Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 17
Found at i:3106933 original size:15 final size:15
Alignment explanation
Indices: 3106910--3106972 Score: 90
Period size: 15 Copynumber: 4.2 Consensus size: 15
3106900 CGTAGGACTC
3106910 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
* *
3106925 CTACGTCCCGAATGA
1 CTACATCCCGAAGGA
3106940 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
* *
3106955 CTACGTCCTGAAGGA
1 CTACATCCCGAAGGA
3106970 CTA
1 CTA
3106973 TTATACCCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:3106946 original size:30 final size:30
Alignment explanation
Indices: 3106910--3106972 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
3106900 CGTAGGACTC
*
3106910 CTACATCCCGAAGGACTACGTCCCGAATGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
*
3106940 CTACATCCCGAAGGACTACGTCCTGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
3106970 CTA
1 CTA
3106973 TTATACCCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (30 bp):
CTACATCCCGAAGGACTACGTCCCGAAGGA
Found at i:3107099 original size:29 final size:29
Alignment explanation
Indices: 3107057--3107134 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
3107047 TTTCATATGT
3107057 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
3107085 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
3107114 TCATGTAGCTCATGTCATTTC
1 TCATGTAGCTCATGTCATTTC
3107135 ATATCATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.14
29 42 0.86
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:3107163 original size:12 final size:12
Alignment explanation
Indices: 3107146--3107191 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
3107136 TATCATGTTC
*
3107146 TCATATCACAGG
1 TCATATCACAGA
*
3107158 TCATATCACATA
1 TCATATCACAGA
*
3107170 TCATATCACATA
1 TCATATCACAGA
*
3107182 GCATATCACA
1 TCATATCACA
3107192 TGAACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:3107177 original size:24 final size:24
Alignment explanation
Indices: 3107146--3107192 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3107136 TATCATGTTC
*
3107146 TCATATCACA-GGTCATATCACATA
1 TCATATCACATAG-CATATCACATA
3107170 TCATATCACATAGCATATCACAT
1 TCATATCACATAGCATATCACAT
3107193 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (24 bp):
TCATATCACATAGCATATCACATA
Found at i:3107192 original size:12 final size:12
Alignment explanation
Indices: 3107159--3107192 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3107149 TATCACAGGT
*
3107159 CATATCACATAT
1 CATATCACATAG
3107171 CATATCACATAG
1 CATATCACATAG
3107183 CATATCACAT
1 CATATCACAT
3107193 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (12 bp):
CATATCACATAG
Found at i:3107609 original size:64 final size:64
Alignment explanation
Indices: 3107541--3107661 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 64
3107531 CATAAAAGGT
* ** * *
3107541 ATTCGATGTAGTATTATTGCTGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGC
1 ATTCGATGTAGTACTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCACCAATTGC
**
3107605 ATTCGATGTTTTACTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCAC
1 ATTCGATGTAGTACTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCAC
3107662 ATTCATACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (64 bp):
ATTCGATGTAGTACTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCACCAATTGC
Found at i:3108606 original size:12 final size:10
Alignment explanation
Indices: 3108580--3108609 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
3108570 TTAGAATTAA
3108580 TTATATATTT
1 TTATATATTT
3108590 TTATATATTT
1 TTATATATTT
3108600 TTATATATTT
1 TTATATATTT
3108610 AAAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATATATTT
Found at i:3124566 original size:6 final size:6
Alignment explanation
Indices: 3124548--3124577 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3124538 TCGGAGATTT
3124548 GTTCGG G-TCGG GTTCGG GTTCGG GTTCGG G
1 GTTCGG GTTCGG GTTCGG GTTCGG GTTCGG G
3124578 GCAAGGTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GTTCGG
Found at i:3124629 original size:9 final size:9
Alignment explanation
Indices: 3124603--3124670 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
3124593 CGATTATATA
*
3124603 TATATATATA
1 TATATAT-TT
3124613 TATAATATTT
1 TAT-ATATTT
3124623 TATATATTT
1 TATATATTT
*
3124632 TATAT-TAAT
1 TATATAT-TT
*
3124641 TATATA-TA
1 TATATATTT
3124649 TA-ATATTT
1 TATATATTT
*
3124657 TATATTTTT
1 TATATATTT
3124666 TATAT
1 TATAT
3124671 TAATTATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
7 3 0.06
8 6 0.13
9 27 0.57
10 7 0.15
11 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TATATATTT
Found at i:3124645 original size:25 final size:25
Alignment explanation
Indices: 3124617--3124681 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
3124607 TATATATATA
3124617 ATATTTTATATATTTTATATTAATT
1 ATATTTTATATATTTTATATTAATT
* **
3124642 ATA-TATATAATATTTTATATTTTTT
1 ATATTTTAT-ATATTTTATATTAATT
3124667 ATATTAATTATATAT
1 ATATT--TTATATAT
3124682 AAAATATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 4 0.12
25 20 0.62
26 1 0.03
27 4 0.12
28 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATATTTTATATATTTTATATTAATT
Found at i:3124646 original size:34 final size:34
Alignment explanation
Indices: 3124607--3124691 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
3124597 TATATATATA
3124607 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
3124641 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
3124675 TATATATAAAATATTTT
1 TATATATATAATATTTT
3124692 CGGGTTCGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:3125636 original size:13 final size:13
Alignment explanation
Indices: 3125618--3125642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3125608 AAACTTAAAG
3125618 ATTTATAATTATT
1 ATTTATAATTATT
3125631 ATTTATAATTAT
1 ATTTATAATTAT
3125643 ACTAACATTT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTATAATTATT
Found at i:3127160 original size:22 final size:19
Alignment explanation
Indices: 3127118--3127167 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
3127108 ATAAAGCTAA
3127118 AAATAAAAAAATATTAAAT
1 AAATAAAAAAATATTAAAT
* *
3127137 AAAT-CAAAAATA-TATAT
1 AAATAAAAAAATATTAAAT
3127154 AAGATAAAAAAATA
1 AA-ATAAAAAAATA
3127168 CAAGAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.23
18 9 0.35
19 11 0.42
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AAATAAAAAAATATTAAAT
Found at i:3127163 original size:18 final size:18
Alignment explanation
Indices: 3127118--3127164 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3127108 ATAAAGCTAA
3127118 AAATAAAAAAATATTAAAT
1 AAAT-AAAAAATATTAAAT
* *
3127137 AAATCAAAAATA-TATAT
1 AAATAAAAAATATTAAAT
3127154 AAGATAAAAAA
1 AA-ATAAAAAA
3127165 ATACAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 6 0.25
18 14 0.58
19 4 0.17
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
AAATAAAAAATATTAAAT
Found at i:3127370 original size:20 final size:20
Alignment explanation
Indices: 3127345--3127383 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3127335 TGCAATACAA
3127345 AAATAA-AAAAAGTAAAAAAT
1 AAATAATAAAAA-TAAAAAAT
*
3127365 AAATAATAATAATAAAAAA
1 AAATAATAAAAATAAAAAA
3127384 GAATTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (20 bp):
AAATAATAAAAATAAAAAAT
Found at i:3128544 original size:17 final size:16
Alignment explanation
Indices: 3128516--3128550 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3128506 GGAAAAAAAC
*
3128516 AAAAAAAGAAATTAAT
1 AAAAAAAGAAATAAAT
3128532 AAAAAAAGAAAATAAAT
1 AAAAAAAG-AAATAAAT
3128549 AA
1 AA
3128551 TAATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (16 bp):
AAAAAAAGAAATAAAT
Found at i:3128721 original size:38 final size:37
Alignment explanation
Indices: 3128634--3129015 Score: 296
Period size: 38 Copynumber: 10.5 Consensus size: 37
3128624 AAAAAAAATC
* *
3128634 AAAACTATATATTATAT-AGTTTTC-AAAAT-TAATAT
1 AAAACTATATATTATATAAGTTTTCAAAAATGT-TTTT
3128669 AAAA--A-ATATTATATAAGTTTTCAAAAAATGTTTTT
1 AAAACTATATATTATATAAGTTTTC-AAAAATGTTTTT
* *
3128704 AAAACCATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAAGTTTTCAAAAATGTTTTT
* *
3128741 AAAACTATATA-TATATAACTTTTTTCAAAAATGTTTTA
1 AAAACTATATATTATATAA--GTTTTCAAAAATGTTTTT
*
3128779 AAAAC--TATA-TATATAAGTTTTTTCAAAAATG-TTTA
1 AAAACTATATATTATATAAG--TTTTCAAAAATGTTTTT
* *
3128814 AAAACTATATATTATATAAGTTTTCAAAATTGTTTTA
1 AAAACTATATATTATATAAGTTTTCAAAAATGTTTTT
* * *
3128851 AAAACTATATATTATATACA-TATTTCCAAAATGATTTC
1 AAAACTATATATTATATA-AGT-TTTCAAAAATGTTTTT
* * **
3128889 AAAACTATATATTAAATATA-TTTTCAAAAGCA-CTTTCA
1 AAAACTATATATTATATA-AGTTTTCAAAA--ATGTTTTT
* * * **
3128927 AAAATTATACATTATATATGTTTTC-AAAAT-TTTCC
1 AAAACTATATATTATATAAGTTTTCAAAAATGTTTTT
* * *
3128962 AAAACTATATAATATATATA-TTTTC-GAAATGCTTTT
1 AAAACTATATATTATATA-AGTTTTCAAAAATGTTTTT
* *
3128998 GAAACTATATAGTATATA
1 AAAACTATATATTATATA
3129016 TATTTTAGAA
Statistics
Matches: 291, Mismatches: 33, Indels: 45
0.79 0.09 0.12
Matches are distributed among these distances:
32 9 0.03
33 8 0.03
35 53 0.18
36 60 0.21
37 60 0.21
38 100 0.34
39 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (37 bp):
AAAACTATATATTATATAAGTTTTCAAAAATGTTTTT
Found at i:3129736 original size:84 final size:84
Alignment explanation
Indices: 3129648--3130476 Score: 735
Period size: 84 Copynumber: 10.0 Consensus size: 84
3129638 ACTATGTTGT
* * * * * * ** *
3129648 AAATGATTTGTCTTGGAACTGAGCGTAGTAGAACTCGAATATCTTTGGTTGGAAGATAACCCTTC
1 AAATGATGTGCCTTCGAACTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
3129713 TAGCCTTGAGTTATGCAGC
66 TAGCCTTGAGTTATGCAGC
* * * * * *
3129732 AAATGATATGCCCTCGAAGCTAAGTGTAATCGAACTCG-AGG---GTGTTTGGCAGATAGCCCTT
