Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003132.1 Hibiscus syriacus cultivar Beakdansim tig00006570_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: 1555756
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1350684 original size:23 final size:24
Alignment explanation
Indices: 1350658--1350703 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1350648 TGTTGTTCGT
* *
1350658 GAACATTTTCGTTTA-ATGTTCAC
1 GAACATGTTCATTTATATGTTCAC
*
1350681 GAACGTGTTCATTTATATGTTCA
1 GAACATGTTCATTTATATGTTCA
1350704 TAAATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (24 bp):
GAACATGTTCATTTATATGTTCAC
Found at i:1351460 original size:22 final size:22
Alignment explanation
Indices: 1351430--1351485 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
1351420 GACTGTGGTG
1351430 TTTC-TGATTTAGTGAAACTCT
1 TTTCTTGATTTAGTGAAACTCT
1351451 TTTCTTGATTTAGTGAAACTCT
1 TTTCTTGATTTAGTGAAACTCT
*
1351473 TTTTTTGATTTAG
1 TTTCTTGATTTAG
1351486 AAGAAGATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.21, C:0.11, G:0.14, T:0.54
Consensus pattern (22 bp):
TTTCTTGATTTAGTGAAACTCT
Found at i:1354092 original size:18 final size:18
Alignment explanation
Indices: 1354069--1354103 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1354059 AGGGATATAC
1354069 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1354087 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1354104 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1355917 original size:12 final size:11
Alignment explanation
Indices: 1355897--1355932 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1355887 GAATTCAGCT
1355897 GCATTATTGCA
1 GCATTATTGCA
*
1355908 GCACTTATTGCT
1 GCA-TTATTGCA
1355920 GCATTATTGCA
1 GCATTATTGCA
1355931 GC
1 GC
1355933 CCGCTCACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:1356048 original size:15 final size:15
Alignment explanation
Indices: 1356030--1356063 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1356020 TGAAACATAA
1356030 AAGAAAGAAAGGGAG
1 AAGAAAGAAAGGGAG
* *
1356045 AAGATAGCAAGGGAG
1 AAGAAAGAAAGGGAG
1356060 AAGA
1 AAGA
1356064 TAGTAGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.38, T:0.03
Consensus pattern (15 bp):
AAGAAAGAAAGGGAG
Found at i:1356064 original size:15 final size:15
Alignment explanation
Indices: 1356038--1356066 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1356028 AAAAGAAAGA
1356038 AAGGGAGAAGATAGC
1 AAGGGAGAAGATAGC
1356053 AAGGGAGAAGATAG
1 AAGGGAGAAGATAG
1356067 TAGAGAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.41, T:0.07
Consensus pattern (15 bp):
AAGGGAGAAGATAGC
Found at i:1356148 original size:8 final size:9
Alignment explanation
Indices: 1356118--1356155 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1356108 GAGGCAAGTT
1356118 TTTTAATTA
1 TTTTAATTA
1356127 TTTTAATTA
1 TTTTAATTA
*
1356136 GTTT-ATTA
1 TTTTAATTA
1356144 TTTTAAATTA
1 TTTT-AATTA
1356154 TT
1 TT
1356156 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:1356247 original size:21 final size:20
Alignment explanation
Indices: 1356191--1356239 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
1356181 AAAACAAAAT
1356191 TTTAGTTAATTAGTTAGTTAG
1 TTTAGTTAATTA-TTAGTTAG
1356212 TTTAAGTTATATTATT-GTTAG
1 TTT-AGTTA-ATTATTAGTTAG
1356233 TTTAGTT
1 TTTAGTT
1356240 TAAGTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.15
21 11 0.42
22 7 0.27
23 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.57
Consensus pattern (20 bp):
TTTAGTTAATTATTAGTTAG
Found at i:1356363 original size:27 final size:28
Alignment explanation
Indices: 1356310--1356368 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
1356300 AAAAAAACAA
*
1356310 TTAATTAGTGTGTTAGTTAGTCTAATAT
1 TTAATTAGTGTGTTAGTTAGTCTAATAG
*
1356338 TTAATTAGTTTG-TAGTTAGT-TAAATAG
1 TTAATTAGTGTGTTAGTTAGTCT-AATAG
1356365 TTAA
1 TTAA
1356369 GTTATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 1 0.04
27 16 0.57
28 11 0.39
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (28 bp):
TTAATTAGTGTGTTAGTTAGTCTAATAG
Found at i:1356599 original size:21 final size:21
Alignment explanation
Indices: 1356574--1356613 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1356564 GTTAATTAGT
1356574 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
1356595 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
1356614 AATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:1356826 original size:30 final size:30
Alignment explanation
Indices: 1356792--1356856 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
1356782 ATTACTTAAT
* *
1356792 TAGTTTTTTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTAAAGTTATATTAAAGAA
*
1356822 TAGTTTATTAGTTAAAGTTGTATTAAAGAA
1 TAGTTTATTAGTTAAAGTTATATTAAAGAA
1356852 TAGTT
1 TAGTT
1356857 AAATTCATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (30 bp):
TAGTTTATTAGTTAAAGTTATATTAAAGAA
Found at i:1356857 original size:22 final size:22
Alignment explanation
Indices: 1356830--1356892 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 22
1356820 AATAGTTTAT
1356830 TAGTTAAAGTTGTATTAAAGAA
1 TAGTTAAAGTTGTATTAAAGAA
*
1356852 TAGTTAAA-TTCATATTAAAGAA
1 TAGTTAAAGTT-GTATTAAAGAA
1356874 TAGTTTAATAGTTGT-TTAA
1 TAG-TTAA-AGTTGTATTAA
1356893 GGAAAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 21 0.60
23 8 0.23
24 2 0.06
25 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (22 bp):
TAGTTAAAGTTGTATTAAAGAA
Found at i:1359230 original size:59 final size:56
Alignment explanation
Indices: 1359167--1359287 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 56
1359157 TATTATAATT
* * *
1359167 TCATTACTAGTAATCATTAGTAAATCATTAATATCAAATAATTAAATATTAATAATAAA
1 TCATTACTAATAATAATTACTAAATCATTAATATCAAATAATTAAATATT--TAA-AAA
* * * *
1359226 TCATTATTAATAATAATTACTAAATCATTAGTATTAAATCATTAAATATTTAAAAA
1 TCATTACTAATAATAATTACTAAATCATTAATATCAAATAATTAAATATTTAAAAA
1359282 TCATTA
1 TCATTA
1359288 ATAAATTCGA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
56 9 0.16
57 3 0.05
59 43 0.78
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (56 bp):
TCATTACTAATAATAATTACTAAATCATTAATATCAAATAATTAAATATTTAAAAA
Found at i:1359234 original size:24 final size:24
Alignment explanation
Indices: 1359178--1359255 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
1359168 CATTACTAGT
*
1359178 AATCATTAGTAAATCATTAAT-ATCA
1 AATCATTATTAAAT-ATTAATAAT-A
1359203 AAT-A--ATTAAATATTAATAATA
1 AATCATTATTAAATATTAATAATA
* *
1359224 AATCATTATT-AATAATAATTACTA
1 AATCATTATTAAATATTAA-TAATA
1359248 AATCATTA
1 AATCATTA
1359256 GTATTAAATC
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
21 10 0.22
22 9 0.20
23 7 0.16
24 16 0.36
25 3 0.07
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (24 bp):
AATCATTATTAAATATTAATAATA
Found at i:1359237 original size:14 final size:14
Alignment explanation
Indices: 1359209--1359269 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
1359199 ATCAAATAAT
*
1359209 TAAAT-ATTAATAA
1 TAAATCATTATTAA
1359222 TAAATCATTATTAA
1 TAAATCATTATTAA
*
1359236 T-AAT-A--ATTAC
1 TAAATCATTATTAA
* *
1359246 TAAATCATTAGTAT
1 TAAATCATTATTAA
1359260 TAAATCATTA
1 TAAATCATTA
1359270 AATATTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 5 0.13
11 3 0.08
12 2 0.05
13 8 0.21
14 21 0.54
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.41
Consensus pattern (14 bp):
TAAATCATTATTAA
Found at i:1359264 original size:38 final size:37
Alignment explanation
Indices: 1359142--1359269 Score: 104
Period size: 38 Copynumber: 3.5 Consensus size: 37
1359132 ACAATGATTT
* *
1359142 TTAGTATCAAATCATTATTATAATTTCATTACTAGTAATCA
1 TTAGTATTAAATCATTATTATAA--TAATTACTA--AATCA
* * * *
1359183 TTAG---TAAATCATTAATATCA-AATAATTAAAT-A
1 TTAGTATTAAATCATTATTATAATAATTACTAAATCA
* *
1359215 TTAATAATAAATCATTATTAATAATAATTACTAAATCA
1 TTAGTATTAAATCATTATT-ATAATAATTACTAAATCA
1359253 TTAGTATTAAATCATTA
1 TTAGTATTAAATCATTA
1359270 AATATTTAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
32 4 0.06
33 3 0.04
