Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003752.1 Hibiscus syriacus cultivar Beakdansim tig00008030_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: 153864
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:749 original size:21 final size:22
Alignment explanation
Indices: 714--754 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
704 AAATAATAAA
714 ATATCAAAAAATTAATTCGATT
1 ATATCAAAAAATTAATTCGATT
*
736 ATAT-AAAAATTTAATTCGA
1 ATATCAAAAAATTAATTCGA
755 ACATAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (22 bp):
ATATCAAAAAATTAATTCGATT
Found at i:760 original size:19 final size:20
Alignment explanation
Indices: 719--760 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
709 ATAAAATATC
*
719 AAAAAATTAATTCGATTATAT
1 AAAAAATTAATTCGA-TACAT
*
740 AAAAATTTAATTCGA-ACAT
1 AAAAAATTAATTCGATACAT
759 AA
1 AA
761 CATTAATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
21 14 0.74
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAAAATTAATTCGATACAT
Found at i:1353 original size:16 final size:15
Alignment explanation
Indices: 1332--1367 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1322 ACTTGATTAT
1332 TAAAAATAAGAAAAAA
1 TAAAAATAA-AAAAAA
1348 TAAAAATAAAAAAAA
1 TAAAAATAAAAAAAA
1363 -AAAAA
1 TAAAAA
1368 GCCTCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 6 0.30
16 9 0.45
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (15 bp):
TAAAAATAAAAAAAA
Found at i:4115 original size:3 final size:3
Alignment explanation
Indices: 4107--4133 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4097 CACTAATCCC
4107 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
4134 GTTTGGGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13639 original size:21 final size:21
Alignment explanation
Indices: 13613--13652 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13603 AACAAAATGG
13613 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
13634 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
13653 CATTAAACAT
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:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:17311 original size:23 final size:22
Alignment explanation
Indices: 17284--17326 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
17274 ATATCATTCC
17284 ATAATAGTTTAATAAATTTAACA
1 ATAATAGTTTAA-AAATTTAACA
* *
17307 ATAATTGTTTAAAATTTTAA
1 ATAATAGTTTAAAAATTTAA
17327 TTATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATAATAGTTTAAAAATTTAACA
Found at i:21060 original size:114 final size:113
Alignment explanation
Indices: 20928--21147 Score: 379
Period size: 113 Copynumber: 1.9 Consensus size: 113
20918 TTTGTTTCTG
* *
20928 TTTTTTACCCACCATTAAAAAATTTACGGTGATGATGATGTTGCAT-TTTTTAAATTATTTTTTC
1 TTTTTTACCCACCATTAAAAAATTAACGGCGATGATGATG-TG-ATATTTTTAAATTATTTTTTC
20992 ACTTCACACTTAATTATTATTTTATTATTTTTTGACAAGATGGTTTCTTT
64 ACTTCACACTTAATTATTATTTTATTATTTTTTGACAAGATGGTTTCTTT
*
21042 TTTTTTACCCACCATTAAAAAATTAACGGCGATGTTGATGTGATATTTTTAAATTATTTTTTCAC
1 TTTTTTACCCACCATTAAAAAATTAACGGCGATGATGATGTGATATTTTTAAATTATTTTTTCAC
*
21107 TTCACACTTAATTATTCTTTTATTATTTTTTGACAAGATGG
66 TTCACACTTAATTATTATTTTATTATTTTTTGACAAGATGG
21148 AGAAGGTTAA
Statistics
Matches: 101, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
112 2 0.02
113 62 0.61
114 37 0.37
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (113 bp):
TTTTTTACCCACCATTAAAAAATTAACGGCGATGATGATGTGATATTTTTAAATTATTTTTTCAC
TTCACACTTAATTATTATTTTATTATTTTTTGACAAGATGGTTTCTTT
Found at i:24476 original size:50 final size:52
Alignment explanation
Indices: 24417--24554 Score: 163
Period size: 59 Copynumber: 2.6 Consensus size: 52
24407 CACACTCCAA
* *
24417 TTTGCCTTTTCATTGCGACGAGGAGGGTT-GG-TTAGAGTCATATTATTGAG
1 TTTGCCTTTTCATTGCGACTAGGAGGGTTAGGATTAGAGTCATATTATCGAG
*
24467 TTTGTCTTTTCATTGCGACTAGGAGGGTTCGATAGGACACTTAGAGTCATATTATCGAG
1 TTTGCCTTTTCATTGCGACTAGGAGGG-T---TAGG--A-TTAGAGTCATATTATCGAG
*
24526 TTTGCCTTTTCATTGCGACTTGGAGGGTT
1 TTTGCCTTTTCATTGCGACTAGGAGGGTT
24555 CAATAGGACA
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
50 25 0.34
51 1 0.01
54 1 0.01
55 3 0.04
58 1 0.01
59 43 0.58
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (52 bp):
TTTGCCTTTTCATTGCGACTAGGAGGGTTAGGATTAGAGTCATATTATCGAG
Found at i:24540 original size:59 final size:59
Alignment explanation
Indices: 24448--24568 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
24438 GGAGGGTTGG
* * *
24448 TTAGAGTCATATTATTGAGTTTGTCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGTCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGGACAC
*
24507 TTAGAGTCATATTATCGAGTTTGCCTTTTCATTGCGACTTGGAGGGTTCAATAGGACAC
1 TTAGAGTCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGGACAC
24566 TTA
1 TTA
24569 TCCATCTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (59 bp):
TTAGAGTCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGGACAC
Found at i:25938 original size:10 final size:10
Alignment explanation
Indices: 25905--25959 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
