Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2818
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: 118939
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Found at i:15946 original size:21 final size:22
Alignment explanation
Indices: 15889--15946 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
15879 GAATGGTATC
*
15889 TACAAATCAAATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATG
* *
15911 TACAAAATCATATCTCTAGGA-G
1 TAC-AAATCAAATCTCTAAGATG
*
15933 TACATATCAAATCT
1 TACAAATCAAATCT
15947 ACGATTGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 9 0.30
22 6 0.20
23 15 0.50
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATG
Found at i:21076 original size:22 final size:22
Alignment explanation
Indices: 21018--21076 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
21008 GAATGGTATC
21018 TACAAATCAAATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATT
*
21040 TACAAAATCATATCTCCTAAGA-T
1 TAC-AAATCAAATCT-CTAAGATT
*
21063 TACATATCAAATCT
1 TACAAATCAAATCT
21077 ACGATTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 14 0.44
24 6 0.19
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATT
Found at i:21356 original size:43 final size:43
Alignment explanation
Indices: 21246--22222 Score: 769
Period size: 43 Copynumber: 23.1 Consensus size: 43
21236 ACCCATGACA
* * * * **
21246 CTAGTTTGCCGATGGTGTCCGAGGCTCCCACAC-ATCCCAGCAC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGC
* *
21289 CTAGG-GGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
** * *
21331 CTATTTTACCGATGGTGCCCCAGGCTCCCGCACGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
* * * * *
21374 TTAGTTTGCCGATGGTGCTCGAGCCTCTCGCACGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
* * ** **
21417 CTAGGTTACCGATAGTGCGGGAGGCTCCCGCAC-ATCCAAGCAC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGC
* * *
21460 CAAGG-TGCCGATGGTGCTCGAGGCTCCCGCACGACCAACGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
*** * * * **
21502 CTAGGTTGCCGACAATGTCCGAGACTCCCGCAC-ATCATAGCAC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCA-AGGGC
* *
21545 CGAGGTT-CCGATGGTGCCCGAGGCTCCCGTACGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
* * * * **
21587 CTAGTTTGCCGATGGTGTCCGAGGCTCCCGGAC-ATCCCAGCCC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGC
* *
21630 CTAGG-GGCCGATGGTGGCCGAGGCTCCCGCACGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
**
21672 CTATTTTG--GATGGTG-CCGAGGCTCCCGCACGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
* * * *
21712 TTA-G-TGCCGATGGTGCTCGAGCCT-TCGCACGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
* * * *
21752 CTAGGTTACCGATGGTGCGCGAGGTTCCCGCACGACAAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
* * ** * * * **
21795 CTAGGTGGCTGACAGTGTCCGAGGCTCCCGGAC-ATCATAGCAC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCA-AGGGC
*
21838 CGA-GTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
* * * **
21880 CTAGGTTGCCGATGGTGCGCGAGGTTCTCGCAC-ATCCAAGCAC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGC
* * *
21923 CAAGG-TGCTGATGGTGCTCGAGGCTCCCGCACGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
** * * * **
21965 CTAGGTTGCCGACAGTGTCTGAGGCTCCCGCAC-ATCATAGCAC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCA-AGGGC
* * *
22008 CGAGG-TACCGATGGTGCCTGAGGCTCCCGCACGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
* * ***
22050 CTAGGTTGCCGATGGTGTCCGAGGCTCCCGCAC-ATCGAAATAC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGC
* * * * * *
22093 CGAGG-TGCCGATGGCGCCCGAGGATCCTGTATGACCAAGGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
* * * * * * **
22135 TTAGTTTGCCGATGGTGTCCGAGGCTCCTGTAC-ATCCTAGCAC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGC
* * *
22178 CAAGG-TACCGATGGTGCCCGAGGCTCCCGCACGACCAAAGGC
1 CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
22220 CTA
1 CTA
22223 TGCTACCGGA
Statistics
Matches: 720, Mismatches: 183, Indels: 63
0.75 0.19 0.07
Matches are distributed among these distances:
38 2 0.00
40 51 0.07
41 14 0.02
42 299 0.42
43 354 0.49
ACGTcount: A:0.19, C:0.33, G:0.31, T:0.17
Consensus pattern (43 bp):
CTAGGTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
Found at i:21815 original size:208 final size:211
Alignment explanation
Indices: 21246--21997 Score: 589
Period size: 213 Copynumber: 3.5 Consensus size: 211
21236 ACCCATGACA
* * * * *
