Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003391.1 Hibiscus syriacus cultivar Beakdansim tig00007137_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: 193384
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:3813 original size:62 final size:62
Alignment explanation
Indices: 3731--3849 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 62
3721 ATGTTTGCAT
*
3731 ATCAAATACTGCAAAGCTCTGATATCTATGATCGATCGAAACTGGATCGTG-ACAGAAATTTG
1 ATCAAATACTGCAAAGCTCTGATATCTATGACCGATCGAAACTGGATCG-GAACAGAAATTTG
* * * * * *
3793 ATCAAATATTGCAGAGCTCTGATGTCTATTACCGATCGGAATTGGATCGGAACAGAA
1 ATCAAATACTGCAAAGCTCTGATATCTATGACCGATCGAAACTGGATCGGAACAGAA
3850 TTCCGGTGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 1 0.02
62 48 0.98
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (62 bp):
ATCAAATACTGCAAAGCTCTGATATCTATGACCGATCGAAACTGGATCGGAACAGAAATTTG
Found at i:8634 original size:54 final size:54
Alignment explanation
Indices: 8559--8696 Score: 188
Period size: 54 Copynumber: 2.6 Consensus size: 54
8549 TAGTAACCCC
* * * *
8559 TGCCCACGCCTTAACTAAAGACCTCTTCTGCGATAGCTTAGAATGAATAAGCCG
1 TGCCCACGCCTTAACTGAAGACCTCTTCTGCAATAGCTCAAAATGAATAAGCCG
*
8613 TGCCCACGCCTTAACTGAAGACCTTTTCTGCAATAGCTCAAAATGAATAAGCCG
1 TGCCCACGCCTTAACTGAAGACCTCTTCTGCAATAGCTCAAAATGAATAAGCCG
* * *
8667 TGCCCATGCCTTATGCGGAA-ACCTCTTCTG
1 TGCCCACGCCTTA-ACTGAAGACCTCTTCTG
8697 GTCTTTTCGT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 70 0.95
55 4 0.05
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (54 bp):
TGCCCACGCCTTAACTGAAGACCTCTTCTGCAATAGCTCAAAATGAATAAGCCG
Found at i:9175 original size:24 final size:23
Alignment explanation
Indices: 9110--9185 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
9100 CACTACGGTG
*
9110 AAATTCTACGTGGCACTTCAGTGC
1 AAATTCTACGTGGCACTTC-GGGC
*
9134 --ATCTCTACGCGGTC-CTTCGGGAC
1 AAAT-TCTACGTGG-CACTTCGGG-C
9157 AAATTCTACGTGGCACTTCGGTGC
1 AAATTCTACGTGGCACTTCGG-GC
9181 AAATT
1 AAATT
9186 TATATGAGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
22 4 0.10
23 14 0.33
24 21 0.50
25 3 0.07
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (23 bp):
AAATTCTACGTGGCACTTCGGGC
Found at i:16025 original size:54 final size:54
Alignment explanation
Indices: 15947--16087 Score: 203
Period size: 54 Copynumber: 2.6 Consensus size: 54
15937 AACTAGTAAC
* * *
15947 CCGTGCCCACGCCTTAACTAAAGACCTCTTCTGCGATAGCTTAGAATGAATAAG
1 CCGTGCCCACGCCTTAACTGAAGACCTCTTCTGCGATAGCTCAAAATGAATAAG
* *
16001 CCGTGCCCACGCCTTAACTGAAGACCTTTTTTGCGATAGCTCAAAATGAATAAG
1 CCGTGCCCACGCCTTAACTGAAGACCTCTTCTGCGATAGCTCAAAATGAATAAG
* *
16055 CCGTGCCCACGCCTTATGC-GAAAACCTCTTCTG
1 CCGTGCCCACGCCTTA-ACTGAAGACCTCTTCTG
16088 GTCTTTTCGT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 76 0.99
55 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (54 bp):
CCGTGCCCACGCCTTAACTGAAGACCTCTTCTGCGATAGCTCAAAATGAATAAG
Found at i:16566 original size:24 final size:24
Alignment explanation
Indices: 16488--16576 Score: 98
Period size: 23 Copynumber: 3.8 Consensus size: 24
16478 ACATATTATA
*
16488 TGGCACTACGGTG-AAATTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
16511 TGGCACTTCGGTGC--ATCTCTACG
1 TGGCACTTCGGTGCAAAT-TCTACG
*
16534 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-CAAATTCTACG
16558 TGGCACTTCGGTGCAAATT
1 TGGCACTTCGGTGCAAATT
16577 TATATGAGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
22 3 0.05
23 28 0.51
24 21 0.38
25 3 0.05
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:18091 original size:123 final size:123
Alignment explanation
Indices: 17869--18114 Score: 483
Period size: 123 Copynumber: 2.0 Consensus size: 123
17859 ACACACTTTC
17869 TTGACACAATTGTTCGAACTCAGAACTCCTTTCTTTTACCATAAACACCATTTAATGGGTAGATT
1 TTGACACAATTGTTCGAACTCAGAACTCCTTTCTTTTACCATAAACACCATTTAATGGGTAGATT
17934 TTTATCTAAGAAACATCATTTTAGAAATAATACAAATACGTCAAAATCTATATAAAAA
66 TTTATCTAAGAAACATCATTTTAGAAATAATACAAATACGTCAAAATCTATATAAAAA
17992 TTGACACAATTGTTCGAACTCAGAACTCCTTTCTTTTACCATAAACACCATTTAATGGGTAGATT
1 TTGACACAATTGTTCGAACTCAGAACTCCTTTCTTTTACCATAAACACCATTTAATGGGTAGATT
*
18057 TTTATCTAAGAAACATCATTTTAGAAATATTACAAATACGTCAAAATCTATATAAAAA
66 TTTATCTAAGAAACATCATTTTAGAAATAATACAAATACGTCAAAATCTATATAAAAA
18115 GGGTAAATTA
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 122 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (123 bp):
TTGACACAATTGTTCGAACTCAGAACTCCTTTCTTTTACCATAAACACCATTTAATGGGTAGATT
TTTATCTAAGAAACATCATTTTAGAAATAATACAAATACGTCAAAATCTATATAAAAA
Found at i:19837 original size:2 final size:2
Alignment explanation
Indices: 19799--19823 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19789 ACACAGATAG
19799 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 A
19824 CCATCAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20281 original size:2 final size:2
Alignment explanation
Indices: 20274--20310 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20264 TGCCATGCGT
20274 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
20311 TTTAGGGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:25605 original size:17 final size:17
Alignment explanation
Indices: 25583--25616 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25573 TGTTGAACCC
*
25583 TAATTTGTTTTTTTATT
1 TAATTTATTTTTTTATT
25600 TAATTTATTTTTTTATT
1 TAATTTATTTTTTTATT
25617 CACTATAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TAATTTATTTTTTTATT
Found at i:29275 original size:34 final size:34
Alignment explanation
Indices: 29235--29316 Score: 128
Period size: 34 Copynumber: 2.4 Consensus size: 34
29225 CCGATTATAC
29235 ATATATAATATTTTATATATTTTATATTAATTAT
1 ATATATAATATTTTATATATTTTATATTAATTAT
* * *
29269 ATATATAATATATAATATTTTTTATATTAATTAT
1 ATATATAATATTTTATATATTTTATATTAATTAT
*
29303 ATATAAAATATTTT
1 ATATATAATATTTT
29317 CGGGTTCGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
ATATATAATATTTTATATATTTTATATTAATTAT
Found at i:30944 original size:6 final size:6
Alignment explanation
Indices: 30935--31113 Score: 299
Period size: 6 Copynumber: 30.2 Consensus size: 6
30925 ATATGTATAT
* *
30935 GCATAG GCATAG GTATAG GTATAG GCATAG GCATAG GCATAG GCATAG
1 GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG
30983 GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG
1 GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG
* * *
31031 GCATAG GCATAG GCATAG GC--AG GCATAG GCTTAG GCTTAG GCTTAG
1 GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG
31077 GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG G
1 GCATAG GCATAG GCATAG GCATAG GCATAG GCATAG G
31114 TATATGTATA
Statistics
Matches: 167, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
4 4 0.02
6 163 0.98
ACGTcount: A:0.31, C:0.16, G:0.34, T:0.19
Consensus pattern (6 bp):
GCATAG
Found at i:32356 original size:29 final size:29
Alignment explanation
Indices: 32314--32425 Score: 215
Period size: 29 Copynumber: 3.9 Consensus size: 29
32304 GTACCGGGGT
32314 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
32343 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
32372 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
32401 AGGTCGCCATGCACGCCCTGCGACC
1 AGGTCGCCATGCACGCCCGGCGACC
32426 TACCCCACGA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 82 1.00
ACGTcount: A:0.20, C:0.45, G:0.28, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:32468 original size:30 final size:30
Alignment explanation
Indices: 32432--32541 Score: 184
Period size: 30 Copynumber: 3.7 Consensus size: 30
32422 GACCTACCCC
32432 ACGACCTCCATGCACGCCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
* * *
32462 ACGACCTCCATGCATGCCCAGGCACGTCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
*
32492 ACGACCTCCATGCACGGCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
32522 ACGACCTCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCA
32542 GCTCGCCAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.24, C:0.47, G:0.18, T:0.11
Consensus pattern (30 bp):
ACGACCTCCATGCACGCCCATGCACGCCCA
Found at i:33183 original size:21 final size:21
Alignment explanation
Indices: 33158--33201 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
33148 AATTTAGTTA
33158 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
33179 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
33200 AT
1 AT
33202 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:33215 original size:28 final size:28
