Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 43
Found at i:1331679 original size:19 final size:18
Alignment explanation
Indices: 1331657--1331703 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1331647 AAATAAAGTC
1331657 AAATAATAAAATAAATAAA
1 AAAT-ATAAAATAAATAAA
*
1331676 AAATATTAAATAAATAAA
1 AAATATAAAATAAATAAA
1331694 AGAAT-TAAAA
1 A-AATATAAAA
1331704 AGTAAATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAATATAAAATAAATAAA
Found at i:1332771 original size:9 final size:9
Alignment explanation
Indices: 1332759--1332808 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
1332749 TTAAATAAGT
*
1332759 AATAATATA
1 AATAATAAA
*
1332768 AATAAAAAA
1 AATAATAAA
1332777 AATAATAAA
1 AATAATAAA
1332786 AATAAT--A
1 AATAATAAA
*
1332793 TATAATAAA
1 AATAATAAA
1332802 AATAATA
1 AATAATA
1332809 TGTTTTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
7 6 0.18
9 28 0.82
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AATAATAAA
Found at i:1332779 original size:25 final size:25
Alignment explanation
Indices: 1332751--1332808 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1332741 AAATTAAGTT
*
1332751 AAATAAGTAATAAT-ATAAATAAAAA
1 AAATAA-TAAAAATAATAAATAAAAA
* *
1332776 AAATAATAAAAATAATATATAATAA
1 AAATAATAAAAATAATAAATAAAAA
1332801 AAATAATA
1 AAATAATA
1332809 TGTTTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 6 0.21
25 23 0.79
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (25 bp):
AAATAATAAAAATAATAAATAAAAA
Found at i:1332797 original size:16 final size:16
Alignment explanation
Indices: 1332759--1332809 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
1332749 TTAAATAAGT
1332759 AATAATATA-AAT-AA
1 AATAATATATAATAAA
1332773 AA-AA-A-ATAATAAA
1 AATAATATATAATAAA
1332786 AATAATATATAATAAA
1 AATAATATATAATAAA
1332802 AATAATAT
1 AATAATAT
1332810 GTTTTCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 1 0.03
12 4 0.12
13 6 0.19
14 4 0.12
15 1 0.03
16 16 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAATATATAATAAA
Found at i:1332825 original size:24 final size:25
Alignment explanation
Indices: 1332798--1332845 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1332788 TAATATATAA
1332798 TAAA-AATA-ATATGTTTTCAAAAAT
1 TAAATAATATATATG-TTTCAAAAAT
*
1332822 TAAATATTATATATGTTTCAAAAA
1 TAAATAATATATATGTTTCAAAAA
1332846 AATCATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 12 0.57
26 5 0.24
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
TAAATAATATATATGTTTCAAAAAT
Found at i:1332945 original size:38 final size:35
Alignment explanation
Indices: 1332880--1332995 Score: 151
Period size: 36 Copynumber: 3.1 Consensus size: 35
1332870 TATATATATT
*
1332880 TTTTCAAAATATGTTTTCAAAACTATATTATATACG
1 TTTTCAAAA-ATGTTTTTAAAACTATATTATATACG
*
1332916 TTTTCAAAAATCGTTTTTAAAACTATATATATTATTCG
1 TTTTCAAAAAT-GTTTTTAAAACTATAT-TA-TATACG
*
1332954 TTTTCAAAAATGTGTTTTCAAAACTATATTATATATG
1 TTTTCAAAAATGT-TTTT-AAAACTATATTATATACG
1332991 TTTTC
1 TTTTC
1332996 CAAACTATAT
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
35 2 0.03
36 24 0.34
37 13 0.18
38 22 0.31
39 10 0.14
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.47
Consensus pattern (35 bp):
TTTTCAAAAATGTTTTTAAAACTATATTATATACG
Found at i:1333011 original size:25 final size:23
Alignment explanation
Indices: 1332966--1333022 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1332956 TTCAAAAATG
1332966 TGTTTTCAAAACTATATTATATA
1 TGTTTTCAAAACTATATTATATA
*
1332989 TGTTTTCCAAACTATATTATATA
1 TGTTTTCAAAACTATATTATATA
*
1333012 TGTTTTTAAAA
1 TGTTTTCAAAA
1333023 TTGTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (23 bp):
TGTTTTCAAAACTATATTATATA
Found at i:1333038 original size:36 final size:36
Alignment explanation
Indices: 1332997--1333116 Score: 152
Period size: 36 Copynumber: 3.3 Consensus size: 36
1332987 TATGTTTTCC
*
1332997 AAACTATATTA-TATATGTTTTTAAAATTGTTTTAAA
1 AAACTATA-TACTATATGTTTTTAAAACTGTTTTAAA
* *
1333033 AAACTATATACTATATGTTTTCAAAACCGTTTTTAAAA
1 AAACTATATACTATATGTTTTTAAAACTG-TTTT-AAA
* * *
1333071 AAACTATATATTATACGTTTTTAAAACTATTTTAAA
1 AAACTATATACTATATGTTTTTAAAACTGTTTTAAA
1333107 AAACTATATA
1 AAACTATATA
1333117 TTATTATATA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 2 0.03
36 36 0.49
37 8 0.11
38 27 0.37
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.43
Consensus pattern (36 bp):
AAACTATATACTATATGTTTTTAAAACTGTTTTAAA
Found at i:1334513 original size:13 final size:12
Alignment explanation
Indices: 1334484--1334512 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1334474 AAATAAAAAT
1334484 AAAAAGTCAAGG
1 AAAAAGTCAAGG
1334496 AAAAAGTCAAGG
1 AAAAAGTCAAGG
1334508 AAAAA
1 AAAAA
1334513 ATAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (12 bp):
AAAAAGTCAAGG
Found at i:1334616 original size:2 final size:2
Alignment explanation
Indices: 1334609--1334660 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1334599 AATTAGAAAC
1334609 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1334651 AT AT AT AT AT
1 AT AT AT AT AT
1334661 GATTAGAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1336147 original size:34 final size:34
Alignment explanation
Indices: 1336075--1336254 Score: 190
Period size: 34 Copynumber: 5.2 Consensus size: 34
1336065 GAAGGTTTGG
* *
1336075 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTT
1 TGTTTCAAGAGAAACAATTTCAAAGG-TTTTTTTA
*
1336110 TGTGATTCAAGAGAAACAATTTCAAAGGTTTTTTTG
1 TGT--TTCAAGAGAAACAATTTCAAAGGTTTTTTTA
*
1336146 TGTGTCAAGAGAAACAATGTT-AAAGGTTTTTTTA
1 TGTTTCAAGAGAAACAAT-TTCAAAGGTTTTTTTA
* * *
1336180 TGTTTTAAGAGAAAC--TGTCTTAAGGTTTTTTTA
1 TGTTTCAAGAGAAACAATTTC-AAAGGTTTTTTTA
*
1336213 TGTTTCAAGA-AAA-AATGTTTCAAAGGTTTTTTTC
1 TGTTTCAAGAGAAACAA--TTTCAAAGGTTTTTTTA
1336247 TGTTTCAA
1 TGTTTCAA
1336255 AGGTTTTTTT
Statistics
Matches: 124, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
31 1 0.01
32 4 0.03
33 21 0.17
34 58 0.47
35 8 0.06
36 10 0.08
37 22 0.18
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (34 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTA
Found at i:1336222 original size:67 final size:68
Alignment explanation
Indices: 1336075--1336254 Score: 199
Period size: 67 Copynumber: 2.6 Consensus size: 68
1336065 GAAGGTTTGG
* * *
1336075 TGTTTCAAGAGAAAC-ATTTTCAAAGGTTTTTTTTTTGTGATTCAAGAGAAACAATTTCAAAGGT
1 TGTTTCAAGAGAAACAATGTTCAAAGG-TTTTTTTATGT--TTCAAGAGAAAC-ATGTCAAAGGT
*
1336139 TTTTTTG
62 TTTTTTA
* * *
1336146 TGTGTCAAGAGAAACAATGTT-AAAGGTTTTTTTATGTTTTAAGAGAAAC-TGTCTTAAGGTTTT
1 TGTTTCAAGAGAAACAATGTTCAAAGGTTTTTTTATGTTTCAAGAGAAACATGTC-AAAGGTTTT
1336209 TTTA
65 TTTA
*
1336213 TGTTTCAAGA-AAA-AATGTTTCAAAGGTTTTTTTCTGTTTCAA
1 TGTTTCAAGAGAAACAATG-TTCAAAGGTTTTTTTATGTTTCAA
1336255 AGGTTTTTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
65 4 0.04
66 8 0.08
67 39 0.41
68 11 0.12
70 10 0.11
71 19 0.20
72 4 0.04
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (68 bp):
TGTTTCAAGAGAAACAATGTTCAAAGGTTTTTTTATGTTTCAAGAGAAACATGTCAAAGGTTTTT
TTA
Found at i:1336252 original size:19 final size:20
Alignment explanation
Indices: 1336227--1336274 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1336217 TCAAGAAAAA
1336227 ATGTTTCAAAGG-TTTTTTT
1 ATGTTTCAAAGGTTTTTTTT
*
1336246 CTGTTTCAAAGGTTTTTTTT
1 ATGTTTCAAAGGTTTTTTTT
1336266 ATGTTTCAA
1 ATGTTTCAA
1336275 GATAAACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (20 bp):
ATGTTTCAAAGGTTTTTTTT
Found at i:1336350 original size:37 final size:36
Alignment explanation
Indices: 1336300--1336528 Score: 206
Period size: 36 Copynumber: 6.6 Consensus size: 36
1336290 AGATTGGTGC
*
1336300 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* *
1336337 TTCAAGGGAAACTGTCTTAAGAGAGACAAAATTTGA
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * *
1336373 TTCAAGGGAAAATGTCTCAATAGAGA-AAATTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * * *
1336408 TTTAAGAGAAAATGTCTCAAGGGAGACGAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
1336444 TTTAAGGAAAACAGAT-TC-A-A-AG----ATTTTGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTTGT
1336473 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* ** *
1336509 TTTAAAAGAAAATGTCTCAA
1 TTCAAGGGAAACTGTCTCAA
1336529 AAGAAAGAAA
Statistics
Matches: 154, Mismatches: 28, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.01
29 19 0.12
30 1 0.01
31 1 0.01
32 2 0.01
33 2 0.01
35 30 0.19
36 68 0.44
37 30 0.19
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (36 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:1336440 original size:71 final size:72
Alignment explanation
Indices: 1336300--1336528 Score: 195
Period size: 65 Copynumber: 3.3 Consensus size: 72
1336290 AGATTGGTGC
* * * *
1336300 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTTAAGAGAGACA
1 TTCAAGAGAAAATGTCTCAAGAGAGA-AAAACTTTGTTTCAAGAGAAAATGTCTCAAGAGAGACA
1336365 AAATTTGA
65 AAATTTGA
* * * * * *
1336373 TTCAAGGGAAAATGTCTCAATAGAG-AAAATTTTGTTTTAAGAGAAAATGTCTCAAGGGAGACGA
1 TTCAAGAGAAAATGTCTCAAGAGAGAAAAACTTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAA
*
1336437 AATTTGT
66 AATTTGA
* *** * * * *
1336444 TTTAAG-GAAAA-----C-AGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTCAAGAGAAAATGTCTCAAGAGAGAAAAACTTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAA
*
1336502 AATTTGT
66 AATTTGA
* *
1336509 TTTAAAAGAAAATGTCTCAA
1 TTCAAGAGAAAATGTCTCAA
1336529 AAGAAAGAAA
Statistics
Matches: 125, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
64 2 0.02
65 46 0.37
66 5 0.04
70 5 0.04
71 44 0.35
72 1 0.01
73 22 0.18
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (72 bp):
TTCAAGAGAAAATGTCTCAAGAGAGAAAAACTTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAA
AATTTGA
Found at i:1336529 original size:65 final size:66
Alignment explanation
Indices: 1336332--1336529 Score: 213
Period size: 65 Copynumber: 2.9 Consensus size: 66
1336322 GAGACAAAAC
* * * *
1336332 TTTGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAATTTGATTCAAGGGAAAATGTCTCAATAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAGGAAAATGTCTC-A-A-A
1336397 GAAAAT
63 G--AAT
* * * * * *
1336403 TTTGTTTTAAGAGAAAATGTCTCAAGGGAGACGAAATTTGTTTT-AAGGAAAACAGAT-TCAAAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAGGAAAA-TG-TCTCAAAG
1336466 -AT
64 AAT
*
1336468 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAAATGTCTCAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAGGAAAATGTCTCAAA
1336530 AGAAAGAAAG
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
64 1 0.01
65 47 0.44
66 7 0.07
68 2 0.02
69 1 0.01
70 8 0.08
71 39 0.37
72 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (66 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAGGAAAATGTCTCAAAGAA
T
Found at i:1343714 original size:18 final size:16
Alignment explanation
Indices: 1343674--1343721 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 16
1343664 CAAAGGGTTA
1343674 AAAATAAAGTCAAATAAT
1 AAAATAAA-T-AAATAAT
1343692 AAAATAAATAAATAAT
1 AAAATAAATAAATAAT
1343708 ATTAAATAAATAAA
1 A--AAATAAATAAA
1343722 AGAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.29
17 1 0.04
18 19 0.68
