Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011155.1 Kokia drynarioides strain JFW-HI SEQ_126129, 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: 337589
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 49 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:149053 original size:41 final size:41
Alignment explanation
Indices: 149003--149102 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
148993 GCTGCTATTA
149003 CTCTGACCTTTAGCGGTGCTTTCCCACAAGCATCGCTAATG
1 CTCTGACCTTTAGCGGTGCTTTCCCACAAGCATCGCTAATG
* * * * *
149044 CTCTTACCTTTAACGGCGCTTTCCCATAAGCGTCGCTAATG
1 CTCTGACCTTTAGCGGTGCTTTCCCACAAGCATCGCTAATG
149085 CTCTGACCTTTAGCGGTG
1 CTCTGACCTTTAGCGGTG
149103 TTTATGAGGA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.31, G:0.20, T:0.31
Consensus pattern (41 bp):
CTCTGACCTTTAGCGGTGCTTTCCCACAAGCATCGCTAATG
Found at i:149116 original size:41 final size:40
Alignment explanation
Indices: 149071--149148 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
149061 GCTTTCCCAT
* *
149071 AAGCGTCGCTAATGCTCTGACCTTTAGCGGTGTTTATGAGG
1 AAGCGCCGCTAATACT-TGACCTTTAGCGGTGTTTATGAGG
* * *
149112 AAGCGCCGCTATTACTTTACCTTTTGCGGTGTTTATG
1 AAGCGCCGCTAATACTTGACCTTTAGCGGTGTTTATG
149149 GAAAAACGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 19 0.59
41 13 0.41
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (40 bp):
AAGCGCCGCTAATACTTGACCTTTAGCGGTGTTTATGAGG
Found at i:149170 original size:40 final size:40
Alignment explanation
Indices: 149090--149177 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
149080 TAATGCTCTG
* * *
149090 ACCTTTAGCGGTGTTTATGAGGAAGCGCCGCTATTACTTT
1 ACCTTTTGCGGTGTTTATGAGAAAACGCCGCTATTACTTT
* * *
149130 ACCTTTTGCGGTGTTTATG-GAAAAACGTCGTTATTGCTTT
1 ACCTTTTGCGGTGTTTATGAG-AAAACGCCGCTATTACTTT
149170 ACCTTTTG
1 ACCTTTTG
149178 TGATGTTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.02
40 40 0.98
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (40 bp):
ACCTTTTGCGGTGTTTATGAGAAAACGCCGCTATTACTTT
Found at i:151124 original size:24 final size:24
Alignment explanation
Indices: 151092--151159 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
151082 ACACTTCTGC
151092 GCCAATAGAGAATTGTTCACCTGT
1 GCCAATAGAGAATTGTTCACCTGT
*
151116 GCCAATAGAGAATTGTTCATCTGT
1 GCCAATAGAGAATTGTTCACCTGT
* *
151140 ACCAATAGAGAAATGTTCAC
1 GCCAATAGAGAATTGTTCAC
151160 TGAGTTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (24 bp):
GCCAATAGAGAATTGTTCACCTGT
Found at i:153659 original size:94 final size:94
Alignment explanation
Indices: 153501--153816 Score: 424
Period size: 94 Copynumber: 3.4 Consensus size: 94
153491 CAAATTCTCG
* * * *
153501 TCAGCTTAGTGTGAGCAACATCGT-TA-AGG-AACAATTATATGTACAAATACCATATCGATGGC
1 TCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACCGTATCGATGGC
* *
153563 TGAGGTACCGTATATGTTGCGAGTCCTCA
66 TGAGGTACCGCATATGTTACGAGTCCTCA
* * *
153592 TCAGCTTAGAT-TGAGCAGCATTGTATACCGGTAACAATTACATGTACAGATACCGTATCGATGG
1 TCAGCTTAG-TGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACCGTATCGATGG
**
153656 CTGAGGTACCGCATATGTTACGAGTCCTTG
65 CTGAGGTACCGCATATGTTACGAGTCCTCA
* * * * * *
153686 TTAGCTTAGTGTGAGCAACATCGTATACTAGTAACAGTTATATGTAAAGATACCGTATTGATGGC
1 TCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACCGTATCGATGGC
*
153751 TGAGGTACCGCATATGTTACGAGCCCTCA
66 TGAGGTACCGCATATGTTACGAGTCCTCA
*
153780 TCAGTTTAGTGTGAGCAGCATCGTATACTGGTAACAA
1 TCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAA
153817 AGATAATTTT
Statistics
Matches: 193, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
91 20 0.10
92 3 0.02
93 3 0.02
94 167 0.87
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (94 bp):
TCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACCGTATCGATGGC
TGAGGTACCGCATATGTTACGAGTCCTCA
Found at i:154590 original size:21 final size:21
Alignment explanation
Indices: 154566--154614 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
154556 CTAGAGTTTG
154566 TTGTATCGGTAGAAGTAATAA
1 TTGTATCGGTAGAAGTAATAA
* *
154587 TTGTATCGGTAGAAGTCATAC
1 TTGTATCGGTAGAAGTAATAA
154608 TTGTATC
1 TTGTATC
154615 AGTAAAACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTAATAA
Found at i:160609 original size:28 final size:28
Alignment explanation
Indices: 160578--160639 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
160568 AAAATTTGAT
* *
160578 TTTTGGATAATCGAGAG-TAAAATGGTAA
1 TTTTGGACAATCG-GAGCCAAAATGGTAA
* *
160606 TTTTGGACACTCGGGGCCAAAATGGTAA
1 TTTTGGACAATCGGAGCCAAAATGGTAA
160634 TTTTGG
1 TTTTGG
160640 GAAAGTTCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.32
Consensus pattern (28 bp):
TTTTGGACAATCGGAGCCAAAATGGTAA
Found at i:160754 original size:59 final size:59
Alignment explanation
Indices: 160682--161006 Score: 220
Period size: 60 Copynumber: 5.5 Consensus size: 59
160672 AGTTTAGGGG
* * *
160682 TAAAAAAGTAATTTTTGAAAAGTTTAGGGGTTAAATGGTAGTTTTTGGTAAAATCGAGGT
1 TAAAATAG-AATTTTTGAAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGT
* * * * *
160742 TAAAATAGAATTTTT-TAAA-TTTTGAGGGTAAAATGGTAATTTTTAGTGAAATCGGGGT
1 TAAAATAGAATTTTTGAAAAGTTTAG-GGGTAAAATGGTAATTTTTGGTAAAATCGAGGT
* * * * * * *
160800 TAAAAATGGAA-TTTTGGAAAGTTAGAGGGGTAAAATGGTAATTTTTGATGAAATTGGGGT
1 T-AAAATAGAATTTTTGAAAAGTT-TAGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGT
* * * *
160860 TAAAAAATTGGAA-TTTTGGAAAGTTT-GGGGTAAAATGATAA-TTTTGGCAAAATC-AGGGTT
1 T--AAAA-TAGAATTTTTGAAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCGA-GG-T
* * * * * *
160920 TAAAATAGAATTTTAG-AAAGTTCATGGGTAAAAAT-GTAATTTTTAG-AAAGTTTGAGGGT
1 TAAAATAGAATTTTTGAAAAGTTTAGGGGT-AAAATGGTAATTTTTGGTAAA-ATCGA-GGT
* * *
160979 TAAAATATAATTTTTGGATAGTTTAGGG
1 TAAAATAGAATTTTTGAAAAGTTTAGGG
161007 ACCTTTAAGG
Statistics
Matches: 214, Mismatches: 35, Indels: 32
0.76 0.12 0.11
Matches are distributed among these distances:
57 14 0.07
58 54 0.25
59 55 0.26
60 68 0.32
61 6 0.03
62 17 0.08
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (59 bp):
TAAAATAGAATTTTTGAAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGT
Found at i:160983 original size:119 final size:121
Alignment explanation
Indices: 160677--160963 Score: 277
Period size: 118 Copynumber: 2.4 Consensus size: 121
160667 TGGAAAGTTT
* * * * * * * * *
160677 AGGGGTAAAAA-AGTAATTTTTGAAAAGTT-TAGGGGTTAAATGGTAGTTTTTGGTAAAATCGAG
1 AGGGTTAAAAATAG-AATTTTAG-AAAGTTACAGGGGTAAAATGGTAATTTTTGATGAAATTGGG
* ** * * **
160740 GTT--AAAA-TAGAATTTTTTAAATTTTGAGGGTAAAATGGTAATTTTTAGTGAAATC
64 GTTAAAAAATTGGAATTTTGGAAAGTTTGAGGGTAAAATGATAATTTTTAGCAAAATC
* * * *
160795 GGGGTTAAAAATGGAATTTTGGAAAGTTAGAGGGGTAAAATGGTAATTTTTGATGAAATTGGGGT
1 AGGGTTAAAAATAGAATTTTAGAAAGTTACAGGGGTAAAATGGTAATTTTTGATGAAATTGGGGT
*
160860 TAAAAAATTGGAATTTTGGAAAGTTTG-GGGTAAAATGATAA-TTTTGGCAAAATC
66 TAAAAAATTGGAATTTTGGAAAGTTTGAGGGTAAAATGATAATTTTTAGCAAAATC
* *
160914 AGGGTTTAAAATAGAATTTTAGAAAGTT-CATGGGTAAAAAT-GTAATTTTT
1 AGGGTTAAAAATAGAATTTTAGAAAGTTACAGGGGT-AAAATGGTAATTTTT
160964 AGAAAGTTTG
Statistics
Matches: 138, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
117 6 0.04
118 60 0.43
119 40 0.29
120 17 0.12
121 15 0.11
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (121 bp):
AGGGTTAAAAATAGAATTTTAGAAAGTTACAGGGGTAAAATGGTAATTTTTGATGAAATTGGGGT
TAAAAAATTGGAATTTTGGAAAGTTTGAGGGTAAAATGATAATTTTTAGCAAAATC
Found at i:160984 original size:30 final size:30
Alignment explanation
Indices: 160624--161006 Score: 147
Period size: 30 Copynumber: 12.9 Consensus size: 30
160614 ACTCGGGGCC
* * *
160624 AAAATGGTAATTTTGGGAAAGTTCG-GGGTCA
1 AAAAT-GTAATTTTTGGAAAGTTTGAGGGT-T
*
160655 AAAATAG-AA-TTTTGGAAAGTTT-AGGGGTA
1 AAAAT-GTAATTTTTGGAAAGTTTGA-GGGTT
* *
160684 AAAAAGTAATTTTTGAAAAGTTT-AGGGGTT
1 AAAATGTAATTTTTGGAAAGTTTGA-GGGTT
* * *
160714 -AAATGGTAGTTTTTGGTAAA-ATCGA-GGTT
1 AAAAT-GTAATTTTTGG-AAAGTTTGAGGGTT
* *
160743 AAAATAG-AATTTTT-TAAATTTTGAGGG-T
1 AAAAT-GTAATTTTTGGAAAGTTTGAGGGTT
*
160771 AAAATGGTAATTTTTAGTGAAA--TCG-GGGTT
1 AAAAT-GTAATTTTT-G-GAAAGTTTGAGGGTT
* * *
160801 AAAAATGGAA-TTTTGGAAAGTTAGAGGGGT
1 -AAAATGTAATTTTTGGAAAGTTTGAGGGTT
160831 AAAATGGTAATTTTTGATGAAA--TTG-GGGTT
1 AAAAT-GTAATTTTTG--GAAAGTTTGAGGGTT
*
160861 AAAAAATTGGAA-TTTTGGAAAGTTTG-GGG-T
1 --AAAA-TGTAATTTTTGGAAAGTTTGAGGGTT
* *
160891 AAAATGATAA-TTTTGGCAAA--ATCAGGGTTT
1 AAAATG-TAATTTTTGG-AAAGTTTGAGGG-TT
* * *
160921 AAAATAG-AA-TTTTAGAAAG-TTCATGGGTA
1 AAAAT-GTAATTTTTGGAAAGTTTGA-GGGTT
*
160950 AAAATGTAATTTTTAGAAAGTTTGAGGGTT
1 AAAATGTAATTTTTGGAAAGTTTGAGGGTT
* *
160980 AAAATATAATTTTTGGATAGTTT-AGGG
1 AAAATGTAATTTTTGGAAAGTTTGAGGG
161007 ACCTTTAAGG
Statistics
Matches: 276, Mismatches: 37, Indels: 80
0.70 0.09 0.20
Matches are distributed among these distances:
27 10 0.04
28 31 0.11
29 83 0.30
30 100 0.36
31 37 0.13
32 10 0.04
33 5 0.02
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTTGAGGGTT
Found at i:161609 original size:17 final size:17
Alignment explanation
Indices: 161587--161661 Score: 80
Period size: 17 Copynumber: 4.4 Consensus size: 17
161577 AAGTTTAAGT
*
161587 TTTAAAAT-TATTTCAAA
1 TTTAAAATAAATTT-AAA
*
161604 TTTAAACTAAATTTAAA
1 TTTAAAATAAATTTAAA
*
161621 TTTAAAACAAATTTAAA
1 TTTAAAATAAATTTAAA
* *
161638 TCTAAAAATGAATTTAAA
1 T-TTAAAATAAATTTAAA
161656 TTTAAA
1 TTTAAA
161662 TTTAAAGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 30 0.62
18 18 0.38
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:161622 original size:6 final size:6
