Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015381.1 Kokia drynarioides strain JFW-HI SEQ_130428, 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: 2291099
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 587 characters in sequence are not A, C, G, or T
File 5 of 8
Found at i:1113877 original size:23 final size:23
Alignment explanation
Indices: 1113851--1113900 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1113841 TCATATTTAC
* *
1113851 ATTTAAACAGAAATCACGTTAAT
1 ATTTAAACACAAATCACATTAAT
* *
1113874 ATTTGACCACAAATCACATTAAT
1 ATTTAAACACAAATCACATTAAT
1113897 ATTT
1 ATTT
1113901 TTTTGTGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (23 bp):
ATTTAAACACAAATCACATTAAT
Found at i:1117266 original size:23 final size:23
Alignment explanation
Indices: 1117236--1117286 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1117226 CAAAAAAATA
*
1117236 TTTAAGCACAAATCACA-TACACT
1 TTTAAGCAAAAATCACATTA-ACT
*
1117259 TTTAAGCAAAAATTACATTAACT
1 TTTAAGCAAAAATCACATTAACT
1117282 TTTAA
1 TTTAA
1117287 CAGATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (23 bp):
TTTAAGCAAAAATCACATTAACT
Found at i:1117758 original size:36 final size:36
Alignment explanation
Indices: 1117680--1117766 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
1117670 TTAGCACAAT
* * * *
1117680 ATATTCATTATCACATGGCATGAATAACATGCCCAT
1 ATATTTATTATCACATGACATGAATAACATACCCAC
* *
1117716 AAATTTATTATCTCATGACATGAATAACATACCCAC
1 ATATTTATTATCACATGACATGAATAACATACCCAC
1117752 ATATTTACTT-TCACA
1 ATATTTA-TTATCACA
1117767 ACAGTCAGCA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
36 40 0.95
37 2 0.05
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (36 bp):
ATATTTATTATCACATGACATGAATAACATACCCAC
Found at i:1131804 original size:21 final size:21
Alignment explanation
Indices: 1131780--1131835 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
1131770 TAGAAGTAAG
*
1131780 ACTTGTATCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
* * * *
1131801 ACTTGTACCAGTAAAACTGTC
1 ACTTGTATCGGTAGAACAGTC
1131822 ACTTGTATCGGTAG
1 ACTTGTATCGGTAG
1131836 GAGTCTGCAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:1135432 original size:26 final size:26
Alignment explanation
Indices: 1135400--1135485 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 26
1135390 AAATTTATTT
1135400 TTTTAAAATATAAAATTTTTAAATTA
1 TTTTAAAATATAAAATTTTTAAATTA
*
1135426 TTTTAAAAT-T--AA--TTT-AATTT
1 TTTTAAAATATAAAATTTTTAAATTA
* *
1135446 TTTTAAAT-ATAAAATTATTGAAATTA
1 TTTTAAAATATAAAATT-TTTAAATTA
1135472 TTTTAAAATTATAA
1 TTTTAAAA-TATAA
1135486 CCATCATCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
20 12 0.26
21 3 0.07
22 2 0.04
23 2 0.04
25 3 0.07
26 20 0.43
28 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
TTTTAAAATATAAAATTTTTAAATTA
Found at i:1135454 original size:45 final size:46
Alignment explanation
Indices: 1135391--1135482 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
1135381 AAAATGATTA
*
1135391 AATTTATTTTTTTAAAATATAAAATT-TTTAAATTATTTTAAAATT
1 AATTTATTTTTTTAAAATATAAAATTATTGAAATTATTTTAAAATT
1135436 AATTTAATTTTTTT-AAATATAAAATTATTGAAATTATTTTAAAATT
1 AATTT-ATTTTTTTAAAATATAAAATTATTGAAATTATTTTAAAATT
1135482 A
1 A
1135483 TAACCATCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
45 17 0.39
46 27 0.61
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (46 bp):
AATTTATTTTTTTAAAATATAAAATTATTGAAATTATTTTAAAATT
Found at i:1135524 original size:6 final size:6
Alignment explanation
Indices: 1135506--1135539 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
1135496 CTTGAGTTTT
1135506 TTCCCC TTTCCCC TTCCCC TTCCCC TTCCCC TTC
1 TTCCCC -TTCCCC TTCCCC TTCCCC TTCCCC TTC
1135540 AACAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
TTCCCC
Found at i:1140475 original size:21 final size:20
Alignment explanation
Indices: 1140451--1140501 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1140441 AAAGTTTTTA
1140451 GTATCGGTAGAAGTAAG-ACTT
1 GTATCGGTAGAAG--AGCACTT
*
1140472 GTATCTGTAGAAGAGTCACTT
1 GTATCGGTAGAAGAG-CACTT
1140493 GTATCGGTA
1 GTATCGGTA
1140502 AAACTATCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
21 24 0.92
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31
Consensus pattern (20 bp):
GTATCGGTAGAAGAGCACTT
Found at i:1141260 original size:16 final size:17
Alignment explanation
Indices: 1141236--1141269 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1141226 ACAGTACACA
*
1141236 AATATAATTGA-CTCGC
1 AATACAATTGAGCTCGC
1141252 AATACAATTGAGCTCGC
1 AATACAATTGAGCTCGC
1141269 A
1 A
1141270 CTTAGCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (17 bp):
AATACAATTGAGCTCGC
Found at i:1141731 original size:2 final size:2
Alignment explanation
Indices: 1141671--1141711 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1141661 ACACACACAC
1141671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1141712 ACACCCACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1141786 original size:17 final size:17
Alignment explanation
Indices: 1141766--1141832 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
1141756 AACTCATATG
1141766 AAATAACAGTTCATACC
1 AAATAACAGTTCATACC
* * *
1141783 AAATGATAGTTTC-TTCC
1 AAATAACAG-TTCATACC
* * *
1141800 AATTAACAGTTCATGCA
1 AAATAACAGTTCATACC
1141817 AAATAACAGTTCATAC
1 AAATAACAGTTCATAC
1141833 TCCATCATAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
16 3 0.08
17 32 0.84
18 3 0.08
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (17 bp):
AAATAACAGTTCATACC
Found at i:1142961 original size:25 final size:26
Alignment explanation
Indices: 1142899--1142964 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 26
1142889 TATAAACCTA
1142899 TATATATTATATAATAAAACCCACACG
1 TATATATTATAT-ATAAAACCCACACG
*
1142926 TA-ATATT-TATATACAACCC-CAC-
1 TATATATTATATATAAAACCCACACG
1142948 TCATATATTATATATAA
1 T-ATATATTATATATAA
1142965 TACGCATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 1 0.03
23 4 0.12
24 13 0.38
25 9 0.26
26 5 0.15
27 2 0.06
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (26 bp):
TATATATTATATATAAAACCCACACG
Found at i:1144005 original size:21 final size:21
Alignment explanation
Indices: 1143979--1144021 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1143969 TGTTGAGGTG
*
1143979 TTTGGATAGCTATAAAATCAC
1 TTTGGATAGCTAGAAAATCAC
1144000 TTTGGATAGCTAGAAAATCAC
1 TTTGGATAGCTAGAAAATCAC
1144021 T
1 T
1144022 AAGGATGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
TTTGGATAGCTAGAAAATCAC
Found at i:1144027 original size:21 final size:21
Alignment explanation
Indices: 1143982--1144027 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1143972 TGAGGTGTTT
* **
1143982 GGATAGCTATAAAATCACTTT
1 GGATAGCTAGAAAATCACTAA
1144003 GGATAGCTAGAAAATCACTAA
1 GGATAGCTAGAAAATCACTAA
1144024 GGAT
1 GGAT
1144028 GAGTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (21 bp):
GGATAGCTAGAAAATCACTAA
Found at i:1144856 original size:14 final size:15
Alignment explanation
Indices: 1144825--1144857 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1144815 ATTTTCATCC
1144825 AAAATTTAAATATTT
1 AAAATTTAAATATTT
*
1144840 AAAATTT-AATTTTT
1 AAAATTTAAATATTT
1144854 AAAA
1 AAAA
1144858 CTAGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTTAAATATTT
Found at i:1161005 original size:18 final size:17
Alignment explanation
Indices: 1160982--1161024 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
1160972 GTCCTTGCAT
1160982 TTGTGGTGGTAATCGC-GA
1 TTGTGGT-GTAATC-CTGA
1161000 TTGTGGCTGTAATCCTGA
1 TTGTGG-TGTAATCCTGA
1161018 TTGTGGT
1 TTGTGGT
1161025 TGCATCTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.09
18 20 0.87
19 1 0.04
ACGTcount: A:0.14, C:0.12, G:0.35, T:0.40
Consensus pattern (17 bp):
TTGTGGTGTAATCCTGA
Found at i:1164217 original size:20 final size:18
Alignment explanation
Indices: 1164192--1164240 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1164182 TTCCTCCAAT
1164192 TAACAATTCATAACAACACA
1 TAACAATTCATAACAA-A-A
* *
1164212 TAACAATTTAT-GCAAAA
1 TAACAATTCATAACAAAA
1164229 TAACAATTCATA
1 TAACAATTCATA
1164241 CTCCATCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 11 0.44
18 1 0.04
19 3 0.12
20 10 0.40
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.27
Consensus pattern (18 bp):
TAACAATTCATAACAAAA
Found at i:1164892 original size:18 final size:18
Alignment explanation
Indices: 1164866--1164917 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1164856 CACAGTTTGG
1164866 CAAATTAATACAATTCAC
1 CAAATTAATACAATTCAC
*
1164884 CATATTAATACAGA-TCAC
1 CAAATTAATACA-ATTCAC
* *
1164902 TAAATTAACACAATTC
1 CAAATTAATACAATTC
1164918 GTCATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (18 bp):
CAAATTAATACAATTCAC
Found at i:1167041 original size:28 final size:28
Alignment explanation
Indices: 1166993--1167067 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
1166983 AATGTACAGA
* * *
1166993 CACAAGGGCAAGCACATGGTCATGTGGAC
1 CACACGGGC-AGCACACGGTCATGTAGAC
1167022 CACACGGGCAGCACACGGTCATGTAGAC
1 CACACGGGCAGCACACGGTCATGTAGAC
* *
1167050 CACACAGACAGCACACGG
1 CACACGGGCAGCACACGG
1167068 ACGTGTGACC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 33 0.80
29 8 0.20
ACGTcount: A:0.32, C:0.31, G:0.28, T:0.09
Consensus pattern (28 bp):
CACACGGGCAGCACACGGTCATGTAGAC
Found at i:1180608 original size:15 final size:15
Alignment explanation
Indices: 1180590--1180627 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1180580 AAAAGAAACT
1180590 GAAGAGGAGAAGGAG
1 GAAGAGGAGAAGGAG
* *
1180605 GAAGAGAAGAAGGAT
1 GAAGAGGAGAAGGAG
1180620 GAAGAGGA
1 GAAGAGGA
1180628 TGTAGATGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (15 bp):
GAAGAGGAGAAGGAG
Found at i:1181038 original size:17 final size:17
Alignment explanation
Indices: 1181013--1181055 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1181003 ATGCATTTCA
1181013 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
* **
1181030 TTTAGTTGTTGTTGCAT
1 TTTAATTGTCATTGCAT
*
1181047 TTTACTTGT
1 TTTAATTGT
1181056 TAATTCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.58
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:1181056 original size:17 final size:17
Alignment explanation
Indices: 1181024--1181056 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1181014 TTAATTGTCA
*
1181024 TTGCATTTTAGTTGTTG
1 TTGCATTTTACTTGTTG
1181041 TTGCATTTTACTTGTT
1 TTGCATTTTACTTGTT
1181057 AATTCATTTG
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:0.12, C:0.09, G:0.18, T:0.61
Consensus pattern (17 bp):
TTGCATTTTACTTGTTG
Found at i:1181201 original size:61 final size:61
Alignment explanation
Indices: 1181127--1181251 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