35 16 0.24
36 3 0.04
37 9 0.13
38 29 0.43
41 4 0.06
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (37 bp):
TTAGTATTAAATCATTATTATAATAATTACTAAATCA
Found at i:1359437 original size:26 final size:26
Alignment explanation
Indices: 1359359--1359503 Score: 197
Period size: 26 Copynumber: 5.7 Consensus size: 26
1359349 TTATTCCATA
* * *
1359359 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATG
* *
1359383 ATTATTATAAAATCATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATG
1359408 ATTATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
1359434 ATTATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* *
1359460 ATTATTACTAAATTATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
*
1359486 ATTATTATCAAATCATTA
1 ATTATTATTAAATCATTA
1359504 CTAAATCATC
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
24 7 0.06
25 34 0.31
26 68 0.62
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (26 bp):
ATTATTATTAAATCATTATTATAATG
Found at i:1359514 original size:14 final size:13
Alignment explanation
Indices: 1359372--1359503 Score: 139
Period size: 14 Copynumber: 10.1 Consensus size: 13
1359362 ATTAGTAATA
1359372 ATTATTAAATCATT
1 ATTA-TAAATCATT
1359386 ATTATAAAATCATT
1 ATTAT-AAATCATT
1359400 A-T-TAAATCATT
1 ATTATAAATCATT
1359411 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
1359425 ATTAT-AATGATT
1 ATTATAAATCATT
1359437 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
1359451 ATTAT-AATGATT
1 ATTATAAATCATT
*
1359463 ATTACTAAATTATT
1 ATTA-TAAATCATT
*
1359477 ATTAT-AATGATT
1 ATTATAAATCATT
1359489 ATTATCAAATCATT
1 ATTAT-AAATCATT
1359503 A
1 A
1359504 CTAAATCATC
Statistics
Matches: 102, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
11 9 0.09
12 33 0.32
13 7 0.07
14 53 0.52
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:1360659 original size:17 final size:17
Alignment explanation
Indices: 1360637--1360675 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1360627 TAGTATAAAA
1360637 TAAACACTAA-ATATTTT
1 TAAACAC-AATATATTTT
*
1360654 TAAACACAATATTTTTT
1 TAAACACAATATATTTT
1360671 TAAAC
1 TAAAC
1360676 GGGAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAACACAATATATTTT
Found at i:1361051 original size:28 final size:28
Alignment explanation
Indices: 1361020--1361073 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1361010 ATAATCTAAT
*
1361020 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
1361048 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
1361074 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:1361080 original size:28 final size:28
Alignment explanation
Indices: 1361016--1361080 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
1361006 TTATATAATC
*
1361016 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
1361044 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
1361072 TAATTTATA
1 TAATATATA
1361081 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:1361083 original size:21 final size:21
Alignment explanation
Indices: 1361050--1361098 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1361040 TTAATATAAT
1361050 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1361071 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1361092 ATTAACT
1 A-TAACT
1361099 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1362705 original size:30 final size:31
Alignment explanation
Indices: 1362666--1362730 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
1362656 AAGTTTGAGG
*
1362666 TTTTCTTTAAA-ATAAAATTAGAA-TTTTTAA
1 TTTTCTTTAAATAT-AAATTAAAATTTTTTAA
* *
1362696 TTTTTTTTAAATATATATTAAAATTTTTTAA
1 TTTTCTTTAAATATAAATTAAAATTTTTTAA
1362727 TTTT
1 TTTT
1362731 AAATAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTTCTTTAAATATAAATTAAAATTTTTTAA
Found at i:1366742 original size:20 final size:19
Alignment explanation
Indices: 1366694--1366744 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1366684 TTGAAAAGGT
* *
1366694 ATAATAAAATAAAATAAATA
1 ATAAT-AAATAAAAGAAAAA
1366714 ATAATAAATAAAAGGAAAAA
1 ATAATAAATAAAA-GAAAAA
1366734 ATAATAAATAA
1 ATAATAAATAA
1366745 TAGTAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (19 bp):
ATAATAAATAAAAGAAAAA
Found at i:1366746 original size:23 final size:23
Alignment explanation
Indices: 1366694--1366746 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1366684 TTGAAAAGGT
*
1366694 ATAATAAAATAAAATAAATAATA
1 ATAATAAAAGAAAATAAATAATA
*
1366717 ATAAATAAAAGGAAA-AAATAATAA
1 AT-AATAAAAGAAAATAAATAAT-A
1366741 ATAATA
1 ATAATA
1366747 GTAGTAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (23 bp):
ATAATAAAAGAAAATAAATAATA
Found at i:1367480 original size:85 final size:82
Alignment explanation
Indices: 1367450--1367626 Score: 275
Period size: 84 Copynumber: 2.1 Consensus size: 82
1367440 CAATTTAAAC
1367450 TAAAATACCTAAAACAAAGATAAAATAAAATACTATTTAAAATAATATCCTAAATCCTAATTGAA
1 TAAAATACCTAAAACAAAGATAAAATAAAATA--ATTTAAAATAATATCCTAAATCCTAATTGAA
*
1367515 ATACTAAAACCTATTTAAAC
64 ATACTAAAA-CAATTTAAAC
1367535 TAAAATACCTAAAACAAAGATAAAATAAAATATTATTT-AAATAATATCCTAAATCCTAATTGAA
1 TAAAATACCTAAAACAAAGATAAAATAAAATA--ATTTAAAATAATATCCTAAATCCTAATTGAA
*
1367599 ATACTAAAAGATATTTAAAC
64 ATACTAAAACA-ATTTAAAC
1367619 TAAAATAC
1 TAAAATAC
1367627 AAAAATCAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
84 51 0.58
85 37 0.42
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (82 bp):
TAAAATACCTAAAACAAAGATAAAATAAAATAATTTAAAATAATATCCTAAATCCTAATTGAAAT
ACTAAAACAATTTAAAC
Found at i:1367597 original size:84 final size:84
Alignment explanation
Indices: 1367402--1367626 Score: 353
Period size: 85 Copynumber: 2.7 Consensus size: 84
1367392 AAATAATTCC
* * * * *
1367402 TAAAATAATATCTTAAATCTTAATTAAAACACTTAAAACAATTTAAACTAAAATACCTAAAACAA
1 TAAAATAATATCCTAAATCCTAATTGAAATAC-TAAAACTATTTAAACTAAAATACCTAAAACAA
1367467 AGATAAAATAAAATACTATT
65 AGATAAAATAAAATACTATT
1367487 TAAAATAATATCCTAAATCCTAATTGAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA
1 TAAAATAATATCCTAAATCCTAATTGAAATACTAAAA-CTATTTAAACTAAAATACCTAAAACAA
*
1367552 AGATAAAATAAAATATTATT
65 AGATAAAATAAAATACTATT
*
1367572 T-AAATAATATCCTAAATCCTAATTGAAATACTAAAAGATATTTAAACTAAAATAC
1 TAAAATAATATCCTAAATCCTAATTGAAATACTAAAA-CTATTTAAACTAAAATAC
1367627 AAAAATCAAA
Statistics
Matches: 131, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
84 57 0.44
85 74 0.56
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (84 bp):
TAAAATAATATCCTAAATCCTAATTGAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAA
GATAAAATAAAATACTATT
Found at i:1368987 original size:2 final size:2
Alignment explanation
Indices: 1368982--1369019 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1368972 CGAAACAGTG
1368982 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
1369020 TCTCGTGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1369987 original size:31 final size:30
Alignment explanation
Indices: 1369895--1369988 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
1369885 GAAGGACCTA
* * * * *
1369895 TCCAGAGGTCACACAGA-CCCCGATAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1369924 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1369954 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
1369985 TCCA
1 TCCA
1369989 TATGTTCCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 15 0.26
30 34 0.59
31 9 0.16
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1370018 original size:31 final size:31
Alignment explanation
Indices: 1369976--1370076 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
1369966 AAAGATCCTC
*
1369976 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * * *
1370007 GGTATATTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
1370038 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
1370070 GGTAAAC
1 GGTAAAC
1370077 CCTCGACTCT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 32 0.56
32 25 0.44
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:1371517 original size:21 final size:21