Alignment explanation
Indices: 33178--33232 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
33168 TAGTATAAAT
*
33178 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
33206 TATTAATTTGTTAGTTTAAGTTATATT
1 TATTAATTTGTTAGTTTAAGTTATATT
33233 TAGATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:36334 original size:21 final size:21
Alignment explanation
Indices: 36307--36454 Score: 69
Period size: 21 Copynumber: 7.3 Consensus size: 21
36297 AGATTTAGTA
36307 ATGATTAGTAATGATGAAATT
1 ATGATTAGTAATGATGAAATT
* * *
36328 ATTATTAATTATGTATG--ATT
1 ATGATTAGTAATG-ATGAAATT
** * *
36348 -TGA-TAGTAATGATTTAGTA
1 ATGATTAGTAATGATGAAATT
*
36367 ATGATTAGTAATAATGAAATT
1 ATGATTAGTAATGATGAAATT
* * *
36388 ATTATTAATTATGTATG--ATT
1 ATGATTAGTAATG-ATGAAATT
** * *
36408 -TGA-TAGTAATGATTTAGTA
1 ATGATTAGTAATGATGAAATT
*
36427 ATGATTAGTAATAATGAAATT
1 ATGATTAGTAATGATGAAATT
*
36448 ATTATTA
1 ATGATTA
36455 ATTTTTAATG
Statistics
Matches: 87, Mismatches: 30, Indels: 20
0.64 0.22 0.15
Matches are distributed among these distances:
17 4 0.05
18 12 0.14
19 6 0.07
20 12 0.14
21 47 0.54
22 6 0.07
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.45
Consensus pattern (21 bp):
ATGATTAGTAATGATGAAATT
Found at i:36367 original size:11 final size:11
Alignment explanation
Indices: 36351--36498 Score: 52
Period size: 11 Copynumber: 12.6 Consensus size: 11
36341 TATGATTTGA
36351 TAGTAATGATT
1 TAGTAATGATT
36362 TAGTAATGATT
1 TAGTAATGATT
* *
36373 AGTAATAATGAAAT
1 --TAGTAATG-ATT
* * *
36387 TA-TTATTAAT
1 TAGTAATGATT
36397 TATGT-ATGATT
1 TA-GTAATGATT
36408 TGATAGTAATGATT
1 T-A--GTAATGATT
36422 TAGTAATGATT
1 TAGTAATGATT
* *
36433 AGTAATAATGAAAT
1 --TAGTAATG-ATT
* * *
36447 TATTATTAATT
1 TAGTAATGATT
*
36458 T-TTAATGATTT
1 TAGTAATGA-TT
36469 GATAGTAATGATT
1 --TAGTAATGATT
36482 TAGTAATGA-T
1 TAGTAATGATT
36492 TAGTAAT
1 TAGTAAT
36499 AATGAAATTA
Statistics
Matches: 106, Mismatches: 16, Indels: 31
0.69 0.10 0.20
Matches are distributed among these distances:
10 18 0.17
11 42 0.40
12 9 0.08
13 20 0.19
14 17 0.16
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:36369 original size:60 final size:61
Alignment explanation
Indices: 36298--36790 Score: 851
Period size: 60 Copynumber: 8.2 Consensus size: 61
36288 GTATTTATAA
*
36298 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAATGATTTGATAGTAAT
36358 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAATGATTTGATAGTAAT
*
36418 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAATGATTTGATAGTAAT
36478 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAATGATTTGATAGTAAT
* *
36538 GACTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAATGATTTGATAGTAAT
* * *
36598 GATTTAGTAATGATTAGTAATAAT-AATTTATTATTAA-TATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAATGATTTGATAGTAAT
36657 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAATGATTTGATAGTAAT
*
36717 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAATGATTTGATAGTAAT
36777 GATTTAGTAATGAT
1 GATTTAGTAATGAT
36791 AATTTATTAT
Statistics
Matches: 414, Mismatches: 12, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
58 1 0.00
59 61 0.15
60 346 0.84
61 6 0.01
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (61 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAATGATTTGATAGTAAT
Found at i:36647 original size:21 final size:22
Alignment explanation
Indices: 36618--36667 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
36608 TGATTAGTAA
36618 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
36639 TAATGATTTGATATTAATGATT
1 TAATAATTTGATATTAATGATT
*
36661 TAGTAAT
1 TAATAAT
36668 GATTAGTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:36787 original size:25 final size:25
Alignment explanation
Indices: 36759--36856 Score: 114
Period size: 25 Copynumber: 4.0 Consensus size: 25
36749 TATTAATTTT
36759 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
* *
36784 TAATGATAATTTATTATTAAT-A-TT--
1 TAATGAT--TTGA-TAGTAATGATTTAG
*
36808 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
36833 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
36857 CGACTTGAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
21 7 0.11
22 4 0.06
23 2 0.03
24 7 0.11
25 30 0.48
26 2 0.03
27 4 0.06
28 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:36826 original size:14 final size:14
Alignment explanation
Indices: 36808--36855 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
36798 TATTAATATT
*
36808 TAATGATTTGATAT
1 TAATGATTTGATAG
36822 TAATGA-TT--TAG
1 TAATGATTTGATAG
36833 TAATGATTTGATAG
1 TAATGATTTGATAG
36847 TAATGATTT
1 TAATGATTT
36856 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:36837 original size:49 final size:50
Alignment explanation
Indices: 36721--36839 Score: 188
Period size: 49 Copynumber: 2.4 Consensus size: 50
36711 AGTAATGATT
* *
36721 TAGTAATGA-TTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTTAGTAATGATGAAATTATTATTAATATTTAATGATTTGA
*
36770 TAGTAATGATTTAGTAATGAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTTAGTAATGATGAAATTATTATTAATATTTAATGATTTGA
*
36819 TATTAATGATTTAGTAATGAT
1 TAGTAATGATTTAGTAATGAT
36840 TTGATAGTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
49 55 0.85
50 10 0.15
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (50 bp):
TAGTAATGATTTAGTAATGATGAAATTATTATTAATATTTAATGATTTGA
Found at i:36841 original size:239 final size:239
Alignment explanation
Indices: 36301--36792 Score: 787
Period size: 239 Copynumber: 2.1 Consensus size: 239
36291 TTTATAAGAT
* * *
36301 TTAGTAATGATTAGTAATGATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGATTTAG
1 TTAGTAATGATAAGTAATAATGAAATTATGATTAATTAT-TAATGATTT-ATAGTAATGATTTAG
36365 TAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAATG
64 TAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAATG
*
36430 ATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGATTAG
129 ATTAGTAATAATGAAATTATTATTAATTTGTAATGATTTGATAGTAATGATTTAGTAATGATTAG
36495 TAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGAC
194 TAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGAC
* * *
36541 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGT
1 TTAGTAATGATAAGTAATAATGAAATTATGATTAATTATTAATGATTT-ATAGTAATGATTTAGT
* * *
36606 AATGATTAGTAATAAT-AATTTATTATTAA-TATTTAATGATTTGATATTAATGATTTAGTAATG
65 AATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGATTTAGTAATG
36669 ATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGATTTAGTAATGATTA
129 ATTAGTAATAATGAAATTATTATTAATT-TGTAATGATTTGATAGTAATGATTTAGTAATGATTA
* *
36733 GTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAATGAT
193 GTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGAC
36780 TTAGTAATGATAA
1 TTAGTAATGATAA
36793 TTTATTATTA
Statistics
Matches: 239, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
238 6 0.03
239 154 0.64
240 79 0.33
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (239 bp):
TTAGTAATGATAAGTAATAATGAAATTATGATTAATTATTAATGATTTATAGTAATGATTTAGTA
ATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAATGAT
TAGTAATAATGAAATTATTATTAATTTGTAATGATTTGATAGTAATGATTTAGTAATGATTAGTA
ATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGAC
Found at i:36940 original size:7 final size:7
Alignment explanation
Indices: 36928--36954 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
36918 ATTTTTGGTT
36928 CAATGAA
1 CAATGAA
36935 CAATGAA
1 CAATGAA
36942 CAATGAA
1 CAATGAA
36949 CAATGA
1 CAATGA
36955 TTTAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CAATGAA
Found at i:36989 original size:26 final size:26
Alignment explanation
Indices: 36950--37087 Score: 103
Period size: 26 Copynumber: 5.5 Consensus size: 26
36940 AACAATGAAC
*
36950 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAATAATAATCATTATAAA
*
36976 AATGA-TT--TAATAATGATT-T--A
1 AATGATTTAATAATAATCATTATAAA
* * * **
36996 AAT-ATTTAATGATTTGATGATT-TAGT
1 AATGATTTAAT-A-ATAATCATTATAAA
* **
37022 AATGATTTGATAATAATCATTATAGT
1 AATGATTTAATAATAATCATTATAAA
*
37048 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAATAATAATCATTATAAA
37074 AATGATTTAATAAT
1 AATGATTTAATAAT
37088 GATTTAAATA
Statistics
Matches: 90, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
19 1 0.01
20 6 0.07
22 2 0.02
23 11 0.12
24 8 0.09
25 8 0.09
26 48 0.53
27 6 0.07
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (26 bp):
AATGATTTAATAATAATCATTATAAA