1 AAATGATGTGCCTTCGAA-CTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
* *
3129793 CTAGCCTTGAGTTATACCGC
65 CTAGCCTTGAGTTATGCAGC
* * * *
3129813 AAATGATGTGTCGTT-GAGA-TGAGTGTAATCGAACTCAAAGGTCTTT-GTTGACAGATAATCCT
1 AAATGATGTG-CCTTCGA-ACTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCT
*
3129875 TCTAGCCTTGAGTTTTGCTA-C
64 TCTAGCCTTGAGTTATGC-AGC
* * * * * *
3129896 AAATGATGTGCCCTCGAAGTTGATTATAATCAAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTT
1 AAATGATGTGCCTTCGAA-CTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
* * * *
3129961 CTCGACTTAAGCTATGCCA-C
65 CTAGCCTTGAGTTATG-CAGC
* * * * * *
3129981 AAATGATGTGCCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTAT-GTTGGTAGATAACCCTTC
1 AAATGATGTGCCTTCGAACTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* *
3130045 TAGCCTTAAGTTATGCTGC
66 TAGCCTTGAGTTATGCAGC
* * * * *
3130064 AAAAGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAAGGTTTTTGGTTGGCGGATAACCCTT
1 AAATGATGTGCCTTCGAA-CTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
*
3130129 CT---C--GA-TTATGCTGC
65 CTAGCCTTGAGTTATGCAGC
* * * * * * *
3130143 AAATAATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGTAGATAACCC-TC
1 AAATGATGTGCCTTCGAACTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* *
3130207 TTAGCCTTGAGTTATACTGC
66 -TAGCCTTGAGTTATGCAGC
* * * * * * * *
3130227 AAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCATATAGCCCTTC
1 AAATGATGTGCCTTCGAACTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
*
3130292 TAGCCTTGAGCTATGCTAG-
66 TAGCCTTGAGTTATGC-AGC
* * * * * * *
3130311 AAATGTTGCGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGG-TGGCAGATAACCCTT
1 AAATGATGTGCCTTCGAACTGAGTGTAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTT
3130375 CTAGCCTTGAGTTATGCTA-C
65 CTAGCCTTGAGTTATGC-AGC
* * * *
3130395 AAATGATCTGCCCTCAAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTT
1 AAATGATGTGCCTTCGAA-CTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
3130460 CTAGCCTTGAGTTATGC
65 CTAGCCTTGAGTTATGC
3130477 TGTAAATAAA
Statistics
Matches: 605, Mismatches: 111, Indels: 57
0.78 0.14 0.07
Matches are distributed among these distances:
77 2 0.00
78 38 0.06
79 22 0.04
80 17 0.03
81 49 0.08
82 8 0.01
83 86 0.14
84 247 0.41
85 135 0.22
86 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
AAATGATGTGCCTTCGAACTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
TAGCCTTGAGTTATGCAGC
Found at i:3130024 original size:168 final size:168
Alignment explanation
Indices: 3129648--3130463 Score: 884
Period size: 168 Copynumber: 4.9 Consensus size: 168
3129638 ACTATGTTGT
* * * * * ** *
3129648 AAATGATTTGTCTTGGAACTGAGCGTAGTAGAACTCGAATATCTTTGGTTGGAAGATAACCCTTC
1 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTC
* *
3129713 TAGCCTTGAGTTATGC-AGCAAATGATATGCCCTCGAAGCTAAGTGTAATCGAACTCG-AGG---
65 TAGCCTTGAGTTATGCTA-CAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCT
* * * * * * *
3129773 GTGTTTGGCAGATAGCCCTTCTAGCCTTGAGTTATACCGC
129 TTGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCCAC
* * * * * * * *
3129813 AAATGATGTGTCGTTGAGATGAGTGTAATCGAACTCAAAGGTCTTTGTTGACAGATAATCCTTCT
1 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
* * * * *
3129878 AGCCTTGAGTTTTGCTACAAATGATGTGCCCTCGAAGTTGATTATAATCAAACTCGAAGGTCTTT
66 AGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT
*
3129943 GGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCCAC
131 GGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCCAC
* * * *
3129981 AAATGATGTGCCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTATGTTGGTAGATAACCCTTCT
1 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
* * * * *
3130046 AGCCTTAAGTTATGCTGCAAAAGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAAGGTTTTT
66 AGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT
* * * *
3130111 GGTTGGCGGATAACCCTTCTCGA-TTATGC--TG---C
131 GGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCCAC
* *
3130143 AAATAATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGTAGATAACCC-TC
1 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTC
* * * * * *
3130207 TTAGCCTTGAGTTATACTGCAAATGATGTGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCT
65 -TAGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCT
* * * * * * *
3130271 TTTGTTAGCATATAGCCCTTCTAGCCTTGAGCTATGCTAG
129 TTGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCCAC
* * * * *
3130311 AAATGTTGCGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTGGCAGATAACCCTTC
1 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTC
* *
3130376 TAGCCTTGAGTTATGCTACAAATGATCTGCCCTCAAAGCTGAGTGTAATCGAACTCGAAGGTCTT
65 TAGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTT
* *
3130441 TTGTTGGCAGATAACCCTTCTAG
130 TGGTTGGCAGATAGCCCTTCTAG
3130464 CCTTGAGTTA
Statistics
Matches: 543, Mismatches: 93, Indels: 26
0.82 0.14 0.04
Matches are distributed among these distances:
162 85 0.16
163 51 0.09
164 63 0.12
165 43 0.08
167 5 0.01
168 247 0.45
169 49 0.09
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (168 bp):
AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
AGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT
GGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCCAC
Found at i:3130456 original size:331 final size:332
Alignment explanation
Indices: 3129659--3130462 Score: 951
Period size: 331 Copynumber: 2.4 Consensus size: 332
3129649 AATGATTTGT
* * *
3129659 CTTGGAACTGAGCGTAGTAGAACTCGAATATCTTTGGTTGGAAGATAACCCTTCTAGCCTTGAGT
1 CTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGG-TGGAAGATAACCCTTCTAGCCTTGAGT
* * *
3129724 TATGC-AGCAAATGATATGCCCTCGAAGCTAAGTGTAATCGAACTCG-AGG-GTGT-TTGGCAGA
65 TATGCTA-CAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTTTTTGTTGGCAGA
* * * *
3129785 TAGCCCTTCTAGCCTTGAGTTATACCGCAAATGATGTGTCGTTGAGATGAGTGTAATCGAACTCA
129 TAACCCTTCTA--C-TGAGTTATACCGCAAATAATGTGCCGTTGAGATGAGCGTAATCGAACTCA
* * * *
3129850 AAGGTCTTTGTTGACAGATAATCCTTCTAGCCTTGAGTTTTGCTACAAATGATGTGCCCTCGAAG
191 AAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTACAAATGATGTGCCCTAGAAG
* ** * *
3129915 TTGATTATAATCAAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCCA
256 CTGAGCATAATCAAACTCGAAGGTCTTTGGTTAGCAGATAGCCCTTCTAGACTTAAGCTATGCCA
*
3129980 CAAATGATGTGC
321 CAAATGATGCGC
* * * * * * * *
3129992 CTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTATGTTGGTAGATAACCCTTCTAGCCTTAAGTT
1 CTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTGGAAGATAACCCTTCTAGCCTTGAGTT
* * * * *
3130057 ATGCTGCAAAAGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAAGGTTTTTGGTTGGCGGAT
66 ATGCTACAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTTTTT-GTTGGCAGAT
* * * * * *
3130122 AACCCTTCT-C-GA-TTATGCTGCAAATAATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGG
130 AACCCTTCTACTGAGTTATACCGCAAATAATGTGCCGTTGAGATGAGCGTAATCGAACTCAAAGG
** * *
3130184 TCTTTTGTTGGTAGATAACCC-TCTTAGCCTTGAGTTATACTGCAAATGATGTGCCTTAG-AGCT
195 TC-TTTGTTGACAGATAACCCTTC-TAGCCTTGAGTTATACTACAAATGATGTGCCCTAGAAGCT
* * * * * * * * *
3130247 GAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCATATAGCCCTTCTAGCCTTGAGCTATGCTAGA
258 GAGCATAATCAAACTCGAAGGTCTTTGGTTAGCAGATAGCCCTTCTAGACTTAAGCTATGCCACA
*
3130312 AATGTTGCGC
323 AATGATGCGC
*
3130322 CTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTGGCAGATAACCCTTCTAGCCTTGAGT
1 CTTGGAGCTGAGCGTAGTCGAACTCGAAGATC-TTTGGTGGAAGATAACCCTTCTAGCCTTGAGT
* *
3130387 TATGCTACAAATGATCTGCCCTCAAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGA
65 TATGCTACAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGT-TTTTGTTGGCAGA
3130452 TAACCCTTCTA
129 TAACCCTTCTA
3130463 GCCTTGAGTT
Statistics
Matches: 394, Mismatches: 67, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
330 136 0.35
331 139 0.35
332 69 0.18
333 32 0.08
334 2 0.01
336 16 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (332 bp):
CTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTGGAAGATAACCCTTCTAGCCTTGAGTT
ATGCTACAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTTTTTGTTGGCAGATA
ACCCTTCTACTGAGTTATACCGCAAATAATGTGCCGTTGAGATGAGCGTAATCGAACTCAAAGGT
CTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTACAAATGATGTGCCCTAGAAGCTGAG
CATAATCAAACTCGAAGGTCTTTGGTTAGCAGATAGCCCTTCTAGACTTAAGCTATGCCACAAAT
GATGCGC
Found at i:3131786 original size:95 final size:94
Alignment explanation
Indices: 3131597--3131857 Score: 337
Period size: 95 Copynumber: 2.7 Consensus size: 94
3131587 GACTAGCTGG
* * * * *
3131597 ATCCATAAAGCCGAGTCGTTTAACCAATTGCTCTAGAGGGATAGCTCAATATCATTGTATAG-AT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGA-AACTC-A-AGC-TT-TATTGTAT
3131661 ATTATAATCACCTTTATCAAGCTAGCTGAATATT
61 ATTATAATCACCTTTATCAAGCTAGCTGAATATT
* * *
3131695 ATCCATAGAGCCGGGGCGTTTAACCAATTGCTCTAGCGGGACAACTCGAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGA-AACTCAAGCTTTATTGTATATTA
* *
3131760 TAATCACCTTTATCAGGCTAGCTGAATCTT
65 TAATCACCTTTATCAAGCTAGCTGAATATT
* *
3131790 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGAAAGCTCAAGCTTTATTGTATA-TA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGAAA-CTCAAGCTTTATTGTATATTA
3131854 TAAT
65 TAAT
3131858 ATTATAATCT
Statistics
Matches: 145, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
94 12 0.08
95 90 0.62
96 2 0.01
98 41 0.28
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (94 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGAAACTCAAGCTTTATTGTATATTAT
AATCACCTTTATCAAGCTAGCTGAATATT
Found at i:3134493 original size:22 final size:22
Alignment explanation
Indices: 3134448--3134528 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 22
3134438 AAATTAAATG