1181117 GGGATAACGC
1181127 AGACATTAAGTTTAGGGGAAATTTGTGTGAAATGGTAATGCAATTGCACCCACATATTTGA
1 AGACATTAAGTTTAGGGGAAATTTGTGTGAAATGGTAATGCAATTGCACCCACATATTTGA
1181188 AGACATTAAGTTTAGGGGAAATTTGTGTGAAATGGTAATGCAATTGCACCCACATATTTGA
1 AGACATTAAGTTTAGGGGAAATTTGTGTGAAATGGTAATGCAATTGCACCCACATATTTGA
1181249 AGA
1 AGA
1181252 GTTTACTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (61 bp):
AGACATTAAGTTTAGGGGAAATTTGTGTGAAATGGTAATGCAATTGCACCCACATATTTGA
Found at i:1181712 original size:15 final size:15
Alignment explanation
Indices: 1181692--1181724 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1181682 AGTCACGTAT
1181692 AAAAAAAG-AGAAGAA
1 AAAAAAAGCA-AAGAA
1181707 AAAAAAAGCAAAGAA
1 AAAAAAAGCAAAGAA
1181722 AAA
1 AAA
1181725 GAGAAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAGCAAAGAA
Found at i:1185872 original size:55 final size:55
Alignment explanation
Indices: 1185813--1185920 Score: 139
Period size: 55 Copynumber: 2.0 Consensus size: 55
1185803 TATTTTGAGG
* *
1185813 CACATGGGCGA-GTGCTAGACCGT-ATGTGTATACTATTTTGAGACACACGGGCAGA
1 CACATGGGC-ATGTGCTAGACCATGA-GTGTATACTATTTTAAGACACACGGGCAGA
* * *
1185868 CACATGGGCATGTGCTAGACCATGAGTGTATATTGTTTTAAGACACATGGGCA
1 CACATGGGCATGTGCTAGACCATGAGTGTATACTATTTTAAGACACACGGGCA
1185921 TGTGCCAGGC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
54 1 0.02
55 44 0.96
56 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (55 bp):
CACATGGGCATGTGCTAGACCATGAGTGTATACTATTTTAAGACACACGGGCAGA
Found at i:1199996 original size:42 final size:42
Alignment explanation
Indices: 1199937--1200019 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1199927 ACTTTTTCAA
1199937 GTGCACTTTTAAATGCATAATCTCGTATCTTCATGTATCTCT
1 GTGCACTTTTAAATGCATAATCTCGTATCTTCATGTATCTCT
* *
1199979 GTGCACTTTTAAATGCATCATCTCGTATCTTCGTGTATCTC
1 GTGCACTTTTAAATGCATAATCTCGTATCTTCATGTATCTC
1200020 CAATAAGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (42 bp):
GTGCACTTTTAAATGCATAATCTCGTATCTTCATGTATCTCT
Found at i:1200235 original size:3 final size:3
Alignment explanation
Indices: 1200227--1200261 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1200217 TTCCTCAGGA
1200227 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1200262 AGCTTGTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1202124 original size:17 final size:17
Alignment explanation
Indices: 1202102--1202134 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1202092 GATTCAATAC
1202102 TTTAATTCGGGTAATTT
1 TTTAATTCGGGTAATTT
*
1202119 TTTAATTCGGTTAATT
1 TTTAATTCGGGTAATT
1202135 CGGGTAATTT
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:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (17 bp):
TTTAATTCGGGTAATTT
Found at i:1212241 original size:122 final size:122
Alignment explanation
Indices: 1212089--1212504 Score: 503
Period size: 122 Copynumber: 3.4 Consensus size: 122
1212079 GAGTTTCACC
* ** * * * ** *
1212089 TCATTGTTTTGGTCCGCTTCTCTGTATCTCATCAGGAAGATGACCACTTCGTTGTCAAACCCAAT
1 TCATTGATTTGGTCTACTTCTCTGTATCTCACCAGAAAGATAACCACTTCGTTGTCTGACCCACT
* *
1212154 TCTCTGTATCTCATCAAGAAGATAAGGTTTCAAAGTTTTACTCACGTGAGTTCTGCT
66 TCTCTGTATCTCATCAAGAAGATAGGGTTTCAAAGTTTTACTCACATGAGTTCTGCT
** * * ** * * *
1212211 TCATTGATTTGGTCTACTTCTCTGTATCTCATAAAAAAGATGACCGTTTTGTTGTCTGGCCTACT
1 TCATTGATTTGGTCTACTTCTCTGTATCTCACCAGAAAGATAACCACTTCGTTGTCTGACCCACT
* * *
1212276 TCTCTGTATCTCATCAAGAAGATGGGGTTTCAAAGTTTTACTTACATGAGCTCTGCT
66 TCTCTGTATCTCATCAAGAAGATAGGGTTTCAAAGTTTTACTCACATGAGTTCTGCT
* *
1212333 TCATTGATTTGGTCTACTTCTCTATATCTCACCAGAAAGATAACCACTTCATTGTCTGACCCACT
1 TCATTGATTTGGTCTACTTCTCTGTATCTCACCAGAAAGATAACCACTTCGTTGTCTGACCCACT
* * * * *
1212398 TCTTTGTATCTCATTAGGAACATAGGGTTTCAAAGTTTTACTCACATGAGCTT-TACCT
66 TCTCTGTATCTCATCAAGAAGATAGGGTTTCAAAGTTTTACTCACATGAG-TTCT-GCT
* * *
1212456 T-ATTTATTTGGTCTACTTCTCTGTATCTCACCAGGAAGATAATCACTTC
1 TCATTGATTTGGTCTACTTCTCTGTATCTCACCAGAAAGATAACCACTTC
1212505 ACTTCTTTGT
Statistics
Matches: 250, Mismatches: 42, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
122 246 0.98
123 4 0.02
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (122 bp):
TCATTGATTTGGTCTACTTCTCTGTATCTCACCAGAAAGATAACCACTTCGTTGTCTGACCCACT
TCTCTGTATCTCATCAAGAAGATAGGGTTTCAAAGTTTTACTCACATGAGTTCTGCT
Found at i:1213015 original size:99 final size:98
Alignment explanation
Indices: 1212831--1213048 Score: 242
Period size: 99 Copynumber: 2.2 Consensus size: 98
1212821 TATAAGGTCT
* * * * * * *
1212831 ACCGTTGCGACCTCAA-CTCTTCCCTTCATATCTTTATGGTACCGGGTTCCCCGTTATGGCCCCA
1 ACCGTTGCAACCTCAATC-CTTCCCATCACATCTTTAAGGTACCGAGTTCACCGTTACGGCCCCA
* *
1212895 ACCTTTCCCATCATATGTTCATGGCAC-CGAATTC
65 ACCTTTCCCATCATATCTTCATGGCACAAG-ATTC
* * *
1212929 ACCGTTGCAACCTCAATCCTTCCCATCACATCTTCTAAGGTATCGAGTTTACCGTTACGGCCTCA
1 ACCGTTGCAACCTCAATCCTTCCCATCACATCTT-TAAGGTACCGAGTTCACCGTTACGGCCCCA
* *
1212994 ACCTTTCCCTTCATATCTTCATGGTACAAGATTC
65 ACCTTTCCCATCATATCTTCATGGCACAAGATTC
* * *
1213028 ATCGTTGTAGCCTCAATCCTT
1 ACCGTTGCAACCTCAATCCTT
1213049 TCCTTCATAT
Statistics
Matches: 100, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
98 29 0.29
99 70 0.70
100 1 0.01
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.33
Consensus pattern (98 bp):
ACCGTTGCAACCTCAATCCTTCCCATCACATCTTTAAGGTACCGAGTTCACCGTTACGGCCCCAA
CCTTTCCCATCATATCTTCATGGCACAAGATTC
Found at i:1213085 original size:148 final size:148
Alignment explanation
Indices: 1212830--1213296 Score: 462
Period size: 148 Copynumber: 3.2 Consensus size: 148
1212820 GTATAAGGTC
* * * ** * ** * * *
1212830 TACCGTTGCGACCTCAA-CTCTTCCCTTCATATCTTTATGGTACCGGGTTCCCCGTTATGGCCCC
1 TACCGTTACGGCCTCAACCT-TTCCCTTCATATCTTCATGGTACAAGATTCATCGTTGTAGCCTC
* * * * * *
1212894 AA-CCTTTCCCATCATATGTTCATGGCACCGAATTCACCGTTGCAACCTCAATCCTTCCCATCAC
65 AATCCTTT-CCTTCATATATTCATGGTACCGGATTCGCCGTTGCAACCTCAATCCTTCCTATCAC
*
1212958 ATCTTCTAAGGTATCGAGTT
129 ATCTTCTAAGGTATCGGGTT
1212978 TACCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACAAGATTCATCGTTGTAGCCTCA
1 TACCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACAAGATTCATCGTTGTAGCCTCA
* *
1213043 ATCCTTTCCTTCATATATTCATGGTACCGGATTCGCCATTGCATCCTCAATCCTTCCTATCACAT
66 ATCCTTTCCTTCATATATTCATGGTACCGGATTCGCCGTTGCAACCTCAATCCTTCCTATCACAT
* *
1213108 CTTTTAAGGTATTGGGTT
131 CTTCTAAGGTATCGGGTT
* ** ** * *
1213126 TACCATTACGGCCTCAACCTTTCCCTTCATATC-TCTATGGTATTAGATTTGTCGTTGCAGCCTT
1 TACCGTTACGGCCTCAACCTTTCCCTTCATATCTTC-ATGGTACAAGATTCATCGTTGTAGCCTC
* * * ** * * * * *
1213190 AATCC-TTCCTATTACATCTTCATGGTATTGGATTTGCTGTTACGACCTCAATCCTTCCTATCAT
65 AATCCTTTCCT-TCATATATTCATGGTACCGGATTCGCCGTTGCAACCTCAATCCTTCCTATCAC
* *
1213254 ATCTTC-ATGGTA-CGGGGT
129 ATCTTCTAAGGTATCGGGTT
1213272 T-CGCTGTTACGGCCTCAACCTTTCC
1 TAC-C-GTTACGGCCTCAACCTTTCC
1213297 ATCACATCTT
Statistics
Matches: 267, Mismatches: 46, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
145 1 0.00
146 6 0.02
147 31 0.12
148 222 0.83
149 7 0.03
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (148 bp):
TACCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACAAGATTCATCGTTGTAGCCTCA
ATCCTTTCCTTCATATATTCATGGTACCGGATTCGCCGTTGCAACCTCAATCCTTCCTATCACAT
CTTCTAAGGTATCGGGTT
Found at i:1213331 original size:98 final size:100
Alignment explanation
Indices: 1213037--1213610 Score: 406
Period size: 99 Copynumber: 5.8 Consensus size: 100
1213027 CATCGTTGTA
* ** *
1213037 GCCTCAATCCTTT-CCTTCATATATTCATGGTACCGGATTCGCCATTGCATCCTCAATCCTTCCT
1 GCCTCAATCCTTTCCCTTCATATCTTCATGGTACCGGATTCGCTGTTGCAGCCTCAATCCTTCCT
1213101 ATCACATCTTTTAAGGTATTGGGTTTACCATTACG
66 ATCACATCTTTTAAGGTATTGGGTTTACCATTACG
*** * *
1213136 GCCTCAA-CCTTTCCCTTCATATC-TCTATGGTATTAGATTTG-TCGTTGCAGCCTTAATCCTTC
1 GCCTCAATCCTTTCCCTTCATATCTTC-ATGGTACCGGATTCGCT-GTTGCAGCCTCAATCCTTC
* * * * * **
1213198 CTATTACATC-TTCATGGTATTGGATTTGCTGTTACG
64 CTATCACATCTTTTAAGGTATTGGGTTTACCATTACG
* * * * *
1213234 ACCTCAATCC-TT-CCTATCATATCTTCATGGTACGGGGTTCGCTGTTACGGCCTCAA-CCTTTC
1 GCCTCAATCCTTTCCCT-TCATATCTTCATGGTACCGGATTCGCTGTTGCAGCCTCAATCC-TTC
*
1213296 C-ATCACATCTTTTAAGGTATCGGGTTTACCATTACG
64 CTATCACATCTTTTAAGGTATTGGGTTTACCATTACG
* * * ** * *
1213332 GCCTCAA-GCTTTCCCTTCATATCTTTAATGGTATCAAATTCGCCGTTGCAGCCTTAATCCTTCC
1 GCCTCAATCCTTTCCCTTCATATC-TTCATGGTACCGGATTCGCTGTTGCAGCCTCAATCCTTCC
* * * ** * **
1213396 CATCATATCTTCTAAGGTATTGGGTTTGTCGTCGCG
65 TATCACATCTTTTAAGGTATTGGGTTTACCATTACG
* * ** * * * *
1213432 ACTTCAA-CCTTTCCCTT--TAT-TTCCATGGTACTAGATTTG-TCGTTGCTGCCTCGATCTTTC
1 GCCTCAATCCTTTCCCTTCATATCTT-CATGGTACCGGATTCGCT-GTTGCAGCCTCAATCCTTC
* ** * ** * * *
1213492 CCATCATGTCTTCTAAGGTACAGGGTTTGCCGTTACA
64 CTATCACATCTTTTAAGGTATTGGGTTTACCATTACG
* * ** * * * *
1213529 GCCTCAA-CATTTCCCTTCATAACTTCATGGTATTGGATTCACCGTTGCGGCCTCAATCCTTCCC
1 GCCTCAATCCTTTCCCTTCATATCTTCATGGTACCGGATTCGCTGTTGCAGCCTCAATCCTTCCT
*
1213593 ATCACATCTTCTAAGGTA
66 ATCACATCTTTTAAGGTA
1213611 CAAGGTTCGC
Statistics
Matches: 368, Mismatches: 87, Indels: 40
0.74 0.18 0.08
Matches are distributed among these distances:
96 2 0.01
97 83 0.23
98 103 0.28
99 135 0.37
100 45 0.12
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (100 bp):
GCCTCAATCCTTTCCCTTCATATCTTCATGGTACCGGATTCGCTGTTGCAGCCTCAATCCTTCCT
ATCACATCTTTTAAGGTATTGGGTTTACCATTACG
Found at i:1213390 original size:197 final size:198
Alignment explanation
Indices: 1213038--1213610 Score: 574
Period size: 196 Copynumber: 2.9 Consensus size: 198
1213028 ATCGTTGTAG
* *
1213038 CCTCAATCCTTTCCTTCATATATTCATGGTACCGGATTCGCCATTGCATCCTCAATCCTTCCTAT
1 CCTCAATCCTTTCCTTCATATATTCATGGTACCGGATTCGCCATTACAGCCTCAATCCTTCCTAT
*
1213103 CACATCTTTTAAGGTATTGGGTTTACCATTACGGCCTCAACCTTTCCCTTCATATCTCTATGGTA
66 CACATCTTTTAAGGTATCGGGTTTACCATTACGGCCTCAACCTTTCCCTTCATATCTCTATGGTA
* * * * * * *
1213168 TTAGATTTGTCGTTGCAGCCTTAATCCTTCCTATTACATCTTC-ATGGTATTGGATTTGCTGTTA
131 TCAAATTCGCCGTTGCAGCCTTAATCCTTCCCATCACATCTTCTAAGGTATTGGATTTGCTGTTA
1213232 CGA
196 CGA
* * * ** *
1213235 CCTCAATCC-TTCCTATCATATCTTCATGGTACGGGGTTCGCTGTTACGGCCTCAA-CCTTTCC-
1 CCTCAATCCTTTCCT-TCATATATTCATGGTACCGGATTCGCCATTACAGCCTCAATCC-TTCCT
* *
1213297 ATCACATCTTTTAAGGTATCGGGTTTACCATTACGGCCTCAAGCTTTCCCTTCATATCTTTAATG
64 ATCACATCTTTTAAGGTATCGGGTTTACCATTACGGCCTCAACCTTTCCCTTCATATCTCT-ATG
* *
1213362 GTATCAAATTCGCCGTTGCAGCCTTAATCCTTCCCATCATATCTTCTAAGGTATTGGGTTTG-TC
128 GTATCAAATTCGCCGTTGCAGCCTTAATCCTTCCCATCACATCTTCTAAGGTATTGGATTTGCT-
**
1213426 GTCGCGA
192 GTTACGA
* ** * * * * * * * *
1213433 CTTCAA-CCTTTCCCTT--TAT-TTCCATGGTACTAGATTTGTCGTTGCTGCCTCGATCTTTCCC
1 CCTCAATCCTTT-CCTTCATATATT-CATGGTACCGGATTCGCCATTACAGCCTCAATCCTTCCT
** * * * * * *
1213494 ATCATGTCTTCTAAGGTA-CAGGGTTTGCCGTTACAGCCTCAACATTTCCCTTCATAACT-TCAT
64 ATCACATCTTTTAAGGTATC-GGGTTTACCATTACGGCCTCAACCTTTCCCTTCATATCTCT-AT
