Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007897.1 Hibiscus syriacus cultivar Beakdansim tig00110283_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 862109
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:832 original size:33 final size:33
Alignment explanation
Indices: 787--901 Score: 196
Period size: 33 Copynumber: 3.5 Consensus size: 33
777 TCTTTTGGTT
787 GAAATGAAAATCGCAACGAGAG-ATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
819 GAGGATGACAATCGCAACGAGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGAGAGAATCGCAACGC
853 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
886 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
902 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
32 2 0.03
33 63 0.82
34 12 0.16
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:847 original size:14 final size:14
Alignment explanation
Indices: 795--884 Score: 65
Period size: 14 Copynumber: 5.7 Consensus size: 14
785 TTGAAATGAA
795 AATCGCAACGAGAG
1 AATCGCAACGAGAG
809 -ATCGCAACGCGAGGATG
1 AATCGCAA--CGA-GA-G
826 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
842 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
861 AATCGCAACGAGAG
1 AATCGCAACGAGAG
875 AATCGCAACG
1 AATCGCAACG
885 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 24
0.70 0.02 0.27
Matches are distributed among these distances:
13 7 0.11
14 20 0.32
15 4 0.06
16 5 0.08
17 5 0.08
18 4 0.06
19 10 0.16
20 7 0.11
ACGTcount: A:0.41, C:0.23, G:0.27, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:866 original size:19 final size:19
Alignment explanation
Indices: 842--906 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
832 GCAACGAGAG
842 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
861 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
875 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
894 AATCGCAATGCGA
1 AATCGCAACGCGA
907 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:937 original size:14 final size:14
Alignment explanation
Indices: 918--972 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
908 TTTGGTTTCG
918 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
932 CGTTGCGATTTTCATTTCT
1 CGTTGCGA--TTC---TCT
951 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
965 CGTTGCGA
1 CGTTGCGA
973 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 19 0.53
16 3 0.08
17 3 0.08
19 11 0.31
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:955 original size:33 final size:33
Alignment explanation
Indices: 902--994 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
892 AAAATCGCAA
** *
902 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCTCGTTGCGATTCTCTCGT
935 TGCGATTTTCATTTCTCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCTCGTTGCGATTCTCTCGT
***
968 TGCGACAGTCATTCTCTCGTTGCGATT
1 TGCGATTTTCATT-TCTCGTTGCGATT
995 TTCATTTATC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.75
34 13 0.25
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCTCGTTGCGATTCTCTCGT
Found at i:999 original size:20 final size:20
Alignment explanation
Indices: 925--1013 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 20
915 TCGCGTTGCG
925 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
945 ATT-TCTCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
958 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
978 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
998 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1014 CTCTTCTGCA
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
13 3 0.05
14 10 0.18
19 10 0.18
20 21 0.37
21 13 0.23
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1133 original size:32 final size:32
Alignment explanation
Indices: 1094--1162 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
1084 ACTAACTTGA
*
1094 AAATCGCAACGAGAGAATAGCAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
* *
1126 AAATCGCAACGACAGAATCGTAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
1158 AAATC
1 AAATC
1163 TAAGTGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (32 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATG
Found at i:1136 original size:18 final size:18
Alignment explanation
Indices: 1113--1162 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
1103 CGAGAGAATA
1113 GCAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
*
1131 GCAA--CGACA-G-AATC
1 GCAACGCGAAATGAAATC
*
1145 GTAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
1163 TAAGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 8 0.32
17 1 0.04
18 8 0.32
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
GCAACGCGAAATGAAATC
Found at i:1391 original size:21 final size:22
Alignment explanation
Indices: 1340--1393 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1330 TGGTTGTGAG
**
1340 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1362 GGAAATCTTCGGAGAT-GGGAC
1 GGATTTCTTCGGAGATGGGGAC
1383 GGATTTCTTCG
1 GGATTTCTTCG
1394 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1559 original size:20 final size:20
Alignment explanation
Indices: 1534--1725 Score: 226
Period size: 20 Copynumber: 9.6 Consensus size: 20
1524 CTTTAAATAT
1534 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1554 CGCGTTGCGATTTATGTATTA
1 CGCGTTGCGATTTACGGA-TA
*
1575 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1594 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1614 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1634 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1654 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1674 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1694 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1714 CGCGTTGCGATT
1 CGCGTTGCGATT
1726 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 141 0.97
21 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1627 original size:60 final size:60
Alignment explanation
Indices: 1534--1725 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1524 CTTTAAATAT
*
1534 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
* * ***
1594 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCA-TACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTA-GCGTTGCGATTTACGGATA
* * * * ** *
1654 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
1714 CGCGTTGCGATT
1 CGCGTTGCGATT
1726 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
59 2 0.02
60 108 0.97
61 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
Found at i:1813 original size:20 final size:20
Alignment explanation
Indices: 1790--1832 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1780 GTTGCGATTT
1790 TGGAAACTGATTTGCAATTC
1 TGGAAACTGATTTGCAATTC
*
1810 TGGAAACTGATTTGCGATTC
1 TGGAAACTGATTTGCAATTC
1830 TGG
1 TGG
1833 GGATCGCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (20 bp):
TGGAAACTGATTTGCAATTC
Found at i:2547 original size:23 final size:23
Alignment explanation
Indices: 2520--2566 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
2510 GACTATCGTC
2520 TTAAAA-TTTTTATATTTTATATT
1 TTAAAACTTTTTATATTTT-TATT
2543 TTAAAACTTTTTTATATTTTTATT
1 TTAAAAC-TTTTTATATTTTTATT
2567 GATATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.27
24 4 0.18
25 12 0.55
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
TTAAAACTTTTTATATTTTTATT
Found at i:3477 original size:23 final size:23
Alignment explanation
Indices: 3451--3496 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3441 TACCACAGCT
*
3451 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCAAAGTGCCA
**
3474 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCAAAGTGCCA
3497 TATAATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCAAAGTGCCA
Found at i:3778 original size:30 final size:29
Alignment explanation
Indices: 3725--3783 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
3715 TGTAAACATA
* *
3725 TCACATATTCATATAAGCTCGTAGCTTCAT
1 TCACATATACATATAAGCACGTAG-TTCAT
* *
3755 TCACATATACATGTAATCACGTAGTTCAT
1 TCACATATACATATAAGCACGTAGTTCAT
3784 GTAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (29 bp):
TCACATATACATATAAGCACGTAGTTCAT
Found at i:4273 original size:25 final size:24
Alignment explanation
Indices: 4228--4274 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
4218 TCTAAACATA
*
4228 TATATACACTTAATCATATTTATT
1 TATATACACTTAATCACATTTATT
4252 TATATACTACTTTAATC-CATTTA
1 TATATAC-AC-TTAATCACATTTA
4275 ATTAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 7 0.35
26 6 0.30
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATACACTTAATCACATTTATT
Found at i:15157 original size:7 final size:7
Alignment explanation
Indices: 15151--15182 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
15141 GATATTGTCG
*
15151 CAGGTCG
1 CAGGTCA
15158 CAGGTCA
1 CAGGTCA
15165 CAGGTCA
1 CAGGTCA
15172 CAGGTCA
1 CAGGTCA
15179 CAGG
1 CAGG
15183 CTCTTAGCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CAGGTCA
Found at i:16657 original size:41 final size:41
Alignment explanation
Indices: 16600--16681 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
16590 ATAACATCGT
16600 AAGCCTAGTGGCAATCTCATTCCATTCCCTTACCTTGAAGA
1 AAGCCTAGTGGCAATCTCATTCCATTCCCTTACCTTGAAGA
16641 AAGCCTAGTGGCAATCTCATTCCATTCCCTTACCTTGAAGA
1 AAGCCTAGTGGCAATCTCATTCCATTCCCTTACCTTGAAGA
16682 TTCACGAAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (41 bp):
AAGCCTAGTGGCAATCTCATTCCATTCCCTTACCTTGAAGA
Found at i:17223 original size:20 final size:20
Alignment explanation
Indices: 17198--17339 Score: 142
Period size: 21 Copynumber: 7.0 Consensus size: 20
17188 GTAATACGAA
*
17198 TACGTAAATCGCAACGCGAT
1 TACGTAAATCGCAATGCGAT
17218 TACGTAAATCGCAATGCGAAT
1 TACGTAAATCGCAATGCG-AT
* *
17239 T-CGGAAAATCGCAATGCGAA
1 TAC-GTAAATCGCAATGCGAT
* *
17259 TATGTAAATCACAATGCGAT
1 TACGTAAATCGCAATGCGAT
17279 TACGTAAATCGCAATGCGAAT
1 TACGTAAATCGCAATGCG-AT
* * *
17300 TAGGAAAATCGCAACGCGAAT
1 TACGTAAATCGCAATGCG-AT
** *
17321 TTGGGAAATCGCAATGCGA
1 TACGTAAATCGCAATGCGA
17340 ATCTGACTAT
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
20 51 0.50
21 52 0.50
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (20 bp):
TACGTAAATCGCAATGCGAT
Found at i:17249 original size:21 final size:21
Alignment explanation
Indices: 17223--17359 Score: 131
Period size: 21 Copynumber: 6.7 Consensus size: 21
17213 GCGATTACGT
17223 AAATCGCAATGCGAATTCGGA
1 AAATCGCAATGCGAATTCGGA
*
17244 AAATCGCAATGCGAATAT--GT
1 AAATCGCAATGCGAAT-TCGGA
* *
17264 AAATCACAATGCG-ATTAC-GT
1 AAATCGCAATGCGAATT-CGGA
*
17284 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTCGGA
* * *
17305 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTCGGA
*
17326 AAATCGCAATGCGAA-TCTGA
1 AAATCGCAATGCGAATTCGGA
**
17346 CTATCGCAATGCGA
1 AAATCGCAATGCGA
17360 TTTACATAGC
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 41 0.42
21 52 0.54
