Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007466.1 Hibiscus syriacus cultivar Beakdansim tig00020485_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: 207968
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1072 original size:9 final size:9
Alignment explanation
Indices: 1058--1092 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
1048 ATTTCTCATC
1058 TTCTTTTTT
1 TTCTTTTTT
1067 TTC-TTTTT
1 TTCTTTTTT
1075 TTCTTTTTT
1 TTCTTTTTT
1084 TTCTTTTTT
1 TTCTTTTTT
1093 CTGATGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:1073 original size:8 final size:8
Alignment explanation
Indices: 1062--1092 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1052 CTCATCTTCT
1062 TTTTTTTC
1 TTTTTTTC
1070 TTTTTTTC
1 TTTTTTTC
1078 TTTTTTTTC
1 -TTTTTTTC
1087 TTTTTT
1 TTTTTT
1093 CTGATGAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1078 original size:17 final size:17
Alignment explanation
Indices: 1058--1092 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1048 ATTTCTCATC
1058 TTCTTTTTTTTCTTTTT
1 TTCTTTTTTTTCTTTTT
1075 TTCTTTTTTTTCTTTTT
1 TTCTTTTTTTTCTTTTT
1092 T
1 T
1093 CTGATGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTCTTTTTTTTCTTTTT
Found at i:3473 original size:16 final size:16
Alignment explanation
Indices: 3452--3485 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3442 GTCGAAATCC
3452 TTATTTTAATGAATGA
1 TTATTTTAATGAATGA
*
3468 TTATTTTAATGCATGA
1 TTATTTTAATGAATGA
3484 TT
1 TT
3486 TGGAAATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (16 bp):
TTATTTTAATGAATGA
Found at i:3569 original size:16 final size:17
Alignment explanation
Indices: 3548--3584 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3538 AAATTTATGA
3548 AAAAATAA-AA-ATAAAT
1 AAAAATAAGAAGA-AAAT
3564 AAAAATAAGAAGAAAAT
1 AAAAATAAGAAGAAAAT
3581 AAAA
1 AAAA
3585 TGGTTAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 10 0.53
18 1 0.05
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAAATAAGAAGAAAAT
Found at i:6520 original size:3 final size:3
Alignment explanation
Indices: 6512--6566 Score: 101
Period size: 3 Copynumber: 18.0 Consensus size: 3
6502 AATATTTATT
6512 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
6558 TAA TAA TAA
1 TAA TAA TAA
6567 AATCATAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:11031 original size:36 final size:36
Alignment explanation
Indices: 10992--11375 Score: 347
Period size: 36 Copynumber: 10.7 Consensus size: 36
10982 CATGGATAAA
* * *
10992 ATATCATGCTTATAATCATTATTCGCAAGCACATGA
1 ATATCATGCATATAATCATTATTAGCAAGCACATGT
** * **
11028 ATATCATGCATATAATCATTAGCAACAAGCGTATGT
1 ATATCATGCATATAATCATTATTAGCAAGCACATGT
* ** *
11064 ATATCATGCATGTAATCATTGGTAGCAAGCACATCT
1 ATATCATGCATATAATCATTATTAGCAAGCACATGT
* * * * *
11100 ATATCATACATATGATCATCATTAGCAGGCGCATGT
1 ATATCATGCATATAATCATTATTAGCAAGCACATGT
* *
11136 ATACCATGCATATAATCATTATTAGCAAGCATATGT
1 ATATCATGCATATAATCATTATTAGCAAGCACATGT
* * * * *
11172 ATACCATGTATATAATCATTATTAGTAGGCGCATGT
1 ATATCATGCATATAATCATTATTAGCAAGCACATGT
** *
11208 ATATCATGCATATAATCATTATTAGCAAGTGCATAT
1 ATATCATGCATATAATCATTATTAGCAAGCACATGT
* * *
11244 GTATCATGCATATGATCATTATTAG-AAGGCGCATGT
1 ATATCATGCATATAATCATTATTAGCAA-GCACATGT
* * ** ** ** *
11280 ATACCATGCATATGATCATTAACAATAAGCGTATAT
1 ATATCATGCATATAATCATTATTAGCAAGCACATGT
* * ** *
11316 ATATCATGCATGTAATCATTAGTAGCAAGCGTAGGT
1 ATATCATGCATATAATCATTATTAGCAAGCACATGT
*
11352 ATATCATGCATATGATCATTATTA
1 ATATCATGCATATAATCATTATTA
11376 ACATGTGCAT
Statistics
Matches: 281, Mismatches: 65, Indels: 4
0.80 0.19 0.01
Matches are distributed among these distances:
35 2 0.01
36 277 0.99
37 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (36 bp):
ATATCATGCATATAATCATTATTAGCAAGCACATGT
Found at i:11388 original size:72 final size:72
Alignment explanation
Indices: 10992--11390 Score: 388
Period size: 72 Copynumber: 5.5 Consensus size: 72
10982 CATGGATAAA
* * * ** *
10992 ATATCATGCTTATAATCATTATTCGCAAGCACATGA-ATATCATGCATATAATCATTAGCAACAA
1 ATATCATGCATATAATCATTATTAGCAAGCGCAT-ATATATCATGCATATAATCATTATTAGCAA
*
11056 GCGTATGT
65 GCGCATGT
* ** * * * * * *
11064 ATATCATGCATGTAATCATTGGTAGCAAGCACATCTATATCATACATATGATCATCATTAGCAGG
1 ATATCATGCATATAATCATTATTAGCAAGCGCATATATATCATGCATATAATCATTATTAGCAAG
11129 CGCATGT
66 CGCATGT
* ** * * * * *
11136 ATACCATGCATATAATCATTATTAGCAAGCATATGTATACCATGTATATAATCATTATTAGTAGG
1 ATATCATGCATATAATCATTATTAGCAAGCGCATATATATCATGCATATAATCATTATTAGCAAG
11201 CGCATGT
66 CGCATGT
* * *
11208 ATATCATGCATATAATCATTATTAGCAAGTGCATATGTATCATGCATATGATCATTATTAG-AAG
1 ATATCATGCATATAATCATTATTAGCAAGCGCATATATATCATGCATATAATCATTATTAGCAA-
11272 GCGCATGT
65 GCGCATGT
* * ** ** * * *
11280 ATACCATGCATATGATCATTAACAATAAGCGTATATATATCATGCATGTAATCATTAGTAGCAAG
1 ATATCATGCATATAATCATTATTAGCAAGCGCATATATATCATGCATATAATCATTATTAGCAAG
* *
11345 CGTAGGT
66 CGCATGT
* * * *
11352 ATATCATGCATATGATCATTATTAACATGTGCATATATA
1 ATATCATGCATATAATCATTATTAGCAAGCGCATATATA
11391 CCATACGTAT
Statistics
Matches: 267, Mismatches: 57, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
71 1 0.00
72 264 0.99
73 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (72 bp):
ATATCATGCATATAATCATTATTAGCAAGCGCATATATATCATGCATATAATCATTATTAGCAAG
CGCATGT
Found at i:11391 original size:108 final size:107
Alignment explanation
Indices: 10992--11432 Score: 314
Period size: 108 Copynumber: 4.1 Consensus size: 107
10982 CATGGATAAA
* * * * * * * **
10992 ATATCATGCTTATAATCATTATTCGCAAGCACATGAATATCATGCATATAATCATTAGCAACA-A
1 ATATCATGCATATAATCATTAGTAGCAAGCGCAGGTATATCATGCATATGATCATTATTAACAGA
* * * *** ** * *
11056 GCGTATGTATATCATGCATGTAATCATTGGTAGCAAGCACATCT
66 GC--ATATATACCATGCATATAATCATTAACAATAAGCGCATAT
* * * * * * * * *
11100 ATATCATACATATGATCATCATTAGCAGGCGCATGTATACCATGCATATAATCATTATTAGCA-A
1 ATATCATGCATATAATCATTAGTAGCAAGCGCAGGTATATCATGCATATGATCATTATTAACAGA
* ** * * *
11164 GCATATGTATACCATGTATATAATCATTATTAGTAGGCGCATGT
66 GCATA--TATACCATGCATATAATCATTAACAATAAGCGCATAT
* * ** *
11208 ATATCATGCATATAATCATTATTAGCAAGTGCATATGTATCATGCATATGATCATTATTAGA-AG
1 ATATCATGCATATAATCATTAGTAGCAAGCGCAGGTATATCATGCATATGATCATTATTA-ACA-
* * * *
11272 GCGCATGTATACCATGCATATGATCATTAACAATAAGCGTATAT
64 GAGCATATATACCATGCATATAATCATTAACAATAAGCGCATAT
* *
11316 ATATCATGCATGTAATCATTAGTAGCAAGCGTAGGTATATCATGCATATGATCATTATTAACATG
1 ATATCATGCATATAATCATTAGTAGCAAGCGCAGGTATATCATGCATATGATCATTATTAACA-G
* * * * * *
11381 TGCATATATACCATACGTATAAT-TTATAACAATAAGCACATGT
65 AGCATATATACCATGCATATAATCAT-TAACAATAAGCGCATAT
11424 ATCATCATG
1 AT-ATCATG
11433 AAATATTATC
Statistics
Matches: 266, Mismatches: 59, Indels: 15
0.78 0.17 0.04
Matches are distributed among these distances:
106 2 0.01
107 2 0.01
108 252 0.95
109 6 0.02
110 4 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (107 bp):
ATATCATGCATATAATCATTAGTAGCAAGCGCAGGTATATCATGCATATGATCATTATTAACAGA
GCATATATACCATGCATATAATCATTAACAATAAGCGCATAT
Found at i:12313 original size:38 final size:38
Alignment explanation
Indices: 12230--12333 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 38
12220 TACTTACCCT
* *
12230 TAAAGATCTGGTTTCCAACCTAAAATCTTATTTACAACC
1 TAAA-ATCTGGTTTCCAACCTAAAATCTGATTTACAACA
* * *
12269 TAAAATCTGGTTTCTAACCTAAAATCTGATTTCCAATA
1 TAAAATCTGGTTTCCAACCTAAAATCTGATTTACAACA
* * * *
12307 TGAAATCTGGGTTCCACCCTCAAATCT
1 TAAAATCTGGTTTCCAACCTAAAATCT
12334 AGTTTCTAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 51 0.93
39 4 0.07
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.34
Consensus pattern (38 bp):
TAAAATCTGGTTTCCAACCTAAAATCTGATTTACAACA
Found at i:12350 original size:19 final size:19
Alignment explanation
Indices: 12230--12361 Score: 106
Period size: 19 Copynumber: 6.9 Consensus size: 19
12220 TACTTACCCT
*
12230 TAAAGATCTGGTTTCCAACC
1 TAAA-ATCTAGTTTCCAACC
*
12250 TAAAATCTTA-TTTACAACC
1 TAAAATC-TAGTTTCCAACC
* *
12269 TAAAATCTGGTTTCTAACC
1 TAAAATCTAGTTTCCAACC
**
12288 TAAAATCT-GATTTCCAATA
1 TAAAATCTAG-TTTCCAACC
* * * *
12307 TGAAATCTGGGTTCCACCC
1 TAAAATCTAGTTTCCAACC
* *
12326 TCAAATCTAGTTTCTAACC
1 TAAAATCTAGTTTCCAACC
*
12345 TAAAATTTAGTTTCCAA
1 TAAAATCTAGTTTCCAA
12362 ATCATAATTC
Statistics
Matches: 87, Mismatches: 21, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
18 2 0.02
19 79 0.91
20 6 0.07
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (19 bp):
TAAAATCTAGTTTCCAACC
Found at i:12816 original size:85 final size:84
Alignment explanation
Indices: 12668--12833 Score: 228
Period size: 85 Copynumber: 2.0 Consensus size: 84
12658 TTATGATAGG
* * *
12668 AATTTATGACACACATTTATGACGTGCATTGCGCGTCATTGAAGCCTCCGTCATAAATGAAGATG
1 AATTTATGACACACATTTATGACGTACATTGCGCGTCATTGAAGCCACCGT-ATAAATAAAGATG
*
12733 ACACACATTTGTGTGTCATA
65 ACACACATTCGTGTGTCATA
* *
12753 AATTTATGACACACATTTATGACTTACATTGCGTGTCATTGAAGCACACACCGT-TAAA-AAAGA
1 AATTTATGACACACATTTATGACGTACATTGCGCGTCATTGAAG--C-CACCGTATAAATAAAGA
12816 TGACACACATTCGTGTGT
63 TGACACACATTCGTGTGT
12834 TGTGATTGTA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
85 62 0.86
86 4 0.06
87 1 0.01
88 5 0.07
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (84 bp):
AATTTATGACACACATTTATGACGTACATTGCGCGTCATTGAAGCCACCGTATAAATAAAGATGA
CACACATTCGTGTGTCATA
Found at i:19703 original size:83 final size:83
Alignment explanation
Indices: 19417--19740 Score: 340
Period size: 83 Copynumber: 4.0 Consensus size: 83
19407 GAAATAAATG
* * * * *
19417 TTTAATATT-TAAATTTAAATAATATTATTATCTATTTAAGTTTA-ACTATTAAAAAAAGTTTTT
1 TTTAATATTATAAATTTAAAAAATATTATAATATATTTAAATTTAGA-TATT-AAAAAAGTTTTG
*
19480 GTTAGAGTAAAACT-TTTTGA
64 GTTAGAGTAAAACTCTTAT-A
* * * *
19500 TTTAATATTATAAATTTAAAAGATATTATAATATGTTTAAATTTATATATTAAAAAATTTTTGGT
1 TTTAATATTATAAATTTAAAAAATATTATAATATATTTAAATTTAGATATTAAAAAAGTTTTGGT
* * **
19565 TAGAGAAAAATTCTTAGG
66 TAGAGTAAAACTCTTATA
* *
19583 TTTAATATTATAAATTTAAAAGATATTATAATATATTTAAATTTAGATATTAAAAGAGTTTTGGT
1 TTTAATATTATAAATTTAAAAAATATTATAATATATTTAAATTTAGATATTAAAAAAGTTTTGGT
*
19648 TAGAGTAAAACTCTCATA
66 TAGAGTAAAACTCTTATA
* * ** * *
19666 TTTAATATTTTAAATTTAAAAAATA--AT-AT-TATCTATTTTTAGATATTAAAAGTA-TTTTAG
