Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008301.1 Hibiscus syriacus cultivar Beakdansim tig00110987_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: 3376434
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 18
Found at i:2350659 original size:9 final size:9
Alignment explanation
Indices: 2350647--2350711 Score: 71
Period size: 9 Copynumber: 7.3 Consensus size: 9
2350637 AATTTTTTCA
2350647 TTTTTTCCC
1 TTTTTTCCC
2350656 -TTTTT-CC
1 TTTTTTCCC
* *
2350663 TTTTTTTCT
1 TTTTTTCCC
2350672 TTTTTTCCCC
1 TTTTTT-CCC
*
2350682 CTTTTTCCC
1 TTTTTTCCC
*
2350691 TTTTTTCCT
1 TTTTTTCCC
2350700 TTTTTTCCC
1 TTTTTTCCC
2350709 TTT
1 TTT
2350712 CCCCCTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
7 2 0.04
8 10 0.22
9 28 0.61
10 6 0.13
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTTCCC
Found at i:2350704 original size:8 final size:8
Alignment explanation
Indices: 2350639--2350704 Score: 60
Period size: 8 Copynumber: 7.8 Consensus size: 8
2350629 CTTGGTTTAA
*
2350639 TTTTTTCA
1 TTTTTTCC
2350647 TTTTTTCC
1 TTTTTTCC
*
2350655 CTTTTTCC
1 TTTTTTCC
*
2350663 TTTTTTTCT
1 -TTTTTTCC
2350672 TTTTTTCCCCC
1 TTTTTT---CC
*
2350683 TTTTTCCC
1 TTTTTTCC
2350691 TTTTTTCC
1 TTTTTTCC
2350699 TTTTTT
1 TTTTTT
2350705 TCCCTTTCCC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
8 35 0.74
9 6 0.13
11 6 0.13
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTTCC
Found at i:2350718 original size:18 final size:18
Alignment explanation
Indices: 2350675--2350723 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2350665 TTTTTCTTTT
2350675 TTTCCCCC--TTTTTCCC
1 TTTCCCCCTTTTTTTCCC
***
2350691 TTTTTTCCTTTTTTTCCC
1 TTTCCCCCTTTTTTTCCC
2350709 TTTCCCCCTTTTTTT
1 TTTCCCCCTTTTTTT
2350724 TTCAAGTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 5 0.20
18 20 0.80
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTCCCCCTTTTTTTCCC
Found at i:2356376 original size:23 final size:23
Alignment explanation
Indices: 2356341--2356384 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2356331 ATATATATAT
*
2356341 ATATATATATATTTATAAATAAG
1 ATATATATATATTTAGAAATAAG
* *
2356364 ATATTTATTTATTTAGAAATA
1 ATATATATATATTTAGAAATA
2356385 TCAGAAAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATATATATATATTTAGAAATAAG
Found at i:2356551 original size:126 final size:125
Alignment explanation
Indices: 2356346--2356576 Score: 290
Period size: 126 Copynumber: 1.8 Consensus size: 125
2356336 TATATATATA
* * * * *
2356346 TATATATTTATAAATAAGATATTTATTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTACTTTA
1 TATATATTTATAAATAAAATATTTATTTATTTAAAAATATAAGAAAAGAGATTCCAGGTACTTTA
* *
2356411 AGACATCTCTTTTCTTAATATT-AAAATATAAATAAATATTAATAAAACATTTATTAAAAT
66 AGACAGCTCCTTTCTTAATATTGAAAA-ATAAATAAATATTAATAAAACATTTATTAAAAT
* *
2356471 TATA-ATTTATAAAAGTAAAATATTTATTTATTTAAAAATATAAGAAAATG-GATATCCAGTTGC
1 TATATATTTAT-AAA-TAAAATATTTATTTATTTAAAAATATAAGAAAA-GAGAT-TCCAGGTAC
* *
2356534 TTTAAGACCGC-CCTTTCTTAATATTGAAAAATAAATATATATT
62 TTTAAGACAGCTCCTTTCTTAATATTGAAAAATAAATAAATATT
2356577 TAAAATATAA
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
124 6 0.07
125 7 0.08
126 57 0.63
127 20 0.22
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (125 bp):
TATATATTTATAAATAAAATATTTATTTATTTAAAAATATAAGAAAAGAGATTCCAGGTACTTTA
AGACAGCTCCTTTCTTAATATTGAAAAATAAATAAATATTAATAAAACATTTATTAAAAT
Found at i:2358131 original size:3 final size:3
Alignment explanation
Indices: 2358125--2358162 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2358115 ATTTTTTATT
2358125 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2358163 AACGAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2366189 original size:4 final size:4
Alignment explanation
Indices: 2366180--2366231 Score: 60
Period size: 4 Copynumber: 14.0 Consensus size: 4
2366170 TTTTTTATCC
2366180 ATTT ATTT ATTT ATTT ATTT ATTT A-TT A-TT A-TT A-TT A-TT ATTTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT
2366224 ATTT ATTT
1 ATTT ATTT
2366232 TTATTATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 15 0.33
4 28 0.61
5 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:2366210 original size:3 final size:3
Alignment explanation
Indices: 2366202--2366258 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
2366192 ATTTATTTAT
* **
2366202 TTA TTA TTA TTA TTA TTA TT- TTA TTTA TTT TTA TTA TTA TTA AAA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
2366247 TTA TTA TTA TTA
1 TTA TTA TTA TTA
2366259 CAAACATGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2366217 original size:24 final size:25
Alignment explanation
Indices: 2366190--2366242 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
2366180 ATTTATTTAT
2366190 TTATTTA-TTTATTTATTATTATTA
1 TTATTTATTTTATTTATTATTATTA
*
2366214 TTA-TTATTTTATTTATTTTTATTA
1 TTATTTATTTTATTTATTATTATTA
2366238 TTATT
1 TTATT
2366243 AAAATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 3 0.12
24 22 0.85
25 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (25 bp):
TTATTTATTTTATTTATTATTATTA
Found at i:2366242 original size:36 final size:36
Alignment explanation
Indices: 2366185--2366257 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
2366175 TATCCATTTA
**
2366185 TTTATTTATTTATTTATTTATTATTATTATTATTAT
1 TTTATTTATTTATTTATTTATTAAAATTATTATTAT
*
2366221 TTTATTTATTTTTATTA-TTATTAAAATTATTATTAT
1 TTTATTTATTTAT-TTATTTATTAAAATTATTATTAT
2366257 T
1 T
2366258 ACAAACATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 30 0.91
37 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (36 bp):
TTTATTTATTTATTTATTTATTAAAATTATTATTAT
Found at i:2366243 original size:24 final size:24
Alignment explanation
Indices: 2366197--2366243 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2366187 TATTTATTTA
2366197 TTTATTTATTATTATTATTATTAT
1 TTTATTTATTATTATTATTATTAT
*
2366221 TTTATTTATTTTTATTATTATTA
1 TTTATTTATTATTATTATTATTA
2366244 AAATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTATTTATTATTATTATTATTAT
Found at i:2367671 original size:16 final size:16
Alignment explanation
Indices: 2367650--2367680 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2367640 TTTTACTTTC
*
2367650 ATATATTTATGATTAT
1 ATATATTTATCATTAT
2367666 ATATATTTATCATTA
1 ATATATTTATCATTA
2367681 GTATTACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
ATATATTTATCATTAT
Found at i:2368095 original size:11 final size:13
Alignment explanation
Indices: 2368058--2368097 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
2368048 TGTTTAATAA
2368058 AATATA-TATATT
1 AATATATTATATT
*
2368070 AATATATTATCTT
1 AATATATTATATT
2368083 AA-A-ATTATATT
1 AATATATTATATT
2368094 AATA
1 AATA
2368098 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:2368600 original size:3 final size:3
Alignment explanation
Indices: 2368594--2368619 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2368584 TTTTAAATAC
2368594 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2368620 TTTTATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2375823 original size:20 final size:21
Alignment explanation
Indices: 2375798--2375857 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 21
2375788 TTTTGGTGCA
*
2375798 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
*
2375818 GAGGGAACCGATTCCCCCCTTT
1 GAGGGAACCGATTCCCCCC-AT
2375840 GAAGGGGAACCGATTCCC
1 G-A-GGGAACCGATTCCC
2375858 TTCCAGGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.29
21 7 0.21
22 2 0.06
23 1 0.03
24 14 0.41
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:2379678 original size:43 final size:43
Alignment explanation
Indices: 2379611--2379693 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
2379601 TGGCTTTAGA
* * *
2379611 GAAGTTAGGAGGGAAAGTTATCCCCTATATGTAAAGGTTTGCT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTGCT
* *
2379654 GAAGTTAGGACTGAAAGATGTCCCCTATATGTAAAAGTTT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTT
2379694 TGTTTGATGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (43 bp):
GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTGCT
Found at i:2379983 original size:14 final size:14
Alignment explanation
Indices: 2379945--2379983 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2379935 ATTTTAAATA
**
2379945 ATTTACATTTATAT
1 ATTTACATTTGCAT
*
2379959 TTTTACATTTGCAT
1 ATTTACATTTGCAT
2379973 ATTTACATTTG
1 ATTTACATTTG
2379984 GAATCTTTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.56
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:2399267 original size:43 final size:44
Alignment explanation
Indices: 2399200--2399286 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
2399190 TGGCTTTAGA
* *
2399200 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTTGTT
* *
2399243 GAAGTTAGGACTGAAAGATGTCCCCTATATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTTGTT
2399287 TGATGCACGG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTTGTT
Found at i:2399572 original size:14 final size:14
Alignment explanation
Indices: 2399534--2399572 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2399524 ATTTTAAATA
*
2399534 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
2399548 TTTTACATTTGCAT
1 ATTTACATTTGCAT
2399562 ATTTACATTTG
1 ATTTACATTTG
2399573 GAATCTTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:2405685 original size:70 final size:71
Alignment explanation
Indices: 2405522--2405689 Score: 189
Period size: 75 Copynumber: 2.3 Consensus size: 71
2405512 ATCAACAAGA
* *
2405522 AGCAAATGTTGGGGTATGCTGAAAACCCATTTCAATCATAATCAGGAATATTGAAGTGTTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAAAATCAGGAATA-T-AA--GTTTTGAA
