Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_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: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 20
Found at i:27209 original size:19 final size:19
Alignment explanation
Indices: 27182--27218 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27172 ATGACCAACA
27182 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
*
27201 AAATTGCAATGCGATCTC
1 AAATCGCAATGCGATCTC
27219 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:27548 original size:22 final size:22
Alignment explanation
Indices: 27523--27595 Score: 137
Period size: 22 Copynumber: 3.3 Consensus size: 22
27513 CTACGGCGAC
27523 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
27545 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
27567 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
27589 ATCCGTC
1 ATCCGTC
27596 TCTATTTCTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.45, G:0.15, T:0.19
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:28030 original size:20 final size:20
Alignment explanation
Indices: 27982--28032 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
27972 TCAAATTTGC
**
27982 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
28002 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
28022 GTTGCGATTTT
1 GTTGCGATTTT
28033 AAGTTTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:28039 original size:20 final size:20
Alignment explanation
Indices: 27996--28039 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
27986 CGATAGTCAT
* *
27996 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
28016 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
28036 TTTC
1 TTTC
28040 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:29995 original size:20 final size:20
Alignment explanation
Indices: 29970--30018 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
29960 AAACTTAAAA
*
29970 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
29990 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
30010 ATCGCAACG
1 ATCGCAACG
30019 AGATAATCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:30116 original size:19 final size:19
Alignment explanation
Indices: 30094--30147 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
30084 CGGGAATTTA
30094 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
30113 GTTTCGCGTTGCGATTTTT
1 GTTTCGCGTTGCGATTTTG
* *
30132 ATTTCGCATTGCGATT
1 GTTTCGCGTTGCGATT
30148 ATCCCGTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:30178 original size:20 final size:20
Alignment explanation
Indices: 30152--30220 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
30142 GCGATTATCC
*
30152 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
30172 TGTTGCGATAGTC-ATTTCTG
1 CGTTGCGATAGTCAATTTC-G
*
30192 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
30212 CGTTGCGAT
1 CGTTGCGAT
30221 TTTTAAGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.09
20 35 0.81
21 4 0.09
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:30246 original size:20 final size:21
Alignment explanation
Indices: 30207--30250 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
30197 CGATAGTCAT
30207 TTTCGCGTTGCGATTTTTAAG
1 TTTCGCGTTGCGATTTTTAAG
*
30228 TTTCGTGTTGCGA-TTTTAAG
1 TTTCGCGTTGCGATTTTTAAG
30248 TTT
1 TTT
30251 TAGAAACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (21 bp):
TTTCGCGTTGCGATTTTTAAG
Found at i:30804 original size:42 final size:42
Alignment explanation
Indices: 30738--30849 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
30728 CTGTCATCGT
* * *
30738 TCAAGAGGTCTCTCCTATCATTCAAGAGGCCCCTATCATCCA
1 TCAAGAGGTCCCTCCCACCATTCAAGAGGCCCCTATCATCCA
* * **
30780 TCAAGA-GTCCCCTCCCACCGTTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGT-CCCTCCCACCATTCAAGAGGCCCCTATCATCCA
*
30822 TGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCAAGAGGTCCCTCCCACCATTCAAGAG
30850 TCCGATTCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.03
42 55 0.93
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAAGAGGTCCCTCCCACCATTCAAGAGGCCCCTATCATCCA
Found at i:30822 original size:21 final size:21
Alignment explanation
Indices: 30727--30834 Score: 83
Period size: 21 Copynumber: 5.1 Consensus size: 21
30717 CACTGACTCA
*
30727 CCTGTCATCGTTCAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
* * *
30748 TCT-CCTATCATTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
30769 CCTATCATCCATCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
30790 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
30811 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
30832 CCT
1 CCT
30835 CCCACCATTC
Statistics
Matches: 65, Mismatches: 20, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:30848 original size:21 final size:21
Alignment explanation
Indices: 30737--30849 Score: 77
Period size: 21 Copynumber: 5.4 Consensus size: 21
30727 CCTGTCATCG
* * *
30737 TTCAAGAGGTCTCTCCTATCA
1 TTCAAGAGGTCCCTCCCACCA
* **
30758 TTCAAGAGGCCCCTATCATCCA
1 TTCAAGAGGTCCCTCCCA-CCA
*
30780 -TCAAGA-GTCCCCTCCCACCG
1 TTCAAGAGGT-CCCTCCCACCA
* ** * *
30800 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGTCCCTCCCACCA
*
30821 TTGAAGAGGTCCCTCCCACCA
1 TTCAAGAGGTCCCTCCCACCA
30842 TTCAAGAG
1 TTCAAGAG
30850 TCCGATTCAT
Statistics
Matches: 67, Mismatches: 21, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
20 3 0.04
21 61 0.91
22 3 0.04
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGTCCCTCCCACCA
Found at i:32396 original size:20 final size:20
Alignment explanation
Indices: 32371--32448 Score: 113
Period size: 20 Copynumber: 3.9 Consensus size: 20
32361 AGGTACACTT
*
32371 TCGCAATGCTAAACTCAAAA
1 TCGCAATGCGAAACTCAAAA
*
32391 TCGCAATGCGAAAGTCAAAA
1 TCGCAATGCGAAACTCAAAA
32411 TCGCAATGCGAAAGC-CAAAA
1 TCGCAATGCGAAA-CTCAAAA
*
32431 TCGCAATGCGAAAGTCAA
1 TCGCAATGCGAAACTCAA
32449 TTCGCGTTGC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (20 bp):
TCGCAATGCGAAACTCAAAA
Found at i:32415 original size:40 final size:40
Alignment explanation
Indices: 32371--32448 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 40
32361 AGGTACACTT
*
32371 TCGCAATGCTAAA-CTCAAAATCGCAATGCGAAAGTCAAAA
1 TCGCAATGCGAAAGC-CAAAATCGCAATGCGAAAGTCAAAA
32411 TCGCAATGCGAAAGCCAAAATCGCAATGCGAAAGTCAA
1 TCGCAATGCGAAAGCCAAAATCGCAATGCGAAAGTCAA
32449 TTCGCGTTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 35 0.97
41 1 0.03
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (40 bp):
TCGCAATGCGAAAGCCAAAATCGCAATGCGAAAGTCAAAA
Found at i:32496 original size:34 final size:34
Alignment explanation
Indices: 32452--32583 Score: 194
Period size: 34 Copynumber: 3.9 Consensus size: 34
32442 AAGTCAATTC
* * *
32452 GCGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-T
*
32487 -CGTTGCGATAGTCAAATTCGCGTTGCAATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
* *
32520 GCGTTACAATAGTCAAATTCGCGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
32554 GCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGAT
32584 AGTCAAATTC
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
33 1 0.01
34 86 0.99
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (34 bp):
GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:32512 original size:20 final size:20
Alignment explanation
Indices: 32437--32611 Score: 118
Period size: 20 Copynumber: 9.7 Consensus size: 20
32427 AAAATCGCAA
*
32437 TGCGAAAGTC-AATTCGCGT
1 TGCGATAGTCAAATTCGCGT
* * *
32456 TGCGATAGTCTAATACGCTT
1 TGCGATAGTCAAATTCGCGT
*
32476 TGCGAT--T----TTCTCGT
1 TGCGATAGTCAAATTCGCGT
32490 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCGCGT
* *
32510 TGC-A-A-T---TTTTGCGT
1 TGCGATAGTCAAATTCGCGT
* *
32524 TACAATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCGCGT
*
32544 TGCGAT--T----TTTGCGT
1 TGCGATAGTCAAATTCGCGT
32558 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCGCGT
32578 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCGCGT
*
32598 TGCGATATTCAAAT
1 TGCGATAGTCAAAT
32612 GAATGTGTAA
Statistics
Matches: 120, Mismatches: 17, Indels: 37
0.69 0.10 0.21
Matches are distributed among these distances:
14 30 0.25
15 1 0.01
16 3 0.03
17 2 0.02
18 3 0.03
19 10 0.08
20 71 0.59
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (20 bp):
TGCGATAGTCAAATTCGCGT
Found at i:32834 original size:140 final size:140
Alignment explanation
Indices: 32582--33004 Score: 792
Period size: 140 Copynumber: 3.0 Consensus size: 140
32572 TCGCGTTGCG
* *
32582 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATAACA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
32647 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAAATGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
32712 AATACACATA
131 AATACACATA
*
32722 ATAGTCAAATTCGTGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
32787 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTATACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
*
32852 AATACTCATA
131 AATACACATA
32862 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
32927 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
32992 AATACACATA
131 AATACACATA
33002 ATA
1 ATA
33005 CAACGTTTGC
Statistics
Matches: 274, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 274 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:35378 original size:24 final size:24
Alignment explanation
Indices: 35344--35397 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
35334 CTGAAACATC