1 TTTAATATTATAAATTTAAAAAATATTATAATATATTTAAATTTAGATATTAAAA-AAGTTTTGG
*
19726 TTGGAGTAAAACTCT
65 TTAGAGTAAAACTCT
19741 ATCGAAATTC
Statistics
Matches: 207, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
79 38 0.18
80 3 0.01
81 2 0.01
83 128 0.62
84 35 0.17
85 1 0.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (83 bp):
TTTAATATTATAAATTTAAAAAATATTATAATATATTTAAATTTAGATATTAAAAAAGTTTTGGT
TAGAGTAAAACTCTTATA
Found at i:20225 original size:13 final size:13
Alignment explanation
Indices: 20207--20236 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20197 TATTATCTTA
20207 GGCTTCTCTGGTG
1 GGCTTCTCTGGTG
*
20220 GGCTTCTCTGTTG
1 GGCTTCTCTGGTG
20233 GGCT
1 GGCT
20237 CCAGACTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.37, T:0.40
Consensus pattern (13 bp):
GGCTTCTCTGGTG
Found at i:25347 original size:13 final size:13
Alignment explanation
Indices: 25329--25358 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25319 TATTATCTTA
25329 GGCTTCTCTGGTG
1 GGCTTCTCTGGTG
*
25342 GGCTTCTCTGTTG
1 GGCTTCTCTGGTG
25355 GGCT
1 GGCT
25359 CCAGACTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.37, T:0.40
Consensus pattern (13 bp):
GGCTTCTCTGGTG
Found at i:32965 original size:20 final size:19
Alignment explanation
Indices: 32940--32979 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
32930 GAAAAACAAC
32940 AAAAAGAAAAACCAGAAAAA
1 AAAAAGAAAAA-CAGAAAAA
*
32960 AAAAAGAAAAAGAGAAAAA
1 AAAAAGAAAAACAGAAAAA
32979 A
1 A
32980 CTGAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAACAGAAAAA
Found at i:32969 original size:19 final size:20
Alignment explanation
Indices: 32940--32979 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
32930 GAAAAACAAC
*
32940 AAAAAGAAAAACCAGAAAAA
1 AAAAAGAAAAAACAGAAAAA
*
32960 AAAAAG-AAAAAGAGAAAAA
1 AAAAAGAAAAAACAGAAAAA
32979 A
1 A
32980 CTGAAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAACAGAAAAA
Found at i:33020 original size:6 final size:6
Alignment explanation
Indices: 33009--33065 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
32999 AAATTGGTGA
*
33009 TTTATG TTTATG TTTATG TTTATA TGTT-T- TTTATG TTTACT- TTTAT-
1 TTTATG TTTATG TTTATG TTTATG T-TTATG TTTATG TTTA-TG TTTATG
33055 TTTAT- TTTATG
1 TTTATG TTTATG
33066 AAGATTAGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
4 2 0.04
5 13 0.29
6 27 0.60
7 3 0.07
ACGTcount: A:0.18, C:0.02, G:0.11, T:0.70
Consensus pattern (6 bp):
TTTATG
Found at i:33057 original size:17 final size:17
Alignment explanation
Indices: 33009--33064 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
32999 AAATTGGTGA
*
33009 TTTATGTTTATGTTTATG
1 TTTATATTTAT-TTTATG
33027 TTTATATGTT-TTTTATG
1 TTTATAT-TTATTTTATG
33044 TTTACT-TTTATTTTAT-
1 TTTA-TATTTATTTTATG
33060 TTTAT
1 TTTAT
33065 GAAGATTAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 1 0.03
16 6 0.18
17 17 0.50
18 8 0.24
19 2 0.06
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (17 bp):
TTTATATTTATTTTATG
Found at i:33062 original size:23 final size:24
Alignment explanation
Indices: 33008--33062 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
32998 AAAATTGGTG
*
33008 ATTTATGTTTATGTTTATGTTTAT
1 ATTTATTTTTATGTTTATGTTTAT
*
33032 ATGT-TTTTTATGTTTACT-TTTAT
1 ATTTATTTTTATGTTTA-TGTTTAT
33055 -TTTATTTT
1 ATTTATTTT
33063 ATGAAGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 2 0.08
23 20 0.77
24 4 0.15
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (24 bp):
ATTTATTTTTATGTTTATGTTTAT
Found at i:33896 original size:20 final size:20
Alignment explanation
Indices: 33871--33908 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33861 TTAGTTTAGA
33871 TATTTTCAAGAATTATCTCT
1 TATTTTCAAGAATTATCTCT
* *
33891 TATTTTTAGGAATTATCT
1 TATTTTCAAGAATTATCT
33909 TTTCATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (20 bp):
TATTTTCAAGAATTATCTCT
Found at i:37858 original size:19 final size:20
Alignment explanation
Indices: 37822--37869 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
37812 TCTAAATCCT
* *
37822 TTTTCAAAATATCATTTTGG
1 TTTTCAAAATACCATTTTAG
37842 TTTTCAAAAT-CCATTTTAG
1 TTTTCAAAATACCATTTTAG
*
37861 CTTTCAAAA
1 TTTTCAAAA
37870 GAAAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (20 bp):
TTTTCAAAATACCATTTTAG
Found at i:41895 original size:83 final size:83
Alignment explanation
Indices: 41784--42106 Score: 448
Period size: 83 Copynumber: 4.0 Consensus size: 83
41774 TGAAATATAT
* *
41784 GTTTAATATT-TAAATTTAAACAATATTATTATCTATTTAAATTTAGGTATTAAAAGAGTTTTGG
1 GTTTAATATTATAAATTTAAACAATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
41848 TTGGAGTAAAACTCTCAA
66 TTGGAGTAAAACTCTCAA
* * *
41866 GTTTAATATTATAAATTTAAA-AGATATTATAATCTATTTAAATGTAGACATTAAAAGAGTTTTT
1 GTTTAATATTATAAATTTAAACA-ATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTG
* *
41930 GTTGGATTAAAGCTCTCAA
65 GTTGGAGTAAAACTCTCAA
41949 GTTTAATATTATAAATTTAAA-AGATATTATAATCTATTTAAATTTAGATATT--AAGAGTTTTG
1 GTTTAATATTATAAATTTAAACA-ATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTG
**
42011 GTTATAGTAAAACTCTCAA
65 GTTGGAGTAAAACTCTCAA
* * * *
42030 ATTTAATATTTTAAATTTAAACAATATTATTATCTA-TT---TTTAGATATTAAAAGAGTTTTAG
1 GTTTAATATTATAAATTTAAACAATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
42091 TTGGAGTAAAACTCTC
66 TTGGAGTAAAACTCTC
42107 TCAAAATTCC
Statistics
Matches: 216, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
77 10 0.05
79 24 0.11
80 2 0.01
81 55 0.25
82 12 0.06
83 113 0.52
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (83 bp):
GTTTAATATTATAAATTTAAACAATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
TTGGAGTAAAACTCTCAA
Found at i:42067 original size:164 final size:160
Alignment explanation
Indices: 41784--42106 Score: 454
Period size: 164 Copynumber: 2.0 Consensus size: 160
41774 TGAAATATAT
* *
41784 GTTTAATATTTAAATTTAAACAATATTATTATCTATTTAAATTTAGGTATTAAAAGAGTTTTGGT
1 GTTTAATATTTAAATTTAAACAATATTATAATCTATTTAAATTTAGATATT-AAAGAGTTTTGGT
* *
41849 TGGAGTAAAACTCTCAAGTTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATGTAGA
65 TAGAGTAAAACTCTCAAATTTAATATTATAAATTTAAAAGATATTATAATCTATTT---T-TAGA
* * *
41914 CATTAAAAGAGTTTTTGTTGGATTAAAGCTCTCAA
126 CATTAAAAGAGTTTTAGTTGGAGTAAAACTCTCAA
41949 GTTTAATATTATAAATTTAAA-AGATATTATAATCTATTTAAATTTAGATATT-AAGAGTTTTGG
1 GTTTAATATT-TAAATTTAAACA-ATATTATAATCTATTTAAATTTAGATATTAAAGAGTTTTGG
* * * *
42012 TTATAGTAAAACTCTCAAATTTAATATTTTAAATTTAAACA-ATATTATTATCTATTTTTAGATA
64 TTAGAGTAAAACTCTCAAATTTAATATTATAAATTTAAA-AGATATTATAATCTATTTTTAGACA
42076 TTAAAAGAGTTTTAGTTGGAGTAAAACTCTC
128 TTAAAAGAGTTTTAGTTGGAGTAAAACTCTC
42107 TCAAAATTCC
Statistics
Matches: 144, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
160 33 0.23
161 1 0.01
164 61 0.42
165 12 0.08
166 37 0.26
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (160 bp):
GTTTAATATTTAAATTTAAACAATATTATAATCTATTTAAATTTAGATATTAAAGAGTTTTGGTT
AGAGTAAAACTCTCAAATTTAATATTATAAATTTAAAAGATATTATAATCTATTTTTAGACATTA
AAAGAGTTTTAGTTGGAGTAAAACTCTCAA
Found at i:44444 original size:35 final size:35
Alignment explanation
Indices: 44398--44465 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
44388 AATTGTTTAC
*
44398 ATCAAACTTAATGGGTATCTATATCTATAAATACA
1 ATCAAACTTAATGGGTAACTATATCTATAAATACA
44433 ATCAAACTTAATGGGTAACTATATCTATAAATA
1 ATCAAACTTAATGGGTAACTATATCTATAAATA
44466 AAACCAACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (35 bp):
ATCAAACTTAATGGGTAACTATATCTATAAATACA
Found at i:44560 original size:3 final size:3
Alignment explanation
Indices: 44552--44587 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
44542 CTTTATTAGT
44552 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44588 AATACATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:46167 original size:33 final size:33
Alignment explanation
Indices: 46125--46193 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
46115 GTTGATGAAT
*
46125 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
46158 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
46191 GAA
1 GAA
46194 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:51833 original size:33 final size:33
Alignment explanation
Indices: 51791--51859 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
51781 GTTGATGAAT
*
51791 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
51824 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
51857 GAA
1 GAA
51860 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:54237 original size:131 final size:131
Alignment explanation
Indices: 54051--54392 Score: 366
Period size: 131 Copynumber: 2.6 Consensus size: 131
54041 CATTTCGGTC
* ** * * * *
54051 GGAGTAATAAATGACTGCTTTAAGGCA-TAAGAGGTAATTTATTCTCTATTGGAAATAATTTGAT
1 GGAGTAAAAAATGACTATTTTAATGCACGAA-AGGTCATTTATTCTCTATTGGAAATAATTAGAT
* * * ** * *
54115 ATTGTCGTTTTCTCTCGAATTAATA-TCAATTTTTTTGACGGAATAT-TAATATCTCTTTATTTT
65 ATTATCGTTTTCACTCGAATAAATATTCAA-TTTTAAGACGAAAT-TGTAATATCTCTTTATTTC
54178 AATT
128 AATT
* * * * * * *
54182 GGGGTAATAAATGACTATTTTAATGCACGAAATGTCATTTATTTTCGATTGGAAATCATTAGATG
1 GGAGTAAAAAATGACTATTTTAATGCACGAAAGGTCATTTATTCTCTATTGGAAATAATTAGATA
** * * * *
54247 TTATTATTTTCACTTGAGTAAATATTGAATTTTAAGATGAAATTGTAATATCTCTTTATTTCAAT
66 TTATCGTTTTCACTCGAATAAATATTCAATTTTAAGACGAAATTGTAATATCTCTTTATTTCAAT
54312 T
131 T
* * *
54313 GGAGTAAAAAATGACTGTTTTAATGCACGAAAGGTCATTTATTCTATATTGGAAATAAATAGATA
1 GGAGTAAAAAATGACTATTTTAATGCACGAAAGGTCATTTATTCTCTATTGGAAATAATTAGATA
54378 TTATCGTTTTCACTC
66 TTATCGTTTTCACTC
54393 TTAAAATTAT
Statistics
Matches: 170, Mismatches: 38, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
130 1 0.01
131 164 0.96
132 5 0.03
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (131 bp):
GGAGTAAAAAATGACTATTTTAATGCACGAAAGGTCATTTATTCTCTATTGGAAATAATTAGATA
TTATCGTTTTCACTCGAATAAATATTCAATTTTAAGACGAAATTGTAATATCTCTTTATTTCAAT
T
Found at i:55716 original size:47 final size:47
Alignment explanation
Indices: 55602--55722 Score: 129
Period size: 47 Copynumber: 2.6 Consensus size: 47
55592 AATTTCCAAA
* * * **