Alignment explanation
Indices: 161565--161682 Score: 75
Period size: 6 Copynumber: 20.0 Consensus size: 6
161555 ATGGACTTTG
* * * *
161565 AATTTA ATTTTA AAGTTTA AGTTTTA AAATT- -ATTTCA AATTTA AA-CTA
1 AATTTA AATTTA AA-TTTA A-ATTTA AATTTA AATTT-A AATTTA AATTTA
** * ** *
161613 AATTTA AATTTA AA-ACA AATTTA AATCTA AAAATG AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
161660 AATTTA AA-GTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA
161683 GAAATAAGTC
Statistics
Matches: 83, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
4 3 0.04
5 11 0.13
6 55 0.66
7 14 0.17
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:161628 original size:18 final size:18
Alignment explanation
Indices: 161596--161661 Score: 82
Period size: 17 Copynumber: 3.7 Consensus size: 18
161586 TTTTAAAATT
161596 ATTTCAAATTT-AAACTAA
1 ATTT-AAATTTAAAACTAA
161614 ATTTAAATTTAAAAC-AA
1 ATTTAAATTTAAAACTAA
* * *
161631 ATTTAAATCTAAAAATGA
1 ATTTAAATTTAAAACTAA
161649 ATTTAAATTTAAA
1 ATTTAAATTTAAA
161662 TTTAAAGTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 21 0.50
18 21 0.50
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (18 bp):
ATTTAAATTTAAAACTAA
Found at i:161674 original size:17 final size:17
Alignment explanation
Indices: 161596--161682 Score: 66
Period size: 17 Copynumber: 4.6 Consensus size: 17
161586 TTTTAAAATT
*
161596 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAAGTAA
**
161614 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAGTAA
*
161631 ATTTAAATCTAAAAATGAATTTAA
1 ATTTAAAT-T-TAAA-G----TAA
161655 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAGTAA
161672 ATTTAAATTTA
1 ATTTAAATTTA
161683 GAAATAAGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
17 33 0.59
18 5 0.09
19 3 0.05
21 1 0.02
22 3 0.05
23 1 0.02
24 10 0.18
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAGTAA
Found at i:162415 original size:206 final size:206
Alignment explanation
Indices: 162051--162924 Score: 1295
Period size: 206 Copynumber: 4.2 Consensus size: 206
162041 TCTGGTTTCA
* * * ** * * *
162051 TTGACTTGGCCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTTGATTCAG-T
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTG-TTTCAATCCGCT
* * * * * * *
162115 TCTCTGTGTTTCATCAGGAAGACGGATTAGGTTCACTTCTCCGTATCTCATCAAGAAGCTAACCA
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * **
162180 CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTATTCATA
130 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATA
* *
162245 TCGAGCATGGGT
195 TCGAGCGTGAGT
* *
162257 TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACTGCATCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* *
162322 CTTTGTATCTCATCAGGAAGTCGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
162387 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
162452 CGAGCGTGAGT
196 CGAGCGTGAGT
*
162463 TTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* *
162528 CTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCGGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
162593 TTTATTACTTCAACCTACTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
162658 CGAGCGTGAGT
196 CGAGCGTGAGT
*
162669 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG-TCGACCGCATCGTTTGTTTCAATCTGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT-GACCGCATCGTTTGTTTCAATCCGCT
*
162733 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCA
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * *
162798 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTAGGGTTCGAAGATTTGCTCGCT
130 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC-AT
* * **
162863 -TTGAGCCTTGTTT
194 ATCGAG-CGTGAGT
*
162876 CATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATC
1 --TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATC
162925 ATTGTTTGTG
Statistics
Matches: 611, Mismatches: 50, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
205 8 0.01
206 553 0.91
207 5 0.01
209 44 0.07
210 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
CGAGCGTGAGT
Found at i:163277 original size:101 final size:101
Alignment explanation
Indices: 163093--163287 Score: 259
Period size: 101 Copynumber: 1.9 Consensus size: 101
163083 TACAACTTCG
* * * * *
163093 CTGCAACTTCAGGAAATAGGATTTGATGTTGAAGCTCCATCTTGCTCTTACTACAACTTCAGAGA
1 CTGCAACTTCAAGAAATAGGAATTGACGTTAAAGCTCCATCTTGCTCTTACTACAACTTCAAAGA
163158 GATAAAGACTTACTATTGT-TTTTAATCCAACTTTA
66 GATAAAGACTTACTATTGTATTTTAATCCAACTTTA
* * * *
163193 CTGCAACTTCAAGAGGATAGGAATTGACGTTAAAGCTTCATTTTGCTCTTACTGCAACTTCAAAG
1 CTGCAACTTCAAGA-AATAGGAATTGACGTTAAAGCTCCATCTTGCTCTTACTACAACTTCAAAG
*
163258 AGATAAAGACTT-GTCATTGTAGTTTTAATC
65 AGATAAAGACTTACT-ATTGTA-TTTTAATC
163288 TGATCCACTA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
100 14 0.17
101 59 0.73
103 8 0.10
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (101 bp):
CTGCAACTTCAAGAAATAGGAATTGACGTTAAAGCTCCATCTTGCTCTTACTACAACTTCAAAGA
GATAAAGACTTACTATTGTATTTTAATCCAACTTTA
Found at i:163460 original size:50 final size:50
Alignment explanation
Indices: 163406--163812 Score: 273
Period size: 50 Copynumber: 8.1 Consensus size: 50
163396 AAATCTTCGG
*
163406 GGTACTAGATTCGCTGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGA
1 GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGA
* * * * *
163456 GGTAC-ACG-GTCTGCCATTACGACTTAAA-CTTTTCCCTT-TTGTATCTT-TGT
1 GGTACTA-GATTC-GCCGTTGCGGCTTAAATC-TTTCCCTTCTTG--TCTTCTGA
* * * * *
163506 GGTACTGGATCCGTCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTC--A
1 GGTACTAGATTCGCCGTTGCGG-CTTAAATCTTTCCCTTCTTGTCTTCTGA
* * * *
163555 TGGTACTAGATTCACCGTTACGGCTTAAATCTTTCCCTTCATATCTTCTGA
1 -GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGA
* * * * * *
163606 GGTAC-ACGGTCTTGCCGTTGCGACTTAGACCTTTCCCTT-TTGTATCTT-TGT
1 GGTACTA-GAT-TCGCCGTTGCGGCTTAAATCTTTCCCTTCTTG--TCTTCTGA
* * * *
163657 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTTCCTTCGTGTCTTTTGA
1 GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGA
* * * * * *
163707 GGTAC-ACGGTCCTGCCGTTGCGACTTAGACCTTTCCCTT-TTGTATCTT-TGT
1 GGTACTA-GATTC-GCCGTTGCGGCTTAAATCTTTCCCTTCTTG--TCTTCTGA
* * * *
163758 GGTACTAGATCCGCCGTTACGGCTTAAATCTTTTCCTTCGTGTCTTCTGA
1 GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGA
163808 GGTAC
1 GGTAC
163813 ACGGTCCTGC
Statistics
Matches: 270, Mismatches: 59, Indels: 56
0.70 0.15 0.15
Matches are distributed among these distances:
49 39 0.14
50 132 0.49
51 87 0.32
52 12 0.04
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (50 bp):
GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGA
Found at i:163683 original size:101 final size:101
Alignment explanation
Indices: 163555--163846 Score: 494
Period size: 101 Copynumber: 2.9 Consensus size: 101
163545 CATGTCTTCA
* * * * *
163555 TGGTACTAGATTCACCGTTACGGCTTAAATCTTTCCCTTCATATCTTCTGAGGTACACGGTCTTG
1 TGGTACTAGATTCGCCGTTACGGCTTAAATCTTTTCCTTCGTGTCTTCTGAGGTACACGGTCCTG
163620 CCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTG
66 CCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTG
* * *
163656 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTTCCTTCGTGTCTTTTGAGGTACACGGTCCTG
1 TGGTACTAGATTCGCCGTTACGGCTTAAATCTTTTCCTTCGTGTCTTCTGAGGTACACGGTCCTG
163721 CCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTG
66 CCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTG
*
163757 TGGTACTAGATCCGCCGTTACGGCTTAAATCTTTTCCTTCGTGTCTTCTGAGGTACACGGTCCTG
1 TGGTACTAGATTCGCCGTTACGGCTTAAATCTTTTCCTTCGTGTCTTCTGAGGTACACGGTCCTG
*
163822 CCGTTGCTACTTAGACCTTTCCCTT
66 CCGTTGCGACTTAGACCTTTCCCTT
163847 CATGTCTTCA
Statistics
Matches: 178, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 178 1.00
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.39
Consensus pattern (101 bp):
TGGTACTAGATTCGCCGTTACGGCTTAAATCTTTTCCTTCGTGTCTTCTGAGGTACACGGTCCTG
CCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTG
Found at i:163688 original size:150 final size:149
Alignment explanation
Indices: 163356--163702 Score: 451
Period size: 150 Copynumber: 2.3 Consensus size: 149
163346 ATGTTTGTAA
* * ** ** ** * * *
163356 GGTACTGGGTTCGCCATTGCAACTTAAGCCTTTCCCCTTCAAATCTTCGGGGTACTAGATTCGCT
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTT-CCCTTCATGTCTTCAGGGTACTAGATTCACC
* * * *
163421 GTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACACGGTCTGCCATTACGACTTAAACT
65 GTTACGGCTTAAATCTTTCCCTTCATATCTTCTGAGGTACACGGTCTGCCATTACGACTTAAACC
163486 TTTCCCTTTTGTATCTTTGT
130 TTTCCCTTTTGTATCTTTGT
* * * *
163506 GGTACTGGATCCGTCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGGTACTAGATTCACC
1 GGTACTGGATTCGCCGTTGCGG-CTTAAATCTTTCCCTTCATGTCTTCAGGGTACTAGATTCACC
* * *
163571 GTTACGGCTTAAATCTTTCCCTTCATATCTTCTGAGGTACACGGTCTTGCCGTTGCGACTTAGAC
65 GTTACGGCTTAAATCTTTCCCTTCATATCTTCTGAGGTACACGGTC-TGCCATTACGACTTAAAC
163636 CTTTCCCTTTTGTATCTTTGT
129 CTTTCCCTTTTGTATCTTTGT
* *
163657 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTTCCTTCGTGTCTT
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT
163703 TTGAGGTACA
Statistics
Matches: 168, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
150 105 0.62
151 63 0.38
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.39
Consensus pattern (149 bp):
GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCAGGGTACTAGATTCACCG
TTACGGCTTAAATCTTTCCCTTCATATCTTCTGAGGTACACGGTCTGCCATTACGACTTAAACCT
