Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007741.1 Hibiscus syriacus cultivar Beakdansim tig00110004_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: 1550271
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1178319 original size:33 final size:33
Alignment explanation
Indices: 1178277--1178459 Score: 179
Period size: 33 Copynumber: 5.4 Consensus size: 33
1178267 TCGCAGCGCG
* *
1178277 GAAATGAAAATCGCGACGAGAGAATCGCAATAC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
* * *
1178310 GAAATGAAAATCGCAACGACAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
* * *
1178343 AAAACT-AAAATCGCAACGCGGAAATGACTATCACAATGC
1 GAAA-TGAAAATCGCAA--C-GAGA-GA--ATCGCAATGC
*
1178382 GAAATGAAAATCGCAACGAGAGAATCGTAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
* * * *
1178415 GAAATGAAAATCGTAAAGAGGGAATCGCAAAGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1178448 GAAATGAAAATC
1 GAAATGAAAATC
1178460 ACGTTGCGAA
Statistics
Matches: 123, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
33 89 0.72
34 1 0.01
35 3 0.02
36 6 0.05
37 2 0.02
38 1 0.01
39 21 0.17
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:1178335 original size:14 final size:13
Alignment explanation
Indices: 1178316--1178346 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1178306 ATACGAAATG
1178316 AAAATCGCAACGAC
1 AAAATCGCAACG-C
1178330 AAAATCGCAACGC
1 AAAATCGCAACGC
1178343 AAAA
1 AAAA
1178347 CTAAAATCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.55, C:0.26, G:0.13, T:0.06
Consensus pattern (13 bp):
AAAATCGCAACGC
Found at i:1178336 original size:86 final size:86
Alignment explanation
Indices: 1178184--1178369 Score: 318
Period size: 86 Copynumber: 2.2 Consensus size: 86
1178174 ATGTCTATCA
* * *
1178184 CAACGCAGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGACAAAAT
1 CAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGACAAAAT
*
1178249 CGCAACGCGAAACTAAAATCG
66 CGCAACGCAAAACTAAAATCG
* *
1178270 CAGCGCGGAAATGAAAATCGCGACGAGAGAATCGCAATACGAAATGAAAATCGCAACGACAAAAT
1 CAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGACAAAAT
1178335 CGCAACGCAAAACTAAAATCG
66 CGCAACGCAAAACTAAAATCG
1178356 CAACGCGGAAATGA
1 CAACGCGGAAATGA
1178370 CTATCACAAT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 93 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.10
Consensus pattern (86 bp):
CAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGACAAAAT
CGCAACGCAAAACTAAAATCG
Found at i:1178428 original size:19 final size:19
Alignment explanation
Indices: 1178377--1178430 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
1178367 TGACTATCAC
*
1178377 AATGCGAAATGAAAATCGC
1 AATGCGAAATGAAAATCGT
*
1178396 AA--CG--A-GAGAATCGT
1 AATGCGAAATGAAAATCGT
1178410 AATGCGAAATGAAAATCGT
1 AATGCGAAATGAAAATCGT
1178429 AA
1 AA
1178431 AGAGGGAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 12 0.44
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.17
Consensus pattern (19 bp):
AATGCGAAATGAAAATCGT
Found at i:1181982 original size:20 final size:20
Alignment explanation
Indices: 1181959--1182014 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1181949 TGAAATGAAA
1181959 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
1181979 ATCGCAACGTG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
*
1181999 ATCGCAATGAGAGAAT
1 ATCGCAACGAGAGAAT
1182015 CGCAACGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:1182034 original size:19 final size:18
Alignment explanation
Indices: 1182012--1182104 Score: 76
Period size: 19 Copynumber: 5.4 Consensus size: 18
1182002 GCAATGAGAG
1182012 AATCGCAACGCAAAATGAA
1 AATCGCAACGC-AAATGAA
*
1182031 AATCGCAACG---A-GAG
1 AATCGCAACGCAAATGAA
*
1182045 AATCGCAACGCAAAATTAA
1 AATCGCAACGC-AAATGAA
*
1182064 AATCGCAACG---A-GAG
1 AATCGCAACGCAAATGAA
1182078 AATCGCAACGCGAAATGAA
1 AATCGCAACGC-AAATGAA
1182097 AATCGCAA
1 AATCGCAA
1182105 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 23 0.40
15 2 0.03
18 2 0.03
19 31 0.53
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (18 bp):
AATCGCAACGCAAATGAA
Found at i:1182036 original size:33 final size:33
Alignment explanation
Indices: 1181999--1182104 Score: 185
Period size: 33 Copynumber: 3.2 Consensus size: 33
1181989 GGAAATGACT
*
1181999 ATCGCAATGAGAGAATCGCAACGCAAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGCAAAATGAAA
*
1182032 ATCGCAACGAGAGAATCGCAACGCAAAATTAAA
1 ATCGCAACGAGAGAATCGCAACGCAAAATGAAA
*
1182065 ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGCAAAATGAAA
1182098 ATCGCAA
1 ATCGCAA
1182105 TGCGATTTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAACGCAAAATGAAA
Found at i:1182048 original size:14 final size:14
Alignment explanation
Indices: 1182031--1182087 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1182021 GCAAAATGAA
1182031 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
1182045 AATCGCAACGCAAAATTAA
1 AATCGCAACG----A-GAG
1182064 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1182078 AATCGCAACG
1 AATCGCAACG
1182088 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.62
15 1 0.03
18 1 0.03
19 11 0.32
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1182127 original size:19 final size:19
Alignment explanation
Indices: 1182105--1182149 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1182095 AAAATCGCAA
** *
1182105 TGCGATTTTGGTTTTGCGT
1 TGCGATTTTCATTTCGCGT
1182124 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
1182143 TGCGATT
1 TGCGATT
1182150 CTCTCGTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1182174 original size:21 final size:21
Alignment explanation
Indices: 1182148--1182211 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1182138 CGCGTTGCGA
1182148 TTCTCTCGTTACGATTTTCAT
1 TTCTCTCGTTACGATTTTCAT
**
1182169 TTCTCTCGTTACGATAGTCAT
1 TTCTCTCGTTACGATTTTCAT
*
1182190 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTACGATTTTCAT
1182210 TT
1 TT
1182212 TCATTAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTACGATTTTCAT
Found at i:1183159 original size:26 final size:26
Alignment explanation
Indices: 1183120--1183169 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1183110 ATGTACCTTT
*
1183120 CACTTCATTAATTTCATAGCATGTTC
1 CACTCCATTAATTTCATAGCATGTTC
*
1183146 CACTCCATTTATTTCATAGCATGT
1 CACTCCATTAATTTCATAGCATGT
1183170 ATCATTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (26 bp):
CACTCCATTAATTTCATAGCATGTTC
Found at i:1183175 original size:21 final size:24
Alignment explanation
Indices: 1183118--1183184 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 24
1183108 ACATGTACCT
1183118 TTCACTTCATTAATTTCATAGCATG
1 TTCAC-TCATTAATTTCATAGCATG
*
1183143 TTCCACTCCATTTATTTCATAGCATG
1 TT-CACT-CATTAATTTCATAGCATG
*
1183169 TATCATTCATTTAATT
1 T-TCACTCA-TTAATT
1183185 CACTTCGTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
25 5 0.14
26 29 0.83
27 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (24 bp):
TTCACTCATTAATTTCATAGCATG
Found at i:1183401 original size:48 final size:47
Alignment explanation
Indices: 1183346--1183647 Score: 259
Period size: 48 Copynumber: 6.3 Consensus size: 47
1183336 TGCATAAGTA
* * *
1183346 ACGTCAGACGTGCTAGGTACCATTGATAGGAGCACCACCGA-CACACAG
1 ACGTCAGACGTGCTAGTTACCATT-ATAGTAGCACCACC-ATCACAAAG
* *
1183394 ACGTCAGACGTGCTAGGTACCATTGGTAGTAGCACCACCATCACAAAG
1 ACGTCAGACGTGCTAGTTACCATT-ATAGTAGCACCACCATCACAAAG
* * * *
1183442 ACGTCAGACATGCTATTTACCATTATAGTAGCACCACCGTCATAAAG
1 ACGTCAGACGTGCTAGTTACCATTATAGTAGCACCACCATCACAAAG
* ** * * * * *
1183489 ACGTCAAATATGATATTTATCATTAATAGTTGCACCACCATCGCAAAG
1 ACGTCAGACGTGCTAGTTACCATT-ATAGTAGCACCACCATCACAAAG
* * * *
1183537 ACGTCAAACGTGCTAATTATCATTAGTAGTAGCACCACCATCACACAG
1 ACGTCAGACGTGCTAGTTACCATTA-TAGTAGCACCACCATCACAAAG
* * ** * *
1183585 ACGTCAGCCGTGCTAATTATTATTAATAGTAGTACCA-CAGTCGCACAA-
1 ACGTCAGACGTGCTAGTTACCATT-ATAGTAGCACCACCA-TCACA-AAG
*
1183633 ACGTCAGAGGTGCTA
1 ACGTCAGACGTGCTA
1183648 AATGTTCCAC
Statistics
Matches: 216, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
47 44 0.20
48 170 0.79
49 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (47 bp):
ACGTCAGACGTGCTAGTTACCATTATAGTAGCACCACCATCACAAAG
Found at i:1183991 original size:20 final size:20
Alignment explanation
Indices: 1183966--1184003 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1183956 AGACGTAATT
*
1183966 TAATAAAATAATATGAAATA
1 TAATAAAACAATATGAAATA
*
1183986 TAATAAAACAATTTGAAA
1 TAATAAAACAATATGAAA
1184004 ACATTTTCTT
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:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAATAAAACAATATGAAATA
Found at i:1185824 original size:22 final size:20
Alignment explanation
Indices: 1185799--1185852 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 20
1185789 CCTTAGTTCT
1185799 TTAACTCCATGTTTCTAGTATC
1 TTAAC-CCA-GTTTCTAGTATC
1185821 TTAA-CCAGTTTCTAGTATC
1 TTAACCCAGTTTCTAGTATC
1185840 TTAA-CCAGTTTCT
1 TTAACCCAGTTTCT
1185853 TTAACCAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 25 0.78
20 3 0.09
22 4 0.12
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.44
Consensus pattern (20 bp):
TTAACCCAGTTTCTAGTATC
Found at i:1185833 original size:19 final size:19
Alignment explanation
Indices: 1185809--1185852 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
1185799 TTAACTCCAT
1185809 GTTTCTAGTATCTTAACCA
1 GTTTCTAGTATCTTAACCA
1185828 GTTTCTAGTATCTTAACCA
1 GTTTCTAGTATCTTAACCA
1185847 GTTTCT
1 GTTTCT
1185853 TTAACCAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.45
Consensus pattern (19 bp):
GTTTCTAGTATCTTAACCA
Found at i:1192952 original size:24 final size:25
Alignment explanation
Indices: 1192925--1192973 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1192915 AAGATGCTTA
*
1192925 TTTCATATGT-TATA-ATATAGTTAT
1 TTTCATATATATATATATATA-TTAT
1192949 TTTCATATATATATATATATATTAT
1 TTTCATATATATATATATATATTAT
1192974 ATCTATAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 8 0.36
26 5 0.23
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (25 bp):
TTTCATATATATATATATATATTAT
Found at i:1194484 original size:17 final size:18
Alignment explanation
Indices: 1194462--1194506 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
1194452 AAATTGGAGT
1194462 ACAAAAAGAAAG-AAAAG
1 ACAAAAAGAAAGAAAAAG
1194479 ACAAAAAG-AAGAAAAAG
1 ACAAAAAGAAAGAAAAAG
1194496 A-AGAAAAGAAA
1 ACA-AAAAGAAA
1194507 AAGAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.16
17 19 0.76
18 2 0.08
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (18 bp):
ACAAAAAGAAAGAAAAAG
Found at i:1194510 original size:20 final size:20
Alignment explanation
Indices: 1194464--1194511 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1194454 ATTGGAGTAC
1194464 AAAAAGAAAGAAAAGACAAA
1 AAAAAGAAAGAAAAGACAAA
*
1194484 AAGAAGAAA-AAGAAGA-AAA
