Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008011.1 Hibiscus syriacus cultivar Beakdansim tig00110474_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: 1648842
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1025294 original size:61 final size:61
Alignment explanation
Indices: 1025206--1025340 Score: 173
Period size: 61 Copynumber: 2.2 Consensus size: 61
1025196 AAATATATAA
* * * *
1025206 GGATCAAATTGAACAAATTTTAAATATGAAGCTTAAACTAATAAATTATAA-CATTAAATTT
1 GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAACTAATAAATTA-AATCATTAAATTT
* * *
1025267 GGATTAAATTGAAAAAAGTTGAAATATGTAGCTTAAATTAATATATTAAATCATTAAATTT
1 GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAACTAATAAATTAAATCATTAAATTT
* *
1025328 GGACTCAATTGAA
1 GGATTAAATTGAA
1025341 TAAATTAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 2 0.03
61 62 0.97
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (61 bp):
GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAACTAATAAATTAAATCATTAAATTT
Found at i:1028219 original size:23 final size:24
Alignment explanation
Indices: 1028193--1028242 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
1028183 TAATATTTTT
1028193 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
*
1028216 TTTATTTAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1028240 TTT
1 TTT
1028243 TTCTTTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1028330 original size:26 final size:22
Alignment explanation
Indices: 1028264--1028321 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
1028254 ATTAATAATG
1028264 TTTTATCTAATTTATATTTAAATAA
1 TTTTAT-TAATTT-TA-TTAAATAA
*
1028289 ATTTATTAATTTTATTAAATAA
1 TTTTATTAATTTTATTAAATAA
1028311 TTTTATATAAT
1 TTTTAT-TAAT
1028322 ATGTCTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 13 0.43
23 6 0.20
24 6 0.20
25 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTATTAATTTTATTAAATAA
Found at i:1030938 original size:43 final size:42
Alignment explanation
Indices: 1030841--1030938 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 42
1030831 AGAAAAAGTG
* * *
1030841 TTATTAAAAAATTTAATATTTTTTTAATATTTTATATAGAGTA
1 TTATTAAAATA-TTAATAATTTTTAAATATTTTATATAGAGTA
1030884 TTATTATAAATATTAATAATTTTTAAATATTTT-TGATAGAGTA
1 TTATTA-AAATATTAATAATTTTTAAATATTTTAT-ATAGAGTA
1030927 TTATTTAAAATA
1 TTA-TTAAAATA
1030939 GAGAAAATCG
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
42 1 0.02
43 41 0.84
44 7 0.14
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (42 bp):
TTATTAAAATATTAATAATTTTTAAATATTTTATATAGAGTA
Found at i:1031081 original size:20 final size:20
Alignment explanation
Indices: 1031058--1031109 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1031048 AACGCGATCC
1031058 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1031078 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1031098 CCAAAATCGCAA
1 CCAGAATCGCAA
1031110 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1031190 original size:20 final size:20
Alignment explanation
Indices: 1031165--1031358 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
1031155 GATTTTCCAT
* *
1031165 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1031185 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1031205 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1031225 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
1031245 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
1031265 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1031285 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1031305 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1031326 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1031346 AATCGCAACGCGA
1 AATCGCAACGCGA
1031359 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1031210 original size:40 final size:39
Alignment explanation
Indices: 1031161--1031358 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
1031151 TTGCGATTTT
* ** *
1031161 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
1031199 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
1031240 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
1031280 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
1031319 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1031359 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:1031248 original size:60 final size:60
Alignment explanation
Indices: 1031165--1031357 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1031155 GATTTTCCAT
* ** * *
1031165 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
1031225 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
1031285 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
1031346 AATCGCAACGCG
1 AATCGCAACGCG
1031358 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:1031778 original size:33 final size:33
Alignment explanation
Indices: 1031739--1031809 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1031729 TTCACTTAGA
*
1031739 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1031772 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1031805 TTTCA
1 TTTCA
1031810 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1031949 original size:14 final size:14
Alignment explanation
Indices: 1031930--1031965 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1031920 AGAATGACTG
1031930 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1031944 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1031958 TCGCAACG
1 TCGCAACG
1031966 CGAAACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.25, G:0.28, T:0.08
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1031999 original size:19 final size:19
Alignment explanation
Indices: 1031977--1032074 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1031967 GAAACCAAAA
*
1031977 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1031996 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1032010 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1032029 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1032043 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1032062 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1032075 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1032018 original size:14 final size:14
Alignment explanation
Indices: 1031999--1032088 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1031989 TTTCATTTCG
1031999 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1032013 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1032032 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1032046 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1032063 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1032079 CGTTGCGATT
1 CGTTGCGATT
1032089 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1032024 original size:33 final size:33
Alignment explanation
Indices: 1031982--1032096 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1031972 CAAAATCGCA
1031982 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1032015 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1032048 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1032081 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1032097 AACCAAAATA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1034025 original size:185 final size:185
Alignment explanation
Indices: 1033795--1034266 Score: 926
Period size: 185 Copynumber: 2.6 Consensus size: 185
1033785 TAGATTGCTT
*
1033795 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1033860 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1033925 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1033980 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1034045 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
1034110 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1034165 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1034230 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
1034267 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 285 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1034109 original size:93 final size:93
Alignment explanation
Indices: 1033795--1034266 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
1033785 TAGATTGCTT
*
1033795 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1033860 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1033888 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1033952 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1033980 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1034045 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1034073 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1034137 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1034165 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1034230 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1034258 AGTAAATTT
1 AGTAAATTT
1034267 ATCCATTCAA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.49
93 191 0.51
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1034350 original size:19 final size:19
Alignment explanation
Indices: 1034310--1034438 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1034300 TAGTTTACTT
* *