35344 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
35368 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
35392 ATCAAA
1 ATCAAA
35398 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:35411 original size:24 final size:24
Alignment explanation
Indices: 35344--35411 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
35334 CTGAAACATC
* * *
35344 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
35368 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
35392 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
35412 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:36249 original size:20 final size:20
Alignment explanation
Indices: 36216--36345 Score: 111
Period size: 20 Copynumber: 6.5 Consensus size: 20
36206 TTGAAATTCA
* *
36216 GCGTTGCAACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
36236 GTGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
**
36256 GCGTTGCGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
*
36277 ACGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* * * *
36297 GCGTTGTGAT-TTACATATTC
1 GCGTTGCGATAGT-CAGAATC
* *
36317 GCATTGCGATAGTCAAAATC
1 GCGTTGCGATAGTCAGAATC
36337 GCGTTGCGA
1 GCGTTGCGA
36346 ATCTGGAAAC
Statistics
Matches: 85, Mismatches: 20, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
19 3 0.04
20 65 0.76
21 15 0.18
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:36283 original size:41 final size:40
Alignment explanation
Indices: 36238--36345 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 40
36228 TCAGAATCGT
**
36238 GTTGCGATAGTCAGAATCGCGTTGCGA-TTATGTATTATCAC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTTACATA-T-TCAC
* *
36279 GTTGCGATAGTCAGAATCGCGTTGTGATTTACATATTCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTTACATATTCAC
* *
36319 ATTGCGATAGTCAAAATCGCGTTGCGA
1 GTTGCGATAGTCAGAATCGCGTTGCGA
36346 ATCTGGAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 27 0.46
41 27 0.46
42 5 0.08
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (40 bp):
GTTGCGATAGTCAGAATCGCGTTGCGATTTACATATTCAC
Found at i:36383 original size:20 final size:19
Alignment explanation
Indices: 36360--36405 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
36350 GGAAACTGAT
* *
36360 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
36380 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
36399 TTGCGAT
1 TTGCGAT
36406 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:36395 original size:19 final size:19
Alignment explanation
Indices: 36371--36407 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
36361 TGCGATACTG
*
36371 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
36390 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
36408 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:39460 original size:21 final size:21
Alignment explanation
Indices: 39436--39484 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
39426 ACTTGTTGTC
39436 GTTGCTAAAAAACAAGTTGAG
1 GTTGCTAAAAAACAAGTTGAG
39457 GTTGCTAAAAAACAAGTTGAG
1 GTTGCTAAAAAACAAGTTGAG
39478 GTTGCTA
1 GTTGCTA
39485 GTCTTGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (21 bp):
GTTGCTAAAAAACAAGTTGAG
Found at i:48031 original size:20 final size:20
Alignment explanation
Indices: 48006--48052 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
47996 AACAAGGGTG
*
48006 AAGGATCTGTTGGCGCAGTA
1 AAGGATCTGTTGGCGCAGCA
48026 AAGGATCTGTTGGCGCAGCA
1 AAGGATCTGTTGGCGCAGCA
48046 AAGGATC
1 AAGGATC
48053 CTGAAGGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (20 bp):
AAGGATCTGTTGGCGCAGCA
Found at i:55839 original size:16 final size:17
Alignment explanation
Indices: 55807--55839 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
55797 ATAAAATTTA
*
55807 AAATTAACATTATTAAT
1 AAATTAACATAATTAAT
55824 AAATTAA-ATAATTAAT
1 AAATTAACATAATTAAT
55840 CAAAGAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTAACATAATTAAT
Found at i:63819 original size:23 final size:23
Alignment explanation
Indices: 63793--63844 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
63783 TCTCCTCTTC
63793 GAAAACCTACCCTTTATTACCTA
1 GAAAACCTACCCTTTATTACCTA
63816 GAAAACCTACCCTTTATTACCTA
1 GAAAACCTACCCTTTATTACCTA
63839 GAAAAC
1 GAAAAC
63845 TAGAGACCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.29, G:0.06, T:0.27
Consensus pattern (23 bp):
GAAAACCTACCCTTTATTACCTA
Found at i:64615 original size:3 final size:3
Alignment explanation
Indices: 64591--64648 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
64581 TACAAAAATG
* *
64591 TAA TAA T-A TAT TAA -AA 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
64637 TAA TAA TAA TAA
1 TAA TAA TAA TAA
64649 AAGACTCGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 4 0.08
3 45 0.92
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:67754 original size:3 final size:3
Alignment explanation
Indices: 67746--67804 Score: 109
Period size: 3 Copynumber: 19.3 Consensus size: 3
67736 CTGCAAAAAT
67746 ATA ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
67792 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
67805 AGACTCGGAC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:73010 original size:23 final size:23
Alignment explanation
Indices: 72983--73033 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
72973 AGAACAAATT
72983 AGTGAATTTGTTAGAAAATCCTA
1 AGTGAATTTGTTAGAAAATCCTA
*
73006 AGTGAATTTGTTAGAAAATCTTA
1 AGTGAATTTGTTAGAAAATCCTA
73029 AGTGA
1 AGTGA
73034 TGAGCTTAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (23 bp):
AGTGAATTTGTTAGAAAATCCTA
Found at i:73042 original size:23 final size:23
Alignment explanation
Indices: 72983--73042 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
72973 AGAACAAATT
**
72983 AGTGAATTTGTTAGAAAATCCTA
1 AGTGAATGAGTTAGAAAATCCTA
** *
73006 AGTGAATTTGTTAGAAAATCTTA
1 AGTGAATGAGTTAGAAAATCCTA
73029 AGTG-ATGAGCTTAG
1 AGTGAATGAG-TTAG
73043 GTAGTGAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 3 0.09
23 30 0.91
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.35
Consensus pattern (23 bp):
AGTGAATGAGTTAGAAAATCCTA
Found at i:73978 original size:51 final size:51
Alignment explanation
Indices: 73869--74056 Score: 231
Period size: 50 Copynumber: 3.7 Consensus size: 51
73859 TGTATATACA
* * *
73869 TACACCAGTGTAAGTATGTGTTAAGTGTTAC--TCTTTTATTTTATTTACT
1 TACACCGGTGTAAGTATGTGTTAAGTGTTACATTTTTTTATTTTATTCACT
* * *
73918 TATGA-CGGTGTAAGTATCTGTTAAGTGTTACATTTTTTTATTGTATTCACT
1 TA-CACCGGTGTAAGTATGTGTTAAGTGTTACATTTTTTTATTTTATTCACT
* * * *
73969 TACACCGGTGT-AGTATGTGTTAAGTGTTATACTTGTTTATTTTATTCATT
1 TACACCGGTGTAAGTATGTGTTAAGTGTTACATTTTTTTATTTTATTCACT
* *
74019 TACACCGATGTAAGTATGTGTTAAGTGCTACATTTTTT
1 TACACCGGTGTAAGTATGTGTTAAGTGTTACATTTTTT
74057 GTAGTATGAA
Statistics
Matches: 116, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
49 26 0.22
50 45 0.39
51 45 0.39
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (51 bp):
TACACCGGTGTAAGTATGTGTTAAGTGTTACATTTTTTTATTTTATTCACT
Found at i:74033 original size:101 final size:100
Alignment explanation
Indices: 73869--74056 Score: 256
Period size: 101 Copynumber: 1.9 Consensus size: 100
73859 TGTATATACA
* * *
73869 TACACCAGTGTAAGTATGTGTTAAGTGTTACTCTTTTATTTTATTTACTTATGACGGTGTAAGTA
1 TACACCAGTGTAAGTATGTGTTAAGTGTTACTCTTTTATTTTATTCACTTATCACGATGTAAGTA
*
73934 TCTGTTAAGTGTTACATTTTTTTATTGTATTCACT
66 TCTGTTAAGTGCTACATTTTTTTATTGTATTCACT
* *
73969 TACACCGGTGT-AGTATGTGTTAAGTGTTA-TACTTGTTTATTTTATTCATTTA-CACCGATGTA
1 TACACCAGTGTAAGTATGTGTTAAGTGTTACT-C-T-TTTATTTTATTCACTTATCA-CGATGTA
*
74031 AGTATGTGTTAAGTGCTACATTTTTT
62 AGTATCTGTTAAGTGCTACATTTTTT
74057 GTAGTATGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
98 1 0.01
99 19 0.25
100 12 0.16
101 45 0.58
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (100 bp):
TACACCAGTGTAAGTATGTGTTAAGTGTTACTCTTTTATTTTATTCACTTATCACGATGTAAGTA
TCTGTTAAGTGCTACATTTTTTTATTGTATTCACT
Found at i:79446 original size:15 final size:16
Alignment explanation
Indices: 79406--79446 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
79396 TTGGTTTGTT
*
79406 TTTAAAT-AATCTTTT
1 TTTAAATAAATCTTTA
79421 TTTAAATTAAAT-TTTA
1 TTTAAA-TAAATCTTTA
79437 TTTAAATAAA
1 TTTAAATAAA
79447 AAACTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 10 0.43
17 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTAAATAAATCTTTA
Found at i:87245 original size:2 final size:2
Alignment explanation
Indices: 87238--87263 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
87228 GTTGATGAAT
87238 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
87264 AATAAAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:109221 original size:26 final size:26
Alignment explanation
Indices: 109191--109240 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
109181 TCAAATGACT
109191 GAAATGTA-TAAAAAGTAGAAGTCATG
1 GAAAT-TACTAAAAAGTAGAAGTCATG
*
109217 GAAATTACTACAAAGTAGAAGTCA
1 GAAATTACTAAAAAGTAGAAGTCA
109241 CTGCAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.22
Consensus pattern (26 bp):
GAAATTACTAAAAAGTAGAAGTCATG
Found at i:111334 original size:12 final size:12
Alignment explanation
Indices: 111317--111341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
111307 ATGTTAAGTT
111317 TTTATTTTTTTA
1 TTTATTTTTTTA
111329 TTTATTTTTTTA
1 TTTATTTTTTTA
111341 T
1 T
111342 CACATAACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:112275 original size:2 final size:2
Alignment explanation
Indices: 112268--112293 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
