Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007936.1 Hibiscus syriacus cultivar Beakdansim tig00110346_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: 2869312
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:968575 original size:23 final size:23
Alignment explanation
Indices: 968539--968588 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
968529 ATAACTATAG
*
968539 ATAATATATATAT-ATATATGATA
1 ATAATATATATATAACATATGA-A
968562 ATAAT-TATATTATAACATATGAA
1 ATAATATATA-TATAACATATGAA
968585 ATAA
1 ATAA
968589 GCATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.17
23 13 0.54
24 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
ATAATATATATATAACATATGAA
Found at i:969900 original size:22 final size:23
Alignment explanation
Indices: 969857--969901 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
969847 GTTTTCACAT
* *
969857 GTTTTTTTTTTAAAATGAGAAAA
1 GTTTATTTTTTAAAATCAGAAAA
*
969880 GTTTATTTTTT-AAATCTGAAAA
1 GTTTATTTTTTAAAATCAGAAAA
969902 TTGAAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (23 bp):
GTTTATTTTTTAAAATCAGAAAA
Found at i:971230 original size:37 final size:36
Alignment explanation
Indices: 971181--971542 Score: 432
Period size: 37 Copynumber: 9.8 Consensus size: 36
971171 AAAGAGAATG
*
971181 TATATATTATATAGTTTTTGAAAACATTTTGAAAATA
1 TATATAATATATAG-TTTTGAAAACATTTTGAAAATA
971218 TATATAATATATAGTTTTTGAAAACATTTTGAATATATA
1 TATATAATATATAG-TTTTGAAAACATTTTGAA-A-ATA
* *
971257 TATATAGTATATAGTTTTTGGAAACATTTT-AAAACCT-
1 TATATAATATATAG-TTTTGAAAACATTTTGAAAA--TA
*
971294 TATATAATATATAGTTTTGAAATCATTTTGAAAA-A
1 TATATAATATATAGTTTTGAAAACATTTTGAAAATA
*
971329 CTTATATAATATATAGTTTTGAAATCATTTTGAAAACT-
1 --TATATAATATATAGTTTTGAAAACATTTTGAAAA-TA
*
971367 TATATAATATATAGTTTTGAAAACATTTTTTGAAAACA
1 TATATAATATATAGTTTTGAAAACA--TTTTGAAAATA
* *
971405 TATATAATATATAGTTTTAAAAACATTTTTTGAAAACA
1 TATATAATATATAGTTTTGAAAACA--TTTTGAAAATA
971443 TATATAATATATAGTTTT-AAAACATTATTGAAAACTA
1 TATATAATATATAGTTTTGAAAACATT-TTGAAAA-TA
*
971480 TATA-AATATATAGTTTTGAAAACATTTTTAAAATA
1 TATATAATATATAGTTTTGAAAACATTTTGAAAATA
* *
971515 TATATTATATATAGTTTT-AAAATATTTT
1 TATATAATATATAGTTTTGAAAACATTTT
971543 TTTTAAAATA
Statistics
Matches: 295, Mismatches: 13, Indels: 36
0.86 0.04 0.10
Matches are distributed among these distances:
35 17 0.06
36 76 0.26
37 103 0.35
38 68 0.23
39 31 0.11
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
TATATAATATATAGTTTTGAAAACATTTTGAAAATA
Found at i:971399 original size:13 final size:13
Alignment explanation
Indices: 971381--971405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
971371 TAATATATAG
971381 TTTTGAAAACATT
1 TTTTGAAAACATT
971394 TTTTGAAAACAT
1 TTTTGAAAACAT
971406 ATATAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAACATT
Found at i:971403 original size:112 final size:108
Alignment explanation
Indices: 971181--971536 Score: 436
Period size: 112 Copynumber: 3.2 Consensus size: 108
971171 AAAGAGAATG
* *
971181 TATATATTATATAGTTTTTGAAAACATTTTGAAAA-TATATATAATATATAGTTTTTGAAAACAT
1 TATATAATATATAG-TTTTAAAAACATTTTGAAAACT-TATATAATATATAG-TTTTGAAAACAT
* *
971245 TTTGAATATA-TATATATAGTATATAGTTTTTGGAAACA-TTTTAAAACCT
63 TTTGAA-A-ACT-TATATAATATATAG-TTTTGAAAACATTTTTAAAA-CT
* * *
971294 TATATAATATATAGTTTTGAAATCATTTTGAAAAACTTATATAATATATAGTTTTGAAATCATTT
1 TATATAATATATAGTTTTAAAAACATTTTG-AAAACTTATATAATATATAGTTTTGAAAACATTT
*
971359 TGAAAACTTATATAATATATAGTTTTGAAAACATTTTTTGAAAACA
65 TGAAAACTTATATAATATATAGTTTTGAAAACA-TTTTT-AAAACT
*
971405 TATATAATATATAGTTTTAAAAACATTTTTTGAAAACATATATAATATATAGTTTT-AAAACATT
1 TATATAATATATAGTTTTAAAAACA--TTTTGAAAACTTATATAATATATAGTTTTGAAAACATT
971469 ATTGAAAAC-TATATAAATATATAGTTTTGAAAACATTTTTAAAA-T
64 -TTGAAAACTTATAT-AATATATAGTTTTGAAAACATTTTTAAAACT
*
971514 ATATATTATATATAGTTTTAAAA
1 -TATATAATATATAGTTTTAAAA
971537 TATTTTTTTT
Statistics
Matches: 220, Mismatches: 12, Indels: 25
0.86 0.05 0.10
Matches are distributed among these distances:
109 10 0.05
110 39 0.18
111 47 0.21
112 87 0.40
113 36 0.16
114 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (108 bp):
TATATAATATATAGTTTTAAAAACATTTTGAAAACTTATATAATATATAGTTTTGAAAACATTTT
GAAAACTTATATAATATATAGTTTTGAAAACATTTTTAAAACT
Found at i:971589 original size:19 final size:20
Alignment explanation
Indices: 971567--971611 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
971557 ATTATCATTA
*
971567 TTATTTATTTTATTGTA-TT
1 TTATTTACTTTATTGTATTT
* *
971586 TTATTAACTTTATTTTATTT
1 TTATTTACTTTATTGTATTT
971606 TTATTT
1 TTATTT
971612 TTTGGTCCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (20 bp):
TTATTTACTTTATTGTATTT
Found at i:972401 original size:6 final size:6
Alignment explanation
Indices: 972390--972554 Score: 54
Period size: 6 Copynumber: 26.7 Consensus size: 6
972380 TTTAACCCAA
* *
972390 TTTTAT TTTTAT TATTAT TATTTAT TTATT-T TATTTCAT TGTT-T TTTTA-
1 TTTTAT TTTTAT TTTTAT T-TTTAT TT-TTAT T-TTT-AT TTTTAT TTTTAT
* * ** * *
972439 TTTTAT TATTTCT ACTCAAT TTTATTT TTTTAT ATTTAT TTTT-T TCATTTAT
1 TTTTAT T-TTTAT -TTTTAT TTT-TAT TTTTAT TTTTAT TTTTAT T--TTTAT
* * * * * * *
972491 TATTAT TATTAT TATTAT TATATTAA TATT-T TTTTAT TCTT-T TTTCAT
1 TTTTAT TTTTAT TTTTAT T-T-TTAT TTTTAT TTTTAT TTTTAT TTTTAT
972539 TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTT
972555 GCAATTTAAT
Statistics
Matches: 116, Mismatches: 26, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
5 17 0.15
6 68 0.59
7 23 0.20
8 8 0.07
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (6 bp):
TTTTAT
Found at i:972493 original size:3 final size:3
Alignment explanation
Indices: 972487--972520 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
972477 TTTTTTTCAT
*
972487 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
972521 TTTTTATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:972493 original size:16 final size:15
Alignment explanation
Indices: 972390--972554 Score: 64
Period size: 14 Copynumber: 11.1 Consensus size: 15
972380 TTTAACCCAA
972390 TTTTATTT-TTATTAT
1 TTTTATTTATTATT-T
* *
972405 TATTATTTA-T-TTA
1 TTTTATTTATTATTT
*
972418 TTTTATTTCATTGTTT
1 TTTTATTT-ATTATTT
972434 TTTTATTTTATTATTT
1 TTTTA-TTTATTATTT
* * *
972450 CTACTCAATT-TTATTT
1 -T-TTTATTTATTATTT
*
972466 TTTTATAT-TTATTT
1 TTTTATTTATTATTT
972480 TTTTCATTTATTA--T
1 TTTT-ATTTATTATTT
* *
972494 TATTA-TTATTATTA
1 TTTTATTTATTATTT
* *
972508 TTATA-TTAATATTT
1 TTTTATTTATTATTT
*
972522 TTTTATTCT-TTTTTCAT
1 TTTTATT-TATTATT--T
972539 TTTTATTT-TTATTT
1 TTTTATTTATTATTT
972553 TT
1 TT
972555 GCAATTTAAT
Statistics
Matches: 112, Mismatches: 23, Indels: 31
0.67 0.14 0.19
Matches are distributed among these distances:
12 6 0.05
13 8 0.07
14 37 0.33
15 17 0.15
16 28 0.25
17 14 0.12
18 2 0.02
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (15 bp):
TTTTATTTATTATTT
Found at i:974231 original size:23 final size:23
Alignment explanation
Indices: 974205--974258 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
974195 CTTTAAAATG
*
974205 TTTTTGT-CTCTTAATAAATAACA
1 TTTTTGTCCT-TTAATAAATAAAA
974228 TTTTT-TCCTTTAATAAATAAAA
1 TTTTTGTCCTTTAATAAATAAAA
974250 TTTTTGTCC
1 TTTTTGTCC
974259 CAATAAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTTTGTCCTTTAATAAATAAAA
Found at i:974263 original size:21 final size:21
Alignment explanation
Indices: 974217--974264 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
974207 TTTGTCTCTT
* *
974217 AATAAATAACATTTTTTCCTTT
1 AATAAATAAAATTTTTTCC-TC
974239 AATAAATAAAATTTTTGTCC-C
1 AATAAATAAAATTTTT-TCCTC
974260 AATAA
1 AATAA
974265 GAATTGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 15 0.65
23 3 0.13
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (21 bp):
AATAAATAAAATTTTTTCCTC
Found at i:977695 original size:86 final size:86
Alignment explanation
Indices: 977545--977709 Score: 260
Period size: 86 Copynumber: 1.9 Consensus size: 86
977535 TCGCAAAGAG
* *
977545 GAACCACCTGAGGAATATCTCACGTGACTTTCCCATGAAGGGGAGTAATCCAAAGATCATCTCAC
1 GAACAACCTGAGGAATATCTCACATGACTTTCCCATGAAGGGGAGTAATCCAAAGATCATCTCAC
977610 CTGGTTCAGACCCGCTAAGGA
66 CTGGTTCAGACCCGCTAAGGA
* * * *
977631 GAACAACCTGAGGAATATAC-CACATGGCTTTCCCGTGAAGGGGGGTCATCCAAAGATCATCTCA
1 GAACAACCTGAGGAATAT-CTCACATGACTTTCCCATGAAGGGGAGTAATCCAAAGATCATCTCA
977695 CCTGGTTCAGACCCG
65 CCTGGTTCAGACCCG
977710 TGAAGGGGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
86 71 0.99
87 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (86 bp):
GAACAACCTGAGGAATATCTCACATGACTTTCCCATGAAGGGGAGTAATCCAAAGATCATCTCAC
CTGGTTCAGACCCGCTAAGGA
Found at i:978048 original size:85 final size:83
Alignment explanation
Indices: 977776--978060 Score: 277
Period size: 85 Copynumber: 3.4 Consensus size: 83
977766 TATGGTAGAA
* * * *
977776 AAAAACCTTCGAGTTTGATTACATTCAGCTCAAGGGCATATCAATTTACAGCATAGCTCAAGGCG
1 AAAAA-CTTCGAGTTCGATTACATTCAGCTCAAGAGCATTTAAATTTACAGCATAGCTCAAGGCG
977841 AGAAAGGATATCTATCAAC
65 AGAAAGGATATCTATCAAC
* * * * *
977860 AACGACCTTCGAATTCGATTACATTCAGCTCAA-AGGCATATCAAATTTACAGCATAGCTGAAGG
1 AA-AAACTTCGAGTTCGATTACATTCAGCTCAAGA-GCAT-TTAAATTTACAGCATAGCTCAAGG
* *
977924 CGA-TAAGGATTATCTGTCAAC
63 CGAGAAAGGA-TATCTATCAAC
* * * * * *
977945 AAATAACTTCAAGATCGATTCCATTCAGCTCAAGAACATGTTAAATTTACAGCATAGCTTAAGTC
1 AAA-AACTTCGAGTTCGATTACATTCAGCTCAAGAGCAT-TTAAATTTACAGCATAGCTCAAGGC
* **
978010 GAGAAAAGCCATCTATCAAC
64 GAGAAAGGATATCTATCAAC
* **
978030 AAAAATTGTCGAGTTCGATGCCATTCAGCTC
1 AAAAACT-TCGAGTTCGATTACATTCAGCTC
978061 GATGACACAT
Statistics
Matches: 162, Mismatches: 31, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
84 39 0.24
85 119 0.73
86 4 0.02
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (83 bp):
AAAAACTTCGAGTTCGATTACATTCAGCTCAAGAGCATTTAAATTTACAGCATAGCTCAAGGCGA
GAAAGGATATCTATCAAC
Found at i:978800 original size:10 final size:11
Alignment explanation
Indices: 978779--978811 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
978769 TTTCGTTCAG
978779 ATTTT-TTATT
1 ATTTTATTATT
978789 ATTTTATT-TT
1 ATTTTATTATT
978799 ATTTTATTATT
1 ATTTTATTATT
978810 AT
1 AT
978812 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:978850 original size:15 final size:15
Alignment explanation
Indices: 978827--978859 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
978817 TATATTATAA
978827 TTTTTGAAAAT-ATT
1 TTTTTGAAAATGATT
