Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007931.1 Hibiscus syriacus cultivar Beakdansim tig00110339_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: 2341804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1236534 original size:82 final size:82
Alignment explanation
Indices: 1236442--1236620 Score: 225
Period size: 82 Copynumber: 2.2 Consensus size: 82
1236432 GTTTATACAA
* * *
1236442 AAAAACGCCACTATTGATT-ACACTATTGTGGCGTTTGTAAAAAAAACGCCACTAATGATTAAAA
1 AAAAACGCCACTATTGATTAACACTATTATGGCATTTGT-AAAAAAACACCACTAATGATTAAAA
* * *
1236506 CTATTGCGGTATTTTTAT
65 CTATTGCGGCATTTTAAG
** * * *
1236524 AAAAACGCCACTATTGATTAACACTATTATGGCATTTGTCTAAAAACACCACTATTTATTATAAC
1 AAAAACGCCACTATTGATTAACACTATTATGGCATTTGTAAAAAAACACCACTAATGATTAAAAC
1236589 TATTGCGGCATTTTAAG
66 TATTGCGGCATTTTAAG
*
1236606 AATAAATGCCACTAT
1 AA-AAACGCCACTAT
1236621 ATGTGTAATC
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
82 55 0.66
83 28 0.34
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (82 bp):
AAAAACGCCACTATTGATTAACACTATTATGGCATTTGTAAAAAAACACCACTAATGATTAAAAC
TATTGCGGCATTTTAAG
Found at i:1236653 original size:42 final size:41
Alignment explanation
Indices: 1236607--1236735 Score: 131
Period size: 42 Copynumber: 3.1 Consensus size: 41
1236597 CATTTTAAGA
*
1236607 ATAAATGCCACTATATGTGTAATCTATTGCGGTGTTTGTGGT
1 ATAAATGCCACTATATGT-TAATCTATTGCGGCGTTTGTGGT
* * * *
1236649 ATAAACGCCGCTA-AT-TTACCGATCTATTGTGGCATTT-TGGCT
1 ATAAATGCCACTATATGTTA---ATCTATTGCGGCGTTTGTGG-T
*
1236691 A-AAATGCCACTATATGTTAATCTATAGCGGCGTTTGTGGT
1 ATAAATGCCACTATATGTTAATCTATTGCGGCGTTTGTGGT
1236731 ATAAA
1 ATAAA
1236736 CACCGTTAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
39 2 0.03
40 16 0.23
41 20 0.29
42 28 0.41
43 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (41 bp):
ATAAATGCCACTATATGTTAATCTATTGCGGCGTTTGTGGT
Found at i:1240828 original size:35 final size:36
Alignment explanation
Indices: 1240697--1240977 Score: 211
Period size: 36 Copynumber: 8.2 Consensus size: 36
1240687 GTAACCGTAC
*
1240697 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1240733 TTTGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1240769 CTTAG-TTCCAGAAAAACTGTCTCAAGAAAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* **
1240805 TTTGTTTCAA-AGAAACTGTCTCAAGGGAGATGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1240840 TTTGTTTCAAGGGAAACATAT-TC-A-A-AG----AT
1 TTTGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAA
* * *
1240869 TTTGTTTCAAGGGAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAA
* *
1240898 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACCAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1240934 TTTGTTTCAAGGGAAATTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1240970 TTTTGTTT
1 -TTTGTTT
1240978 TGAGTAAATT
Statistics
Matches: 206, Mismatches: 25, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.00
29 47 0.23
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
35 35 0.17
36 105 0.51
37 12 0.06
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1240880 original size:29 final size:29
Alignment explanation
Indices: 1240840--1240914 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
1240830 GGAGATGAAA
*
1240840 TTTGTTTCAAGGGAAACATATTCAAAGAT
1 TTTGTTTCAAGGGAAACAGATTCAAAGAT
1240869 TTTGTTTCAAGGGAAACAGATTCAAAGAT
1 TTTGTTTCAAGGGAAACAGATTCAAAGAT
1240898 TTTGTTTCAAGGGAAAC
1 TTTGTTTCAAGGGAAAC
1240915 TGTCTCAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (29 bp):
TTTGTTTCAAGGGAAACAGATTCAAAGAT
Found at i:1240994 original size:37 final size:37
Alignment explanation
Indices: 1240898--1240994 Score: 119
Period size: 36 Copynumber: 2.7 Consensus size: 37
1240888 ATTCAAAGAT
* *
1240898 TTTGTTTCAAGGGAAACT-GTCTCAAGAGAGACCAAA
1 TTTGTTTCAAGGGAAATTAGTCTCAAGAGAGACAAAA
1240934 TTTGTTTCAAGGGAAATTA-TCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAATTAGTCTCAAGAGAGACAAAA
** *
1240970 TTTTGTTTTGA-GTAAATTAGTCTCA
1 -TTTGTTTCAAGGGAAATTAGTCTCA
1240995 TGCGAGACGA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 40 0.75
37 13 0.25
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (37 bp):
TTTGTTTCAAGGGAAATTAGTCTCAAGAGAGACAAAA
Found at i:1241916 original size:32 final size:32
Alignment explanation
Indices: 1241880--1241962 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
1241870 TTCACATCTA
1241880 GAATCCCCAAAGATGCCCCAATATTCGATGTT
1 GAATCCCCAAAGATGCCCCAATATTCGATGTT
* * *
1241912 GAATCTCCGAAA-ATGCCTCAATATTTGATGTT
1 GAATC-CCCAAAGATGCCCCAATATTCGATGTT
** *
1241944 GAATCTTCAAAGATACCCC
1 GAATCCCCAAAGATGCCCC
1241963 CATTGTTCCT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
31 3 0.07
32 33 0.80
33 5 0.12
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (32 bp):
GAATCCCCAAAGATGCCCCAATATTCGATGTT
Found at i:1243037 original size:12 final size:11
Alignment explanation
Indices: 1243015--1243068 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 11
1243005 ATGCGTCTTG
*
1243015 TTTTTTCTCTC
1 TTTTTTTTCTC
1243026 TTTTTTATTCTC
1 TTTTTT-TTCTC
1243038 TTTGCTTTTTCT-
1 TTT--TTTTTCTC
1243050 TTATTTTTTCTC
1 TT-TTTTTTCTC
1243062 TTTTTTT
1 TTTTTTT
1243069 CTTTTTGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
11 18 0.49
12 11 0.30
13 5 0.14
14 3 0.08
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:1243079 original size:11 final size:10
Alignment explanation
Indices: 1243010--1243079 Score: 50
Period size: 12 Copynumber: 6.1 Consensus size: 10
1243000 TGCTTATGCG
1243010 TCTTGTTTTTT
1 TCTT-TTTTTT
1243021 CTCTCTTTTTTAT
1 -TCT-TTTTTT-T
1243034 TCTCTTTGCTTTT
1 TCT-TTT--TTTT
1243047 TCTTTATTTTT
1 TCTTT-TTTTT
*
1243058 TCTCTTTTTT
1 TCTTTTTTTT
1243068 TCTTTTTGTTT
1 TCTTTTT-TTT
1243079 T
1 T
1243080 GATTAGATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
10 11 0.22
11 12 0.24
12 17 0.34
13 7 0.14
14 3 0.06
ACGTcount: A:0.03, C:0.16, G:0.04, T:0.77
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:1246105 original size:3 final size:3
Alignment explanation
Indices: 1246099--1246142 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
1246089 AAATTAATTA
*
1246099 AAT AAT AAT AAT AAT AAT AA- AAT AAT AGA- AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
1246143 TATCTAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 3 0.08
3 32 0.89
4 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1246121 original size:20 final size:20
Alignment explanation
Indices: 1246093--1246137 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1246083 GTAAAAAAAT
*
1246093 TAATTAAATAATA-ATAATAA
1 TAATAAAATAATAGA-AATAA
1246113 TAATAAAATAATAGAAATAA
1 TAATAAAATAATAGAAATAA
1246133 TAATA
1 TAATA
1246138 CTAATTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
TAATAAAATAATAGAAATAA
Found at i:1256361 original size:22 final size:23
Alignment explanation
Indices: 1256321--1256365 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1256311 AGACAGTTGT
*
1256321 ATAATATAAATTAAATTAAAAAA
1 ATAATATAAAGTAAATTAAAAAA
*
1256344 ATAAT-TAAAGTAATTTAAAAAA
1 ATAATATAAAGTAAATTAAAAAA
1256366 TTGAAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
ATAATATAAAGTAAATTAAAAAA
Found at i:1260477 original size:28 final size:29
Alignment explanation
Indices: 1260438--1260546 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
1260428 CTAGTGGAAA
*
1260438 TACCTAATTTTCCAATATTAAATGAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
*
1260467 TACCT-ATTTTCCAATATTCAATAAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
1260495 TACCTAATTTTCCAATATTCAATGAGCATT
1 TACCTAATTTTCCAATATTCAATGAGCA-T
1260525 TACCTAATTTTCCAATA-TCAAT
1 TACCTAATTTTCCAATATTCAAT
1260547 ATTCAATGAG
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
28 26 0.35
29 31 0.41
30 18 0.24
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (29 bp):
TACCTAATTTTCCAATATTCAATGAGCAT
Found at i:1260501 original size:57 final size:58
Alignment explanation
Indices: 1260438--1260547 Score: 188
Period size: 57 Copynumber: 1.9 Consensus size: 58
1260428 CTAGTGGAAA
1260438 TACCTAATTTTCCAATATTAAATGAGCA-TTACCT-ATTTTCCAATATTCAATAAGCAT
1 TACCTAATTTTCCAATATTAAATGAGCATTTACCTAATTTTCCAATA-TCAATAAGCAT
*
1260495 TACCTAATTTTCCAATATTCAATGAGCATTTACCTAATTTTCCAATATCAATA
1 TACCTAATTTTCCAATATTAAATGAGCATTTACCTAATTTTCCAATATCAATA
1260548 TTCAATGAGC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
57 27 0.54
58 12 0.24
59 11 0.22
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (58 bp):
TACCTAATTTTCCAATATTAAATGAGCATTTACCTAATTTTCCAATATCAATAAGCAT
Found at i:1267090 original size:23 final size:23
Alignment explanation
Indices: 1267043--1267090 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1267033 GACCCAAATA
* *
1267043 AAAATAAAATTAAATAAATTAAT
1 AAAATAAAAGTAAATAAAGTAAT
1267066 AAAATAAAAGTAAA-AAAGTAGAT
1 AAAATAAAAGTAAATAAAGTA-AT
1267089 AA
1 AA
1267091 GAAAACGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (23 bp):
AAAATAAAAGTAAATAAAGTAAT
Found at i:1267308 original size:2 final size:2
Alignment explanation
Indices: 1267303--1267398 Score: 60
Period size: 2 Copynumber: 49.5 Consensus size: 2
1267293 TTTCAAAAAT
* * *
1267303 TA TA TA TA T- TA TA TA TT TT TA -A AA T- TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1267341 TA TT TT TA -A AA T- TA TA TA TA CA 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
1267381 TGA TCA TA TA TA CTA TA T
1 T-A T-A TA TA TA -TA TA T
1267399 GATGTAATTA
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
1 6 0.08
2 65 0.84
3 6 0.08
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1267310 original size:19 final size:19
Alignment explanation
Indices: 1267260--1267312 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 19
1267250 TGAAAACTAT
*
1267260 ATTATATATGTTTTAAAAA
1 ATTATATATATTTTAAAAA
*
1267279 ATTATACTATATATTTTCAAAA
1 A-T-TA-TATATATTTTAAAAA
1267301 ATTATATATATT
1 ATTATATATATT
1267313 ATATATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 3 0.10
22 14 0.48
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTATATATATTTTAAAAA
Found at i:1267310 original size:21 final size:21
Alignment explanation
Indices: 1267237--1267360 Score: 79
Period size: 23 Copynumber: 5.4 Consensus size: 21
1267227 AAACTATATA
* * *
1267237 TATATATATATATTGAAAACT
1 TATATATATATTTTAAAAAAT
*
1267258 ATATTATATATGTTTTAAAAAAT
1 -TA-TATATATATTTTAAAAAAT
1267281 TATACTATATATTTTCAAAAATTAT
1 TATA-TATATATTTT-AAAAA--AT
*
1267306 ATATATTATATATTTTTAAAATTAT
1 -TATA-TATATA-TTTTAAAA-AAT
*
1267331 ATATATTATATATTTT-TAAAAT
1 -TATA-TATATATTTTAAAAAAT