55602 AAAAATGCATGCGAAGTAGAGATCATGCGGTTAGGTTTATTTTTCTTG
1 AAAAA-GCATGTGAAGTAGATATCATGCGATTAGGTTTATTTTTAATG
* *
55650 AAAAAGCATGTGAATTAGATATCATGCGATTAGGATTTTTTTTTAAT-
1 AAAAAGCATGTGAAGTAGATATCATGCGATTAGG-TTTATTTTTAATG
*
55697 AACAAAGCATGTG-GGTAGATATCATG
1 AA-AAAGCATGTGAAGTAGATATCATG
55723 TTGGGTAGGA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
47 38 0.61
48 24 0.39
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (47 bp):
AAAAAGCATGTGAAGTAGATATCATGCGATTAGGTTTATTTTTAATG
Found at i:58644 original size:98 final size:99
Alignment explanation
Indices: 58525--58717 Score: 300
Period size: 98 Copynumber: 2.0 Consensus size: 99
58515 CCAGAATGTA
* *
58525 ATTATATATGTATACAAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAATGCCC-GACT
1 ATTATATATATATACAAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCTGACT
*
58589 TTATGGATAAGATTCAGCTAGCCTGATAAAAGTG
66 TTATGGATAAGATGCAGCTAGCCTGATAAAAGTG
* * *
58623 ATTATAATATATATAC-AATAAAGTTTGAGTTGTCCCTCTAGAGTAATTGGTTAAACGCCCTGGC
1 ATTAT-ATATATATACAAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCTGAC
*
58687 TTTATGGATATGATGCAGCTAGCCTGATAAA
65 TTTATGGATAAGATGCAGCTAGCCTGATAAA
58718 GGCAAACTAC
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
98 46 0.53
99 40 0.47
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (99 bp):
ATTATATATATATACAAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCTGACT
TTATGGATAAGATGCAGCTAGCCTGATAAAAGTG
Found at i:61724 original size:221 final size:225
Alignment explanation
Indices: 61227--61773 Score: 674
Period size: 221 Copynumber: 2.4 Consensus size: 225
61217 CTGAAGATGA
* *
61227 TAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCAGGTCATCTGTAT
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAT
* * * * * *
61292 GTCTTTCAAGCAAGATTATAAGTTTTTCAGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCAC
66 GCCTTTCGAGCAAGATGATAAG----T-----CATCAAGAAGACCTTCAGGCAAGATGTTTTAAC
* * * **
61357 ATGGATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCCCATTTAATGTTTTTAGAAAATAAAAT
122 ATGAATTTGAAAAATGAG-AAGCAATTTTCAAAGTTTCCCATTTAATATTTCCAGAAAATAAAAT
61422 CTTTGAAAAATAAGAAATCGATTTCCAAAGTTTCTTACTTAG
186 CTTT--AAAATAAGAAATCGATTTCCAAAGTTTCTTACTTAG
* *
61464 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTTGGGTCATCTGTAT
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAT
* *
61529 GCCTTTCGAGCAAGATGATAAGTC-TCAAGAAGACCTTCGGGCAGGATGTTTTAACATGAATTTG
66 GCCTTTCGAGCAAGATGATAAGTCATCAAGAAGACCTTCAGGCAAGATGTTTTAACATGAATTTG
* * * *
61593 AAAAATGAG-AGCAATTTTCAAAGTTTCTCATTTAAATATTTCCAGAAGAA-GAAAT-TTT-TAG
131 AAAAATGAGAAGCAATTTTCAAAGTTTCCCATTT-AATATTTCCAGAA-AATAAAATCTTTAAAA
61654 TAAGAAA-CGATTTCCAAAGTTTCTTACTTAG
194 TAAGAAATCGATTTCCAAAGTTTCTTACTTAG
* * * * *
61685 TAAGTCCTTCAGACCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCTTCGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAT
* *
61750 GCCTTTTGAGTAAGATGATAAGTC
66 GCCTTTCGAGCAAGATGATAAGTC
61774 CTTCGGGCCA
Statistics
Matches: 278, Mismatches: 30, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
221 104 0.37
222 8 0.03
225 25 0.09
226 14 0.05
227 45 0.16
228 1 0.00
233 1 0.00
237 80 0.29
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (225 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAT
GCCTTTCGAGCAAGATGATAAGTCATCAAGAAGACCTTCAGGCAAGATGTTTTAACATGAATTTG
AAAAATGAGAAGCAATTTTCAAAGTTTCCCATTTAATATTTCCAGAAAATAAAATCTTTAAAATA
AGAAATCGATTTCCAAAGTTTCTTACTTAG
Found at i:61963 original size:233 final size:233
Alignment explanation
Indices: 61685--62281 Score: 962
Period size: 233 Copynumber: 2.6 Consensus size: 233
61675 TCTTACTTAG
* *
61685 TAAGTCCTTCAGACCATCAGTAAGTCTTTCGAA-CATGATGCTTAAATCCTTCGGGTCATCTGTA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTC-AAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
61749 AGCCTTTTGAGTAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCA
65 AGCCTTTTGAGTAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCA
* * *
61814 CATGTCTATCAAAATATGAGAAAGGTTTCTCATTTAAACCTGAAATTTGAAATTTTTGAAAAGTA
130 CATATCTATCAAAATATGAGAAAGGTTTCTCATTTAAACCTGAAAATCGAAATTTTTGAAAAGTA
* ** *
61879 AGAAAGGTTTCTTACCTAGTAAACTATTTTTAAAATTTA
195 AGAAAGGTTTCTTACCTAGTAAAATATTTCCAAAATATA
61918 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
* * * *
61983 GTCTTTTGAGTAAGATTATAAGTCTTTCGGGCCATCAATAAGACCTTTGGGCAGGATGTTTTCAC
66 GCCTTTTGAGTAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCAC
* *
62048 ATATCTATCGAAATATGAGAAAGGTTTCTCATTTAAATCTGAAAATCGAAATTTTTGAAAAGTAA
131 ATATCTATCAAAATATGAGAAAGGTTTCTCATTTAAACCTGAAAATCGAAATTTTTGAAAAGTAA
62113 GAAAGGTTTCTTACCTAGTAAAATATTTCCAAAATATA
196 GAAAGGTTTCTTACCTAGTAAAATATTTCCAAAATATA
* * * *
62151 TAAGTCATTCGAGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
* * * * *
62216 GCCTTTCGTGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTGGGCAGGATATTTTCAC
66 GCCTTTTGAGTAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCAC
62281 A
131 A
62282 GATCCCTCTT
Statistics
Matches: 335, Mismatches: 28, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
232 2 0.01
233 333 0.99
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (233 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
GCCTTTTGAGTAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCAC
ATATCTATCAAAATATGAGAAAGGTTTCTCATTTAAACCTGAAAATCGAAATTTTTGAAAAGTAA
GAAAGGTTTCTTACCTAGTAAAATATTTCCAAAATATA
Found at i:62205 original size:42 final size:41
Alignment explanation
Indices: 62158--62251 Score: 116
Period size: 42 Copynumber: 2.3 Consensus size: 41
62148 ATATAAGTCA
* * *
62158 TTCGAGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCC
1 TTCGAGCCATCAGTAAGCCTTTCGAGCAAGATG-ATAAATCC
* * * *
62200 TTCGAGTCATCTGTAAGCCTTTCGTGCAAGATGATAAGTCC
1 TTCGAGCCATCAGTAAGCCTTTCGAGCAAGATGATAAATCC
62241 TTCGAGCCATC
1 TTCGAGCCATC
62252 CATAAGACCT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 16 0.36
42 28 0.64
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (41 bp):
TTCGAGCCATCAGTAAGCCTTTCGAGCAAGATGATAAATCC
Found at i:62263 original size:42 final size:42
Alignment explanation
Indices: 62150--62263 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 42
62140 TCCAAAATAT
* * *
62150 ATAAGTCATTCGAGCCAT-CAGTAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCGAGCCATCCA-TAAGCCTTTCGAGCAAGATGC
* * * ** *
62192 TTAAATCCTTCGAGTCATCTGTAAGCCTTTCGTGCAAGATG-
1 ATAAGTCCTTCGAGCCATCCATAAGCCTTTCGAGCAAGATGC
62233 ATAAGTCCTTCGAGCCATCCATAAGACCTTT
1 ATAAGTCCTTCGAGCCATCCATAAG-CCTTT
62264 GGGCAGGATA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 20 0.36
42 36 0.64
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (42 bp):
ATAAGTCCTTCGAGCCATCCATAAGCCTTTCGAGCAAGATGC
Found at i:62523 original size:3 final size:3
Alignment explanation
Indices: 62508--62589 Score: 141
Period size: 3 Copynumber: 28.0 Consensus size: 3
62498 TCTAGTATCT
*
62508 TTA TTA GTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62555 TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62590 AATACATTTA
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 4 0.05
3 71 0.95
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:64832 original size:131 final size:131
Alignment explanation
Indices: 64666--65033 Score: 425
Period size: 131 Copynumber: 2.8 Consensus size: 131
64656 CGACAATGAC
** * * * *
64666 AATAGTAATATC-CTTTCATTTCGGTCGGAGTAATAAATGACTGCTTTAAGGCA-TAAGAGGTCA
1 AATAGTAATATCTCTTT-ATTTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAA-AGGTCA
* * * * * * * *
64729 TTTATTCTTTATTGCAAATAATTTGATATTGTCGTTTTCTCTCGAATTAATATCGATTTTTTAGA
64 TTTATTCTTAATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATCGAATTTTAAGA
64794 CGA
129 CGA
* * * * *
64797 AATATTAATATCTCTTTATTTCAATTGGGGTAATAAATGATTGTTTTAATGCACGAAACGTCGTT
1 AATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAAAGGTCATT
* * * ** * * * * *
64862 TATTCTTGATTGGAAATCATTAGATGTTATTATTTTCACTTGAGTCAATTTTGAATTTTAAGATG
66 TATTCTTAATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATCGAATTTTAAGACG
64927 A
131 A
*
64928 AATAGTAATATCTTTTTATTTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAAAGGTCATT
1 AATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAAAGGTCATT
*
64993 TATTCTCAATTGGAAATAATTAGATATTATCGTTTTCACTC
66 TATTCTTAATTGGAAATAATTAGATATTATCGTTTTCACTC
65034 TTAAAATTAT
Statistics
Matches: 194, Mismatches: 41, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
131 188 0.97
132 6 0.03
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (131 bp):
AATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAAAGGTCATT
TATTCTTAATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATCGAATTTTAAGACG
A
Found at i:69338 original size:99 final size:99
Alignment explanation
Indices: 69167--69362 Score: 286
Period size: 99 Copynumber: 2.0 Consensus size: 99
69157 TCAGAATGTA
* * * *
69167 ATTATATATGTATACAAATAAAGCTTGAGATGTCCCTCTAAAACAATTGGTTAAACTCCCCGACT
1 ATTATATATATATACAAATAAAGCCTGAGATATCCCTCTAAAACAATTGGTTAAACGCCCCGACT
*
69232 TTATGGATAAGATTCAGCTAGCCTGATAAAGGTG
66 TTATGGATAAGATTCAACTAGCCTGATAAAGGTG
* * * * *
69266 ATTATAATATATATAC-AATAAAGCCTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCTCGGC
1 ATTAT-ATATATATACAAATAAAGCCTGAGATATCCCTCTAAAACAATTGGTTAAACGCCCCGAC
69330 TTTATGGATAAGATTCAACTAGCCTGATAAAGG
65 TTTATGGATAAGATTCAACTAGCCTGATAAAGG
69363 CAAACTACAA
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 77 0.90
100 9 0.10
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (99 bp):
ATTATATATATATACAAATAAAGCCTGAGATATCCCTCTAAAACAATTGGTTAAACGCCCCGACT
TTATGGATAAGATTCAACTAGCCTGATAAAGGTG
Found at i:72353 original size:131 final size:130
Alignment explanation
Indices: 72185--72554 Score: 410
Period size: 131 Copynumber: 2.8 Consensus size: 130
72175 ATCGACAATG
** * *
72185 AGAATAGTAATATC-CTTTCATTTCGGTTGGAGAAATAAATGATTGTTTTAAGTCA-TAAGAGGT
1 AGAATAGTAATATCTCTTT-ATTTCAATTGGAGTAATAAATGATTGTTTTAAGTCACGAA-AGGT
* * * *
72248 CATCTATTCTCTATTGGAAATAATTTGATATTATCGTTTTCTA-TCGAAGT-AATATTGATTTTT