112258 ATTTTAGTTA
112268 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
112294 TTCTAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112525 original size:34 final size:34
Alignment explanation
Indices: 112480--112546 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
112470 AATAGGAATT
*
112480 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATA
112515 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
112547 CTCTAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:129794 original size:21 final size:21
Alignment explanation
Indices: 129768--129810 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
129758 CCTTGAGCTA
129768 TCGAGTCAAAAAGTAAAAAAC
1 TCGAGTCAAAAAGTAAAAAAC
129789 TCGAGTCAAAAAGTAAAAAAC
1 TCGAGTCAAAAAGTAAAAAAC
129810 T
1 T
129811 AAAAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.16
Consensus pattern (21 bp):
TCGAGTCAAAAAGTAAAAAAC
Found at i:134290 original size:14 final size:15
Alignment explanation
Indices: 134271--134300 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
134261 AATACTTCAT
134271 ACATATTTTA-TAAA
1 ACATATTTTATTAAA
134285 ACATATTTTATTAAA
1 ACATATTTTATTAAA
134300 A
1 A
134301 GGGACATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
ACATATTTTATTAAA
Found at i:135728 original size:15 final size:15
Alignment explanation
Indices: 135708--135738 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
135698 CCCCGAACAA
135708 TATAAGAATCAGTAC
1 TATAAGAATCAGTAC
135723 TATAAGAATCAGTAC
1 TATAAGAATCAGTAC
135738 T
1 T
135739 GAACATCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (15 bp):
TATAAGAATCAGTAC
Found at i:136899 original size:22 final size:22
Alignment explanation
Indices: 136871--136923 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
136861 TCTAAATACT
* *
136871 AATACTAAATAAAAGGAATTTG
1 AATACTAAATAAAAGAAATTCG
136893 AATACTAAATAAAAGAAATTCG
1 AATACTAAATAAAAGAAATTCG
136915 AATATCTAA
1 AATA-CTAA
136924 CTAATATCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.26
Consensus pattern (22 bp):
AATACTAAATAAAAGAAATTCG
Found at i:137726 original size:22 final size:22
Alignment explanation
Indices: 137698--137739 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
137688 TATAATTTTT
137698 TATAAAATTAAAGAATTAAATA
1 TATAAAATTAAAGAATTAAATA
137720 TATAAAATTAAAGAATTAAA
1 TATAAAATTAAAGAATTAAA
137740 GAAAAAGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
TATAAAATTAAAGAATTAAATA
Found at i:140117 original size:17 final size:17
Alignment explanation
Indices: 140083--140116 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
140073 ACACAATATA
140083 TATTTAATATTTATTTT
1 TATTTAATATTTATTTT
*
140100 TATTT-ATATTTCTTTT
1 TATTTAATATTTATTTT
140116 T
1 T
140117 TGGTTGTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTAATATTTATTTT
Found at i:140909 original size:21 final size:21
Alignment explanation
Indices: 140883--140933 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
140873 GCCACTTCGT
140883 TCTTTTTCTCCAAGCTACTTC
1 TCTTTTTCTCCAAGCTACTTC
* * *
140904 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTCTCCAAGCTACTTC
140925 TCTTTTTCT
1 TCTTTTTCT
140934 AATTCACTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.10, C:0.27, G:0.08, T:0.55
Consensus pattern (21 bp):
TCTTTTTCTCCAAGCTACTTC
Found at i:141469 original size:22 final size:22
Alignment explanation
Indices: 141444--141486 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
141434 TTATTTTACA
* *
141444 TTTTGACTTTT-TTTTGTTTGG
1 TTTTTACTTTTATCTTGTTTGG
*
141465 TTTTTTCTTTTATCTTGTTTGG
1 TTTTTACTTTTATCTTGTTTGG
141487 AAAAACTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.05, C:0.07, G:0.16, T:0.72
Consensus pattern (22 bp):
TTTTTACTTTTATCTTGTTTGG
Found at i:142166 original size:13 final size:13
Alignment explanation
Indices: 142148--142174 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
142138 TTTTCTATTT
142148 TCTCTTTTATTAA
1 TCTCTTTTATTAA
142161 TCTCTTTTATTAA
1 TCTCTTTTATTAA
142174 T
1 T
142175 TTTAAATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTCTTTTATTAA
Found at i:142199 original size:131 final size:132
Alignment explanation
Indices: 141965--142227 Score: 467
Period size: 131 Copynumber: 2.0 Consensus size: 132
141955 TTCGATATGT
* *
141965 TTTACCGAGAAGGTCTATGGTTCGAGTCTGTATAGCCCTATATTTTCTATTTTCTCTTTATTAAT
1 TTTACCGAGAAGGTCTATGGTTCGAGCCCGTATAGCCCTATATTTTCTATTTTCTCTTTATTAAT
*
142030 CTCTTTTATTAATTTTAAATATTCGTTAAAATAATAAAAATGAAAATAA-ATTCTTAAAACTAAA
66 CTCTTTTATTAATTTTAAATATTCATTAAAATAATAAAAATGAAAATAATATTCTTAAAACTAAA
142094 AA
131 AA
142096 TTTACCGAGAAGGTCTATGGTTCGAGCCCGTATAGCCCTATATTTTCTATTTTCTCTTTTATTAA
1 TTTACCGAGAAGGTCTATGGTTCGAGCCCGTATAGCCCTATATTTTCTATTTTCTC-TTTATTAA
*
142161 TCTCTTTTATTAATTTTAAATA-TCATTAAATTAATAAAAATGAAAATAATATTCTTAAAACTAA
65 TCTCTTTTATTAATTTTAAATATTCATTAAAATAATAAAAATGAAAATAATATTCTTAAAACTAA
142225 AAA
130 AAA
142228 AACTAAAGCA
Statistics
Matches: 126, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
131 79 0.63
132 47 0.37
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (132 bp):
TTTACCGAGAAGGTCTATGGTTCGAGCCCGTATAGCCCTATATTTTCTATTTTCTCTTTATTAAT
CTCTTTTATTAATTTTAAATATTCATTAAAATAATAAAAATGAAAATAATATTCTTAAAACTAAA
AA
Found at i:158168 original size:33 final size:33
Alignment explanation
Indices: 158131--158196 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
158121 AAAAATTTTA
158131 TAAACATTTTAAAGGTGAACACATATATTATTG
1 TAAACATTTTAAAGGTGAACACATATATTATTG
158164 TAAACATTTTAAAGGTGAACACATATATTATTG
1 TAAACATTTTAAAGGTGAACACATATATTATTG
158197 ATATAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (33 bp):
TAAACATTTTAAAGGTGAACACATATATTATTG
Found at i:159895 original size:185 final size:185
Alignment explanation
Indices: 159662--160051 Score: 660
Period size: 185 Copynumber: 2.1 Consensus size: 185
159652 TTTTCTAATT
* * * *
159662 TATATAA-AAATTAAATGTTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
159726 TTATAAAATAAAAAATTCAAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAAATTCAAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
*
159791 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGG-TTGAGCCCATATGTTA
159846 TATATAATATATTTAATATTTTTTAATT-AAAAAAATAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAA-AGTTTACAATTAATTTAAATAATATATA
* * * *
159910 ATTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 ATTATAAAATAAAAAATTCAAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
159975 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
130 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
160031 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
160052 AAAATTTAAT
Statistics
Matches: 194, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
184 16 0.08
185 178 0.92
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAAATTCAAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
Found at i:167277 original size:24 final size:24
Alignment explanation
Indices: 167250--167402 Score: 297
Period size: 24 Copynumber: 6.4 Consensus size: 24
167240 ATTTTATTAC
*
167250 TTTATATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
167274 TTTACATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
167298 TTTACATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
167322 TTTACATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
167346 TTTACATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
167370 TTTACATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
167394 TTTACATCA
1 TTTACATCA
167403 GCACTCGTAA
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
24 128 1.00
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (24 bp):
TTTACATCAACCAGTTATCTGTCA
Found at i:169790 original size:18 final size:18
Alignment explanation
Indices: 169767--169801 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
169757 AGAAAAAAAT
*
169767 TAATAAATAAATTAATAA
1 TAATAAATAAATAAATAA
169785 TAATAAATAAATAAATA
1 TAATAAATAAATAAATA
169802 TTTTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAATAAATAAATAAATAA
Found at i:177411 original size:5 final size:5
Alignment explanation
Indices: 177396--177490 Score: 59
Period size: 5 Copynumber: 18.0 Consensus size: 5
177386 TACAACTAAT
* * * *
177396 TAAAA TGAAA TAAAA TAAAA T-AAA TAAAA CAAAA CAAAA CAAAATA TACAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA -TAAA-A TA-AAA
* *
177448 TAAAA TAAAGA TGAAAA TGAAAA TGAAAA AAAAA CAAAA -AAAA
1 TAAAA TAAA-A T-AAAA T-AAAA T-AAAA TAAAA TAAAA TAAAA
177491 AACAAAAACA
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
4 8 0.10
5 41 0.53
6 22 0.29
7 6 0.08
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (5 bp):
TAAAA
Found at i:177487 original size:11 final size:11
Alignment explanation
Indices: 177473--177507 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
177463 AATGAAAATG
177473 AAAAAAAAACA
1 AAAAAAAAACA
177484 AAAAAAAAACA
1 AAAAAAAAACA
*
177495 AAAACAAAACA
1 AAAAAAAAACA
177506 AA
1 AA
177508 TTATAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:177598 original size:12 final size:12
Alignment explanation
Indices: 177583--177608 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
177573 GTTTTCAAAC
177583 TTATATACTATT
1 TTATATACTATT
177595 TTATATACTATT
1 TTATATACTATT
177607 TT
1 TT
177609 CAAAAGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATATACTATT
Found at i:177630 original size:42 final size:40
Alignment explanation
Indices: 177561--177658 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 40