1267353 TATATATA
1 TATATATA
1267361 CATATATATA
Statistics
Matches: 85, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.05
21 6 0.07
22 15 0.18
23 22 0.26
24 4 0.05
25 16 0.19
26 14 0.16
27 4 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TATATATATATTTTAAAAAAT
Found at i:1267332 original size:25 final size:25
Alignment explanation
Indices: 1267257--1267369 Score: 149
Period size: 25 Copynumber: 4.5 Consensus size: 25
1267247 TATTGAAAAC
*
1267257 TATATTATATATGTTTTAAAA-AAT-
1 TATATTATATAT-TTTTAAAATTATA
* *
1267281 TATACTATATATTTTCAAAAATTATA
1 TATATTATATATTTT-TAAAATTATA
1267307 TATATTATATATTTTTAAAATTATA
1 TATATTATATATTTTTAAAATTATA
1267332 TATATTATATATTTTTAAAATTATA
1 TATATTATATATTTTTAAAATTATA
*
1267357 TATACATATATAT
1 TATA-TTATATAT
1267370 ATATATATAT
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
23 3 0.04
24 15 0.19
25 40 0.51
26 21 0.27
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (25 bp):
TATATTATATATTTTTAAAATTATA
Found at i:1267365 original size:24 final size:24
Alignment explanation
Indices: 1267233--1267367 Score: 143
Period size: 25 Copynumber: 5.6 Consensus size: 24
1267223 TAAAAAACTA
* * *
1267233 TATATATATATATATATTGAAAAC
1 TATATATATATATATTTTTAAAAT
*
1267257 TATAT-TATATAT-GTTTTAAAA-
1 TATATATATATATATTTTTAAAAT
* *
1267278 AAT-TATACTATATATTTTCAAAAAT
1 TATATATA-TATATATTTT-TAAAAT
1267303 TATATATATTATATATTTTTAAAAT
1 TATATATA-TATATATTTTTAAAAT
1267328 TATATATATTATATATTTTTAAAAT
1 TATATATA-TATATATTTTTAAAAT
*
1267353 TATATATACATATAT
1 TATATATATATATAT
1267368 ATATATATAT
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.01
21 4 0.04
22 11 0.12
23 10 0.11
24 15 0.16
25 40 0.42
26 14 0.15
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (24 bp):
TATATATATATATATTTTTAAAAT
Found at i:1267788 original size:14 final size:14
Alignment explanation
Indices: 1267771--1267803 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1267761 ATTTCTATGT
*
1267771 AGGGAATTATTTGC
1 AGGGAATTATTTAC
1267785 AGGGAATTATTTAC
1 AGGGAATTATTTAC
1267799 AGGGA
1 AGGGA
1267804 TTACTCCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:1270396 original size:5 final size:6
Alignment explanation
Indices: 1270379--1270403 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1270369 CCTTTTAGAT
1270379 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
1270404 AACGATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:1282146 original size:25 final size:25
Alignment explanation
Indices: 1282118--1282190 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 25
1282108 AAATCTTTTT
1282118 TATACACATAAAAAATACATATAAA
1 TATACACATAAAAAATACATATAAA
* *
1282143 TATATA-ATTAAAAAAT-CATTTAAA
1 TATACACA-TAAAAAATACATATAAA
* * *
1282167 TGTAC-CATACAAAATATA-ATAAA
1 TATACACATAAAAAATACATATAAA
1282190 T
1 T
1282191 TGGTTGGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
23 12 0.32
24 13 0.34
25 13 0.34
ACGTcount: A:0.59, C:0.10, G:0.01, T:0.30
Consensus pattern (25 bp):
TATACACATAAAAAATACATATAAA
Found at i:1295095 original size:26 final size:26
Alignment explanation
Indices: 1295066--1295117 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1295056 TGTTATTGTG
1295066 TGATATTTTCTACTTGTCTTTATCTA
1 TGATATTTTCTACTTGTCTTTATCTA
1295092 TGATATTTTCTACTTGTCTTTATCTA
1 TGATATTTTCTACTTGTCTTTATCTA
1295118 GGTATATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (26 bp):
TGATATTTTCTACTTGTCTTTATCTA
Found at i:1296825 original size:15 final size:15
Alignment explanation
Indices: 1296807--1296857 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1296797 AAAATAAATT
*
1296807 TTAAAGTTAGAGTGA
1 TTAAAGTTAGAGTAA
1296822 TTAAA-TTAAGAGTAA
1 TTAAAGTT-AGAGTAA
1296837 TTTGAAAGTTA-AGTAA
1 -TT-AAAGTTAGAGTAA
1296853 TTAAA
1 TTAAA
1296858 TAAAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 5 0.16
15 13 0.42
16 7 0.23
17 4 0.13
18 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (15 bp):
TTAAAGTTAGAGTAA
Found at i:1300459 original size:46 final size:45
Alignment explanation
Indices: 1300367--1300490 Score: 178
Period size: 46 Copynumber: 2.8 Consensus size: 45
1300357 GTAAGCATGC
*
1300367 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
1300411 AAATAAGCTTACGAGCTTATGTAATTAAATGGTAAGTGTTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TAAATGGTAAGTATATTGGTA
* *
1300457 AAATAAGCTTACGATCTTATGGGATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA
1300491 TAGATTTTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
44 23 0.32
45 11 0.15
46 37 0.52
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1306887 original size:213 final size:213
Alignment explanation
Indices: 1306520--1306950 Score: 799
Period size: 213 Copynumber: 2.0 Consensus size: 213
1306510 GGAAAGGTCA
* *
1306520 GAAAAATCGGATAGCAGATTCTGCAAAACAGATTCTGTTGATCAACTTTAAAAATTCACCATAAA
1 GAAAAATCGAACAGCAGATTCTGCAAAACAGATTCTGTTGATCAACTTTAAAAATTCACCATAAA
* *
1306585 TTGTAAATAATGAATTAGAAGGAGTTATTTATATGGATAGATTCGTATTTAAGTCTAGTTTTTAA
66 TTGTAAAGAATGAATTAGAAGGAGTTATTTATATGGATAGATTCGTATTCAAGTCTAGTTTTTAA
* *
1306650 CTAAATAAACATAATTGAATTCCAGTGTGTATATCAATACAGAATACTGATTCTTTAAAGGTAGT
131 CGAAAGAAACATAATTGAATTCCAGTGTGTATATCAATACAGAATACTGATTCTTTAAAGGTAGT
1306715 ACGAATTGTCTGAATATG
196 ACGAATTGTCTGAATATG
1306733 GAAAAATCGAACAGCAGATTCTGCAAAACAGATTCTGTTGATCAACTTTAAAAATTCACCATAAA
1 GAAAAATCGAACAGCAGATTCTGCAAAACAGATTCTGTTGATCAACTTTAAAAATTCACCATAAA
*
1306798 TTGTAAAGAATGAATTAGAAGGAGTTATTTATATGGATAGATTCTTATTCAAGTCTAGTTTTTAA
66 TTGTAAAGAATGAATTAGAAGGAGTTATTTATATGGATAGATTCGTATTCAAGTCTAGTTTTTAA
1306863 CGAAAGAAACATAATTGAATTCCAGTGTGTATATCAATACAGAATACTGATTCTTTAAAGGTAGT
131 CGAAAGAAACATAATTGAATTCCAGTGTGTATATCAATACAGAATACTGATTCTTTAAAGGTAGT
1306928 ACGAATTGTCTGAATATG
196 ACGAATTGTCTGAATATG
1306946 GAAAA
1 GAAAA
1306951 TTGATGGGTT
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
213 211 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (213 bp):
GAAAAATCGAACAGCAGATTCTGCAAAACAGATTCTGTTGATCAACTTTAAAAATTCACCATAAA
TTGTAAAGAATGAATTAGAAGGAGTTATTTATATGGATAGATTCGTATTCAAGTCTAGTTTTTAA
CGAAAGAAACATAATTGAATTCCAGTGTGTATATCAATACAGAATACTGATTCTTTAAAGGTAGT
ACGAATTGTCTGAATATG
Found at i:1308667 original size:21 final size:21
Alignment explanation
Indices: 1308625--1308668 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1308615 TGGGTGTTAT
* *
1308625 AATACAAGAAATCATACGAGA
1 AATACAAAAAATCATACAAGA
1308646 AATACAAAAAAT-ATTACAAGA
1 AATACAAAAAATCA-TACAAGA
1308667 AA
1 AA
1308669 AAATACGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.64, C:0.11, G:0.09, T:0.16
Consensus pattern (21 bp):
AATACAAAAAATCATACAAGA
Found at i:1309260 original size:18 final size:18
Alignment explanation
Indices: 1309233--1309280 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1309223 AAAATCACAC
*
1309233 ATAT-TTATATGTTATAT
1 ATATATTATATATTATAT
*
1309250 ATATATTATATATTGTAT
1 ATATATTATATATTATAT
*
1309268 AAATATTAT-TATT
1 ATATATTATATATT
1309281 TTAGTAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
ATATATTATATATTATAT
Found at i:1311757 original size:13 final size:13
Alignment explanation
Indices: 1311724--1311748 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1311714 CCTAATCGTT
1311724 TGTTTTTTTCTTA
1 TGTTTTTTTCTTA
1311737 TGTTTTTTTCTT
1 TGTTTTTTTCTT
1311749 GTTATTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.08, G:0.08, T:0.80
Consensus pattern (13 bp):
TGTTTTTTTCTTA
Found at i:1321251 original size:52 final size:52
Alignment explanation
Indices: 1321170--1321269 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
1321160 AATACTTCGC
* *
1321170 TTAGGATGAAAACCCGAGAGGGCGTCCT-AAGTTGAAAAAAAAAAAAAAACGT
1 TTAGGATGAAAACCCGAGAGGGCGCCCTAAAATT-AAAAAAAAAAAAAAACGT
* *
1321222 TTAGGGTGAAAACCCGAGAGGGCGCCCTAAAATTAAAAAAAAGAAAAA
1 TTAGGATGAAAACCCGAGAGGGCGCCCTAAAATTAAAAAAAAAAAAAA
1321270 GAAAAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 39 0.91
53 4 0.09
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.14
Consensus pattern (52 bp):
TTAGGATGAAAACCCGAGAGGGCGCCCTAAAATTAAAAAAAAAAAAAAACGT
Found at i:1322196 original size:105 final size:105
Alignment explanation
Indices: 1322014--1322684 Score: 1144
Period size: 105 Copynumber: 6.4 Consensus size: 105
1322004 AGGTTTTACC
* * *
1322014 CAGAGCCAATTTCAGCTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1322079 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1322119 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1322184 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1322224 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1322289 ACGAAGGGACCGCTGGTTGTCGACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1322329 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1322394 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1322434 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1322499 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
1322539 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGCTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * ** * * *
1322604 ACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* ** *
1322645 CAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1322685 GGAACAATGC
Statistics
Matches: 542, Mismatches: 23, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 498 0.92
106 44 0.08
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:1323219 original size:18 final size:18
Alignment explanation
Indices: 1323192--1323239 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1323182 AAAATCACAC
*
1323192 ATAT-TTATATGTTATAT
1 ATATATTATATATTATAT
*
1323209 ATATATTATATATTGTAT
1 ATATATTATATATTATAT
*
1323227 AAATATTAT-TATT
1 ATATATTATATATT
1323240 TTAGTAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
ATATATTATATATTATAT
Found at i:1326660 original size:163 final size:163
Alignment explanation
Indices: 1326390--1326712 Score: 583
Period size: 163 Copynumber: 2.0 Consensus size: 163
1326380 ATGTTTTAGA
* *
1326390 TTTTTAAGGGTATTCGTTTAAATCGATCGGAGGTAAGTAATTTGGATTAAACTTTACTTTTTAAT
1 TTTTTAAGGGTATTCGTTCAAATCGATCGGAGGTAAGTAATTTGGATCAAACTTTACTTTTTAAT
*
1326455 TTAACTTACAATTTTCTCAATTAAGACAACTGAAAATTAATTAGTAGCGAAAGGGCAGTTCAAGG
66 TTAACTTACAATTTTCTCAATTAAGACAACTGAAAATTAATTAGTACCGAAAGGGCAGTTCAAGG
* *
1326520 GTGTTAATCCTTCATTGACTGTAACCGACTAAC
131 GTGCTAATCCTTCATTGACTATAACCGACTAAC
*
1326553 TTTTTAAGGGTATTCGTTCAAATCTATCGGAGGTAAGTAATTTGGATCAAACTTTACTTTTTAAT
1 TTTTTAAGGGTATTCGTTCAAATCGATCGGAGGTAAGTAATTTGGATCAAACTTTACTTTTTAAT