22 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (21 bp):
AAATCGCAATGCGAATTCGGA
Found at i:17259 original size:61 final size:61
Alignment explanation
Indices: 17194--17320 Score: 209
Period size: 61 Copynumber: 2.1 Consensus size: 61
17184 ATTCGTAATA
* * *
17194 CGAATACGTAAATCGCAACGCGATTACGTAAATCGCAATGCGAATTCGGAAAATCGCAATG
1 CGAATACGTAAATCACAACGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAACG
* *
17255 CGAATATGTAAATCACAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAACG
1 CGAATACGTAAATCACAACGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAACG
17316 CGAAT
1 CGAAT
17321 TTGGGAAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (61 bp):
CGAATACGTAAATCACAACGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAACG
Found at i:17955 original size:21 final size:21
Alignment explanation
Indices: 17894--17972 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
17884 TTCTAAACGT
17894 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
17914 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
17934 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
17955 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
17973 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:17990 original size:33 final size:33
Alignment explanation
Indices: 17949--18018 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
17939 CGCAACGAGA
17949 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
17982 GAAATGAAAATCGCAACGATATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
18015 GAAA
1 GAAA
18019 CCAAAATCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:18025 original size:33 final size:33
Alignment explanation
Indices: 17955--18026 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
17945 GAGAGAAATG
**
17955 AAAATCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
* *
17988 AAAATCGCAACGATATAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
18021 AAAATC
1 AAAATC
18027 ACATTGCGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:18086 original size:33 final size:33
Alignment explanation
Indices: 18030--18099 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
18020 CAAAATCACA
* * *
18030 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCAATTTTAATTTAGCATTGCGATTCTCTCG
*
18063 TTGCAATTTTAATTTAGCGTTGCGATTCTCTCG
1 TTGCAATTTTAATTTAGCATTGCGATTCTCTCG
18096 TTGC
1 TTGC
18100 GATAGTCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCAATTTTAATTTAGCATTGCGATTCTCTCG
Found at i:18128 original size:20 final size:21
Alignment explanation
Indices: 18088--18151 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
18078 AGCGTTGCGA
* **
18088 TTCTCTCGTTGCGATAGTCAT
1 TTCTCACGTTGCGATTTTCAT
18109 TTC-CACGTTGCGATTTTCA-
1 TTCTCACGTTGCGATTTTCAT
*
18128 TTCTCTCGTTGCGATTTTCAT
1 TTCTCACGTTGCGATTTTCAT
18149 TTC
1 TTC
18152 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.08
20 28 0.76
21 6 0.16
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (21 bp):
TTCTCACGTTGCGATTTTCAT
Found at i:20051 original size:94 final size:94
Alignment explanation
Indices: 19842--20121 Score: 448
Period size: 94 Copynumber: 3.1 Consensus size: 94
19832 TAGATTGCTT
* * *
19842 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
19903 ATTTGTCTTT-TGTTGTCTTTTGGTT-AA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
19930 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
19995 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
20024 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
20089 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
20117 AGTAA
1 AGTAA
20122 TGCAATCAAT
Statistics
Matches: 179, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
88 34 0.19
90 3 0.02
91 2 0.01
92 29 0.16
93 20 0.11
94 91 0.51
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:20239 original size:20 final size:20
Alignment explanation
Indices: 20214--20256 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
20204 TTTTGGTTAA
20214 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
20234 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
20254 AAT
1 AAT
20257 TGCAACGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:20317 original size:19 final size:17
Alignment explanation
Indices: 20295--20391 Score: 62
Period size: 19 Copynumber: 5.7 Consensus size: 17
20285 GAAACTATAA
20295 TCGCGTTGCGACTTTCATT
1 TCGCGTTGCGA-TTTC-TT
*
20314 TCGCATTGCGA-TTC--
1 TCGCGTTGCGATTTCTT
*
20328 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTC-TT
*
20347 TCGTGTTGCGA-TTC--
1 TCGCGTTGCGATTTCTT
*
20361 TCTCGTTGCGATTTTCGTT
1 TCGCGTTGCGA-TTTC-TT
20380 TCGCGTTGCGAT
1 TCGCGTTGCGAT
20392 AGTCATTTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 21
0.67 0.09 0.24
Matches are distributed among these distances:
14 18 0.30
16 6 0.10
17 6 0.10
18 1 0.02
19 29 0.48
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.44
Consensus pattern (17 bp):
TCGCGTTGCGATTTCTT
Found at i:20338 original size:14 final size:14
Alignment explanation
Indices: 20319--20373 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
20309 TCATTTCGCA
20319 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
20333 TTGCGATTTTCATTTCGTG
1 TTGCGA--TTC-TCTC--G
20352 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
20366 TTGCGATT
1 TTGCGATT
20374 TTCGTTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 15 0.44
16 6 0.18
17 6 0.18
19 7 0.21
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:20344 original size:33 final size:33
Alignment explanation
Indices: 20298--20391 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
20288 ACTATAATCG
* *
20298 CGTTGCGACTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
20331 CGTTGCGATTTTCATTTCGTGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
20364 CGTTGCGATTTTCGTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
20392 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:20893 original size:21 final size:21
Alignment explanation
Indices: 20869--20935 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
20859 TCATTCCTCG
20869 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
20890 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
20911 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
20932 AGAG
1 AGAG
20936 CTCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:20893 original size:42 final size:42
Alignment explanation
Indices: 20817--20935 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
20807 AACTCGCCTG
* * * * * * *
20817 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
20859 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
20901 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
20936 CTCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:22306 original size:14 final size:14
Alignment explanation
Indices: 22287--22322 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
22277 ATTGTTTAAT
22287 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
22301 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
22315 TGATTTGT
1 TGATTTGT
22323 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:22466 original size:33 final size:33
Alignment explanation
Indices: 22429--22508 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
22419 AAAATTGACT
* * *
22429 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
22462 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
22495 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
22509 CTAAATTCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:22488 original size:19 final size:19
Alignment explanation
Indices: 22429--22489 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
22419 AAAATTGACT
*
22429 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
22448 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
22462 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
22481 ATCGCAACG
1 ATCGCAACG
22490 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:22536 original size:19 final size:19
Alignment explanation
Indices: 22514--22664 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
22504 CGAAACTAAA
22514 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
22533 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
22548 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
22566 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
22581 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
22599 TTCGCAATGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
22614 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
22632 TTCGCATTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCA-T
22652 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
22665 AGACATTAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 25 0.26
16 9 0.09
17 9 0.09
19 40 0.42
20 13 0.14
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:22560 original size:33 final size:33
Alignment explanation
Indices: 22518--22644 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
22508 ACTAAATTCG
* *
22518 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
22551 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
22584 CGTTGCGATTTTCATTTCGCAATGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
22617 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
22645 AGTCATTTTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:22591 original size:14 final size:14
Alignment explanation
Indices: 22539--22626 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
22529 TCATTTCGCT
*
22539 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
22553 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
22570 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
22586 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
22603 CAATGCGATTCTCTCG
1 --TTGCGATTCTCTCG
22619 TTGCGATT
1 TTGCGATT
22627 TTCATTTCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 19 0.33
16 14 0.25
17 13 0.23
19 11 0.19
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.43
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:22656 original size:20 final size:20
Alignment explanation
Indices: 22631--22671 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
22621 GCGATTTTCA
*
22631 TTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGACAT
*
22651 TTTCGCGTTGCGATAGACAT
1 TTTCGCATTGCGATAGACAT
22671 T
1 T
22672 AAGATGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
TTTCGCATTGCGATAGACAT
Found at i:22710 original size:20 final size:20
Alignment explanation
Indices: 22638--22710 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
22628 TCATTTCGCA
* *
22638 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTACGTG
* *
22658 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTACG-TG
*
22678 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTACGTG
22699 TTGCGATAGTCA