1034310 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1034330 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1034349 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1034368 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1034382 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1034401 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1034415 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1034434 TCGCA
1 TCGCA
1034439 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1034389 original size:33 final size:32
Alignment explanation
Indices: 1034346--1034438 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1034336 CGCGAAACCA
**
1034346 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1034378 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1034411 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1034439 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1034436 original size:52 final size:52
Alignment explanation
Indices: 1034310--1034438 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1034300 TAGTTTACTT
**
1034310 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1034362 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1034415 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1034439 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1034456 original size:19 final size:19
Alignment explanation
Indices: 1034434--1034568 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1034424 GAAACCAAAA
*
1034434 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1034453 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1034469 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1034486 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1034502 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1034519 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1034538 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1034558 TCGTGTTGCGA
1 TCGCGTTGCGA
1034569 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1034475 original size:14 final size:14
Alignment explanation
Indices: 1034456--1034512 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1034446 TTTCATTTCG
1034456 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1034470 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1034487 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1034503 CGTTGCGATT
1 CGTTGCGATT
1034513 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1034481 original size:33 final size:33
Alignment explanation
Indices: 1034439--1034531 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1034429 CAAAATCGCA
*
1034439 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1034472 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1034505 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1034532 TTGGTTTCGC
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:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1036492 original size:14 final size:14
Alignment explanation
Indices: 1036473--1036508 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1036463 ATTGTTTAAT
1036473 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1036487 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1036501 TGATTTGT
1 TGATTTGT
1036509 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1036631 original size:19 final size:19
Alignment explanation
Indices: 1036615--1036716 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1036605 AAAAATGACT
1036615 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1036634 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1036653 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1036667 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1036686 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1036706 ATCGCAATGCG
1 ATCGCAATGCG
1036717 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1036769 original size:19 final size:19
Alignment explanation
Indices: 1036745--1037037 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
1036735 GATTATCTTG
1036745 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1036764 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1036783 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1036797 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1036816 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1036835 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1036854 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1036873 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1036892 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1036911 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
1036925 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1036944 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1036963 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1036977 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1036997 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1037011 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1037030 TTGCGATT
1 TTGCGATT
1037038 GTATTTTCCG
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 29 0.12
16 24 0.10
17 20 0.08
18 3 0.01
19 157 0.64
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1036785 original size:52 final size:53
Alignment explanation
Indices: 1036723--1037037 Score: 350
Period size: 52 Copynumber: 5.9 Consensus size: 53
1036713 TGCGTTTATA
*
1036723 ATTTCGCATTGCGATTATCTT-GTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTCTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1036775 ATTTCGCATTGCGATTCT-TTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTCTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1036827 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC--TTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1036884 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTT--CTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
1036936 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC--TTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* * *
1036988 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTTCTTCGTTGCGATTTTCATTTCGCATTGCGATT
1037038 GTATTTTCCG
Statistics
Matches: 238, Mismatches: 9, Indels: 31
0.86 0.03 0.11
Matches are distributed among these distances:
48 5 0.02
50 4 0.02
51 7 0.03
52 128 0.54
53 23 0.10
54 4 0.02
55 7 0.03
57 60 0.25
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (53 bp):
ATTTCGCATTGCGATTTTCTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1036893 original size:128 final size:122
Alignment explanation
Indices: 1036745--1037009 Score: 194
Period size: 128 Copynumber: 2.1 Consensus size: 122
1036735 GATTATCTTG
*
1036745 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
1036807 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1036871 CA
121 CA
* * *
1036873 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
1036935 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
1036995 CA
121 CA
1036997 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1037010 GTTGGGATTT
Statistics
Matches: 125, Mismatches: 5, Indels: 18
0.84 0.03 0.12
Matches are distributed among these distances:
121 7 0.06
122 4 0.03
123 18 0.14
124 18 0.14
125 2 0.02
126 2 0.02
128 74 0.59
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:1039337 original size:12 final size:12
Alignment explanation
Indices: 1039320--1039344 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1039310 TCTTCGGGGA
1039320 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1039332 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1039344 C
1 C
1039345 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1039553 original size:24 final size:24
Alignment explanation
Indices: 1039519--1039565 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1039509 CTGAAACATC
1039519 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1039543 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1039566 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1040276 original size:20 final size:20
Alignment explanation
Indices: 1040248--1040616 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
1040238 AAATTTAAGT
* * * *
1040248 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1040268 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1040288 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1040308 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1040328 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1040348 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1040368 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1040388 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1040408 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1040428 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1040448 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
1040468 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1040488 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1040508 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1040528 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1040548 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1040568 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1040588 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1040608 GTTGCGATT