25895 AGGGCTGGAA
25905 ACCGGTTT-G
1 ACCGGTTTCG
* *
25914 ATCGGTTTTCA
1 ACCGG-TTTCG
*
25925 ACCGATTTCG
1 ACCGGTTTCG
25935 ACCGGTTTCG
1 ACCGGTTTCG
*
25945 TCCGGTTT-G
1 ACCGGTTTCG
25954 ACCGGT
1 ACCGGT
25960 ATGAACCGGC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 10 0.28
10 23 0.64
11 3 0.08
ACGTcount: A:0.13, C:0.25, G:0.27, T:0.35
Consensus pattern (10 bp):
ACCGGTTTCG
Found at i:29109 original size:39 final size:38
Alignment explanation
Indices: 29066--29139 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
29056 AAGGGCTGGA
* *
29066 AACCGGTTTGACCGTTTTCAACCGGTTTCGACCGGTTCG
1 AACCGGTTTGACCGGTATCAACCGGTTT-GACCGGTTCG
*
29105 AACCGGTTTGACCGGTATGAACCGGTTTGACCGGT
1 AACCGGTTTGACCGGTATCAACCGGTTTGACCGGT
29140 CTGACCCGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 7 0.22
39 25 0.78
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (38 bp):
AACCGGTTTGACCGGTATCAACCGGTTTGACCGGTTCG
Found at i:29118 original size:9 final size:9
Alignment explanation
Indices: 29067--29145 Score: 77
Period size: 10 Copynumber: 8.3 Consensus size: 9
29057 AGGGCTGGAA
29067 ACCGGTTTG
1 ACCGGTTTG
* *
29076 ACCGTTTTCA
1 ACCGGTTT-G
29086 ACCGGTTTCG
1 ACCGGTTT-G
*
29096 ACCGGTTCG
1 ACCGGTTTG
29105 AACCGGTTTG
1 -ACCGGTTTG
*
29115 ACCGGTATG
1 ACCGGTTTG
29124 AACCGGTTTG
1 -ACCGGTTTG
*
29134 ACCGGTCTG
1 ACCGGTTTG
29143 ACC
1 ACC
29146 CGACCCGACT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
9 27 0.47
10 31 0.53
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:29138 original size:19 final size:18
Alignment explanation
Indices: 29066--29139 Score: 94
Period size: 19 Copynumber: 3.9 Consensus size: 18
29056 AAGGGCTGGA
* *
29066 AACCGGTTTGACCGTTTTC
1 AACCGGTTTGACCG-GTTG
29085 AACCGGTTTCGACCGGTTCG
1 AACCGGTTT-GACCGGTT-G
29105 AACCGGTTTGACCGGTATG
1 AACCGGTTTGACCGGT-TG
29124 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
29140 CTGACCCGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
19 35 0.70
20 15 0.30
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (18 bp):
AACCGGTTTGACCGGTTG
Found at i:29167 original size:19 final size:19
Alignment explanation
Indices: 29143--29188 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
29133 GACCGGTCTG
29143 ACCCGACCCGACTGACCCA
1 ACCCGACCCGACTGACCCA
* *
29162 ACCCGACCCGATTGACCCG
1 ACCCGACCCGACTGACCCA
29181 ACCCGACC
1 ACCCGACC
29189 GTTGACCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.24, C:0.52, G:0.17, T:0.07
Consensus pattern (19 bp):
ACCCGACCCGACTGACCCA
Found at i:30668 original size:2 final size:2
Alignment explanation
Indices: 30661--30694 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
30651 AGGGGGTTAC
*
30661 AT AT AT AT AT AT AT AT AT AT AT AT GAC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A
30695 AAATATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.97
3 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:31735 original size:26 final size:26
Alignment explanation
Indices: 31681--31742 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
31671 AAAGTTGATG
* *
31681 GAAGAAAAAGAAATGGGTTTATAGAA
1 GAAGAAGAAGAAACGGGTTTATAGAA
* * *
31707 GAAGAAGAAGAAACGTGTTTATGGGA
1 GAAGAAGAAGAAACGGGTTTATAGAA
*
31733 GAAGTAGAAG
1 GAAGAAGAAG
31743 GGTTCTGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.48, C:0.02, G:0.32, T:0.18
Consensus pattern (26 bp):
GAAGAAGAAGAAACGGGTTTATAGAA
Found at i:40382 original size:2 final size:2
Alignment explanation
Indices: 40339--40364 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40329 TTAGTAATTG
40339 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
40365 TAGTTAATTT
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:40960 original size:21 final size:21
Alignment explanation
Indices: 40919--40962 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40909 TTAAATAATA
**
40919 AATATATAATAATAAGTTTAT
1 AATATATAATAATAAAATTAT
40940 AATATTATAA-AATAAAATTAT
1 AATA-TATAATAATAAAATTAT
40961 AA
1 AA
40963 AATAGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AATATATAATAATAAAATTAT
Found at i:43628 original size:2 final size:2
Alignment explanation
Indices: 43621--43698 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
43611 TGAAATTTGG
43621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43663 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43699 GAACTCAATT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48799 original size:35 final size:36
Alignment explanation
Indices: 48753--48831 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
48743 TTTAAATTTT
48753 AAGACTAATATTATATAT-AAAAAATAAGTAGTACA
1 AAGACTAATATTATATATAAAAAAATAAGTAGTACA
*
48788 AAGACTAATATTATATATAAAAAAATAAGTGGTACA
1 AAGACTAATATTATATATAAAAAAATAAGTAGTACA
48824 AAGACTAA
1 AAGACTAA
48832 ATCTGATACT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 18 0.43
36 24 0.57
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (36 bp):
AAGACTAATATTATATATAAAAAAATAAGTAGTACA
Found at i:50352 original size:27 final size:28