1 TTGCGATAGTCA
22711 AATGAATGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTACGTG
Found at i:25209 original size:24 final size:24
Alignment explanation
Indices: 25182--25235 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
25172 CTGAAAAATC
* *
25182 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATCGACCAAG
* *
25206 ATCAAAGTCCGGGTATCGACCAAG
1 ATCAAAATCCGAGTATCGACCAAG
25230 ATCAAA
1 ATCAAA
25236 TTTTGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATCGACCAAG
Found at i:26305 original size:21 final size:21
Alignment explanation
Indices: 26098--26327 Score: 179
Period size: 20 Copynumber: 11.3 Consensus size: 21
26088 AGAATCTCAT
26098 TGCGATTTAC-TAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
26118 TGCGA-TTACGTAAATTGCAA
1 TGCGATTTACGTAAATCGCAA
* * * *
26138 TGCGAATTAGGAAAATCACAA
1 TGCGATTTACGTAAATCGCAA
* * *
26159 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
26180 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* *
26200 TGCGA-ATACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
* *
26219 TGCGATTTACGT-AATCACAT
1 TGCGATTTACGTAAATCGCAA
*
26239 TGCGATTTACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
* * * * **
26259 TGCGATTTTCCTAATTTGCGT
1 TGCGATTTACGTAAATCGCAA
*
26280 TGCGATTTTCGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
26301 CGCGAATTT-GGGAAATCGCAA
1 TGCG-ATTTACGTAAATCGCAA
*
26322 TACGAT
1 TGCGAT
26328 AGTCAGAATC
Statistics
Matches: 177, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.09
20 85 0.48
21 72 0.41
22 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:27105 original size:2 final size:2
Alignment explanation
Indices: 27098--27123 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27088 AATTCAAATA
27098 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27124 CAATGAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39380 original size:213 final size:213
Alignment explanation
Indices: 39013--39437 Score: 850
Period size: 213 Copynumber: 2.0 Consensus size: 213
39003 AAGCTAAATC
39013 CATCCACGTAGCAGCAGAGAAGATAATTCATGAAGTTCATTTCATATTCAATCACTTTACAGTTG
1 CATCCACGTAGCAGCAGAGAAGATAATTCATGAAGTTCATTTCATATTCAATCACTTTACAGTTG
39078 GTGGGATCTCTATCGTGAAGTAAAGATGGTTGATATTTCTTCCTAAGTTGCTTAACTATAATGGT
66 GTGGGATCTCTATCGTGAAGTAAAGATGGTTGATATTTCTTCCTAAGTTGCTTAACTATAATGGT
39143 ATCACAGTTCAACTACAAAAGCCAAGGAAGGAACTACAATTCTCATTCTCACACAACCAATAAAA
131 ATCACAGTTCAACTACAAAAGCCAAGGAAGGAACTACAATTCTCATTCTCACACAACCAATAAAA
39208 ATTGAGAATTTTAACGAA
196 ATTGAGAATTTTAACGAA
39226 CATCCACGTAGCAGCAGAGAAGATAATTCATGAAGTTCATTTCATATTCAATCACTTTACAGTTG
1 CATCCACGTAGCAGCAGAGAAGATAATTCATGAAGTTCATTTCATATTCAATCACTTTACAGTTG
39291 GTGGGATCTCTATCGTGAAGTAAAGATGGTTGATATTTCTTCCTAAGTTGCTTAACTATAATGGT
66 GTGGGATCTCTATCGTGAAGTAAAGATGGTTGATATTTCTTCCTAAGTTGCTTAACTATAATGGT
39356 ATCACAGTTCAACTACAAAAGCCAAGGAAGGAACTACAATTCTCATTCTCACACAACCAATAAAA
131 ATCACAGTTCAACTACAAAAGCCAAGGAAGGAACTACAATTCTCATTCTCACACAACCAATAAAA
39421 ATTGAGAATTTTAACGA
196 ATTGAGAATTTTAACGA
39438 TCTTGTTTTC
Statistics
Matches: 212, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 212 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (213 bp):
CATCCACGTAGCAGCAGAGAAGATAATTCATGAAGTTCATTTCATATTCAATCACTTTACAGTTG
GTGGGATCTCTATCGTGAAGTAAAGATGGTTGATATTTCTTCCTAAGTTGCTTAACTATAATGGT
ATCACAGTTCAACTACAAAAGCCAAGGAAGGAACTACAATTCTCATTCTCACACAACCAATAAAA
ATTGAGAATTTTAACGAA
Found at i:40395 original size:21 final size:20
Alignment explanation
Indices: 40365--40404 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40355 AGGATACTTA
*
40365 CTGCAACTTCCTGCATTAAGT
1 CTGCAACTTCC-GCAATAAGT
*
40386 CTGCAGCTTCCGCAATAAG
1 CTGCAACTTCCGCAATAAG
40405 GCCCTGATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (20 bp):
CTGCAACTTCCGCAATAAGT
Found at i:41931 original size:23 final size:23
Alignment explanation
Indices: 41899--41947 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
41889 GTTATTATTC
* *
41899 TTTTTCATTTTGACCATCAACTT
1 TTTTTAATTTTGACAATCAACTT
*
41922 TTTTTAATTTTGTCAATCAACTT
1 TTTTTAATTTTGACAATCAACTT
41945 TTT
1 TTT
41948 AATTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTTAATTTTGACAATCAACTT
Found at i:54506 original size:197 final size:197
Alignment explanation
Indices: 54171--54564 Score: 761
Period size: 197 Copynumber: 2.0 Consensus size: 197
54161 AATATAATTA
54171 ATGTAGTTGGAGATATTGTAGATTATGATATGATCATAGTACAATATTTTTATGGAGTATTCTAT
1 ATGTAGTTGGAGATATTGTAGATTATGATATGATCATAGTACAATATTTTTATGGAGTATTCTAT
*
54236 ACATACAGGGACTCCTGTACAAACCTATATACAATTTTGGAATATCAACAATGTAGTCTTACCTT
66 ACATACAGGGACTCCTGTACAAACCTATATACAATTTTGGAATATCAACAATGTAATCTTACCTT
*
54301 CAAAAAAAGAAAAAGACAACGTAGTATGAATGTTGGCTACTATGGTTGAACCATTTATTCCTTTG
131 CAAAAAAAGAAAAAGACAACGTAGTATGAATGTTGGCTACTATGGTCGAACCATTTATTCCTTTG
54366 TG
196 TG
54368 ATGTAGTTGGAGATATTGTAGATTATGATATGATCATAGTACAATATTTTTATGGAGTATTCTAT
1 ATGTAGTTGGAGATATTGTAGATTATGATATGATCATAGTACAATATTTTTATGGAGTATTCTAT
*
54433 ACATACAGGGATTCCTGTACAAACCTATATACAATTTTGGAATATCAACAATGTAATCTTACCTT
66 ACATACAGGGACTCCTGTACAAACCTATATACAATTTTGGAATATCAACAATGTAATCTTACCTT
54498 CAAAAAAAGAAAAAGACAACGTAGTATGAATGTTGGCTACTATGGTCGAACCATTTATTCCTTTG
131 CAAAAAAAGAAAAAGACAACGTAGTATGAATGTTGGCTACTATGGTCGAACCATTTATTCCTTTG
54563 TG
196 TG
54565 TTCTTCTGAT
Statistics
Matches: 194, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
197 194 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (197 bp):
ATGTAGTTGGAGATATTGTAGATTATGATATGATCATAGTACAATATTTTTATGGAGTATTCTAT
ACATACAGGGACTCCTGTACAAACCTATATACAATTTTGGAATATCAACAATGTAATCTTACCTT
CAAAAAAAGAAAAAGACAACGTAGTATGAATGTTGGCTACTATGGTCGAACCATTTATTCCTTTG
TG
Found at i:58983 original size:23 final size:23
Alignment explanation
Indices: 58953--58998 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
58943 TTTAACGTTC
58953 ATCGTCGATATCTATTCTTTGTT
1 ATCGTCGATATCTATTCTTTGTT
58976 ATCGTCGATATCTATTCTTTGTT
1 ATCGTCGATATCTATTCTTTGTT
58999 TGAGTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.52
Consensus pattern (23 bp):
ATCGTCGATATCTATTCTTTGTT
Found at i:70969 original size:15 final size:15
Alignment explanation
Indices: 70949--70981 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
70939 ACATTACCCA
70949 CCCCGCATCCGCCCG
1 CCCCGCATCCGCCCG
70964 CCCCGCATCCGCCCG
1 CCCCGCATCCGCCCG
70979 CCC
1 CCC
70982 AGTTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.70, G:0.18, T:0.06
Consensus pattern (15 bp):
CCCCGCATCCGCCCG
Found at i:75388 original size:42 final size:46
Alignment explanation
Indices: 75324--75447 Score: 125
Period size: 47 Copynumber: 2.8 Consensus size: 46
75314 TTTGTTTTTA
*
75324 TATTATTAAAATATATT-CTTTAATCATTAAAA-AT-AT-AA-ACAT
1 TATTA-TAAAATATATTATTTTAATCATTAAAATATAATAAATACAT
* *
75366 TATTATAAAATAAATTATTTTAA-CTATTTAAAATATAATAAATATAT
1 TATTATAAAATATATTATTTTAATC-A-TTAAAATATAATAAATACAT
* * *
75413 TATTACAAAATATATTATTTTAATTATTAATATAT
1 TATTATAAAATATATTATTTTAATCATTAAAATAT
75448 TCAGATCGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
41 11 0.16
42 11 0.16
43 6 0.09
44 2 0.03
45 2 0.03
46 10 0.15
47 25 0.37
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (46 bp):
TATTATAAAATATATTATTTTAATCATTAAAATATAATAAATACAT
Found at i:75393 original size:24 final size:24
Alignment explanation
Indices: 75364--75441 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
75354 AAATATAAAC
75364 ATTATTATAAAATAAATTATTTTA
1 ATTATTATAAAATAAATTATTTTA
* * * *
75388 ACTATT-TAAAATATAATAAATAT-
1 ATTATTATAAAATA-AATTATTTTA
* *
75411 ATTATTACAAAATATATTATTTTA
1 ATTATTATAAAATAAATTATTTTA
75435 ATTATTA
1 ATTATTA
75442 ATATATTCAG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
23 17 0.41
24 24 0.59
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTATTATAAAATAAATTATTTTA
Found at i:76401 original size:32 final size:32
Alignment explanation
Indices: 76363--76453 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
76353 CCGAGATTTC
* * *
76363 AAATGTTACAAAATAGTCATTAAATTTTATTA
1 AAATGTTACAAAATAATCATTAAATTTCATCA
* *
76395 AAATGTTATAAAATAATCATTAAATTTCATCG
1 AAATGTTACAAAATAATCATTAAATTTCATCA
* *
76427 AACTGTTACAAAACAATCATTAAATTT
1 AAATGTTACAAAATAATCATTAAATTT
76454 ATAAAAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.37
Consensus pattern (32 bp):
AAATGTTACAAAATAATCATTAAATTTCATCA
Found at i:80538 original size:21 final size:21
Alignment explanation
Indices: 80512--80551 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
80502 GGGTTTTCGG
80512 AAAATGAATTACTGGAATTGA
1 AAAATGAATTACTGGAATTGA
*
80533 AAAATGAATTATTGGAATT
1 AAAATGAATTACTGGAATT
80552 TGAATTCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (21 bp):
AAAATGAATTACTGGAATTGA
Found at i:80828 original size:49 final size:50
Alignment explanation
Indices: 80731--80850 Score: 115
Period size: 49 Copynumber: 2.5 Consensus size: 50
80721 TACAAATATT
*
80731 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
80781 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
** *
80830 TTA-ATAA-AAATAATAATATTT
1 AAATATAATAAATAATATTATTT
80851 TTATATTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
48 19 0.33
49 31 0.53
50 8 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:80873 original size:32 final size:32
Alignment explanation
Indices: 80809--80871 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
80799 TTTATTATTA
* *
80809 AATATTATTTTTATAATTTTATTAATAAAAAT
1 AATAATATTTTTATAATTTTATAAATAAAAAT
80841 AATAATATTTTTAT-ATTTTAGTGAAATAAAA
1 AATAATATTTTTATAATTTTA-T-AAATAAAA
80872 TATTATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 6 0.22
32 14 0.52
33 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
AATAATATTTTTATAATTTTATAAATAAAAAT
Found at i:81018 original size:51 final size:53
Alignment explanation
Indices: 80951--81079 Score: 126
Period size: 51 Copynumber: 2.5 Consensus size: 53
80941 TTTAAATATC
* *
80951 TTTATTAAAATATTATTTAAATATATAA-ATAAT-TCATTAT-TAAATATAATTT
1 TTTATT-ATATATTATTTAAATATATAATATAATATC-TTATATAAATATAATTG
* * *
81003 TTTATTATATATTATTAAAATA-AAAATATAATATCTTATATATATATAATTG
1 TTTATTATATATTATTTAAATATATAATATAATATCTTATATAAATATAATTG
* *
81055 ATTATT-TATA-TAATTAACATATATA
1 TTTATTATATATTATTTAA-ATATATA
81080 TTATTTATTA
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
50 8 0.13
51 30 0.48
52 25 0.40
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (53 bp):
TTTATTATATATTATTTAAATATATAATATAATATCTTATATAAATATAATTG
Found at i:81625 original size:25 final size:25
Alignment explanation
Indices: 81605--81658 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
81595 CCTAAATTTT
*
81605 CATAAACTTTAAATCATTAAATCTC
1 CATAAACCTTAAATCATTAAATCTC
*
81630 CATAAACCTTAAATCATTAAATATC
1 CATAAACCTTAAATCATTAAATCTC
81655 CATA
1 CATA
81659 CTCAAATCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.33
Consensus pattern (25 bp):
CATAAACCTTAAATCATTAAATCTC
Found at i:90310 original size:15 final size:16