978841 TTTTTAGAAAATGATT
1 TTTTT-GAAAATGATT
978857 TTT
1 TTT
978860 GAAAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (15 bp):
TTTTTGAAAATGATT
Found at i:978897 original size:37 final size:37
Alignment explanation
Indices: 978856--979253 Score: 403
Period size: 37 Copynumber: 10.8 Consensus size: 37
978846 AGAAAATGAT
* *
978856 TTTTGAAAATGTATATATTATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
978893 TTTTGAAAATATATATAATATATAATTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
978930 TTTTGAATATATATATAAATAATATATAGTTTTTGAAAACA
1 TTTTGAA-A-ATATAT--ATAATATATAGTTTTTGAAAACA
* * *
978971 TTTTTAAAACT-TATATAATATATAG-TTTCGAAATCA
1 TTTTGAAAA-TATATATAATATATAGTTTTTGAAAACA
*
979007 TTTTGAAAA-ACTTATATAATATATA-TTTTTGAAATCA
1 TTTTGAAAATA--TATATAATATATAGTTTTTGAAAACA
* * *
979044 TTTTGATAAACT-TATATAATAAATAG-CTTTGAAATCA
1 TTTTGA-AAA-TATATATAATATATAGTTTTTGAAAACA
979081 TTTTGAAAACT-TATATAATATATAG-TTTTGAAAACA
1 TTTTGAAAA-TATATATAATATATAGTTTTTGAAAACA
* **
979117 TTTTTGAAAACATATATAATATATAG-TTTCAAAAACA
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * *
979154 TTTTTTGAAAACATATA-AATGTATA-TTTTT-AATACA
1 --TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
979190 TTATTGAAAA-CTATATAATATATAG-TTTTGAAAAC-
1 TT-TTGAAAATATATATAATATATAGTTTTTGAAAACA
*
979225 TTTTTAAAATATATATAATATATAGTTTT
1 TTTTGAAAATATATATAATATATAGTTTT
979254 AAAATGTTTT
Statistics
Matches: 313, Mismatches: 25, Indels: 47
0.81 0.06 0.12
Matches are distributed among these distances:
34 12 0.04
35 34 0.11
36 56 0.18
37 151 0.48
38 20 0.06
39 10 0.03
40 2 0.01
41 28 0.09
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:979306 original size:10 final size:9
Alignment explanation
Indices: 979282--979330 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
979272 AAAATATATA
979282 TTATTATTAT
1 TTATT-TTAT
979292 TTATTTTAT
1 TTATTTTAT
979301 TGTATTTTAT
1 T-TATTTTAT
* *
979311 TAACTTTAT
1 TTATTTTAT
*
979320 TTTTTTTAT
1 TTATTTTAT
979329 TT
1 TT
979331 TTTGGTCTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
9 19 0.58
10 14 0.42
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (9 bp):
TTATTTTAT
Found at i:979393 original size:19 final size:19
Alignment explanation
Indices: 979369--979419 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
979359 CCAGGTCCAG
* *
979369 ACCGGGTGTGGGCTGCCCA
1 ACCGGGTTTGGGCTACCCA
*
979388 ACCGGGTTTAGGCTACCCA
1 ACCGGGTTTGGGCTACCCA
979407 ACCGGGTTTGGGC
1 ACCGGGTTTGGGC
979420 CTCACCCAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.37, T:0.20
Consensus pattern (19 bp):
ACCGGGTTTGGGCTACCCA
Found at i:980542 original size:22 final size:21
Alignment explanation
Indices: 980514--980560 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
980504 TTTTTGTTAA
980514 TATTTATCTTCTTAACATTTTT
1 TATTTAT-TTCTTAACATTTTT
* **
980536 TATTTATTTTTTTTCATTTTT
1 TATTTATTTCTTAACATTTTT
980557 TATT
1 TATT
980561 ATTATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (21 bp):
TATTTATTTCTTAACATTTTT
Found at i:980554 original size:10 final size:11
Alignment explanation
Indices: 980529--980600 Score: 59
Period size: 10 Copynumber: 7.0 Consensus size: 11
980519 ATCTTCTTAA
980529 CATTTTTTATT
1 CATTTTTTATT
*
980540 TATTTTTT-TT
1 CATTTTTTATT
980550 CATTTTTTATT
1 CATTTTTTATT
*
980561 -ATTATTATATT
1 CATT-TTTTATT
980572 -A-TTTTT-TT
1 CATTTTTTATT
980580 -ATTTTTTTATT
1 CA-TTTTTTATT
980591 C-TTTTTTATT
1 CATTTTTTATT
980601 TTTATTTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
10 27 0.53
11 18 0.35
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (11 bp):
CATTTTTTATT
Found at i:980581 original size:8 final size:8
Alignment explanation
Indices: 980533--980609 Score: 57
Period size: 8 Copynumber: 8.6 Consensus size: 8
980523 TCTTAACATT
980533 TTTTATTTA
1 TTTT-TTTA
980542 TTTTTTTTCA
1 -TTTTTTT-A
980552 TTTTTTATTA
1 -TTTTT-TTA
980562 TTATTATATTA
1 TT-TT-T-TTA
980573 TTTTTTTA
1 TTTTTTTA
980581 TTTTTTTA
1 TTTTTTTA
980589 TTCTTTTT-
1 TT-TTTTTA
*
980597 TATTTTTA
1 TTTTTTTA
980605 TTTTT
1 TTTTT
980610 GTAATATAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
7 5 0.08
8 18 0.31
9 11 0.19
10 16 0.27
11 9 0.15
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTA
Found at i:980587 original size:30 final size:27
Alignment explanation
Indices: 980535--980603 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 27
980525 TTAACATTTT
980535 TTATTTATTTTTTTTCATTTTTTATTA
1 TTATTTATTTTTTTTCATTTTTTATTA
* *
980562 TTATTATATTATTTTTTTATTTTTTTATTC
1 TTATT-TATT-TTTTTTCA-TTTTTTATTA
*
980592 TTTTTTATTTTT
1 TTATTTATTTTT
980604 ATTTTTGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.14
28 7 0.19
29 11 0.31
30 13 0.36
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (27 bp):
TTATTTATTTTTTTTCATTTTTTATTA
Found at i:980608 original size:11 final size:11
Alignment explanation
Indices: 980532--980608 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
980522 TTCTTAACAT
980532 TTTTTA-TTTA
1 TTTTTATTTTA
*
980542 TTTTT-TTTCA
1 TTTTTATTTTA
980552 TTTTTTATTATTA
1 -TTTTTATT-TTA
980565 TTATATTATTTT-
1 TT-T-TTATTTTA
*
980577 TTTATTTTTTTA
1 TTT-TTATTTTA
*
980589 TTCTT-TTTTA
1 TTTTTATTTTA
980599 TTTTTATTTT
1 TTTTTATTTT
980609 TGTAATATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
10 17 0.31
11 19 0.35
12 8 0.15
13 5 0.09
14 5 0.09
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:980625 original size:46 final size:48
Alignment explanation
Indices: 980533--980625 Score: 111
Period size: 46 Copynumber: 2.0 Consensus size: 48
980523 TCTTAACATT
* * *
980533 TTTTATTTATTTTTTTTCATTTTTTATTATTATTATATTATTTTTTTA
1 TTTTATTTATTTTTTTTCATTTTTTATTATTATAATATAATGTTTTTA
* *
980581 TTTT-TTTATTCTTTTTT-A-TTTTTATTTTTGTAATATAATGTTTTT
1 TTTTATTTATT-TTTTTTCATTTTTTATTATTATAATATAATGTTTTT
980626 GACTTTTTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
46 22 0.56
47 7 0.18
48 10 0.26
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (48 bp):
TTTTATTTATTTTTTTTCATTTTTTATTATTATAATATAATGTTTTTA
Found at i:981327 original size:21 final size:21
Alignment explanation
Indices: 981302--981344 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
981292 AATTAACCAC
*
981302 TGATT-TGGTTTGATTTGGTGT
1 TGATTCTGATTTG-TTTGGTGT
*
981323 TGATTCTGATTTGTTTTGTGT
1 TGATTCTGATTTGTTTGGTGT
981344 T
1 T
981345 TTAGAAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.09, C:0.02, G:0.28, T:0.60
Consensus pattern (21 bp):
TGATTCTGATTTGTTTGGTGT
Found at i:981889 original size:37 final size:36
Alignment explanation
Indices: 981836--981986 Score: 159
Period size: 37 Copynumber: 4.2 Consensus size: 36
981826 AATAATAAAA
* *
981836 ATATATATGATAATATATATTTTCAAAAACTACATATT
1 ATATATATTAT-ATATATA-TTTCAAAAACTATATATT
* * **
981874 TTATATATTATATATATA-TTCAAAAAATATACGTT
1 ATATATATTATATATATATTTCAAAAACTATATATT
*
981909 ATATAT-TT-TAT-T-TATTTAAAAAACTATATATT
1 ATATATATTATATATATATTTCAAAAACTATATATT
* *
981941 ATGTATATTATAGATATATTGTCAAAAACTATATATT
1 ATATATATTATATATATATT-TCAAAAACTATATATT
981978 ATATATATT
1 ATATATATT
981987 TTTCGAAACT
Statistics
Matches: 92, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
31 2 0.02
32 19 0.21
33 5 0.05
34 4 0.04
35 19 0.21
36 4 0.04
37 30 0.33
38 9 0.10
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (36 bp):
ATATATATTATATATATATTTCAAAAACTATATATT
Found at i:981930 original size:31 final size:34
Alignment explanation
Indices: 981839--981983 Score: 93
Period size: 35 Copynumber: 4.2 Consensus size: 34
981829 AATAAAAATA
* * **
981839 TATATGATAATATATATTTTC-AAAAACTACATATTT
1 TATAT-ATTATATATATATTCAAAAAACT--ATACGT
981875 TATATATTATATATATATTCAAAAAA-TATACGT
1 TATATATTATATATATATTCAAAAAACTATACGT
* * **
981908 TATATATT-T-TATTTATTTAAAAAACTATATAT
1 TATATATTATATATATATTCAAAAAACTATACGT
* **
981940 TATGTATATTATAGATATATTGTC-AAAAACTATATAT
1 TA--TATATTATATATATA-T-TCAAAAAACTATACGT
981977 TATATAT
1 TATATAT
981984 ATTTTTCGAA
Statistics
Matches: 90, Mismatches: 11, Indels: 17
0.76 0.09 0.14
Matches are distributed among these distances:
31 13 0.14
32 8 0.09
33 12 0.13
34 6 0.07
35 20 0.22
36 14 0.16
37 16 0.18
38 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (34 bp):
TATATATTATATATATATTCAAAAAACTATACGT
Found at i:981975 original size:28 final size:28
Alignment explanation
Indices: 981944--982040 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 28
981934 ATATATTATG
* *
981944 TATATTATAGATATATTGTCAAAAACTA
1 TATATTATATATATATTTTCAAAAACTA
*
981972 TATATTATATATAT-TTTTC-GAAACTA
1 TATATTATATATATATTTTCAAAAACTA
* *
981998 TTTATTAAATATATATATTTTCAAAAATTA
1 TATATT--ATATATATATTTTCAAAAACTA
982028 TATA-TAT-TATATA
1 TATATTATATATATA
982041 CATTATACTA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
26 17 0.29
27 6 0.10
28 21 0.36
29 6 0.10
30 8 0.14
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (28 bp):
TATATTATATATATATTTTCAAAAACTA
Found at i:983812 original size:21 final size:22
Alignment explanation
Indices: 983788--983828 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
983778 AAATCATAGA
* *
983788 TAATGACAAGTAT-ATAATGTT
1 TAATGAAAAGAATCATAATGTT
983809 TAATGAAAAGAATCATAATG
1 TAATGAAAAGAATCATAATG
983829 GTTTCATAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.32
Consensus pattern (22 bp):
TAATGAAAAGAATCATAATGTT
Found at i:988245 original size:101 final size:101
Alignment explanation
Indices: 988070--988272 Score: 352
Period size: 101 Copynumber: 2.0 Consensus size: 101
988060 AAAAGGATAG
* *
988070 TGTTAGAATATATGTTCAATATATTCTGTTTATAGTGTGTATCATTAGTTTAGAATGTATATCTT
1 TGTTAGAATACATGTTCAATATATTCTGTTTATAGTGTGTATCATTAATTTAGAATGTATATCTT
*
988135 TTTTTCCTTAATTATAGCCTAATTGATCTCTTGTAA
66 TGTTTCCTTAATTATAGCCTAATTGATCTCTTGTAA
* *
988171 TGTTAGAATACATGTTCAATATATTCTGTTTATAGTGTGTATCGTTAATTTATAATGTATATCTT
1 TGTTAGAATACATGTTCAATATATTCTGTTTATAGTGTGTATCATTAATTTAGAATGTATATCTT
*
988236 TGTTTCCTTAATTGTAGCCTAATTGATCTCTTGTAA
66 TGTTTCCTTAATTATAGCCTAATTGATCTCTTGTAA
988272 T
1 T
988273 CATGTATATA
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.49
Consensus pattern (101 bp):
TGTTAGAATACATGTTCAATATATTCTGTTTATAGTGTGTATCATTAATTTAGAATGTATATCTT
TGTTTCCTTAATTATAGCCTAATTGATCTCTTGTAA
Found at i:996709 original size:13 final size:13
Alignment explanation
Indices: 996691--996727 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