1 GTTGCGATT
1040617 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1044652 original size:21 final size:21
Alignment explanation
Indices: 1044623--1044680 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1044613 CCTTCATCCA
* *
1044623 CATATCCTCCTGCACCTTCTG
1 CATACCCTCCTCCACCTTCTG
1044644 CATACCCTCCTCCACCTTCTG
1 CATACCCTCCTCCACCTTCTG
*
1044665 CATACCCTCCACCACC
1 CATACCCTCCTCCACC
1044681 AGCACCTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.17, C:0.52, G:0.05, T:0.26
Consensus pattern (21 bp):
CATACCCTCCTCCACCTTCTG
Found at i:1044725 original size:36 final size:36
Alignment explanation
Indices: 1044676--1044804 Score: 153
Period size: 33 Copynumber: 3.8 Consensus size: 36
1044666 ATACCCTCCA
* * *
1044676 CCACCAGCACCTTCATCGTATCCCCAATCTACATAC
1 CCACCACCACCTTCATCGTATCCCCCATCTACATAT
* * *
1044712 CCACCACCGCCTTCATCGTATCCCCCGTCTGCATAT
1 CCACCACCACCTTCATCGTATCCCCCATCTACATAT
1044748 CCA-CA--ACCTTCATCGTATCCCCCATCTACATAT
1 CCACCACCACCTTCATCGTATCCCCCATCTACATAT
*
1044781 ---CCACCACCTTCATCATATCCCCCA
1 CCACCACCACCTTCATCGTATCCCCCA
1044805 GGTAACTTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
31 2 0.03
33 43 0.54
35 2 0.03
36 33 0.41
ACGTcount: A:0.24, C:0.47, G:0.05, T:0.24
Consensus pattern (36 bp):
CCACCACCACCTTCATCGTATCCCCCATCTACATAT
Found at i:1044799 original size:18 final size:18
Alignment explanation
Indices: 1044743--1044800 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
1044733 CCCCCGTCTG
*
1044743 CATATCCACAACCTTCAT
1 CATATCCACCACCTTCAT
* * *
1044761 CGTATCCCCCATC-T-A-
1 CATATCCACCACCTTCAT
1044776 CATATCCACCACCTTCAT
1 CATATCCACCACCTTCAT
1044794 CATATCC
1 CATATCC
1044801 CCCAGGTAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
15 10 0.33
16 2 0.07
17 2 0.07
18 16 0.53
ACGTcount: A:0.28, C:0.43, G:0.02, T:0.28
Consensus pattern (18 bp):
CATATCCACCACCTTCAT
Found at i:1047006 original size:22 final size:21
Alignment explanation
Indices: 1046980--1047021 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
1046970 GGCAATGAAG
1046980 TATGTGAAGAAACATAGCTCGA
1 TATGTGAAGAAACATA-CTCGA
1047002 TATGTGAAGAAACATACTCG
1 TATGTGAAGAAACATACTCG
1047022 TACTCGATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24
Consensus pattern (21 bp):
TATGTGAAGAAACATACTCGA
Found at i:1050498 original size:6 final size:5
Alignment explanation
Indices: 1050444--1050494 Score: 75
Period size: 5 Copynumber: 9.6 Consensus size: 5
1050434 CGCCGCCGTC
1050444 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TC-GGG TCG-GG TCG-GG
1050492 TCG
1 TCG
1050495 TGGTAATACG
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 28 0.64
6 16 0.36
ACGTcount: A:0.00, C:0.20, G:0.57, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:1053349 original size:35 final size:35
Alignment explanation
Indices: 1053303--1053372 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1053293 AAAATAGTCC
*
1053303 TCAATTTCATTCTAAATCCC-AAATTCCAAAATAAT
1 TCAATTACATTCTAAA-CCCAAAATTCCAAAATAAT
1053338 TCAATTACATTCTAAACCCAAAATTCCAAAATAAT
1 TCAATTACATTCTAAACCCAAAATTCCAAAATAAT
1053373 ATTGATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 3 0.09
35 30 0.91
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCAAAATTCCAAAATAAT
Found at i:1055969 original size:32 final size:32
Alignment explanation
Indices: 1055933--1056040 Score: 171
Period size: 32 Copynumber: 3.4 Consensus size: 32
1055923 GTTCTACGGA
* *
1055933 ACATATGGACAGAATTACCTATGTCTTTCGGG
1 ACATATGGACAGAATTACCTATGTCTTTTGAG
* *
1055965 ACATATGGACAAAATTGCCTATGTCTTTTGAG
1 ACATATGGACAGAATTACCTATGTCTTTTGAG
*
1055997 ACATATGAACAGAATTACCTATGTCTTTTGAG
1 ACATATGGACAGAATTACCTATGTCTTTTGAG
1056029 ACATATGGACAG
1 ACATATGGACAG
1056041 TATAACTATG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTTGAG
Found at i:1062263 original size:35 final size:35
Alignment explanation
Indices: 1062217--1062290 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
1062207 CAATGTTATT
1062217 TTGAAGTATTTTAGAATTTTG-GGTTTAGAAT-ATAA
1 TTGAAGTATTTTAGAA-TTTGAGGTTTAGAATGA-AA
* *
1062252 TTGAATTATTTTGGAATTTGAGGTTTAGAATGAAA
1 TTGAAGTATTTTAGAATTTGAGGTTTAGAATGAAA
1062287 TTGA
1 TTGA
1062291 GGATTGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 4 0.11
35 30 0.86
36 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.45
Consensus pattern (35 bp):
TTGAAGTATTTTAGAATTTGAGGTTTAGAATGAAA
Found at i:1069749 original size:125 final size:125
Alignment explanation
Indices: 1069538--1069794 Score: 372
Period size: 125 Copynumber: 2.1 Consensus size: 125
1069528 GTGATACCAA
* * * * * *
1069538 TTTTTTTATTGTTGTGTATAATAAAATCGATAAAAATTATTGAAAAAATTATTATTTCTATTGGA
1 TTTTGTTATTGTTGTGAATAACAAAACCGATAAAAATTATTCAAAAAATTATTATTTCTATCGGA
* * * * *
1069603 TTTGTTATTATTTTAGTATTTTATCGGGTTTCTTAACAAAACCGGTAAAAGCGCTATCGG
66 TTTGTTATTATGTTAGCATTTTACCGGGTTTCTTAACAAAACCGATAAAAGCGCTACCGG
*
1069663 TTTTGTTATTGTTGTGAATAACAAAACCGGTAAAAATTA-TCAAAAATATTATTATTTCTATCGG
1 TTTTGTTATTGTTGTGAATAACAAAACCGATAAAAATTATTCAAAAA-ATTATTATTTCTATCGG
* *
1069727 TTTTGTTATTATGTTGGCATTTTACCGGGTTTCTTAACAAAACCGATAAAAGCGCTACCGG
65 ATTTGTTATTATGTTAGCATTTTACCGGGTTTCTTAACAAAACCGATAAAAGCGCTACCGG
1069788 TTTTGTT
1 TTTTGTT
1069795 GTTTTTTTAT
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
124 6 0.05
125 111 0.95
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (125 bp):
TTTTGTTATTGTTGTGAATAACAAAACCGATAAAAATTATTCAAAAAATTATTATTTCTATCGGA
TTTGTTATTATGTTAGCATTTTACCGGGTTTCTTAACAAAACCGATAAAAGCGCTACCGG
Found at i:1070536 original size:199 final size:199
Alignment explanation
Indices: 1070131--1070652 Score: 565
Period size: 198 Copynumber: 2.6 Consensus size: 199
1070121 TAAATATATA
* *
1070131 TGTCGATACATTT-TCTAAAAGTATCGA-CCCAAAAACA-CGAAACTGATAATTATAATGTAATA
1 TGTCGATACATTTAT-TAAAAGTATCGATCTCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * * * *
1070193 GGTAAATTTATAATGTAAACGGTATAAATATATC-AGTTTTATAATAGAATATGTCAACATAATG
65 AGTAAATTTACAATGT-AACGGTATAAATATACCGA-TTTTATAAGAAAATAAGTCAACATAAAG
* * *
1070257 TATCGACACAAATTTAAAAAGTGTCGATACATTTTGTCCAGAATGAATGTCAAACGAGGTGCACG
128 CATCGACACAAATTTAAAAAGTGACGATACATTTTGTCCAGAATGAATGCCAAACGAGGTGCACG
1070322 CACAAAG
193 CACAAAG
* * * * *
1070329 TATCGATACATTTATTAAAAGTATCGATATCAAAAACATAGAAACCGATAATTACAATGTAATAT
1 TGTCGATACATTTATTAAAAGTATCGATCTCAAAAACATCGAAACCGATAATTATAATGTAATAA
* * * *
1070394 GTAAATTTACAATGTACCCGGTAAAAATATACCGATTTTATGAGAAAATAAGTCTACATAAAGCA
66 GTAAATTTACAATGTA-ACGGTATAAATATACCGATTTTATAAGAAAATAAGTCAACATAAAGCA
** *** * * *
1070459 TCGACAC-GTTTTAAGTTTGTGACGATAC-TTTTTTTCAGAATGAATGCCCAACGAGGTGCACGC
130 TCGACACAAATTTAA-AAAGTGACGATACATTTTGTCCAGAATGAATGCCAAACGAGGTGCACGC
*
1070522 ATAAAG
194 ACAAAG
* * *
1070528 TGTCGATACATTTA--AAATTGTATCGATCTCAAAAACATCGAAACCAATCATTATAATGTAATA
1 TGTCGATACATTTATTAAA-AGTATCGATCTCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * * * *
1070591 AATAAATTTACAATGTTATCGGTATAAATATACCGGTTTAATTAGAAAATAGGTCAATATAA
65 AGTAAATTTACAATG-TAACGGTATAAATATACCGATTTTATAAGAAAATAAGTCAACATAA
1070653 GTACTACTTA
Statistics
Matches: 270, Mismatches: 46, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
197 3 0.01
198 112 0.41
199 66 0.24
200 88 0.33
201 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (199 bp):
TGTCGATACATTTATTAAAAGTATCGATCTCAAAAACATCGAAACCGATAATTATAATGTAATAA
GTAAATTTACAATGTAACGGTATAAATATACCGATTTTATAAGAAAATAAGTCAACATAAAGCAT
CGACACAAATTTAAAAAGTGACGATACATTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCAC
AAAG
Found at i:1070752 original size:64 final size:64
Alignment explanation
Indices: 1070667--1070813 Score: 206
Period size: 64 Copynumber: 2.3 Consensus size: 64
1070657 TACTTATTAC
* * *
1070667 ATTATATAAGCGCGACCTAATATGTTATTATACTTAATAATATTTCCGGTTAAATG-TATATTTT
1 ATTATATAAACGCTACCTAATATGTTATTATACTTAATAATATTTCCGATTAAATGCT-TATTTT
* * * * *
1070731 ATTATATAAACGCTACTTAATATGTTATTGTATTTGATAATATTTTCGATTAAATGCTTATTTT
1 ATTATATAAACGCTACCTAATATGTTATTATACTTAATAATATTTCCGATTAAATGCTTATTTT
1070795 ATTATATAAACGCTACCTA
1 ATTATATAAACGCTACCTA
1070814 TTACATTATA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 72 0.99
65 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.45
Consensus pattern (64 bp):
ATTATATAAACGCTACCTAATATGTTATTATACTTAATAATATTTCCGATTAAATGCTTATTTT
Found at i:1070844 original size:23 final size:23
Alignment explanation
Indices: 1070794--1070845 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1070784 ATGCTTATTT
* *
1070794 TATTATATAAACGCTACCTATTA
1 TATTATATAAACGATACCTAATA
* * *
1070817 CATTATATAAGCGATACTTAATA
1 TATTATATAAACGATACCTAATA
1070840 TATTAT
1 TATTAT
1070846 TGTACTTGAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (23 bp):
TATTATATAAACGATACCTAATA
Found at i:1075911 original size:16 final size:16
Alignment explanation
Indices: 1075886--1075920 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1075876 GTCGTCATTT
*
1075886 TATGTTTGCATGTATA
1 TATGTATGCATGTATA
*
1075902 TATGTATGCATGTGTA
1 TATGTATGCATGTATA
1075918 TAT
1 TAT
1075921 ATGCATTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.49
Consensus pattern (16 bp):