Alignment explanation
Indices: 90272--90314 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
90262 ACAGAACCTC
*
90272 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
90288 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
90304 T-AATCATTCAG
1 TGAATCATTCAG
90315 AAGTAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:95648 original size:20 final size:20
Alignment explanation
Indices: 95623--95675 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
95613 ACCAACAAAT
95623 TCGCAACGCGAATTCCAATA
1 TCGCAACGCGAATTCCAATA
* * *
95643 TCGCAAC-CCAGTTTCCAATT
1 TCGCAACGCGA-ATTCCAATA
95663 TCGCAACGCGAAT
1 TCGCAACGCGAAT
95676 ATGTAAATCG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATTCCAATA
Found at i:95722 original size:20 final size:20
Alignment explanation
Indices: 95699--95763 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
95689 TGCGATTTTC
*
95699 CAAATTCTCAACGCGATAGT
1 CAAATTCTCAACGCGAAAGT
95719 CAAATTCTCAACGCGAAAGT
1 CAAATTCTCAACGCGAAAGT
*
95739 CAAATTCGCAACGCGAAAGT
1 CAAATTCTCAACGCGAAAGT
95759 CAAAT
1 CAAAT
95764 GTTTTTACGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (20 bp):
CAAATTCTCAACGCGAAAGT
Found at i:95916 original size:22 final size:22
Alignment explanation
Indices: 95891--95941 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
95881 CTACGGTGAC
95891 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
95913 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
95935 ATTCGTC
1 ATCCGTC
95942 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:96171 original size:13 final size:13
Alignment explanation
Indices: 96153--96184 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
96143 AGTATTTGTC
96153 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
96166 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
96179 TTTGTT
1 TTTGTT
96185 GAAAAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTGTTTTGTCTT
Found at i:96272 original size:21 final size:20
Alignment explanation
Indices: 96234--96272 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
96224 AACTAAAATC
**
96234 GCGTTGCGATTTTCGTTTTT
1 GCGTTGCGATTTAAGTTTTT
96254 GCGTTGCGAATTTAAGTTT
1 GCGTTGCG-ATTTAAGTTT
96273 CATAAACTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.49
Consensus pattern (20 bp):
GCGTTGCGATTTAAGTTTTT
Found at i:98491 original size:21 final size:21
Alignment explanation
Indices: 98467--98509 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
98457 ATCATCATCG
*
98467 AAGAAGCCCCTCCCATCGTTC
1 AAGAAGCCACTCCCATCGTTC
* **
98488 AAGATGCCACTGTCATCGTTC
1 AAGAAGCCACTCCCATCGTTC
98509 A
1 A
98510 CCGTTTAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (21 bp):
AAGAAGCCACTCCCATCGTTC
Found at i:99940 original size:14 final size:14
Alignment explanation
Indices: 99921--99960 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
99911 TTTTTATTAA
99921 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
99935 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
99949 TTGATTTGTAAA
1 TTGATTTGTAAA
99961 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:99943 original size:60 final size:64
Alignment explanation
Indices: 99871--100010 Score: 164
Period size: 66 Copynumber: 2.2 Consensus size: 64
99861 TTTTACATTG
99871 AAAGTTGATTTGTTACAATTGATGAGGAAAT-A-AA-ATTTATTT-TTT-ATTAATTGATTTGTA
1 AAAGTTGATTTGTTA-AATTGATGAGGAAATAAGAATATTTATTTGTTTGATTAATTGATTTGTA
* ** * * *
99931 AAAGTTGATTTGTTTAATTTGATTTGTAAATAAGAATTATTTTTTTGTTTGTTTAATTGATTTGT
1 AAAGTTGATTTG-TTAAATTGATGAGGAAATAAGAA-TATTTATTTGTTTGATTAATTGATTTGT
99996 A
64 A
99997 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
100011 GTTTTTAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
60 23 0.34
61 4 0.06
62 2 0.03
64 7 0.10
65 5 0.07
66 26 0.39
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (64 bp):
AAAGTTGATTTGTTAAATTGATGAGGAAATAAGAATATTTATTTGTTTGATTAATTGATTTGTA
Found at i:100118 original size:20 final size:20
Alignment explanation
Indices: 100095--100139 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
100085 AATAAGCGTT
100095 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
* *
100115 GCGAAAGTCAAATTCGTAAC
1 GCGATAGTCAAATTCGCAAC
100135 GCGAT
1 GCGAT
100140 TTTCGGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:100476 original size:18 final size:18
Alignment explanation
Indices: 100453--100488 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
100443 AAGCCGGTTG
*
100453 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
100471 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
100489 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:102773 original size:24 final size:24
Alignment explanation
Indices: 102739--102792 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
102729 CCATCACATC
102739 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
102763 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
102787 ATCAAA
1 ATCAAA
102793 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:102937 original size:12 final size:12
Alignment explanation
Indices: 102916--102949 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
102906 GGTTGTGGGT
*
102916 TTTGAGATTGTG
1 TTTGATATTGTG
102928 TTTGATATTGTG
1 TTTGATATTGTG
*
102940 TTTGGTATTG
1 TTTGATATTG
102950 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:103719 original size:19 final size:20
Alignment explanation
Indices: 103695--103819 Score: 98
Period size: 20 Copynumber: 6.4 Consensus size: 20
103685 ACTAAAATCT
103695 GTTGCGAAATT-AAATTCGC
1 GTTGCGAAATTGAAATTCGC
* *
103714 GTTGCGAATTTGAAATTC-A
1 GTTGCGAAATTGAAATTCGC
* *
103733 GTTGCGAAATTGAAA-ACTGG
1 GTTGCGAAATTGAAATTC-GC
* * *
103753 GTTGGGAAATTGGAAACT-GG
1 GTTGCGAAATT-GAAATTCGC
*
103773 GTTGCGAAATTGGAATTCGC
1 GTTGCGAAATTGAAATTCGC
* * *
103793 GTTGCGAATTTGAGA-TCTC
1 GTTGCGAAATTGAAATTCGC
103812 GTTGCGAA
1 GTTGCGAA
103820 TTTGTTGGTC
Statistics
Matches: 85, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.01
19 39 0.46
20 41 0.48
21 4 0.05
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (20 bp):
GTTGCGAAATTGAAATTCGC
Found at i:103731 original size:20 final size:20
Alignment explanation
Indices: 103695--103823 Score: 88
Period size: 19 Copynumber: 6.6 Consensus size: 20
103685 ACTAAAATCT
*
103695 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
103714 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
* * *
103733 GTTGCGAAATTGAAA-ACTGG
1 GTTGCGAATTTGAAATTC-GC
* * * *
103753 GTTGGGAAATTGGAAACT-GG
1 GTTGCG-AATTTGAAATTCGC
* *
103773 GTTGCGAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGC
* *
103793 GTTGCGAATTTGAGA-TCTC
1 GTTGCGAATTTGAAATTCGC
103812 GTTGCGAATTTG
1 GTTGCGAATTTG
103824 TTGGTCATTT
Statistics
Matches: 85, Mismatches: 19, Indels: 12
0.73 0.16 0.10
Matches are distributed among these distances:
18 1 0.01
19 46 0.54
20 31 0.36
21 7 0.08
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:136446 original size:26 final size:26
Alignment explanation
Indices: 136409--136470 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
136399 CATCACCTAC
136409 CGAAACACACTGCTAATGCGACACAT
1 CGAAACACACTGCTAATGCGACACAT
* *
136435 TGAAACACACTGTTAATGCGACACAT
1 CGAAACACACTGCTAATGCGACACAT
136461 CGAAACACAC
1 CGAAACACAC
136471 CACTAACTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.16
Consensus pattern (26 bp):
CGAAACACACTGCTAATGCGACACAT
Found at i:144370 original size:3 final size:3
Alignment explanation
Indices: 144362--144395 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
144352 AAGGTAAATG
144362 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
144396 CCTATTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:147107 original size:30 final size:30
Alignment explanation
Indices: 147059--147127 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
147049 ATAATTTTTG
*
147059 AAAATTTACACTTTTAATC-CTTAAACTTTT
1 AAAATTTACACTTTTAATCTC-TAAACTTTC
147089 ACAAATTTACAC-TTTAATCTCTAAACTTTC
1 A-AAATTTACACTTTTAATCTCTAAACTTTC
147119 AAAATTTAC
1 AAAATTTAC
147128 TTTTCAATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 8 0.22
30 17 0.47
31 11 0.31
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (30 bp):
AAAATTTACACTTTTAATCTCTAAACTTTC
Found at i:147136 original size:29 final size:28
Alignment explanation
Indices: 147059--147136 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 28
147049 ATAATTTTTG
*
147059 AAAATTTACACTTTTAATCCTTAAACTTTT
1 AAAATTT--ACTTTTAATCCTTAAACTTTC
*
147089 ACAAATTTACACTTTAAT-CTCTAAACTTTC
1 A-AAATTTAC-TTTTAATCCT-TAAACTTTC
147119 AAAATTTACTTTTCAATC
1 AAAATTTACTTTT-AATC
147137 ACTAGTCCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
28 3 0.08
29 15 0.38
30 16 0.40
31 6 0.15
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (28 bp):
AAAATTTACTTTTAATCCTTAAACTTTC
Found at i:149241 original size:21 final size:21
Alignment explanation
Indices: 149215--149259 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
149205 ATTATATGTA
149215 GTCTTTTGGGACATCTACGTG
1 GTCTTTTGGGACATCTACGTG
149236 GTCTTTTGGGACATCTACGTG
1 GTCTTTTGGGACATCTACGTG
149257 GTC
1 GTC
149260 CTTCGAGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.20, G:0.29, T:0.38
Consensus pattern (21 bp):
GTCTTTTGGGACATCTACGTG
Found at i:149269 original size:21 final size:21
Alignment explanation
Indices: 149224--149269 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
149214 AGTCTTTTGG
* * *
149224 GACATCTACGTGGTCTTTTGG
1 GACATCTACGTGGTCCTTCGA
149245 GACATCTACGTGGTCCTTCGA
1 GACATCTACGTGGTCCTTCGA
149266 GACA
1 GACA
149270 AATTCTACGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (21 bp):
GACATCTACGTGGTCCTTCGA
Found at i:163465 original size:16 final size:16
Alignment explanation
Indices: 163444--163475 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
163434 ATCACTTTTA
*
163444 GTGACATATGGCATAT
1 GTGACATATGACATAT
163460 GTGACATATGACATAT
1 GTGACATATGACATAT
163476 CATCACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (16 bp):
GTGACATATGACATAT
Found at i:164454 original size:47 final size:47
Alignment explanation
Indices: 164375--164464 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
164365 TTTATACACA
*
164375 GTTGTTCTTGGTAAATGTTGTCACAAACAAGAGTTGTTCTCAGCATG
1 GTTGTTCTTGATAAATGTTGTCACAAACAAGAGTTGTTCTCAGCATG
* * *
164422 GTTGTTCTTGATAGAA-GTTGTCCCGAATAAGAGTTGTTCTCAG
1 GTTGTTCTTGATA-AATGTTGTCACAAACAAGAGTTGTTCTCAG
164465 TAAAAGTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
47 36 0.95
48 2 0.05
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (47 bp):
GTTGTTCTTGATAAATGTTGTCACAAACAAGAGTTGTTCTCAGCATG
Found at i:166390 original size:20 final size:20
Alignment explanation
Indices: 166362--166408 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
166352 AAACCCAAGC
*
166362 AACTCGACTTGAATTTTATA
1 AACTCGACTCGAATTTTATA
*
166382 AACTTGACTCGAATTTTATA