Found at i:37119 original size:98 final size:98
Alignment explanation
Indices: 36950--37168 Score: 404
Period size: 98 Copynumber: 2.2 Consensus size: 98
36940 AACAATGAAC
36950 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
*
37015 ATTTAGTAATGATTTGATAATAATCATTATAGT
66 ATTTAGTAATGATTTGATAATAATCATTATAAT
37048 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
37113 ATTTAGTAATGATTTGATAATAATCATTATAAT
66 ATTTAGTAATGATTTGATAATAATCATTATAAT
*
37146 AATGATTTTA-TAATAATTATTAT
1 AATGA-TTTAGTAATAATCATTAT
37169 GTTATTATTT
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
98 114 0.97
99 4 0.03
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (98 bp):
AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
ATTTAGTAATGATTTGATAATAATCATTATAAT
Found at i:37148 original size:26 final size:26
Alignment explanation
Indices: 37021--37168 Score: 121
Period size: 26 Copynumber: 5.9 Consensus size: 26
37011 GATGATTTAG
*
37021 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
37047 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
37073 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
37096 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
37119 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* *
37145 TAATGATTTTATAATAATTATTAT
1 TAATGATTTGATAATAATCATTAT
37169 GTTATTATTT
Statistics
Matches: 95, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.04
22 3 0.03
23 12 0.13
24 7 0.07
25 7 0.07
26 61 0.64
27 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:37202 original size:24 final size:24
Alignment explanation
Indices: 37130--37221 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
37120 AATGATTTGA
*
37130 TAATAATCATTA-TAATAATGATT
1 TAATAATTATTACTAATAATGATT
* * * * * *
37153 TTATAATAATTATTATGTTATTATT
1 TAATAATTATTACTA-ATAATGATT
*
37178 TAGTAATTATTTA-TAATAATGATT
1 TAATAATTA-TTACTAATAATGATT
37202 TAATAATTATTACTAATAAT
1 TAATAATTATTACTAATAAT
37222 TATAGAATAC
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
23 13 0.25
24 23 0.43
25 14 0.26
26 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (24 bp):
TAATAATTATTACTAATAATGATT
Found at i:37218 original size:13 final size:12
Alignment explanation
Indices: 37129--37224 Score: 81
Period size: 11 Copynumber: 7.9 Consensus size: 12
37119 TAATGATTTG
*
37129 ATAATAATCATT
1 ATAATAATTATT
*
37141 ATAATAATGATTTT
1 ATAATAAT--TATT
37155 ATAATAATTATT
1 ATAATAATTATT
* *
37167 AT-GTTATTATT
1 ATAATAATTATT
*
37178 -TAGTAATTATTT
1 ATAATAATTA-TT
*
37190 ATAATAATGATT
1 ATAATAATTATT
37202 -TAATAATTATT
1 ATAATAATTATT
37213 ACTAATAATTAT
1 A-TAATAATTAT
37225 AGAATACTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 1 0.01
11 23 0.34
12 17 0.25
13 17 0.25
14 10 0.15
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:37230 original size:24 final size:24
Alignment explanation
Indices: 37181--37230 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
37171 TATTATTTAG
**
37181 TAATTATTTATAATAATGATTTAA
1 TAATTATTTATAATAATGATAGAA
*
37205 TAATTA-TTACTAATAATTATAGAA
1 TAATTATTTA-TAATAATGATAGAA
37229 TA
1 TA
37231 CTAACAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TAATTATTTATAATAATGATAGAA
Found at i:37329 original size:14 final size:14
Alignment explanation
Indices: 37310--37350 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
37300 TTTAAATATT
37310 TAATGATTTGATAC
1 TAATGATTTGATAC
37324 TAATGA-TT--TAC
1 TAATGATTTGATAC
*
37335 TAATTATTTGATAC
1 TAATGATTTGATAC
37349 TA
1 TA
37351 GTAATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 2 0.09
14 11 0.48
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (14 bp):
TAATGATTTGATAC
Found at i:39538 original size:15 final size:14
Alignment explanation
Indices: 39515--39545 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
39505 TACAACACTA
39515 AACTTTAATATAAT
1 AACTTTAATATAAT
39529 AACTTATAATATAAT
1 AACTT-TAATATAAT
39544 AA
1 AA
39546 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:39553 original size:16 final size:16
Alignment explanation
Indices: 39520--39566 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
39510 CACTAAACTT
*
39520 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
39535 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
39551 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
39567 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:39677 original size:32 final size:34
Alignment explanation
Indices: 39602--39683 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
39592 CCAAAGCCTT
* *
39602 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
39635 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
39668 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
39684 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:39689 original size:12 final size:12
Alignment explanation
Indices: 39664--39716 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
39654 TTTTTCATTA
*
39664 TAATATACT-AC
1 TAATAAACTAAC
*
39675 TAATAAACTTAC
1 TAATAAACTAAC
39687 TAACTAAAACTAAC
1 TAA-T-AAACTAAC
39701 TAATAAACTAAC
1 TAATAAACTAAC
39713 TAAT
1 TAAT
39717 TTTTTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 8 0.22
12 17 0.46
13 2 0.05
14 10 0.27
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (12 bp):
TAATAAACTAAC
Found at i:39847 original size:43 final size:47
Alignment explanation
Indices: 39743--39849 Score: 118
Period size: 46 Copynumber: 2.3 Consensus size: 47
39733 TCAACAAACA
39743 AATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAAATTTTTT
1 AATATAAC-TAACTA-TTAACTAACAAAAACTAATTAAATAAATTTTTT
* *
39792 TATATAACTAACTATTAAC-AA-AACAAACTAATT-AAT-TATTTTTT
1 AATATAACTAACTATTAACTAACAA-AAACTAATTAAATAAATTTTTT
39836 AACTAT-A-TAACTAT
1 AA-TATAACTAACTAT
39850 CAAACATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
43 7 0.13
44 9 0.17
45 8 0.15
46 11 0.21
47 5 0.09
48 6 0.11
49 7 0.13
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (47 bp):
AATATAACTAACTATTAACTAACAAAAACTAATTAAATAAATTTTTT
Found at i:39904 original size:41 final size:40
Alignment explanation
Indices: 39816--39904 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
39806 TTAACAAAAC
* *
39816 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
39857 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
39898 AAACTAA
1 AAACTAA
39905 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:39969 original size:16 final size:18
Alignment explanation
Indices: 39940--39978 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
39930 ACTAATTAAC
*
39940 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
39958 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
39974 ATTTA
1 ATTTA
39979 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:40244 original size:49 final size:47
Alignment explanation
Indices: 40190--40295 Score: 162
Period size: 49 Copynumber: 2.2 Consensus size: 47
40180 TAGGATCACA
40190 TGGCATGCTAT-AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGC-ATCAGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTAT-T
40239 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGCAT-CAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
40287 TGGC-TGCAT
1 TGGCATGCAT
40296 GTGCATGCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
47 5 0.09
48 7 0.13
49 32 0.58
50 11 0.20
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.21
Consensus pattern (47 bp):
TGGCATGCATCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
Found at i:40261 original size:50 final size:47
Alignment explanation
Indices: 40201--40296 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 47
40191 GGCATGCTAT
40201 AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCTTGGCATGCATGC
1 AGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTAT-TTGGC-TGCATGC
40251 AGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATTTGGCTGCATG
1 AGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATTTGGCTGCATG
40297 TGCATGCATG
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 6 0.13
48 5 0.11
49 24 0.52
50 11 0.24
ACGTcount: A:0.24, C:0.19, G:0.39, T:0.19
Consensus pattern (47 bp):
AGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATTTGGCTGCATGC
Found at i:40361 original size:17 final size:17
Alignment explanation
Indices: 40339--40390 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
40329 GGGGCGACCC