TTCCCTTTTGTATCTTTGT
Found at i:163774 original size:151 final size:151
Alignment explanation
Indices: 163428--163863 Score: 381
Period size: 151 Copynumber: 2.9 Consensus size: 151
163418 GCTGTTGCGG
* * * * * * *
163428 CTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACACGGTCT-GCCATTACGACTTAAACTTTTCCC
1 CTTAAACCTTTCCCTTCATATCTTCTGAGGTACACGATCTCGCCGTTGCGACTTAAACCTTTCCC
* *
163492 TTTTGTATCTTTGTGGTACTGGATCCGTCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATG
66 TTTTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTCCCTTCATGTCTTCATG
* *
163557 GTACTAGATTCACCGTTACGG
131 GTACTAGATCCACCGTTACGA
* * * *
163578 CTTAAATCTTTCCCTTCATATCTTCTGAGGTACACGGTCTTGCCGTTGCGACTTAGACCTTTCCC
1 CTTAAACCTTTCCCTTCATATCTTCTGAGGTACACGATCTCGCCGTTGCGACTTAAACCTTTCCC
* * * *
163643 TTTTGTATCTTTGTGGTACTGGATTCGCCGTTGCGG-CTTAAATCTTTTCCTTCGTGTCTT-TTG
66 TTTTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTCCCTTCATGTCTTCAT-
* * *
163706 AGGTAC-ACGGTCCTGCCGTTGCGA
130 -GGTACTA-GATCC-ACCGTTACGA
* ** * * * * *
163730 CTTAGACCTTTCCCTTTTGTATCTT-TGTGGTACTA-GATC-CGCCGTTACGGCTTAAATCTTTT
1 CTTAAACCTTTCCC-TTCATATCTTCTGAGGTAC-ACGATCTCGCCGTTGCGACTTAAACCTTTC
* * * * * *
163792 CC-TTCGTGTCTTCTGAGGTACACGG-TCCTGCCGTTGC--TACTTAGACCTTTCCCTTCATGTC
64 CCTTTTGTATCTT-TGTGGTAC-TGGATCC-GCCGTTGCGGT-CTTAAATCTTTCCCTTCATGTC
163853 TTCATGGTACT
125 TTCATGGTACT
163864 GAGACTTGTA
Statistics
Matches: 233, Mismatches: 39, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
149 1 0.00
150 68 0.29
151 95 0.41
152 59 0.25
153 10 0.04
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (151 bp):
CTTAAACCTTTCCCTTCATATCTTCTGAGGTACACGATCTCGCCGTTGCGACTTAAACCTTTCCC
TTTTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTCCCTTCATGTCTTCATG
GTACTAGATCCACCGTTACGA
Found at i:164922 original size:3 final size:3
Alignment explanation
Indices: 164909--164950 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
164899 CTTTCCCTTT
164909 TTC TTC TTTC TTC TT- TTAC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC -TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TT
164951 TTTGTATTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.06
3 29 0.81
4 5 0.14
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:170685 original size:59 final size:58
Alignment explanation
Indices: 170616--170782 Score: 171
Period size: 59 Copynumber: 2.8 Consensus size: 58
170606 TTGGAAAGTT
* * * *
170616 TAAGGGTAAAAATGTAATTTTTGAAAAGTTTAGGGGTTAAATGATAATTTTTGGTGA-A
1 TAAGGTTAAAAATGTAATTTTT-AAAAGTTTAGGGGTAAAATGGTAATTTTTAGTGAGA
* ** *
170674 TCGAGGTTAAAAATAG-AATTTTTTTAAGTTTAAGGGTAAAATGGTAATTTTTAGTGAGA
1 T-AAGGTTAAAAAT-GTAATTTTTAAAAGTTTAGGGGTAAAATGGTAATTTTTAGTGAGA
*
170733 TAAGGTTCAAAAA--TAGATTTTTAGAAAGTTTGGGGGTAAAATGGTAATTT
1 TAAGGTT-AAAAATGTA-ATTTTTA-AAAGTTTAGGGGTAAAATGGTAATTT
170783 GGGTAAAATC
Statistics
Matches: 89, Mismatches: 13, Indels: 13
0.77 0.11 0.11
Matches are distributed among these distances:
57 1 0.01
58 40 0.45
59 47 0.53
60 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (58 bp):
TAAGGTTAAAAATGTAATTTTTAAAAGTTTAGGGGTAAAATGGTAATTTTTAGTGAGA
Found at i:170725 original size:58 final size:57
Alignment explanation
Indices: 170622--170831 Score: 192
Period size: 58 Copynumber: 3.6 Consensus size: 57
170612 AGTTTAAGGG
* * * *
170622 TAAAAAT-GTAATTTTTGAAAAGTTTAGGGGTTAAATGATAATTTTTGGTGAATCGAGGT
1 TAAAAATAG-AATTTTT-TAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGAATC-AGGT
* * *
170681 TAAAAATAGAATTTTTTTAAGTTTAAGGGTAAAATGGTAATTTTTAGTGAGATAAGGT
1 TAAAAATAGAATTTTTTAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGA-ATCAGGT
* ** * * *
170739 TCAAAAATAG-ATTTTTAGAAAGTTTGGGGGTAAAATGGTAA-TTTGGGTAAAATCAGGGG
1 T-AAAAATAGAATTTTT-TAAAGTTTAAGGGTAAAATGGTAATTTTTGGT-GAATCA-GGT
* *
170798 TCAAAATAGAATTTTATAAAGTTTAAGGGTAAAA
1 TAAAAATAGAATTTTTTAAAGTTTAAGGGTAAAA
170832 ATGTGATTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
58 69 0.56
59 53 0.43
60 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.36
Consensus pattern (57 bp):
TAAAAATAGAATTTTTTAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGAATCAGGT
Found at i:170753 original size:117 final size:117
Alignment explanation
Indices: 170632--170844 Score: 272
Period size: 117 Copynumber: 1.8 Consensus size: 117
170622 TAAAAATGTA
* * * *
170632 ATTTTT-GAAAAGTTTAGGGGTTAAATGATAATTTTTGGT-GAATC-GAGGTTAAAAATAGAATT
1 ATTTTTAG-AAAGTTTAGGGGTAAAATGATAA-TTTGGGTAAAATCAG-GGGTAAAAATAGAATT
* *
170694 TTTTTAAGTTTAAGGGT-AAAATGGTAATTTTTAGTGAGATAAGGTTCAAAAATAG
63 TTATAAAGTTTAAGGGTAAAAAT-GTAATTTTTAGTGAGATAAGGTTCAAAAATAG
* * *
170749 ATTTTTAGAAAGTTTGGGGGTAAAATGGTAATTTGGGTAAAATCAGGGGTCAAAATAGAATTTTA
1 ATTTTTAGAAAGTTTAGGGGTAAAATGATAATTTGGGTAAAATCAGGGGTAAAAATAGAATTTTA
*
170814 TAAAGTTTAAGGGTAAAAATGTGATTTTTAG
66 TAAAGTTTAAGGGTAAAAATGTAATTTTTAG
170845 AAAGTTCGAG
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
116 6 0.07
117 69 0.84
118 7 0.09
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (117 bp):
ATTTTTAGAAAGTTTAGGGGTAAAATGATAATTTGGGTAAAATCAGGGGTAAAAATAGAATTTTA
TAAAGTTTAAGGGTAAAAATGTAATTTTTAGTGAGATAAGGTTCAAAAATAG
Found at i:170834 original size:59 final size:59
Alignment explanation
Indices: 170682--170831 Score: 169
Period size: 59 Copynumber: 2.6 Consensus size: 59
170672 AATCGAGGTT
* * * * * *
170682 AAAAATAGAATTTTTTTAAGTTTAAGGGTAAAATGGTAATTTTTAGTGAGATAAGGTTC
1 AAAAATAGAATTTTATAAAGTTTAAGGGTAAAATGGTAATTTTGAGTAAAATAAGGGTC
* * ** * *
170741 AAAAATAGATTTTTAGAAAGTTTGGGGGTAAAATGGTAA-TTTGGGTAAAATCAGGGGTC
1 AAAAATAGAATTTTATAAAGTTTAAGGGTAAAATGGTAATTTTGAGTAAAAT-AAGGGTC
170800 -AAAATAGAATTTTATAAAGTTTAAGGGTAAAA
1 AAAAATAGAATTTTATAAAGTTTAAGGGTAAAA
170832 ATGTGATTTT
Statistics
Matches: 74, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
58 36 0.49
59 38 0.51
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (59 bp):
AAAAATAGAATTTTATAAAGTTTAAGGGTAAAATGGTAATTTTGAGTAAAATAAGGGTC
Found at i:170849 original size:30 final size:30
Alignment explanation
Indices: 170565--170882 Score: 116
Period size: 30 Copynumber: 10.8 Consensus size: 30
170555 ACTAAGGGGC
**
170565 AAAATGGTAATTTTGGGAAAGTTT--GGGTCA
1 AAAAT-GTAATTTTTAGAAAGTTTAAGGGT-A
* *
170595 AAAATGGAA-TTTTGGAAAGTTTAAGGGTA
1 AAAATGTAATTTTTAGAAAGTTTAAGGGTA
*
170624 AAAATGTAATTTTT-GAAAAGTTTAGGGGT-
1 AAAATGTAATTTTTAG-AAAGTTTAAGGGTA
* * * ** *
170653 TAAATGATAATTTTTGGTGAA--TCGAGGTTA
1 AAAATG-TAATTTTTAG-AAAGTTTAAGGGTA
**
170683 AAAATAG-AATTTTT-TTAAGTTTAAGGGT-
1 AAAAT-GTAATTTTTAGAAAGTTTAAGGGTA
** * *
170711 AAAATGGTAATTTTTAGTGAG-ATAAGGTTCA
1 AAAAT-GTAATTTTTAGAAAGTTTAAGGGT-A
**
170742 AAAA--TAGATTTTTAGAAAGTTTGGGGGT-
1 AAAATGTA-ATTTTTAGAAAGTTTAAGGGTA
* * * *
170770 AAAATGGTAATTTGGGTA-AAA--TCAGGGGTC
1 AAAAT-GTAATTT--TTAGAAAGTTTAAGGGTA
*
170800 AAAATAG-AA-TTTTATAAAGTTTAAGGGTA
1 AAAAT-GTAATTTTTAGAAAGTTTAAGGGTA
* ** *
170829 AAAATGTGATTTTTAGAAAGTTCGAGGGTT
1 AAAATGTAATTTTTAGAAAGTTTAAGGGTA
* *
170859 AAAATGTAATTTTTGGATAGTTTA
1 AAAATGTAATTTTTAGAAAGTTTA
170883 GGACCTTCAA
Statistics
Matches: 215, Mismatches: 46, Indels: 54
0.68 0.15 0.17
Matches are distributed among these distances:
26 2 0.01
27 5 0.02
28 27 0.13
29 77 0.36
30 89 0.41
31 13 0.06
32 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTTAGAAAGTTTAAGGGTA
Found at i:171557 original size:23 final size:23
Alignment explanation
Indices: 171531--171581 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
171521 GATGTAAGCG
171531 CCGTCGACTCC-TCCTGCCACGCA
1 CCGTCGACTCCGT-CTGCCACGCA
*
171554 CCGTCGACTCCGTCTGCCACGCG
1 CCGTCGACTCCGTCTGCCACGCA
171577 CCGTC
1 CCGTC
171582 CTCGAGGCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.10, C:0.51, G:0.22, T:0.18
Consensus pattern (23 bp):
CCGTCGACTCCGTCTGCCACGCA
Found at i:172054 original size:38 final size:36
Alignment explanation
Indices: 172005--172075 Score: 106
Period size: 38 Copynumber: 1.9 Consensus size: 36
171995 ATTATTATAT
*
172005 TATTAATATTAATGCTTATTAATATCATTTAATATTAC
1 TATTAATATTAATGC-TATTAAAAT-ATTTAATATTAC
*
172043 TATTATTATTAATGCTATTAAAATATTTAATAT
1 TATTAATATTAATGCTATTAAAATATTTAATAT
172076 ATGTATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 9 0.29
37 8 0.26
38 14 0.45
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.51
Consensus pattern (36 bp):
TATTAATATTAATGCTATTAAAATATTTAATATTAC
Found at i:172832 original size:17 final size:17
Alignment explanation
Indices: 172807--172883 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
172797 TTTTAAAATT
172807 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAACTAA
*
172825 ATTTAAATTAAAAAC-AA
1 ATTTAAATT-TAAACTAA
* *
172842 TTTTAAATTTAAAGTAA
1 ATTTAAATTTAAACTAA
*
172859 ATTTAAATTTAGAAATAA
1 ATTTAAATTTA-AACTAA
*
172877 ATCTAAA
1 ATTTAAA
172884 ATAATTTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 3 0.06
17 27 0.55
18 19 0.39
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAACTAA
Found at i:173414 original size:21 final size:21
Alignment explanation
Indices: 173390--173442 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
173380 CTAGAGTTTG
**
173390 TTGTATCGGTAGAAGTGTTAC
1 TTGTATCGGTAGAAGTCATAC
* *
173411 TTGTTTTCGGTAGTAGTCATAC
1 TTG-TATCGGTAGAAGTCATAC
173433 TTGTATCGGT
1 TTGTATCGGT
173443 CGAACTATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.43
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTCATAC
Found at i:175032 original size:51 final size:51