1 AACTCGACTCGAATTTTATA
*
166402 TACTCGA
1 AACTCGA
166409 TTGGACTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (20 bp):
AACTCGACTCGAATTTTATA
Found at i:167558 original size:20 final size:21
Alignment explanation
Indices: 167521--167559 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
167511 ATAGCAGGGT
167521 TAAAGTAATTTTTATTTTACA
1 TAAAGTAATTTTTATTTTACA
167542 TAAA-TAATATTTT-TTTTA
1 TAAAGTAAT-TTTTATTTTA
167560 ATTGAGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (21 bp):
TAAAGTAATTTTTATTTTACA
Found at i:167868 original size:20 final size:22
Alignment explanation
Indices: 167829--167869 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
167819 TTTTTGAAAA
*
167829 TTTATTTTTGAATAATTGGTTT
1 TTTATTTTTAAATAATTGGTTT
167851 TTTA-TTTTAAAT-ATTGGTT
1 TTTATTTTTAAATAATTGGTT
167870 AAATTTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.63
Consensus pattern (22 bp):
TTTATTTTTAAATAATTGGTTT
Found at i:167876 original size:22 final size:23
Alignment explanation
Indices: 167826--167878 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
167816 TCTTTTTTGA
*
167826 AAATTTATTTTTGAATAATTGGTT
1 AAATTTA-TTTTAAATAATTGGTT
*
167850 --TTTTATTTTAAAT-ATTGGTT
1 AAATTTATTTTAAATAATTGGTT
167870 AAATTTATT
1 AAATTTATT
167879 CCCATTCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.58
Consensus pattern (23 bp):
AAATTTATTTTAAATAATTGGTT
Found at i:168710 original size:135 final size:137
Alignment explanation
Indices: 168453--168729 Score: 339
Period size: 135 Copynumber: 2.0 Consensus size: 137
168443 ATTTTTGTGG
* * *
168453 GTTTTAATATCAGGTGAATAATAATCATTCTCCTGGTATACAATTAGTTGATTCTTTAACCATGA
1 GTTTTAATATCAGATGAAAAATAATCATTCACCTGGTATACAATTAGTTGATTCTTTAACCATGA
* * *
168518 ACTGGTTTTGTTTGGTTTCCAAGAAAAACATGTGAAAATCAATAATGCTATTCAAAAAGAAAAAT
66 ACTGGTTTTGTTTGGTTGCCAAGAAAAACATGAGAAAAGCAATAATGCTATTCAAAAAGAAAAAT
168583 GAACTTT
131 GAACTTT
** * **
168590 -TTTTAA-ATCAGATGAAAAATAATCATTCACCTGGTATACCGTTATTTGATTCTTTAATTATGA
1 GTTTTAATATCAGATGAAAAATAATCATTCACCTGGTATACAATTAGTTGATTCTTTAACCATGA
* * * * *
168653 AC-GAGTTTTGTTTGGTTGCCAAG-AATACATGAGGAAAGCAATAAT-CTTGTTGGAAAAAGGAA
66 ACTG-GTTTTGTTTGGTTGCCAAGAAAAACATGAGAAAAGCAATAATGC-TATT-CAAAAAGAAA
*
168715 AATGAGCTTT
128 AATGAACTTT
168725 GTTTT
1 GTTTT
168730 CAAGAATCCA
Statistics
Matches: 119, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
133 1 0.01
134 22 0.18
135 86 0.72
136 10 0.08
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (137 bp):
GTTTTAATATCAGATGAAAAATAATCATTCACCTGGTATACAATTAGTTGATTCTTTAACCATGA
ACTGGTTTTGTTTGGTTGCCAAGAAAAACATGAGAAAAGCAATAATGCTATTCAAAAAGAAAAAT
GAACTTT
Found at i:170398 original size:165 final size:165
Alignment explanation
Indices: 170217--170530 Score: 531
Period size: 165 Copynumber: 1.9 Consensus size: 165
170207 ACGTTTTGGT
* * *
170217 TCTCCCTGCGGAAGGTCATATGGATTCCTCAG-AAGAAAAGGGGAATGAAGAATCTAATGATGAT
1 TCTCCCTGCAGAAGGTCATATGGATTCCTCAGCAA-AAAAGGGAAATAAAGAATCTAATGATGAT
** *
170281 GATGCATTCCTTGATGAATTGGACATCAACAATGACACAGGATCTGAAAGTAAATCACTAGCTGA
65 GATGCATTCCTTGACAAATCGGACATCAACAATGACACAGGATCTGAAAGTAAATCACTAGCTGA
170346 AGAGCAAATCACTGCTGATGCTCAAAGTATTCCAGA
130 AGAGCAAATCACTGCTGATGCTCAAAGTATTCCAGA
* *
170382 TCTCCCTGCAGAAGGTCATATGGATTCCTCTGCAAAGAAGGGAAATAAAGAATCTAATGATGATG
1 TCTCCCTGCAGAAGGTCATATGGATTCCTCAGCAAAAAAGGGAAATAAAGAATCTAATGATGATG
*
170447 ATGCATTCCTTGGCAAATCGGACATCAACAATGACACAGGATCTGAAAGTAAATCACTAGCTGAA
66 ATGCATTCCTTGACAAATCGGACATCAACAATGACACAGGATCTGAAAGTAAATCACTAGCTGAA
170512 GAGCAAATCACTGCTGATG
131 GAGCAAATCACTGCTGATG
170531 ACAGCACAGT
Statistics
Matches: 139, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
165 137 0.99
166 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (165 bp):
TCTCCCTGCAGAAGGTCATATGGATTCCTCAGCAAAAAAGGGAAATAAAGAATCTAATGATGATG
ATGCATTCCTTGACAAATCGGACATCAACAATGACACAGGATCTGAAAGTAAATCACTAGCTGAA
GAGCAAATCACTGCTGATGCTCAAAGTATTCCAGA
Found at i:188507 original size:3 final size:3
Alignment explanation
Indices: 188493--188522 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
188483 AATATTTTCT
*
188493 AGA AGT AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
188523 CCAGTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:194879 original size:20 final size:19
Alignment explanation
Indices: 194842--194902 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
194832 GTATCGATCC
*
194842 AAAACGAT-ATACCAGGTAA
1 AAAACGATAAAACC-GGTAA
* * *
194861 AAATATGATAAAATCGGTATC
1 AAA-ACGATAAAACCGGTA-A
194882 AAAACGATAAAACCGGTAA
1 AAAACGATAAAACCGGTAA
194901 AA
1 AA
194903 GGTTACCGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 5 0.16
20 21 0.66
21 6 0.19
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.18
Consensus pattern (19 bp):
AAAACGATAAAACCGGTAA
Found at i:194980 original size:181 final size:181
Alignment explanation
Indices: 194644--195116 Score: 682
Period size: 181 Copynumber: 2.6 Consensus size: 181
194634 GATCCAAATT
* * * *
194644 AAAAATGTGTCGATCCAAAACGATATAAAAGGTAAAATTATGACAAAACCGGTAT-AGAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCA-AAATGAT
* * *
194708 AAAACCGGT-AAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACT
65 AAAACCGGTAAAAG-GATACCGGATATA-TTAAAGTGTCGATACTTTAATATAAGGATCGACACT
* * *
194772 TCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
128 TCGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* * *
194826 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAATCGGTATCAAAACGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
194891 AAACCGGTAAAAGGTTACCGGATATATTAATAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAAGGATACCGGATATATTAA-AGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
194955 GTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
130 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
195007 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
195072 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTTGATACTTT
66 AAACCGGTAAAAGGATACCGGATATATT-AAAGTGTCGATACTTT
195117 CGTAAGTACG
Statistics
Matches: 262, Mismatches: 25, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
181 167 0.64
182 90 0.34
183 5 0.02
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAAGGATACCGGATATATTAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:195060 original size:20 final size:19
Alignment explanation
Indices: 195037--195083 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
195027 CGATATAACA
195037 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
195057 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
195077 GGTAAAA
1 GGTAAAA
195084 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:195085 original size:17 final size:19
Alignment explanation
Indices: 195046--195088 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
195036 AGGTAAAAAT
195046 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
195066 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
195083 ATGATA
1 ATGATA
195089 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:197328 original size:21 final size:21
Alignment explanation
Indices: 197304--197347 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
197294 AAGACAATCA
197304 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
197325 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
197346 AG
1 AG
197348 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:197412 original size:25 final size:25
Alignment explanation
Indices: 197384--197438 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
197374 TAGATGGAGT
*
197384 GGTGAAAGAAGTAGAGGTGTTGAGG
1 GGTGAAAGAAGTAGAGGTGTTAAGG
* *
197409 GGTGAAAGAAGTTGGGGTGTTAAGG
1 GGTGAAAGAAGTAGAGGTGTTAAGG
197434 GGTGA
1 GGTGA
197439 TATTAAGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.49, T:0.22
Consensus pattern (25 bp):
GGTGAAAGAAGTAGAGGTGTTAAGG
Found at i:197662 original size:19 final size:19
Alignment explanation
Indices: 197623--197662 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
197613 AAAAAATATG
*
197623 AAGAAGAAAAGAGGGAGGA
1 AAGAAGAAAAGAGGGAAGA
* *
197642 AAGAAGAAGAGATGGAAGA
1 AAGAAGAAAAGAGGGAAGA
197661 AA
1 AA
197663 TGAGGAGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.03
Consensus pattern (19 bp):
AAGAAGAAAAGAGGGAAGA
Found at i:199250 original size:19 final size:19
Alignment explanation
Indices: 199226--199274 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
199216 AATGTAAGGT
199226 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
199245 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
199264 TATTTTTGTAT
1 TAATTTTGTAT
199275 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:199734 original size:199 final size:199
Alignment explanation
Indices: 199393--200930 Score: 2449
Period size: 199 Copynumber: 7.9 Consensus size: 199
199383 CAATATGGCC
* *
199393 AACAGGGTGCAACCATAAAGTGTCGAACCATATATAAAAAGTGTCGATCCCAAAAAAATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
*
199458 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACAAGTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
199523 GAATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
199588 TGGAA
195 TGGAA
*
199593 AACAGGGTGCAACCATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
199658 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* * *
199723 AATATGTCTAAATAATGTATTGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
199788 GGAA
196 GGAA
* * * *
199792 AACAGTGTGCAACCATAAGGTGTCGATCC-----CAAAAA----C-AT--C-----GA---AACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
199837 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCTGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
199902 AATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
199967 GGAA
196 GGAA
* *
199971 AACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAAGTGGCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
* *
200036 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTAATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
200101 AATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
200166 GGAA
196 GGAA
200170 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
200235 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
** **** *
200300 AATATGTCTAAATAATGTGTCGACAC-CATTTAAAAAGTGTCGATA-TTTTGGTTCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
200363 GGAA
196 GGAA
200367 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
200431 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
** ****
200496 AATATGTCT--A-AA--TGTCGACAC-CATTTAAAAAGTGTCGATATTTTTGGTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
200555 GGAA
196 GGAA
* *
200559 AACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAAAGTGTCGATCCTAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
200624 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACTGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* * ****