*
2405587 TATTCACGTC
62 TATTCACATC
* * * *
2405597 AACAAATGCTGGGGCATGCTGAAAACCCATTTTAATCAGAAAT-TGGAATA-ACA-TTTTGAATA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAATCA-AAATCAGGAATATA-AGTTTTGAATA
*
2405659 TTCATATC
64 TTCACATC
2405667 AGCAAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
2405690 GGCCCACATC
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
70 36 0.44
72 1 0.01
73 1 0.01
75 40 0.49
76 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (71 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAAAATCAGGAATATAAGTTTTGAATATT
CACATC
Found at i:2407708 original size:113 final size:111
Alignment explanation
Indices: 2407430--2407852 Score: 542
Period size: 113 Copynumber: 3.8 Consensus size: 111
2407420 AAAATAGATT
* * * *
2407430 AACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATATGAATAAGGAAGAGGAAGTTCATAATG
1 AACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * *
2407495 AGAAGAACTTGTTTAACCTTTTGTTCAAATCCATAAC-AATGGATC
66 AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTGATGGATC
* * *
2407540 AACATTTCTACAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
1 AACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * **
2407605 AGAAGAATTTGTTCAACCTTTTGCTCGAATCCATCACTTGATGTTTC
66 AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCAC-TGATGGATC
* * ** *
2407652 AGCATTGCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAATAAACAAGAAATTCATAAT
1 AACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
* * *
2407717 GAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGGATC
65 GAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACT-GATGGATC
* * * * *
2407765 AACTTTTCCAGAGAAGGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGGAGTTCATAAT
1 AACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
*
2407830 GAGAAGAACTTGTTCGACCTTTT
65 GAGAAGAACTTGTTCAACCTTTT
2407853 ACATGACTTT
Statistics
Matches: 268, Mismatches: 41, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
110 90 0.34
112 14 0.05
113 164 0.61
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (111 bp):
AACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTGATGGATC
Found at i:2407942 original size:123 final size:123
Alignment explanation
Indices: 2407762--2408464 Score: 1185
Period size: 123 Copynumber: 5.7 Consensus size: 123
2407752 CACTCGATGG
* * *
2407762 ATCAACTTTTCCAGAGAAG-GTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGGAGTTCA
1 ATCAACATTTCC--AGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCA
2407826 TAATGAGAAGAACTTGTTCGACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
64 TAATGAGAAGAACTTGTTCGACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
* *
2407886 ATCAACATTTCCAAAAGTGTTCATAATGAGAAGAACTCATCTAAAGAAAGAAGAAGGAGTTCATA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATA
*
2407951 ATGAGAAGAACTTGTTCAACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
66 ATGAGAAGAACTTGTTCGACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
* * *
2408009 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAAATCATCTAAAGAAAGAAGAAGGATTTCATA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATA
* *
2408074 ATGATAAGAGCTTGTTCGACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
66 ATGAGAAGAACTTGTTCGACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
* *
2408132 ATCAACATTTCCAGAAGTGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAATGAGTTCATA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATA
2408197 ATGAGAAGAACTTGTTCGACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
66 ATGAGAAGAACTTGTTCGACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
* * *
2408255 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTTATCTGAAGAAAGAAGAAAGAGTTTATA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATA
2408320 ATGAGAAGAACTTGTTCGACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
66 ATGAGAAGAACTTGTTCGACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
* * *
2408378 ATCAACATTTCCAGAAGTGTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATA
* *
2408442 ATGAGAAGAATTTGTTCAACCTT
66 ATGAGAAGAACTTGTTCGACCTT
2408465 GCCTTAATTC
Statistics
Matches: 547, Mismatches: 31, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
122 39 0.07
123 497 0.91
124 11 0.02
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (123 bp):
ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATA
ATGAGAAGAACTTGTTCGACCTTTTACATGACTTTATCACAGAAGGAGATATATCATC
Found at i:2408838 original size:3 final size:3
Alignment explanation
Indices: 2408832--2408894 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
2408822 AATTTATTTG
2408832 TTA TTA TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
**
2408877 TTA AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
2408895 CAAACAGGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2410695 original size:11 final size:13
Alignment explanation
Indices: 2410655--2410697 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 13
2410645 TCTTGTTTAA
2410655 TAATATATATATAT
1 TAATATAT-TATAT
*
2410669 TAATATATTATCT
1 TAATATATTATAT
2410682 TAA-A-ATTATAT
1 TAATATATTATAT
2410693 TAATA
1 TAATA
2410698 AACTTAACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 9 0.35
12 2 0.08
13 7 0.27
14 8 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATATATTATAT
Found at i:2413408 original size:11 final size:11
Alignment explanation
Indices: 2413392--2413447 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
2413382 TAATAAAAAT
2413392 ATAAAAAATAA
1 ATAAAAAATAA
2413403 AT-AAAAATAA
1 ATAAAAAATAA
2413413 ATAAGAAAA-AA
1 ATAA-AAAATAA
*
2413424 ATATAAAGA-AA
1 ATA-AAAAATAA
*
2413435 ATAGAAAATAA
1 ATAAAAAATAA
2413446 AT
1 AT
2413448 GAAGACAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 13 0.34
11 20 0.53
12 5 0.13
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:2413425 original size:21 final size:22
Alignment explanation
Indices: 2413383--2413447 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 22
2413373 TAAAGAACCT
2413383 AATAAAAAT--ATAA-AAAATA
1 AATAAAAATAAATAAGAAAATA
2413402 AATAAAAATAAATAAGAAAA-A
1 AATAAAAATAAATAAGAAAATA
2413423 AATATAAAGA-AAAT-AGAAAATA
1 AATA-AAA-ATAAATAAGAAAATA
2413445 AAT
1 AAT
2413448 GAAGACAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
19 9 0.22
21 15 0.38
22 15 0.38
23 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (22 bp):
AATAAAAATAAATAAGAAAATA
Found at i:2413429 original size:17 final size:17
Alignment explanation
Indices: 2413386--2413430 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2413376 AGAACCTAAT
*
2413386 AAAAATATAAAAAATAA
1 AAAAATATAAAAAAGAA
*
2413403 ATAAAA-ATAAATAAGAA
1 A-AAAATATAAAAAAGAA
2413420 AAAAATATAAA
1 AAAAATATAAA
2413431 GAAAATAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAAATATAAAAAAGAA
Found at i:2413429 original size:34 final size:34
Alignment explanation
Indices: 2413386--2413452 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
2413376 AGAACCTAAT
2413386 AAAAATATAAAAAATAAATA-AAAATAAAT-AAGAA
1 AAAAATAT-AAAAA-AAATAGAAAATAAATGAAGAA
*
2413420 AAAAATATAAAGAAAATAGAAAATAAATGAAGA
1 AAAAATATAAAAAAAATAGAAAATAAATGAAGA
2413453 CAAAGGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 5 0.17
33 13 0.43
34 12 0.40
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.16
Consensus pattern (34 bp):
AAAAATATAAAAAAAATAGAAAATAAATGAAGAA
Found at i:2413432 original size:14 final size:13
Alignment explanation
Indices: 2413394--2413435 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2413384 ATAAAAATAT
*
2413394 AAAAAATAAATAA
1 AAAAAATAAAGAA
2413407 AAATAAAT-AAGAA
1 AAA-AAATAAAGAA
2413420 AAAAATATAAAGAA
1 AAAAA-ATAAAGAA
2413434 AA
1 AA
2413436 TAGAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 2 0.08
13 12 0.48
14 11 0.44
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAATAAAGAA
Found at i:2413578 original size:37 final size:36
Alignment explanation
Indices: 2413529--2413638 Score: 101
Period size: 37 Copynumber: 3.2 Consensus size: 36
2413519 AAAAGGTAAA
*
2413529 ATATAAGT-TAAAAGTAAAATAGTAATAATAATAGTC
1 ATATAA-TATAAAAATAAAATAGTAATAATAATAGTC
2413565 ATATAATTATAAAAATAAAATA-TACAT-AT-ATA--C
1 ATATAA-TATAAAAATAAAATAGTA-ATAATAATAGTC
* *
2413598 AT-TGATAGTAAAAAT-AAATAGTAATAATAATAGTT
1 ATATAATA-TAAAAATAAAATAGTAATAATAATAGTC
2413633 ATATAA
1 ATATAA
2413639 AAATATATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
31 9 0.15
32 13 0.22
33 6 0.10
35 5 0.08
36 13 0.22
37 14 0.23
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (36 bp):
ATATAATATAAAAATAAAATAGTAATAATAATAGTC
Found at i:2419734 original size:46 final size:46
Alignment explanation
Indices: 2419684--2419787 Score: 156
Period size: 46 Copynumber: 2.3 Consensus size: 46
2419674 TTTACGCGGC
* *
2419684 CCTTCGGGATATAGT-TGTCCTTTGGGACATATGTGTTATATGTGGT
1 CCTTCGGGACATAGTGT-TCCTTCGGGACATATGTGTTATATGTGGT
2419730 CCTTCGGGACATAGTGTTCCTTCGGGACATATGTGTTATATGTGGT
1 CCTTCGGGACATAGTGTTCCTTCGGGACATATGTGTTATATGTGGT
* *
2419776 CATTCGAGACAT
1 CCTTCGGGACAT
2419788 CTACGCGGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
46 52 0.98
47 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.38
Consensus pattern (46 bp):
CCTTCGGGACATAGTGTTCCTTCGGGACATATGTGTTATATGTGGT
Found at i:2419752 original size:18 final size:19
Alignment explanation
Indices: 2419721--2419766 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
2419711 CATATGTGTT
*
2419721 ATATGTGGTCCTTCGGGAC
1 ATATGTGTTCCTTCGGGAC
2419740 ATA-GTGTTCCTTCGGGAC
1 ATATGTGTTCCTTCGGGAC
2419758 ATATGTGTT
1 ATATGTGTT
2419767 ATATGTGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.37