177551 TAACTTAAAA
* ** *
177561 ATTTTCAAAATAGTTTTCAAACTTATATACTATTTTATATACT
1 ATTTTCAAAATAGTTTTAAAAAATATATA-TATTATA-ATA-T
*
177604 ATTTTCAAAA-GGTTTTAAAAAATATATATATTATAATAT
1 ATTTTCAAAATAGTTTTAAAAAATATATATATTATAATAT
177643 -TTTTCAAAATAGTTTT
1 ATTTTCAAAATAGTTTT
177659 TCCAAAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
38 9 0.19
39 6 0.12
40 3 0.06
41 6 0.12
42 14 0.29
43 10 0.21
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (40 bp):
ATTTTCAAAATAGTTTTAAAAAATATATATATTATAATAT
Found at i:177676 original size:81 final size:77
Alignment explanation
Indices: 177520--177677 Score: 185
Period size: 81 Copynumber: 2.0 Consensus size: 77
177510 ATAAAGTATG
* * * * *
177520 TATATTATTTTCAAAGGTTTTCAAAACTATATAACTTAAAAATTTTCAAAATAGTTTTCAAACTT
1 TATACTATTTTCAAAAGTTTTAAAAAATATATAACTTAAAAATTTTCAAAATAGTTTTCAAAATT
177585 ATATACTATTTTA
66 ATATA-TATTTTA
*
177598 TATACTATTTTCAAAAGGTTTTAAAAAATATATATA-TTATAATATTTTTCAAAATAGTTTTTCC
1 TATACTATTTTCAAAA-GTTTTAAAAAATATATA-ACTTA-AA-AATTTTCAAAATAG-TTTT-C
177662 AAAATTATAT-TATTTT
60 AAAATTATATATATTTT
177678 CAAAAGGTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
78 14 0.21
79 18 0.26
80 3 0.04
81 19 0.28
82 4 0.06
83 10 0.15
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (77 bp):
TATACTATTTTCAAAAGTTTTAAAAAATATATAACTTAAAAATTTTCAAAATAGTTTTCAAAATT
ATATATATTTTA
Found at i:177688 original size:29 final size:31
Alignment explanation
Indices: 177633--177693 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
177623 AAATATATAT
*
177633 ATTATAATATTTTTCAAAATAGTTTTTCCAAA
1 ATTATAATATTTTTCAAAATAGGTTTT-CAAA
*
177665 ATTATATTA-TTTTC-AAA-AGGTTTTCAAA
1 ATTATAATATTTTTCAAAATAGGTTTTCAAA
177693 A
1 A
177694 CTGTTGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 6 0.22
30 3 0.11
31 5 0.19
32 8 0.30
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (31 bp):
ATTATAATATTTTTCAAAATAGGTTTTCAAA
Found at i:180025 original size:21 final size:21
Alignment explanation
Indices: 179986--180025 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
179976 AAGACTTTAT
*
179986 TTTCAAAATACAAAGATGATA
1 TTTCAAAATACAAAAATGATA
**
180007 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
180026 AAATAGTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:183900 original size:22 final size:22
Alignment explanation
Indices: 183832--183907 Score: 93
Period size: 23 Copynumber: 3.4 Consensus size: 22
183822 CAGGAAGGAT
*
183832 CGATACCCCCTTTGCATGGGTAC
1 CGATACCCCC-TTGAATGGGTAC
183855 CGATACCCTCCTTGAATGGGTAC
1 CGATACCC-CCTTGAATGGGTAC
183878 CGATACCCCCATATG-A-GGGTAC
1 CGATACCCCC-T-TGAATGGGTAC
183900 CGATACCC
1 CGATACCC
183908 TACACGGGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
22 16 0.33
23 29 0.59
24 4 0.08
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.22
Consensus pattern (22 bp):
CGATACCCCCTTGAATGGGTAC
Found at i:187453 original size:66 final size:68
Alignment explanation
Indices: 187330--187459 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 68
187320 ATTAACTCAA
187330 CAAAAACTATATAATGTATAATGTTTTTCAAAATAGGTTTCAAACTTATATACTATTTTCAAAAG
1 CAAAAACTATATAATGTATAATGTTTTTCAAAATAGGTTTCAAACTTATATA-TATTTTCAAAAG
187395 TTTT
65 TTTT
*
187399 CAAAAA-TATAT-AT-TATAATAG-TTTTCAAAATAGTTTTCCCAAAAC-TATAT-TATTTTCAA
1 CAAAAACTATATAATGTATAAT-GTTTTTCAAAATAGGTTT--C-AAACTTATATATATTTTCAA
187458 AA
62 AA
187460 CTATATTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
66 32 0.57
67 3 0.05
68 11 0.20
69 10 0.18
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (68 bp):
CAAAAACTATATAATGTATAATGTTTTTCAAAATAGGTTTCAAACTTATATATATTTTCAAAAGT
TTT
Found at i:187460 original size:17 final size:17
Alignment explanation
Indices: 187438--187476 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
187428 ATAGTTTTCC
187438 CAAAACTATATTATTTT
1 CAAAACTATATTATTTT
187455 CAAAACTATATTATTTT
1 CAAAACTATATTATTTT
187472 CAAAA
1 CAAAA
187477 GGTTTTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (17 bp):
CAAAACTATATTATTTT
Found at i:188122 original size:111 final size:110
Alignment explanation
Indices: 187921--188425 Score: 523
Period size: 111 Copynumber: 4.6 Consensus size: 110
187911 TAATGGAATT
* * ** * * * * *
187921 TTGAACAAGTTTTTCTCATTAATAACTTCTTTTATCTCATC-GAGCGAGTTCTTCTCATTATGAA
1 TTGAAGAAGTTCTTCTCATTAGGAACTTATTCTCTCTCATCAGA-TGAGTTATTCTCATTATGAA
* *
187985 CCCTCTTATTAGAAATATTCGATCCACCTCTGTGATGGATGCCAAGA
65 CCCTCATATTA-AAATGTTCGATCCACCTCTGTGATGGATGCCAAGA
* * * * * * *
188032 TTGGAGAAGTTTTTCTCATTAGGAACTTCTTCTCGCTCGTCAAATGAGTTATTCTCATTATAAAC
1 TTGAAGAAGTTCTTCTCATTAGGAACTTATTCTCTCTCATCAGATGAGTTATTCTCATTATGAAC
* *
188097 CCTCCTATTAAACATGTTC-AGTCCACCTCTGTGATGGATGCCAGGA
66 CCTCATATTAAA-ATGTTCGA-TCCACCTCTGTGATGGATGCCAAGA
* * *
188143 TTGAAGAAGTTCTTCTCATTAGGAACTTTTTCTCTCTCATTAGACGAGTTATTCTCATTATGAAC
1 TTGAAGAAGTTCTTCTCATTAGGAACTTATTCTCTCTCATCAGATGAGTTATTCTCATTATGAAC
* * * *
188208 CCTCATATTGGAAATGTTCGATCCACTTCTGTGATAGATGCCAAGG
66 CCTCATATT-AAAATGTTCGATCCACCTCTGTGATGGATGCCAAGA
* * * * * *
188254 TTGAAGAAGTTTTTCTCATTA-TAAATTAATTCTCTTTCATCGGATGAGTTCTTCTCATTATGAA
1 TTGAAGAAGTTCTTCTCATTAGGAACTT-ATTCTCTCTCATCAGATGAGTTATTCTCATTATGAA
* * * *
188318 CCCTCATATTAGAATGTTCGATCCACCTCTGTGATGAAGGCCAAGG
65 CCCTCATATTAAAATGTTCGATCCACCTCTGTGATGGATGCCAAGA
* * * * * * *
188364 TTGAAAAAGTTCTTCTCATTAGTAAC-TACTTTTCTTTCATCAGACGAGTTCTTCTTATTATG
1 TTGAAGAAGTTCTTCTCATTAGGAACTTA-TTCTCTCTCATCAGATGAGTTATTCTCATTATG
188426 GACTCTTATA
Statistics
Matches: 334, Mismatches: 52, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
109 1 0.00
110 86 0.26
111 243 0.73
112 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.38
Consensus pattern (110 bp):
TTGAAGAAGTTCTTCTCATTAGGAACTTATTCTCTCTCATCAGATGAGTTATTCTCATTATGAAC
CCTCATATTAAAATGTTCGATCCACCTCTGTGATGGATGCCAAGA
Found at i:188322 original size:222 final size:220
Alignment explanation
Indices: 187921--188446 Score: 623
Period size: 222 Copynumber: 2.4 Consensus size: 220
187911 TAATGGAATT
* * * *
187921 TTGAACAAGTTTTTCTCATTAATAACTTCTTT-TATCTCA-TCGAGCGAGTTCTTCTCATTATGA
1 TTGAAAAAGTTCTTCTCATTAGTAACTT-TTTCT-TCTCATTAGA-CGAGTTCTTCTCATTATGA
* * * * *
187984 ACCCTCTTATTAGAAATATTCGATCCACCTCTGTGATGGATGCCAAGATTGGAGAAGTTTTTCTC
63 ACCCTCATATTGGAAATGTTCGATCCACCTCTGTGATAGATGCCAAGATTGAAGAAGTTTTTCTC
* * * *
188049 ATTAGGAACTTCTTCTCGCTCGTCAAATGAGTTATTCTCATTATAAACCCTCCTATTAAACATGT
128 ATTAGGAAATTATTCTCGCTCATCAAATGAGTTATTCTCATTATAAACCCTCATATTAAA-ATGT
* *
188114 TC-AGTCCACCTCTGTGATGGATGCC-AGG
192 TCGA-TCCACCTCTGTGATGAAGGCCAAGG
* * *
188142 ATTGAAGAAGTTCTTCTCATTAGGAACTTTTTCTCTCTCATTAGACGAGTTATTCTCATTATGAA
1 -TTGAAAAAGTTCTTCTCATTAGTAACTTTTTCT-TCTCATTAGACGAGTTCTTCTCATTATGAA
* *
188207 CCCTCATATTGGAAATGTTCGATCCACTTCTGTGATAGATGCCAAGGTTGAAGAAGTTTTTCTCA
64 CCCTCATATTGGAAATGTTCGATCCACCTCTGTGATAGATGCCAAGATTGAAGAAGTTTTTCTCA
* ** ** * * *
188272 TTA-TAAATTAATTCTCTTTCATCGGATGAGTTCTTCTCATTATGAACCCTCATATTAGAATGTT
129 TTAGGAAATT-ATTCTCGCTCATCAAATGAGTTATTCTCATTATAAACCCTCATATTAAAATGTT
188336 CGATCCACCTCTGTGATGAAGGCCAAGG
193 CGATCCACCTCTGTGATGAAGGCCAAGG
* * *
188364 TTGAAAAAGTTCTTCTCATTAGTAACTACTTTTCTT-TCATCAGACGAGTTCTTCTTATTATGGA
1 TTGAAAAAGTTCTTCTCATTAGTAACT--TTTTCTTCTCATTAGACGAGTTCTTCTCATTATGAA
* *
188428 CTCTTATATTGGAAATGTT
64 CCCTCATATTGGAAATGTT
188447 GACTTATTTC
Statistics
Matches: 261, Mismatches: 36, Indels: 15
0.84 0.12 0.05
Matches are distributed among these distances:
221 98 0.38
222 154 0.59
223 9 0.03
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (220 bp):
TTGAAAAAGTTCTTCTCATTAGTAACTTTTTCTTCTCATTAGACGAGTTCTTCTCATTATGAACC
CTCATATTGGAAATGTTCGATCCACCTCTGTGATAGATGCCAAGATTGAAGAAGTTTTTCTCATT
AGGAAATTATTCTCGCTCATCAAATGAGTTATTCTCATTATAAACCCTCATATTAAAATGTTCGA
TCCACCTCTGTGATGAAGGCCAAGG
Found at i:191163 original size:2 final size:2
Alignment explanation
Indices: 191156--191184 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
191146 GACTATTTGA
191156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
191185 ATGTTAATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:192696 original size:16 final size:17
Alignment explanation
Indices: 192675--192710 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
192665 GTGTGTTTCA
192675 TTGTATAT-TATATAGT
1 TTGTATATATATATAGT
192691 TTGTATATACTATATAGT
1 TTGTATATA-TATATAGT
192709 TT
1 TT
192711 ACATTTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.56
Consensus pattern (17 bp):
TTGTATATATATATAGT
Found at i:196697 original size:6 final size:6
Alignment explanation
Indices: 196665--196728 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
196655 AATAAAAGTG
* * * *
196665 AAAT-A AAAT-A AAATAA ATATGA AAATAA AAATAA AAACAA AAACAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* *
196711 AAACAA AAA-CA AAATAA A
1 AAATAA AAATAA AAATAA A
196729 TTATAAACTA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
5 13 0.26
6 37 0.74
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.12
Consensus pattern (6 bp):
AAATAA
Found at i:196707 original size:18 final size:17
Alignment explanation
Indices: 196686--196728 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
196676 AATAAATATG
*
196686 AAAATAAAAATAAAAAC
1 AAAATAAAAACAAAAAC
*
196703 AAAAACAAAAACAAAAAC
1 -AAAATAAAAACAAAAAC
196721 AAAATAAA
1 AAAATAAA
196729 TTATAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.07
Consensus pattern (17 bp):
AAAATAAAAACAAAAAC
Found at i:196793 original size:67 final size:68
Alignment explanation
Indices: 196733--197060 Score: 335