1 AAAAAGAAAGAA-AAGACAAA
1194503 GAAAAAGAA
1 -AAAAAGAA
1194512 TAAATTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAGAAAAGACAAA
Found at i:1197373 original size:2 final size:2
Alignment explanation
Indices: 1197366--1197396 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1197356 ATAATATAGT
1197366 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 T
1197397 TATGATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1200855 original size:32 final size:33
Alignment explanation
Indices: 1200799--1200860 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1200789 GAAAGAGAAG
*
1200799 TAAAAAATATAAAACAATGTTTAAAATTAACAA
1 TAAAAAATAAAAAACAATGTTTAAAATTAACAA
1200832 TAAAAAATGAAAAAAC-ATG-TTAAAATTAA
1 TAAAAAAT-AAAAAACAATGTTTAAAATTAA
1200861 AAGGGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 10 0.37
33 11 0.41
34 6 0.22
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (33 bp):
TAAAAAATAAAAAACAATGTTTAAAATTAACAA
Found at i:1202239 original size:35 final size:35
Alignment explanation
Indices: 1202159--1202549 Score: 173
Period size: 37 Copynumber: 10.8 Consensus size: 35
1202149 TATTTTTTAG
* *
1202159 AAAACTATATA-TTATATACGTTTTCAAAAATATTTTCC
1 AAAACTATATATTTATATA--TTTT-TAAAACATTTT-C
1202197 AAAA-TATATA-TTATATATTTTTAAAACATTTT-
1 AAAACTATATATTTATATATTTTTAAAACATTTTC
* * *
1202229 AAAGCTATATATTATATATATTTTCAAAAATATTTTC
1 AAAACTATATATT-TATATATTTT-TAAAACATTTTC
1202266 AAAACTATATATTTTATATATATTTTTTTCAAAA-ATGTTTTC
1 AAAACTATATA--TT-TATATA--TTTTT-AAAACA--TTTTC
* * * * * *
1202308 AAAACTATATATATATATATATAT-ATATA-TAT-
1 AAAACTATATATTTATATATTTTTAAAACATTTTC
* * ** *
1202340 -ATA-TATATATATATATA-TTCCAAAA-ATGTTTT
1 AAAACTATATATTTATATATTTTTAAAACAT-TTTC
* * *
1202372 AATACTATATAGTATACATATTTTTGAAAA-ATGTTTTC
1 AAAACTATATA-TTTATATATTTTT-AAAACA--TTTTC
* * **
1202410 AAAACTATATA-TTATATATTTTCAAAAAAAAATTC
1 AAAACTATATATTTATATATTTT-TAAAACATTTTC
**
1202445 AAAACTATATATTATATATATTTTTGGAAAATGTTTTC
1 AAAACTATATATT-TATATATTTTT--AAAACATTTTC
* *
1202483 AAAACTATATA-TTATATATATTTCAAAAAATGTTTTC
1 AAAACTATATATTTATATAT-TTTTAAAACA--TTTTC
*
1202520 AAAACTATATAATATATATATTTTTTAAAA
1 AAAACTATAT-ATTTATATA-TTTTTAAAA
1202550 ATGTATTTTC
Statistics
Matches: 279, Mismatches: 38, Indels: 71
0.72 0.10 0.18
Matches are distributed among these distances:
29 2 0.01
30 16 0.06
31 4 0.01
32 3 0.01
33 11 0.04
34 16 0.06
35 41 0.15
36 33 0.12
37 61 0.22
38 36 0.13
39 29 0.10
40 3 0.01
41 8 0.03
42 16 0.06
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (35 bp):
AAAACTATATATTTATATATTTTTAAAACATTTTC
Found at i:1202308 original size:42 final size:43
Alignment explanation
Indices: 1202234--1202331 Score: 148
Period size: 42 Copynumber: 2.3 Consensus size: 43
1202224 ATTTTAAAGC
1202234 TATATAT-TATATA-TATTTTCAAAAATATTTTCAAAACTATA
1 TATATATATATATATTATTTTCAAAAATATTTTCAAAACTATA
* * *
1202275 TAT-TTTATATATATTTTTTTCAAAAATGTTTTCAAAACTATA
1 TATATATATATATATTATTTTCAAAAATATTTTCAAAACTATA
1202317 TATATATATATATAT
1 TATATATATATATAT
1202332 ATATATATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 2 0.04
41 9 0.18
42 29 0.58
43 10 0.20
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (43 bp):
TATATATATATATATTATTTTCAAAAATATTTTCAAAACTATA
Found at i:1202320 original size:2 final size:2
Alignment explanation
Indices: 1202313--1202357 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1202303 TTTTCAAAAC
1202313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1202355 TA T
1 TA T
1202358 TCCAAAAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1202403 original size:37 final size:38
Alignment explanation
Indices: 1202339--1202564 Score: 246
Period size: 37 Copynumber: 6.0 Consensus size: 38
1202329 TATATATATA
* ** *
1202339 TATATATATATATATATATTCCAAAAATGTTTT-AATAC
1 TATATAT-TATATATATTTTTAAAAAATGTTTTCAAAAC
* * *
1202377 TATATAGTATACATATTTTTGAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTTAAAAAATGTTTTCAAAAC
* ***
1202415 TATATA-T-TATATATTTTCAAAAAA-AAATTCAAAAC
1 TATATATTATATATATTTTTAAAAAATGTTTTCAAAAC
**
1202450 TATATATTATATATATTTTTGGAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTTAAAAAATGTTTTCAAAAC
*
1202488 TATATATTATATATA-TTTCAAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTTAAAAAATGTTTTCAAAAC
* *
1202525 TATATAATATATATATTTTTTAAAAATGTATTTTCAAAAC
1 TATATATTATATATATTTTTAAAAAATG--TTTTCAAAAC
1202565 CATGCAATGT
Statistics
Matches: 157, Mismatches: 24, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
35 14 0.09
36 15 0.10
37 69 0.44
38 49 0.31
40 10 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATATTATATATATTTTTAAAAAATGTTTTCAAAAC
Found at i:1202584 original size:73 final size:73
Alignment explanation
Indices: 1202343--1202564 Score: 286
Period size: 73 Copynumber: 3.0 Consensus size: 73
1202333 TATATATATA
* * * * *
1202343 TATATATATATATATTCCAAAAATGTTTT-AATACTATATAGTATACATATTTTTGAAAAATGTT
1 TATATATATATATTTTCAAAAAATGTTTTCAAAACTATATAATATATATATTTTTGAAAAATGTT
1202407 TTCAAAAC
66 TTCAAAAC
*** * *
1202415 TATATATTATATATTTTCAAAAAA-AAATTCAAAACTATATATTATATATATTTTTGGAAAATGT
1 TATATA-TATATATTTTCAAAAAATGTTTTCAAAACTATATAATATATATATTTTTGAAAAATGT
1202479 TTTCAAAAC
65 TTTCAAAAC
*
1202488 TATATATTATATATATTTCAAAAAATGTTTTCAAAACTATATAATATATATATTTTTTAAAAATG
1 TATATA-TATATAT-TTTCAAAAAATGTTTTCAAAACTATATAATATATATATTTTTGAAAAATG
1202553 TATTTTCAAAAC
64 --TTTTCAAAAC
1202565 CATGCAATGT
Statistics
Matches: 129, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
72 8 0.06
73 68 0.53
74 10 0.08
75 33 0.26
77 10 0.08
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (73 bp):
TATATATATATATTTTCAAAAAATGTTTTCAAAACTATATAATATATATATTTTTGAAAAATGTT
TTCAAAAC
Found at i:1216238 original size:31 final size:32
Alignment explanation
Indices: 1216160--1216254 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 32
1216150 ATTTTTTAGA
**
1216160 AAACTATATATTATATATGTTTTCAAAAATATTTTTT
1 AAACTATATATTATATA--TTTTC--AAA-ACGTTTT
1216197 AAACTATATA-T-TATATTTTCAAAACGTTTT
1 AAACTATATATTATATATTTTCAAAACGTTTT
1216227 AAAGCTATATATTATATATTTTCAAAAC
1 AAA-CTATATATTATATATTTTCAAAAC
1216255 TATATTATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
30 8 0.15
31 10 0.19
32 1 0.02
33 19 0.36
35 4 0.08
36 1 0.02
37 10 0.19
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.46
Consensus pattern (32 bp):
AAACTATATATTATATATTTTCAAAACGTTTT
Found at i:1216273 original size:25 final size:23
Alignment explanation
Indices: 1216223--1216278 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 23
1216213 TTTCAAAACG
*
1216223 TTTT-AAAGCTATATATTATATA
1 TTTTCAAAACTATATATTATATA
1216245 TTTTCAAAACTATATTATATATATA
1 TTTTCAAAACTATA-TAT-TATATA
1216270 TTTTCAAAA
1 TTTTCAAAA
1216279 ATGTTTCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 4 0.13
23 8 0.27
24 3 0.10
25 15 0.50
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTCAAAACTATATATTATATA
Found at i:1216299 original size:2 final size:2
Alignment explanation
Indices: 1216292--1216365 Score: 127
Period size: 2 Copynumber: 38.5 Consensus size: 2
1216282 TTTCCAAAAC
1216292 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1216332 TA TA -A 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 T
1216366 TTCAAAAATG
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 66 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1216463 original size:144 final size:143
Alignment explanation
Indices: 1216357--1216651 Score: 355
Period size: 144 Copynumber: 2.0 Consensus size: 143
1216347 TATATATATA
*
1216357 TATATATATTTCAAAAATGTTTT-AAAACTATATATATACATATTTTCGAAAAAAAAAATCAAAA
1 TATATAT-TTTCAAAAATGTTTTCAAAACTACATAT-TACATATTTTCG-AAAAAAAAATCAAAA
* *
1216421 CTATATA-T-TATATATTTTCAAAAAAAATG-TTTCAAAACTATATATTATATATATTTTCGAAA
63 CTACATATTATATATATTTTC--AAAAAATGTTTTCAAAACTATATATTATATATATTATC-AAA
* *
1216483 AATGTTTTCAAAACTACAT
125 AATATTATCAAAACTACAT
* * *****
1216502 TATATATTTTGAAAAATGTTTTCAAAACTACATATTATATATTTTCGAAAATGTTTTCAAAACTA
1 TATATATTTTCAAAAATGTTTTCAAAACTACATATTACATATTTTCGAAAAAAAAATCAAAACTA
* *
1216567 CATATTATATATATTTTCGAAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAAATATT
66 CATATTATATATATTTTCAAAAAATGTTTTCAAAACTATATATTATATATATTATCAAAAATATT
* * *
1216632 CTCAAAACTATAA
131 ATCAAAACTACAT
1216645 TATATAT
1 TATATAT
1216652 ATATATATAT
Statistics
Matches: 132, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
143 48 0.36
144 55 0.42
145 29 0.22
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (143 bp):
TATATATTTTCAAAAATGTTTTCAAAACTACATATTACATATTTTCGAAAAAAAAATCAAAACTA
CATATTATATATATTTTCAAAAAATGTTTTCAAAACTATATATTATATATATTATCAAAAATATT
ATCAAAACTACAT
Found at i:1216485 original size:37 final size:38
Alignment explanation
Indices: 1216347--1216657 Score: 355
Period size: 37 Copynumber: 8.4 Consensus size: 38
1216337 TATATATATA
1216347 TATATATATATATATATATTTC-AAAAATGTTTT-AAAAC
1 TATATAT-TATATATAT-TTTCGAAAAATGTTTTCAAAAC
* *****
1216385 TATATA-TATACATATTTTCGAAAAAAAAAATCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
*
1216422 TATATA-T-TATATATTTTCAAAAAAAATG-TTTCAAAAC
1 TATATATTATATATATTTTC--GAAAAATGTTTTCAAAAC
1216459 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
*
1216497 --TACA-T-TATATATTTT-GAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
*
1216530 TACATA-T-TATATATTTTCG-AAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
*
1216565 TACATATTATATATATTTTCGAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
* *
1216603 TATATATTATATATATTTTC-AAAAATATTCTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
1216640 TATAATATATATATATAT
1 TAT-ATAT-TATATATAT
1216658 ATATATATAT
Statistics
Matches: 239, Mismatches: 19, Indels: 29
0.83 0.07 0.10
Matches are distributed among these distances:
33 18 0.08
34 10 0.04
35 40 0.17
36 29 0.12
37 62 0.26
38 60 0.25
39 20 0.08
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (38 bp):
TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
Found at i:1216652 original size:73 final size:73
Alignment explanation
Indices: 1216349--1216653 Score: 351
Period size: 75 Copynumber: 4.2 Consensus size: 73
1216339 TATATATATA
* *
1216349 TATATATATATATATATTTC-AAAAATGTTTT-AAAACTATATATATACATATTTTCGAAAAAAA
1 TATA-ATATATATAT-TTTCGAAAAATGTTTTCAAAACTATATATATATATATTTTCGAAAAATA
***
1216412 AAATCAAAAC
64 TTTTCAAAAC
*
1216422 TAT-ATATTATATATTTTCAAAAAAAATG-TTTCAAAACTATATATTATATATATTTTCGAAAAA
1 TATAATA-TATATATTTTC--GAAAAATGTTTTCAAAACTATATA-TATATATATTTTCGAAAAA
*
1216485 TGTTTTCAAAAC
62 TATTTTCAAAAC
* * *
1216497 TA-CAT-TATATATTTT-GAAAAATGTTTTCAAAACTACATAT-TATATATTTTCG-AAAATGTT
1 TATAATATATATATTTTCGAAAAATGTTTTCAAAACTATATATATATATATTTTCGAAAAATATT
1216557 TTCAAAAC
66 TTCAAAAC
*
1216565 TACATATTATATATATTTTCGAAAAATGTTTTCAAAACTATATATTATATATATTTTC-AAAAAT
1 T--ATAATATATATATTTTCGAAAAATGTTTTCAAAACTATATA-TATATATATTTTCGAAAAAT
*
1216629 ATTCTCAAAAC
63 ATTTTCAAAAC