TATGTATGCATGTATA
Found at i:1080065 original size:14 final size:14
Alignment explanation
Indices: 1080048--1080077 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1080038 TACCATTGTT
1080048 CTCATATAGATCTC
1 CTCATATAGATCTC
*
1080062 CTCATCTAGATCTC
1 CTCATATAGATCTC
1080076 CT
1 CT
1080078 TTCAAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (14 bp):
CTCATATAGATCTC
Found at i:1106976 original size:7 final size:7
Alignment explanation
Indices: 1106964--1106994 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1106954 ATATAAGCCA
1106964 AAAAAAG
1 AAAAAAG
1106971 AAAAAAG
1 AAAAAAG
1106978 AAAAAAG
1 AAAAAAG
1106985 AAAAAA-
1 AAAAAAG
1106991 AAAA
1 AAAA
1106995 GATAGCATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1111180 original size:21 final size:21
Alignment explanation
Indices: 1111155--1111212 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
1111145 CCTAATATTG
1111155 CAATGTTAAAATTAGGTGCAA
1 CAATGTTAAAATTAGGTGCAA
*
1111176 CAATGTCAAAATTAGGTGCAA
1 CAATGTTAAAATTAGGTGCAA
*
1111197 TAATGTTTGAAAATTA
1 CAATG-TT-AAAATTA
1111213 AATAGGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 24 0.75
22 1 0.03
23 7 0.22
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (21 bp):
CAATGTTAAAATTAGGTGCAA
Found at i:1111245 original size:14 final size:14
Alignment explanation
Indices: 1111226--1111263 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
1111216 AGGTAAATTA
1111226 TAAACTTTAGTCAC
1 TAAACTTTAGTCAC
1111240 TAAACTTTAGTCAC
1 TAAACTTTAGTCAC
1111254 TAAACTTTAG
1 TAAACTTTAG
1111264 GATATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (14 bp):
TAAACTTTAGTCAC
Found at i:1115861 original size:21 final size:21
Alignment explanation
Indices: 1115836--1115883 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1115826 CCTAATATTG
1115836 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
1115857 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
1115878 TAATGT
1 CAATGT
1115884 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:1123936 original size:20 final size:20
Alignment explanation
Indices: 1123907--1123944 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1123897 TTTGGTTCAC
*
1123907 GGAATGTAAGATTACCAGTG
1 GGAATATAAGATTACCAGTG
1123927 GGAATATAAGATTACCAG
1 GGAATATAAGATTACCAG
1123945 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (20 bp):
GGAATATAAGATTACCAGTG
Found at i:1123949 original size:18 final size:19
Alignment explanation
Indices: 1123907--1123950 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1123897 TTTGGTTCAC
*
1123907 GGAATGTAAGATTACCAGTG
1 GGAATATAAGATTACCAG-G
1123927 GGAATATAAGATTACCA-G
1 GGAATATAAGATTACCAGG
1123945 GGAATA
1 GGAATA
1123951 GGATTACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.41, C:0.09, G:0.27, T:0.23
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:1125818 original size:14 final size:14
Alignment explanation
Indices: 1125799--1125841 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
1125789 GAAACATAAG
1125799 ATATATGATATGAT-
1 ATATATGATAT-ATC
1125813 ATATATGATTATATGC
1 ATATATGA-TATAT-C
1125829 ATATATGATATAT
1 ATATATGATATAT
1125842 GCTATGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 10 0.38
15 8 0.31
16 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (14 bp):
ATATATGATATATC
Found at i:1126084 original size:15 final size:15
Alignment explanation
Indices: 1126066--1126115 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
1126056 CGAGGGTATT
*
1126066 GTAGTCCTTCAGGAC
1 GTAGTCCTTCGGGAC
*
1126081 GTAGTCCATCGGGAC
1 GTAGTCCTTCGGGAC
*
1126096 GTAGTTCTTCGGGAC
1 GTAGTCCTTCGGGAC
1126111 GTAGT
1 GTAGT
1126116 GGTCCTACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.18, C:0.22, G:0.32, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:1136050 original size:111 final size:110
Alignment explanation
Indices: 1135857--1136077 Score: 406
Period size: 111 Copynumber: 2.0 Consensus size: 110
1135847 TGAAAATCAT
*
1135857 ATATCTCTACACTTTGCTGATACGGTAACATTTAACGTTTTAATTTAATTTAAATTATTAGTAAT
1 ATATCTCGACACTTTGCTGATACGGTAACATTTAACGTTTTAATTTAATTTAAATTATTAGTAAT
* *
1135922 ATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 AATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
1135967 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACA-TTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1136032 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
65 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
1136078 TTTTTTTAAT
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
110 29 0.27
111 78 0.73
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (110 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTAACGTTTTAATTTAATTTAAATTATTAGTAAT
AATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1155396 original size:30 final size:30
Alignment explanation
Indices: 1155362--1155418 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1155352 TGTTTTTATT
1155362 CTTAAATTTTATCAAACAATTATAAAATGA
1 CTTAAATTTTATCAAACAATTATAAAATGA
**
1155392 CTTAAATTTTATCAAATTATTATAAAA
1 CTTAAATTTTATCAAACAATTATAAAA
1155419 CGACCCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (30 bp):
CTTAAATTTTATCAAACAATTATAAAATGA
Found at i:1162678 original size:10 final size:10
Alignment explanation
Indices: 1162663--1162690 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1162653 TTTTTTTTTA
1162663 ATTAAAATAT
1 ATTAAAATAT
1162673 ATTAAAATAT
1 ATTAAAATAT
1162683 ATTAAAAT
1 ATTAAAAT
1162691 TAGATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:1162734 original size:8 final size:9
Alignment explanation
Indices: 1162713--1162744 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
1162703 CATATTATTT
1162713 TTTTTGTAA
1 TTTTTGTAA
1162722 TTTTTGTAA
1 TTTTTGTAA
1162731 TTTTTGTAA
1 TTTTTGTAA
1162740 TTTTT
1 TTTTT
1162745 TTATATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (9 bp):
TTTTTGTAA
Found at i:1167878 original size:20 final size:20
Alignment explanation
Indices: 1167855--1167942 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
1167845 GAATATGTAA
* *
1167855 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
1167875 ATCGCAACGTGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
1167895 ATCGCAACGAGATTCTAACT
1 ATCGCAACGCGATTCTGACT
1167915 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1167935 GTCGCAAC
1 ATCGCAAC
1167943 ACTGAATTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1168776 original size:24 final size:24
Alignment explanation
Indices: 1168744--1168797 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1168734 GTATTCGAAA
1168744 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1168768 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1168792 TTTGAT
1 TTTGAT
1168798 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1170264 original size:23 final size:23
Alignment explanation
Indices: 1170238--1170315 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
1170228 CACCACAGCT
1170238 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
1170261 CATATAATTGCACCGGAGTG-CA
1 CATATAATTGCACCGAAGTGCCA
* * *
1170283 GCGTAGAATTGCACCGTAGTGCCA
1 -CATATAATTGCACCGAAGTGCCA
*
1170307 TATAATAAT
1 CAT-ATAAT
1170316 ATCCATAAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.04
23 37 0.82
24 6 0.13
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:1170516 original size:103 final size:103
Alignment explanation
Indices: 1170330--1170520 Score: 310
Period size: 103 Copynumber: 1.9 Consensus size: 103
1170320 ATAAGGACCA
* * * *
1170330 CATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACA
1 CATATACATATACCAAGGATCAAGTATATATCTCACCAGACTTCACACATGTTCCAAAGAATACA
* * *
1170395 TATATGTCTCGAATGACCACATATCATTCCTTAAGAAT
66 CATATGTCCCGAAGGACCACATATCATTCCTTAAGAAT
*
1170433 CATATACATATGCCAAGGATCAAGTATATATCTCACCAGACTTCACACATGTTCCAAAGAATACA
1 CATATACATATACCAAGGATCAAGTATATATCTCACCAGACTTCACACATGTTCCAAAGAATACA
1170498 CATATGTCCCGAAGGACCACATA
66 CATATGTCCCGAAGGACCACATA
1170521 GACCCTCGAC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 80 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
CATATACATATACCAAGGATCAAGTATATATCTCACCAGACTTCACACATGTTCCAAAGAATACA
CATATGTCCCGAAGGACCACATATCATTCCTTAAGAAT
Found at i:1174960 original size:64 final size:64
Alignment explanation
Indices: 1174887--1175048 Score: 159
Period size: 64 Copynumber: 2.5 Consensus size: 64
1174877 ATTGTTTGAA
* *** *
1174887 GGTGTATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAATCTAA-AAACATCGAATAAAAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCATC-CCAGTAAT-AAACAAACATCGAATAAAAT
1174950 T
64 T
* * ** *
1174951 GGTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAAACAAACATCGAATGTATTT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATAAAATT
** *
1175015 TATGCACCGATGCACAGGTAGTGCATCGATGCAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCAT
1175049 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
63 6 0.08
64 68 0.86
65 5 0.06
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (64 bp):
GGTGCATCGATGCACAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATAAAATT
Found at i:1176016 original size:103 final size:103
Alignment explanation