21246 CTAGTTTGCCGATGGTGTC-CGAGGCTCCCACACATCCCAGCACCTAGGGGCCGATGGTGGC-CG
1 CTAGGTTG-CGATGGTG-CGCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGT-GCTCG
* ** * *
21309 AGGCTCCCGCACGACCAAGGGCCTATTTTACCGATGGTGCCCCAGGCTCCCGCACGACCAAGGGC
63 AGCCTCCCGCACGACCAAGGGCCTAGGTT-CCGATGGTGCCCGAGGCTCCCGCACGACAAAGGGC
* * * ** * * * * ** * ** * **
21374 TTAGTTTGCCGATGGTG-CTCGAGCCTCTCGCACGACCA-AGGGCCTAGGTTACCGATAGTGCGG
127 CTAGGTGGCCGACAGTGTC-CGAGGCTCCCGGAC-ATCACAGCACCGAGG-GGCCGATGGTGCCC
**
21437 GAGGCTCCCGCAC-ATCCAAGCAC
189 GAGGCTCCCGCACGA-CCAAGGGC
* * * * ***
21460 CAAGG-TGCCGATGGTGCTCGAGGCTCCCGCACGA-CCAA-CGGCCTAGGTTGCCGACAATG-TC
1 CTAGGTTG-CGATGGTGCGCGAGGCTCCCGCAC-ATCCAAGC-ACCAAGG-TGCCGATGGTGCT-
* * ** * * *
21521 CGAGACTCCCGCAC-ATCATAGCACCGAGGTTCCGATGGTGCCCGAGGCTCCCGTACGACCAAGG
61 CGAGCCTCCCGCACGACCA-AGGGCCTAGGTTCCGATGGTGCCCGAGGCTCCCGCACGACAAAGG
* * ** * * * *
21585 GCCTAGTTTGCCGATGGTGTCCGAGGCTCCCGGACATCCCAGCCCCTAGGGGCCGATGGTGGCCG
125 GCCTAGGTGGCCGACAGTGTCCGAGGCTCCCGGACATCACAGCACCGAGGGGCCGATGGTGCCCG
21650 AGGCTCCCGCACGACCAAGGGC
190 AGGCTCCCGCACGACCAAGGGC
** ** **
21672 CTATTTTG-GATGGTGC-CGAGGCTCCCGCACGA-CCAAGGGCTTA-GTGCCGATGGTGCTCGAG
1 CTAGGTTGCGATGGTGCGCGAGGCTCCCGCAC-ATCCAAGCACCAAGGTGCCGATGGTGCTCGAG
* * *
21733 CCT-TCGCACGACCAAGGGCCTAGGTTACCGATGGTGCGCGAGGTTCCCGCACGACAAAGGGCCT
65 CCTCCCGCACGACCAAGGGCCTAGGTT-CCGATGGTGCCCGAGGCTCCCGCACGACAAAGGGCCT
* * **
21797 AGGTGGCTGACAGTGTCCGAGGCTCCCGGACATCATAGCACCGAGTTGCCGATGGTGCCCGAGGC
129 AGGTGGCCGACAGTGTCCGAGGCTCCCGGACATCACAGCACCGAGGGGCCGATGGTGCCCGAGGC
21862 TCCCGCACGACCAAGGGC
194 TCCCGCACGACCAAGGGC
* * *
21880 CTAGGTTGCCGATGGTGCGCGAGGTTCTCGCACATCCAAGCACCAAGGTGCTGATGGTGCTCGAG
1 CTAGGTTG-CGATGGTGCGCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAG
* ** * *
21945 GCTCCCGCACGACCAAGGGCCTAGGTTGCCGACAGTGTCTGAGGCTCCCGCAC
65 CCTCCCGCACGACCAAGGGCCTAGGTT-CCGATGGTGCCCGAGGCTCCCGCAC
21998 ATCATAGCAC
Statistics
Matches: 435, Mismatches: 82, Indels: 43
0.78 0.15 0.08
Matches are distributed among these distances:
207 14 0.03
208 127 0.29
209 2 0.00
210 33 0.08
211 27 0.06
212 52 0.12
213 149 0.34
214 31 0.07
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (211 bp):
CTAGGTTGCGATGGTGCGCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGC
CTCCCGCACGACCAAGGGCCTAGGTTCCGATGGTGCCCGAGGCTCCCGCACGACAAAGGGCCTAG
GTGGCCGACAGTGTCCGAGGCTCCCGGACATCACAGCACCGAGGGGCCGATGGTGCCCGAGGCTC
CCGCACGACCAAGGGC
Found at i:22083 original size:85 final size:84
Alignment explanation
Indices: 21254--22222 Score: 633
Period size: 85 Copynumber: 11.5 Consensus size: 84
21244 CACTAGTTTG
* * * ** * *
21254 CCGATGGTGTCCGAGGCTCCCACAC-ATCCCAGCACCTAGG-GGCCGATGGTGGCCGAGGCTCCC
1 CCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTGCCGATGGTGTCCGAGGCTCCC
* ** * **
21317 GCACGACCAAGGGCCTATTTTA
65 GCAC-ATCAAGCACCGA-GGTA
* * * * *
21339 CCGATGGTGCCCCAGGCTCCCGCACGACCAAGGGCTTAGTTTGCCGATGGTG-CTCGAGCCTCTC
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGTC-CGAGGCTCCC
* ** *
21403 GCACGACCAAGGGCCTAGGTTA
65 GCAC-ATCAAGCACCGAGG-TA
* ** ** *
21425 CCGATAGTGCGGGAGGCTCCCGCAC-ATCCAAGCACCAAGG-TGCCGATGGTG-CTCGAGGCTCC
1 CCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTGCCGATGGTGTC-CGAGGCTCC
* * * *
21487 CGCACGACCAA-CGGCCTAGGTTG
64 CGCAC-ATCAAGC-ACCGAGG-TA
*** * * * ** * *
21510 CCGACAATGTCCGAGACTCCCGCAC-ATCATAGCACCGAGGTT-CCGATGGTGCCCGAGGCTCCC
1 CCGATGGTGCCCGAGGCTCCCGCACGACCA-AGGGCCTAGGTTGCCGATGGTGTCCGAGGCTCCC
* * ** * * *
21573 GTACGACCAAGGGCCTAGTTTG
65 GCAC-ATCAAGCACCGAG-GTA
* * * ** * *
21595 CCGATGGTGTCCGAGGCTCCCGGAC-ATCCCAGCCCCTAGG-GGCCGATGGTGGCCGAGGCTCCC
1 CCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTGCCGATGGTGTCCGAGGCTCCC
* ** * * *
21658 GCACGACCAAGGGCCTA-TTT
65 GCAC-ATCAAGCACCGAGGTA
** * * *
21678 TGGATGGTG-CCGAGGCTCCCGCACGACCAAGGGCTTA-G-TGCCGATGGTG-CTCGAGCCT-TC
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGTC-CGAGGCTCCC
* ** *
21738 GCACGACCAAGGGCCTAGGTTA
65 GCAC-ATCAAGCACCGAGG-TA
* * * * * **
21760 CCGATGGTGCGCGAGGTTCCCGCACGACAAAGGGCCTAGGTGGCTGACAGTGTCCGAGGCTCCCG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGTCCGAGGCTCCCG
* * *
21825 GACATCATAGCACCGAGTTG
66 CACATCA-AGCACCGAGGTA
* *
21845 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTG-CGCGAGGTTCTC
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGTC-CGAGGCTCCC
* *
21909 GCACATCCAAGCACCAAGGTG
65 GCACAT-CAAGCACCGAGGTA
* * ** *