1216640 TATAATATATATAT
1 TATAATATATATAT
1216654 ATATATATAT
Statistics
Matches: 202, Mismatches: 14, Indels: 32
0.81 0.06 0.13
Matches are distributed among these distances:
68 17 0.08
69 12 0.06
70 9 0.04
71 22 0.11
72 17 0.08
73 51 0.25
74 19 0.09
75 55 0.27
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (73 bp):
TATAATATATATATTTTCGAAAAATGTTTTCAAAACTATATATATATATATTTTCGAAAAATATT
TTCAAAAC
Found at i:1222540 original size:41 final size:43
Alignment explanation
Indices: 1222474--1222565 Score: 113
Period size: 41 Copynumber: 2.2 Consensus size: 43
1222464 AACAAGTAAT
* *
1222474 AAAT-AACACCATAACACCATTAAGTCTC-A-AAGTCTAAAATA
1 AAATCAACACCATAACACAATAAAGTCTCAATAAGTCT-AAATA
1222515 AAA-CAACA-CATAACACTAATAAAGTCTCAATAAGTCTAAATA
1 AAATCAACACCATAACAC-AATAAAGTCTCAATAAGTCTAAATA
1222557 AAATCAACA
1 AAATCAACA
1222566 TAAAATAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
40 8 0.18
41 16 0.36
42 9 0.20
43 11 0.25
ACGTcount: A:0.54, C:0.21, G:0.04, T:0.21
Consensus pattern (43 bp):
AAATCAACACCATAACACAATAAAGTCTCAATAAGTCTAAATA
Found at i:1223890 original size:41 final size:41
Alignment explanation
Indices: 1223822--1223941 Score: 161
Period size: 40 Copynumber: 3.0 Consensus size: 41
1223812 GATTTTGCCT
* *
1223822 CATTACATTCTTGCAAAGACGCCTCAAGTTTCTGTTTTCCC
1 CATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTCCC
* * **
1223863 CGTTGCATTCTTGCAAAGATGCTTCAAGTTTCTG-TTTCTT
1 CATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTCCC
* *
1223903 CATTACATTCTTGCAAACATGCTTCAACTTTCTGTTTTC
1 CATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTC
1223942 TTCCTTGCAG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 34 0.50
41 34 0.50
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (41 bp):
CATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTCCC
Found at i:1223925 original size:40 final size:41
Alignment explanation
Indices: 1223821--1223944 Score: 169
Period size: 41 Copynumber: 3.0 Consensus size: 41
1223811 AGATTTTGCC
* * *
1223821 TCATTACATTCTTGCAAAGACGCCTCAAGTTTCTGTTTTCC
1 TCATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTCT
* * *
1223862 CCGTTGCATTCTTGCAAAGATGCTTCAAGTTTCTG-TTTCT
1 TCATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTCT
* *
1223902 TCATTACATTCTTGCAAACATGCTTCAACTTTCTGTTTTCT
1 TCATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTCT
1223943 TC
1 TC
1223945 CTTGCAGTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 34 0.48
41 37 0.52
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (41 bp):
TCATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTCT
Found at i:1232112 original size:45 final size:45
Alignment explanation
Indices: 1232051--1232139 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
1232041 TAAGCAGGAG
*
1232051 AAAAACAATGTAAAAGCAA-CAAGAGGAA-TTTTATTTAAAAGAAGA
1 AAAAACAATGTAAAAGCAATCAA-AAGAAGTTTTA-TTAAAAGAAGA
1232096 AAAAACAATGTAAAAGCAATCAAAAGAAGGTTTTATTAAAAGAA
1 AAAAACAATGTAAAAGCAATCAAAAGAA-GTTTTATTAAAAGAA
1232140 CCCAATTACA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
45 23 0.57
46 12 0.30
47 5 0.12
ACGTcount: A:0.58, C:0.07, G:0.15, T:0.20
Consensus pattern (45 bp):
AAAAACAATGTAAAAGCAATCAAAAGAAGTTTTATTAAAAGAAGA
Found at i:1233661 original size:145 final size:148
Alignment explanation
Indices: 1233492--1233784 Score: 565
Period size: 145 Copynumber: 2.0 Consensus size: 148
1233482 AGGAAAATGT
1233492 TAAAAATTAATTCAAAAAAACTAACAAAATAAATATGTGAATAGAATCAACTGCATTGACAAATG
1 TAAAAATTAATTCAAAAAAACTAACAAAATAAATATGTGAATAGAATCAACTGCATTGACAAATG
1233557 AA-CACAACATGAGATTAAACTACTG-AAGATCACCGACAATCGCGAATCAGAATCGAGCG-TGT
66 AACCACAACATGAGATTAAACTACTGAAAGATCACCGACAATCGCGAATCAGAATCGAGCGTTGT
1233619 GATAAAACTATCTTTGAA
131 GATAAAACTATCTTTGAA
1233637 TAAAAATTAATTCAAAAAAACTAACAAAATAAATATGTGAATAGAATCAACTGCATTGACAAATG
1 TAAAAATTAATTCAAAAAAACTAACAAAATAAATATGTGAATAGAATCAACTGCATTGACAAATG
1233702 AACCACAACATGAGATTAAACTACTGAAAGATCACCGACAATCGCGAATCAGAATCGAGCGTTGT
66 AACCACAACATGAGATTAAACTACTGAAAGATCACCGACAATCGCGAATCAGAATCGAGCGTTGT
1233767 GATAAAACTATCTTTGAA
131 GATAAAACTATCTTTGAA
1233785 CGTAAATTAC
Statistics
Matches: 145, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
145 67 0.46
146 23 0.16
147 34 0.23
148 21 0.14
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (148 bp):
TAAAAATTAATTCAAAAAAACTAACAAAATAAATATGTGAATAGAATCAACTGCATTGACAAATG
AACCACAACATGAGATTAAACTACTGAAAGATCACCGACAATCGCGAATCAGAATCGAGCGTTGT
GATAAAACTATCTTTGAA
Found at i:1235480 original size:19 final size:18
Alignment explanation
Indices: 1235443--1235481 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1235433 ACGAAAAAGA
*
1235443 TTATTATTAGATAATAAT
1 TTATTATTAGATAAGAAT
*
1235461 TTATTATTATGATAGGAAT
1 TTATTATTA-GATAAGAAT
1235480 TT
1 TT
1235482 TGATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (18 bp):
TTATTATTAGATAAGAAT
Found at i:1235873 original size:16 final size:16
Alignment explanation
Indices: 1235852--1235882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1235842 CGAAGCCATA
*
1235852 ATATTATTTTTATATT
1 ATATTATATTTATATT
1235868 ATATTATATTTATAT
1 ATATTATATTTATAT
1235883 AAACAACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATTATATTTATATT
Found at i:1240334 original size:33 final size:33
Alignment explanation
Indices: 1240230--1240337 Score: 173
Period size: 33 Copynumber: 3.2 Consensus size: 33
1240220 CGGAAATTAC
1240230 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
1240263 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
1240297 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1240330 AATCGCAA
1 AATCGCAA
1240338 TGCGAAATGA
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.01
33 37 0.54
34 29 0.43
35 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1240335 original size:19 final size:19
Alignment explanation
Indices: 1240244--1240356 Score: 129
Period size: 19 Copynumber: 6.4 Consensus size: 19
1240234 GCAACGAGAG
1240244 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1240263 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1240277 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1240297 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1240311 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1240330 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1240349 AATCGCAA
1 AATCGCAA
1240357 CGAGAGAATC
Statistics
Matches: 79, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
14 22 0.28
15 1 0.01
16 3 0.04
17 2 0.03
18 2 0.03
19 36 0.46
20 13 0.16
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1240357 original size:52 final size:53
Alignment explanation
Indices: 1240272--1240378 Score: 207
Period size: 52 Copynumber: 2.0 Consensus size: 53
1240262 AAATCCCAAC
1240272 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1240325 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1240377 AT
1 AT
1240379 TATAAACGCA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 38 0.70
53 16 0.30
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1240427 original size:19 final size:19
Alignment explanation
Indices: 1240403--1240496 Score: 116
Period size: 19 Copynumber: 5.4 Consensus size: 19
1240393 GATTCTCTCG
1240403 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1240422 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
1240440 TTGCGA--TTC---TCG--
1 TTGCGATTTTCATTTCGCA
1240452 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1240471 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1240490 TTGCGAT
1 TTGCGAT
1240497 AGTCATTTTG
Statistics
Matches: 67, Mismatches: 0, Indels: 16
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.09
14 6 0.09
16 3 0.04
17 3 0.04
18 10 0.15
19 34 0.51
20 5 0.07
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1240471 original size:49 final size:51
Alignment explanation
Indices: 1240385--1240496 Score: 185
Period size: 49 Copynumber: 2.2 Consensus size: 51
1240375 AAATTATAAA
1240385 CGCATTGCGATTCTCTCGTTGCGATTTCATTTCCGCATTGCGATTTTCA-TT
1 CGCATTGCGA-TCTCTCGTTGCGATTTCATTTCCGCATTGCGATTTTCATTT
1240436 CGCATTGCGAT-TCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATCTCTCGTTGCGA-TTTCATTTCCGCATTGCGATTTTCATTT
1240486 CGCATTGCGAT
1 CGCATTGCGAT
1240497 AGTCATTTTG
Statistics
Matches: 59, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
49 27 0.46
50 22 0.37
51 10 0.17
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (51 bp):
CGCATTGCGATCTCTCGTTGCGATTTCATTTCCGCATTGCGATTTTCATTT
Found at i:1240502 original size:19 final size:19
Alignment explanation
Indices: 1240461--1240504 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1240451 GTTGCGATTT
**
1240461 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
1240480 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
1240499 TCATTT
1 TCATTT
1240505 TGCCTTCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1240621 original size:14 final size:14
Alignment explanation
Indices: 1240602--1240638 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1240592 CATCAATTAC
1240602 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1240616 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1240630 ACAAATCAA
1 ACAAATCAA
1240639 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1242615 original size:14 final size:14
Alignment explanation
Indices: 1242596--1242652 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1242586 GCGAAATGAA
*
1242596 AATCGCAACGACAG
1 AATCGCAACGAAAG
1242610 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1242627 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1242643 AATCGCAACG
1 AATCGCAACG
1242653 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1242623 original size:33 final size:33
Alignment explanation
Indices: 1242577--1242669 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1242567 GCGAAACCAA
*
1242577 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1242610 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1242643 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1242670 TGCTCTTCCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1242634 original size:19 final size:19
Alignment explanation
Indices: 1242540--1242669 Score: 127
Period size: 19 Copynumber: 7.3 Consensus size: 19
1242530 TAGTTTACTT
* *
1242540 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1242560 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1242579 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1242598 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1242612 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1242631 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1242645 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1242664 TCGCAA
1 TCGCAA
1242670 TGCTCTTCCT
Statistics