Consensus pattern (19 bp):
ATATGTGTTCCTTCGGGAC
Found at i:2434861 original size:19 final size:19
Alignment explanation
Indices: 2434837--2434878 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2434827 AATACCAGAA
*
2434837 CCCTAGGGGGTATCGATTC
1 CCCTAGGGGGAATCGATTC
*
2434856 CCCTAGGGGGAATCGGTTC
1 CCCTAGGGGGAATCGATTC
2434875 CCCT
1 CCCT
2434879 TCAAAGGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.24
Consensus pattern (19 bp):
CCCTAGGGGGAATCGATTC
Found at i:2434908 original size:23 final size:24
Alignment explanation
Indices: 2434861--2434911 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
2434851 GATTCCCCTA
2434861 GGGGGAATCGGTTCCCCTTCAAAG
1 GGGGGAATCGGTTCCCCTTCAAAG
2434885 GGGGGAATCGGTTCCCCTTC-AAG
1 GGGGGAATCGGTTCCCCTTCAAAG
2434908 GGGG
1 GGGG
2434912 TATCGATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.18, C:0.24, G:0.39, T:0.20
Consensus pattern (24 bp):
GGGGGAATCGGTTCCCCTTCAAAG
Found at i:2441932 original size:64 final size:63
Alignment explanation
Indices: 2441852--2442010 Score: 168
Period size: 64 Copynumber: 2.5 Consensus size: 63
2441842 ATCCCTTGAC
*
2441852 GGGTGCATCGATGCACT-GTCTATGCATC-AGTGCA-TAAAT-CCTATTCGATGTTT-ATATTTT
1 GGGTGCATCGATGCACTCCT-TATGCATCGA-TGCACT-AATGCC-ATTCGATGTTTCAT-TTTT
2441912 AAGT
61 AA-T
* *
2441916 GGGTGTATCGATGCACTCCTTATGCATCGATGCACTAATGGCATTCGATGTTTCCATTTTTAAT
1 GGGTGCATCGATGCACTCCTTATGCATCGATGCACTAATGCCATTCGATGTTT-CATTTTTAAT
*
2441980 GGGTGCATCGATGCACTTCC-TGTGCATCGAT
1 GGGTGCATCGATGCAC-TCCTTATGCATCGAT
2442011 ACACACTGAA
Statistics
Matches: 83, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
64 68 0.82
65 13 0.16
66 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (63 bp):
GGGTGCATCGATGCACTCCTTATGCATCGATGCACTAATGCCATTCGATGTTTCATTTTTAAT
Found at i:2446597 original size:64 final size:64
Alignment explanation
Indices: 2446520--2446678 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 64
2446510 ATCCCTTGAC
* *
2446520 GGGTGCATCGATGCACT-ATCTATGCATCGGTGCA-TAAAT-CCTATTCGATGTTTGT-A-TTTT
1 GGGTGCATCGATGCACTCCT-TATGCATCGATGCACT-AATGCC-ATTCGATGTTT-TCATTTTT
2446580 AAGT
62 AA-T
* *
2446584 GGGTGCATTGATGCACTCCTTATGCATCGATGCACTAATGGCATTCGATGTTTTCATTTTTAAT
1 GGGTGCATCGATGCACTCCTTATGCATCGATGCACTAATGCCATTCGATGTTTTCATTTTTAAT
*
2446648 GGGTGCATCGATGCACGTCC-TGTGCATCGAT
1 GGGTGCATCGATGCAC-TCCTTATGCATCGAT
2446679 ACACACTGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
63 1 0.01
64 70 0.84
65 12 0.14
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (64 bp):
GGGTGCATCGATGCACTCCTTATGCATCGATGCACTAATGCCATTCGATGTTTTCATTTTTAAT
Found at i:2453412 original size:23 final size:23
Alignment explanation
Indices: 2453382--2453459 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
2453372 ATTTTCTTAA
2453382 AGAAGAAATGAAAAA-AGAAAATG
1 AGAA-AAATGAAAAATAGAAAATG
*
2453405 AGAAGAAATGAAAAATAAAAAAT-
1 AGAA-AAATGAAAAATAGAAAATG
*
2453428 A-AAAAAT-AAAAATTGAAAA-G
1 AGAAAAATGAAAAATAGAAAATG
2453448 AGAAAAATGAAA
1 AGAAAAATGAAA
2453460 TGAACAAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
20 11 0.23
21 10 0.21
22 5 0.10
23 16 0.33
24 6 0.12
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (23 bp):
AGAAAAATGAAAAATAGAAAATG
Found at i:2453420 original size:7 final size:7
Alignment explanation
Indices: 2453387--2453480 Score: 65
Period size: 7 Copynumber: 13.4 Consensus size: 7
2453377 CTTAAAGAAG
2453387 AAATGAA
1 AAATGAA
*
2453394 AAAAG-A
1 AAATGAA
2453400 AAATGAGAA
1 AAAT--GAA
2453409 GAAATGAA
1 -AAATGAA
*
2453417 AAATAAA
1 AAATGAA
*
2453424 AAATAAA
1 AAATGAA
2453431 AAAT-AA
1 AAATGAA
2453437 AAATTGAA
1 AAA-TGAA
2453445 AAGA-GAA
1 AA-ATGAA
2453452 AAATG--
1 AAATGAA
2453457 AAATGAA
1 AAATGAA
2453464 CAAATGAA
1 -AAATGAA
2453472 AAA-GAA
1 AAATGAA
2453478 AAA
1 AAA
2453481 ACAAAAGAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 23
0.74 0.03 0.23
Matches are distributed among these distances:
5 5 0.07
6 16 0.22
7 31 0.42
8 15 0.21
9 2 0.03
10 4 0.05
ACGTcount: A:0.73, C:0.01, G:0.14, T:0.12
Consensus pattern (7 bp):
AAATGAA
Found at i:2453480 original size:6 final size:6
Alignment explanation
Indices: 2453442--2453507 Score: 50
Period size: 6 Copynumber: 10.8 Consensus size: 6
2453432 AATAAAAATT
*
2453442 GAAAAGA GAAAAA TG-AAAT GAACAAA TGAAAAA GAAAAA -ACAAAA GAAAAA
1 GAAAA-A GAAAAA -GAAAAA GAA-AAA -GAAAAA GAAAAA GA-AAAA GAAAAA
2453493 G--AAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAA
2453508 GAATAAAAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
4 4 0.08
5 2 0.04
6 28 0.57
7 12 0.24
8 3 0.06
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:2453481 original size:28 final size:27
Alignment explanation
Indices: 2453410--2453515 Score: 85
Period size: 28 Copynumber: 3.8 Consensus size: 27
2453400 AAATGAGAAG
*
2453410 AAATGAAAAATAAAAAATAAAAAATAA
1 AAATGAAAAAGAAAAAATAAAAAATAA
*
2453437 AAATTG-AAAAGAGAAAAAT--GAAATGAA
1 AAA-TGAAAAAGA-AAAAATAAAAAAT-AA
*
2453464 CAAATGAAAAAGAAAAAACAAAAGAA-AA
1 -AAATGAAAAAGAAAAAATAAAA-AATAA
*
2453492 AGAAAGAAAAAGAAAAGAATAAAA
1 A-AATGAAAAAGAAAA-AATAAAA
2453516 GGGGTTCAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
26 4 0.06
27 18 0.29
28 32 0.51
29 7 0.11
30 2 0.03
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.09
Consensus pattern (27 bp):
AAATGAAAAAGAAAAAATAAAAAATAA
Found at i:2453485 original size:18 final size:18
Alignment explanation
Indices: 2453448--2453496 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
2453438 AATTGAAAAG
*
2453448 AGAAAAATGAAATGAACAAA
1 AGAAAAA-GAAA-AAACAAA
*
2453468 TGAAAAAGAAAAAACAAA
1 AGAAAAAGAAAAAACAAA
2453486 AGAAAAAGAAA
1 AGAAAAAGAAA
2453497 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 16 0.62
19 4 0.15
20 6 0.23
ACGTcount: A:0.76, C:0.04, G:0.14, T:0.06
Consensus pattern (18 bp):
AGAAAAAGAAAAAACAAA
Found at i:2453497 original size:10 final size:10
Alignment explanation
Indices: 2453469--2453506 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2453459 ATGAACAAAT
2453469 GAAAAAGAAA
1 GAAAAAGAAA
*
2453479 -AAACA-AAA
1 GAAAAAGAAA
2453487 GAAAAAGAAA
1 GAAAAAGAAA
2453497 GAAAAAGAAA
1 GAAAAAGAAA
2453507 AGAATAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 3 0.12
9 8 0.33
10 13 0.54
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:2454943 original size:54 final size:55
Alignment explanation
Indices: 2454861--2455117 Score: 347
Period size: 54 Copynumber: 4.7 Consensus size: 55
2454851 ATTTTATGAC
* *
2454861 GTTCGAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACGTTT-CTGAAGATT
1 GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGGACACGTTTGCTGAAGATT
* * * * *
2454915 GTTCGAGTCCTATACTCTCTAAAGAAATAGGGAGCGAACACGTTTGTTGAAGATT
1 GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGGACACGTTTGCTGAAGATT
* *
2454970 GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGACACGTTTGTTGAAGATT
1 GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGGACACGTTTGCTGAAGATT
* * ** *
2455025 GATCGAGTCTTATACTCCCTG-ACAAATAGGGAGCAAACACATTTGCTGAAGATT
1 GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGGACACGTTTGCTGAAGATT
* * *
2455079 GTTTGAGTCTTATACTCCCTGAAGGAATAGGAAGCGGAC
1 GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGGAC
2455118 CGTCATTCAA
Statistics
Matches: 181, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
54 91 0.50
55 90 0.50
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (55 bp):
GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGGACACGTTTGCTGAAGATT
Found at i:2455052 original size:109 final size:109
Alignment explanation
Indices: 2454861--2455109 Score: 356
Period size: 109 Copynumber: 2.3 Consensus size: 109
2454851 ATTTTATGAC
* * * *
2454861 GTTCGAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACGTTTCTGAAGATTGTTCGAGTCCT
1 GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGACACGTTTCTGAAGATTGATCGAGTCCT
* * * * *
2454926 ATACTCTCTAAAGAAATAGGGAGCGAACACGTTTGTTGAAGATT
66 ATACTCCCTAAACAAATAGGGAGCAAACACATTTGCTGAAGATT
* *
2454970 GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGACACGTTTGTTGAAGATTGATCGAGTCT
1 GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGACACGTTT-CTGAAGATTGATCGAGTCC
*
2455035 TATACTCCCT-GACAAATAGGGAGCAAACACATTTGCTGAAGATT
65 TATACTCCCTAAACAAATAGGGAGCAAACACATTTGCTGAAGATT
* *
2455079 GTTTGAGTCTTATACTCCCTGAAGGAATAGG
1 GTTCGAGTCTTATACTCCCTGAAGAAATAGG
2455110 AAGCGGACCG
Statistics
Matches: 125, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
109 100 0.80
110 25 0.20
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (109 bp):
GTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGACACGTTTCTGAAGATTGATCGAGTCCT
ATACTCCCTAAACAAATAGGGAGCAAACACATTTGCTGAAGATT
Found at i:2459275 original size:30 final size:31
Alignment explanation
Indices: 2459241--2459300 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
2459231 TGATAACTAA
*
2459241 ATCTACTAACTCCATCGACCTACAA-TAGTT
1 ATCTACCAACTCCATCGACCTACAAGTAGTT
2459271 ATCTACCAACTCCATCGACCTACAAGTAGT
1 ATCTACCAACTCCATCGACCTACAAGTAGT
2459301 AATATTACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.33, C:0.32, G:0.08, T:0.27
Consensus pattern (31 bp):
ATCTACCAACTCCATCGACCTACAAGTAGTT
Found at i:2459915 original size:3 final size:3
Alignment explanation
Indices: 2459907--2459997 Score: 141
Period size: 3 Copynumber: 30.7 Consensus size: 3
2459897 TTTACCCATA
2459907 TAT TAT TAT TA- TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2459953 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAA TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
2459998 AACATATATA
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.05