40339 ACTACAAGGTCGCCGGG
1 ACTACAAGGTCGCCGGG
* *
40356 ACTACATGG-CGAC---
1 ACTACAAGGTCGCCGGG
40369 -CTACAAGGTCGCCGGG
1 ACTACAAGGTCGCCGGG
40385 ACTACA
1 ACTACA
40391 TGGCGACCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
12 7 0.27
13 3 0.12
16 3 0.12
17 13 0.50
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.13
Consensus pattern (17 bp):
ACTACAAGGTCGCCGGG
Found at i:40376 original size:29 final size:29
Alignment explanation
Indices: 40340--40428 Score: 151
Period size: 29 Copynumber: 3.1 Consensus size: 29
40330 GGGCGACCCA
40340 CTACAAGGTCGCCGGGACTACATGGCGAC
1 CTACAAGGTCGCCGGGACTACATGGCGAC
40369 CTACAAGGTCGCCGGGACTACATGGCGAC
1 CTACAAGGTCGCCGGGACTACATGGCGAC
** *
40398 CTACAAGGTCGCCCAGACTGCATGGCGAC
1 CTACAAGGTCGCCGGGACTACATGGCGAC
40427 CT
1 CT
40429 CTCTTTTGGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.24, C:0.33, G:0.29, T:0.15
Consensus pattern (29 bp):
CTACAAGGTCGCCGGGACTACATGGCGAC
Found at i:40461 original size:24 final size:24
Alignment explanation
Indices: 40416--40463 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
40406 TCGCCCAGAC
**
40416 TGCATGGCGACCTCTCTTTTGGCT
1 TGCATGGCGACCTCTCCGTTGGCT
40440 TGCATGGCGACCTCTCCGTTGGCT
1 TGCATGGCGACCTCTCCGTTGGCT
40464 GGCTCGTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.08, C:0.31, G:0.27, T:0.33
Consensus pattern (24 bp):
TGCATGGCGACCTCTCCGTTGGCT
Found at i:42920 original size:101 final size:101
Alignment explanation
Indices: 42745--42982 Score: 422
Period size: 101 Copynumber: 2.4 Consensus size: 101
42735 GCGTTATGTT
* * * *
42745 ATTCGAATTCTTAAATTTCTTCTATATAAACATCGTATATTTACCACGAATCAAGTAATCTCGGT
1 ATTCGAATTCTTCATTTTCTTCTATATAAACATCATATATTTACCACGAATCAAATAATCTCGGT
42810 AATAAAGAAATTATTATTATTCTCGGAGGTTTCGGG
66 AATAAAGAAATTATTATTATTCTCGGAGGTTTCGGG
*
42846 ATTCGAATTCTTCATTTTCTTCTATATAAACATCATATATTTAGCACGAATCAAATAATCTCGGT
1 ATTCGAATTCTTCATTTTCTTCTATATAAACATCATATATTTACCACGAATCAAATAATCTCGGT
42911 AATAAAGAAATTATTATTATTCTCGGAGGTTTCGGG
66 AATAAAGAAATTATTATTATTCTCGGAGGTTTCGGG
*
42947 ATTCGAAATCTTCATTTTCTTCTATATAAACATCAT
1 ATTCGAATTCTTCATTTTCTTCTATATAAACATCAT
42983 TTTCTTTGCA
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 131 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (101 bp):
ATTCGAATTCTTCATTTTCTTCTATATAAACATCATATATTTACCACGAATCAAATAATCTCGGT
AATAAAGAAATTATTATTATTCTCGGAGGTTTCGGG
Found at i:45464 original size:15 final size:15
Alignment explanation
Indices: 45444--45483 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
45434 AAGATCATAA
45444 TTTAAATTTAATTAG
1 TTTAAATTTAATTAG
45459 TTTAAATTTAATTAG
1 TTTAAATTTAATTAG
45474 TTTAAATTTA
1 TTTAAATTTA
45484 TTCTATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (15 bp):
TTTAAATTTAATTAG
Found at i:45936 original size:29 final size:30
Alignment explanation
Indices: 45903--45977 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
45893 TAAAAATATA
45903 ATAATTTAGGGGCTTAAAG-AAAAAGAAAT
1 ATAATTTAGGGGCTTAAAGAAAAAAGAAAT
*
45932 ATAATTTAGGGGCTTAAAGAAAAAAGGAAT
1 ATAATTTAGGGGCTTAAAGAAAAAAGAAAT
*
45962 ATAGTTT-GGGGACTTA
1 ATAATTTAGGGG-CTTA
45978 TTTTGATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
29 23 0.55
30 19 0.45
ACGTcount: A:0.45, C:0.04, G:0.24, T:0.27
Consensus pattern (30 bp):
ATAATTTAGGGGCTTAAAGAAAAAAGAAAT
Found at i:46176 original size:17 final size:19
Alignment explanation
Indices: 46144--46178 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
46134 TCAATTCACA
46144 TAATCATAATTTTTAGGTT
1 TAATCATAATTTTTAGGTT
46163 TAAT-ATAA-TTTTAGGT
1 TAATCATAATTTTTAGGT
46179 GCCTAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (19 bp):
TAATCATAATTTTTAGGTT
Found at i:46901 original size:5 final size:5
Alignment explanation
Indices: 46891--46916 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46881 TATTATTATT
46891 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
46917 GAAACCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:49582 original size:17 final size:18
Alignment explanation
Indices: 49548--49584 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
49538 TTTAAGATTT
49548 TATATTCGATTCAAAATTA
1 TATATTCGATTC-AAATTA
49567 TATATTCGATTC-AATTA
1 TATATTCGATTCAAATTA
49584 T
1 T
49585 TCGAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTCAAATTA
Found at i:49806 original size:35 final size:35
Alignment explanation
Indices: 49758--49835 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
49748 AACAAGTATC
49758 GATACCCCTCAAACATTGAATGCAAAAGAGGTACG
1 GATACCCCTCAAACATTGAATGCAAAAGAGGTACG
*
49793 GGTACCCCTCAAACATTGAATGCAAAAGAGGTACG
1 GATACCCCTCAAACATTGAATGCAAAAGAGGTACG
49828 GATACCCC
1 GATACCCC
49836 ACAAGGTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.17
Consensus pattern (35 bp):
GATACCCCTCAAACATTGAATGCAAAAGAGGTACG
Found at i:51921 original size:12 final size:12
Alignment explanation
Indices: 51906--51942 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
51896 TTAAATATAA
51906 AAAATCTAATTT
1 AAAATCTAATTT
51918 AAAATCTAATTT
1 AAAATCTAATTT
51930 AAAATCTAATTT
1 AAAATCTAATTT
51942 A
1 A
51943 TACACATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATCTAATTT
Found at i:54974 original size:19 final size:19
Alignment explanation
Indices: 54932--54996 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
54922 TTTGAAATTA
54932 TTAATAA-TTATTAATGAA-
1 TTAATAATTTATTAAT-AAT
* * *
54950 TTAATATTTTCTTATTAAT
1 TTAATAATTTATTAATAAT
54969 TTAATAATTTATTAATAAT
1 TTAATAATTTATTAATAAT
54988 TTAAATAAT
1 TT-AATAAT
54997 CAAAATAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 8 0.21
19 24 0.63
20 6 0.16
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TTAATAATTTATTAATAAT
Found at i:55705 original size:23 final size:23
Alignment explanation
Indices: 55679--55735 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
55669 TAATAACCAA
*
55679 AAAACATGTAAAAAAAACATAAG
1 AAAACATGCAAAAAAAACATAAG
* * * *
55702 AAAACGTGCCATAAAAACATATG
1 AAAACATGCAAAAAAAACATAAG
*
55725 AAAACGTGCAA
1 AAAACATGCAA
55736 TACAGACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (23 bp):
AAAACATGCAAAAAAAACATAAG
Found at i:58692 original size:2 final size:2
Alignment explanation
Indices: 58685--58738 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
58675 TACATATAAG
58685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58726 TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA
58739 CACTTAGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60283 original size:54 final size:54
Alignment explanation
Indices: 60118--60284 Score: 246
Period size: 54 Copynumber: 3.1 Consensus size: 54
60108 ACTAAGGTAA
* *
60118 CGAAATGGTAATTCACAAACTCATTATGAATA-TCATGGGTTGTACACATAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATACT-ATGGGTTGCACACATAGTGT
* * * *
60172 CAAAATTGTAATTCACAAACTCATTATGAATACCATGGGTTGCACACATAGTAT
1 CGAAATGGTAATTCACAAACTCATTATGAATACTATGGGTTGCACACATAGTGT
* *
60226 CGAAATGGTAATTTACAAACTCATTATAAATACTATGGGTTGCACACATAGTGT
1 CGAAATGGTAATTCACAAACTCATTATGAATACTATGGGTTGCACACATAGTGT
60280 CGAAA
1 CGAAA
60285 GTACACATAA
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
54 100 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (54 bp):
CGAAATGGTAATTCACAAACTCATTATGAATACTATGGGTTGCACACATAGTGT
Found at i:62331 original size:23 final size:23
Alignment explanation
Indices: 62288--62331 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
62278 AATTAGGTTT
*
62288 TTAAAATATTAATGGGTTTAAAG
1 TTAAAATATTAATAGGTTTAAAG
*
62311 TTAAAAT-TTATTAGGTCTTAA
1 TTAAAATATTAATAGGT-TTAA
62332 TATTTTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (23 bp):
TTAAAATATTAATAGGTTTAAAG
Found at i:66609 original size:60 final size:60
Alignment explanation
Indices: 66493--66665 Score: 195
Period size: 60 Copynumber: 2.9 Consensus size: 60
66483 ACCATAACCT
* * * * ** * *
66493 TCATTTTAAATTTA-TCCTTAAACTTTTGAATGTTCTAATGTCATCTTTAAACTATGACCC
1 TCATTCTAAA-TTAGTCCTTAAACTTTTGAATATTTTAATTTCATCCCTAAATTATGACCA
* **
66553 TCATTCTAAATTAGTCTTTAAACTTTTGAATATTTTAATTTCATCCCTAAATTATGATTA
1 TCATTCTAAATTAGTCCTTAAACTTTTGAATATTTTAATTTCATCCCTAAATTATGACCA
* * * *
66613 TCTTTCTAAGTTAGTCCTTAAACTTTTGAATATTTCAATTTCATCCCCAAATT
1 TCATTCTAAATTAGTCCTTAAACTTTTGAATATTTTAATTTCATCCCTAAATT
66666 CATCCATATA
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 3 0.03
60 93 0.97
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCTTAAACTTTTGAATATTTTAATTTCATCCCTAAATTATGACCA