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (16 bp):
AAAATAAATAAATAAT
Found at i:1344830 original size:9 final size:9
Alignment explanation
Indices: 1344808--1344851 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
1344798 ATTAAATAAG
1344808 AAATAAAA-
1 AAATAAAAT
1344816 AAATAAAAT
1 AAATAAAAT
1344825 AAATAAAAT
1 AAATAAAAT
*
1344834 AAATAATAT
1 AAATAAAAT
1344843 ATAATAAAA
1 A-AATAAAA
1344852 ATAATATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 8 0.25
9 18 0.56
10 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1344858 original size:14 final size:14
Alignment explanation
Indices: 1344801--1344857 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
1344791 AAATGAAATT
*
1344801 AAATAAGAAATAAAA
1 AAATAA-AAATAATA
1344816 AAAT-AAAATAAATA
1 AAATAAAAAT-AATA
1344830 AAATAAATAAT-ATA
1 AAATAAA-AATAATA
*
1344844 TAATAAAAATAATA
1 AAATAAAAATAATA
1344858 TGTTTTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 7 0.19
14 20 0.56
15 6 0.17
16 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (14 bp):
AAATAAAAATAATA
Found at i:1344897 original size:59 final size:59
Alignment explanation
Indices: 1344834--1344954 Score: 131
Period size: 59 Copynumber: 2.0 Consensus size: 59
1344824 TAAATAAAAT
* * *
1344834 AAATAATATATAATAAAA-ATA-ATATGTTTTCAAAAATTAAATATTATATATG-TTTCAAA
1 AAATAATATATAAAAAAACATATATATGTTTTC-AAAAGT--ATATTATATACGTTTTCAAA
* * *
1344893 AAATAGTTTTTAAAAAAACTATATATATGTTTTCAAAAGTATATTATATACGTTTTCAAA
1 AAATAATATATAAAAAAAC-ATATATATGTTTTCAAAAGTATATTATATACGTTTTCAAA
1344953 AA
1 AA
1344955 TCATTTTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
59 25 0.48
60 9 0.17
61 8 0.15
62 10 0.19
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (59 bp):
AAATAATATATAAAAAAACATATATATGTTTTCAAAAGTATATTATATACGTTTTCAAA
Found at i:1344930 original size:23 final size:23
Alignment explanation
Indices: 1344898--1344954 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1344888 TCAAAAAATA
* *
1344898 GTTTTTAAAAAAACTA-TATATAT
1 GTTTTCAAAAAAA-TATTATATAC
**
1344921 GTTTTCAAAAGTATATTATATAC
1 GTTTTCAAAAAAATATTATATAC
1344944 GTTTTCAAAAA
1 GTTTTCAAAAA
1344955 TCATTTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (23 bp):
GTTTTCAAAAAAATATTATATAC
Found at i:1345078 original size:35 final size:34
Alignment explanation
Indices: 1344920--1345127 Score: 190
Period size: 35 Copynumber: 5.8 Consensus size: 34
1344910 ACTATATATA
* *
1344920 TGTTTTCAAAAGTATATTATATACGTTTTCAAAAATC
1 TGTTTT-AAAACTATA-TATATATGTTTTCAAAAA-C
*
1344957 AT-TTTTAAAACTATATATATTATTCGTTTTCAAAAATG
1 -TGTTTTAAAACTATATATA-TA-T-GTTTTCAAAAA-C
*
1344995 TGTTTTCAAAACTATATTATATATTTTTTCAAAAAC
1 TGTTTT-AAAACTATA-TATATATGTTTTCAAAAAC
*
1345031 T-TTTAAAAACTATATACTATATGTTTTC-AAAAC
1 TGTTTTAAAACTATATA-TATATGTTTTCAAAAAC
*
1345064 TGTTTTAAATACTATATATGATATGTTTT-TAAAAC
1 TGTTTTAAA-ACTATATAT-ATATGTTTTCAAAAAC
*
1345099 TATTTTAAAAACTATATATTATATGTTTT
1 TGTTTT-AAAACTATATA-TATATGTTTT
1345128 TTTTAAATAA
Statistics
Matches: 148, Mismatches: 9, Indels: 29
0.80 0.05 0.16
Matches are distributed among these distances:
33 8 0.05
34 26 0.18
35 51 0.34
36 15 0.10
37 15 0.10
38 18 0.12
39 11 0.07
40 4 0.03
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (34 bp):
TGTTTTAAAACTATATATATATGTTTTCAAAAAC
Found at i:1345082 original size:71 final size:71
Alignment explanation
Indices: 1344920--1345127 Score: 223
Period size: 75 Copynumber: 2.9 Consensus size: 71
1344910 ACTATATATA
* * *
1344920 TGTTTTCAAAAGTATATTATATACGTTTTCAAAAATCATTTTTAAAACTATATATATTATTCGTT
1 TGTTTTCAAAACTATATTATATACTTTTTCAAAAA-CATTTTAAAAACTATATATA-TA-T-GTT
*
1344985 TTCAAAAATG
62 TTCAAAAATC
*
1344995 TGTTTTCAAAACTATATTATATATTTTTTCAAAAAC-TTTTAAAAACTATATACTATATGTTTTC
1 TGTTTTCAAAACTATATTATATACTTTTTCAAAAACATTTTAAAAACTATATA-TATATGTTTTC
1345059 -AAAA-C
65 AAAAATC
*
1345064 TGTTTT-AAATACTATA-TATGATA-TGTTTT-TAAAACTATTTTAAAAACTATATATTATATGT
1 TGTTTTCAAA-ACTATATTAT-ATACT-TTTTCAAAAAC-ATTTTAAAAACTATATA-TATATGT
1345125 TTT
61 TTT
1345128 TTTTAAATAA
Statistics
Matches: 120, Mismatches: 7, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
68 12 0.10
69 19 0.16
70 30 0.25
71 6 0.05
72 1 0.01
73 17 0.14
74 3 0.03
75 32 0.27
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (71 bp):
TGTTTTCAAAACTATATTATATACTTTTTCAAAAACATTTTAAAAACTATATATATATGTTTTCA
AAAATC
Found at i:1345130 original size:37 final size:37
Alignment explanation
Indices: 1345007--1345166 Score: 145
Period size: 35 Copynumber: 4.4 Consensus size: 37
1344997 TTTTCAAAAC
*
1345007 TATATTATATATTTTTTCAAAA-ACTTTTAAAAACTA
1 TATATTATATGTTTTTTCAAAATACTTTTAAAAACTA
* * *
1345043 TATACTATATG--TTTTCAAAACT-GTTTTAAATACTA
1 TATATTATATGTTTTTTCAAAA-TACTTTTAAAAACTA
*
1345078 TATATGATATG-TTTTT-AAAACTA-TTTTAAAAACTA
1 TATATTATATGTTTTTTCAAAA-TACTTTTAAAAACTA
** * *
1345113 TATATTATATGTTTTTTTTAAATAAGTTTCCAAAAACTA
1 TATATTATATGTTTTTTCAAAAT-ACTTT-TAAAAACTA
*
1345152 TATATTATATATTTT
1 TATATTATATGTTTT
1345167 CAAAAACCAT
Statistics
Matches: 104, Mismatches: 11, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
34 9 0.09
35 47 0.45
36 19 0.18
37 4 0.04
38 3 0.03
39 22 0.21
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (37 bp):
TATATTATATGTTTTTTCAAAATACTTTTAAAAACTA
Found at i:1345698 original size:17 final size:17
Alignment explanation
Indices: 1345671--1345711 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1345661 GAGATAGTTC
*
1345671 CTCATTGATGCAAATGA
1 CTCATTTATGCAAATGA
* *
1345688 TTCATTTATGCAGATGA
1 CTCATTTATGCAAATGA
1345705 CTCATTT
1 CTCATTT
1345712 GTTGTGAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (17 bp):
CTCATTTATGCAAATGA
Found at i:1350084 original size:23 final size:23
Alignment explanation
Indices: 1350048--1350111 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1350038 GTCGAGGGTT
* *
1350048 CTATGTGGTACTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAA
* *
1350071 CTATGTAGTCCTTCGGGATAAAA
1 CTATGTGGTCCTTCGGGACAAAA
*
1350094 CTATGTGGTCATTCGGGA
1 CTATGTGGTCCTTCGGGA
1350112 AATATATGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:1354762 original size:37 final size:36
Alignment explanation
Indices: 1354703--1354870 Score: 141
Period size: 37 Copynumber: 5.0 Consensus size: 36
1354693 CGAAGGTTTG
*
1354703 GTGT-TTCAAGAGAAACATTTTCAAAGGTTTTTTTT
1 GTGTGTTCAAGAGAAACAATTTCAAAGGTTTTTTTT
*
1354738 TTGTGATTCAAGAGAAACAATTTCAAAGGTTTTTTTT
1 GTGTG-TTCAAGAGAAACAATTTCAAAGGTTTTTTTT
1354775 GTGTG-TC-A-AGAAACAATGTT-AAAGG-TTTTTTT
1 GTGTGTTCAAGAGAAACAAT-TTCAAAGGTTTTTTTT
* *
1354807 GT-T-TT-AAGAGAAAC--TGTCTTAAGG-TTTTTTT
1 GTGTGTTCAAGAGAAACAATTTC-AAAGGTTTTTTTT
* *
1354838 ATGT-TTCAAGA-AAA-ATGTTTCAAAGGTTTTTTT
1 GTGTGTTCAAGAGAAACA-ATTTCAAAGGTTTTTTT
1354871 CTGTTTCAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 29
0.75 0.05 0.20
Matches are distributed among these distances:
29 1 0.01
30 1 0.01
31 15 0.14
32 21 0.19
33 22 0.20
34 12 0.11
35 5 0.05
37 34 0.31
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (36 bp):
GTGTGTTCAAGAGAAACAATTTCAAAGGTTTTTTTT
Found at i:1354837 original size:33 final size:32
Alignment explanation
Indices: 1354704--1354879 Score: 123
Period size: 33 Copynumber: 5.2 Consensus size: 32
1354694 GAAGGTTTGG
*
1354704 TGTTTCAAGAGAAACAT-TTTCAAAGGTTTTTTTTT
1 TGTTTCAAGA-AAA-ATGTTT-AAAGG-TTTTTTTA
*
1354739 TGTGATTCAAGAGAAACAAT-TTCAAAGGTTTTTTT-
1 TGT--TTC-A-AGAAA-AATGTTTAAAGGTTTTTTTA
1354774 TGTGTGTCAAGAAACAATG-TTAAAGG-TTTTTT-
1 TGT-T-TCAAGAAA-AATGTTTAAAGGTTTTTTTA
* *
1354806 TGTTTTAAGAGAAACTGTCTT-AAGGTTTTTTTA
1 TGTTTCAAGA-AAAATGT-TTAAAGGTTTTTTTA
*
1354839 TGTTTCAAGAAAAATGTTTCAAAGGTTTTTTTC
1 TGTTTCAAGAAAAATGTTT-AAAGGTTTTTTTA
1354872 TGTTTCAA
1 TGTTTCAA
1354880 AGGTTTTTTT
Statistics
Matches: 119, Mismatches: 8, Indels: 30
0.76 0.05 0.19
Matches are distributed among these distances:
30 8 0.07
31 9 0.08
32 23 0.19
33 43 0.36
34 2 0.02
35 8 0.07
36 7 0.06
37 8 0.07
38 7 0.06
39 4 0.03
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (32 bp):
TGTTTCAAGAAAAATGTTTAAAGGTTTTTTTA
Found at i:1354877 original size:19 final size:20
Alignment explanation
Indices: 1354852--1354899 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1354842 TTCAAGAAAA
1354852 ATGTTTCAAAGG-TTTTTTT
1 ATGTTTCAAAGGTTTTTTTT
*
1354871 CTGTTTCAAAGGTTTTTTTT
1 ATGTTTCAAAGGTTTTTTTT
1354891 ATGTTTCAA
1 ATGTTTCAA
1354900 GATAAACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (20 bp):
ATGTTTCAAAGGTTTTTTTT
Found at i:1354975 original size:37 final size:36
Alignment explanation
Indices: 1354925--1355153 Score: 199
Period size: 36 Copynumber: 6.6 Consensus size: 36
1354915 AGATTGGTGC
*
1354925 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGT
*
1354962 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGA
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * *
1354998 TTCAAGGGAAAATGTCTCAATAGAGA-AAATTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
** * * *
1355033 CTT-AAGAAAAAATGTCTCAAGGGAGACGAAATTTGT
1 -TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
1355069 TTTAAGGAAAACAGAT-TC-A-A-AG----ATTTTGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTTGT
1355098 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* ** *
1355134 TTTAAAAGAAAATGTCTCAA
1 TTCAAGGGAAACTGTCTCAA
1355154 AAGAAAGAAA
Statistics
Matches: 155, Mismatches: 25, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.01
29 19 0.12
30 1 0.01
31 1 0.01
32 2 0.01
33 2 0.01
35 29 0.19
36 69 0.45
37 31 0.20
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (36 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:1355059 original size:71 final size:72
Alignment explanation
Indices: 1354925--1355153 Score: 179
Period size: 65 Copynumber: 3.3 Consensus size: 72
1354915 AGATTGGTGC
* ** *
1354925 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TTCAAGAGAAAATGTCTCAAGAGAGA-AAAACTTTGTTTCAAGAAAAAATGTCTCAAGAGAGACA
1354990 AAATTTGA
65 AAATTTGA
* * * * *
1354998 TTCAAGGGAAAATGTCTCAATAGAG-AAAATTTTGTCTT-AAGAAAAAATGTCTCAAGGGAGACG
1 TTCAAGAGAAAATGTCTCAAGAGAGAAAAACTTTGT-TTCAAGAAAAAATGTCTCAAGAGAGACA
*
1355061 AAATTTGT
65 AAATTTGA
* *** * * ** *
1355069 TTTAAG-GAAAA-----C-AGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTCAAGAGAAAATGTCTCAAGAGAGAAAAACTTTGTTTCAAGAAAAAATGTCTCAAGAGAGACAA
*
1355127 AATTTGT
66 AATTTGA
* *
1355134 TTTAAAAGAAAATGTCTCAA
1 TTCAAGAGAAAATGTCTCAA
1355154 AAGAAAGAAA
Statistics
Matches: 124, Mismatches: 22, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
64 4 0.03
65 43 0.35
66 5 0.04
70 5 0.04
71 42 0.34
72 3 0.02
73 22 0.18
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (72 bp):
TTCAAGAGAAAATGTCTCAAGAGAGAAAAACTTTGTTTCAAGAAAAAATGTCTCAAGAGAGACAA
AATTTGA
Found at i:1355154 original size:65 final size:66
Alignment explanation
Indices: 1354957--1355154 Score: 206
Period size: 65 Copynumber: 2.9 Consensus size: 66
1354947 GAGACAAAAC
* * *
1354957 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGATTCAAGGGAAAATGTCTCAATAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAGGAAAATGTCTC-A-A-A
1355022 GAAAAT
63 G--AAT
** * * * *
1355028 TTTGTCTT-AAGAAAAAATGTCTCAAGGGAGACGAAATTTGTTTT-AAGGAAAACAGAT-TCAAA