*** * * *
1213557 GGTATTGGATTCACCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTA
127 GGTATCAAATTCGCCGTTGCAGCCTTAATCCTTCCCATCACATCTTCTAAGGTA
1213611 CAAGGTTCGC
Statistics
Matches: 315, Mismatches: 50, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
195 2 0.01
196 145 0.46
197 139 0.44
198 26 0.08
199 3 0.01
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (198 bp):
CCTCAATCCTTTCCTTCATATATTCATGGTACCGGATTCGCCATTACAGCCTCAATCCTTCCTAT
CACATCTTTTAAGGTATCGGGTTTACCATTACGGCCTCAACCTTTCCCTTCATATCTCTATGGTA
TCAAATTCGCCGTTGCAGCCTTAATCCTTCCCATCACATCTTCTAAGGTATTGGATTTGCTGTTA
CGA
Found at i:1213536 original size:97 final size:96
Alignment explanation
Indices: 1213281--1213664 Score: 294
Period size: 99 Copynumber: 3.9 Consensus size: 96
1213271 TTCGCTGTTA
* * * * * *
1213281 CGGCCTCAA-CCTTTCCATCACATCTTTTAAGGTATC-GGGTTTACCATTACGGCCTCAAGC-TT
1 CGGCCTCAATCCTTCCCATCATATCTTCTAAGGTA-CAGGGTTTGCCGTTGC-GCCTCAA-CATT
** * *
1213343 TCCCTTCATATCTTTAATGGTA-TCAAATTCGCCGTTG
63 TCCCTT--TAT-TTCCATGGTACT-AGATTCACCGTTG
* * ** * * * *
1213380 CAGCCTTAATCCTTCCCATCATATCTTCTAAGGTATTGGGTTTGTCGTCGCGACTTCAACCTTTC
1 CGGCCTCAATCCTTCCCATCATATCTTCTAAGGTACAGGGTTTGCCGTTGCG-CCTCAACATTTC
***
1213445 CCTTTATTTCCATGGTACTAGATTTGTCGTTG
65 CCTTTATTTCCATGGTACTAGATTCACCGTTG
* * * * *
1213477 CTGCCTCGATCTTTCCCATCATGTCTTCTAAGGTACAGGGTTTGCCGTTACAGCCTCAACATTTC
1 CGGCCTCAATCCTTCCCATCATATCTTCTAAGGTACAGGGTTTGCCGTTGC-GCCTCAACATTTC
* * *
1213542 CCTTCATAACTT-CATGGTATTGGATTCACCGTTG
65 CCTT--T-ATTTCCATGGTACTAGATTCACCGTTG
* * * * * *
1213576 CGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTCGCCATTGTGGCCTTAACATTT-
1 CGGCCTCAATCCTTCCCATCATATCTTCTAAGGTACAGGGTTTGCCGTTG-CGCCTCAACATTTC
1213640 CCTTTATTTCCATGGTACTAGATTC
65 CCTTTATTTCCATGGTACTAGATTC
1213665 GTTGTTGTGG
Statistics
Matches: 225, Mismatches: 49, Indels: 25
0.75 0.16 0.08
Matches are distributed among these distances:
95 3 0.01
96 14 0.06
97 73 0.32
98 9 0.04
99 79 0.35
100 47 0.21
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (96 bp):
CGGCCTCAATCCTTCCCATCATATCTTCTAAGGTACAGGGTTTGCCGTTGCGCCTCAACATTTCC
CTTTATTTCCATGGTACTAGATTCACCGTTG
Found at i:1213592 original size:49 final size:49
Alignment explanation
Indices: 1212832--1213603 Score: 291
Period size: 49 Copynumber: 15.7 Consensus size: 49
1212822 ATAAGGTCTA
* * * * **
1212832 CCGTTGCGACCTCAA-CTCTTCCCTTCATATCTTTATGGTACCGGGTTCC
1 CCGTTGCGGCCTCAATC-CTTCCCTTCATATCTTCATGGTACTGGATTTG
** * * * * * * **
1212881 CCGTTATGGCCCCAA-CCTTTCCCATCATATGTTCATGGCACCGAATTCA
1 CCGTTGCGGCCTCAATCC-TTCCCTTCATATCTTCATGGTACTGGATTTG
** * * * * *
1212930 CCGTTGCAACCTCAATCCTTCCCATCACATCTTCTAAGGTA-TCGAGTTTA
1 CCGTTGCGGCCTCAATCCTTCCCTTCATATCTTC-ATGGTACTGGA-TTTG
* ** **
1212980 CCGTTACGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACAAGATTCA
1 CCGTTGCGGCCTCAATCC-TTCCCTTCATATCTTCATGGTACTGGATTTG
* ** * * * *
1213029 TCGTTGTAGCCTCAATCCTTTCCTTCATATATTCATGGTACCGGATTCG
1 CCGTTGCGGCCTCAATCCTTCCCTTCATATCTTCATGGTACTGGATTTG
* ** * * * * * *
1213078 CCATTGCATCCTCAATCCTT-CCTATCACATCTTTTAAGGTATTGGGTTTA
1 CCGTTGCGGCCTCAATCCTTCCCT-TCATATC-TTCATGGTACTGGATTTG
* * * *
1213128 CCATTACGGCCTCAA-CCTTTCCCTTCATATC-TCTATGGTATTAGATTTG
1 CCGTTGCGGCCTCAATCC-TTCCCTTCATATCTTC-ATGGTACTGGATTTG
* * * * * *
1213177 TCGTTGCAGCCTTAATCCTT-CCTATTACATCTTCATGGTATTGGATTTG
1 CCGTTGCGGCCTCAATCCTTCCCT-TCATATCTTCATGGTACTGGATTTG
* * * * * *
1213226 CTGTTACGACCTCAATCCTT-CCTATCATATCTTCATGGTACGGGGTTCG
1 CCGTTGCGGCCTCAATCCTTCCCT-TCATATCTTCATGGTACTGGATTTG
* * * * * * * * *
1213275 CTGTTACGGCCTCAA-CCTTTCCATCACATCTTTTAAGGTA-TCGGGTTTA
1 CCGTTGCGGCCTCAATCCTTCCCTTCATATC-TTCATGGTACT-GGATTTG
* * * * * ** *
1213324 CCATTACGGCCTCAAGCTTTCCCTTCATATCTTTAATGGTA-TCAAATTCG
1 CCGTTGCGGCCTCAATCCTTCCCTTCATATC-TTCATGGTACT-GGATTTG
* * * * * *
1213374 CCGTTGCAGCCTTAATCCTTCCCATCATATCTTCTAAGGTATTGGGTTTG
1 CCGTTGCGGCCTCAATCCTTCCCTTCATATCTTC-ATGGTACTGGATTTG
* * * * *
1213424 TCGTCGCGACTTCAA-CCTTTCCCTT--TAT-TTCCATGGTACTAGATTTG
1 CCGTTGCGGCCTCAATCC-TTCCCTTCATATCTT-CATGGTACTGGATTTG
* * * * * * * * *
1213471 TCGTTGCTGCCTCGATCTTTCCCATCATGTCTTCTAAGGTACAGGGTTTG
1 CCGTTGCGGCCTCAATCCTTCCCTTCATATCTTC-ATGGTACTGGATTTG
* * * * * **
1213521 CCGTTACAGCCTCAA-CATTTCCCTTCATAACTTCATGGTATTGGATTCA
1 CCGTTGCGGCCTCAATC-CTTCCCTTCATATCTTCATGGTACTGGATTTG
* *
1213570 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTC
1 CCGTTGCGGCCTCAATCCTTCCCTTCATATCTTC
1213604 TAAGGTACAA
Statistics
Matches: 533, Mismatches: 160, Indels: 60
0.71 0.21 0.08
Matches are distributed among these distances:
47 29 0.05
48 23 0.04
49 294 0.55
50 183 0.34
51 4 0.01
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.36
Consensus pattern (49 bp):
CCGTTGCGGCCTCAATCCTTCCCTTCATATCTTCATGGTACTGGATTTG
Found at i:1225747 original size:56 final size:56
Alignment explanation
Indices: 1225661--1225793 Score: 239
Period size: 56 Copynumber: 2.4 Consensus size: 56
1225651 CAATTTATCC
* **
1225661 TTGATAAGTAAATGTGTTATGGCACATTACTTATGAACGATTGACTAAACTAATCT
1 TTGATAAGTAAATGTGTTATGACACATTACTTATGAACGACCGACTAAACTAATCT
1225717 TTGATAAGTAAATGTGTTATGACACATTACTTATGAACGACCGACTAAACTAATCT
1 TTGATAAGTAAATGTGTTATGACACATTACTTATGAACGACCGACTAAACTAATCT
1225773 TTGATAAGTAAATGTGTTATG
1 TTGATAAGTAAATGTGTTATG
1225794 GTACAAACAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (56 bp):
TTGATAAGTAAATGTGTTATGACACATTACTTATGAACGACCGACTAAACTAATCT
Found at i:1228868 original size:17 final size:17
Alignment explanation
Indices: 1228848--1228880 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1228838 GAAGGTATGG
*
1228848 AATCTTAGAGGATTTGT
1 AATCTTAGAAGATTTGT
1228865 AATCTTAGAAGATTTG
1 AATCTTAGAAGATTTG
1228881 ATTATGTAAA
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:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (17 bp):
AATCTTAGAAGATTTGT
Found at i:1228888 original size:23 final size:22
Alignment explanation
Indices: 1228858--1228907 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1228848 AATCTTAGAG
*
1228858 GATTTGT-AATCTTAGAAGATTT
1 GATTTGTAAATCTAAG-AGATTT
*
1228880 GATTATGTAAATCTAAGATATTT
1 GATT-TGTAAATCTAAGAGATTT
1228903 GATTT
1 GATTT
1228908 TTTAGATTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 5 0.21
23 12 0.50
24 7 0.29
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (22 bp):
GATTTGTAAATCTAAGAGATTT
Found at i:1233280 original size:83 final size:82
Alignment explanation
Indices: 1233122--1233372 Score: 263
Period size: 83 Copynumber: 3.0 Consensus size: 82
1233112 ACAACAAAGT
* * * * *
1233122 AATCATACTCGCACGTAAGTGCATCATCAAATGTATCGGAAAAAAA-ATACTAGCATGTAAGTGC
1 AATCATACTGGCACGTAAGTGCATCATC-GATGTA-C-CAAAAAAATATAATAGCACGTAAGTGC
*
1233186 ATCATCGGATATACTGAAGC
63 ATCATCAGATATACTGAAGC
* *
1233206 AATCATACTGGCACATAAGTGCATCATCGACTGTACTAAAAAAATATAATAGCACGTAAGTGCAT
1 AATCATACTGGCACGTAAGTGCATCATCGA-TGTACCAAAAAAATATAATAGCACGTAAGTGCAT
*
1233271 CATCAGATATAC-CAACGC
65 CATCAGATATACTGAA-GC
* * * * * *
1233289 AATCATACTGGCACGTAACTGCATCATTAGATGCACCAAAGAAAATATATTTGGCACGTAATTGC
1 AATCATACTGGCACGTAAGTGCATCA-TCGATGTACCAAA-AAAATATA-ATAGCACGTAAGTGC
* *
1233354 ATCATCAGCTAAACTGAAG
63 ATCATCAGATATACTGAAG
1233373 TATATACTTG
Statistics
Matches: 141, Mismatches: 19, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
82 9 0.06
83 64 0.45
84 41 0.29
85 25 0.18
86 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (82 bp):
AATCATACTGGCACGTAAGTGCATCATCGATGTACCAAAAAAATATAATAGCACGTAAGTGCATC
ATCAGATATACTGAAGC
Found at i:1233312 original size:42 final size:41
Alignment explanation
Indices: 1233116--1233361 Score: 172
Period size: 42 Copynumber: 5.9 Consensus size: 41
1233106 TCGGTTACAA
* * * *
1233116 CAAAGTAATCATACTCGCACGTAAGTGCATCATCAAATGTATC
1 CAAAGAAAT-ATACTGGCACGTAAGTGCATCATCAGATATA-C
* * * * *
1233159 GGAAA-AAAAATACTAGCATGTAAGTGCATCATCGGATATAC
1 -CAAAGAAATATACTGGCACGTAAGTGCATCATCAGATATAC
** * * *
1233200 TGAAGCAATCATACTGGCACATAAGTGCATCATC-GACTGTAC
1 CAAAGAAAT-ATACTGGCACGTAAGTGCATCATCAGA-TATAC
* * * *
1233242 TAAAAAAATATAATAGCACGTAAGTGCATCATCAGATATAC
1 CAAAGAAATATACTGGCACGTAAGTGCATCATCAGATATAC
* * * * **
1233283 CAACGCAATCATACTGGCACGTAACTGCATCATTAGATGCAC
1 CAAAGAAAT-ATACTGGCACGTAAGTGCATCATCAGATATAC
* *
1233325 CAAAGAAAATATATTTGGCACGTAATTGCATCATCAG
1 CAAAG-AAATATA-CTGGCACGTAAGTGCATCATCAG
1233362 CTAAACTGAA
Statistics
Matches: 157, Mismatches: 38, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
40 2 0.01
41 35 0.22
42 92 0.59
43 25 0.16
44 3 0.02
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (41 bp):
CAAAGAAATATACTGGCACGTAAGTGCATCATCAGATATAC
Found at i:1238525 original size:37 final size:37
Alignment explanation
Indices: 1238470--1238549 Score: 142
Period size: 37 Copynumber: 2.1 Consensus size: 37
1238460 TAAATGAGAG
*
1238470 AGCACATAGTTAGAAAATAAATGAAACCACTCATTAGA
1 AGCA-ATAGTGAGAAAATAAATGAAACCACTCATTAGA
1238508 AGCAATAGTGAGAAAATAAATGAAACCACTCATTAGA
1 AGCAATAGTGAGAAAATAAATGAAACCACTCATTAGA
1238545 AGCAA
1 AGCAA
1238550 CCCTCTATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 37 0.90
38 4 0.10
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (37 bp):
AGCAATAGTGAGAAAATAAATGAAACCACTCATTAGA
Found at i:1246110 original size:17 final size:17
Alignment explanation
Indices: 1246081--1246114 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1246071 GTAATTTTAC
1246081 TTTTATAAATTTAAAAA
1 TTTTATAAATTTAAAAA
1246098 TTTTA-AAATTTTAAAAA
1 TTTTATAAA-TTTAAAAA
1246115 ATCAAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTATAAATTTAAAAA
Found at i:1249193 original size:18 final size:18
Alignment explanation
Indices: 1249172--1249206 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1249162 AATGATATAT
*
1249172 TAATTAATAATAATATTA
1 TAATAAATAATAATATTA
1249190 TAATAAATAATAATATT
1 TAATAAATAATAATATT
1249207 TTATTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATAATAATATTA
Found at i:1250280 original size:18 final size:18
Alignment explanation
Indices: 1250244--1250281 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1250234 GGTATTGGAC
*
1250244 AAAAATGAGAATGATGTG
1 AAAAATGAGAATGAAGTG
1250262 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAA-TGAAGTG
1250280 AA
1 AA
1250282 TTTTGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (18 bp):
AAAAATGAGAATGAAGTG
Found at i:1256388 original size:18 final size:18
Alignment explanation
Indices: 1256362--1256396 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1256352 AATGATATAT
* *
1256362 TAATTAATAATATTATTA
1 TAATAAATAATAATATTA
1256380 TAATAAATAATAATATT
1 TAATAAATAATAATATT
1256397 TTATTATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATAAATAATAATATTA
Found at i:1256742 original size:22 final size:22