Indices: 1175791--1176008 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1175781 GTCGAGGGTC
1175791 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1175856 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1175894 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1175959 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1175997 TATGTGGTCCTT
1 TATGTGGTCCTT
1176009 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1176058 original size:23 final size:23
Alignment explanation
Indices: 1176025--1176090 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
1176015 ATTATTATAT
*
1176025 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* * * *
1176048 GGCACTCCGGTGTAATTATATGT
1 GGCACTACGGTGCAATTATACGC
* *
1176071 GGCACTTCGGTTCAATTATA
1 GGCACTACGGTGCAATTATA
1176091 TGAGATGTGG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1176091 original size:23 final size:23
Alignment explanation
Indices: 1176015--1176092 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
1176005 CCTTATGGAC
* *
1176015 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTTCA
* * * *
1176039 ATTCTACGCGGCACTCCGGTGT-A
1 ATTATATGTGGCACTACGGT-TCA
*
1176062 ATTATATGTGGCACTTCGGTTCA
1 ATTATATGTGGCACTACGGTTCA
1176085 ATTATATG
1 ATTATATG
1176093 AGATGTGGTG
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
22 1 0.02
23 38 0.90
24 3 0.07
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTTCA
Found at i:1178605 original size:18 final size:18
Alignment explanation
Indices: 1178584--1178626 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1178574 CAAGAAAAAG
1178584 GCAATCAAAATCAAAATT
1 GCAATCAAAATCAAAATT
1178602 GCAATCAAAATCAAAATT
1 GCAATCAAAATCAAAATT
*
1178620 CCAATCA
1 GCAATCA
1178627 CAACCGGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.21, G:0.05, T:0.21
Consensus pattern (18 bp):
GCAATCAAAATCAAAATT
Found at i:1178839 original size:20 final size:20
Alignment explanation
Indices: 1178796--1179143 Score: 298
Period size: 20 Copynumber: 18.7 Consensus size: 20
1178786 TTACACATTC
*
1178796 ATTTGAATATCGCAACGCG-
1 ATTTGACTATCGCAACGCGA
*
1178815 ATTTGACTATCGCAACGCGG
1 ATTTGACTATCGCAACGCGA
* *
1178835 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
1178854 A----A-AATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
1178869 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1178889 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
1178908 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1178923 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1178943 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1178963 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
1178983 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1179003 ATTTGACTATCGCAA--CGA
1 ATTTGACTATCGCAACGCGA
**
1179021 A----AAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1179037 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * * *
1179057 ATTTGATTATCACAACGGGT
1 ATTTGACTATCGCAACGCGA
* * *
1179077 ATTCGATTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
1179097 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
1179111 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1179131 A-TTGACTTTCGCA
1 ATTTGACTATCGCA
1179144 TTGCGATTTT
Statistics
Matches: 269, Mismatches: 35, Indels: 50
0.76 0.10 0.14
Matches are distributed among these distances:
14 36 0.13
15 6 0.02
16 5 0.02
18 5 0.02
19 33 0.12
20 184 0.68
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1178885 original size:54 final size:54
Alignment explanation
Indices: 1178804--1179073 Score: 380
Period size: 54 Copynumber: 4.9 Consensus size: 54
1178794 TCATTTGAAT
* *
1178804 ATCGCAACGCG-ATTTGACTATCGCAACGCGGATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCAAAA
* *
1178857 ATCGCAACACGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCAAAA
* *
1178911 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGC-AA----A-A
* * *
1178971 ATCACAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCAAAA
* *
1179025 ATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATCACAACG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACG
1179074 GGTATTCGAT
Statistics
Matches: 197, Mismatches: 13, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
53 10 0.05
54 133 0.68
55 3 0.02
59 3 0.02
60 48 0.24
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCAAAA
Found at i:1178979 original size:94 final size:93
Alignment explanation
Indices: 1178857--1179143 Score: 310
Period size: 94 Copynumber: 3.1 Consensus size: 93
1178847 CAACTCAAAA
* *
1178857 ATCGCAACACGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCAAAAATCGCAACGCG
1 ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGCAAC-CAAAAATCGCAACGCG
*
1178922 AATTTGACTATCGCAACGCGAATTTGACT
65 AATTAGACTATCGCAACGCGAATTTGACT
* * * * *
1178951 ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGACTATCGCAACGC-GAATTTGACTATCG
1 ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGCAAC-CAAAAATCG-C-AACG
** * **
1179015 C-AACGAAAAAATCGCAACGCGAATTTGACT
63 CGAATTAGACTATCGCAACGCGAATTTGACT
* * * * * * *
1179045 ATCGCAACGTGAATTTGATTATCACAACGGGTATTCGATTATCGCAACGAGAAAATCGCAAAGCG
1 ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGCAACCA-AAAATCGCAACGCG
*
1179110 TATTAGACTATCGCAACGCGAA-TTGACT
65 AATTAGACTATCGCAACGCGAATTTGACT
*
1179138 TTCGCA
1 ATCGCA
1179144 TTGCGATTTT
Statistics
Matches: 155, Mismatches: 33, Indels: 11
0.78 0.17 0.06
Matches are distributed among these distances:
93 18 0.12
94 129 0.83
95 8 0.05
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (93 bp):
ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGCAACCAAAAATCGCAACGCGA
ATTAGACTATCGCAACGCGAATTTGACT
Found at i:1179029 original size:74 final size:74
Alignment explanation
Indices: 1178911--1179143 Score: 270
Period size: 74 Copynumber: 3.1 Consensus size: 74
1178901 CAACTCAAAA
** *
1178911 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCAC
1 ATCGCAACGCGAATTTGACTATCGCAA--CGAA----AAAATCGCAACGCGAATTTGACTATCGC
1178976 AACGCGAATTTGACT
60 AACGCGAATTTGACT
*
1178991 ATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGAATTTGACTATCGCAACGTG
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGAATTTGACTATCGCAACGCG
*
1179056 AATTTGATT
66 AATTTGACT
* * * * * * * * *
1179065 ATCACAACGGGTATTCGATTATCGCAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAACGCG
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGAATTTGACTATCGCAACGCG
1179130 AA-TTGACT
66 AATTTGACT
*
1179138 TTCGCA
1 ATCGCA
1179144 TTGCGATTTT
Statistics
Matches: 135, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
73 9 0.07
74 95 0.70
78 4 0.03
80 27 0.20
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGAATTTGACTATCGCAACGCG
AATTTGACT
Found at i:1179161 original size:20 final size:20
Alignment explanation
Indices: 1179136--1179174 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1179126 CGCGAATTGA
*
1179136 CTTTCGCATTGCGATTTTGG
1 CTTTCGCATTACGATTTTGG
1179156 CTTTCGCATTACGATTTTG
1 CTTTCGCATTACGATTTTG
1179175 AGTTTAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (20 bp):
CTTTCGCATTACGATTTTGG
Found at i:1180782 original size:42 final size:42
Alignment explanation
Indices: 1180733--1180828 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
1180723 GGACCTATTC
* *
1180733 AACGATGACAGTGACCTCTTGAACGGT-GGGAGAGGACTCTTG
1 AACGATGACAGGGACCTCTTGAACGATAGGG-GAGGACTCTTG
** * * *
1180775 AGGGATGATAGGGGCCTCTTGAACGATAGGGGAGGCCTCTTG
1 AACGATGACAGGGACCTCTTGAACGATAGGGGAGGACTCTTG
1180817 AACGATGACAGG
1 AACGATGACAGG
1180829 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
42 40 0.93
43 3 0.07
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.20
Consensus pattern (42 bp):
AACGATGACAGGGACCTCTTGAACGATAGGGGAGGACTCTTG
Found at i:1181408 original size:20 final size:20
Alignment explanation
Indices: 1181383--1181430 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1181373 GCGATTCTTT
1181383 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
1181403 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCAAATTCG
1181423 CGTTGCGA
1 CGTTGCGA
1181431 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1183199 original size:20 final size:20
Alignment explanation
Indices: 1183176--1183263 Score: 88
Period size: 20 Copynumber: 4.5 Consensus size: 20
1183166 TCTGAAACTT
1183176 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
1183196 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
1183216 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * *
1183236 ACTATCGCTACGCG-AAATG
1 AAAATCGCAACACGAAAATG
1183255 AAAATCGCA
1 AAAATCGCA
1183264 TTGCGATTCT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
19 9 0.16
20 48 0.84
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1183895 original size:20 final size:20
Alignment explanation
Indices: 1183865--1183958 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
1183855 ACGCTTTGAA
*
1183865 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* * *
1183885 CATCGCGTTGCGACAGTCCG
1 AATCGCGTTGCGATAGTCAG
* *
1183905 AATCTCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
1183925 AATCGCGTTGTGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
1183945 AATCGCATTGCGAT
1 AATCGCGTTGCGAT