Matches: 93, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 43 0.46
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1243802 original size:14 final size:14
Alignment explanation
Indices: 1243783--1243872 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1243773 TTGAAATGAA
1243783 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1243797 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
1243816 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1243830 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1243849 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1243863 AATCGCAACG
1 AATCGCAACG
1243873 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1243813 original size:33 final size:33
Alignment explanation
Indices: 1243775--1243889 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
1243765 TCTTTTGGTT
1243775 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1243808 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1243841 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1243874 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1243890 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1243821 original size:19 final size:19
Alignment explanation
Indices: 1243797--1243894 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1243787 GCAACGAGAG
*
1243797 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
1243816 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1243830 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1243849 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1243863 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1243882 AATCGCAATGCGA
1 AATCGCAACGCGA
1243895 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1243925 original size:14 final size:14
Alignment explanation
Indices: 1243906--1243962 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1243896 TTTGGTTTCG
1243906 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1243920 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1243939 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1243953 CGTTGCGATT
1 CGTTGCGATT
1243963 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1243938 original size:33 final size:33
Alignment explanation
Indices: 1243890--1244010 Score: 143
Period size: 33 Copynumber: 3.4 Consensus size: 33
1243880 AAAATCGCAA
**
1243890 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1243923 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1243956 TGCGATTGTCATTTCTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCGT
1243997 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1244011 ATCTCGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
33 41 0.54
34 2 0.03
35 7 0.09
37 1 0.01
38 1 0.01
39 2 0.03
40 2 0.03
41 20 0.26
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1243977 original size:21 final size:21
Alignment explanation
Indices: 1243947--1244022 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1243937 CGCGTTGCGA
1243947 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
* **
1243968 TTCTCGCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
1243988 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
1244009 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1244023 CTTCTGCAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:1244003 original size:41 final size:41
Alignment explanation
Indices: 1243946--1244023 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
1243936 TCGCGTTGCG
*
1243946 ATTCTCTCGTTGCGATTGTCATTTCTCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCGCGTTGCGACAGTC
* *
1243987 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCGCGTTGCGAC
1244024 TTCTGCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.42
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCGCGTTGCGACAGTC
Found at i:1244142 original size:33 final size:33
Alignment explanation
Indices: 1244100--1244170 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
1244090 AATACTAACT
*
1244100 TGAAAATCGCAACGAGAGAAT-AGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATCA-CAACGCGAAA
*
1244133 TGAAAATCGCAACGACAGAATCATAACGCGAAA
1 TGAAAATCGCAACGACAGAATCACAACGCGAAA
1244166 TGAAA
1 TGAAA
1244171 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATCACAACGCGAAA
Found at i:1244376 original size:21 final size:23
Alignment explanation
Indices: 1244352--1244404 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
1244342 TGTGAGGGAT
1244352 TTCGCCGAGAT-GGACGGA-ATC
1 TTCGCCGAGATGGGACGGATATC
*
1244373 TTCG--GAGATGGGGACGGATTTC
1 TTCGCCGAGAT-GGGACGGATATC
1244395 TTCGCCGAGA
1 TTCGCCGAGA
1244405 GAGTGAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 5 0.19
21 11 0.42
22 6 0.23
24 4 0.15
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.23
Consensus pattern (23 bp):
TTCGCCGAGATGGGACGGATATC
Found at i:1244568 original size:20 final size:20
Alignment explanation
Indices: 1244543--1244715 Score: 215
Period size: 20 Copynumber: 8.6 Consensus size: 20
1244533 CTTTAAATAT
1244543 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1244563 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1244585 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1244604 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1244624 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1244644 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1244664 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1244684 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
1244704 CGCGTTGCGATT
1 CGCGTTGCGATT
1244716 CATATTCGCG
Statistics
Matches: 131, Mismatches: 18, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 112 0.85
21 15 0.11
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1244708 original size:60 final size:60
Alignment explanation
Indices: 1244545--1244715 Score: 243
Period size: 60 Copynumber: 2.8 Consensus size: 60
1244535 TTAAATATCG
** *
1244545 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
1244606 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
1244666 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATT
1244716 CATATTCGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 68 0.72
61 26 0.28
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:1244751 original size:21 final size:21
Alignment explanation
Indices: 1244721--1244803 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1244711 CGATTCATAT
*
1244721 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1244742 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1244763 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1244784 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1244804 CTGATTTACG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1250204 original size:3 final size:3
Alignment explanation
Indices: 1250196--1250250 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
1250186 TAAACACACT
*
1250196 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1250243 TAA TAA TA
1 TAA TAA TA
1250251 TTTTTTAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 1 0.02
3 48 0.98
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1253234 original size:36 final size:36
Alignment explanation
Indices: 1253125--1253223 Score: 189
Period size: 36 Copynumber: 2.8 Consensus size: 36
1253115 GGCTCCCTCT
1253125 AATGATGAAGAGAAGTCCACGTAATTGGCTCATTGC
1 AATGATGAAGAGAAGTCCACGTAATTGGCTCATTGC
*
1253161 AATGATGAAGAGAAGTCCACGTAATTGGCTCCTTGC
1 AATGATGAAGAGAAGTCCACGTAATTGGCTCATTGC
1253197 AATGATGAAGAGAAGTCCACGTAATTG
1 AATGATGAAGAGAAGTCCACGTAATTG
1253224 CGTGGTTGCA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.24
Consensus pattern (36 bp):
AATGATGAAGAGAAGTCCACGTAATTGGCTCATTGC
Found at i:1255404 original size:2 final size:2
Alignment explanation
Indices: 1255397--1255421 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1255387 TAGAATCTGG
1255397 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 T
1255422 TAAACATATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1255476 original size:12 final size:12
Alignment explanation
Indices: 1255455--1255490 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1255445 TATATTTTTT
*
1255455 TATAAAATTAAC
1 TATAAAATTAAA
*
1255467 TATTAAATTAAA
1 TATAAAATTAAA
1255479 TATAAAATTAAA
1 TATAAAATTAAA
1255491 GGAATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
TATAAAATTAAA
Found at i:1256356 original size:30 final size:29
Alignment explanation
Indices: 1256294--1256605 Score: 200
Period size: 30 Copynumber: 10.6 Consensus size: 29
1256284 CAGAACAATA
* **
1256294 AAAAATTTAAAGGACCAAAATATGATTAA-
1 AAAAACTTAAAGGACCAAAATA-GAAAAAC
*
1256323 AAAAACTT-GAGGACCAAAATAGCAAAAAC
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* *
1256352 AAAAACTTAAAGGACTAAAATAGAAAAAT
1 AAAAACTTAAAGGACCAAAATAGAAAAAC
* * * * *
1256381 AGAAATTTAAAGGACTAAAATAGCACAAAT
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* ** *
1256411 AGAAACTTAAACTACTAAAATA-ACAAAA-
1 AAAAACTTAAAGGACCAAAATAGA-AAAAC
* * *
1256439 ATAAAACTTAAAGGACTAAAATAGCACAAAG
1 A-AAAACTTAAAGGACCAAAATAG-AAAAAC
* * * *
1256470 AGAAACTTAAAGGACTAAAATAGCATAAAT
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* * *
1256500 AGAAACTTAAAGGACTAAAATAGCACAAAC
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* * *
1256530 AAAAATTTAAAGGACTAAAATAGCACAAAC
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* * * * *
1256560 AGAAACTTAAAGAACTAAAATATCACAAAC
1 AAAAACTTAAAGGACCAAAATA-GAAAAAC
*
1256590 AAAAATTTAAAGGACC
1 AAAAACTTAAAGGACC
1256606 GAATCATAAA
Statistics
Matches: 240, Mismatches: 33, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.00
28 17 0.07
29 62 0.26
30 158 0.66
31 2 0.01
ACGTcount: A:0.59, C:0.12, G:0.11, T:0.17
Consensus pattern (29 bp):
AAAAACTTAAAGGACCAAAATAGAAAAAC
Found at i:1256527 original size:60 final size:60
Alignment explanation
Indices: 1256332--1256604 Score: 379
Period size: 60 Copynumber: 4.6 Consensus size: 60
1256322 AAAAAACTTG
* * *
1256332 AGGACCAAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAG-AAAAATAGAAATTTAA
1 AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAA
* * ** *
1256391 AGGACTAAAATAGCACAAATAGAAACTTAAACTACTAAAATAACAAAAATA-AAACTTAA
1 AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAA
* * *
1256450 AGGACTAAAATAGCACAAAGAGAAACTTAAAGGACTAAAATAGCATAAATAGAAACTTAA
1 AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAA
* * *
1256510 AGGACTAAAATAGCACAAACAAAAATTTAAAGGACTAAAATAGCACAAACAGAAACTTAA
1 AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAA
* * *
1256570 AGAACTAAAATATCACAAACAAAAATTTAAAGGAC
1 AGGACTAAAATAGCACAAACAAAAACTTAAAGGAC
1256605 CGAATCATAA
Statistics
Matches: 192, Mismatches: 20, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
59 89 0.46