Alignment explanation
Indices: 1256714--1256765 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1256704 ATAGAAAATG
1256714 ATTAGAAGATGAATTCTAGCTT
1 ATTAGAAGATGAATTCTAGCTT
1256736 ATTAGAAGATGAATTCTAGCTT
1 ATTAGAAGATGAATTCTAGCTT
1256758 ATTAGAAG
1 ATTAGAAG
1256766 TGTGGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (22 bp):
ATTAGAAGATGAATTCTAGCTT
Found at i:1257479 original size:18 final size:18
Alignment explanation
Indices: 1257443--1257480 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1257433 GATATGGGAC
*
1257443 AAAAATGAGAATGATGTG
1 AAAAATGAGAATGAAGTG
1257461 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAA-TGAAGTG
1257479 AA
1 AA
1257481 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (18 bp):
AAAAATGAGAATGAAGTG
Found at i:1259626 original size:20 final size:20
Alignment explanation
Indices: 1259594--1259631 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1259584 TACTCACTAT
*
1259594 GTTAAAAAGTAAATAAATTG
1 GTTAAAAAGTAAACAAATTG
1259614 GTTAGAAAA-TAAACAAAT
1 GTTA-AAAAGTAAACAAAT
1259632 GAAAAGGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
GTTAAAAAGTAAACAAATTG
Found at i:1264637 original size:41 final size:41
Alignment explanation
Indices: 1264585--1264703 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 41
1264575 GAAAACGCCG
*
1264585 CTATTGTTTAACCTTTAGCGGCGTTTTCCTCATAAACACCA
1 CTATTGCTTAACCTTTAGCGGCGTTTTCCTCATAAACACCA
* * * *
1264626 CTATTGCTTAACCTTTAGCGGTGTTTTTCTCATAAACGCCT
1 CTATTGCTTAACCTTTAGCGGCGTTTTCCTCATAAACACCA
* *
1264667 CTAATGCTCTTTACCTATT-GCGGCGTTTTCC-CATAAA
1 CTATTG--CTTAACCT-TTAGCGGCGTTTTCCTCATAAA
1264704 TATCGCTCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
41 41 0.62
42 6 0.09
43 17 0.26
44 2 0.03
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (41 bp):
CTATTGCTTAACCTTTAGCGGCGTTTTCCTCATAAACACCA
Found at i:1265545 original size:12 final size:12
Alignment explanation
Indices: 1265528--1265601 Score: 80
Period size: 12 Copynumber: 6.3 Consensus size: 12
1265518 ATAACATCCA
1265528 AACAACCAAAAT
1 AACAACCAAAAT
*
1265540 AACAACCAAAAC
1 AACAACCAAAAT
* *
1265552 AGCAACAAAAAT
1 AACAACCAAAAT
* *
1265564 AAC-AGCAAAAC
1 AACAACCAAAAT
*
1265575 AACAACAAAAAT
1 AACAACCAAAAT
1265587 AACAA-CAAAAT
1 AACAACCAAAAT
1265598 AACA
1 AACA
1265602 GGAAAAATAG
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
11 17 0.35
12 32 0.65
ACGTcount: A:0.69, C:0.23, G:0.03, T:0.05
Consensus pattern (12 bp):
AACAACCAAAAT
Found at i:1265572 original size:23 final size:23
Alignment explanation
Indices: 1265528--1265619 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
1265518 ATAACATCCA
*
1265528 AACAACCAAAATAACAACCAAAAC
1 AACAACAAAAATAACAA-CAAAAC
* *
1265552 AGCAACAAAAATAACAGCAAAAC
1 AACAACAAAAATAACAACAAAAC
*
1265575 AACAACAAAAATAACAACAAAAT
1 AACAACAAAAATAACAACAAAAC
**
1265598 AACAGGAAAAATAGA-AACAAAA
1 AACAACAAAAATA-ACAACAAAA
1265620 AAAATATCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
23 44 0.75
24 15 0.25
ACGTcount: A:0.70, C:0.20, G:0.05, T:0.05
Consensus pattern (23 bp):
AACAACAAAAATAACAACAAAAC
Found at i:1265579 original size:20 final size:20
Alignment explanation
Indices: 1265514--1265579 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
1265504 AAAAAGGCAT
1265514 AAAAATAACATCC-AAACAAC
1 AAAAATAACA-CCAAAACAAC
*
1265534 CAAAATAACAACCAAAACAGCAAC
1 AAAAATAAC-ACC-AAA-A-CAAC
*
1265558 AAAAATAACAGCAAAACAAC
1 AAAAATAACACCAAAACAAC
1265578 AA
1 AA
1265580 CAAAAATAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
20 16 0.42
21 2 0.05
22 5 0.13
23 3 0.08
24 12 0.32
ACGTcount: A:0.67, C:0.24, G:0.03, T:0.06
Consensus pattern (20 bp):
AAAAATAACACCAAAACAAC
Found at i:1265607 original size:11 final size:11
Alignment explanation
Indices: 1265559--1265607 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
1265549 AACAGCAACA
1265559 AAAATAACAGC
1 AAAATAACAGC
* *
1265570 AAAACAACAAC
1 AAAATAACAGC
*
1265581 AAAAATAACAAC
1 -AAAATAACAGC
*
1265593 AAAATAACAGG
1 AAAATAACAGC
1265604 AAAA
1 AAAA
1265608 ATAGAAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.71, C:0.16, G:0.06, T:0.06
Consensus pattern (11 bp):
AAAATAACAGC
Found at i:1265674 original size:18 final size:18
Alignment explanation
Indices: 1265651--1265744 Score: 102
Period size: 18 Copynumber: 5.1 Consensus size: 18
1265641 AAAAAACAGC
*
1265651 AACCAAAATAGTAAAAAA
1 AACCAAAACAGTAAAAAA
*
1265669 AACCAAAACAG--CAAAA
1 AACCAAAACAGTAAAAAA
*
1265685 AACTAAAACAGTAAAAAA
1 AACCAAAACAGTAAAAAA
1265703 ATACCAAAACAGTAAAAAAAA
1 A-ACCAAAACAGT--AAAAAA
*
1265724 CAACCAAAACAATAAAAAA
1 -AACCAAAACAGTAAAAAA
1265743 AA
1 AA
1265745 GAGCACCAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
16 14 0.22
18 17 0.27
19 16 0.25
21 16 0.25
22 1 0.02
ACGTcount: A:0.72, C:0.16, G:0.04, T:0.07
Consensus pattern (18 bp):
AACCAAAACAGTAAAAAA
Found at i:1265686 original size:16 final size:16
Alignment explanation
Indices: 1265664--1265722 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
1265654 CAAAATAGTA
1265664 AAAAAAACCAAAACAG
1 AAAAAAACCAAAACAG
* *
1265680 CAAAAAACTAAAACAG
1 AAAAAAACCAAAACAG
1265696 TAAAAAAATACCAAAACAG
1 --AAAAAA-ACCAAAACAG
1265715 TAAAAAAA
1 -AAAAAAA
1265723 ACAACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 14 0.40
17 1 0.03
18 11 0.31
19 9 0.26
ACGTcount: A:0.73, C:0.15, G:0.05, T:0.07
Consensus pattern (16 bp):
AAAAAAACCAAAACAG
Found at i:1265703 original size:19 final size:19
Alignment explanation
Indices: 1265651--1265744 Score: 97
Period size: 19 Copynumber: 5.1 Consensus size: 19
1265641 AAAAAACAGC
*
1265651 AACCAAAATAGT-AAAAAA
1 AACCAAAACAGTAAAAAAA
*
1265669 AACCAAAACAG---CAAAA
1 AACCAAAACAGTAAAAAAA
*
1265685 AACTAAAACAGTAAAAAAA
1 AACCAAAACAGTAAAAAAA
*
1265704 TACCAAAACAGTAAAAAAAA
1 AACCAAAACAGT-AAAAAAA
*
1265724 CAACCAAAACAATAAAAAAA
1 -AACCAAAACAGTAAAAAAA
1265744 A
1 A
1265745 GAGCACCAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
16 14 0.22
18 10 0.16
19 15 0.24
20 14 0.22
21 10 0.16
ACGTcount: A:0.72, C:0.16, G:0.04, T:0.07
Consensus pattern (19 bp):
AACCAAAACAGTAAAAAAA
Found at i:1265709 original size:35 final size:34
Alignment explanation
Indices: 1265655--1265721 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
1265645 AACAGCAACC
*
1265655 AAAATAGTAAAAAAAACCAAAACAGCAAAAAACT
1 AAAACAGTAAAAAAAACCAAAACAGCAAAAAACT
*
1265689 AAAACAGTAAAAAAATACCAAAACAGTAAAAAA
1 AAAACAGTAAAAAAA-ACCAAAACAGCAAAAAA
1265722 AACAACCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 14 0.47
35 16 0.53
ACGTcount: A:0.72, C:0.13, G:0.06, T:0.09
Consensus pattern (34 bp):
AAAACAGTAAAAAAAACCAAAACAGCAAAAAACT
Found at i:1265723 original size:21 final size:20
Alignment explanation
Indices: 1265681--1265744 Score: 85
Period size: 21 Copynumber: 3.2 Consensus size: 20
1265671 CCAAAACAGC
*
1265681 AAAAAACTAAAACAGT-AAA
1 AAAAAACCAAAACAGTAAAA
*
1265700 AAAATACCAAAACAGTAAAA
1 AAAAAACCAAAACAGTAAAA
*
1265720 AAAACAACCAAAACAATAAAA
1 AAAA-AACCAAAACAGTAAAA
1265741 AAAA
1 AAAA
1265745 GAGCACCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.36
20 7 0.18
21 18 0.46
ACGTcount: A:0.75, C:0.14, G:0.03, T:0.08
Consensus pattern (20 bp):
AAAAAACCAAAACAGTAAAA
Found at i:1265742 original size:23 final size:23
Alignment explanation
Indices: 1265697--1265761 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 23
1265687 CTAAAACAGT
* *
1265697 AAAAA-AATACCAAAACAGTAAA
1 AAAAAGAACACCAAAACAATAAA
*
1265719 AAAAA-CA-ACCAAAACAATAAA
1 AAAAAGAACACCAAAACAATAAA
* *
1265740 AAAAAGAGCACCAAAATAATAA
1 AAAAAGAACACCAAAACAATAA
1265762 TATAATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.50
22 6 0.17
23 12 0.33
ACGTcount: A:0.72, C:0.15, G:0.05, T:0.08
Consensus pattern (23 bp):
AAAAAGAACACCAAAACAATAAA
Found at i:1266520 original size:20 final size:20
Alignment explanation
Indices: 1266481--1266520 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1266471 CCGCTAAATG
* *
1266481 TCAGAGTATTAGCGGCGTTT
1 TCAGAGCATTAGCGGAGTTT
*
1266501 TCAGAGCATTAGTGGAGTTT
1 TCAGAGCATTAGCGGAGTTT
1266521 ATAGGAAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (20 bp):
TCAGAGCATTAGCGGAGTTT
Found at i:1266563 original size:41 final size:41
Alignment explanation
Indices: 1266505--1266585 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
1266495 GCGTTTTCAG
*
1266505 AGCATTAGTGGAGTTTATAGG-AAAACGCCGTTAAAGGTCAA
1 AGCATTAGCGGAGTTTAT-GGAAAAACGCCGTTAAAGGTCAA
* *
1266546 AGCATTAGCGGTA-TTTATGGAAAAATGCTGTTAAAGGTCA
1 AGCATTAGCGG-AGTTTATGGAAAAACGCCGTTAAAGGTCA
1266586 GAACAAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 2 0.06
41 32 0.91
42 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (41 bp):
AGCATTAGCGGAGTTTATGGAAAAACGCCGTTAAAGGTCAA
Found at i:1267285 original size:22 final size:22
Alignment explanation
Indices: 1267259--1267305 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1267249 AAAATATTAC
*
1267259 ATTACATTACAAGTTAAAATGT
1 ATTACATTACAAGTTAAAATAT
1267281 ATTACATTACAAGTTAAAATAT
1 ATTACATTACAAGTTAAAATAT
1267303 ATT
1 ATT
1267306 TCAATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (22 bp):
ATTACATTACAAGTTAAAATAT
Found at i:1267718 original size:47 final size:48
Alignment explanation
Indices: 1267653--1267752 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
1267643 TCTCATCTCT
1267653 CAAATTTATCTGAACCTT-AATTCCTAATTTCTCCTCTCTCAAAACCC
1 CAAATTTATCTGAACCTTAAATTCCTAATTTCTCCTCTCTCAAAACCC
* * * *
1267700 CAAATTTGTCT-AATCCTTAAATTCTTAATTTCTCCTCTCTCAAAGCCT
1 CAAATTTATCTGAA-CCTTAAATTCCTAATTTCTCCTCTCTCAAAACCC
1267748 CAAAT
1 CAAAT
1267753 CCCTCGTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
46 2 0.04
47 14 0.30
48 31 0.66
ACGTcount: A:0.30, C:0.29, G:0.03, T:0.38
Consensus pattern (48 bp):
CAAATTTATCTGAACCTTAAATTCCTAATTTCTCCTCTCTCAAAACCC
Found at i:1268019 original size:14 final size:14
Alignment explanation
Indices: 1268000--1268027 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1267990 TTTGTATTCT
1268000 GTTTACTGGTATGG
1 GTTTACTGGTATGG
1268014 GTTTACTGGTATGG
1 GTTTACTGGTATGG
1268028 TTGGTGTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.36, T:0.43
Consensus pattern (14 bp):
GTTTACTGGTATGG
Found at i:1271557 original size:28 final size:28
Alignment explanation
Indices: 1271495--1271549 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1271485 ATGTTGAAAG
1271495 AATAATTTATTATAAATTAATAATATAC
1 AATAATTTATTATAAATTAATAATATAC
1271523 AATAATTTATTATAAATTAATAATATA
1 AATAATTTATTATAAATTAATAATATA
1271550 TTCAAATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
AATAATTTATTATAAATTAATAATATAC
Found at i:1273331 original size:43 final size:43
Alignment explanation
Indices: 1273284--1273432 Score: 208