Alignment explanation
Indices: 174913--175053 Score: 135
Period size: 50 Copynumber: 2.8 Consensus size: 51
174903 NNNNNNNNNN
* * *
174913 AGGTACACGGTCCTGCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTG
1 AGGTACACGGTCCTGCCGTTACGACTTAAACCTTTCCCTTTCGTATCTTTG
* * * * * *
174964 TGGTACTA-GATCC-GCCGTTACGGCTTAAATCTTTTCC-TTCGTGTCTTCTG
1 AGGTAC-ACGGTCCTGCCGTTACGACTTAAACCTTTCCCTTTCGTATCTT-TG
* * *
175014 AGGTACACGGTCCTGCCGTTGCTACTTAGACCTTTCCCTT
1 AGGTACACGGTCCTGCCGTTACGACTTAAACCTTTCCCTT
175054 CATGTCTTCA
Statistics
Matches: 68, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
49 9 0.13
50 30 0.44
51 27 0.40
52 2 0.03
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.37
Consensus pattern (51 bp):
AGGTACACGGTCCTGCCGTTACGACTTAAACCTTTCCCTTTCGTATCTTTG
Found at i:175054 original size:51 final size:51
Alignment explanation
Indices: 174913--175062 Score: 162
Period size: 51 Copynumber: 3.0 Consensus size: 51
174903 NNNNNNNNNN
* *
174913 AGGTACACGGTCCTGCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTT-TG
1 AGGTACACGGTCCTGCCGTTGCGACTTAGACCTTTCCC-TTCGTGTCTTCTG
* * * * * * *
174964 TGGTACTA-GATCC-GCCGTTACGGCTTAAATCTTTTCCTTCGTGTCTTCTG
1 AGGTAC-ACGGTCCTGCCGTTGCGACTTAGACCTTTCCCTTCGTGTCTTCTG
* *
175014 AGGTACACGGTCCTGCCGTTGCTACTTAGACCTTTCCCTTCATGTCTTC
1 AGGTACACGGTCCTGCCGTTGCGACTTAGACCTTTCCCTTCGTGTCTTC
175063 ATGGTACTGA
Statistics
Matches: 77, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
49 9 0.12
50 30 0.39
51 37 0.48
52 1 0.01
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.37
Consensus pattern (51 bp):
AGGTACACGGTCCTGCCGTTGCGACTTAGACCTTTCCCTTCGTGTCTTCTG
Found at i:176129 original size:3 final size:3
Alignment explanation
Indices: 176116--176157 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
176106 CTTTCCCTTT
176116 TTC TTC TTTC TTC TT- TTAC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC -TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TT
176158 TTTGTATTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.06
3 29 0.81
4 5 0.14
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:181892 original size:59 final size:58
Alignment explanation
Indices: 181823--181989 Score: 171
Period size: 59 Copynumber: 2.8 Consensus size: 58
181813 TTGGAAAGTT
* * * *
181823 TAAGGGTAAAAATGTAATTTTTGAAAAGTTTAGGGGTTAAATGATAATTTTTGGTGA-A
1 TAAGGTTAAAAATGTAATTTTT-AAAAGTTTAGGGGTAAAATGGTAATTTTTAGTGAGA
* ** *
181881 TCGAGGTTAAAAATAG-AATTTTTTTAAGTTTAAGGGTAAAATGGTAATTTTTAGTGAGA
1 T-AAGGTTAAAAAT-GTAATTTTTAAAAGTTTAGGGGTAAAATGGTAATTTTTAGTGAGA
*
181940 TAAGGTTCAAAAA--TAGATTTTTAGAAAGTTTGGGGGTAAAATGGTAATTT
1 TAAGGTT-AAAAATGTA-ATTTTTA-AAAGTTTAGGGGTAAAATGGTAATTT
181990 GGGTAAAATC
Statistics
Matches: 89, Mismatches: 13, Indels: 13
0.77 0.11 0.11
Matches are distributed among these distances:
57 1 0.01
58 40 0.45
59 47 0.53
60 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (58 bp):
TAAGGTTAAAAATGTAATTTTTAAAAGTTTAGGGGTAAAATGGTAATTTTTAGTGAGA
Found at i:181932 original size:58 final size:57
Alignment explanation
Indices: 181829--182038 Score: 192
Period size: 58 Copynumber: 3.6 Consensus size: 57
181819 AGTTTAAGGG
* * * *
181829 TAAAAAT-GTAATTTTTGAAAAGTTTAGGGGTTAAATGATAATTTTTGGTGAATCGAGGT
1 TAAAAATAG-AATTTTT-TAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGAATC-AGGT
* * *
181888 TAAAAATAGAATTTTTTTAAGTTTAAGGGTAAAATGGTAATTTTTAGTGAGATAAGGT
1 TAAAAATAGAATTTTTTAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGA-ATCAGGT
* ** * * *
181946 TCAAAAATAG-ATTTTTAGAAAGTTTGGGGGTAAAATGGTAA-TTTGGGTAAAATCAGGGG
1 T-AAAAATAGAATTTTT-TAAAGTTTAAGGGTAAAATGGTAATTTTTGGT-GAATCA-GGT
* *
182005 TCAAAATAGAATTTTATAAAGTTTAAGGGTAAAA
1 TAAAAATAGAATTTTTTAAAGTTTAAGGGTAAAA
182039 ATGTGATTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
58 69 0.56
59 53 0.43
60 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.36
Consensus pattern (57 bp):
TAAAAATAGAATTTTTTAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGAATCAGGT
Found at i:181960 original size:117 final size:117
Alignment explanation
Indices: 181839--182051 Score: 272
Period size: 117 Copynumber: 1.8 Consensus size: 117
181829 TAAAAATGTA
* * * *
181839 ATTTTT-GAAAAGTTTAGGGGTTAAATGATAATTTTTGGT-GAATC-GAGGTTAAAAATAGAATT
1 ATTTTTAG-AAAGTTTAGGGGTAAAATGATAA-TTTGGGTAAAATCAG-GGGTAAAAATAGAATT
* *
181901 TTTTTAAGTTTAAGGGT-AAAATGGTAATTTTTAGTGAGATAAGGTTCAAAAATAG
63 TTATAAAGTTTAAGGGTAAAAAT-GTAATTTTTAGTGAGATAAGGTTCAAAAATAG
* * *
181956 ATTTTTAGAAAGTTTGGGGGTAAAATGGTAATTTGGGTAAAATCAGGGGTCAAAATAGAATTTTA
1 ATTTTTAGAAAGTTTAGGGGTAAAATGATAATTTGGGTAAAATCAGGGGTAAAAATAGAATTTTA
*
182021 TAAAGTTTAAGGGTAAAAATGTGATTTTTAG
66 TAAAGTTTAAGGGTAAAAATGTAATTTTTAG
182052 AAAGTTCGAG
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
116 6 0.07
117 69 0.84
118 7 0.09
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (117 bp):
ATTTTTAGAAAGTTTAGGGGTAAAATGATAATTTGGGTAAAATCAGGGGTAAAAATAGAATTTTA
TAAAGTTTAAGGGTAAAAATGTAATTTTTAGTGAGATAAGGTTCAAAAATAG
Found at i:182041 original size:59 final size:59
Alignment explanation
Indices: 181889--182038 Score: 169
Period size: 59 Copynumber: 2.6 Consensus size: 59
181879 AATCGAGGTT
* * * * * *
181889 AAAAATAGAATTTTTTTAAGTTTAAGGGTAAAATGGTAATTTTTAGTGAGATAAGGTTC
1 AAAAATAGAATTTTATAAAGTTTAAGGGTAAAATGGTAATTTTGAGTAAAATAAGGGTC
* * ** * *
181948 AAAAATAGATTTTTAGAAAGTTTGGGGGTAAAATGGTAA-TTTGGGTAAAATCAGGGGTC
1 AAAAATAGAATTTTATAAAGTTTAAGGGTAAAATGGTAATTTTGAGTAAAAT-AAGGGTC
182007 -AAAATAGAATTTTATAAAGTTTAAGGGTAAAA
1 AAAAATAGAATTTTATAAAGTTTAAGGGTAAAA
182039 ATGTGATTTT
Statistics
Matches: 74, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
58 36 0.49
59 38 0.51
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (59 bp):
AAAAATAGAATTTTATAAAGTTTAAGGGTAAAATGGTAATTTTGAGTAAAATAAGGGTC
Found at i:182056 original size:30 final size:30
Alignment explanation
Indices: 181772--182089 Score: 116
Period size: 30 Copynumber: 10.8 Consensus size: 30
181762 ACTAAGGGGC
**
181772 AAAATGGTAATTTTGGGAAAGTTT--GGGTCA
1 AAAAT-GTAATTTTTAGAAAGTTTAAGGGT-A
* *
181802 AAAATGGAA-TTTTGGAAAGTTTAAGGGTA
1 AAAATGTAATTTTTAGAAAGTTTAAGGGTA
*
181831 AAAATGTAATTTTT-GAAAAGTTTAGGGGT-
1 AAAATGTAATTTTTAG-AAAGTTTAAGGGTA
* * * ** *
181860 TAAATGATAATTTTTGGTGAA--TCGAGGTTA
1 AAAATG-TAATTTTTAG-AAAGTTTAAGGGTA
**
181890 AAAATAG-AATTTTT-TTAAGTTTAAGGGT-
1 AAAAT-GTAATTTTTAGAAAGTTTAAGGGTA
** * *
181918 AAAATGGTAATTTTTAGTGAG-ATAAGGTTCA
1 AAAAT-GTAATTTTTAGAAAGTTTAAGGGT-A
**
181949 AAAA--TAGATTTTTAGAAAGTTTGGGGGT-
1 AAAATGTA-ATTTTTAGAAAGTTTAAGGGTA
* * * *
181977 AAAATGGTAATTTGGGTA-AAA--TCAGGGGTC
1 AAAAT-GTAATTT--TTAGAAAGTTTAAGGGTA
*
182007 AAAATAG-AA-TTTTATAAAGTTTAAGGGTA
1 AAAAT-GTAATTTTTAGAAAGTTTAAGGGTA
* ** *
182036 AAAATGTGATTTTTAGAAAGTTCGAGGGTT
1 AAAATGTAATTTTTAGAAAGTTTAAGGGTA
* *
182066 AAAATGTAATTTTTGGATAGTTTA
1 AAAATGTAATTTTTAGAAAGTTTA
182090 GGACCTTCAA
Statistics
Matches: 215, Mismatches: 46, Indels: 54
0.68 0.15 0.17
Matches are distributed among these distances:
26 2 0.01
27 5 0.02
28 27 0.13
29 77 0.36
30 89 0.41
31 13 0.06
32 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTTAGAAAGTTTAAGGGTA
Found at i:182764 original size:23 final size:23
Alignment explanation
Indices: 182738--182788 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
182728 GATGTAAGCG
182738 CCGTCGACTCC-TCCTGCCACGCA
1 CCGTCGACTCCGT-CTGCCACGCA
*
182761 CCGTCGACTCCGTCTGCCACGCG
1 CCGTCGACTCCGTCTGCCACGCA
182784 CCGTC
1 CCGTC
182789 CTCGAGGCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.10, C:0.51, G:0.22, T:0.18
Consensus pattern (23 bp):
CCGTCGACTCCGTCTGCCACGCA
Found at i:183261 original size:38 final size:36
Alignment explanation
Indices: 183212--183282 Score: 106
Period size: 38 Copynumber: 1.9 Consensus size: 36
183202 ATTATTATAT
*
183212 TATTAATATTAATGCTTATTAATATCATTTAATATTAC
1 TATTAATATTAATGC-TATTAAAAT-ATTTAATATTAC
*
183250 TATTATTATTAATGCTATTAAAATATTTAATAT
1 TATTAATATTAATGCTATTAAAATATTTAATAT
183283 ATGTATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 9 0.29
37 8 0.26
38 14 0.45
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.51
Consensus pattern (36 bp):
TATTAATATTAATGCTATTAAAATATTTAATATTAC
Found at i:184039 original size:17 final size:17
Alignment explanation
Indices: 184014--184090 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
184004 TTTTAAAATT
184014 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAACTAA
*
184032 ATTTAAATTAAAAAC-AA
1 ATTTAAATT-TAAACTAA
* *
184049 TTTTAAATTTAAAGTAA
1 ATTTAAATTTAAACTAA
*
184066 ATTTAAATTTAGAAATAA
1 ATTTAAATTTA-AACTAA
*
184084 ATCTAAA
1 ATTTAAA
184091 ATAATTTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 3 0.06
17 27 0.55
18 19 0.39
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAACTAA
Found at i:184621 original size:21 final size:21
Alignment explanation
Indices: 184597--184649 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
184587 CTAGAGTTTG
**
184597 TTGTATCGGTAGAAGTGTTAC
1 TTGTATCGGTAGAAGTCATAC
* *
184618 TTGTTTTCGGTAGTAGTCATAC
1 TTG-TATCGGTAGAAGTCATAC
184640 TTGTATCGGT
1 TTGTATCGGT
184650 CGAACTATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.43
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTCATAC
Found at i:186219 original size:137 final size:137
Alignment explanation
Indices: 185973--186246 Score: 548
Period size: 137 Copynumber: 2.0 Consensus size: 137
185963 ATTAATCACT