64 CATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC-ACTCG-AGTCAATATTGAATTTT
*
72311 TAGA
127 AAGA
* *
72315 CAGAATATTAATATCTCTTTATTTCAATTGGGGTAATAAATGATTGTTTTAA-TGCACGAAAGGT
1 -AGAATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATGATTGTTTTAAGT-CACGAAAGGT
* * * * ** * *
72379 CGTTTACTCTCGATTGGAAATCATTAGATGTTATTATTTTCACTTGAGTCGATATTGAATTTTAA
64 CATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAGTCAATATTGAATTTTAA
72444 GA
129 GA
* * * *
72446 TGAAATAGTAATATTTCTTTATTTCAATTGAAGTAATAAATGATTGTTTTAATGT-ACGAAATGT
1 AG-AATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATGATTGTTTTAA-GTCACGAAAGGT
*
72510 CATTTATTTTCGATTGGAAATAATTAGATATTATCGTTTTCACTC
64 CATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTC
72555 TTAAAATTAT
Statistics
Matches: 198, Mismatches: 33, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
130 6 0.03
131 185 0.93
132 6 0.03
133 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.43
Consensus pattern (130 bp):
AGAATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATGATTGTTTTAAGTCACGAAAGGTCA
TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAGTCAATATTGAATTTTAAGA
Found at i:74249 original size:60 final size:60
Alignment explanation
Indices: 74128--74259 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
74118 GCATATACCT
* * * * * **
74128 ATAGTTTG-GGATGAAGTTGAAATGTTTAAAATTTTGGGGACTAATTTTGAATAAAGGTC
1 ATAGTTTGAGGATGAAGTTAAAATATTTAAAAATTTGAGGACTAATATAAAATAAAGGTC
*
74187 ATAGTTTGAGGATGAAGTTAAAATATTTAAAAATTTGAGGACTAATATAAAATGAAA-TTC
1 ATAGTTTGAGGATGAAGTTAAAATATTTAAAAATTTGAGGACTAATATAAAAT-AAAGGTC
*
74247 ATAATTTGAGGAT
1 ATAGTTTGAGGAT
74260 AAAACTAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 8 0.13
60 51 0.82
61 3 0.05
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (60 bp):
ATAGTTTGAGGATGAAGTTAAAATATTTAAAAATTTGAGGACTAATATAAAATAAAGGTC
Found at i:79864 original size:13 final size:13
Alignment explanation
Indices: 79848--79879 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
79838 GTAACGATTA
79848 ATTTAAAATTTAG
1 ATTTAAAATTTAG
79861 ATTTAAAATTTAG
1 ATTTAAAATTTAG
79874 AGTTTA
1 A-TTTA
79880 GGATCAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (13 bp):
ATTTAAAATTTAG
Found at i:84311 original size:18 final size:18
Alignment explanation
Indices: 84288--84342 Score: 101
Period size: 18 Copynumber: 3.1 Consensus size: 18
84278 TTATACCTTT
84288 TATGTCCCGAATGACCAC
1 TATGTCCCGAATGACCAC
84306 TATGTCCCGAATGACCAC
1 TATGTCCCGAATGACCAC
*
84324 TATGTCCCGAAGGACCAC
1 TATGTCCCGAATGACCAC
84342 T
1 T
84343 GAAAATCCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (18 bp):
TATGTCCCGAATGACCAC
Found at i:87560 original size:14 final size:14
Alignment explanation
Indices: 87541--87569 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
87531 CAGATCTTAA
87541 GAGCGAACACTACC
1 GAGCGAACACTACC
87555 GAGCGAACACTACC
1 GAGCGAACACTACC
87569 G
1 G
87570 CAACCATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.34, G:0.24, T:0.07
Consensus pattern (14 bp):
GAGCGAACACTACC
Found at i:89839 original size:20 final size:20
Alignment explanation
Indices: 89804--89855 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
89794 TACGGTTTCA
*
89804 TTGCTTCAGATTCATGAACTC
1 TTGCTTCA-TTTCATGAACTC
89825 TTGCTTCATTTCATGAACTC
1 TTGCTTCATTTCATGAACTC
89845 TTGCTTCATTT
1 TTGCTTCATTT
89856 GTCAGATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (20 bp):
TTGCTTCATTTCATGAACTC
Found at i:91155 original size:18 final size:18
Alignment explanation
Indices: 91128--91174 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
91118 TATTTTTCCT
91128 GAAGGACCACTATGTCCC
1 GAAGGACCACTATGTCCC
*
91146 GAATGACCACTATGTCCC
1 GAAGGACCACTATGTCCC
91164 GAAGGACCACT
1 GAAGGACCACT
91175 GAAAATCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (18 bp):
GAAGGACCACTATGTCCC
Found at i:98542 original size:14 final size:13
Alignment explanation
Indices: 98509--98550 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
98499 AGCCTCCTAA
98509 AAATCCTAAAAAT
1 AAATCCTAAAAAT
*
98522 AACTCCTAAAAGAT
1 AAATCCTAAAA-AT
98536 AAATCCTAATAAAT
1 AAATCCTAA-AAAT
98550 A
1 A
98551 GGAAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.40
14 13 0.52
15 2 0.08
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (13 bp):
AAATCCTAAAAAT
Found at i:99572 original size:55 final size:55
Alignment explanation
Indices: 99489--99592 Score: 199
Period size: 55 Copynumber: 1.9 Consensus size: 55
99479 TTTATTTACT
99489 CTCTTAATTGCTTATGCCTTGAATGTTTGAGTGAGATGGTGTAAATAATAAACAA
1 CTCTTAATTGCTTATGCCTTGAATGTTTGAGTGAGATGGTGTAAATAATAAACAA
*
99544 CTCTTAATTGCTTATGCCTTGAATGTTTGAGTGAGCTGGTGTAAATAAT
1 CTCTTAATTGCTTATGCCTTGAATGTTTGAGTGAGATGGTGTAAATAAT
99593 TTTCATTGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (55 bp):
CTCTTAATTGCTTATGCCTTGAATGTTTGAGTGAGATGGTGTAAATAATAAACAA
Found at i:102532 original size:18 final size:19
Alignment explanation
Indices: 102509--102544 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
102499 GAGATTTTTT
102509 AAAAGAAAGATT-GATTTC
1 AAAAGAAAGATTGGATTTC
102527 AAAAGAAAGATTGGATTT
1 AAAAGAAAGATTGGATTT
102545 TGAAGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.19, T:0.28
Consensus pattern (19 bp):
AAAAGAAAGATTGGATTTC
Found at i:102963 original size:62 final size:60
Alignment explanation
Indices: 102879--102994 Score: 151
Period size: 62 Copynumber: 1.9 Consensus size: 60
102869 TGTACTTTAT
* * * * *
102879 ATTATATTCTTATATAATTATATACATATAATGAATGCATAGGTATAAATGTATAATGTAC
1 ATTATATACTTATATAAATATATACATATAATCAACGCATAAGTAT-AATGTATAATGTAC
* *
102940 ATTATATACTTTATATAAATATATACTTATAATCTACGCATAAGTATAATGTATA
1 ATTATATAC-TTATATAAATATATACATATAATCAACGCATAAGTATAATGTATA
102995 TATATATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 16 0.34
62 31 0.66
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (60 bp):
ATTATATACTTATATAAATATATACATATAATCAACGCATAAGTATAATGTATAATGTAC
Found at i:105819 original size:15 final size:16
Alignment explanation
Indices: 105788--105820 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
105778 TGCAAAGTAT
105788 ATTATTGCTGATGTTG
1 ATTATTGCTGATGTTG
*
105804 ATTATTG-TGATTTTG
1 ATTATTGCTGATGTTG
105819 AT
1 AT
105821 GAAATTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.21, C:0.03, G:0.21, T:0.55
Consensus pattern (16 bp):
ATTATTGCTGATGTTG
Found at i:106286 original size:2 final size:2
Alignment explanation
Indices: 106279--106315 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
106269 TTTTGCAGTG
106279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
106316 GTTATAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:113183 original size:6 final size:6
Alignment explanation
Indices: 113041--113182 Score: 248
Period size: 6 Copynumber: 23.7 Consensus size: 6
113031 ATATACATAT
*
113041 ACATAC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
1 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
113089 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
1 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
* * *
113137 ACATGC ACATGC ACATGC ACATGC ACATAC ACATAC ACATAC ACAT
1 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACAT
113183 ATACATATAT
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 134 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (6 bp):
ACATGC
Found at i:113265 original size:51 final size:51
Alignment explanation
Indices: 113196--113322 Score: 139
Period size: 51 Copynumber: 2.5 Consensus size: 51
113186 CATATATATA
* * *
113196 TATATA-TATAAGTGTAATGTATACATTACAAATAAAATGTATACTTAAAT
1 TATATACTTTAAGTATAATGTATACATTACAAATAAAATATATACTTAAAT
* * * ** *
113246 TATATACTTTAAGTATAATGTATATATTATAAGTATGATATATACTTATAT
1 TATATACTTTAAGTATAATGTATACATTACAAATAAAATATATACTTAAAT
* *
113297 TATATTCTTATAATTATAATGTATAC
1 TATATACTT-TAAGTATAATGTATAC
113323 TTATATTATA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
50 6 0.10
51 43 0.68
52 14 0.22
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (51 bp):
TATATACTTTAAGTATAATGTATACATTACAAATAAAATATATACTTAAAT
Found at i:113289 original size:20 final size:20
Alignment explanation
Indices: 113246--113289 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
113236 ATACTTAAAT
*
113246 TATATACTTTAAGTATAATG
1 TATATACTTTAAGTATAATA
*
113266 TATATA-TTATAAGTATGATA
1 TATATACTT-TAAGTATAATA
113286 TATA
1 TATA
113290 CTTATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (20 bp):
TATATACTTTAAGTATAATA
Found at i:113300 original size:13 final size:13
Alignment explanation
Indices: 113284--113340 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
113274 ATAAGTATGA
113284 TATATACTTATAT
1 TATATACTTATAT
*
113297 TATATTCTTATAATT
1 TATATACTTAT-A-T
113312 ATAATGTATACTTATAT
1 -T-A--TATACTTATAT
113329 TATATACTTATA
1 TATATACTTATA
113341 AGTATAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
15 2 0.06
16 2 0.06
17 2 0.06
18 1 0.03
19 8 0.22
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (13 bp):
TATATACTTATAT
Found at i:113309 original size:32 final size:32
Alignment explanation
Indices: 113272--113365 Score: 136
Period size: 32 Copynumber: 3.0 Consensus size: 32
113262 AATGTATATA
* *
113272 TTATAAGTATGATATATACTTATATTATATTC
1 TTATAAGTATAATGTATACTTATATTATATTC
* *
113304 TTATAATTATAATGTATACTTATATTATATAC
1 TTATAAGTATAATGTATACTTATATTATATTC
*
113336 TTATAAGTATAATGTATACTTACA-TATATT
1 TTATAAGTATAATGTATACTTATATTATATT
113366 ATATATACAC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 5 0.09
32 50 0.91
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.49
Consensus pattern (32 bp):
TTATAAGTATAATGTATACTTATATTATATTC
Found at i:113340 original size:19 final size:18
Alignment explanation
Indices: 113286--113333 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
113276 AAGTATGATA
*
113286 TATACTTATATTATATTCT
1 TATA-TTATATTATATACT
* *
113305 TATAATTATAATGTATACT
1 TAT-ATTATATTATATACT
113324 TATATTATAT
1 TATATTATAT