Found at i:68362 original size:22 final size:23
Alignment explanation
Indices: 68332--68377 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
68322 TGAAAATAAG
* *
68332 TTAACAAAATTATATTTATTTAA
1 TTAACAAAATAATATTTAATTAA
68355 TTAA-AAAATAATATTTAATTAA
1 TTAACAAAATAATATTTAATTAA
68377 T
1 T
68378 GTAGAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAACAAAATAATATTTAATTAA
Found at i:68978 original size:21 final size:22
Alignment explanation
Indices: 68952--69003 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
68942 ATATATGTAT
68952 TAAAAATATTATTTTATT-AAA
1 TAAAAATATTATTTTATTGAAA
*
68973 TAAAAACA-TATTTTATTGAAA
1 TAAAAATATTATTTTATTGAAA
*
68994 -AAAAGTATTA
1 TAAAAATATTA
69004 AGAGGGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (22 bp):
TAAAAATATTATTTTATTGAAA
Found at i:70399 original size:2 final size:2
Alignment explanation
Indices: 70394--70428 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
70384 ACTTACTTAA
70394 AT AT AT 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 AT AT AT A
70429 GAAATAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:74509 original size:59 final size:60
Alignment explanation
Indices: 74428--74542 Score: 153
Period size: 59 Copynumber: 1.9 Consensus size: 60
74418 TTAAATATTT
** ** * *
74428 TAATTTCATCCCTAAATTATGACTTTTATTCTAAATTAATCCA-TAAACTTTTGAACCTCC
1 TAATTTCATCCCTAAAACATGACACTCATTCTAAATT-AGCCACTAAACTTTTGAACCTCC
74488 TAATTT-ATCCCTAAAACATGACACTCATTCTAAATTAGCCACTAAACTTTTGAAC
1 TAATTTCATCCCTAAAACATGACACTCATTCTAAATTAGCCACTAAACTTTTGAAC
74543 ATTCAAGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 4 0.08
59 38 0.79
60 6 0.12
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (60 bp):
TAATTTCATCCCTAAAACATGACACTCATTCTAAATTAGCCACTAAACTTTTGAACCTCC
Found at i:78876 original size:60 final size:58
Alignment explanation
Indices: 78811--78948 Score: 134
Period size: 60 Copynumber: 2.3 Consensus size: 58
78801 TTTAAATATT
* ** * * *
78811 TTAATTTCATCCTTAAATTATGACTTTTATTCTAAATTA-ATACCTAAACTTTTGAACC
1 TTAATTTCATCCATAAATTATGACCCTCATTCTAAATTAGACA-CTAAACTTTTGAACA
* * ** *
78869 TCCTAATTTTATCCCTAAAACATGACCCTCATTCTAAATTAGCCACTAAACTTTTGAACA
1 T--TAATTTCATCCATAAATTATGACCCTCATTCTAAATTAGACACTAAACTTTTGAACA
78929 TTAAGTTTCATCCATAAATT
1 TTAA-TTTCATCCATAAATT
78949 CATCCAAATA
Statistics
Matches: 62, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
58 4 0.06
59 11 0.18
60 46 0.74
61 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (58 bp):
TTAATTTCATCCATAAATTATGACCCTCATTCTAAATTAGACACTAAACTTTTGAACA
Found at i:80670 original size:3 final size:3
Alignment explanation
Indices: 80662--80687 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
80652 TTTGATTGAT
80662 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
80688 GTTGTTGCAG
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:86869 original size:19 final size:19
Alignment explanation
Indices: 86823--86870 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
86813 ATTTATTTAA
* * *
86823 AATAAATAAATAAAAATAC
1 AATAAAAAAAGAAAAAGAC
* *
86842 GATATAAAAAGAAAAAGAC
1 AATAAAAAAAGAAAAAGAC
86861 AATAAAAAAA
1 AATAAAAAAA
86871 AACCAATGAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (19 bp):
AATAAAAAAAGAAAAAGAC
Found at i:88563 original size:27 final size:27
Alignment explanation
Indices: 88528--88687 Score: 176
Period size: 27 Copynumber: 5.9 Consensus size: 27
88518 TTATAAAGCC
** *
88528 AACTTCACTCTCCTATTCATCTTCAGA
1 AACTTCACTCTCAGATTCAGCTTCAGA
* * *
88555 AACCTCACTCTCAGGTTCAGTTTCAGA
1 AACTTCACTCTCAGATTCAGCTTCAGA
*
88582 AACTTCATTCTCAGATTCAGCTTCAGA
1 AACTTCACTCTCAGATTCAGCTTCAGA
*
88609 AACTTCATTCTCAGATTCAGCTTCAGA
1 AACTTCACTCTCAGATTCAGCTTCAGA
* * * * *
88636 AACTTCATTCTTAAATTCATCTTTAGA
1 AACTTCACTCTCAGATTCAGCTTCAGA
* * *
88663 GATTTTACTCTCAGATTCAGCTTCA
1 AACTTCACTCTCAGATTCAGCTTCA
88688 AATGGGCACG
Statistics
Matches: 111, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 111 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (27 bp):
AACTTCACTCTCAGATTCAGCTTCAGA
Found at i:107491 original size:231 final size:231
Alignment explanation
Indices: 106842--107688 Score: 1163
Period size: 231 Copynumber: 3.7 Consensus size: 231
106832 ATCATCTCTA
* *
106842 TCACCTATATGTATTTTTTTCAAACCCATAATTCATATAAATTTCAAATGATTTAAAAGCATAAA
1 TCACCTATATGTATTTTTTTCAAACTCATAATTCACATAAATTTCAAATGA-TTAAAAGCATAAA
* * *
106907 TAAC---CAATACTAAAATATTAAGTG----GAAATCAAAGATTGAGATAAACATACCACGAAAA
65 TAACTAATAATACTAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATACCACGAAAA
* * **
106965 GGAGAATCAGGAAACTGACAATCAAATTCATCTTCAATTGGGACATTGTTATCATCTACAGGAAC
130 GGAGAATCGGGAAACTGAGAATCAAATTCATCTTCAATTGAAACATTGTTATCATCTACAGGAAC
* *
107030 CGTATCTTGAAGAAAGTTTAATTCATTTTCACACCCG
195 CGTATCTTGAAGAAAGTTTAATTCATTATCACAACCG
* *
107067 TCACCTATATGTATTTTTTTCAAACTCATAATTCACATAAATTTCAAATAATTGAAAGCATAAAT
1 TCACCTATATGTATTTTTTTCAAACTCATAATTCACATAAATTTCAAATGATTAAAAGCATAAAT
* * * *
107132 AACTAATAATACTAAAATATTAAGCGAAAGAATAATCAAAGATTGTGATAAACATACCACGATAT
66 AACTAATAATACTAAAATATTAAGCGAAA-AAAAATCAAAGATTGAGATAAACATACCACGAAAA
* * * * *
107197 GGAGAATCGGGTAACTGAGAGTCAAATTCATCTTCAATTGTAGCATTGTTATCATCCACAGGAAC
130 GGAGAATCGGGAAACTGAGAATCAAATTCATCTTCAATTGAAACATTGTTATCATCTACAGGAAC
107262 CGTATCTTGAAGAAAGTTTAATTCATTATCACAACCG
195 CGTATCTTGAAGAAAGTTTAATTCATTATCACAACCG
* *
107299 TCACCTATATGT-TTTTTTTCCAAACTCGTAATTCACATAAATTTCAAATGATTCAAAGCATAAA
1 TCACCTATATGTATTTTTTT-CAAACTCATAATTCACATAAATTTCAAATGATTAAAAGCATAAA
* * * * *
107363 TAACTAATAATTCTACAATATTAATCCAAAAAAAATCAAAGATTGAGATAAACATACCACGAAAT
65 TAACTAATAATACTAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATACCACGAAAA
* * * ** *
107428 GGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATAGAAACATTGTTGTTGTCTACAGGAAT
130 GGAGAATCGGGAAACTGAGAATCAAATTCATCTTCAATTGAAACATTGTTATCATCTACAGGAAC
* * *
107493 AGTATCTTGTAGAAAGTTCAATTCATTATCACAACCG
195 CGTATCTTGAAGAAAGTTTAATTCATTATCACAACCG
* * * * *
107530 TCACCTCTATGAATTTTTTT-AAAGCTCGTAATTCACATAAATTTCAAATGATTTAAAGCGTAAA
1 TCACCTATATGTATTTTTTTCAAA-CTCATAATTCACATAAATTTCAAATGATTAAAAGCATAAA
* * * * *
107594 TAACTAATAATACTAAAATATTAAGGGGAAAAGAATCAAAGATTGAGATAAATATACCAGGAAAA
65 TAACTAATAATACTAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATACCACGAAAA
107659 GGAGAATCGGGAAACTGAGAATCAAATTCA
130 GGAGAATCGGGAAACTGAGAATCAAATTCA
107689 AAGGGCTGGG
Statistics
Matches: 553, Mismatches: 58, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
224 16 0.03
225 48 0.09
227 18 0.03
230 3 0.01
231 261 0.47
232 207 0.37
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.30
Consensus pattern (231 bp):
TCACCTATATGTATTTTTTTCAAACTCATAATTCACATAAATTTCAAATGATTAAAAGCATAAAT
AACTAATAATACTAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATACCACGAAAAG
GAGAATCGGGAAACTGAGAATCAAATTCATCTTCAATTGAAACATTGTTATCATCTACAGGAACC
GTATCTTGAAGAAAGTTTAATTCATTATCACAACCG
Found at i:108305 original size:24 final size:24
Alignment explanation
Indices: 108256--108334 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
108246 ATTTCTATTC
*
108256 TTCACGAATA-TGTTCGCTTA-ATG
1 TTCACGAA-AGTGTTCGTTTATATG
*
108279 TTCA-TAAATGTGTTCGTTTATATG
1 TTCACGAAA-GTGTTCGTTTATATG
**
108303 TTCACGAAAGTGTTTATTTATATG
1 TTCACGAAAGTGTTCGTTTATATG
*
108327 TTTACGAA
1 TTCACGAA
108335 TATGTTCATT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.02
22 2 0.04
23 13 0.28
24 27 0.59
25 3 0.07
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.44
Consensus pattern (24 bp):
TTCACGAAAGTGTTCGTTTATATG
Found at i:108340 original size:24 final size:24
Alignment explanation
Indices: 108288--108354 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
108278 GTTCATAAAT
*
108288 GTGTTCGTTTATATGTTCACGAAA
1 GTGTTCATTTATATGTTCACGAAA
* *
108312 GTGTTTATTTATATGTTTACGAATA
1 GTGTTCATTTATATGTTCACGAA-A
*
108337 -TGTTCATTTA-GTGTTCAC
1 GTGTTCATTTATATGTTCAC
108355 AAATATATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 6 0.17
24 29 0.81
25 1 0.03
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (24 bp):
GTGTTCATTTATATGTTCACGAAA
Found at i:108359 original size:23 final size:23
Alignment explanation
Indices: 108256--108375 Score: 89
Period size: 23 Copynumber: 5.1 Consensus size: 23
108246 ATTTCTATTC
* *
108256 TTCACGAATATGTTCGCTTAATG
1 TTCACAAATATGTTCGTTTAATG
* *
108279 TTCATAAATGTGTTCGTTTATATG
1 TTCACAAATATGTTCGTTTA-ATG
* **