21930 CTGATGGTGCTCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGACAGTGTCTGAGGCTCCCG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGTCCGAGGCTCCCG
21995 CACATCATAGCACCGAGGTA
66 CACATCA-AGCACCGAGGTA
*
22015 CCGATGGTGCCTGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGTCCGAGGCTCCCG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGTCCGAGGCTCCCG
** *
22080 CACATCGAAATACCGAGGTG
66 CACATC-AAGCACCGAGGTA
* * * * * * * *
22100 CCGATGGCGCCCGAGGATCCTGTATGACCAAGGGCTTAGTTTGCCGATGGTGTCCGAGGCTCCTG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGTCCGAGGCTCCCG
* * *
22165 TACATCCTAGCACCAAGGTA
66 CACAT-CAAGCACCGAGGTA
*
22185 CCGATGGTGCCCGAGGCTCCCGCACGACCAAAGGCCTA
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTA
22223 TGCTACCGGA
Statistics
Matches: 722, Mismatches: 133, Indels: 58
0.79 0.15 0.06
Matches are distributed among these distances:
80 19 0.03
81 17 0.02
82 29 0.04
83 34 0.05
84 6 0.01
85 531 0.74
86 86 0.12
ACGTcount: A:0.19, C:0.33, G:0.31, T:0.17
Consensus pattern (84 bp):
CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGTCCGAGGCTCCCG
CACATCAAGCACCGAGGTA
Found at i:22260 original size:24 final size:22
Alignment explanation
Indices: 22233--22301 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 22
22223 TGCTACCGGA
22233 ACGGTTCACCGGAGCACCGACGGG
1 ACGGTTC-CCGGAGCACCG-CGGG
*
22257 ACGGTTCGCGGAGCA-C-CGGG
1 ACGGTTCCCGGAGCACCGCGGG
*
22277 ACGGATCGCCGGAGCACCGCCGGG
1 ACGGTTC-CCGGAGCACCG-CGGG
22301 A
1 A
22302 ACCTAACCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 10 0.26
21 7 0.18
22 2 0.05
23 7 0.18
24 12 0.32
ACGTcount: A:0.19, C:0.33, G:0.41, T:0.07
Consensus pattern (22 bp):
ACGGTTCCCGGAGCACCGCGGG
Found at i:22278 original size:20 final size:21
Alignment explanation
Indices: 22253--22295 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
22243 GGAGCACCGA
*
22253 CGGGACGGTTCG-CGGAGCAC
1 CGGGACGGATCGCCGGAGCAC
22273 CGGGACGGATCGCCGGAGCAC
1 CGGGACGGATCGCCGGAGCAC
22294 CG
1 CG
22296 CCGGGAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.16, C:0.33, G:0.44, T:0.07
Consensus pattern (21 bp):
CGGGACGGATCGCCGGAGCAC
Found at i:22581 original size:42 final size:42
Alignment explanation
Indices: 22508--22837 Score: 248
Period size: 42 Copynumber: 7.8 Consensus size: 42
22498 ACTTTAGCTT
* * * *
22508 TGGTGCTCAAGGCTCCCGCTCATCCATGCACCAAGGTGCCGA
1 TGGTTCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
*
22550 TGGTTCTCGAGGCTCCCGTACATCCAAGCACCAAGGTGCCGA
1 TGGTTCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
* * *
22592 TGGTGCTCGAGGCTCCCGCACGA-CCAA-CGGCCTAGGTTGCCGA
1 TGGTTCTCGAGGCTCCCGCAC-ATCCAAGC-ACCAAGG-TGCCGA
** * * *
22635 CAGTGTC-CGAGGCTCTCGCACAT-CATAGCACCGAGGTGCAGA
1 TGGT-TCTCGAGGCTCCCGCACATCCA-AGCACCAAGGTGCCGA
* ** * *
22677 TGG-TCTCTGAGGCTCCC-CACAACCAAGGGCCTAGTTTGCCG-
1 TGGTTCTC-GAGGCTCCCGCACATCCAAGCACCAAG-GTGCCGA
* * *
22718 TGGTGTC-CGATGCTCCCGCACATCCATG-ACCAAGGTGCCGG
1 TGGT-TCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
* * *
22759 TGGTGCTCGAGGCTCCCGCACATCCAAGCATCAAGGTTACCGA
1 TGGTTCTCGAGGCTCCCGCACATCCAAGCACCAAGG-TGCCGA
** *
22802 TGGTGTCT-GAGGCTCCTACACATCCGAGCCACCAAG
1 TGGT-TCTCGAGGCTCCCGCACATCCAAG-CACCAAG
22838 TTGATGGAGG
Statistics
Matches: 226, Mismatches: 42, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
40 8 0.04
41 50 0.22
42 103 0.46
43 55 0.24
44 10 0.04
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.19
Consensus pattern (42 bp):
TGGTTCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
Found at i:22658 original size:85 final size:84
Alignment explanation
Indices: 22557--22785 Score: 286
Period size: 85 Copynumber: 2.7 Consensus size: 84
22547 CGATGGTTCT
* *
22557 CGAGGCTCCCGTACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACGACCAACGG
1 CGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACAACCAACGG
22622 CCTAGGTTGCCGACAGTGTC
66 CCTAGGTTGCCG-CAGTGTC
* * * *
22642 CGAGGCTCTCGCACAT-CATAGCACCGAGGTGCAGATGGT-CTCTGAGGCTCCC-CACAACCAAG
1 CGAGGCTCCCGCACATCCA-AGCACCAAGGTGCCGATGGTGCTC-GAGGCTCCCGCACAACCAAC
* **
22704 GGCCTAGTTTGCCGTGGTGTC
64 GGCCTAGGTTGCCGCAGTGTC
* * * *
22725 CGATGCTCCCGCACATCCATG-ACCAAGGTGCCGGTGGTGCTCGAGGCTCCCGCACATCCAA
1 CGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACAACCAA
22786 GCATCAAGGT
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
82 23 0.19
83 31 0.25
84 28 0.23
85 41 0.33
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.17