185973 TTCTACGAGGCTCTCCAAGTGTCCTAATTATTGACACATTACCTCAACTAGGATGCTAGATGCCT
1 TTCTACGAGGCTCTCCAAGTGTCCTAATTATTGACACATTACCTCAACTAGGATGCTAGATGCCT
186038 TAAACTTGTCATACAAGCTATTATACTCACTTTAAAAGTGACCCAAAACACAGGTGGCAATCTTA
66 TAAACTTGTCATACAAGCTATTATACTCACTTTAAAAGTGACCCAAAACACAGGTGGCAATCTTA
186103 TTAGCGG
131 TTAGCGG
186110 TTCTACGAGGCTCTCCAAGTGTCCTAATTATTGACACATTACCTCAACTAGGATGCTAGATGCCT
1 TTCTACGAGGCTCTCCAAGTGTCCTAATTATTGACACATTACCTCAACTAGGATGCTAGATGCCT
186175 TAAACTTGTCATACAAGCTATTATACTCACTTTAAAAGTGACCCAAAACACAGGTGGCAATCTTA
66 TAAACTTGTCATACAAGCTATTATACTCACTTTAAAAGTGACCCAAAACACAGGTGGCAATCTTA
186240 TTAGCGG
131 TTAGCGG
186247 GAAAGTCCGC
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (137 bp):
TTCTACGAGGCTCTCCAAGTGTCCTAATTATTGACACATTACCTCAACTAGGATGCTAGATGCCT
TAAACTTGTCATACAAGCTATTATACTCACTTTAAAAGTGACCCAAAACACAGGTGGCAATCTTA
TTAGCGG
Found at i:190858 original size:71 final size:71
Alignment explanation
Indices: 190693--190839 Score: 188
Period size: 71 Copynumber: 2.1 Consensus size: 71
190683 ACAACATTGA
* * * ** * *** *
190693 TGAATGCTCC-CCTGTAAGTTTGAAGTTTGTTGTCGCGACATTGAGTGGTTGTTGTTGTGACATT
1 TGAATGCTCCTCCTCTAGGTTCGAAGTTTGTTGTCGCGACATTGAGTCATTGTTATCACGACATC
190757 GAAGGC
66 GAAGGC
190763 TGAATGCTCCTCCTCTAGGTTCGAAGTTTGTTGTCGCGACATTGAGTCATTGTTATCACGACATC
1 TGAATGCTCCTCCTCTAGGTTCGAAGTTTGTTGTCGCGACATTGAGTCATTGTTATCACGACATC
*
190828 GATGGC
66 GAAGGC
190834 TGAATG
1 TGAATG
190840 TTCTCCTTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
70 10 0.15
71 55 0.85
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (71 bp):
TGAATGCTCCTCCTCTAGGTTCGAAGTTTGTTGTCGCGACATTGAGTCATTGTTATCACGACATC
GAAGGC
Found at i:193666 original size:17 final size:16
Alignment explanation
Indices: 193643--193683 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
193633 GATAATAAAA
193643 TATAATTTTACTAT-TT
1 TATAATTTTA-TATATT
193659 TAATAA-TTTATATATT
1 T-ATAATTTTATATATT
193675 TATAATTTT
1 TATAATTTT
193684 TAAAGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.32
16 11 0.50
17 4 0.18
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:193713 original size:30 final size:31
Alignment explanation
Indices: 193673--193735 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
193663 AATTTATATA
* *
193673 TTTATAATTTTTAAAGAATTAAATTA-AATT
1 TTTATAATTTTTAAAAAATTAAAATATAATT
*
193703 TTTATCATTTTTAAAAAATTAAAATATAATT
1 TTTATAATTTTTAAAAAATTAAAATATAATT
193734 TT
1 TT
193736 ACTATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (31 bp):
TTTATAATTTTTAAAAAATTAAAATATAATT
Found at i:201351 original size:5 final size:5
Alignment explanation
Indices: 201341--201371 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
201331 TAGGGCTGTG
201341 GAAAT GAAAT GAAAT GAAAT GAAAT GGAAAT
1 GAAAT GAAAT GAAAT GAAAT GAAAT -GAAAT
201372 TTAAATTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (5 bp):
GAAAT
Found at i:203428 original size:19 final size:19
Alignment explanation
Indices: 203406--203450 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
203396 TTATATTAGG
203406 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
203425 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
203444 ATTTAAT
1 ATTTAAT
203451 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:204134 original size:21 final size:22
Alignment explanation
Indices: 204097--204138 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
204087 ATTTCTTTCG
204097 ATTCTGTTTTCTTTTATTTTTA
1 ATTCTGTTTTCTTTTATTTTTA
204119 ATTCTGTTTT-TTTTATTTTT
1 ATTCTGTTTTCTTTTATTTTT
204139 CCTTAGATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (22 bp):
ATTCTGTTTTCTTTTATTTTTA
Found at i:209548 original size:20 final size:22
Alignment explanation
Indices: 209512--209572 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 22
209502 CATTCTAATT
*
209512 TTTTTAA-ATATA-ATTTATAA
1 TTTTTAATATATATTTTTATAA
209532 TTTTT-ATATAT-TTTTTAT--
1 TTTTTAATATATATTTTTATAA
209550 TTTTTGAATATATATTTTTATAA
1 TTTTT-AATATATATTTTTATAA
209573 AATTCTGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
18 5 0.15
19 1 0.03
20 20 0.61
21 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTTAATATATATTTTTATAA
Found at i:214651 original size:18 final size:18
Alignment explanation
Indices: 214628--214665 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
214618 GGTTTTCTGA
*
214628 AAAATGGAAATGA-AAATG
1 AAAAT-GAAATAAGAAATG
214646 AAAATGAAATAAGAAATG
1 AAAATGAAATAAGAAATG
214664 AA
1 AA
214666 TTAATTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (18 bp):
AAAATGAAATAAGAAATG
Found at i:214843 original size:26 final size:26
Alignment explanation
Indices: 214807--214859 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
214797 AAATATATTT
*
214807 TCTTCATAATTTTACTAGGGGTAAAA
1 TCTTCATAATTTTACTAGGAGTAAAA
*
214833 TCTTTATAATTTTACTAGGAGTAAAA
1 TCTTCATAATTTTACTAGGAGTAAAA
214859 T
1 T
214860 TGGGATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (26 bp):
TCTTCATAATTTTACTAGGAGTAAAA
Found at i:221312 original size:14 final size:13
Alignment explanation
Indices: 221289--221319 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
221279 ACTTTTCAAC
221289 AAAAAAATAAAAT
1 AAAAAAATAAAAT
221302 AAAATAAATAAAAT
1 AAAA-AAATAAAAT
221316 AAAA
1 AAAA
221320 CATCAGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:222538 original size:23 final size:25
Alignment explanation
Indices: 222496--222547 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
222486 AAGATAAAAT
** *
222496 AAAATTCAAATTAAATAAAC-A-CA
1 AAAATTCAAAAAAAAAAAACTAGCA
222519 AAAATTCAAAAAAAAAAAACTAGCA
1 AAAATTCAAAAAAAAAAAACTAGCA
222544 AAAA
1 AAAA
222548 GTACATGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 1 0.04
25 6 0.25
ACGTcount: A:0.71, C:0.12, G:0.02, T:0.15
Consensus pattern (25 bp):
AAAATTCAAAAAAAAAAAACTAGCA
Found at i:223315 original size:23 final size:22
Alignment explanation
Indices: 223282--223336 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
223272 AAATTTAACA
223282 TTTAATGTTTAGTTCTT-TTATTAT
1 TTTAAT-TTTA-TTCTTCTTA-TAT
* *
223306 TTTGATTTTATTTTTCTTATAT
1 TTTAATTTTATTCTTCTTATAT
223328 TTTAATTTT
1 TTTAATTTT
223337 TAACCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 15 0.56
23 7 0.26
24 5 0.19
ACGTcount: A:0.20, C:0.04, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTAATTTTATTCTTCTTATAT
Found at i:224972 original size:25 final size:23
Alignment explanation
Indices: 224944--224989 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
224934 GTTGGATCCA
224944 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
224969 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
224990 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:225076 original size:13 final size:13
Alignment explanation
Indices: 225055--225088 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
225045 ACAATATAAT
225055 AATAATAATCCTA
1 AATAATAATCCTA
*
225068 AATATTAATCCTA
1 AATAATAATCCTA
*
225081 AAAAATAA
1 AATAATAA
225089 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:226074 original size:15 final size:13
Alignment explanation
Indices: 226056--226092 Score: 56
Period size: 13 Copynumber: 2.7 Consensus size: 13
226046 TTTTTTCGAC
226056 TTTTTTTTTCATATA
1 TTTTTTTTT-AT-TA
226071 TTTTTTTTTATTA
1 TTTTTTTTTATTA
226084 TTTTTTTTT
1 TTTTTTTTT
226093 TCTAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.50
14 2 0.09
15 9 0.41
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTATTA
Found at i:226093 original size:15 final size:14
Alignment explanation
Indices: 226029--226094 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
226019 TTTCTTCTTC
*
226029 TTTTTTTCAATTTTCT
1 TTTTTTTC-ATATT-T
* *
226045 TTTTTTTC-GACTT
1 TTTTTTTCATATTT
226058 TTTTTTTCATATATT
1 TTTTTTTCATAT-TT
226073 TTTTTTT-ATTATTT
1 TTTTTTTCA-TATTT
226087 TTTTTTTC
1 TTTTTTTC
226095 TAAATAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 9 0.22
14 12 0.29
15 12 0.29
16 8 0.20
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTTTCATATTT
Found at i:227037 original size:6 final size:6
Alignment explanation
Indices: 227026--227079 Score: 67
Period size: 6 Copynumber: 9.3 Consensus size: 6
227016 GTGCATAATG
* * *
227026 AAAATA AAAATA AAAAT- AAAAT- AAAATA AAACTA AAAATA AAATTG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
227072 AAAATA AA
1 AAAATA AA
227080 TATACTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
5 10 0.24
6 31 0.76
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:227040 original size:5 final size:5
Alignment explanation
Indices: 227026--227079 Score: 54
Period size: 5 Copynumber: 9.6 Consensus size: 5
227016 GTGCATAATG
227026 AAAAT AAAAAT AAAAAT AAAAT AAAAT AAAACT AAAAAT AAAATT GAAAAT
1 AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAA-T -AAAAT
227077 AAA
1 AAA
227080 TATACTAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 21 0.48
6 15 0.34
7 8 0.18
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:227176 original size:14 final size:14
Alignment explanation
Indices: 227138--227179 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
227128 TTAATTTTTT
227138 TAAAAAAAATGAAAG
1 TAAAAAAAAT-AAAG
*
227153 TAAAATAAATAAA-
1 TAAAAAAAATAAAG
227166 TAAATAAAAATAAA
1 TAAA-AAAAATAAA
227180 AATACTCGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 11 0.46
15 9 0.38
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (14 bp):