1183959 TTACATATTC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:1190793 original size:45 final size:45
Alignment explanation
Indices: 1190723--1190873 Score: 205
Period size: 45 Copynumber: 3.4 Consensus size: 45
1190713 CACTCTTTTG
* * * *
1190723 AGAAGTACGAGTCAGAAAGGCACATCAGAAACAGAAAACCGCTCG
1 AGAAGTACGAGTCGGAAAGGTACATCAGAAACAGAAAACCGTTCC
*
1190768 ACAAGTACGAGTCGGAAAGGTACATCAGAAACA-AAACACCGTTCC
1 AGAAGTACGAGTCGGAAAGGTACATCAGAAACAGAAA-ACCGTTCC
* * *
1190813 AGAAGTGCGAGTCGAAAAGGTACATCAGAAACAGAAAACCGTTCT
1 AGAAGTACGAGTCGGAAAGGTACATCAGAAACAGAAAACCGTTCC
*
1190858 AGAAGTACAAGTCGGA
1 AGAAGTACGAGTCGGA
1190874 GTCGTCCCAC
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
44 3 0.03
45 86 0.93
46 3 0.03
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.13
Consensus pattern (45 bp):
AGAAGTACGAGTCGGAAAGGTACATCAGAAACAGAAAACCGTTCC
Found at i:1197925 original size:9 final size:9
Alignment explanation
Indices: 1197911--1197953 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
1197901 GAGTCGAATA
1197911 CACCTTCAC
1 CACCTTCAC
*
1197920 CACCTTCAT
1 CACCTTCAC
**
1197929 CGTCTTCAC
1 CACCTTCAC
1197938 CACCTTCAC
1 CACCTTCAC
1197947 CACCTTC
1 CACCTTC
1197954 GTCTTCAACT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.19, C:0.51, G:0.02, T:0.28
Consensus pattern (9 bp):
CACCTTCAC
Found at i:1197955 original size:24 final size:26
Alignment explanation
Indices: 1197910--1197969 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 26
1197900 GGAGTCGAAT
1197910 ACACCTTCACCACCTTCATCGTCTTCA
1 ACACCTTCACCACCTT-ATCGTCTTCA
*
1197937 CCACCTTCACCACC-T-TCGTCTTCA
1 ACACCTTCACCACCTTATCGTCTTCA
*
1197961 ACTCCTTCA
1 ACACCTTCA
1197970 TCCTCTTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.53
26 1 0.03
27 13 0.43
ACGTcount: A:0.20, C:0.47, G:0.03, T:0.30
Consensus pattern (26 bp):
ACACCTTCACCACCTTATCGTCTTCA
Found at i:1200659 original size:2 final size:2
Alignment explanation
Indices: 1200652--1200682 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1200642 ATTCTAACTT
1200652 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
1200683 GTAAATCAGG
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:1203250 original size:80 final size:81
Alignment explanation
Indices: 1203143--1203304 Score: 254
Period size: 80 Copynumber: 2.0 Consensus size: 81
1203133 TTGTACCAAA
* * *
1203143 ATTTGTAGACATACATTTGAATATATATTAAGGAATTTTATAATTTAAATA-TTTTAAAAAAATT
1 ATTTATAGACATACATTTGAATATATATCAAGGAATATTATAATTTAAATATTTTTAAAAAAATT
*
1203207 GAGAATATTTATTTAT
66 AAGAATATTTATTTAT
*
1203223 ATTTATAGACATACATTTGAATATATATCGAGGAATATTATAATTTAAATATTTTTTTAAAAAAA
1 ATTTATAGACATACATTTGAATATATATCAAGGAATATTATAATTTAAATA--TTTTTAAAAAAA
1203288 TTAAGAATATTTATTTA
64 TTAAGAATATTTATTTA
1203305 ATACTCAAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
80 47 0.64
83 27 0.36
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (81 bp):
ATTTATAGACATACATTTGAATATATATCAAGGAATATTATAATTTAAATATTTTTAAAAAAATT
AAGAATATTTATTTAT
Found at i:1208422 original size:15 final size:15
Alignment explanation
Indices: 1208383--1208422 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1208373 TAAAAAAGAA
* *
1208383 ATAAATATCTAATTT
1 ATAAATATATAAATT
1208398 ATAAAT-TATAAATT
1 ATAAATATATAAATT
1208412 ATAAATATATA
1 ATAAATATATA
1208423 TATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATATATAAATT
Found at i:1230717 original size:11 final size:11
Alignment explanation
Indices: 1230687--1230720 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1230677 TTGTTAGCTT
* *
1230687 CTCAACACACT
1 CTCAACACTCA
1230698 CTCAACACTCA
1 CTCAACACTCA
1230709 CTCAACACTCA
1 CTCAACACTCA
1230720 C
1 C
1230721 GTATCCTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (11 bp):
CTCAACACTCA
Found at i:1250255 original size:31 final size:31
Alignment explanation
Indices: 1250217--1250278 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1250207 GTATTCATTA
**
1250217 TTTTTTTT-ATTTTGTTATATTATATCTTTAT
1 TTTTTTTTAATTTTAATA-ATTATATCTTTAT
*
1250248 TTTTTTTTAATTTTAATAATTTTATCTTTAT
1 TTTTTTTTAATTTTAATAATTATATCTTTAT
1250279 GACACTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.73
Consensus pattern (31 bp):
TTTTTTTTAATTTTAATAATTATATCTTTAT
Found at i:1250963 original size:21 final size:20
Alignment explanation
Indices: 1250929--1250971 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1250919 TTAAAAAATC
1250929 GAATCAAACATCATAAAATTT
1 GAATCAAACATCAT-AAATTT
** *
1250950 GAATCAAATTTCATTAATTT
1 GAATCAAACATCATAAATTT
1250970 GA
1 GA
1250972 TCCATCATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (20 bp):
GAATCAAACATCATAAATTT
Found at i:1262656 original size:19 final size:18
Alignment explanation
Indices: 1262632--1262684 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
1262622 TTATTAAAAG
1262632 TTATAAAATGATTATTTAA
1 TTATAAAAT-ATTATTTAA
* *
1262651 TTATAAAATATCATTTTA
1 TTATAAAATATTATTTAA
*
1262669 TTAAAAAATTATTATT
1 TTATAAAA-TATTATT
1262685 AAAAGTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TTATAAAATATTATTTAA
Found at i:1262671 original size:18 final size:19
Alignment explanation
Indices: 1262632--1262677 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
1262622 TTATTAAAAG
*
1262632 TTATAAAATGATTATTTAA
1 TTATAAAATGATCATTTAA
*
1262651 TTATAAAAT-ATCATTTTA
1 TTATAAAATGATCATTTAA
*
1262669 TTAAAAAAT
1 TTATAAAAT
1262678 TATTATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
TTATAAAATGATCATTTAA
Found at i:1269462 original size:2 final size:2
Alignment explanation
Indices: 1269455--1269514 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1269445 GCGATATGTG
1269455 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
1269497 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1269515 GAGAGAGAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1271541 original size:23 final size:23
Alignment explanation
Indices: 1271514--1271560 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1271504 CCGGTCGTCA
1271514 ACCCTCACGTCACCGTTCGATCC
1 ACCCTCACGTCACCGTTCGATCC
1271537 ACCCTCACGTCACCGTTCGATCC
1 ACCCTCACGTCACCGTTCGATCC
1271560 A
1 A
1271561 TCAGAAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.47, G:0.13, T:0.21
Consensus pattern (23 bp):
ACCCTCACGTCACCGTTCGATCC
Found at i:1275459 original size:23 final size:23
Alignment explanation
Indices: 1275395--1275459 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
1275385 CTTATATGGT
*
1275395 ACTTCGTTGCATTTCTACGCGGC
1 ACTTCGGTGCATTTCTACGCGGC
* * *
1275418 ACTACGGTGCAATTCTACGTGGC
1 ACTTCGGTGCATTTCTACGCGGC
*
1275441 ACTTCGGTGCATTTATACG
1 ACTTCGGTGCATTTCTACG
1275460 AGCTGTAATG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.32
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGC
Found at i:1279870 original size:2 final size:2
Alignment explanation
Indices: 1279819--1279852 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1279809 GTATTTGCAG
1279819 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
1279853 GAATAAGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1281352 original size:2 final size:2
Alignment explanation
Indices: 1281347--1281371 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1281337 TAAATTCATA
1281347 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1281372 GTTTACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1284984 original size:2 final size:2
Alignment explanation
Indices: 1284977--1285020 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1284967 TTCATCAAAT
* *
1284977 TA TA TA TA TC TA TA TA TA TA TA TA TA TA AA 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
1285019 TA
1 TA
1285021 CATCTAGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1300920 original size:19 final size:19
Alignment explanation
Indices: 1300896--1300934 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1300886 TCGAATGCAT
1300896 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1300915 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1300934 T
1 T
1300935 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1300951 original size:65 final size:63
Alignment explanation
Indices: 1300833--1301041 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 63
1300823 TATTCAAAGG
* *
1300833 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGCA
*
1300895 TTC
61 TTT
1300898 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * * **
1300963 GATGCATCGATGCACAAGCCATGTATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATTT
*
1301027 CATGCATCGATGCAC
1 CATGCACCGATGCAC
1301042 ACTTGGTGCA
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 7 0.06
64 53 0.42
65 63 0.50
66 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTT
Found at i:1301034 original size:64 final size:65
Alignment explanation
Indices: 1300882--1301042 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
1300872 GAATTAATTG
* * *** *
1300882 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* * **
1300947 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGTATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
1301010 A
65 A
1301011 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1301043 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1301057 original size:64 final size:64