108303 TTCACGAAA-GTGTTTATTTATATG
1 TTCAC-AAATATGTTCGTTTA-ATG
* * * *
108327 TTTACGAATATGTTCATTTAGTG
1 TTCACAAATATGTTCGTTTAATG
* *
108350 TTCACAAATATATTCGTTTAGTG
1 TTCACAAATATGTTCGTTTAATG
108373 TTC
1 TTC
108376 TTTTATTATT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
23 42 0.54
24 33 0.42
25 3 0.04
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.46
Consensus pattern (23 bp):
TTCACAAATATGTTCGTTTAATG
Found at i:108620 original size:12 final size:12
Alignment explanation
Indices: 108604--108650 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
108594 AAACAAGTTG
108604 ATAAACGAGCTC
1 ATAAACGAGCTC
* * *
108616 CTAAACAAGCTT
1 ATAAACGAGCTC
*
108628 ATAAATGAGCTC
1 ATAAACGAGCTC
108640 ATAAACGAGCT
1 ATAAACGAGCT
108651 TATTCATAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (12 bp):
ATAAACGAGCTC
Found at i:108621 original size:24 final size:24
Alignment explanation
Indices: 108592--108653 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
108582 ATGAACATAA
108592 ATAAACAAG-TTGATAAACGAGCTC
1 ATAAACAAGCTT-ATAAACGAGCTC
* *
108616 CTAAACAAGCTTATAAATGAGCTC
1 ATAAACAAGCTTATAAACGAGCTC
*
108640 ATAAACGAGCTTAT
1 ATAAACAAGCTTAT
108654 TCATAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.24
Consensus pattern (24 bp):
ATAAACAAGCTTATAAACGAGCTC
Found at i:108926 original size:34 final size:34
Alignment explanation
Indices: 108873--108957 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 34
108863 AAATAAATTT
* * *
108873 ATTC-AATAGTAAATTTTGATATTGTAAAAGATC
1 ATTCTAATAATAAATCTTGATATTGTAAAAAATC
*
108906 ATTCTAATAATAAATCTTGATATTGTAAAAAATT
1 ATTCTAATAATAAATCTTGATATTGTAAAAAATC
*
108940 ATTCTAATAATATATCTT
1 ATTCTAATAATAAATCTT
108958 TTTTAATATC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 4 0.09
34 42 0.91
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (34 bp):
ATTCTAATAATAAATCTTGATATTGTAAAAAATC
Found at i:111374 original size:39 final size:39
Alignment explanation
Indices: 111320--111397 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
111310 ATGCTACTTT
111320 CACTGTCACAGCTTTCACTGGATTCAACAGTTTGTTTCC
1 CACTGTCACAGCTTTCACTGGATTCAACAGTTTGTTTCC
111359 CACTGTCACAGCTTTCACTGGATTCAACAGTTTGTTTCC
1 CACTGTCACAGCTTTCACTGGATTCAACAGTTTGTTTCC
111398 TTCCTCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (39 bp):
CACTGTCACAGCTTTCACTGGATTCAACAGTTTGTTTCC
Found at i:116189 original size:14 final size:15
Alignment explanation
Indices: 116160--116191 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
116150 AAATAATTAA
116160 AATAATATATTTTAT
1 AATAATATATTTTAT
116175 AATAATATA-TTTAT
1 AATAATATATTTTAT
116189 AAT
1 AAT
116192 TATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:116414 original size:22 final size:22
Alignment explanation
Indices: 116387--116430 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
116377 AAGACCACTC
116387 GGTTCATGCTTAAATAATATAT
1 GGTTCATGCTTAAATAATATAT
116409 GGTTCATGCTTAAATAATATAT
1 GGTTCATGCTTAAATAATATAT
116431 TTGAATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (22 bp):
GGTTCATGCTTAAATAATATAT
Found at i:124738 original size:30 final size:29
Alignment explanation
Indices: 124699--124764 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
124689 TTTTAAAAAG
*
124699 TATATTATTTTTTAAAAACTATATATA-ATA
1 TATACTATTTTTT-AAAACTATATATATA-A
124729 TATACTA-TTTTTAAAACTATATATATAA
1 TATACTATTTTTTAAAACTATATATATAA
124757 TATACTAT
1 TATACTAT
124765 ATATATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 21 0.64
29 6 0.18
30 6 0.18
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (29 bp):
TATACTATTTTTTAAAACTATATATATAA
Found at i:124751 original size:2 final size:2
Alignment explanation
Indices: 124746--124856 Score: 68
Period size: 2 Copynumber: 55.0 Consensus size: 2
124736 TTTTTAAAAC
* * *
124746 TA TA TA TA TA -A TA TA CTA TA TA TA TA TA TA TA TA TT TA AA AA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
124788 TA TA TA TA CTA T- TT TCA AA AA CTA TA -A TA TA TT TT TA -A AA
1 TA TA TA TA -TA TA TA T-A TA TA -TA TA TA TA TA TA TA TA TA TA
124828 CTA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
124857 CTATTTTTTC
Statistics
Matches: 90, Mismatches: 10, Indels: 18
0.76 0.08 0.15
Matches are distributed among these distances:
1 4 0.04
2 80 0.89
3 6 0.07
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:124793 original size:63 final size:61
Alignment explanation
Indices: 124726--124893 Score: 168
Period size: 61 Copynumber: 2.7 Consensus size: 61
124716 ACTATATATA
* *
124726 ATATATACTATTTTTAAAACTATATATATAATATACTATATA-TATATATATATATTTAAAAAT
1 ATATATACTATTTTTAAAACTATATATAT-AT-TACTA-AAACTATATATATATATATAAAAAT
* ** * *
124789 ATATATACTATTTTCAAAAACTATA-ATATATTTTTAAAACTATATATATATATATATATAT
1 ATATATACTATTTT-TAAAACTATATATATATTACTAAAACTATATATATATATATAAAAAT
124850 ATATATACTATTTTTTCAAAATCTATATAT-T-TT-C-AAAACTATAT
1 ATATATACTA-TTTTT-AAAA-CTATATATATATTACTAAAACTATAT
124894 TATTTTCAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
60 12 0.13
61 31 0.34
62 12 0.13
63 24 0.27
64 11 0.12
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (61 bp):
ATATATACTATTTTTAAAACTATATATATATTACTAAAACTATATATATATATATAAAAAT
Found at i:124891 original size:127 final size:124
Alignment explanation
Indices: 124718--124948 Score: 285
Period size: 127 Copynumber: 1.8 Consensus size: 124
124708 TTTTAAAAAC
*
124718 TATATATAATATATACTATTTTTAAAACTATATATATAATATACTATATATATATAT-ATATA-T
1 TATATATAATATATACTATTTTTAAAACTATATATATAATATACTATAT-TAT-TATCA-AAACT
*
124781 TTAAAA-ATATATATACTATTTTCAAAAACTA-TAATATATTTTTAAAACTATATATATATA
63 ATAAAATATATATATACTATTTTCAAAAACTACTAATATATTTTTAAAACTATATATATATA
* *
124841 TATATATATATATATACTATTTTTTCAAAATCTATATATTTTCAA-A-ACTATATTATTTTCAAA
1 TATATATA-ATATATACTA-TTTTT-AAAA-CTATATA-TAT-AATATACTATATTATTATCAAA
*
124904 ACTATAAAATATATTTATACTATTTTCAAAAACTACCTAATATAT
60 ACTATAAAATATATATATACTATTTTCAAAAACTA-CTAATATAT
124949 ATTATTTTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 16
0.81 0.04 0.14
Matches are distributed among these distances:
123 8 0.09
124 10 0.11
125 9 0.10
126 14 0.15
127 38 0.41
128 3 0.03
129 10 0.11
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.45
Consensus pattern (124 bp):
TATATATAATATATACTATTTTTAAAACTATATATATAATATACTATATTATTATCAAAACTATA
AAATATATATATACTATTTTCAAAAACTACTAATATATTTTTAAAACTATATATATATA
Found at i:124893 original size:16 final size:17
Alignment explanation
Indices: 124858--124909 Score: 81
Period size: 17 Copynumber: 3.1 Consensus size: 17
124848 ATATATATAC
124858 TATT-TTTTCAAAATCTA
1 TATTATTTTCAAAA-CTA
124875 TA-TATTTTCAAAACTA
1 TATTATTTTCAAAACTA
124891 TATTATTTTCAAAACTA
1 TATTATTTTCAAAACTA
124908 TA
1 TA
124910 AAATATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.18
17 27 0.82
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTATTTTCAAAACTA
Found at i:124946 original size:31 final size:31
Alignment explanation
Indices: 124889--124953 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
124879 TTTTCAAAAC
* *
124889 TATATTATTTTCAAAACTATAAAATATAT-T
1 TATACTATTTTCAAAACTACAAAATATATAT
**
124919 TATACTATTTTCAAAAACTACCTAATATATAT
1 TATACTATTTTC-AAAACTACAAAATATATAT
124951 TAT
1 TAT
124954 TTTATTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 11 0.38
31 14 0.48
32 4 0.14
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (31 bp):
TATACTATTTTCAAAACTACAAAATATATAT
Found at i:125363 original size:46 final size:46
Alignment explanation
Indices: 125313--125646 Score: 158
Period size: 45 Copynumber: 7.5 Consensus size: 46
125303 AAAATATATG
* * * *
125313 CTCCACTACTCTTTAAGGAAGATCAGATCTGGAAAATTTTGATTCA
1 CTCCACTGCTCTTCAGGGAAGATCAAATCTGGAAAATTTTGATTCA
* ** *
125359 CTCCACTGCTCTTCAGGGAAGATTAAATC-GG----GGTAGATTCA
1 CTCCACTGCTCTTCAGGGAAGATCAAATCTGGAAAATTTTGATTCA
* * * * *** *
125400 CTTCGCTGCTCTTTAGGGAAGACCAAATCTGGAAAA-AGGGATAT-G
1 CTCCACTGCTCTTCAGGGAAGATCAAATCTGGAAAATTTTGAT-TCA
* * * *
125445 TTCCACTACTCTTCATGGAAGATCAGATCTGGAAAATTTTGATTCA
1 CTCCACTGCTCTTCAGGGAAGATCAAATCTGGAAAATTTTGATTCA
* ** ** * **
125491 CTCCACTGCTCTTCAGGAAAAGATTGAAT-T-G---AGGTAGATTTG
1 CTCCACTGCTCTTCAGG-GAAGATCAAATCTGGAAAATTTTGATTCA
* * * **
125533 CTCCACTTCTCTTCAGGGAATATCAAATCT--AGAATTAGGAATCTC-
1 CTCCACTGCTCTTCAGGGAAGATCAAATCTGGAAAATTTTG-AT-TCA
*** * * *
125578 CTCTGTTGCTCTTTAGGGAATATCAGATCTGGAAAATTTTGATTCA
1 CTCCACTGCTCTTCAGGGAAGATCAAATCTGGAAAATTTTGATTCA
* *