Alignment explanation
Indices: 1371487--1371531 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1371477 ATTCTGTCGT
* *
1371487 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1371508 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1371529 TTG
1 TTG
1371532 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1374501 original size:30 final size:30
Alignment explanation
Indices: 1374442--1374530 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
1374432 CCCGAAGGAC
* * *
1374442 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1374471 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1374501 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1374531 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1374568 original size:31 final size:31
Alignment explanation
Indices: 1374526--1374626 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
1374516 AAAGATCCTC
*
1374526 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * * *
1374557 GGTATATTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
1374588 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
1374620 GGTAAAC
1 GGTAAAC
1374627 CCTCGACTCT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 32 0.56
32 25 0.44
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:1376071 original size:21 final size:21
Alignment explanation
Indices: 1376041--1376085 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1376031 ATTCTGTCGT
* *
1376041 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1376062 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1376083 TTG
1 TTG
1376086 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1379058 original size:30 final size:30
Alignment explanation
Indices: 1378999--1379087 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
1378989 CCCGAAGGAC
* * *
1378999 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1379028 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1379058 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1379088 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1379125 original size:31 final size:31
Alignment explanation
Indices: 1379083--1379183 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
1379073 AAAGATCCTC
*
1379083 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * * *
1379114 GGTATATTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
1379145 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
1379177 GGTAAAC
1 GGTAAAC
1379184 CCTCGACTCT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 32 0.56
32 25 0.44
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:1380557 original size:21 final size:21
Alignment explanation
Indices: 1380527--1380571 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1380517 ATTCTGTCGT
* *
1380527 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1380548 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1380569 TTG
1 TTG
1380572 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1384960 original size:20 final size:20
Alignment explanation
Indices: 1384935--1385008 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
1384925 TGAAAATGTA
1384935 TAATAAAATAAAATGAATAG
1 TAATAAAATAAAATGAATAG
* *
1384955 TAAT-AAATAAAAGGGAA-AA
1 TAATAAAATAAAA-TGAATAG
1384974 TAATAAAATAATAAAT-AATAG
1 TAATAAAAT-A-AAATGAATAG
*
1384995 TAGTAAAGATAAAA
1 TAATAAA-ATAAAA
1385009 AGGGTTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 13 0.30
20 16 0.37
21 9 0.21
22 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (20 bp):
TAATAAAATAAAATGAATAG
Found at i:1385053 original size:18 final size:18
Alignment explanation
Indices: 1385032--1385074 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1385022 GATGTTTTTA
*
1385032 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
1385050 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1385068 AAATAAA
1 AAATAAA
1385075 TAATTTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1385774 original size:85 final size:86
Alignment explanation
Indices: 1385672--1385897 Score: 388
Period size: 85 Copynumber: 2.7 Consensus size: 86
1385662 ATATAATTCC
* * * *
1385672 TAAAATAATATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACA
1 TAAAATAATATCCTAAATCCTAATTGAAATACTTAAAACCTATTTAAACTAAAATACATAAAACA
1385736 AAGATAAAATAAAATATTATT
66 AAGATAAAATAAAATATTATT
1385757 TAAAATAATATCCTAAATCCTAATTGAAATA-TTAAAACCTATTTAAACTAAAATACATAAAACA
1 TAAAATAATATCCTAAATCCTAATTGAAATACTTAAAACCTATTTAAACTAAAATACATAAAACA
1385821 AAGATAAAATAAAATATTATT
66 AAGATAAAATAAAATATTATT
1385842 T-AAATAATATCCTAAATCCTAATTGAAATAC-TAAAACCTATTTAAACTAAAATACA
1 TAAAATAATATCCTAAATCCTAATTGAAATACTTAAAACCTATTTAAACTAAAATACA
1385898 AAGATAAAAT
Statistics
Matches: 135, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
84 60 0.44
85 75 0.56
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (86 bp):
TAAAATAATATCCTAAATCCTAATTGAAATACTTAAAACCTATTTAAACTAAAATACATAAAACA
AAGATAAAATAAAATATTATT
Found at i:1398530 original size:43 final size:43
Alignment explanation
Indices: 1398469--1398787 Score: 392
Period size: 43 Copynumber: 7.4 Consensus size: 43
1398459 TTTTTGTTGG
*
1398469 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCA
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
*
1398512 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCA
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
** *
1398555 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGTATTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
* * *
1398598 ACAAATGCCGCAATAGGTGTTAAGATTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
*
1398641 ACAAACGCTGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC-
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCG-TTTTTCCA
* * * * *
1398684 ATAAACGCCGCAATAGGTCTTGAGATTTAACGGTGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
* * * * * **
1398727 ACAAACACCGCAAAAGAT-CTG-GTATATAGCGGCGTTTTTTAGA
1 ACAAACGCCGCAATAGGTGTTGAG-ATTTAGCGGCG-TTTTTCCA
*
1398770 ACAAACGCCGCAAAAGGT
1 ACAAACGCCGCAATAGGT
1398788 CATATTTATA
Statistics
Matches: 243, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
41 1 0.00
42 17 0.07
43 218 0.90
44 7 0.03
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
Found at i:1398961 original size:21 final size:21
Alignment explanation
Indices: 1398935--1398993 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1398925 ATTTTCCAAT
*
1398935 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* * *
1398956 AAACTTAAAATCCAAAACAAG
1 AAACTTGAAATCCATAACAAC
**
1398977 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
1398994 TAATAAATCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.58, C:0.20, G:0.05, T:0.17
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:1402187 original size:41 final size:41
Alignment explanation
Indices: 1401942--1402290 Score: 165
Period size: 41 Copynumber: 8.4 Consensus size: 41
1401932 GCATTTTCTA
* * * *
1401942 AAAAATGCCGCTAAAGTACATA-TTTTTTGCGGCGTTTGTGT
1 AAAAACGCCGCTAAAGTAC-TACTCTATTGCGGCGTTTGTAT
* * * * * * * *
1401983 AAAAACGCCGCTAAAGTTCTAATATGTTGCAGCATTTATTAGA
1 AAAAACGCCGCTAAAGTACTACTCTATTGCGGCGTTT-GTA-T
* * * * ** * * *
1402026 AAAAAAGCCACTATAGGAGAACTCTATTGTGGCATTTTTAT
1 AAAAACGCCGCTAAAGTACTACTCTATTGCGGCGTTTGTAT
* * * *
1402067 AAAAACGCCGCTAAAGTA-TAAATCTTTTGCGGCATTTGTTAGA
1 AAAAACGCCGCTAAAGTACT-ACTCTATTGCGGCGTTTG-TA-T
* * * *
1402110 AAAAACGCCACTATAG-A-TGGAC-CTATTGCAGAGTTTGTAT
1 AAAAACGCCGCTAAAGTACT--ACTCTATTGCGGCGTTTGTAT
* *
1402150 AAAAACGCCGCTAAAGTACTACTCTGTTGTGGCGTTTGT-T
1 AAAAACGCCGCTAAAGTACTACTCTATTGCGGCGTTTGTAT
* ** * * *
1402190 GAAAAACGTCATTACA-TATGTAC-CTATTGCGGCGTTTATAT
1 -AAAAACGCCGCTAAAGTA-CTACTCTATTGCGGCGTTTGTAT
* * * * *
1402231 AAAAATGCCGCTATAGTACTACTCTATAGCGGTGTTTGTTT
1 AAAAACGCCGCTAAAGTACTACTCTATTGCGGCGTTTGTAT
1402272 AAGAAACGCCGCTAAAGTA
1 AA-AAACGCCGCTAAAGTA
1402291 TCATTTTGTG
Statistics
Matches: 225, Mismatches: 67, Indels: 31