Alignment explanation
Indices: 50321--50376 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
50311 TTTTTATATT
50321 TTTAA-TTTTGTAAA-AAAATTATATAAA
1 TTTAATTTTTGTAAAGAAAA-TATATAAA
*
50348 TTTAATTTTTTTAAAGAAAATATATAAA
1 TTTAATTTTTGTAAAGAAAATATATAAA
50376 T
1 T
50377 ATTTTTTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 5 0.19
28 17 0.65
29 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (28 bp):
TTTAATTTTTGTAAAGAAAATATATAAA
Found at i:50798 original size:20 final size:20
Alignment explanation
Indices: 50753--50798 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
50743 GACCAACAAA
*
50753 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
50773 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
50792 ATCGCAA
1 ATCGCAA
50799 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:50902 original size:20 final size:20
Alignment explanation
Indices: 50877--50969 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
50867 TTTTCCCAAT
50877 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
50897 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
50917 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
50938 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
50959 TCGCAATGCGA
1 TCGCAATGCGA
50970 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:50919 original size:41 final size:41
Alignment explanation
Indices: 50874--50969 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
50864 CGATTTTCCC
50874 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
50915 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
50956 AAATCGCAATGCGA
1 AATTCGCAATGCGA
50970 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:50923 original size:21 final size:20
Alignment explanation
Indices: 50877--50969 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
50867 TTTTCCCAAT
*
50877 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
50897 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
50917 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
50938 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
50959 TCGCAATGCGA
1 TCGCAATGCGA
50970 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:51048 original size:20 final size:20
Alignment explanation
Indices: 51001--51051 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
50991 AATAAAAAAC
* *
51001 CGCAACGAGATACTTACTTT
1 CGCAACGCGATACTGACTTT
51021 CGCAACGCGATACTGACTTT
1 CGCAACGCGATACTGACTTT
51041 CGCAACGCGAT
1 CGCAACGCGAT
51052 TTACTTAGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (20 bp):
CGCAACGCGATACTGACTTT
Found at i:51598 original size:19 final size:19
Alignment explanation
Indices: 51555--51619 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
51545 CGAGAATGAG
* *
51555 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATAAA
*
51575 TATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
51594 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
51613 AATCGCA
1 AATCGCA
51620 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:51651 original size:19 final size:19
Alignment explanation
Indices: 51615--51692 Score: 120
Period size: 19 Copynumber: 4.0 Consensus size: 19
51605 GAAACCAAAA
*
51615 TCGCATTGCGATTTTTCATT
1 TCGCGTTGCGA-TTTTCATT
51635 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
51654 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
51673 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
51693 GACATTAAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 30 0.56
20 24 0.44
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.49
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:51682 original size:39 final size:39
Alignment explanation
Indices: 51615--51692 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
51605 GAAACCAAAA
51615 TCGCATTGCGATTTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTTCATTTCGCGTTGCGATTTTCATT
*
51654 TCGCGTTGCGATTTTT-ATTTCGCGGTTGCGATTTTCATT
1 TCGCATTGCGATTTTTCATTTCGC-GTTGCGATTTTCATT
51693 GACATTAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 7 0.19
39 30 0.81
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.49
Consensus pattern (39 bp):
TCGCATTGCGATTTTTCATTTCGCGTTGCGATTTTCATT
Found at i:53591 original size:42 final size:42
Alignment explanation
Indices: 53531--53653 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
53521 GCCCGACTCG
* * *
53531 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
53573 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
53615 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
53654 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:53611 original size:21 final size:21
Alignment explanation
Indices: 53587--53653 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
53577 TCATTCCTCG
53587 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
53608 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
53629 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
53650 AGAG
1 AGAG
53654 CCCGATTCAC
