTTTCTCA
1 TTTTTCTTTTTTCAT-TTTTTTCTTTT-TCTTTTT-TCA
69475 TTTTTCTTTTTTCATCTTTTTTCTTTTTTCTTT
1 TTTTTCTTTTTTCAT-TTTTTTC-TTTTTCTTT
69508 CTTTGTTGGA
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
34 7 0.11
35 13 0.21
36 3 0.05
37 1 0.02
38 5 0.08
39 29 0.47
40 4 0.06
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (36 bp):
TTTTTCTTTTTTCATTTTTTTCTTTTTCTTTTTTCA
Found at i:72268 original size:20 final size:20
Alignment explanation
Indices: 72239--72287 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
72229 TTATGCAAAG
*
72239 ATGCAAATACAAACATGAAA
1 ATGCAAATACAAACATAAAA
* *
72259 ATGTAAATACAAACGTAAAA
1 ATGCAAATACAAACATAAAA
72279 ATGCAAATA
1 ATGCAAATA
72288 TGCAAAATGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.10, T:0.18
Consensus pattern (20 bp):
ATGCAAATACAAACATAAAA
Found at i:72312 original size:35 final size:34
Alignment explanation
Indices: 72243--72312 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
72233 GCAAAGATGC
*
72243 AAATACAAACATGAAAATGTAAATACAAACGTAA
1 AAATACAAACATGAAAATGCAAATACAAACGTAA
* * * *
72277 AAATGCAAATATGCAAAATGCAAATGCAAATGTAA
1 AAATACAAACATG-AAAATGCAAATACAAACGTAA
72312 A
1 A
72313 TATATGAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 11 0.37
35 19 0.63
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (34 bp):
AAATACAAACATGAAAATGCAAATACAAACGTAA
Found at i:72390 original size:7 final size:8
Alignment explanation
Indices: 72372--72410 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
72362 ATAAAAGTAT
72372 AAATGCAA
1 AAATGCAA
72380 AAATG-AA
1 AAATGCAA
72387 AAATGCAA
1 AAATGCAA
*
72395 AGATGC-A
1 AAATGCAA
72402 AAATGCAA
1 AAATGCAA
72410 A
1 A
72411 TGTATGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (8 bp):
AAATGCAA
Found at i:72390 original size:15 final size:15
Alignment explanation
Indices: 72372--72410 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
72362 ATAAAAGTAT
72372 AAATGCAAAAATGAA
1 AAATGCAAAAATGAA
* *
72387 AAATGCAAAGATGCA
1 AAATGCAAAAATGAA
72402 AAATGCAAA
1 AAATGCAAA
72411 TGTATGTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (15 bp):
AAATGCAAAAATGAA
Found at i:75314 original size:27 final size:28
Alignment explanation
Indices: 75259--75314 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
75249 ATTTCAAAAT
75259 TATAATTATGAAAAAATATATTAATTTA
1 TATAATTATGAAAAAATATATTAATTTA
75287 TATATATTAT-AAATAAATAT-TT-ATTTA
1 TATA-ATTATGAAA-AAATATATTAATTTA
75314 T
1 T
75315 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 6 0.23
28 9 0.35
29 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TATAATTATGAAAAAATATATTAATTTA
Found at i:76893 original size:3 final size:3
Alignment explanation
Indices: 76885--76945 Score: 86
Period size: 3 Copynumber: 19.7 Consensus size: 3
76875 ATATTTATTA
**
76885 AAT AAT AAT ATAT ATAT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
76932 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
76946 AACGAAATGA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 46 0.87
4 7 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:79014 original size:32 final size:32
Alignment explanation
Indices: 78973--79034 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
78963 ACAATATTGA
*
78973 ATTGATTGATTTGTGATTCGAGTCAATATCAC
1 ATTGATTGATTTGTGAGTCGAGTCAATATCAC
* * * *
79005 ATTGGTTGATTTTTTAGTCGGGTCAATATC
1 ATTGATTGATTTGTGAGTCGAGTCAATATC
79035 GAATCATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (32 bp):
ATTGATTGATTTGTGAGTCGAGTCAATATCAC
Found at i:80793 original size:24 final size:24
Alignment explanation
Indices: 80761--80806 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
80751 TCTTCCAGAT
80761 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
80785 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
80807 CATGTCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:81387 original size:30 final size:30
Alignment explanation
Indices: 81348--81413 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
81338 CATTCACAAC
* * * *
81348 TTTTCCAAAATTACCGAATTGTTCCCCCAAT
1 TTTTCAAAAATTACAGAA-TGGTCCCCAAAT
81379 TTTTCAAAAATTACAGAATGGTCCCCAAAT
1 TTTTCAAAAATTACAGAATGGTCCCCAAAT
81409 TTTTC
1 TTTTC
81414 TAAGGCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (30 bp):
TTTTCAAAAATTACAGAATGGTCCCCAAAT
Found at i:81473 original size:20 final size:20
Alignment explanation
Indices: 81435--81473 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
81425 GAATATTTCC
*
81435 TATATTATTTACATCCTTTA
1 TATATTATTTACATACTTTA
* *
81455 TATATTTTTTCCATACTTT
1 TATATTATTTACATACTTT
81474 TTCTTACTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATTATTTACATACTTTA
Found at i:82149 original size:29 final size:30
Alignment explanation
Indices: 82107--82165 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
82097 AATTACCATT
82107 AAACCAAGACACCT-ACCCTTATCATCTTC
1 AAACCAAGACACCTAACCCTTATCATCTTC
82136 AAACCAAGACACCTAACCCTTATCATCTTC
1 AAACCAAGACACCTAACCCTTATCATCTTC
82166 CATAAGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.36, C:0.37, G:0.03, T:0.24
Consensus pattern (30 bp):
AAACCAAGACACCTAACCCTTATCATCTTC
Done.