1 TTTGT-TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAGGAAAA-TG-TCTCAAA
1355090 G-AT
63 GAAT
*
1355093 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAAATGTCTCAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAGGAAAATGTCTCAAA
1355155 AGAAAGAAAG
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
64 3 0.03
65 44 0.42
66 7 0.07
68 2 0.02
69 1 0.01
70 8 0.08
71 37 0.35
72 3 0.03
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.29
Consensus pattern (66 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAGGAAAATGTCTCAAAGAA
T
Found at i:1362070 original size:18 final size:20
Alignment explanation
Indices: 1362039--1362083 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
1362029 AAAGGGTTAA
1362039 AAATAAAGTCAATAATAAAT
1 AAATAAAGTCAATAATAAAT
*
1362059 AAATAAA-T-AATATTAAAT
1 AAATAAAGTCAATAATAAAT
1362077 AAATAAA
1 AAATAAA
1362084 AGAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.67
19 1 0.04
20 7 0.29
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATAAAGTCAATAATAAAT
Found at i:1363225 original size:8 final size:8
Alignment explanation
Indices: 1363182--1363227 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
1363172 TTAAATAAGA
*
1363182 AATAAAAA
1 AATAAAAT
*
1363190 AATAAAAA
1 AATAAAAT
1363198 AATAAAAT
1 AATAAAAT
1363206 AATAATATAT
1 AATAA-A-AT
1363216 AATAAAAT
1 AATAAAAT
1363224 AATA
1 AATA
1363228 TGTTTTCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
8 26 0.74
9 2 0.06
10 7 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:1363331 original size:58 final size:58
Alignment explanation
Indices: 1363225--1363345 Score: 151
Period size: 58 Copynumber: 2.1 Consensus size: 58
1363215 TAATAAAATA
* *
1363225 ATATGTTTTCAAAAATTAAATATTATATATGTTTCAAAAAATAGTTTTTAAAAAACTATAT
1 ATATGTTTTCAAAAAGT-AATATTATATACGTTTCAAAAAATAGTTTTT--AAAACTATAT
1363286 ATATGTTTTC-AAAAGT-ATATTATATACGTTTTC-AAAAATCA-TTTTTAAAACTATAT
1 ATATGTTTTCAAAAAGTAATATTATATACG-TTTCAAAAAAT-AGTTTTTAAAACTATAT
1363342 ATAT
1 ATAT
1363346 TATTCGTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
56 14 0.25
58 22 0.39
59 5 0.09
60 5 0.09
61 10 0.18
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (58 bp):
ATATGTTTTCAAAAAGTAATATTATATACGTTTCAAAAAATAGTTTTTAAAACTATAT
Found at i:1363417 original size:34 final size:33
Alignment explanation
Indices: 1363291--1363531 Score: 186
Period size: 35 Copynumber: 6.9 Consensus size: 33
1363281 TATATATATG
* * **
1363291 TTTTCAAAAGTATATTATATACGTTTTCAAAAATC
1 TTTTTAAAACTATA-TATATATTTTTTCAAAAA-C
1363326 ATTTTTAAAACTATATATATTATTCGTTTTCAAAAA-
1 -TTTTTAAAACTATATATA-TATT--TTTTCAAAAAC
*
1363362 TTTTTCAAACTATATTATATATTTTTTCAAAAAC
1 TTTTTAAAACTATA-TATATATTTTTTCAAAAAC
* *
1363396 TTTTAAAAACTATATACTATATTTTTTC-TAAAC
1 TTTTTAAAACTATATA-TATATTTTTTCAAAAAC
1363429 TGTTTTAAATACTATATATGATATGTTTTT--AAAAC
1 T-TTTTAAA-ACTATATAT-ATAT-TTTTTCAAAAAC
* *
1363464 TATTTTAAAACTATATATTATATGTTTTTTTAAATAAG
1 T-TTTTAAAACTATATA-TATA--TTTTTTCAAA-AAC
** *
1363502 TTTCCAAAACTAT-TATATATATTTTCAAAA
1 TTTTTAAAACTATATATATATTTTTTCAAAA
1363532 CCATATTTGA
Statistics
Matches: 173, Mismatches: 16, Indels: 36
0.77 0.07 0.16
Matches are distributed among these distances:
32 1 0.01
33 25 0.14
34 41 0.24
35 55 0.32
36 26 0.15
37 12 0.07
38 13 0.08
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (33 bp):
TTTTTAAAACTATATATATATTTTTTCAAAAAC
Found at i:1363474 original size:69 final size:65
Alignment explanation
Indices: 1363291--1363497 Score: 184
Period size: 69 Copynumber: 3.0 Consensus size: 65
1363281 TATATATATG
* * * *
1363291 TTTTCAAAAGTATATTATATACGTTTTCAAAAATCATTTTTAAAACTATATATATTATTCGTTTT
1 TTTTTAAAACTATATTATATA-TTTTTTAAAAA-C-TTTTTAAAACTATATATA-TATT--TTTT
*
1363356 CAAAAA
60 CTAAAA
* *
1363362 TTTTTCAAACTATATTATATATTTTTTCAAAAACTTTTAAAAACTATATACTATATTTTTTCTAA
1 TTTTTAAAACTATATTATATATTTTTT-AAAAACTTTTTAAAACTATATA-TATATTTTTTCTAA
*
1363427 AC
64 AA
1363429 TGTTTTAAATACTATA-TATGATATGTTTTT-AAAACTATTTTAAAACTATATATTATATGTTTT
1 T-TTTTAAA-ACTATATTAT-ATAT-TTTTTAAAAACT-TTTTAAAACTATATA-TATAT-TTTT
*
1363492 TTTAAA
59 TCTAAA
1363498 TAAGTTTCCA
Statistics
Matches: 116, Mismatches: 12, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
67 9 0.08
68 15 0.13
69 48 0.41
70 21 0.18
71 23 0.20
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (65 bp):
TTTTTAAAACTATATTATATATTTTTTAAAAACTTTTTAAAACTATATATATATTTTTTCTAAAA
Found at i:1363532 original size:69 final size:66
Alignment explanation
Indices: 1363303--1363532 Score: 180
Period size: 69 Copynumber: 3.3 Consensus size: 66
1363293 TTCAAAAGTA
** * * * *
1363303 TATTATATACGTTTTCAAAAATCATTTTTAAAACTATATA-TATTATTCGTTTTCAAAAATTTTT
1 TATTATATATATTTTC-AAAA-C-TTTTAAAAACTATATACTA-TATT--TTTTCTAAACTGTTT
1363367 CAAACTA-
60 CAAA-TAC
* *
1363374 TATTATATATTTTTTCAAAAACTTTTAAAAACTATATACTATATTTTTTCTAAACTGTTTTAAAT
1 TATTATATATATTTTC-AAAACTTTTAAAAACTATATACTATATTTTTTCTAAACTGTTTCAAAT
1363439 AC
65 AC
* * * * *
1363441 TATATATGATATGTTTTTAAAACTATTTTAAAACTATATATTATATGTTTTTTTAAA-TAAGTTT
1 TAT-TAT-ATATATTTTCAAAACT-TTTAAAAACTATATACTATAT-TTTTTCTAAACT--GTTT
1363505 CCAAA-AC
60 -CAAATAC
1363512 TATTATATATATTTTCAAAAC
1 TATTATATATATTTTCAAAAC
1363533 CATATTTGAA
Statistics
Matches: 135, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
66 2 0.01
67 18 0.13
68 9 0.07
69 60 0.44
70 15 0.11
71 28 0.21
72 3 0.02
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.48
Consensus pattern (66 bp):
TATTATATATATTTTCAAAACTTTTAAAAACTATATACTATATTTTTTCTAAACTGTTTCAAATA
C
Found at i:1364056 original size:17 final size:17
Alignment explanation
Indices: 1364029--1364069 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1364019 GAGATAGTTC
*
1364029 CTCATTGATGCAAATGA
1 CTCATTTATGCAAATGA
* *
1364046 TTCATTTATGCAGATGA
1 CTCATTTATGCAAATGA
1364063 CTCATTT
1 CTCATTT
1364070 GTTGAAGTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (17 bp):
CTCATTTATGCAAATGA
Found at i:1365581 original size:27 final size:21
Alignment explanation
Indices: 1365528--1365569 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1365518 AGGTTCAATT
1365528 GATCATATTGAGTTTGCACCA
1 GATCATATTGAGTTTGCACCA
1365549 GATCATATTGAGTTTGCACCA
1 GATCATATTGAGTTTGCACCA
1365570 ATTCTGCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (21 bp):
GATCATATTGAGTTTGCACCA
Found at i:1368384 original size:23 final size:23
Alignment explanation
Indices: 1368348--1368408 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
1368338 GTCGAGGGTT
* *
1368348 CTATGTGGTACTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAA
* *
1368371 CTATGTAGTCCTTC-GGATAAAA
1 CTATGTGGTCCTTCGGGACAAAA
*
1368393 CTATGTGGTCATTCGG
1 CTATGTGGTCCTTCGG
1368409 AAATATATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:1372046 original size:280 final size:280
Alignment explanation
Indices: 1371541--1372101 Score: 1024
Period size: 280 Copynumber: 2.0 Consensus size: 280
1371531 TTAGAAATTT
*
1371541 CAGGAACTTCACCTCCTCTTTTCCTTTATTGGCTCATTTACTACTAGCACGTCCTCTTTGAATGG
1 CAGGAACTTCACATCCTCTTTTCCTTTATTGGCTCATTTACTACTAGCACGTCCTCTTTGAATGG
1371606 TTTTCAAGTTGTCTCTGGGGTAAGTAGACTTTTGGGAGTATTACTTCCCAACAGTATGCCCCACT
66 -TTTCAAGTTGTCTCTGGGGTAAGTAGACTTTTGGGAGTATTACTTCCCAACAGTATGCCCCACT
1371671 TCGTTGATATCTTCCTTTAAAGTGCTTATTACATTCATACTTCCAATGCACTTGTTTGTTGTCTT
130 TCGTTGATATCTTCCTTTAAAGTGCTTATTACATTCATACTTCCAATGCACTTGTTTGTTGTCTT
1371736 TGTAAGGAAAGGTCTTGGTGCGACTATCACCACCTTTATTGGTGTTTTATCTGTTTCTTTAACTT
195 TGTAAGGAAAGGTCTTGGTGCGACTATCACCACCTTTATTGGTGTTTTATCTGTTTCTTTAACTT
1371801 TGGGGTGA-TATCAAAAGATG
260 TGGGGTGATTATCAAAAGATG
1371821 CAGGAACTTCACATCCTCTTTTTCCTTTA-TGGCTCATTTACTACTAGCACGT-C-CTTTGAATG
1 CAGGAACTTCACATCCTC-TTTTCCTTTATTGGCTCATTTACTACTAGCACGTCCTCTTTGAATG
1371883 G-TTCAAGTTGTCTCTGGGGTAAGTTAGACTTTTGGGAGTATTACTTCCCAACAGTATGCCCCAC
65 GTTTCAAGTTGTCTCTGGGGTAAG-TAGACTTTTGGGAGTATTACTTCCCAACAGTATGCCCCAC
1371947 TTCGTTGATATCTTCCTTTAAAGTGCTTATTTGACATTCATACTTCCAATGCACTTGTTTGTTGT
129 TTCGTTGATATCTTCCTTTAAAGTGCTTA-TT-ACATTCATACTTCCAATGCACTTGTTTGTTGT
1372012 CTTTGTAAGGAAAAGGTCTTGGTGCGACTATCACCACCTTTATTGGTGTTTTATCTGTTTCTTTA
192 CTTTGTAAGG-AAAGGTCTTGGTGCGACTATCACCACCTTTATTGGTGTTTTATCTGTTTCTTTA
1372077 ACTTTGGGGTGATTATCAAAAGATG
256 ACTTTGGGGTGATTATCAAAAGATG
1372102 GCCCGTGCCA
Statistics
Matches: 274, Mismatches: 1, Indels: 11
0.96 0.00 0.04
Matches are distributed among these distances:
276 22 0.08
277 69 0.25
278 12 0.04
279 43 0.16
280 106 0.39
281 22 0.08
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (280 bp):
CAGGAACTTCACATCCTCTTTTCCTTTATTGGCTCATTTACTACTAGCACGTCCTCTTTGAATGG
TTTCAAGTTGTCTCTGGGGTAAGTAGACTTTTGGGAGTATTACTTCCCAACAGTATGCCCCACTT
CGTTGATATCTTCCTTTAAAGTGCTTATTACATTCATACTTCCAATGCACTTGTTTGTTGTCTTT
GTAAGGAAAGGTCTTGGTGCGACTATCACCACCTTTATTGGTGTTTTATCTGTTTCTTTAACTTT
GGGGTGATTATCAAAAGATG
Found at i:1376284 original size:2 final size:2
Alignment explanation
Indices: 1376273--1376354 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
1376263 TTTTAAGAAT
1376273 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1376314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1376355 TCAGGTTGTG
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1390062 original size:3 final size:3
Alignment explanation
Indices: 1390054--1390082 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1390044 AGTTAGTAAG
1390054 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1390083 GAAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1391576 original size:9 final size:9
Alignment explanation
Indices: 1391564--1391615 Score: 63
Period size: 9 Copynumber: 5.9 Consensus size: 9
1391554 TTAAATAAGT
1391564 AATAATATA
1 AATAATATA
*
1391573 AATAAAAATA
1 AAT-AATATA
1391583 AATAATATA
1 AATAATATA
1391592 AATAATAT-
1 AATAATATA
*
1391600 -ATAATAAA
1 AATAATATA
1391608 AATAATAT
1 AATAATAT
1391616 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 6 0.17
9 22 0.61
10 8 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAATATA
Found at i:1391576 original size:16 final size:15
Alignment explanation
Indices: 1391555--1391614 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 15
1391545 AAAATGAAGT
1391555 TAAATAAGTAATAATA
1 TAAATAA-TAATAATA
1391571 TAAATAAAAATAAATAATA
1 TAAAT---AAT-AATAATA
1391590 TAAATAATATATAATA
1 TAAATAATA-ATAATA
*
1391606 AAAATAATA
1 TAAATAATA
1391615 TGTTTTCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 1 0.03
16 22 0.58
18 1 0.03
19 14 0.37
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
TAAATAATAATAATA
Found at i:1391614 original size:19 final size:19
Alignment explanation
Indices: 1391557--1391606 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1391547 AATGAAGTTA
*
1391557 AATAAGTAATAATATAAAT
1 AATAAATAATAATATAAAT
1391576 AA-AAATAAATAATATAAAT
1 AATAAAT-AATAATATAAAT
*
1391595 AATATATAATAA
1 AATAAATAATAA
1391607 AAATAATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AATAAATAATAATATAAAT
Found at i:1391615 original size:16 final size:16
Alignment explanation
Indices: 1391564--1391615 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
1391554 TTAAATAAGT
1391564 AATAATATA-AATAAA
1 AATAATATATAATAAA
*
1391579 AAT-A-A-ATAATATA
