Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 23
Found at i:4342464 original size:36 final size:37
Alignment explanation
Indices: 4342380--4342511 Score: 119
Period size: 37 Copynumber: 3.6 Consensus size: 37
4342370 GTCTTCACCA
* * * **
4342380 AAGAGTAGTGAAGCAAATCCATTTTGAGCTTTCA-CTA
1 AAGAGTAGTGAAGCAAA-CCATCTTAAGCCTTCATCGG
4342417 AAGAGTAGTGAAGCAAACCATCTTAAGCCTTCATC-G
1 AAGAGTAGTGAAGCAAACCATCTTAAGCCTTCATCGG
* * * *
4342453 AAGAGTAGTGAAGCATATCCTTTTTAAACCTTC-TCGG
1 AAGAGTAGTGAAGCA-AACCATCTTAAGCCTTCATCGG
*
4342490 AAGAGT-GTTGGAGCAAACCATC
1 AAGAGTAG-TGAAGCAAACCATC
4342512 AGACTATCAG
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
36 35 0.44
37 44 0.56
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (37 bp):
AAGAGTAGTGAAGCAAACCATCTTAAGCCTTCATCGG
Found at i:4342937 original size:54 final size:54
Alignment explanation
Indices: 4342872--4343117 Score: 438
Period size: 54 Copynumber: 4.6 Consensus size: 54
4342862 GTAGTAAAGC
4342872 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
4342926 AGAAGGAGATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCAGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
4342980 AGAAGAAGATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
4343034 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCATA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
4343088 AGAAGAAGATGTTCGAGTTCTATACTCCCT
1 AGAAGAAGATGTTCGAGTTCCATACTCCCT
4343118 GAACGAATAG
Statistics
Matches: 184, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 184 1.00
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
Found at i:4343175 original size:55 final size:54
Alignment explanation
Indices: 4342984--4343297 Score: 248
Period size: 54 Copynumber: 5.9 Consensus size: 54
4342974 CCAGTAAGAA
* * * * ** **
4342984 GAAGATGTTTGAGTTCC-ATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTAAGAA
1 GAAGATGTTCGAG-TCCTATACTCCCTGAAAG-AATAGGGAGCGGACCCGTTTGTT
* * * * ** **
4343038 GAAGATGTTCGAGTTCC-ATACTCCCT-AGAGAAAGAGGGAGCGAACCCATAAGAA
1 GAAGATGTTCGAG-TCCTATACTCCCTGAAAG-AATAGGGAGCGGACCCGTTTGTT
* * *
4343092 GAAGATGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCATTTGTT
1 GAAGATGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTTGTT
* * * *
4343146 GAAGATTGTTCGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGTTTATT
1 GAAGA-TGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTTGTT
* * *
4343201 GAAGA---TCGAGTCTTATACTCTCTGAAGGAAT-GGGAGCGGACCCGTTTGTT
1 GAAGATGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTTGTT
* * * *
4343251 GAAGATTTTTTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACC
1 GAAGA-TGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC
4343298 GTCATTCGAA
Statistics
Matches: 227, Mismatches: 25, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
50 22 0.10
51 24 0.11
53 2 0.01
54 119 0.52
55 60 0.26
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (54 bp):
GAAGATGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTTGTT
Found at i:4343266 original size:105 final size:106
Alignment explanation
Indices: 4343100--4343292 Score: 291
Period size: 105 Copynumber: 1.8 Consensus size: 106
4343090 AAGAAGATGT
4343100 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCATTTGTTGAAGATTGTTCGAGTCCTA
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCATTTGTTGAAGATTGTTCGAGTCCTA
* *
4343165 TACTCTCTGAATGAATAGGGAGCGGACACGTTTATTGAAGA
66 TACTCCCTGAAAGAATAGGGAGCGGACACGTTTATTGAAGA
* * * * * *
4343206 TCGAG-TCTTATACTCTCTGAAGGAAT-GGGAGCGGACCCGTTTGTTGAAGATTTTTTGAGTCTT
1 TCGAGTTC-TATACTCCCTGAACGAATAGGGAGCGGACCCATTTGTTGAAGATTGTTCGAGTCCT
4343269 ATACTCCCTGAAAGAATAGGGAGC
65 ATACTCCCTGAAAGAATAGGGAGC
4343293 AGACCGTCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
105 57 0.73
106 21 0.27
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (106 bp):
TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCATTTGTTGAAGATTGTTCGAGTCCTA
TACTCCCTGAAAGAATAGGGAGCGGACACGTTTATTGAAGA
Found at i:4343309 original size:54 final size:55
Alignment explanation
Indices: 4343099--4343322 Score: 200
Period size: 55 Copynumber: 4.2 Consensus size: 55
4343089 GAAGAAGATG
* *
4343099 TTCGAGT-TCTATACTCCCTGAACGAATAGGGAGCGGACC--CATTTGTTGAAGATTG
1 TTCGAGTCT-TATACTCCCTGAAAGAATAGGGAGCGGACCGTCA--TGTTGAAGATTT
* * * * *
4343154 TTCGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGT-TTATTGAAGA---
1 TTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGAC-CGTCATGTTGAAGATTT
* * *
4343206 -TCGAGTCTTATACTCTCTGAAGGAAT-GGGAGCGGACCCGT-TTGTTGAAGATTT
1 TTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGA-CCGTCATGTTGAAGATTT
* * *
4343259 TTTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACCGTCAT-TCGAAGATTT
1 TTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGACCGTCATGTTGAAGATTT
*
4343313 TTCAAGTCTT
1 TTCGAGTCTT
4343323 GCTTATCCTG
Statistics
Matches: 142, Mismatches: 16, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
50 21 0.15
51 25 0.18
54 44 0.31
55 51 0.36
56 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (55 bp):
TTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGACCGTCATGTTGAAGATTT
Found at i:4352265 original size:19 final size:19
Alignment explanation
Indices: 4352241--4352279 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4352231 CATATTCGCA
4352241 TTGCGATAGTTC-AAGTTCG
1 TTGCGATAG-TCGAAGTTCG
4352260 TTGCGATAGTCGAAGTTCG
1 TTGCGATAGTCGAAGTTCG
4352279 T
1 T
4352280 GTTGCGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCGAAGTTCG
Found at i:4352304 original size:21 final size:21
Alignment explanation
Indices: 4352280--4352589 Score: 331
Period size: 21 Copynumber: 14.4 Consensus size: 21
4352270 CGAAGTTCGT
4352280 GTTGCGATTTATTCCAAATTC
1 GTTGCGATTTATTCCAAATTC
*
4352301 GTTGCGATTTATTCCAAGTTCGC
1 GTTGCGATTTATTCCAAATT--C
* *
4352324 GTTGCGATTTATTTCAAGTTCGC
1 GTTGCGATTTATTCCAAATT--C
*
4352347 GTTACGATTTATTCCAAATTC
1 GTTGCGATTTATTCCAAATTC
* * *
4352368 GTTGCGA--TAGTCGAAGTTCGC
1 GTTGCGATTTATTCCAAATT--C
*
4352389 GTTGCGATTTATTTCAAATTC
1 GTTGCGATTTATTCCAAATTC
4352410 GTTGCGATTTATTCCAAATTC
1 GTTGCGATTTATTCCAAATTC
4352431 GTTGCGATTTATTCCAAATTC
1 GTTGCGATTTATTCCAAATTC
* *
4352452 GTTGCGATTTATTCTAAGTTCGC
1 GTTGCGATTTATTCCAAATT--C
*
4352475 GTTGCGATTTATTCCAAATTT
1 GTTGCGATTTATTCCAAATTC
*
4352496 GTTGCGATTTATTCCAAGTTCGC
1 GTTGCGATTTATTCCAAATT--C
*
4352519 GTTGCGATTTATTTCAAATTC
1 GTTGCGATTTATTCCAAATTC
* * *
4352540 GTTGCGA--TAGTCGAAGTTCAC
1 GTTGCGATTTATTCCAAATT--C
*
4352561 GTTGCGATTTATTCCAAGTTC
1 GTTGCGATTTATTCCAAATTC
4352582 GTTGCGAT
1 GTTGCGAT
4352590 AGTCCAAAAT
Statistics
Matches: 246, Mismatches: 29, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
19 15 0.06
21 138 0.56
23 93 0.38
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (21 bp):
GTTGCGATTTATTCCAAATTC
Found at i:4352415 original size:130 final size:129
Alignment explanation
Indices: 4352280--4352589 Score: 466
Period size: 130 Copynumber: 2.4 Consensus size: 129
4352270 CGAAGTTCGT
4352280 GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATT-TCAAGTT
1 GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTT--CGTTGCGATTTATTCT-AAGTT
*
4352344 CGCGTTACGATTTATTCCAAATTCGTTGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTTCAAAT
63 CGCGTTACGATTTATTCCAAATTCGTTGCGATTAGTCCAAGTTCGCGTTGCGATTTATTTCAAAT
4352408 TC
128 TC
*
4352410 GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCTAAGTTCGC
1 GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCTAAGTTCGC
* * *
4352475 GTTGCGATTTATTCCAAATTTGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTTCAAATTC
66 GTTACGATTTATTCCAAATTCGTTGCGA-TTAGTCCAAGTTCGCGTTGCGATTTATTTCAAATTC
* * *
4352540 GTTGCGA--TAGTCGAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGCGAT
1 GTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAGTTCGTTGCGAT
4352590 AGTCCAAAAT
Statistics
Matches: 166, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
128 56 0.34
129 1 0.01
130 109 0.66
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (129 bp):
GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCTAAGTTCGC
GTTACGATTTATTCCAAATTCGTTGCGATTAGTCCAAGTTCGCGTTGCGATTTATTTCAAATTC
Found at i:4352542 original size:172 final size:171
Alignment explanation
Indices: 4352280--4352589 Score: 496
Period size: 172 Copynumber: 1.8 Consensus size: 171
4352270 CGAAGTTCGT
* *
4352280 GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTTCAAGTTC
1 GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTC-CGTTGCGATTTATTCCAAGTTC
* *
4352345 GCGTTACGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAATTC
65 GCGTTACGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTC
4352410 GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTC
130 GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTC
* * *
4352452 GTTGCGATTTATTCTAAGTTCGCGTTGCGATTTATTCCAAATT-TGTTGCGATTTATTCCAAGTT
1 GTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATTCCGTTGCGATTTATTCCAAGTT
* * *
4352516 CGCGTTGCGATTTATTTCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAGTT
64 CGCGTTACGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATT
4352581 CGTTGCGAT
129 CGTTGCGAT
4352590 AGTCCAAAAT
Statistics
Matches: 126, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
172 106 0.84
174 20 0.16
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (171 bp):
GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCCGTTGCGATTTATTCCAAGTTCG
CGTTACGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCG
TTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTC
Found at i:4352593 original size:42 final size:43
Alignment explanation
Indices: 4352280--4352589 Score: 380
Period size: 42 Copynumber: 7.2 Consensus size: 43
4352270 CGAAGTTCGT
* *
4352280 GTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAGTTCGC
1 GTTGCGA-TTATTCCAAGTTCGCGTTGCGATTTATTCCAAATT--C
* *
4352324 GTTGCGATTTATTTCAAGTTCGCGTTACGATTTATTCCAAATTC
1 GTTGCGA-TTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
* * *
4352368 GTTGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTTCAAATTC
1 GTTGCGATTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
*
4352410 GTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATTC
1 GTTGCGA-TTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
* *
4352452 GTTGCGATTTATTCTAAGTTCGCGTTGCGATTTATTCCAAATTT
1 GTTGCGA-TTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
*
4352496 GTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTTCAAATTC
1 GTTGCGA-TTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
* * * *
4352540 GTTGCGA-TAGTCGAAGTTCACGTTGCGATTTATTCCAAGTTC
1 GTTGCGATTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
4352582 GTTGCGAT
1 GTTGCGAT
4352590 AGTCCAAAAT
Statistics
Matches: 235, Mismatches: 24, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
42 113 0.48
44 103 0.44
46 19 0.08
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (43 bp):
GTTGCGATTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
Found at i:4352977 original size:45 final size:45
Alignment explanation
Indices: 4352922--4353015 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
4352912 TTGATTGTAG
4352922 ATTGACATTTAATTATGACATATTTAATCGTATAATACTAATGCA
1 ATTGACATTTAATTATGACATATTTAATCGTATAATACTAATGCA
* *
4352967 ATTGATATTTAATTATGACATATTTAATCGTATAATATTAATGCA
1 ATTGACATTTAATTATGACATATTTAATCGTATAATACTAATGCA
4353012 ATTG
1 ATTG
4353016 GTTAAAATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.43
Consensus pattern (45 bp):
ATTGACATTTAATTATGACATATTTAATCGTATAATACTAATGCA
Found at i:4353240 original size:12 final size:11
Alignment explanation
Indices: 4353210--4353243 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
4353200 GCCGTCTATC
4353210 TCGGGTCG-GG
1 TCGGGTCGTGG
4353220 TCGGGTCGTGG
1 TCGGGTCGTGG
4353231 TCGTGGTCGTGG
1 TCG-GGTCGTGG
4353243 T
1 T
4353244 AATACGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:4353391 original size:21 final size:21
Alignment explanation
Indices: 4353361--4353428 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
4353351 AATATGTAAA
4353361 TCGCAATGCGATAGTCCAAGT
1 TCGCAATGCGATAGTCCAAGT
* * * *
4353382 TCGCATTGCGATTGT-CGACT
1 TCGCAATGCGATAGTCCAAGT
4353402 ATCGCAATGCGATAGTCCAAGT
1 -TCGCAATGCGATAGTCCAAGT
4353424 TCGCA
1 TCGCA
4353429 TTATCGCATT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.08
21 31 0.84
22 3 0.08
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGATAGTCCAAGT
Found at i:4353538 original size:62 final size:62
Alignment explanation
Indices: 4353472--4353629 Score: 282
Period size: 62 Copynumber: 2.5 Consensus size: 62
4353462 GATTTACATA
* *
4353472 TTCGCATTGCGATAGT-CGACTATCGCATTGCGATTTACATATTCGTATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAGT-TCGCATTGCGATTTACATATTCGTATTGCGATAGTCCAAG
4353534 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGTATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGTATTGCGATAGTCCAAG
4353596 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGAT
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGAT
4353630 AGTCGAAGTT
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
62 90 0.97
63 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGTATTGCGATAGTCCAAG
Found at i:4353584 original size:41 final size:42
Alignment explanation
Indices: 4353432--4353649 Score: 200
Period size: 41 Copynumber: 5.3 Consensus size: 42
4353422 GTTCGCATTA
* * * *
4353432 TCGCATTGCGATAGT-CGACTATCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTACAAGT-TCGCATTGCGATAGTCCA-AGT
* * * *
4353473 TCGCATTGCGATAGT-CGACTATCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTACAAGT-TCGCATTGCGATAGTCCA-AGT
* *
4353514 TCGTATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAGT
* *
4353556 TCGCATTGCGAT-TTACATA-TTCGTATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTACA-AGTTCGCATTGCGATAGTCCAAGT
* *
4353597 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAGT
*
4353639 TCGCGTTGCGA
1 TCGCATTGCGA
4353650 ATCTGGAAAC
Statistics
Matches: 157, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
41 105 0.67
42 52 0.33
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (42 bp):
TCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAGT
Found at i:4353638 original size:21 final size:21
Alignment explanation
Indices: 4353432--4353649 Score: 209
Period size: 21 Copynumber: 10.5 Consensus size: 21
4353422 GTTCGCATTA
* *
4353432 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
4353452 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
* *
4353473 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
4353493 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
*
4353514 TCGTATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
4353535 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
4353556 TCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTCCA-AGT
*
4353576 TCGTATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
4353597 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
4353618 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
4353639 TCGCGTTGCGA
1 TCGCATTGCGA
4353650 ATCTGGAAAC
Statistics
Matches: 167, Mismatches: 18, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.01
20 44 0.26
21 120 0.72
22 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:4353925 original size:20 final size:20
Alignment explanation
Indices: 4353897--4353936 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4353887 TTGGTAATAT
* * *
4353897 TGAGCAAAAATTATGAATTA
1 TGAGAAAAAAATATAAATTA
4353917 TGAGAAAAAAATATAAATTA
1 TGAGAAAAAAATATAAATTA
4353937 GATGTAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (20 bp):
TGAGAAAAAAATATAAATTA
Found at i:4354001 original size:2 final size:2
Alignment explanation
Indices: 4353984--4354024 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
4353974 ATAATCTTTT
*
4353984 TA TA TA T- TA AA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4354024 T
1 T
4354025 GAAATATCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4356991 original size:2 final size:2
Alignment explanation
Indices: 4356980--4357025 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
4356970 AAAAGAAAAA
*
4356980 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4357022 AT AT
1 AT AT
4357026 CAAAGTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4357531 original size:18 final size:17
Alignment explanation
Indices: 4357510--4357552 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
4357500 ATATATACAT
4357510 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
4357528 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
4357545 ATAA-AATA
1 ATAATAATA
4357553 TTCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:4357987 original size:37 final size:36
Alignment explanation
Indices: 4357944--4358045 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 36
4357934 TTAGTAGAAC
4357944 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
4357981 GT-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 -TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
4358015 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
4358046 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:4358809 original size:105 final size:106
Alignment explanation
Indices: 4358593--4359048 Score: 657
Period size: 105 Copynumber: 4.3 Consensus size: 106
4358583 CATTGTTCCA
* * * ** *
4358593 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
4358658 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * *
4358699 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* * *
4358763 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
4358804 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
4358868 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
*
4358908 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 -AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
4358973 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
4359015 AGTGCCACGATATCCTCCGTTGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
4359049 CGCGGATGGC
Statistics