996681 GTTTGCTAAT
996691 GAGAAGGAAATGA
1 GAGAAGGAAATGA
*
996704 GAGAAGGAAACGA
1 GAGAAGGAAATGA
*
996717 GAGAAGAAAAT
1 GAGAAGGAAAT
996728 ATAAGAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.57, C:0.03, G:0.35, T:0.05
Consensus pattern (13 bp):
GAGAAGGAAATGA
Found at i:1002634 original size:21 final size:21
Alignment explanation
Indices: 1002608--1002652 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1002598 CGTGTTGGGC
1002608 CTATCATCCACTGCATTGAAT
1 CTATCATCCACTGCATTGAAT
*
1002629 CTATCATCCATTGCATTGAAT
1 CTATCATCCACTGCATTGAAT
1002650 CTA
1 CTA
1002653 GCTCGAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.36
Consensus pattern (21 bp):
CTATCATCCACTGCATTGAAT
Found at i:1003865 original size:21 final size:21
Alignment explanation
Indices: 1003839--1003883 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1003829 CGTGTTGGGC
1003839 CTATCATCCACTGCATTGAAT
1 CTATCATCCACTGCATTGAAT
*
1003860 CTATCATCCATTGCATTGAAT
1 CTATCATCCACTGCATTGAAT
1003881 CTA
1 CTA
1003884 GCTCGAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.36
Consensus pattern (21 bp):
CTATCATCCACTGCATTGAAT
Found at i:1005150 original size:23 final size:23
Alignment explanation
Indices: 1005123--1005167 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1005113 TGAAAAACAA
*
1005123 TTTTATGAAAAACAATAGTATAG
1 TTTTATGAAAAACAATAATATAG
1005146 TTTTATGAAAAACAATAATATA
1 TTTTATGAAAAACAATAATATA
1005168 CACATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (23 bp):
TTTTATGAAAAACAATAATATAG
Found at i:1005641 original size:20 final size:20
Alignment explanation
Indices: 1005616--1005681 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
1005606 CTAAAAACAA
1005616 TATCGATACTATACGAGTAG
1 TATCGATACTATACGAGTAG
*
1005636 TATCGATACCATACAAGAGTAG
1 TATCGATACTATAC--GAGTAG
* **
1005658 TATCAATACTATGTGAGTAG
1 TATCGATACTATACGAGTAG
1005678 TATC
1 TATC
1005682 AATAGCAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 23 0.59
22 16 0.41
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (20 bp):
TATCGATACTATACGAGTAG
Found at i:1037226 original size:11 final size:11
Alignment explanation
Indices: 1037197--1037229 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1037187 GCCAATACCT
*
1037197 CCTCTTAACCA
1 CCTCTTATCCA
1037208 CCTCTTATCCA
1 CCTCTTATCCA
1037219 CCTCTTATCCA
1 CCTCTTATCCA
1037230 TAGCACCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.33
Consensus pattern (11 bp):
CCTCTTATCCA
Found at i:1061130 original size:17 final size:17
Alignment explanation
Indices: 1061108--1061146 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1061098 AAAAATGAAC
*
1061108 TAAAAGAAATAATACAG
1 TAAAAGAAACAATACAG
* *
1061125 TAAAAGTAACAATATAG
1 TAAAAGAAACAATACAG
1061142 TAAAA
1 TAAAA
1061147 TATACCATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (17 bp):
TAAAAGAAACAATACAG
Found at i:1068907 original size:22 final size:22
Alignment explanation
Indices: 1068882--1068930 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1068872 CATCCTATCT
1068882 AGAACGTGATAGCTTCGGGGTA
1 AGAACGTGATAGCTTCGGGGTA
*
1068904 AGAACGTGATAGCTTTGGGGTA
1 AGAACGTGATAGCTTCGGGGTA
1068926 AGAAC
1 AGAAC
1068931 TATAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.35, T:0.22
Consensus pattern (22 bp):
AGAACGTGATAGCTTCGGGGTA
Found at i:1069296 original size:16 final size:16
Alignment explanation
Indices: 1069275--1069316 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1069265 CTTGTTGCTC
1069275 ATTAAGCTCGTCACTT
1 ATTAAGCTCGTCACTT
*
1069291 ATTAAGCTCGTTACTT
1 ATTAAGCTCGTCACTT
*
1069307 GTTAAGCTCG
1 ATTAAGCTCG
1069317 ATGCCCATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (16 bp):
ATTAAGCTCGTCACTT
Found at i:1069617 original size:20 final size:20
Alignment explanation
Indices: 1069584--1069638 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1069574 AAAATTATAT
* * *
1069584 AAAAAATTAACGAGTTGTTC
1 AAAAACTTATCGAGTTGTGC
1069604 AAAAACTTATCGAGTTGTGC
1 AAAAACTTATCGAGTTGTGC
*
1069624 ACAAACTTATCGAGT
1 AAAAACTTATCGAGT
1069639 CGATTTGGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (20 bp):
AAAAACTTATCGAGTTGTGC
Found at i:1081594 original size:20 final size:19
Alignment explanation
Indices: 1081566--1081616 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1081556 ATAACCATGA
*
1081566 TATCTATACTCCT-CTTGGGG
1 TATCGATACTCCTCCTT--GG
1081586 TATCGATACTCCTGCCTTGG
1 TATCGATACTCCT-CCTTGG
1081606 TATCGATACTC
1 TATCGATACTC
1081617 AGTAGTAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 25 0.89
22 3 0.11
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (19 bp):
TATCGATACTCCTCCTTGG
Found at i:1085057 original size:13 final size:14
Alignment explanation
Indices: 1085033--1085071 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
1085023 GCCTAAATAT
*
1085033 ATAAAGAAAAATGA
1 ATAAATAAAAATGA
1085047 AT-AATAAAAATGA
1 ATAAATAAAAATGA
1085060 ATAAATAAAAAT
1 ATAAATAAAAAT
1085072 AAAAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (14 bp):
ATAAATAAAAATGA
Found at i:1088064 original size:22 final size:22
Alignment explanation
Indices: 1088039--1088106 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
1088029 CAAGTAAACT
1088039 AAAAAAAATAAAATTAAAGAAA
1 AAAAAAAATAAAATTAAAGAAA
1088061 AAAATAAAATAAAATT-AAGAAA
1 AAAA-AAAATAAAATTAAAGAAA
* *
1088083 AAAGAAAAGTAAATTGTAAAGAAA
1 AAA-AAAAATAAAAT-TAAAGAAA
1088107 TAATTAAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
22 21 0.52
23 13 0.32
24 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (22 bp):
AAAAAAAATAAAATTAAAGAAA
Found at i:1096223 original size:20 final size:20
Alignment explanation
Indices: 1096198--1096237 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1096188 GCATATGCAT
* *
1096198 AAAATACACATAAATAAATA
1 AAAATACAAATAAAAAAATA
*
1096218 AAAATATAAATAAAAAAATA
1 AAAATACAAATAAAAAAATA
1096238 CATACACTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAATACAAATAAAAAAATA
Found at i:1097663 original size:67 final size:65
Alignment explanation
Indices: 1097588--1097747 Score: 203
Period size: 66 Copynumber: 2.4 Consensus size: 65
1097578 CAAGAGAAGT
*
1097588 TATCTCAAGTGAGTCGAAACTTTGTTTCTAGTGAAACAATTTCAAAATTTGCGTTTCAAGGGAAA
1 TATCTCAAGTGAGACGAAA-TTTGTTT-TAGTGAAACAATTTCAAAATTTGCGTTTCAAGGGAAA
1097653 AC
64 AC
* * * * * *
1097655 TATCTCAAGTGAGACAAAATTTATTTTAAATGAAATAATTTCAAAATTTGTGTTTCGAGGGAAAA
1 TATCTCAAGTGAGACGAAATTTGTTTT-AGTGAAACAATTTCAAAATTTGCGTTTCAAGGGAAAA
1097720 C
65 C
* * *
1097721 TGTCTTAAGCGAGACGAAATTTGTTTT
1 TATCTCAAGTGAGACGAAATTTGTTTT
1097748 TAGGAAAATA
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
65 1 0.01
66 62 0.77
67 17 0.21
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (65 bp):
TATCTCAAGTGAGACGAAATTTGTTTTAGTGAAACAATTTCAAAATTTGCGTTTCAAGGGAAAAC
Found at i:1097846 original size:102 final size:102
Alignment explanation
Indices: 1097648--1097848 Score: 228
Period size: 102 Copynumber: 2.0 Consensus size: 102
1097638 GCGTTTCAAG
* * * * * *
1097648 GGAAAACTATCTCAAGTGAGACAAAATTTATTTTAAATGAAATAATTTCAAAATTTGTGTTTCGA
1 GGAAAACTATCTCAAGTGAGACAAAATTTATTTCAAATGAAACAACTTCAAAATTTGGGCTTCAA
* *
1097713 GGGAAAACTGTCTTAAGCGAGACGAAATTTGTTTTTA
66 GGGAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTA
* * *
1097750 GGAAAA-TAATCTCAAGTGAGATC-AATTTTGTTTCAAGTGAAACAACTTCAAAATTTGGGCTTC
1 GGAAAACT-ATCTCAAGTGAGA-CAAAATTTATTTCAAATGAAACAACTTCAAAATTTGGGCTTC
* * *
1097813 AATGG-AAATTGTCTCAAGCGAGATAAAACTTTGTTT
64 AAGGGAAAACTGTCTCAAGCGAGACAAAA-TTTGTTT
1097849 CGAGAGAAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
101 20 0.24
102 61 0.74
103 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (102 bp):
GGAAAACTATCTCAAGTGAGACAAAATTTATTTCAAATGAAACAACTTCAAAATTTGGGCTTCAA
GGGAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTA
Found at i:1097909 original size:67 final size:66
Alignment explanation
Indices: 1097759--1097954 Score: 236
Period size: 67 Copynumber: 3.0 Consensus size: 66
1097749 AGGAAAATAA
* * * * * * ** * *
1097759 TCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTTCAAA-ATTTGGGCTTCAATG-GAAAT
1 TCTCAAGCGAGATAAACTTTGTTTCGAGAGAAACAACTTCAAAGGTTTATGTTTCAA-GAGAAAA
1097822 TG
65 TG
1097824 TCTCAAGCGAGATAAAACTTTGTTTCGAGAGAAACAACTTCAAAGGTTTATGTTTCAAGAGAAAA
1 TCTCAAGCGAGAT-AAACTTTGTTTCGAGAGAAACAACTTCAAAGGTTTATGTTTCAAGAGAAAA
1097889 TG
65 TG
*
1097891 TCTCAAGCGAGATGAAACTTTGTTTCGAGCGAAACAA-TCTCAAAGGTTTATGTTTCAAGAGAAA
1 TCTCAAGCGAGAT-AAACTTTGTTTCGAGAGAAACAACT-TCAAAGGTTTATGTTTCAAGAGAAA
1097955 CAATCTCAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
65 12 0.10
66 28 0.24
67 75 0.65
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (66 bp):
TCTCAAGCGAGATAAACTTTGTTTCGAGAGAAACAACTTCAAAGGTTTATGTTTCAAGAGAAAAT
G
Found at i:1098019 original size:36 final size:35
Alignment explanation
Indices: 1097971--1098095 Score: 109
Period size: 36 Copynumber: 3.7 Consensus size: 35
1097961 CAAAGGTTTA
*
1097971 TGTTTCAAGAGAAATTGTCTCAAGTGAGACGAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGTGAGACGAAAT
** **
1098006 TGGTTTCAAGAGAAACAATCTCAA---AG--G-TTT
1 T-GTTTCAAGAGAAACTGTCTCAAGTGAGACGAAAT
* * *
1098036 ATGTTTCAAGAGAAATTTTCTCAAGTGAGACAAAAT
1 -TGTTTCAAGAGAAACTGTCTCAAGTGAGACGAAAT
1098072 CTGTTTCAAGAGAAACTGTCTCAA
1 -TGTTTCAAGAGAAACTGTCTCAA
1098096 AGGTGACAGA
Statistics
Matches: 68, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
30 20 0.29
31 2 0.03
33 4 0.06
35 1 0.01
36 41 0.60
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGTGAGACGAAAT
Found at i:1098023 original size:66 final size:66
Alignment explanation
Indices: 1097941--1098099 Score: 266
Period size: 66 Copynumber: 2.4 Consensus size: 66
1097931 CAAAGGTTTA
*
1097941 TGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGTGAGACGAAAT
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGTGAGACAAAAT
1098006 -
66 C
*
1098006 TGGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAATTTTCTCAAGTGAGACAAAA
1 T-GTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGTGAGACAAAA
1098071 TC
65 TC
**
1098073 TGTTTCAAGAGAAACTGTCTCAAAGGT
1 TGTTTCAAGAGAAACAATCTCAAAGGT
1098100 GACAGACAAT
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
65 1 0.01
66 86 0.98