1 AATAATATATAATAAA
1391592 AATAATATATAATAAA
1 AATAATATATAATAAA
1391608 AATAATAT
1 AATAATAT
1391616 GTTTTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 1 0.03
13 9 0.29
14 2 0.06
15 4 0.13
16 15 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATATATAATAAA
Found at i:1391776 original size:75 final size:74
Alignment explanation
Indices: 1391659--1391878 Score: 254
Period size: 75 Copynumber: 3.0 Consensus size: 74
1391649 AAAAATCGTT
*
1391659 TTTTAAAAAACTATATGTATATATATT-TTTTC-AAAATATGTTTTCAAAACTATATTATATACG
1 TTTTAAAAAACTATA--TATAT-TATTGTTTTCAAAAATGTGTTTTCAAAACTATATTATATACG
1391722 TTTTCAAATATCA
63 TTTTCAAA-ATCA
* *
1391735 TTTT-TAAAACTATATATATTATTCGTTTTCAAAAATGTGTTTTCAAAACTATATTATATATGTT
1 TTTTAAAAAACTATATATATTATT-GTTTTCAAAAATGTGTTTTCAAAACTATATTATATACGTT
**
1391799 TTCAAAATTG
65 TTCAAAATCA
** * *
1391809 TTTTAAAAAACTATATACTA-TA-TGTTTTCAAAACCGTTTTTTAAAAACTATA-TATTATACGT
1 TTTTAAAAAACTATATA-TATTATTGTTTTCAAAAATGTGTTTTCAAAACTATATTA-TATACGT
1391871 TTTCAAAA
64 TTTCAAAA
1391879 CTATATATTA
Statistics
Matches: 127, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
72 6 0.05
73 44 0.35
74 12 0.09
75 59 0.46
76 6 0.05
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (74 bp):
TTTTAAAAAACTATATATATTATTGTTTTCAAAAATGTGTTTTCAAAACTATATTATATACGTTT
TCAAAATCA
Found at i:1391800 original size:37 final size:37
Alignment explanation
Indices: 1391631--1391878 Score: 199
Period size: 36 Copynumber: 6.6 Consensus size: 37
1391621 CAAAAATTAA
*
1391631 ATATTATATATG-TTTCAAAAAAATCGTTTTTTAAAAAACT
1 ATATTATATATGTTTTC--AAAAAT-GTGTTTT-AAAAACT
* * *
1391671 ATATGTATATATATTTTTTC-AAAATATGTTTTCAAAACT
1 ATA--T-TATATATGTTTTCAAAAATGTGTTTTAAAAACT
* * *
1391710 ATATTATATACGTTTTCAAATATCAT-TTTT-AAAACT
1 ATATTATATATGTTTTCAAAAAT-GTGTTTTAAAAACT
*
1391746 ATA-TATATTATTCGTTTTCAAAAATGTGTTTTCAAAACT
1 ATATTATA-TA-T-GTTTTCAAAAATGTGTTTTAAAAACT
1391785 ATATTATATATGTTTTC-AAAAT-TGTTTTAAAAAACT
1 ATATTATATATGTTTTCAAAAATGTGTTTT-AAAAACT
** *
1391821 ATA-TACTATATGTTTTCAAAACCGTTTTTTAAAAACT
1 ATATTA-TATATGTTTTCAAAAATGTGTTTTAAAAACT
*
1391858 ATA-TATTATACGTTTTCAAAA
1 ATATTA-TATATGTTTTCAAAA
1391879 CTATATATTA
Statistics
Matches: 176, Mismatches: 16, Indels: 35
0.78 0.07 0.15
Matches are distributed among these distances:
35 12 0.07
36 47 0.27
37 45 0.26
38 23 0.13
39 20 0.11
40 12 0.07
41 5 0.03
42 1 0.01
43 7 0.04
44 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (37 bp):
ATATTATATATGTTTTCAAAAATGTGTTTTAAAAACT
Found at i:1391879 original size:37 final size:37
Alignment explanation
Indices: 1391656--1391880 Score: 174
Period size: 37 Copynumber: 6.0 Consensus size: 37
1391646 CAAAAAAATC
**
1391656 GTTTTTTAAAAAACTATATGTATATATATTTTTTCAAAA-T
1 GTTTTTT-AAAAACTATA--TAT-TATACGTTTTCAAAACT
* * *
1391696 ATGTTTTCAAAACTATAT-TATATACGTTTTCAAATA-T
1 GTTTTTTAAAAACTATATAT-TATACGTTTTCAAA-ACT
** * *
1391733 CATTTTT-AAAACTATATATATTATTCGTTTTCAAAAAT
1 GTTTTTTAAAAAC--TATATATTATACGTTTTCAAAACT
* * * *
1391771 GTGTTTTCAAAACTATAT-TATATATGTTTTCAAAATT
1 GTTTTTTAAAAACTATATAT-TATACGTTTTCAAAACT
* * * *
1391808 G-TTTTAAAAAACTATATACTATATGTTTTCAAAACC
1 GTTTTTTAAAAACTATATATTATACGTTTTCAAAACT
1391844 GTTTTTTAAAAACTATATATTATACGTTTTCAAAACT
1 GTTTTTTAAAAACTATATATTATACGTTTTCAAAACT
1391881 ATATATTATT
Statistics
Matches: 151, Mismatches: 25, Indels: 21
0.77 0.13 0.11
Matches are distributed among these distances:
36 49 0.32
37 59 0.39
38 23 0.15
39 15 0.10
40 5 0.03
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (37 bp):
GTTTTTTAAAAACTATATATTATACGTTTTCAAAACT
Found at i:1393151 original size:21 final size:20
Alignment explanation
Indices: 1393121--1393190 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 20
1393111 TAATAATAAT
*
1393121 AATAATAATAAATGTTAAAAA
1 AATAAAAATAAATG-TAAAAA
*
1393142 AATAAAAATAAATG-GAAAA
1 AATAAAAATAAATGTAAAAA
* *
1393161 AAT-AAAA-AAATATATAAA
1 AATAAAAATAAATGTAAAAA
1393179 AATAAAAATAAA
1 AATAAAAATAAA
1393191 AAGTCAAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
17 4 0.10
18 10 0.24
19 11 0.27
20 3 0.07
21 13 0.32
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (20 bp):
AATAAAAATAAATGTAAAAA
Found at i:1393162 original size:19 final size:17
Alignment explanation
Indices: 1393138--1393190 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 17
1393128 ATAAATGTTA
1393138 AAAAAATAAAAATAAAT
1 AAAAAATAAAAATAAAT
1393155 GGAAAAAATAAAAA-AATAT
1 --AAAAAATAAAAATAA-AT
1393174 ATAAAAATAAAAATAAA
1 A-AAAAATAAAAATAAA
1393191 AAGTCAAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.03
18 14 0.45
19 16 0.52
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (17 bp):
AAAAAATAAAAATAAAT
Found at i:1394821 original size:34 final size:34
Alignment explanation
Indices: 1394742--1394975 Score: 206
Period size: 34 Copynumber: 6.7 Consensus size: 34
1394732 GAAGGTTTGG
* *
1394742 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG---TTTTTTTA
1394779 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTA
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTA
* *
1394813 TGTGTCAAGAGAAACAATTTTAAAGGTCTTTTTTA
1 TGTTTCAAGAGAAACAATTTCAAAGGT-TTTTTTA
* *** *
1394848 GTGTTTCAATAGAAATTGTCTC-AAGGTTTTTTTTTA
1 -TGTTTCAAGAGAAACAATTTCAAAGG--TTTTTTTA
*
1394884 TGTTTCAAGA-AAA-AATGTTTCAAAGGTTTTTTTC
1 TGTTTCAAGAGAAACAA--TTTCAAAGGTTTTTTTA
**** *
1394918 TGTTTCAAGA-AAATTGCTTCAAAGGTTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTA
* *
1394951 TGTTTCATGATAAACAATTTCAAAG
1 TGTTTCAAGAGAAACAATTTCAAAG
1394976 ATTGGTGCTT
Statistics
Matches: 163, Mismatches: 25, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
33 24 0.15
34 65 0.40
35 23 0.14
36 25 0.15
37 26 0.16
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (34 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTA
Found at i:1394828 original size:71 final size:69
Alignment explanation
Indices: 1394742--1394975 Score: 244
Period size: 71 Copynumber: 3.4 Consensus size: 69
1394732 GAAGGTTTGG
***
1394742 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTT
1 TGTTTCAAGAGAAACATTTTCAAAGG--TTTTTTTTGTGTTTCAAGAGAAATTGTTTCAAAGGTT
1394807 TTTTTA
64 TTTTTA
* * * *
1394813 TGTGTCAAGAGAAACAATTTT-AAAGGTCTTTTTTAGTGTTTCAATAGAAATTGTCTC-AAGGTT
1 TGTTTCAAGAGAAAC-ATTTTCAAAGGT-TTTTTTTGTGTTTCAAGAGAAATTGTTTCAAAGG--
1394876 TTTTTTTA
62 TTTTTTTA
* * *
1394884 TGTTTCAAGA-AAAAATGTTTCAAAGG-TTTTTTTCTGTTTCAAGA-AAATTGCTTCAAAGGTTT
1 TGTTTCAAGAGAAACAT-TTTCAAAGGTTTTTTTTGTGTTTCAAGAGAAATTGTTTCAAAGGTTT
*
1394946 TTTTG
65 TTTTA
* * *
1394951 TGTTTCATGATAAACAATTTCAAAG
1 TGTTTCAAGAGAAACATTTTCAAAG
1394976 ATTGGTGCTT
Statistics
Matches: 137, Mismatches: 18, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
67 24 0.18
68 12 0.09
69 26 0.19
70 29 0.21
71 41 0.30
72 5 0.04
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (69 bp):
TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTGTGTTTCAAGAGAAATTGTTTCAAAGGTTTT
TTTA
Found at i:1394914 original size:69 final size:70
Alignment explanation
Indices: 1394797--1394949 Score: 176
Period size: 69 Copynumber: 2.2 Consensus size: 70
1394787 GAGAAACAAT
* *
1394797 TTCAAAGG--TTTTTTTATGTGTCAAGAGAAACAATTTTAAAGGTCTTTTTTAGTGTTTCAATAG
1 TTCAAAGGTTTTTTTTTATGTGTCAAGAGAAACAATTTTAAAGG-CTTTTTTACTGTTTCAAGA-
1394860 AAATTG-
64 AAATTGC
* *
1394866 TCTC-AAGGTTTTTTTTTATGTTTCAAGA-AAA-AATGTTTCAAAGG-TTTTTTTCTGTTTCAAG
1 T-TCAAAGGTTTTTTTTTATGTGTCAAGAGAAACAAT-TTT-AAAGGCTTTTTTACTGTTTCAAG
1394927 AAAATTGC
63 AAAATTGC
1394935 TTCAAAGGTTTTTTT
1 TTCAAAGGTTTTTTT
1394950 GTGTTTCATG
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
68 8 0.11
69 35 0.48
70 8 0.11
71 22 0.30
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.46
Consensus pattern (70 bp):
TTCAAAGGTTTTTTTTTATGTGTCAAGAGAAACAATTTTAAAGGCTTTTTTACTGTTTCAAGAAA
ATTGC
Found at i:1395073 original size:36 final size:36
Alignment explanation
Indices: 1394984--1395402 Score: 327
Period size: 36 Copynumber: 12.1 Consensus size: 36
1394974 AGATTGGTGC
* * *
1394984 TTCAAGAGAAATTTTCTCAAGAGAGATAAAACTTTGT
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAA-TTTGT
* * *
1395021 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGA
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
* * *
1395057 TTCAAGGGAAAATGTCTCAATAGAGAC-AATTTTGT
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
* * *
1395092 TTTAAGAGAAAATGTCTCAAGGGAGACGAAATTTGT
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
* * *
1395128 TTTAAG-GAAAACATAT-TC-A-A-AG----ATTTTGT
1 TTCAAGAG-AAA-ATGTCTCAAGAGAGACAAAATTTGT
* * *
1395157 TTCAAGGGAAACTGTTTCAAGAGAGAC--AATTTGT
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
* *
1395191 TTTAAAAGAAAATGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
* *
1395227 TTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAA-TTTGT
* *** ***
1395264 TTCAAG-GAAAA---C-AAATTCA-AC-GTTTTTGT
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
* * **
1395293 TTCAAGGGTAACCGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
* *
1395329 TTTAAGAGAAAATGTCTCAAGAGTGACAAAATTTGT
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
* * *
1395365 TTTAAGAGAAACTGTCTCAAGAGAGACAAACTTTGT
1 TTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
1395401 TT
1 TT
1395403 TGAGTAAATT
Statistics
Matches: 307, Mismatches: 55, Indels: 41
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.01
29 27 0.09
30 5 0.02
31 3 0.01
32 5 0.02
33 4 0.01
34 31 0.10
35 33 0.11
36 157 0.51
37 40 0.13
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (36 bp):
TTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
Found at i:1395181 original size:136 final size:137
Alignment explanation
Indices: 1395016--1395403 Score: 586
Period size: 136 Copynumber: 2.8 Consensus size: 137
1395006 GAGATAAAAC
* * * *
1395016 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGATTCAAGGGAAAATGTCTCAATAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
* * * *
1395081 GAC-AATTTTGTTTTAAGAGAAAATGTCTCAAGGGAGACGAAA-TTTGTTTTAAGGAAAACATAT
66 GACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC-AAACTTTGTTTTAAGGAAAACAAAT
1395144 TCAAAGAT
130 TCAAAGAT
* *
1395152 TTTGTTTCAAGGGAAACTGTTTCAAGAGAGAC--AATTTGTTTTAAAAGAAAATGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
*
1395215 GACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAAT
66 GACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC-AAACTTTGTTTTAAGGAAAACAAAT
* *
1395280 TCAACGTT
130 TCAAAGAT
* * *
1395288 TTTGTTTCAAGGGTAACCGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
1395353 GACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAACTTTGTTTT
66 GACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAACTTTGTTTT
1395404 GAGTAAATTA
Statistics
Matches: 228, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
134 29 0.13
135 35 0.15
136 85 0.37
137 11 0.05
138 68 0.30
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (137 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
GACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAACTTTGTTTTAAGGAAAACAAATT
CAAAGAT
Found at i:1395229 original size:99 final size:101
Alignment explanation
Indices: 1395052--1395237 Score: 295