TAAAAAAAATAAAG
Found at i:232627 original size:13 final size:13
Alignment explanation
Indices: 232596--232651 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
232586 ATAAAAGGGA
232596 AAAAAATCAAAAT
1 AAAAAATCAAAAT
*
232609 AGAAAAAT-TAAAT
1 A-AAAAATCAAAAT
* *
232622 TAAAAATGAAAAT
1 AAAAAATCAAAAT
*
232635 AATAAAATAAAAAT
1 AA-AAAATCAAAAT
232649 AAA
1 AAA
232652 TAATAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 6 0.17
13 11 0.31
14 18 0.51
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (13 bp):
AAAAAATCAAAAT
Found at i:232641 original size:26 final size:26
Alignment explanation
Indices: 232597--232660 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
232587 TAAAAGGGAA
* * *
232597 AAAAATCAAAATAGAAAAATTAAATT
1 AAAAATAAAAATAGAAAAATAAAAAT
*
232623 AAAAATGAAAATA-ATAAAATAAAAAT
1 AAAAATAAAAATAGA-AAAATAAAAAT
232649 AAATAATAAAAA
1 AAA-AATAAAAA
232661 ATGGTTAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 1 0.03
26 24 0.75
27 7 0.22
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (26 bp):
AAAAATAAAAATAGAAAAATAAAAAT
Found at i:232647 original size:14 final size:13
Alignment explanation
Indices: 232596--232660 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
232586 ATAAAAGGGA
*
232596 AAAAAATCAAAAT
1 AAAAAATAAAAAT
*
232609 AGAAAAAT-TAAAT
1 A-AAAAATAAAAAT
* *
232622 TAAAAATGAAAAT
1 AAAAAATAAAAAT
232635 AATAAAATAAAAAT
1 AA-AAAATAAAAAT
*
232649 AAATAATAAAAA
1 AAAAAATAAAAA
232661 ATGGTTAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.14
13 19 0.44
14 18 0.42
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:233752 original size:25 final size:23
Alignment explanation
Indices: 233724--233769 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
233714 GTTGGATCCA
233724 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
233749 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
233770 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:248527 original size:29 final size:30
Alignment explanation
Indices: 248490--248551 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
248480 AGGAGAGTTC
*
248490 GGGATGAAAACGTG-ATTTTTGAAGAATTTG
1 GGGATGAAAA-GTGAATTTTTGAAAAATTTG
*
248520 GGGA-GAAAATTGAAATTTTTGAAAAATTTG
1 GGGATGAAAAGTG-AATTTTTGAAAAATTTG
248550 GG
1 GG
248552 ATTGAAGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
29 5 0.18
30 21 0.75
ACGTcount: A:0.37, C:0.02, G:0.29, T:0.32
Consensus pattern (30 bp):
GGGATGAAAAGTGAATTTTTGAAAAATTTG
Found at i:248662 original size:30 final size:28
Alignment explanation
Indices: 248612--248836 Score: 144
Period size: 30 Copynumber: 7.6 Consensus size: 28
248602 GCTCAAGGGT
* *
248612 AAAATGGTGATTTTTGGAAGTTTGGGAGAA
1 AAAAT-GTAATTTTTGGAAGTTCGGG-GAA
*
248642 AAAATGTAATTTTTGAGAAGTTCAGGGGTA
1 AAAATGTAATTTTTG-GAAGTTC-GGGGAA
** * *
248672 AAAATGTGTTTTTTGAAAGTACGGGGATA
1 AAAATGTAATTTTTGGAAGTTCGGGGA-A
* * **
248701 AAAATGTGATTTTAGGAAGTTCGAGGGTC
1 AAAATGTAATTTTTGGAAGTTCG-GGGAA
* * *
248730 AAAATATAATTTTTGGAAAGTTCCAGGGCA
1 AAAATGTAATTTTTGG-AAGTT-CGGGGAA
* **
248760 AAAATGTAATTTTTGGAAGTTTGAGGGTC
1 AAAATGTAATTTTTGGAAGTTCG-GGGAA
* ** **
248789 AAAATGTTATTTTTAAAAAGTTCGAGGGTC
1 AAAATGTAATTTTT-GGAAGTTCG-GGGAA
*
248819 AAAATGTGATTTTTGGAA
1 AAAATGTAATTTTTGGAA
248837 AATTTAAGGA
Statistics
Matches: 155, Mismatches: 32, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
28 4 0.03
29 70 0.45
30 77 0.50
31 4 0.03
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTCGGGGAA
Found at i:248685 original size:59 final size:56
Alignment explanation
Indices: 248583--248836 Score: 195
Period size: 59 Copynumber: 4.3 Consensus size: 56
248573 GATTGAGGGT
* * * * *
248583 AAAATGGTAATTTTAGGATGCTCAAGGGTAAAATGGTGATTTTTGGAAGTTTGGGAGAA
1 AAAAT-GTAATTTTTGGAAGTTCGAGGGTAAAAT-GTGATTTTTGGAAGTTCGGG-GAA
* * *
248642 AAAATGTAATTTTTGAGAAGTTC-AGGGGTAAAAATGTGTTTTTTGAAAGTACGGGGATA
1 AAAATGTAATTTTTG-GAAGTTCGA-GGGT-AAAATGTGATTTTTGGAAGTTCGGGGA-A
* * * * * *
248701 AAAATGTGATTTTAGGAAGTTCGAGGGTCAAAATATAATTTTTGGAAAGTTCCAGGGCA
1 AAAATGTAATTTTTGGAAGTTCGAGGGT-AAAATGTGATTTTTGG-AAGTT-CGGGGAA
* * ** **
248760 AAAATGTAATTTTTGGAAGTTTGAGGGTCAAAATGTTATTTTTAAAAAGTTCGAGGGTC
1 AAAATGTAATTTTTGGAAGTTCGAGGGT-AAAATGTGATTTTT-GGAAGTTCG-GGGAA
*
248819 AAAATGTGATTTTTGGAA
1 AAAATGTAATTTTTGGAA
248837 AATTTAAGGA
Statistics
Matches: 158, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
58 36 0.23
59 113 0.72
60 9 0.06
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (56 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGTGATTTTTGGAAGTTCGGGGAA
Found at i:248733 original size:29 final size:29
Alignment explanation
Indices: 248565--248836 Score: 198
Period size: 29 Copynumber: 9.3 Consensus size: 29
248555 GAAGTCGAAC
248565 TTTTGGAAGATT-GAGGGT-AAAATGGTAAT
1 TTTTGGAAG-TTCGAGGGTCAAAAT-GTAAT
* * * * *
248594 TTTAGGATGCTCAAGGGT-AAAATGGTGAT
1 TTTTGGAAGTTCGAGGGTCAAAAT-GTAAT
* **
248623 TTTTGGAAGTTTG-GGAGAAAAAATGTAAT
1 TTTTGGAAGTTCGAGG-GTCAAAATGTAAT
* **
248652 TTTTGAGAAGTTC-AGGGGTAAAAATGTGTT
1 TTTTG-GAAGTTCGA-GGGTCAAAATGTAAT
* * * *
248682 TTTTGAAAGTACG-GGGATAAAAATGTGAT
1 TTTTGGAAGTTCGAGGG-TCAAAATGTAAT
* *
248711 TTTAGGAAGTTCGAGGGTCAAAATATAAT
1 TTTTGGAAGTTCGAGGGTCAAAATGTAAT
*
248740 TTTTGGAAAGTTCCAGGG-CAAAAATGTAAT
1 TTTTGG-AAGTTCGAGGGTC-AAAATGTAAT
* *
248770 TTTTGGAAGTTTGAGGGTCAAAATGTTAT
1 TTTTGGAAGTTCGAGGGTCAAAATGTAAT
** *
248799 TTTTAAAAAGTTCGAGGGTCAAAATGTGAT
1 TTTT-GGAAGTTCGAGGGTCAAAATGTAAT
248829 TTTTGGAA
1 TTTTGGAA
248837 AATTTAAGGA
Statistics
Matches: 193, Mismatches: 37, Indels: 26
0.75 0.14 0.10
Matches are distributed among these distances:
28 6 0.03
29 105 0.54
30 80 0.41
31 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
TTTTGGAAGTTCGAGGGTCAAAATGTAAT
Found at i:249906 original size:10 final size:10
Alignment explanation
Indices: 249891--249961 Score: 54
Period size: 10 Copynumber: 6.7 Consensus size: 10
249881 TTCAGCTTCT
249891 TTTATTATTA
1 TTTATTATTA
*
249901 TTTATTAAATA
1 TTTATT-ATTA
249912 TTATTATTATTA
1 -T-TTATTATTA
*
249924 TTCATTATTCA
1 TTTATTATT-A
*
249935 TTTATTACTA
1 TTTATTATTA
*
249945 TGCT-TTATTA
1 T-TTATTATTA
249955 TTTATTA
1 TTTATTA
249962 ATTACTATCT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 1 0.02
10 24 0.51
11 13 0.28
12 4 0.09
13 5 0.11
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTATTATTA
Found at i:250576 original size:26 final size:26
Alignment explanation
Indices: 250547--250596 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
250537 TTTAAGTCTG
250547 TTTGGAATTGT-TTTTGGACATTTTTA
1 TTTGGAATTGTATTTTGGAC-TTTTTA
**
250573 TTTGGGCTTGTATTTTGGACTTTT
1 TTTGGAATTGTATTTTGGACTTTT
250597 AAACTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.14, C:0.06, G:0.22, T:0.58
Consensus pattern (26 bp):
TTTGGAATTGTATTTTGGACTTTTTA
Found at i:250621 original size:23 final size:23
Alignment explanation
Indices: 250594--250737 Score: 105
Period size: 23 Copynumber: 6.0 Consensus size: 23
250584 ATTTTGGACT
* * *
250594 TTTAAACTAAATTTAAAATTAAG
1 TTTAAAATAAATTTAAATTTAAA
**
250617 TTTAAAA-CCATTTCAAATTTTAAA
1 TTTAAAATAAATTT-AAA-TTTAAA
250641 TTTAAAATAAATTTAAATTTAAA
1 TTTAAAATAAATTTAAATTTAAA
*
250664 CTTAAAATAAATTTAAATTTCAAA
1 TTTAAAATAAATTTAAATTT-AAA
*
250688 --TAAATTTAAATTTAAAACAAATTTAAA
1 TTTAAA-ATAAATTT-----AAATTTAAA
* *
250715 CTTAAAATAAATTTAAAATTAAA
1 TTTAAAATAAATTTAAATTTAAA
250738 AGTTGGATTT
Statistics
Matches: 98, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
22 8 0.08
23 49 0.50
24 17 0.17
25 4 0.04
27 3 0.03
28 13 0.13
29 4 0.04
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.39
Consensus pattern (23 bp):
TTTAAAATAAATTTAAATTTAAA
Found at i:250657 original size:17 final size:17
Alignment explanation
Indices: 250654--250738 Score: 125
Period size: 17 Copynumber: 5.0 Consensus size: 17
250644 AAAATAAATT
250654 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
* *
250671 TAAATTTAAATTTCAAA
1 TAAATTTAAACTTAAAA
*
250688 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
*
250705 CAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
*
250722 TAAATTTAAAATTAAAA
1 TAAATTTAAACTTAAAA
250739 GTTGGATTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 61 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:250738 original size:6 final size:6
Alignment explanation
Indices: 250635--250737 Score: 83
Period size: 6 Copynumber: 18.0 Consensus size: 6
250625 CATTTCAAAT
* * *
250635 TTTAAA TTTAAA -ATAAA TTTAAA TTTAAA CTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * *
250681 TTTCAAA --TAAA TTTAAA TTTAAA -ACAAA TTTAAA CTTAAA -ATAAA
1 TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
250726 TTTAAA ATTAAA
1 TTTAAA TTTAAA
250738 AGTTGGATTT
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
4 3 0.04
5 16 0.21
6 55 0.71
7 3 0.04
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (6 bp):
TTTAAA
Found at i:251291 original size:78 final size:79
Alignment explanation
Indices: 251188--251632 Score: 265
Period size: 78 Copynumber: 5.7 Consensus size: 79
251178 AGAGATTGGA
* * * *
251188 TGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATCGTATGACTACAATCTGCCCT-AGAC
1 TGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGACTGCAATCTGCCCTCAG-C
251252 TTAG-AGTAAGAGAT
65 TTAGTAGTAAGAGAT
* * * ** * *
251266 TGGTTGATGGTAATCTGCCCTAGGCTCAGGGTAAAAGATCGAATGGTTGTAATCTG-CCTCAGGT