67 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (66 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGTGAGACAAAAT
C
Found at i:1098059 original size:30 final size:30
Alignment explanation
Indices: 1097911--1098050 Score: 147
Period size: 30 Copynumber: 4.5 Consensus size: 30
1097901 GATGAAACTT
* *
1097911 TGTTTCGAGCGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1097941 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
*** *
1097971 TGTTTCAAGAGAAATTGTCTCAAGTGAGACGAAATT-
1 TGTTTCAAGAGAAACAATCTCAA---AG--G--TTTA
*
1098007 GGTTTCAAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1098037 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
1098051 TTTTCTCAAG
Statistics
Matches: 90, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.02
30 61 0.68
31 1 0.01
33 4 0.04
35 1 0.01
36 19 0.21
37 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:1098059 original size:96 final size:97
Alignment explanation
Indices: 1097844--1098050 Score: 328
Period size: 97 Copynumber: 2.1 Consensus size: 97
1097834 GATAAAACTT
* *
1097844 TGTTTCGAGAGAAACAA-CTTCAAAGGTTTATGTTTCAAGAGAAAATGTCTCAAGCGAGATGAAA
1 TGTTTCAAGAGAAACAATC-TCAAAGGTTTATGTTTCAAGAGAAAATGTCTCAAGCGAGACGAAA
* * *
1097908 CTTTGTTTCGAGCGAAACAATCTCAAAGGTTTA
65 CTTGGTTTCAAGAGAAACAATCTCAAAGGTTTA
* *
1097941 TGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGTGAGACGAAA-
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAAATGTCTCAAGCGAGACGAAAC
1098005 TTGGTTTCAAGAGAAACAATCTCAAAGGTTTA
66 TTGGTTTCAAGAGAAACAATCTCAAAGGTTTA
1098037 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
1098051 TTTTCTCAAG
Statistics
Matches: 102, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
96 43 0.42
97 58 0.57
98 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (97 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAAATGTCTCAAGCGAGACGAAAC
TTGGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:1098910 original size:19 final size:20
Alignment explanation
Indices: 1098883--1098920 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1098873 CTTCTGGAGA
*
1098883 GATTATCTT-GTTTGAAAAT
1 GATTATCTTCCTTTGAAAAT
*
1098902 GATTTTCTTCCTTTGAAAA
1 GATTATCTTCCTTTGAAAA
1098921 AATTCAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (20 bp):
GATTATCTTCCTTTGAAAAT
Found at i:1108158 original size:13 final size:13
Alignment explanation
Indices: 1108140--1108164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1108130 AGGGGGAGTA
1108140 ATTTCAAAACTTG
1 ATTTCAAAACTTG
1108153 ATTTCAAAACTT
1 ATTTCAAAACTT
1108165 AAAATTACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
ATTTCAAAACTTG
Found at i:1108487 original size:20 final size:21
Alignment explanation
Indices: 1108459--1108509 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1108449 AGAGGGAACT
*
1108459 GATTCCCCCCCAAGGGGTATC
1 GATTCCCCCCCAAGGGGTACC
*
1108480 GATTCCCCCCCAGGGGGTACC
1 GATTCCCCCCCAAGGGGTACC
*
1108501 AATTCCCCC
1 GATTCCCCC
1108510 TTGTATAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.18
Consensus pattern (21 bp):
GATTCCCCCCCAAGGGGTACC
Found at i:1113470 original size:12 final size:12
Alignment explanation
Indices: 1113441--1113472 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
1113431 GTATTTTCGG
1113441 AGTTACTGTAGC
1 AGTTACTGTAGC
1113453 --TTACTGTAGC
1 AGTTACTGTAGC
1113463 AGTTACTGTA
1 AGTTACTGTA
1113473 AAAGGGGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.56
12 8 0.44
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (12 bp):
AGTTACTGTAGC
Found at i:1113531 original size:13 final size:13
Alignment explanation
Indices: 1113513--1113548 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1113503 CCGATTCCCC
1113513 ACTGTTCA-TGGGT
1 ACTGTTCACT-GGT
1113526 ACTGTTCACTGGT
1 ACTGTTCACTGGT
1113539 ACTGTTCACT
1 ACTGTTCACT
1113549 ATTCATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 21 0.95
14 1 0.05
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (13 bp):
ACTGTTCACTGGT
Found at i:1116299 original size:268 final size:266
Alignment explanation
Indices: 1115805--1116338 Score: 831
Period size: 268 Copynumber: 2.0 Consensus size: 266
1115795 TTTGGTTAAC
* *
1115805 GGTTAAAGAAAAACAATTCGGTTAATTCAGTTAATGGTAATTCGGTTCAGTCTGTGCCGAATTAA
1 GGTTAAAGAAAAACAATTCGGTTAATTCAATTAATGGTAATTCAGTTCAGTCTGTGCCGAATTAA
*
1115870 ACGTTTGAACACCACTATTAGTTTTAGTTGTCATATTTTTATTTTAATATTTAAGTTTTTGATTA
66 ACGTTTGAACACCACTATTAGTTTTAGTGGTCATATTTTTATTTTAATATTTAAGTTTTTGATTA
1115935 TTTTATAAAATTAAGAAATGAAAGTAATTAGAGATATAACAATAATTTTGGTTAACATTAGAATT
131 TTTTATAAAATTAAGAAATGAAAGTAATTAGAGATATAACAATAATTTTGGTTAACATTAGAATT
** * *
1116000 TAAAATATAATGAAATTGTATTATGTGAAGATATATTATAAAGCAAGATTATTTGAAATATATAT
196 TAAAATATAATGAAATTGTATTACATGAAGATATATTATAAAACAAAATTATTTGAAATATATAT
1116065 TATAGA
261 TATAGA
* ** *
1116071 GGTTAAATAAATAA-AAGTTCGGTTAATTCAATTAATGGTAATTCAGTTTGGTC-GATGGTCGAA
1 GGTTAAAGAAA-AACAA-TTCGGTTAATTCAATTAATGGTAATTCAGTTCAGTCTG-T-GCCGAA
** *
1116134 TTAATTGTTTGAACACC-CTATTAGTTTTAGTGGTCATCTTTTTTATTTTAATATTTAAGTTTTT
62 TTAAACGTTTGAACACCACTATTAGTTTTAGTGGTCAT-ATTTTTATTTTAATATTTAAGTTTTT
* * * *
1116198 GGTTATTTTATAAAATTAAGAAATGAAAGTAATTATAGATATAGCAATAATTTTGGTTAAGATTA
126 GATTATTTTATAAAATTAAGAAATGAAAGTAATTAGAGATATAACAATAATTTTGGTTAACATTA
*
1116263 GAATTTAAATTATAATGAAATTGTATTACATGAAGATATATTATAAAACAAAATTATTTGAAATA
191 GAATTTAAAATATAATGAAATTGTATTACATGAAGATATATTATAAAACAAAATTATTTGAAATA
1116328 TATATTATAGA
256 TATATTATAGA
1116339 AGATAAAGTA
Statistics
Matches: 244, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
266 13 0.05
267 54 0.22
268 177 0.73
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (266 bp):
GGTTAAAGAAAAACAATTCGGTTAATTCAATTAATGGTAATTCAGTTCAGTCTGTGCCGAATTAA
ACGTTTGAACACCACTATTAGTTTTAGTGGTCATATTTTTATTTTAATATTTAAGTTTTTGATTA
TTTTATAAAATTAAGAAATGAAAGTAATTAGAGATATAACAATAATTTTGGTTAACATTAGAATT
TAAAATATAATGAAATTGTATTACATGAAGATATATTATAAAACAAAATTATTTGAAATATATAT
TATAGA
Found at i:1122296 original size:45 final size:45
Alignment explanation
Indices: 1122224--1122413 Score: 283
Period size: 45 Copynumber: 4.2 Consensus size: 45
1122214 AAATGAATGA
*
1122224 ATAAATGAAATGCATAATGGTGCATTAACGACATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTAACGACATGAAAGGATGCC
* *
1122269 ATAAATGAAATGCATAACGGTGTATTAACAACATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTAACGACATGAAAGGATGCC
* *
1122314 ATAAATGAAATGCATAACGGTGCATTAACGGCATGAAAGGATGTC
1 ATAAATGAAATGCATAACGGTGCATTAACGACATGAAAGGATGCC
* * * *
1122359 ATAAATGAAATGCATAACAGTGCATTATAAG-CATGAAACGATGCT
1 ATAAATGAAATGCATAACGGTGCATTA-ACGACATGAAAGGATGCC
1122404 ATAAATGAAA
1 ATAAATGAAA
1122414 ATAAATGATA
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
45 130 0.98
46 2 0.02
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.23
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTAACGACATGAAAGGATGCC
Found at i:1127113 original size:45 final size:45
Alignment explanation
Indices: 1127062--1127251 Score: 301
Period size: 45 Copynumber: 4.2 Consensus size: 45
1127052 AGATGAATGA
*
1127062 ATAAATGAAATACATAACGGTGCATTAACGACATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTAACGACATGAAAGGATGCC
* *
1127107 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTAACGACATGAAAGGATGCC
* *
1127152 ATAAATGAAATGCATAACGGTGTATTAACGACATGAAAGGATACC
1 ATAAATGAAATGCATAACGGTGCATTAACGACATGAAAGGATGCC
* *
1127197 ATAAATGAAATGCATAACGGTGCATTATAAG-CATGAAAGGATGCT
1 ATAAATGAAATGCATAACGGTGCATTA-ACGACATGAAAGGATGCC
1127242 ATAAATGAAA
1 ATAAATGAAA
1127252 ATAAAGGATA
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 131 0.98
46 2 0.02
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTAACGACATGAAAGGATGCC
Found at i:1134334 original size:68 final size:68
Alignment explanation
Indices: 1134253--1134386 Score: 223
Period size: 68 Copynumber: 2.0 Consensus size: 68
1134243 TGCTACTCAG
* * **
1134253 CAATACTAATGCTATCAAAAGTGCACAACAAATCAATTACGTATATTTCTAGAAAATAATTGAAA
1 CAATACCAATGCTATCAAAAGTGCACAACAAATCAATCAAATATATTTCTAGAAAATAATTGAAA
1134318 AAA
66 AAA
*
1134321 CAATACCAATGCTATCAAAAGTGTACAACAAATCAATCAAATATATTTCTAGAAAATAATTGAAA
1 CAATACCAATGCTATCAAAAGTGCACAACAAATCAATCAAATATATTTCTAGAAAATAATTGAAA
1134386 A
66 A
1134387 CACCATACTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (68 bp):
CAATACCAATGCTATCAAAAGTGCACAACAAATCAATCAAATATATTTCTAGAAAATAATTGAAA
AAA
Found at i:1138869 original size:5 final size:5
Alignment explanation
Indices: 1138859--1138887 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1138849 ACTCATACAC
1138859 ATCAT ATCAT ATCAT ATCAT ATCAT ATCA
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCA
1138888 CCAAACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (5 bp):
ATCAT
Found at i:1139111 original size:22 final size:22
Alignment explanation
Indices: 1139045--1139111 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
1139035 GGCATATGAA
*
1139045 ATATGTCCCAAAGGACCTATGC
1 ATATGTCCCAAAGGACCTATGT
* * *
1139067 ACATGTCCCAAAGGACATGTGT
1 ATATGTCCCAAAGGACCTATGT
1139089 ATATGTCCCGAAA-GACCTATGT
1 ATATGTCCC-AAAGGACCTATGT
1139111 A
1 A
1139112 ACCCTCGACT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
22 34 0.92
23 3 0.08
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (22 bp):
ATATGTCCCAAAGGACCTATGT
Found at i:1150375 original size:19 final size:21
Alignment explanation
Indices: 1150343--1150394 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1150333 TGCAAAAATG
* *
1150343 GTATCGATATCGTA-ATA-TA
1 GTATCAATACCGTAGATAGTA
1150362 GTATCAATACCGTAGTATAGTA
1 GTATCAATACCGTAG-ATAGTA
1150384 GTATCAATACC
1 GTATCAATACC
1150395 ATGGTAGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
21 3 0.11
22 13 0.46
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (21 bp):
GTATCAATACCGTAGATAGTA
Found at i:1150807 original size:57 final size:57
Alignment explanation
Indices: 1150739--1150901 Score: 249
Period size: 57 Copynumber: 2.9 Consensus size: 57
1150729 CAAATGGCAC
* ** * *
1150739 TGTGTGTAAAAAGTTAAGAAATTTGTACTAAGTGTATGAATTTTTGTATGGGCACTT
1 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGGCACTA
* *
1150796 TGTGTGCAAAAAGTTAAGAAATTCATATTAAGTGTATGAATTTCCGTATGGGCACTA
1 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGGCACTA
1150853 TGTGTGC-AAAA-TTAAGAAATTCATACTAAGTGTATGAATTTTCGTATGG