Period size: 67 Copynumber: 4.9 Consensus size: 68
196723 AATAAATTAT
*
196733 AAACTATGTATATTATTTTTAAAAGTTTTCAAAACTATATAACTTA-AA-ATTTTTCAAAATAGT
1 AAACTAT-TATATTATTTTCAAAAGTTTTCAAAACTATATAACTTATAATATTTTTCAAAATAGT
196796 TTTC
65 TTTC
* **
196800 AAACT-TATATACTATTTTCAAAAGGTTTTCAAAA--ATATATTTTATAATATTTTTCAAAATAG
1 AAACTAT-TATATTATTTTCAAAA-GTTTTCAAAACTATATAACTTATAATATTTTTCAAAATAG
196862 TTTTCCC
64 TTTT--C
*
196869 AAA--ATTATATTATTTTCAAAAGTTTTTCAAAACTATATAA-TGTATAATATTTTTTAAAATAG
1 AAACTATTATATTATTTTCAAAAG-TTTTCAAAACTATATAACT-TATAATATTTTTCAAAATAG
196931 TTTTC
64 TTTTC
* * * * *
196936 -AA-TCTTATACTATTTTCAAAAGGTTTCAAAAATATAT-A-TTATAATATTTGTCAAAAATAGT
1 AAACTATTATATTATTTTCAAAAGTTTTCAAAACTATATAACTTATAATATTTTTC-AAAATAGT
196997 TTTCC
65 TTT-C
* * *
197002 AAA--ACTATATTATTTTCAAAAGGTTTTCAAAATTATATAA-TATATAATGTTTTTCAAAA
1 AAACTATTATATTATTTTCAAAA-GTTTTCAAAACTATATAACT-TATAATATTTTTCAAAA
197061 CATTTTTAAA
Statistics
Matches: 223, Mismatches: 21, Indels: 33
0.81 0.08 0.12
Matches are distributed among these distances:
64 11 0.05
65 21 0.09
66 49 0.22
67 91 0.41
68 8 0.04
69 43 0.19
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (68 bp):
AAACTATTATATTATTTTCAAAAGTTTTCAAAACTATATAACTTATAATATTTTTCAAAATAGTT
TTC
Found at i:196798 original size:37 final size:36
Alignment explanation
Indices: 196756--196937 Score: 101
Period size: 31 Copynumber: 5.2 Consensus size: 36
196746 TATTTTTAAA
196756 AGTTTTCAAAACTATATAACTTAAAATTTTTCAAAAT
1 AGTTTTCAAAACTATATAACTT-AAATTTTTCAAAAT
196793 AGTTTTC-AAACT-TATATAC-T--A-TTTTCAAAA-
1 AGTTTTCAAAACTATATA-ACTTAAATTTTTCAAAAT
* * **
196823 GGTTTTCAAAAATATAT-TTTATAATATTTTTCAAAAT
1 AGTTTTCAAAACTATATAACT-TAA-ATTTTTCAAAAT
196860 AGTTTTCCCAAAA-T-TAT-A-TT--A-TTTTC-AAA-
1 AGTTTT--CAAAACTATATAACTTAAATTTTTCAAAAT
* *
196889 AGTTTTTCAAAACTATATAATGTATAATATTTTTTAAAAT
1 AG-TTTTCAAAACTATATAA-CT-TAA-ATTTTTCAAAAT
196929 AGTTTTCAA
1 AGTTTTCAA
196938 TCTTATACTA
Statistics
Matches: 113, Mismatches: 7, Indels: 48
0.67 0.04 0.29
Matches are distributed among these distances:
28 5 0.04
29 3 0.03
30 16 0.14
31 19 0.17
32 6 0.05
33 1 0.01
34 1 0.01
35 7 0.06
36 17 0.15
37 16 0.14
38 5 0.04
39 15 0.13
40 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.45
Consensus pattern (36 bp):
AGTTTTCAAAACTATATAACTTAAATTTTTCAAAAT
Found at i:196984 original size:133 final size:134
Alignment explanation
Indices: 196741--197060 Score: 472
Period size: 133 Copynumber: 2.4 Consensus size: 134
196731 ATAAACTATG
*
196741 TATATTATTTTTAAAAGTTTTCAAAACTATATAACTTA-AA-ATTTTTCAAAATAGTTTTCAAAC
1 TATATTATTTTCAAAAGTTTTCAAAACTATATAA-TTATAATATTTTTCAAAATAGTTTTCAAAC
* *
196804 TTATATACTATTTTCAAAAGGTTTTCAAAAATATATTTTATAATATTTTTC-AAAATAGTTTTCC
65 TTATATACTATTTTCAAAAGGTTTTCAAAAATATATATTATAATATTTGTCAAAAATAGTTTT-C
*
196868 CAAAAT
129 CAAAAC
* *
196874 TATATTATTTTCAAAAGTTTTTCAAAACTATATAATGTATAATATTTTTTAAAATAGTTTTCAAT
1 TATATTATTTTCAAAAG-TTTTCAAAACTATATAAT-TATAATATTTTTCAAAATAGTTTTCAAA
196939 C-T-TATACTATTTTCAAAAGG-TTTCAAAAATATATATTATAATATTTGTCAAAAATAGTTTTC
64 CTTATATACTATTTTCAAAAGGTTTTCAAAAATATATATTATAATATTTGTCAAAAATAGTTTTC
197001 CAAAAC
129 CAAAAC
* *
197007 TATATTATTTTCAAAAGGTTTTCAAAATTATATAATATATAATGTTTTTCAAAA
1 TATATTATTTTCAAAA-GTTTTCAAAACTATATAAT-TATAATATTTTTCAAAA
197061 CATTTTTAAA
Statistics
Matches: 171, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
133 98 0.57
134 49 0.29
135 3 0.02
136 21 0.12
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (134 bp):
TATATTATTTTCAAAAGTTTTCAAAACTATATAATTATAATATTTTTCAAAATAGTTTTCAAACT
TATATACTATTTTCAAAAGGTTTTCAAAAATATATATTATAATATTTGTCAAAAATAGTTTTCCA
AAAC
Found at i:200928 original size:24 final size:25
Alignment explanation
Indices: 200901--200959 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
200891 TAAATTAATT
200901 TTTTAATAATTTAA-TT-TTGAAGTA
1 TTTTAATAATTTAATTTATTGAA-TA
*
200925 TTTTTAT-ATTTAATTTATTGAATA
1 TTTTAATAATTTAATTTATTGAATA
*
200949 TCTTAATAATT
1 TTTTAATAATT
200960 GTTTATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 6 0.21
24 15 0.52
25 8 0.28
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (25 bp):
TTTTAATAATTTAATTTATTGAATA
Found at i:204363 original size:106 final size:106
Alignment explanation
Indices: 203822--205218 Score: 2166
Period size: 106 Copynumber: 13.4 Consensus size: 106
203812 CATTGTTCCA
* * * ** * *
203822 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTT-GTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
* * * *
203886 CAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** * * *
203927 AGTCCAACATCCTTCGTTGTGAAGTTGAAATTGATTCTG-AA-T--GAA-AT-TTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
203986 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
204027 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
*
204091 CAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
204132 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA--AATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
* * *
204195 CAGCGGTCCCTTCGTCGTGAAGTTAAACATACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
204236 AGTCCAATATCCTTCGATGTGAAGTCGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
204301 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
204342 AGTCCAATATCCTCCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
204407 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * * *
204448 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGATTCTG-AA-T--GAA-AT-TTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
204507 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
204548 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
204612 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * ** *
204653 AGTCCAATACCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA--AATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
* *
204716 CAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
204757 AGTCCAATATCCTTCGATGTGAAGTCGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
204822 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
204863 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGATTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
204928 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
204969 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
205034 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
205075 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
205140 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
205181 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
205219 AAAGGCTGTA
Statistics
Matches: 1203, Mismatches: 70, Indels: 37
0.92 0.05 0.03
Matches are distributed among these distances:
99 3 0.00
100 168 0.14
101 6 0.00
102 5 0.00
104 198 0.16
105 234 0.19
106 589 0.49
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:204860 original size:521 final size:521
Alignment explanation
Indices: 203822--205218 Score: 2481
Period size: 521 Copynumber: 2.7 Consensus size: 521
203812 CATTGTTCCA
* * ** * *
203822 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTT-GTGACAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
* * * * *
203886 CAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAACATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
203951 TTGAAATTGATTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
131 TTGAAATTGATTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
204016 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGT
196 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGT
*
204081 TGTTGACAAGCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTT
261 TGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTT
204146 CGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTTGTTGACAACCAGCGGTCCCTTCGTC
326 CGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTTGTTGACAACCAGCGGTCCCTTCGTC
204211 GTGAAGTTAAACATACGTTGTCTGGAGTCCAATATCCTTCGATGTGAAGTCGAAATTGGCTCTGA
391 GTGAAGTTAAACATACGTTGTCTGGAGTCCAATATCCTTCGATGTGAAGTCGAAATTGGCTCTGA
204276 AATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
456 AATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
204341 G
521 G
*
204342 AGTCCAATATCCTCCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
204407 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
204472 TTGAAATTGATTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
131 TTGAAATTGATTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
204537 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGT
196 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGT
*
204602 TGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATACCCTT
261 TGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTT
204667 CGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTTGTTGACAACCAGCGGTCCCTTCGTC
326 CGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTTGTTGACAACCAGCGGTCCCTTCGTC
*
204732 GTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGATGTGAAGTCGAAATTGGCTCTGA
391 GTGAAGTTAAACATACGTTGTCTGGAGTCCAATATCCTTCGATGTGAAGTCGAAATTGGCTCTGA
204797 AATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
456 AATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
204862 G
521 G
* * *
204863 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGATTATTGACAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
204928 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