1 TGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGACTGCAATCTGCCCTCAGCT
* *
251330 TCGTGGTAAGAGAT
66 TAGTAGTAAGAGAT
* * *
251344 TTGCTGATGATGATCTGCCCTAGGCTTGGGGTAAAAGATCGAATGACTGCAATCTGCCC-CAAG-
1 TGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGACTGCAATCTGCCCTC-AGC
* **
251407 TTCGGGGTAAGAGAT
65 TTAGTAGTAAGAGAT
* * * * * * * * * * * **
251422 TGACTGGTGATGATTTGCCCCAAGCTCGAGGTAAGAGATCTG-CTGGCTGCAATTTATCC-CAGG
1 TGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATC-GAATGACTGCAATCTGCCCTCA-G
* **
251485 C-TCGGGGTAAGAGAT
64 CTTAGTAGTAAGAGAT
* * ** * * * *
251500 TTGTTGATAATGGTCTG-CCTAAGGCTCGGGGTAAGAGATCGAAT-AGCTGCCATTTG-CCTCAG
1 TGGCTGATGGTGATCTGCCCT-AGGCTCGGGGTAAAAGATCGAATGA-CTGCAATCTGCCCTCA-
*
251562 GC-TCG-AGGTAAGAGAT
63 GCTTAGTA-GTAAGAGAT
* * * *
251578 TGGCTG-TGATGATCTGCCC-AGGCTCGGGGTAAGAGATCTG-CTGGCTGCAATCTGC
1 TGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATC-GAATGACTGCAATCTGC
251633 TCTAGGCTCG
Statistics
Matches: 291, Mismatches: 60, Indels: 33
0.76 0.16 0.09
Matches are distributed among these distances:
76 28 0.10
77 21 0.07
78 237 0.81
79 5 0.02
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (79 bp):
TGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGACTGCAATCTGCCCTCAGCT
TAGTAGTAAGAGAT
Found at i:251360 original size:39 final size:39
Alignment explanation
Indices: 251317--251809 Score: 213
Period size: 39 Copynumber: 12.7 Consensus size: 39
251307 AATGGTTGTA
* *
251317 ATCTGCCTCAGGTTCGTGGTAAGAGATTTGCTGATGATG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* *
251356 ATCTGCC-CTAGGCTTGGGGTAAAAGA--T-C-GAATGACTG
1 ATCTGCCTC-AGGCTCGGGGTAAGAGATTTGCTG-ATGA-TG
* * * *
251393 CAATCTGCCCCAAGTTCGGGGTAAGAGA-TTGACTGGTGATG
1 --ATCTGCCTCAGGCTCGGGGTAAGAGATTTG-CTGATGATG
* * * * * *
251434 ATTTGCCCCAAGCTCGAGGTAAGAGATCTGCTG--GCTG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* * * *
251471 CAATTTATCC-CAGGCTCGGGGTAAGAGATTTGTTGATAATG
1 --ATCT-GCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* * *
251512 GTCTGCCTAAGGCTCGGGGTAAGAGA--T-C-GAATAGCTG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTG-AT-GATG
* * *
251549 CCATTTGCCTCAGGCTCGAGGTAAGAGATTGGCTG-TGATG
1 --ATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* *
251589 ATCTGCC-CAGGCTCGGGGTAAGAGATCTGCTG--GCTG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* *
251625 CAATCTG-CTCTAGGCTCGGGGTAAGAGATTTGTTAATGATG
1 --ATCTGCCTC-AGGCTCGGGGTAAGAGATTTGCTGATGATG
* * * * * *
251666 ACCAGCCCCAGGCTCGGGGTAAGAGATTGGATGATGGTG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* * * * * * * * * *
251705 ATCTATCC-CAAGATTGAGGTAAAAG-GTTGAATGGCTG-TA
1 ATCT-GCCTCAGGCTCGGGGTAAGAGATTTG-CT-GATGATG
251744 ATCTGCC-CTAGGCTCGGGGTAAGAGA-TTGACTGATGATG
1 ATCTGCCTC-AGGCTCGGGGTAAGAGATTTG-CTGATGATG
* * *
251783 ATCTGCCCCAAGCTCGAGGTAAGAGAT
1 ATCTGCCTCAGGCTCGGGGTAAGAGAT
251810 CGAATCTTCA
Statistics
Matches: 341, Mismatches: 73, Indels: 79
0.69 0.15 0.16
Matches are distributed among these distances:
35 2 0.01
36 10 0.03
37 32 0.09
38 23 0.07
39 242 0.71
40 17 0.05
41 8 0.02
42 5 0.01
43 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (39 bp):
ATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATG
Found at i:263720 original size:30 final size:30
Alignment explanation
Indices: 263638--263849 Score: 175
Period size: 30 Copynumber: 7.2 Consensus size: 30
263628 GAAGTCGAAC
*
263638 TTTTGA-AAGATTGAGGGT-AAAATGGTAA-
1 TTTTGAGAAGTTTGAGGGTCAAAAT-GTAAT
* * * * * * *
263666 TTTTAAGATGCTCGACGGTAAAAATGTGAT
1 TTTTGAGAAGTTTGAGGGTCAAAATGTAAT
* * *
263696 TTTTGAGAAGTTCGAGGTTTAAAATGTAAT
1 TTTTGAGAAGTTTGAGGGTCAAAATGTAAT
* * *
263726 TTTT-AGAAAGTTTAAGGCTAAAAATGTAAT
1 TTTTGAG-AAGTTTGAGGGTCAAAATGTAAT
*
263756 TTTTG-GAAGTTTGAGAGTCAAAATGTAAT
1 TTTTGAGAAGTTTGAGGGTCAAAATGTAAT
263785 TTTTG-GAAAGTTTGAGGGTCAAAATGTAAT
1 TTTTGAG-AAGTTTGAGGGTCAAAATGTAAT
* * * * *
263815 TTTTGAAAAGTTCGAGGGTCCAAATATGAT
1 TTTTGAGAAGTTTGAGGGTCAAAATGTAAT
263845 TTTTG
1 TTTTG
263850 GAAAATTCAG
Statistics
Matches: 150, Mismatches: 27, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
28 5 0.03
29 38 0.25
30 107 0.71
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (30 bp):
TTTTGAGAAGTTTGAGGGTCAAAATGTAAT
Found at i:263779 original size:59 final size:60
Alignment explanation
Indices: 263684--263831 Score: 201
Period size: 59 Copynumber: 2.5 Consensus size: 60
263674 TGCTCGACGG
* *
263684 TAAAAATGTGATTTTTGAGAAGTTCGAGGTTTAAAATGTAATTTTTAGAAAGTTTAAGGC
1 TAAAAATGTAATTTTTGAGAAGTTCGAGGTTCAAAATGTAATTTTTAGAAAGTTTAAGGC
* * * *
263744 TAAAAATGTAATTTTTG-GAAGTTTGAGAG-TCAAAATGTAATTTTTGGAAAGTTTGAGGG
1 TAAAAATGTAATTTTTGAGAAGTTCGAG-GTTCAAAATGTAATTTTTAGAAAGTTTAAGGC
* *
263803 TCAAAATGTAATTTTTGAAAAGTTCGAGG
1 TAAAAATGTAATTTTTGAGAAGTTCGAGG
263832 GTCCAAATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 52 0.68
60 25 0.32
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.37
Consensus pattern (60 bp):
TAAAAATGTAATTTTTGAGAAGTTCGAGGTTCAAAATGTAATTTTTAGAAAGTTTAAGGC
Found at i:263847 original size:89 final size:89
Alignment explanation
Indices: 263686--263852 Score: 203
Period size: 89 Copynumber: 1.9 Consensus size: 89
263676 CTCGACGGTA
* * * *
263686 AAAATGTGATTTTTGAGAAGTTCGAGGTTTAAAATGTAATTTTTAGAAAGTTTAAGGCTAAAAAT
1 AAAATGTAATTTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTTAGAAAGTTCAAGGCTAAAAAT
*
263751 GTAATTTTTGGAAGTTTGAGAGTC
66 ATAATTTTTGGAAGTTTGAGAGTC
* * * **
263775 AAAATGTAATTTTTG-GAAAGTTTGAGGGTCAAAATGTAATTTTT-GAAAAGTTCGAGGGTCCAA
1 AAAATGTAATTTTTGAG-AAGTTCGAGGGTCAAAATGTAATTTTTAG-AAAGTTCAAGGCTAAAA
*
263838 ATATGATTTTTGGAA
64 ATATAATTTTTGGAA
263853 AATTCAGGGA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
88 2 0.03
89 63 0.97
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (89 bp):
AAAATGTAATTTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTTAGAAAGTTCAAGGCTAAAAAT
ATAATTTTTGGAAGTTTGAGAGTC
Found at i:264927 original size:10 final size:10
Alignment explanation
Indices: 264912--264979 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 10
264902 TTCAGCTTCT
264912 TTTATTATTA
1 TTTATTATTA
*
264922 TTTATTA-AA
1 TTTATTATTA
264931 TATTATTATTA
1 T-TTATTATTA
*
264942 TTTGTTATTCA
1 TTTATTATT-A
*
264953 TTTATTACTA
1 TTTATTATTA
*
264963 TGCT-TTATTA
1 T-TTATTATTA
264973 TTTATTA
1 TTTATTA
264980 GTTACTATCT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
9 3 0.07
10 31 0.69
11 11 0.24
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTATTATTA
Found at i:265676 original size:17 final size:17
Alignment explanation
Indices: 265646--265741 Score: 75
Period size: 17 Copynumber: 5.2 Consensus size: 17
265636 AAACCATTTC
265646 AAATTTTAAATTTAAAAT
1 AAATTTT-AATTTAAAAT
*
265664 AAATTTTAATTTAAACTTAAA
1 AAATTTTAATTT-AA---AAT
*
265685 ATAATTTTAAATTTCAAAT
1 A-AATTTT-AATTTAAAAT
* *
265704 AAATTTAAATTTAAAAC
1 AAATTTTAATTTAAAAT
* *
265721 AAATTTAAACTTAAAAT
1 AAATTTTAATTTAAAAT
265738 AAAT
1 AAAT
265742 CTAAAATTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
17 32 0.50
18 14 0.22
19 3 0.05
21 3 0.05
22 7 0.11
23 5 0.08
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTTTAATTTAAAAT
Found at i:265684 original size:47 final size:47
Alignment explanation
Indices: 265609--265719 Score: 109
Period size: 47 Copynumber: 2.4 Consensus size: 47
265599 ATTTGGGACT
* ** * *
265609 TTTAAACTAAATTTAAAATTAAGTTTAAAACCATTTCAAATTTTAAA
1 TTTAAAATAAATTTAAAATTAAACTTAAAACAATTTCAAATTTCAAA
* * * *
265656 TTTAAAATAAATTTTAATTTAAACTTAAAATAATTTTAAATTTCAAA
1 TTTAAAATAAATTTAAAATTAAACTTAAAACAATTTCAAATTTCAAA
*
265703 --TAAATTTAAATTTAAAA
1 TTTAAA-ATAAATTTAAAA
265720 CAAATTTAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
45 4 0.08
46 9 0.18
47 38 0.75
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (47 bp):
TTTAAAATAAATTTAAAATTAAACTTAAAACAATTTCAAATTTCAAA
Found at i:265697 original size:23 final size:24
Alignment explanation
Indices: 265641--265741 Score: 75
Period size: 23 Copynumber: 4.1 Consensus size: 24
265631 GTTTAAAACC
* *
265641 ATTTCAAATTTTAAATTTAAAATAA
1 ATTTTAAA-TTTAAACTTAAAATAA
265666 ATTTT-AATTTAAACTTAAAAT-A
1 ATTTTAAATTTAAACTTAAAATAA
*
265688 ATTTTAAATTTCAAA--TAAATTTAA
1 ATTTTAAATTT-AAACTTAAA-ATAA
*
265712 ATTTAAAACAAATTTAAACTTAAAATAA
1 ATTT----TAAATTTAAACTTAAAATAA
265740 AT
1 AT
265742 CTAAAATTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
22 10 0.16
23 19 0.31
24 10 0.16
25 4 0.07
27 3 0.05
28 11 0.18
29 4 0.07
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTTTAAATTTAAACTTAAAATAA
Found at i:265735 original size:40 final size:39
Alignment explanation
Indices: 265651--265735 Score: 91
Period size: 40 Copynumber: 2.1 Consensus size: 39
265641 ATTTCAAATT
* **
265651 TTAAATTTAAAATAAATTTTAATTTAAACTTAAAATAATT
1 TTAAATTTAAAATAAATTTAAATTTAAAC-TAAAATAAAC
* *
265691 TTAAATTTCAAATAAATTTAAATTTAAAAC-AAATTTAAAC
1 TTAAATTTAAAATAAATTTAAATTT-AAACTAAA-ATAAAC
265731 TTAAA
1 TTAAA
265736 ATAAATCTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 3 0.08
40 31 0.82
41 4 0.11
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (39 bp):
TTAAATTTAAAATAAATTTAAATTTAAACTAAAATAAAC
Found at i:265746 original size:17 final size:17
Alignment explanation
Indices: 265671--265753 Score: 103
Period size: 17 Copynumber: 4.9 Consensus size: 17
265661 AATAAATTTT
265671 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
* * *
265688 ATTTTAAATTTCAAATA
1 AATTTAAACTTAAAATA