Alignment explanation
Indices: 1300833--1301062 Score: 216
Period size: 64 Copynumber: 3.6 Consensus size: 64
1300823 TATTCAAAGG
* * * *
1300833 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
1300895 TTC
62 TTT
* * *
1300898 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** * **
1300963 GATGCATCGATGCACAAGCCATGTATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
1301027 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
1301063 AGTGTTCCAA
Statistics
Matches: 137, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
63 6 0.04
64 68 0.50
65 63 0.46
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:1306773 original size:20 final size:21
Alignment explanation
Indices: 1306744--1306799 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1306734 TTTGCACTTC
*
1306744 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1306764 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1306786 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1306800 AAGACTATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:1308378 original size:21 final size:21
Alignment explanation
Indices: 1308336--1308379 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1308326 ACCCCGGGAG
*
1308336 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1308357 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1308378 CT
1 CT
1308380 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1309427 original size:19 final size:19
Alignment explanation
Indices: 1309403--1309441 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1309393 TCGAATGCAT
1309403 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1309422 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1309441 T
1 T
1309442 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1309460 original size:65 final size:63
Alignment explanation
Indices: 1309359--1309548 Score: 222
Period size: 65 Copynumber: 3.0 Consensus size: 63
1309349 ATGCATCAGT
* * * * **
1309359 CCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCATTCCATGCACCGATGCACTC
1 CCATGCATCGATGCATC-A-GAATAT-TTTCAAACATCGAATGCATTTCATGCATCGATGCACAA
*
1309422 T
63 G
* *
1309423 CCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAAG
1 CCATGCATCGATGCA-TCAGAATATTTTC-AAACATCGAATGCATTTCATGCATCGATGCACAAG
**
1309488 CCATGCATCGATGCATCAGGCTATTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
1 CCATGCATCGATGCATCAGAATATTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
1309549 CTTGGTGCAC
Statistics
Matches: 109, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
63 38 0.35
64 26 0.24
65 45 0.41
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (63 bp):
CCATGCATCGATGCATCAGAATATTTTCAAACATCGAATGCATTTCATGCATCGATGCACAAG
Found at i:1309540 original size:63 final size:65
Alignment explanation
Indices: 1309389--1309548 Score: 225
Period size: 65 Copynumber: 2.5 Consensus size: 65
1309379 GAATTAATTG
* * *** *
1309389 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
1309454 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
1309517 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1309549 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
63 32 0.38
64 10 0.12
65 43 0.51
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1309563 original size:63 final size:64
Alignment explanation
Indices: 1309347--1309568 Score: 227
Period size: 63 Copynumber: 3.5 Consensus size: 64
1309337 AGGCATGAAC
* * * *
1309347 CGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCATTCCATG
1 CGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCATTTCATG
*
1309409 CAC
62 CAT
* * *
1309412 CGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTGATGCAT
1 CGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTTCATGCAT
** **
1309477 CGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTC-AAACATCGAATGCATTTCATGCAT
1 CGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTTCATGCAT
*** *
1309540 CGATGCACACTTGGTGCACCGATGCATCA
1 CGATGCACACTCCATGCATCGATGCATCA
1309569 AGTGTTCCAA
Statistics
Matches: 132, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
63 52 0.39
64 28 0.21
65 52 0.39
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
CGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTTCATGCAT
Found at i:1325053 original size:87 final size:87
Alignment explanation
Indices: 1324886--1325125 Score: 299
Period size: 87 Copynumber: 2.8 Consensus size: 87
1324876 ATATGATTTA
* * * * * *
1324886 ACTGAAAATATTATTAAA-ATAAT-A-A-ATTAGGTAGCGCTTATATAATGTAATAGATATTGTT
1 ACTGAAAATATTATCAAACACAATAACATATTAGATAACGCTTATATAATGTAATAGGTAGTGTT
*
1324947 TATATAATAAAATATGTTAATT
66 TATATAATAAAATAGGTTAATT
* * *
1324969 ACTGGAAATATTATCAAACACAATAACATATTAGATAACGTTTATATAATGTAATAGGTAGTGCT
1 ACTGAAAATATTATCAAACACAATAACATATTAGATAACGCTTATATAATGTAATAGGTAGTGTT
1325034 TATATAATAAAATAGGTTAATT
66 TATATAATAAAATAGGTTAATT
** * * * * *
1325056 ACTGAAAATATTATCAAGTATAATAATATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGTT
1 ACTGAAAATATTATCAAACACAATAACATATTAGATAACGCTTATATAATGTAATAGGTAGTGTT
1325121 TATAT
66 TATAT
1325126 TGACTTATTC
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
83 16 0.12
84 4 0.03
85 1 0.01
86 1 0.01
87 111 0.83
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (87 bp):
ACTGAAAATATTATCAAACACAATAACATATTAGATAACGCTTATATAATGTAATAGGTAGTGTT
TATATAATAAAATAGGTTAATT
Found at i:1325113 original size:23 final size:23
Alignment explanation
Indices: 1325078--1325125 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1325068 ATCAAGTATA
*
1325078 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
* *
1325101 ATAATGTAATAGGTAGCGTTTAT
1 ATAATATAATAGGTAGCGCTTAT
1325124 AT
1 AT
1325126 TGACTTATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:1325533 original size:198 final size:199
Alignment explanation
Indices: 1325127--1325806 Score: 883
Period size: 200 Copynumber: 3.4 Consensus size: 199
1325117 CGTTTATATT
* * * **
1325127 GACTTATTCTATCATAAAATCGGTATATTTATATCAGTAACATTACAAATTTACCTATTACATTA
1 GACTTATTCTCTCATAAAACCGGTATATTTATACCAGTAACATTGTAAATTTACCTATTACATTA
* * * *
1325192 TAATTATCGGTTTCGATGTTTTTGGGATCAATACAATTT--TAAATGTATCGACACTTTATGCGT
66 TAATTATCGGTTTCGATGTTTTTGAGATCGATAC-TTTTAATAAATGTATCGACACTTTATGTGT
* *
1325255 GCACCTCGTTGGGCATTCATTCTGG-AAAAAAGTATCGACACAAACTTAAAACGTGTCGATACAT
130 GCACCTCGTT-GGCATTCATTCTGGAAAAAAATTATCGACACAAACTTAAAATGTGTCGATACAT
1325319 TATGTA
194 TATGTA
* * * *
1325325 GACCTATTTTCTCATAAAACCGGTATATTTCTACCGGGT-ACATTGTAAA-TTACCTATTACATT
1 GACTTATTCTCTCATAAAACCGGTATATTTATACC-AGTAACATTGTAAATTTACCTATTACATT
* *
1325388 ATAATTATCGGTTTTGAT-TTTTTAAGATCGATACTTTTAATAAATGTATCGACACTTTATGTGT
65 ATAATTATCGGTTTCGATGTTTTTGAGATCGATACTTTTAATAAATGTATCGACACTTTATGTGT
* *
1325452 GCACCTCGTTGGACATTAATTCTGGAAAAAAATTATAGACACAAACTTAAAATGTGTCGATACAT
130 GCACCTCGTTGG-CATTCATTCTGGAAAAAAATTATCGACACAAACTTAAAATGTGTCGATACAT
1325517 TATGTA
194 TATGTA
* * * * * *
1325523 GACTTATTTTCTCATAAAACCGATATATTTCTACTA-AATACATTGTAAATTTACATATTACATT
1 GACTTATTCTCTCATAAAACCGGTATATTTATACCAGTA-ACATTGTAAATTTACCTATTACATT
* * *
1325587 GTAATTATCGGTTTCGATGTTTTTGTGATCGATACTTTTAATAAATATATCGACACTTTATGTGT
65 ATAATTATCGGTTTCGATGTTTTTGAGATCGATACTTTTAATAAATGTATCGACACTTTATGTGT
* *** *
1325652 GCACCTCGTTTGGCATTCATTCT-GAACAAAATGTATCGACAC-TTTTTAAATTTGTGTCGATAC
130 GCACCTCG-TTGGCATTCATTCTGGAAAAAAAT-TATCGACACAAACTTAAA-ATGTGTCGATAC
1325715 ATTATGTA
192 ATTATGTA
* * ** *
1325723 GACATATTCTCTCATAAAATCGGTATATTTATACTGGTAACATTGTAAATTTATCTATTACATTA
1 GACTTATTCTCTCATAAAACCGGTATATTTATACCAGTAACATTGTAAATTTACCTATTACATTA
1325788 TAATTATCGGTTTCGATGT
66 TAATTATCGGTTTCGATGT
1325807 AACATATGTG
Statistics
Matches: 422, Mismatches: 47, Indels: 24
0.86 0.10 0.05
Matches are distributed among these distances:
195 3 0.01
196 15 0.04
197 75 0.18
198 121 0.29
199 44 0.10
200 159 0.38
201 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (199 bp):
GACTTATTCTCTCATAAAACCGGTATATTTATACCAGTAACATTGTAAATTTACCTATTACATTA
TAATTATCGGTTTCGATGTTTTTGAGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTG
CACCTCGTTGGCATTCATTCTGGAAAAAAATTATCGACACAAACTTAAAATGTGTCGATACATTA
TGTA
Found at i:1325948 original size:31 final size:30
Alignment explanation
Indices: 1325907--1326000 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
1325897 TTATAATAAA
*
1325907 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
1325937 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
* * *
1325967 TTATAAAAT-T-ATAGAT-ATAATATTTTAA
1 TAATAAAATATAATA-ATAATAATTTTTTAT
1325995 TAATAA
1 TAATAA
1326001 TATTGACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
28 18 0.33
29 5 0.09
30 24 0.44
31 8 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:1326000 original size:14 final size:14
Alignment explanation
Indices: 1325918--1326004 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
1325908 AATAAATATA
**
1325918 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
1325933 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
1325946 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
1325960 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
1325974 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
1325988 ATTTTAATAATAAT
1 ATTTTAATAATAAT
1326002 ATT
1 ATT