* * *
3134448 AAAAATAAAGCTAAAAAAAGTAA
1 AAAAATAAA-ATAAAAATATTAA
3134471 AAAAATAAAATAAAAATATTAA
1 AAAAATAAAATAAAAATATTAA
* ** *
3134493 ATAAACCAAA-AAATATATATAA
1 AAAAATAAAATAAAAATAT-TAA
3134515 GATAAAATAAAATA
1 -A-AAAATAAAATA
3134529 CAAGAAAGAA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
21 7 0.16
22 20 0.45
23 10 0.23
24 6 0.14
25 1 0.02
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (22 bp):
AAAAATAAAATAAAAATATTAA
Found at i:3134496 original size:18 final size:20
Alignment explanation
Indices: 3134473--3134528 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
3134463 AAAAGTAAAA
3134473 AAATAAAATAAAA-ATAT-T
1 AAATAAAATAAAATATATAT
*
3134491 AAATAAACCAAAAAATATATAT
1 AAATAAA--ATAAAATATATAT
3134513 AAGATAAAATAAAATA
1 AA-ATAAAATAAAATA
3134529 CAAGAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 7 0.23
20 5 0.16
21 11 0.35
22 3 0.10
23 5 0.16
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (20 bp):
AAATAAAATAAAATATATAT
Found at i:3134738 original size:3 final size:3
Alignment explanation
Indices: 3134732--3134763 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3134722 GTAAAAAATA
3134732 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3134764 AGAATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3135288 original size:31 final size:32
Alignment explanation
Indices: 3135236--3135318 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 32
3135226 TAATATAATA
3135236 TAAACTATATAATATATATTTTAAAAATA-TTTT-
1 TAAACTATAT-AT-TATATTTTAAAAA-AGTTTTC
3135269 TAAACTATATATTATATTTTTAAAAAAGTTTTC
1 TAAACTATATATTATA-TTTTAAAAAAGTTTTC
*
3135302 AAAACTATATATTATAT
1 TAAACTATATATTATAT
3135319 AGTTTTGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 5 0.11
32 16 0.35
33 25 0.54
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (32 bp):
TAAACTATATATTATATTTTAAAAAAGTTTTC
Found at i:3135318 original size:38 final size:37
Alignment explanation
Indices: 3135237--3135698 Score: 249
Period size: 39 Copynumber: 12.6 Consensus size: 37
3135227 AATATAATAT
*
3135237 AAACTATATA--ATATATA-TTTTAAAAATA-TTTT-T
1 AAACTATATATTATATATATTTTTAAAAA-AGTTTTCA
3135270 AAAC--TATA-TAT-TATATTTTTAAAAAAGTTTTCA
1 AAACTATATATTATATATATTTTTAAAAAAGTTTTCA
* *
3135303 AAACTATATATTATATA-GTTTTGAAAATTAA--TTT--
1 AAACTATATATTATATATATTTTTAAAA--AAGTTTTCA
* *
3135337 AAA--A-ATATTATATA-AGTTTTCAAAAAATGTTTTTA
1 AAACTATATATTATATATA-TTTTTAAAAAA-GTTTTCA
* * * *
3135372 AAACCATACATTATATA-ATTTTTCAAAAATGTTTTTA
1 AAACTATATATTATATATATTTTT-AAAAAAGTTTTCA
* * *
3135409 AAACTATATATTATATAAATTTTTTCAAAAATGTTTTAA
1 AAACTATATATTATATATA-TTTTT-AAAAAAGTTTTCA
* *
3135448 AAACTATATATTATATA-AGCTTTTTCAAAAATGTTTTAA
1 AAACTATATATTATATATA--TTTTT-AAAAAAGTTTTCA
* *
3135487 AAACTATATATTATATA-AGTTTTCAAAAAATGTTTTAA
1 AAACTATATATTATATATA-TTTTTAAAAAA-GTTTTCA
* * *
3135525 AAACTATATATTATATATATATATTTCCAAAATGATTTCA
1 AAACTATATATTATATATAT-T-TTT-AAAAAAGTTTTCA
* * *
3135565 AAACTATATATTATATATATATATT-CAAAAGCACTTTCAA
1 AAACTATATATTATATATAT-TTTTAAAAAAG--TTTTC-A
* * *
3135605 AAACTATACATTATATAT-GTTTT-CAAAA-TTTTCCA
1 AAACTATATATTATATATATTTTTAAAAAAGTTTT-CA
* * ** * *
3135640 AAACTATATAATATATATA-TATTCGAAATGTTTAT-G
1 AAACTATATATTATATATATTTTTAAAAAAGTTT-TCA
*
3135676 AAACTATATAGTATATATATTTT
1 AAACTATATATTATATATATTTT
3135699 AGAAAATCGT
Statistics
Matches: 356, Mismatches: 36, Indels: 70
0.77 0.08 0.15
Matches are distributed among these distances:
30 2 0.01
31 19 0.05
32 24 0.07
33 11 0.03
34 3 0.01
35 30 0.08
36 36 0.10
37 43 0.12
38 57 0.16
39 80 0.22
40 47 0.13
41 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
AAACTATATATTATATATATTTTTAAAAAAGTTTTCA
Found at i:3135444 original size:39 final size:38
Alignment explanation
Indices: 3135341--3135698 Score: 315
Period size: 39 Copynumber: 9.4 Consensus size: 38
3135331 TAATTTAAAA
* * *
3135341 ATATTATAT-AAGTTTTCAAAAAATGTTTTTAAAACCAT
1 ATATTATATAAATTTTTC-AAAAATGTTTTAAAAACTAT
* *
3135379 ACATTATAT-AATTTTTCAAAAATGTTTTTAAAACTAT
1 ATATTATATAAATTTTTCAAAAATGTTTTAAAAACTAT
3135416 ATATTATATAAATTTTTTCAAAAATGTTTTAAAAACTAT
1 ATATTATATAAA-TTTTTCAAAAATGTTTTAAAAACTAT
*
3135455 ATATTATATAAGCTTTTTCAAAAATGTTTTAAAAACTAT
1 ATATTATATAA-ATTTTTCAAAAATGTTTTAAAAACTAT
*
3135494 ATATTATAT-AAGTTTTCAAAAAATGTTTTAAAAACTAT
1 ATATTATATAAATTTTTC-AAAAATGTTTTAAAAACTAT
* * * *
3135532 ATATTATATATATATATTTCCAAAATGATTTCAAAACTAT
1 ATATTATATA-A-ATTTTTCAAAAATGTTTTAAAAACTAT
* * * *
3135572 ATATTATATATATATATTCAAAAGCA-CTTTCAAAAACTAT
1 ATATTATATAAAT-TTTTCAAAA--ATGTTTTAAAAACTAT
* **
3135612 ACATTATAT--ATGTTTTC-AAAAT-TTTCCAAAACTAT
1 ATATTATATAAAT-TTTTCAAAAATGTTTTAAAAACTAT
* * * * *
3135647 ATAATATATATA-TATTC-GAAATG-TTTATGAAACTAT
1 ATATTATATAAATTTTTCAAAAATGTTTTA-AAAACTAT
* *
3135683 ATAGTATATATATTTT
1 ATATTATATAAATTTT
3135699 AGAAAATCGT
Statistics
Matches: 270, Mismatches: 34, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
35 30 0.11
36 18 0.07
37 38 0.14
38 55 0.20
39 77 0.29
40 46 0.17
41 6 0.02
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.43
Consensus pattern (38 bp):
ATATTATATAAATTTTTCAAAAATGTTTTAAAAACTAT
Found at i:3135682 original size:36 final size:36
Alignment explanation
Indices: 3135361--3135851 Score: 193
Period size: 39 Copynumber: 13.2 Consensus size: 36
3135351 AGTTTTCAAA
* * * * *
3135361 AAATGTTTTTAAAACCATACATTATATA-ATTTTTCAA
1 AAATGTTTATAAAACTATATAATATATATA-TTTTC-G
* * * *
3135398 AAATGTTTTTAAAACTATATATTATATAAATTTTTTCAA
1 AAATGTTTATAAAACTATATA--ATATATATATTTTC-G
* *
3135437 AAATGTTT-TAAAAACTATATATTATATA-AGCTTTTTCAA
1 AAATGTTTAT-AAAACTATATAATATATATA---TTTTC-G
* *
3135476 AAATGTTT-TAAAAACTATATATTATATA-AGTTTTCAAA
1 AAATGTTTAT-AAAACTATATAATATATATA-TTTTC--G
*
3135514 AAATGTTT-TAAAAACTATATATTATATATATATATTTCCA
1 AAATGTTTAT-AAAACTATATA--ATATATATAT-TTT-CG
* *
3135554 AAATGATTT-CAAAACTATATATTATATATATATATTC-
1 AAATG-TTTATAAAACTATATA--ATATATATATTTTCG
* * * * *
3135591 AAAAGCACTTTCA-AAAACTATACATTATATATGTTTTCA
1 AAATG---TTT-ATAAAACTATATAATATATATATTTTCG
** *
3135630 AAAT-TTTCCAAAACTATATAATATATATATATTCG
1 AAATGTTTATAAAACTATATAATATATATATTTTCG
* * *
3135665 AAATGTTTATGAAACTATATAGTATATATATTTTAG
1 AAATGTTTATAAAACTATATAATATATATATTTTCG
* * * * **
3135701 AAAATCGTTTAAAAACACTTTCA-AAGAT-TATATTATAT
1 -AAAT-GTTTATAAA-ACTAT-ATAATATATATATTTTCG
* * * * * * *
3135739 TACT-TTCA-AAAACTATACATTATATATGTTTTCA
1 AAATGTTTATAAAACTATATAATATATATATTTTCG
** *
3135773 AAAT-TTTCCAAACCTATATAATATATATATTTTCG
1 AAATGTTTATAAAACTATATAATATATATATTTTCG
* * *
3135808 AAATGTTTTTGAAACTATATAGTATATATATTTTCG
1 AAATGTTTATAAAACTATATAATATATATATTTTCG
3135844 AAATGTTT
1 AAATGTTT
3135852 TCAAAAAATA
Statistics
Matches: 363, Mismatches: 62, Indels: 59
0.75 0.13 0.12
Matches are distributed among these distances:
32 1 0.00
33 7 0.02
34 13 0.04
35 56 0.15
36 59 0.16
37 39 0.11
38 51 0.14
39 82 0.23
40 47 0.13
41 7 0.02
42 1 0.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (36 bp):
AAATGTTTATAAAACTATATAATATATATATTTTCG
Found at i:3139950 original size:63 final size:63
Alignment explanation
Indices: 3139837--3139972 Score: 143
Period size: 63 Copynumber: 2.2 Consensus size: 63
3139827 TTCAATGTGT
* *
3139837 ATCGATGCACTCTCAAATAAATAAACATCGAATGCAATTAATGCATCGATGCATAAGGA-A-TGC
1 ATCGATGCACTCCCAAATAAATAAACATCGAATGCAATTAATGCACCGATG--TAAGGATAGTGC
** * ** * *
3139900 ATCGATGCACTCCCTTA-AAATGAAACATCGAATGTAATTTGTGTACCGATGTATGGATAGTGC
1 ATCGATGCACTCCCAAATAAAT-AAACATCGAATGCAATTAATGCACCGATGTAAGGATAGTGC
3139963 ATCGATGCAC
1 ATCGATGCAC
3139973 ATGTTAAGGA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
61 5 0.08
62 5 0.08
63 51 0.84
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (63 bp):
ATCGATGCACTCCCAAATAAATAAACATCGAATGCAATTAATGCACCGATGTAAGGATAGTGC
Found at i:3140707 original size:32 final size:31
Alignment explanation
Indices: 3140666--3140787 Score: 111
Period size: 32 Copynumber: 3.8 Consensus size: 31
3140656 AGTCGAGGGT
3140666 TTACCTATGTTCTACGGAACATATGGATAGAA
1 TTACCTATG-TCTACGGAACATATGGATAGAA
* * * *
3140698 TTACCTATGTCTTTCGGGACATATGAACAGAA
1 TTACCTATGTC-TACGGAACATATGGATAGAA
*** *
3140730 TTACCTATGTCTTTTGAGACATATGGATAGTA
1 TTACCTATGTCTACGGA-ACATATGGATAGAA
* *
3140762 -TATCTATGTTCTAAGGAACATATGGA
1 TTACCTATG-TCTACGGAACATATGGA
3140788 CAGTTTACAT
Statistics
Matches: 73, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
31 21 0.29
32 52 0.71
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (31 bp):
TTACCTATGTCTACGGAACATATGGATAGAA
Found at i:3144315 original size:20 final size:20
Alignment explanation
Indices: 3144290--3144353 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
3144280 GAATCCCCTA
**
3144290 GAACCAATTTGAGTCAAGTC
1 GAACCAATTTGAGTCAACCC
* *
3144310 GAACCAGTCTGAGTCAACCC
1 GAACCAATTTGAGTCAACCC
3144330 GAACCGAA-TTGAGTCAACCC
1 GAACC-AATTTGAGTCAACCC
3144350 GAAC
1 GAAC
3144354 AAACCCACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 36 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.17
Consensus pattern (20 bp):
GAACCAATTTGAGTCAACCC
Found at i:3147849 original size:4 final size:4
Alignment explanation
Indices: 3147835--3147877 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
3147825 TTTGGTAGAG
*
3147835 AGAA GGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA
3147878 CAGAGAAAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:3151827 original size:90 final size:90
Alignment explanation
Indices: 3151676--3151856 Score: 344
Period size: 90 Copynumber: 2.0 Consensus size: 90
3151666 CAGATGCAAC
* *
3151676 CTGCAGCTGCGACGTCGGCACCATCATCGTCATCGCCTCCCCCTCCGGCTGATCAGAATTCTGAG
1 CTGCAGCTGCGACGGCAGCACCATCATCGTCATCGCCTCCCCCTCCGGCTGATCAGAATTCTGAG
3151741 AAATGGGGGACGCATATCATGGGAG
66 AAATGGGGGACGCATATCATGGGAG