Consensus pattern (84 bp):
CGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACAACCAACGG
CCTAGGTTGCCGCAGTGTC
Found at i:22824 original size:84 final size:85
Alignment explanation
Indices: 22508--22826 Score: 314
Period size: 84 Copynumber: 3.8 Consensus size: 85
22498 ACTTTAGCTT
* * * *
22508 TGGTGCTCAAGGCTCCCGCTCATCCATGCACCAAGG-TGCCGATGGT-TCTCGAGGCTCCCGTAC
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTTGCCGATGGTGTC-CGAGGCTCCCGCAC
*
22571 ATCCAAGCACCAAGGTGCCGA
65 ATCCATGCACCAAGGTGCCGA
* * ** *
22592 TGGTGCTCGAGGCTCCCGCACGA-CCAA-CGGCCTAGGTTGCCGACAGTGTCCGAGGCTCTCGCA
1 TGGTGCTCGAGGCTCCCGCAC-ATCCAAGC-ACCAAGGTTGCCGATGGTGTCCGAGGCTCCCGCA
* *
22655 CAT-CATAGCACCGAGGTGCAGA
64 CATCCAT-GCACCAAGGTGCCGA
* ** * * *
22677 TGGT-CTCTGAGGCTCCC-CACAACCAAGGGCCTAGTTTGCCG-TGGTGTCCGATGCTCCCGCAC
1 TGGTGCTC-GAGGCTCCCGCACATCCAAGCACCAAGGTTGCCGATGGTGTCCGAGGCTCCCGCAC
*
22739 ATCCATG-ACCAAGGTGCCGG
65 ATCCATGCACCAAGGTGCCGA
* * * **
22759 TGGTGCTCGAGGCTCCCGCACATCCAAGCATCAAGGTTACCGATGGTGTCTGAGGCTCCTACACA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTTGCCGATGGTGTCCGAGGCTCCCGCACA
22824 TCC
66 TCC
22827 GAGCCACCAA
Statistics
Matches: 191, Mismatches: 32, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
82 23 0.12
83 42 0.22
84 75 0.39
85 49 0.26
86 2 0.01
ACGTcount: A:0.19, C:0.34, G:0.28, T:0.19
Consensus pattern (85 bp):
TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTTGCCGATGGTGTCCGAGGCTCCCGCACA
TCCATGCACCAAGGTGCCGA
Found at i:30824 original size:85 final size:84
Alignment explanation
Indices: 30649--31319 Score: 428
Period size: 85 Copynumber: 7.9 Consensus size: 84
30639 CCAGGCACCA
* * * * *
30649 AGGTGCCGATGGGTGCCCGAGGCTCCTGTACATCCAAGCACCAAGTTGCCGATAGTGTCCGAGGC
1 AGGTGCCGAT-GGTGCCCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGTGCCCGAGGC
** * *
30714 TCCCGCACCTCCTAGTCACCG
65 TCCCGCACGACCAAG-GACCG
*
30735 AGGTGCCGATGCTGCCCGAGGCTCCCGCACATCCAAGCCACCAAGGTGCCGATGGTGCCCGAGGC
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACATCCAAG-CACCAAGGTGCCGATGGTGCCCGAGGC
*
30800 TCCCGCACGACCAAGGGCCG
65 TCCCGCACGACCAAGGACCG
* * ** ***
30820 AGGTGCCGATGGTGGCCGAGGC-CCCGCATGA-CCAAGGGCCTATTTTGCCGATGGTGCCCGAGG
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCA-CATCCAAGCACC-AAGGTGCCGATGGTGCCCGAGG
* **
30883 CTCCCGCACGACCAAGGGCTT
64 CTCCCGCACGACCAAGGACCG
* * * * * * *** * *
30904 AGTTTGCCAATAGTGTCCGAGCCTCTCGCACGA-CCAAGGGTCTAGGCTGCCGATGGTGCGCGAG
1 AG-GTGCCGATGGTGCCCGAGGCTCCCGCAC-ATCCAAGCACCAAGG-TGCCGATGGTGCCCGAG
* ** * *
30968 GTTTTCGCA-AATCC-AGGCACCA
63 GCTCCCGCACGA-CCAAGG-ACCG
* * ** * * ** *
30990 AGGTGCCGATGGTACTCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTTCCGACAGTGTCCGAGG
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCAC-ATCCAAGCACCAAGG-TGCCGATGGTGCCCGAGG
* *
31054 CTCCCGCAC-ATCATAGCACCG
64 CTCCCGCACGACCA-AGGACCG
** *
31075 AGGTGCCGATGGTGCCCGAGGCT-CC-CACATGACCAAGGGCCTAGGTTG-CGATGGTGCCCGAG
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACAT--CCAAGCACCAAGG-TGCCGATGGTGCCCGAG
* *
31137 GCTCCCGCAC-ATCGAAGCACCG
63 GCTCCCGCACGA-CCAAGGACCG
** * * * * **
31159 AAATGCCGATGGCGCCCGAGGGTCCCGCACATCGAAGCACCGAGGTGCCGATGACGCCCGAGGCT
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCT
* * * **
31224 CCTGCATGACCAAGGGCTT
66 CCCGCACGACCAAGGACCG
* * * ** * * * *
31243 AGTTTGCCGATGGTGTCCGGGGCTCCTACACATCCTAGCACCGAGTTGTCGATGGTGCCCGAGGC
1 AG-GTGCCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGTGCCCGAGGC
31308 TCCCGCACGACC
65 TCCCGCACGACC
31320 TAGGGCCTAT
Statistics
Matches: 461, Mismatches: 103, Indels: 43
0.76 0.17 0.07
Matches are distributed among these distances:
82 1 0.00
83 7 0.02
84 137 0.30
85 222 0.48
86 94 0.20
ACGTcount: A:0.19, C:0.34, G:0.31, T:0.16
Consensus pattern (84 bp):
AGGTGCCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCT
CCCGCACGACCAAGGACCG
Found at i:30839 original size:42 final size:42
Alignment explanation
Indices: 30649--31319 Score: 426
Period size: 42 Copynumber: 15.8 Consensus size: 42
30639 CCAGGCACCA
* * * *
30649 AGGTGCCGATGGGTGCCCGAGGCTCCTGTAC-ATCCAAGCACCA
1 AGGTGCCGAT-GGTGCCCGAGGCTCCCGCACGA-CCAAGGACCG
* * * ** * *
30692 AGTTGCCGATAGTGTCCGAGGCTCCCGCACCTCCTAGTCACCG
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAG-GACCG
* * *
30735 AGGTGCCGATGCTGCCCGAGGCTCCCGCAC-ATCCAAGCCACCA
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAG-GACCG
*
30778 AGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCG
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGACCG
* * * *
30820 AGGTGCCGATGGTGGCCGAGGC-CCCGCATGACCAAGGGCCT
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGACCG
** * **
30861 ATTTTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTT
1 A-GGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGACCG
* * * * * * ** *
30904 AGTTTGCCAATAGTGTCCGAGCCTCTCGCACGACCAAGGGTCT
1 AG-GTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGACCG
* * ** * *
30947 AGGCTGCCGATGGTGCGCGAGGTTTTCGCA-AATCC-AGGCACCA
1 AGG-TGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGG-ACCG
* * * *
30990 AGGTGCCGATGGTACTCGAGGCTCCCGCACGACCAAGGGCCT
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGACCG
* ** * * *
31032 AGGTTTCCGACAGTGTCCGAGGCTCCCGCAC-ATCATAGCACCG
1 AGG-TGCCGATGGTGCCCGAGGCTCCCGCACGACCA-AGGACCG
* * * *
31075 AGGTGCCGATGGTGCCCGAGGCTCCCACATGACCAAGGGCCT
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGACCG
* *
31117 AGGTTG-CGATGGTGCCCGAGGCTCCCGCAC-ATCGAAGCACCG
1 AGG-TGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGACCG
** * * * *
31159 AAATGCCGATGGCGCCCGAGGGTCCCGCAC-ATCGAAGCACCG
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGACCG
** * * * **
31201 AGGTGCCGATGACGCCCGAGGCTCCTGCATGACCAAGGGCTT
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGACCG
* * * ** * *
31243 AGTTTGCCGATGGTGTCCGGGGCTCCTACAC-ATCCTAGCACCG
1 AG-GTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGACCG
* *
31286 AGTTGTCGATGGTGCCCGAGGCTCCCGCACGACC
1 AGGTGCCGATGGTGCCCGAGGCTCCCGCACGACC
31320 TAGGGCCTAT
Statistics
Matches: 492, Mismatches: 114, Indels: 45
0.76 0.18 0.07
Matches are distributed among these distances:
41 21 0.04
42 244 0.50
43 226 0.46
44 1 0.00
ACGTcount: A:0.19, C:0.34, G:0.31, T:0.16
Consensus pattern (42 bp):
AGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGACCG
Found at i:30898 original size:127 final size:127
Alignment explanation
Indices: 30629--31326 Score: 520
Period size: 127 Copynumber: 5.5 Consensus size: 127
30619 TCTTCTTTAG
* * * ** *
30629 CCCGCACATCCCAGGCACCAAGGTGCCGATGGGTGCCCGAGGCTCCTGTAC-ATCCAAGCACCAA
1 CCCGCACAT-CCAAGCACCAAGGTGCCGAT-GGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCGA
* * * *** * ** * *
30693 GTTGCCGATAGTGTCCGAGGCTCCCGCACCTCCTAGTCACCGAGG-TGCCGATGCTGCCCGAGGC
63 GGTGCCGATGGTGCCCGAGGCTCCCGCATGACCAAG-GGCCTAGGTTGCCGATGGTGCCCGAGGC
30757 T
127 T
30758 CCCGCACATCCAAGCCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCGAGG
1 CCCGCACATCCAAG-CACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCGAGG
* **
30823 TGCCGATGGTGGCCGAGGC-CCCGCATGACCAAGGGCCTATTTTGCCGATGGTGCCCGAGGCT
65 TGCCGATGGTGCCCGAGGCTCCCGCATGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCT
** ** * * * * * * * *
30885 CCCGCACGA-CCAAGGGCTTAGTTTGCCAATAGTGTCCGAGCCTCTCGCACGACCAAGGGTCTAG
1 CCCGCAC-ATCCAAGCACCAAG-GTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCGAG
* * ** * * * * *
30949 GCTGCCGATGGTGCGCGAGGTTTTCGCA-AATCC-AGGCACCAAGG-TGCCGATGGTACTCGAGG
64 G-TGCCGATGGTGCCCGAGGCTCCCGCATGA-CCAAGG-GCCTAGGTTGCCGATGGTGCCCGAGG
31011 CT
126 CT
** * * ** * * **
31013 CCCGCACGA-CCAAGGGCCTAGGTTTCCGACAGTGTCCGAGGCTCCCGCAC-ATCATAGCACCGA
1 CCCGCAC-ATCCAAGCACCAAGG-TGCCGATGGTGCCCGAGGCTCCCGCACGACCA-AGGGCCGA
*
31076 GGTGCCGATGGTGCCCGAGGCTCCCACATGACCAAGGGCCTAGGTTG-CGATGGTGCCCGAGGCT
63 GGTGCCGATGGTGCCCGAGGCTCCCGCATGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCT
* * * * * **
31140 CCCGCACATCGAAGCACCGAA-ATGCCGATGGCGCCCGAGGGTCCCGCAC-ATCGAAGCACCGAG
1 CCCGCACATCCAAGCACC-AAGGTGCCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCGAG
** * * * * *
31203 GTGCCGATGACGCCCGAGGCTCCTGCATGACCAAGGGCTTAGTTTGCCGATGGTGTCCGGGGCT
64 GTGCCGATGGTGCCCGAGGCTCCCGCATGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCT
** * * * * *
31267 CCTACACATCCTAGCACCGAGTTGTCGATGGTGCCCGAGGCTCCCGCACGACCTAGGGCC
1 CCCGCACATCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCC
31327 TATGCTACCA
Statistics
Matches: 450, Mismatches: 99, Indels: 42
0.76 0.17 0.07
Matches are distributed among these distances:
126 79 0.18
127 194 0.43
128 143 0.32
129 34 0.08
ACGTcount: A:0.19, C:0.34, G:0.31, T:0.16
Consensus pattern (127 bp):
CCCGCACATCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCGAGGT
GCCGATGGTGCCCGAGGCTCCCGCATGACCAAGGGCCTAGGTTGCCGATGGTGCCCGAGGCT
Found at i:31401 original size:24 final size:24
Alignment explanation