Matches: 319, Mismatches: 24, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
104 1 0.00
105 196 0.61
106 95 0.30
107 4 0.01
109 23 0.07
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
Found at i:4358945 original size:210 final size:212
Alignment explanation
Indices: 4358593--4359048 Score: 666
Period size: 211 Copynumber: 2.1 Consensus size: 212
4358583 CATTGTTCCA
* *
4358593 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAACCGGGAAATTGTTTGTTGACAAC
* *
4358658 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTCGTGAAG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTCGTGAAG
* * * *
4358723 TTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTT
*
4358787 GAACTTGCATTGTCTGG
196 GAACTTGCATTGTCTCG
* * ** * *
4358804 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACAAG
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAACCGGGAAATTGTTTGTTGACAAC
* *
4358868 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAAGTCCAATATCCTTCGTTGTGAA
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG-AGTCCAATATCCTTCGTCGTGAA
*
4358932 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
130 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGT
**
4358997 TGAACTTGTGTTGTCTCG
195 TGAACTTGCATTGTCTCG
*
4359015 AGTGCCACGATATCCTCCGTTGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTCCGTTGTGAAGTTGAAAT
4359049 CGCGGATGGC
Statistics
Matches: 217, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
209 1 0.00
210 93 0.43
211 98 0.45
212 3 0.01
214 22 0.10
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (212 bp):
AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAACCGGGAAATTGTTTGTTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTCGTGAAG
TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTT
GAACTTGCATTGTCTCG
Found at i:4360028 original size:21 final size:22
Alignment explanation
Indices: 4359977--4360030 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4359967 TTGTGTTTGG
*
4359977 TCAAATGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
4359999 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
4360021 TC-AAGGTTTG
1 TCAAAGGTTTG
4360031 ATGGGGTAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:4360689 original size:13 final size:12
Alignment explanation
Indices: 4360646--4360690 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
4360636 TTCTTTTTGA
*
4360646 TTTTTGTTCTTTC
1 TTTTTTTTC-TTC
4360659 TTTTGTTTTCTTC
1 TTTT-TTTTCTTC
*
4360672 TTTTTTTGCTTC
1 TTTTTTTTCTTC
4360684 TTTTTTT
1 TTTTTTT
4360691 ACCCTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 14 0.48
13 11 0.38
14 4 0.14
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:4364820 original size:37 final size:36
Alignment explanation
Indices: 4364777--4364878 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 36
4364767 TTAGTAGAAC
4364777 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
4364814 GT-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 -TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
4364848 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
4364879 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:4366623 original size:6 final size:6
Alignment explanation
Indices: 4366612--4366686 Score: 96
Period size: 6 Copynumber: 12.2 Consensus size: 6
4366602 GACACGTATT
* * * *
4366612 ACCACG ACCACG ACCACACG ACCACG ACCTCG ACCTCG ACCTCG ACCTCG
1 ACCACG ACCACG A-C-CACG ACCACG ACCACG ACCACG ACCACG ACCACG
4366662 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
4366687 GCCGAGCCGA
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
6 58 0.89
7 2 0.03
8 5 0.08
ACGTcount: A:0.29, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:4366633 original size:14 final size:14
Alignment explanation
Indices: 4366614--4366640 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4366604 CACGTATTAC
4366614 CACGACCACGACCA
1 CACGACCACGACCA
4366628 CACGACCACGACC
1 CACGACCACGACC
4366641 TCGACCTCGA
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:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (14 bp):
CACGACCACGACCA
Found at i:4366694 original size:5 final size:5
Alignment explanation
Indices: 4366684--4366732 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
4366674 ACCACGACCA
* * * *
4366684 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
4366733 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:4372255 original size:21 final size:22
Alignment explanation
Indices: 4372226--4372275 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
4372216 TCAGCTGTTA
*
4372226 TAACTCCCGAAATTATATCATG
1 TAACTCCCGAAATTAAATCATG
* **
4372248 TAAC-CCCGGAATTAAATCAAA
1 TAACTCCCGAAATTAAATCATG
4372269 TAACTCC
1 TAACTCC
4372276 TGTAACTCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (22 bp):
TAACTCCCGAAATTAAATCATG
Found at i:4372564 original size:6 final size:6
Alignment explanation
Indices: 4372553--4372607 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
4372543 GACACGTATT
* *
4372553 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
4372601 ACCACG A
1 ACCACG A
4372608 GCCGAGCCGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:4372615 original size:5 final size:5
Alignment explanation
Indices: 4372605--4372652 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
4372595 ACCACGACCA
* * * *
4372605 CGAGC CGAGC CGAGC CGAGC CGTGC CGTG- CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
4372653 ACGGACGGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
4 4 0.10
5 35 0.90
ACGTcount: A:0.17, C:0.35, G:0.42, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:4373396 original size:13 final size:13
Alignment explanation
Indices: 4373359--4373398 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
4373349 TCGATATTGA
4373359 AAAATAAATA-TT
1 AAAATAAATATTT
*
4373371 AAAATAATTTATTT
1 AAAATAA-ATATTT
4373385 AAAATAAATATTT
1 AAAATAAATATTT
4373398 A
1 A
4373399 TTTATTGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:4374812 original size:3 final size:3
Alignment explanation
Indices: 4374804--4374866 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
4374794 AATATATATT
* *
4374804 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4374852 AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
4374867 ATCAATATGG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4376300 original size:20 final size:20
Alignment explanation
Indices: 4376275--4376367 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
4376265 TTTTCCCAAT
4376275 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
4376295 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
4376315 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
4376336 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
4376357 TCGCAATGCGA
1 TCGCAATGCGA
4376368 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:4376317 original size:41 final size:41
Alignment explanation
Indices: 4376272--4376367 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
4376262 CGATTTTCCC
4376272 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
4376313 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
4376354 AAATCGCAATGCGA
1 AATTCGCAATGCGA
4376368 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:4376321 original size:21 final size:20
Alignment explanation
Indices: 4376275--4376367 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
4376265 TTTTCCCAAT
*
4376275 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
4376295 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
4376315 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
4376336 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
4376357 TCGCAATGCGA
1 TCGCAATGCGA
4376368 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:4376380 original size:41 final size:41
Alignment explanation
Indices: 4376294--4376428 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
4376284 GAATAAGTAA
* * *
4376294 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
4376335 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
4376376 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
4376417 TTCGCAACGCGA
1 ATCGCAACGCGA
4376429 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:4376381 original size:20 final size:20
Alignment explanation
Indices: 4376356--4376449 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
4376346 AATTGGGAAA
*
4376356 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
4376376 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
4376397 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
4376417 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
4376437 TTCGCAACGCGAT
1 ATCGCAACGCGAT
4376450 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:4377004 original size:19 final size:19
Alignment explanation
Indices: 4376966--4377032 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
4376956 TTCGAGAATG
*
4376966 AAAATCGCAAAGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