** * *
204993 TTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGATTCTG-AA-TGA-AA-TT--TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
* *
205058 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
190 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGA
* *
205123 AGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
255 AGTT-GTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
*
205188 TATCCTTCGTTGTGAAGTTGAAATTGGCTCT
319 TATCCTTCGCTGTGAAGTTGAAATTGGCTCT
205219 AAAGGCTGTA
Statistics
Matches: 840, Mismatches: 29, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
520 50 0.06
521 594 0.71
522 2 0.00
523 3 0.00
524 2 0.00
525 2 0.00
527 100 0.12
528 87 0.10
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (521 bp):
AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGATTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGT
TGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTT
CGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTTGTTGACAACCAGCGGTCCCTTCGTC
GTGAAGTTAAACATACGTTGTCTGGAGTCCAATATCCTTCGATGTGAAGTCGAAATTGGCTCTGA
AATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
G
Found at i:207020 original size:26 final size:25
Alignment explanation
Indices: 206966--207022 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
206956 GAGACATGTG
*
206966 AATGCAATGAAAAAAAAGGAATCAT
1 AATGCAATGAAAAAAAAGGAATCAA
* *
206991 AATGCGAATGTAAAGAAAAGTAA-CAA
1 AATGC-AATG-AAAAAAAAGGAATCAA
207017 AATGCA
1 AATGCA
207023 CAACATGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 6 0.22
26 11 0.41
27 10 0.37
ACGTcount: A:0.58, C:0.09, G:0.18, T:0.16
Consensus pattern (25 bp):
AATGCAATGAAAAAAAAGGAATCAA
Found at i:210781 original size:27 final size:27
Alignment explanation
Indices: 210735--210786 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
210725 ATGTTTTCTA
*
210735 ATTTTCAAAAAATAAAAAATGAAAACT
1 ATTTTCAAAAAATAAAAAATAAAAACT
*
210762 ATTTTCCAAAAAA-AAGAAATAAAAA
1 ATTTT-CAAAAAATAAAAAATAAAAA
210787 TAGAGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (27 bp):
ATTTTCAAAAAATAAAAAATAAAAACT
Found at i:215039 original size:2 final size:2
Alignment explanation
Indices: 215028--215056 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
215018 GCCCAAAGGT
215028 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
215057 AATATTCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:224269 original size:17 final size:17
Alignment explanation
Indices: 224249--224281 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
224239 TGTATTTTAA
224249 ATTAATAAA-ATATTTTT
1 ATTAA-AAATATATTTTT
224266 ATTAAAAATATATTTT
1 ATTAAAAATATATTTT
224282 AACCTCTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTAAAAATATATTTTT
Found at i:224514 original size:12 final size:12
Alignment explanation
Indices: 224497--224534 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
224487 TCGGTTGGCT
224497 TAACTGCTAATA
1 TAACTGCTAATA
*
224509 TAACTG--AATT
1 TAACTGCTAATA
224519 TAACTGCTAATA
1 TAACTGCTAATA
224531 TAAC
1 TAAC
224535 ATTGGCAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (12 bp):
TAACTGCTAATA
Found at i:230321 original size:15 final size:15
Alignment explanation
Indices: 230292--230331 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
230282 GATTTTGTGA
230292 TTTTGAAA-T-CAAG
1 TTTTGAAATTACAAG
230305 TTTTGAAATTACAAG
1 TTTTGAAATTACAAG
230320 TTTTGAAATTAC
1 TTTTGAAATTAC
230332 TCCCCCTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 8 0.32
14 1 0.04
15 16 0.64
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (15 bp):
TTTTGAAATTACAAG
Found at i:231309 original size:26 final size:26
Alignment explanation
Indices: 231280--231336 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
231270 GATGAACATA
231280 GTTTCTTGTTAGGAACAAGATTTACG
1 GTTTCTTGTTAGGAACAAGATTTACG
231306 GTTTCTTGTTAGGAACAAGATTTACG
1 GTTTCTTGTTAGGAACAAGATTTACG
231332 GTTTC
1 GTTTC
231337 AACAATTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (26 bp):
GTTTCTTGTTAGGAACAAGATTTACG
Found at i:232501 original size:20 final size:20
Alignment explanation
Indices: 232464--232502 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
232454 AGATTGAGTG
* * *
232464 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
232484 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
232503 AGTTTAGGAG
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:232725 original size:20 final size:21
Alignment explanation
Indices: 232680--232740 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
232670 TTACCCTGTG
232680 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
232703 GGGGGAATCGGTTCCCT-AAA
1 GGGGGAATCGGTTCCCTCAAA
*
232723 GGGGGAATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
232741 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 19 0.53
21 1 0.03
22 3 0.08
23 13 0.36
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:239516 original size:344 final size:343
Alignment explanation
Indices: 238889--239580 Score: 1258
Period size: 344 Copynumber: 2.0 Consensus size: 343
238879 CCCCTTAAAA
* * *
238889 AGCATATATGATTTTTTCTGCTATTTTTCTGACCTTGGATGGCCTTGCACGCTCCCCCACGCACC
1 AGCATATAGGAATTTTTCTGCTATTTTTCTGACCTTGGATGGCCCTGCACGCTCCCCCACGCACC
*
238954 GTCGCTGCACGTGGGGAAATCCCACTGCATGGTGGGTTTCTAGAAACGAGCTGACCCGATCCGAC
66 GTCGCTACACGTGGGGAAATCCCACTGCATGGTGGGTTTCTAGAAACGAGCTGACCCGATCCGAC
*
239019 CCACCTGTCCGACCCGACCTACCGGGTCCAACCCGAACCGAATATGTAAGCCGTTGACCATTGAT
131 CCACCTGTCCAACCCGACCTACCGGGTCCAACCCGAACCGAATATGTAAGCCGTTGACCATTGAT
239084 CGTTGATCATTAACAAACCATTAAAGTTTTTCAAAAACTTTTATCTGGACGTTTTTCGACGTTCT
196 CGTTGATCATTAACAAACCATTAAAGTTTTTCAAAAACTTTTATCTGGACGTTTTTCGACGTTCT
*
239149 GAGTCTAATTTTACAATTTGTTTTGCCAAATTATGACCCAAAAACCCTAAATTGACCCGTTAATC
261 GAGTCTAATTTTACAATTTGTTTTGCCAAATTATGACCC-AAAACCCTAAATAGACCCGTTAATC
239214 CAAAAATGCTTAGTATTTT
325 CAAAAATGCTTAGTATTTT
239233 AGCATATAGGAATTTTTCTGCTATTTTTCTGACCTTGGATGGCCCTGCACGCTCCCCCACGCACC
1 AGCATATAGGAATTTTTCTGCTATTTTTCTGACCTTGGATGGCCCTGCACGCTCCCCCACGCACC
239298 GTCGCTACACGTGGGGAAATCCCACTGCATGGTGGGTTTCTAGAAACGAGCTGACCCGATCCGAC
66 GTCGCTACACGTGGGGAAATCCCACTGCATGGTGGGTTTCTAGAAACGAGCTGACCCGATCCGAC
*
239363 CCACCTGTCCAACCCGACCTACCGGGTCCAACTCGAACCGAATATGTAAGCCGTTGACCATTGAT
131 CCACCTGTCCAACCCGACCTACCGGGTCCAACCCGAACCGAATATGTAAGCCGTTGACCATTGAT
* * * *
239428 CGTTGATCATTGACAAACCATTAAATTTTTTCAAAAACTTTTATCTTGATGTTTTTCGACGTTCT
196 CGTTGATCATTAACAAACCATTAAAGTTTTTCAAAAACTTTTATCTGGACGTTTTTCGACGTTCT
* *
239493 GAGTCTAATTTTACAATTTGTTTTGCCAAATTATGACTCAAAAGCCTAAATAGACCCGTTAATCC
261 GAGTCTAATTTTACAATTTGTTTTGCCAAATTATGACCCAAAACCCTAAATAGACCCGTTAATCC
239558 AAAAATGCTTAGTATTTT
326 AAAAATGCTTAGTATTTT
239576 AGCAT
1 AGCAT
239581 TTTTGCTTAT
Statistics
Matches: 335, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
343 47 0.14
344 288 0.86
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (343 bp):
AGCATATAGGAATTTTTCTGCTATTTTTCTGACCTTGGATGGCCCTGCACGCTCCCCCACGCACC
GTCGCTACACGTGGGGAAATCCCACTGCATGGTGGGTTTCTAGAAACGAGCTGACCCGATCCGAC
CCACCTGTCCAACCCGACCTACCGGGTCCAACCCGAACCGAATATGTAAGCCGTTGACCATTGAT
CGTTGATCATTAACAAACCATTAAAGTTTTTCAAAAACTTTTATCTGGACGTTTTTCGACGTTCT
GAGTCTAATTTTACAATTTGTTTTGCCAAATTATGACCCAAAACCCTAAATAGACCCGTTAATCC
AAAAATGCTTAGTATTTT
Found at i:239589 original size:21 final size:21
Alignment explanation
Indices: 239563--239603 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
239553 AATCCAAAAA
239563 TGCTTA-GTATTTTAGCATTTT
1 TGCTTATGTATTTTAG-ATTTT
*
239584 TGCTTATTTATTTTAGATTT
1 TGCTTATGTATTTTAGATTT
239604 GGTTATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.20, C:0.07, G:0.12, T:0.61
Consensus pattern (21 bp):
TGCTTATGTATTTTAGATTTT
Found at i:241662 original size:91 final size:89
Alignment explanation
Indices: 241560--241724 Score: 267
Period size: 91 Copynumber: 1.8 Consensus size: 89
241550 ATTTAATTTC
*
241560 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCCCAATATGATTAGAGTAACT
1 AATTAATTAAATATAGATTTAATTAATTTAAAATAAT-AAAA-CCCCAATATGATTAGAGTAACT
241625 TGGATATAAAATGATTATTGAATATT
64 TGGATATAAAATGATTATTGAATATT
** *
241651 AATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCTTAATATGATTAGGGTAACTTG
1 AATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCCAATATGATTAGAGTAACTTG
*
241716 GCTATAAAA
66 GATATAAAA
241725 GGGTGTGTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
89 29 0.42
90 4 0.06
91 36 0.52
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (89 bp):
AATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCCAATATGATTAGAGTAACTTG
GATATAAAATGATTATTGAATATT
Found at i:254850 original size:37 final size:36
Alignment explanation
Indices: 254794--254874 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 36
254784 ACCATTCTTA
*
254794 TTTTC-AACAAACATCTACCAAACTTTGAAAAACATT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACA-T
*
254830 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
254866 TTTTCAAAG
1 TTTTCAAAG
254875 TTGGTTGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 15 0.36
37 27 0.64
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
Found at i:263007 original size:24 final size:24
Alignment explanation
Indices: 262980--263099 Score: 113
Period size: 23 Copynumber: 5.1 Consensus size: 24
262970 CGAACCTGTT
262980 AATGAACACGTTCGTGAACATATA
1 AATGAACACGTTCGTGAACATATA
*
263004 AATGAACACGTTCGCGAACAT-TA
1 AATGAACACGTTCGTGAACATATA
* * * *
263027 AACGAATATGTTCATGAACATATA
1 AATGAACACGTTCGTGAACATATA
* * * *
263051 AACGAACACATT-TTTAA-ATATTA
1 AATGAACACGTTCGTGAACATA-TA
*
263074 AATGAACATGTTCGTGAACA-ATA