1 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATGG
1150902 AAACTATATG
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
55 36 0.37
56 4 0.04
57 57 0.59
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (57 bp):
TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGGCACTA
Found at i:1150924 original size:55 final size:55
Alignment explanation
Indices: 1150734--1150937 Score: 232
Period size: 55 Copynumber: 3.7 Consensus size: 55
1150724 ATTACCAAAT
* * ** *
1150734 GGCACTGTGTGT-AAAAAGTTAAGAAATTTGTACTAAGTGTATGAATTTTTGTATG
1 GGCACTATGTGTGCAAAA-TTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * *
1150789 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATATTAAGTGTATGAATTTCCGTATG
1 GGCACTATGTGTGC-AAAA-TTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
1150846 GGCACTATGTGTGCAAAATTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
1 GGCACTATGTGTGCAAAATTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
** * * * *
1150901 GAAACTATATGTGTAGACA-TAAGAAATTCATAATAAG
1 GGCACTATGTGTGCA-AAATTAAGAAATTCATACTAAG
1150938 GAGGTGGATT
Statistics
Matches: 130, Mismatches: 16, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
55 74 0.57
56 6 0.05
57 50 0.38
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (55 bp):
GGCACTATGTGTGCAAAATTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
Found at i:1156614 original size:30 final size:30
Alignment explanation
Indices: 1156569--1156641 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1156559 TGATATGTTA
* *
1156569 AGATATGATTGTTTATTGATGTTTACTAGT
1 AGATTTGAGTGTTTATTGATGTTTACTAGT
1156599 AGATTTGAGTGTTTATTGATGTTTACTAGT
1 AGATTTGAGTGTTTATTGATGTTTACTAGT
1156629 AGATTTGACGTGT
1 AGATTTGA-GTGT
1156642 CAAAGAGGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 36 0.90
31 4 0.10
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (30 bp):
AGATTTGAGTGTTTATTGATGTTTACTAGT
Found at i:1157061 original size:19 final size:21
Alignment explanation
Indices: 1157037--1157090 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
1157027 TGCAAAAATG
1157037 GTATCGATACCATA-ATAG-A
1 GTATCGATACCATAGATAGTA
*
1157056 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
*
1157078 GTATCAATACCAT
1 GTATCGATACCAT
1157091 CGTAGGGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 13 0.45
21 4 0.14
22 12 0.41
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:1157488 original size:57 final size:57
Alignment explanation
Indices: 1157426--1157766 Score: 517
Period size: 57 Copynumber: 6.0 Consensus size: 57
1157416 ATTACCAAAT
* * *
1157426 GGCACTTTGTGTGTAAAAAGTTAAGAAATTCATGCTAAGTGTATGAATTTTTGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * *
1157483 GGCACTTTATGTGCAAAAGGTTAAGAAATTCATACTAAGTGTATGAATTTT-GTATA
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * *
1157539 GGCACTTTATGTACAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
*
1157596 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * *
1157653 GGCACTTTGTGTGCAAAAAGTTAAGAAGTTCATACTAAGTGTATAAATTTTCCTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * *
1157710 GGCACTATGTGTG-TAAAA-TTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
1157765 GG
1 GG
1157767 TACTATATGT
Statistics
Matches: 260, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
55 35 0.13
56 56 0.22
57 169 0.65
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (57 bp):
GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
Found at i:1157624 original size:113 final size:113
Alignment explanation
Indices: 1157426--1157757 Score: 508
Period size: 113 Copynumber: 2.9 Consensus size: 113
1157416 ATTACCAAAT
* * **
1157426 GGCACTTTGTGTGTAAAAAGTTAAGAAATTCATGCTAAGTGTATGAATTTTTGTATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
* *
1157491 ATGTGCAAAAGGTTAAGAAATTCATACTAAGTGTATGAATTTTGTATA
66 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTGTATA
* *
1157539 GGCACTTTATGTACAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
*
1157604 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATG
66 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAA-TTTTGTATA
* * *
1157653 GGCACTTTGTGTGCAAAAAGTTAAGAAGTTCATACTAAGTGTATAAATTTTCC-TATGGGCACTA
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAA-TTTCCGTATGGGCACTT
*
1157717 TGTGTG-TAAAA-TTAAGAAATTCATACTAAGTGTATGAATTT
65 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTT
1157758 CCGTATGGGT
Statistics
Matches: 202, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
111 3 0.01
112 27 0.13
113 100 0.50
114 67 0.33
115 5 0.02
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (113 bp):
GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTGTATA
Found at i:1157625 original size:170 final size:169
Alignment explanation
Indices: 1157426--1157766 Score: 549
Period size: 170 Copynumber: 2.0 Consensus size: 169
1157416 ATTACCAAAT
* *
1157426 GGCACTTTGTGTGTAAAAAGTTAAGAAATTCATGCTAAGTGTATGAATTTTTGTATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTTT
* * * *
1157491 ATGTGCAAAAGGTTAAGAAATTCATACTAAGTGTATGAATTTT-GTATAGGCACTTTATGTACAA
66 ATGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATAAATTTTCCTATAGGCACTATATGT-CAA
1157555 AAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
130 AAA-TTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1157596 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTTT
* * * * **
1157661 GTGTGCAAAAAGTTAAGAAGTTCATACTAAGTGTATAAATTTTCCTATGGGCACTATGTGTGTAA
66 ATGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATAAATTTTCCTATAGGCACTATATGTCAAA
1157726 AATTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
131 AATTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1157765 GG
1 GG
1157767 TACTATATGT
Statistics
Matches: 158, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
169 39 0.25
170 106 0.67
171 13 0.08
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (169 bp):
GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTTT
ATGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATAAATTTTCCTATAGGCACTATATGTCAAA
AATTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
Found at i:1163832 original size:21 final size:21
Alignment explanation
Indices: 1163790--1163828 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1163780 CATTAAGGCC
*
1163790 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCATGAAATCT
*
1163811 TTTGTCGAGGCCAT-AAAT
1 TTTGTCGAAGCCATGAAAT
1163829 TCTTGCAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (21 bp):
TTTGTCGAAGCCATGAAATCT
Found at i:1179437 original size:21 final size:21
Alignment explanation
Indices: 1179413--1179459 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1179403 ACTACAGGAA
* *
1179413 TTAATGGCCTCGACAAAAAAT
1 TTAATGGCCTCAACAAAAAAC
* *
1179434 TTAATGGCTTCAACAAAGAAC
1 TTAATGGCCTCAACAAAAAAC
1179455 TTAAT
1 TTAAT
1179460 ACACGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.28
Consensus pattern (21 bp):
TTAATGGCCTCAACAAAAAAC
Found at i:1190559 original size:79 final size:76
Alignment explanation
Indices: 1190433--1190576 Score: 175
Period size: 79 Copynumber: 1.9 Consensus size: 76
1190423 TAAAATATTG
* *
1190433 TTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTGAATTATAATC-TTTAATGTTTA
1 TTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTTTAATGTTTA
1190497 TTTAAAACTTA
66 TTTAAAACTTA
* * * *
1190508 TTTAATT-ATTCTGAATTATATATACCAATTAAAAGAGTTGTAATCTAAATTACATTCTTTTAAT
1 TTTAATTAATTC--AATTAAATATA-C-ATT-AAAGACTTATAATCTAAATTACAATCTTTTAAT
1190572 GTTTA
61 GTTTA
1190577 CTTACTATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
74 4 0.07
75 7 0.12
76 10 0.18
77 1 0.02
78 3 0.05
79 21 0.37
80 11 0.19
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (76 bp):
TTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTTTAATGTTTA
TTTAAAACTTA
Found at i:1198647 original size:36 final size:36
Alignment explanation
Indices: 1198607--1198681 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
1198597 ATGGCCATTC
1198607 ATTTCTAGTCTCACTCAATAAAGTGGCATGTGATAT
1 ATTTCTAGTCTCACTCAATAAAGTGGCATGTGATAT
1198643 ATTTCTAGTCTCACTCAATAAAGTGGCATGTGATAT
1 ATTTCTAGTCTCACTCAATAAAGTGGCATGTGATAT
1198679 ATT
1 ATT
1198682 CAACAACAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (36 bp):
ATTTCTAGTCTCACTCAATAAAGTGGCATGTGATAT
Found at i:1213670 original size:20 final size:20
Alignment explanation
Indices: 1213634--1213671 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1213624 ATCCTATTCC
**
1213634 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1213654 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1213672 ATGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1217007 original size:54 final size:54
Alignment explanation
Indices: 1216939--1217602 Score: 815
Period size: 54 Copynumber: 12.4 Consensus size: 54
1216929 CTAAGTGTAC
* * * * * **
1216939 TATAGGCACTATGTGTGTAACCCACGGAATTTATCATATGTTAATGAACAACTA
1 TATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * * *
1216993 TATAGGCACCATGTGTGCAACCCATGGAATTCATCATATGTTGCTGAACAACCG
1 TATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * * * *
1217047 TATAGGCACTATGTGTACAACCCAC-AGAATTAATCATATGTTGTTAAATGATCG
1 TATAGGCACTATGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
*
1217101 TCTAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
** ***
1217155 TATACACACTATGTGCATAACCCACGAAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * * * *
1217209 TATAGGCACTATGTTTGCAACCAACAAAAGTCATCATATATTGATGAACAACCG
1 TATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * * *
1217263 TATATGCACTATGTTTGCAACCAAC-AGAATTCATCATATGTTGATGAACAACCA
1 TATAGGCACTATGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
* * *
1217317 TATAGGCACTATATGTGCAACCAACGAAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
1217371 TATAAGAACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * *
1217425 TATAGGCACTATATGTGCATCCCACAAAATTCATCATATGTTGATGAACGACTG
1 TATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* *
1217479 TATAGGCACAATGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
1217533 TATAGGCACTA--TGTG----CCAC-ATAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTATGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
1217581 TATAGGCACTATGTGTGCAACC