Period size: 43 Copynumber: 3.5 Consensus size: 43
1273274 AAAGCACCGC
* * *
1273284 TAAAGACCATGTTTTTTAGCGGCATTTGTGAGGAAAGCGTCGT
1 TAAAGACCATGTTCTTTAGCGGCGTTTGTGAGGAAAGCGTCAT
* *
1273327 TAAAGACCATGTTCTTTAGTGGCGTTTTTGAGGAAAGCGTCAT
1 TAAAGACCATGTTCTTTAGCGGCGTTTGTGAGGAAAGCGTCAT
* * * * *
1273370 TAAAGACCATGTTCTTTAGCAGCGTTTGTGTGAAAAGCGCCAC
1 TAAAGACCATGTTCTTTAGCGGCGTTTGTGAGGAAAGCGTCAT
1273413 TAAAGACCATGTTCTTTAGC
1 TAAAGACCATGTTCTTTAGC
1273433 AACCATGCTC
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (43 bp):
TAAAGACCATGTTCTTTAGCGGCGTTTGTGAGGAAAGCGTCAT
Found at i:1273364 original size:86 final size:86
Alignment explanation
Indices: 1273257--1273431 Score: 208
Period size: 86 Copynumber: 2.0 Consensus size: 86
1273247 ACATTATCTG
* * * * *
1273257 TAGTGGTGTTTGTGGGAAAAGCACCGCTAAAGACCATGTTTTTTAGCGGCATTTGTGAGGAAAGC
1 TAGTGGCGTTTGTGGGAAAAGCACCACTAAAGACCATGTTCTTTAGCAGCATTTGTGAGAAAAGC
* **
1273322 GTCGTTAAAGACCATGTTCTT
66 GCCACTAAAGACCATGTTCTT
* ** * * *
1273343 TAGTGGCGTTTTTGAGG-AAAGCGTCATTAAAGACCATGTTCTTTAGCAGCGTTTGTGTGAAAAG
1 TAGTGGCGTTTGTG-GGAAAAGCACCACTAAAGACCATGTTCTTTAGCAGCATTTGTGAGAAAAG
1273407 CGCCACTAAAGACCATGTTCTT
65 CGCCACTAAAGACCATGTTCTT
1273429 TAG
1 TAG
1273432 CAACCATGCT
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
86 72 0.97
87 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (86 bp):
TAGTGGCGTTTGTGGGAAAAGCACCACTAAAGACCATGTTCTTTAGCAGCATTTGTGAGAAAAGC
GCCACTAAAGACCATGTTCTT
Found at i:1273433 original size:43 final size:43
Alignment explanation
Indices: 1273264--1273433 Score: 187
Period size: 43 Copynumber: 4.0 Consensus size: 43
1273254 CTGTAGTGGT
* * * * *
1273264 GTTTGTGGGAAAAGCACCGCTAAAGACCATGTTTTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTTTAGCAGC
* * * ** **
1273307 ATTTGTGAGGAAAGCGTCGTTAAAGACCATGTTCTTTAGTGGC
1 GTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTTTAGCAGC
* * * *
1273350 GTTTTTGAGGAAAGCGTCATTAAAGACCATGTTCTTTAGCAGC
1 GTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTTTAGCAGC
*
1273393 GTTTGTGTGAAAAGCGCCACTAAAGACCATGTTCTTTAGCA
1 GTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTTTAGCA
1273434 ACCATGCTCT
Statistics
Matches: 109, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 109 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (43 bp):
GTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTTTAGCAGC
Found at i:1274283 original size:42 final size:40
Alignment explanation
Indices: 1274236--1274460 Score: 209
Period size: 42 Copynumber: 5.5 Consensus size: 40
1274226 CTCTTACGCT
* *
1274236 CTTTACCTTTTGTGGTGTTTTCCCATAAACGCCACTATTG
1 CTTTACCTTTTGCGGCGTTTTCCCATAAACGCCACTATTG
*** * *
1274276 CTTTTTACCTTTTGCGGCGTTTATGGGA-AAGCGTCACTATTG
1 C--TTTACCTTTTGCGGCGTTT-TCCCATAAACGCCACTATTG
* * * * * *
1274318 CTCTACTTTTTACGGTGTTTTACCATAAACGCCGCTATTG
1 CTTTACCTTTTGCGGCGTTTTCCCATAAACGCCACTATTG
* * * *
1274358 CTCTTTACCTTTTGTGGCGTTTTTCCATAAATGCCACCATTG
1 --CTTTACCTTTTGCGGCGTTTTCCCATAAACGCCACTATTG
* *
1274400 CTTTACCTTTTGCGGCGTTTTTCCCATAAAAGCCGCTATTG
1 CTTTACCTTTTGCGGCG-TTTTCCCATAAACGCCACTATTG
*
1274441 CTTTACCTTTTGCGGTGTTT
1 CTTTACCTTTTGCGGCGTTT
1274461 ATGGGAAAGC
Statistics
Matches: 146, Mismatches: 32, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
39 2 0.01
40 46 0.32
41 35 0.24
42 61 0.42
43 2 0.01
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.42
Consensus pattern (40 bp):
CTTTACCTTTTGCGGCGTTTTCCCATAAACGCCACTATTG
Found at i:1274361 original size:40 final size:40
Alignment explanation
Indices: 1274312--1274460 Score: 154
Period size: 41 Copynumber: 3.6 Consensus size: 40
1274302 GAAAGCGTCA
* * * *
1274312 CTATTGCTCTACTTTTTACGGTGTTTTACCATAAACGCCG
1 CTATTGCTCTACCTTTTGCGGCGTTTTACCATAAAAGCCG
* * * *
1274352 CTATTGCTCTTTACCTTTTGTGGCGTTTTTCCATAAATGCCA
1 CTATTGCTC--TACCTTTTGCGGCGTTTTACCATAAAAGCCG
* * *
1274394 CCATTGCTTTACCTTTTGCGGCGTTTTTCCCATAAAAGCCG
1 CTATTGCTCTACCTTTTGCGGCG-TTTTACCATAAAAGCCG
* *
1274435 CTATTGCTTTACCTTTTGCGGTGTTT
1 CTATTGCTCTACCTTTTGCGGCGTTT
1274461 ATGGGAAAGC
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
40 25 0.27
41 35 0.38
42 31 0.34
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.43
Consensus pattern (40 bp):
CTATTGCTCTACCTTTTGCGGCGTTTTACCATAAAAGCCG
Found at i:1274400 original size:82 final size:81
Alignment explanation
Indices: 1274239--1274462 Score: 238
Period size: 82 Copynumber: 2.8 Consensus size: 81
1274229 TTACGCTCTT
** * * **
1274239 TACCTTTTGTGGTGTTTTCCCATAAACGCCACTATTGCTTTTTACCTTTTGCGGCGTTTATGGGA
1 TACCTTTTACGGTGTTTTCCCATAAACGCCGCTATTGCTCTTTACCTTTTGCGGCGTTTATCAGA
*
1274304 AAGCGTCACTATTGCTC
66 AAGCG-CACCATTGCTC
* * * * *
1274321 TACTTTTTACGGTGTTTTACCATAAACGCCGCTATTGCTCTTTACCTTTTGTGGCGTTTTTCCAT
1 TACCTTTTACGGTGTTTTCCCATAAACGCCGCTATTGCTCTTTACCTTTTGCGGCGTTTAT-CAG
*
1274386 AAATGC-CACCATTGCTT
65 AAA-GCGCACCATTGCTC
* * * *
1274403 TACCTTTTGCGGCGTTTTTCCCATAAAAGCCGCTATTG--CTTTACCTTTTGCGGTGTTTAT
1 TACCTTTTACGGTG-TTTTCCCATAAACGCCGCTATTGCTCTTTACCTTTTGCGGCGTTTAT
1274463 GGGAAAGCAT
Statistics
Matches: 118, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
81 19 0.16
82 73 0.62
83 24 0.20
84 2 0.02
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.42
Consensus pattern (81 bp):
TACCTTTTACGGTGTTTTCCCATAAACGCCGCTATTGCTCTTTACCTTTTGCGGCGTTTATCAGA
AAGCGCACCATTGCTC
Found at i:1274451 original size:124 final size:122
Alignment explanation
Indices: 1274211--1274460 Score: 288
Period size: 124 Copynumber: 2.0 Consensus size: 122
1274201 TTAGTGTCTT
* * * *
1274211 TTTTTCCATAAACGCCTCTTACGCTCTTTACCTTTTGTGGTGTTTTCCCATAAACGCCACTATTG
1 TTTTACCATAAACGCCGCTTACGCTCTTTACCTTTTGTGGCGTTTTCCCATAAACGCCACCATTG
*** ** *
1274276 CTTTTTACCTTTTGCGGCGTTTATGGGAAAGCGTCACTATTGCTCTACTTTTTACGGTG
66 C-TTTTACCTTTTGCGGCGTTTATCCCAAAAAGCCACTATTGCTCTAC-TTTTACGGTG
* * *
1274335 TTTTACCATAAACGCCGC-TATTGCTCTTTACCTTTTGTGGCGTTTTTCCATAAATGCCACCATT
1 TTTTACCATAAACGCCGCTTA-CGCTCTTTACCTTTTGTGGCGTTTTCCCATAAACGCCACCATT
* * * *
1274399 GC-TTTACCTTTTGCGGCGTTTTTCCCATAAAAGCCGCTATTGCTTTACCTTTTGCGGTG
65 GCTTTTACCTTTTGCGGCGTTTATCCCA-AAAAGCCACTATTGCTCTA-CTTTTACGGTG
1274458 TTT
1 TTT
1274461 ATGGGAAAGC
Statistics
Matches: 106, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
122 21 0.20
123 28 0.26
124 57 0.54
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.42
Consensus pattern (122 bp):
TTTTACCATAAACGCCGCTTACGCTCTTTACCTTTTGTGGCGTTTTCCCATAAACGCCACCATTG
CTTTTACCTTTTGCGGCGTTTATCCCAAAAAGCCACTATTGCTCTACTTTTACGGTG
Found at i:1274488 original size:40 final size:40
Alignment explanation
Indices: 1274396--1274540 Score: 150
Period size: 40 Copynumber: 3.6 Consensus size: 40
1274386 AAATGCCACC
* **
1274396 ATTGCTTTACCTTTTGCGGCGTTTTTCCCATAAAAGC--CGCT
1 ATTGCTTTACCTTTTGCGGCGTTTAT-GGA-AAAA-CATCGCT
* * *
1274437 ATTGCTTTACCTTTTGCGGTGTTTATGGGAAAGCATCGCT
1 ATTGCTTTACCTTTTGCGGCGTTTATGGAAAAACATCGCT
* * **
1274477 ATTGCTTTACCTTTTGCGGCATTTATTGAAAAATGTCGCT
1 ATTGCTTTACCTTTTGCGGCGTTTATGGAAAAACATCGCT
*
1274517 ATTGCTTTACTTTTTGCGGCGTTT
1 ATTGCTTTACCTTTTGCGGCGTTT
1274541 TCGGTCCAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
38 1 0.01
39 3 0.03
40 59 0.68
41 24 0.28
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (40 bp):
ATTGCTTTACCTTTTGCGGCGTTTATGGAAAAACATCGCT
Found at i:1282293 original size:89 final size:93
Alignment explanation
Indices: 1282129--1282319 Score: 237
Period size: 89 Copynumber: 2.1 Consensus size: 93
1282119 TTAATATAAT
* * * * * * *
1282129 ATTTGGTATTTGAACATGATATTTTTTTATTAATTTGGTACTTAAATTTTTTTCTGGTCCAATTT
1 ATTTGGTACTTAAACATGACATCTTTTTATTAAGTTGATACTTAAATTTTTTTCGGGTCCAATTT
**
1282194 GGTATTTAAACTTGACGTTTTCTCT-TA
66 GGTACCTAAACTTGACGTTTTCTCTCTA
*
1282221 ATTTGGTACTTAAACATGACA-CTTTTT-TTAAGTTGATACTTAAA-TTTTTTGGGGTCCAATTT
1 ATTTGGTACTTAAACATGACATCTTTTTATTAAGTTGATACTTAAATTTTTTTCGGGTCCAATTT
* * *
1282283 GGTACCTAAACTTGACTTTTTTTTTCTA
66 GGTACCTAAACTTGACGTTTTCTCTCTA
1282311 ATTTGGTAC
1 ATTTGGTAC
1282320 CTAATTTTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
89 36 0.42
90 26 0.31
91 5 0.06
92 18 0.21
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.50
Consensus pattern (93 bp):
ATTTGGTACTTAAACATGACATCTTTTTATTAAGTTGATACTTAAATTTTTTTCGGGTCCAATTT
GGTACCTAAACTTGACGTTTTCTCTCTA
Found at i:1282564 original size:27 final size:27
Alignment explanation
Indices: 1282538--1282628 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 27
1282528 GTTCAGGTAT
*
1282538 CAAATTGGGTCAAAAAAGTTTAAGTAT
1 CAAATTGGGTCAAAAAAGTTTAAGTAC
* * * * *
1282565 CAAATTAAGATAAAATATTAAGTTCAGGTAC
1 CAAATT-GGGTCAAA-A--AAGTTTAAGTAC
1282596 CAAATTGGGTCAAAAAAGTTTAAGTAC
1 CAAATTGGGTCAAAAAAGTTTAAGTAC
1282623 CAAATT
1 CAAATT
1282629 AAAAAAAATA
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
27 22 0.45
28 5 0.10
29 2 0.04
30 5 0.10
31 15 0.31
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (27 bp):
CAAATTGGGTCAAAAAAGTTTAAGTAC
Found at i:1282588 original size:58 final size:57
Alignment explanation
Indices: 1282490--1282639 Score: 201
Period size: 58 Copynumber: 2.6 Consensus size: 57
1282480 TTGAATCTAA
* * * * * *
1282490 AAAAAAGCTTACGTACCAATTTAGGAAAAAAATGTCAAGTTCAGGTATCAAATTGGGTC
1 AAAAAAGTTTAAGTACCAAATTA--AAAAAAATATTAAGTTCAGGTACCAAATTGGGTC
* *
1282549 AAAAAAGTTTAAGTATCAAATTAAGATAAAATATTAAGTTCAGGTACCAAATTGGGTC
1 AAAAAAGTTTAAGTACCAAATTAA-AAAAAATATTAAGTTCAGGTACCAAATTGGGTC
1282607 AAAAAAGTTTAAGTACCAAATTAAAAAAAATAT
1 AAAAAAGTTTAAGTACCAAATTAAAAAAAATAT
1282640 CACATTTAGA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
57 9 0.11
58 52 0.65
59 19 0.24
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (57 bp):
AAAAAAGTTTAAGTACCAAATTAAAAAAAATATTAAGTTCAGGTACCAAATTGGGTC
Found at i:1282655 original size:57 final size:58
Alignment explanation
Indices: 1282490--1282657 Score: 196
Period size: 58 Copynumber: 2.9 Consensus size: 58
1282480 TTGAATCTAA
* * * * * * *
1282490 AAAAAAGCTTACGTACCAATTTAGGAAAAAAATGTCAAGTTCAGGTATCAAATTGGGTC
1 AAAAAAGTTTAAGTACCAAATTAAG-AAAAAATATCAAGTTCAGATACCAAATTGGGTC
* * * *
1282549 AAAAAAGTTTAAGTATCAAATTAAGATAAAATATTAAGTTCAGGTACCAAATTGGGTC
1 AAAAAAGTTTAAGTACCAAATTAAGAAAAAATATCAAGTTCAGATACCAAATTGGGTC
*
1282607 AAAAAAGTTTAAGTACCAAATTAA-AAAAAATATCACA-TTTAGATACCAAAT
1 AAAAAAGTTTAAGTACCAAATTAAGAAAAAATATCA-AGTTCAGATACCAAAT
1282658 ATTATATTAA
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
57 21 0.22
58 53 0.56
59 20 0.21
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (58 bp):
AAAAAAGTTTAAGTACCAAATTAAGAAAAAATATCAAGTTCAGATACCAAATTGGGTC
Found at i:1282893 original size:20 final size:20
Alignment explanation
Indices: 1282868--1282907 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1282858 AAATAAGAAT
*
1282868 TATAAAACAAACATTA-ATAA