4376986 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
4377005 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
4377024 AAAATCGCA
1 AAAATCGCA
4377033 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:4377050 original size:19 final size:19
Alignment explanation
Indices: 4377028--4377097 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
4377018 GAAACCAAAA
*
4377028 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4377047 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
4377066 TCGCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4377085 TCGCGTTGCGATT
1 TCGCGTTGCGATT
4377098 CTCTCGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4377108 original size:38 final size:38
Alignment explanation
Indices: 4377028--4377135 Score: 118
Period size: 38 Copynumber: 3.0 Consensus size: 38
4377018 GAAACCAAAA
* * *
4377028 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
*
4377066 TCGCGTTGTGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
* **
4377101 T--CGTCGCGATAGTCATTTCGCGTTGCGATTCTCAT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCAT
4377136 TGCGATAGTC
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
33 28 0.46
35 1 0.02
38 32 0.52
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
Found at i:4377144 original size:31 final size:32
Alignment explanation
Indices: 4377080--4377167 Score: 119
Period size: 33 Copynumber: 2.8 Consensus size: 32
4377070 GTTGTGATTT
4377080 TCATTTCGCGTTGCGATTCTC-TCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCAT--TCGCGATAG
4377113 TCATTTCGCGTTGCGATTCTCATT-GCGATAG
1 TCATTTCGCGTTGCGATTCTCATTCGCGATAG
*
4377144 TCATTTCCGCGTTGCAATT-TCATT
1 TCATTT-CGCGTTGCGATTCTCATT
4377168 ATCTCGTTGC
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
31 18 0.35
32 12 0.23
33 21 0.40
34 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (32 bp):
TCATTTCGCGTTGCGATTCTCATTCGCGATAG
Found at i:4380664 original size:14 final size:14
Alignment explanation
Indices: 4380645--4380680 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4380635 ATTGTTTAAT
4380645 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
4380659 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
4380673 TGATTTGT
1 TGATTTGT
4380681 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:4381399 original size:17 final size:18
Alignment explanation
Indices: 4381339--4381401 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
4381329 GAAATGAAAA
4381339 TCGCATTGCGATTTC---
1 TCGCATTGCGATTTCATT
4381354 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
4381371 TCGCATTGCGATTTCATT
1 TCGCATTGCGATTTCATT
4381389 TCGCA-TGCGATTT
1 TCGCATTGCGATTT
4381402 TCTCGTTGCG
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.14
14 4 0.10
15 3 0.07
17 11 0.26
18 12 0.29
19 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:4381403 original size:18 final size:19
Alignment explanation
Indices: 4381357--4381403 Score: 80
Period size: 18 Copynumber: 2.6 Consensus size: 19
4381347 CGATTTCTCG
4381357 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4381376 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4381394 -TGCGATTTTC
1 TTGCGATTTTC
4381404 TCGTTGCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.19
18 16 0.59
19 6 0.22
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4381538 original size:14 final size:13
Alignment explanation
Indices: 4381519--4381554 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
4381509 CATCAATTAA
4381519 ACAAATCAACATTT
1 ACAAATCAAC-TTT
*
4381533 ACAAATCATCTTT
1 ACAAATCAACTTT
4381546 ACAAATCAA
1 ACAAATCAA
4381555 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (13 bp):
ACAAATCAACTTT
Found at i:4382008 original size:19 final size:16
Alignment explanation
Indices: 4381967--4382017 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 16
4381957 CGAAATGAAA
4381967 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
4381983 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
4381997 ATTTCGCATTGCGA-TTTC
1 ---TCGCATTGCGATTTTC
4382015 TCG
1 TCG
4382018 TTGCGATAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
14 11 0.37
15 3 0.10
16 3 0.10
17 3 0.10
18 4 0.13
19 6 0.20
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.45
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:4382020 original size:32 final size:32
Alignment explanation
Indices: 4381967--4382043 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
4381957 CGAAATGAAA
***
4381967 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGA-TTTCTCGTTGCGATAGCCATT
4382000 TCGCATTGCGATTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTCTCGTTGCGATAGCCATT
*
4382032 TCGCGTTGCGAT
1 TCGCATTGCGAT
4382044 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 29 0.73
33 11 0.28
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (32 bp):
TCGCATTGCGATTTCTCGTTGCGATAGCCATT
Found at i:4384104 original size:19 final size:19
Alignment explanation
Indices: 4383992--4384113 Score: 101
Period size: 19 Copynumber: 6.6 Consensus size: 19
4383982 TAGTTTACTT
* *
4383992 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
4384012 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
4384031 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
4384051 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4384070 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
4384084 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4384103 TCGCAATGCGA
1 TCGCAACGCGA
4384114 TTTGTGTTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 39 0.46
20 29 0.35
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:4384169 original size:32 final size:32
Alignment explanation
Indices: 4384120--4384228 Score: 193
Period size: 32 Copynumber: 3.4 Consensus size: 32
4384110 GCGATTTGTG
4384120 TTTCGCGTTGCGA-TTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
4384151 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
*
4384183 TTTCGCGTTGCGCTTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
*
4384215 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
4384229 AGCCATTTCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
31 13 0.18
32 61 0.82
ACGTcount: A:0.09, C:0.20, G:0.25, T:0.46
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:4384175 original size:14 final size:14
Alignment explanation
Indices: 4384125--4384212 Score: 70
Period size: 14 Copynumber: 5.8 Consensus size: 14
4384115 TTGTGTTTCG
4384125 CGTTGCGA-TTTGT
1 CGTTGCGATTTTGT
*
4384138 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
4384154 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
4384170 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
4384186 CGCGTTGCGCTTTTGT
1 --CGTTGCGATTTTGT
4384202 CGTTGCGATTT
1 CGTTGCGATTT
4384213 CATTTCGCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
13 8 0.13
14 23 0.38
16 8 0.13
18 21 0.35
ACGTcount: A:0.08, C:0.19, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4384247 original size:20 final size:19
Alignment explanation
Indices: 4384213--4384267 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
4384203 GTTGCGATTT
*
4384213 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
4384232 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
4384252 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
4384268 AAGTAAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:4384746 original size:18 final size:18
Alignment explanation
Indices: 4384720--4384764 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4384710 GGCGATCAGA
*
4384720 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
4384738 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
4384756 TGATGGCTC
1 TGATGGCTC
4384765 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:4385733 original size:28 final size:27
Alignment explanation
Indices: 4385696--4385748 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
4385686 AAGATATACC
4385696 AAAACAATAATAAACATAAATAGTACA
1 AAAACAATAATAAACATAAATAGTACA
4385723 AAAACCAATAATAAACATAAATAGTA
1 AAAA-CAATAATAAACATAAATAGTA
4385749 GTAGTTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.66, C:0.11, G:0.04, T:0.19
Consensus pattern (27 bp):
AAAACAATAATAAACATAAATAGTACA
Found at i:4386449 original size:20 final size:20
Alignment explanation
Indices: 4386363--4386457 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
4386353 GCGATTATGT
*
4386363 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
4386383 TATCGTGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
4386403 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
4386424 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
4386444 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
4386458 TTTCCCAATT
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:4386475 original size:21 final size:21
Alignment explanation
Indices: 4386446--4386540 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
4386436 ATAGTCAGTA
*
4386446 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