Indices: 31339--31411 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
31329 TGCTACCAGA
*
31339 ACGGTTCGCCGGAGCACCGACGGG
1 ACGGTTCGCCGGAGCACCGCCGGG
* *
31363 ACGGTTCACCAGAGCACCGCCGGG
1 ACGGTTCGCCGGAGCACCGCCGGG
* * *
31387 ACGGATCGCTGGAGCACCACCGGG
1 ACGGTTCGCCGGAGCACCGCCGGG
31411 A
1 A
31412 ACCTAACCGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.34, G:0.37, T:0.08
Consensus pattern (24 bp):
ACGGTTCGCCGGAGCACCGCCGGG
Found at i:36743 original size:14 final size:14
Alignment explanation
Indices: 36724--36751 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36714 AACTGCGCTA
36724 CTACCAGGTGACAT
1 CTACCAGGTGACAT
36738 CTACCAGGTGACAT
1 CTACCAGGTGACAT
36752 TCATGTGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (14 bp):
CTACCAGGTGACAT
Found at i:36871 original size:42 final size:42
Alignment explanation
Indices: 36822--37156 Score: 351
Period size: 42 Copynumber: 7.9 Consensus size: 42
36812 ACTTTAGCTT
* * *
36822 TGGTGCTCAAGGCTCCCGCTCATCCATGCACCAAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
36864 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
** *
36906 TGGTGCTCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTGCCGA
1 TGGTGCTCGAGGCTCCCGCAC-ATCCAAGCACCAAGG-TGCCGA
* * *
36949 TAGTG-TCCGAGCCTCCCGTACAT-CATAGCACCAAGGTGCCGA
1 TGGTGCT-CGAGGCTCCCGCACATCCA-AGCACCAAGGTGCCGA
* ** * *
36991 TGGT-CTCCGAGGCTCCC-CACAACCAAGGGCCTAGTTTGCCGA
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAG-GTGCCGA
* *
37033 TGGTG-TCCGATGCTCCCGCACATCCATGCACCAAGGTGCCGA
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
* *
37075 TGGTGCTCGAGGCTCCCGCACATCCAAGCATCAAGGTTACCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGG-TGCCGA
* *
37118 TGGTGGCT-GAGGCTCCCACACATCCGAGCCACCAAGGTG
1 TGGT-GCTCGAGGCTCCCGCACATCCAAG-CACCAAGGTG
37157 ATGGAGGCTC
Statistics
Matches: 244, Mismatches: 35, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
41 9 0.04
42 154 0.63
43 71 0.29
44 10 0.04
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.18
Consensus pattern (42 bp):
TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
Found at i:47268 original size:39 final size:39
Alignment explanation
Indices: 47225--47443 Score: 271
Period size: 39 Copynumber: 5.6 Consensus size: 39
47215 ATACAACCTA
* *
47225 CTAGGCATATAGCCCGAATAATCACCGGCACAGAGCCTG
1 CTAGGCACATAGCCCGAATAATCACCGGCACACAGCCTG
* * * *
47264 CTAGGCACAAAGCCCGAATAATTACCGACACACTA-CTTG
1 CTAGGCACATAGCCCGAATAATCACCGGCACAC-AGCCTG
* *
47303 CTAGGCACATAGCCTGAATAATCACTGGCACACAGCCTG
1 CTAGGCACATAGCCCGAATAATCACCGGCACACAGCCTG
*
47342 CTAGGCACAT-GCCTCGAATAATCAACGGCACACAGCCTG
1 CTAGGCACATAGCC-CGAATAATCACCGGCACACAGCCTG
* * * *
47381 CTAGGCACATAGCCCAAATAATTACCGGCACACAACTTG
1 CTAGGCACATAGCCCGAATAATCACCGGCACACAGCCTG
* *
47420 CTAAGCACATAGCTCGAATAATCA
1 CTAGGCACATAGCCCGAATAATCA
47444 TTATATTTCT
Statistics
Matches: 152, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
38 4 0.03
39 144 0.95
40 4 0.03
ACGTcount: A:0.34, C:0.31, G:0.18, T:0.17
Consensus pattern (39 bp):
CTAGGCACATAGCCCGAATAATCACCGGCACACAGCCTG
Found at i:47431 original size:117 final size:117
Alignment explanation
Indices: 47225--47443 Score: 334
Period size: 117 Copynumber: 1.9 Consensus size: 117
47215 ATACAACCTA
* * * *
47225 CTAGGCATATAGCCCGAATAATCACCGGCACAGAGCCTGCTAGGCACAAAGCCCGAATAATTACC
1 CTAGGCACATAGCCCGAATAATCAACGGCACACAGCCTGCTAGGCACAAAGCCCAAATAATTACC
* *
47290 GACACACTACTTGCTAGGCACATAGC-CTGAATAATCACTGGCACACAGCCTG
66 GACACACAACTTGCTAAGCACATAGCTC-GAATAATCACTGGCACACAGCCTG
*
47342 CTAGGCACAT-GCCTCGAATAATCAACGGCACACAGCCTGCTAGGCACATAGCCCAAATAATTAC
1 CTAGGCACATAGCC-CGAATAATCAACGGCACACAGCCTGCTAGGCACAAAGCCCAAATAATTAC
*
47406 CGGCACACAACTTGCTAAGCACATAGCTCGAATAATCA
65 CGACACACAACTTGCTAAGCACATAGCTCGAATAATCA
47444 TTATATTTCT
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
116 3 0.03
117 88 0.96
118 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.18, T:0.17
Consensus pattern (117 bp):
CTAGGCACATAGCCCGAATAATCAACGGCACACAGCCTGCTAGGCACAAAGCCCAAATAATTACC
GACACACAACTTGCTAAGCACATAGCTCGAATAATCACTGGCACACAGCCTG
Found at i:60443 original size:21 final size:21
Alignment explanation
Indices: 60417--60457 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
60407 AGACGAGCAA
* *
60417 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
60438 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