200689 AATATGTCTAAATAATGTGTCGACACCAT-TTAAAACAGTGTCGATATTTTTGGTCCAGAATGAA
131 AATATGTCTAAATAATGTGTCGACA-CTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
200753 TGGAA
195 TGGAA
* *
200758 AACAGTGTGCAACCATAAGGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
200822 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
200886 AATATGTCTAAATAATGTGTCGACACTT-TTTAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATA
200931 CTAATTTAAA
Statistics
Matches: 1256, Mismatches: 53, Indels: 62
0.92 0.04 0.05
Matches are distributed among these distances:
179 159 0.13
182 1 0.00
184 5 0.00
187 1 0.00
188 1 0.00
189 4 0.00
190 1 0.00
191 29 0.02
192 70 0.06
193 88 0.07
194 6 0.00
195 1 0.00
196 104 0.08
197 158 0.13
198 35 0.03
199 535 0.43
200 58 0.05
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (199 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
GGAA
Found at i:200128 original size:378 final size:376
Alignment explanation
Indices: 199433--200930 Score: 2170
Period size: 378 Copynumber: 3.9 Consensus size: 376
199423 TATATAAAAA
* *
199433 GTGTCGATCCCAAAAAAATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTG
1 GTGTCGATCCCAAAAACATCG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCG
** *
199498 GTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGT
65 GTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTGTTTAAATAGT
*
199563 GTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATTCATATAT
130 GTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATAT
199628 AAAAAGTGTCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
195 AAAAAGTGTCGATCCC-AAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
* * *
199693 ACTGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTATTGACACTTTTTTAGT
259 ACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC-TTTTTAGT
199758 TTGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGTGTGCAACCAT-AAG
323 TTGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGTGTGCAACCATAAAG
199811 GTGTCGATCCCAAAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCG
1 GTGTCGATCCCAAAAACATCG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCG
* ** *
199876 GTACAAGTATACCTGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGT
65 GTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTGTTTAAATAGT
*
199941 GTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAATGTCGATCCATATAT
130 GTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATAT
*
200006 AAAAAGTGGCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
195 AAAAAGTGTCGATCCC-AAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
* *
200071 ACCGGTACAAGTATACCAGTTTAATGAGAGAATATGTCTAAATAATGTGTCGACACTTGTTTAGT
259 ACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTT-TTTAGT
*
200136 TTGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCG
323 TTGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGTGTGCAACCATAAA-----G
200195 ATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATT
1 ---------------GTGTCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATT
200260 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACA
51 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACA
** * *
200325 C-CATTTAAAAAGTGTCGATA-TTTTGGTTCAGAATGAATGGAAAACAGGGTGCAACCATAAAGT
116 CTTGTTTAAATAGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGT
200388 GTCGATCCATATATAAAAAGTGTCGATCCCAAAACATCGAACCCAAAAGTATAATGTAATATGTA
181 GTCGATCCATATATAAAAAGTGTCGATCCCAAAACATCGAACCCAAAAGTATAATGTAATATGTA
200453 ATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCT--A-AA--TGTCG
246 ATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCG
** ****
200513 ACACCATTTAAAAAGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAA
311 ACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACA----G------T---
*
200578 GTGTCAATCCATATATAAAAA
363 GTG-CAA-CC----AT-AAAG
*
200599 GTGTCGATCCTAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG
1 GTGTCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG
* * * *
200664 TACAAGTATACTGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACCAT-TTAAAACAGT
66 TACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACA-CTTGTTTAAATAGT
* *
200728 GTCGATATTTTTGGTCCAGAATGAATGGAAAACAGTGTGCAACCATAAGGTGTCGATCCATATAT
130 GTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATAT
200793 AAAAAGTGTCGATCCCAAAACATCGAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAA
195 AAAAAGTGTCGATCCCAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
*
200857 CCGGTATAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTAGTTT
260 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTAGTTT
200922 GTGTCGATA
325 GTGTCGATA
200931 CTAATTTAAA
Statistics
Matches: 1023, Mismatches: 47, Indels: 83
0.89 0.04 0.07
Matches are distributed among these distances:
377 2 0.00
378 360 0.35
379 2 0.00
384 1 0.00
389 153 0.15
390 96 0.09
391 84 0.08
392 3 0.00
393 4 0.00
395 107 0.10
396 70 0.07
397 13 0.01
398 94 0.09
399 21 0.02
402 3 0.00
403 3 0.00
404 2 0.00
408 2 0.00
409 3 0.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (376 bp):
GTGTCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG
TACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTGTTTAAATAGTG
TCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATA
AAAAGTGTCGATCCCAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
CGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTAGTTTG
TGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGTGTGCAACCATAAAG
Found at i:200622 original size:389 final size:391
Alignment explanation
Indices: 199811--200898 Score: 1858
Period size: 389 Copynumber: 2.8 Consensus size: 391
199801 CAACCATAAG
199811 GTGTCGATCCCAAAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCG
1 GTGTCGATCCCAAAAACATCG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCG
* ** ****
199876 GTACAAGTATACCTGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGT
65 GTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC-CATTTAAAAAGT
*
199941 GTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAATGTCGATCCATATAT
129 GTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATAT
*
200006 AAAAAGTGGCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
194 AAAAAGTGTCGATCCC-AAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
* * ** **
200071 ACCGGTACAAGTATACCAGTTTAATGAGAGAATATGTCTAAATAATGTGTCGACACTTGTTTAGT
258 ACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCT--A-AA--TGTCGACACTCATTTAAA
** *
200136 TTGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCAT
318 AAGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCAATCCAT
200201 ATATAAAAA
383 ATATAAAAA
200210 GTGTCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG
1 GTGTCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG
200275 TACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACCATTTAAAAAGTGT
66 TACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACCATTTAAAAAGTGT
*
200340 CGATA-TTTTGGTTCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAA
131 CGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAA
200404 AAAGTGTCGATCCCAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC
196 AAAGTGTCGATCCCAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC
200469 GGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATGTCGACAC-CATTTAAAAAGTGTCG
261 GGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATGTCGACACTCATTTAAAAAGTGTCG
200533 ATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAA
326 ATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAA
200598 A
391 A
*
200599 GTGTCGATCCTAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG
1 GTGTCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG
*
200664 TACAAGTATACTGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACCATTTAAAACAGTG
66 TACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACCATTTAAAA-AGTG
* *
200729 TCGATATTTTTGGTCCAGAATGAATGGAAAACAGTGTGCAACCATAAGGTGTCGATCCATATATA
130 TCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATA
200794 AAAAGTGTCGATCCCAAAACATCGAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAAC
195 AAAAGTGTCGATCCCAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
200858 CGGTATAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
260 CGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
200899 AATGTGTCGA
Statistics
Matches: 662, Mismatches: 25, Indels: 13
0.95 0.04 0.02
Matches are distributed among these distances:
389 198 0.30
390 94 0.14
391 84 0.13
392 2 0.00
393 1 0.00
395 85 0.13
396 70 0.11
397 13 0.02
398 94 0.14
399 21 0.03
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (391 bp):
GTGTCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG
TACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACCATTTAAAAAGTGT
CGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAA
AAAGTGTCGATCCCAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC
GGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATGTCGACACTCATTTAAAAAGTGTCG
ATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAA
A
Found at i:200773 original size:588 final size:592
Alignment explanation
Indices: 199811--200911 Score: 1901
Period size: 588 Copynumber: 1.9 Consensus size: 592
199801 CAACCATAAG
199811 GTGTCGATCCCAAAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCG
1 GTGTCGATCCCAAAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCG
* ** ****
199876 GTACAAGTATACCTGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTGTTTAGTTTGT
66 GTACAAGTATACCGGTTTTATGAGAGAATATGTCT-AATAA-GTGTCGACACTCATTTAAAAAGT
*
199941 GTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAATGTCGATCCATATAT
129 GTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAATGTCAATCCATATAT
200006 AAAAAGTGGCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
194 AAAAAGTGGCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
* * **
200071 ACCGGTACAAGTATACCAGTTTAATGAGAGAATATGTCTAAATAATGTGTCGACACTTGTTTAGT
259 ACCGGTACAAGTATACCAGTTTAATGAGAGAATATGTCTAAATAATGTGTCGACACATGTTAAAA
**
200136 TTGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCAT
324 CAGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCAT
200201 ATATAAAAAGTGTCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAA
389 ATATAAAAAGTGTCGATCCC-AAAACATCGAACCC-AAAGTATAATGTAATATGTAATTTTTCAA
200266 TCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACCATTT
452 TCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACCATTT
200331 AAAAAGTGTCGATATTTTGGTTCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCC
517 AAAAAGTGTCGATATTTTGGTTCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCC
200396 ATATATAAAAA
582 ATATATAAAAA
200407 GTGTCGATCCC-AAAACATCG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCG
1 GTGTCGATCCCAAAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCG
200470 GTACAAGTATACCGGTTTTATGAGAGAATATGTCT-A-AA-TGTCGACAC-CATTTAAAAAGTGT
66 GTACAAGTATACCGGTTTTATGAGAGAATATGTCTAATAAGTGTCGACACTCATTTAAAAAGTGT
*
200531 CGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAA
131 CGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAATGTCAATCCATATATAA
* *
200596 AAAGTGTCGATCCTAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
196 AAAGTGGCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
** *
200661 CGGTACAAGTATACTGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACCAT-TTAAAAC
261 CGGTACAAGTATACCAGTTTAATGAGAGAATATGTCTAAATAATGTGTCGACA-CATGTTAAAAC
* *
200725 AGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGTGTGCAACCATAAGGTGTCGATCCATA
325 AGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
200790 TATAAAAAGTGTCGATCCCAAAACATCGAACCCAAAGTATAATGTAATATGTAATTTTTCAATCT
390 TATAAAAAGTGTCGATCCCAAAACATCGAACCCAAAGTATAATGTAATATGTAATTTTTCAATCT
*
200855 AACCGGTATAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC
455 AACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC
200912 TTTTTAGTTT
Statistics
Matches: 481, Mismatches: 23, Indels: 12
0.93 0.04 0.02
Matches are distributed among these distances:
586 88 0.18
587 14 0.03
588 268 0.56
589 11 0.02
591 2 0.00
592 1 0.00
594 77 0.16
595 9 0.02
596 11 0.02
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (592 bp):
GTGTCGATCCCAAAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCG
GTACAAGTATACCGGTTTTATGAGAGAATATGTCTAATAAGTGTCGACACTCATTTAAAAAGTGT
CGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAATGTCAATCCATATATAA
AAAGTGGCGATCCCAAAAACATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
CGGTACAAGTATACCAGTTTAATGAGAGAATATGTCTAAATAATGTGTCGACACATGTTAAAACA
GTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATAT
ATAAAAAGTGTCGATCCCAAAACATCGAACCCAAAGTATAATGTAATATGTAATTTTTCAATCTA
ACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACCATTTAAAA
AGTGTCGATATTTTGGTTCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATAT
ATAAAAA
Found at i:202403 original size:6 final size:6
Alignment explanation
Indices: 202392--202461 Score: 59
Period size: 6 Copynumber: 11.7 Consensus size: 6
202382 CAAGCGGTCA
* * * * *
202392 ATGAAG ATGAAG TTGACG ATGAAG ATGACG ATGATG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * *
202440 CTGACG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGA
202462 TGATCCAAAC
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (6 bp):
ATGAAG
Found at i:202414 original size:12 final size:12
Alignment explanation
Indices: 202392--202461 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 12
202382 CAAGCGGTCA
*
202392 ATGAAGATGAAG
1 ATGACGATGAAG
*
202404 TTGACGATGAAG
1 ATGACGATGAAG
*
202416 ATGACGATGATG
1 ATGACGATGAAG
202428 ATGACGATGAAG
1 ATGACGATGAAG
* *
202440 CTGACGATGATG
1 ATGACGATGAAG
*
202452 ATGATGATGA
1 ATGACGATGA
202462 TGATCCAAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:202429 original size:3 final size:3
Alignment explanation
Indices: 202409--202465 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
202399 TGAAGTTGAC
* * * * * *
202409 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GAC GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
202457 GAT GAT GAT
1 GAT GAT GAT
202466 CCAAACAAGT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.35, C:0.07, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:203677 original size:16 final size:16
Alignment explanation
Indices: 203656--203689 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
203646 TATCCACAAC
*
203656 AAAGTGTCGATTTAAA
1 AAAGTGTCGATTGAAA
203672 AAAGTGTCGATTGAAA
1 AAAGTGTCGATTGAAA
203688 AA
1 AA
203690 TATAATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (16 bp):
AAAGTGTCGATTGAAA
Found at i:204081 original size:23 final size:23
Alignment explanation
Indices: 204050--204122 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
204040 ATAGGTAAAA
*
204050 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
204073 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
204096 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
204119 ATAT
1 ATAT
204123 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:207021 original size:21 final size:24
Alignment explanation
Indices: 206997--207055 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
206987 TTTCATTAAA
206997 TTAGGTATATACAAT-A-AC-TAT
1 TTAGGTATATACAATAACACATAT
*
207018 TTAGGTATGTACAATAACTACATAT
1 TTAGGTATATACAATAAC-ACATAT
207043 TTAGGTATATACA
1 TTAGGTATATACA
207056 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 14 0.44
22 1 0.03
24 2 0.06
25 15 0.47
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (24 bp):
TTAGGTATATACAATAACACATAT
Found at i:207368 original size:23 final size:23
Alignment explanation
Indices: 207337--207398 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
207327 ATAGGTAAAA
*
207337 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
*
207360 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGTTT
207383 ATATAATGTAATAGGT
1 ATATAATGTAATAGGT
207399 TGTGGTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:207407 original size:23 final size:22
Alignment explanation
Indices: 207337--207409 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
207327 ATAGGTAAAA
* * *
207337 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTTGTG-TT
207360 ATATAATGTAATAGGTATCGT-TT
1 ATATAATGTAATAGGT-T-GTGTT
207383 ATATAATGTAATAGGTTGTGGTT
1 ATATAATGTAATAGGTTGT-GTT
207406 ATAT
1 ATAT
207410 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
21 2 0.05
22 1 0.02
23 39 0.91
25 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (22 bp):
ATATAATGTAATAGGTTGTGTT
Found at i:213393 original size:259 final size:259
Alignment explanation
Indices: 212929--213452 Score: 1030
Period size: 259 Copynumber: 2.0 Consensus size: 259
212919 GAGGCCCCGG
212929 ACCTACAGGCTCCTTGAAAGACCCTAATGTAGTTCCAGAGGAATCTTTTAAAACTCCTCCTAAAC
1 ACCTACAGGCTCCTTGAAAGACCCTAATGTAGTTCCAGAGGAATCTTTTAAAACTCCTCCTAAAC
212994 CACTCTTCTTCCAATCCTTAGTCGTAGCTGTATCAACATTAATTTTCACAAAACCCATAGGAGGA
66 CACTCTTCTTCCAATCCTTAGTCGTAGCTGTATCAACATTAATTTTCACAAAACCCATAGGAGGA
213059 GGATGCCACGGAATAGTAGACACAATCATATTAGAATGGGTGGAACAAACGTCCCCTAAGGAGGG
131 GGATGCCACGGAATAGTAGACACAATCATATTAGAATGGGTGGAACAAACGTCCCCTAAGGAGGG
213124 GTCTGAAATGAGAGAGTCTTTAAGAATATGCACCCCTTTATTCTTCGCTAGGAACCATGAAGCA
196 GTCTGAAATGAGAGAGTCTTTAAGAATATGCACCCCTTTATTCTTCGCTAGGAACCATGAAGCA
*
213188 ACCTGCAGGCTCCTTGAAAGACCCTAATGTAGTTCCAGAGGAATCTTTTAAAACTCCTCCTAAAC
1 ACCTACAGGCTCCTTGAAAGACCCTAATGTAGTTCCAGAGGAATCTTTTAAAACTCCTCCTAAAC
213253 CACTCTTCTTCCAATCCTTAGTCGTAGCTGTATCAACATTAATTTTCACAAAACCCATAGGAGGA
66 CACTCTTCTTCCAATCCTTAGTCGTAGCTGTATCAACATTAATTTTCACAAAACCCATAGGAGGA
213318 GGATGCCACGGAATAGTAGACACAATCATATTAGAATGGGTGGAACAAACGTCCCCTAAGGAGGG
131 GGATGCCACGGAATAGTAGACACAATCATATTAGAATGGGTGGAACAAACGTCCCCTAAGGAGGG
213383 GTCTGAAATGAGAGAGTCTTTAAGAATATGCACCCCTTTATTCTTCGCTAGGAACCATGAAGCA
196 GTCTGAAATGAGAGAGTCTTTAAGAATATGCACCCCTTTATTCTTCGCTAGGAACCATGAAGCA
213447 AGCCTA
1 A-CCTA
213453 AACCTTGCTA
Statistics
Matches: 262, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
259 259 0.99
260 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (259 bp):
ACCTACAGGCTCCTTGAAAGACCCTAATGTAGTTCCAGAGGAATCTTTTAAAACTCCTCCTAAAC
CACTCTTCTTCCAATCCTTAGTCGTAGCTGTATCAACATTAATTTTCACAAAACCCATAGGAGGA
GGATGCCACGGAATAGTAGACACAATCATATTAGAATGGGTGGAACAAACGTCCCCTAAGGAGGG
GTCTGAAATGAGAGAGTCTTTAAGAATATGCACCCCTTTATTCTTCGCTAGGAACCATGAAGCA
Found at i:219503 original size:217 final size:219
Alignment explanation
Indices: 219099--219514 Score: 667
Period size: 217 Copynumber: 1.9 Consensus size: 219
219089 TTTCGGGTTA
* * *
219099 GGTCGGTTTTTTTAAGTGTGATATTTGGGTCGGGTCGAGTTTGGGTTTAGGGTGAAAAAAACTCG
1 GGTCGATTTTTTTAAGTGTGATA-TT--GTCGGGTCGAGTTCGAGTTTAGGGTGAAAAAAACTCG
*
219164 AATCGAAAATATATATAATTTTACCTTATATATTTAAGAATAATTACAAGAATACCCCTCTATAT
63 AACCGAAAATATATATAATTTTACCTTATATATTTAAGAATAATTACAAGAATACCCCTCTATAT
* * *
219229 ATAATTTTTTTCAATTAAGTCACTGTTTTTGTTGAATAAAAATATTTTTTTTATTATTTCGGGTC
128 ATAATTTTTTTCAATCAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTC
219294 GGGTGAAACTTTATTTTGGTCTGGTCG
193 GGGTGAAACTTTATTTTGGTCTGGTCG
* *
219321 GGTCGATTTTTTTAAGTGTGATA-T-TCGGGTCGAGTTCGAGTTTAGGGTGAAAAATA-TCCGAC
1 GGTCGATTTTTTTAAGTGTGATATTGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAAAACT-CGAA
**
219383 CCGAAAATATATATAATTTTACCTTATATATTTAAGAATAATTACATTAATACCCCTCTATATAT
65 CCGAAAATATATATAATTTTACCTTATATATTTAAGAATAATTACAAGAATACCCCTCTATATAT
*
219448 AATTTTTTTCAATCAAGTCATTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGG
130 AATTTTTTTCAATCAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGG
219513 GT
195 GT
219515 CGGATTTCTA
Statistics
Matches: 181, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
216 1 0.01
217 157 0.87
220 1 0.01
222 22 0.12
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (219 bp):
GGTCGATTTTTTTAAGTGTGATATTGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAAAACTCGAAC
CGAAAATATATATAATTTTACCTTATATATTTAAGAATAATTACAAGAATACCCCTCTATATATA
ATTTTTTTCAATCAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGG
TGAAACTTTATTTTGGTCTGGTCG
Found at i:219728 original size:253 final size:246
Alignment explanation
Indices: 219287--219826 Score: 814
Period size: 253 Copynumber: 2.2 Consensus size: 246
219277 TTTTATTATT
*
219287 TCGGGTCGGGTGAAACTTTATTTTGGTCTGGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTC
1 TCGGGTC-GGTGAAACTTTATTTTGGTCGGGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTC
* * *
219352 GAGTTCGAGTTTAGGGTGAAAAATATCCGACCCGAAAATATATATAATTTTACCTTATATATTTA
65 GAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATATTACCTTATATATTTA
* *
219417 AGAATAATTACATTAATACCCCTCTATATATAATTTTTTTCAATCAAGTCATTGTTTTTATTGAA
130 AGAATAATTACAATAATACCCCTC---ATATAATTTTTTTCAATCAAGTCACTGTTTTTATTGAA
219482 TAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
192 TAAAAATAA--TTTTT-TTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
* *
219540 TCGGGTCAGGTGAAATTTTATTTTGGTCGGGTCGGGTCAGTTTTTTTTAAGTGTGATATTCGGGT
1 TCGGGTC-GGTGAAACTTTATTTTGGTCGGGTCGGGTC-GATTTTTTTAAGTGTGATATTCGGGT
219605 CGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAAATATATAATATTACCTTATAT
64 CGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCG----AAAAAATATATAATATTACCTTATAT
* * *
219670 ATTTAGGAATAATTACAATCATACCCCTC-TAT-ATTTTTTTCAATTAAGTCACTGTTTTTATTG
125 ATTTAAGAATAATTACAATAATACCCCTCATATAATTTTTTTCAATCAAGTCACTGTTTTTATTG
* * *
219733 AATAAAAATAATTTTTTTATTTCGGGTCGGGTCGGGTTTTTAATTCATATGTTCGGG
190 AATAAAAATAATTTTTTTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
*
219790 TCGAGTCGGTGAAACTTTATTTTGGTCGGGTCGGGTC
1 TCGGGTCGGTGAAACTTTATTTTGGTCGGGTCGGGTC