60 103 0.54
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (60 bp):
AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAA
Found at i:1257959 original size:3 final size:3
Alignment explanation
Indices: 1257951--1258003 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
1257941 ATATGTATAT
* * *
1257951 TAA TAA TAA TAA TAA AAA TAA TAA TAC TAA TAC TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1257999 TAA TA
1 TAA TA
1258004 GTATTTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1258460 original size:130 final size:130
Alignment explanation
Indices: 1258200--1258549 Score: 443
Period size: 130 Copynumber: 2.7 Consensus size: 130
1258190 GGTCATCTAA
* * * * **
1258200 GGGTGAGACGTCTCCTACGTGATGAGGAGATCTGGTCGGGGTATGA-TACGGTTCCTACACGATG
1 GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACTA--GTTCCTACGTGATG
* * * *
1258264 AGGATGATA-GACCATGTTTAGGGAGGGTGATAACACGGTTCCTACGTGATAAGGATGACTGGTT
64 AGGACGACATG-CCATCTTTA--G-GGGTGATAACACGGTTCCTACGTGATAAGGACGACTGGTT
1258328 ATCAAG
125 ATCAAG
* **
1258334 GGGTGACATGACTCCTACACGATGAGGAGGTCTGGTCGGGGGATGACTAGTTCCTACGTGATGAG
1 GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACTAGTTCCTACGTGATGAG
* * * * *
1258399 GACGACATGCCATCTTTAGGGGTGATAACATGGTTCCTACGTTATGAGGGCGACTGGTTATCTAG
66 GACGACATGCCATCTTTAGGGGTGATAACACGGTTCCTACGTGATAAGGACGACTGGTTATCAAG
*
1258464 GGGTGGCACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACATAGTTCCTACGTGATGA
1 GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGAC-TAGTTCCTACGTGATGA
*
1258529 GGACGGCATGCCATCTTTAGG
65 GGACGACATGCCATCTTTAGG
1258550 AATAATGGTT
Statistics
Matches: 190, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
130 83 0.44
131 38 0.20
133 27 0.14
134 40 0.21
135 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (130 bp):
GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACTAGTTCCTACGTGATGAG
GACGACATGCCATCTTTAGGGGTGATAACACGGTTCCTACGTGATAAGGACGACTGGTTATCAAG
Found at i:1258680 original size:66 final size:65
Alignment explanation
Indices: 1258558--1258701 Score: 175
Period size: 66 Copynumber: 2.2 Consensus size: 65
1258548 GGAATAATGG
* *
1258558 TTTCAAGGGAAACTGACTCAAAGATGATGCTTCAAGAGAAGCTGTCTCAAGAGAGACAAAA-TTC
1 TTTCAAGGGAAACTGACCCAAAGATGATGCTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-
1258622 A
65 A
* * * *
1258623 TTTCAAGGGAAAC-GATCCCAAAGATGGGTGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAACT
1 TTTCAAGGGAAACTGA-CCCAAAGAT-GATGCTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
*
1258687 TG
64 TA
*
1258689 TTTAAAGGGAAAC
1 TTTCAAGGGAAAC
1258702 AACTCAAATA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 2 0.03
65 21 0.31
66 43 0.63
67 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (65 bp):
TTTCAAGGGAAACTGACCCAAAGATGATGCTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
Found at i:1258914 original size:36 final size:36
Alignment explanation
Indices: 1258830--1258939 Score: 118
Period size: 36 Copynumber: 3.0 Consensus size: 36
1258820 GAAACAAACT
*
1258830 CAAAATTTGTTTCTCAAAGGAAAA-TGTCTCAAGCAAG-A
1 CAAAATTTGTTT-T--AA-GAAAACTGTCTCAAGCGAGAA
* *
1258868 CAAAATTTGTTTTAGTGAAAACTGTCTCGAGCGAGAA
1 CAAAATTTGTTTTA-AGAAAACTGTCTCAAGCGAGAA
1258905 CAAAA-TTGTTTTAAGAAAACTTGTCTCAAGCGAGA
1 CAAAATTTGTTTTAAGAAAAC-TGTCTCAAGCGAGA
1258940 CAACCCATTG
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
35 12 0.19
36 32 0.51
37 7 0.11
38 12 0.19
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (36 bp):
CAAAATTTGTTTTAAGAAAACTGTCTCAAGCGAGAA
Found at i:1260143 original size:26 final size:27
Alignment explanation
Indices: 1260103--1260190 Score: 101
Period size: 26 Copynumber: 3.3 Consensus size: 27
1260093 TTTTCATGTA
1260103 TTTCTTGTCCATTTTTCTTTGTTTTTTT
1 TTTCTT-TCCATTTTTCTTTGTTTTTTT
*
1260131 TTTCTTT-CATTTTCCTTT-TCTTTTTT
1 TTTCTTTCCATTTTTCTTTGT-TTTTTT
* *
1260157 TTTCTTTGC-TTTTTCTTTGCTATTTTT
1 TTTCTTTCCATTTTTCTTTG-TTTTTTT
1260184 TTTCTTT
1 TTTCTTT
1260191 GCCCTTTATC
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
25 1 0.02
26 31 0.58
27 14 0.26
28 7 0.13
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (27 bp):
TTTCTTTCCATTTTTCTTTGTTTTTTT
Found at i:1260163 original size:15 final size:16
Alignment explanation
Indices: 1260115--1260168 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 16
1260105 TCTTGTCCAT
*
1260115 TTTTCTTTGTTTTTT-
1 TTTTCTTTCTTTTTTC
* *
1260130 TTTTCTTTCATTTTCC
1 TTTTCTTTCTTTTTTC
1260146 TTTTCTTT-TTTTTTC
1 TTTTCTTTCTTTTTTC
*
1260161 TTTGCTTT
1 TTTTCTTT
1260169 TTCTTTGCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 24 0.75
16 8 0.25
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTTCTTTCTTTTTTC
Found at i:1260170 original size:27 final size:26
Alignment explanation
Indices: 1260115--1260192 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
1260105 TCTTGTCCAT
*
1260115 TTTTCTTTGTTTTTTTTTTCTTT-CA
1 TTTTCTTTGCTTTTTTTTTCTTTGCA
* *
1260140 TTTTCCTTTTCTTTTTTTTTCTTTGCT
1 TTTT-CTTTGCTTTTTTTTTCTTTGCA
1260167 TTTTCTTTGCTATTTTTTTTCTTTGC
1 TTTTCTTTGCT-TTTTTTTTCTTTGC
1260193 CCTTTATCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.09
26 23 0.50
27 19 0.41
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTTCTTTGCTTTTTTTTTCTTTGCA
Found at i:1273283 original size:27 final size:27
Alignment explanation
Indices: 1273253--1273335 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 27
1273243 AATATTTAAG
1273253 GAAATATAATAGAAACAAATGTGATGA
1 GAAATATAATAGAAACAAATGTGATGA
* * * * * *
1273280 GAAATGTAAAATAAA-ATAT-TTAAG-
1 GAAATATAATAGAAACAAATGTGATGA
* *
1273304 GAAATCTAATAGAAACAAATGTGATTA
1 GAAATATAATAGAAACAAATGTGATGA
1273331 GAAAT
1 GAAAT
1273336 GTAAAATAAA
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
24 12 0.30
25 6 0.15
26 5 0.12
27 17 0.43
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (27 bp):
GAAATATAATAGAAACAAATGTGATGA
Found at i:1273319 original size:51 final size:51
Alignment explanation
Indices: 1273243--1273352 Score: 202
Period size: 51 Copynumber: 2.2 Consensus size: 51
1273233 GAATATTATT
1273243 AATATTTAAGGAAATATAATAGAAACAAATGTGATGAGAAATGTAAAATAA
1 AATATTTAAGGAAATATAATAGAAACAAATGTGATGAGAAATGTAAAATAA
* *
1273294 AATATTTAAGGAAATCTAATAGAAACAAATGTGATTAGAAATGTAAAATAA
1 AATATTTAAGGAAATATAATAGAAACAAATGTGATGAGAAATGTAAAATAA
1273345 AATATTTA
1 AATATTTA
1273353 CAACATAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.55, C:0.03, G:0.14, T:0.28
Consensus pattern (51 bp):
AATATTTAAGGAAATATAATAGAAACAAATGTGATGAGAAATGTAAAATAA
Found at i:1273505 original size:29 final size:28
Alignment explanation
Indices: 1273456--1273512 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
1273446 AAAAATTTAA
*
1273456 AGGACCAAAATATGACTAACATAAACTTG
1 AGGACCAAAATATGAC-AACAGAAACTTG
1273485 AGGACCAAAATAGTAGA-AACAGAAACTT
1 AGGACCAAAATA-T-GACAACAGAAACTT
1273513 AAAAGATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 22 0.88
30 1 0.04
31 2 0.08
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.18
Consensus pattern (28 bp):
AGGACCAAAATATGACAACAGAAACTTG
Found at i:1273527 original size:30 final size:30
Alignment explanation
Indices: 1273452--1273752 Score: 317
Period size: 30 Copynumber: 10.2 Consensus size: 30
1273442 AATAAAAAAT
* * *
1273452 TTAAAGGACCAAAATATG-ACTAACATAAAC
1 TTAAAGGACTAAAATA-GCACAAACAGAAAC
* * * *
1273482 TT-GAGGACCAAAATAGTAGAAACAGAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* * * * * *
1273511 TTAAAAGATTAAAATAGAAAAAATAGAAAT
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* *
1273541 TTAAAGGACTAAAATAGTACAAATAGAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* *
1273571 TTAAAAGACTAAAATA--A-AAA-AAAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
1273597 TTAAAGGACTAAAATAGCACAAACAGAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
*
1273627 TTAAAGGACTAAAATAGCACAAACATAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* * * *
1273657 TTAAAGGACTAAAATAGCATAAATATAAAT
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* *
1273687 TTAAAGGACTAAAATAGCATAAACAAAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* *
1273717 TTAAAGGACTAAAATAGCACAAACATAAAT
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
1273747 TTAAAG
1 TTAAAG
1273753 AATCGAATCA
Statistics
Matches: 234, Mismatches: 31, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
26 20 0.09
27 3 0.01
28 3 0.01
29 26 0.11
30 182 0.78
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.19
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCACAAACAGAAAC
Found at i:1273661 original size:146 final size:145
Alignment explanation
Indices: 1273445--1273732 Score: 380
Period size: 146 Copynumber: 2.0 Consensus size: 145
1273435 ATAGAACAAT
* * * * * *
1273445 AAAAAATTTAAAGGACCAAAATATGACTAACATAAACTTGAGGACCAAAATAGTAGAAACAGAAA
1 AAAAAACTTAAAGGACCAAAATATGACAAACAGAAACTTAAGGACCAAAATAGCACAAACAGAAA
* * * *
1273510 CTTAAAAGATTAAAATAGAAAAAATAGAAATTTAAAGGACTAAAATAGTACAAATAGAAACTTAA
66 CTTAAAAGACTAAAATAGAAAAAATAGAAATTTAAAGGACTAAAATAGCACAAACAAAAACTTAA
1273575 AAGACTAAAATAAAA
131 AAGACTAAAATAAAA
* * *
1273590 AAAAAACTTAAAGGACTAAAATA-GCACAAACAGAAACTTAAAGGACTAAAATAGCACAAACATA
1 AAAAAACTTAAAGGACCAAAATATG-ACAAACAGAAACTT-AAGGACCAAAATAGCACAAACAGA
* * * * *
1273654 AACTTAAAGGACTAAAATAGCATAAATATAAATTTAAAGGACTAAAATAGCATAAACAAAAACTT
64 AACTTAAAAGACTAAAATAGAAAAAATAGAAATTTAAAGGACTAAAATAGCACAAACAAAAACTT
*
1273719 AAAGGACTAAAATA
129 AAAAGACTAAAATA
1273733 GCACAAACAT
Statistics
Matches: 122, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
144 1 0.01
145 33 0.27
146 88 0.72
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (145 bp):
AAAAAACTTAAAGGACCAAAATATGACAAACAGAAACTTAAGGACCAAAATAGCACAAACAGAAA
CTTAAAAGACTAAAATAGAAAAAATAGAAATTTAAAGGACTAAAATAGCACAAACAAAAACTTAA
AAGACTAAAATAAAA
Found at i:1284410 original size:45 final size:44
Alignment explanation
Indices: 1284360--1284548 Score: 218
Period size: 45 Copynumber: 4.5 Consensus size: 44
1284350 TTTTATGTTG
**
1284360 ATAATGCACCCATATGCATTTCAACTTTGACATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACTAAG-CATCCTTTCATGCCA
*
1284405 ATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACTAA-GCATCCTTTCATGCCA
* *
1284450 ATAATGCACCCATATGCA-TT--A-T-----T-CTTTTATGCCG
1 ATAATGCACCCATATGCATTTCAACTAAGCATCCTTTCATGCCA
* *
1284484 ATAATGCACCCATATGCATTTCAGCTAAGTCATCCTTTTATGCCA
1 ATAATGCACCCATATGCATTTCAACTAAG-CATCCTTTCATGCCA
1284529 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
1284549 ATTCTTTTGA
Statistics
Matches: 124, Mismatches: 8, Indels: 24
0.79 0.05 0.15
Matches are distributed among these distances:
34 27 0.22
35 3 0.02
38 1 0.01
41 1 0.01
44 3 0.02
45 88 0.71
46 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (44 bp):
ATAATGCACCCATATGCATTTCAACTAAGCATCCTTTCATGCCA
Found at i:1284482 original size:34 final size:34