1326618 TTAACTTACAATTTTCTCAATTAAGACAACTGAAAATTAATTAGTACCGAAAGGGCAGTTCAAGG
66 TTAACTTACAATTTTCTCAATTAAGACAACTGAAAATTAATTAGTACCGAAAGGGCAGTTCAAGG
*
1326683 GTGCTAATCCTTCCTTGACTATAACCGACT
131 GTGCTAATCCTTCATTGACTATAACCGACT
1326713 CCCGAATCCG
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
163 153 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (163 bp):
TTTTTAAGGGTATTCGTTCAAATCGATCGGAGGTAAGTAATTTGGATCAAACTTTACTTTTTAAT
TTAACTTACAATTTTCTCAATTAAGACAACTGAAAATTAATTAGTACCGAAAGGGCAGTTCAAGG
GTGCTAATCCTTCATTGACTATAACCGACTAAC
Found at i:1329692 original size:13 final size:13
Alignment explanation
Indices: 1329674--1329698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1329664 TACTTTGAAT
1329674 TTTATTTTCCATG
1 TTTATTTTCCATG
1329687 TTTATTTTCCAT
1 TTTATTTTCCAT
1329699 TTTCCATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTATTTTCCATG
Found at i:1338724 original size:2 final size:2
Alignment explanation
Indices: 1338713--1338753 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1338703 ATATTATACA
1338713 AT AT -T 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
1338754 TATTTATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1339215 original size:22 final size:23
Alignment explanation
Indices: 1339170--1339217 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1339160 AAAAGGAAAA
* *
1339170 AAATACATAAGAAATCATACGAG
1 AAATACATAAGAAATCACAAGAG
*
1339193 AAATACATAA-AAATTACAAGAG
1 AAATACATAAGAAATCACAAGAG
1339215 AAA
1 AAA
1339218 ATACGAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (23 bp):
AAATACATAAGAAATCACAAGAG
Found at i:1339219 original size:23 final size:24
Alignment explanation
Indices: 1339169--1339221 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
1339159 GAAAAGGAAA
* *
1339169 AAAATACATAAGAAATCATACGAG
1 AAAATACATAAGAAATCACAAGAG
*
1339193 -AAATACATAA-AAATTACAAGAG
1 AAAATACATAAGAAATCACAAGAG
1339215 AAAATAC
1 AAAATAC
1339222 GAGAGAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.17
Consensus pattern (24 bp):
AAAATACATAAGAAATCACAAGAG
Found at i:1339895 original size:5 final size:5
Alignment explanation
Indices: 1339887--1339914 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1339877 TTAACCGTTT
1339887 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1339915 TTTTCTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:1339943 original size:6 final size:6
Alignment explanation
Indices: 1339932--1339978 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
1339922 CTCTTATTGT
*
1339932 TTTTTA TTTTTA TTTTTA TCTTTT- TTTATT- TTTTTA TATTTA TTTTT
1 TTTTTA TTTTTA TTTTTA T-TTTTA TTT-TTA TTTTTA TTTTTA TTTTT
1339979 TTGAATTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 28 0.78
7 4 0.11
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:1339958 original size:24 final size:23
Alignment explanation
Indices: 1339925--1339980 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
1339915 TTTTCTTCTC
*
1339925 TTATTGTTTTTTA--TTTTTATTT
1 TTATT-TTTTTTATTTTTTTATAT
1339947 TTATCTTTTTTTATTTTTTTATAT
1 TTAT-TTTTTTTATTTTTTTATAT
1339971 TTATTTTTTT
1 TTATTTTTTT
1339981 GAATTGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 11 0.37
23 7 0.23
24 12 0.40
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (23 bp):
TTATTTTTTTTATTTTTTTATAT
Found at i:1339980 original size:32 final size:32
Alignment explanation
Indices: 1339902--1339980 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
1339892 TTTAATTTAA
*
1339902 TTTA-ATTTAATTTTTTTCTTCTCTTATTGTT
1 TTTATATTTATTTTTTTTCTTCTCTTATTGTT
* *
1339933 TTT-TATTT-TTATTTTTATCTTTTTTTATT-TT
1 TTTATATTTATT-TTTTT-TCTTCTCTTATTGTT
1339964 TTTATATTTATTTTTTT
1 TTTATATTTATTTTTTT
1339981 GAATTGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
30 1 0.03
31 17 0.43
32 20 0.50
33 2 0.05
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.78
Consensus pattern (32 bp):
TTTATATTTATTTTTTTTCTTCTCTTATTGTT
Found at i:1339990 original size:24 final size:23
Alignment explanation
Indices: 1339939--1340001 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
1339929 TGTTTTTTAT
* * *
1339939 TTTTATTTTTATCTTTTTTTATTT
1 TTTTATATTTAT-TTTTTTAATTG
1339963 TTTTATATTTATTTTTTTGAATTG
1 TTTTATATTTATTTTTTT-AATTG
*
1339987 TTTTTTATATTATTT
1 TTTTATAT-TTATTT
1340002 CTCTTTTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 6 0.18
24 21 0.64
25 6 0.18
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (23 bp):
TTTTATATTTATTTTTTTAATTG
Found at i:1340081 original size:17 final size:18
Alignment explanation
Indices: 1340047--1340084 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1340037 CATTTATTTC
*
1340047 TTTTTTTAGTTTAGCCTT
1 TTTTTTTAGTTTACCCTT
*
1340065 TTTTTTTA-TTTTCCCTT
1 TTTTTTTAGTTTACCCTT
1340082 TTT
1 TTT
1340085 AGTAGCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTTTTAGTTTACCCTT
Found at i:1341723 original size:17 final size:18
Alignment explanation
Indices: 1341701--1341738 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1341691 GATAATTCAT
1341701 TAAAAATATA-ATTATAA
1 TAAAAATATATATTATAA
*
1341718 TAAAAATATATTTTATAA
1 TAAAAATATATATTATAA
1341736 TAA
1 TAA
1341739 CTTATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAAATATATATTATAA
Found at i:1342616 original size:31 final size:31
Alignment explanation
Indices: 1342578--1342637 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1342568 AGGAGAAATA
* *
1342578 AATGAAAAATACTTTAATATAAAACTTTAAT
1 AATGAAAAAGACCTTAATATAAAACTTTAAT
*
1342609 AATGAAAAAGACCTTAATATAAAATTTTA
1 AATGAAAAAGACCTTAATATAAAACTTTA
1342638 TATAGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (31 bp):
AATGAAAAAGACCTTAATATAAAACTTTAAT
Found at i:1343183 original size:20 final size:20
Alignment explanation
Indices: 1343151--1343188 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1343141 TACTATAATT
1343151 CCTTTTTCCAAAA-AAAATC
1 CCTTTTTCCAAAAGAAAATC
*
1343170 CCTTTTTCTTAAAAGAAAA
1 CCTTTTTC-CAAAAGAAAA
1343189 AAAGTACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
20 4 0.25
21 4 0.25
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (20 bp):
CCTTTTTCCAAAAGAAAATC
Found at i:1345637 original size:18 final size:18
Alignment explanation
Indices: 1345614--1345663 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1345604 CTGCGCTTAT
1345614 TTTTCAAAATCAAAATAG
1 TTTTCAAAATCAAAATAG
1345632 TTTTCAAAATCAAAATAG
1 TTTTCAAAATCAAAATAG
1345650 TTTTCAAAATCAAA
1 TTTTCAAAATCAAA
1345664 GATCGACTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (18 bp):
TTTTCAAAATCAAAATAG
Found at i:1355268 original size:16 final size:16
Alignment explanation
Indices: 1355247--1355277 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1355237 ATTAAAAATT
1355247 GATTTATTTGAGTAGC
1 GATTTATTTGAGTAGC
1355263 GATTTATTTGAGTAG
1 GATTTATTTGAGTAG
1355278 AGATCCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.45
Consensus pattern (16 bp):
GATTTATTTGAGTAGC
Found at i:1357100 original size:21 final size:21
Alignment explanation
Indices: 1357049--1357100 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1357039 CATTTTATTT
*
1357049 TTGATTTTTAAGCTTACATGA
1 TTGATTTTTGAGCTTACATGA
1357070 TTGATTTTTGAGCTTACATGA
1 TTGATTTTTGAGCTTACATGA
1357091 TTGATTTTTG
1 TTGATTTTTG
1357101 GACTAAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.08, G:0.17, T:0.52
Consensus pattern (21 bp):
TTGATTTTTGAGCTTACATGA
Found at i:1358440 original size:20 final size:20
Alignment explanation
Indices: 1358412--1358457 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1358402 TAATATAGTA
*
1358412 GTATAGATACCATGGTAAGG
1 GTATCGATACCATGGTAAGG
1358432 GTATCGATACCATGGTAAGG
1 GTATCGATACCATGGTAAGG
1358452 GTATCG
1 GTATCG
1358458 TTACTGGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.26
Consensus pattern (20 bp):
GTATCGATACCATGGTAAGG
Found at i:1358506 original size:115 final size:115
Alignment explanation
Indices: 1358317--1358543 Score: 274
Period size: 115 Copynumber: 2.0 Consensus size: 115
1358307 CGATGAGGTA
* * * *
1358317 GTATCGATATAATGTTAAGGGTATCGATACTAGGTAACATCAAACCTAATTTTTGTATAAATACC
1 GTATCGATACAATGGTAAGGGTATCGATACTAGGCAACATCAAACCTAATTTTGGTATAAATACC
* * * *
1358382 ATAAAGGGGTATCGGTGCCATAATATAGTAGTATAGATACCATGGTAAGG
66 AGAAAGGGGTATCGATACCATAATAGAGTAGTATAGATACCATGGTAAGG
* * * * * * **
1358432 GTATCGATACCATGGTAAGGGTATCGTTACTGGGCCACATCGAATCTAATTTTGGTATCGATACC
1 GTATCGATACAATGGTAAGGGTATCGATACTAGGCAACATCAAACCTAATTTTGGTATAAATACC
* * * *
1358497 AGAAGGGGGTATCGATACCATAGTAGGGTAGTATCGATACCATGGTA
66 AGAAAGGGGTATCGATACCATAATAGAGTAGTATAGATACCATGGTA
1358544 GGAGCATCAT
Statistics
Matches: 92, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
115 92 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (115 bp):
GTATCGATACAATGGTAAGGGTATCGATACTAGGCAACATCAAACCTAATTTTGGTATAAATACC
AGAAAGGGGTATCGATACCATAATAGAGTAGTATAGATACCATGGTAAGG
Found at i:1358525 original size:19 final size:19
Alignment explanation
Indices: 1358485--1358545 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 19
1358475 ATCTAATTTT
* *
1358485 GGTATCGATACCAGAAG-GG
1 GGTATCGATACCA-TAGTAG
1358504 GGTATCGATACCATAGTAGG
1 GGTATCGATACCATAGTA-G
*
1358524 GTAGTATCGATACCATGGTAG
1 G--GTATCGATACCATAGTAG
1358545 G
1 G
1358546 AGCATCATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 2 0.06
19 13 0.37
20 2 0.06
21 2 0.06
22 16 0.46
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.23
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:1358559 original size:23 final size:22
Alignment explanation
Indices: 1358505--1358559 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1358495 CCAGAAGGGG
*
1358505 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGCA
*
1358527 GTATCGATACCATGGTAGGAGCA
1 GTATCGATACCATAGTAGG-GCA
1358550 -TCATCGATAC
1 GT-ATCGATAC
1358560 TGAGGAACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 19 0.66
23 10 0.34
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGCA
Found at i:1359839 original size:94 final size:94
Alignment explanation
Indices: 1359693--1359909 Score: 258
Period size: 94 Copynumber: 2.3 Consensus size: 94
1359683 CCCAAGCAAT
* * *
1359693 GTGGTATCGATACCATGGTAAGGGTATCGATATATGTCAACATCGAATCTAATTTTGGTATCAAT
1 GTGGTATCGATACCATGGTAAGGGTATCGATACATGACAACATCGAAGCTAATTTTGGTATCAAT
* *
1359758 ACCT-AAGGGTGTATCGATACCATAGCATA
66 A-CTGAAGGGGGTATCGATACCATAGCAGA
* * * **
1359787 GTGGTATCGATACCATGGTGATGGTATCGATACCA-GACTACATCGAAGCTAATTTTGGTATTGA
1 GTGGTATCGATACCATGGTAAGGGTATCGATA-CATGACAACATCGAAGCTAATTTTGGTATCAA
* *
1359851 TATTGGAAGGGGGTATCGATACCATAGTAGA