3151766 CTGCAGCTGCGACGGCAGCACCATCATCGTCATCGCCTCCCCCTCCGGCTGATCAGAATTCTGAG
1 CTGCAGCTGCGACGGCAGCACCATCATCGTCATCGCCTCCCCCTCCGGCTGATCAGAATTCTGAG
3151831 AAATGGGGGACGCATATCATGGGAG
66 AAATGGGGGACGCATATCATGGGAG
3151856 C
1 C
3151857 ACCGGCCGTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.22, C:0.31, G:0.28, T:0.19
Consensus pattern (90 bp):
CTGCAGCTGCGACGGCAGCACCATCATCGTCATCGCCTCCCCCTCCGGCTGATCAGAATTCTGAG
AAATGGGGGACGCATATCATGGGAG
Found at i:3155380 original size:20 final size:20
Alignment explanation
Indices: 3155355--3155395 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3155345 CTACTATGGA
3155355 GGATATTTCATAATTCGGAG
1 GGATATTTCATAATTCGGAG
3155375 GGATATTTCATAATTCGGAG
1 GGATATTTCATAATTCGGAG
3155395 G
1 G
3155396 TTTCTTACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (20 bp):
GGATATTTCATAATTCGGAG
Found at i:3156781 original size:40 final size:40
Alignment explanation
Indices: 3156733--3156825 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 40
3156723 CTCCACGTTC
3156733 CAGCAGCTTCCAGCAACAACAGCTGGTTC-CTCACTCCACA
1 CAGCAGCTTCCAGCAACAACAGCTGGTTCTC-CACTCCACA
* * *
3156773 CAGCAGCTTCCGGCAACAACATCTGGTTCTCCACTCCACG
1 CAGCAGCTTCCAGCAACAACAGCTGGTTCTCCACTCCACA
*
3156813 CAGCAGCTGCCAG
1 CAGCAGCTTCCAG
3156826 TATCCCAGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 46 0.98
41 1 0.02
ACGTcount: A:0.25, C:0.40, G:0.18, T:0.17
Consensus pattern (40 bp):
CAGCAGCTTCCAGCAACAACAGCTGGTTCTCCACTCCACA
Found at i:3157795 original size:2 final size:2
Alignment explanation
Indices: 3157788--3157812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3157778 ATTAATTCTT
3157788 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3157813 GCATGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3170945 original size:20 final size:20
Alignment explanation
Indices: 3170920--3170958 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3170910 TTTTCAAGGG
3170920 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
3170940 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
3170959 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:3176923 original size:24 final size:23
Alignment explanation
Indices: 3176896--3176977 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 23
3176886 ACACTTAACA
3176896 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCCTTTGAAT
* *
3176920 GTGCATCGATTCACCATGTTG-A-
1 GTGCATCGATGCACCCT-TTGAAT
*
3176942 -TGCACCGATGCACGCC-TTGAAT
1 GTGCATCGATGCAC-CCTTTGAAT
3176964 GTGCATCGATGCAC
1 GTGCATCGATGCAC
3176978 AGGGTCATGC
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
20 3 0.06
21 12 0.26
22 1 0.02
23 16 0.34
24 15 0.32
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACCCTTTGAAT
Found at i:3179290 original size:16 final size:16
Alignment explanation
Indices: 3179269--3179301 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3179259 AGGGAGAAGT
3179269 GTAAAATGTTTTAAAG
1 GTAAAATGTTTTAAAG
3179285 GTAAAATGTTTTAAAG
1 GTAAAATGTTTTAAAG
3179301 G
1 G
3179302 GGGAGAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.36
Consensus pattern (16 bp):
GTAAAATGTTTTAAAG
Found at i:3179312 original size:19 final size:19
Alignment explanation
Indices: 3179272--3179327 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 19
3179262 GAGAAGTGTA
*
3179272 AAATGTTTTAAA--GGTA-
1 AAATGTTTTAAAGGGGGAG
3179288 AAATGTTTTAAAGGGGGAG
1 AAATGTTTTAAAGGGGGAG
*
3179307 AAATGTTATAGTAAGGGGGAG
1 AAATGTTTTA--AAGGGGGAG
3179328 TAATTTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 12 0.36
18 3 0.09
19 9 0.27
21 9 0.27
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (19 bp):
AAATGTTTTAAAGGGGGAG
Found at i:3179687 original size:20 final size:20
Alignment explanation
Indices: 3179662--3179700 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3179652 TTTTCAAGGG
3179662 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
3179682 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
3179701 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:3179769 original size:45 final size:46
Alignment explanation
Indices: 3179720--3179809 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 46
3179710 GAACATCGAA
* * * *
3179720 TGCATTTTATGCATCGATGCAC-ATACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATACACTCAG
3179765 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATACACTCA
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATACACTCA
3179810 AGCTTTTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATACACTCAG
Found at i:3191353 original size:23 final size:23
Alignment explanation
Indices: 3191327--3191392 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 23
3191317 TGTTGTGTGT
3191327 AAGGGTAAGCCTTACAGTTTCCC
1 AAGGGTAAGCCTTACAGTTTCCC
* * * *
3191350 AA-GGT--TCCTTTACTGTGT-GC
1 AAGGGTAAGCC-TTACAGTTTCCC
3191370 AAGGGTAAGCCTTACAGTTTCCC
1 AAGGGTAAGCCTTACAGTTTCCC
3191393 TAGGTTCCTT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
20 5 0.17
21 10 0.33
22 10 0.33
23 5 0.17
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (23 bp):
AAGGGTAAGCCTTACAGTTTCCC
Found at i:3191355 original size:43 final size:43
Alignment explanation
Indices: 3191278--3191733 Score: 594
Period size: 43 Copynumber: 10.6 Consensus size: 43
3191268 TCCTCTACTA
* * * * *
3191278 TGTGCAAGGGTAAGTTCTTACCGTTACCACAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGTTCCTTTGCTG
* * *
3191322 TGTGTAAGGGTAAGCCTTACAGTTTCCCAAGGTTCCTTTACTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
*
3191365 TGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* * *
3191408 TGTACAAGGGTAAGCCTTACAGTTTCCCCGGGTTCCTTAGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
3191451 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
*
3191494 TGTGCAAGGGTAAGCCTTACAGTTT-CCCAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* *
3191536 TGTGCAAGGGTAAGCCTTACAATTTCCCCAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* * *
3191579 TGTGCCAGGGTAAGCCTTACAGTTTCCCCATGTTCATTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* * * * *
3191622 TGTACGAA-GGTAAGCCTTACAGTTTCCCCATGCTCCTTTGTTA
1 TGTGC-AAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* * * * *
3191665 TGTGCAAGGGTAAGACCTTACCGTTT-CTCAGGCTCTTTTGCTA
1 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGTTCCTTTGCTG
*
3191708 TGTGCAAGGGTAAGACCTTACCGTTT
1 TGTGCAAGGGTAAG-CCTTACAGTTT
3191734 TTGCATGCTC
Statistics
Matches: 371, Mismatches: 37, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
42 42 0.11
43 305 0.82
44 24 0.06
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (43 bp):
TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
Found at i:3191676 original size:214 final size:216
Alignment explanation
Indices: 3191265--3191733 Score: 658
Period size: 214 Copynumber: 2.2 Consensus size: 216
3191255 AAGTATTTCT
* * ** * *
3191265 GGCTCCTCTACTATGTGCAAGGGTAAGTTCTTACCGTTACCACAGGTTCCTTTGTTGTGTGTAAG
1 GGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCGTTTCCACAGGTTCCTTTGTTGTGTGCAAG
* *
3191330 GGTAAGCCTTACAGTTTCCCAAGGTTCCTTTACTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTA
66 GGTAAGCCTTACAATTTCCCAAGGTTCCTTTACTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA
* * * *
3191395 GGTTCCTTTGCTGTGTACAAGGGTAAGCCTTACAGTTTCCCCGGGTTCCTTAGCTGTGTGCAAGG
131 GGTTCATTTGCTGTGTACAAGGGTAAGCCTTACAGTTTCCCCAGGCTCCTTAGCTATGTGCAAGG
3191460 GTAAG-CCTTACAGTTTCCCCA
196 GTAAGACCTTACAGTTT-CCCA
* * *
3191481 GGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTTTCC-CAGGTTCCTTTGTTGTGTGCAAG
1 GGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCGTTTCCACAGGTTCCTTTGTTGTGTGCAAG
* ** *
3191544 GGTAAGCCTTACAATTTCCCCAGGTTCCTTTGTTGTGTGCCAGGGTAAGCCTTACAGTTTCCCCA
66 GGTAAGCCTTACAATTTCCCAAGGTTCCTTTACTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA
* * * *
3191609 TGTTCATTTGCTGTGTACGAA-GGTAAGCCTTACAGTTTCCCCATGCTCCTTTGTTATGTGCAAG
131 GGTTCATTTGCTGTGTAC-AAGGGTAAGCCTTACAGTTTCCCCAGGCTCCTTAGCTATGTGCAAG
* *
3191673 GGTAAGACCTTACCGTTTCTCA
195 GGTAAGACCTTACAGTTTCCCA
*
3191695 GGCTCTTTTGCTATGTGCAAGGGTAAGACCTTACCGTTT
1 GGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCGTTT
3191734 TTGCATGCTC
Statistics
Matches: 222, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
214 167 0.75
215 32 0.14
216 23 0.10
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (216 bp):
GGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCGTTTCCACAGGTTCCTTTGTTGTGTGCAAG
GGTAAGCCTTACAATTTCCCAAGGTTCCTTTACTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA
GGTTCATTTGCTGTGTACAAGGGTAAGCCTTACAGTTTCCCCAGGCTCCTTAGCTATGTGCAAGG
GTAAGACCTTACAGTTTCCCA
Found at i:3192708 original size:70 final size:70
Alignment explanation
Indices: 3192595--3192740 Score: 274
Period size: 70 Copynumber: 2.1 Consensus size: 70
3192585 CCAAAGTTCA
3192595 CCAAATCATATTTTATAAAATTATGCATATACACGGGCCAGAACATTAAGCATGGAAAGATATTG
1 CCAAATCATATTTTATAAAATTATGCATATACACGGGCCAGAACATTAAGCATGGAAAGATATTG
3192660 CAAGT
66 CAAGT
* *
3192665 CCAAATCATATTTTATAAAATTATGTATATAGACGGGCCAGAACATTAAGCATGGAAAGATATTG
1 CCAAATCATATTTTATAAAATTATGCATATACACGGGCCAGAACATTAAGCATGGAAAGATATTG
3192730 CAAGT
66 CAAGT
3192735 CCAAAT
1 CCAAAT
3192741 GTCAGTCAAG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (70 bp):
CCAAATCATATTTTATAAAATTATGCATATACACGGGCCAGAACATTAAGCATGGAAAGATATTG
CAAGT
Found at i:3194996 original size:149 final size:149
Alignment explanation
Indices: 3194726--3195024 Score: 598
Period size: 149 Copynumber: 2.0 Consensus size: 149
3194716 CATGTTACGC
3194726 ATTAGTTGTCCTATTTTGAGTTGAGAACAATTTTAAAAAATAATATAATAATTGGATAGTGTTAT
1 ATTAGTTGTCCTATTTTGAGTTGAGAACAATTTTAAAAAATAATATAATAATTGGATAGTGTTAT