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:55028 original size:14 final size:14
Alignment explanation
Indices: 55009--55044 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
54999 ATTGTTTAAT
55009 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
55023 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
55037 TGATTTGT
1 TGATTTGT
55045 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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:55245 original size:19 final size:19
Alignment explanation
Indices: 55223--55289 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
55213 CGAAATTAAA
*
55223 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
55242 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
55257 --CTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
55274 TTCGCATTGCGATTTT
1 TTCGCATTGCGATTTT
55290 GTCGTTTCCG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
13 9 0.23
15 3 0.08
17 3 0.08
19 24 0.62
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:57599 original size:12 final size:12
Alignment explanation
Indices: 57582--57606 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57572 TCTTCGGGGA
57582 CTTTTTCTTCTT
1 CTTTTTCTTCTT
57594 CTTTTTCTTCTT
1 CTTTTTCTTCTT
57606 C
1 C
57607 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:59101 original size:14 final size:14
Alignment explanation
Indices: 59082--59118 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
59072 CATCAATTAA
59082 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
59096 ACAAATCATCTTTT
1 ACAAATCAACATTT
59110 ACAAATCAA
1 ACAAATCAA
59119 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:59690 original size:14 final size:14
Alignment explanation
Indices: 59671--59707 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
59661 CATCAATTAA
59671 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
59685 ACAAATCATCTTTT
1 ACAAATCAACATTT
59699 ACAAATCAA
1 ACAAATCAA
59708 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:61596 original size:20 final size:19
Alignment explanation
Indices: 61561--61627 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
61551 GAAACTTAAA
61561 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
61580 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
61600 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
61619 ATCGCAACG
1 ATCGCAACG
61628 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:61635 original size:14 final size:14
Alignment explanation
Indices: 61616--61673 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
61606 ATGCGAAATG
61616 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
61630 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
61646 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
61662 AAAATCGCAACG
1 AAAATCGCAACG
61674 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:61658 original size:32 final size:33
Alignment explanation
Indices: 61600--61678 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
61590 GGAAATGGCT
*
61600 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
61633 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
61665 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
61679 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:61712 original size:19 final size:18
Alignment explanation
Indices: 61690--61749 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
61680 ACAAATCGCA
61690 TTGCGATTTTCATTTTGCG
1 TTGCGA-TTTCATTTTGCG
*
61709 TTGCGA-TT--TTGT-CG
1 TTGCGATTTCATTTTGCG
*
61723 TTGCGATTTCATTTCGCG
1 TTGCGATTTCATTTTGCG
61741 TTGCGATTT
1 TTGCGATTT
61750 TGTCGTTGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 8 0.24
15 5 0.15
17 4 0.12
18 11 0.32
19 6 0.18
ACGTcount: A:0.10, C:0.17, G:0.23, T:0.50
Consensus pattern (18 bp):
TTGCGATTTCATTTTGCG
Found at i:61724 original size:14 final size:14
Alignment explanation
Indices: 61701--61764 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
61691 TGCGATTTTC
61701 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
61714 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
61728 ATTTCATTTCGCGTTGCG
1 ATTT--TGT--CGTTGCG
61746 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
61760 ATTTT
1 ATTTT
61765 CATTTCGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.14
14 23 0.52
16 4 0.09
18 11 0.25
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:61771 original size:33 final size:33
Alignment explanation
Indices: 61690--61780 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
61680 ACAAATCGCA
*
61690 TTGCGATTTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
61723 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
61755 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
61781 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:61779 original size:19 final size:17
Alignment explanation
Indices: 61685--61780 Score: 69
Period size: 14 Copynumber: 5.6 Consensus size: 17
61675 GAAACACAAA