113334 ACTTATAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 6 0.25
19 17 0.71
20 1 0.04
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (18 bp):
TATATTATATTATATACT
Found at i:113378 original size:21 final size:21
Alignment explanation
Indices: 113353--113393 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
113343 TATAATGTAT
113353 ACTTACATATATTATATATAC
1 ACTTACATATATTATATATAC
**
113374 ACTTATGTATATTATATATA
1 ACTTACATATATTATATATA
113394 TAAAAACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.46
Consensus pattern (21 bp):
ACTTACATATATTATATATAC
Found at i:114074 original size:21 final size:21
Alignment explanation
Indices: 114048--114092 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
114038 TCTAAAAAAG
*
114048 ACCCGAACTGATTTGACTCGA
1 ACCCGAACTGATCTGACTCGA
* * *
114069 ACCCGACCTTATCTGAGTCGA
1 ACCCGAACTGATCTGACTCGA
114090 ACC
1 ACC
114093 ATCAAATTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (21 bp):
ACCCGAACTGATCTGACTCGA
Found at i:121536 original size:4 final size:4
Alignment explanation
Indices: 121527--121552 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
121517 TATTTAAAGA
121527 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
121553 TAATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:123007 original size:3 final size:3
Alignment explanation
Indices: 122999--123037 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
122989 AATGTAATTT
122999 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
123038 GATAGAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:123352 original size:47 final size:46
Alignment explanation
Indices: 123234--123353 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 46
123224 CATCTTTAGG
* * *
123234 AAGGGTGATAACACTGTTCCTACATGATGAGGACGGCTGGTTATCT
1 AAGGGTGATGACACTGTTCCTACGTGATGAGGACGGCTGGTCATCT
* * *
123280 AA-GG-G-TGACACAGCTCCTACGTGATGAGGA-GGTCTGGTCGTCT
1 AAGGGTGATGACACTGTTCCTACGTGATGAGGACGG-CTGGTCATCT
*
123323 AAGGGTAGATGACACTGTTCATACGTGATGA
1 AAGGGT-GATGACACTGTTCCTACGTGATGA
123354 AGAATTCTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
42 2 0.03
43 31 0.52
44 3 0.05
45 2 0.03
46 3 0.05
47 19 0.32
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (46 bp):
AAGGGTGATGACACTGTTCCTACGTGATGAGGACGGCTGGTCATCT
Found at i:123386 original size:141 final size:141
Alignment explanation
Indices: 123192--123459 Score: 380
Period size: 141 Copynumber: 1.9 Consensus size: 141
123182 TGTTGGGGAC
*
123192 GACACTGCTCATACGCGATGAAGAAGTTTGGCCATCTTTAGGAAGGGTGATAACACTGTTCCTAC
1 GACACTGCTCATACGCGATGAAGAAGTTTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTAC
* *
123257 ATGATGAGGACGGCTGGTTAT-CTAAGGGTGACACAGCTCCTACGTGA-TGAGGAGGTCTGGTCG
66 ATGATGAGGACGGCTGGTTATCCTAAGGGTGACAC-GCTCCTACGT-ACCGAGGAGATCTGGTCG
123320 TCTAAGGGTAGAT
129 TCTAAGGGTAGAT
* * *
123333 GACACTGTTCATACGTGATGAAGAA-TTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
1 GACACTGCTCATACGCGATGAAGAAGTT-TGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTA
** * * * *
123397 TGTGATGAGGATGGCTGGTTATCCTAATGTTGACACTCTCCTACGTACCGAGGAGATCTGGTC
65 CATGATGAGGACGGCTGGTTATCCTAAGGGTGACACGCTCCTACGTACCGAGGAGATCTGGTC
123460 AGTTGCTGTT
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
140 3 0.03
141 98 0.88
142 11 0.10
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (141 bp):
GACACTGCTCATACGCGATGAAGAAGTTTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTAC
ATGATGAGGACGGCTGGTTATCCTAAGGGTGACACGCTCCTACGTACCGAGGAGATCTGGTCGTC
TAAGGGTAGAT
Found at i:124530 original size:9 final size:9
Alignment explanation
Indices: 124481--124535 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
124471 TTTTCTTTTG
*
124481 TTTTTCTCA
1 TTTTTTTCA
124490 TTTTTTCTCA
1 TTTTTT-TCA
124500 -TTTTTTCA
1 TTTTTTTCA
124508 --TTTTTCA
1 TTTTTTTCA
124515 TTTTTTTCA
1 TTTTTTTCA
124524 TTTTTTTC-
1 TTTTTTTCA
124532 TTTT
1 TTTT
124536 CTTTTTTTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
7 7 0.17
8 7 0.17
9 25 0.60
10 3 0.07
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:124542 original size:13 final size:14
Alignment explanation
Indices: 124502--124551 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 14
124492 TTTTCTCATT
*
124502 TTTTCATTTTTCATTT
1 TTTTCATTTTT--TTC
124518 TTTTCATTTTTTTC
1 TTTTCATTTTTTTC
124532 TTTTC-TTTTTTTC
1 TTTTCATTTTTTTC
124545 TTCTTCA
1 TT-TTCA
124552 AGTGTAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 10 0.32
14 10 0.32
16 11 0.35
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCATTTTTTTC
Found at i:137466 original size:3 final size:3
Alignment explanation
Indices: 137458--137487 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
137448 AATGTAATTT
137458 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
137488 GATAGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:146869 original size:29 final size:29
Alignment explanation
Indices: 146809--146892 Score: 134
Period size: 29 Copynumber: 2.9 Consensus size: 29
146799 TCCCAACACA
146809 TAGGTCGCCATGCCCTCC-GGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
146837 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
* * *
146866 TAGGCCACCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
146893 ACCCTCGCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 18 0.35
29 34 0.65
ACGTcount: A:0.13, C:0.39, G:0.29, T:0.19
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:146937 original size:33 final size:33
Alignment explanation
Indices: 146896--146963 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
146886 GCGACCTACC
*
146896 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
146929 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
146962 CT
1 CT
146964 TGTTCGGATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.09, C:0.41, G:0.24, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:146952 original size:10 final size:10
Alignment explanation
Indices: 146908--147034 Score: 56
Period size: 10 Copynumber: 11.3 Consensus size: 10
146898 CGCTCGGCTT
*
146908 CCCTCGGATT
1 CCCTCGGATG
*
146918 CCCTCGCATAG
1 CCCTCGGAT-G
*
146929 CTCGCTCGGTTG
1 C-C-CTCGGATG
146941 CCCTCGGATG
1 CCCTCGGATG
*
146951 CCCTCGCATAG
1 CCCTCGGAT-G
**
146962 CTTGTTCGGATGG
1 C--CCTCGGAT-G
146975 CCTCGGTCGGATG
1 CC-C--TCGGATG
*
146988 GCCTCGGATG
1 CCCTCGGATG
*
146998 CTCTCGGATGG
1 CCCTCGGAT-G
147009 CCTCGGTCGGATG
1 CC-C--TCGGATG
147022 CCCTCGGATG
1 CCCTCGGATG
147032 CCC
1 CCC
147035 AGCGTGTTGG
Statistics
Matches: 88, Mismatches: 16, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
10 47 0.53
11 6 0.07
12 6 0.07
13 17 0.19
14 12 0.14
ACGTcount: A:0.09, C:0.35, G:0.31, T:0.24
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:146979 original size:33 final size:33
Alignment explanation
Indices: 146896--146980 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
146886 GCGACCTACC
* * *
146896 CTCGCTCGGCTTCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
*
146929 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
* * *
146962 CTTGTTCGGATGGCCTCGG
1 CTCGCTCGGATGCCCTCGG
146981 TCGGATGGCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.08, C:0.38, G:0.27, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
Found at i:146986 original size:14 final size:14
Alignment explanation
Indices: 146967--147028 Score: 61
Period size: 14 Copynumber: 4.0 Consensus size: 14
146957 CATAGCTTGT
146967 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
146981 TCGGATGGCCTCGGATG
1 TCGGATGGCCTC-G--G
146998 CTCTCGGATGGCCTCGG
1 ---TCGGATGGCCTCGG
*
147015 TCGGATGCCCTCGG
1 TCGGATGGCCTCGG
147029 ATGCCCAGCG
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
17 2 0.05
19 1 0.02
20 12 0.29
ACGTcount: A:0.08, C:0.31, G:0.39, T:0.23
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:147010 original size:34 final size:34
Alignment explanation
Indices: 146944--147032 Score: 124
Period size: 34 Copynumber: 2.5 Consensus size: 34
146934 TCGGTTGCCC
* *
146944 TCGGATGCCCTCGCATAGCTTGTTCGGATGGCCTCGG
1 TCGGATGCCCTCGGAT-GC-T-CTCGGATGGCCTCGG
*
146981 TCGGATGGCCTCGGATGCTCTCGGATGGCCTCGG
1 TCGGATGCCCTCGGATGCTCTCGGATGGCCTCGG
147015 TCGGATGCCCTCGGATGC
1 TCGGATGCCCTCGGATGC
147033 CCAGCGTGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
34 31 0.65
35 1 0.02
36 2 0.04
37 14 0.29
ACGTcount: A:0.10, C:0.30, G:0.35, T:0.25
Consensus pattern (34 bp):
TCGGATGCCCTCGGATGCTCTCGGATGGCCTCGG
Found at i:150479 original size:38 final size:39
Alignment explanation
Indices: 150437--150513 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 39
150427 TTACTTTTTG
150437 AAATTTAGG-TTTTATAATAATTAT-AATT-TATATATTAT
1 AAATTT-GGTTTTTATAATAATT-TCAATTCTATATATTAT
* *
150475 AAATTTGGTTTTTATATTAATTTCAATTCTTTATATTAT
1 AAATTTGGTTTTTATAATAATTTCAATTCTATATATTAT
150514 TTATATTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 3 0.09
38 22 0.65
39 9 0.26
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (39 bp):
AAATTTGGTTTTTATAATAATTTCAATTCTATATATTAT
Found at i:153354 original size:12 final size:12
Alignment explanation
Indices: 153337--153367 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
153327 CGGGAGTAGG
153337 AGTCAAAGCCAA
1 AGTCAAAGCCAA
153349 AGTCAAAGCCAA
1 AGTCAAAGCCAA
*
153361 AGCCAAA
1 AGTCAAA
153368 AACATAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.26, G:0.16, T:0.06
Consensus pattern (12 bp):
AGTCAAAGCCAA
Found at i:154213 original size:60 final size:61
Alignment explanation
Indices: 154095--154213 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 61
154085 TTTAATGTAG
* * ** * * * *
154095 TACATATTTAATGATTTAATTTATTAATTTGAGTTTCATATTTCAATTTTTTTTAATTTAA
1 TACATATTTAATGATTCAATTTATTAATTTAAACTTCATATTTAAAATTTGTTCAATTTAA
154156 TACA-ATTTAATG-TTACAATTTATTAATTTAAACTTCATATTTAAAATTTGTTCAATTT
1 TACATATTTAATGATT-CAATTTATTAATTTAAACTTCATATTTAAAATTTGTTCAATTT
154214 GATCATTATA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 2 0.04
60 43 0.88
61 4 0.08
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (61 bp):