3 74 0.91
4 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2472834 original size:1 final size:1
Alignment explanation
Indices: 2472823--2472906 Score: 69
Period size: 1 Copynumber: 84.0 Consensus size: 1
2472813 ATGCTTGAAG
* * * * * * * *
2472823 AAAAAAGAAAAAAAAAGAAAAGAAAGAAAATAAAAAAAAAAAAAAAAAAAAAGAGAAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** *
2472888 AAAAAGGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAA
2472907 GGGGGTCAAG
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.87, C:0.00, G:0.12, T:0.01
Consensus pattern (1 bp):
A
Found at i:2472852 original size:24 final size:23
Alignment explanation
Indices: 2472825--2472906 Score: 96
Period size: 24 Copynumber: 3.6 Consensus size: 23
2472815 GCTTGAAGAA
2472825 AAAAGAAAAAAAAAGAAAAGAAAG
1 AAAAGAAAAAAAAAGAAAA-AAAG
* *
2472849 AAAATAAAAAAAAA-AAAAAAAA
1 AAAAGAAAAAAAAAGAAAAAAAG
*
2472871 AAAAGAGAAAAAAAAGAAAAAAGG
1 AAAAGA-AAAAAAAAGAAAAAAAG
*
2472895 AAAA-AAGAAAAA
1 AAAAGAAAAAAAA
2472907 GGGGGTCAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
22 14 0.28
23 13 0.26
24 23 0.46
ACGTcount: A:0.87, C:0.00, G:0.12, T:0.01
Consensus pattern (23 bp):
AAAAGAAAAAAAAAGAAAAAAAG
Found at i:2472861 original size:33 final size:32
Alignment explanation
Indices: 2472820--2472907 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
2472810 ATTATGCTTG
2472820 AAGAAAAAAGAAAAAAAAAGAAAAGA-AAGAAAA
1 AAGAAAAAAGAAAAAAAAA-AAAAGAGAA-AAAA
2472853 TAA-AAAAAA-AAAAAAAAAAAAAGAGAAAAAA
1 -AAGAAAAAAGAAAAAAAAAAAAAGAGAAAAAA
* *
2472884 AAGAAAAAAGGAAAAAAGAAAAAG
1 AAGAAAAAAGAAAAAAAAAAAAAG
2472908 GGGGTCAAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
30 2 0.04
31 16 0.33
32 23 0.47
33 6 0.12
34 2 0.04
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (32 bp):
AAGAAAAAAGAAAAAAAAAAAAAGAGAAAAAA
Found at i:2472900 original size:9 final size:9
Alignment explanation
Indices: 2472823--2472892 Score: 86
Period size: 9 Copynumber: 7.4 Consensus size: 9
2472813 ATGCTTGAAG
2472823 AAAAAAGAAA
1 AAAAAAG-AA
2472833 AAAAAAGAA
1 AAAAAAGAA
*
2472842 AAGAAAGAA
1 AAAAAAGAA
*
2472851 AATAAAAAAA
1 AA-AAAAGAA
*
2472861 AAAAAAAAA
1 AAAAAAGAA
2472870 AAAAAGAGAA
1 AAAAA-AGAA
2472880 AAAAAAGAA
1 AAAAAAGAA
2472889 AAAA
1 AAAA
2472893 GGAAAAAAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
9 32 0.59
10 22 0.41
ACGTcount: A:0.89, C:0.00, G:0.10, T:0.01
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:2473242 original size:16 final size:16
Alignment explanation
Indices: 2473216--2473260 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2473206 TTTGAATACA
*
2473216 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
2473233 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
2473248 ATTCAATTTATTT
1 ATTCAATTTATTT
2473261 TTGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:2474208 original size:114 final size:114
Alignment explanation
Indices: 2474006--2474225 Score: 395
Period size: 114 Copynumber: 1.9 Consensus size: 114
2473996 TCATGTTCTG
*
2474006 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
2474071 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
2474120 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
2474185 GGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
2474226 ATGCATGATC
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:2475198 original size:114 final size:111
Alignment explanation
Indices: 2474921--2475540 Score: 761
Period size: 114 Copynumber: 5.5 Consensus size: 111
2474911 GAAAGATTAG
2474921 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTT-CAGAGAAA-TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* *
2474986 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAT
64 GAAGAATTTGTTCAACCTTTTACCTGAATTCATC-ATTTGATGGATCAT
*
2475035 CTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG-TCATAATGA
1 CTTTT-CAGAGAA-ATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* *
2475099 GAAGAATTTGTTCAACCTTTTACCCGAATCCATCATTTGATGGATCAGT
64 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCA-T
* *
2475148 CTTTTCAGAGAAACTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 CTTTTCAGAGAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
** * *
2475213 AGAATTTGTTCAACCTTTTTTCTGAATTCATCAAGTTGATGGATTAT
66 AGAATTTGTTCAACCTTTTACCTGAATTCATC-ATTTGATGGATCAT
* * *
2475260 CTTTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATTGAAGAAGGAAGAAGAAGTTCATAA
1 CTTT-TCAGAG-A-AATTCATAATGAGAAGAACTCATC--TGAAGAAGGAAGAAGAAGTTCATAA
* * * * *
2475324 TGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCAA
61 TGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCAT
* *
2475375 CTTTGCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAA
1 CTTTTCAGAG-A-AATTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAA
* * * *
2475439 TGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCA-TTGATGGATCAAT
61 TGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATC-AT
**
2475490 C--CCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAG-AGAAG
1 CTTTTCAG-AGAAA-TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
2475541 CATTTATTCA
Statistics
Matches: 457, Mismatches: 33, Indels: 37
0.87 0.06 0.07
Matches are distributed among these distances:
109 5 0.01
110 4 0.01
111 50 0.11
112 64 0.14
113 66 0.14
114 125 0.27
115 81 0.18
116 58 0.13
117 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (111 bp):
CTTTTCAGAGAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCAT
Found at i:2475507 original size:228 final size:223
Alignment explanation
Indices: 2474927--2475540 Score: 800
Period size: 225 Copynumber: 2.7 Consensus size: 223
2474917 TTAGCTTTTC
2474927 CAGAGAAAGTTCATAATGAGAAGAA--CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
1 CAGAG-AAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
* * *
2474990 AATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCAT
65 AATTTGTTCAACCTTTT-CTTGAATTCATC-AATTGATGGATTATC--TCCCAGAGAAAGTTCAT
*
2475055 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTCATAATGAGAAGAATTTGTTCAACCTTTT
126 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTCATAATGAGAAGAACTTGTTCAACCTTTT
* *
2475120 ACCCGAATCCATCATTTGATGGATCAGTCTTTT
191 ACCCGAATCCATCATTTGATGGATCAGACTTTG
**
2475153 CAGAGAAACTCATAATGAGAAGAACT-T-ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CAGAGAAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* * *
2475216 ATTTGTTCAACCTTTTTTCTGAATTCATCAAGTTGATGGATTATCTTTGCCAG-GTAGAGTTCAT
66 ATTTGTTCAACCTTTTCT-TGAATTCATCAA-TTGATGGATTATC--TCCCAGAG-AAAGTTCAT
* *
2475280 AATGAGAAGAACTCGTCATTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCT
126 AATGAGAAGAACTCATC--TGAAGAAGGAAGAAGAAG-TCATAATGAGAAGAACTTGTTCAACCT
* ** *
2475345 TTTGCTTGAATTCATCATTTGATGGATCA-ACTTTG
188 TTTACCCGAATCCATCATTTGATGGATCAGACTTTG
2475380 CAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 CAGAG-A-AGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
2475444 AGAACTTGTTCAATCTTTTGCTTGAATTCATC-ATTGATGGATCAATC-CCCAGCAGAAAGTTCA
63 AGAATTTGTTCAACCTTTT-CTTGAATTCATCAATTGATGGAT-TATCTCCCAG-AGAAAGTTCA
2475507 TAATGAGAAGAACTCATCTGAAGAA-GAAG-AGAAG
125 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
2475541 CATTTATTCA
Statistics
Matches: 346, Mismatches: 25, Indels: 36
0.85 0.06 0.09
Matches are distributed among these distances:
224 8 0.02
225 126 0.36
226 14 0.04
227 30 0.09
228 92 0.27
229 10 0.03
230 5 0.01
231 60 0.17
232 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (223 bp):
CAGAGAAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
ATTTGTTCAACCTTTTCTTGAATTCATCAATTGATGGATTATCTCCCAGAGAAAGTTCATAATGA
GAAGAACTCATCTGAAGAAGGAAGAAGAAGTCATAATGAGAAGAACTTGTTCAACCTTTTACCCG
AATCCATCATTTGATGGATCAGACTTTG
Found at i:2475678 original size:3 final size:3
Alignment explanation
Indices: 2475670--2475758 Score: 114
Period size: 3 Copynumber: 30.7 Consensus size: 3
2475660 TTTTTACCCA
*
2475670 TAT TAT TAT TA- TAT TAT TA- TAG TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2475715 TAT TAT TAT TAT TAT CAT TAT TAT TA- TAT TAT TAA TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
2475759 AACATATATA
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
2 8 0.11
3 65 0.86
4 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2475685 original size:11 final size:11
Alignment explanation
Indices: 2475669--2475758 Score: 119
Period size: 11 Copynumber: 7.8 Consensus size: 11
2475659 TTTTTTACCC
2475669 ATATTATTATT
1 ATATTATTATT
2475680 ATATTATTATAGT
1 ATATTATTAT--T
2475693 ATTATTATTATT
1 A-TATTATTATT
2475705 ATATTATTATT
1 ATATTATTATT
2475716 ATTATTATTATT
1 A-TATTATTATT
2475728 ATCATTATTATT
1 AT-ATTATTATT
*
2475740 ATATTATTAAT
1 ATATTATTATT
2475751 ATA-TATTA
1 ATATTATTA
2475759 AACATATATA
Statistics
Matches: 73, Mismatches: 1, Indels: 11
0.86 0.01 0.13
Matches are distributed among these distances:
10 5 0.07
11 33 0.45
12 24 0.33
13 2 0.03
14 9 0.12
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (11 bp):
ATATTATTATT
Found at i:2475703 original size:17 final size:17
Alignment explanation
Indices: 2475673--2475758 Score: 120
Period size: 17 Copynumber: 5.0 Consensus size: 17
2475663 TTACCCATAT
2475673 TATTATTA-TATTATTA
1 TATTATTATTATTATTA
*
2475689 TAGTATTATTATTATTA
1 TATTATTATTATTATTA
2475706 TATTATTATTATTATTA
1 TATTATTATTATTATTA
*
2475723 TTATTATCATTATTATTA
1 -TATTATTATTATTATTA
*
2475741 TATTATTAATATATATTA
1 TATTATTATTAT-TATTA
2475759 AACATATATA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
16 7 0.11
17 34 0.55
18 21 0.34
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:2478478 original size:19 final size:19