1 AATGAACACGTTCGTGAACATATA
263097 AAT
1 AAT
263100 AAACGAGAAG
Statistics
Matches: 76, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
22 3 0.04
23 37 0.49
24 35 0.46
25 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (24 bp):
AATGAACACGTTCGTGAACATATA
Found at i:274140 original size:48 final size:47
Alignment explanation
Indices: 274041--274140 Score: 119
Period size: 47 Copynumber: 2.1 Consensus size: 47
274031 TCATCCAACT
** * * *
274041 ATAATGACTCATTTTTGTGCCACAAGCTTATGTAATGTCTTGTAACT
1 ATAATGACTCATTTTTGCCCCACAAGCATATGTAATATCTTGTAACC
** *
274088 ATAATGACTCATTTTTGCCCCGTAAGCCATATGTAATATTTTGTAACC
1 ATAATGACTCATTTTTGCCCCACAAG-CATATGTAATATCTTGTAACC
274136 ATAAT
1 ATAAT
274141 TACTATGGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 22 0.50
48 22 0.50
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (47 bp):
ATAATGACTCATTTTTGCCCCACAAGCATATGTAATATCTTGTAACC
Found at i:274725 original size:69 final size:69
Alignment explanation
Indices: 274614--274753 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 69
274604 TCGAACTTCA
274614 AATTTAAATAAACTATTCTATTGTTCTAATCAAATTTCACCGAGTCACTAAGAAAAGAACATACA
1 AATTTAAATAAACTATTCTATTGTTCTAATCAAATTTCACCGAGTCACTAAGAAAAGAACATACA
274679 TTGT
66 TTGT
* *
274683 AATTTAAATCAATTATTCTATTGTTCTAATCAAATTTCACCGAGTCACTAAGAAAAGAACATACA
1 AATTTAAATAAACTATTCTATTGTTCTAATCAAATTTCACCGAGTCACTAAGAAAAGAACATACA
274748 TTGT
66 TTGT
274752 AA
1 AA
274754 ATGTCTAATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.34
Consensus pattern (69 bp):
AATTTAAATAAACTATTCTATTGTTCTAATCAAATTTCACCGAGTCACTAAGAAAAGAACATACA
TTGT
Found at i:275281 original size:31 final size:31
Alignment explanation
Indices: 275245--275304 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
275235 AACTTAAAAG
* *
275245 AGTTTTGCAATACCGAGATTTAAATAATTTT
1 AGTTTTACAATACCGAAATTTAAATAATTTT
**
275276 AGTTTTACAATATTGAAATTTAAATAATT
1 AGTTTTACAATACCGAAATTTAAATAATT
275305 CATACAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACCGAAATTTAAATAATTTT
Found at i:275816 original size:20 final size:19
Alignment explanation
Indices: 275740--275816 Score: 54
Period size: 20 Copynumber: 4.1 Consensus size: 19
275730 TAACAAATCC
*
275740 AAAA-AAATATTAT-ATTT
1 AAAATAAATATAATAATTT
* *
275757 AAACTTAAATCAAAATAA-TT
1 AAA-ATAAAT-ATAATAATTT
275777 AAAATAAATATAA-AATTTT
1 AAAATAAATATAATAA-TTT
*
275796 AATAATATATATAATAATTT
1 AA-AATAAATATAATAATTT
275816 A
1 A
275817 TATGATATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
17 5 0.11
18 3 0.07
19 13 0.28
20 22 0.48
21 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATAAATATAATAATTT
Found at i:275825 original size:21 final size:20
Alignment explanation
Indices: 275775--275815 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
275765 ATCAAAATAA
*
275775 TTAA-AATAAATATAAAATT
1 TTAATAATATATATAAAATT
275794 TTAATAATATATATAATAATT
1 TTAATAATATATATAA-AATT
275815 T
1 T
275816 ATATGATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATAATATATATAAAATT
Found at i:275896 original size:12 final size:12
Alignment explanation
Indices: 275879--275982 Score: 74
Period size: 12 Copynumber: 8.7 Consensus size: 12
275869 ATTTATTTAA
275879 AAAATTAATATT
1 AAAATTAATATT
275891 AAAATTAATATCT
1 AAAATTAATAT-T
*
275904 ATAATATAATATT
1 AAAAT-TAATATT
*
275917 AAAAATTATTATT
1 -AAAATTAATATT
* *
275930 -TAATTTAT-TT
1 AAAATTAATATT
275940 AAAAATTAATATT
1 -AAAATTAATATT
*
275953 AAAATCAA-A-T
1 AAAATTAATATT
*
275963 ATAATATAATA-T
1 AAAAT-TAATATT
275975 AAAATTAA
1 AAAATTAA
275983 ATATAAAACC
Statistics
Matches: 72, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
10 7 0.10
11 11 0.15
12 30 0.42
13 14 0.19
14 10 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:275942 original size:63 final size:62
Alignment explanation
Indices: 275824--275983 Score: 230
Period size: 63 Copynumber: 2.5 Consensus size: 62
275814 TTATATGATA
275824 TAAAATTAAATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTTAAAAAATTAATA
1 TAAAATT-AATATCTATAATATAATATT--AAAAATTAATATTTAATTTATTT-AAAAATTAATA
275889 T
62 T
*
275890 TAAAATTAATATCTATAATATAATATTAAAAATTATTATTTAATTTATTTAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAATTAATAT
* * *
275952 TAAAATCAAATATAATATAATATAAAATTAAA
1 TAAAAT-TAATAT-CTATAATATAATATTAAA
275984 TATAAAACCT
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
62 18 0.20
63 27 0.31
64 16 0.18
65 20 0.23
66 7 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (62 bp):
TAAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAATTAATAT
Found at i:275979 original size:22 final size:23
Alignment explanation
Indices: 275946--275988 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
275936 ATTTAAAAAT
275946 TAATATTAAAATCAAATATAATA
1 TAATATTAAAATCAAATATAATA
*
275969 TAATA-TAAAATTAAATATAA
1 TAATATTAAAATCAAATATAA
275989 AACCTCTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAATATTAAAATCAAATATAATA
Found at i:275987 original size:12 final size:11
Alignment explanation
Indices: 275840--275990 Score: 56
Period size: 12 Copynumber: 12.9 Consensus size: 11
275830 TAAATATCTA
*
275840 TAATATAATAT
1 TAATATAAAAT
275851 TAA-A-AAAAT
1 TAATATAAAAT
* *
275860 TAATATTTAATT
1 TAATA-TAAAAT
* *
275872 TATTTAAAAAAT
1 TA-ATATAAAAT
275884 TAATATTAAAAT
1 TAATA-TAAAAT
*
275896 TAATATCTATAAT
1 TAATA--TAAAAT
275909 ATAATATTAAAAAT
1 -TAATA-T-AAAAT
* **
275923 TATTATTTAAT
1 TAATATAAAAT
* *
275934 TTATTTAAAAAT
1 TAATAT-AAAAT
275946 TAATATTAAAAT
1 TAATA-TAAAAT
* *
275958 CAA-ATATAAT
1 TAATATAAAAT
275968 ATAATATAAAAT
1 -TAATATAAAAT
275980 TAAATATAAAA
1 T-AATATAAAA
275991 CCTCTTTGAA
Statistics
Matches: 100, Mismatches: 27, Indels: 25
0.66 0.18 0.16
Matches are distributed among these distances:
9 7 0.07
10 7 0.07
11 15 0.15
12 49 0.49
13 13 0.13
14 9 0.09
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATATAAAAT
Found at i:279539 original size:27 final size:28
Alignment explanation
Indices: 279477--279541 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
279467 TACATAATAT
* **
279477 TTTGAA-AAATTATAATAATAAAAGGTT
1 TTTGAATAAAATATAATAATAAAAGGAA
279504 TTCTGGAATAAAATATAATAATAAAA-GAA
1 TT-T-GAATAAAATATAATAATAAAAGGAA
279533 TTTGAATAA
1 TTTGAATAA
279542 GTAATTAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 8 0.25
28 2 0.06
29 6 0.19
30 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.34
Consensus pattern (28 bp):
TTTGAATAAAATATAATAATAAAAGGAA
Found at i:279546 original size:21 final size:21
Alignment explanation
Indices: 279518--279557 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
279508 GGAATAAAAT
279518 ATAATAATAAAAG-AATTTGA
1 ATAATAATAAAAGTAATTTGA
*
279538 ATAAGTAATTAAAGTAATTT
1 ATAA-TAATAAAAGTAATTT
279558 ACAACATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (21 bp):
ATAATAATAAAAGTAATTTGA
Found at i:279830 original size:31 final size:30
Alignment explanation
Indices: 279759--279854 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 30
279749 TTAGTAAAAA
* * *
279759 AAATTAATTTTAAATTTAACTTCTAAATTTT
1 AAATTAATATT-AATTTAACCTCTAAAATTT
*
279790 AAATAAATATTAATTTAACCTCTAAAAATTT
1 AAATTAATATTAATTTAACCTCT-AAAATTT
*
279821 AAATTAATA-TAATTATAACC-CTTAAACTTT
1 AAATTAATATTAATT-TAACCTC-TAAAATTT
279851 AAAT
1 AAAT
279855 AAAATATCAG
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
30 27 0.48
31 29 0.52
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATTAATATTAATTTAACCTCTAAAATTT
Found at i:279861 original size:31 final size:30
Alignment explanation
Indices: 279771--279857 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
279761 ATTAATTTTA
* *
279771 AATTTAACTTC-TAAATTTTAAATAAATATT
1 AATTTAACCTCTTAAAATTTAAATAAATA-T
* *
279801 AATTTAACCTCTAAAAATTTAAATTAATAT
1 AATTTAACCTCTTAAAATTTAAATAAATAT
*
279831 AATTATAACC-CTTAAACTTTAAATAAA
1 AATT-TAACCTCTTAAAATTTAAATAAA
279858 ATATCAGTCT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 29 0.60
31 19 0.40
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.40
Consensus pattern (30 bp):
AATTTAACCTCTTAAAATTTAAATAAATAT
Found at i:283061 original size:22 final size:21
Alignment explanation
Indices: 283027--283067 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
283017 ATAATTATTT
283027 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
283048 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
283068 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:284582 original size:30 final size:29
Alignment explanation
Indices: 284519--284583 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
284509 TCTCACAACT
*
284519 TCCTCTCAACCAAAAAACTAATACAATAA
1 TCCTCTCAACCAAAAAACTAATACAAAAA
**
284548 TCCTCTCAACCAGTAAA-TAATACACGAAAA
1 TCCTCTCAACCAAAAAACTAATACA--AAAA
284578 TCCTCT
1 TCCTCT
284584 TATATTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 15 0.48
30 9 0.29
ACGTcount: A:0.45, C:0.29, G:0.03, T:0.23
Consensus pattern (29 bp):
TCCTCTCAACCAAAAAACTAATACAAAAA
Found at i:285675 original size:12 final size:12
Alignment explanation
Indices: 285658--285722 Score: 60
Period size: 12 Copynumber: 5.1 Consensus size: 12
285648 AAAAAAATTA
285658 ATTAAATAAAAT
1 ATTAAATAAAAT
285670 ATTAAAATAATTAAAT
1 ATT-AAAT-A--AAAT
285686 AATTAAATAAAAT
1 -ATTAAATAAAAT
*
285699 ACT-AATAAAAT
1 ATTAAATAAAAT
*
285710 ATTAAATATAAT
1 ATTAAATAAAAT
285722 A
1 A
285723 AAATATACCT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 10 0.23
12 13 0.30
13 8 0.18
14 1 0.02
15 1 0.02
16 8 0.18
17 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:285684 original size:17 final size:17