3194791 AATGTAGTATTTGTTAAGAATTTTTTTAATTTATTGACAATACATGCATCTTGAAGGAGTTAATC
66 AATGTAGTATTTGTTAAGAATTTTTTTAATTTATTGACAATACATGCATCTTGAAGGAGTTAATC
3194856 GAACTCGAATAGTTTAAGT
131 GAACTCGAATAGTTTAAGT
3194875 ATTAGTTGTCCTATTTTGAGTTGAGAACAATTTTAAAAAATAATATAATAATTGGATAGTGTTAT
1 ATTAGTTGTCCTATTTTGAGTTGAGAACAATTTTAAAAAATAATATAATAATTGGATAGTGTTAT
3194940 AATGTAGTATTTGTTAAGAATTTTTTTAATTTATTGACAATACATGCATCTTGAAGGAGTTAATC
66 AATGTAGTATTTGTTAAGAATTTTTTTAATTTATTGACAATACATGCATCTTGAAGGAGTTAATC
3195005 GAACTCGAATAGTTTAAGT
131 GAACTCGAATAGTTTAAGT
3195024 A
1 A
3195025 GAATAAAATA
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (149 bp):
ATTAGTTGTCCTATTTTGAGTTGAGAACAATTTTAAAAAATAATATAATAATTGGATAGTGTTAT
AATGTAGTATTTGTTAAGAATTTTTTTAATTTATTGACAATACATGCATCTTGAAGGAGTTAATC
GAACTCGAATAGTTTAAGT
Found at i:3201670 original size:20 final size:21
Alignment explanation
Indices: 3201636--3201679 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
3201626 ATAAATTACA
3201636 TAATTCTTTTAAATTAATATC
1 TAATTCTTTTAAATTAATATC
*
3201657 TAATT-TTTTCAATTAATATC
1 TAATTCTTTTAAATTAATATC
3201677 TAA
1 TAA
3201680 ATTAGATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATTCTTTTAAATTAATATC
Found at i:3204163 original size:57 final size:58
Alignment explanation
Indices: 3204097--3204211 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 58
3204087 CGAAAATGTT
3204097 AATATTTTTTTTATCATTTTCAGTATAACACTACCTAAAATGTTAATTCGTTACCTAA
1 AATATTTTTTTTATCATTTTCAGTATAACACTACCTAAAATGTTAATTCGTTACCTAA
3204155 AATA-TTTTTTTATCATTTTCAGTATAACACTACCTAAAATGTTAATTCGTTACCTAA
1 AATATTTTTTTTATCATTTTCAGTATAACACTACCTAAAATGTTAATTCGTTACCTAA
3204212 TATGATAATC
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 53 0.93
58 4 0.07
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (58 bp):
AATATTTTTTTTATCATTTTCAGTATAACACTACCTAAAATGTTAATTCGTTACCTAA
Found at i:3204320 original size:21 final size:21
Alignment explanation
Indices: 3204296--3204352 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
3204286 AAACGTTAAA
*
3204296 AAATTAACATTTTAGATAATG
1 AAATTAGCATTTTAGATAATG
*
3204317 AAATTAGCTTTTTAGATAATG
1 AAATTAGCATTTTAGATAATG
*
3204338 AAATTAGCACTTTAG
1 AAATTAGCATTTTAG
3204353 GTAGCGCTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (21 bp):
AAATTAGCATTTTAGATAATG
Found at i:3205040 original size:22 final size:22
Alignment explanation
Indices: 3204997--3205038 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3204987 TTATATTTTA
*
3204997 TTTAGGGTTTAAAGATTTAAAT
1 TTTAAGGTTTAAAGATTTAAAT
*
3205019 TTTAAGGTTTATA-ATTTAAA
1 TTTAAGGTTTAAAGATTTAAA
3205039 ATCTAATCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (22 bp):
TTTAAGGTTTAAAGATTTAAAT
Found at i:3205956 original size:46 final size:46
Alignment explanation
Indices: 3205903--3205993 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
3205893 CGGGTTAACC
* ** *
3205903 TTTAGATTTTCGGGTCAATTTGGGTTGGTTTCGGTTCAAGTCAACA
1 TTTAGATTTTCAGGTCAATTCAGGTTGGTTTCAGTTCAAGTCAACA
*
3205949 TTTAGATTTTTAGGTCAATTCAGGTTGGTTTCAGTTCAAGTCAAC
1 TTTAGATTTTCAGGTCAATTCAGGTTGGTTTCAGTTCAAGTCAAC
3205994 TGTCACCACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (46 bp):
TTTAGATTTTCAGGTCAATTCAGGTTGGTTTCAGTTCAAGTCAACA
Found at i:3206450 original size:2 final size:2
Alignment explanation
Indices: 3206443--3206470 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3206433 AATGAGAATA
3206443 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
3206471 TATTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3208676 original size:24 final size:24
Alignment explanation
Indices: 3208649--3208704 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
3208639 CTATTCTTTC
3208649 GCTTCAATTAAGCTCAAATTTTAG
1 GCTTCAATTAAGCTCAAATTTTAG
*
3208673 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTAAGCTCAAATTTTAG
3208697 GCTTCAAT
1 GCTTCAAT
3208705 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (24 bp):
GCTTCAATTAAGCTCAAATTTTAG
Found at i:3209332 original size:23 final size:26
Alignment explanation
Indices: 3209280--3209336 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
3209270 ATATATGACG
3209280 AAAATATATAAAAATGTATATTATAC
1 AAAATATATAAAAATGTATATTATAC
3209306 -AAATATATAAAATAT-TA-A-TA-AC
1 AAAATATATAAAA-ATGTATATTATAC
3209328 AAAATATAT
1 AAAATATAT
3209337 CTTCAACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 2 0.07
23 10 0.34
24 1 0.03
25 14 0.48
26 2 0.07
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAATATATAAAAATGTATATTATAC
Found at i:3209466 original size:21 final size:21
Alignment explanation
Indices: 3209433--3209494 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 21
3209423 ATCTGATTTG
* *
3209433 TTTAAATTATTTAAATTTAAA
1 TTTAATTTTTTTAAATTTAAA
* *
3209454 TTTAATTTTTTTACATATTAAT
1 TTTAATTTTTTTAAAT-TTAAA
* *
3209476 TTTATTTTTCTTTGAATTT
1 TTTAATTTT-TTTAAATTT
3209495 TCAAGTATCA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 13 0.41
22 14 0.44
23 5 0.16
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTAATTTTTTTAAATTTAAA
Found at i:3213384 original size:14 final size:15
Alignment explanation
Indices: 3213365--3213393 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3213355 AAAAAATATT
3213365 TGGGTGA-CAAAATG
1 TGGGTGATCAAAATG
3213379 TGGGTGATCAAAATG
1 TGGGTGATCAAAATG
3213394 AAATCAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.07, G:0.34, T:0.24
Consensus pattern (15 bp):
TGGGTGATCAAAATG
Found at i:3213391 original size:74 final size:74
Alignment explanation
Indices: 3213304--3213451 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
3213294 ATTTTTAACG
3213304 GTGGGTGATCAAAATGAAATCAAAGTGTAACATTAGGTATGATTTTGAAACAAAAAATATTTGGG
1 GTGGGTGATCAAAATGAAATCAAAGTGTAACATTAGGTATGATTTTGAAACAAAAAATATTTGGG
3213369 TGACAAAAT
66 TGACAAAAT
3213378 GTGGGTGATCAAAATGAAATCAAAGTGTAACATTAGGTATGATTTTGAAACAAAAAATATTTGGG
1 GTGGGTGATCAAAATGAAATCAAAGTGTAACATTAGGTATGATTTTGAAACAAAAAATATTTGGG
3213443 TGACAAAAT
66 TGACAAAAT
3213452 ATAACAAAAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (74 bp):
GTGGGTGATCAAAATGAAATCAAAGTGTAACATTAGGTATGATTTTGAAACAAAAAATATTTGGG
TGACAAAAT
Found at i:3221051 original size:22 final size:22
Alignment explanation
Indices: 3221017--3221073 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
3221007 TAAAAATTAT
3221017 TAATT-ATATTTATTAAATATAA
1 TAATTAATA-TTATTAAATATAA
* *
3221039 TAATTAATATTATTTATTATAA
1 TAATTAATATTATTAAATATAA
3221061 -AA--AATATTATTAA
1 TAATTAATATTATTAA
3221074 TTTTAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 10 0.32
21 2 0.06
22 16 0.52
23 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATTAATATTATTAAATATAA
Found at i:3221066 original size:26 final size:25
Alignment explanation
Indices: 3221008--3221075 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
3220998 GTAATTTTTT
*
3221008 AAAAATTATTAATTATATTTATTAA
1 AAAAATAATTAATTATATTTATTAA
*
3221033 ATATAATAATTAA-TATTATTTATTATA
1 A-AAAATAATTAATTA-TATTTATTA-A
3221060 AAAAATATTATTAATT
1 AAAAATA--ATTAATT
3221076 TTAAAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
25 3 0.09
26 23 0.68
27 2 0.06
28 5 0.15
29 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAAATAATTAATTATATTTATTAA
Found at i:3221080 original size:19 final size:19
Alignment explanation
Indices: 3221044--3221081 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3221034 TATAATAATT
*
3221044 AATATTATTTATTATAAAA
1 AATATTATTAATTATAAAA
*
3221063 AATATTATTAATTTTAAAA
1 AATATTATTAATTATAAAA
3221082 TATTATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATTATTAATTATAAAA
Found at i:3221387 original size:21 final size:21
Alignment explanation
Indices: 3221357--3221396 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3221347 TTTAATTGAA
* * *
3221357 AAAATTAAAATATCGATAATC
1 AAAATAAAAAAATAGATAATC
3221378 AAAATAAAAAAATAGATAA
1 AAAATAAAAAAATAGATAA
3221397 ATAATAATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAATAAAAAAATAGATAATC
Found at i:3229455 original size:183 final size:183
Alignment explanation
Indices: 3229147--3229511 Score: 730
Period size: 183 Copynumber: 2.0 Consensus size: 183
3229137 AAAGTCTTGG
3229147 AATTCAAATGTTTTTGGCTCTATTACCCATCAAAAGAAGACTGTAATGGCAAGACTATACGACAT
1 AATTCAAATGTTTTTGGCTCTATTACCCATCAAAAGAAGACTGTAATGGCAAGACTATACGACAT
3229212 TAAAAAAAGTATTGACCGAAGGCACAATCATTTTCTCATCACCTTGGAGGCACAACTTCAACTCG
66 TAAAAAAAGTATTGACCGAAGGCACAATCATTTTCTCATCACCTTGGAGGCACAACTTCAACTCG
3229277 AACTTGAAAAGATTCTTGATCAGGAAGAACTTATTTGGAAACTAAAATCCCGA
131 AACTTGAAAAGATTCTTGATCAGGAAGAACTTATTTGGAAACTAAAATCCCGA
3229330 AATTCAAATGTTTTTGGCTCTATTACCCATCAAAAGAAGACTGTAATGGCAAGACTATACGACAT
1 AATTCAAATGTTTTTGGCTCTATTACCCATCAAAAGAAGACTGTAATGGCAAGACTATACGACAT
3229395 TAAAAAAAGTATTGACCGAAGGCACAATCATTTTCTCATCACCTTGGAGGCACAACTTCAACTCG
66 TAAAAAAAGTATTGACCGAAGGCACAATCATTTTCTCATCACCTTGGAGGCACAACTTCAACTCG
3229460 AACTTGAAAAGATTCTTGATCAGGAAGAACTTATTTGGAAACTAAAATCCCG
131 AACTTGAAAAGATTCTTGATCAGGAAGAACTTATTTGGAAACTAAAATCCCG
3229512 GATGGATTGG
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 182 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (183 bp):
AATTCAAATGTTTTTGGCTCTATTACCCATCAAAAGAAGACTGTAATGGCAAGACTATACGACAT
TAAAAAAAGTATTGACCGAAGGCACAATCATTTTCTCATCACCTTGGAGGCACAACTTCAACTCG
AACTTGAAAAGATTCTTGATCAGGAAGAACTTATTTGGAAACTAAAATCCCGA
Found at i:3230598 original size:19 final size:20
Alignment explanation
Indices: 3230574--3230617 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3230564 TAATTTAATC
*
3230574 GAATATATAAT-TTAAAATT
1 GAATATAAAATCTTAAAATT
3230593 GAATATAAAATCTTAAAATT
1 GAATATAAAATCTTAAAATT
*
3230613 CAATA
1 GAATA
3230618 ATACTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