TACATATTTAATGATTCAATTTATTAATTTAAACTTCATATTTAAAATTTGTTCAATTTAA
Found at i:154303 original size:18 final size:18
Alignment explanation
Indices: 154280--154347 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
154270 TAATATGTAG
154280 TTTATATATACTATATAA
1 TTTATATATACTATATAA
154298 TTTATATATACTA-ATGAA
1 TTTATATATACTATAT-AA
* *
154316 -CTATATA-A-TATATAG
1 TTTATATATACTATATAA
* *
154331 TTTGTATATACCATATA
1 TTTATATATACTATATA
154348 CTATATAGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 3 0.08
16 8 0.20
17 9 0.22
18 20 0.50
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (18 bp):
TTTATATATACTATATAA
Found at i:154325 original size:51 final size:54
Alignment explanation
Indices: 154270--154401 Score: 171
Period size: 58 Copynumber: 2.4 Consensus size: 54
154260 ATTAATAAAT
*
154270 TAATATGTAGTTTATATATACTATA-TA-AT-TTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTATACTATATGTTATATATACTAATGAACTATA
*
154321 TAATATATAGTTTGTATATACCATATACTATATAGGTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATA-C-TATACTATAT--GTTATATATACTAATGAACTATA
* *
154379 TAGTATATAGGTTATATATACTA
1 TAATATATAGTTTATATATACTA
154402 ATGAACTATA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
51 18 0.26
52 1 0.01
53 4 0.06
54 2 0.03
55 2 0.03
56 2 0.03
57 1 0.01
58 39 0.57
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (54 bp):
TAATATATAGTTTATATATACTATACTATATGTTATATATACTAATGAACTATA
Found at i:154328 original size:33 final size:33
Alignment explanation
Indices: 154284--154470 Score: 212
Period size: 33 Copynumber: 5.9 Consensus size: 33
154274 ATGTAGTTTA
* *
154284 TATATACTATATAATTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
154317 TATATAATATATAGTTTGTATATAC-------C
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
154343 -ATATACTATATAGGTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
154375 TATATAGTATATAGGTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
154408 TATATAGTATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
154441 TATATATAATGTATAGTTTATATATA-TAAT
1 --TATATAATATATAGTTTATATATACTAAT
154471 ATATAATATA
Statistics
Matches: 134, Mismatches: 10, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
25 21 0.16
26 1 0.01
32 1 0.01
33 85 0.63
34 4 0.03
35 22 0.16
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:154361 original size:58 final size:58
Alignment explanation
Indices: 154285--154466 Score: 211
Period size: 58 Copynumber: 3.0 Consensus size: 58
154275 TGTAGTTTAT
* *
154285 ATATACTATATAATTTATATATACTAATGAACTATATAATATATAGTTTGTATATACC
1 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
* *
154343 ATATACTATATAGGTTATATATACTAATGAACTATATAGTATATAGGTTATATATACTAATGAAC
1 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATA-G-T-T-TATA-T-AT--AC
*
154408 T
58 C
* *
154409 ATATAGTATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATA
1 ATATACTATATAGTTTATATATACTAATGAAC--TATATAATATATAGTTTATATATA
154467 TAATATATAA
Statistics
Matches: 105, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
58 42 0.40
59 1 0.01
60 2 0.02
61 1 0.01
62 5 0.05
63 2 0.02
64 6 0.06
65 1 0.01
66 33 0.31
67 1 0.01
68 11 0.10
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (58 bp):
ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
Found at i:154431 original size:20 final size:19
Alignment explanation
Indices: 154408--154555 Score: 77
Period size: 20 Copynumber: 7.4 Consensus size: 19
154398 ACTAATGAAC
*
154408 TATATAGTATATAGTTTATA
1 TATATAGTATATA-TATATA
*
154428 TATACTAATGA-ACTATATATAA
1 TATA-TAGT-ATA-TATATAT-A
* *
154450 TGTATAGTTTATATATATAA
1 TATATAGTATATATATAT-A
* *
154470 TATATAATATATAAATATA
1 TATATAGTATATATATATA
* *
154489 AACTATAGTATGTAGTATATA
1 TA-TATAGTATATA-TATATA
* * *
154510 AATATA-AACTATAATTTATA
1 TATATAGTA-TAT-ATATATA
154530 TATATAGTATATAT-TATA
1 TATATAGTATATATATATA
*
154548 TAAATAGT
1 TATATAGT
154556 GTATGTAGTT
Statistics
Matches: 99, Mismatches: 19, Indels: 22
0.71 0.14 0.16
Matches are distributed among these distances:
18 11 0.11
19 5 0.05
20 55 0.56
21 21 0.21
22 7 0.07
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (19 bp):
TATATAGTATATATATATA
Found at i:154472 original size:7 final size:7
Alignment explanation
Indices: 154442--154550 Score: 77
Period size: 7 Copynumber: 16.1 Consensus size: 7
154432 CTAATGAACT
154442 ATATATA
1 ATATATA
*
154449 ATGTATA
1 ATATATA
* *
154456 GTTTAT-
1 ATATATA
154462 ATATATA
1 ATATATA
154469 ATATATA
1 ATATATA
154476 ATATATA
1 ATATATA
154483 A-ATATA
1 ATATATA
154489 A-ACTATA
1 ATA-TATA
* *
154496 GTATGTA
1 ATATATA
*
154503 GTATATA
1 ATATATA
154510 A-ATATA
1 ATATATA
154516 A-ACTATA
1 ATA-TATA
*
154523 ATTTAT-
1 ATATATA
154529 ATATATA
1 ATATATA
*
154536 GTATATA
1 ATATATA
*
154543 TTATATA
1 ATATATA
154550 A
1 A
154551 ATAGTGTATG
Statistics
Matches: 82, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
6 23 0.28
7 58 0.71
8 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:154495 original size:27 final size:27
Alignment explanation
Indices: 154465--154535 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
154455 AGTTTATATA
154465 TATAATATATAATATATAAATATAAAC
1 TATAATATATAATATATAAATATAAAC
* * *
154492 TATAGTATGTAGTATATAAATATAAAC
1 TATAATATATAATATATAAATATAAAC
*
154519 TATAATTTAT-ATATATA
1 TATAATATATAATATATA
154536 GTATATATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 6 0.16
27 31 0.84
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (27 bp):
TATAATATATAATATATAAATATAAAC
Found at i:154633 original size:33 final size:32
Alignment explanation
Indices: 154596--154662 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
154586 AGTTCATAGG
*
154596 TAAACTATAGTTCATATATATAGTATATAAATA
1 TAAACTATAGTTCATATAAATAGTATA-AAATA
*
154629 TAAACTATAGTTTATATAAATAGTATAAAATA
1 TAAACTATAGTTCATATAAATAGTATAAAATA
154661 TA
1 TA
154663 GTATATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.22
33 25 0.78
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (32 bp):
TAAACTATAGTTCATATAAATAGTATAAAATA
Found at i:154637 original size:20 final size:20
Alignment explanation
Indices: 154613--154686 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
154603 TAGTTCATAT
154613 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
154633 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
154658 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
154678 TTATAGTAT
1 ATATAGTAT
154687 GTAGCTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 19 0.41
21 1 0.02
22 7 0.15
23 7 0.15
24 1 0.02
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:154662 original size:25 final size:23
Alignment explanation
Indices: 154613--154673 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
154603 TAGTTCATAT
154613 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
154633 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
154658 ATATAGTATATAAATA
1 ATATAGTATATAAATA
154674 TAAATTATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.15
22 5 0.15
23 12 0.35
24 1 0.03
25 11 0.32
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATAGTATATAAATAGTATAAA
Found at i:154665 original size:12 final size:13
Alignment explanation
Indices: 154626--154675 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
154616 TAGTATATAA
154626 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
154640 TTATATAA-ATAGT
1 ATATA-AATATAGT
154653 ATA-AAATATAGT
1 ATATAAATATAGT
154665 ATATAAATATA
1 ATATAAATATA
154676 AATTATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:154674 original size:29 final size:29
Alignment explanation
Indices: 154642--154710 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
154632 ACTATAGTTT
154642 ATATAAATAGTATAAAATATAG-TATATAA
1 ATATAAATA-TATAAAATATAGCTATATAA
** *
154671 ATATAAAT-TATAGTATGTAGCTTATATAA
1 ATATAAATATATAAAATATAGC-TATATAA
154700 ATATAAATATA
1 ATATAAATATA
154711 AACCCTAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
29 23 0.68
30 2 0.06
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (29 bp):
ATATAAATATATAAAATATAGCTATATAA
Found at i:154871 original size:9 final size:10
Alignment explanation
Indices: 154789--154876 Score: 51
Period size: 11 Copynumber: 8.8 Consensus size: 10
154779 AATTTATACA
154789 ATATAT-ATT
1 ATATATAATT
*
154798 ATTTATAATT
1 ATATATAATT
* *
154808 ATACATAA-C
1 ATATATAATT
154817 ATATA-AATAT
1 ATATATAAT-T
*
154827 AAATATAAATT
1 ATATAT-AATT
*
154838 GTATAGT--TT
1 ATATA-TAATT
154847 ATATATAATT
1 ATATATAATT
154857 CATATATAATTT
1 -ATATATAA-TT
154869 ATATATAA
1 ATATATAA
154877 ACTATGTAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
8 3 0.05
9 15 0.25
10 15 0.25
11 20 0.34
12 6 0.10
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (10 bp):
ATATATAATT
Found at i:154874 original size:13 final size:11
Alignment explanation
Indices: 154839--154876 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
154829 ATATAAATTG
*
154839 TATAGTTTATA
1 TATAATTTATA
*
154850 TATAATTCATA
1 TATAATTTATA
154861 TATAATTTATA
1 TATAATTTATA
154872 TATAA
1 TATAA
154877 ACTATGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TATAATTTATA
Found at i:154968 original size:27 final size:28
Alignment explanation
Indices: 154922--154982 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
154912 ATATATAAAC
* **
154922 TATATAGTATTATAGTTTATACATGGTA
1 TATATAGTATTATACTTTATACATAATA
154950 TATATAGT-TTATACTTTATACATAATA
1 TATATAGTATTATACTTTATACATAATA
154977 TATATA
1 TATATA
154983 TAAACTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (28 bp):
TATATAGTATTATACTTTATACATAATA
Found at i:154981 original size:2 final size:2
Alignment explanation
Indices: 154974--155055 Score: 51
Period size: 2 Copynumber: 39.5 Consensus size: 2
154964 TTTATACATA
* * *
154974 AT AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT A- AT AC AT AT ACT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * *
155018 TT AT AT AT AA ACT AT AT AGT TT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT A
155056 CCTATATTAG