0.70 0.21 0.10
Matches are distributed among these distances:
40 47 0.21
41 104 0.46
42 34 0.15
43 40 0.18
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGTACTACTCTATTGCGGCGTTTGTAT
Found at i:1402241 original size:81 final size:83
Alignment explanation
Indices: 1401968--1402255 Score: 278
Period size: 84 Copynumber: 3.5 Consensus size: 83
1401958 TACATATTTT
* * * * * * * *
1401968 TTGCGGCGTTTGTGTAAAAACGCCGCTAAAGTTCTAATATGTTGCAGCATTTATTAGAAAAAAAG
1 TTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCATTTGTTAGAAAAAACG
* *
1402033 CCACTATAGGA-GAACTCTA
66 CCACTACA-GATGGAC-CTA
* * * * *
1402052 TTGTGGCATTTTTATAAAAACGCCGCTAAAGTA-TAAATCTTTTGCGGCATTTGTTAGAAAAAAC
1 TTGCGGCGTTTATATAAAAACGCCGCTAAAGTACT-ACTCTGTTGCGGCATTTGTTAGAAAAAAC
*
1402116 GCCACTATAGATGGACCTA
65 GCCACTACAGATGGACCTA
* * * * *
1402135 TTGCAGAGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGTGGCGTTTGTT-G-AAAAACG
1 TTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCATTTGTTAGAAAAAACG
* * * *
1402198 TCATTACATATGTACCTA
66 CCACTACAGATGGACCTA
* *
1402216 TTGCGGCGTTTATATAAAAATGCCGCTATAGTACTACTCT
1 TTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTACTCT
1402256 ATAGCGGTGT
Statistics
Matches: 171, Mismatches: 30, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
81 55 0.32
82 1 0.01
83 50 0.29
84 65 0.38
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (83 bp):
TTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCATTTGTTAGAAAAAACG
CCACTACAGATGGACCTA
Found at i:1402268 original size:81 final size:82
Alignment explanation
Indices: 1402064--1402279 Score: 220
Period size: 81 Copynumber: 2.6 Consensus size: 82
1402054 GTGGCATTTT
* * * * * * * * *
1402064 TATAAAAACGCCGCTAAAGTA-TAAATCTTTTGCGGCATTTGTTAGAAAAAACGCCACTATAGAT
1 TATAAAAACGCCGCTAAAGTACT-ACTCTATAGCGGCGTTTGTT-GAAGAAACGTCATTACATAT
* *
1402128 GGACCTATTGCAGAGTTTG
64 GTACCTATTGCAGAGTTTA
* * *
1402147 TATAAAAACGCCGCTAAAGTACTACTCTGTTGTGGCGTTTGTTGAA-AAACGTCATTACATATGT
1 TATAAAAACGCCGCTAAAGTACTACTCTATAGCGGCGTTTGTTGAAGAAACGTCATTACATATGT
* *
1402211 ACCTATTGCGGCGTTTA
66 ACCTATTGCAGAGTTTA
* * * *
1402228 TATAAAAATGCCGCTATAGTACTACTCTATAGCGGTGTTTGTTTAAGAAACG
1 TATAAAAACGCCGCTAAAGTACTACTCTATAGCGGCGTTTGTTGAAGAAACG
1402280 CCGCTAAAGT
Statistics
Matches: 112, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
81 66 0.59
82 8 0.07
83 37 0.33
84 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (82 bp):
TATAAAAACGCCGCTAAAGTACTACTCTATAGCGGCGTTTGTTGAAGAAACGTCATTACATATGT
ACCTATTGCAGAGTTTA
Found at i:1418124 original size:16 final size:16
Alignment explanation
Indices: 1418103--1418135 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1418093 GAAAATATTT
*
1418103 ATTATAAATATATAAA
1 ATTATAAATATAGAAA
1418119 ATTATAAATATAGAAA
1 ATTATAAATATAGAAA
1418135 A
1 A
1418136 ATAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
ATTATAAATATAGAAA
Found at i:1418139 original size:14 final size:15
Alignment explanation
Indices: 1418105--1418142 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1418095 AAATATTTAT
*
1418105 TATAAATATATAAAA
1 TATAAATATAGAAAA
1418120 TTATAAATATAGAAAA
1 -TATAAATATAGAAAA
1418136 -ATAAATA
1 TATAAATA
1418143 ATATTATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
16 14 0.67
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
TATAAATATAGAAAA
Found at i:1418176 original size:20 final size:22
Alignment explanation
Indices: 1418132--1418189 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
1418122 ATAAATATAG
* *
1418132 AAAAATAAATAATATTATTTGTT
1 AAAAAT-ATTAATAATATTTGTT
1418155 AAAAA-ATTAATAATATTT-TT
1 AAAAATATTAATAATATTTGTT
1418175 AAAAATATTAA-AATA
1 AAAAATATTAATAATA
1418190 ATTTATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.34
21 16 0.50
23 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAATATTAATAATATTTGTT
Found at i:1418194 original size:19 final size:20
Alignment explanation
Indices: 1418153--1418194 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1418143 ATATTATTTG
*
1418153 TTAAAAAATTAATAATATTT
1 TTAAAAAATTAATAATATAT
1418173 TTAAAAATATTAA-AATA-AT
1 TTAAAAA-ATTAATAATATAT
1418192 TTA
1 TTA
1418195 TTTAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAAAAATTAATAATATAT
Found at i:1418198 original size:23 final size:23
Alignment explanation
Indices: 1418142--1418206 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
1418132 AAAAATAAAT
*
1418142 AATATTATTTGTTAAAAA-ATT--
1 AATAATATTT-TTAAAAATATTAA
1418163 AATAATATTTTTAAAAATATTAA
1 AATAATATTTTTAAAAATATTAA
*
1418186 AATAAT-TTATTTAATAATATT
1 AATAATATT-TTTAAAAATATT
1418207 TATGTCAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.18
21 12 0.32
22 2 0.05
23 17 0.45
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATAATATTTTTAAAAATATTAA
Found at i:1418303 original size:26 final size:24
Alignment explanation
Indices: 1418261--1418339 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
1418251 ATAAATAATT
*
1418261 ATATATTGTTA-AAATAAAAATACA
1 ATATATTATTATAAATAAAAATA-A
* *
1418285 ATATATTATTAT-AATATAATTAA
1 ATATATTATTATAAATAAAAATAA
1418308 ATATATTATTATAACACTAAAAAATATA
1 ATATATTATTATAA-A-T-AAAAATA-A
1418336 ATAT
1 ATAT
1418340 TCTACATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
23 13 0.30
24 19 0.43
25 1 0.02
26 1 0.02
27 5 0.11
28 5 0.11
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (24 bp):
ATATATTATTATAAATAAAAATAA
Found at i:1418314 original size:23 final size:23
Alignment explanation
Indices: 1418246--1418340 Score: 93
Period size: 23 Copynumber: 4.0 Consensus size: 23
1418236 TCTATAATAA
*
1418246 ATAATATAAATAATTATATATTGTT
1 ATAATATAAATAA--ATATATTATT
* *
1418271 AAAATAAAAATACAATATATTATT
1 ATAATATAAATA-AATATATTATT
*
1418295 ATAATATAATTAAATATATTATT
1 ATAATATAAATAAATATATTATT
* *
1418318 ATAACACTAAA-AAATATAATATT
1 ATAATA-TAAATAAATATATTATT
1418341 CTACATTAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
23 27 0.46
24 21 0.36
25 10 0.17
26 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (23 bp):
ATAATATAAATAAATATATTATT
Found at i:1421430 original size:42 final size:41
Alignment explanation
Indices: 1421370--1421476 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 41
1421360 CATAATGGTC
* * *
1421370 TTTGAG-AGTAGAAAAGAGTTTAA-TT-ATGTGAGCATAACATA
1 TTTGAGAAGTA-AAAAGAGTTCAATTTCATG-GA-CAGAACAAA
1421411 TTTGAGAAGTAAAATAGAGTTCAATTTCATGGACAGAACAAA
1 TTTGAGAAGTAAAA-AGAGTTCAATTTCATGGACAGAACAAA
*
1421453 TTCGAGAAGTAAAAA-A-TTCAATTT
1 TTTGAGAAGTAAAAAGAGTTCAATTT
1421477 TTGCGAGTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
39 8 0.14
40 1 0.02
41 10 0.17
42 32 0.55
43 4 0.07
44 3 0.05
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (41 bp):
TTTGAGAAGTAAAAAGAGTTCAATTTCATGGACAGAACAAA
Found at i:1422685 original size:12 final size:12
Alignment explanation
Indices: 1422656--1422689 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1422646 TATCGATATT
*
1422656 TATTATTTTTTA
1 TATTATATTTTA
1422668 TA-TATATTTTA
1 TATTATATTTTA
1422679 TATTATATTTT
1 TATTATATTTT
1422690 TGTTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:1422703 original size:17 final size:17
Alignment explanation
Indices: 1422681--1422713 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1422671 ATATTTTATA
*
1422681 TTATATTTTTGTTTTTC
1 TTATATTTTAGTTTTTC
1422698 TTATATTTTAGTTTTT
1 TTATATTTTAGTTTTT
1422714 AATAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (17 bp):
TTATATTTTAGTTTTTC
Found at i:1428697 original size:20 final size:20
Alignment explanation
Indices: 1428685--1428721 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1428675 TATGTTTTTC
1428685 TTAA-ATATATTATTTTTGT
1 TTAACATATATTATTTTTGT
1428704 TTAACATATATTATTTTT
1 TTAACATATATTATTTTT
1428722 AATATGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTAACATATATTATTTTTGT
Found at i:1428993 original size:2 final size:2
Alignment explanation
Indices: 1428986--1429029 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1428976 GGGAGTGAGT