4386467 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
4386488 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
* *
4386508 TCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
4386529 T-GCGTTGCGATT
1 TCGCGTTGCGATT
4386541 ACTTATTCGC
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
20 25 0.40
21 38 0.60
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:4386554 original size:39 final size:41
Alignment explanation
Indices: 4386465--4386560 Score: 160
Period size: 39 Copynumber: 2.4 Consensus size: 41
4386455 GATTTTCCCA
* *
4386465 ATTCGCGTTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTT
4386506 ATTCGCATTGCGAATTTCCCAATT-GCGTTGCGA-TTACTT
1 ATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTT
4386545 ATTCGCATTGCGAATT
1 ATTCGCATTGCGAATT
4386561 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
39 22 0.42
40 9 0.17
41 22 0.42
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (41 bp):
ATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTT
Found at i:4390288 original size:2 final size:2
Alignment explanation
Indices: 4390281--4390363 Score: 152
Period size: 2 Copynumber: 42.5 Consensus size: 2
4390271 GATCCTAACC
4390281 TA TA TA TA TA TA -A TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4390321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4390363 T
1 T
4390364 TCATGAGAAT
Statistics
Matches: 79, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 77 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4390996 original size:14 final size:14
Alignment explanation
Indices: 4390997--4391037 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
4390987 CTAGAATGCA
4390997 AATGTATATTCCAG
1 AATGTATATTCCAG
4391011 AATGTATATTCCAG
1 AATGTATATTCCAG
*
4391025 AATGCATATTCCA
1 AATGTATATTCCA
4391038 ATATTCTCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (14 bp):
AATGTATATTCCAG
Found at i:4391000 original size:20 final size:20
Alignment explanation
Indices: 4390977--4391014 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4390967 ACACGTTAAC
*
4390977 AATGCATATTCTAGAATGCA
1 AATGCATATTCCAGAATGCA
*
4390997 AATGTATATTCCAGAATG
1 AATGCATATTCCAGAATG
4391015 TATATTCCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
AATGCATATTCCAGAATGCA
Found at i:4391189 original size:35 final size:33
Alignment explanation
Indices: 4391140--4391236 Score: 142
Period size: 35 Copynumber: 2.8 Consensus size: 33
4391130 TAGTAAATCA
4391140 TCCGTTCTAGTTGAATCGAAAGTGCGATGCTTCCT
1 TCCGTTC-A-TTGAATCGAAAGTGCGATGCTTCCT
4391175 TCCGTTCGAATTGAATCGAAAGTGCGATGCTTCCT
1 TCCGTTC--ATTGAATCGAAAGTGCGATGCTTCCT
*
4391210 TCTGTTC-TTGAATCGAAAGTGCGATGC
1 TCCGTTCATTGAATCGAAAGTGCGATGC
4391237 CTCCCTTCGT
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
32 20 0.34
35 38 0.64
36 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (33 bp):
TCCGTTCATTGAATCGAAAGTGCGATGCTTCCT
Found at i:4391226 original size:32 final size:31
Alignment explanation
Indices: 4391150--4391249 Score: 137
Period size: 35 Copynumber: 3.0 Consensus size: 31
4391140 TCCGTTCTAG
4391150 TTGAATCGAAAGTGCGATGCTTCCTTCCGTTC
1 TTGAATCGAAAGTGCGATGCTTCCTT-CGTTC
4391182 GAATTGAATCGAAAGTGCGATGCTTCCTTCTGTTC
1 ---TTGAATCGAAAGTGCGATGCTTCCTTC-GTTC
*
4391217 TTGAATCGAAAGTGCGATGCCTCCCTTCGTTC
1 TTGAATCGAAAGTGCGATG-CTTCCTTCGTTC
4391249 T
1 T
4391250 ACTATAGACG
Statistics
Matches: 62, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
32 24 0.39
33 7 0.11
34 1 0.02
35 30 0.48
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (31 bp):
TTGAATCGAAAGTGCGATGCTTCCTTCGTTC
Found at i:4392916 original size:14 final size:14
Alignment explanation
Indices: 4392899--4392939 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
4392889 CTAGAATGCA
*
4392899 AATGTATATTTCAG
1 AATGTATATTCCAG
4392913 AATGTATATTCCAG
1 AATGTATATTCCAG
*
4392927 AATGCATATTCCA
1 AATGTATATTCCA
4392940 ATACGGACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (14 bp):
AATGTATATTCCAG
Found at i:4393995 original size:2 final size:2
Alignment explanation
Indices: 4393988--4394051 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
4393978 TTTTTGAAAC
4393988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4394030 AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
4394052 GAACATATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4395335 original size:20 final size:19
Alignment explanation
Indices: 4395312--4395537 Score: 181
Period size: 20 Copynumber: 11.3 Consensus size: 19
4395302 AATTTGTAAA
*
4395312 TCGCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
*
4395332 TCGCAACACTGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
* *
4395352 TCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
* *
4395372 TCACAACGCGATAGTCAAAA
1 TCGCAACGCGA-AGTCAAAT
*
4395392 TCGCAAGGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
*
4395412 TTGCAACGCGAA-TCTGTAAA-
1 TCGCAACGCGAAGTC---AAAT
4395432 TCGCAACGCGAATTTGT-AAA-
1 TCGCAACGCGAA---GTCAAAT
*
4395452 TCGCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
* *
4395472 TCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
*
4395492 TCACAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
4395512 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCG-AAGTCAAAT
4395532 TCGCAA
1 TCGCAA
4395538 AGCGCGTTTA
Statistics
Matches: 174, Mismatches: 19, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.02
19 6 0.03
20 156 0.90
21 7 0.04
24 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (19 bp):
TCGCAACGCGAAGTCAAAT
Found at i:4395460 original size:120 final size:120
Alignment explanation
Indices: 4395287--4395537 Score: 382
Period size: 120 Copynumber: 2.1 Consensus size: 120
4395277 ACCCAGTTTC
* *
4395287 CAAATTCGCAACGCAAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACTGAAGTCAAAT
1 CAAATTCGCAACGCAAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAAT
* *
4395352 TCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAAATCGCAAGGCGATAGT
66 TCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAAATCGCAACGCGAAAGT
* * *
4395407 CAAATTTGCAACGCGAATCTGTAAATCGCAACGC-GAATTTGT-AAA-TCGCAACACAGAAGTCA
1 CAAATTCGCAACGCAAATCTGTAAATCGCAACACAGAA---GTCAAATTCGCAACACAGAAGTCA
*
4395469 AATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTCGCAACGCGAAAGT
63 AATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAAATCGCAACGCGAAAGT
4395527 CAAATTCGCAA
1 CAAATTCGCAA
4395538 AGCGCGTTTA
Statistics
Matches: 119, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
119 3 0.03
120 111 0.93
121 3 0.03
122 2 0.02
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.19
Consensus pattern (120 bp):
CAAATTCGCAACGCAAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAAT
TCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAAATCGCAACGCGAAAGT
Found at i:4396115 original size:14 final size:14
Alignment explanation
Indices: 4396081--4396123 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4396071 ACACGAAAAT
*
4396081 GAAAATCGCAACAC
1 GAAAATCGCAACGC
*
4396095 -CAAATCGCAACGC
1 GAAAATCGCAACGC
*
4396108 GAAAATCGCAATGC
1 GAAAATCGCAACGC
4396122 GA
1 GA
4396124 TTTTAGTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGC
Found at i:4397849 original size:15 final size:15
Alignment explanation
Indices: 4397831--4397878 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
4397821 GAGGGTATAA
4397831 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
4397846 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
4397861 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
4397876 TAG
1 TAG
4397879 GAGTCCTACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:4401833 original size:17 final size:17
Alignment explanation
Indices: 4401811--4401851 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
4401801 CTAAATCGAA
4401811 TTAAAGATGAAAAGTGT
1 TTAAAGATGAAAAGTGT
4401828 TTAAAGATGAAAAGTGT
1 TTAAAGATGAAAAGTGT
4401845 TTAAAGA
1 TTAAAGA
4401852 GGATACAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (17 bp):
TTAAAGATGAAAAGTGT
Found at i:4404537 original size:12 final size:12
Alignment explanation
Indices: 4404519--4404554 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4404509 TATATATGTT
4404519 CATGTGATATGA
1 CATGTGATATGA
*
4404531 TATGTGATATGA
1 CATGTGATATGA
*
4404543 CCTGTGATATGA
1 CATGTGATATGA
4404555 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:4404717 original size:15 final size:15
Alignment explanation
Indices: 4404699--4404746 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
4404689 GAGGGTATAA
4404699 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
4404714 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
4404729 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
4404744 TAG
1 TAG
4404747 GAGTCCTACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:4407009 original size:75 final size:74
Alignment explanation
Indices: 4406845--4407053 Score: 242
Period size: 75 Copynumber: 2.8 Consensus size: 74
4406835 CAAAGCCAAA
* * * **