Alignment explanation
Indices: 1284439--1284556 Score: 119
Period size: 34 Copynumber: 3.1 Consensus size: 34
1284429 CTAAGGCATC
*
1284439 CTTTCATGCCAATAATGCACCCATATGCATTATT
1 CTTTTATGCCAATAATGCACCCATATGCATTATT
*
1284473 CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTAAGTCAT
1 CTTTTATGCCAATAATGCACCCATATGCA--T----T-A-T--T
1284517 CCTTTTATGCCAATAATGCACCCATATGCATTATT
1 -CTTTTATGCCAATAATGCACCCATATGCATTATT
1284552 CTTTT
1 CTTTT
1284557 GATCATTCGT
Statistics
Matches: 70, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
34 32 0.46
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
45 28 0.40
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.37
Consensus pattern (34 bp):
CTTTTATGCCAATAATGCACCCATATGCATTATT
Found at i:1284530 original size:79 final size:79
Alignment explanation
Indices: 1284394--1284556 Score: 290
Period size: 79 Copynumber: 2.1 Consensus size: 79
1284384 CTTTGACATC
*
1284394 CTTTCATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCAC
1 CTTTTATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCAC
1284459 CCATATGCATTATT
66 CCATATGCATTATT
* * *
1284473 CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTAAGTCATCCTTTTATGCCAATAATGCAC
1 CTTTTATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCAC
1284538 CCATATGCATTATT
66 CCATATGCATTATT
1284552 CTTTT
1 CTTTT
1284557 GATCATTCGT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (79 bp):
CTTTTATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCAC
CCATATGCATTATT
Found at i:1287079 original size:3 final size:3
Alignment explanation
Indices: 1287067--1287116 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
1287057 TGCAAAAATG
*
1287067 TAA T-A TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
1287112 TAA TA
1 TAA TA
1287117 GTATTTTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1287965 original size:12 final size:12
Alignment explanation
Indices: 1287948--1287986 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1287938 GACTCAAAAA
*
1287948 TCAAATCGTTTT
1 TCAAATCATTTT
1287960 TCAAATCATTTT
1 TCAAATCATTTT
*
1287972 TCAAATCATATT
1 TCAAATCATTTT
1287984 TCA
1 TCA
1287987 TCGTTCCCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (12 bp):
TCAAATCATTTT
Found at i:1288970 original size:31 final size:31
Alignment explanation
Indices: 1288935--1288996 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1288925 ATCTTGTTGG
*
1288935 TACTAA-TTCATTTTTTTTCTTTTGTTTGTGT
1 TACTAACTT-ATTTCTTTTCTTTTGTTTGTGT
1288966 TACTAACTTATTTCTTTTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTTTCTTTTGTTTGTGT
1288997 CACTTTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.13, C:0.11, G:0.10, T:0.66
Consensus pattern (31 bp):
TACTAACTTATTTCTTTTCTTTTGTTTGTGT
Found at i:1290958 original size:33 final size:33
Alignment explanation
Indices: 1290897--1290964 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
1290887 GAATCAGTGC
* * *
1290897 TGAAGCAATCAACATCGAGTATTGGGGCATCTT
1 TGAAGCAATCAACATCAAATATTGGGGCAACTT
* *
1290930 TGAAGCAATCAACATCAAATGTTTGGGCAACTT
1 TGAAGCAATCAACATCAAATATTGGGGCAACTT
1290963 TG
1 TG
1290965 GGGATTCAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (33 bp):
TGAAGCAATCAACATCAAATATTGGGGCAACTT
Found at i:1291122 original size:36 final size:36
Alignment explanation
Indices: 1291080--1291170 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 36
1291070 CAAAGTGTCA
* **
1291080 TCTCGCTAGAGACAATTTTCTTAAAAACA-AATTTTG
1 TCTCGCTTGAGACAATTTTCGCAAAAA-AGAATTTTG
* *
1291116 TCTCGCTTGAGATAGTTTTCGCAAAAAATGAATTTTG
1 TCTCGCTTGAGACAATTTTCGCAAAAAA-GAATTTTG
*
1291153 TCTCACTTGAGACAATTT
1 TCTCGCTTGAGACAATTT
1291171 CTTTCGAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
35 1 0.02
36 22 0.49
37 22 0.49
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (36 bp):
TCTCGCTTGAGACAATTTTCGCAAAAAAGAATTTTG
Found at i:1291388 original size:38 final size:39
Alignment explanation
Indices: 1291341--1291448 Score: 173
Period size: 39 Copynumber: 2.8 Consensus size: 39
1291331 TTTTCTTGAG
1291341 AAATCTTTGAGTCTGTTTCACTTGAAACAAAA-CAAAAA
1 AAATCTTTGAGTCTGTTTCACTTGAAACAAAATCAAAAA
* *
1291379 AAATATTTGAGTCTGTTTCACTTGAAACAAAATGAAAAA
1 AAATCTTTGAGTCTGTTTCACTTGAAACAAAATCAAAAA
* *
1291418 AAATCTTTGAGTCTATTTCCCTTGAAACAAA
1 AAATCTTTGAGTCTGTTTCACTTGAAACAAA
1291449 GTTTTTTCTC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
38 31 0.48
39 33 0.52
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (39 bp):
AAATCTTTGAGTCTGTTTCACTTGAAACAAAATCAAAAA
Found at i:1291481 original size:137 final size:135
Alignment explanation
Indices: 1291276--1291670 Score: 546
Period size: 137 Copynumber: 3.0 Consensus size: 135
1291266 ATTTTCTTTT
1291276 AAAAAAAATC--TGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTCTTG
1 AAAAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTCTTG
*
1291339 AGAAATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAAAAAATATTTGAGTCTGTTTCACTTGA
66 AGAAATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAAAAAATCTTTGAGTCTGTTTCACTTGA
1291404 AACAAAA
131 AAC--AA
* * *
1291411 TGAAAAAAAATCTTTGAGTCTATTTCCCTTGAAACAAAGTTTT-T-TCTCTTGAGACAGTTTTTT
1 --AAAAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTCT
* * *
1291474 TGAGAAATCTTTGAGTCTATTTTACTTGAAAC---A-AAAAAAGATCTTTGAGTCTGTTTCACTT
64 TGAGAAATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAAAAAATCTTTGAGTCTGTTTCACTT
1291535 G----AA
129 GAAACAA
* *
1291538 AAAAAAAATCTTTGAGTTTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTCTTG
1 AAAAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTCTTG
* * *
1291603 AGAAATTTTTGAG-CATGTTTCACTTGAAACAAAACAAAAAAAATCTTTGAGTCGGTTTCTCTTG
66 AGAAATCTTTGAGTC-TGTTTCACTTGAAACAAAACAAAAAAAATCTTTGAGTCTGTTTCACTTG
1291667 AAAC
130 AAAC
1291671 CATTATCCCT
Statistics
Matches: 228, Mismatches: 17, Indels: 28
0.84 0.06 0.10
Matches are distributed among these distances:
125 39 0.17
126 2 0.01
127 46 0.20
130 1 0.00
131 26 0.11
133 27 0.12
134 1 0.00
137 58 0.25
138 1 0.00
139 27 0.12
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (135 bp):
AAAAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTCTTG
AGAAATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAAAAAATCTTTGAGTCTGTTTCACTTGA
AACAA
Found at i:1291523 original size:34 final size:33
Alignment explanation
Indices: 1291478--1291573 Score: 133
Period size: 31 Copynumber: 2.9 Consensus size: 33
1291468 TTTTTTTGAG
* *
1291478 AAATCTTTGAGTCTATTTTACTTGAAACAAAAA
1 AAATCTTTGAGTCTGTTTCACTTGAAACAAAAA
1291511 AAGATCTTTGAGTCTGTTTCACTTG-AA-AAAAA
1 AA-ATCTTTGAGTCTGTTTCACTTGAAACAAAAA
* *
1291543 AAATCTTTGAGTTTGTTTCCCTTGAAACAAA
1 AAATCTTTGAGTCTGTTTCACTTGAAACAAA
1291574 GTTTTGTCTC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
31 20 0.36
32 9 0.16
33 7 0.12
34 20 0.36
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (33 bp):
AAATCTTTGAGTCTGTTTCACTTGAAACAAAAA
Found at i:1292115 original size:132 final size:129
Alignment explanation
Indices: 1291675--1292153 Score: 520
Period size: 127 Copynumber: 3.7 Consensus size: 129
1291665 TGAAACCATT
** ** * * *
1291675 ATCCCTAAAGATGACATGTCATCCTCATCACGTAGGAACCATGTCATCCACTGACCAGACCTCCT
1 ATCCCTAAAGATGGTATAACATCCTCATCACGTATGAA-CGTGTCATCCACCGACCAGACCTCCT
* * * * *
1291740 CATCATGTAGGAGTCGTGTCAACCTCAGATAACCAGCCGTCTTCATCACGTAGGAATCGTGTTAT
65 CATCACGTAGGAGCCGTGTC-ACCCCAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTAT
1291805 C
129 C
* * *
1291806 ATCCCTAAAGATGGTATACCATCCTCATCACGTATGAACTGTTTCATCC-CCTAACCAGA---CC
1 ATCCCTAAAGATGGTATAACATCCTCATCACGTATGAAC-GTGTCATCCACC-GACCAGACCTCC
* * * * * *
1291867 TCATCACGTAGGAGCCGTGTCACCCCTGATAACCAGTCATCCTAATCATGTAGGAACTGTGTTAT
64 TCATCACGTAGGAGCCGTGTCACCCCAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTAT
1291932 C
129 C
** * *
1291933 ATCCCTAAAGATGGTATGTCATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGACCTCCT
1 ATCCCTAAAGATGGTATAACATCCTCATCACGTATGAA-CGTGTCATCCACCGACCAGACCTCCT
** *
1291998 CATCACGTAGGAGCCGTGTCACCCCAGATAATAAG-CGTCCTCATCGCGTAGGAACCGTGTTATC
65 CATCACGTAGGAGCCGTGTCACCCCAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
* * * * *
1292062 ACTCTCCCTAAAGATGGCCAAAAC-TCTTCATCACGTATGAGTCGTGTCATCCACCGACCAGATC
1 A---TCCCTAAAGATGG-TATAACATCCTCATCACGTATGA-ACGTGTCATCCACCGACCAGACC
*
1292126 TCCTTATCACGTAGGAGCCGTGTCACCC
61 TCCTCATCACGTAGGAGCCGTGTCACCC
1292154 TTAAACGACC
Statistics
Matches: 292, Mismatches: 44, Indels: 23
0.81 0.12 0.06
Matches are distributed among these distances:
127 84 0.29
128 24 0.08
129 25 0.09
130 37 0.13
131 46 0.16
132 74 0.25
133 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (129 bp):
ATCCCTAAAGATGGTATAACATCCTCATCACGTATGAACGTGTCATCCACCGACCAGACCTCCTC
ATCACGTAGGAGCCGTGTCACCCCAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
Found at i:1296003 original size:24 final size:24
Alignment explanation
Indices: 1295975--1296026 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1295965 TAAACCGATT
*
1295975 GAACCGCTACTAGTGAACCGGCTA
1 GAACCGCTACTAGTGAACCGGCCA
* *
1295999 GAACCGTTATTAGTGAACCGGCCA
1 GAACCGCTACTAGTGAACCGGCCA
1296023 GAAC
1 GAAC
1296027 TGTTGAACCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (24 bp):
GAACCGCTACTAGTGAACCGGCCA
Found at i:1300001 original size:2 final size:2
Alignment explanation
Indices: 1299994--1300020 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1299984 GCAATATGTA
1299994 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 A
1300021 AAGTCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1304048 original size:18 final size:18
Alignment explanation
Indices: 1304025--1304062 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1304015 CATTTGATCT
*
1304025 TCTGGTCGTGCTTGTTCC
1 TCTGGTCGAGCTTGTTCC
*
1304043 TCTGGTGGAGCTTGTTCC
1 TCTGGTCGAGCTTGTTCC
1304061 TC
1 TC
1304063 GTGCTGTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.26, G:0.29, T:0.42
Consensus pattern (18 bp):
TCTGGTCGAGCTTGTTCC
Found at i:1305718 original size:21 final size:21
Alignment explanation
Indices: 1305650--1305707 Score: 89
Period size: 22 Copynumber: 2.7 Consensus size: 21
1305640 GGGGTATCGA
* *
1305650 TTCCCCTACAGGGGGAATCAG
1 TTCCCCTTCAAGGGGAATCAG
1305671 TTCCCCTTCAAAGGGGAATCAG
1 TTCCCCTTC-AAGGGGAATCAG
1305693 TTCCCCTTCAAGGGG
1 TTCCCCTTCAAGGGG
1305708 TATCGATTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 14 0.41
22 20 0.59
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.22
Consensus pattern (21 bp):
TTCCCCTTCAAGGGGAATCAG
Found at i:1312187 original size:15 final size:15
Alignment explanation
Indices: 1312167--1312199 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1312157 CTGGGTAGCC
1312167 TTAACTTCCACCCAT
1 TTAACTTCCACCCAT
1312182 TTAACTTCCACCCAT
1 TTAACTTCCACCCAT
1312197 TTA
1 TTA
1312200 GAAACATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAACTTCCACCCAT
Found at i:1316900 original size:13 final size:13
Alignment explanation
Indices: 1316875--1316975 Score: 64
Period size: 14 Copynumber: 7.3 Consensus size: 13
1316865 AGAATTACAG
1316875 ATAAAGATAAAA-A
1 ATAAA-ATAAAATA
1316888 TATAAGAATAAAATA
1 -ATAA-AATAAAATA
1316903 ATAAAAT-AAATA
1 ATAAAATAAAATA
1316915 ATAAAATATAAATTA
1 ATAAAATA-AAA-TA
* * *
1316930 TTTTAAATAGAAT-
1 -ATAAAATAAAATA
*
1316943 ATAAGGATAAAATA
1 ATAA-AATAAAATA
1316957 ATAAAATAATAAATA
1 ATAAAAT-A-AAATA
1316972 ATAA
1 ATAA
1316976 TTATAAGATA
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
12 14 0.20
13 11 0.16
14 23 0.33
15 15 0.22
16 6 0.09
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (13 bp):
ATAAAATAAAATA
Found at i:1316915 original size:12 final size:12
Alignment explanation
Indices: 1316875--1316922 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
1316865 AGAATTACAG
*
1316875 ATAAAGATAAAAA
1 ATAAA-ATAAATA
1316888 TATAAGAATAAAATA
1 -ATAA-AAT-AAATA
1316903 ATAAAATAAATA
1 ATAAAATAAATA
1316915 ATAAAATA
1 ATAAAATA
1316923 TAAATTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 13 0.42
13 3 0.10
14 10 0.32
15 5 0.16
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (12 bp):
ATAAAATAAATA
Found at i:1316917 original size:20 final size:20
Alignment explanation
Indices: 1316875--1316926 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1316865 AGAATTACAG
1316875 ATAAAGATA-AAAATATAAGA
1 ATAAA-ATATAAAATATAAGA
*
1316895 ATAAAATAATAAAATA-AATA
1 ATAAAAT-ATAAAATATAAGA
1316915 ATAAAATATAAA
1 ATAAAATATAAA
1316927 TTATTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.24
20 16 0.55
21 6 0.21
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (20 bp):
ATAAAATATAAAATATAAGA
Found at i:1316998 original size:46 final size:42
Alignment explanation
Indices: 1316903--1316998 Score: 97
Period size: 42 Copynumber: 2.2 Consensus size: 42
1316893 GAATAAAATA
* * *
1316903 ATAAA-AT-AAATAATAAAATATAAATTATTTTAAATAGAAT
1 ATAAAGATAAAATAATAAAATATAAATAATATTAAAGAGAAT
* *
1316943 ATAAGGATAAAATAATAAAATAATAAATAATAATTATAAGATAAT
1 ATAAAGATAAAATAATAAAAT-ATAAATAAT-ATTA-AAGAGAAT
1316988 GATAAAGATAA
1 -ATAAAGATAA
1316999 CAAGGGAGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
40 4 0.09
41 2 0.05
42 12 0.27
43 8 0.18
44 3 0.07
45 6 0.14
46 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (42 bp):
ATAAAGATAAAATAATAAAATATAAATAATATTAAAGAGAAT
Found at i:1317848 original size:7 final size:7
Alignment explanation
Indices: 1317836--1317865 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1317826 CTTCGCATCA
1317836 TATTCTT
1 TATTCTT
*
1317843 TATTCTA
1 TATTCTT
1317850 TATTCTT
1 TATTCTT
1317857 TATTCTT
1 TATTCTT
1317864 TA
1 TA
1317866 CATTCCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTCTT
Found at i:1321134 original size:25 final size:25
Alignment explanation
Indices: 1321118--1321187 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 25
1321108 GAAAGAAAAG
1321118 AAGAAAAAGGAA-AAAGAAAAAATAA
1 AAGAAAAA-GAATAAAGAAAAAATAA
1321143 AAGAAAAAGAATAAAGAATAAAGA-ATA
1 AAGAAAAAGAATAAAGAA-AAA-ATA-A
1321170 AAG-AAAAGAA-AAAGAAAA
1 AAGAAAAAGAATAAAGAAAA
1321188 GAAAAAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
24 5 0.12
25 20 0.49
26 11 0.27
27 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.06
Consensus pattern (25 bp):
AAGAAAAAGAATAAAGAAAAAATAA
Found at i:1321136 original size:6 final size:6
Alignment explanation
Indices: 1321118--1321193 Score: 86
Period size: 6 Copynumber: 12.3 Consensus size: 6
1321108 GAAAGAAAAG
1321118 AAGAAA AAGGAAA AAGAAA AA-ATAA AAGAAA AAGAATA AAGAATA AAGAATA
1 AAGAAA AA-GAAA AAGAAA AAGA-AA AAGAAA AAGAA-A AAGAA-A AAGAA-A
1321170 AAG-AA AAGAAA AAG-AA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AA
1321194 AATAAGAGGT
Statistics
Matches: 64, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
5 10 0.16
6 29 0.45
7 25 0.39
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:1321138 original size:14 final size:13
Alignment explanation
Indices: 1321109--1321194 Score: 90
Period size: 12 Copynumber: 6.8 Consensus size: 13
1321099 TACATATAAG
1321109 AAAGAAAAGAAGAA
1 AAAGAAAA-AAGAA
*
1321123 AAAGGAAAAAGAA
1 AAAGAAAAAAGAA
*
1321136 AAA-ATAAAAGAA
1 AAAGAAAAAAGAA
*
1321148 AAAGAATAAAGAA
1 AAAGAAAAAAGAA
*
1321161 TAAAGAATAAAG-A
1 -AAAGAAAAAAGAA
1321174 AAAG-AAAAAG-A
1 AAAGAAAAAAGAA
1321185 AAAGAAAAAA
1 AAAGAAAAAA
1321195 ATAAGAGGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
11 10 0.16
12 19 0.30
13 16 0.25
14 18 0.29
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:1321177 original size:32 final size:31
Alignment explanation
Indices: 1321109--1321187 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
1321099 TACATATAAG
*
1321109 AAAGAAAAGAAGAAAAAGGAAAAAGAAAAAATA
1 AAAG-AAA-AAGAAAAAGGAAAAAGAAAAAAGA
*
1321142 AAAGAAAAAGAATAAA-GAATAAAGAATAAAGA
1 AAAGAAAAAGAA-AAAGGAA-AAAGAAAAAAGA
1321174 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
1321188 GAAAAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 10 0.24
32 28 0.67
33 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (31 bp):
AAAGAAAAAGAAAAAGGAAAAAGAAAAAAGA
Found at i:1322517 original size:136 final size:135
Alignment explanation
Indices: 1322132--1322538 Score: 472
Period size: 136 Copynumber: 3.0 Consensus size: 135
1322122 TAAACTGATC
* * **
1322132 AACATTTTTGATGGAGAGCTCATAATGATAAGAATTCATTTGACAGAGGGAGAAGAAGTTCATAA
1 AACATTTTCGATGGAGAGTTCATAATGATAAGAATTCATCCGACAGAGGGAGAAGAAGTTCATAA
* * *
1322197 TGAGAAGAACTTGTTTGACCTATTGCTCAATTCACCATACTTCAAATTAGCAACACCTCGCTTGA
66 TGAGAAGAACTTGTTTGACCTATTGCTCAATTCA-CAAACTTCAAATCAACAACACCTCGCTTGA
1322262 GGGATT
130 GGGATT
* * * * *
1322268 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACACAGGGAGAAGAAGTTCATAA
1 AACATTTTCGATGGAGAGTTCATAATGATAAGAATTCATCCGACAGAGGGAGAAGAAGTTCATAA
* ** * * **
1322333 TGAGAAGAACTTGTTTGACCTATTGTTTGATACACAACACTTCGAATCAACAATGCCTCGCTTGA
66 TGAGAAGAACTTGTTTGACCTATTGCTCAATTCACAA-ACTTCAAATCAACAACACCTCGCTTGA
1322398 GGGATT
130 GGGATT
* * * * * *
1322404 GACGTTTTCGATGGAGAGTTTATAATGATAAGAATTAATCCAAAAGAGGGAGAAGAAGTTCATAA
1 AACATTTTCGATGGAGAGTTCATAATGATAAGAATTCATCCGACAGAGGGAGAAGAAGTTCATAA
* * * * * * * * * *
1322469 TGAGAAGAAATTGTTCGACCTGTTGCTCAATTTATAAAGCTTTAAATCAGCGACACATCACTTGA
66 TGAGAAGAACTTGTTTGACCTATTGCTCAATTCACAAA-CTTCAAATCAACAACACCTCGCTTGA
1322534 GGGAT
130 GGGAT
1322539 CAATATTTCC
Statistics
Matches: 222, Mismatches: 47, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
135 3 0.01
136 219 0.99
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (135 bp):
AACATTTTCGATGGAGAGTTCATAATGATAAGAATTCATCCGACAGAGGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTTGACCTATTGCTCAATTCACAAACTTCAAATCAACAACACCTCGCTTGAG
GGATT
Found at i:1324596 original size:20 final size:19
Alignment explanation
Indices: 1324552--1324663 Score: 84
Period size: 21 Copynumber: 5.6 Consensus size: 19
1324542 AATAAAGTTA
*
1324552 AAAAAGATAGAAAATGAAAATG
1 AAAAA-ATA-AAAAAGAAAA-G
1324574 AAAAAATGAAAAAAGAAAAG
1 AAAAAAT-AAAAAAGAAAAG
1324594 AAAAAA-AAAGAAAGAAAGAG
1 AAAAAATAAA-AAAGAAA-AG
* *
1324614 TAAAGATAGAAAAAGAAGAAG
1 AAAAAATA-AAAAAGAA-AAG
* * *
1324635 AAAAAGTGAAAAAGAGAA-
1 AAAAAATAAAAAAGAAAAG
1324653 AAAAAATAAAA
1 AAAAAATAAAA
1324664 TAAATCAAGT
Statistics
Matches: 74, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
18 12 0.16
19 9 0.12
20 20 0.27
21 24 0.32
22 9 0.12
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAAAATAAAAAAGAAAAG
Found at i:1324600 original size:15 final size:14
Alignment explanation
Indices: 1324551--1324610 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 14
1324541 CAATAAAGTT
*
1324551 AAAAAAGATAGAAA
1 AAAAAAGAAAGAAA
*
1324565 ATGAAAATGAAA-AAA
1 A--AAAAAGAAAGAAA
1324580 TGAAAAAAGAAAAGAAA
1 --AAAAAAG-AAAGAAA
1324597 AAAAAAGAAAGAAA
1 AAAAAAGAAAGAAA
1324611 GAGTAAAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
14 8 0.22
15 15 0.41
16 10 0.27
17 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAAAAGAAAGAAA
Found at i:1324652 original size:28 final size:28
Alignment explanation
Indices: 1324589--1324658 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
1324579 ATGAAAAAAG
*
1324589 AAAAGA-AAAAAAAAGAAAGAAAGAGTA
1 AAAAGAGAAAAAAAAGAAAGAAAAAGTA
* * *
1324616 AAGATAGAAAAAGAAG-AAGAAAAAGTGA
1 AAAAGAGAAAAAAAAGAAAGAAAAAGT-A
1324644 AAAAGAGAAAAAAAA
1 AAAAGAGAAAAAAAA
1324659 TAAAATAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
27 13 0.38
28 21 0.62
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (28 bp):
AAAAGAGAAAAAAAAGAAAGAAAAAGTA
Found at i:1326737 original size:54 final size:54
Alignment explanation
Indices: 1326640--1327309 Score: 925
Period size: 54 Copynumber: 12.4 Consensus size: 54
1326630 TTCCTTGGTT
* * * * * *
1326640 TTGCACACAGAGGGCCGATACAATAATTCACAAGCTCATTATGAATTA-TATGGG
1 TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACT-TAGG
* * * *
1326694 TTGTACGCATAGTGTCAATACGATAATTCACAAACTCGTTATGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGG
* * * *
1326748 TTGCACCCATAGTTCCAATACAATAATTCACAAACTTATTATGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGG
*
1326802 TTGCACACATAGTGCTAATACGATAATTCACAAACAT-ATTATGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGATAATTCACAAAC-TCATTATGAATTACTTAGG
* * *
1326856 TTGCACACATAGTGTCAATACGGTAATTCACAAACTTATTATGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGG
* *
1326910 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTTGG
1 TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGG
* *
1326964 TTGCACACATAGTGGCAATAC-AGTAATTCACAAACTCATTGTGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGA-TAATTCACAAACTCATTATGAATTACTTAGG
* * * * *
1327018 TTGCACACATAGTGTCAATACGGTAATTCAAAAACTCATTGTCAATTACTTAGG
1 TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGG
* * *
1327072 TTGCACACATAGTGCCAATACGGTAATTAACAAACTCATTGTGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGG
* * *
1327126 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTGTGAATTACTTGGG
1 TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGG
* * * *
1327180 CTGGACACATAGTGCCAATACGGTAATTCACAAACTCATTTTGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGG
* *
1327234 TTGCATACATAGTGCCAATAC-ATTAATTCACAAACTCATTATGAATTACTTGGG
1 TTGCACACATAGTGCCAATACGA-TAATTCACAAACTCATTATGAATTACTTAGG
1327288 TTGCACACATAGTGCCAATACG
1 TTGCACACATAGTGCCAATACG
1327310 GTAAATGCAA
Statistics
Matches: 557, Mismatches: 52, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
53 1 0.00
54 554 0.99
55 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGG
Found at i:1326865 original size:27 final size:27
Alignment explanation
Indices: 1326784--1326920 Score: 72
Period size: 27 Copynumber: 5.1 Consensus size: 27
1326774 TTCACAAACT