61685 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
* *
61704 TTGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
61720 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
61736 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
61752 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
61769 TCGCATTGCGAT
1 TCGC-TTGCGAT
61781 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
14 15 0.25
15 3 0.05
16 11 0.18
17 4 0.07
18 13 0.21
19 15 0.25
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:61799 original size:20 final size:19
Alignment explanation
Indices: 61765--61819 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
61755 TTGCGATTTT
*
61765 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
61784 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
61804 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
61820 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:62318 original size:18 final size:18
Alignment explanation
Indices: 62292--62336 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
62282 GTCGATCAGA
*
62292 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
62310 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
62328 TGATGGCTC
1 TGATGGCTC
62337 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:63680 original size:20 final size:20
Alignment explanation
Indices: 63655--63708 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
63645 AATAGTTTCT
63655 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
63675 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
63695 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
63709 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:63967 original size:22 final size:22
Alignment explanation
Indices: 63942--63985 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
63932 GATTTAGATA
63942 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
63964 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
63986 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:64198 original size:20 final size:20
Alignment explanation
Indices: 64173--64266 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
64163 GATTATGTAT
64173 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
64193 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
64213 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
64234 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
64254 TATCGCATTGCGA
1 TATCGCGTTGCGA
64267 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:64238 original size:41 final size:42
Alignment explanation
Indices: 64193--64328 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
64183 CGAAAGTCAG
* * * *
64193 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
64234 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
64276 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
64317 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
64329 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:64267 original size:20 final size:20
Alignment explanation
Indices: 64153--64267 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
64143 CGCTTTGAAA
*
64153 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
64174 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
64194 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
64214 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
64235 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
64255 ATCGCATTGCGAT
1 ATCGCATTGCGAT
64268 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:64300 original size:20 final size:20
Alignment explanation
Indices: 64256--64348 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
64246 ATAGTCAGTA
*
64256 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
64277 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
64297 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
64318 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
64338 TCGCATTGCGA
1 TCGCATTGCGA
64349 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:64329 original size:41 final size:41
Alignment explanation
Indices: 64256--64351 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
64246 ATAGTCAGTA
* *
64256 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
64297 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
64338 TCGCATTGCGAATT
1 TCGCATTGCGAATT
64352 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:65311 original size:2 final size:2
Alignment explanation
Indices: 65304--65349 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
65294 AGTATATGTT
65304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65346 TA TA
1 TA TA
65350 AGCCATTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:91823 original size:88 final size:88
Alignment explanation
Indices: 91674--91850 Score: 327
Period size: 88 Copynumber: 2.0 Consensus size: 88
91664 GTTTGTTGAT
*
91674 GTATGTGGTGTATTTTCTTTATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCG
1 GTATGAGGTGTATTTTCTTTATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCG
*
91739 TTGAGGTACTTATGTACAGCGAC
66 CTGAGGTACTTATGTACAGCGAC
91762 GTATGAGGTGTATTTTCTTTATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCG
1 GTATGAGGTGTATTTTCTTTATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCG
*
91827 CTGAGGTACTTATGTACAGTGAC
66 CTGAGGTACTTATGTACAGCGAC
91850 G
1 G
91851 AGTATGAAGG
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (88 bp):
GTATGAGGTGTATTTTCTTTATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCG
CTGAGGTACTTATGTACAGCGAC
Found at i:91883 original size:88 final size:87
Alignment explanation
Indices: 91694--91873 Score: 245
Period size: 88 Copynumber: 2.0 Consensus size: 87
91684 TATTTTCTTT
*
91694 ATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCGTTGAGGTACTTATGTACAGC
1 ATGGAAT-AAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCGCTGAGGTACTTATGTACAGC
* ** *
91759 GACGTATGAGGTGTATTTTCTTT
65 GACGTATGAGGGGTATTTTAATG
*
91782 ATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCGCTGAGGTACTTATGTACAGT
1 ATGGAAT-AAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCGCTGAGGTACTTATGTACAGC
91847 GACGAGTATGAAGGGGGT-TTTTAATG
65 GAC--GTATG-A-GGGGTATTTTAATG
91873 A
1 A
91874 GGCCTAATTT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
88 66 0.80
90 5 0.06
91 7 0.09
92 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (87 bp):
ATGGAATAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCGCTGAGGTACTTATGTACAGCG
ACGTATGAGGGGTATTTTAATG
Found at i:98507 original size:353 final size:353
Alignment explanation
Indices: 97861--98919 Score: 2093
Period size: 353 Copynumber: 3.0 Consensus size: 353
97851 ACGGATCATG
97861 ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
1 ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
97926 AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
66 AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
97991 AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
131 AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
98056 TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
196 TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
98121 GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
261 GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
98186 GAATTTTGATCAAAATATCCAATCAGAT
326 GAATTTTGATCAAAATATCCAATCAGAT
98214 ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
1 ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
98279 AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
66 AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
98344 AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
131 AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
*
98409 TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATAGGCA
196 TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
98474 GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
261 GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
98539 GAATTTTGATCAAAATATCCAATCAGAT
326 GAATTTTGATCAAAATATCCAATCAGAT
98567 ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
1 ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
98632 AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
66 AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
98697 AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
131 AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
98762 TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
196 TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
*
98827 GTACAGGAAAGGAAAA-ATGCACTCTGACAACATTCAACTGTTGAGAAAGTCGTACCTAAATCTT
261 GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
98891 GAATTTTGATCAAAATATCCAATCAGAT
326 GAATTTTGATCAAAATATCCAATCAGAT
98919 A
1 A
98920 ACAAACAGAA
Statistics
Matches: 703, Mismatches: 3, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
352 76 0.11
353 627 0.89
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (353 bp):
ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
GAATTTTGATCAAAATATCCAATCAGAT
Found at i:99833 original size:21 final size:21
Alignment explanation
Indices: 99785--99834 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
99775 ATGACTATCG
*
99785 CAATGCGATTTTCCAATTTCG
1 CAATGCGATTTTCCAATTTCA
**
99806 CGTTGCGATTTTCCCAA-TTCA
1 CAATGCGATTTT-CCAATTTCA
99827 CAATGCGA
1 CAATGCGA
99835 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (21 bp):
CAATGCGATTTTCCAATTTCA
Found at i:99852 original size:20 final size:21
Alignment explanation
Indices: 99827--99875 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
99817 TCCCAATTCA
*
99827 CAATGCGAA-TAAGTAAATCG
1 CAATGCGAATTAAGAAAATCG
**
99847 CAATGCGAATTTGGAAAATCG
1 CAATGCGAATTAAGAAAATCG
99868 CAATGCGA
1 CAATGCGA
99876 TACTGACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
CAATGCGAATTAAGAAAATCG
Found at i:99919 original size:21 final size:20
Alignment explanation
Indices: 99885--99938 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