1 TATAGGCACTATGTGTGCAACC
1217603 TCTTTTAAAT
Statistics
Matches: 531, Mismatches: 68, Indels: 22
0.86 0.11 0.04
Matches are distributed among these distances:
47 1 0.00
48 42 0.08
50 4 0.01
52 4 0.01
53 1 0.00
54 477 0.90
55 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (54 bp):
TATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
Found at i:1217167 original size:27 final size:27
Alignment explanation
Indices: 1217137--1217223 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
1217127 AAATTCATCA
1217137 TATGTTGATGAACGACCGTATACACAC
1 TATGTTGATGAACGACCGTATACACAC
* * *
1217164 TATG-TGCAT-AAC-CCACGAAATTCATCA-
1 TATGTTG-ATGAACGAC-CG-TATACA-CAC
**
1217191 TATGTTGATGAACGACCGTATAGGCAC
1 TATGTTGATGAACGACCGTATACACAC
1217218 TATGTT
1 TATGTT
1217224 TGCAACCAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 16
0.65 0.12 0.24
Matches are distributed among these distances:
25 1 0.02
26 9 0.20
27 24 0.55
28 9 0.20
29 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (27 bp):
TATGTTGATGAACGACCGTATACACAC
Found at i:1217695 original size:48 final size:47
Alignment explanation
Indices: 1217625--1217797 Score: 177
Period size: 48 Copynumber: 3.6 Consensus size: 47
1217615 CTAATGGTGT
*
1217625 ATTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGAAAATGATGC
1 ATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAATGATGC
** ** * *
1217672 ATTCTTGGCAGAAAGGTATCACTAATGCAAGTTA-ACCACCTAATGATAC
1 ATT-TTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA--AAATGATGC
* * *
1217721 ATTTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAGAACGGTGC
1 ATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAA-AATGATGC
*
1217769 ATTATTGGCATGAAAGGATGCCACAAATG
1 ATT-TTGGCA-GAAAGG-TGCCACTAATG
1217798 AAAATACATA
Statistics
Matches: 100, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
47 5 0.05
48 62 0.62
49 18 0.18
50 6 0.06
51 9 0.09
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.25
Consensus pattern (47 bp):
ATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAATGATGC
Found at i:1223163 original size:54 final size:54
Alignment explanation
Indices: 1223096--1223876 Score: 1073
Period size: 54 Copynumber: 14.4 Consensus size: 54
1223086 CTAAGTGTAC
* * * * *
1223096 TATAGGCATTATGTGTGCAACCCACGGAATTCATCATATGTTGATAAACGATCA
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * *
1223150 TATAGGCACTATGTATACAA-CCACAAAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* *
1223203 TATAGGCACTATGTGTGGAACCCACAGAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * * *
1223257 TATAGACACTATATGTGCAATCCACGGAATTCATCATATGTTGATGAACGACTG
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * *
1223311 TATAGGCACTATGCGTGCAACCCACAGAA-TAATCATATATTGATGAATGACCG
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * *
1223364 TATAGGCACTATGTTTGCAACCTACAAAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
*
1223418 TATAGGCACTATGTGTGCAACCCATAGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* *
1223472 TATAGGCACTATGTGTGTAACCCA-AGGAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTATGTGTGCAACCCACA-GAATTCATCATATGTTGATGAACGACCG
* *
1223526 TATAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGACCGACCG
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * *
1223580 TATAGGCACTATATGTGCAACCCACGGAATTCATCGTATGTTGATGAACGACCG
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * *
1223634 TATATGCACTATGTTTGCAACCAACAGAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * * * * *
1223688 TATAGGCATTATGTGTGCAACCTAAAAAATTCATCATATCTTGATAAACGACCA
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* *
1223742 TATAGGCACTATGCATGTGTGCAACCCACAGAATTCATCATATGTTAATGAACAACCG
1 TATAGGCAC--T--ATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * *
1223800 TATAGGCACTATGCGTGCAACCCACGGAATTTATCATATGTTGATGAACGACCG
1 TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
*
1223854 TATAGGCACTATATGTGCAACCC
1 TATAGGCACTATGTGTGCAACCC
1223877 CTTTTAAATG
Statistics
Matches: 639, Mismatches: 80, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
53 91 0.14
54 501 0.78
56 2 0.00
58 45 0.07
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (54 bp):
TATAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
Found at i:1223430 original size:27 final size:27
Alignment explanation
Indices: 1223400--1223485 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
1223390 AAATTCATCA
1223400 TATGTTGATGAACGACCGTATAGGCAC
1 TATGTTGATGAACGACCGTATAGGCAC
* * **
1223427 TATG-TG-TGCAAC--CCATAGAATTCATC
1 TATGTTGATG-AACGACCGTA-TAGGCA-C
1223453 ATATGTTGATGAACGACCGTATAGGCAC
1 -TATGTTGATGAACGACCGTATAGGCAC
1223481 TATGT
1 TATGT
1223486 GTGTAACCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
24 4 0.09
25 5 0.12
26 6 0.14
27 13 0.30
28 6 0.14
29 5 0.12
30 4 0.09
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (27 bp):
TATGTTGATGAACGACCGTATAGGCAC
Found at i:1223538 original size:27 final size:27
Alignment explanation
Indices: 1223400--1223539 Score: 64
Period size: 27 Copynumber: 5.2 Consensus size: 27
1223390 AAATTCATCA
*
1223400 TATGTTGATGAACGACCGTATAGGCAC
1 TATGTTGATGAACGACCATATAGGCAC
* **
1223427 TATG-TG-TGCAAC--CCATAGAATTCATC
1 TATGTTGATG-AACGACCATA-TAGGCA-C
*
1223453 ATATGTTGATGAACGACCGTATAGGCAC
1 -TATGTTGATGAACGACCATATAGGCAC
* **
1223481 TATG-TG-TGTAAC--CCA-AGGAATTCATC
1 TATGTTGATG-AACGACCATA--TAGGCA-C
1223507 ATATGTTGATGAACGACCATATAGGCAC
1 -TATGTTGATGAACGACCATATAGGCAC
1223535 TATGT
1 TATGT
1223540 GTGCAACCCA
Statistics
Matches: 80, Mismatches: 15, Indels: 36
0.61 0.11 0.27
Matches are distributed among these distances:
23 1 0.01
24 6 0.08
25 10 0.12
26 12 0.15
27 21 0.26
28 12 0.15
29 10 0.12
30 7 0.09
31 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (27 bp):
TATGTTGATGAACGACCATATAGGCAC
Found at i:1224040 original size:49 final size:48
Alignment explanation
Indices: 1223892--1224046 Score: 168
Period size: 49 Copynumber: 3.2 Consensus size: 48
1223882 AAATGCCTAG
* * * *
1223892 CGGTGCATTTTTTGCAAAAAGGTGCTACTAATGCAAGTTAGATGAAAA
1 CGGTGCATTTTTGGCAGAAAGGTGCCACTAATACAAGTTAGATGAAAA
* * ** * * * *
1223940 TGATGTGTTCTTGGTAGAAAGGTGCCACTAATACAAGTTAAAT-ATCTAA
1 CGGTGCATTTTTGGCAGAAAGGTGCCACTAATACAAGTTAGATGA--AAA
1223989 CGGTGCATTTTTGGCAGAAAGGTGCCACTAATACAAGTTAGATGAAGAA
1 CGGTGCATTTTTGGCAGAAAGGTGCCACTAATACAAGTTAGATGAA-AA
1224038 CGGTGCATT
1 CGGTGCATT
1224047 ATCAGCTTGA
Statistics
Matches: 83, Mismatches: 20, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
47 1 0.01
48 32 0.39
49 49 0.59
50 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (48 bp):
CGGTGCATTTTTGGCAGAAAGGTGCCACTAATACAAGTTAGATGAAAA
Found at i:1231451 original size:24 final size:25
Alignment explanation
Indices: 1231406--1231452 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1231396 ATAGGCTGAG
* *
1231406 TTACAACATTGAGTCTTACTAGGAT
1 TTACAACATCGAGTCCTACTAGGAT
*
1231431 TTACAACA-CGAGTCCTGCTAGG
1 TTACAACATCGAGTCCTACTAGG
1231453 TGTTTACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (25 bp):
TTACAACATCGAGTCCTACTAGGAT
Found at i:1232727 original size:17 final size:17
Alignment explanation
Indices: 1232705--1232737 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1232695 TTTATTTTAT
1232705 TAAAAAAATAAAGATAG
1 TAAAAAAATAAAGATAG
*
1232722 TAAAAATATAAAGATA
1 TAAAAAAATAAAGATA
1232738 TTATTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
TAAAAAAATAAAGATAG
Found at i:1233279 original size:20 final size:20
Alignment explanation
Indices: 1233254--1233292 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1233244 AAAGGATAAA
1233254 TAAAAA-AAGACCAAAGAACT
1 TAAAAATAAG-CCAAAGAACT
*
1233274 TAAAAATATGCCAAAGAAC
1 TAAAAATAAGCCAAAGAAC
1233293 ATAAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.62, C:0.15, G:0.10, T:0.13
Consensus pattern (20 bp):
TAAAAATAAGCCAAAGAACT
Found at i:1233758 original size:19 final size:20
Alignment explanation
Indices: 1233735--1233779 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
1233725 TTATTCAGGC
1233735 TTGATAATTTTATTGATTTG
1 TTGATAATTTTATTGATTTG
* *
1233755 -TGAT-GTTTTATTGGTTTG
1 TTGATAATTTTATTGATTTG
1233773 TTGATAA
1 TTGATAA
1233780 CAAAATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 4
0.74 0.11 0.15
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.58
Consensus pattern (20 bp):
TTGATAATTTTATTGATTTG
Found at i:1234193 original size:12 final size:12
Alignment explanation
Indices: 1234176--1234220 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
1234166 TCAGAACTAT
1234176 TATATTTATATA
1 TATATTTATATA
1234188 TATA-TTAT-TA
1 TATATTTATATA
1234198 TATAATTTATAT-
1 TAT-ATTTATATA
*
1234210 TATTTTTATAT
1 TATATTTATAT
1234221 TAACATTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 5 0.17
11 12 0.41
12 11 0.38
13 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTTATATA
Found at i:1234195 original size:17 final size:16
Alignment explanation
Indices: 1234173--1234220 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1234163 TAATCAGAAC
1234173 TATTATATTTATATATA
1 TATTAT-TTTATATATA
* *
1234190 TATTATTATATAATTTA
1 TATTATTTTAT-ATATA
1234207 TATTATTTT-TATAT
1 TATTATTTTATATAT
1234221 TAACATTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 5 0.19
17 18 0.69
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATTTTATATATA
Found at i:1234198 original size:20 final size:18
Alignment explanation
Indices: 1234173--1234221 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
1234163 TAATCAGAAC
1234173 TATTATATTTATATATATAT
1 TATTATATTT-TATAT-TAT
1234193 TATTATATAATTTATATTAT
1 TATTATAT--TTTATATTAT
*
1234213 TTTTATATT
1 TATTATATT
1234222 AACATTGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.04
20 18 0.69
21 5 0.19
22 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTATATTTTATATTAT
Found at i:1234209 original size:23 final size:20
Alignment explanation
Indices: 1234179--1234220 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
1234169 GAACTATTAT
1234179 ATTTATATATATATTATTATATA
1 ATTTATAT-TAT-TT-TTATATA
1234202 ATTTATATTATTTTTATAT
1 ATTTATATTATTTTTATAT
1234221 TAACATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 2 0.11
22 3 0.16
23 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTATATTATTTTTATATA
Found at i:1241224 original size:23 final size:23
Alignment explanation
Indices: 1241198--1241273 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
1241188 CCATAGCTCG
*
1241198 TATAAATGTACCAAAGTGCCACA
1 TATAAATGCACCAAAGTGCCACA
* * *
1241221 TATAATTACACCGAAGTGCCACA
1 TATAAATGCACCAAAGTGCCACA
* * * *
1241244 TAGAAATGCACCGAAGTTCCATA
1 TATAAATGCACCAAAGTGCCACA
1241267 TA-AAATG
1 TATAAATG
1241274 TCCAAAAGGA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 5 0.11
23 39 0.89
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.22
Consensus pattern (23 bp):
TATAAATGCACCAAAGTGCCACA
Found at i:1252703 original size:23 final size:23
Alignment explanation
Indices: 1252677--1252745 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1252667 CACCACAGCT
1252677 CGTATAAATGCACCGAAGTGCCA
1 CGTATAAATGCACCGAAGTGCCA
* * * *
1252700 CGTAGAATTACACCGAAGTGTCA
1 CGTATAAATGCACCGAAGTGCCA
*
1252723 CGTATAAATGCATCGAAGTGCCA
1 CGTATAAATGCACCGAAGTGCCA
1252746 TATAAAATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (23 bp):
CGTATAAATGCACCGAAGTGCCA
Found at i:1258285 original size:20 final size:20
Alignment explanation
Indices: 1258260--1258298 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1258250 TTTTCAAGGG
1258260 CATGCATCGATGCACCAATC
1 CATGCATCGATGCACCAATC
*
1258280 CATGCATCGATGCATCAAT
1 CATGCATCGATGCACCAAT
1258299 TAATTTCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (20 bp):
CATGCATCGATGCACCAATC
Found at i:1258349 original size:26 final size:26
Alignment explanation
Indices: 1258318--1258369 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1258308 GAACATCGAA
*
1258318 TGCATTTTATGCATCGATACACTCAG
1 TGCATTTGATGCATCGATACACTCAG
*
1258344 TGCATTTGATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATACACTCAG
1258370 GCTTTTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (26 bp):
TGCATTTGATGCATCGATACACTCAG
Found at i:1266086 original size:45 final size:46
Alignment explanation
Indices: 1266037--1266125 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 46
1266027 ACATCGAATA
* *
1266037 CATTTTATGCATCGATGCAC-ATACCATGCATCGATGAACTCAGTG
1 CATTTGATGCATCGATGCACAAGACCATGCATCGATGAACTCAGTG
* * *
1266082 CATTTGATGCATCGATGCACAAGACTATGTATCGATGCACTCAG
1 CATTTGATGCATCGATGCACAAGACCATGCATCGATGAACTCAG
1266126 GCTTTTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
45 19 0.50
46 19 0.50
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (46 bp):
CATTTGATGCATCGATGCACAAGACCATGCATCGATGAACTCAGTG
Found at i:1266253 original size:21 final size:21
Alignment explanation
Indices: 1266227--1266277 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1266217 TACACTGATA
1266227 CATCGATGCACCACGGGTATG
1 CATCGATGCACCACGGGTATG
*
1266248 CATCGATGCACCATGGGTATG
1 CATCGATGCACCACGGGTATG
1266269 CATCGATGC
1 CATCGATGC
1266278 GCTGACGCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (21 bp):
CATCGATGCACCACGGGTATG
Found at i:1280470 original size:18 final size:18
Alignment explanation
Indices: 1280439--1280486 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1280429 AATTCAAGTA
*
1280439 GTATCGATACTATTATGG
1 GTATCAATACTATTATGG
*
1280457 GTATCAATATTATTATGG
1 GTATCAATACTATTATGG
*
1280475 GTATCGATACTA
1 GTATCAATACTA
1280487 AGAGGAAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (18 bp):
GTATCAATACTATTATGG
Found at i:1282078 original size:81 final size:81
Alignment explanation
Indices: 1281973--1282492 Score: 664
Period size: 81 Copynumber: 6.4 Consensus size: 81
1281963 ACATCGTTTA
* * * * * * * *
1281973 TGTCAAAATGCATTGTTAAGCATTTAGTCTTTTACCCAAAGGTATTTAGCCTTTCATCTAACTTG
1 TGTC-AAATGCATAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGG
*
1282038 CATGATTGACACCTTTC
65 CATAATTGACACCTTTC
* * * * * * **
1282055 TGCCAAATGCATAGCTAGGCATTTAATCTTTAACTTAAAGGCATTTAGCCTTTCATCTAACTTAC
1 TGTCAAATGCATAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGC
* *
1282120 ATAGTTGACACCTTTT
66 ATAATTGACACCTTTC
* * * *
1282136 TGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGTATTCAACCATTCATCTAACTGGC
1 TGTCAAATGCATAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGC
1282201 ATAATTGACACCTTTC
66 ATAATTGACACCTTTC
* * *
1282217 TGTCAAATGCACAGCTAGGTAATTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGC
1 TGTCAAATGCATAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGC
*
1282282 ATAATTGACACATTTC
66 ATAATTGACACCTTTC
* *
1282298 TTTCAAATGCATAGCTAGGTAATTAATCTTTTACTCAAAGGTATTTAACAC-TTCATCTAACTGG
1 TGTCAAATGCATAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC-CTTTCATCTAACTGG
1282362 CATAATTGACACCTTTC
65 CATAATTGACACCTTTC
* ** * * * *
1282379 TGACAAATGCATAGCTAGGTTATTAATCATTTACTCAAAGTTATTTAACATTTTATCTAACTGGC
1 TGTCAAATGCATAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGC
1282444 ATAATTGACACCTTTC
66 ATAATTGACACCTTTC
* * *
1282460 TGTTAAATGCACAACTAGGCAATTAATCTTTTA
1 TGTCAAATGCATAGCTAGGCAATTAATCTTTTA
1282493 TTTAAAATAG
Statistics
Matches: 385, Mismatches: 51, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
81 381 0.99
82 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (81 bp):
TGTCAAATGCATAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGC
ATAATTGACACCTTTC
Found at i:1288844 original size:81 final size:80
Alignment explanation
Indices: 1288740--1289259 Score: 626
Period size: 81 Copynumber: 6.4 Consensus size: 80
1288730 ACACTATTTA
* * * * * ** * * *
1288740 TGTCAAAATGCACAGTTAAGCATTTAGTCTTTTACCCAAACACGTTTAGCCTTTCATCTAACTTG
1 TGTC-AAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGG
*
1288805 CATGATTGACACCATTC
65 CATAATTGACA-CATTC
* * * * * *
1288822 TGTCAAATGCACATCTAGGCATTTAATCTTTAACTAAAAGGCATTTAGCCTTTCATATAACTGGC
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGC
** *
1288887 ATAATTGACATTTTTT
66 ATAATTGACA-CATTC
* * * * *
1288903 TCTCAAATGCACAGCTAGGCAATTAATCTTTTACTAAAAGGTATTTAACCTTTCATCTAATTGTC
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGC
1288968 ATAATTGACACATTTC
66 ATAATTGACACA-TTC
*
1288984 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAAATGGC
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGC
*
1289049 ATAATTAACACATTTC
66 ATAATTGACACA-TTC
* * *
1289065 TGTCAAATGCACAGCTAGGCAATTAATCTTTTATTCAAATGTATTTAACCTTTCATCTAACTGGC
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGC
*
1289130 ATAATTGACACTTTTC
66 ATAATTGACAC-ATTC
* * * *
1289146 TGTCAAATGCACATCTATGCACTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGC
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGC
* *
1289211 ATAATTAACATCTTTC
66 ATAATTGACA-CATTC
*
1289227 TGTCAAATGCACAACTAGGCAATTAATCATTTT
1 TGTCAAATGCACAGCTAGGCAATTAATC-TTTT
1289260 TTTAAAACAG
Statistics
Matches: 384, Mismatches: 50, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
81 375 0.98
82 9 0.02
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (80 bp):
TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGC
ATAATTGACACATTC
Found at i:1289174 original size:243 final size:243
Alignment explanation
Indices: 1288729--1289259 Score: 697
Period size: 243 Copynumber: 2.2 Consensus size: 243
1288719 ATCAATAAAC
* * * * * * *
1288729 GACACTATTTATGTCAAAATGCACAGTTAAGCATTTAGTCTTTTACCCAAACACGTTTAGCCTTT
1 GACAC-ATTTCTGTC-AAATGCACAGCTAGGCAATTAATCTTTTACCCAAACACATTTAACCTTT
* * * * * *
1288794 CATCTAACTTGCATGATTGACACCATTCTGTCAAATGCACATCTAGGCATTTAATCTTTAACTAA
64 CATCTAAATGGCATAATTAACACCATTCTGTCAAATGCACAGCTAGGCAATTAATCTTTAACTAA
* * *
1288859 AAGGCATTTAGCCTTTCATATAACTGGCATAATTGACATTTTTTTCTCAAATGCACAGCTAGGCA
129 AAGGCATTTAACCTTTCATATAACTGGCATAATTGACACTTTTCTCTCAAATGCACAGCTAGGCA
* *
1288924 ATTAATCTTTTACTAAAAGGTATTTAACCTTTCATCTAATTGTCATAATT
194 ATTAATCTTTTACTAAAAGGTATTTAACCTTTCATCTAACTGGCATAATT
* **
1288974 GACACATTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAACCTTTCA
1 GACACATTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACCCAAACACATTTAACCTTTCA
* * *
1289039 TCTAAATGGCATAATTAACA-CATTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTATTCAA
66 TCTAAATGGCATAATTAACACCA-TTCTGTCAAATGCACAGCTAGGCAATTAATCTTTAACTAAA
* * * * * * *
1289103 ATGTATTTAACCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACATCTATGCAC
130 AGGCATTTAACCTTTCATATAACTGGCATAATTGACACTTTTCTCTCAAATGCACAGCTAGGCAA
*
1289168 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATT
195 TTAATCTTTTACTAAAAGGTATTTAACCTTTCATCTAACTGGCATAATT
* *
1289217 AACATC-TTTCTGTCAAATGCACAACTAGGCAATTAATCATTTT
1 GACA-CATTTCTGTCAAATGCACAGCTAGGCAATTAATC-TTTT
1289260 TTTAAAACAG
Statistics
Matches: 249, Mismatches: 34, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
242 2 0.01
243 229 0.92
244 13 0.05
245 5 0.02
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (243 bp):
GACACATTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACCCAAACACATTTAACCTTTCA
TCTAAATGGCATAATTAACACCATTCTGTCAAATGCACAGCTAGGCAATTAATCTTTAACTAAAA
GGCATTTAACCTTTCATATAACTGGCATAATTGACACTTTTCTCTCAAATGCACAGCTAGGCAAT
TAATCTTTTACTAAAAGGTATTTAACCTTTCATCTAACTGGCATAATT
Found at i:1289695 original size:22 final size:22
Alignment explanation
Indices: 1289670--1289718 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1289660 CATGGTATCA
1289670 ATACTTCTATATTGTGGTACCG
1 ATACTTCTATATTGTGGTACCG
1289692 ATACTTCTATATTGTGGTACCG
1 ATACTTCTATATTGTGGTACCG
1289714 ATACT
1 ATACT
1289719 CCCTTTCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (22 bp):
ATACTTCTATATTGTGGTACCG
Found at i:1289824 original size:94 final size:95
Alignment explanation
Indices: 1289690--1289867 Score: 279
Period size: 94 Copynumber: 1.9 Consensus size: 95
1289680 ATTGTGGTAC
* *
1289690 CGATACTTCTATATTGTGGTACCGATACTCCCTTTCAGTATCGATACCATTTCT-ACATTCT-GG
1 CGATACTTCTATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTT-TGACATTCTAGA
*
1289753 ATCTATGGTATCGATACTTTTCTTCAAGTAT
65 ATCCATGGTATCGATACTTTTCTTCAAGTAT
* **
1289784 CGATACTTCTATATTATGGTACTGATACTCCCTTTCAGTATCGATACCATTTTGGTATTCTAGAA
1 CGATACTTCTATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTTGACATTCTAGAA
1289849 TCCATGGTATCGATACTTT
66 TCCATGGTATCGATACTTT
1289868 CCTTTTTGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
93 1 0.01
94 55 0.72
95 20 0.26
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (95 bp):
CGATACTTCTATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTTGACATTCTAGAA
TCCATGGTATCGATACTTTTCTTCAAGTAT
Found at i:1290941 original size:59 final size:59
Alignment explanation
Indices: 1290814--1290942 Score: 168
Period size: 59 Copynumber: 2.2 Consensus size: 59
1290804 CGTAGTGCAA
* * * **
1290814 TCCCGAATATGACACATAAGGTCGTGTCCACTATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* * ** *
1290873 TCCCAAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
1290932 TCCCGAATATG
1 TCCCGAATATG
1290943 CAGCCTGCTG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:1296363 original size:20 final size:20
Alignment explanation
Indices: 1296338--1296379 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1296328 TATATTGGGC
* *
1296338 TATTGTAGATTGTTTATGGT
1 TATTGTAGATGGTATATGGT
*
1296358 TATTGTATATGGTATATGGT
1 TATTGTAGATGGTATATGGT
1296378 TA
1 TA
1296380 AGGAATAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (20 bp):
TATTGTAGATGGTATATGGT
Found at i:1296428 original size:24 final size:24
Alignment explanation
Indices: 1296400--1296472 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
1296390 GCAAGTGTAT
1296400 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
* * *
1296424 TGGTACAAAT--G-GTA--AGTATTT
1 TGGTA-AAATAAGCTTACGAG-CTTA
1296445 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
1296469 TGGT
1 TGGT
1296473 TAATAAATGG
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 6 0.17
21 7 0.19
22 3 0.08
23 3 0.08
24 11 0.31
25 6 0.17
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (24 bp):
TGGTAAAATAAGCTTACGAGCTTA
Found at i:1296959 original size:7 final size:7
Alignment explanation
Indices: 1296947--1296982 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1296937 TGCATCGATA
1296947 CACTGTT
1 CACTGTT
1296954 CACTGTT
1 CACTGTT
1296961 -ACTGTT
1 CACTGTT
1296967 CACTGTT
1 CACTGTT
*
1296974 CACTATT
1 CACTGTT
1296981 CA
1 CA
1296983 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.42
Consensus pattern (7 bp):
CACTGTT
Found at i:1296966 original size:13 final size:13
Alignment explanation
Indices: 1296948--1296973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1296938 GCATCGATAC
1296948 ACTGTTCACTGTT
1 ACTGTTCACTGTT
1296961 ACTGTTCACTGTT
1 ACTGTTCACTGTT
1296974 CACTATTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
ACTGTTCACTGTT
Found at i:1299280 original size:6 final size:6
Alignment explanation
Indices: 1299261--1299362 Score: 107
Period size: 6 Copynumber: 16.8 Consensus size: 6
1299251 TATAATATAA
* *
1299261 AAAAAG AAACAG AAAAAG AAAAAG AATGAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG AAAAAG
* * * * * *
1299310 AGAAAG AGAAAG AGAAAA- AAATAG AGAAAG AAAAAG AAAACG AAGAAG
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1299358 AAAAA
1 AAAAA
1299363 AAGAAATAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
5 3 0.04
6 68 0.86
7 8 0.10
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:1303287 original size:24 final size:24
Alignment explanation
Indices: 1303259--1303331 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
1303249 GCAAGTGTAT
1303259 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
* * *
1303283 TGGTACAAAT--G-GTA--AGTATTT
1 TGGTA-AAATAAGCTTACGAG-CTTA
1303304 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
1303328 TGGT
1 TGGT
1303332 TAATAAATGG
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 6 0.17
21 7 0.19
22 3 0.08
23 3 0.08
24 11 0.31
25 6 0.17
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (24 bp):
TGGTAAAATAAGCTTACGAGCTTA
Found at i:1306223 original size:37 final size:36
Alignment explanation
Indices: 1306176--1306247 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
1306166 TAATAGAAAA
*
1306176 AAAGAAATAGA-AAAATAAAGAAGAAAAATAAAAAGAG
1 AAAGAAATAGAGAAAA-AAA-AAGAAAAAGAAAAAGAG
* *
1306213 AAAGAGATAGAGAAAAAAATAGAAAAAGAAAAAGA
1 AAAGAAATAGAGAAAAAAAAAGAAAAAGAAAAAGA
1306248 AAACAAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 14 0.45
37 13 0.42
38 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (36 bp):
AAAGAAATAGAGAAAAAAAAAGAAAAAGAAAAAGAG
Found at i:1306250 original size:6 final size:6
Alignment explanation
Indices: 1306174--1306250 Score: 66
Period size: 6 Copynumber: 12.7 Consensus size: 6
1306164 TATAATAGAA
* * * * * *
1306174 AAAAAG AAATAG AAAAAT AAAGAAG AAAAAT AAAAAG AGAAAG AGATAG
1 AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG
*
1306223 AGAAAA- AAATAG AAAAAG AAAAAG AAAA
1 A-AAAAG AAAAAG AAAAAG AAAAAG AAAA
1306251 CAAAGAAGAA
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
5 3 0.05
6 46 0.82
7 7 0.12
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAAAG
Found at i:1306939 original size:20 final size:20
Alignment explanation
Indices: 1306914--1306958 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1306904 TTGTATATTG
* *
1306914 GGTTATTGTCTATTGTTTAT
1 GGTTATTGTCTATGGTATAT
1306934 GGTTATTGTCTATGGTATAT
1 GGTTATTGTCTATGGTATAT
1306954 GGTTA
1 GGTTA
1306959 ATGAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.04, G:0.24, T:0.53
Consensus pattern (20 bp):
GGTTATTGTCTATGGTATAT
Found at i:1315112 original size:10 final size:10
Alignment explanation
Indices: 1315099--1315213 Score: 58
Period size: 10 Copynumber: 10.7 Consensus size: 10
1315089 ACACGCTGGG
1315099 CATCCGAGGC
1 CATCCGAGGC
1315109 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
*
1315123 CATCCGAAAG-
1 CATCCG-AGGC
1315133 CATCCGAGGC
1 CATCCGAGGC
1315143 CATCCGAGAG-
1 CATCCGAG-GC
1315153 CATCCGACCGAGGC
1 CAT----CCGAGGC
*
1315167 CATCCGAAAG-
1 CATCCG-AGGC
*
1315177 CATCCAAGGC
1 CATCCGAGGC
1315187 CATCCGAGAG-
1 CATCCGAG-GC
*
1315197 CATCTGAGGC
1 CATCCGAGGC
1315207 CATCCGA
1 CATCCGA
1315214 CCGAGGCCAT
Statistics
Matches: 81, Mismatches: 8, Indels: 32
0.67 0.07 0.26
Matches are distributed among these distances:
9 5 0.06
10 49 0.60
11 8 0.10
13 3 0.04
14 16 0.20
ACGTcount: A:0.27, C:0.37, G:0.26, T:0.10
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:1315121 original size:14 final size:14
Alignment explanation
Indices: 1315102--1315173 Score: 62
Period size: 14 Copynumber: 5.0 Consensus size: 14
1315092 CGCTGGGCAT
1315102 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
1315116 CCGAGGCCATCCGAAAGCA
1 CCGAGGCCATCC----G-A
1315135 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
1315150 --GA-G-CATCCGA
1 CCGAGGCCATCCGA
1315160 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
1315174 AAGCATCCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
10 7 0.15
11 1 0.02
12 4 0.08
13 1 0.02
14 19 0.40
15 1 0.02
16 1 0.02
18 1 0.02
19 1 0.02
20 12 0.25
ACGTcount: A:0.25, C:0.39, G:0.28, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:1315141 original size:20 final size:20
Alignment explanation
Indices: 1315116--1315213 Score: 124
Period size: 20 Copynumber: 4.7 Consensus size: 20
1315106 GGCCATCCGA
1315116 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
1315136 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
1315156 CCGACCGAGGCCATCCGAAAGCAT
1 ----CCGAGGCCATCCGAAAGCAT
* *
1315180 CCAAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
1315200 CTGAGGCCATCCGA
1 CCGAGGCCATCCGA
1315214 CCGAGGCCAT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
20 49 0.72
24 19 0.28
ACGTcount: A:0.28, C:0.36, G:0.27, T:0.10
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:1315149 original size:44 final size:44
Alignment explanation
Indices: 1315099--1315200 Score: 179
Period size: 44 Copynumber: 2.3 Consensus size: 44
1315089 ACACGCTGGG
*
1315099 CATCCGAG-GCCATCCGACCGAGGCCATCCGAAAGCATCCGAGGC
1 CATCCGAGAG-CATCCGACCGAGGCCATCCGAAAGCATCCAAGGC
1315143 CATCCGAGAGCATCCGACCGAGGCCATCCGAAAGCATCCAAGGC
1 CATCCGAGAGCATCCGACCGAGGCCATCCGAAAGCATCCAAGGC
1315187 CATCCGAGAGCATC
1 CATCCGAGAGCATC
1315201 TGAGGCCATC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
44 55 0.98
45 1 0.02
ACGTcount: A:0.27, C:0.37, G:0.25, T:0.10
Consensus pattern (44 bp):
CATCCGAGAGCATCCGACCGAGGCCATCCGAAAGCATCCAAGGC
Found at i:1315221 original size:14 final size:14
Alignment explanation
Indices: 1315202--1315232 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1315192 GAGAGCATCT
*
1315202 GAGGCCATCCGACC
1 GAGGCCATCCGAAC
1315216 GAGGCCATCCGAAC
1 GAGGCCATCCGAAC
1315230 GAG
1 GAG
1315233 CTATGCGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.32, T:0.06
Consensus pattern (14 bp):
GAGGCCATCCGAAC
Found at i:1315227 original size:10 final size:10
Alignment explanation
Indices: 1315116--1315213 Score: 60
Period size: 10 Copynumber: 9.4 Consensus size: 10
1315106 GGCCATCCGA
1315116 CCGAGGCCAT
1 CCGAGGCCAT
*
1315126 CCGAAAG-CAT
1 CCG-AGGCCAT
1315136 CCGAGGCCAT
1 CCGAGGCCAT
1315146 CCGAGAG-CAT
1 CCGAG-GCCAT
1315156 CCGACCGAGGCCAT
1 ----CCGAGGCCAT
*
1315170 CCGAAAG-CAT
1 CCG-AGGCCAT
*
1315180 CCAAGGCCAT
1 CCGAGGCCAT
1315190 CCGAGAG-CAT
1 CCGAG-GCCAT
*
1315200 CTGAGGCCAT
1 CCGAGGCCAT
1315210 CCGA
1 CCGA
1315214 CCGAGGCCAT
Statistics
Matches: 68, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
9 5 0.07
10 48 0.71
11 6 0.09
13 1 0.01
14 8 0.12
ACGTcount: A:0.28, C:0.36, G:0.27, T:0.10
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:1315271 original size:33 final size:33
Alignment explanation
Indices: 1315214--1315298 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
1315204 GGCCATCCGA
* * * *
1315214 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
*
1315247 CCGAGGGCAACCGAGCGAGTTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1315280 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
1315299 GGTAGGTCGC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.26, C:0.27, G:0.38, T:0.09
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:1315393 original size:32 final size:31
Alignment explanation
Indices: 1315331--1315396 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
1315321 GCGACCTACC
*
1315331 CTCACTCGGTTGCTCGGATTCCCTCGCATAG
1 CTCACTCGGTTGCTCAGATTCCCTCGCATAG
*
1315362 CTCACTCGGTTGCCCTCAGA-TGCCTCGCATAG
1 CTCACTCGGTTG--CTCAGATTCCCTCGCATAG
1315394 CTC
1 CTC
1315397 GTTCGGATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 12 0.39
32 14 0.45
33 5 0.16
ACGTcount: A:0.14, C:0.38, G:0.21, T:0.27
Consensus pattern (31 bp):
CTCACTCGGTTGCTCAGATTCCCTCGCATAG
Done.