Period size: 99 Copynumber: 1.9 Consensus size: 101
1395042 AGAGACAAAA
* * *
1395052 TTTGATTCAAGGGAAAATGTCTCAATAGAGACAATTTTGTTTTAAGAGAAAATGTCTCAAGGGAG
1 TTTGATTCAAGGGAAAATGTCTCAAGAGAGACAATTTTGTTTTAAAAGAAAATGTCTCAAGAGAG
*
1395117 ACGAAATTTGTTTTAAG-GAAAACATATTCAAAGAT
66 ACAAAATTTGTTTTAAGAGAAAACATATTCAAAGAT
* * *
1395152 TTTGTTTCAAGGGAAACTGTTTCAAGAGAGACAA-TTTGTTTTAAAAGAAAATGTCTCAAGAGAG
1 TTTGATTCAAGGGAAAATGTCTCAAGAGAGACAATTTTGTTTTAAAAGAAAATGTCTCAAGAGAG
1395216 ACAAAATTTGTTTTAAGAGAAA
66 ACAAAATTTGTTTTAAGAGAAA
1395238 CTGTCTCAAG
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 44 0.56
100 34 0.44
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (101 bp):
TTTGATTCAAGGGAAAATGTCTCAAGAGAGACAATTTTGTTTTAAAAGAAAATGTCTCAAGAGAG
ACAAAATTTGTTTTAAGAGAAAACATATTCAAAGAT
Found at i:1395337 original size:21 final size:21
Alignment explanation
Indices: 1395311--1395373 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
1395301 TAACCGTCTC
1395311 AAGAGAGACAAAATTTGTTTT
1 AAGAGAGACAAAATTTGTTTT
* *
1395332 -A-AGAG--AAAA--TGTCTC
1 AAGAGAGACAAAATTTGTTTT
*
1395347 AAGAGTGACAAAATTTGTTTT
1 AAGAGAGACAAAATTTGTTTT
1395368 AAGAGA
1 AAGAGA
1395374 AACTGTCTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 4 0.13
16 1 0.03
17 7 0.23
19 8 0.27
20 1 0.03
21 9 0.30
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (21 bp):
AAGAGAGACAAAATTTGTTTT
Found at i:1396832 original size:83 final size:89
Alignment explanation
Indices: 1396701--1396927 Score: 236
Period size: 95 Copynumber: 2.6 Consensus size: 89
1396691 GGCTAGCTGA
* * * *
1396701 ATCCTTAAAGTCGAGGCGTTTAACCAGTTG-CTCTAGAGGGATAGCTCAA-TA-TGCA-A-AT-A
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCCT-TAGAGGGACAGCTCAATTATTGCATAGATAA
* *
1396760 T-CTTTATCAGGGTAGCTGAATCTT
65 TCCTTTATCAGGCTAGCTGAATATT
* *
1396784 ATCCATAAAG-CTGGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTGTATAGT
1 ATCCATAAAGTC-GGGGCGTTTAACCAATTGCCTTAGAGGGACAGCTCAA---TTATTGCATAG-
1396848 ATAATCACCTTTATCAGGCTAGCTGAATATT
61 ATAAT--CCTTTATCAGGCTAGCTGAATATT
* *
1396879 ATCCATAAAGTCGGGGCATTTAACCAATTGCTTTAGAGGGACAGCTCAA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCCTTAGAGGGACAGCTCAA
1396928 GTTTTATTGT
Statistics
Matches: 118, Mismatches: 11, Indels: 18
0.80 0.07 0.12
Matches are distributed among these distances:
82 1 0.01
83 39 0.33
84 2 0.02
87 2 0.02
88 3 0.03
89 1 0.01
91 2 0.02
92 2 0.02
95 65 0.55
96 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (89 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCCTTAGAGGGACAGCTCAATTATTGCATAGATAAT
CCTTTATCAGGCTAGCTGAATATT
Found at i:1396927 original size:95 final size:95
Alignment explanation
Indices: 1396761--1396940 Score: 290
Period size: 95 Copynumber: 1.9 Consensus size: 95
1396751 ATGCAAATAT
* * *
1396761 CTTTATCAGGGTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAATTGCCTTAGAGGGAC
1 CTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGGGGCATTTAACCAATTGCCTTAGAGGGAC
1396826 AACTCAAGCTTTATTGTATAGTATAATCAC
66 AACTCAAGCTTTATTGTATAGTATAATCAC
*
1396856 CTTTATCAGGCTAGCTGAATATTATCCATAAAG-TCGGGGCATTTAACCAATTGCTTTAGAGGGA
1 CTTTATCAGGCTAGCTGAATATTATCCATAAAGCT-GGGGCATTTAACCAATTGCCTTAGAGGGA
* *
1396920 CAGCTCAAGTTTTATTGTATA
65 CAACTCAAGCTTTATTGTATA
1396941 TAAATAATAT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 1 0.01
95 77 0.99
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (95 bp):
CTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGGGGCATTTAACCAATTGCCTTAGAGGGAC
AACTCAAGCTTTATTGTATAGTATAATCAC
Found at i:1398624 original size:21 final size:21
Alignment explanation
Indices: 1398600--1398640 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1398590 CCCCTTAGAC
1398600 CATCTTCATCTGATCTTCTAA
1 CATCTTCATCTGATCTTCTAA
* **
1398621 CATCTTGATCTTCTCTTCTA
1 CATCTTCATCTGATCTTCTA
1398641 TCTTTTTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.46
Consensus pattern (21 bp):
CATCTTCATCTGATCTTCTAA
Found at i:1400880 original size:19 final size:21
Alignment explanation
Indices: 1400837--1400882 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
1400827 AAAAAGTCAA
*
1400837 AAATGTTAGTAATAATAATAAT
1 AAATGTTAG-AATAATAAAAAT
1400859 AAATGTTA-AATAA-AAAAAT
1 AAATGTTAGAATAATAAAAAT
1400878 AAATG
1 AAATG
1400883 GAAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
20 5 0.22
22 8 0.35
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (21 bp):
AAATGTTAGAATAATAAAAAT
Found at i:1401525 original size:20 final size:20
Alignment explanation
Indices: 1401495--1401660 Score: 165
Period size: 20 Copynumber: 8.2 Consensus size: 20
1401485 TTCAAGATTT
1401495 GCAACGCGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
** *
1401515 GCATTGCGATTTTCCGACTATC
1 GCAACGCGA--TTCTGACTATC
* * * *
1401537 GCAATGCGAATATGTA-AATC
1 GCAACGCGATTCTG-ACTATC
* * *
1401557 GCAATGCGAGTATGACTATC
1 GCAACGCGATTCTGACTATC
1401577 GCAACGCGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
*
1401597 GCAACGAGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
1401617 GCAACGCGATTCTGAC-AGTC
1 GCAACGCGATTCTGACTA-TC
* *
1401637 GCAACGTGATGCTGACTATC
1 GCAACGCGATTCTGACTATC
1401657 GCAA
1 GCAA
1401661 TACGATTTTC
Statistics
Matches: 123, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.02
20 101 0.82
21 2 0.02
22 18 0.15
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (20 bp):
GCAACGCGATTCTGACTATC
Found at i:1401840 original size:22 final size:22
Alignment explanation
Indices: 1401815--1401857 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1401805 GGCGACATCC
1401815 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1401837 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
1401858 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1402297 original size:20 final size:19
Alignment explanation
Indices: 1402243--1402297 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
1402233 AGAATCGCAA
1402243 TGCGATTTTAGTTTCGCGT
1 TGCGATTTTAGTTTCGCGT
* * * *
1402262 TGCGATAGTCATTTTCGTGT
1 TGCGAT-TTTAGTTTCGCGT
1402282 TGCGATTTTAAGTTTC
1 TGCGATTTT-AGTTTC
1402298 AGAAACTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.47
Consensus pattern (19 bp):
TGCGATTTTAGTTTCGCGT
Found at i:1404040 original size:18 final size:17
Alignment explanation
Indices: 1404017--1404066 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 17
1404007 TTTACTCGTA
1404017 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATT-ACC
1404035 ATTTCACTTAGATGTACC
1 ATTTCACTTAGAT-TACC
1404053 ATTTCACTTAGATT
1 ATTTCACTTAGATT
1404067 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (17 bp):
ATTTCACTTAGATTACC
Found at i:1404326 original size:18 final size:19
Alignment explanation
Indices: 1404284--1404330 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
1404274 GCGATTCTCT
1404284 TGTTGCGATAGTCATTTTCG
1 TGTTGCGATAGTCA-TTTCG
* *
1404304 CGTTGTGATAGTCA-TTCG
1 TGTTGCGATAGTCATTTCG
1404322 TGTTGCGAT
1 TGTTGCGAT
1404331 TTTAAGTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 11 0.48
20 12 0.52
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.43
Consensus pattern (19 bp):
TGTTGCGATAGTCATTTCG
Found at i:1406356 original size:14 final size:14
Alignment explanation
Indices: 1406322--1406383 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
1406312 TTGCTTGTTT
*
1406322 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
1406336 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1406350 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1406365 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1406379 TAATT
1 -AATT
1406384 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1406535 original size:20 final size:20
Alignment explanation
Indices: 1406497--1406535 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1406487 ACGCTAAACT
* **
1406497 CAAAATCGCAATGTGAAAGA
1 CAAAATCGCAACGCAAAAGA
1406517 CAAAATCGCAACGCAAAAG
1 CAAAATCGCAACGCAAAAG
1406536 TCAATTCGCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.21, G:0.18, T:0.10
Consensus pattern (20 bp):
CAAAATCGCAACGCAAAAGA
Found at i:1406612 original size:20 final size:20
Alignment explanation
Indices: 1406598--1406760 Score: 115
Period size: 20 Copynumber: 8.4 Consensus size: 20
1406588 GTCAAATACC
* *
1406598 CGTTGCGATAATCAAATTCG
1 CGTTGCGATACTCAAATTCA
1406618 CGTTGCGATACTCAAATTCA
1 CGTTGCGATACTCAAATTCA
**
1406638 CGTTGCGATACTCAAATTTG
1 CGTTGCGATACTCAAATTCA
*
1406658 CGTTGCGAT--T----TTCT
1 CGTTGCGATACTCAAATTCA
* * *
1406672 CGTTGTGATAGTCAAATAGC-
1 CGTTGCGATACTCAAAT-TCA
* *
1406692 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATACTCAAATTCA
* * *
1406712 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATACTCAAATTCA
* ** *
1406732 TGTTGCGATAGACAAATTCG
1 CGTTGCGATACTCAAATTCA
1406752 CGTTGCGAT
1 CGTTGCGAT
1406761 TTTTGCGTTG
Statistics
Matches: 122, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
14 10 0.08
16 1 0.01
18 1 0.01
19 1 0.01
20 108 0.89
21 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATACTCAAATTCA
Found at i:1406688 original size:54 final size:54
Alignment explanation
Indices: 1406618--1406720 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
1406608 ATCAAATTCG
* *
1406618 CGTTGCGATACTCAAAT-TCACGTTGCGATACTCAAATTTGCGTTGCGATTTTCT
1 CGTTGCGATACTCAAATAGC-CGTTGCGATACTCAAATTCGCGTTGCGATTTTCT
* * * *
1406672 CGTTGTGATAGTCAAATAGCCGTTGCGATAGTCAAATTCGTGTTGCGAT
1 CGTTGCGATACTCAAATAGCCGTTGCGATACTCAAATTCGCGTTGCGAT
1406721 AGTCAAATTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 41 0.98
55 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (54 bp):
CGTTGCGATACTCAAATAGCCGTTGCGATACTCAAATTCGCGTTGCGATTTTCT
Found at i:1406699 original size:94 final size:94
Alignment explanation
Indices: 1406566--1406812 Score: 325
Period size: 94 Copynumber: 2.6 Consensus size: 94
1406556 CTAATACGCT
* * * *
1406566 TTGCAATTTTCTCGTTACAATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGATACTC
1 TTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATACTC
* *
1406631 AAATTCACGTTGCGATACTCAAATTTGCG
66 AAATTCACGTTGCGATACACAAATTCGCG
* * * *
1406660 TTGCGATTTTCTCGTTGTGATAGTCAAATAGCCGTTGCGATAGTCAAATTCGTGTTGCGATAGTC
1 TTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATACTC
** *
1406725 AAATTCGTGTTGCGATAGACAAATTCGCG
66 AAATTCACGTTGCGATACACAAATTCGCG
* * **
1406754 TTGCGATTTT-TGCGTTGCGATAGTCATATTCATGTTGCGATAGTCAAATTCGCGTTGCG
1 TTGCGATTTTCT-CGTTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCG
1406813 GTTTTTGAGT
Statistics
Matches: 132, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
93 1 0.01
94 131 0.99
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (94 bp):
TTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATACTC
AAATTCACGTTGCGATACACAAATTCGCG
Found at i:1406792 original size:20 final size:20
Alignment explanation
Indices: 1406767--1406812 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1406757 CGATTTTTGC
* *
1406767 GTTGCGATAGTCATATTCAT
1 GTTGCGATAGTCAAATTCGT
*
1406787 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGT
1406807 GTTGCG
1 GTTGCG
1406813 GTTTTTGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGT
Found at i:1406843 original size:74 final size:73
Alignment explanation
Indices: 1406599--1406856 Score: 227
Period size: 74 Copynumber: 3.5 Consensus size: 73
1406589 TCAAATACCC
* * * *
1406599 GTTGCGATAATCAAATTCGCGTTGCGATACTCAAATTCACGTTGCGATACTCAAATTTGCGTTGC
1 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCATGTTGCGATAGTCAAATTCGCGTTGC
*
1406664 GATTTTCTC
66 GATTTT-TA
* * * * *
1406673 GTTGTGATAGTCAAA-TAGCCGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGTGTTG
1 GTTGCGATAATCAAATTCG-CGTTGCGATAGTCAAATTCATGTTGCGATAGTCAAATTCGCGTTG
****
1406737 CGATAGACAA
65 CGAT-TTTTA
* ** * *
1406747 ATTCGCG-T--TGCGATTTTTGCGTTGCGATAGTCATATTCATGTTGCGATAGTCAAATTCGCGT
1 GTT-GCGATAAT-C-AAATTCGCGTTGCGATAGTCAAATTCATGTTGCGATAGTCAAATTCGCGT
*
1406809 TGCGGTTTTTGA
63 TGCGATTTTT-A
* *
1406821 GTTGTGATAATCAAATTCGCGTTGCGATATTCAAAT
1 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAAT
1406857 GAATGTGTAA
Statistics
Matches: 140, Mismatches: 34, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
72 1 0.01
73 5 0.04
74 128 0.91
75 5 0.04
76 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (73 bp):
GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCATGTTGCGATAGTCAAATTCGCGTTGC
GATTTTTA
Found at i:1406855 original size:54 final size:54
Alignment explanation
Indices: 1406713--1406856 Score: 207
Period size: 54 Copynumber: 2.7 Consensus size: 54
1406703 TCAAATTCGT
* *
1406713 GTTGCGATAGTCAAATTCGTGTTGCGATAGACAAATTCGCGTTGCGATTTTTGC
1 GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
* * *
1406767 GTTGCGATAGTCATATTCATGTTGCGATAGTCAAATTCGCGTTGCGGTTTTTGA
1 GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
* * * *
1406821 GTTGTGATAATCAAATTCGCGTTGCGATATTCAAAT
1 GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAAT
1406857 GAATGTGTAA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (54 bp):
GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
Found at i:1407083 original size:140 final size:140
Alignment explanation
Indices: 1406831--1407096 Score: 514
Period size: 140 Copynumber: 1.9 Consensus size: 140
1406821 GTTGTGATAA
* *
1406831 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGAGATAACAACTGAACAGATCATAGC
1406896 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
1406961 CAAATAATAG
131 CAAATAATAG
1406971 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGAGATAACAACTGAACAGATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGAGATAACAACTGAACAGATCATAGC
1407036 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1407097 TACAACGTTT
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (140 bp):
TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGAGATAACAACTGAACAGATCATAGC
AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
CAAATAATAG
Found at i:1407197 original size:11 final size:12
Alignment explanation
Indices: 1407171--1407198 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1407161 GGGATTTTGA
1407171 TTTTGATTGCCT
1 TTTTGATTGCCT
1407183 TTTTGATTGCCT
1 TTTTGATTGCCT
1407195 TTTT
1 TTTT
1407199 CTTGACACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.14, T:0.64
Consensus pattern (12 bp):
TTTTGATTGCCT
Found at i:1410352 original size:20 final size:20
Alignment explanation
Indices: 1410327--1410374 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1410317 GAAATTTAGT
1410327 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1410347 GTTGCGATAGTTAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1410367 ATTGCGAT
1 GTTGCGAT
1410375 TTACATATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1411535 original size:20 final size:20
Alignment explanation
Indices: 1411510--1411556 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
1411500 AAATTGTAAA
1411510 TATAAATAAAT-ATATAAAT-
1 TATAAATAAATCATA-AAATG
1411529 TATTAAA-AAATCATAAAATG
1 TA-TAAATAAATCATAAAATG
1411549 TATAAATA
1 TATAAATA
1411557 TTAGTAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
TATAAATAAATCATAAAATG
Found at i:1417351 original size:195 final size:195
Alignment explanation
Indices: 1417004--1417365 Score: 661
Period size: 195 Copynumber: 1.9 Consensus size: 195
1416994 ATTAAATCCG
1417004 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
1417069 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACATTGCTCAGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
* * *
1417134 TTGTCATGCCAAAGATTTTGTGATGAGACGAACCCTTTAGTGATTATAATACTAAGTTGTCCTTC
131 TTGTCAGGACAAAGACTTTGTGATGAGACGAACCCTTTAGTGATTATAATACTAAGTTGTCCTTC
* *
1417199 TAAAGCTGAGCTATTTCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCTCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1417264 ATAGATTACATTCAAACCATGACATTGCTCAGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACATTGCTCAGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
1417329 TTGTCAGGACAAAGACTTTGTGATGAGACGAACCCTT
131 TTGTCAGGACAAAGACTTTGTGATGAGACGAACCCTT
1417366 CAGTTAAACA
Statistics
Matches: 160, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
195 160 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (195 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACATTGCTCAGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
TTGTCAGGACAAAGACTTTGTGATGAGACGAACCCTTTAGTGATTATAATACTAAGTTGTCCTTC
Found at i:1418576 original size:52 final size:52
Alignment explanation
Indices: 1418509--1418610 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
1418499 GTTTTTTTTA
* *
1418509 AAACATACTTTGTCTCACTTGAGAATGTTTTACTCGAAAGAAGATTTATTTC
1 AAACAGACTTTGTCTCACTTGAGAATGTTTTACTCGAAAGAAGAATTATTTC
* * *
1418561 AAACAGACTTTGTCTCACTTGAGACTGTTTTACTTGGAAGAAGAATTATT
1 AAACAGACTTTGTCTCACTTGAGAATGTTTTACTCGAAAGAAGAATTATT
1418611 GTACTCAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (52 bp):
AAACAGACTTTGTCTCACTTGAGAATGTTTTACTCGAAAGAAGAATTATTTC
Found at i:1418762 original size:21 final size:21
Alignment explanation
Indices: 1418736--1418785 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1418726 TGAGATAGTT
*
1418736 TCTCTTGAAACAGATTTTATC
1 TCTCTTGAAACAAATTTTATC
*
1418757 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTATC
*
1418778 TCCCTTGA
1 TCTCTTGA
1418786 GACATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTATC
Found at i:1418926 original size:37 final size:37
Alignment explanation
Indices: 1418870--1418942 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
1418860 CCTTAAAATG
*
1418870 AATTTTGTCTCTCTCGAGATAGGTTCTCTTGAAACAA
1 AATTTTGTCTCCCTCGAGATAGGTTCTCTTGAAACAA
* *
1418907 AATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTCGAGATAGGTTCTCTTGAAACA
1418943 TAAACATTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (37 bp):
AATTTTGTCTCCCTCGAGATAGGTTCTCTTGAAACAA
Found at i:1418933 original size:102 final size:103
Alignment explanation
Indices: 1418811--1419016 Score: 308
Period size: 102 Copynumber: 2.0 Consensus size: 103
1418801 ACTAAGTTTC
* *
1418811 GTCTCTCTTGAGACAATTTCTCTTAAAACATAAATATTGAAAA-ACTTTCCCTTAAAATGAATTT
1 GTCTCCCTTGAGACAATTTCTCTTAAAACATAAACATTGAAAACA-TTTCCCTTAAAATGAATTT
1418875 TGTCTCTCTCGAGATAGGTTCTCTTGAAACAAAAT-TTT
65 TGTCTCTCTCGAGATAGGTTCTCTTGAAACAAAATCTTT
* * *
1418913 GTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAATGAATTTT
1 GTCTCCCTTGAGACAATTTCTCTTAAAACATAAACATTGAAAACATTTCCCTTAAAATGAATTTT
* * * *
1418978 GTCTCTCTTGAGATAGTTTTTCTTGAAACGAAATCTTT
66 GTCTCTCTCGAGATAGGTTCTCTTGAAACAAAATCTTT
1419016 G
1 G
1419017 AATCTGTTTC
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
102 88 0.95
103 5 0.05
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (103 bp):
GTCTCCCTTGAGACAATTTCTCTTAAAACATAAACATTGAAAACATTTCCCTTAAAATGAATTTT
GTCTCTCTCGAGATAGGTTCTCTTGAAACAAAATCTTT
Found at i:1419027 original size:65 final size:65
Alignment explanation
Indices: 1418901--1419055 Score: 179
Period size: 65 Copynumber: 2.4 Consensus size: 65
1418891 GGTTCTCTTG
1418901 AAACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTT
1 AAAC-AAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTT
1418966 A
65 A
** * * * * * *
1418967 AAATGAATTTTGTCTCTCTTGAGATAGTTTTTCTTGAAACGA-AATCTTTG-AATCTGTTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAAC-ATAAACATTGAAAAC-ATTTCCCT
*
1419030 TG
64 TA
*
1419032 AAACAAATTTCGTCTCCCTTGAGA
1 AAACAAATTTTGTCTCCCTTGAGA
1419056 CATTTTCTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
64 3 0.04
65 67 0.91
66 4 0.05
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTA
Found at i:1419080 original size:102 final size:101
Alignment explanation
Indices: 1418958--1419344 Score: 463
Period size: 102 Copynumber: 3.8 Consensus size: 101
1418948 ATTGAAAACA
* ** * * * * * *
1418958 TTTCCCTTAAAATGAATTTTGTCTCTCTTGAGATAGTTTTTCTTGAAACGA-AATCTTTG-AATC
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-ATAAACATTGAAAAC
* * * * *
1419021 TGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAT
65 -ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
** * * * * *
1419059 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAATTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
**
1419124 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
65 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
*
1419161 GTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
**
1419226 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
65 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
*
1419263 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
1419328 GTTTCCTTTGAAACAAA
66 -TTTCCCTTGAAACAAA
1419345 ATCTTTGAAT
Statistics
Matches: 249, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
101 60 0.24
102 186 0.75
103 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (101 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
Found at i:1419121 original size:269 final size:266
Alignment explanation
Indices: 1418714--1419283 Score: 911
Period size: 269 Copynumber: 2.2 Consensus size: 266
1418704 TTTAAAGAAG
* * *
1418714 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAGATTTT--ATC----TCTCTTGAAACAAATT
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGAATCTGTTTCCCTTGAAACAAATT
*
1418773 TTGTCTCCCTTGAGACATTTTTTTTAGAACTAAGTTTCGTCTCTCTTGAGACAATTTCTCTTAAA
66 TCGTCTCCCTTGAGACATTTTTTTTAGAACTAAGTTTCGTCTCTCTTGAGACAATTTCTCTTAAA
* *
1418838 ACATAAATATTGAAAA-ACTTTCCCTTAAAATGAATTTTGTCTCTCTCGAGATAGGTTCTCTTGA
131 ACATAAACATTGAAAACA-TTTCCCTTAAAATGAATTTTGTCTCTCTCGAGATAGGTTCCCTTGA
*
1418902 AACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTA
195 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTA
1418967 AAATGAA
260 AAATGAA
**
1418974 TTTTGTCTCTCTTGAGATAGTTTTTCTTGAAACGAAATCTTTGAATCTGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAAT-TTTGAATCTGTTTCCCTTGAAACAAA
* * *
1419039 TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAATTTCTCTT
64 TTTCGTCTCCCTTGAGACATTTT-TTTTAGAACTAAGTTTCGTCTCTCTTGAGACAATTTCTCTT
* * *
1419104 GAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGGTTCCCTT
128 AAAACATAAACATTGAAAACATTTCCCTTAAAATGAATTTTGTCTCTCTCGAGATAGGTTCCCTT
1419169 GAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCT
193 GAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCT
*
1419234 TGAAATGAA
258 TAAAATGAA
1419243 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTG
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTG
1419284 TCTCCCTTGA
Statistics
Matches: 284, Mismatches: 16, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
260 32 0.11
261 3 0.01
262 3 0.01
264 3 0.01
267 4 0.01
268 39 0.14
269 199 0.70
270 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (266 bp):
TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGAATCTGTTTCCCTTGAAACAAATT
TCGTCTCCCTTGAGACATTTTTTTTAGAACTAAGTTTCGTCTCTCTTGAGACAATTTCTCTTAAA
ACATAAACATTGAAAACATTTCCCTTAAAATGAATTTTGTCTCTCTCGAGATAGGTTCCCTTGAA
ACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAA
AATGAA
Found at i:1419186 original size:37 final size:37
Alignment explanation
Indices: 1419126--1419211 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
1419116 TTGAAAACAT
** * *
1419126 TTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAGG
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGG
*
1419162 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGT
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGG
*
1419199 TTCTCTTGAAACA
1 TTCCCTTGAAACA
1419212 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 11 0.26
37 32 0.74
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (37 bp):
TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGG
Found at i:1419249 original size:167 final size:162
Alignment explanation
Indices: 1418907--1419276 Score: 408
Period size: 167 Copynumber: 2.2 Consensus size: 162
1418897 CTTGAAACAA
*
1418907 AATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAATG
1 AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAATG
* ** *
1418972 AATTTTGTCTCTCTTGAGATAGTTTTTCTTGAAACGAAATCTTTGAATCTGTTTCCCTTGAAACA
66 AATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATCTTTG-ATC---TTCCCTTGAAACA
* * * * ** *
1419037 AATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACT
127 AATTTCGACTACATTGAAACATTTTCCCTTGGAAAT
* *
1419073 AAGTTTTGTCTCTCTTGAGATAATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AA-TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAAT
* **
1419138 GAATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAAT-TTTG-TC-TCCCTTGAGACAGTT
65 GAATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATCTTTGATCTTCCCTTGAAACAAAT
1419200 TCTCTTGAAACATAAACATTGAAAACA-TTTCCCTT-GAAAT
130 T-TC--G--AC-T--ACATTG-AAACATTTTCCCTTGGAAAT
*
1419240 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 -AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1419277 AATTTTGTCT
Statistics
Matches: 174, Mismatches: 19, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
160 13 0.07
161 2 0.01
163 1 0.01
164 2 0.01
165 1 0.01
166 7 0.04
167 132 0.76
168 12 0.07
169 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (162 bp):
AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAATG
AATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATCTTTGATCTTCCCTTGAAACAAATT
TCGACTACATTGAAACATTTTCCCTTGGAAAT
Found at i:1419274 original size:36 final size:36
Alignment explanation
Indices: 1419227--1419312 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 36
1419217 ATTGAAAACA
** * *
1419227 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1419263 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
1419299 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1419313 TAAACTTTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:1419329 original size:30 final size:30
Alignment explanation
Indices: 1419295--1419353 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1419285 CTCCCTTGAG
1419295 ACAGTTT-CTCTTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCT-TTGAAACA-AAATCTTTGAAA
1419325 ACAGTTTCCTTTGAAACAAAATCTTTGAA
1 ACAGTTTCCTTTGAAACAAAATCTTTGAA
1419354 TATGTTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 3 0.11
30 22 0.81
31 2 0.07
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (30 bp):
ACAGTTTCCTTTGAAACAAAATCTTTGAAA
Found at i:1419428 original size:34 final size:34
Alignment explanation
Indices: 1419385--1419476 Score: 87
Period size: 36 Copynumber: 2.6 Consensus size: 34
1419375 TTCGTCTCCT
* * *
1419385 TTGACACAGTTTATTTTGGAAGC-TTTTGTCTCTC
1 TTGAGACAGTTTATCTT-GAAACATTTTGTCTCTC
*
1419419 TTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTATCTTGAAAC--ATTTTGTCTCTC
* **
1419455 TTGAGATAGTTTCCCTTGAAAC
1 TTGAGACAGTTTATCTTGAAAC
1419477 TTCAATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 4 0.08
34 14 0.29
36 31 0.63
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.42
Consensus pattern (34 bp):
TTGAGACAGTTTATCTTGAAACATTTTGTCTCTC
Found at i:1419450 original size:36 final size:36
Alignment explanation
Indices: 1419408--1419476 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1419398 TTTTGGAAGC
*
1419408 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
1419444 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1419477 TTCAATCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1419536 original size:35 final size:35
Alignment explanation
Indices: 1419494--1419583 Score: 153
Period size: 35 Copynumber: 2.6 Consensus size: 35
1419484 TTTGAATACA
* *
1419494 GTTTCTCTTGAAACACCAAAAAACCCTTTGAAATT
1 GTTTCTCTTGAAACACCAAAAAAACCTTTGAAAAT
*
1419529 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACCAAAAAAACCTTTGAAAAT
1419564 GTTTCTCTTGAAACACCAAA
1 GTTTCTCTTGAAACACCAAA
1419584 CCCTCGAGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (35 bp):
GTTTCTCTTGAAACACCAAAAAAACCTTTGAAAAT
Found at i:1419716 original size:84 final size:84
Alignment explanation
Indices: 1419587--1419821 Score: 247
Period size: 84 Copynumber: 2.8 Consensus size: 84
1419577 CACCAAACCC
* ** * * * * * *
1419587 TCGAGTTCGATTACAATCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTATAAGGGT
1 TCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGC
** *
1419652 TATGTGTC-ACCAAAAGACCT
65 TAAATGCCAACC-AAAGACCT
* * * * **
1419672 TCGAGTTCGACTATGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAATCAAGAAGGGCT
1 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGCT
*
1419737 AAATGCCAACCAAATACCT
66 AAATGCCAACCAAAGACCT
* * *
1419756 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAATTACAGCATAGTTCAAGGCAAGATGGGCT
1 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGCT
1419821 A
66 A
1419822 TCTGTCAACA
Statistics
Matches: 122, Mismatches: 27, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
84 102 0.84
85 20 0.16
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (84 bp):
TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGCT
AAATGCCAACCAAAGACCT
Found at i:1422316 original size:2 final size:2
Alignment explanation
Indices: 1422309--1422340 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1422299 TTCCTTTTTG
1422309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1422341 TTCTTTAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1425001 original size:3 final size:3
Alignment explanation
Indices: 1424993--1425043 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
1424983 AACCGTTAAA
* * *
1424993 TAT TAT TAT TA- TAA TAT TAG TAT AAAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
1425038 TAT TAT
1 TAT TAT
1425044 AAAATTGGGC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1433724 original size:19 final size:18
Alignment explanation
Indices: 1433700--1433792 Score: 89
Period size: 19 Copynumber: 4.9 Consensus size: 18
1433690 AAAGAAAGTA
1433700 AAAAAAAAGAGAAAATAGG
1 AAAAAAAAGAGAAAA-AGG
*
1433719 AAAAAACAGA-AAAAAGAG
1 AAAAAAAAGAGAAAAAG-G
* *
1433737 AAAAAAAGAAAAAAGAAAGAG
1 AAAAAAA-AGAGAA-AAAG-G
*
1433758 AAAAAATAGTAGAAAAAGG
1 AAAAAAAAG-AGAAAAAGG
1433777 AAAAAAAAGAGAAAAA
1 AAAAAAAAGAGAAAAA
1433793 AAGAAGAAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
17 2 0.03
18 18 0.29
19 20 0.32
20 7 0.11
21 15 0.24
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.03
Consensus pattern (18 bp):
AAAAAAAAGAGAAAAAGG
Found at i:1433730 original size:9 final size:8
Alignment explanation
Indices: 1433687--1433809 Score: 65
Period size: 9 Copynumber: 14.4 Consensus size: 8
1433677 AAAAACACAT
1433687 AAAAAAGA
1 AAAAAAGA
1433695 AAGTAAAA-A
1 AA--AAAAGA
*
1433704 AAAAGAGA
1 AAAAAAGA
* *
1433712 AAATAGGA
1 AAAAAAGA
1433720 AAAAACAGA
1 AAAAA-AGA
1433729 AAAAAGAGA
1 AAAAA-AGA
1433738 AAAAAAG-
1 AAAAAAGA
1433745 AAAAAAG-
1 AAAAAAGA
*
1433752 -AAAGAGA
1 AAAAAAGA
1433759 AAAAATAGTA
1 AAAAA-AG-A
*
1433769 GAAAAAGGAAA
1 -AAAAA--AGA
1433780 AAAAAGAGA
1 AAAAA-AGA
1433789 AAAAAAGA
1 AAAAAAGA
1433797 AGAAAGAAGA
1 A-AAA-AAGA
1433807 AAA
1 AAA
1433810 TAGACATATC
Statistics
Matches: 91, Mismatches: 12, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
6 5 0.05
7 10 0.11
8 21 0.23
9 33 0.36
10 15 0.16
11 6 0.07
12 1 0.01
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1433742 original size:51 final size:50
Alignment explanation
Indices: 1433687--1433797 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 50
1433677 AAAAACACAT
* *
1433687 AAAAAAGAAAGTAAAAAAAAAGAGAAAATAG-GAAAAAACAGAAAAAAGAGA
1 AAAAAAGAAA--AAAAAAAAAGAAAAAATAGAGAAAAAACAAAAAAAAGAGA
* * **
1433738 AAAAAAGAAAAAAGAAAGAGAAAAAATAGTAGAAAAAGGAAAAAAAAGAGA
1 AAAAAAGAAAAAAAAAAAAGAAAAAATAG-AGAAAAAACAAAAAAAAGAGA
1433789 AAAAAAGAA
1 AAAAAAGAA
1433798 GAAAGAAGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
49 16 0.31
51 36 0.69
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (50 bp):
AAAAAAGAAAAAAAAAAAAGAAAAAATAGAGAAAAAACAAAAAAAAGAGA
Found at i:1433754 original size:41 final size:40
Alignment explanation
Indices: 1433674--1433801 Score: 104
Period size: 41 Copynumber: 3.1 Consensus size: 40
1433664 TTAAAGATAT
* * *
1433674 AGAAAAAACACATAAAAA-AGAAAGTAAAA-AAAAAGAGAAAAT
1 AGAAAAAACAGAGAAAAAGAGAAA--AAAAGAAAAA-AG-AAAG
1433716 AGGAAAAAACAGA-AAAAAGAGAAAAAAAGAAAAAAGAAAG
1 A-GAAAAAACAGAGAAAAAGAGAAAAAAAGAAAAAAGAAAG
* *
1433756 AGAAAAAATAGTAGAAAAAG-GAAAAAAAAGAGAAAA-AAAG
1 AGAAAAAACAG-AGAAAAAGAG-AAAAAAAGAAAAAAGAAAG
1433796 AAGAAA
1 -AGAAA
1433802 GAAGAAAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
39 9 0.12
40 10 0.13
41 30 0.40
42 11 0.15
43 15 0.20
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (40 bp):
AGAAAAAACAGAGAAAAAGAGAAAAAAAGAAAAAAGAAAG
Found at i:1433760 original size:30 final size:28
Alignment explanation
Indices: 1433699--1433809 Score: 61
Period size: 26 Copynumber: 3.9 Consensus size: 28
1433689 AAAAGAAAGT
* *
1433699 AAAAAAAAAGAGAAAATAGGAAAAAACAG
1 AAAAAAAAAGAGAAAAAAAGAAAAAA-AG
1433728 ---AAAAAAGAGAAAAAAAG-AAAAAAG
1 AAAAAAAAAGAGAAAAAAAGAAAAAAAG
* *
1433752 AAAGAGAAAAAATAGTAGAAAAAGGAAAAAAAAG
1 -AA-A-AAAAAAGAG-A-AAAAAAG-AAAAAAAG
* *
1433786 AGAAAAAAAGA-AGAAAGAAGAAAA
1 AAAAAAAAAGAGA-AAAAAAGAAAA
1433810 TAGACATATC
Statistics
Matches: 64, Mismatches: 8, Indels: 21
0.69 0.09 0.23
Matches are distributed among these distances:
24 2 0.03
25 5 0.08
26 15 0.23
28 4 0.06
29 7 0.11
30 8 0.12
31 8 0.12
32 7 0.11
33 1 0.02
34 7 0.11
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (28 bp):