GAATATAAAATCTTAAAATT
Found at i:3230990 original size:9 final size:9
Alignment explanation
Indices: 3230976--3231010 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
3230966 TCAAATTAAA
3230976 CATTCAAAC
1 CATTCAAAC
3230985 CATTCAAAC
1 CATTCAAAC
3230994 CATTCAAAC
1 CATTCAAAC
3231003 CATTCAAA
1 CATTCAAA
3231011 TCCAAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (9 bp):
CATTCAAAC
Found at i:3231038 original size:22 final size:22
Alignment explanation
Indices: 3231012--3231055 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3231002 CCATTCAAAT
*
3231012 CCAAAACAAACATATCCAAAAC
1 CCAAAACAAACAAATCCAAAAC
*
3231034 CCAAAACACACAAATCCAAAAC
1 CCAAAACAAACAAATCCAAAAC
3231056 ATTCAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.34, G:0.00, T:0.07
Consensus pattern (22 bp):
CCAAAACAAACAAATCCAAAAC
Found at i:3235188 original size:17 final size:17
Alignment explanation
Indices: 3235166--3235199 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3235156 GAAATTACTC
3235166 CCCCTTACTTTAACACT
1 CCCCTTACTTTAACACT
3235183 CCCCTTACTTTAACACT
1 CCCCTTACTTTAACACT
3235200 TCTCTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (17 bp):
CCCCTTACTTTAACACT
Found at i:3237482 original size:21 final size:21
Alignment explanation
Indices: 3237456--3237495 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3237446 CAGAACCCCA
*
3237456 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3237477 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3237496 TCAAAGGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3245594 original size:40 final size:40
Alignment explanation
Indices: 3245545--3245638 Score: 163
Period size: 40 Copynumber: 2.3 Consensus size: 40
3245535 CCTCCATTTT
3245545 TGTCGTTAAGC-TCTATAAACCGACTCTTATCTTCGGTCATA
1 TGTC-TTAAGCATC-ATAAACCGACTCTTATCTTCGGTCATA
3245586 TGTCTTAAGCATCATAAACCGACTCTTATCTTCGGTCATA
1 TGTCTTAAGCATCATAAACCGACTCTTATCTTCGGTCATA
3245626 TGTCTTAAGCATC
1 TGTCTTAAGCATC
3245639 CACTATCAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
40 46 0.88
41 6 0.12
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (40 bp):
TGTCTTAAGCATCATAAACCGACTCTTATCTTCGGTCATA
Found at i:3248414 original size:19 final size:20
Alignment explanation
Indices: 3248390--3248428 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3248380 TAATTTAATC
*
3248390 GAATATATAAT-TTAAAATT
1 GAATATAAAATCTTAAAATT
3248409 GAATATAAAATCTTAAAATT
1 GAATATAAAATCTTAAAATT
3248429 CAATGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
GAATATAAAATCTTAAAATT
Found at i:3250295 original size:20 final size:21
Alignment explanation
Indices: 3250258--3250296 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3250248 CGACTCGAAA
*
3250258 TAATAAAAAATATTATTTATT
1 TAATAAAAAATATGATTTATT
*
3250279 TAATAAAACA-ATGATTTA
1 TAATAAAAAATATGATTTA
3250297 ATTGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (21 bp):
TAATAAAAAATATGATTTATT
Found at i:3255237 original size:28 final size:28
Alignment explanation
Indices: 3255146--3255258 Score: 208
Period size: 29 Copynumber: 4.0 Consensus size: 28
3255136 AGTGTTGGCC
3255146 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCC-GGCGACCTT
3255175 GTAGGTCGCCATGCACTCCGGTCGACCTT
1 GTAGGTCGCCATGCACTCCGG-CGACCTT
3255204 GTAGGTCGCCATGCACTCCGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGCGACCTT
3255232 GTAGGTCGCCATGCACTCCGGCGACCT
1 GTAGGTCGCCATGCACTCCGGCGACCT
3255259 ACCCTTGCTC
Statistics
Matches: 83, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
28 36 0.43
29 47 0.57
ACGTcount: A:0.14, C:0.35, G:0.29, T:0.21
Consensus pattern (28 bp):
GTAGGTCGCCATGCACTCCGGCGACCTT
Found at i:3255243 original size:57 final size:57
Alignment explanation
Indices: 3255146--3255258 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
3255136 AGTGTTGGCC
3255146 GTAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACTCCGGTCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACTCCGG-CGACCTT
3255204 GTAGGTCGCCATGCACTCC-GGCGACCTTGTAGGTCGCCATGCACTCCGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACTCCGGCGACCT
3255259 ACCCTTGCTC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
56 6 0.11
57 30 0.55
58 19 0.35
ACGTcount: A:0.14, C:0.35, G:0.29, T:0.21
Consensus pattern (57 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACTCCGGCGACCTT
Found at i:3255432 original size:20 final size:20
Alignment explanation
Indices: 3255409--3255491 Score: 136
Period size: 20 Copynumber: 4.3 Consensus size: 20
3255399 GCTCGGCTTC
3255409 CCTCGGATGCTCTCGGATGG
1 CCTCGGATGCTCTCGGATGG
3255429 CCTCGGATGCTCTCGGATGG
1 CCTCGGATGCTCTCGGATGG
*
3255449 CCTC-GATACTCTCGGATGG
1 CCTCGGATGCTCTCGGATGG
3255468 CCTC-GAT-CTCTCGGATGG
1 CCTCGGATGCTCTCGGATGG
3255486 CCTCGG
1 CCTCGG
3255492 TCGATGGCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
18 15 0.25
19 22 0.36
20 24 0.39
ACGTcount: A:0.11, C:0.33, G:0.31, T:0.25
Consensus pattern (20 bp):
CCTCGGATGCTCTCGGATGG
Found at i:3255462 original size:19 final size:18
Alignment explanation
Indices: 3255418--3255490 Score: 119
Period size: 19 Copynumber: 3.9 Consensus size: 18
3255408 CCCTCGGATG
3255418 CTCTCGGATGGCCTCGGAT
1 CTCTCGGATGGCCTC-GAT
3255437 GCTCTCGGATGGCCTCGAT
1 -CTCTCGGATGGCCTCGAT
3255456 ACTCTCGGATGGCCTCGAT
1 -CTCTCGGATGGCCTCGAT
3255475 CTCTCGGATGGCCTCG
1 CTCTCGGATGGCCTCG
3255491 GTCGATGGCC
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
18 16 0.31
19 21 0.40
20 15 0.29
ACGTcount: A:0.11, C:0.33, G:0.30, T:0.26
Consensus pattern (18 bp):
CTCTCGGATGGCCTCGAT
Found at i:3255466 original size:39 final size:37
Alignment explanation
Indices: 3255409--3255490 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 37
3255399 GCTCGGCTTC
*
3255409 CCTCGGATGCTCTCGGATGGCCTCGGATGCTCTCGGATGG
1 CCTC-GATACTCTCGGATGGCCTC-GAT-CTCTCGGATGG
3255449 CCTCGATACTCTCGGATGGCCTCGATCTCTCGGATGG
1 CCTCGATACTCTCGGATGGCCTCGATCTCTCGGATGG
3255486 CCTCG
1 CCTCG
3255491 GTCGATGGCC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
37 16 0.39
38 3 0.07
39 18 0.44
40 4 0.10
ACGTcount: A:0.11, C:0.33, G:0.30, T:0.26
Consensus pattern (37 bp):
CCTCGATACTCTCGGATGGCCTCGATCTCTCGGATGG
Found at i:3255490 original size:10 final size:10
Alignment explanation
Indices: 3255409--3255507 Score: 77
Period size: 10 Copynumber: 9.9 Consensus size: 10
3255399 GCTCGGCTTC
3255409 CCTCGGAT-G
1 CCTCGGATGG
3255418 CTCTCGGATGG
1 C-CTCGGATGG
3255429 CCTCGGAT-G
1 CCTCGGATGG
3255438 CTCTCGGATGG
1 C-CTCGGATGG
*
3255449 CCTC-GAT-A
1 CCTCGGATGG
3255457 CTCTCGGATGG
1 C-CTCGGATGG
3255468 CCTC-GAT--
1 CCTCGGATGG
3255475 CTCTCGGATGG
1 C-CTCGGATGG
3255486 CCTCGGTCGATGG
1 CCTC-G--GATGG
3255499 CCTCGGATG
1 CCTCGGATG
3255508 CCCAGCGTGT
Statistics
Matches: 74, Mismatches: 2, Indels: 27
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.01
8 4 0.05
9 15 0.20
10 37 0.50
11 7 0.09
12 1 0.01
13 9 0.12
ACGTcount: A:0.11, C:0.31, G:0.32, T:0.25
Consensus pattern (10 bp):
CCTCGGATGG
Found at i:3258780 original size:48 final size:48
Alignment explanation
Indices: 3258709--3258804 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
3258699 TTTCTCTATT
3258709 ATCGGAAGAAAGCTAGAATGTTTTGGGATGATTTTGAAGCTAAATGAG
1 ATCGGAAGAAAGCTAGAATGTTTTGGGATGATTTTGAAGCTAAATGAG
3258757 ATCGGAAGAAAGCTAGAATGTTTTGGGATGATTTTGAAGCTAAATGAG
1 ATCGGAAGAAAGCTAGAATGTTTTGGGATGATTTTGAAGCTAAATGAG
3258805 CTAGAGTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (48 bp):
ATCGGAAGAAAGCTAGAATGTTTTGGGATGATTTTGAAGCTAAATGAG
Found at i:3269353 original size:12 final size:12
Alignment explanation
Indices: 3269326--3269361 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
3269316 TTGGTAATCA
3269326 CCGCCCCGATTAC
1 CCGCCCCGA-TAC
3269339 CCGCCCCGATAC
1 CCGCCCCGATAC
*
3269351 CCGACCCGATA
1 CCGCCCCGATA
3269362 AATATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.19, C:0.53, G:0.17, T:0.11
Consensus pattern (12 bp):
CCGCCCCGATAC
Found at i:3269388 original size:2 final size:2
Alignment explanation
Indices: 3269381--3269412 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3269371 AATAATTATT
3269381 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3269413 TAATAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3269507 original size:12 final size:12
Alignment explanation
Indices: 3269492--3269526 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
3269482 CGATTCTCGG
3269492 CCCAATACCCGA
1 CCCAATACCCGA
*
3269504 CCCAATACCCGG
1 CCCAATACCCGA
3269516 CCCAATACCCG
1 CCCAATACCCG
3269527 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:3280500 original size:18 final size:18
Alignment explanation
Indices: 3280477--3280552 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 18
3280467 GCGTAGAATT
3280477 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3280495 TGTCCCAAAGGACCACATATCACATA
1 TGTCCCGAAGG---AC----CAC-TA
3280521 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3280539 TGTCCCGAATGACC
1 TGTCCCGAAGGACC
3280553 GTGTAGAACC
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
18 25 0.53
19 3 0.06
21 2 0.04
23 2 0.04
25 3 0.06
26 12 0.26
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3286132 original size:20 final size:21
Alignment explanation
Indices: 3286096--3286137 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
3286086 ATGTTATAGG
*
3286096 GGTATCGATACCCCTGCTACA
1 GGTACCGATACCCCTGCTACA
3286117 GGTACCGATA-CCCTGCTACA
1 GGTACCGATACCCCTGCTACA
3286137 G
1 G
3286138 TACTGTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTACCGATACCCCTGCTACA
Found at i:3286897 original size:24 final size:24
Alignment explanation
Indices: 3286865--3286920 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