99875 ATACTGACTA
* * *
99885 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTACCT-AT
*
99906 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACCTAT
*
99926 TCGCGTTGCGATT
1 TCGCATTGCGATT
99939 GCGAATACGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACCTAT
Found at i:99963 original size:20 final size:20
Alignment explanation
Indices: 99938--99982 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
99928 GCGTTGCGAT
99938 TGCGAATACGTA-AATCGCAA
1 TGCGAAT-CGTACAATCGCAA
* *
99958 TGCGAATCTTACTATCGCAA
1 TGCGAATCGTACAATCGCAA
99978 TGCGA
1 TGCGA
99983 TTTACATAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
TGCGAATCGTACAATCGCAA
Found at i:100561 original size:19 final size:19
Alignment explanation
Indices: 100537--100581 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
100527 GCAACTAGAG
*
100537 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
100556 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
100575 AATCGCA
1 AATCGCA
100582 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:100628 original size:33 final size:34
Alignment explanation
Indices: 100582--100645 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
100572 CAAAATCGCA
**
100582 TTGCGATTTTCATTT-CGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTCTCG
100615 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
100646 ATTATCTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.42
Consensus pattern (34 bp):
TTGCGATAGTCATTTCCGCGTTGCGATTCTCTCG
Found at i:100647 original size:20 final size:19
Alignment explanation
Indices: 100577--100670 Score: 81
Period size: 20 Copynumber: 5.1 Consensus size: 19
100567 GAAACCAAAA
* *
100577 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
100596 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
100612 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
100629 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
100649 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
100669 TC
1 TC
100671 AACCAAAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
14 11 0.18
16 1 0.02
17 1 0.02
19 16 0.27
20 30 0.50
21 1 0.02
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:102839 original size:42 final size:42
Alignment explanation
Indices: 102763--102851 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
102753 GACTCGCCTG
* * *
102763 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
102805 TCATTCCTCGAGAGTCCTCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
102847 TCATC
1 TCATC
102852 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:103889 original size:20 final size:20
Alignment explanation
Indices: 103800--103891 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
103790 TGCGAATTTG
* *
103800 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
103820 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
103840 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
103861 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
103881 GAAAATCGCAA
1 GAAAATCGCAA
103892 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:104126 original size:20 final size:20
Alignment explanation
Indices: 104101--104152 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
104091 ATCGCAACGG
104101 GGAAATCGCAACGCGAAAAT
1 GGAAATCGCAACGCGAAAAT
*
104121 GGAAATCACAACGCGAAAAT
1 GGAAATCGCAACGCGAAAAT
**
104141 GGCTATCGCAAC
1 GGAAATCGCAAC
104153 TAGAAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (20 bp):
GGAAATCGCAACGCGAAAAT
Found at i:104220 original size:19 final size:19
Alignment explanation
Indices: 104198--104246 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
104188 GCTTTTCTCG
104198 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
104217 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
104236 TTGCGATTTTC
1 TTGCGATTTTC
104247 TCGTTGCGAT
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:0.16, C:0.20, G:0.14, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:106311 original size:21 final size:21
Alignment explanation
Indices: 106285--106339 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
106275 GAAACTTAAA
106285 ATCGCAATGCGAAAAATGACT
1 ATCGCAATGCGAAAAATGACT
* * *
106306 ATCGCAACGCG-GAAATGGCT
1 ATCGCAATGCGAAAAATGACT
106326 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
106340 TGCAAATCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (21 bp):
ATCGCAATGCGAAAAATGACT
Found at i:106362 original size:14 final size:14
Alignment explanation
Indices: 106343--106397 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
106333 TGCGAAATGC
106343 AAATCGCAACGACA
1 AAATCGCAACGACA
*
106357 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
106373 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
106389 AAATCGCAA
1 AAATCGCAA
106398 TGCGAAACAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 18 0.51
16 8 0.23
18 9 0.26
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:106384 original size:32 final size:33