1428986 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1429028 GA
1 GA
1429030 ATTCCCTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1429742 original size:7 final size:7
Alignment explanation
Indices: 1429720--1429754 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1429710 TCCAGAGTTC
1429720 TCTT-CT
1 TCTTCCT
1429726 TCTT-CT
1 TCTTCCT
1429732 TCTTCCT
1 TCTTCCT
1429739 TCTTCCT
1 TCTTCCT
1429746 TCTTCCT
1 TCTTCCT
1429753 TC
1 TC
1429755 CTTTCCTACG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 10 0.36
7 18 0.64
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (7 bp):
TCTTCCT
Found at i:1430889 original size:22 final size:22
Alignment explanation
Indices: 1430860--1430954 Score: 129
Period size: 22 Copynumber: 4.3 Consensus size: 22
1430850 AGTCGAGGGT
*
1430860 TTCATAGGTCATTTGGGACATA
1 TTCATAGGTCATTCGGGACATA
*
1430882 CTCATAGGTCATTCGGGACATA
1 TTCATAGGTCATTCGGGACATA
1430904 TTCATAGGTTC-TTCGGGACATA
1 TTCATAGG-TCATTCGGGACATA
* *
1430926 TTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCATTCGGGACATA
1430948 TATCATA
1 T-TCATA
1430955 TGCCACTCAG
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
21 2 0.03
22 57 0.86
23 7 0.11
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (22 bp):
TTCATAGGTCATTCGGGACATA
Found at i:1437702 original size:22 final size:22
Alignment explanation
Indices: 1437674--1437736 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
1437664 GTCGAGGGTT
* *
1437674 TCATAGGTCCTTTGGGACATAC
1 TCATAGGTCATTCGGGACATAC
*
1437696 TCATAGGTCATTCGGGACATAT
1 TCATAGGTCATTCGGGACATAC
1437718 TCATAGGTCATTCGGGACA
1 TCATAGGTCATTCGGGACA
1437737 AATATCATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (22 bp):
TCATAGGTCATTCGGGACATAC
Found at i:1444141 original size:6 final size:6
Alignment explanation
Indices: 1444130--1444981 Score: 1630
Period size: 6 Copynumber: 143.0 Consensus size: 6
1444120 TAGACCTAAA
1444130 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444178 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444226 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444274 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444322 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444370 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATG- -TATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444416 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444464 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATG-
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444511 -TATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444558 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATG-
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444605 -TATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444652 ATATGT ATATGT ATATGT ATATGT ATATGTAT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATG--T ATATGT ATATGT ATATGT
1444702 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444750 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444798 ATATG- -TATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444844 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444892 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444940 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1444982 GTATACGTGT
Statistics
Matches: 836, Mismatches: 0, Indels: 20
0.98 0.00 0.02
Matches are distributed among these distances:
4 16 0.02
6 814 0.97
8 6 0.01
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:1451129 original size:31 final size:31
Alignment explanation
Indices: 1451094--1451202 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
1451084 TAGGTCCCGA
* *
1451094 AGAACCTAGGTAAACTGTCCATATGTTCCTT
1 AGAACATAGGTAAACTGTCCATATGTTCCAT
* * * *
1451125 AGAACATAGGTATATTGTCCATATGTCTCAAA
1 AGAACATAGGTAAACTGTCCATATGT-TCCAT
* * *
1451157 AG-ACATAGGTAATTCTATCCATATGTTCCGT
1 AGAACATAGGTAA-ACTGTCCATATGTTCCAT
1451188 AGAACATAGGTAAAC
1 AGAACATAGGTAAAC
1451203 CATCGACTCT
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
31 37 0.61
32 24 0.39
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATGTTCCAT
Found at i:1452352 original size:19 final size:19
Alignment explanation
Indices: 1452328--1452398 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
1452318 TTTAAGGGGG
*
1452328 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTTCTTA
1452347 TGCATCGATGCACTTCTTA
1 TGCATCGATGCACTTCTTA
1452366 TGCATCGATGCACTTCTTA
1 TGCATCGATGCACTTCTTA
1452385 TGCATCGATGCACT
1 TGCATCGATGCACT
1452399 AATTGCATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (19 bp):
TGCATCGATGCACTTCTTA
Found at i:1456118 original size:15 final size:15
Alignment explanation
Indices: 1456088--1456130 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
1456078 TTTTAGTTAG
*
1456088 CTTTACTTTTTACTTT
1 CTTTAATTTTT-CTTT
1456104 CTTTAATTTTTCTTT
1 CTTTAATTTTTCTTT
*
1456119 ATTT-ATTTTTCT
1 CTTTAATTTTTCT
1456131 AGGTACATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.32
15 7 0.28
16 10 0.40
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (15 bp):
CTTTAATTTTTCTTT
Found at i:1469379 original size:22 final size:22
Alignment explanation
Indices: 1469354--1469410 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1469344 CACTCTCTAC
*
1469354 GGCGACATCCGTCCCCATCTCA
1 GGCGAAATCCGTCCCCATCTCA
* * *
1469376 GGCGAAATCCATCCTCATCTCC
1 GGCGAAATCCGTCCCCATCTCA
*
1469398 GACGAAATCCGTC
1 GGCGAAATCCGTC
1469411 TTACTTCATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.23, C:0.40, G:0.18, T:0.19
Consensus pattern (22 bp):
GGCGAAATCCGTCCCCATCTCA
Found at i:1469763 original size:20 final size:20
Alignment explanation
Indices: 1469740--1469778 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1469730 TTTGAAACTT
1469740 AAATTCAAAACACGAAAATG
1 AAATTCAAAACACGAAAATG
* *
1469760 AAATTTACAACACGAAAAT
1 AAATTCAAAACACGAAAAT
1469779 CGCAACGCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.15, G:0.08, T:0.18
Consensus pattern (20 bp):
AAATTCAAAACACGAAAATG
Found at i:1469807 original size:19 final size:20
Alignment explanation
Indices: 1469785--1469838 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1469775 AAATCGCAAC
1469785 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
* *
1469804 GCGATTTTCATTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
*
1469824 ACGATTTTAAGTTTC
1 GCGATTTTAAGTTTC
1469839 AGAAACTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.48
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:1471217 original size:42 final size:42
Alignment explanation
Indices: 1471158--1471254 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
1471148 CCCCACTTCG
* * * * * *
1471158 AGAGCCATCACTTGATCGAGCCGATTCTATAGCTCGACACCC
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACC
*
1471200 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACG
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACC
1471242 AGAGCCATCACCT
1 AGAGCCATCACCT
1471255 ATTCCATCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.19
Consensus pattern (42 bp):
AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACC
Found at i:1481247 original size:21 final size:21
Alignment explanation
Indices: 1481198--1481247 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1481188 GTTAGGGGAG
*
1481198 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
** *
1481219 TTGTGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
1481240 TTACGTGA
1 TTACGTGA
1481248 CGACAATGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.12, G:0.34, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:1481479 original size:4 final size:4
Alignment explanation
Indices: 1481470--1481503 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
1481460 TTTTTCGACA
* *
1481470 TTAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1481504 TTAGCGGCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:1481675 original size:21 final size:21