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
1 2 0.03
2 54 0.89
3 5 0.08
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:154991 original size:22 final size:20
Alignment explanation
Indices: 154975--155033 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
154965 TTATACATAA
*
154975 TATATATATAAACTATATAGTT
1 TATATATATAAACTATACA--T
154997 TATATATATAATACATATAC-T
1 TATATATATAA-AC-TATACAT
155018 T-TATATATAAACTATA
1 TATATATATAAACTATA
155034 TAGTTTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 9 0.26
21 2 0.06
22 11 0.32
23 2 0.06
24 4 0.12
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (20 bp):
TATATATATAAACTATACAT
Found at i:155000 original size:20 final size:20
Alignment explanation
Indices: 154977--155043 Score: 91
Period size: 20 Copynumber: 3.2 Consensus size: 20
154967 ATACATAATA
154977 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
*
154997 TATATATATAA-TACATATACTT
1 TATATATA-AACT--ATATAGTT
155019 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
155039 TATAT
1 TATAT
155044 TATATATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 21 0.51
21 4 0.10
22 16 0.39
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATATAAACTATATAGTT
Found at i:155033 original size:42 final size:40
Alignment explanation
Indices: 154950--155062 Score: 151
Period size: 42 Copynumber: 2.8 Consensus size: 40
154940 ATACATGGTA
154950 TATATAGTTTATACTT-TATACATA-A-TATATATATAAAC
1 TATATAGTTTATA-TTATATACATATACTATATATATAAAC
*
154988 TATATAGTTTATATATATAATACATATACTTTATATATAAAC
1 TATATAGTTTATAT-TAT-ATACATATACTATATATATAAAC
*
155030 TATATAGTTTATATTATATATATATACCTATAT
1 TATATAGTTTATATTATATACATATA-CTATAT
155063 TAGTTGTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
37 1 0.02
38 14 0.21
39 1 0.02
40 15 0.23
41 9 0.14
42 26 0.39
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (40 bp):
TATATAGTTTATATTATATACATATACTATATATATAAAC
Found at i:155053 original size:20 final size:20
Alignment explanation
Indices: 154948--155055 Score: 82
Period size: 20 Copynumber: 5.4 Consensus size: 20
154938 TTATACATGG
154948 TATATATAGTTTATACTT-TA
1 TATATATAGTTTATA-TTATA
* *
154968 TACATA-A-TATATA-TATA
1 TATATATAGTTTATATTATA
*
154985 AACTATATAGTTTATATATATAA
1 TA-TATATAGTTTATAT-TAT-A
* *
155008 TACATATACTTTATA-TATA
1 TATATATAGTTTATATTATA
*
155027 AACTATATAGTTTATATTATA
1 TA-TATATAGTTTATATTATA
155048 TATATATA
1 TATATATA
155056 CCTATATTAG
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
16 1 0.01
17 3 0.04
18 8 0.12
19 4 0.06
20 30 0.45
21 5 0.07
22 14 0.21
23 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (20 bp):
TATATATAGTTTATATTATA
Found at i:155478 original size:216 final size:216
Alignment explanation
Indices: 155087--155906 Score: 1341
Period size: 216 Copynumber: 3.8 Consensus size: 216
155077 TTTTTTCTCA
* * * *
155087 ACTTATTACTTATTTCTATTTATT-AATTGGCCCATAACTTTTTAAATGAGTATAATTTATTACA
1 ACTTATTACTTATTTATATTT-TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
* * *
155151 TTTTTATATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGAT-CCT--T---T-TGTGT
65 TTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGT
*
155209 TGTTTAATATATTTAAATTTTTATTTGTAAGTTCATATTTGTTCAATTTAGTCCTCCAAATTTTA
130 TGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTA
*
155274 TTTGCACCTGAAATTGACCCAT
195 TTTGCATCTGAAATTGACCCAT
*
155296 ACTTAATACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
*
155361 TTTTGTATTAATTTCAACATCACAATTTAAAATCATTTCGATTTGATCCCTCATCAATGTGTGTT
66 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
*
155426 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTTAT
131 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
*
155491 TTGCATCTGAAATTGACCTAT
196 TTGCATCTGAAATTGACCCAT
155512 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
*
155577 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCGTCAATGTGTGTT
66 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
* *
155642 GTATAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
131 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
* *
155707 TTGCATGTGAAATTGATCCAT
196 TTGCATCTGAAATTGACCCAT
* * * *
155728 ACTTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTTTAAATGGATATAATTTAGTACTT
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* * *
155793 TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTTGATTTGATCCCTAATCAATGTGTGTT
66 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
*
155858 GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
131 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
155907 ATTCTTAAAT
Statistics
Matches: 572, Mismatches: 31, Indels: 9
0.93 0.05 0.01
Matches are distributed among these distances:
208 2 0.00
209 100 0.17
210 3 0.01
212 1 0.00
215 1 0.00
216 465 0.81
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (216 bp):
ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
TTGCATCTGAAATTGACCCAT
Found at i:157234 original size:20 final size:20
Alignment explanation
Indices: 157209--157251 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
157199 CAACGTGCTT
*
157209 GGTGTGAGCATGGTAGACAG
1 GGTGTGAGCATGATAGACAG
157229 GGTGTGAGCATGATAGACAG
1 GGTGTGAGCATGATAGACAG
157249 GGT
1 GGT
157252 TCGCGCTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.44, T:0.21
Consensus pattern (20 bp):
GGTGTGAGCATGATAGACAG
Found at i:159059 original size:2 final size:2
Alignment explanation
Indices: 159052--159088 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
159042 TTTAAAGTAA
* *
159052 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
159089 AGCATGATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:159366 original size:24 final size:24
Alignment explanation
Indices: 159306--159370 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
159296 TTAAAAGACT
* *
159306 AAAATTAAAGT-ATTGAAAAATAT
1 AAAATTAAAGTAATTAAAAAATAG
*** *
159329 AAAGCAAAAATAATTAAAAAATAG
1 AAAATTAAAGTAATTAAAAAATAG
159353 AAAATTAAAGTAA-TAAAA
1 AAAATTAAAGTAATTAAAA
159371 TTAAATAACT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (24 bp):
AAAATTAAAGTAATTAAAAAATAG
Found at i:159372 original size:14 final size:13
Alignment explanation
Indices: 159353--159398 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
159343 TAAAAAATAG
159353 AAAATTAAAGTAAT
1 AAAATTAAA-TAAT
159367 AAAATTAAATAACT
1 AAAATTAAATAA-T
*
159381 GAAATTAAATAAAT
1 AAAATTAAAT-AAT
159395 AAAA
1 AAAA
159399 AGTAAATGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 23 0.82
15 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (13 bp):
AAAATTAAATAAT
Found at i:159459 original size:18 final size:19
Alignment explanation
Indices: 159433--159485 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
159423 AAAGTAAAGG
159433 ACTAAAATAAAAGATAA-AA
1 ACTAAAATAAAAGA-AACAA
*
159452 A-TATAATATAAAGAAACAA
1 ACTAAAATA-AAAGAAACAA
159471 ACTAAAATAAAAGAA
1 ACTAAAATAAAAGAA
159486 CTAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 8 0.28
19 15 0.52
20 6 0.21
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (19 bp):
ACTAAAATAAAAGAAACAA
Found at i:159489 original size:14 final size:14
Alignment explanation
Indices: 159470--159498 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
159460 TAAAGAAACA
159470 AACTAAAATAAAAG
1 AACTAAAATAAAAG
159484 AACTAAAATAAAAG
1 AACTAAAATAAAAG
159498 A
1 A
159499 TATCAGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AACTAAAATAAAAG
Found at i:159495 original size:19 final size:19
Alignment explanation
Indices: 159435--159496 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
159425 AGTAAAGGAC
159435 TAAAATAAAAG-A-TAAAAA
1 TAAAATAAAAGAACT-AAAA
* *
159453 TATAATATAAAGAAAC-AAAC
1 TAAAATA-AAAG-AACTAAAA
159473 TAAAATAAAAGAACTAAAA
1 TAAAATAAAAGAACTAAAA
159492 TAAAA
1 TAAAA
159497 GATATCAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
18 9 0.26
19 16 0.46
20 9 0.26
21 1 0.03
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.18
Consensus pattern (19 bp):
TAAAATAAAAGAACTAAAA
Found at i:160677 original size:45 final size:45
Alignment explanation
Indices: 160522--161371 Score: 1210
Period size: 45 Copynumber: 19.0 Consensus size: 45
160512 TAAAATCTCC
* ** * ** *
160522 TTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCTTGAAGGAC
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGG-T
* * * *
160568 TTTAAAAACATCAC-GCACTGGAGATATTACAGATGACCCGAAGGTT
1 TTTGAAAACATC-CTGCACTGAAGGTCTTACAGATGACCCGAAGG-T
*
160614 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
* * *
160659 TTTGAAAACATCATGCACTGAAGGTCTTATAGATGACTCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
*
160704 TTTGGAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
160749 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
* *
160794 TTTGAAAACATCCTGCACTGAAGGTCTTATAGATGACCGGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
* * *
160839 TTTGAAAACATCCTACACTGAAGGTCTTACAGATGACCCAAATGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
*
160884 TTTGAAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
160929 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
* *
160974 TTTGAAAATATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
* * * *
161019 TTTGAAAACATCCTGCACTAAAGGTATTATAGATGACTCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
161064 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
161109 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
* *
161154 TTTGAAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGA
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
* * * * *
161199 TTT--CAACATCTTGTACTGAAGGACTTACAGATGACTCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
* * *
161242 TTTGAAAACATCCTGCACTGAAGGTCTTATAGATAACCCGAAGGA
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
* * * *
161287 TTT--CAACATCTTGCACTGAAGGTCTTATAGATGACCCGAAGGA
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
* * * *
161330 TTT--CAGCATCTTGCACTGAAGGTCTTACAGATGGCCCGAAGG