3286855 CATATATGTA
3286865 CCGAAGGAACACGTAAAGTTTGTC
1 CCGAAGGAACACGTAAAGTTTGTC
3286889 CCGAAGGAACACGTAAAGTTTGTC
1 CCGAAGGAACACGTAAAGTTTGTC
3286913 CCGAAGGA
1 CCGAAGGA
3286921 CCGAGTAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.18
Consensus pattern (24 bp):
CCGAAGGAACACGTAAAGTTTGTC
Found at i:3287047 original size:30 final size:31
Alignment explanation
Indices: 3287013--3287076 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
3287003 TTATATTGCG
* *
3287013 TAGACATATTA-TTTCCATACTTTTATCACA
1 TAGACATATTATTTTCCACACCTTTATCACA
3287043 TAGACATATTATTTTCCACACCTTTATCACA
1 TAGACATATTATTTTCCACACCTTTATCACA
3287074 TAG
1 TAG
3287077 CTCATATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (31 bp):
TAGACATATTATTTTCCACACCTTTATCACA
Found at i:3292986 original size:29 final size:29
Alignment explanation
Indices: 3292928--3293088 Score: 150
Period size: 29 Copynumber: 5.7 Consensus size: 29
3292918 TTTTTTTAAA
* *
3292928 TAATTACCAAAATAGC-CCT-TTTCGAAT
1 TAATTCCCAAAATAGCACCTATTTCAAAT
*
3292955 TAATTCCCAAAATAGCACCAATTTCAAAT
1 TAATTCCCAAAATAGCACCTATTTCAAAT
* * * *
3292984 TAATTCCCAGAATATCA-CTTTTTCAAAA
1 TAATTCCCAAAATAGCACCTATTTCAAAT
* * * *
3293012 AAATTACCAAAATAGCACCCATTTCGAAT
1 TAATTCCCAAAATAGCACCTATTTCAAAT
* *
3293041 TAATTCCCAGAATAGCA-CTATTACCAAAT
1 TAATTCCCAAAATAGCACCTATT-TCAAAT
* *
3293070 TAATTCCCAGAATAACACC
1 TAATTCCCAAAATAGCACC
3293089 GGTCATCGGT
Statistics
Matches: 106, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
27 15 0.14
28 27 0.25
29 63 0.59
30 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.29
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCTATTTCAAAT
Found at i:3293114 original size:13 final size:13
Alignment explanation
Indices: 3293096--3293125 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3293086 ACCGGTCATC
*
3293096 GGTCAACTGGTCG
1 GGTCAACGGGTCG
3293109 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3293122 GGTC
1 GGTC
3293126 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.23, G:0.43, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3293127 original size:18 final size:17
Alignment explanation
Indices: 3293104--3293142 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
3293094 TCGGTCAACT
3293104 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAAC-GGTCG
3293122 GGTCGGGTCAACGGTCG
1 GGTCGGGTCAACGGTCG
3293139 GGTC
1 GGTC
3293143 AACGGGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCAACGGTCG
Found at i:3293139 original size:12 final size:12
Alignment explanation
Indices: 3293122--3293147 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3293112 CAACGGGTCG
3293122 GGTCGGGTCAAC
1 GGTCGGGTCAAC
3293134 GGTCGGGTCAAC
1 GGTCGGGTCAAC
3293146 GG
1 GG
3293148 GTAAACGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:3299939 original size:11 final size:11
Alignment explanation
Indices: 3299925--3299955 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
3299915 TGTTTCTATG
3299925 TTGTTTTTTTT
1 TTGTTTTTTTT
3299936 TTG-TTTTTTT
1 TTGTTTTTTTT
3299946 TTGTTTTTTT
1 TTGTTTTTTT
3299956 CCTCTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTGTTTTTTTT
Found at i:3306212 original size:214 final size:214
Alignment explanation
Indices: 3305843--3306233 Score: 692
Period size: 214 Copynumber: 1.8 Consensus size: 214
3305833 CATTCATAAG
* *
3305843 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAATGATGTTTTAAGAAGATGGAAT
1 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAAGAAGATGAAAT
** *
3305908 TTTTGAAAATGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
66 TTTTGAAAACAAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
*
3305973 GTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGT
131 GTCTTTCGAGCATGATGCTTAAATCTTTCGGGTAATCTGTAAGCCTTTAGAGCAAGATGATAAGT
3306038 CCTTCGGACCATCCGTAAA
196 CCTTCGGACCATCCGTAAA
* *
3306057 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATGAAAAACGATGTTTTGAGAAGATGAAAT
1 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAAGAAGATGAAAT
*
3306122 TTTTGAAAACAAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCGGTCCATCAGTAA
66 TTTTGAAAACAAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
*
3306187 GTCTTTCGAGCATGATGCTTAAATCTTTCGGGTAATTTGTAAGCCTT
131 GTCTTTCGAGCATGATGCTTAAATCTTTCGGGTAATCTGTAAGCCTT
3306234 CACCGAAGAG
Statistics
Matches: 167, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
214 167 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (214 bp):
ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAAGAAGATGAAAT
TTTTGAAAACAAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
GTCTTTCGAGCATGATGCTTAAATCTTTCGGGTAATCTGTAAGCCTTTAGAGCAAGATGATAAGT
CCTTCGGACCATCCGTAAA
Found at i:3306275 original size:13 final size:13
Alignment explanation
Indices: 3306257--3306281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3306247 TGAAGCAAAC
3306257 CCATCAGTAAGTG
1 CCATCAGTAAGTG
3306270 CCATCAGTAAGT
1 CCATCAGTAAGT
3306282 CTTTTGAGCA
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:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:3306331 original size:20 final size:20
Alignment explanation
Indices: 3306269--3306332 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
3306259 ATCAGTAAGT
*
3306269 GCCATCAGTAAGTCTTTTGA
1 GCCATCAGTAAGTCTTTCGA
* * *
3306289 G-CATGATGATGAAATCCTTCGA
1 GCCATCA-G-T-AAGTCTTTCGA
3306311 GCCATCAGTAAGTCTTTCGA
1 GCCATCAGTAAGTCTTTCGA
3306331 GC
1 GC
3306333 ATGATGATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
19 4 0.12
20 13 0.39
21 2 0.06
22 10 0.30
23 4 0.12
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (20 bp):
GCCATCAGTAAGTCTTTCGA
Found at i:3306333 original size:42 final size:42
Alignment explanation
Indices: 3306269--3306351 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
3306259 ATCAGTAAGT
*
3306269 GCCATCAGTAAGTCTTTTGAGCATGATGATGAAATCCTTCGA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGA
*
3306311 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCG
3306352 GATAATTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGA
Found at i:3306461 original size:42 final size:41
Alignment explanation
Indices: 3306398--3306484 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 41
3306388 AAATTCATCA
*
3306398 GTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCGAGCATGATGAT-AAATCCTTCGGGCCATTT
* *
3306440 GTAAGTCTTTCGAGTGA-GATGATAAGTCCTTCGGGCCATTT
1 GTAAGTCTTTCGAG-CATGATGATAAATCCTTCGGGCCATTT
3306481 -TAAG
1 GTAAG
3306485 CCTTCTCGGA
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 20 0.49
43 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (41 bp):
GTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGCCATTT
Found at i:3306919 original size:53 final size:53
Alignment explanation
Indices: 3306856--3307058 Score: 273
Period size: 53 Copynumber: 3.8 Consensus size: 53
3306846 AGAATTACAC
* *
3306856 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAAG
3306909 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAAG
* * * ***
3306962 CAGAAGATTGTTCGAGTTCTACTTCCTGAAGAAATAGGGAGCGAACTCGTTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAAG
* * * *
3307015 TAGAAGATTGTTCAAGTTCCTTAATCCCTGAA-CAAGATGGAGCG
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCG
3307059 GACACATCAT
Statistics
Matches: 133, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
53 114 0.86
54 10 0.08
55 9 0.07
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAAG
Found at i:3313902 original size:29 final size:29
Alignment explanation
Indices: 3313870--3314036 Score: 100
Period size: 29 Copynumber: 5.7 Consensus size: 29
3313860 CTTTTTTAAA
* ** *
3313870 TAATTACCAAAATAGCACCCTTTTCGAAT
1 TAATTCCCAAAATAGCACCAATTTCAAAT
3313899 TAATTCCCAAAATAGCACCAATTTCAAAT
1 TAATTCCCAAAATAGCACCAATTTCAAAT
* * **** *
3313928 TAATTCCCAGAATATCATTTTTTTTTTCAAAA
1 TAATTCCCAAAATAGCA---CCAATTTCAAAT
* * *
3313960 AAATTACCAAAATAGCACCCATTTCAAAT
1 TAATTCCCAAAATAGCACCAATTTCAAAT
* * * * ** *
3313989 TAATTCCTAGAATATCACTAAAATCGAAT
1 TAATTCCCAAAATAGCACCAATTTCAAAT
* *
3314018 TAATTCCCAGAATAACACC
1 TAATTCCCAAAATAGCACC
3314037 GGTCAACGGT
Statistics
Matches: 102, Mismatches: 33, Indels: 6
0.72 0.23 0.04
Matches are distributed among these distances:
29 82 0.80
32 20 0.20
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.31
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCAATTTCAAAT
Found at i:3314979 original size:65 final size:65
Alignment explanation
Indices: 3314863--3315025 Score: 206
Period size: 64 Copynumber: 2.5 Consensus size: 65
3314853 AATTAAATTG
* * *
3314863 AACATCGAAGGCATTTCATGCATCGACGATGCA-CATACCATGCATCGATGCACTGAGGAT-TTT
1 AACATCGAATGCATTTGATGCAT---CGATGCACCATACCATGCATCGATGCACTCAGGATATTT
3314926 ATGAA
63 -TG-A
* *
3314931 AACATCGAATGCATTTGATGCATCGATGCACCA-ACCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCATCGATGCACTCAGGATATTTTGA
*
3314995 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
3315026 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
64 31 0.36
65 30 0.34
66 5 0.06
68 21 0.24
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCATCGATGCACTCAGGATATTTTGA
Found at i:3318860 original size:15 final size:15
Alignment explanation
Indices: 3318836--3318870 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3318826 ATCAAAGGAA
3318836 GAAACAAAAAATGAG
1 GAAACAAAAAATGAG
*
3318851 GAAACGAAAAATGAG
1 GAAACAAAAAATGAG
3318866 GAAAC
1 GAAAC
3318871 TCATGATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.23, T:0.06
Consensus pattern (15 bp):
GAAACAAAAAATGAG
Found at i:3323027 original size:2 final size:2
Alignment explanation
Indices: 3323020--3323046 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3323010 CAGCTTAAGC