125624 CTCAACTGCTCTTCAGGGTAGAT
1 CTCCACTGCTCTTCAGGGAAGAT
125647 TTGCTCCACT
Statistics
Matches: 204, Mismatches: 66, Indels: 36
0.67 0.22 0.12
Matches are distributed among these distances:
41 38 0.19
42 25 0.12
44 2 0.01
45 63 0.31
46 63 0.31
47 13 0.06
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (46 bp):
CTCCACTGCTCTTCAGGGAAGATCAAATCTGGAAAATTTTGATTCA
Found at i:125465 original size:132 final size:132
Alignment explanation
Indices: 125270--125647 Score: 432
Period size: 133 Copynumber: 2.8 Consensus size: 132
125260 CGGTTCGCTT
* * * **
125270 CACTGCTCTTCAGGGAAGATCGAACCTAGAAAAAAAATATATGCTCCACTACTCTTTAAGGAAGA
1 CACTGCTCTTCAGGGAAGACCAAATCTAGAAAAAGGA-ATATGCTCCACTACTCTTTAAGGAAGA
*
125335 TCAGATCTGGAAAATTTTGATTCACTCCACTGCTCTTCAGGGAAGATTAAATCGGGGTAGATTCA
65 TCAGATCTGGAAAATTTTGATTCACTCCACTGCTCTTCAGGGAAGATTAAATCGAGGTAGATTCA
*
125400 CTT
130 CTC
* * * * * * *
125403 CGCTGCTCTTTAGGGAAGACCAAATCTGGAAAAAGGGATATGTTCCACTACTCTTCATGGAAGAT
1 CACTGCTCTTCAGGGAAGACCAAATCTAGAAAAAGGAATATGCTCCACTACTCTTTAAGGAAGAT
* * * **
125468 CAGATCTGGAAAATTTTGATTCACTCCACTGCTCTTCAGGAAAAGATTGAATTGAGGTAGATTTG
66 CAGATCTGGAAAATTTTGATTCACTCCACTGCTCTTCAGG-GAAGATTAAATCGAGGTAGATTCA
125533 CTC
130 CTC
* * * ** * * *** * * *
125536 CACTTCTCTTCAGGGAATATCAAATCTAGAATTAGGAATCTCCTCTGTTGCTCTTTAGGGAATAT
1 CACTGCTCTTCAGGGAAGACCAAATCTAGAAAAAGGAATATGCTCCACTACTCTTTAAGGAAGAT
* *
125601 CAGATCTGGAAAATTTTGATTCACTCAACTGCTCTTCAGGGTAGATT
66 CAGATCTGGAAAATTTTGATTCACTCCACTGCTCTTCAGGGAAGATT
125648 TGCTCCACTG
Statistics
Matches: 203, Mismatches: 41, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
132 70 0.34
133 133 0.66
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (132 bp):
CACTGCTCTTCAGGGAAGACCAAATCTAGAAAAAGGAATATGCTCCACTACTCTTTAAGGAAGAT
CAGATCTGGAAAATTTTGATTCACTCCACTGCTCTTCAGGGAAGATTAAATCGAGGTAGATTCAC
TC
Found at i:127325 original size:32 final size:32
Alignment explanation
Indices: 127283--127354 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
127273 TTTTATTTTG
* * * *
127283 TTTTTCTTCTTCTTTTTTCTTTTTTTTTTCTT
1 TTTTTTTTCTTCTTTTTTCTTTTCTTTTCCTC
*
127315 TTTTTTTTCTTTTTTTTTCTTTTCTTTTCCTC
1 TTTTTTTTCTTCTTTTTTCTTTTCTTTTCCTC
127347 TTTTTTTT
1 TTTTTTTT
127355 ATTTATTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (32 bp):
TTTTTTTTCTTCTTTTTTCTTTTCTTTTCCTC
Found at i:127353 original size:11 final size:10
Alignment explanation
Indices: 127283--127354 Score: 81
Period size: 11 Copynumber: 6.8 Consensus size: 10
127273 TTTTATTTTG
*
127283 TTTTTCTTCT
1 TTTTTTTTCT
*
127293 TCTTTTTTCTT
1 TTTTTTTTC-T
127304 TTTTTTTTCTT
1 TTTTTTTTC-T
127315 TTTTTTTTCT
1 TTTTTTTTCT
127325 TTTTTTTTCT
1 TTTTTTTTCT
*
127335 TTTCTTTTCCT
1 TTT-TTTTTCT
127346 CTTTTTTTT
1 -TTTTTTTT
127355 ATTTATTTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
10 21 0.39
11 30 0.56
12 3 0.06
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:127354 original size:1 final size:1
Alignment explanation
Indices: 127295--127342 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
127285 TTTCTTCTTC
* * * * *
127295 TTTTTTCTTTTTTTTTTCTTTTTTTTTTCTTTTTTTTTCTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
127343 CCTCTTTTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:127384 original size:21 final size:21
Alignment explanation
Indices: 127335--127384 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
127325 TTTTTTTTCT
**
127335 TTTCTTTTCCTCTTTTTTTTA
1 TTTCTTTTCCTCTTTTTTAAA
*
127356 TTTATTTTCC-CTTTTTTAAA
1 TTTCTTTTCCTCTTTTTTAAA
127376 TGTTCTTTT
1 T-TTCTTTT
127385 TTTTCTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.10, C:0.16, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTCTTTTCCTCTTTTTTAAA
Found at i:129839 original size:28 final size:29
Alignment explanation
Indices: 129789--129848 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
129779 AATCTTGTCG
* *
129789 AAAGTGAGATCAAAGCTTAAAAATAA-GA
1 AAAGTGAGAACAAAGCTTAAAAAAAAGGA
*
129817 AAAGTGAGAACAAATG-TTGAAAAAAAGGA
1 AAAGTGAGAACAAA-GCTTAAAAAAAAGGA
129846 AAA
1 AAA
129849 AGAAATTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.60, C:0.05, G:0.20, T:0.15
Consensus pattern (29 bp):
AAAGTGAGAACAAAGCTTAAAAAAAAGGA
Found at i:130431 original size:31 final size:31
Alignment explanation
Indices: 130393--130491 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 31
130383 TTGTTAGATT
130393 TTAATTTGATCCTTAAATTTTAGATAAAATA
1 TTAATTTGATCCTTAAATTTTAGATAAAATA
*
130424 TTAATTTG-TCCCTAAATTTTAGATAAAATA
1 TTAATTTGATCCTTAAATTTTAGATAAAATA
* * * **
130454 TTGATTTAATCCTTGAACCTTAGATAAAATA
1 TTAATTTGATCCTTAAATTTTAGATAAAATA
130485 TTAATTT
1 TTAATTT
130492 AGCCTTGCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
30 27 0.46
31 32 0.54
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (31 bp):
TTAATTTGATCCTTAAATTTTAGATAAAATA
Found at i:132689 original size:25 final size:28
Alignment explanation
Indices: 132661--132714 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 28
132651 CAAGTTTTGA
132661 TCTTAAATTTTT-T-ATTTAA-TA-TATT
1 TCTT-AATTTTTATGATTTAAGTACTATT
132686 TCTTAATTTTTATGATTTAAGTACTATT
1 TCTTAATTTTTATGATTTAAGTACTATT
132714 T
1 T
132715 AGTGTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 6 0.24
27 2 0.08
28 5 0.20
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.61
Consensus pattern (28 bp):
TCTTAATTTTTATGATTTAAGTACTATT
Found at i:134108 original size:18 final size:19
Alignment explanation
Indices: 134084--134127 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
134074 ATCAGTAATC
134084 ATATTCC-CCGATAATCTT
1 ATATTCCACCGATAATCTT
* * *
134102 TTATTCCACTGGTAATCTT
1 ATATTCCACCGATAATCTT
134121 ATATTCC
1 ATATTCC
134128 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.43
Consensus pattern (19 bp):
ATATTCCACCGATAATCTT
Found at i:136295 original size:59 final size:59
Alignment explanation
Indices: 136199--136310 Score: 199
Period size: 59 Copynumber: 1.9 Consensus size: 59
136189 AACTATGAAT
*
136199 CTCATTCTAAATTGGTCTCATAACTTTTGAATCTTCCAATTTTCATCCCAAATTGTGACC
1 CTCATTCTAAATTGGTCTCACAACTTTTGAATCTTCCAA-TTTCATCCCAAATTGTGACC
136259 CTCATTCTAAATTGGTC-CACAACTTTTGAATCTTCCAATTTCATCCCAAATT
1 CTCATTCTAAATTGGTCTCACAACTTTTGAATCTTCCAATTTCATCCCAAATT
136311 CATCCAAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
58 14 0.27
59 20 0.39
60 17 0.33
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (59 bp):
CTCATTCTAAATTGGTCTCACAACTTTTGAATCTTCCAATTTCATCCCAAATTGTGACC
Found at i:140427 original size:22 final size:24
Alignment explanation
Indices: 140376--140427 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 24
140366 GAAGTACATA
140376 AATGTTTCTGTTTTGCACTCATTGTTC
1 AATGTTTCTGTTTTG-ACTCA-T-TTC
140403 AATGTTTCTGTTTTG-CTCA-TTC
1 AATGTTTCTGTTTTGACTCATTTC
140425 AAT
1 AAT
140428 TATTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.24
25 4 0.16
27 15 0.60
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.52
Consensus pattern (24 bp):
AATGTTTCTGTTTTGACTCATTTC
Found at i:142094 original size:21 final size:20
Alignment explanation
Indices: 142061--142100 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
142051 TTTTTTTTGA
*
142061 ATTTTTTTTTAAAAAATAAT
1 ATTTTTTTATAAAAAATAAT
142081 ATTTTTATTATAAAAAATAA
1 ATTTTT-TTATAAAAAATAA
142101 AAAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTTTTATAAAAAATAAT
Found at i:147887 original size:18 final size:18
Alignment explanation
Indices: 147866--147904 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
147856 AATAAAGCAA
147866 CATCCTGTAATAGGAGAT
1 CATCCTGTAATAGGAGAT
147884 CATCCTGTAATAGGAGAT
1 CATCCTGTAATAGGAGAT
147902 CAT
1 CAT
147905 TTGTGTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (18 bp):
CATCCTGTAATAGGAGAT
Found at i:148476 original size:30 final size:30
Alignment explanation
Indices: 148437--148495 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
148427 ACATTAAATT
148437 ATATATTTAGTATTTAAATTGCTAATTTTG
1 ATATATTTAGTATTTAAATTGCTAATTTTG
* **
148467 ATATTTTTAGTATTTAAATTTTTAATTTT
1 ATATATTTAGTATTTAAATTGCTAATTTT
148496 TTTAAAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (30 bp):
ATATATTTAGTATTTAAATTGCTAATTTTG
Found at i:160439 original size:20 final size:20
Alignment explanation
Indices: 160391--160487 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
160381 CACTGAATAT
*
160391 TTGTCCCGAATGACCACT-A
1 TTGTCCCGAAGGACCACTGA
160410 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