* *
265705 AATTTAAATTTAAAACA
1 AATTTAAACTTAAAATA
265722 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
* *
265739 AATCTAAAATTAAAA
1 AATTTAAACTTAAAA
265754 GTTGGATTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:267866 original size:27 final size:27
Alignment explanation
Indices: 267808--267866 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
267798 CTGTTACAAC
* *
267808 GAACTTTGAAGGAAAGGCACGTATTGA
1 GAACTTTGAAGGAAAGACACGTATAGA
* *
267835 AAACTTTGAAGGAATA-ACATGTATAGA
1 GAACTTTGAAGGAA-AGACACGTATAGA
267862 GAACT
1 GAACT
267867 CGAAAAGGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (27 bp):
GAACTTTGAAGGAAAGACACGTATAGA
Found at i:282814 original size:13 final size:14
Alignment explanation
Indices: 282785--282814 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
282775 CTCAGTACGT
282785 TGACATTTAACCTC
1 TGACATTTAACCTC
282799 TGACATTTAA-CTC
1 TGACATTTAACCTC
282812 TGA
1 TGA
282815 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:284336 original size:168 final size:168
Alignment explanation
Indices: 284058--284387 Score: 624
Period size: 168 Copynumber: 2.0 Consensus size: 168
284048 TGAGCCTCTG
284058 TCAGAATGTCTTGTCTCAAATCAGAATCGTTCGGAATACATACCCTGCCTCTATAATACAACATA
1 TCAGAATGTCTTGTCTCAAATCAGAATCGTTCGGAATACATACCCTGCCTCTATAATACAACATA
* * *
284123 CCCTCTATATCAACTGTAAACCCCGTAGTAGCATCACTCTGTATCTACTCCCTTTTATCTATAAG
66 CCCTCTATATCAACTATAAACCCCGTAGTAGCATCACTCTGTATCTACTCCCATTTAGCTATAAG
284188 CTTTGGATCCTTTCTCTGTACTTCTTGAATTCTGTACT
131 CTTTGGATCCTTTCTCTGTACTTCTTGAATTCTGTACT
*
284226 TCAGAATGTCTTGTCTCAAATCCGAATCGTTCGGAATACATACCCTGCCTCTATAATACAACATA
1 TCAGAATGTCTTGTCTCAAATCAGAATCGTTCGGAATACATACCCTGCCTCTATAATACAACATA
284291 CCCTCTATATCAACTATAAACCCCGTAGTAGCATCACTCTGTATCTACTCCCATTTAGCTATAAG
66 CCCTCTATATCAACTATAAACCCCGTAGTAGCATCACTCTGTATCTACTCCCATTTAGCTATAAG
284356 CTTTGGATCCTTTCTCTGTACTTCTTGAATTC
131 CTTTGGATCCTTTCTCTGTACTTCTTGAATTC
284388 GCTGTAGAAA
Statistics
Matches: 158, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
168 158 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (168 bp):
TCAGAATGTCTTGTCTCAAATCAGAATCGTTCGGAATACATACCCTGCCTCTATAATACAACATA
CCCTCTATATCAACTATAAACCCCGTAGTAGCATCACTCTGTATCTACTCCCATTTAGCTATAAG
CTTTGGATCCTTTCTCTGTACTTCTTGAATTCTGTACT
Found at i:293206 original size:15 final size:14
Alignment explanation
Indices: 293155--293207 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
293145 CAATCATTTG
293155 AAAAAAGAAA-AGA
1 AAAAAAGAAATAGA
* *
293168 AACAAAGTAATAAGA
1 AAAAAAGAAAT-AGA
*
293183 AAAAGAGAAATAGA
1 AAAAAAGAAATAGA
293197 AAGAAAAGAAA
1 AA-AAAAGAAA
293208 GAAAATTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 8 0.26
14 5 0.16
15 18 0.58
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (14 bp):
AAAAAAGAAATAGA
Found at i:300959 original size:12 final size:14
Alignment explanation
Indices: 300942--300973 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
300932 TGTCAACACA
300942 TTTTACA-TTTC-C
1 TTTTACATTTTCAC
300954 TTTTACATTTTCAC
1 TTTTACATTTTCAC
300968 TTTTAC
1 TTTTAC
300974 TTGTTACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 4 0.22
14 7 0.39
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTACATTTTCAC
Found at i:302639 original size:35 final size:35
Alignment explanation
Indices: 302592--302658 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
302582 CTGTAATATA
*
302592 ATTGTCCATGCAT-TATTAATGTCATTGCATTTTTT
1 ATTGTCCATGCATCTA-CAATGTCATTGCATTTTTT
*
302627 ATTGTCGC-TGCATCTACATTGTCATTGCATTT
1 ATTGTC-CATGCATCTACAATGTCATTGCATTT
302659 CCATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
35 25 0.89
36 3 0.11
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (35 bp):
ATTGTCCATGCATCTACAATGTCATTGCATTTTTT
Found at i:306081 original size:18 final size:17
Alignment explanation
Indices: 306050--306096 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
306040 TCAGTCACCT
306050 GAAAAAGAAAAAAATGA
1 GAAAAAGAAAAAAATGA
*
306067 GAAAAAGGAAGAAAAT--
1 GAAAAA-GAAAAAAATGA
306083 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
306097 ATTGTGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 7 0.26
16 6 0.22
17 6 0.22
18 8 0.30
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (17 bp):
GAAAAAGAAAAAAATGA
Found at i:318423 original size:17 final size:16
Alignment explanation
Indices: 318374--318424 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
318364 AATTTAATTT
318374 TAATATAAATATTCAA
1 TAATATAAATATTCAA
*
318390 T-ATGATTAAACAATTCAA
1 TAAT-A-TAAA-TATTCAA
318408 TAATATAAATAGTTCAA
1 TAATATAAATA-TTCAA
318425 AATGTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
15 2 0.07
16 3 0.11
17 13 0.46
18 8 0.29
19 2 0.07
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (16 bp):
TAATATAAATATTCAA
Found at i:318979 original size:18 final size:17
Alignment explanation
Indices: 318955--319000 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
318945 AGGACAAAAA
318955 ATATCGATACTTGTCCAAG
1 ATATCGATACTT-T-CAAG
318974 -TATCGATACCTTTCAAG
1 ATATCGATA-CTTTCAAG
318991 ATATCGATAC
1 ATATCGATAC
319001 ACATAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.20
18 17 0.68
19 3 0.12
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (17 bp):
ATATCGATACTTTCAAG
Found at i:319127 original size:20 final size:21
Alignment explanation
Indices: 319055--319117 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
319045 CAAACAATGA
* *
319055 CAAAAAATATTGATACCTTTT
1 CAAAAAGTATCGATACCTTTT
319076 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTATCGATACCTTTT
319097 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTATCGATACCTTTT
319118 ATCAAGTATC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (21 bp):
CAAAAAGTATCGATACCTTTT
Found at i:319942 original size:181 final size:181
Alignment explanation
Indices: 319632--319994 Score: 609
Period size: 181 Copynumber: 2.0 Consensus size: 181
319622 TTAAACCTTA
*
319632 TCCTCAAAGGTTGCCAAATTAGTGAATTTAGAAAAACCTTTAGTTGTGGAAAGCTATGGTAGTAG
1 TCCTCAAAGGTTGCCAAATTAGTGAATTTAGAAAAACCTTTAGTTGTGAAAAGCTATGGTAGTAG
*
319697 AATAGGCAATTGGGGTCAAACCACTATAAAATTTTGTGTTCTTTGTTGCACAATATTTATTGCTT
66 AATAAGCAATTGGGGTCAAACCACTATAAAATTTTGTGTTCTTTGTTGCACAATATTTATTGCTT
* *
319762 CCACCAAAACATTTCAAAGGCCGATTCAACTTCCCGATTAGTGACCTGGAG
131 CCACCAAAACATTTCAAAGGCCGATTCAACTTCCCAATTACTGACCTGGAG
* * * *
319813 TCCTCCAAGGTTGCCAAATTAGTGAATTTAGAAAAATCTTTAGTTGTGAAAAGTTATGGTAGTGG
1 TCCTCAAAGGTTGCCAAATTAGTGAATTTAGAAAAACCTTTAGTTGTGAAAAGCTATGGTAGTAG
* * *
319878 AATAAGCAATTGGGGTCGAACCACTATAAATTTTTGTGTTCTTTGTTGCATAATATTTATTGCTT
66 AATAAGCAATTGGGGTCAAACCACTATAAAATTTTGTGTTCTTTGTTGCACAATATTTATTGCTT
* *
319943 TCACCACAACATTTCAAAGGCCGATTCAACTTCCCAATTACTGACCTGGAG
131 CCACCAAAACATTTCAAAGGCCGATTCAACTTCCCAATTACTGACCTGGAG
319994 T
1 T
319995 TGATCCTTCC
Statistics
Matches: 169, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
181 169 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (181 bp):
TCCTCAAAGGTTGCCAAATTAGTGAATTTAGAAAAACCTTTAGTTGTGAAAAGCTATGGTAGTAG
AATAAGCAATTGGGGTCAAACCACTATAAAATTTTGTGTTCTTTGTTGCACAATATTTATTGCTT
CCACCAAAACATTTCAAAGGCCGATTCAACTTCCCAATTACTGACCTGGAG
Found at i:320136 original size:20 final size:22
Alignment explanation
Indices: 320105--320149 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
320095 GGGGAGAAAT
*
320105 GGGAAGAAGTAAAAA-TTTTGA
1 GGGAAGAAGTAAAAAGGTTTGA
320126 GGGAA-AAGTAAAAAGGTTTGA
1 GGGAAGAAGTAAAAAGGTTTGA
320147 GGG
1 GGG
320150 CTTGGGGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (22 bp):
GGGAAGAAGTAAAAAGGTTTGA
Found at i:322369 original size:123 final size:123
Alignment explanation
Indices: 322149--322396 Score: 408
Period size: 123 Copynumber: 2.0 Consensus size: 123
322139 CCTCTGACAA
*
322149 GTGATACACTCTCTCACCAATTACTTCACAAGAATTTCCCAATAGTGGTTTACAACTACGGAGAG
1 GTGATACACTCCCTCACCAATTACTTCACAAGAATTTCCCAATAGTGGTTTACAACTACGGAGAG
* **
322214 AACATAAATGAAAATCCAATATTTTTATATATCTTTGGTTCATTTGTTCTATTGGTTT
66 AACATAAATGAAAATCCAATATTTTTAAATATCCCTGGTTCATTTGTTCTATTGGTTT
* * *
322272 GTGATACACTCCCTCACCCAA-TGCTTGACAAGAATTTCCCAATAGTGGTTTACAACTATGGAGA
1 GTGATACACTCCCTCA-CCAATTACTTCACAAGAATTTCCCAATAGTGGTTTACAACTACGGAGA
*
322336 GAACATAAATGAAAATCCAATATTTTTAAATATCCCTGGTTCATTTGTTTTATTGGTTT
65 GAACATAAATGAAAATCCAATATTTTTAAATATCCCTGGTTCATTTGTTCTATTGGTTT
322395 GT
1 GT
322397 AACTGAATAA
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
123 112 0.97
124 4 0.03
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (123 bp):
GTGATACACTCCCTCACCAATTACTTCACAAGAATTTCCCAATAGTGGTTTACAACTACGGAGAG
AACATAAATGAAAATCCAATATTTTTAAATATCCCTGGTTCATTTGTTCTATTGGTTT
Found at i:336727 original size:14 final size:14
Alignment explanation
Indices: 336708--336743 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
336698 TTGTTTGACT
*
336708 GAAAATGGTTTCTG
1 GAAAATGATTTCTG
336722 GAAAATGATTTCTG
1 GAAAATGATTTCTG
*
336736 AAAAATGA
1 GAAAATGA
336744 ATTATTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (14 bp):
GAAAATGATTTCTG
Found at i:336923 original size:22 final size:20
Alignment explanation
Indices: 336891--336930 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
336881 TTATTTTTTC
336891 ATTTTATTTTATATCTATTAA
1 ATTTTATTTTATAT-TATTAA
336912 ATTTATATTTTATATTATT
1 ATTT-TATTTTATATTATT
336931 TCTACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTATTTTATATTATTAA
Done.