3323020 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3323047 TTAATCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3323640 original size:65 final size:63
Alignment explanation
Indices: 3323510--3323719 Score: 228
Period size: 65 Copynumber: 3.3 Consensus size: 63
3323500 ATTTTCAGAG
* * * * **
3323510 TGATGCACCGACGCACCAATCCATGCATCGATGCACCATGGATTAAATTG-AACATCGAATGCAT
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTACGGATTTTA-TGAAACATCGAATGCAT
3323574 T
63 T
*
3323575 TCATGCATCGATGCACATACCATGCATCGATGCACTACGGATTTTATGAAAACATCGAATGCATT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTACGGATTTTATG-AAACATCGAATGCATT
* * * *
3323640 TGATGCATCGATGCACCAGCCATGTATCGATGCACT-CTGGCTATTT-TGAAACATCGAATGCAC
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTAC-GGAT-TTTATGAAACATCGAATGCAT
3323703 T
63 T
3323704 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
3323720 TCTTAGTGCA
Statistics
Matches: 127, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
63 3 0.02
64 56 0.44
65 63 0.50
66 5 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTACGGATTTTATGAAACATCGAATGCATT
Found at i:3323719 original size:17 final size:19
Alignment explanation
Indices: 3323691--3323739 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3323681 TATTTTGAAA
3323691 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3323709 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3323728 CACCGATGCACT
1 CATCGATGCACT
3323740 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3326303 original size:21 final size:21
Alignment explanation
Indices: 3326246--3326293 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
3326236 ATTTGAACTC
3326246 ATATTAAGAAAATATGATAAT
1 ATATTAAGAAAATATGATAAT
3326267 ATATTAAGAAAATATGATAAT
1 ATATTAAGAAAATATGATAAT
3326288 ATATTA
1 ATATTA
3326294 TTAAATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (21 bp):
ATATTAAGAAAATATGATAAT
Found at i:3326490 original size:20 final size:20
Alignment explanation
Indices: 3326465--3326547 Score: 98
Period size: 19 Copynumber: 4.2 Consensus size: 20
3326455 ATACCCCTAT
*
3326465 TACAGGTACCGATACCTTGC
1 TACAGGTACCGATACCCTGC
3326485 TACAGGTACCGATACCCTGC
1 TACAGGTACCGATACCCTGC
* * *
3326505 TACA-GTACTGCTATCCTGC
1 TACAGGTACCGATACCCTGC
* *
3326524 TACA-GTACTGCTACCCTGC
1 TACAGGTACCGATACCCTGC
3326543 TACAG
1 TACAG
3326548 TACTGCTACA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 34 0.60
20 23 0.40
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (20 bp):
TACAGGTACCGATACCCTGC
Found at i:3326517 original size:11 final size:11
Alignment explanation
Indices: 3326501--3326562 Score: 64
Period size: 11 Copynumber: 6.2 Consensus size: 11
3326491 TACCGATACC
3326501 CTGCTACAGTA
1 CTGCTACAGTA
*
3326512 CTGCT--A-TC
1 CTGCTACAGTA
3326520 CTGCTACAGTA
1 CTGCTACAGTA
*
3326531 CTGCTAC---C
1 CTGCTACAGTA
3326539 CTGCTACAGTA
1 CTGCTACAGTA
3326550 CTGCTACAGTA
1 CTGCTACAGTA
3326561 CT
1 CT
3326563 TCCATAAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
8 13 0.32
9 1 0.02
10 1 0.02
11 26 0.63
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:3326522 original size:19 final size:19
Alignment explanation
Indices: 3326477--3326556 Score: 115
Period size: 19 Copynumber: 4.2 Consensus size: 19
3326467 CAGGTACCGA
* * *
3326477 TACCTTGCTACAGGTACCGA
1 TACCCTGCTACA-GTACTGC
3326497 TACCCTGCTACAGTACTGC
1 TACCCTGCTACAGTACTGC
*
3326516 TATCCTGCTACAGTACTGC
1 TACCCTGCTACAGTACTGC
3326535 TACCCTGCTACAGTACTGC
1 TACCCTGCTACAGTACTGC
3326554 TAC
1 TAC
3326557 AGTACTTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 44 0.80
20 11 0.20
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.28
Consensus pattern (19 bp):
TACCCTGCTACAGTACTGC
Found at i:3327458 original size:30 final size:31
Alignment explanation
Indices: 3327424--3327487 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
3327414 TTATATCGCG
* * *
3327424 TAGACATATTA-TTTGCATACTTTTATCACA
1 TAGACATATCATTTTCCATACATTTATCACA
*
3327454 TAGACGTATCATTTTCCATACATTTATCACA
1 TAGACATATCATTTTCCATACATTTATCACA
3327485 TAG
1 TAG
3327488 CTCATATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 9 0.31
31 20 0.69
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.41
Consensus pattern (31 bp):
TAGACATATCATTTTCCATACATTTATCACA
Found at i:3327611 original size:17 final size:17
Alignment explanation
Indices: 3327589--3327630 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
3327579 AAATATTGAA
3327589 TCTAGACTTATCACAAG
1 TCTAGACTTATCACAAG
3327606 TCTAGACTTATCACAAG
1 TCTAGACTTATCACAAG
*
3327623 TCGAGACT
1 TCTAGACT
3327631 GATTATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (17 bp):
TCTAGACTTATCACAAG
Found at i:3337065 original size:16 final size:16
Alignment explanation
Indices: 3337044--3337074 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3337034 TGAAACTCGA
3337044 CTCGAACTCGAAAAAG
1 CTCGAACTCGAAAAAG
3337060 CTCGAACTCGAAAAA
1 CTCGAACTCGAAAAA
3337075 AATTCAAAAG
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:0.45, C:0.26, G:0.16, T:0.13
Consensus pattern (16 bp):
CTCGAACTCGAAAAAG
Found at i:3337913 original size:15 final size:13
Alignment explanation
Indices: 3337893--3337930 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
3337883 CTTTCTTAGC
3337893 ATTATCATATATATT
1 ATTATCAT-TAT-TT
3337908 ATTATCATTATTT
1 ATTATCATTATTT
3337921 A-TATCATTAT
1 ATTATCATTAT
3337931 CATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 3 0.13
15 8 0.35
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATCATTATTT
Found at i:3338208 original size:23 final size:23
Alignment explanation
Indices: 3338190--3338250 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
3338180 CTCGTATATA
3338190 TACACCGAAGTGCCACGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
* *
3338213 TGCACCGTAGTGCCACGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
*
3338236 TGCACC-ATAGTGCCA
1 TACACCGA-AGTGCCA
3338251 TATAATAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (23 bp):
TACACCGAAGTGCCACGTAGAAT
Found at i:3343155 original size:18 final size:17
Alignment explanation
Indices: 3343116--3343156 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
3343106 ACTTTCTTAG
3343116 CATTATCATATATATAT
1 CATTATCATATATATAT
* *
3343133 TATTATCATTATTTATAT
1 CATTATCA-TATATATAT
3343151 CATTAT
1 CATTAT
3343157 TATCAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (17 bp):
CATTATCATATATATAT
Found at i:3343173 original size:21 final size:21
Alignment explanation
Indices: 3343126--3343171 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
3343116 CATTATCATA
3343126 TATAT-ATTATTATCATTATT
1 TATATCATTATTATCATTATT
3343146 TATATCATTATTATCAAATTATT
1 TATATCATTATTATC--ATTATT
3343169 TAT
1 TAT
3343172 CACATGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.22
21 9 0.39
23 9 0.39
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATCATTATTATCATTATT
Found at i:3343298 original size:2 final size:2
Alignment explanation
Indices: 3343291--3343318 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3343281 AAACATATTC
3343291 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
3343319 GTATTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3343452 original size:22 final size:23
Alignment explanation
Indices: 3343427--3343481 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
3343417 CGTATATATA
* *
3343427 CACCGAAGT-ACGCGTAGAATTG
1 CACCGAAGTGACACCTAGAATTG
* *
3343449 CACCGTAGTGCCACCTAGAATTG
1 CACCGAAGTGACACCTAGAATTG
*
3343472 CACCGTAGTG
1 CACCGAAGTG
3343482 CCATATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
CACCGAAGTGACACCTAGAATTG
Found at i:3343468 original size:23 final size:23
Alignment explanation
Indices: 3343441--3343484 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3343431 GAAGTACGCG
3343441 TAGAATTGCACCGTAGTGCCACC
1 TAGAATTGCACCGTAGTGCCACC
3343464 TAGAATTGCACCGTAGTGCCA
1 TAGAATTGCACCGTAGTGCCA
3343485 TATAATAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
TAGAATTGCACCGTAGTGCCACC
Found at i:3349137 original size:6 final size:7
Alignment explanation
Indices: 3349114--3349220 Score: 80
Period size: 7 Copynumber: 15.9 Consensus size: 7
3349104 GTGTATAACT
3349114 TAAACCC
1 TAAACCC
3349121 TAAACCC
1 TAAACCC
3349128 TAAA-CC
1 TAAACCC
3349134 TAAACCC
1 TAAACCC
* *
3349141 CACACCC
1 TAAACCC
3349148 TAAACCC
1 TAAACCC
3349155 TAAA--C
1 TAAACCC
*
3349160 T-AACCT
1 TAAACCC
* *
3349166 TAAATCA
1 TAAACCC
* *
3349173 T-ATCACA
1 TAAAC-CC
3349180 TAAACCC
1 TAAACCC
3349187 TAAACCC
1 TAAACCC
*
3349194 TAAACCA
1 TAAACCC
3349201 TAAACCC
1 TAAACCC
* *
3349208 TAATCTC
1 TAAACCC
3349215 TAAACC
1 TAAACC
3349221 TTTATATTTA
Statistics
Matches: 77, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
6 8 0.10
7 63 0.82
8 2 0.03
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:3349438 original size:14 final size:14
Alignment explanation
Indices: 3349421--3349461 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3349411 TTTATTCATC
3349421 AATAATGTATTTTT
1 AATAATGTATTTTT
3349435 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
3349446 AATAATGTAATTTT
1 AATAATGTATTTTT
3349460 AA
1 AA
3349462 AAAATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:3349468 original size:25 final size:25
Alignment explanation
Indices: 3349421--3349468 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3349411 TTTATTCATC
* * *
3349421 AATAATGTATTTTTAATATATTTTT
1 AATAATGTAATTTTAAAAAATTTTT
3349446 AATAATGTAATTTTAAAAAATTT
1 AATAATGTAATTTTAAAAAATTT
3349469 AAAATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
AATAATGTAATTTTAAAAAATTTTT
Done.