160429 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
* *
160448 -TGTCCCAAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
160467 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
160487 T
1 T
160488 CATCCCTCGA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
18 30 0.46
19 2 0.03
20 33 0.51
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:160445 original size:38 final size:38
Alignment explanation
Indices: 160391--160484 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
160381 CACTGAATAT
*
160391 TTGTCCCGAATG-ACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAA-GAACCACTATGTCCCAAAGGACCACTGA
* *
160429 TTGTTCCGAAGAACCACTATGTCCCAAAGGACCACTGT
1 TTGTCCCGAAGAACCACTATGTCCCAAAGGACCACTGA
*
160467 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGAACCACT
160485 GATCATCCCT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
37 1 0.02
38 49 0.98
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCAAAGGACCACTGA
Found at i:161589 original size:20 final size:20
Alignment explanation
Indices: 161564--161601 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
161554 TTTCCCTTGA
161564 AGTGCATAGATACATTCTAC
1 AGTGCATAGATACATTCTAC
* *
161584 AGTGCATCGATGCATTCT
1 AGTGCATAGATACATTCT
161602 TTAACATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATAGATACATTCTAC
Found at i:161696 original size:64 final size:62
Alignment explanation
Indices: 161609--161764 Score: 168
Period size: 64 Copynumber: 2.5 Consensus size: 62
161599 TCTTTAACAT
* * * * *
161609 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTAAAGGA
* * **
161672 GATGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTAAAGGA
1 G-TGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTAAAGGA
* * *
161736 GTGCATCGATACACTTCATGTGCATCGAT
1 GTGCATCGATGCAC-TCCTATGCATCGAT
161765 GCACCTTCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
63 25 0.32
64 53 0.68
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTAAAGGA
Found at i:171262 original size:30 final size:31
Alignment explanation
Indices: 171197--171264 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
171187 AAAGTACACA
* *
171197 TTTAGTACCTAAACTATTAGTTTTGGTCAAT
1 TTTAGTACCTAAACAATCAGTTTTGGTCAAT
* *
171228 TTTAGTACCTAAACAATCGGTTTT-GTCTAT
1 TTTAGTACCTAAACAATCAGTTTTGGTCAAT
171258 TTTAGTA
1 TTTAGTA
171265 TTTAAACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (31 bp):
TTTAGTACCTAAACAATCAGTTTTGGTCAAT
Found at i:176349 original size:45 final size:45
Alignment explanation
Indices: 176285--176385 Score: 202
Period size: 45 Copynumber: 2.2 Consensus size: 45
176275 CTTGGACTTG
176285 TTGAATGTTTCAAGTTGTTAAAGAAGTAAGGTAACCCAACCCACA
1 TTGAATGTTTCAAGTTGTTAAAGAAGTAAGGTAACCCAACCCACA
176330 TTGAATGTTTCAAGTTGTTAAAGAAGTAAGGTAACCCAACCCACA
1 TTGAATGTTTCAAGTTGTTAAAGAAGTAAGGTAACCCAACCCACA
176375 TTGAATGTTTC
1 TTGAATGTTTC
176386 CTAAGGGGCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (45 bp):
TTGAATGTTTCAAGTTGTTAAAGAAGTAAGGTAACCCAACCCACA
Found at i:178604 original size:30 final size:31
Alignment explanation
Indices: 178539--178606 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
178529 AAAGTACACA
* *
178539 TTTAGTACCTAAACTATTAGTTTTGGTCAAT
1 TTTAGTACCTAAACAATCAGTTTTGGTCAAT
* *
178570 TTTAGTACCTAAACAATCGGTTTT-GTCTAT
1 TTTAGTACCTAAACAATCAGTTTTGGTCAAT
178600 TTTAGTA
1 TTTAGTA
178607 TTTAAACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (31 bp):
TTTAGTACCTAAACAATCAGTTTTGGTCAAT
Found at i:184836 original size:21 final size:18
Alignment explanation
Indices: 184810--184848 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
184800 TTCAAAATAT
184810 ATTATAATTATAATATTATTA
1 ATTAT-ATT-TAATA-TATTA
184831 ATTATATTTAATATATTA
1 ATTATATTTAATATATTA
184849 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 3 0.17
21 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATATTTAATATATTA
Found at i:184924 original size:27 final size:25
Alignment explanation
Indices: 184874--184927 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
184864 TTATTTCAAA
184874 ATTTACAAAATATATTATAATTATT
1 ATTTACAAAATATATTATAATTATT
* *
184899 ATTTATAAAATATCTATTTTAATTATT
1 ATTTACAAAATA--TATTATAATTATT
184926 AT
1 AT
184928 ATTTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.44
27 14 0.56
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTACAAAATATATTATAATTATT
Found at i:184950 original size:17 final size:16
Alignment explanation
Indices: 184930--184973 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
184920 ATTATTATAT
184930 TTATTATTATATTTCAA
1 TTATTATTATATTT-AA
*
184947 TTATTTATTGTATTTAA
1 TTA-TTATTATATTTAA
184964 TTATTATTAT
1 TTATTATTAT
184974 TATTATTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 8 0.33
18 10 0.42
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
TTATTATTATATTTAA
Found at i:184968 original size:26 final size:26
Alignment explanation
Indices: 184913--184968 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
184903 ATAAAATATC
* *
184913 TATTTTAATTATTATATTTATTATTA
1 TATTTCAATTATTATATTTATTAATA
184939 TATTTCAATTATT-TATTGTATTTAAT-
1 TATTTCAATTATTATATT-TA-TTAATA
184965 TATT
1 TATT
184969 ATTATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 18 0.69
27 4 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
TATTTCAATTATTATATTTATTAATA
Found at i:185642 original size:23 final size:24
Alignment explanation
Indices: 185615--185663 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
185605 TCGAGACTGC
185615 CATATAGAAT-TGCACCAAAGTGA
1 CATATAGAATATGCACCAAAGTGA
*
185638 CATATAGAATATGCACCGAAGTGA
1 CATATAGAATATGCACCAAAGTGA
185662 CA
1 CA
185664 CGTAGAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (24 bp):
CATATAGAATATGCACCAAAGTGA
Found at i:185669 original size:24 final size:23
Alignment explanation
Indices: 185618--185670 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
185608 AGACTGCCAT
*
185618 ATAGAATTGCACCAAAGTGACAT
1 ATAGAATTGCACCAAAGTGACAC
*
185641 ATAGAATATGCACCGAAGTGACAC
1 ATAGAAT-TGCACCAAAGTGACAC
*
185665 GTAGAA
1 ATAGAA
185671 ATGTCCCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (23 bp):
ATAGAATTGCACCAAAGTGACAC
Found at i:185692 original size:23 final size:23
Alignment explanation
Indices: 185664--185762 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
185654 CGAAGTGACA
* *
185664 CGTAGAAATGTCCCGAAGAACCA
1 CGTAGAAATGTCCCGAAGGACCG
* *
185687 CATAGATATGTCCCGAAGGACCG
1 CGTAGAAATGTCCCGAAGGACCG
185710 CGTAGAAATGTCCCGAAGGACCG
1 CGTAGAAATGTCCCGAAGGACCG
*
185733 CGTAGAAATGTCCCGAAGGATCG
1 CGTAGAAATGTCCCGAAGGACCG
185756 CGTAGAA
1 CGTAGAA
185763 CCCTCGACTC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.15
Consensus pattern (23 bp):
CGTAGAAATGTCCCGAAGGACCG
Found at i:187230 original size:3 final size:3
Alignment explanation
Indices: 187222--187291 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
187212 GGATGTTACA
187222 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
187270 ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
187292 CTACTACTAC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:192058 original size:41 final size:40
Alignment explanation
Indices: 191984--192259 Score: 178
Period size: 40 Copynumber: 6.8 Consensus size: 40
191974 TAGTGGCATT
* * **
191984 TTTAGCGGCGTTTTT-TGAACAAATGCCGGTAAATACTCGCAC
1 TTTAGCGGCGTTTTTAT--ACAAACGCCGCTAAATACT-ATAC
* * *
192026 TTTAGCGGTGTTTTTATATAAACGCCGCTAAATACTATAA
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAATACTATAC
* * * * * *
192066 TTTAGTGACGTTTTCATATAAACGCGGCTAATTACTATAC
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAATACTATAC
* * *
192106 TTTAGGGGCGTTTTTGTACAAACGCCGCTAAAAACTCATAC
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAATACT-ATAC
* * * ** **
192147 TCTAGCGGCGTTTTAAGCACAAACGCCGCTAAAGGCCCCTAC
1 TTTAGCGGCGTTTTTA-TACAAACGCCGCTAAA-TACTATAC
* ** * * * *
192189 ATTAGTAGCGTTTTCATATAAACGCCACTAATTACTATAC
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAATACTATAC
* * * *
192229 TTTAGC-ACGTTTTTGTGCAAACGCCTCTAAA
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAA
192260 AGCTCTTATT
Statistics
Matches: 177, Mismatches: 53, Indels: 11
0.73 0.22 0.05
Matches are distributed among these distances:
39 18 0.10
40 70 0.40
41 44 0.25
42 43 0.24
43 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTATACAAACGCCGCTAAATACTATAC
Done.