60458 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:78473 original size:35 final size:35
Alignment explanation
Indices: 78405--78496 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 35
78395 GATATTTTAG
* * * *
78405 TTCGCATGTTAAGTATGTCACTATATTGTTTCTGG
1 TTCGCATGTTAAGCATGCCACTATATTGATTCTGA
*
78440 TTTGCATGTTAAGCATGCCACTATACTT-ATTCTGA
1 TTCGCATGTTAAGCATGCCACTATA-TTGATTCTGA
* *
78475 TTCGCATGTAAAACATGCCACT
1 TTCGCATGTTAAGCATGCCACT
78497 GTGTTAAATC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 46 0.96
36 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (35 bp):
TTCGCATGTTAAGCATGCCACTATATTGATTCTGA
Found at i:94993 original size:26 final size:27
Alignment explanation
Indices: 94919--94996 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
94909 TGTTATGACT
*
94919 GAAATACCCCCATAGGGTAAAATGATC
1 GAAATACCCTCATAGGGTAAAATGATC
*
94946 GAAATACCCTCATAGGGTAAAATGATT
1 GAAATACCCTCATAGGGTAAAATGATC
*
94973 GAATTACCCT-ATAGGGTAAAATGA
1 GAAATACCCTCATAGGGTAAAATGA
94997 CTATTATACC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 14 0.29
27 34 0.71
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (27 bp):
GAAATACCCTCATAGGGTAAAATGATC
Found at i:95006 original size:26 final size:26
Alignment explanation
Indices: 94913--95006 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 26
94903 TTACACTGTT
* *
94913 ATGACTGAAATACCCCCATAGGGTAAA
1 ATGACT-ATATACCCTCATAGGGTAAA
* *
94940 ATGATCGAAATACCCTCATAGGGTAAA
1 ATGA-CTATATACCCTCATAGGGTAAA
*
94967 ATGATTGA-ATTACCCT-ATAGGGTAAA
1 ATGACT-ATA-TACCCTCATAGGGTAAA
94993 ATGACTATTATACC
1 ATGACTA-TATACC
95007 TCTAGGAGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
25 1 0.02
26 20 0.35
27 35 0.61
28 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (26 bp):
ATGACTATATACCCTCATAGGGTAAA
Found at i:97913 original size:20 final size:20
Alignment explanation
Indices: 97885--97933 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
97875 GAGTATAGAG
* * *
97885 GTATCGATAATTGGGCGCAA
1 GTATTGATAATTCGGAGCAA
* *
97905 GTATTGATACTTCTGAGCAA
1 GTATTGATAATTCGGAGCAA
97925 GTATTGATA
1 GTATTGATA
97934 CTTCTGAGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (20 bp):
GTATTGATAATTCGGAGCAA
Found at i:97934 original size:20 final size:20
Alignment explanation
Indices: 97901--97942 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
97891 ATAATTGGGC
97901 GCAAGTATTGATACTTCTGA
1 GCAAGTATTGATACTTCTGA
97921 GCAAGTATTGATACTTCTGA
1 GCAAGTATTGATACTTCTGA
97941 GC
1 GC
97943 TAATTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (20 bp):
GCAAGTATTGATACTTCTGA
Found at i:101911 original size:606 final size:606
Alignment explanation
Indices: 100752--102575 Score: 3531
Period size: 606 Copynumber: 3.0 Consensus size: 606
100742 ATCATTAAGG
*
100752 CACGCAACATCCTTGTTGCCATTGAGCATATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
1 CACGCAACATCCTTGTTGCCATTGAGCACATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
100817 GGCCCAGTGCTTTTTGAAGAAGCAACCTGATAAACCATCAGCTTTTCGCTGGTCCATATGGTTAA
66 GGCCCAGTGCTTTTTGAAGAAGCAACCTGATAAACCATCAGCTTTTCGCTGGTCCATATGGTTAA
100882 AAGCAGCAACAATTTCTTCATCAGTAAAGTCCCTGTCCAAGCAAGAGTTCATATTGTCAGTAATG
131 AAGCAGCAACAATTTCTTCATCAGTAAAGTCCCTGTCCAAGCAAGAGTTCATATTGTCAGTAATG
100947 CACGTTTGGATATAATGCATGTCAGGTTCATTACAAGAAACAATGGTTGACTTAAAAAGATCATT
196 CACGTTTGGATATAATGCATGTCAGGTTCATTACAAGAAACAATGGTTGACTTAAAAAGATCATT
*
101012 AAAATAGTCCCATGCAATTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCATTAGAATCTT
261 AAAATAGTCCCATGCAACTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCATTAGAATCTT
* *
101077 TTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCAAGTGAAAATAACCGGTGTTTC
326 TTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAACGGGTGTTTC
* *
101142 TATCACTCTCCGTGAGCCAATTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCCACAGCATAC
391 TATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCCACAGCATAC
101207 AAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTTTGGACCATC
456 AAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTTTGGACCATC
*
101272 CACAAGCTGATTGATCTTCCTTTTCAGACCCCATATTTGGTTCATCATTCTTTTATAACGCTTAT
521 CACAAGCTGATTGATCTTCCTCTTCAGACCCCATATTTGGTTCATCATTCTTTTATAACGCTTAT
*
101337 ACTACCATAACTCAAGCTAAT
586 ACTACCACAACTCAAGCTAAT
*
101358 CACGCAACATCCTTGTTGCCATTGAGCACACCGTGACACAACTTTAAGACATCTTTTCCAACTAC
1 CACGCAACATCCTTGTTGCCATTGAGCACATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