65 TACT-GAAGGGGGTATCGATACCATAGCAGA
* * *
1359882 GTAGTATCGATACCAGGGTAGGGGTATC
1 GTGGTATCGATACCATGGTAAGGGTATC
1359910 AATATTGAAA
Statistics
Matches: 103, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
93 1 0.01
94 56 0.54
95 46 0.45
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (94 bp):
GTGGTATCGATACCATGGTAAGGGTATCGATACATGACAACATCGAAGCTAATTTTGGTATCAAT
ACTGAAGGGGGTATCGATACCATAGCAGA
Found at i:1360328 original size:20 final size:20
Alignment explanation
Indices: 1360305--1360422 Score: 103
Period size: 20 Copynumber: 5.5 Consensus size: 20
1360295 ATGCATTAAA
1360305 GGATGCATAAAGGCATGAAC
1 GGATGCATAAAGGCATGAAC
*
1360325 GGATGCCATAATTGAAAATGCATGAAAC
1 GGATG-C---A-T--AAAGGCATG-AAC
* *
1360353 -GATGCATAAAGTCATGAAA
1 GGATGCATAAAGGCATGAAC
**
1360372 GGATGCATAAAGTTATGAAC
1 GGATGCATAAAGGCATGAAC
1360392 GGATGCATAAAGGCATGAAC
1 GGATGCATAAAGGCATGAAC
1360412 GGATGCCATAA
1 GGATG-CATAA
1360423 TTGAAAATGA
Statistics
Matches: 80, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.03
20 52 0.65
21 6 0.08
22 1 0.01
23 1 0.01
24 1 0.01
25 1 0.01
26 1 0.01
27 12 0.15
28 3 0.04
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (20 bp):
GGATGCATAAAGGCATGAAC
Found at i:1360357 original size:47 final size:47
Alignment explanation
Indices: 1360284--1360466 Score: 184
Period size: 47 Copynumber: 4.0 Consensus size: 47
1360274 AAATCAATTT
* * * *
1360284 CATAATTGGAAATGCATTAAAGGATGCATAAAGGCATGAACGGATGC
1 CATAATTGAAAATGCATGAAACGATGCATAAAGGCATGAAAGGATGC
*
1360331 CATAATTGAAAATGCATGAAACGATGCATAAAGTCATGAAAGGATG-
1 CATAATTGAAAATGCATGAAACGATGCATAAAGGCATGAAAGGATGC
* * *
1360377 C---A-T-AAAGT-TATG-AACGGATGCATAAAGGCATGAACGGATGC
1 CATAATTGAAAATGCATGAAAC-GATGCATAAAGGCATGAAAGGATGC
* * **
1360418 CATAATTGAAAATGAATGAAAGGATGCATTAGTGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAACGATGCA-TAAAGGCATGAAAGGATGC
1360466 C
1 C
1360467 TTAACTGATA
Statistics
Matches: 111, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
39 3 0.03
40 25 0.23
41 5 0.05
42 1 0.01
43 1 0.01
44 1 0.01
45 1 0.01
46 5 0.05
47 50 0.45
48 19 0.17
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (47 bp):
CATAATTGAAAATGCATGAAACGATGCATAAAGGCATGAAAGGATGC
Found at i:1360412 original size:87 final size:87
Alignment explanation
Indices: 1360305--1360465 Score: 270
Period size: 87 Copynumber: 1.8 Consensus size: 87
1360295 ATGCATTAAA
*
1360305 GGATGCATAAAGGCATGAACGGATGCCATAATTGAAAATGCATGAAACGATGCATAAAGT-CATG
1 GGATGCATAAAGGCATGAACGGATGCCATAATTGAAAATGAATGAAACGATGCAT-AAGTGCATG
1360369 AAAGGATGCATAAAGTTATGAAC
65 AAAGGATGCATAAAGTTATGAAC
* *
1360392 GGATGCATAAAGGCATGAACGGATGCCATAATTGAAAATGAATGAAAGGATGCATTAGTGGCATG
1 GGATGCATAAAGGCATGAACGGATGCCATAATTGAAAATGAATGAAACGATGCATAAGT-GCATG
1360457 AAAGGATGC
65 AAAGGATGC
1360466 CTTAACTGAT
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
86 3 0.04
87 53 0.77
88 13 0.19
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (87 bp):
GGATGCATAAAGGCATGAACGGATGCCATAATTGAAAATGAATGAAACGATGCATAAGTGCATGA
AAGGATGCATAAAGTTATGAAC
Found at i:1360560 original size:45 final size:45
Alignment explanation
Indices: 1360509--1360786 Score: 319
Period size: 45 Copynumber: 6.2 Consensus size: 45
1360499 ATAACAGAAT
*** *
1360509 AATGCATATGGGTGCATTATTGGCATG-AAAGTATGCCAGAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATGCTAGAGTTGA
* *
1360554 AATGCATATGGGTGCATTATCCACAGAAAAGTATACTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
*
1360599 AATGCATATGAGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
* * *
1360644 AATGTATATGGGTACATTATCAACAGAAAAGTATACTATGA-TTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTA-GAGTTGA
* * * * * *
1360689 GATGTATATGGGTACATTATCAACATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
* * * * *
1360734 AATGGATATGGGTACATTATCAATAGAAAAG-ATGTTAGAGTTTAA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAG-TTGA
1360779 AATGCATA
1 AATGCATA
1360787 ATGATGTATT
Statistics
Matches: 205, Mismatches: 24, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
44 8 0.04
45 195 0.95
46 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
Found at i:1365187 original size:95 final size:94
Alignment explanation
Indices: 1365024--1365207 Score: 237
Period size: 95 Copynumber: 1.9 Consensus size: 94
1365014 ATACATGTAA
* * * **
1365024 ACATTGAATCTAATTTTGGTATCGATACCTAAGGGGGTATCGGTACCATAGCATAGTGGTATCGA
1 ACATCGAAGCTAATTTTGGTATCGATACCTAAGGGGGTATCGATACCATAGCATAGCAGTATCGA
*
1365089 TACCATGGT-GAGGGTATCGATACTAGACT
66 TACCAGGGTAG-GGGTATCGATACTAGACT
* *
1365118 ACATCGAAGCTAATTTTGGTATTGATA-CTGGAAGGGGGTATCGATACCATAGTATAGCAGTATC
1 ACATCGAAGCTAATTTTGGTATCGATACCT--AAGGGGGTATCGATACCATAGCATAGCAGTATC
* *
1365182 TATACCAGGGTAGGGGTATTGATACT
64 GATACCAGGGTAGGGGTATCGATACT
1365208 GAAAGGCCAT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
93 2 0.03
94 24 0.31
95 50 0.65
96 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (94 bp):
ACATCGAAGCTAATTTTGGTATCGATACCTAAGGGGGTATCGATACCATAGCATAGCAGTATCGA
TACCAGGGTAGGGGTATCGATACTAGACT
Found at i:1365614 original size:20 final size:21
Alignment explanation
Indices: 1365589--1365721 Score: 76
Period size: 20 Copynumber: 5.9 Consensus size: 21
1365579 AATTGAAAAT
1365589 GCATGAAAGGATG-CATAAAG
1 GCATGAAAGGATGCCATAAAG
* *
1365609 GCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCC---A-T--AAAG
1365636 GCATGAAAGGATG-CATAAAG
1 GCATGAAAGGATGCCATAAAG
*
1365656 GCATGAACA-GATGCCATAATTAAAAAT
1 GCATGAA-AGGATGCC---A-T--AAAG
*
1365683 GTATGAAAGGATG-CATAAAG
1 GCATGAAAGGATGCCATAAAG
*
1365703 GCATGAACGGATGCCATAA
1 GCATGAAAGGATGCCATAA
1365722 TTGAAAATGC
Statistics
Matches: 87, Mismatches: 9, Indels: 33
0.67 0.07 0.26
Matches are distributed among these distances:
20 40 0.46
21 8 0.09
22 2 0.02
23 2 0.02
24 2 0.02
25 2 0.02
26 3 0.03
27 28 0.32
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.19
Consensus pattern (21 bp):
GCATGAAAGGATGCCATAAAG
Found at i:1365646 original size:47 final size:47
Alignment explanation
Indices: 1365577--1365745 Score: 302
Period size: 47 Copynumber: 3.6 Consensus size: 47
1365567 AATCAATTTA
1365577 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
*
1365624 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACAGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
* *
1365671 ATAATTAAAAATGTATGAAAGGATGCATAAAGGCATGAACGGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
*
1365718 ATAATTGAAAATGCATGAAATGATGCAT
1 ATAATTGAAAATGCATGAAAGGATGCAT
1365746 GAGTGGTATG
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 115 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.21
Consensus pattern (47 bp):
ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
Found at i:1365859 original size:45 final size:45
Alignment explanation
Indices: 1365808--1366062 Score: 282
Period size: 45 Copynumber: 5.7 Consensus size: 45
1365798 ATAACAGAAC
*** *
1365808 AATGCATATGGGTGCATTATTGGCATG-AAAGTATGCCAGAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATACCAGAGTTGA
*
1365853 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACCAGAGTTGA
*
1365898 AATGCATATGGGTGCATTATCAACA-AAAA-TATATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATA--CCAGAGTTGA
** * ** **
1365943 AATATATATGGGTACATTATCAACAGAAAAGTATAATATTGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACCAGAGTTGA
* * * * * *
1365988 GATGTATATGGGTACATTATCAACATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACCAGAGTTGA
*
1366033 AATGTATATGGGTGCATTATCAACAGAAAA
1 AATGCATATGGGTGCATTATCAACAGAAAA
1366063 CATGTTAAAG
Statistics
Matches: 186, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
43 4 0.02
44 5 0.03
45 169 0.91
46 4 0.02
47 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACCAGAGTTGA
Found at i:1365908 original size:90 final size:90
Alignment explanation
Indices: 1365808--1366062 Score: 341
Period size: 90 Copynumber: 2.8 Consensus size: 90
1365798 ATAACAGAAC
*** * * *
1365808 AATGCATATGGGTGCATTATTGGCATGAAAGTATGCCAGAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTAGAGTTGAAATGTATATGGGTGCATTAT
*
1365873 CAACAGAAAAGTATACTAGAGTTGA
66 CAACAGAAAAGTATAATAGAGTTGA
* * *
1365898 AATGCATATGGGTGCATTATCAACA-AAAATATATGCTAGAGTTGAAATATATATGGGTACATTA
1 AATGCATATGGGTGCATTATCAACATAAAA-GTATGCTAGAGTTGAAATGTATATGGGTGCATTA
**
1365962 TCAACAGAAAAGTATAATATTGTTGA
65 TCAACAGAAAAGTATAATAGAGTTGA
* * * * *
1365988 GATGTATATGGGTACATTATCAACATAAAAGTATACTATAGTTGAAATGTATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTAGAGTTGAAATGTATATGGGTGCATTAT
1366053 CAACAGAAAA
66 CAACAGAAAA
1366063 CATGTTAAAG
Statistics
Matches: 143, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
89 3 0.02
90 136 0.95
91 4 0.03
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (90 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATGCTAGAGTTGAAATGTATATGGGTGCATTAT
CAACAGAAAAGTATAATAGAGTTGA
Found at i:1366097 original size:90 final size:87
Alignment explanation
Indices: 1365845--1366106 Score: 237
Period size: 90 Copynumber: 2.9 Consensus size: 87
1365835 AAAGTATGCC
* ** *
1365845 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAG-TTGAAATGCATATGG
1 AGAGTTGAAATGTATATGGGTGCATTATCAACAGAAAA--ATGTTAAAGTTTGAAATGCATAT--
*
1365909 GTGCATTATCAACA-AAAATATATGCT
62 GTGTATTATCAACATAAAATATA-GCT
* * * * *
1365935 AGAGTTGAAATATATATGGGTACATTATCAACAG-AAAA-GTATAATATTGTTGAGATGTATATG
1 AGAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAATGT-TAA-AGT-TTGAAATGCATATG
*
1365998 GGTACATTATCAACATAAAAGTATA-CT
63 TGT--ATTATCAACATAAAA-TATAGCT
* *
1366025 ATAGTTGAAATGTATATGGGTGCATTATCAACAGAAAACATGTTAAAGTTTAAAATGCATAATGA
1 AGAGTTGAAATGTATATGGGTGCATTATCAACAGAAAA-ATGTTAAAGTTTGAAATGCAT-ATG-
*
1366090 TGTATTATAAACATAAA
63 TGTATTATCAACATAAA
1366107 TGGAGGTTAC
Statistics
Matches: 139, Mismatches: 20, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
87 3 0.02
88 3 0.02
89 3 0.02
90 106 0.76
91 12 0.09
92 10 0.07
93 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (87 bp):
AGAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAATGTTAAAGTTTGAAATGCATATGTGT
ATTATCAACATAAAATATAGCT
Found at i:1366658 original size:2 final size:2
Alignment explanation
Indices: 1366651--1366700 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1366641 TGATGGGATG
1366651 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
1366693 AT AT AT AT
1 AT AT AT AT
1366701 GTACAATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1366808 original size:45 final size:45
Alignment explanation