Alignment explanation
Indices: 1481649--1481765 Score: 121
Period size: 21 Copynumber: 5.6 Consensus size: 21
1481639 TTCACCTGTC
*
1481649 ATCGTTCAAAAGGCCCCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
1481670 ATCGTTCAAGAGGCCCCT-CT
1 ATCGTTCAAGAGGCCCCTCCT
*
1481690 CATCGTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* * *
1481712 ACCGTTCAAGAGGCCTCT-AT
1 ATCGTTCAAGAGGCCCCTCCT
* * *
1481732 CATCATTCAAGAGGTCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
*
1481754 ACCGTTCAAGAG
1 ATCGTTCAAGAG
1481766 CCCGATTTAC
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.03
21 75 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:1481706 original size:42 final size:42
Alignment explanation
Indices: 1481647--1481765 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
1481637 GATTCACCTG
* * * *
1481647 TCATCGTTCAAAAGGCCCCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTA
*
1481689 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCTCTA
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTA
* *
1481731 TCATCATTCAAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAG
1481766 CCCGATTTAC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTA
Found at i:1483379 original size:20 final size:20
Alignment explanation
Indices: 1483356--1483430 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
1483346 ATCGCAACGT
1483356 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCGCGTTGC
* * *
1483376 GAATTTGACTTTTGCATTGT
1 GAATTTGACTTTCGCGTTGC
* *
1483396 GAATTTGACTTTTGCGTAGC
1 GAATTTGACTTTCGCGTTGC
1483416 GAATTTGACTTTCGC
1 GAATTTGACTTTCGC
1483431 AACAATCGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.43
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTGC
Found at i:1483386 original size:49 final size:49
Alignment explanation
Indices: 1483327--1483469 Score: 178
Period size: 49 Copynumber: 3.1 Consensus size: 49
1483317 TTCACGTTTT
1483327 GAATTTGACTTTCGCAACAATCGCAACGTGAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCGCAACAATCGCAACGTGAATTTGACTTTCGCGTTGC
** * *
1483376 GAATTTGACTTT--------T-GCATTGTGAATTTGACTTTTGCGTAGC
1 GAATTTGACTTTCGCAACAATCGCAACGTGAATTTGACTTTCGCGTTGC
*
1483416 GAATTTGACTTTCGCAACAATCGCAACGTGAATTTGACTTTCACGTTGC
1 GAATTTGACTTTCGCAACAATCGCAACGTGAATTTGACTTTCGCGTTGC
1483465 GAATT
1 GAATT
1483470 CAAGGAAACC
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
40 35 0.46
41 1 0.01
48 1 0.01
49 39 0.51
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.36
Consensus pattern (49 bp):
GAATTTGACTTTCGCAACAATCGCAACGTGAATTTGACTTTCGCGTTGC
Found at i:1485996 original size:24 final size:24
Alignment explanation
Indices: 1485962--1486016 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1485952 CTGAAACATC
1485962 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1485986 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1486010 AT-AAAAT
1 ATCAAAAT
1486017 TTCGAATACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1492286 original size:23 final size:21
Alignment explanation
Indices: 1492231--1492292 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
1492221 TTTTGGTGCA
* *
1492231 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCTTT
*
1492251 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTTT
1492272 GAAGGGGAACCGATTCCCCCT
1 G-A-GGGAACCGATTCCCCCT
1492293 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTTT
Found at i:1496597 original size:20 final size:20
Alignment explanation
Indices: 1496562--1496653 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 20
1496552 AAATAAAACT
1496562 TGTTGCGAAATT-AAAATTCG
1 TGTTGCG-AATTCAAAATTCG
1496582 TGTTGCGAATTCAAAAATT-G
1 TGTTGCGAATTC-AAAATTCG
* *
1496602 AGTTACGAATTCAGAAA-TCG
1 TGTTGCGAATTCA-AAATTCG
* * **
1496622 AGTTGCAAATTTGAAATTCAG
1 TGTTGCGAATTCAAAATTC-G
1496643 TGTTGCGAATT
1 TGTTGCGAATT
1496654 TGGAAAGCGC
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
19 9 0.16
20 33 0.57
21 16 0.28
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
TGTTGCGAATTCAAAATTCG
Found at i:1512058 original size:3 final size:3
Alignment explanation
Indices: 1512041--1512080 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
1512031 GACTTTAAAA
* * *
1512041 ATT ATT ATA AAT ATT ATT ATT ATT ATT ACT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1512081 ATTAAACAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1513007 original size:23 final size:23
Alignment explanation
Indices: 1512976--1513029 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1512966 TTTGAGGCCA
1512976 AAGAGATAACCTTACAACTCCCTC
1 AAGA-ATAACCTTACAACTCCCTC
*
1513000 AAGAATAACCTTACAACTCTCTC
1 AAGAATAACCTTACAACTCCCTC
1513023 AAGAATA
1 AAGAATA
1513030 TACCCCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (23 bp):
AAGAATAACCTTACAACTCCCTC
Found at i:1523446 original size:104 final size:101
Alignment explanation
Indices: 1523310--1523495 Score: 293
Period size: 104 Copynumber: 1.8 Consensus size: 101
1523300 TTGTATCACT
1523310 TGTAATACACTAATTATTGTGCTAAAGTGGCTTTACATTT-TATATTATATATAAAATCTTATTA
1 TGTAATACACTAATTATTGTGCTAAAGTGGCTTTACATTTAT-TATTATATATAAAATCTTA-T-
1523374 TATATATGTTTTGTATGGAATCATTAAGTGTTCTCCATG
63 TATATATGTTTTGTATGGAATCATTAAGTGTTCTCCATG
* * *
1523413 TGTAATATACTAATTATGTGTGCTAAAGTGGCTTTGCATTTATTATTATATATACAATCTTATTA
1 TGTAATACACTAATTAT-TGTGCTAAAGTGGCTTTACATTTATTATTATATATAAAATCTTATTA
*
1523478 TATGTGTTTTGTATGGAA
65 TATATGTTTTGTATGGAA
1523496 GAATTAAATG
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
102 19 0.25
103 17 0.22
104 40 0.52
105 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (101 bp):
TGTAATACACTAATTATTGTGCTAAAGTGGCTTTACATTTATTATTATATATAAAATCTTATTAT
ATATGTTTTGTATGGAATCATTAAGTGTTCTCCATG
Found at i:1525561 original size:55 final size:55
Alignment explanation
Indices: 1525476--1525606 Score: 165
Period size: 55 Copynumber: 2.4 Consensus size: 55
1525466 ATGATTCATG
* * * * *
1525476 AAGA-ATCCAATGAATGAAGAAATTTGAAACTGACTGAAGAATGATTCATGAAGA
1 AAGACATCCGATGAATGAAGAAATCTGAAACTGACTGAAGAACGATCCATAAAGA
* * * *
1525530 AGGACATCCGATGACTGAAGAAATCTGAAACTGATTGAAGACCGATCCATAAAGA
1 AAGACATCCGATGAATGAAGAAATCTGAAACTGACTGAAGAACGATCCATAAAGA
*
1525585 AAGACATCTGATGAATGAAGAA
1 AAGACATCCGATGAATGAAGAA
1525607 GTTTGAAGTT
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
54 3 0.05
55 61 0.95
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (55 bp):
AAGACATCCGATGAATGAAGAAATCTGAAACTGACTGAAGAACGATCCATAAAGA
Found at i:1528487 original size:31 final size:31
Alignment explanation
Indices: 1528449--1528511 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1528439 GAATCGAGGG
*
1528449 TTACCTATGTTCTACGGAACATATGGACAGT
1 TTACCTATGTTCTACAGAACATATGGACAGT
* *
1528480 TTACCTATGTTCTTCAGAACATATGGATAGT
1 TTACCTATGTTCTACAGAACATATGGACAGT
1528511 T
1 T
1528512 ACATAGGTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTACAGAACATATGGACAGT
Found at i:1533585 original size:22 final size:22
Alignment explanation
Indices: 1533558--1533601 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1533548 AATAAGGAAG
*
1533558 GAAAAAAGAACGAAAAAAAGAAC
1 GAAAAAA-AAAGAAAAAAAGAAC
1533581 GAAAAAAAAAGAAAAAAAGAA
1 GAAAAAAAAAGAAAAAAAGAA
1533602 AGAATAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.80, C:0.05, G:0.16, T:0.00
Consensus pattern (22 bp):
GAAAAAAAAAGAAAAAAAGAAC
Found at i:1533586 original size:13 final size:12
Alignment explanation
Indices: 1533559--1533601 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
1533549 ATAAGGAAGG
1533559 AAAAAAGAACGA
1 AAAAAAGAACGA
1533571 AAAAAAGAACGA
1 AAAAAAGAACGA
1533583 AAAAAA-AA-GA
1 AAAAAAGAACGA
1533593 AAAAAAGAA
1 AAAAAAGAA
1533602 AGAATAAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.27
11 4 0.13
12 18 0.60
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGAACGA
Found at i:1534911 original size:51 final size:51
Alignment explanation
Indices: 1534773--1535003 Score: 324