101423 GGCCCAGTGCTTTTTGAAGAAGCAACCTGATAAACCATCAGCTTTTCGCTGGTCCATATGGTTAA
66 GGCCCAGTGCTTTTTGAAGAAGCAACCTGATAAACCATCAGCTTTTCGCTGGTCCATATGGTTAA
101488 AAGCAGCAACAATTTCTTCATCAGTAAAGTCCCTGTCCAAGCAAGAGTTCATATTGTCAGTAATG
131 AAGCAGCAACAATTTCTTCATCAGTAAAGTCCCTGTCCAAGCAAGAGTTCATATTGTCAGTAATG
101553 CACGTTTGGATATAATGCATGTCAGGTTCATTACAAGAAACAATGGTTGACTTAAAAAGATCATT
196 CACGTTTGGATATAATGCATGTCAGGTTCATTACAAGAAACAATGGTTGACTTAAAAAGATCATT
101618 AAAATAGTCCCATGCAACTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCATTAGAATCTT
261 AAAATAGTCCCATGCAACTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCATTAGAATCTT
101683 TTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAACGGGTGTTTC
326 TTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAACGGGTGTTTC
101748 TATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCCACAGCATAC
391 TATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCCACAGCATAC
101813 AAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTTTGGACCATC
456 AAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTTTGGACCATC
*
101878 CACAAGCTGATTGATCTTCCTCTTCAAACCCCATATTTGGTTCATCATTCTTTTATAACGCTTAT
521 CACAAGCTGATTGATCTTCCTCTTCAGACCCCATATTTGGTTCATCATTCTTTTATAACGCTTAT
101943 ACTACCACAACTCAAGCTAAT
586 ACTACCACAACTCAAGCTAAT
101964 CACGCAACATCCTTGTTGCCATTGAGCACATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
1 CACGCAACATCCTTGTTGCCATTGAGCACATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
102029 GGCCCAGTGCTTTTTGAAGAAGCAACCTGATAAACCATCAGCTTTTCGCTGGTCCATATGGTTAA
66 GGCCCAGTGCTTTTTGAAGAAGCAACCTGATAAACCATCAGCTTTTCGCTGGTCCATATGGTTAA
*
102094 AAGCAGCAACAATTTCTTCATCAATAAAGTCCCTGTCCAAGCAAGAGTTCATATTGTCAGTAATG
131 AAGCAGCAACAATTTCTTCATCAGTAAAGTCCCTGTCCAAGCAAGAGTTCATATTGTCAGTAATG
102159 CACGTTTGGATATAATGCATGTCAGGTTCATTACAAGAAACAATGGTTGACTTAAAAAGATCATT
196 CACGTTTGGATATAATGCATGTCAGGTTCATTACAAGAAACAATGGTTGACTTAAAAAGATCATT
*
102224 AAAATAGTCCCATGCAACTTTAAAGATGTCCCTCTTGTCTTTTTGCCACGTCCCATTAGAATCTT
261 AAAATAGTCCCATGCAACTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCATTAGAATCTT
102289 TTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAACGGGTGTTTC
326 TTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAACGGGTGTTTC
102354 TATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCCACAGCATAC
391 TATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCCACAGCATAC
*
102419 AAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTATTTGGACCATC
456 AAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTTTGGACCATC
102484 CACAAGCTGATTGATCTTCCTCTTCAGACCCCATATTTGGTTCATCATTCTTTTATAACGCTTAT
521 CACAAGCTGATTGATCTTCCTCTTCAGACCCCATATTTGGTTCATCATTCTTTTATAACGCTTAT
102549 ACTACCACAACTCAAGCTAAT
586 ACTACCACAACTCAAGCTAAT
102570 CACGCA
1 CACGCA
102576 CCTTATCCAT
Statistics
Matches: 1203, Mismatches: 15, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
606 1203 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (606 bp):
CACGCAACATCCTTGTTGCCATTGAGCACATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
GGCCCAGTGCTTTTTGAAGAAGCAACCTGATAAACCATCAGCTTTTCGCTGGTCCATATGGTTAA
AAGCAGCAACAATTTCTTCATCAGTAAAGTCCCTGTCCAAGCAAGAGTTCATATTGTCAGTAATG
CACGTTTGGATATAATGCATGTCAGGTTCATTACAAGAAACAATGGTTGACTTAAAAAGATCATT
AAAATAGTCCCATGCAACTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCATTAGAATCTT
TTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAACGGGTGTTTC
TATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCCACAGCATAC
AAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTTTGGACCATC
CACAAGCTGATTGATCTTCCTCTTCAGACCCCATATTTGGTTCATCATTCTTTTATAACGCTTAT
ACTACCACAACTCAAGCTAAT
Found at i:113238 original size:19 final size:19
Alignment explanation
Indices: 113214--113250 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
113204 TCAATATTTG
*
113214 GCTAGCTTATTTCTAAGTA
1 GCTAGCATATTTCTAAGTA
113233 GCTAGCATATTTCTAAGT
1 GCTAGCATATTTCTAAGT
113251 GCATGGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (19 bp):
GCTAGCATATTTCTAAGTA
Found at i:114045 original size:25 final size:25
Alignment explanation
Indices: 113979--114032 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
113969 TCATTAGGGT
* * *
113979 TACCGATTTATAGCTCGTAAGAGCA
1 TACCAATTCATAGCTCATAAGAGCA
114004 TACCAATTCATAGCTCATAAGAGCA
1 TACCAATTCATAGCTCATAAGAGCA
114029 TACC
1 TACC
114033 GATCTTCAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (25 bp):
TACCAATTCATAGCTCATAAGAGCA
Done.