4406845 AATTCCAGATTGCTCAGAGGGAACCAATTCCCCCCCATAGGAGGAACCGATT-CCCCCTTAATGG
1 AATTCCAGA-TGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
4406909 TTTGGCTCCGAG
63 TTTGGCTCCGAG
*
4406921 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
4406986 TTGTTCCGAG
65 TGGCTCCGAG
* * *
4406996 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAG-ATGCTCGGAGGGAACCGAT--TCCCCCATAGGAGGAACCGATTCCCCCCT
4407054 TGTACAACGG
Statistics
Matches: 116, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
74 21 0.18
75 45 0.39
76 43 0.37
77 7 0.06
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (74 bp):
AATTCCAGATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:4414845 original size:15 final size:15
Alignment explanation
Indices: 4414825--4414866 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
4414815 TCAACATTAT
*
4414825 ATTTTGGATTGTTTG
1 ATTTTGGATTGTTGG
4414840 ATTTTGTGGATTGTTGG
1 A-TTT-TGGATTGTTGG
4414857 ATTTTGGATT
1 ATTTTGGATT
4414867 TATGGATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:4414851 original size:17 final size:17
Alignment explanation
Indices: 4414829--4414862 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4414819 CATTATATTT
*
4414829 TGGATTGTTTGATTTTG
1 TGGATTGTTGGATTTTG
4414846 TGGATTGTTGGATTTTG
1 TGGATTGTTGGATTTTG
4414863 GATTTATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTG
Found at i:4415635 original size:74 final size:76
Alignment explanation
Indices: 4415453--4415658 Score: 256
Period size: 75 Copynumber: 2.7 Consensus size: 76
4415443 CAAAGCCAAA
* * * * * **
4415453 AATTCTAGATTGCTCAGAGGGAACTGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTTAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
4415517 TTTGGCTCCGAG
65 TTTGGCTCCGAG
*
4415529 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
4415593 TTTGTTCCGAG
66 TTGGCTCCGAG
* * * *
4415604 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
4415659 TTGTACAACG
Statistics
Matches: 113, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
74 21 0.19
75 62 0.55
76 30 0.27
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:4422063 original size:105 final size:104
Alignment explanation
Indices: 4421875--4422097 Score: 284
Period size: 105 Copynumber: 2.1 Consensus size: 104
4421865 GAGTCGAGGG
* *
4421875 TCTACGTGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGCGACACAT
1 TCTATGTGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACAT
* * *
4421940 ATTTGGTCCTTAGCATATGTATATGATTCTTAAGGAATTT
66 ACTTGATCCTTAGCATATGTATATGATTCTTAA-GAAATT
* * * * * * *
4421980 TCTATGTGGTCCTTCGGGACGTATATGTATTCTTTGGAGCATGTATGAGGTCTTTTGAGACACTT
1 TCTATGTGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACAT
* * *
4422045 ACTTGATCCTTGGTATATGTATATGGTTCTTAAGAAATT
66 ACTTGATCCTTAGCATATGTATATGATTCTTAAGAAATT
* *
4422084 TATATGTGCTCCTT
1 TCTATGTGGTCCTT
4422098 ATGGACAATC
Statistics
Matches: 101, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
104 17 0.17
105 84 0.83
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.40
Consensus pattern (104 bp):
TCTATGTGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACAT
ACTTGATCCTTAGCATATGTATATGATTCTTAAGAAATT
Found at i:4422149 original size:24 final size:24
Alignment explanation
Indices: 4422114--4422163 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
4422104 AATCTTATAT
4422114 GGCACTACGGTGCAAATTCTACGC
1 GGCACTACGGTGCAAATTCTACGC
*
4422138 GGCACTATGGTGCAAATTCTACGC
1 GGCACTACGGTGCAAATTCTACGC
4422162 GG
1 GG
4422164 TACTTCAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (24 bp):
GGCACTACGGTGCAAATTCTACGC
Found at i:4422174 original size:24 final size:24
Alignment explanation
Indices: 4422114--4422176 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
4422104 AATCTTATAT
**
4422114 GGCACTACGGTGCAAATTCTACGC
1 GGCACTATAGTGCAAATTCTACGC
*
4422138 GGCACTATGGTGCAAATTCTACGC
1 GGCACTATAGTGCAAATTCTACGC
*
4422162 GGTACT-TCAGTGCAA
1 GGCACTAT-AGTGCAA
4422177 TTATACGAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (24 bp):
GGCACTATAGTGCAAATTCTACGC
Found at i:4423010 original size:34 final size:34
Alignment explanation
Indices: 4422967--4423034 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
4422957 CCAGATTCGA
4422967 GTATGAAGTTTGCAAGGGTGTATAAACGCTTATT
1 GTATGAAGTTTGCAAGGGTGTATAAACGCTTATT
* *
4423001 GTATGAAGTTTGCAAGGGTGTATGAATGCTTATT
1 GTATGAAGTTTGCAAGGGTGTATAAACGCTTATT
4423035 TTTAAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (34 bp):
GTATGAAGTTTGCAAGGGTGTATAAACGCTTATT
Found at i:4427640 original size:15 final size:16
Alignment explanation
Indices: 4427609--4427642 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4427599 AATGTGTTAT
*
4427609 AAAAACTGATTTATTA
1 AAAAACTGATATATTA
4427625 AAAAACTGATAT-TTA
1 AAAAACTGATATATTA
4427640 AAA
1 AAA
4427643 GAGAGAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (16 bp):
AAAAACTGATATATTA
Found at i:4429988 original size:21 final size:21
Alignment explanation
Indices: 4429959--4430004 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
4429949 CTAGTACGGA
* *
4429959 AATATAATCGTCATGTCCATC
1 AATAAAATCGTAATGTCCATC
*
4429980 AATAAAATCGTAATGTCCGTC
1 AATAAAATCGTAATGTCCATC
4430001 AATA
1 AATA
4430005 CTGGATTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (21 bp):
AATAAAATCGTAATGTCCATC
Found at i:4430077 original size:90 final size:88
Alignment explanation
Indices: 4429924--4430569 Score: 502
Period size: 90 Copynumber: 7.3 Consensus size: 88
4429914 TCGAGGATCA
* * * * * * *
4429924 TTTTCTTGGAGTAAACTACGTTTATCTAGTACGGAAATATAATCGTCATGTCCATCAATAAAATC
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
* *
4429989 GTAATGTCCGTCAATACTGGATTCT
66 ATAATG-CC-TCAATACTGGGTTCT
* * * * *
4430014 TTTTCTTGAAGTAGACGACGTTTATCTAACACGGTAATATAATCATCATGCCCGTCAACAAAATC
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
*
4430079 ATAATGCC-CATTACCTTGAGGTTCT
66 ATAATGCCTCAATA-C-TG-GGTTCT
* * *
4430104 TTTTCTTGAAGTAGACGACGTTTATCTAGTATGGTAGA-ATAATCGTCATGTCCGTCAACACTAA
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTA-ATATAATCGTCATGTCCGTCAACA-AAA
* ** * *
4430168 -CATAAGGCCT-ACCACGGGGTTGT
64 TCATAATGCCTCAATACTGGGTTCT
** * * * * ** * * *
4430191 ACTTCTTGGACTAGAGGGCGTTTATCTAGCATAGTAGCATAATCATCATGTCCATCAATAAAATC
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
* * * *
4430256 GTAATGCCCATCCATATTGAGTTCT
66 ATAATG-CC-TCAATACTGGGTTCT
* ** *
4430281 TTTTCTTGGAGTAGACGGCGTTTATCTAGCATGGTACCATAATCGTCATGTCCGTCAACACTAA-
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACA-AAAT
* *
4430345 CA-AATGGCCT-ATTACGGGGCTT-T
65 CATAAT-GCCTCAATACTGGG-TTCT
* * ** * * ** * *
4430368 ATTTCTTGGAGTAGAGGGTGATTATCTAGCATGGTAGTGGAATCGTCATGTCCATCAATAAAATC
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
* * *
4430433 GTAATATCCGTCAATATTGGGTTCT
66 ATAAT-GCC-TCAATACTGGGTTCT
* * *
4430458 TTTTCTTGGAGTAGACGACGTTTATCTAACACGGTAATATAATCATCATGTCCGTCAACAAAATC
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
*
4430523 ATAATGCC-CATTACCTTGGGGTTC-
66 ATAATGCCTCAATA-C-T-GGGTTCT
* *
4430547 TTTTCTTGAAGTAAACGACGTTT
1 TTTTCTTGGAGTAGACGACGTTT
4430570 CCATTGGTTA
Statistics
Matches: 436, Mismatches: 98, Indels: 45
0.75 0.17 0.08
Matches are distributed among these distances:
86 4 0.01
87 121 0.28
88 12 0.03
89 38 0.09
90 256 0.59
91 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (88 bp):
TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
ATAATGCCTCAATACTGGGTTCT
Found at i:4430240 original size:87 final size:86
Alignment explanation
Indices: 4430105--4430425 Score: 295
Period size: 87 Copynumber: 3.7 Consensus size: 86
4430095 TGAGGTTCTT
* * * * *
4430105 TTTCTTGAAGTAGACGACGTTTATCTAGTATGGTAGAATAATCGTCATGTCCGTCAACACTAACA
1 TTTCTTGGAGTAGAGGGCGTTTATCTAGCATGGTAGCATAATCGTCATGTCCGTCAACACTAACA
4430170 TAAGGCCTACCACGGGGTTGTA
66 TAAGGCCTACCACGGGGTT-TA
* * * * * * *
4430192 CTTCTTGGACTAGAGGGCGTTTATCTAGCATAGTAGCATAATCATCATGTCCATCAATA-AAATC
1 TTTCTTGGAGTAGAGGGCGTTTATCTAGCATGGTAGCATAATCGTCATGTCCGTCAACACTAA-C
* * * ** * *
4430256 GTAATGCCCATCCATATTGAGTTCTT
65 ATAAGGCCTA-CC--ACGGGGTT-TA
* *
4430282 TTTCTTGGAGTAGACGGCGTTTATCTAGCATGGTACCATAATCGTCATGTCCGTCAACACTAACA
1 TTTCTTGGAGTAGAGGGCGTTTATCTAGCATGGTAGCATAATCGTCATGTCCGTCAACACTAACA
**
4430347 -AATGGCCTATTACGGGGCTTTA
66 TAA-GGCCTACCACGGGG-TTTA
* * *** *
4430369 TTTCTTGGAGTAGAGGGTGATTATCTAGCATGGTAGTGGAATCGTCATGTCCATCAA
1 TTTCTTGGAGTAGAGGGCGTTTATCTAGCATGGTAGCATAATCGTCATGTCCGTCAA
4430426 TAAAATCGTA
Statistics
Matches: 181, Mismatches: 46, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
86 2 0.01
87 109 0.60
88 4 0.02
89 2 0.01
90 62 0.34
91 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (86 bp):
TTTCTTGGAGTAGAGGGCGTTTATCTAGCATGGTAGCATAATCGTCATGTCCGTCAACACTAACA
TAAGGCCTACCACGGGGTTTA
Found at i:4430282 original size:177 final size:176
Alignment explanation
Indices: 4430052--4430517 Score: 587
Period size: 177 Copynumber: 2.6 Consensus size: 176
4430042 ACACGGTAAT
* * * * * ** *
4430052 ATAATCATCATGCCCGTCAACAAAATCATAATGCCCAT-TACCTTGAGGTTCTTTTTCTTGAAGT
1 ATAATCATCATGTCCATCAATAAAATCGTAATGCCCATCAATATTGA-GTTCTTTTTCTTGGAGT