Alignment explanation
Indices: 2478454--2478492 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2478444 CCAAACCAAC
2478454 TGAATCCCAATGCTTGGAA
1 TGAATCCCAATGCTTGGAA
2478473 TGAATCCCAATGCTTGGAA
1 TGAATCCCAATGCTTGGAA
2478492 T
1 T
2478493 ATTATCTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (19 bp):
TGAATCCCAATGCTTGGAA
Found at i:2479897 original size:36 final size:35
Alignment explanation
Indices: 2479829--2479915 Score: 138
Period size: 36 Copynumber: 2.5 Consensus size: 35
2479819 AAAAAAAAAA
* *
2479829 AAGTTTGAGTCGGATCAGATCGATTTTTAGAAGAT
1 AAGTTTGGGTCGGGTCAGATCGATTTTTAGAAGAT
*
2479864 AAGTTTGGGTCGGGTCATATCAGATTTTTAGAAGAT
1 AAGTTTGGGTCGGGTCAGATC-GATTTTTAGAAGAT
2479900 AAGTTTGGGTCGGGTC
1 AAGTTTGGGTCGGGTC
2479916 GGATTTAGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 18 0.38
36 30 0.62
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.34
Consensus pattern (35 bp):
AAGTTTGGGTCGGGTCAGATCGATTTTTAGAAGAT
Found at i:2482910 original size:113 final size:113
Alignment explanation
Indices: 2482713--2482939 Score: 429
Period size: 113 Copynumber: 2.0 Consensus size: 113
2482703 CGTCTTCGTG
2482713 AAGGAGAAAAAACAAGGATGATTGTGGATAGAATGATATGGAAGGATAATAAATTTAGGGTCTAA
1 AAGGAGAAAAAACAAGGATGATTGTGGATAGAATGATATGGAAGGATAATAAATTTAGGGTCTAA
2482778 TTGGGCCTTTAGATAAAAGATTATCAAAAGG-CCAACCAAAAAATGAA
66 TTGGGCCTTTAGATAAAAGATTATCAAAAGGCCCAACCAAAAAATGAA
*
2482825 AAGGAGAAAAAACAAGGATGATTTTGGATAGAATGAATATGGAAGGATAATAAATTTAGGGTCTA
1 AAGGAGAAAAAACAAGGATGATTGTGGATAGAATG-ATATGGAAGGATAATAAATTTAGGGTCTA
2482890 ATTGGGCCTTTAGATAAAAGATTATCAAAAGGCCCAACCAAAAAATGAA
65 ATTGGGCCTTTAGATAAAAGATTATCAAAAGGCCCAACCAAAAAATGAA
2482939 A
1 A
2482940 CTTTAAACTA
Statistics
Matches: 112, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
112 34 0.30
113 61 0.54
114 17 0.15
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (113 bp):
AAGGAGAAAAAACAAGGATGATTGTGGATAGAATGATATGGAAGGATAATAAATTTAGGGTCTAA
TTGGGCCTTTAGATAAAAGATTATCAAAAGGCCCAACCAAAAAATGAA
Found at i:2482976 original size:21 final size:21
Alignment explanation
Indices: 2482930--2482979 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2482920 GGCCCAACCA
*
2482930 AAAAATGAAACTTTAAACTAC
1 AAAATTGAAACTTTAAACTAC
*
2482951 AAAATTGAAACTTTAAACTCC
1 AAAATTGAAACTTTAAACTAC
2482972 AAAATTGA
1 AAAATTGA
2482980 TTTGGTCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (21 bp):
AAAATTGAAACTTTAAACTAC
Found at i:2485238 original size:36 final size:36
Alignment explanation
Indices: 2485191--2485269 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
2485181 ATTTCCTCCG
2485191 GATTTGCATTTTCTTCAGCTCCTGATATCTCATCAA
1 GATTTGCATTTTCTTCAGCTCCTGATATCTCATCAA
2485227 GATTTGCATTTTCTTCAGCTCCTGATATCTCATCAA
1 GATTTGCATTTTCTTCAGCTCCTGATATCTCATCAA
2485263 GATTTGC
1 GATTTGC
2485270 GGTTTCACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.42
Consensus pattern (36 bp):
GATTTGCATTTTCTTCAGCTCCTGATATCTCATCAA
Found at i:2489753 original size:84 final size:85
Alignment explanation
Indices: 2489533--2489773 Score: 366
Period size: 85 Copynumber: 2.9 Consensus size: 85
2489523 AAATATGTCA
* *
2489533 ATATAAGCGTTACCTATTA-A--ATATAAGCGCTACGTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
2489595 CCGGTTAAATACTTATTTATT
66 -CGGTTAAATACTTATTTATT
* *
2489616 ATATAAGCACTACCTA-TACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
2489680 CGGTTAAATACTTATTTATT
66 CGGTTAAATACTTATTTATT
** *
2489700 ATATAAGCGCTACCTATTACATTATATAAGTTCTACCTAATATGTCATT-TACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATA-TT
2489764 TCGGTTAAAT
65 TCGGTTAAAT
2489774 GATATAACAT
Statistics
Matches: 144, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
82 2 0.01
83 15 0.10
84 46 0.32
85 81 0.56
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (85 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CGGTTAAATACTTATTTATT
Found at i:2490222 original size:30 final size:30
Alignment explanation
Indices: 2490161--2490223 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
2490151 AGACGTCATG
* * *
2490161 TGTCATATTACCTAAAATAATGTTGGCGTA
1 TGTCACATTACCTAAAATAATGATGGAGTA
* * *
2490191 TGTCACATTATCTAAAGTAATGATGTAGTA
1 TGTCACATTACCTAAAATAATGATGGAGTA
2490221 TGT
1 TGT
2490224 GTCAAACCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (30 bp):
TGTCACATTACCTAAAATAATGATGGAGTA
Found at i:2491094 original size:16 final size:17
Alignment explanation
Indices: 2491070--2491107 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2491060 ATTTCAAAGT
2491070 TATAATTATATA-AAAA
1 TATAATTATATATAAAA
*
2491086 TATATTTATATATAAAA
1 TATAATTATATATAAAA
2491103 TATAA
1 TATAA
2491108 ATAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAATTATATATAAAA
Found at i:2492871 original size:3 final size:3
Alignment explanation
Indices: 2492865--2492915 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
2492855 ATTATTTATT
* * *
2492865 TAA TAA TAA TAA CAA TAA TAA TAT TTA TAA T-A TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
2492910 TAA TAA
1 TAA TAA
2492916 AAGTAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2492889 original size:29 final size:29
Alignment explanation
Indices: 2492851--2492915 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
2492841 TTGTAATTTG
*
2492851 TAATATTATTTAT-T-TAATAATAATAACAA
1 TAATAATATTTATATATAATAATAAT-A-AA
2492880 TAATAATATTTATAATATAATAATAATAAA
1 TAATAATATTTAT-ATATAATAATAATAAA
2492910 TAATAA
1 TAATAA
2492916 AAGTAAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 12 0.38
30 8 0.25
31 2 0.06
32 10 0.31
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TAATAATATTTATATATAATAATAATAAA
Found at i:2493197 original size:76 final size:76
Alignment explanation
Indices: 2493071--2493674 Score: 1073
Period size: 76 Copynumber: 8.0 Consensus size: 76
2493061 GATCTTATAA
*
2493071 ATGACCC-GAAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCCTG-AGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
2493135 CAGGACTTACAG
65 CAGGACTTACAG
2493147 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
*
2493212 ATGACTTACAG
66 AGGACTTACAG
2493223 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
2493288 AGGACTTACAG
66 AGGACTTACAG
2493299 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA-A-CATGCA-TGC
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
2493361 AGGACTTACAG
66 AGGACTTACAG
2493372 ATGA-CCTGAGGATTTGAAAACATCAAAAAGCT-CCGAAGGC-TTTTGGAAACATCATGCACTGC
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
2493434 AGGACTTACAG
66 AGGACTTACAG
2493445 ATGACCCTGAGGATTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGG-AACATCATGCACTGC
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
*
2493508 ATGACTTACAG
66 AGGACTTACAG
2493519 ATGACCCTGAGGATTTGAAAACATCAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCCTGAGGATTTGAAAACATC-AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
2493584 CAGGACTTACAG
65 CAGGACTTACAG
** *
2493596 ATGACCCTGAGGATTTGAAAACATCAAAAATATCTCGAAGGCTTTTTGGAAACATCATGCACTGC
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
2493661 AGGACTTACAG
66 AGGACTTACAG
2493672 ATG
1 ATG
2493675 TGGGAAATAG
Statistics
Matches: 510, Mismatches: 8, Indels: 20
0.95 0.01 0.04
Matches are distributed among these distances:
70 9 0.02
71 9 0.02
72 34 0.07
73 43 0.08
74 84 0.16
75 7 0.01
76 273 0.54
77 51 0.10
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (76 bp):
ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
AGGACTTACAG
Found at i:2494381 original size:20 final size:21
Alignment explanation
Indices: 2494333--2494383 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2494323 TCCCATAAAG
* *
2494333 CTTTCATCTTTGAAAAGAGAAT
1 CTTTCATC-TTAAAAAGAAAAT
*
2494355 CTATCATCTTAAAAAGAAAAT
1 CTTTCATCTTAAAAAGAAAAT
2494376 -TTTCATCT
1 CTTTCATCT
2494384 GAAGTGAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 7 0.28
21 11 0.44
22 7 0.28
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (21 bp):
CTTTCATCTTAAAAAGAAAAT
Found at i:2496801 original size:114 final size:111
Alignment explanation
Indices: 2496638--2496857 Score: 341
Period size: 114 Copynumber: 2.0 Consensus size: 111
2496628 GATCATGCAG
* * *
2496638 TTCATCTTTCAATTCCAATGATTGGTTATGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCATACCAAACCAGATCAGAT-ACTCAAAGA
* *
2496703 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 ACACTTCCAAAAGATGCTATTGAGTCTCCTTA-TT-TACTATGAGCAAA
* *
2496752 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATACTCAAAGAA
1 TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCATACCAAACCAGATCAGATACTCAAAGAA
*
2496817 CACTTCCAAAAGATGCTATTGAGTCTTCTTATTTACTATGA
66 CACTTCCAAAAGATGCTATTGAGTCTCCTTATTTACTATGA
2496858 TCACATGGCA
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
111 8 0.08
112 2 0.02
113 38 0.39
114 50 0.51
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (111 bp):
TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCATACCAAACCAGATCAGATACTCAAAGAA
CACTTCCAAAAGATGCTATTGAGTCTCCTTATTTACTATGAGCAAA
Found at i:2498924 original size:6 final size:6
Alignment explanation
Indices: 2498904--2498953 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
2498894 TTCTCACTTT
* *
2498904 TTTTTC CTTTT- TTTTTC TTTTTC --TTTC TTTTTC TTTTTG TTTTT-
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
2498948 TTTTTC
1 TTTTTC
2498954 AAGTATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.11
5 9 0.24
6 24 0.65
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:2498929 original size:16 final size:16
Alignment explanation
Indices: 2498904--2498951 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