Period size: 50 Copynumber: 4.6 Consensus size: 51
1534763 CCGTGTGGGT
*
1534773 ATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCCATGTGGGGC
1 ATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTAATCCATGTGGGGC
*
1534824 AT-TTGAAGGCTCA-ATCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGC
1 ATCTTGAAGGCTCACATCAGCATG-AAAAGACAGAAGTAATCCATGTGGGGC
* ** * *
1534874 ATCTTGAAGGGTCACATCAGCATGAGGAGACATAAGTAATTCATGT-GGGC
1 ATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTAATCCATGTGGGGC
* * * *
1534924 ATCTTGAAGGGTCACATCAGTATGAAGAGACAGAAGTAATTCATGTGGGGC
1 ATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTAATCCATGTGGGGC
*
1534975 ATCTTGAAGGCTCACACCAGCATGAAAAG
1 ATCTTGAAGGCTCACATCAGCATGAAAAG
1535004 GTTGGGATAT
Statistics
Matches: 161, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
49 9 0.06
50 84 0.52
51 59 0.37
52 9 0.06
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (51 bp):
ATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTAATCCATGTGGGGC
Found at i:1534955 original size:101 final size:101
Alignment explanation
Indices: 1534773--1535003 Score: 322
Period size: 101 Copynumber: 2.3 Consensus size: 101
1534763 CCGTGTGGGT
*
1534773 ATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCCATGTGGGGCATTTGAAGGCTCAA
1 ATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTAATCCATGTGGGGCATTTGAAGGCTCAA
1534838 TCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGC
66 TCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGC
* ** * * *
1534874 ATCTTGAAGGGTCACATCAGCATGAGGAGACATAAGTAATTCATGT-GGGCATCTTGAAGGGTCA
1 ATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTAATCCATGTGGGGCAT-TTGAAGGCTCA
* * * *
1534938 CATCAGTATG-AAGAGACAGAAGTAATTCATGTGGGGC
65 -ATCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGC
*
1534975 ATCTTGAAGGCTCACACCAGCATGAAAAG
1 ATCTTGAAGGCTCACATCAGCATGAAAAG
1535004 GTTGGGATAT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
100 6 0.05
101 99 0.88
102 8 0.07
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (101 bp):
ATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTAATCCATGTGGGGCATTTGAAGGCTCAA
TCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGC
Found at i:1535049 original size:41 final size:40
Alignment explanation
Indices: 1534999--1535079 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
1534989 CACCAGCATG
1534999 AAAAGGTTGGGATATTTTGAAAGTCCATTTTAACTAGAAAT
1 AAAAGGTTGGGATATTTTGAAAGTCCATTTTAAC-AGAAAT
* * * **
1535040 AAAATGTTGGGGTATTTTGAAGGTCTTTTTTAACAGAAAT
1 AAAAGGTTGGGATATTTTGAAAGTCCATTTTAACAGAAAT
1535080 GATCCATGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 6 0.17
41 29 0.83
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.37
Consensus pattern (40 bp):
AAAAGGTTGGGATATTTTGAAAGTCCATTTTAACAGAAAT
Found at i:1536565 original size:43 final size:43
Alignment explanation
Indices: 1536500--1536756 Score: 378
Period size: 43 Copynumber: 6.0 Consensus size: 43
1536490 ATAAGAAACT
*
1536500 AAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
* * *
1536543 AAGCTTGAGGGACCATCATGATATGTA--GGTTCTTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
*
1536584 AAGCTTGAGGGACAAACGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
** *
1536627 AAGCTTGAGGGACCAACAAGATATGTAGGGGATCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
* *
1536670 AAGCTTGAGGAACCACCGTGATATGTAGGGGTTCCTTGATGA-
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
*
1536712 ACA-CTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGGTGAC
1 A-AGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
1536755 AA
1 AA
1536757 CTAAGAAACT
Statistics
Matches: 192, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
41 37 0.19
42 38 0.20
43 117 0.61
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (43 bp):
AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
Found at i:1536641 original size:84 final size:84
Alignment explanation
Indices: 1536500--1536740 Score: 360
Period size: 84 Copynumber: 2.9 Consensus size: 84
1536490 ATAAGAAACT
* *
1536500 AAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAGGGACCATCATGAT
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAGGGACCAACATGAT
* *
1536565 ATGTAGGTTCTTTGATGAC
66 ATGTAGGATCCTTGATGAC
* *
1536584 AAGCTTGAGGGACAAACGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAGGGACCAACAAGAT
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAGGGACCAACATGAT
1536649 ATGTAGGGGATCCTTGATGAC
66 ATGTA--GGATCCTTGATGAC
* * *
1536670 AAGCTTGAGGAACCACCGTGATATGTAGGGGTTCCTTGATGA-ACA-CTTGAGGGACCAACGTGA
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACA-AGCTTGAGGGACCAACATGA
1536733 TATGTAGG
65 TATGTAGG
1536741 GGTTCCTTGG
Statistics
Matches: 143, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
83 2 0.01
84 66 0.46
85 23 0.16
86 52 0.36
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.26
Consensus pattern (84 bp):
AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAGGGACCAACATGAT
ATGTAGGATCCTTGATGAC
Found at i:1536819 original size:20 final size:20
Alignment explanation
Indices: 1536794--1536855 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
1536784 TTTCTTGATA
1536794 AGTAAGTCCTTCGGGCCATC
1 AGTAAGTCCTTCGGGCCATC
* * *
1536814 AGTAAGTCTTTCGAG-CATG
1 AGTAAGTCCTTCGGGCCATC
1536833 ATGCGTAAGTCCTTCGGGCCATC
1 A---GTAAGTCCTTCGGGCCATC
1536856 CATAAGACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.12
20 13 0.41
22 12 0.38
23 3 0.09
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (20 bp):
AGTAAGTCCTTCGGGCCATC
Found at i:1536988 original size:89 final size:90
Alignment explanation
Indices: 1536837--1537123 Score: 472
Period size: 89 Copynumber: 3.2 Consensus size: 90
1536827 AGCATGATGC
*
1536837 GTAAGTCCTTCGGGCCATCCATAAGACCTTTAGTGCAGGATGTTTTCAAATGAGATTTAAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAAC
*
1536902 TAAGCCTT-GGGGGTTTCTTGATTT
66 TAAGCCTTCGAGGGTTTCTTGATTT
1536926 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAAC
*
1536991 TAAGTCTTCGAGGG-TTCTTGATTT
66 TAAGCCTTCGAGGGTTTCTTGATTT
*
1537015 GTAAGTCCTTCGAGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAA-AAA
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGA-TTTAAGAAA
*
1537079 CTAAGCCTTCGAGGGTTTCTTTATTT
65 CTAAGCCTTCGAGGGTTTCTTGATTT
* * *
1537105 TTAAATCCTTCGGGTCATC
1 GTAAGTCCTTCGGGCCATC
1537124 AGTAAGTCTT
Statistics
Matches: 185, Mismatches: 10, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
89 152 0.82
90 33 0.18
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (90 bp):
GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAAC
TAAGCCTTCGAGGGTTTCTTGATTT
Found at i:1537164 original size:42 final size:42
Alignment explanation
Indices: 1537105--1537229 Score: 180
Period size: 42 Copynumber: 3.0 Consensus size: 42
1537095 TTCTTTATTT
*
1537105 TTAAATCCTTCGGGTCATCAGTAAGTCTTTTGAGCATGATGC
1 TTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGC
* *
1537147 TTAAATCTTTCGGGTCATCAATAAGTCTTTCGAGCATGATGC
1 TTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGC
* * *
1537189 TTAAATCCTTCGGATCATCTGTAA-TCCTTTCGAGCAAGATG
1 TTAAATCCTTCGGGTCATCAGTAAGT-CTTTCGAGCATGATG
1537230 ATAAGACCTC
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 1 0.01
42 73 0.99
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (42 bp):
TTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGC
Found at i:1537505 original size:136 final size:136
Alignment explanation
Indices: 1537257--1537603 Score: 524
Period size: 136 Copynumber: 2.6 Consensus size: 136
1537247 AATGTTTTCA
*
1537257 ACATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCTAATAGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAAT
* * *
1537322 GAGAAGAGCTTGTTCGACTTATCACTCGATTCACAACATTTCGAATTAGTTATGCCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCAAATTAGTTACGCCTCGCTTGAG
1537387 AGATTG
131 AGATTG
* * * * * *
1537393 ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATGCGACAGAGGGAGAAGAAGTTTATAAT