1 TATAAAA-AAAAATTACATAA
1282888 TATAAAAAAAAATTACATAA
1 TATAAAAAAAAATTACATAA
1282908 ACTAAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (20 bp):
TATAAAAAAAAATTACATAA
Found at i:1285357 original size:11 final size:12
Alignment explanation
Indices: 1285335--1285359 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1285325 TAATTCGAAA
1285335 TTCAATTTTTTT
1 TTCAATTTTTTT
1285347 TTCAATTTTTTT
1 TTCAATTTTTTT
1285359 T
1 T
1285360 GAATCAAATC
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCAATTTTTTT
Found at i:1287231 original size:16 final size:16
Alignment explanation
Indices: 1287212--1287249 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1287202 CCATAATAAT
1287212 TACTCCACTAACCAAC
1 TACTCCACTAACCAAC
1287228 TACTCCACTAACCAAC
1 TACTCCACTAACCAAC
1287244 TACTCC
1 TACTCC
1287250 TACAACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (16 bp):
TACTCCACTAACCAAC
Found at i:1287739 original size:29 final size:26
Alignment explanation
Indices: 1287696--1287748 Score: 61
Period size: 29 Copynumber: 1.9 Consensus size: 26
1287686 ATTTAAATTA
* *
1287696 GTACTTAAATTTTTTTATTCAATTTG
1 GTACTTAAATTTTTTAATCCAATTTG
1287722 GTACTTAAAATTTATTTTAATCCAATT
1 GTACTT-AAA-TT-TTTTAATCCAATT
1287749 AGACAACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 6 0.27
27 3 0.14
28 2 0.09
29 11 0.50
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (26 bp):
GTACTTAAATTTTTTAATCCAATTTG
Found at i:1289612 original size:26 final size:26
Alignment explanation
Indices: 1289558--1289612 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1289548 AATGATCTAT
* *
1289558 TAAAAATAAAATATTAAATTAACATA
1 TAAAAATAAAATATCAAATTAACACA
*
1289584 TAAAAATTAAATATCAAATTTAA-ACA
1 TAAAAATAAAATATCAAA-TTAACACA
1289610 TAA
1 TAA
1289613 TATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAAAATAAAATATCAAATTAACACA
Found at i:1289985 original size:29 final size:28
Alignment explanation
Indices: 1289923--1290010 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 28
1289913 AATTTACAAG
* *
1289923 AATTGCATCAAATCGAAATTTTATGTATAA
1 AATTGCAT-AAATC-AAAGTTCATGTATAA
*
1289953 AATTGCATAGAATCAAAGTTCATGTATAC
1 AATTGCATA-AATCAAAGTTCATGTATAA
*
1289982 AATTGCACATTAAATCATAGTTCATGTAT
1 AATTG--CA-TAAATCAAAGTTCATGTAT
1290011 GGTTTTGATA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
29 18 0.36
30 12 0.24
31 18 0.36
32 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.35
Consensus pattern (28 bp):
AATTGCATAAATCAAAGTTCATGTATAA
Found at i:1294808 original size:16 final size:16
Alignment explanation
Indices: 1294773--1294810 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1294763 TTAATTTTAC
**
1294773 TTTTTACTTTTTTATT
1 TTTTTACTTTTTTAAA
1294789 TTTTTACTTTTTTAAA
1 TTTTTACTTTTTTAAA
1294805 TTTTTA
1 TTTTTA
1294811 AATTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTACTTTTTTAAA
Found at i:1295012 original size:15 final size:15
Alignment explanation
Indices: 1294992--1295032 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1294982 TATGTATTTT
1294992 ATCATATATATTAAA
1 ATCATATATATTAAA
*
1295007 ATCATATATAATAAA
1 ATCATATATATTAAA
1295022 AT-ATTATATAT
1 ATCA-TATATAT
1295033 GTAACAGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (15 bp):
ATCATATATATTAAA
Found at i:1296188 original size:41 final size:41
Alignment explanation
Indices: 1296137--1296241 Score: 165
Period size: 41 Copynumber: 2.5 Consensus size: 41
1296127 AACTCGATAT
**
1296137 TTAAATGGAAGACTCATGTCTCGGGATGAGAATGAGATCATA
1 TTAAA-GGAAGACTCATGTCTCAAGATGAGAATGAGATCATA
*
1296179 TTAAAGGAAGACTCATGTCTCAAGATGAGAATGAGATTATA
1 TTAAAGGAAGACTCATGTCTCAAGATGAGAATGAGATCATA
*
1296220 TTAAAGGAAGATTCATGTCTCA
1 TTAAAGGAAGACTCATGTCTCA
1296242 GAATGAGCGT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 54 0.92
42 5 0.08
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (41 bp):
TTAAAGGAAGACTCATGTCTCAAGATGAGAATGAGATCATA
Found at i:1303332 original size:40 final size:41
Alignment explanation
Indices: 1303273--1303372 Score: 141
Period size: 40 Copynumber: 2.4 Consensus size: 41
1303263 AACTCGATAT
1303273 TTAAATGGAAGACTCATGTCTCGGGATGAAAATGAA-ATCATA
1 TTAAA-GGAAGACTCATGTCTCGGGATGAAAAT-AAGATCATA
* * *
1303315 TTAAA-GAAGACTTATGTCTCGGGATGAGAATAAGATTATA
1 TTAAAGGAAGACTCATGTCTCGGGATGAAAATAAGATCATA
1303355 TTAAAGGAAGACTCATGT
1 TTAAAGGAAGACTCATGT
1303373 TTCAAAATGA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
39 2 0.04
40 34 0.65
41 11 0.21
42 5 0.10
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (41 bp):
TTAAAGGAAGACTCATGTCTCGGGATGAAAATAAGATCATA
Found at i:1303383 original size:41 final size:40
Alignment explanation
Indices: 1303280--1303392 Score: 93
Period size: 40 Copynumber: 2.8 Consensus size: 40
1303270 TATTTAAATG
*** * *
1303280 GAAGACTCATGTCTCGGGATGAAAATGAA-ATCATATTAAA
1 GAAGACTCATGTCTCAAAATGAGAAT-AAGATTATATTAAA
* ***
1303320 GAAGACTTATGTCTCGGGATGAGAATAAGATTATATTAAA
1 GAAGACTCATGTCTCAAAATGAGAATAAGATTATATTAAA
* * *
1303360 GGAAGACTCATGTTTCAAAATGAGCATGAGATT
1 -GAAGACTCATGTCTCAAAATGAGAATAAGATT
1303393 TGTTTTTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.03
40 34 0.56
41 25 0.41
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (40 bp):
GAAGACTCATGTCTCAAAATGAGAATAAGATTATATTAAA
Found at i:1303455 original size:40 final size:40
Alignment explanation
Indices: 1303402--1303498 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
1303392 TTGTTTTTAA
* * *
1303402 AAAAGGAAGACTTATGTCTCGGTAGAGCATAAGGGTGATT
1 AAAAGGAAGACTTATGACTCGGTAGAGCATAAGAGTAATT
* *
1303442 TAAAGGAAGACTTATCACTCGGTAGAGCATAAGAGTAATT
1 AAAAGGAAGACTTATGACTCGGTAGAGCATAAGAGTAATT
1303482 AAAAGGAAGACTTATGA
1 AAAAGGAAGACTTATGA
1303499 ACCAATGAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (40 bp):
AAAAGGAAGACTTATGACTCGGTAGAGCATAAGAGTAATT
Found at i:1305865 original size:62 final size:62
Alignment explanation
Indices: 1305769--1305889 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 62
1305759 TTATGTTATG
* *
1305769 ATTTTTATTAATTCATATTTTAATAATAATTATATTAATAATGTTATTAAATTATATATTTTT
1 ATTTTTATTAATTCATATTTTAATAATAATTATATTAA-AATATGATTAAATTATATATTTTT
*
1305832 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATGATTAAATTATTTATT
1 ATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAATATGATTAAATTATATATT
1305890 ATTAAATTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
61 18 0.33
62 20 0.37
63 12 0.22
64 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (62 bp):
ATTTTTATTAATTCATATTTTAATAATAATTATATTAAAATATGATTAAATTATATATTTTT
Found at i:1305879 original size:26 final size:26
Alignment explanation
Indices: 1305837--1305923 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 26
1305827 TTTTTATTTT
*
1305837 TATTAAATTATATTTAATAATAATTA
1 TATTAAAATATATTTAATAATAATTA
* *
1305863 TATTAAAATATGA-TTAA-ATTATTTA
1 TATTAAAATAT-ATTTAATAATAATTA
* **
1305888 TTATTAAATTATATTTAATAATAATCC
1 -TATTAAAATATATTTAATAATAATTA
1305915 TATTAAAAT
1 TATTAAAAT
1305924 TTAATAAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
25 7 0.15
26 36 0.75
27 5 0.10
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (26 bp):
TATTAAAATATATTTAATAATAATTA
Found at i:1306591 original size:53 final size:52
Alignment explanation
Indices: 1306495--1306681 Score: 209
Period size: 53 Copynumber: 3.6 Consensus size: 52
1306485 TAGGTGCCGT
*
1306495 CAATGTCAATGACACCACAAAAAAAAATCAAAATTTTTAATTTGGGTGT-T-C
1 CAATGTCAATGACACCGCAAAAAAAAATCAAAATTTTTAATTTGGGT-TCTGC
* * *
1306546 CTAATGTTAACGACACCGCAAAAAAAAAATCAAAATTTTTTATTTGGGTTCTGC
1 C-AATGTCAATGACACCGC-AAAAAAAAATCAAAATTTTTAATTTGGGTTCTGC
* * * * *
1306600 CAATGTCAATGACACTGCAAAAAAAAATCAAAATATTTAATTT-GGTGCCGA
1 CAATGTCAATGACACCGCAAAAAAAAATCAAAATTTTTAATTTGGGTTCTGC
* * * *
1306651 CAATGTCCACGACACCACAGAAAAAAATCAA
1 CAATGTCAATGACACCGCAAAAAAAAATCAA
1306682 TTTTTTGGCA
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
51 32 0.28
52 38 0.33
53 43 0.37
54 2 0.02
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (52 bp):
CAATGTCAATGACACCGCAAAAAAAAATCAAAATTTTTAATTTGGGTTCTGC
Found at i:1310085 original size:17 final size:18
Alignment explanation
Indices: 1310063--1310102 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1310053 ATATTATATT
* *
1310063 TATTTTACTT-TTTTGTA
1 TATTTTAATTATTTTCTA
1310080 TATTTTAATTATTTTCTA
1 TATTTTAATTATTTTCTA
1310098 TATTT
1 TATTT
1310103 GTTCGTGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (18 bp):
TATTTTAATTATTTTCTA
Found at i:1314745 original size:111 final size:111
Alignment explanation
Indices: 1314551--1314772 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
1314541 GATTGAAAAG
*
1314551 TATCTACAAAAAGAATCTCTAAGATTACAATTAAATCTCTAAGATCACAAGGATCATATCTTCTA
1 TATCTACAAAAAGAATCTCTAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTA
*
1314616 AGATTGCCTATCTTGAAGATTACATTTCATATTTGCCGACTTTGTA
66 AGATTGCCTATCTTGAAGATTACATTTCATATTTGCCAACTTTGTA
*
1314662 TATCTACAAAAAGAATCTCTAAGATTATAATCAAATCTCTAAGATCACAAGGATCATATCTTCTA
1 TATCTACAAAAAGAATCTCTAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTA
1314727 AGATTGCCTATCTTGAAGATTACATTTCATATTTGCCAACTTTGTA
66 AGATTGCCTATCTTGAAGATTACATTTCATATTTGCCAACTTTGTA
1314773 GATGGACCTT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (111 bp):
TATCTACAAAAAGAATCTCTAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTA
AGATTGCCTATCTTGAAGATTACATTTCATATTTGCCAACTTTGTA
Found at i:1315316 original size:111 final size:111
Alignment explanation
Indices: 1315122--1315343 Score: 426
Period size: 111 Copynumber: 2.0 Consensus size: 111
1315112 GATTGAAAAG
1315122 TATCTACAAAAAGAATCTCTAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTA
1 TATCTACAAAAAGAATCTCTAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTA
*
1315187 AGATTGCCTATCTTGAAGATTACATTTCATATTTGCCGACTTTGTA
66 AGATTGCCTATCTTGAAGATTACATTTCATATTTGCCAACTTTGTA
*
1315233 TATCTACAAAAAGAATCTCTAAGATTATAATCAAATCTCTAAGATCACAAGGATCATATCTTCTA
1 TATCTACAAAAAGAATCTCTAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTA
1315298 AGATTGCCTATCTTGAAGATTACATTTCATATTTGCCAACTTTGTA
66 AGATTGCCTATCTTGAAGATTACATTTCATATTTGCCAACTTTGTA
1315344 GATGGACCTT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (111 bp):
TATCTACAAAAAGAATCTCTAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTA
AGATTGCCTATCTTGAAGATTACATTTCATATTTGCCAACTTTGTA
Found at i:1315587 original size:571 final size:571
Alignment explanation
Indices: 1314505--1315637 Score: 2203
Period size: 571 Copynumber: 2.0 Consensus size: 571
1314495 GCCTCCACAA
1314505 AATCAATGGTACAGATTAAAGTACATCAATAGCTAAGATTGAAAAGTATCTACAAAAAGAATCTC
1 AATCAATGGTACAGATTAAAGTACATCAATAGCTAAGATTGAAAAGTATCTACAAAAAGAATCTC
*
1314570 TAAGATTACAATTAAATCTCTAAGATCACAAGGATCATATCTTCTAAGATTGCCTATCTTGAAGA