Indices: 1366759--1366860 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 45
1366749 CAAATAGAAC
* *
1366759 ATAAAAGGCATGAAA-AGATGCCATAAAT-GAAAT-GTATAATAGTGT
1 ATAAAA-GCATGAAAGA-ATACCAT-AATGGAAATGGTATAAGAGTGT
*
1366804 ATAAAAGCATGGAAGAATACCATAATGGAAATGGTATAAGAGTGT
1 ATAAAAGCATGAAAGAATACCATAATGGAAATGGTATAAGAGTGT
*
1366849 ATTATAAGCATG
1 A-TAAAAGCATG
1366861 TTGGGATGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
43 3 0.06
44 18 0.37
45 19 0.39
46 9 0.18
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.25
Consensus pattern (45 bp):
ATAAAAGCATGAAAGAATACCATAATGGAAATGGTATAAGAGTGT
Found at i:1369047 original size:23 final size:21
Alignment explanation
Indices: 1369014--1369077 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
1369004 AGTTCAAATT
*
1369014 AAATATTCAAACCATTCAAACA
1 AAATATCCAAA-CATTCAAACA
*
1369036 AATATATCCAAACATCCAATACA
1 AA-ATATCCAAACATTCAA-ACA
*
1369059 CAA-ATCCAAAACATTCAAA
1 AAATATCC-AAACATTCAAA
1369078 ATGTTTTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 5 0.14
22 18 0.51
23 12 0.34
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATATCCAAACATTCAAACA
Found at i:1370505 original size:13 final size:13
Alignment explanation
Indices: 1370486--1370520 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1370476 TAATGGGCAA
*
1370486 GTTTGAAAACTAT
1 GTTTGAAAACAAT
*
1370499 TTTTGAAAACAAT
1 GTTTGAAAACAAT
1370512 GTTTGAAAA
1 GTTTGAAAA
1370521 ATCATAATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (13 bp):
GTTTGAAAACAAT
Found at i:1374219 original size:37 final size:37
Alignment explanation
Indices: 1374166--1374270 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1374156 CATTTTCGTC
1374166 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
1374203 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
1374240 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1374271 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:1378628 original size:183 final size:183
Alignment explanation
Indices: 1378320--1378673 Score: 602
Period size: 183 Copynumber: 1.9 Consensus size: 183
1378310 ATTAAATCCG
*
1378320 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGACTTTATGA
** **
1378385 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTACTT
66 ATAGATTACATTCAAACTATGACACTGCTCGGACACTTGGCAATTCAATGTTTGCTCCACTACTT
*
1378450 TTGTCAAGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAAGCCAAAGACTTTGTGAGGAGATGAACCCTTCAGTGATTTGTCCCTC
1378503 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGACTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGACTTTATGA
* *
1378568 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCAATGTTTGCTCCACTGCT
66 ATAGATTACATTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCAATGTTTGCTCCACTACT
* *
1378632 TTTGTCAGGTCAAAGACTTTGTGAGGAGATGAACCCTTCAGT
130 TTTGTCAAGCCAAAGACTTTGTGAGGAGATGAACCCTTCAGT
1378674 TAAACCTGAT
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
182 1 0.01
183 159 0.99
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGACTTTATGA
ATAGATTACATTCAAACTATGACACTGCTCGGACACTTGGCAATTCAATGTTTGCTCCACTACTT
TTGTCAAGCCAAAGACTTTGTGAGGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:1379868 original size:36 final size:34
Alignment explanation
Indices: 1379828--1379941 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 34
1379818 CACTCAAATT
1379828 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * ** *
1379864 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
1379900 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
1379936 CGTTTT
1 TGTTTT
1379942 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 49 0.83
37 5 0.08
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:1379903 original size:72 final size:75
Alignment explanation
Indices: 1379812--1379986 Score: 218
Period size: 72 Copynumber: 2.4 Consensus size: 75
1379802 ATGCAGATGA
* * * *
1379812 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
1379874 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
1379884 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
1379949 AAGAAGGCAT
66 AAGAAGGCAT
**
1379959 TTCATTTCACTCAAGGCTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
1379987 GAAGATTTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
71 1 0.01
72 50 0.56
73 11 0.12
74 1 0.01
75 8 0.09
76 19 0.21
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:1380016 original size:73 final size:72
Alignment explanation
Indices: 1379828--1380020 Score: 180
Period size: 72 Copynumber: 2.7 Consensus size: 72
1379818 CACTCAAATT
* * * * *
1379828 TGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCGAAAGAAGATTTATTTC
1 TGTTTTTCTT-AAACA-AGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTC
*
1379891 ACTCAAGAT
64 ACTCAAGAC
* *
1379900 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TGTTTTTCTT-AAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAA-G-ATTT-ATT
*
1379965 TCACTCAAGGC
62 TCACTCAAGAC
* * *
1379976 TGTTTTT-TT-AAGAAGATTTTATCTTGCTTGAGATAG-TTTCACTCG
1 TGTTTTTCTTAAACAAGA-TTTATCTCGCTTGAGACAGTTTTCACTCG
1380021 GAACAGAAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
71 1 0.01
72 37 0.36
73 25 0.24
74 16 0.15
75 6 0.06
76 19 0.18
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (72 bp):
TGTTTTTCTTAAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCAC
TCAAGAC
Found at i:1380259 original size:105 final size:104
Alignment explanation
Indices: 1380057--1380373 Score: 482
Period size: 105 Copynumber: 3.1 Consensus size: 104
1380047 ACAGTTTCTC
* * *
1380057 TTGAAAACATTTACCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTTGAAACAGAAAA-
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAGAAAAT
1380121 -TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
1380159 TTGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAGAAAA
1380224 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * *
1380264 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATTGTTTCCCTTGAAAC-G--GAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAGAAAAT
** *
1380326 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
1380365 TTGAAAACA
1 TTGAAAACA
1380374 ATTTAACGAA
Statistics
Matches: 198, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
101 47 0.24
102 22 0.11
103 38 0.19
104 29 0.15
105 62 0.31
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:1380320 original size:36 final size:36
Alignment explanation
Indices: 1380273--1380341 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
1380263 ATTGAAAACA
* *
1380273 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATTG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGATTG
* *
1380309 TTTCCCTTGAAACGGATTTTGTCTCCCTTGAGA
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGA
1380342 CAGTTTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGATTG
Found at i:1380747 original size:105 final size:105
Alignment explanation
Indices: 1380548--1381178 Score: 903
Period size: 105 Copynumber: 6.0 Consensus size: 105
1380538 ATATCGTGAC
* * * * * *
1380548 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
1380613 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1380654 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
1380719 ATTTCAGAGCCAATTTCAGCTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1380759 ACTTCAGACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
1380824 ATCTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
1380864 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTTCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
1380929 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1380969 ACTCCAGACAACGCATGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* * *
1381030 A-TTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * ** * * * *
1381069 ACTCAAGACAACACAAGTTCAGGTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * * *
1381134 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1381175 ACTC
1 ACTC
1381179 GGAACAATGC
Statistics
Matches: 476, Mismatches: 43, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
100 78 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 302 0.63
106 83 0.17
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1381774 original size:37 final size:37
Alignment explanation
Indices: 1381721--1381825 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
1381711 CATTTTCGTC
1381721 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
1381758 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
1381795 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1381826 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:1383326 original size:95 final size:93
Alignment explanation
Indices: 1383151--1383334 Score: 230
Period size: 95 Copynumber: 1.9 Consensus size: 93
1383141 ATACATGTAA
* * *
1383151 ACATCGAATCTAATTTTGGTATCGATACCTAAGGGGGTATCGGTACCATAGCATAGTGGTATCGA
1 ACATCGAAGCTAATTTTGGTATCGATACCTAAGGGGGTATCGATACCATA-CATAGAGGTATCGA
*
1383216 TACCATGATGAGGGTATCGATACTAGACT
65 TACCAGGATGAGGGTATCGATACTAGACT
*
1383245 ACATCGAAGCTAATTTTGGTATTGATA-CTGGAAGGGGGTATCGATACCATA-ATAGAGCAGTAT
1 ACATCGAAGCTAATTTTGGTATCGATACCT--AAGGGGGTATCGATACCATACATAGAG--GTAT
* *
1383308 CGATACCAGGGT-AGGGGTATTGATACT
62 CGATACCAGGATGA-GGGTATCGATACT
1383335 GAAAGGCCAT
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
93 7 0.09
94 26 0.33
95 45 0.58
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (93 bp):
ACATCGAAGCTAATTTTGGTATCGATACCTAAGGGGGTATCGATACCATACATAGAGGTATCGAT
ACCAGGATGAGGGTATCGATACTAGACT
Found at i:1383765 original size:27 final size:27
Alignment explanation
Indices: 1383735--1383862 Score: 113
Period size: 27 Copynumber: 5.3 Consensus size: 27
1383725 GATGCTAAAG
1383735 GCATGAACGGATGCCATAATTGAAAAT
1 GCATGAACGGATGCCATAATTGAAAAT
* *
1383762 GCATGAAAGGATG-C---ATT---AAG
1 GCATGAACGGATGCCATAATTGAAAAT
1383782 GCATGAACGGATGCCATAATTGAAAAT
1 GCATGAACGGATGCCATAATTGAAAAT
* *
1383809 GCATGAAAGGATG-C---A-T--AAAG
1 GCATGAACGGATGCCATAATTGAAAAT
*
1383829 GCATAAACGGATGCCATAATTGAAAAT
1 GCATGAACGGATGCCATAATTGAAAAT
1383856 GCATGAA
1 GCATGAA
1383863 ATGATGCATG
Statistics
Matches: 77, Mismatches: 10, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
20 28 0.36
21 2 0.03
22 1 0.01
23 4 0.05
24 4 0.05
25 1 0.01
26 2 0.03
27 35 0.45
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.20
Consensus pattern (27 bp):
GCATGAACGGATGCCATAATTGAAAAT
Found at i:1383801 original size:47 final size:47
Alignment explanation