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGG
161372 ACTTAAATTC
Statistics
Matches: 729, Mismatches: 71, Indels: 11
0.90 0.09 0.01
Matches are distributed among these distances:
43 112 0.15
45 546 0.75
46 71 0.10
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (45 bp):
TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGT
Found at i:163397 original size:75 final size:74
Alignment explanation
Indices: 163275--163442 Score: 239
Period size: 75 Copynumber: 2.3 Consensus size: 74
163265 TCCATGTGAT
* *
163275 ATGGGCCTTCAGCATGCCCAACATTTGCTAATACAGACGTTCAAAATGCGCCAACATTCCAGA-T
1 ATGGGCTTTCAGCATGCCCAACATTTGCTAATACAAACGTTCAAAATGCGCCAACATTCCA-ATT
163339 TCTGATTGAA
65 TCTGATTGAA
* ** * * *
163349 ATGGGCTTTCAGCATGACCTAGTATTTGCTGATACAAACGTTCAAAATGCGTCAATATTCCAATT
1 ATGGGCTTTCAGCATG-CCCAACATTTGCTAATACAAACGTTCAAAATGCGCCAACATTCCAATT
163414 TCTGATTGAA
65 TCTGATTGAA
163424 ATGGGCTTTCAGCATGCCC
1 ATGGGCTTTCAGCATGCCC
163443 CAGCATTCGC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
74 18 0.22
75 65 0.78
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (74 bp):
ATGGGCTTTCAGCATGCCCAACATTTGCTAATACAAACGTTCAAAATGCGCCAACATTCCAATTT
CTGATTGAA
Found at i:163559 original size:24 final size:24
Alignment explanation
Indices: 163525--163571 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
163515 AATGCCCCAT
*
163525 ATGGATTTGTCTGAAGTGGCCTTC
1 ATGGATCTGTCTGAAGTGGCCTTC
163549 ATGGATCTGTCTGAAGTGGCCTT
1 ATGGATCTGTCTGAAGTGGCCTT
163572 TAAAATGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.36
Consensus pattern (24 bp):
ATGGATCTGTCTGAAGTGGCCTTC
Found at i:165653 original size:72 final size:72
Alignment explanation
Indices: 165543--165679 Score: 247
Period size: 72 Copynumber: 1.9 Consensus size: 72
165533 AGTATAACGA
* *
165543 GCTAGCTGAATATTATCCATAAAGTCGGGGCAATTAACCAATTGCTTTAGGGGGATAACTCAAGC
1 GCTAGCTGAATATTATCCATAAAGCCGAGGCAATTAACCAATTGCTTTAGGGGGATAACTCAAGC
165608 ATAACAG
66 ATAACAG
*
165615 GCTAGCTGAATATTATCCATAAAGCCGAGGCTATTAACCAATTGCTTTAGGGGGATAACTCAAGC
1 GCTAGCTGAATATTATCCATAAAGCCGAGGCAATTAACCAATTGCTTTAGGGGGATAACTCAAGC
165680 TTTATTGTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (72 bp):
GCTAGCTGAATATTATCCATAAAGCCGAGGCAATTAACCAATTGCTTTAGGGGGATAACTCAAGC
ATAACAG
Found at i:167826 original size:12 final size:12
Alignment explanation
Indices: 167802--167835 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
167792 GCAAAGATGC
167802 AAATATAAAATGA
1 AAATAT-AAATGA
*
167815 AAATGTAAATGA
1 AAATATAAATGA
167827 AAATATAAA
1 AAATATAAA
167836 AATGCAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (12 bp):
AAATATAAATGA
Found at i:167839 original size:20 final size:20
Alignment explanation
Indices: 167814--167856 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
167804 ATATAAAATG
* *
167814 AAAATGTAAATGAAAATATA
1 AAAATGCAAATGAAAACATA
*
167834 AAAATGCAAATGCAAACATA
1 AAAATGCAAATGAAAACATA
167854 AAA
1 AAA
167857 GTATGAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.07, G:0.09, T:0.19
Consensus pattern (20 bp):
AAAATGCAAATGAAAACATA
Found at i:167896 original size:7 final size:7
Alignment explanation
Indices: 167862--167901 Score: 57
Period size: 6 Copynumber: 5.9 Consensus size: 7
167852 TAAAAGTATG
167862 AATGCAA
1 AATGCAA
167869 AATG-AA
1 AATGCAA
167875 AATGCAA
1 AATGCAA
167882 AGATGCAA
1 A-ATGCAA
167890 AATGC-A
1 AATGCAA
167896 AATGCA
1 AATGCA
167902 TGTATGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 12 0.40
7 11 0.37
8 7 0.23
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:170991 original size:2 final size:2
Alignment explanation
Indices: 170984--171035 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
170974 CGAATATTTC
170984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
171026 AT AT AT AT AT
1 AT AT AT AT AT
171036 TCATAGGACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:171148 original size:24 final size:24
Alignment explanation
Indices: 171088--171152 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
171078 TTAAAAGACT
* *
171088 AAAATTAAAGT-ATTGAAAAATAT
1 AAAATTAAAGTAATTAAAAAATAG
*** *
171111 AAAGCAAAAATAATTAAAAAATAG
1 AAAATTAAAGTAATTAAAAAATAG
171135 AAAATTAAAGTAA-TAAAA
1 AAAATTAAAGTAATTAAAA
171153 TTAAATAACT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (24 bp):
AAAATTAAAGTAATTAAAAAATAG
Found at i:171154 original size:14 final size:13
Alignment explanation
Indices: 171135--171180 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
171125 TAAAAAATAG
171135 AAAATTAAAGTAAT
1 AAAATTAAA-TAAT
171149 AAAATTAAATAACT
1 AAAATTAAATAA-T
*
171163 GAAATTAAATAAAT
1 AAAATTAAAT-AAT
171177 AAAA
1 AAAA
171181 AGTAAATGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 23 0.82
15 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (13 bp):
AAAATTAAATAAT
Found at i:171213 original size:26 final size:26
Alignment explanation
Indices: 171146--171226 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 26
171136 AAATTAAAGT
* *
171146 AATAAAAT-TAAA-TAACTGAAATTA
1 AATAAAATATAAAGTAAATGACATTA
*
171170 AAT-AAATAAAAAGTAAATGACATTA
1 AATAAAATATAAAGTAAATGACATTA
* *
171195 ATTAAAATATAAAGTAAATGAC-TAA
1 AATAAAATATAAAGTAAATGACATTA
171220 AATAAAA
1 AATAAAA
171227 GAAACAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
23 4 0.09
24 6 0.13
25 20 0.43
26 17 0.36
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (26 bp):
AATAAAATATAAAGTAAATGACATTA
Found at i:176807 original size:22 final size:22
Alignment explanation
Indices: 176782--176833 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
176772 AAATTATTTT
176782 AATTATTTACGTTTATGCGTAA
1 AATTATTTACGTTTATGCGTAA
* *
176804 AATTATTTACGTTTATGTGTAC
1 AATTATTTACGTTTATGCGTAA
176826 AATT-TTTA
1 AATTATTTA
176834 TTGTGTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.50
Consensus pattern (22 bp):
AATTATTTACGTTTATGCGTAA
Found at i:190136 original size:81 final size:81
Alignment explanation
Indices: 189996--190152 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 81
189986 GTCTCTTGCA
* * * *
189996 CAACTGGCTCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCATGTG
1 CAACCGGCTCAGTAACTTCCTACTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCATGTG
190061 CGAACCATTCTCGGTG
66 CGAACCATTCTCGGTG
* * *
190077 CAACCGGCTCAGTAACTTCCTACTCTACACCTCTGCT-AGAGCTTGTTGCTCCGCCATTTCGTGT
1 CAACCGGCTCAGTAACTTCCTACTCTACACCTCTG-TGAGAGCTTGTCGATCCGCCATTTCATGT
190141 GCGAACCATTCT
65 GCGAACCATTCT
190153 TTGTAACTCG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
81 67 0.99
82 1 0.01
ACGTcount: A:0.17, C:0.32, G:0.20, T:0.30
Consensus pattern (81 bp):
CAACCGGCTCAGTAACTTCCTACTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCATGTG
CGAACCATTCTCGGTG
Found at i:190328 original size:55 final size:54
Alignment explanation
Indices: 190269--190569 Score: 284
Period size: 55 Copynumber: 5.5 Consensus size: 54
190259 TAGAATTAAC
*
190269 GATTGAGCACCTCTGTGCTTCAATCGAGATCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGATCTGACACCTCTGTGCAGCCAAAA-T
* **
190324 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAATAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGATCTGACACCTCTGTGCAG---CCA-AAAT
* * * * * * * *
190382 GACTGAGCACCTCTGTGCTTC-AGCCAGGAGCTGACACCTCTGTGTAGCTAAGAC
1 GATTGAGCACCTCTGTGCTTCAATCGA-GATCTGACACCTCTGTGCAGCCAAAAT
*
190436 GATTGAGCACCTCTGTGCTTCAATCAAGGA-CTGACACCTCTGTGCAGCCAAATAT
1 GATTGAGCACCTCTGTGCTTCAATCGA-GATCTGACACCTCTGTGCAGCCAAA-AT
* * * * * ****
190491 GACTAAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA-TTGGAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGA-TCTGACACCTCTGTGCAGCCAAAAT
* *
190545 GATTGAGAACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
190570 TAAAATCAAG
Statistics
Matches: 204, Mismatches: 33, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
54 65 0.32
55 78 0.38
56 15 0.07
57 3 0.01
58 40 0.20
59 3 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGATCTGACACCTCTGTGCAGCCAAAAT
Found at i:190367 original size:27 final size:26
Alignment explanation
Indices: 190276--190480 Score: 105
Period size: 27 Copynumber: 7.4 Consensus size: 26
190266 AACGATTGAG
190276 CACCTCTGTGCTTCAATCGAGATCTGA
1 CACCTCTGTGCTTCAATCGAGA-CTGA
* ** * *
190303 CACCTCTGTG-TAGCCAAAAGTGATTGA
1 CACCTCTGTGCT--TCAATCGAGACTGA
190330 GCACCTCTGTGCTTCAATCGAGAACTGA
1 -CACCTCTGTGCTTCAATCGAG-ACTGA
* **
190358 CACCTCTGTGCAGTTAAAATAAATGACTGA
1 CACCTCTGTGC--TT-CAATCGA-GACTGA
* *
190388 GCACCTCTGTGCTTC-AGCCAGGAGCTGA
1 -CACCTCTGTGCTTCAATCGA-GA-CTGA
* *
190416 CACCTCTGTG-TAGCTAA--GACGATTGA
1 CACCTCTGTGCT-TC-AATCGA-GACTGA
*
190442 GCACCTCTGTGCTTCAATCAAGGACTGA
1 -CACCTCTGTGCTTCAATCGA-GACTGA
190470 CACCTCTGTGC
1 CACCTCTGTGC
190481 AGCCAAATAT
Statistics
Matches: 134, Mismatches: 26, Indels: 36
0.68 0.13 0.18
Matches are distributed among these distances:
26 7 0.05
27 69 0.51
28 31 0.23
29 6 0.04
30 9 0.07
31 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (26 bp):
CACCTCTGTGCTTCAATCGAGACTGA
Found at i:192726 original size:31 final size:31
Alignment explanation
Indices: 192688--192783 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
192678 TTCAAAAACA
*
192688 TAAGATATGATTACTTTCTTTTTTATTTAAT
1 TAAGATATGATTACTTTCGTTTTTATTTAAT
192719 TAAGATATGATTACTTTCGTTTTTATTTAAT
1 TAAGATATGATTACTTTCGTTTTTATTTAAT
*
192750 TAAGATATGATCACTTTCGTTTTTATTTAAT
1 TAAGATATGATTACTTTCGTTTTTATTTAAT
192781 TAA
1 TAA
192784 TATGTAGTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.30, C:0.07, G:0.08, T:0.54
Consensus pattern (31 bp):
TAAGATATGATTACTTTCGTTTTTATTTAAT
Found at i:194714 original size:28 final size:28
Alignment explanation
Indices: 194671--194726 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
194661 TTGATCTTGC
*
194671 ACCATCCATGGTCGCCAATCATCAATAA
1 ACCATCCATGGCCGCCAATCATCAATAA
194699 ACCATCCATGGCCGCCAATCATCAATAA
1 ACCATCCATGGCCGCCAATCATCAATAA
194727 TTGAATAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.34, G:0.11, T:0.20
Consensus pattern (28 bp):
ACCATCCATGGCCGCCAATCATCAATAA
Done.