*
4430116 AGACGACGTTTATCTAGTATGGTAGAATAATCGTCATGTCCGTCAACACTAACATAA-GGCCTAC
65 AGACGACGTTTATCTAGCATGGTA-AATAATCGTCATGTCCGTCAACACTAACA-AATGGCCTAC
*
4430180 CACGGGG-TTGTACTTCTTGGACTAGAGGGCGTTTATCTAGCATAGTAGC
128 CACGGGGCTT-TACTTCTTGGACTAGAGGGCGATTATCTAGCATAGTAGC
*
4430229 ATAATCATCATGTCCATCAATAAAATCGTAATGCCCATCCATATTGAGTTCTTTTTCTTGGAGTA
1 ATAATCATCATGTCCATCAATAAAATCGTAATGCCCATCAATATTGAGTTCTTTTTCTTGGAGTA
* * **
4430294 GACGGCGTTTATCTAGCATGGTACCATAATCGTCATGTCCGTCAACACTAACAAATGGCCTATTA
66 GACGACGTTTATCTAGCATGGTA-AATAATCGTCATGTCCGTCAACACTAACAAATGGCCTACCA
* * * * *
4430359 CGGGGCTTTATTTCTTGGAGTAGAGGGTGATTATCTAGCATGGTAGT
130 CGGGGCTTTACTTCTTGGACTAGAGGGCGATTATCTAGCATAGTAGC
** * ** * *
4430406 GGAATCGTCATGTCCATCAATAAAATCGTAATATCCGTCAATATTGGGTTCTTTTTCTTGGAGTA
1 ATAATCATCATGTCCATCAATAAAATCGTAATGCCCATCAATATTGAGTTCTTTTTCTTGGAGTA
* * *
4430471 GACGACGTTTATCTAACACGGTAATATAATCATCATGTCCGTCAACA
66 GACGACGTTTATCTAGCATGGTAA-ATAATCGTCATGTCCGTCAACA
4430518 AAATCATAAT
Statistics
Matches: 252, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
176 2 0.01
177 243 0.96
178 7 0.03
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (176 bp):
ATAATCATCATGTCCATCAATAAAATCGTAATGCCCATCAATATTGAGTTCTTTTTCTTGGAGTA
GACGACGTTTATCTAGCATGGTAAATAATCGTCATGTCCGTCAACACTAACAAATGGCCTACCAC
GGGGCTTTACTTCTTGGACTAGAGGGCGATTATCTAGCATAGTAGC
Found at i:4430434 original size:21 final size:21
Alignment explanation
Indices: 4430408--4430448 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4430398 ATGGTAGTGG
* *
4430408 AATCGTCATGTCCATCAATAA
1 AATCGTAATATCCATCAATAA
*
4430429 AATCGTAATATCCGTCAATA
1 AATCGTAATATCCATCAATA
4430449 TTGGGTTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (21 bp):
AATCGTAATATCCATCAATAA
Found at i:4432347 original size:24 final size:24
Alignment explanation
Indices: 4432298--4432348 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
4432288 TGAATTAATA
*
4432298 TATTTATTAAACTATTTTTAGTAT
1 TATTTATTAAACTATTTTTAGCAT
* *
4432322 TATTTATTTACCTA-TTTTAGACAT
1 TATTTATTAAACTATTTTTAG-CAT
4432346 TAT
1 TAT
4432349 AGTCTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (24 bp):
TATTTATTAAACTATTTTTAGCAT
Found at i:4434091 original size:2 final size:2
Alignment explanation
Indices: 4434084--4434111 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4434074 ACTAAAATTC
4434084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4434112 TACACGTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4434780 original size:15 final size:15
Alignment explanation
Indices: 4434760--4434797 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
4434750 TTGAGAGGAC
4434760 GAGAAGGGGCTGATG
1 GAGAAGGGGCTGATG
*
4434775 GAGAAGGGGCTGATT
1 GAGAAGGGGCTGATG
4434790 GAGAAGGG
1 GAGAAGGG
4434798 AGAGGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.53, T:0.13
Consensus pattern (15 bp):
GAGAAGGGGCTGATG
Found at i:4442577 original size:60 final size:60
Alignment explanation
Indices: 4442464--4442577 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
4442454 AATAGTTTGG
* * * * **
4442464 TGACCATTTTATAACTTTTAATAGTTGGGAGACTTAACAAAGCAACATGCTATAGTTGAA
1 TGACCATTTTATAACTTTTAATAATCGAGAGACTGAACAAAGCAACACCCTATAGTTGAA
* * **
4442524 TGACCATTTTGTAACTTTTAATAATCGAGTGACTGAACAAAGCATTACCCTATA
1 TGACCATTTTATAACTTTTAATAATCGAGAGACTGAACAAAGCAACACCCTATA
4442578 ATTGGGGGAC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (60 bp):
TGACCATTTTATAACTTTTAATAATCGAGAGACTGAACAAAGCAACACCCTATAGTTGAA
Found at i:4443851 original size:27 final size:27
Alignment explanation
Indices: 4443791--4443852 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
4443781 TAAAATTTAC
* *
4443791 AAAAAATTTAGGTTTTTTATTAAAAAT
1 AAAAATTTTAAGTTTTTTATTAAAAAT
* * **
4443818 TATAATTTTAAGTTTTTTATTTTAAAT
1 AAAAATTTTAAGTTTTTTATTAAAAAT
4443845 AAAAATTT
1 AAAAATTT
4443853 ATATTACCAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (27 bp):
AAAAATTTTAAGTTTTTTATTAAAAAT
Found at i:4444699 original size:18 final size:17
Alignment explanation
Indices: 4444676--4444722 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
4444666 CAACCTCTCC
4444676 ACAAGTGTCACCCCTAA
1 ACAAGTGTCACCCCTAA
* *
4444693 TACAAGTGTCACCTCTCA
1 -ACAAGTGTCACCCCTAA
4444711 A-AAGTGTCACCC
1 ACAAGTGTCACCC
4444723 TGAGGCTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 10 0.38
17 1 0.04
18 15 0.58
ACGTcount: A:0.32, C:0.34, G:0.13, T:0.21
Consensus pattern (17 bp):
ACAAGTGTCACCCCTAA
Found at i:4444717 original size:16 final size:16
Alignment explanation
Indices: 4444668--4444721 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 16
4444658 ATTCCAGACA
*
4444668 ACCTCTCCACAAGTGTC
1 ACCTCT-CAAAAGTGTC
* *
4444685 ACCCCTAATACAAGTGTC
1 ACCTCTCA-A-AAGTGTC
4444703 ACCTCTCAAAAGTGTC
1 ACCTCTCAAAAGTGTC
4444719 ACC
1 ACC
4444722 CTGAGGCTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 11 0.37
17 6 0.20
18 13 0.43
ACGTcount: A:0.30, C:0.37, G:0.11, T:0.22
Consensus pattern (16 bp):
ACCTCTCAAAAGTGTC
Found at i:4454170 original size:18 final size:17
Alignment explanation
Indices: 4454144--4454183 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
4454134 ATTTCAAAGT
4454144 TATAATTATATAAAAAAA
1 TATAATTATAT-AAAAAA
* *
4454162 TATATTTATATATAAAA
1 TATAATTATATAAAAAA
4454179 TATAA
1 TATAA
4454184 ATAAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATAATTATATAAAAAA
Found at i:4454485 original size:3 final size:3
Alignment explanation
Indices: 4454477--4454506 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
4454467 TTTATGACTA
*
4454477 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4454507 TAAGAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4456004 original size:3 final size:3
Alignment explanation
Indices: 4455996--4456050 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
4455986 TTATTTTATT
* * *
4455996 TAA TAA TAA TAA TAA CAA TAA TAA TAT TTA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
4456042 TAA TAA TAA
1 TAA TAA TAA
4456051 AAGTAAATTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4457910 original size:10 final size:10
Alignment explanation
Indices: 4457895--4457924 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
4457885 ATATGAGGAC
4457895 TAAATTAAAA
1 TAAATTAAAA
4457905 TAAATTAAAA
1 TAAATTAAAA
4457915 TAAATTAAAA
1 TAAATTAAAA
4457925 CTCTATGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:4458319 original size:15 final size:15
Alignment explanation
Indices: 4458299--4458330 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4458289 TGTTCATACA
4458299 AAAATTTAAATATTT
1 AAAATTTAAATATTT
*
4458314 AAAATTTATATATTT
1 AAAATTTAAATATTT
4458329 AA
1 AA
4458331 GGAACTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATTTAAATATTT
Found at i:4459377 original size:13 final size:12
Alignment explanation
Indices: 4459352--4459389 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
4459342 TTGCTTCGAA
4459352 AATAAAT-AAAT
1 AATAAATAAAAT
4459363 AATAAATAGAAAT
1 AATAAATA-AAAT
4459376 AAATAAATAAAAT
1 -AATAAATAAAAT
4459389 A
1 A
4459390 CCTCTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 1 0.04
13 8 0.33
14 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AATAAATAAAAT
Found at i:4460484 original size:2 final size:2
Alignment explanation
Indices: 4460479--4460530 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4460469 TATAAAGACG
4460479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4460521 AT AT AT AT AT
1 AT AT AT AT AT
4460531 TAATAATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4468030 original size:3 final size:3
Alignment explanation
Indices: 4468017--4468053 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
4468007 GATAGAAGGG
4468017 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4468054 TTAAAATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:4472544 original size:25 final size:25
Alignment explanation
Indices: 4472509--4472568 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
4472499 CAAATAAGCA
4472509 AGTTAAACTTCAATATGCTATGCTT
1 AGTTAAACTTCAATATGCTATGCTT
* *
4472534 CGTTAAACTTCGATATGCTATGCTT
1 AGTTAAACTTCAATATGCTATGCTT
4472559 AGTTAAACTT
1 AGTTAAACTT
4472569 ACCGCGGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (25 bp):
AGTTAAACTTCAATATGCTATGCTT
Found at i:4475119 original size:21 final size:21
Alignment explanation
Indices: 4475092--4475144 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
4475082 GGTATGAATT
4475092 TTATTTATTGTAAATAATAATG
1 TTATTTATTGTAAATAA-AATG
4475114 -TATTTATTGTAAATAAAATG
1 TTATTTATTGTAAATAAAATG
4475134 TTATTTATTGT
1 TTATTTATTGT
4475145 CAACGTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (21 bp):
TTATTTATTGTAAATAAAATG
Found at i:4478506 original size:26 final size:26
Alignment explanation
Indices: 4478476--4478526 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
4478466 CAATATCTTA
*
4478476 TGTAAAATATCGATATATTGTAGTTT
1 TGTAAAATATCGATATATTATAGTTT
4478502 TGTAAAATATCGATATATTATAGTT
1 TGTAAAATATCGATATATTATAGTT