1 ACATTTCTAATAGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAAT
*
1537458 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCAAATTAGTTACGCCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCAAATTAGTTACGCCTCGCTTGAG
*
1537523 GGATTG
131 AGATTG
* *
1537529 ACATTTCTAATAGAGAGTTCATAATGAGAAGAACTCGTCC-TAA-A-GGAG-A-AAGTTCATAAT
1 ACATTTCTAATAGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAAT
*
1537589 GAGAAGAACTTGTTC
66 GAGAAGAGCTTGTTC
1537604 TTTTCAAATT
Statistics
Matches: 192, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
131 24 0.12
132 1 0.01
133 4 0.02
134 1 0.01
135 1 0.01
136 161 0.84
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (136 bp):
ACATTTCTAATAGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCAAATTAGTTACGCCTCGCTTGAG
AGATTG
Found at i:1537935 original size:107 final size:107
Alignment explanation
Indices: 1537541--1538148 Score: 748
Period size: 105 Copynumber: 5.6 Consensus size: 107
1537531 ATTTCTAATA
* *
1537541 GAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCTT
1 GAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCT
1537606 TTCAAATTCACCACAGAAGGAGGTGAACCAACA-TTTC--TAG
66 TTCAAATTCACCACAGAAGGAGGTGAACCAACATTTTCAGT-G
* *
1537646 AAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCT
1 GAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCT
*
1537711 TTCAAATTCACCACAGAATGAGGTGAACCAACATTTTCA--G
66 TTCAAATTCACCACAGAAGGAGGTGAACCAACATTTTCAGTG
* * * *
1537751 AATAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCT
1 GAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCT
*
1537816 TTCAAATTCACCACAAAAGGAGGTGAACCAACATTTTCAGTG
66 TTCAAATTCACCACAGAAGGAGGTGAACCAACATTTTCAGTG
*
1537858 GAGAGTTCATAATGAGAAGAACTCATCCTAAAGTGA-AATGTTCATAATGAGAAGAACTTGTTCC
1 GAGAGTTCATAATGAGAAGAACTCATCCTAAAG-GAGAAAGTTCATAATGAGAAGAACTTGTTCC
* * * * *
1537922 TTTCAAGTCCACCACAAAATGAAGTG-ACTCAACATTTTCAGTG
65 TTTCAAATTCACCACAGAAGGAGGTGAAC-CAACATTTTCAGTG
* *
1537965 GAGAGTTCATAATGAGAAGAACTCATCCAATAAGGGAGGAGAAGTTCATAATAAGAAGAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCC--TAAAGGA-GA-AAGTTCATAATGAGAAGAACTTGT
* * * * * *
1538030 TCAACCTTGGTTC-GATTCCATCACAGAAGGAAGTGGATCAACATTTCCAGTG
62 T---CC-T--TTCAAATT-CACCACAGAAGGAGGTGAACCAACATTTTCAGTG
* *
1538082 GAGAGTTTATAATGAGAAGAACTCA-CCCAACGAGGAAGAATAAGTTCATAATGAGAAGAACTTG
1 GAGAGTTCATAATGAGAAGAACTCATCCTAA--AGG-AG-A-AAGTTCATAATGAGAAGAACTTG
1538146 TTC
61 TTC
1538149 AACCTTGCAT
Statistics
Matches: 448, Mismatches: 32, Indels: 37
0.87 0.06 0.07
Matches are distributed among these distances:
105 196 0.44
106 6 0.01
107 121 0.27
108 4 0.01
109 4 0.01
110 1 0.00
111 23 0.05
114 5 0.01
115 1 0.00
116 6 0.01
117 80 0.18
118 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (107 bp):
GAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCT
TTCAAATTCACCACAGAAGGAGGTGAACCAACATTTTCAGTG
Found at i:1538185 original size:91 final size:91
Alignment explanation
Indices: 1538073--1538241 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 91
1538063 TGGATCAACA
* * * *
1538073 TTTCCAGTGGAGAGTTTATAATGAGAAGAACTCACCCAACGAG-GAAGAATAAGTTCATAATGAG
1 TTTCCAGTGAAGAGTTCATAATGAGAAGAACTCACCCAACAAGAG-AGAAGAAGTTCATAATGAG
1538137 AAGAACTTGTTCAACCTTGCATCAGTG
65 AAGAACTTGTTCAACCTTGCATCAGTG
*
1538164 TTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGAAGTTCATAATGAGA
1 TTTCCAGTGAAGAGTTCATAATGAGAAGAACTCACCCAACAAGAGAGAAGAAGTTCATAATGAGA
1538229 AGAACTTGTTCAA
66 AGAACTTGTTCAA
1538242 TCCAACAACG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
91 71 0.99
92 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (91 bp):
TTTCCAGTGAAGAGTTCATAATGAGAAGAACTCACCCAACAAGAGAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTGCATCAGTG
Found at i:1538987 original size:11 final size:11
Alignment explanation
Indices: 1538955--1538997 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1538945 TAAACACCCG
*
1538955 AAATGCCACTA
1 AAATCCCACTA
1538966 AAA-CCCTACTA
1 AAATCCC-ACTA
*
1538977 AAATACCACTA
1 AAATCCCACTA
1538988 AAATCCCACT
1 AAATCCCACT
1538998 CAAACACCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 2 0.07
11 23 0.85
12 2 0.07
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.19
Consensus pattern (11 bp):
AAATCCCACTA
Found at i:1539006 original size:22 final size:22
Alignment explanation
Indices: 1538960--1539006 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1538950 ACCCGAAATG
*
1538960 CCACTAAAACCCTACTAAAATA
1 CCACTAAAACCCTACTAAAACA
*
1538982 CCACTAAAATCCC-ACTCAAACA
1 CCACTAAAA-CCCTACTAAAACA
1539004 CCA
1 CCA
1539007 TTATTCGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (22 bp):
CCACTAAAACCCTACTAAAACA
Found at i:1540591 original size:102 final size:102
Alignment explanation
Indices: 1540397--1540597 Score: 271
Period size: 102 Copynumber: 2.0 Consensus size: 102
1540387 TGTCTTGTAT
* * *
1540397 CACGTGTAATACACTAATTATTGTGCTAAAGTGGCTTTACATTTTATATTATATATAAAATTTTT
1 CACGTGTAATACACTAATTATTGTGCTAAAGCGGCTTTACATTTAATATTATATATAAAATTTAT
* * * *
1540462 ATATATATTTTTTTGTATGGAATCATTAAGTGTTCTC
66 ATATATATTGTTTTGTATGAAAGCATTAAATGTTCTC
* * * *
1540499 CACGTGTAATATACTAATTATGTGTGCTAAAGCGGTTTTGCATTTAATATTATATATACAATCTT
1 CACGTGTAATACACTAATTAT-TGTGCTAAAGCGGCTTTACATTTAATATTATATATAAAAT-TT
1540564 AT-TATATA-TGTTTTGTATGAAAGCATTAAATGTT
64 ATATATATATTGTTTTGTATGAAAGCATTAAATGTT
1540598 TTGATATATG
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
102 42 0.49
103 41 0.48
104 3 0.03
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (102 bp):
CACGTGTAATACACTAATTATTGTGCTAAAGCGGCTTTACATTTAATATTATATATAAAATTTAT
ATATATATTGTTTTGTATGAAAGCATTAAATGTTCTC
Found at i:1541122 original size:9 final size:9
Alignment explanation
Indices: 1541096--1541162 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
1541086 GCCCCGATTA
*
1541096 TATATATATA
1 TATATAT-TT
1541106 TATAATATTT
1 TAT-ATATTT
1541116 TATATATTT
1 TATATATTT
*
1541125 TATAT-TAAT
1 TATATAT-TT
*
1541134 TATATA-TG
1 TATATATTT
1541142 TA-ATATTT
1 TATATATTT
1541150 TATAT-TTT
1 TATATATTT
1541158 TATAT
1 TATAT
1541163 TAATTATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 3 0.06
8 14 0.30
9 19 0.40
10 7 0.15
11 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (9 bp):
TATATATTT
Found at i:1541164 original size:33 final size:34
Alignment explanation
Indices: 1541100--1541183 Score: 152
Period size: 33 Copynumber: 2.5 Consensus size: 34
1541090 CGATTATATA
1541100 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
1541134 TATATATGTAATATTTTATAT-TTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
1541167 TATATATATAATATTTT
1 TATATATATAATATTTT
1541184 CGGGTTCGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 28 0.58
34 20 0.42
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:1543733 original size:20 final size:20
Alignment explanation
Indices: 1543708--1543749 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1543698 CGTAAGTGCA
1543708 ATTCCAAAAATATAAATTCG
1 ATTCCAAAAATATAAATTCG
*
1543728 ATTCCAAAAATATAAGTTCG
1 ATTCCAAAAATATAAATTCG
1543748 AT
1 AT
1543750 ACATAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (20 bp):
ATTCCAAAAATATAAATTCG
Found at i:1553906 original size:21 final size:21
Alignment explanation
Indices: 1553882--1553921 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1553872 AAGACTTTAT
1553882 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
1553903 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
1553922 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:1555685 original size:15 final size:15
Alignment explanation
Indices: 1555667--1555700 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1555657 GAATGTATAA
1555667 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
* *
1555682 TAGTCCTTTGGGATG
1 TAGTCCTTCGGGACG
1555697 TAGT
1 TAGT
1555701 GGTCCTATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.32, T:0.35
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Done.