Alignment explanation
Indices: 285649--285728 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 17
285639 TAATTGCACA
* *
285649 AAAAAATTAATTA-AAT
1 AAAATATTAAATATAAT
285665 AAAATATTAAA-ATAAT
1 AAAATATTAAATATAAT
*
285681 TAAATAATTAAATAAAATACTAAT
1 AAAAT-ATTAAAT---AT---AAT
285705 AAAATATTAAATATAAT
1 AAAATATTAAATATAAT
285722 AAAATAT
1 AAAATAT
285729 ACCTTAAGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
15 1 0.02
16 16 0.31
17 16 0.31
20 2 0.04
21 2 0.04
23 7 0.14
24 7 0.14
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATTAAATATAAT
Found at i:285698 original size:29 final size:29
Alignment explanation
Indices: 285656--285729 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
285646 ACAAAAAAAT
285656 TAATTAAATAAAATAT-TAAAATAATTAAA
1 TAATTAAATAAAATATATAAAAT-ATTAAA
285685 TAATTAAATAAAATACTAATAAAATATTAAA
1 TAATTAAATAAAATA-T-ATAAAATATTAAA
285716 T-A-T-AATAAAATATA
1 TAATTAAATAAAATATA
285730 CCTTAAGTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 9 0.21
29 16 0.38
30 2 0.05
31 7 0.17
32 6 0.14
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
TAATTAAATAAAATATATAAAATATTAAA
Found at i:292481 original size:7 final size:7
Alignment explanation
Indices: 292466--292504 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
292456 TAAAGAGAAC
*
292466 AAGATTG
1 AAGAGTG
292473 AAGAGTG
1 AAGAGTG
292480 AAGAGTG
1 AAGAGTG
292487 AAGAGTG
1 AAGAGTG
*
292494 AAGAGTT
1 AAGAGTG
292501 AAGA
1 AAGA
292505 AGGAAAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.36, T:0.18
Consensus pattern (7 bp):
AAGAGTG
Found at i:297990 original size:20 final size:20
Alignment explanation
Indices: 297965--298058 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
297955 GACATTCATT
297965 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
**
297985 TGACTATCGCAATACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
298005 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
298025 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
298045 TGACTATCGCAACG
1 TGACTATCGCAACG
298059 AGAGAATCAC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 64 0.96
21 3 0.04
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.20
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:298100 original size:20 final size:20
Alignment explanation
Indices: 298063--298116 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
298053 GCAACGAGAG
*
298063 AATCACAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
298082 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
298102 AATCGCAATGCGAAA
1 AATCGCAATGCGAAA
298117 TTAGTTTCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 11 0.33
20 22 0.67
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:298188 original size:33 final size:33
Alignment explanation
Indices: 298126--298221 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
298116 ATTAGTTTCG
*
298126 CGTTGCGATTTTCATTTTCGCATTACGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
298160 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* ** *
298193 CATTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
298222 AGTCTTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:298342 original size:14 final size:14
Alignment explanation
Indices: 298323--298359 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
298313 CATCAATTAA
298323 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
298337 ACAAATCATCTTTT
1 ACAAATCAACATTT
298351 ACAAATCAA
1 ACAAATCAA
298360 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:299815 original size:42 final size:42
Alignment explanation
Indices: 299708--299819 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
299698 TCTAGAATGT
* * *
299708 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** * *
299750 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACTA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
299792 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
299820 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:300322 original size:20 final size:20
Alignment explanation
Indices: 300299--300374 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
300289 GAAACTTAAA
300299 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
300319 ATCGCAATGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
300339 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
300359 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
300375 CGCAATGCGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:300437 original size:20 final size:20
Alignment explanation
Indices: 300409--300454 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
300399 CACCAAAATT
300409 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
* **
300429 GCAATGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
300449 GCAACG
1 GCAACG
300455 AGAGAATCGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:300524 original size:20 final size:20
Alignment explanation
Indices: 300499--300639 Score: 195
Period size: 20 Copynumber: 7.3 Consensus size: 20
300489 GATTCTCTCG
**
300499 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
300519 TTGCGATTGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
300539 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
300559 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
300579 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
300593 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
300613 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
300633 TTGCGAT
1 TTGCGAT
300640 TGTAAACTAT
Statistics
Matches: 107, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
14 7 0.07
16 6 0.06
18 6 0.06
20 88 0.82
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:302520 original size:20 final size:20
Alignment explanation
Indices: 302495--302544 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
302485 CTGAAACTTT
302495 AAATCGCAACACAAAAATGA
1 AAATCGCAACACAAAAATGA
*
302515 AAATCGCAACACGAAAATGA
1 AAATCGCAACACAAAAATGA
**
302535 CTATCGCAAC
1 AAATCGCAAC
302545 TTGAATTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACAAAAATGA
Found at i:302662 original size:20 final size:20
Alignment explanation
Indices: 302608--302663 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
302598 GCGATTCTCT
**
302608 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
302628 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
302648 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
302664 CTCGTTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:303240 original size:20 final size:20
Alignment explanation
Indices: 303215--303273 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
303205 TATGTAAATC
303215 GCGTTGCGATTTACGTATTA
1 GCGTTGCGATTTACGTATTA
* *
303235 GCGTTGCGATTTACGTAATC
1 GCGTTGCGATTTACGTATTA
303255 GCGTTGCGATTTACGTATT
1 GCGTTGCGATTTACGTATT
303274 GCGAATTAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
GCGTTGCGATTTACGTATTA
Found at i:304870 original size:43 final size:44
Alignment explanation
Indices: 304809--305026 Score: 198
Period size: 43 Copynumber: 5.1 Consensus size: 44
304799 AAAAATGATT
* *
304809 AAATTAGGGGCTTAAATTATAAAAGTAAAAAGT-ATGATTGAAA
1 AAATTAGGGGCCTCAATTATAAAAGTAAAAAGTGATGATTGAAA
* * * *
304852 AAATTAGGGACCCCAATTATAAAGGTAAAAAGTAAT-ATT-AAA
1 AAATTAGGGGCCTCAATTATAAAAGTAAAAAGTGATGATTGAAA
* * * * *
304894 AAAATAAGGGCATCAATTTTAAACGTAAAAAGTGATGA-TGAAA
1 AAATTAGGGGCCTCAATTATAAAAGTAAAAAGTGATGATTGAAA
* * * * * * *
304937 AAAATAGGGGTCTAAATTATATGAA-TAAAAAATG-GGATTAAAAA
1 AAATTAGGGGCCTCAATTATA-AAAGTAAAAAGTGATGATT-GAAA
*
304981 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAT-ATTGAAA
1 AAATTAGGGGCCTCAATTATAAAAGTAAAAAGTGATGATTGAAA
305024 AAA
1 AAA
305027 GCATGAGCTT
Statistics
Matches: 136, Mismatches: 31, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
42 34 0.25
43 67 0.49
44 35 0.26
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.25
Consensus pattern (44 bp):
AAATTAGGGGCCTCAATTATAAAAGTAAAAAGTGATGATTGAAA
Found at i:304911 original size:42 final size:43
Alignment explanation
Indices: 304823--305176 Score: 172
Period size: 43 Copynumber: 8.2 Consensus size: 43
304813 TAGGGGCTTA
* * * *
304823 AATTATAAAAGTAAAAAGT-ATGATTGAAAAAATTAGGGACCCC
1 AATTATAAAGGTAAAAAGTGAT-ATTAAAAAAATAAGGGACCTC
* *
304866 AATTATAAAGGTAAAAAGTAATATTAAAAAAATAAGGG-CATC
1 AATTATAAAGGTAAAAAGTGATATTAAAAAAATAAGGGACCTC
* * * ** *
304908 AATTTTAAACGTAAAAAGTGATGATGAAAAAAAT-AGGGGTCTA
1 AATTATAAAGGTAAAAAGTGAT-ATTAAAAAAATAAGGGACCTC
* ** * *
304951 AATTATATGAA--TAAAAAATGGGATTAAAAAAAATTAGGGGCCTC
1 AATTATA--AAGGTAAAAAGTGATATT-AAAAAAATAAGGGACCTC
* ** * * *
304995 AATTATAAAGGTAAAAAGTGATATTGAAAAAAGCA-TGAGCTT
1 AATTATAAAGGTAAAAAGTGATATTAAAAAAATAAGGGACCTC
* * ** * *
305037 AATTATAAAGGTACAAGGTGGGATTAAAAAACTTAA--GATCATC
1 AATTATAAAGGTAAAAAGTGATATTAAAAAA-ATAAGGGA-CCTC
* * **
305080 AATTATAAATGTAAAAAAATGGGATTGAAAAAAAATTAA-GGACCTTC
1 AATTATAAAGGT-AAAAAGTGATATT--AAAAAAA-TAAGGGACC-TC
* * * * *
305127 -ATTATAAAGATAAAAAGT-AGGATTACAAAATTTAGGGACCTC
1 AATTATAAAGGTAAAAAGTGA-TATTAAAAAAATAAGGGACCTC
305169 AATTATAA
1 AATTATAA
305177 GTATAAAAAA
Statistics
Matches: 238, Mismatches: 53, Indels: 40
0.72 0.16 0.12
Matches are distributed among these distances:
42 64 0.27
43 102 0.43
44 37 0.16
45 12 0.05
46 19 0.08
47 4 0.02
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (43 bp):
AATTATAAAGGTAAAAAGTGATATTAAAAAAATAAGGGACCTC
Done.