Indices: 1383704--1383891 Score: 306
Period size: 47 Copynumber: 4.0 Consensus size: 47
1383694 AATCAATTTA
1383704 ATAATTGAAAATGCATGAAAGGATGC-TAAAGGCATGAACGGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
*
1383750 ATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
*
1383797 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATAAACGGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
* ** *
1383844 ATAATTGAAAATGCATGAAATGATGCATGAGTGGCATGAAAGGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCAT-AAAGGCATGAACGGATGCC
1383892 TTAACTGATA
Statistics
Matches: 132, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 26 0.20
47 91 0.69
48 15 0.11
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.21
Consensus pattern (47 bp):
ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
Found at i:1391700 original size:173 final size:173
Alignment explanation
Indices: 1391411--1391756 Score: 692
Period size: 173 Copynumber: 2.0 Consensus size: 173
1391401 TTTTCACTTG
1391411 GGGGTATTAGGGTATTCTACAGGGAATTGTAGGCCGCTGTTAAAGGAGATAGAGATGCTTGTGGA
1 GGGGTATTAGGGTATTCTACAGGGAATTGTAGGCCGCTGTTAAAGGAGATAGAGATGCTTGTGGA
1391476 AAATGGGACATTGACACAAGAATTGGTGAAACAGTGGATGATGAGCTCGAGTGTGACATCAGAGC
66 AAATGGGACATTGACACAAGAATTGGTGAAACAGTGGATGATGAGCTCGAGTGTGACATCAGAGC
1391541 ATATAATGTAGCATCCGTTTGGGTCAGGTGTTGCTACGTTAGA
131 ATATAATGTAGCATCCGTTTGGGTCAGGTGTTGCTACGTTAGA
1391584 GGGGTATTAGGGTATTCTACAGGGAATTGTAGGCCGCTGTTAAAGGAGATAGAGATGCTTGTGGA
1 GGGGTATTAGGGTATTCTACAGGGAATTGTAGGCCGCTGTTAAAGGAGATAGAGATGCTTGTGGA
1391649 AAATGGGACATTGACACAAGAATTGGTGAAACAGTGGATGATGAGCTCGAGTGTGACATCAGAGC
66 AAATGGGACATTGACACAAGAATTGGTGAAACAGTGGATGATGAGCTCGAGTGTGACATCAGAGC
1391714 ATATAATGTAGCATCCGTTTGGGTCAGGTGTTGCTACGTTAGA
131 ATATAATGTAGCATCCGTTTGGGTCAGGTGTTGCTACGTTAGA
1391757 TGAGTAATGG
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 173 1.00
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.27
Consensus pattern (173 bp):
GGGGTATTAGGGTATTCTACAGGGAATTGTAGGCCGCTGTTAAAGGAGATAGAGATGCTTGTGGA
AAATGGGACATTGACACAAGAATTGGTGAAACAGTGGATGATGAGCTCGAGTGTGACATCAGAGC
ATATAATGTAGCATCCGTTTGGGTCAGGTGTTGCTACGTTAGA
Found at i:1394849 original size:42 final size:42
Alignment explanation
Indices: 1394746--1394838 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
1394736 ACTTAGTAAG
* * * *
1394746 TCCTTCGGGCAATCAATAATTCTTTCGAGCATGATGCTTAAA
1 TCCTTAGGGCAATCAGTAAGTCTTTCGAGCATGATGATTAAA
*
1394788 TCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTAGGGCAATCAGTAAGTCTTTCGAGCATGATGATTAAA
1394830 TCCTTAGGG
1 TCCTTAGGG
1394839 TAATTTGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (42 bp):
TCCTTAGGGCAATCAGTAAGTCTTTCGAGCATGATGATTAAA
Found at i:1394895 original size:13 final size:13
Alignment explanation
Indices: 1394877--1394901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1394867 TGAAGCAAAC
1394877 CCATCAGTAAGTT
1 CCATCAGTAAGTT
1394890 CCATCAGTAAGT
1 CCATCAGTAAGT
1394902 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (13 bp):
CCATCAGTAAGTT
Found at i:1394929 original size:22 final size:22
Alignment explanation
Indices: 1394898--1394971 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
1394888 TTCCATCAGT
*
1394898 AAGTCTTTCGAGCATGATGATG
1 AAGTCCTTCGAGCATGATGATG
* *
1394920 AAGTCCTTCGGGC-T-ATCA-G
1 AAGTCCTTCGAGCATGATGATG
* *
1394939 TAAGTCTTTCGAGCATGATGATT
1 -AAGTCCTTCGAGCATGATGATG
*
1394962 AAATCCTTCG
1 AAGTCCTTCG
1394972 GGAAATTTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.36
21 2 0.05
22 22 0.56
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (22 bp):
AAGTCCTTCGAGCATGATGATG
Found at i:1394949 original size:20 final size:19
Alignment explanation
Indices: 1394891--1394954 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
1394881 CAGTAAGTTC
1394891 CATCAGTAAGTCTTTCGAG
1 CATCAGTAAGTCTTTCGAG
* * *
1394910 CATGATGATGAAGTCCTTCGGG
1 CATCA-G-T-AAGTCTTTCGAG
1394932 CTATCAGTAAGTCTTTCGAG
1 C-ATCAGTAAGTCTTTCGAG
1394952 CAT
1 CAT
1394955 GATGATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 6 0.17
20 12 0.34
21 2 0.06
22 12 0.34
23 3 0.09
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (19 bp):
CATCAGTAAGTCTTTCGAG
Found at i:1394951 original size:42 final size:42
Alignment explanation
Indices: 1394892--1394973 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
1394882 AGTAAGTTCC
*
1394892 ATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCT
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCT
*
1394934 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
1394974 AAATTTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCT
Found at i:1395008 original size:135 final size:135
Alignment explanation
Indices: 1394757--1395023 Score: 435
Period size: 135 Copynumber: 2.0 Consensus size: 135
1394747 CCTTCGGGCA
* * *
1394757 ATCAATAATTCTTTCGAGCATGATGCTTAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGA
1 ATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGA
* *
1394822 TGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACAGAAGAGTAGTGAAGCAAACCCATCAGTAA
66 TGATTAAATCCTTAGGGAAATTTATAAGCCTTCACAGAAGAGTAGTGAAGCAAACCCATCAGTAA
1394887 GTTCC
131 GTTCC
* * * *
1394892 ATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGA
1 ATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGA
* *
1394957 TGATTAAATCCTTCGGGAAATTTATAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCATCAGTAA
66 TGATTAAATCCTTAGGGAAATTTATAAGCCTTCACAGAAGAGTAGTGAAGCAAACCCATCAGTAA
1395022 GT
131 GT
1395024 CTTTCAAGCA
Statistics
Matches: 121, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 121 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (135 bp):
ATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGA
TGATTAAATCCTTAGGGAAATTTATAAGCCTTCACAGAAGAGTAGTGAAGCAAACCCATCAGTAA
GTTCC
Found at i:1395117 original size:80 final size:80
Alignment explanation
Indices: 1394934--1395129 Score: 295
Period size: 80 Copynumber: 2.5 Consensus size: 80
1394924 CCTTCGGGCT
1394934 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAATTTATAAGCCTTCACGGAAGAG
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAATTTATAAGCCTTCACGGAAGAG
1394999 TAGTGAAGCAAACCC
66 TAGTGAAGCAAACCC
* * * *
1395014 ATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGAAATTTGTAAGCTTTCACAGG-AGT
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAATTTATAAGCCTTCAC-GGAAGA
1395078 GTAGTGAAGCAAACCC
65 GTAGTGAAGCAAACCC
* * * * *
1395094 ATCAGTAAGTTTTTTGAGTATGATGATGAAGTCCTT
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
1395130 TGGGCCATCA
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
80 103 0.98
81 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (80 bp):
ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAATTTATAAGCCTTCACGGAAGAG
TAGTGAAGCAAACCC
Found at i:1395138 original size:122 final size:122
Alignment explanation
Indices: 1395012--1395296 Score: 376
Period size: 122 Copynumber: 2.3 Consensus size: 122
1395002 TGAAGCAAAC
* * *
1395012 CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGAAATTTGTAAGCTTTCACAGGAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACAGAAG
* * * * * * * *
1395077 TGTAGTGAAGCAAACCCATCAGTAAGTTTTTTGAGTATGATGATGAAGTCCTTTGGG
66 AGCAGTGAAGAAAACCCATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTTTGGG
* * *
1395134 CCATCAGTAAGTCTTCCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACAGAAG
*
1395199 AGCAGTGAAGAAAATCCATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTTTGGG
66 AGCAGTGAAGAAAACCCATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTTTGGG
* ** *
1395256 TCATTTGTAAGTCTTTCGAGCAAT-ATGA-TAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGC-ATGATGATTAAATCCTTCGGG
1395297 CCATTTTAAG
Statistics
Matches: 142, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
121 12 0.08
122 128 0.90
123 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (122 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACAGAAG
AGCAGTGAAGAAAACCCATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTTTGGG
Found at i:1395159 original size:42 final size:42
Alignment explanation
Indices: 1395092--1395171 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1395082 TGAAGCAAAC
* ** * *
1395092 CCATCAGTAAGTTTTTTGAGTATGATGATGAAGTCCTTTGGG
1 CCATCAGTAAGTCTTCCGAGCATGATGATGAAATCCTTTGGG
*
1395134 CCATCAGTAAGTCTTCCGAGCATGATGATTAAATCCTT
1 CCATCAGTAAGTCTTCCGAGCATGATGATGAAATCCTT
1395172 CGGGTAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (42 bp):
CCATCAGTAAGTCTTCCGAGCATGATGATGAAATCCTTTGGG
Found at i:1395250 original size:202 final size:203
Alignment explanation
Indices: 1394890--1395272 Score: 597
Period size: 202 Copynumber: 1.9 Consensus size: 203
1394880 TCAGTAAGTT
* *
1394890 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTCCGAGCAT
* * *
1394955 GATGATTAAATCCTTCGGGAAATTTATAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCATCAGT
66 GATGATTAAATCCTTCGGGAAATTTATAAGCCTTCACCGAAGAGCAGTGAAGAAAACCCATCAGT
* *
1395020 AAGTCTTTCAAGCATGATGATTAAATCCTTCGGGAAATTTGTAAG-CTTTCACAGGAGTGTAGTG
131 AAGTCTTTCAAGCATAATGATGAAATCCTTCGGGAAATTTGTAAGTCTTTCACAGGAGTGTAGTG
1395084 AAGCAAAC
196 AAGCAAAC
* * * *
1395092 CCATCAGTAAGTTTTTTGAGTATGATGATGAAGTCCTTTGGGCCATCAGTAAGTCTTCCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTCCGAGCAT
* * *
1395157 GATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGCAGTGAAGAAAATCCATCAGT
66 GATGATTAAATCCTTCGGGAAATTTATAAGCCTTCACCGAAGAGCAGTGAAGAAAACCCATCAGT
* * **
1395222 AAGTCTTTCGAGCATAATGATGAAATCCTTTGGGTCATTTGTAAGTCTTTC
131 AAGTCTTTCAAGCATAATGATGAAATCCTTCGGGAAATTTGTAAGTCTTTC
1395273 GAGCAATATG
Statistics
Matches: 162, Mismatches: 18, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
202 157 0.97
203 5 0.03
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (203 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTCCGAGCAT
GATGATTAAATCCTTCGGGAAATTTATAAGCCTTCACCGAAGAGCAGTGAAGAAAACCCATCAGT
AAGTCTTTCAAGCATAATGATGAAATCCTTCGGGAAATTTGTAAGTCTTTCACAGGAGTGTAGTG
AAGCAAAC
Found at i:1395284 original size:42 final size:41
Alignment explanation
Indices: 1395220--1395306 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 41
1395210 AAATCCATCA
* *
1395220 GTAAGTCTTTCGAGCATAATGATGAAATCCTTTGGGTCATTT
1 GTAAGTCTTTCGAGCATAATGAT-AAATCCTTCGGGCCATTT
*
1395262 GTAAGTCTTTCGAGCA-ATATGATAAGTCCTTCGGGCCATTT
1 GTAAGTCTTTCGAGCATA-ATGATAAATCCTTCGGGCCATTT
1395303 -TAAG
1 GTAAG
1395307 ACTTCTCGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 4 0.10
41 16 0.39
42 21 0.51