AAAAAAAAAGAGAAAAAAAGAAAAAAAG
Found at i:1433762 original size:58 final size:61
Alignment explanation
Indices: 1433687--1433809 Score: 166
Period size: 58 Copynumber: 2.1 Consensus size: 61
1433677 AAAAACACAT
* *
1433687 AAAAAAGAAAGTAAAAAAAAAG-AGAAAATAGGAAAAAACAGA-AAAAAGAGAA-AAA-AAG
1 AAAAAAGAAAGTAAAAAAAAAGTAGAAAA-AGGAAAAAAAAGAGAAAAAAAGAAGAAAGAAG
*
1433745 AAAAAAGAAAG-AGAAAAAATAGTAGAAAAAGGAAAAAAAAGAGAAAAAAAGAAGAAAGAAG
1 AAAAAAGAAAGTA-AAAAAAAAGTAGAAAAAGGAAAAAAAAGAGAAAAAAAGAAGAAAGAAG
1433806 AAAA
1 AAAA
1433810 TAGACATATC
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
57 1 0.02
58 31 0.54
59 15 0.26
60 3 0.05
61 7 0.12
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (61 bp):
AAAAAAGAAAGTAAAAAAAAAGTAGAAAAAGGAAAAAAAAGAGAAAAAAAGAAGAAAGAAG
Found at i:1433800 original size:11 final size:10
Alignment explanation
Indices: 1433701--1433801 Score: 88
Period size: 9 Copynumber: 10.3 Consensus size: 10
1433691 AAGAAAGTAA
1433701 AAAAAAAGAG
1 AAAAAAAGAG
*
1433711 -AAAATAG-G
1 AAAAAAAGAG
*
1433719 -AAAAAACAG
1 AAAAAAAGAG
1433728 -AAAAAAGAG
1 AAAAAAAGAG
*
1433737 AAAAAAAGAA
1 AAAAAAAGAG
1433747 AAAAGAAAGAG
1 AAAA-AAAGAG
1433758 AAAAAATAGTAG
1 AAAAAA-AG-AG
*
1433770 -AAAAAGGA-
1 AAAAAAAGAG
1433778 AAAAAAAGAG
1 AAAAAAAGAG
1433788 AAAAAAAGAAG
1 AAAAAAAG-AG
1433799 AAA
1 AAA
1433802 GAAGAAAATA
Statistics
Matches: 75, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
8 6 0.08
9 23 0.31
10 23 0.31
11 21 0.28
12 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:1433806 original size:10 final size:9
Alignment explanation
Indices: 1433729--1433809 Score: 59
Period size: 8 Copynumber: 9.4 Consensus size: 9
1433719 AAAAAACAGA
1433729 AAAAAG-AG
1 AAAAAGAAG
1433737 AAAAA-AAG
1 AAAAAGAAG
1433745 -AAAA-AAG
1 AAAAAGAAG
*
1433752 AAAGAGAA-
1 AAAAAGAAG
*
1433760 AAAATAGTAG
1 AAAA-AGAAG
*
1433770 AAAAAGGAAA
1 AAAAA-GAAG
1433780 AAAAAG-AG
1 AAAAAGAAG
1433788 AAAAA-AAG
1 AAAAAGAAG
1433796 AAGAAAGAAG
1 AA-AAAGAAG
1433806 AAAA
1 AAAA
1433810 TAGACATATC
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
7 7 0.12
8 23 0.40
9 12 0.21
10 16 0.28
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:1435778 original size:55 final size:55
Alignment explanation
Indices: 1435585--1435946 Score: 417
Period size: 54 Copynumber: 6.6 Consensus size: 55
1435575 ATGTTTTTTT
* ** * *
1435585 AGAAACTAATTCCAATTTTCGGAAGTTTCTTGATCATTTT-AAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTTAA
* * * *
1435639 AGAAACTAAGTCTTATTTTCAGAAGTTTCTTGACGATTTTCAAGTGATTTTTTTAAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGA-GTTTTT-AA
* * * *
1435696 AGAAACTAAGTATGGTTTTCAGAAGTTTCATGATGATTTTCAAGTGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTTAA
* * * * *
1435751 AGAAACTAAGTATGTTTTTTAGAAGTTTCTTGATGA-TTTCAAATAAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTTAA
* * * * *
1435805 CGAAACTAAGTCTGATTTTCAGAGGTTTCATGAT-AATTTCAAATGATTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTTAA
* * * *
1435859 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGCTTTTCAAATGTG-TTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTTAA
* *
1435913 AGAAACTAAGTCTGATTTTCGGAAGCTTCTTGAT
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGAT
1435947 TTTTCTAAAA
Statistics
Matches: 261, Mismatches: 42, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
53 1 0.00
54 157 0.60
55 49 0.19
56 10 0.04
57 44 0.17
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.41
Consensus pattern (55 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTTAA
Found at i:1437070 original size:20 final size:19
Alignment explanation
Indices: 1437008--1437071 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 19
1436998 CCAATGGAGA
1437008 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* *
1437027 CATTCGATGAAGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
1437047 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
1437067 GTTCA
1 GTTCA
1437072 ACCTTAGCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 10 0.29
18 2 0.06
19 3 0.09
20 8 0.23
21 2 0.06
22 10 0.29
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:1437099 original size:139 final size:139
Alignment explanation
Indices: 1436849--1437381 Score: 852
Period size: 139 Copynumber: 3.8 Consensus size: 139
1436839 GGGAAAACCA
* *
1436849 ATCAACATTTCCAATGGAGAGTTCATAACGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* *
1436914 AATGAGAAGAACTTGTTCAACCCTAGATCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
*
1436979 AATCGAGGG
131 ACTCGAGGG
*
1436988 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGAAGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
*
1437053 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAATACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
1437118 ACTCGAGGG
131 ACTCGAGGG
* *
1437127 ATCAGCATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* * *
1437192 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCGTCACATATGGAGTTGAATCAACAACGCCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
1437257 ACTCGAGGG
131 ACTCGAGGG
* * * * *
1437266 ATCAACCTTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCTGAT-AAGGGAGAAGAATTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAA-GGAGAAGAAGTTCA
* * * *
1437330 TAATGAGAAGAACTTGTTCAACCTTAGCTTGTATCCATCGCATAAGGAGTTG
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCG-ATTCATCACATATGGAGTTG
1437382 GGACATCACC
Statistics
Matches: 366, Mismatches: 26, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
138 2 0.01
139 348 0.95
140 16 0.04
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (139 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
ACTCGAGGG
Found at i:1437209 original size:20 final size:19
Alignment explanation
Indices: 1437147--1437210 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
1437137 CCAATGGAGA
1437147 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
1437166 CATCCAATGAAGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
1437186 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
1437206 GTTCA
1 GTTCA
1437211 ACCTTAGCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 10 0.30
18 2 0.06
19 2 0.06
20 7 0.21
21 2 0.06
22 10 0.30
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:1437490 original size:76 final size:75
Alignment explanation
Indices: 1437326--1437492 Score: 214
Period size: 76 Copynumber: 2.2 Consensus size: 75
1437316 GGAGAAGAAT
* * * *
1437326 TTCATAATGAGAAGAACTTGTTCAACCTTAGCTTGTATCCATCGCATAAGGAGTTGGGACATCAC
1 TTCATAATGAGAAGAACTTGTTCAACCTTAGCTTATATCCATCACAGAAGAAGTTGGGACATCAC
1437391 CAGCGAAAAA
66 CAGCGAAAAA
*
1437401 TTCATAATGAGAAGAACTTGTTCAACCTT-GGTTAT-TCCATCACAGAAGAAAG-TGGACTGACA
1 TTCATAATGAGAAGAACTTGTTCAACCTTAGCTTATATCCATCACAGAAG-AAGTTGG---GACA
* *
1437463 TCACCAGCGAAGAG
62 TCACCAGCGAAAAA
1437477 TTCATAATGAGAAGAA
1 TTCATAATGAGAAGAA
1437493 TTCTTTCGAA
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
73 14 0.17
74 6 0.07
75 29 0.36
76 32 0.40
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (75 bp):
TTCATAATGAGAAGAACTTGTTCAACCTTAGCTTATATCCATCACAGAAGAAGTTGGGACATCAC
CAGCGAAAAA
Found at i:1439846 original size:11 final size:11
Alignment explanation
Indices: 1439830--1439858 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1439820 CTCCAAAACA
1439830 TTTCAAAATCT
1 TTTCAAAATCT
1439841 TTTCAAAATCT
1 TTTCAAAATCT
1439852 TTTCAAA
1 TTTCAAA
1439859 GAAAACCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (11 bp):
TTTCAAAATCT
Found at i:1440160 original size:29 final size:30
Alignment explanation
Indices: 1440127--1440183 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
1440117 CTGAATAATC
* *
1440127 ATTTTAACTGACTTGA-TTCTTTTTGTCAA
1 ATTTTAACTAACTTGATTTCCTTTTGTCAA
* *
1440156 ATTTTTACTAACTTTATTTCCTTTTGTC
1 ATTTTAACTAACTTGATTTCCTTTTGTC
1440184 TTGTCTTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.56
Consensus pattern (30 bp):
ATTTTAACTAACTTGATTTCCTTTTGTCAA
Found at i:1441102 original size:41 final size:41
Alignment explanation
Indices: 1441057--1441138 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
1441047 ATGATCCATG
1441057 GGGAGAAGCTACTAGAGGATCCCAATGTAAAAGCTGTGAAT
1 GGGAGAAGCTACTAGAGGATCCCAATGTAAAAGCTGTGAAT
1441098 GGGAGAAGCTACTAGAGGATCCCAATGTAAAAGCTGTGAAT
1 GGGAGAAGCTACTAGAGGATCCCAATGTAAAAGCTGTGAAT
1441139 AAGATGATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.15, G:0.29, T:0.20
Consensus pattern (41 bp):
GGGAGAAGCTACTAGAGGATCCCAATGTAAAAGCTGTGAAT
Found at i:1441169 original size:26 final size:26
Alignment explanation
Indices: 1441140--1441190 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1441130 GCTGTGAATA
**
1441140 AGATGATAAAATGAAGTCGAAGAGTC
1 AGATGATAAAAACAAGTCGAAGAGTC
1441166 AGATGATAAAAACAAGTCGAAGAGT
1 AGATGATAAAAACAAGTCGAAGAGT
1441191 TTTCAGTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.49, C:0.08, G:0.25, T:0.18
Consensus pattern (26 bp):
AGATGATAAAAACAAGTCGAAGAGTC
Found at i:1443832 original size:7 final size:8
Alignment explanation
Indices: 1443813--1443890 Score: 63
Period size: 8 Copynumber: 9.4 Consensus size: 8
1443803 TGAAGAGGAA
1443813 AAAAAATG
1 AAAAAATG
1443821 AAAAAATG
1 AAAAAATG
1443829 AAAAAAATG
1 -AAAAAATG
1443838 AAAAGAAT-
1 AAAA-AATG
*
1443846 AAAAGAA-A
1 AAAA-AATG
1443854 AAATAAAT-
1 AAA-AAATG
1443862 AAAAAATG
1 AAAAAATG
*
1443870 AAAAAAAG
1 AAAAAATG
1443878 AAGAAAATTG
1 AA-AAAA-TG
1443888 AAA
1 AAA
1443891 GGAGGGTTGA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
7 4 0.07
8 36 0.60
9 17 0.28
10 3 0.05
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:1444363 original size:21 final size:23
Alignment explanation
Indices: 1444337--1444379 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1444327 TATAAAAATT
1444337 CCAATTTT-CTCATTT-CAAGCC
1 CCAATTTTGCTCATTTACAAGCC
*
1444358 CCAATTTTGTTCATTTACAAGC
1 CCAATTTTGCTCATTTACAAGC
1444380 ATTTTATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.40
Consensus pattern (23 bp):
CCAATTTTGCTCATTTACAAGCC
Found at i:1447678 original size:22 final size:20
Alignment explanation
Indices: 1447648--1447687 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1447638 CCCTCCTATA
*
1447648 GTACTGATACTTCTCATTTATG
1 GTACCGATAC-TCTC-TTTATG
1447670 GTACCGATACTCTCTTTA
1 GTACCGATACTCTCTTTA
1447688 GTATCGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (20 bp):
GTACCGATACTCTCTTTATG
Found at i:1453898 original size:24 final size:24
Alignment explanation
Indices: 1453880--1454005 Score: 164
Period size: 24 Copynumber: 5.3 Consensus size: 24
1453870 TGAAGTGCCA
1453880 CGTAGAATTTTTCCCGAAGGACCG
1 CGTAGAATTTTTCCCGAAGGACCG
*
1453904 CGTAGAATTTTTCCCTAAGGACCG
1 CGTAGAATTTTTCCCGAAGGACCG
* *
1453928 CGTTGAATATTTCCCGAAGGACCG
1 CGTAGAATTTTTCCCGAAGGACCG
* *
1453952 CGTAGAATTTTTCTCGAAGGACCA
1 CGTAGAATTTTTCCCGAAGGACCG
* * * *
1453976 CATAG-ATTTGTCACGAAGGATCG
1 CGTAGAATTTTTCCCGAAGGACCG
1453999 CGTAGAA
1 CGTAGAA
1454006 CGCTCGAATC
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
23 18 0.21
24 69 0.79
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
CGTAGAATTTTTCCCGAAGGACCG
Done.