219827 TCGGATGGAG
Statistics
Matches: 265, Mismatches: 17, Indels: 14
0.90 0.06 0.05
Matches are distributed among these distances:
249 29 0.11
250 44 0.17
251 5 0.02
253 75 0.28
254 62 0.23
258 50 0.19
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (246 bp):
TCGGGTCGGTGAAACTTTATTTTGGTCGGGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTCG
AGTTCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATATTACCTTATATATTTAA
GAATAATTACAATAATACCCCTCATATAATTTTTTTCAATCAAGTCACTGTTTTTATTGAATAAA
AATAATTTTTTTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
Found at i:219824 original size:254 final size:253
Alignment explanation
Indices: 219295--219826 Score: 757
Period size: 254 Copynumber: 2.1 Consensus size: 253
219285 TTTCGGGTCG
219295 GGTGAAACTTTATTTTGGTC--T--GGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTCGAGT
1 GGTGAAACTTTATTTTGGTCGGTCGGGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTCGAGT
* * *
219356 TCGAGTTTAGGGTGAAAAATATCCGACCCGAAAATATATATAATTTTACCTTATATATTTAAGAA
66 TCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATATTACCTTATATATTTAAGAA
* *
219421 TAATTACATTAATACCCCTCTATATATAATTTTTTTCAATCAAGTCATTGTTTTTATTGAATAAA
131 TAATTACAATAATACCCCTC---ATATAATTTTTTTCAATCAAGTCACTGTTTTTATTGAATAAA
*
219486 AATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCA
193 AATAA-TTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGAGTCA
* *
219548 GGTGAAATTTTA-TTT--T-GGTCGGGTCGGGTCAGTTTTTTTTAAGTGTGATATTCGGGTCGAG
1 GGTGAAACTTTATTTTGGTCGGTCGGGTCGGGTC-GATTTTTTTAAGTGTGATATTCGGGTCGAG
219609 TTCGAGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAAATATATAATATTACCTTATATATTT
65 TTCGAGTTTAGGGTGAAAAATACCCGACCCG----AAAAAATATATAATATTACCTTATATATTT
* * *
219674 AGGAATAATTACAATCATACCCCTC-TAT-ATTTTTTTCAATTAAGTCACTGTTTTTATTGAATA
126 AAGAATAATTACAATAATACCCCTCATATAATTTTTTTCAATCAAGTCACTGTTTTTATTGAATA
* * *
219737 AAAATAA-TTTTT-TTATTTCGGGTCGGGTCGGGTTTTTAATTCATATGTTCGGGTCGAGTC-
191 AAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGAGTCA
219797 GGTGAAACTTTATTTTGGTCGGGTCGGGTC
1 GGTGAAACTTTATTTTGGTC-GGTCGGGTC
219827 TCGGATGGAG
Statistics
Matches: 250, Mismatches: 15, Indels: 27
0.86 0.05 0.09
Matches are distributed among these distances:
249 11 0.04
250 48 0.19
251 6 0.02
252 4 0.02
253 60 0.24
254 71 0.28
258 50 0.20
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (253 bp):
GGTGAAACTTTATTTTGGTCGGTCGGGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTCGAGT
TCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATATTACCTTATATATTTAAGAA
TAATTACAATAATACCCCTCATATAATTTTTTTCAATCAAGTCACTGTTTTTATTGAATAAAAAT
AATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGAGTCA
Found at i:222075 original size:418 final size:420
Alignment explanation
Indices: 221237--222080 Score: 1550
Period size: 419 Copynumber: 2.0 Consensus size: 420
221227 CCCCTGAAGA
*
221237 CTCCATCATCTGAGAAGAGCCACTAAAAATTCCCAGGAAGCATCATACAATCTCTTGAACCATCA
1 CTCCATCATCTGAGAAGAGCCACTAAAAATTCCCAGAAAGCATCATACAATCTCTTGAACCATCA
221302 TCCGTTGGGATCGCTCTTCAAAGTTCATACCCCCAATCTTTGAGGAGACATTTGATATAGCGAAA
66 T-C-TTGGGATCGCTCTTCAAAGTTCATACCCCCAATCTTTGAGGAGACATTTGA-ATAGCGAAA
*
221367 TCTAATATATAAACAACCATGCATGCATAGTCTTCCAACCTATTAGCAGACATTGTGACCATAGT
128 TCTAATATATAAACAACCATGCATGCATAATCTTCCAACCTATTAGCAGACATTGTGACCATAGT
221432 CTTGACACCAGACATGTAGTCAGTGTATTTATACCCCGAAGGAAGGATGAAAGAATGAGTCTTTT
193 CTTGACACCAGACATGTAGTCAGTGTATTTATACCCCGAAGGAAGGATGAAAGAATGAGTCTTTT
* *
221497 TCTCTCTTTTCCAGCTTTTTCATATGTACTATTGATCTTCTCTCATACGCTACTTTTTTTATTCT
258 TATCTCTTTTCCAGCTTTTTCATATGTACTATTGATCTTCTCCCATACGCTACTTTTTTTATTCT
*
221562 CACTCTAATAAAGAATCATCGACTAACAACTATCTTTGCTTCGATAGTGACTCTCTATCCAAACC
323 CACTCTAATAAAGAATCATAGACTAACAACTATCTTTGCTTCGATAGTGACTCTCTATCCAAACC
221627 AGAAAGTGTGAATCGCCAGCGACCAATGCAACC
388 AGAAAGTGTGAATCGCCAGCGACCAATGCAACC
221660 CTCCATCATCTGAGAAGAGCCACTAAAAATTCCCAGAAAGCATCATACAATCTCTTGAACCATCA
1 CTCCATCATCTGAGAAGAGCCACTAAAAATTCCCAGAAAGCATCATACAATCTCTTGAACCATCA
221725 T-TTGGGATCGCTCTTCAAAGTTCATACCCCCAATCTTTGAGGAGACATTTG-ATAGCGAAATCT
66 TCTTGGGATCGCTCTTCAAAGTTCATACCCCCAATCTTTGAGGAGACATTTGAATAGCGAAATCT
* *
221788 AATATATAAACAACCATGCATGCATAATCTTCCAGCCTATTAGCAGACGTTGTGACCATAGTCTT
131 AATATATAAACAACCATGCATGCATAATCTTCCAACCTATTAGCAGACATTGTGACCATAGTCTT
* *
221853 GACACCAGACATGTAGTTAGTGTATTTATACCCCGAAGGAAGGATGAAAGAATGAGTTTTTTTTA
196 GACACCAGACATGTAGTCAGTGTATTTATACCCCGAAGGAAGGATGAAAGAATGAG-TCTTTTTA
221918 TCTCTTTTCCAGCTTTTTCATATGTACTATTGATCTTCTCCCATACGCTACTTTTTTTATTCTCA
260 TCTCTTTTCCAGCTTTTTCATATGTACTATTGATCTTCTCCCATACGCTACTTTTTTTATTCTCA
221983 CTCTAATAAAGAATCATAGACTAACAACTATCTTTGCTTCGATAGTGACTCTCTATCCAAACCAG
325 CTCTAATAAAGAATCATAGACTAACAACTATCTTTGCTTCGATAGTGACTCTCTATCCAAACCAG
222048 AAAGTGTGAATCGCC-GCGACCAATGCAACC
390 AAAGTGTGAATCGCCAGCGACCAATGCAACC
222078 CTC
1 CTC
222081 TCGTTCCCAT
Statistics
Matches: 411, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
418 147 0.36
419 149 0.36
420 50 0.12
423 65 0.16
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (420 bp):
CTCCATCATCTGAGAAGAGCCACTAAAAATTCCCAGAAAGCATCATACAATCTCTTGAACCATCA
TCTTGGGATCGCTCTTCAAAGTTCATACCCCCAATCTTTGAGGAGACATTTGAATAGCGAAATCT
AATATATAAACAACCATGCATGCATAATCTTCCAACCTATTAGCAGACATTGTGACCATAGTCTT
GACACCAGACATGTAGTCAGTGTATTTATACCCCGAAGGAAGGATGAAAGAATGAGTCTTTTTAT
CTCTTTTCCAGCTTTTTCATATGTACTATTGATCTTCTCCCATACGCTACTTTTTTTATTCTCAC
TCTAATAAAGAATCATAGACTAACAACTATCTTTGCTTCGATAGTGACTCTCTATCCAAACCAGA
AAGTGTGAATCGCCAGCGACCAATGCAACC
Found at i:234336 original size:14 final size:14
Alignment explanation
Indices: 234317--234345 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
234307 ACGTGGTTTT
234317 CGACACCAACAAAC
1 CGACACCAACAAAC
234331 CGACACCAACAAAC
1 CGACACCAACAAAC
234345 C
1 C
234346 AATAACAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.45, G:0.07, T:0.00
Consensus pattern (14 bp):
CGACACCAACAAAC
Found at i:235378 original size:9 final size:9
Alignment explanation
Indices: 235356--235588 Score: 57
Period size: 9 Copynumber: 24.9 Consensus size: 9
235346 ATTTATTTAA
*
235356 TATTTTATT
1 TATTTTTTT
*
235365 AATTTTTTT
1 TATTTTTTT
235374 TATTTTATTT
1 TATTTT-TTT
*
235384 CATGTTTTTCTT
1 --TATTTTT-TT
235396 TGATTTTTTT
1 T-ATTTTTTT
* *
235406 TATTTTAATC
1 TATTTT-TTT
235416 TA-TTTTTT
1 TATTTTTTT
*
235424 AATCTTTTTCT
1 TAT-TTTTT-T
** **
235435 CCTTTGATT
1 TATTTTTTT
*
235444 TATTTTTCT
1 TATTTTTTT
*
235453 TA-TTATTT
1 TATTTTTTT
*
235461 TA--TTTAT
1 TATTTTTTT
235468 TATTTCTATTT
1 TATTT-T-TTT
*
235479 TATTTTCTT
1 TATTTTTTT
*
235488 TCTTTTTTCT
1 TATTTTTT-T
*
235498 CTCTTTTGATTT
1 -TATTTT--TTT
*
235510 TA-TTATTT
1 TATTTTTTT
*
235518 TATTATTTT
1 TATTTTTTT
*
235527 T-TTCTTTT
1 TATTTTTTT
* *
235535 GATTTTTAT
1 TATTTTTTT
* *
235544 TATTATTAT
1 TATTTTTTT
235553 TATTTTATTT
1 TATTTT-TTT
*
235563 TATTTTTAT
1 TATTTTTTT
235572 T-TTTTTTT
1 TATTTTTTT
235580 TATGTTTTT
1 TAT-TTTTT
235589 CCTTTGATTT
Statistics
Matches: 161, Mismatches: 41, Indels: 43
0.66 0.17 0.18
Matches are distributed among these distances:
7 5 0.03
8 26 0.16
9 62 0.39
10 36 0.22
11 22 0.14
12 8 0.05
13 2 0.01
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (9 bp):
TATTTTTTT
Found at i:235496 original size:45 final size:42
Alignment explanation
Indices: 235446--235579 Score: 125
Period size: 42 Copynumber: 3.1 Consensus size: 42
235436 CTTTGATTTA
235446 TTTTTCTTATTATTTTATTTATTATTTCTATTTTATTTTCTTTCT
1 TTTTTCTT-TTATTTTATTTATTATTT-TATTTTATTTT-TTTCT
* *
235491 TTTTTCTCTCT-TTTGATTTTATTATTTTA--TTATTTTTTTCT
1 TTTTTCT-TTTATTTTA-TTTATTATTTTATTTTATTTTTTTCT
* *
235532 TTTGAT-TTTTATTATTA-TTATTATTTTATTTTATTTTTATTTT
1 TTT-TTCTTTTATT-TTATTTATTATTTTATTTTATTTTT-TTCT
235575 TTTTT
1 TTTTT
235580 TATGTTTTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
40 13 0.18
41 11 0.15
42 19 0.26
43 6 0.08
44 6 0.08
45 18 0.24
46 1 0.01
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (42 bp):
TTTTTCTTTTATTTTATTTATTATTTTATTTTATTTTTTTCT
Found at i:235516 original size:34 final size:31
Alignment explanation
Indices: 235499--235598 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 31
235489 CTTTTTTCTC
235499 TCTTTTGA-TTTTATTATTTTATTATTTTTT
1 TCTTTTGATTTTTATTATTTTATTATTTTTT
*
235529 TCTTTTGATTTTTATTA--TTATTATTATTT
1 TCTTTTGATTTTTATTATTTTATTATTTTTT
* * * *
235558 TATTTT-ATTTTTATTTTTTTTTTATGTTTT
1 TCTTTTGATTTTTATTATTTTATTATTTTTT
*
235588 TCCTTTGATTT
1 TCTTTTGATTT
235599 ATTTAATACT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
28 9 0.16
29 16 0.28
30 21 0.36
31 12 0.21
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (31 bp):
TCTTTTGATTTTTATTATTTTATTATTTTTT
Found at i:235540 original size:6 final size:5
Alignment explanation
Indices: 235512--235578 Score: 55
Period size: 5 Copynumber: 12.4 Consensus size: 5
235502 TTTGATTTTA
* *
235512 TTATT TTATT ATTTTT TTCTT TTGATTT TTATT ATTATT ATTATT TTATT
1 TTATT TTATT -TTATT TTATT TT-A-TT TTATT -TTATT -TTATT TTATT
235562 TTATTT TTATT TT-TT TT
1 TTA-TT TTATT TTATT TT
235579 TTATGTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
4 4 0.07
5 25 0.46
6 21 0.39
7 4 0.07
ACGTcount: A:0.18, C:0.01, G:0.01, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:235574 original size:11 final size:11
Alignment explanation
Indices: 235442--235587 Score: 75
Period size: 12 Copynumber: 12.3 Consensus size: 11
235432 TCTCCTTTGA
235442 TTTATTTT-TCT
1 TTTATTTTAT-T
235453 TATTATTTTATT
1 T-TTATTTTATT
235465 TATTATTTCTA-T
1 T-TTATTT-TATT
*
235477 TTTATTTTCTT
1 TTTATTTTATT
* *
235488 TCTTTTTTCTCTCT
1 T-TTATTT-TAT-T
235502 TTTGATTTTATTAT
1 TTT-ATTTTA-T-T
235516 TTTATTATT-TT
1 TTTATT-TTATT
*
235527 TTTCTTTTGATT
1 TTTATTTT-ATT
235539 TTTATTATTATT
1 TTTATT-TTATT
*
235551 ATTATTTTA-T
1 TTTATTTTATT
235561 TTTATTTTTATT
1 TTTA-TTTTATT
*
235573 TTTTTTTTATGT
1 TTTATTTTAT-T
235585 TTT
1 TTT
235588 TCCTTTGATT
Statistics
Matches: 109, Mismatches: 10, Indels: 31
0.73 0.07 0.21
Matches are distributed among these distances:
10 7 0.06
11 29 0.27
12 47 0.43
13 14 0.13
14 12 0.11
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:235580 original size:6 final size:6
Alignment explanation
Indices: 235442--235587 Score: 67
Period size: 6 Copynumber: 24.5 Consensus size: 6
235432 TCTCCTTTGA
* * *
235442 TTTATT TTTCTT ATTA-T TTTATT TATTATT TCTA-T TTTATT TTCT-TT
1 TTTATT TTTATT TTTATT TTTATT T-TTATT TTTATT TTTATT TT-TATT
* * * * *
235489 CTTT-TT TCTCTCTT TTGA-T TTTATTAT TTTATT ATT-TT TTTCTT TTGATT
1 -TTTATT T-T-TATT TTTATT TTTA-T-T TTTATT TTTATT TTTATT TTTATT
* *
235539 TTTATT ATTATT ATTA-T TTTA-T TTTATT TTTATT TTT-TT TTTATGT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT-T
235585 TTT
1 TTT
235588 TCCTTTGATT
Statistics
Matches: 109, Mismatches: 16, Indels: 29
0.71 0.10 0.19
Matches are distributed among these distances:
5 31 0.28
6 54 0.50
7 16 0.15
8 8 0.07
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTATT
Done.