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (41 bp):
GTAAGTCTTTCGAGCATAATGATAAATCCTTCGGGCCATTT
Found at i:1395743 original size:53 final size:52
Alignment explanation
Indices: 1395680--1395901 Score: 311
Period size: 53 Copynumber: 4.2 Consensus size: 52
1395670 ATCACACCAT
*
1395680 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTATGTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTA-GCAG
* *
1395733 AAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCTGTAAGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGT-AGCAG
* * * *
1395786 AAGATTATTCAAATTCTACTCCCCGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTA-GCAG
* *
1395839 AAGATTGTTTGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGCTA-CTCG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGC-AG
1395892 AAGATTGTTC
1 AAGATTGTTC
1395902 AAAGAAGAGG
Statistics
Matches: 149, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
52 2 0.01
53 144 0.97
54 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (52 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGCAG
Found at i:1396098 original size:24 final size:24
Alignment explanation
Indices: 1396049--1396099 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
1396039 TTTGTCCGGG
*
1396049 ATTTTTATTGTTTTATTTTATTTT
1 ATTTTTATTGTTTTATTTTATATT
1396073 ATTTTTA-T-TTTTATTATTATAATT
1 ATTTTTATTGTTTTATT-TTAT-ATT
1396097 ATT
1 ATT
1396100 AAATATTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
23 5 0.21
24 12 0.50
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (24 bp):
ATTTTTATTGTTTTATTTTATATT
Found at i:1398930 original size:45 final size:45
Alignment explanation
Indices: 1398866--1399016 Score: 205
Period size: 45 Copynumber: 3.4 Consensus size: 45
1398856 TCGACAGGTG
*
1398866 CATTATCAACAAAAAAGTATGCTAGAGTTGAAATGTATATGGGTA
1 CATTATCAACAAAAAAGTATACTAGAGTTGAAATGTATATGGGTA
* * **
1398911 CATTATCAACAGAAAAGTATAATATG-GTTGAGTTGTATATGGGTA
1 CATTATCAACAAAAAAGTATACTA-GAGTTGAAATGTATATGGGTA
* * *
1398956 CATTATCAACATAAAAGTATACTATAGTTGAAATGTATATGGGTG
1 CATTATCAACAAAAAAGTATACTAGAGTTGAAATGTATATGGGTA
*
1399001 TATTATCAACAAAAAA
1 CATTATCAACAAAAAA
1399017 AAATTAGAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
45 90 0.99
46 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (45 bp):
CATTATCAACAAAAAAGTATACTAGAGTTGAAATGTATATGGGTA
Found at i:1399696 original size:45 final size:45
Alignment explanation
Indices: 1399647--1399738 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 45
1399637 GGAAAACAAA
1399647 AATAGAACATAAAAGGCATGAAA-AGATGCCATAAAT-GAAAT-GTAT
1 AATAGAACATAAAA-GCATGAAAGA-ATGCCAT-AATGGAAATGGTAT
*** *
1399692 AATAGTGTATAAAAGCATGGAAGAATGCCATAATGGAAATGGTAT
1 AATAGAACATAAAAGCATGAAAGAATGCCATAATGGAAATGGTAT
1399737 AA
1 AA
1399739 GAGTGTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
43 3 0.08
44 19 0.47
45 18 0.45
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.22
Consensus pattern (45 bp):
AATAGAACATAAAAGCATGAAAGAATGCCATAATGGAAATGGTAT
Found at i:1399731 original size:44 final size:46
Alignment explanation
Indices: 1399655--1399746 Score: 120
Period size: 45 Copynumber: 2.0 Consensus size: 46
1399645 AAAATAGAAC
*
1399655 ATAAAAGGCATGAAAAGATGCCATAAATGAAAT-GTATAATAGTGT
1 ATAAAAGGCATGAAAAGATGCCATAAATGAAATGGTATAAGAGTGT
*
1399700 ATAAAA-GCATG-GAAGAATGCCAT-AATGGAAATGGTATAAGAGTGT
1 ATAAAAGGCATGAAAAG-ATGCCATAAAT-GAAATGGTATAAGAGTGT
1399745 AT
1 AT
1399747 TATAAGAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
43 6 0.14
44 17 0.40
45 19 0.45
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.24
Consensus pattern (46 bp):
ATAAAAGGCATGAAAAGATGCCATAAATGAAATGGTATAAGAGTGT
Found at i:1403000 original size:13 final size:13
Alignment explanation
Indices: 1402982--1403016 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1402972 TAATGGGCAA
*
1402982 TTTTGAAAACTAT
1 TTTTGAAAACAAT
1402995 TTTTGAAAACAAT
1 TTTTGAAAACAAT
*
1403008 GTTTGAAAA
1 TTTTGAAAA
1403017 ATCATAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (13 bp):
TTTTGAAAACAAT
Found at i:1403564 original size:21 final size:23
Alignment explanation
Indices: 1403507--1403564 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1403497 TACACTTGTG
1403507 AGTGTATTGATACACATTCAATA
1 AGTGTATTGATACACATTCAATA
* *
1403530 AATGTATTGGTACACATTC-AT-
1 AGTGTATTGATACACATTCAATA
*
1403551 AGTGTATCGATACA
1 AGTGTATTGATACA
1403565 TAGCGAGGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 11 0.37
22 2 0.07
23 17 0.57
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (23 bp):
AGTGTATTGATACACATTCAATA
Found at i:1407001 original size:21 final size:21
Alignment explanation
Indices: 1406975--1407033 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1406965 ATATTGTCCA
*
1406975 GGGGTACAGATTCCCCCCCAG
1 GGGGTACAGATTCCCCCCCAC
*
1406996 GGGGTACAGATTCCTCCCCAC
1 GGGGTACAGATTCCCCCCCAC
*
1407017 GGGGTACCGATTCCCCC
1 GGGGTACAGATTCCCCC
1407034 TGTCTAATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.17, C:0.39, G:0.27, T:0.17
Consensus pattern (21 bp):
GGGGTACAGATTCCCCCCCAC
Found at i:1409795 original size:21 final size:21
Alignment explanation
Indices: 1409770--1409830 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
1409760 TTCCCTCCCA
1409770 AGGGGG-ATCGATTCCCCCTC
1 AGGGGGAATCGATTCCCCCTC
** *
1409790 AGGGGGAATAAATTCCCCCCC
1 AGGGGGAATCGATTCCCCCTC
* *
1409811 AGAGGGTA-CTGATTCCCCCT
1 AGGGGGAATC-GATTCCCCCT
1409831 TTCTAATGGT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCCCTC
Found at i:1411149 original size:117 final size:117
Alignment explanation
Indices: 1410934--1411150 Score: 296
Period size: 117 Copynumber: 1.9 Consensus size: 117
1410924 AAATAGAAAG
* *
1410934 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAGAGCTCTAAATCATTCTTTAATATTTCATTT
1 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTTAAAATTTCATTT
* *
1410999 TGATTTTCAAAATTCATTTTAGTTTCTAGAAGAAGTTAGTTTAATTAAAAAA
66 TGATTTTCAAAATTCATTTTACTTTCTAAAAGAAGTTAGTTTAATTAAAAAA
** * *
1411051 TTTCTTTTTCAATGTTTTCAGATTTCATTTTTGAAAGCTCTAACTCATT-TTTCAAAATTTCATT
1 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTT-AAAATTTCATT
* *
1411115 TTGATTTTC-CAAGTCTATTTTGACTTTC-AAAAGAAG
65 TTGATTTTCAAAATTC-ATTTT-ACTTTCTAAAAGAAG
1411151 GTCCTTTTTA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
116 7 0.08
117 75 0.86
118 5 0.06
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (117 bp):
TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTTAAAATTTCATTT
TGATTTTCAAAATTCATTTTACTTTCTAAAAGAAGTTAGTTTAATTAAAAAA
Found at i:1411631 original size:22 final size:22
Alignment explanation
Indices: 1411603--1411678 Score: 134
Period size: 22 Copynumber: 3.5 Consensus size: 22
1411593 TTGGAATGGG
* *
1411603 GTATCGATACCATAGTACAGAA
1 GTATCGATACCATAGTAGAGCA
1411625 GTATCGATACCATAGTAGAGCA
1 GTATCGATACCATAGTAGAGCA
1411647 GTATCGATACCATAGTAGAGCA
1 GTATCGATACCATAGTAGAGCA
1411669 GTATCGATAC
1 GTATCGATAC
1411679 TGAAAGGCCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (22 bp):
GTATCGATACCATAGTAGAGCA
Found at i:1411633 original size:95 final size:96
Alignment explanation
Indices: 1411481--1411656 Score: 225
Period size: 95 Copynumber: 1.8 Consensus size: 96
1411471 AACATCGAAT
* ** *
1411481 CTAATTTTGGTATCGATACCTATGGGGGTATCAATACCATAGCATAGTGGTATCGATACCATGGT
1 CTAATTTTGGTATCGATACCTATGGGGGTATCAATACCATAGCACAGAAGTATCGATACCATAGT
*
1411546 -GAG-GGTATCGATACTATACTACATTAAAG
66 AGAGCAGTATCGATACTATACTACATTAAAG
* * *
1411575 CTAATTTTGGTATCGATA-TTGGAAT-GGGGTATCGATACCATAGTACAGAAGTATCGATACCAT
1 CTAATTTTGGTATCGATACCT---ATGGGGGTATCAATACCATAGCACAGAAGTATCGATACCAT
1411638 AGTAGAGCAGTATCGATAC
63 AGTAGAGCAGTATCGATAC
1411657 CATAGTAGAG
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
93 1 0.01
94 18 0.26
95 35 0.51
96 5 0.07
97 10 0.14
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (96 bp):
CTAATTTTGGTATCGATACCTATGGGGGTATCAATACCATAGCACAGAAGTATCGATACCATAGT
AGAGCAGTATCGATACTATACTACATTAAAG
Found at i:1412093 original size:20 final size:21
Alignment explanation
Indices: 1412061--1412193 Score: 67
Period size: 20 Copynumber: 5.9 Consensus size: 21
1412051 AATTGAAAAT
1412061 GCATGAAAGGATG-CATAAAG
1 GCATGAAAGGATGCCATAAAG
*
1412081 GCATGAACA-GATGCCATAATTGAAAAT
1 GCATGAA-AGGATGCC---A-T--AAAG
*
1412108 TCATGAAAGGATG-CATAAAG
1 GCATGAAAGGATGCCATAAAG
* * *
1412128 GCATGAACGGATGTCATAATTGAAAAT
1 GCATGAAAGGATG-C--CA-T--AAAG
1412155 GCATGAAAGGATG-CATAAAG
1 GCATGAAAGGATGCCATAAAG
*
1412175 GCATGAACGGATGCCATAA
1 GCATGAAAGGATGCCATAA
1412194 TTGAAAATGC
Statistics
Matches: 85, Mismatches: 11, Indels: 33
0.66 0.09 0.26
Matches are distributed among these distances:
20 40 0.47
21 7 0.08
22 2 0.02
23 2 0.02
24 2 0.02
25 2 0.02
26 2 0.02
27 28 0.33
ACGTcount: A:0.43, C:0.13, G:0.25, T:0.20
Consensus pattern (21 bp):
GCATGAAAGGATGCCATAAAG
Found at i:1412118 original size:47 final size:47
Alignment explanation
Indices: 1412049--1412237 Score: 306
Period size: 47 Copynumber: 4.0 Consensus size: 47
1412039 AATCAATTTA
*
1412049 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACAGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
* *
1412096 ATAATTGAAAATTCATGAAAGGATGCATAAAGGCATGAACGGATGTC
1 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
1412143 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
* ** *
1412190 ATAATTGAAAATGCATGAAATGATGCATGAGTGGCATGAAAGGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCAT-AAAGGCATGAACGGATGCC
1412238 TTAACTGATA
Statistics
Matches: 132, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
47 116 0.88
48 16 0.12
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (47 bp):
ATAATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCC
Found at i:1422908 original size:42 final size:42
Alignment explanation
Indices: 1422856--1422948 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
1422846 ACTTAGTAAG
* * *
1422856 TCCTTCGGGCCATCAATAATTCTTTCGAGCATGATGCTTAAA
1 TCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
* *
1422898 TCCTTAGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
1422940 TCCTTAGGG
1 TCCTTAGGG
1422949 TAATTTGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (42 bp):
TCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:1422959 original size:42 final size:42
Alignment explanation
Indices: 1422876--1423094 Score: 145
Period size: 42 Copynumber: 5.0 Consensus size: 42
1422866 CATCAATAAT
* *
1422876 TCTTTCGAGCATGATGCTTAAATCCTTAGGGCCATTAGTAAG
1 TCTTTCGAGCATGATGATTAAATCCTTAGGGCAATTAGTAAG
* *