1326784 TATTATGAATTACTTAGGTTGCACACA
1 TATTATGAATTACTTAGGTTGCACACA
** * *
1326811 TAGTGCT-AA-TACGATA-ATT-CACAAACA
1 TA-TTATGAATTAC-TTAGGTTGCAC--ACA
1326838 TATTATGAATTACTTAGGTTGCACACA
1 TATTATGAATTACTTAGGTTGCACACA
* * * * * *
1326865 TAGTGTCAA-TACGGTA-ATT-CACAAACT
1 TATTATGAATTAC-TTAGGTTGCAC--ACA
1326892 TATTATGAATTACTTAGGTTGCACACA
1 TATTATGAATTACTTAGGTTGCACACA
1326919 TA
1 TA
1326921 GTGCCAATAC
Statistics
Matches: 76, Mismatches: 20, Indels: 28
0.61 0.16 0.23
Matches are distributed among these distances:
25 6 0.08
26 12 0.16
27 40 0.53
28 12 0.16
29 6 0.08
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (27 bp):
TATTATGAATTACTTAGGTTGCACACA
Found at i:1333445 original size:54 final size:54
Alignment explanation
Indices: 1333370--1335060 Score: 2130
Period size: 54 Copynumber: 31.3 Consensus size: 54
1333360 GTGATATTGT
* * * * *
1333370 ACACATAGTGCCGATAGGGTAATTCACAAACTCATTGTGAATTACGTGGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * *
1333424 AAACATAGTGTCAATACGGTAATTCACAAACGCATTATGAATTATTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * *** * * *
1333478 ACCCATAGTTCCAATACAACAATTTATAAACTTATTATGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * * *
1333532 ACACATAGTGCCAATATGGTTATTCACAAACTCATTACGAATTACATAGGTTAC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * *
1333586 ACACATAGTACCAATATGGTAATTCACAAACTCATTATGAATTACTTAGGTTGA
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* ** *
1333640 ACACATATTGCCAATACAATAATTCACAAACTCATTGTGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
*
1333694 ACACTTAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * * * *
1333748 ACGCATAGTGACAATACGGTAAATAACAAACTCATTGTGAATTACTTAGGTTGG
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * *
1333802 ACACATAGTGACAATATGGTAATTCACAAACTCGTTGTGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * *
1333856 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTAC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * *
1333910 ACACATAGTGTCAATACGGTAATTCACAAACTCATTGTGAATTACTTAGATTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * * * *
1333964 ACATATAGTGCTAATATGGTAATTAACAAACTCATTGTGAATTACTTAGGTTTC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
*
1334018 ACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* *
1334072 ACCCATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACATAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * *
1334126 ACCCATAGTGCCAATACGGTAATTCACAAACTTAATATGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* *
1334180 TC-CATAGTGCCATTACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * ** * * **
1334233 ACAAATAGTACCAATACAATAATTTACAAACTCGTTGCGAATTACTTAGGTTG-
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * * * * *
1334286 AGAACATAGTGTCAGTATGGTAATTCATAAACTTATTATAAATTACTTAGGTTGC
1 A-CACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* *
1334341 ACACGTAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTTGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * * *
1334395 ACACATAGTGACAATACAGTAAATCACAAAATCATTGTGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * *
1334449 ACACATAGTGCCAATACTGTAATTCACAAACTCATTGTGAATTA-TGTGGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACT-TAGGTTGC
* ** * * * *
1334503 ACGCATAGTGATAATACGATATTTCACAAACTCATTATGAATTATTTAGGTTCC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * * * * * *
1334557 ACCCATAATGTCAATACGATAATTCAAAAACTTATTATGAATTATTTAGGTTGA
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* *
1334611 ACACATAGTGCGAATACGGTAATTCACAAACTGATTATGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
*
1334665 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTTGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
** * *
1334719 ACACATAGTGATAATACAGTAATTCACAAACTCATTGTGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * *
1334773 AAATATAGTGTCAATACGGTAATTCAAAAACTCATTATGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * *
1334827 ACACATATTGACAATACGATAATTCACAAACTCATTGTGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * * *
1334881 ACACATAGTGTCAATATGGTAATTCTCAAACTCATTGTGAATTA-TGTGGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACT-TAGGTTGC
* * * * *
1334935 ACACATAGTGCAAATACGATAATTCATAATCTCATTTTGAATTACTTAGGTTGC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* * * * * *
1334989 ATACATAGTGCCAATATGGTAATTCACAAACTCATTGTGAATTACGTGGGTTAC
1 ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
* *
1335043 ACACATAATACCAATACG
1 ACACATAGTGCCAATACG
1335061 ATAAATGCAA
Statistics
Matches: 1404, Mismatches: 226, Indels: 14
0.85 0.14 0.01
Matches are distributed among these distances:
53 52 0.04
54 1349 0.96
55 3 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (54 bp):
ACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGC
Found at i:1338831 original size:2 final size:2
Alignment explanation
Indices: 1338824--1338991 Score: 336
Period size: 2 Copynumber: 84.0 Consensus size: 2
1338814 TCATTTCAGG
1338824 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1338866 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1338908 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1338950 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1338992 TACGTACGCA
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 166 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1339004 original size:8 final size:8
Alignment explanation
Indices: 1338993--1339029 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
1338983 ACACACACAT
1338993 ACGTACGC
1 ACGTACGC
1339001 ACGTACGC
1 ACGTACGC
1339009 ACGTACGC
1 ACGTACGC
1339017 ACGTACGC
1 ACGTACGC
1339025 ACGTA
1 ACGTA
1339030 TGTACATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.27, C:0.35, G:0.24, T:0.14
Consensus pattern (8 bp):
ACGTACGC
Found at i:1339049 original size:4 final size:4
Alignment explanation
Indices: 1339040--1339151 Score: 156
Period size: 4 Copynumber: 28.5 Consensus size: 4
1339030 TGTACATATG
* *
1339040 TACA TACA TACA TACA TACA TACA TACA TACG TACA TACA TACA TACG
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
1339088 TACA TACA TACG TAC- -ACA TACA TACG TACA TACA TACG TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
1339134 TATA TACA TACA TACA TA
1 TACA TACA TACA TACA TA
1339152 ATTCTTACAG
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
2 2 0.02
4 93 0.98
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:1339753 original size:41 final size:41
Alignment explanation
Indices: 1339651--1339761 Score: 102
Period size: 41 Copynumber: 2.7 Consensus size: 41
1339641 AAGTCTTTCG
* * * * *
1339651 GGCCGTCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTC
1 GGCCATCAGTAAGTCCTTCGAGCAAGATGCATAAATCCTTA
* *
1339692 GGTCATCTA-TAAG-CCTTTCGAGCAAGATG-ATAAGTCCTTA
1 GGCCATC-AGTAAGTCC-TTCGAGCAAGATGCATAAATCCTTA
*
1339732 GAGCCATCAGTAAGTCCTTCGAGCAGGATG
1 G-GCCATCAGTAAGTCCTTCGAGCAAGATG
1339762 TTTTCGCATG
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
40 11 0.20
41 42 0.75
42 3 0.05
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (41 bp):
GGCCATCAGTAAGTCCTTCGAGCAAGATGCATAAATCCTTA
Found at i:1341210 original size:37 final size:37
Alignment explanation
Indices: 1341168--1341239 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
1341158 ATTCATTCCC
*
1341168 GTGGAAGCTTATTGTGTGAGGATTCAACATATTCTTT
1 GTGGAAGCTTATTGTGTGAGGATTCAAAATATTCTTT
*
1341205 GTGGAAGCTTGTTGTGTGAGGATTCAAAATATTCT
1 GTGGAAGCTTATTGTGTGAGGATTCAAAATATTCT
1341240 ATTAGTTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.25, C:0.10, G:0.26, T:0.39
Consensus pattern (37 bp):
GTGGAAGCTTATTGTGTGAGGATTCAAAATATTCTTT
Found at i:1346365 original size:18 final size:17
Alignment explanation
Indices: 1346342--1346384 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1346332 AAATAATAAA
1346342 TTTATTCTTTCATTTAT-T
1 TTTATT-TTT-ATTTATAT
*
1346360 TTTATTTTTATTTTTAT
1 TTTATTTTTATTTATAT
1346377 TTTATTTT
1 TTTATTTT
1346385 GTGTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 12 0.52
18 6 0.26
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTTATTTATAT
Found at i:1346373 original size:5 final size:6
Alignment explanation
Indices: 1346354--1346384 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1346344 TATTCTTTCA
1346354 TTTATT TTTATT TTTATT TTTA-T TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT
1346385 GTGTATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:1351253 original size:134 final size:134
Alignment explanation
Indices: 1350953--1351639 Score: 803
Period size: 134 Copynumber: 5.1 Consensus size: 134
1350943 GCAATTCGAA
* * * * *
1350953 CTCGATTCAATCTTCCCTGAGTAACAGTGAAATGAATCAACA-TCCCCAGATGTGATTTTTCCTA
1 CTCGATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAA-AGTCCCCAGATCTGATTTTCCCTC
* *
1351017 AAGAAGAAGTGAAACAAATCCCTCTCTTTTAAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
65 AAGAAGAAGCGAAACAAATCCCTCTCTTTT-CAGATTTGATATTCCCTGAGTAACAGTGGAACAA
1351082 GTCTGC
129 GTCTGC
* * * * *
1351088 CTCTATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAAAGTCCCCAGATATGATTTTACCTTA
1 CTCGATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
* * * *
1351153 GGAAGAAGCGAAACATATCCCTCTCTTTTCAGATTTGATATTCCTTGATTAACAGTGGAACAAGT
66 AGAAGAAGCGAAACAAATCCCTCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
1351218 CTGC
131 CTGC
* * * * * *
1351222 CTCGATTCAATATTCCCTAAGTCACATTGGAATGAATCAACGTCCCCATATCTGATTTTCCCCCA
1 CTCGATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
* * ** *
1351287 AGAAGAAGTGTAACATGTCCCTCTCTTTTCAGATTTGATATTCCCTGAGTAACAATGGAACAAGT
66 AGAAGAAGCGAAACAAATCCCTCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
1351352 CTGC
131 CTGC
* * * * * * * *
1351356 CACAATTCAATCTTCCCTGAA-TGATAGTAGAATGAATCAACA-TCCCTATATCTAATTTTCCCT
1 CTCGATTCAATCTTCCCT-AAGTAACAGTGGAATGAATCAA-AGTCCCCAGATCTGATTTTCCCT
* * * * *
1351419 CAAGAAAAAG-TAGAACAAATCCATCTC-TTTCAAGATTTGATATTCCCTGAGTAATAGTGGAAA
64 CAAGAAGAAGCGA-AACAAATCCCTCTCTTTTC-AGATTTGATATTCCCTGAGTAACAGTGGAAC
*
1351482 AAGTTTGC
127 AAGTCTGC
* * * * *
1351490 CTCGATTCAATTTTCCCTGAGTAACAGTGGAGTGAATCAATG-CCCCTTGATCTGATTTTCCCTC
1 CTCGATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAAAGTCCCC-AGATCTGATTTTCCCTC
* * *
1351554 AAGAAGAAGCGAAACAGATCCCTCTC-TTTCAAGATTTGATATTCCCTTAGTAACAGCGGAACAA
65 AAGAAGAAGCGAAACAAATCCCTCTCTTTTC-AGATTTGATATTCCCTGAGTAACAGTGGAACAA
1351618 GTCTGC
129 GTCTGC
*
1351624 CTTGATTCAATCTTCC
1 CTCGATTCAATCTTCC
1351640 ATGAAGAACA
Statistics
Matches: 468, Mismatches: 75, Indels: 19
0.83 0.13 0.03
Matches are distributed among these distances:
133 8 0.02
134 375 0.80
135 85 0.18
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
AGAAGAAGCGAAACAAATCCCTCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTGC
Done.