2498894 TTCTCACTTT
2498904 TTTTTCCTTTTTTTTTC
1 TTTTT-CTTTTTTTTTC
*
2498921 TTTTTCTTTCTTTTTC
1 TTTTTCTTTTTTTTTC
*
2498937 TTTTTGTTTTTTTTT
1 TTTTTCTTTTTTTTT
2498952 TCAAGTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:2498951 original size:10 final size:10
Alignment explanation
Indices: 2498900--2498950 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
2498890 CAACTTCTCA
*
2498900 CTTTTTTTTC
1 CTTTTTTTTT
2498910 CTTTTTTTTT
1 CTTTTTTTTT
*
2498920 CTTTTTCTTT
1 CTTTTTTTTT
2498930 CTTTTTCTTTT
1 CTTTTT-TTTT
2498941 -TGTTTTTTTT
1 CT-TTTTTTTT
2498951 TTCAAGTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 29 0.81
11 7 0.19
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:2503203 original size:18 final size:18
Alignment explanation
Indices: 2503182--2503233 Score: 79
Period size: 18 Copynumber: 2.8 Consensus size: 18
2503172 ATTAAAATAA
2503182 AATATATATATAAAAAAT
1 AATATATATATAAAAAAT
2503200 AATATA-ATATAAATAAAT
1 AATATATATATAAA-AAAT
2503218 AATATGATATATAAAA
1 AATAT-ATATATAAAA
2503234 TTTTGAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.23
18 15 0.48
19 2 0.06
20 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AATATATATATAAAAAAT
Found at i:2503215 original size:21 final size:20
Alignment explanation
Indices: 2503175--2503232 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2503165 ACATGAAATT
*
2503175 AAAATAAAATATATATATAA
1 AAAATAAAATATATAAATAA
*
2503195 AAAATAATATAATATAAATAA
1 AAAATAAAAT-ATATAAATAA
* **
2503216 ATAATATGATATATAAA
1 AAAATAAAATATATAAA
2503233 ATTTTGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATAAAATATATAAATAA
Found at i:2503725 original size:16 final size:15
Alignment explanation
Indices: 2503701--2503736 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2503691 ATTTCAAAGT
2503701 TATAATTATATAAAAA
1 TATAATTATAT-AAAA
*
2503717 TATATTTATATAAAA
1 TATAATTATATAAAA
2503732 TATAA
1 TATAA
2503737 ATAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAATTATATAAAA
Found at i:2503753 original size:28 final size:28
Alignment explanation
Indices: 2503710--2503764 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2503700 TTATAATTAT
2503710 ATAAAAATATATTTATATA-AAATATAA
1 ATAAAAATATATTTATATAGAAATATAA
* *
2503737 ATAAAATATTTATTTATTTAGAAATATA
1 ATAAAA-ATATATTTATATAGAAATATA
2503765 GAAAAAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 11 0.46
29 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
ATAAAAATATATTTATATAGAAATATAA
Found at i:2503770 original size:28 final size:25
Alignment explanation
Indices: 2503707--2503770 Score: 65
Period size: 28 Copynumber: 2.4 Consensus size: 25
2503697 AAGTTATAAT
*
2503707 TATATAAAAATATATTTATATAAAA
1 TATAAAAAAATATATTTATATAAAA
*
2503732 TATAAATAAAATATTTATTTATTTAGAAA
1 TATAAA-AAAATA--TATTTATATA-AAA
*
2503761 TATAGAAAAA
1 TATAAAAAAA
2503771 GGACTTCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 5 0.16
26 6 0.19
28 13 0.41
29 8 0.25
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (25 bp):
TATAAAAAAATATATTTATATAAAA
Found at i:2503851 original size:21 final size:22
Alignment explanation
Indices: 2503826--2503871 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2503816 AAAAATATAT
*
2503826 AAAATAATTA-ATATGATTTAA
1 AAAATAAATATATATGATTTAA
* *
2503847 AAAATAAATATTTATTATTTAA
1 AAAATAAATATATATGATTTAA
2503869 AAA
1 AAA
2503872 TATCAGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATAAATATATATGATTTAA
Found at i:2504020 original size:17 final size:18
Alignment explanation
Indices: 2503988--2504021 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2503978 TTAATAAATA
2503988 AAATAAATATTATTTATT
1 AAATAAATATTATTTATT
*
2504006 AAATACATA-TATTTAT
1 AAATAAATATTATTTAT
2504022 GACTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAAATATTATTTATT
Found at i:2504612 original size:219 final size:218
Alignment explanation
Indices: 2504226--2504663 Score: 819
Period size: 219 Copynumber: 2.0 Consensus size: 218
2504216 TTTGGTGACT
2504226 AAATAAAATTAATATAAAATTCAAATATCAGATTAAAATAAATTAAAATATGTACTCGGGATTAA
1 AAATAAAATTAATATAAAATTCAAATATCAGATTAAAATAAATTAAAATATGTACTCGGGATTAA
2504291 AATATATTATTAAAATTAAAGGACTAAATATGATATTTACCCTAAATATATTATTAATATAAAGG
66 AATATATTATTAAAATTAAAGGACTAAATATGATATTTACCCTAAATATATTATTAATATAAAGG
2504356 ATTAAAATAAATAAAATTAAAATTAAAGAACCGAATTATAAAGATCTAAAATTGGG-TCAGTGAC
131 ATTAAAATAAATAAAATTAAAATTAAAGAACCGAATTATAAAGATCTAAAATTGGGTTCAGTGAC
2504420 TAAAATGTAAGGATTACAAATTA
196 TAAAATGTAAGGATTACAAATTA
2504443 AAATAAAATT-ATATAAAATTCAAATATCAGATTAAAATAAATTAAAAATATGTACTC-GGATTA
1 AAATAAAATTAATATAAAATTCAAATATCAGATTAAAATAAATT-AAAATATGTACTCGGGATTA
2504506 AAATATTAATTATTAAAATTAAAGGACTAAATATGATATTTACCCTAAATATATTATTTAATATA
65 AAATA-T-ATTATTAAAATTAAAGGACTAAATATGATATTTACCCTAAATATATTA-TTAATATA
2504571 AAGGATTAAAATAAATAAAATTAAAATTAAAGAACCGAATTATAAAGATCTAAAATTGGGTTCAG
127 AAGGATTAAAATAAATAAAATTAAAATTAAAGAACCGAATTATAAAGATCTAAAATTGGGTTCAG
2504636 TGACTAAAATGTAAGGATTACAAATTA
192 TGACTAAAATGTAAGGATTACAAATTA
2504663 A
1 A
2504664 GATGGCTGCG
Statistics
Matches: 216, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
216 44 0.20
217 24 0.11
218 48 0.22
219 68 0.31
220 32 0.15
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (218 bp):
AAATAAAATTAATATAAAATTCAAATATCAGATTAAAATAAATTAAAATATGTACTCGGGATTAA
AATATATTATTAAAATTAAAGGACTAAATATGATATTTACCCTAAATATATTATTAATATAAAGG
ATTAAAATAAATAAAATTAAAATTAAAGAACCGAATTATAAAGATCTAAAATTGGGTTCAGTGAC
TAAAATGTAAGGATTACAAATTA
Found at i:2505761 original size:3 final size:3
Alignment explanation
Indices: 2505748--2505796 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
2505738 TTATTTTATT
* * *
2505748 TAA TAA T-A TAA TAA CAA TAA TAA TAT TTA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2505794 TAA
1 TAA
2505797 AAAGTAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2506321 original size:66 final size:66
Alignment explanation
Indices: 2506244--2506439 Score: 233
Period size: 63 Copynumber: 3.0 Consensus size: 66
2506234 TTAGGGATTT
*
2506244 TTTAGGATAAACTACCTATTTGGTCACTTATATTATCTAATTTATTTTTTGGTCACTCGATTATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATTATCTAATTTATTTTTTGGTCACTCGATTATT
2506309 A
66 A
* * ** * *
2506310 TTTAGGGTAAACTACCTATTTGGTCACTTATTTATTATCTAATATAATTCAT-AT-A-T--ATTT
1 TTTAGGGTAAACTACCTATTTGGTCACTTA--TATTATCTAATTTATTTTTTGGTCACTCGATTA
2506370 TTA
64 TTA
*
2506373 TTTAGGGTAAACTA-CTGATTTGGTCACTTATAAATTATCTAATTTATGTTTTGGTCACTCGATT
1 TTTAGGGTAAACTACCT-ATTTGGTCACTTAT--ATTATCTAATTTATTTTTTGGTCACTCGATT
2506437 ATT
63 ATT
2506440 TTTTTTTAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
61 1 0.01
62 2 0.02
63 47 0.44
64 1 0.01
65 2 0.02
66 31 0.29
67 1 0.01
68 21 0.20
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (66 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATTATCTAATTTATTTTTTGGTCACTCGATTATT
A
Found at i:2506567 original size:32 final size:32
Alignment explanation
Indices: 2506521--2506584 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
2506511 TGCTAACATG
*
2506521 ACATTTTATTATTATGTTTGGATGTTGGACTA
1 ACATTTTATTATTATGTTTGGATGTTGAACTA
2506553 ACATTTT-TTAATTATGTTTGGATGTTGAACTA
1 ACATTTTATT-ATTATGTTTGGATGTTGAACTA
2506585 TGTAATTCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 2 0.07
32 28 0.93
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (32 bp):
ACATTTTATTATTATGTTTGGATGTTGAACTA
Found at i:2521292 original size:11 final size:11
Alignment explanation
Indices: 2521276--2521328 Score: 78
Period size: 11 Copynumber: 5.2 Consensus size: 11
2521266 CCAGGCAACC
2521276 TTATACGAGAG
1 TTATACGAGAG
2521287 TTATACGAGAG
1 TTATACGAGAG
2521298 -T-TACGAGAG
1 TTATACGAGAG
2521307 TTATACGAGAG
1 TTATACGAGAG
2521318 -T-TACGAGAG
1 TTATACGAGAG
2521327 TT
1 TT
2521329 TGCATGAGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
9 16 0.41
10 4 0.10
11 19 0.49
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (11 bp):
TTATACGAGAG
Found at i:2521304 original size:9 final size:9
Alignment explanation
Indices: 2521279--2521328 Score: 64
Period size: 9 Copynumber: 5.1 Consensus size: 9
2521269 GGCAACCTTA
2521279 TACGAGAGTT
1 TACGAGAG-T
2521289 ATACGAGAGT
1 -TACGAGAGT
2521299 TACGAGAGTT
1 TACGAGAG-T
2521309 ATACGAGAGT
1 -TACGAGAGT
2521319 TACGAGAGT
1 TACGAGAGT
2521328 T
1 T
2521329 TGCATGAGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 18 0.49
10 3 0.08
11 16 0.43
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (9 bp):
TACGAGAGT
Found at i:2521304 original size:20 final size:20
Alignment explanation
Indices: 2521279--2521328 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
2521269 GGCAACCTTA
2521279 TACGAGAGTTATACGAGAGT
1 TACGAGAGTTATACGAGAGT
2521299 TACGAGAGTTATACGAGAGT
1 TACGAGAGTTATACGAGAGT
2521319 TACGAGAGTT
1 TACGAGAGTT
2521329 TGCATGAGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (20 bp):
TACGAGAGTTATACGAGAGT
Found at i:2521736 original size:13 final size:13
Alignment explanation
Indices: 2521713--2521759 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2521703 CAACCGAGAA
2521713 AGAAA-GAAAGGG
1 AGAAAGGAAAGGG
*
2521725 AGAAAGGAAAGGA
1 AGAAAGGAAAGGG
*
2521738 AGAAGAAGAAAGGG
1 AGAA-AGGAAAGGG
2521752 AGATAAGG
1 AGA-AAGG
2521760 CACTTGTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 12 0.43
15 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.02
Consensus pattern (13 bp):
AGAAAGGAAAGGG
Found at i:2524603 original size:24 final size:23
Alignment explanation
Indices: 2524556--2524613 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
2524546 CATTAGTATC
*
2524556 AAATCATTA--AATATTAATAAT