1422918 TCTTTCGAGCATGATGATTAAATCCTTAGGGTAATTTGTAAG
1 TCTTTCGAGCATGATGATTAAATCCTTAGGGCAATTAGTAAG
* * * * ** * *
1422960 CCTTCATAGAAGAGCAGTGAAGCA--AACCCATCACTAAGTTCCATCAGTAAG
1 TCTT--T---CGAGCA-TGATG-ATTAA---ATC-CTTAGGGCAATTAGTAAG
* * * * *
1423011 TCTTTCGAGCATGATGATGAAGTCCTTCGGGCTATCAGTAAG
1 TCTTTCGAGCATGATGATTAAATCCTTAGGGCAATTAGTAAG
* * *
1423053 TCTTTCGAGCATGATGATTAAATCCTTCGGGAAATTTGTAAG
1 TCTTTCGAGCATGATGATTAAATCCTTAGGGCAATTAGTAAG
1423095 CCTTCACGGA
Statistics
Matches: 135, Mismatches: 29, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
42 90 0.67
43 2 0.01
44 2 0.01
45 4 0.03
46 7 0.05
47 7 0.05
48 4 0.03
49 2 0.01
50 3 0.02
51 14 0.10
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (42 bp):
TCTTTCGAGCATGATGATTAAATCCTTAGGGCAATTAGTAAG
Found at i:1423039 original size:22 final size:22
Alignment explanation
Indices: 1423008--1423081 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
1422998 TTCCATCAGT
*
1423008 AAGTCTTTCGAGCATGATGATG
1 AAGTCCTTCGAGCATGATGATG
* *
1423030 AAGTCCTTCGGGC-T-ATCA-G
1 AAGTCCTTCGAGCATGATGATG
* *
1423049 TAAGTCTTTCGAGCATGATGATT
1 -AAGTCCTTCGAGCATGATGATG
*
1423072 AAATCCTTCG
1 AAGTCCTTCG
1423082 GGAAATTTGT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.36
21 2 0.05
22 22 0.56
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (22 bp):
AAGTCCTTCGAGCATGATGATG
Found at i:1423059 original size:20 final size:19
Alignment explanation
Indices: 1423001--1423064 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
1422991 CACTAAGTTC
1423001 CATCAGTAAGTCTTTCGAG
1 CATCAGTAAGTCTTTCGAG
* * *
1423020 CATGATGATGAAGTCCTTCGGG
1 CATCA-G-T-AAGTCTTTCGAG
1423042 CTATCAGTAAGTCTTTCGAG
1 C-ATCAGTAAGTCTTTCGAG
1423062 CAT
1 CAT
1423065 GATGATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 6 0.17
20 12 0.34
21 2 0.06
22 12 0.34
23 3 0.09
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (19 bp):
CATCAGTAAGTCTTTCGAG
Found at i:1423107 original size:135 final size:135
Alignment explanation
Indices: 1422865--1423133 Score: 412
Period size: 135 Copynumber: 2.0 Consensus size: 135
1422855 GTCCTTCGGG
* * * *
1422865 CCATCAATAATTCTTTCGAGCATGATGCTTAAATCCTTAGGGCCATTAGTAAGTCTTTCGAGCAT
1 CCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCAT
* *
1422930 GATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCATAGAAGAGCAGTGAAGCAAACCCATCACT
66 GATGATTAAATCCTTAGGGAAATTTGTAAGCCTTCACAGAAGAGCAGTGAAGCAAACCCATCACT
1422995 AAGTT
131 AAGTT
* * * *
1423000 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCAT
1 CCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCAT
* * * *
1423065 GATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCATCAGT
66 GATGATTAAATCCTTAGGGAAATTTGTAAGCCTTCACAGAAGAGCAGTGAAGCAAACCCATCACT
1423130 AAGT
131 AAGT
1423134 CTTTCGAGCA
Statistics
Matches: 120, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
135 120 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (135 bp):
CCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCAT
GATGATTAAATCCTTAGGGAAATTTGTAAGCCTTCACAGAAGAGCAGTGAAGCAAACCCATCACT
AAGTT
Found at i:1423143 original size:80 final size:80
Alignment explanation
Indices: 1423044--1423239 Score: 331
Period size: 80 Copynumber: 2.5 Consensus size: 80
1423034 CCTTCGGGCT
*
1423044 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCAC-GGAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGG-AGA
1423108 GTAGTGAAGCAAACCC
65 GTAGTGAAGCAAACCC
1423124 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGGAGAG
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGGAGAG
1423189 TAGTGAAGCAAACCC
66 TAGTGAAGCAAACCC
* * * *
1423204 ATCAGTAAGTTTTTCGAGTATGATGATGAAGTCCTT
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
1423240 TGGGCCATCA
Statistics
Matches: 110, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
80 108 0.98
81 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (80 bp):
ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGGAGAG
TAGTGAAGCAAACCC
Found at i:1423248 original size:122 final size:122
Alignment explanation
Indices: 1423122--1423406 Score: 380
Period size: 122 Copynumber: 2.3 Consensus size: 122
1423112 TGAAGCAAAC
*
1423122 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGGAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGAAG
* * * *
1423187 AGTAGTGAAGCAAACCCATCAGTAAGT-TTTTCGAGTATGATGATGAAGTCCTTTGGG
66 AGTAGTGAAGCAAACCCATCAGTAAGTCTTTT-GAGCATAATGATGAAATCCTTCGGG
* * *
1423244 CCATCAGTAAGTC-TTCTGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
1 CCATCAGTAAGTCTTTC-GAGCATGATGATTAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGAA
*
1423308 GAGTAGTGAAGCAAATCCATCAGTAAGTCTTTTGAGCATAATGATGAAATCCTTCGGG
65 GAGTAGTGAAGCAAACCCATCAGTAAGTCTTTTGAGCATAATGATGAAATCCTTCGGG
* * ** * *
1423366 TCTTTTGTAAGTCTTTCGAGTAAT-ATGA-TAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAG-CATGATGATTAAATCCTTCGGG
1423407 CCATTTTAAG
Statistics
Matches: 144, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
121 15 0.10
122 120 0.83
123 9 0.06
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (122 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGAAG
AGTAGTGAAGCAAACCCATCAGTAAGTCTTTTGAGCATAATGATGAAATCCTTCGGG
Found at i:1423250 original size:42 final size:42
Alignment explanation
Indices: 1423202--1423281 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
1423192 TGAAGCAAAC
* * *
1423202 CCATCAGTAAGT-TTTTCGAGTATGATGATGAAGTCCTTTGGG
1 CCATCAGTAAGTCTTCT-GAGCATGATGATGAAATCCTTTGGG
*
1423244 CCATCAGTAAGTCTTCTGAGCATGATGATTAAATCCTT
1 CCATCAGTAAGTCTTCTGAGCATGATGATGAAATCCTT
1423282 CGGGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 30 0.91
43 3 0.09
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (42 bp):
CCATCAGTAAGTCTTCTGAGCATGATGATGAAATCCTTTGGG
Found at i:1423376 original size:202 final size:202
Alignment explanation
Indices: 1423000--1423365 Score: 626
Period size: 202 Copynumber: 1.8 Consensus size: 202
1422990 TCACTAAGTT
*
1423000 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
*
1423065 GATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCATCAGT
66 GATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACCCATCAGT
* *
1423130 AAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGGAGAGTAGTGA
131 AAGTCTTTCGAGCATAATGATGAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGGAGAGTAGTGA
1423195 AGCAAAC
196 AGCAAAC
* * *
1423202 CCATCAGTAAGTTTTTCGAGTATGATGATGAAGTCCTTTGGGCCATCAGTAAGTC-TTCTGAGCA
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTC-GAGCA
* *
1423266 TGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
65 TGATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACCCATCAG
*
1423331 TAAGTCTTTTGAGCATAATGATGAAATCCTTCGGG
130 TAAGTCTTTCGAGCATAATGATGAAATCCTTCGGG
1423366 TCTTTTGTAA
Statistics
Matches: 153, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
201 3 0.02
202 150 0.98
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (202 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
GATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACCCATCAGT
AAGTCTTTCGAGCATAATGATGAAATCCTTCGGGAAAGTTGTAAGCCTTCACAGGAGAGTAGTGA
AGCAAAC
Found at i:1423853 original size:53 final size:53
Alignment explanation
Indices: 1423790--1423992 Score: 300
Period size: 53 Copynumber: 3.8 Consensus size: 53
1423780 ATCACACCAT
*
1423790 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTATGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAG
*
1423843 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAG
* * * * * *
1423896 AAGATTATTCAAATTCTACTCCCCGAAGTAAGAGGGATG-GAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGA-GCGAACCCGTAAGCAG
* *
1423949 AAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGCAAACC
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACC
1423993 TTCTAGTCGT
Statistics
Matches: 132, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
52 1 0.01
53 130 0.98
54 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAG
Found at i:1426985 original size:45 final size:45
Alignment explanation
Indices: 1426921--1427071 Score: 205
Period size: 45 Copynumber: 3.4 Consensus size: 45
1426911 TCGACATGTG
** *
1426921 CATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGTTA
1 CATTATCAACAGAAAAGTATAATAGAGTTGAAATGTATATGGGTA
*
1426966 CATTATCAACAGAAAAGTATAATATG-GTTGAGATGTATATGGGTA
1 CATTATCAACAGAAAAGTATAATA-GAGTTGAAATGTATATGGGTA
* * * *
1427011 CATTATCAACATAAAAGTATATTATAGTTGAAATGTATATGGGTG
1 CATTATCAACAGAAAAGTATAATAGAGTTGAAATGTATATGGGTA
*
1427056 CATTATCAACATAAAA
1 CATTATCAACAGAAAA
1427072 CATGTTAGAT
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
45 94 0.99
46 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (45 bp):
CATTATCAACAGAAAAGTATAATAGAGTTGAAATGTATATGGGTA
Found at i:1427090 original size:45 final size:45
Alignment explanation
Indices: 1426921--1427090 Score: 155
Period size: 45 Copynumber: 3.8 Consensus size: 45
1426911 TCGACATGTG
* * ** * *
1426921 CATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGTTA
1 CATTATCAACATAAAAGCATATTAGAGTTAAAATGTATATGGGTA
* * * * *
1426966 CATTATCAACAGAAAAGTATAATATG-GTTGAGATGTATATGGGTA
1 CATTATCAACATAAAAGCATATTA-GAGTTAAAATGTATATGGGTA
* * * *
1427011 CATTATCAACATAAAAGTATATTATAGTTGAAATGTATATGGGTG
1 CATTATCAACATAAAAGCATATTAGAGTTAAAATGTATATGGGTA
* *
1427056 CATTATCAACATAAAA-CATGTTAGATTTTAAAATG
1 CATTATCAACATAAAAGCATATTAGA-GTTAAAATG
1427091 CAAAATGATG
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
44 6 0.06
45 101 0.94
46 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (45 bp):
CATTATCAACATAAAAGCATATTAGAGTTAAAATGTATATGGGTA
Found at i:1430000 original size:22 final size:22
Alignment explanation
Indices: 1429984--1430045 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
1429974 TTCAAATTAA
*
1429984 ATATTCAAACCATTCAAACAAAT
1 ATATCCAAA-CATTCAAACAAAT
*
1430007 ATATCCAAACATTCAATACACA-
1 ATATCCAAACATTCAA-ACAAAT
1430029 A-ATCCAAAACATTCAAA
1 ATATCC-AAACATTCAAA
1430046 ATGTTTTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 5 0.14
22 18 0.51
23 12 0.34
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.23
Consensus pattern (22 bp):
ATATCCAAACATTCAAACAAAT
Found at i:1430877 original size:15 final size:15
Alignment explanation
Indices: 1430857--1430885 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1430847 AATTTCTTTT
1430857 TCGTTATCTAAACCC
1 TCGTTATCTAAACCC
1430872 TCGTTATCTAAACC
1 TCGTTATCTAAACC
1430886 AAAGGTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (15 bp):
TCGTTATCTAAACCC
Done.