4478527 CAACTGTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (26 bp):
TGTAAAATATCGATATATTATAGTTT
Found at i:4479156 original size:44 final size:45
Alignment explanation
Indices: 4479076--4479164 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 45
4479066 CAATTTTTCC
*
4479076 CATGCAACCACCCTTTGGAAATCCCAGCGTCTTTAGGCTTAATGG
1 CATGCAACCACCCTTTGGAAATCCCAGCGTCCTTAGGCTTAATGG
*
4479121 CATGCAACCA-CCTTTGGAAGTAT-CGA-CGTCCTTAGGCTTAATGG
1 CATGCAACCACCCTTTGGAA--ATCCCAGCGTCCTTAGGCTTAATGG
4479165 GGGTTGAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 26 0.65
45 12 0.30
46 2 0.05
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (45 bp):
CATGCAACCACCCTTTGGAAATCCCAGCGTCCTTAGGCTTAATGG
Found at i:4479994 original size:4 final size:4
Alignment explanation
Indices: 4479985--4480027 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
4479975 AGTTTAGCCT
4479985 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
4480028 TTTCTTTAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
ATTA
Found at i:4481851 original size:2 final size:2
Alignment explanation
Indices: 4481844--4481881 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4481834 AATATTATGC
4481844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4481882 TATTGTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4484030 original size:29 final size:31
Alignment explanation
Indices: 4483973--4484032 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
4483963 CAATTTAAGG
*
4483973 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
4484004 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
4484033 TTCAAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:4484125 original size:19 final size:19
Alignment explanation
Indices: 4484098--4484163 Score: 105
Period size: 19 Copynumber: 3.5 Consensus size: 19
4484088 TGTGTTTTTA
* *
4484098 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
4484117 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
*
4484136 TGAACAGTAAATCACTATT
1 TGAACAGTAAATTACTATT
4484155 TGAACAGTA
1 TGAACAGTA
4484164 CCCAGAGGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:4490446 original size:22 final size:21
Alignment explanation
Indices: 4490404--4490443 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4490394 GAGTTTATTT
*
4490404 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
4490425 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4490444 ATAATTTCTC
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:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:4492538 original size:62 final size:61
Alignment explanation
Indices: 4492389--4492543 Score: 165
Period size: 62 Copynumber: 2.5 Consensus size: 61
4492379 GTTTCAAACA
4492389 AGAGTGCATCGATGCATGGTTGTGCATCGATGCATAAAGCATTCGATGTTTTCATAAAACCC
1 AGAGTGCATCGATGCATGGTTGTGCATCGATGCATAAAGCATTCGATG-TTTCATAAAACCC
* * * ** **
4492451 CGAGTGCATCAATGC-TAGTATGTGCATCGATGCATAAATGCATTCGATG-TTCA-ATTTATTC
1 AGAGTGCATCGATGCATGGT-TGTGCATCGATGCATAAA-GCATTCGATGTTTCATA-AAACCC
4492512 AG-GTGCATCGATGCATGGATTGGTGCATCGAT
1 AGAGTGCATCGATGCATGG-TT-GTGCATCGAT
4492544 ACACTCTTTG
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
60 12 0.16
61 13 0.17
62 42 0.55
63 10 0.13
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (61 bp):
AGAGTGCATCGATGCATGGTTGTGCATCGATGCATAAAGCATTCGATGTTTCATAAAACCC
Found at i:4493712 original size:20 final size:20
Alignment explanation
Indices: 4493687--4493839 Score: 252
Period size: 20 Copynumber: 7.7 Consensus size: 20
4493677 TTTTCCTAAT
4493687 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
4493707 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
4493727 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
4493747 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
4493767 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
* *
4493787 TCGCAATTCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
4493807 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
4493827 TCGCAACGCGAAT
1 TCGCAATGCGAAT
4493840 CTGACTATCG
Statistics
Matches: 123, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 123 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:4493763 original size:60 final size:60
Alignment explanation
Indices: 4493687--4493857 Score: 272
Period size: 60 Copynumber: 2.9 Consensus size: 60
4493677 TTTTCCTAAT
4493687 TCGCAATGCGAATACGTAAATCGCAATGCGAATATGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATATGTAAATCGCAATGCGAATACGTAAA
* *
4493747 TCGCAATGCGAATACGTAAATCGCAATGCGAATATGTAAATCGCAATTCAAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATATGTAAATCGCAATGCGAATACGTAAA
* * * *
4493807 TCGCAATGCGAATATGTAAATCGCAACGCGAATCTG-ACTATCGCAATGCGA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATATGTA-AATCGCAATGCGA
4493858 TTTACATAGC
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 1 0.01
60 101 0.99
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATATGTAAATCGCAATGCGAATACGTAAA
Found at i:4494061 original size:22 final size:22
Alignment explanation
Indices: 4494036--4494101 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
4494026 GGCGACATCT
4494036 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
4494058 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
4494080 GTCTCCATCTCC-AGCGAAATCA
1 GTCCCCATCTCCGA-CGAAATCA
4494102 TTCACGATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 1 0.03
22 39 0.98
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:4494514 original size:20 final size:20
Alignment explanation
Indices: 4494438--4494507 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
4494428 CGATTCTGTC
*
4494438 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
**
4494457 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
4494477 GTTGCAATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
4494497 GTTGCGATTTT
1 GTTGCGATTTT
4494508 AAGTTTCAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 11 0.26
20 32 0.74
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:4496442 original size:33 final size:33
Alignment explanation
Indices: 4496382--4496538 Score: 143
Period size: 33 Copynumber: 4.5 Consensus size: 33
4496372 ATAGTTTACT
*
4496382 ATCGCAATGCAAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGACTATCGCAACGAGAGA
** * * * *
4496416 ATCGCAATGCGAAATGAAAATTGCAACAACAAA
1 ATCGCAATGCGAAATGACTATCGCAACGAGAGA
* *
4496449 ATCGCAACGCGAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAATGACTATCGCAA--CG-AGA-GA
*
4496486 CTATCGCAATGCGAATTTGACTATCGCAACGAGAGA
1 --ATCGCAATGCGAA-ATGACTATCGCAACGAGAGA
*
4496522 ATCGCAATACGAAATGA
1 ATCGCAATGCGAAATGA
4496539 AAATCGCATT
Statistics
Matches: 97, Mismatches: 19, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
33 41 0.42
34 22 0.23
35 1 0.01
36 4 0.04
37 3 0.03
38 2 0.02
39 12 0.12
40 12 0.12
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGACTATCGCAACGAGAGA
Found at i:4496485 original size:20 final size:20
Alignment explanation
Indices: 4496449--4496514 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
4496439 CAACAACAAA
*
4496449 ATCGCAACGCG-AAATGACT
1 ATCGCAATGCGAAAATGACT
4496468 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
4496488 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
4496508 ATCGCAA
1 ATCGCAA
4496515 CGAGAGAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
19 10 0.23
20 33 0.77
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:4496586 original size:20 final size:20
Alignment explanation
Indices: 4496561--4496687 Score: 173
Period size: 20 Copynumber: 6.3 Consensus size: 20
4496551 GATTCTCTCG
**
4496561 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
4496581 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
4496601 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
4496621 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
* *
4496641 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCA
* *
4496661 TTGCGATAGTCATTTTCACG
1 TTGCGATAGTCATTTTCGCA
4496681 TTGCGAT
1 TTGCGAT
4496688 TTTAAGTTTC
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 101 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:4497244 original size:21 final size:21
Alignment explanation
Indices: 4497220--4497278 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
4497210 CTATCATCCC
4497220 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* * **
4497241 TCAAGAGGCCACTGTCACCGT
1 TCAAGAGTCCCCTCCCACCGT
*
4497262 TGAAGAGGT-CCCTCCCA
1 TCAAGA-GTCCCCTCCCA
4497279 ACATTCTAGA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.22, C:0.39, G:0.20, T:0.19
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:4498681 original size:14 final size:14
Alignment explanation
Indices: 4498662--4498697 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4498652 ATTGTTTAAT
4498662 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
4498676 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
4498690 TGATTTGT
1 TGATTTGT
4498698 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Done.