66 TAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTAAGATTGCCTATCTTGAAGA
1314635 TTACATTTCATATTTGCCGACTTTGTATATCTACAAAAAGAATCTCTAAGATTATAATCAAATCT
131 TTACATTTCATATTTGCCGACTTTGTATATCTACAAAAAGAATCTCTAAGATTATAATCAAATCT
1314700 CTAAGATCACAAGGATCATATCTTCTAAGATTGCCTATCTTGAAGATTACATTTCATATTTGCCA
196 CTAAGATCACAAGGATCATATCTTCTAAGATTGCCTATCTTGAAGATTACATTTCATATTTGCCA
1314765 ACTTTGTAGATGGACCTTCAATCTCTCCAAGCACTAGGCCAGTCTAAGTGGGCCAAAAGACCTCC
261 ACTTTGTAGATGGACCTTCAATCTCTCCAAGCACTAGGCCAGTCTAAGTGGGCCAAAAGACCTCC
1314830 TTTGAACTCGATGGATCACACAAGTGTGCCATGGTTGCGGGCTCCCATGCGCAACCCATGTCATT
326 TTTGAACTCGATGGATCACACAAGTGTGCCATGGTTGCGGGCTCCCATGCGCAACCCATGTCATT
1314895 CTCCCCCACCGAATCTAGCGACGTCCTCGTTGCATCTTTTACATGGAACTGGTCTATCTTGTTTG
391 CTCCCCCACCGAATCTAGCGACGTCCTCGTTGCATCTTTTACATGGAACTGGTCTATCTTGTTTG
1314960 GAACTGCCACAAGGCCTCGACGGGTTCCCAACTTCTCTTACTTTCGAGAAATTCTTTCCATCGAA
456 GAACTGCCACAAGGCCTCGACGGGTTCCCAACTTCTCTTACTTTCGAGAAATTCTTTCCATCGAA
*
1315025 CTAAATATTCATCCCGCGGTCGGTAGTACTTCCTTCTGAACAATGGTACAG
521 CTAAATATTCATCCCGCGGTCGGAAGTACTTCCTTCTGAACAATGGTACAG
1315076 AATCAATGGTACAGATTAAAGTACATCAATAGCTAAGATTGAAAAGTATCTACAAAAAGAATCTC
1 AATCAATGGTACAGATTAAAGTACATCAATAGCTAAGATTGAAAAGTATCTACAAAAAGAATCTC
1315141 TAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTAAGATTGCCTATCTTGAAGA
66 TAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTAAGATTGCCTATCTTGAAGA
1315206 TTACATTTCATATTTGCCGACTTTGTATATCTACAAAAAGAATCTCTAAGATTATAATCAAATCT
131 TTACATTTCATATTTGCCGACTTTGTATATCTACAAAAAGAATCTCTAAGATTATAATCAAATCT
1315271 CTAAGATCACAAGGATCATATCTTCTAAGATTGCCTATCTTGAAGATTACATTTCATATTTGCCA
196 CTAAGATCACAAGGATCATATCTTCTAAGATTGCCTATCTTGAAGATTACATTTCATATTTGCCA
** *
1315336 ACTTTGTAGATGGACCTTCAATCTCTTTAAGCACTAGGCCAGTCTGAGTGGGCCAAAAGACCTCC
261 ACTTTGTAGATGGACCTTCAATCTCTCCAAGCACTAGGCCAGTCTAAGTGGGCCAAAAGACCTCC
1315401 TTTGAACTCGATGGATCACACAAGTGTGCCATGGTTGCGGGCTCCCATGCGCAACCCATGTCATT
326 TTTGAACTCGATGGATCACACAAGTGTGCCATGGTTGCGGGCTCCCATGCGCAACCCATGTCATT
1315466 CTCCCCCACCGAATCTAGCGACGTCCTCGTTGCATCTTTTACATGGAACTGGTCTATCTTGTTTG
391 CTCCCCCACCGAATCTAGCGACGTCCTCGTTGCATCTTTTACATGGAACTGGTCTATCTTGTTTG
1315531 GAACTGCCACAAGGCCTCGACGGGTTCCCAACTTCTCTTACTTTCGAGAAATTCTTTCCATCGAA
456 GAACTGCCACAAGGCCTCGACGGGTTCCCAACTTCTCTTACTTTCGAGAAATTCTTTCCATCGAA
**
1315596 CTAAATATTCATGTCGCGGTCGGAAGTACTTCCTTCTGAACA
521 CTAAATATTCATCCCGCGGTCGGAAGTACTTCCTTCTGAACA
1315638 CATAGTCTGC
Statistics
Matches: 555, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
571 555 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (571 bp):
AATCAATGGTACAGATTAAAGTACATCAATAGCTAAGATTGAAAAGTATCTACAAAAAGAATCTC
TAAGATTACAATCAAATCTCTAAGATCACAAGGATCATATCTTCTAAGATTGCCTATCTTGAAGA
TTACATTTCATATTTGCCGACTTTGTATATCTACAAAAAGAATCTCTAAGATTATAATCAAATCT
CTAAGATCACAAGGATCATATCTTCTAAGATTGCCTATCTTGAAGATTACATTTCATATTTGCCA
ACTTTGTAGATGGACCTTCAATCTCTCCAAGCACTAGGCCAGTCTAAGTGGGCCAAAAGACCTCC
TTTGAACTCGATGGATCACACAAGTGTGCCATGGTTGCGGGCTCCCATGCGCAACCCATGTCATT
CTCCCCCACCGAATCTAGCGACGTCCTCGTTGCATCTTTTACATGGAACTGGTCTATCTTGTTTG
GAACTGCCACAAGGCCTCGACGGGTTCCCAACTTCTCTTACTTTCGAGAAATTCTTTCCATCGAA
CTAAATATTCATCCCGCGGTCGGAAGTACTTCCTTCTGAACAATGGTACAG
Found at i:1319995 original size:20 final size:20
Alignment explanation
Indices: 1319970--1320007 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1319960 TCTACAAAAA
*
1319970 AAATCTCTAAGATTACAATC
1 AAATCTCTAAGATCACAATC
1319990 AAATCTCTAAGATCACAA
1 AAATCTCTAAGATCACAA
1320008 GGATCATATC
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:0.47, C:0.21, G:0.05, T:0.26
Consensus pattern (20 bp):
AAATCTCTAAGATCACAATC
Found at i:1320501 original size:18 final size:19
Alignment explanation
Indices: 1320464--1320507 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1320454 AAGTTTATAA
* *
1320464 TATTATATATTATGTTATT
1 TATTATATATTATATAATT
1320483 T-TTATATATTATATAATT
1 TATTATATATTATATAATT
1320501 TATTATA
1 TATTATA
1320508 CATTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTATATATTATATAATT
Found at i:1320506 original size:25 final size:26
Alignment explanation
Indices: 1320457--1320506 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1320447 CCGTTTTAAG
*
1320457 TTTATAATATTATATATTATGTTATT
1 TTTATAATATTATATATTATATTATT
1320483 TTTAT-ATATTATATAATT-TATTAT
1 TTTATAATATTATAT-ATTATATTAT
1320507 ACATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTATAATATTATATATTATATTATT
Found at i:1320650 original size:22 final size:22
Alignment explanation
Indices: 1320622--1320666 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1320612 ATAAAATTAT
1320622 TAAATA-TTAAAATAAAATAAAA
1 TAAATATTTAAAA-AAAATAAAA
1320644 TAAATATTTTAAAAAAAATAAAA
1 TAAATA-TTTAAAAAAAATAAAA
1320667 ATAATATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 9 0.43
24 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAATATTTAAAAAAAATAAAA
Found at i:1320943 original size:44 final size:46
Alignment explanation
Indices: 1320849--1320943 Score: 124
Period size: 44 Copynumber: 2.1 Consensus size: 46
1320839 GGTTCGTTGT
* *
1320849 AATGGAATAGGGCTGTAATCAGTAATTCAGTTGTTTGGTTGAATAG
1 AATGGAATAGAGCTGTAATCAGTAATTCAGTTGTTTAGTTGAATAG
* *
1320895 AATGGAATAGAGCTGTAAT-AGT-ATT-ATTATGTTTAGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAGT-TGTTTAGTTGAATAG
1320939 AATGG
1 AATGG
1320944 TGATGTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 2 0.05
44 21 0.48
45 3 0.07
46 18 0.41
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCAGTTGTTTAGTTGAATAG
Found at i:1321091 original size:59 final size:57
Alignment explanation
Indices: 1321023--1321161 Score: 174
Period size: 59 Copynumber: 2.4 Consensus size: 57
1321013 GATTAATATT
*
1321023 ATTAAATTTTAATA-AGATTATTATTAAATAT-AATTTAATAAAAAATAATAAATAATTCA
1 ATTATATTTTAATATA-ATTATTATTAAAT-TCAATTTAAT--AAAATAATAAATAATTCA
* * *
1321082 ATTATATTTTAACATAATTATTATTAAATTCAATTTAATAAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATTCAATTTAATAAAATAATAAATAATTCA
*
1321139 ATAATATTTTTAATATAATTATT
1 ATTATA-TTTTAATATAATTATT
1321162 GTTATTATTA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
57 21 0.30
58 16 0.23
59 33 0.46
60 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (57 bp):
ATTATATTTTAATATAATTATTATTAAATTCAATTTAATAAAATAATAAATAATTCA
Found at i:1322171 original size:21 final size:21
Alignment explanation
Indices: 1322147--1322212 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1322137 ATAAATAGTC
1322147 TAAAATTTGGTACCAACATAA
1 TAAAATTTGGTACCAACATAA
* * *
1322168 TAAAACTAT-GTA--AATAGT-C
1 TAAAA-TTTGGTACCAACA-TAA
1322187 TAAAATTTGGTACCAACATAA
1 TAAAATTTGGTACCAACATAA
1322208 TAAAA
1 TAAAA
1322213 CTATATAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
18 2 0.06
19 11 0.33
20 2 0.06
21 16 0.48
22 2 0.06
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (21 bp):
TAAAATTTGGTACCAACATAA
Found at i:1322193 original size:40 final size:40
Alignment explanation
Indices: 1322134--1322236 Score: 170
Period size: 40 Copynumber: 2.5 Consensus size: 40
1322124 CTGCAACATT
1322134 TATATAAATAGTCTAAAATTTGGTACCAACATAATAAAAC
1 TATATAAATAGTCTAAAATTTGGTACCAACATAATAAAAC
*
1322174 TATGTAAATAGTCTAAAATTTGGTACCAACATAATAAAAC
1 TATATAAATAGTCTAAAATTTGGTACCAACATAATAAAAC
*
1322214 TATATAAAATAGTTTGAAAATTT
1 TATAT-AAATAGTCT-AAAATTT
1322237 TATTTTTCTA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 43 0.74
41 8 0.14
42 7 0.12
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.33
Consensus pattern (40 bp):
TATATAAATAGTCTAAAATTTGGTACCAACATAATAAAAC
Found at i:1330805 original size:6 final size:6
Alignment explanation
Indices: 1330791--1330860 Score: 74
Period size: 6 Copynumber: 12.0 Consensus size: 6
1330781 TTAAATTTGT
* * *
1330791 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TTTAAA TTT-AA TTTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
1330837 TTTAAA TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA
1330861 ATTATGTCCC
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
5 12 0.23
6 36 0.69
7 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:1330805 original size:17 final size:17
Alignment explanation
Indices: 1330780--1330865 Score: 73
Period size: 17 Copynumber: 4.6 Consensus size: 17
1330770 CTAAGTTTAT
*
1330780 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
1330797 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
1330814 TTTAAATTTAAATTTAATTTAAG
1 TTTAAATTT--A--T--TTTAAA
1330837 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
*
1330855 TTTAAAATTAT
1 TTTAAATTTAT
1330866 GTCCCAATAC
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
17 26 0.46
18 12 0.21
19 2 0.04
21 2 0.04
23 14 0.25
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:1330811 original size:11 final size:11
Alignment explanation
Indices: 1330775--1330858 Score: 55
Period size: 11 Copynumber: 7.4 Consensus size: 11
1330765 CACTTCTAAG
1330775 TTTATTTTAAA
1 TTTATTTTAAA
*
1330786 TTTGTTTTAAA
1 TTTATTTTAAA
* *
1330797 TTTAGATTT-AT
1 TTTA-TTTTAAA
*
1330808 TTTAAATTTAAA
1 TTT-ATTTTAAA
*
1330820 TTTAAATTT-AA
1 TTT-ATTTTAAA
*
1330831 TTTAAGTTTAAA
1 TTT-ATTTTAAA
1330843 TTTATTTTCAAA
1 TTTATTTT-AAA
1330855 TTTA
1 TTTA
1330859 AAATTATGTC
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
11 35 0.57
12 26 0.43
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:1330817 original size:23 final size:23
Alignment explanation
Indices: 1330791--1330846 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1330781 TTAAATTTGT
* *
1330791 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTAAATTTAATTTAAA
*
1330814 TTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTAAATTTAATTTAAA
1330837 TTTAAATTTA
1 TTTAAATTTA
1330847 TTTTCAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATTTAAA
Found at i:1332331 original size:29 final size:29
Alignment explanation
Indices: 1332299--1332390 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 29
1332289 AGAAATTATG
*
1332299 TTTTGACCCTAAAACTTCCAAAAATTCCA
1 TTTTAACCCTAAAACTTCCAAAAATTCCA
*
1332328 TTTTCAACCCCAAAACTTTCC-AAAATTCCA
1 TTTT-AACCCTAAAAC-TTCCAAAAATTCCA
* * **
1332358 TTTTTATCCTCGAACTTCCAAAAATTCCA
1 TTTTAACCCTAAAACTTCCAAAAATTCCA
1332387 TTTT
1 TTTT
1332391 TTACCTTGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.08
29 23 0.43
30 22 0.42
31 4 0.08
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (29 bp):
TTTTAACCCTAAAACTTCCAAAAATTCCA
Found at i:1332391 original size:29 final size:30
Alignment explanation
Indices: 1332299--1332391 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
1332289 AGAAATTATG
* *
1332299 TTTTGACCCTAAAACTTCCAAAAATTCCAT
1 TTTTAACCCCAAAACTTCCAAAAATTCCAT