1326005 GACATAAATT
Statistics
Matches: 53, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
13 10 0.19
14 38 0.72
15 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:1326000 original size:28 final size:28
Alignment explanation
Indices: 1325932--1326000 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
1325922 ATAATAATTT
*
1325932 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
1325959 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
1325987 TATTTTAATAATAA
1 TATTTTAATAATAA
1326001 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:1326176 original size:2 final size:2
Alignment explanation
Indices: 1326169--1326223 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1326159 ATATTGTAAT
1326169 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
1326211 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1326224 TATTTGAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1326447 original size:21 final size:21
Alignment explanation
Indices: 1326405--1326448 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1326395 TCGGTAAAAA
* *
1326405 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATCAATATTT
* *
1326426 TTACCTAAAATATCAATGTTT
1 TTACCTAAAACATCAATATTT
1326447 TT
1 TT
1326449 TAACATTTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (21 bp):
TTACCTAAAACATCAATATTT
Found at i:1326811 original size:14 final size:14
Alignment explanation
Indices: 1326729--1326830 Score: 50
Period size: 14 Copynumber: 7.2 Consensus size: 14
1326719 AAAAAATATA
**
1326729 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
1326744 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
1326757 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * *
1326771 -TTTTTATCTATAAA
1 ATTTTAAT-AATAAT
*
1326785 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
1326799 ATTTTAATAATAAT
1 ATTTTAATAATAAT
1326813 A-TTTACATAAATAAT
1 ATTTTA-AT-AATAAT
1326828 ATT
1 ATT
1326831 AAATAAATTA
Statistics
Matches: 65, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
13 18 0.28
14 30 0.46
15 14 0.22
16 3 0.05
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:1326836 original size:14 final size:15
Alignment explanation
Indices: 1326794--1326838 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
1326784 AATTATAGAT
*
1326794 ATAATATTTTAAT-A
1 ATAATATTTAAATAA
*
1326808 ATAATATTTACATAA
1 ATAATATTTAAATAA
1326823 ATAATA-TTAAATAA
1 ATAATATTTAAATAA
1326837 AT
1 AT
1326839 TATTCTAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATATTTAAATAA
Found at i:1326870 original size:20 final size:21
Alignment explanation
Indices: 1326847--1326894 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1326837 ATTATTCTAG
1326847 TATTTTAAAAAT-AATAATAT
1 TATTTTAAAAATAAATAATAT
**
1326867 TATTTTATTAATAAATAATAT
1 TATTTTAAAAATAAATAATAT
1326888 TATTTTA
1 TATTTTA
1326895 TTGTATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTTAAAAATAAATAATAT
Found at i:1327179 original size:23 final size:23
Alignment explanation
Indices: 1327153--1327202 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1327143 ACCTATTTTA
*
1327153 TTATATAAGCACTACCTATTACG
1 TTATATAAGCACTACCTAATACG
*
1327176 TTATATAAGCACTACCTAATATG
1 TTATATAAGCACTACCTAATACG
1327199 TTAT
1 TTAT
1327203 TGTCCTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (23 bp):
TTATATAAGCACTACCTAATACG
Found at i:1327346 original size:87 final size:86
Alignment explanation
Indices: 1327135--1327363 Score: 323
Period size: 86 Copynumber: 2.7 Consensus size: 86
1327125 TAACAAATTA
* * * *
1327135 AATAATTAACCTATTTTATTATATAAGCACTACCTATTACGTTATATAAGCACTACCTAATATGT
1 AATAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGTACTACATAATATGT
1327200 TATTGTCCTTAATAATTTTCC
66 TATTGTCCTTAATAATTTTCC
**
1327221 AATAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGTTGTACATAATATGT
1 AATAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGTACTACATAATATGT
** * *
1327286 TATTGTGTTTGATAATGTTTTC
66 TATTGTCCTTAATAAT-TTTCC
* * * *
1327308 AGTAATTAACCTATTTTATTATGTAAACGCTACCTATTACATTATATAAGTGCTAC
1 AATAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGTACTAC
1327364 TTATTACATT
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 72 0.57
87 55 0.43
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.43
Consensus pattern (86 bp):
AATAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGTACTACATAATATGT
TATTGTCCTTAATAATTTTCC
Found at i:1327351 original size:23 final size:23
Alignment explanation
Indices: 1327316--1327533 Score: 155
Period size: 23 Copynumber: 9.7 Consensus size: 23
1327306 TCAGTAATTA
** * *
1327316 ACCTATTTTATTATGTAAACGCT
1 ACCTATTACATTATATAAGCGCT
*
1327339 ACCTATTACATTATATAAGTGCT
1 ACCTATTACATTATATAAGCGCT
*
1327362 ACTTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
* *
1327385 ACTTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
* ** *** *
1327408 ACCTAATATGTTATTATATTTGAT
1 ACCTATTACATTA-TATAAGCGCT
* * *
1327432 A-ATGTTTACAGTA-ATTAA----T
1 ACCT-ATTACATTATA-TAAGCGCT
**
1327451 A--TATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
1327472 ACATATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
1327495 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
1327518 ACCTATTACATCATAT
1 ACCTATTACATTATAT
1327534 TTTTACCTGT
Statistics
Matches: 154, Mismatches: 31, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
17 8 0.05
18 2 0.01
19 2 0.01
21 2 0.01
22 1 0.01
23 128 0.83
24 11 0.07
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:1327479 original size:133 final size:133
Alignment explanation
Indices: 1327229--1327533 Score: 457
Period size: 133 Copynumber: 2.3 Consensus size: 133
1327219 CCAATAATTA
** ** * *
1327229 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGTTGTACATAATATGTTATTGTGT
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGGTACATAATATGTTATTATAT
* * * * *
1327294 TTGATAATGTTTTCAGTAATTAACCTATTTTATTATGTAAACGCTACCTATTACATTATATAAGT
66 TTGATAATGTTTACAGTAATTAACATATTTTATTATATAAACGCTACATATTACATTATATAAGC
1327359 GCT
131 GCT
* * *
1327362 ACTTATTACATTATATAAGCGCTACTTATTACATTATATAAGCGGTACCTAATATGTTATTATAT
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGGTACATAATATGTTATTATAT
* *
1327427 TTGATAATGTTTACAGTAATTAATATATTTTATTATATAAGCGCTACATATTACATTATATAAGC
66 TTGATAATGTTTACAGTAATTAACATATTTTATTATATAAACGCTACATATTACATTATATAAGC
1327492 GCT
131 GCT
*
1327495 ACCTATTACATTATATAAGCGCTACCTATTACATCATAT
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATAT
1327534 TTTTACCTGT
Statistics
Matches: 153, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
133 153 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (133 bp):
ACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGGTACATAATATGTTATTATAT
TTGATAATGTTTACAGTAATTAACATATTTTATTATATAAACGCTACATATTACATTATATAAGC
GCT
Found at i:1329209 original size:2 final size:2
Alignment explanation
Indices: 1329204--1329233 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1329194 TATAAAAAGC
1329204 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
1329234 GGTATTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1338151 original size:22 final size:23
Alignment explanation
Indices: 1338126--1338177 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1338116 AAATTATATA
*
1338126 ATATAATTTA-TTAACTTTAATT
1 ATATAATATATTTAACTTTAATT
* *
1338148 ATAT-ATATATTTCATTTTAATT
1 ATATAATATATTTAACTTTAATT
1338170 ATATAATA
1 ATATAATA
1338178 ATGTTTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.16
22 18 0.72
23 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATAATATATTTAACTTTAATT
Found at i:1356301 original size:18 final size:18
Alignment explanation
Indices: 1356278--1356316 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1356268 TCAAACAAAA
1356278 TTTAAATTCAAGATTTAC
1 TTTAAATTCAAGATTTAC
1356296 TTTAAATTCAAGATTTAC
1 TTTAAATTCAAGATTTAC
1356314 TTT
1 TTT
1356317 CTCGTTTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTAAATTCAAGATTTAC
Found at i:1357495 original size:40 final size:40
Alignment explanation
Indices: 1357433--1357539 Score: 119
Period size: 40 Copynumber: 2.6 Consensus size: 40
1357423 TTTAAACATA
** * *
1357433 TAGCGGCGTTTACATTCCAAACGCC-ACAAAATAGTAACTT
1 TAGCGGCGTTTTTATACAAAACGCCGACAAAATAGT-ACTT
*
1357473 TAGCGGCGTTTTTATACAAAACGCCGCGACAAAGTAGTACTT
1 TAGCGGCGTTTTTATACAAAACG-C-CGACAAAATAGTACTT
*
1357515 TAGCGGTGTTTTTATA-AAAACGCCG
1 TAGCGGCGTTTTTATACAAAACGCCG
1357540 CTATAGACTC
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.03
40 20 0.34
41 7 0.12
42 20 0.34
43 9 0.16
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (40 bp):
TAGCGGCGTTTTTATACAAAACGCCGACAAAATAGTACTT
Found at i:1357526 original size:42 final size:42
Alignment explanation
Indices: 1357458--1357540 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
1357448 TCCAAACGCC
1357458 ACAAAATAGTAACTTTAGCGGCGTTTTTATACAAAACGCCGCG
1 ACAAAATAGTAACTTTAGCGGCGTTTTTATA-AAAACGCCGCG
* *
1357501 ACAAAGTAGT-ACTTTAGCGGTGTTTTTATAAAAACGCCGC
1 ACAAAATAGTAACTTTAGCGGCGTTTTTATAAAAACGCCGC
1357541 TATAGACTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 10 0.26
42 19 0.50
43 9 0.24
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (42 bp):
ACAAAATAGTAACTTTAGCGGCGTTTTTATAAAAACGCCGCG
Done.