1 AAATCATTATTAATAATAATAAT
*
2524577 AAATCATTATTAATAATAATTACT
1 AAATCATTATTAATAATAA-TAAT
2524601 AAATCATTATTAA
1 AAATCATTATTAA
2524614 ATCATTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 9 0.28
23 7 0.22
24 16 0.50
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATCATTATTAATAATAATAAT
Found at i:2524614 original size:11 final size:11
Alignment explanation
Indices: 2524576--2524743 Score: 93
Period size: 11 Copynumber: 14.1 Consensus size: 11
2524566 ATATTAATAA
2524576 TAAATCATTAT
1 TAAATCATTAT
* *
2524587 TAATAATAATTAC
1 T-A-AATCATTAT
2524600 TAAATCATTAT
1 TAAATCATTAT
*
2524611 TAAATCATTAA
1 TAAATCATTAT
* *
2524622 TATCATTATTAT
1 TA-AATCATTAT
*
2524634 CAAATCATTAT
1 TAAATCATTAT
*
2524645 TAAAATAATTATT
1 T-AAATCATTA-T
2524658 ACTAAATCATTAT
1 --TAAATCATTAT
*
2524671 TATAATGATTATT
1 TA-AATCATTA-T
*
2524684 ATCAAATCATTAC
1 -T-AAATCATTAT
* *
2524697 TAAATCATCAG
1 TAAATCATTAT
* * *
2524708 TACATTAAATAT
1 TA-AATCATTAT
2524720 TAAAATCATTAT
1 T-AAATCATTAT
2524732 TAAATCATTAT
1 TAAATCATTAT
2524743 T
1 T
2524744 GTCAAATATT
Statistics
Matches: 117, Mismatches: 27, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
11 50 0.43
12 37 0.32
13 12 0.10
14 16 0.14
15 2 0.02
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.42
Consensus pattern (11 bp):
TAAATCATTAT
Found at i:2524638 original size:23 final size:23
Alignment explanation
Indices: 2524606--2524695 Score: 74
Period size: 26 Copynumber: 3.7 Consensus size: 23
2524596 TTACTAAATC
* *
2524606 ATTATTAAATCATTAATATCATT
1 ATTATCAAATCATTAATATAATT
*
2524629 ATTATCAAATCATTATTAAAATAATT
1 ATTATCAAATC---ATTAATATAATT
*
2524655 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTA--AT-ATAATT
2524681 ATTATCAAATCATTA
1 ATTATCAAATCATTA
2524696 CTAAATCATC
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
23 14 0.26
25 2 0.04
26 37 0.69
27 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (23 bp):
ATTATCAAATCATTAATATAATT
Found at i:2524646 original size:26 final size:26
Alignment explanation
Indices: 2524617--2524704 Score: 101
Period size: 26 Copynumber: 3.4 Consensus size: 26
2524607 TTATTAAATC
2524617 ATTAATATCATTATTATCAAATCATT
1 ATTAATATCATTATTATCAAATCATT
* *
2524643 ATTAAAATAATTATTA-CTAAATCATT
1 ATTAATATCATTATTATC-AAATCATT
*
2524669 ATT-ATAATGATTATTATCAAATCATT
1 ATTAAT-ATCATTATTATCAAATCATT
*
2524695 ACTAA-ATCAT
1 ATTAATATCAT
2524705 CAGTACATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 6 0.12
26 44 0.85
27 2 0.04
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.43
Consensus pattern (26 bp):
ATTAATATCATTATTATCAAATCATT
Found at i:2524693 original size:86 final size:84
Alignment explanation
Indices: 2524495--2524743 Score: 217
Period size: 86 Copynumber: 2.9 Consensus size: 84
2524485 TTCGACATAT
*
2524495 TTATAATGATTATTAGTATCAAATCATTATTATAATTTCATTACTAATAATCATTAGTATCAAAT
1 TTATAATGATTA-T--TATCAAATCATTATTA-AA--TCA-T--TAAT-ATCATTAATATCAAAT
*
2524560 C---ATTAAATATTAATAATAAATCATTA
56 CATTATTAAATATTATTAATAAATCATTA
*
2524586 TTAATAAT-A--ATTA-CTAAATCATTATTAAATCATTAATATCATTATTATCAAATCATTATTA
1 TT-ATAATGATTATTATC-AAATCATTATTAAATCATTAATATCATTAATATCAAATCATTATT-
*
2524647 AAATAATTATTACTAAATCATTA
63 AAAT-ATTATTAATAAATCATTA
* * * *
2524670 TTATAATGATTATTATCAAATCATTACTAAATCATCAGTA-CATTAAATATTAAAATCATTATTA
1 TTATAATGATTATTATCAAATCATTATTAAATCATTAATATCATT-AATA-TCAAATCATTATTA
2524734 AATCATTATT
64 AAT-ATTATT
2524744 GTCAAATATT
Statistics
Matches: 136, Mismatches: 9, Indels: 31
0.77 0.05 0.18
Matches are distributed among these distances:
79 16 0.12
80 4 0.03
82 4 0.03
83 12 0.09
84 19 0.14
85 7 0.05
86 51 0.38
87 13 0.10
88 1 0.01
89 1 0.01
91 3 0.02
92 5 0.04
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (84 bp):
TTATAATGATTATTATCAAATCATTATTAAATCATTAATATCATTAATATCAAATCATTATTAAA
TATTATTAATAAATCATTA
Found at i:2524771 original size:35 final size:34
Alignment explanation
Indices: 2524578--2524670 Score: 64
Period size: 35 Copynumber: 2.6 Consensus size: 34
2524568 ATTAATAATA
*
2524578 AATCATTATTAAT-AATAATTA-CTAAATCATTATTA
1 AATCATTATT-ATAAAT-ATTATC-AAATCATTACTA
* * * *
2524613 AATCATTAATATCATTATTATCAAATCATTATTAA
1 AATCATTATTATAAATATTATCAAATCATTACT-A
*
2524648 AATAATTATTACTAAATCATTAT
1 AATCATTATTA-TAAAT-ATTAT
2524671 TATAATGATT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
34 17 0.36
35 22 0.47
36 3 0.06
37 5 0.11
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (34 bp):
AATCATTATTATAAATATTATCAAATCATTACTA
Found at i:2525077 original size:24 final size:23
Alignment explanation
Indices: 2525021--2525101 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 23
2525011 CATTATTACT
2525021 AATCATTACTTAATCATTAAT-ATAA
1 AATCATTA-TTAAT-ATTAATAAT-A
2525046 AATCATTA--AATATTAATAATA
1 AATCATTATTAATATTAATAATA
* *
2525067 AATCATTATTAATAATAATTACTA
1 AATCATTATTAATATTAA-TAATA
2525091 AATCATTATTA
1 AATCATTATTA
2525102 TCAAATCATT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
21 15 0.30
22 5 0.10
23 7 0.14
24 15 0.30
25 8 0.16
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.41
Consensus pattern (23 bp):
AATCATTATTAATATTAATAATA
Found at i:2525078 original size:38 final size:38
Alignment explanation
Indices: 2525036--2525115 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
2525026 TTACTTAATC
*
2525036 ATTAATATAAAATCATTAAAT-ATTAATAAT-AAATCATT
1 ATTAATA-AAAATCACTAAATCATT-ATAATCAAATCATT
* * *
2525074 ATTAATAATAATTACTAAATCATTATTATCAAATCATT
1 ATTAATAAAAATCACTAAATCATTATAATCAAATCATT
2525112 ATTA
1 ATTA
2525116 TAATGGTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 14 0.39
38 22 0.61
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (38 bp):
ATTAATAAAAATCACTAAATCATTATAATCAAATCATT
Found at i:2525079 original size:14 final size:14
Alignment explanation
Indices: 2525052--2525141 Score: 70
Period size: 14 Copynumber: 6.9 Consensus size: 14
2525042 ATAAAATCAT
*
2525052 TAAAT-ATTAATAA
1 TAAATCATTATTAA
2525065 TAAATCATTATTAA
1 TAAATCATTATTAA
*
2525079 T-AAT-A--ATTAC
1 TAAATCATTATTAA
2525089 TAAATCATTATT-A
1 TAAATCATTATTAA
2525102 TCAAATCATTATT-A
1 T-AAATCATTATTAA
** *
2525116 T-AATGGTTATTAC
1 TAAATCATTATTAA
2525129 TAAATCATTATTA
1 TAAATCATTATTA
2525142 TGGTTAATTG
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
10 5 0.08
11 3 0.05
12 10 0.16
13 10 0.16
14 33 0.54
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (14 bp):
TAAATCATTATTAA
Found at i:2525425 original size:60 final size:60
Alignment explanation
Indices: 2525351--2525465 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 60
2525341 GATTACTAAT
* *
2525351 CATTACTTTTAAATCATTAAATATTAATAATAATTTCATGATTACTAATCATTACCAAAG
1 CATTACTATCAAATCATTAAATATTAATAATAATTTCATGATTACTAATCATTACCAAAG
*
2525411 CATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 CATTACTATCAAATCATTAAATATTAATAATAATTTCATGATTACTAATCATTAC
2525466 TATCAAATCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (60 bp):
CATTACTATCAAATCATTAAATATTAATAATAATTTCATGATTACTAATCATTACCAAAG
Found at i:2525459 original size:109 final size:109
Alignment explanation
Indices: 2525331--2525576 Score: 402
Period size: 109 Copynumber: 2.3 Consensus size: 109
2525321 AATCATTATT
* * * * *
2525331 ATAATTGCATGATTACTAATCATTACTTTTAAATCATTAAATATTAATAATAATTTCATGATTAC
1 ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATGATTAC
2525396 TAATCATTACCAAAGCATTACTATCAAATCATTAAATATTAATA
66 TAATCATTACCAAAGCATTACTATCAAATCATTAAATATTAATA
*
2525440 ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTAC
1 ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATGATTAC
* *
2525505 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
66 TAATCATTACCAAAGCATTACTATCAAATCATTAAATATTAATA
* *
2525549 ATAATTTCATTATTATTAATCATGACTA
1 ATAATTTCATTATTACTAATCATTACTA
2525577 AATAATTATT
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 127 1.00
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.41
Consensus pattern (109 bp):
ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATGATTAC
TAATCATTACCAAAGCATTACTATCAAATCATTAAATATTAATA
Found at i:2525465 original size:49 final size:49
Alignment explanation
Indices: 2525411--2525576 Score: 206
Period size: 49 Copynumber: 3.2 Consensus size: 49
2525401 ATTACCAAAG
2525411 CATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAAT
1 CATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAAT
*
2525460 CATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTAAAT
1 CATTACTATCAAATCATTAAATA-T--TAATAA--TAA-T-TT-C--ATTATTACT-AAT
*
2525520 CATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTATTAAT
1 CATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAAT
*
2525569 CATGACTA
1 CATTACTA
2525577 AATAATTATT
Statistics
Matches: 102, Mismatches: 4, Indels: 22
0.80 0.03 0.17
Matches are distributed among these distances:
49 33 0.32
50 8 0.08
52 7 0.07
53 2 0.02
54 4 0.04
55 4 0.04
56 2 0.02
57 7 0.07
59 9 0.09
60 26 0.25
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (49 bp):
CATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAAT
Found at i:2525485 original size:21 final size:20
Alignment explanation
Indices: 2525461--2525545 Score: 61
Period size: 21 Copynumber: 4.2 Consensus size: 20
2525451 ATTACTAATC
2525461 ATTACTATCAAATCATTAAAT
1 ATTACTATC-AATCATTAAAT
* *
2525482 ATTA--AT-AATAATTTAATT
1 ATTACTATCAATCA-TTAAAT
* *
2525500 ATTACTAATC-ATTACTAAAT
1 ATTACT-ATCAATCATTAAAT
2525520 CATTACTATCAAATCATTAAAT
1 -ATTACTATC-AATCATTAAAT
2525542 ATTA
1 ATTA
2525546 ATAATAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
17 4 0.08
18 9 0.18
19 2 0.04
20 7 0.14
21 19 0.39
22 8 0.16
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTACTATCAATCATTAAAT
Found at i:2525498 original size:60 final size:60
Alignment explanation
Indices: 2525374--2525555 Score: 194
Period size: 60 Copynumber: 3.0 Consensus size: 60
2525364 TCATTAAATA
* * * * *
2525374 TTAATAATAATTTCATGATTACTAATCATTAC---CAAAGCATT-ACTATCAAATCATTAAAT
1 TTAATAATAATTTCATCATTACTAATCATTACTATCAAATCATTAAATAT-TAAT-AAT-AAT
*
2525433 ATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAT
1 -TTAATAATAATTTCATCATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAT
* * * *
2525494 TTAATTATTA-CTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAT
1 TTAATAATAATTTCATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAT
2525554 TT
1 TT
2525556 CATTATTATT
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
59 9 0.08
60 78 0.73
61 3 0.03
62 2 0.02
63 11 0.10
64 4 0.04
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (60 bp):
TTAATAATAATTTCATCATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAT
Found at i:2525561 original size:60 final size:60
Alignment explanation
Indices: 2525451--2525584 Score: 225
Period size: 60 Copynumber: 2.2 Consensus size: 60
2525441 TAATTTCATT
2525451 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATC
* *
2525510 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATC
* *
2525570 ATGACTAAATAATTA
1 ATTACTAAATCATTA
2525585 TTATAATTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
59 6 0.09
60 64 0.91
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATC
Found at i:2529659 original size:28 final size:28
Alignment explanation
Indices: 2529624--2529677 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
2529614 ATAATCTAAT
2529624 ATATAACTTAAACTAACAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
*
2529652 ATATAACTTAAACTAACAAAGTAATA
1 ATATAACTTAAACTAACAAACTAATA
2529678 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:2529684 original size:28 final size:28
Alignment explanation
Indices: 2529620--2529684 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
2529610 TTATATAATC
2529620 TAATATATAACTTAAACTAACAAACTAA
1 TAATATATAACTTAAACTAACAAACTAA
*
2529648 T-ATAATATAACTTAAACTAACAAAGTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
2529676 TAATTTATA
1 TAATATATA
2529685 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:2529687 original size:21 final size:21
Alignment explanation
Indices: 2529654--2529702 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2529644 CTAATATAAT
*
2529654 ATAACTTAAACTAACAAAGTA
1 ATAACTTAAACTAACAAACTA
* *
2529675 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2529696 ATTAACT
1 A-TAACT
2529703 AAATTTCTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2532147 original size:3 final size:3
Alignment explanation
Indices: 2532139--2532180 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
2532129 AAAGAGTGTT
2532139 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2532181 GAAAAGAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2538667 original size:20 final size:21
Alignment explanation
Indices: 2538622--2538682 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
2538612 TTCCCCTGAG
*
2538622 GGGGGAATCAGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
2538645 GGGGGAATCGGTTCCCT-AAA
1 GGGGGAATCGGTTCCCTCAAA
** *
2538665 GGGAAAATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2538683 TACACCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 17 0.52
21 1 0.03
22 3 0.09
23 12 0.36
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2540116 original size:12 final size:12
Alignment explanation
Indices: 2540101--2540155 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
2540091 GTTATTTAAA
2540101 CGGGTATTGGGC
1 CGGGTATTGGGC
*
2540113 CGGGTATTGGGT
1 CGGGTATTGGGC
* *
2540125 CAGGTATTGGGT
1 CGGGTATTGGGC
* * *
2540137 CGAGAATCGGGC
1 CGGGTATTGGGC
2540149 CGGGTAT
1 CGGGTAT
2540156 ATATATATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.15, C:0.15, G:0.45, T:0.25
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:2545896 original size:21 final size:19
Alignment explanation
Indices: 2545872--2545912 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2545862 TTAGGTTTAA
2545872 TAGTTGAATTTTCATGTATTT
1 TAGTTGAA-TTT-ATGTATTT
*
2545893 TAGTTTAATTTATGTATTT
1 TAGTTGAATTTATGTATTT
2545912 T
1 T
2545913 TTAATTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 3 0.16
21 7 0.37
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.61
Consensus pattern (19 bp):
TAGTTGAATTTATGTATTT
Found at i:2546850 original size:15 final size:14
Alignment explanation
Indices: 2546814--2546876 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 14
2546804 GACTTATTAT
2546814 ATAAAATTATTT-A
1 ATAAAATTATTTAA
2546827 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
2546841 ATGTAAATTATAT-A
1 AT-AAAATTATTTAA
*
2546855 A-AACATTA-TT-A
1 ATAAAATTATTTAA
2546866 ATAAAATTATT
1 ATAAAATTATT
2546877 GGCATTGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 3 0.08
12 11 0.28
13 13 0.32
14 5 0.12
15 8 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:2546936 original size:23 final size:24
Alignment explanation
Indices: 2546899--2546949 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
2546889 TGATTAAATA
2546899 TAAATTAATATAGTTTAATTTATC
1 TAAATTAATATAGTTTAATTTATC
*
2546923 TAAATT-ATATAGTTTAATTTATG
1 TAAATTAATATAGTTTAATTTATC
2546946 TAAA
1 TAAA
2546950 GAAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
TAAATTAATATAGTTTAATTTATC
Found at i:2547231 original size:11 final size:11
Alignment explanation
Indices: 2547198--2547238 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2547188 TGATAATGAT
*
2547198 AATTTAAATAA
1 AATTTGAATAA
2547209 AATTTGATATAA
1 AATTTGA-ATAA
2547221 AATTTGAATAA
1 AATTTGAATAA
*
2547232 CATTTGA
1 AATTTGA
2547239 GTTAATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (11 bp):
AATTTGAATAA
Found at i:2547737 original size:20 final size:20
Alignment explanation
Indices: 2547699--2547737 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2547689 GTTACTTTGG
** *
2547699 ACAGAAGCATCCTTTAAAAA
1 ACAGAAGCATCAATAAAAAA
2547719 ACAGAAGCATCAATAAAAA
1 ACAGAAGCATCAATAAAAA
2547738 TTGGTTTTAG
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:0.56, C:0.18, G:0.10, T:0.15
Consensus pattern (20 bp):
ACAGAAGCATCAATAAAAAA
Found at i:2548943 original size:25 final size:25
Alignment explanation
Indices: 2548909--2548958 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2548899 ATTCAGGTTC
*
2548909 AGGTTCAGGTTTGGGTTTGGGTTTA
1 AGGTTCAGGTTTGGGTTCGGGTTTA
*
2548934 AGGTTTAGGTTTGGGTTCGGGTTTA
1 AGGTTCAGGTTTGGGTTCGGGTTTA
2548959 TATTTAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.04, G:0.40, T:0.44
Consensus pattern (25 bp):
AGGTTCAGGTTTGGGTTCGGGTTTA
Found at i:2548970 original size:25 final size:24
Alignment explanation
Indices: 2548915--2548966 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
2548905 GTTCAGGTTC
*
2548915 AGGTTTGGGTTTGGGTTTAAGGTTT
1 AGGTTTGGGTTCGGGTTTAA-GTTT
2548940 AGGTTTGGGTTCGGGTTTATA-TTT
1 AGGTTTGGGTTCGGGTTTA-AGTTT
2548964 AGG
1 AGG
2548967 GTTTAAGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 18 0.72
26 1 0.04
ACGTcount: A:0.13, C:0.02, G:0.38, T:0.46
Consensus pattern (24 bp):
AGGTTTGGGTTCGGGTTTAAGTTT
Found at i:2549796 original size:6 final size:6
Alignment explanation
Indices: 2549759--2549836 Score: 53
Period size: 6 Copynumber: 13.3 Consensus size: 6
2549749 ACTATTTATA
2549759 ATTAAT ATTAAAAT AATTATAT ATT-AT AATTAAT ATTAAT -TT-A- ATTAAT
1 ATTAAT ATT--AAT -ATTA-AT ATTAAT -ATTAAT ATTAAT ATTAAT ATTAAT
*
2549808 ATTAAT ATTAA- CTT-AT ATTAAT A-TAAT AT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT
2549837 AGTTTATAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 24
0.69 0.02 0.29
Matches are distributed among these distances:
4 4 0.07
5 14 0.24
6 26 0.45
7 6 0.10
8 5 0.09
9 3 0.05
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTAAT
Found at i:2549834 original size:21 final size:20
Alignment explanation
Indices: 2549785--2549836 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
2549775 TTATATATTA
*
2549785 TAAT-TAATATTAATTTAAT
1 TAATATAATATTAACTTAAT
2549804 TAATATTAATATTAACTTATAT
1 TAATA-TAATATTAACTTA-AT
2549826 TAATATAATAT
1 TAATATAATAT
2549837 AGTTTATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
21 18 0.62
22 7 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATATAATATTAACTTAAT
Found at i:2549847 original size:43 final size:41
Alignment explanation
Indices: 2549727--2549847 Score: 106
Period size: 43 Copynumber: 2.9 Consensus size: 41
2549717 CAATTTCATC
*
2549727 AATATATAATTTATATTAATA-AA-CTATTTATAATTAATATT
1 AATAT-TAA-TTATATTAATATAATATATTTATAATTAATATT
* * *
2549768 AA-AATAATTATA-TATTATAATTAATATTAATTTAATTAATATT
1 AATATTAATTATATTAATATAA-T-ATATT--TATAATTAATATT
2549811 AATATTAACTTATATTAATATAATATAGTTTATAATT
1 AATATTAA-TTATATTAATATAATATA-TTTATAATT
2549848 TGTAATTATA
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
37 4 0.06
38 7 0.11
39 3 0.05
40 1 0.02
41 6 0.10
43 20 0.32
44 7 0.11
45 8 0.13
46 7 0.11
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (41 bp):
AATATTAATTATATTAATATAATATATTTATAATTAATATT
Found at i:2549947 original size:21 final size:21
Alignment explanation
Indices: 2549923--2549967 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2549913 AATATAAATA
* *
2549923 ATAGTTTATAAATTATATACT
1 ATAGGTTATAAAGTATATACT
*
2549944 ATAGGTTATATAGTATATACT
1 ATAGGTTATAAAGTATATACT
2549965 ATA
1 ATA
2549968 TATTACACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (21 bp):
ATAGGTTATAAAGTATATACT
Done.