*
1332329 TTTCAACCCCAAAACTTTCC-AAAATTCCAT
1 TTTTAACCCCAAAAC-TTCCAAAAATTCCAT
* * *
1332359 TTTTATCCTC-GAACTTCCAAAAATTCCAT
1 TTTTAACCCCAAAACTTCCAAAAATTCCAT
1332388 TTTT
1 TTTT
1332392 TACCTTGAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
28 4 0.07
29 17 0.31
30 29 0.54
31 4 0.07
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (30 bp):
TTTTAACCCCAAAACTTCCAAAAATTCCAT
Found at i:1332411 original size:30 final size:30
Alignment explanation
Indices: 1332349--1332421 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
1332339 AAAACTTTCC
*
1332349 AAAATTCCA-TTTTTATCCTCGAACTTCCA
1 AAAATTCCATTTTTTATCCTCGAACTTCAA
* *
1332378 AAAATTCCATTTTTTA-CCTTGAAGCTTTAA
1 AAAATTCCATTTTTTATCCTCGAA-CTTCAA
1332408 AAAATTACCATTTT
1 AAAATT-CCATTTT
1332422 ACCCCCTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 15 0.39
30 16 0.42
31 7 0.18
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (30 bp):
AAAATTCCATTTTTTATCCTCGAACTTCAA
Found at i:1344614 original size:115 final size:115
Alignment explanation
Indices: 1344407--1344623 Score: 353
Period size: 115 Copynumber: 1.9 Consensus size: 115
1344397 ATGAAACGAG
* * * *
1344407 GCTCTAAGCGAGCAAATCTTTGAACCCCAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGTA
1 GCTCAAAGCGAGCAAATCTTTAAACCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGTA
1344472 ATAAAATGGTTAGCTTCCTAATAAGATACAGAGAAGTAAATCAAACCCAC
66 ATAAAATGGTTAGCTTCCTAATAAGATACAGAGAAGTAAATCAAACCCAC
* *
1344522 GCTCAAAGCGAGCAAATCTTTAAACCCCAGCTTCCTAATGAGATACTGAGAAGCGGGTCGAAGTA
1 GCTCAAAGCGAGCAAATCTTTAAACCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGTA
* * *
1344587 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGT
66 ATAAAATGGTTAGCTTCCTAATAAGATACAGAGAAGT
1344624 GGACCAAATT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 93 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (115 bp):
GCTCAAAGCGAGCAAATCTTTAAACCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGTA
ATAAAATGGTTAGCTTCCTAATAAGATACAGAGAAGTAAATCAAACCCAC
Found at i:1345064 original size:194 final size:194
Alignment explanation
Indices: 1344523--1345503 Score: 1214
Period size: 194 Copynumber: 5.0 Consensus size: 194
1344513 CAAACCCACG
* * ** * *
1344523 CTCAAAGCGAGCAAATCTTTAAACCCCAGCTTCCTAATGAGATACTGAGAAGCGGGTCGAAGTAA
1 CTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAA
* * * * *
1344588 TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGGTAC
66 TAAAAAGGTTAGCTTCCTGATGAAACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTAC
* * * *
1344653 AAAGAAGCGGATTGAAACAAGTAAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAAC
131 AGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACC-A-
1344718 TTGA
194 ---A
* * * *
1344722 GGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTTCTGATGAGATACTGAGAAGCAGGTCAAAGC
1 --CTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGT
* * * *
1344787 AAT---AAGGTTAGCTTCCTGATGAGACGCTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGGT
64 AATAAAAAGGTTAGCTTCCTGATGAAACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGT
*
1344849 ACAGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGGTATAGAGAAGTATACCA
129 ACAGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCA
1344914 A
194 A
*
1344915 CTCAATACGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAA
1 CTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAA
* * * *
1344980 TAAAAAGGTCAGCTTCCTGATGAAACACTAAGAAGTGAACCAAATCCGTCTTCTTGATGAGGTAC
66 TAAAAAGGTTAGCTTCCTGATGAAACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTAC
* * *
1345045 AGAGAAGCGGATTGAAACAAACT-AGGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAA
131 AGAGAAGCGGATTGAAAC-AAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAA
*
1345109 CTCAATGCGAACAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAA
1 CTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAA
*
1345174 TAAAAAGGTTAGCTTCCTGAT-AAGACACTGAGAAGTGAACCAAAATCGTCTTCCTGATGAGGTA
66 TAAAAAGGTTAGCTTCCTGATGAA-ACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTA
* * * * *
1345238 TAGAGAAGCGGATTGAAACAAATGGGGGGGTTATCTTCCTGATGAGATATAGAGAAGTATACCAA
130 CAGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAA
* * *
1345303 CTCAGGGCTCGATGTGAACAAATCTTCGAATCCCAGCTTCTTGATGAGATACTGAG-A--A-G-C
1 CTCA-------ATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTC
* * * * **
1345363 -AA-CAATAAAATGGTTAGCTTCTTGATGAAATACTGAGAAGCAAACCAAATTCGTCTTCCTGAT
59 GAAGTAATAAAAAGGTTAGCTTCCTGATGAAACACTGAGAAGTGAACCAAATTCGTCTTCCTGAT
* ** * * *
1345426 GAGGTACAGAGAAGCGGATTGAAACAAGCGATACGGTAATCTTCGTGATAAGATACTA-AGAAGT
124 GAGGTACAGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATA-TAGAGAAGT
*
1345490 AGACCAA
188 ATACCAA
*
1345497 ATCAATG
1 CTCAATG
1345504 ACACCTAACC
Statistics
Matches: 695, Mismatches: 70, Indels: 44
0.86 0.09 0.05
Matches are distributed among these distances:
187 3 0.00
191 61 0.09
193 6 0.01
194 397 0.57
195 9 0.01
196 1 0.00
197 2 0.00
198 114 0.16
200 1 0.00
201 101 0.15
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (194 bp):
CTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAA
TAAAAAGGTTAGCTTCCTGATGAAACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTAC
AGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAA
Found at i:1345811 original size:11 final size:11
Alignment explanation
Indices: 1345795--1345899 Score: 69
Period size: 11 Copynumber: 9.7 Consensus size: 11
1345785 AGGCCCCTTC
1345795 TAAATTTATTT
1 TAAATTTATTT
*
1345806 TAAATTTGTTT
1 TAAATTTATTT
1345817 T-AA---A-TT
1 TAAATTTATTT
*
1345823 TAGATTTATTT
1 TAAATTTATTT
*
1345834 TAAATTTAAATT
1 TAAATTT-ATTT
*
1345846 TAAATTTACTT
1 TAAATTTATTT
**
1345857 TAAATTTA-AA
1 TAAATTTATTT
*
1345867 TATAATTTAAGTT
1 TA-AATTT-ATTT
1345880 TAAATTTATTT
1 TAAATTTATTT
1345891 TCAAATTTA
1 T-AAATTTA
1345900 AAATTATGTC
Statistics
Matches: 73, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
6 3 0.04
7 1 0.01
10 5 0.07
11 39 0.53
12 23 0.32
13 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (11 bp):
TAAATTTATTT
Found at i:1345829 original size:6 final size:6
Alignment explanation
Indices: 1345815--1345901 Score: 83
Period size: 6 Copynumber: 15.0 Consensus size: 6
1345805 TTAAATTTGT
* * *
1345815 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
1345861 TTTAAA TAT-AA TTTAAG TTTAAA TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
1345902 ATTATGTCCC
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
5 15 0.23
6 45 0.70
7 4 0.06
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:1345829 original size:17 final size:17
Alignment explanation
Indices: 1345804--1345906 Score: 89
Period size: 17 Copynumber: 5.6 Consensus size: 17
1345794 CTAAATTTAT
*
1345804 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
1345821 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
1345838 TTTAAATTTAAATTTACTTTAAA
1 TTTAAATTT--A--T--TTTAAA
* * *
1345861 TTTAAATATAATTTAAG
1 TTTAAATTTATTTTAAA
1345878 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
*
1345896 TTTAAAATTAT
1 TTTAAATTTAT
1345907 GTCCCAATAC
Statistics
Matches: 69, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
17 40 0.58
18 12 0.17
19 1 0.01
21 2 0.03
23 14 0.20
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:1345841 original size:23 final size:22
Alignment explanation
Indices: 1345815--1345887 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 22
1345805 TTAAATTTGT
*
1345815 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTA-ATTTACTTTAAA
1345838 TTTAAATTTAAATTTACTTTAAA
1 TTTAAATTT-AATTTACTTTAAA
* *
1345861 TTTAAATATAATTTAAGTTTAAA
1 TTTAAATTTAATTT-ACTTTAAA
1345884 TTTA
1 TTTA
1345888 TTTTCAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
22 5 0.11
23 39 0.87
24 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (22 bp):
TTTAAATTTAATTTACTTTAAA
Found at i:1347280 original size:29 final size:28
Alignment explanation
Indices: 1347248--1347477 Score: 139
Period size: 29 Copynumber: 7.9 Consensus size: 28
1347238 AGAAATTATG
* *
1347248 TTTTGACCCTCGAACTTTTAAAAATTCCA
1 TTTT-ACCCTCAAACTTTCAAAAATTCCA
** *
1347277 TTTTAACCCTCAAAACTTTTGAAGATTACCA
1 TTTT-ACCCTC-AAACTTTCAAAAATT-CCA
* *
1347308 TTTTACCC-CAAAC-ATCCAAAATTCCA
1 TTTTACCCTCAAACTTTCAAAAATTCCA
* *
1347334 TTTTCGACCCTAAAAC-TTCTAAAATTTACCA
1 TTTT--ACCCTCAAACTTTC-AAAAATT-CCA
*
1347365 TTTTACCC-CTAAACTTCCAAAAATTCCA
1 TTTTACCCTC-AAACTTTCAAAAATTCCA
* *
1347393 TTTTTGA-CCTCGAAACTTTCTAGAATTCCAA
1 -TTTT-ACCCTC-AAACTTTCAAAAATTCC-A
* ** *
1347424 TTTTATCCTTGAACTTCCAAAAATTCCA
1 TTTTACCCTCAAACTTTCAAAAATTCCA
1347452 TTTTTACCC-CAAAGCTTTCAAAAATT
1 -TTTTACCCTCAAA-CTTTCAAAAATT
1347478 ACCTAATTAC
Statistics
Matches: 157, Mismatches: 28, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
26 7 0.04
27 6 0.04
28 14 0.09
29 69 0.44
30 46 0.29
31 15 0.10
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (28 bp):
TTTTACCCTCAAACTTTCAAAAATTCCA
Found at i:1347337 original size:57 final size:59
Alignment explanation
Indices: 1347267--1347396 Score: 178
Period size: 57 Copynumber: 2.2 Consensus size: 59
1347257 TCGAACTTTT
* *
1347267 AAAAATTCCATTTT-AACCCTCAAAACTTTTGAAGA-TTACCATTTTACCCC-AAACATCC
1 AAAAATTCCATTTTCAACCCT-AAAACTTCT-AAAATTTACCATTTTACCCCTAAACATCC
* *
1347325 -AAAATTCCATTTTCGACCCTAAAACTTCTAAAATTTACCATTTTACCCCTAAACTTCC
1 AAAAATTCCATTTTCAACCCTAAAACTTCTAAAATTTACCATTTTACCCCTAAACATCC
1347383 AAAAATTCCATTTT
1 AAAAATTCCATTTT
1347397 TGACCTCGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
56 3 0.05
57 36 0.56
58 12 0.19
59 13 0.20
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (59 bp):
AAAAATTCCATTTTCAACCCTAAAACTTCTAAAATTTACCATTTTACCCCTAAACATCC
Found at i:1347409 original size:59 final size:58
Alignment explanation
Indices: 1347267--1347480 Score: 206
Period size: 59 Copynumber: 3.7 Consensus size: 58
1347257 TCGAACTTTT
* * * *
1347267 AAAAATTCCA-TTTTAACCCTCAAAACTTTTGAAGATTACCATTTTACCCC-AAACATCC
1 AAAAATTCCATTTTTGA-CCTCAAAACTTCT-AAAATTACCATTTTACCCCTAAACTTCC
*
1347325 -AAAATTCCATTTTCGACC-CTAAAACTTCTAAAATTTACCATTTTACCCCTAAACTTCC
1 AAAAATTCCATTTTTGACCTC-AAAACTTCTAAAA-TTACCATTTTACCCCTAAACTTCC
* * * * *
1347383 AAAAATTCCATTTTTGACCTCGAAACTTTCTAGAATT-CCAATTTTATCCTTGAACTTCC
1 AAAAATTCCATTTTTGACCTCAAAAC-TTCTAAAATTACC-ATTTTACCCCTAAACTTCC
* * *
1347442 AAAAATTCCATTTTT-ACCCCAAAGCTTTCAAAAATTACC
1 AAAAATTCCATTTTTGACCTCAAAAC-TTCTAAAATTACC
1347481 TAATTACCCT
Statistics
Matches: 131, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
56 4 0.03
57 34 0.26
58 29 0.22
59 56 0.43
60 8 0.06
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAAATTCCATTTTTGACCTCAAAACTTCTAAAATTACCATTTTACCCCTAAACTTCC
Done.