Alignment explanation
Indices: 106326--106415 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 33
106316 GGAAATGGCT
106326 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
106359 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
**
106391 ATCGCAATGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCA
106416 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAA
Found at i:106454 original size:19 final size:20
Alignment explanation
Indices: 106440--106483 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
106430 TTGCGATTTT
106440 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
106459 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
106479 CATTT
1 CATTT
106484 TCATGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:107002 original size:18 final size:18
Alignment explanation
Indices: 106976--107020 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
106966 GTCGATCAGA
*
106976 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
106994 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
107012 TGATGGCTC
1 TGATGGCTC
107021 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:108366 original size:20 final size:20
Alignment explanation
Indices: 108341--108383 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
108331 AATAGTTTCT
108341 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
108361 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
108381 GAA
1 GAA
108384 TTTGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:108389 original size:20 final size:20
Alignment explanation
Indices: 108351--108423 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
108341 GAAAATGAAA
* **
108351 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATTTGACT
108371 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
108391 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
108411 ATCGCAACGCGAA
1 ATCGCAACGCGAA
108424 ACTAAAATCG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:108685 original size:20 final size:21
Alignment explanation
Indices: 108660--108709 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
108650 CTCTGAGAGA
108660 TGGAGAT-AGACGGATTTCGC
1 TGGAGATGAGACGGATTTCGC
*
108680 TGGAGATGGGGACGGATTTCG-
1 TGGAGAT-GAGACGGATTTCGC
108701 TCGGAGATG
1 T-GGAGATG
108710 GGTGAGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.27
21 2 0.08
22 17 0.65
ACGTcount: A:0.22, C:0.12, G:0.42, T:0.24
Consensus pattern (21 bp):
TGGAGATGAGACGGATTTCGC
Found at i:108696 original size:22 final size:22
Alignment explanation
Indices: 108668--108711 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
108658 GATGGAGATA
108668 GACGGATTTCG-CTGGAGATGGG
1 GACGGATTTCGTC-GGAGATGGG
108690 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
108712 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:108925 original size:20 final size:20
Alignment explanation
Indices: 108900--108951 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
108890 ATTATGTATT
108900 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
108920 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
108940 ATCTCGTTGCGA
1 ATCGCGTTGCGA
108952 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:108985 original size:20 final size:20
Alignment explanation
Indices: 108879--108989 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
108869 CGCTTTGAAA
*
108879 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
108900 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
108920 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
108940 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
108961 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
108981 ATCGCATTG
1 ATCGCATTG
108990 TGATTTTCCT
Statistics
Matches: 73, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.07
20 43 0.59
21 23 0.32
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:109012 original size:41 final size:41
Alignment explanation
Indices: 108920--109014 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
108910 GAAAGTCAGA
* * * * *
108920 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCTAAT
* *
108961 ATCGCATTGCGATAGTCAGTATCGCATTGTGATTTTCCTAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CTAAT
109003 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
109015 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 42 0.93
42 3 0.07
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCTAAT
Found at i:109015 original size:21 final size:20
Alignment explanation
Indices: 108982--109033 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
108972 ATAGTCAGTA
* *
108982 TCGCATTGTGATTTTCCTAAT
1 TCGCATTGCGA-TTTACTAAT
* *
109003 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
109023 TCGCATTGCGA
1 TCGCATTGCGA
109034 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:109104 original size:21 final size:21
Alignment explanation
Indices: 109064--109104 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
109054 ACTGTAGACC
** *
109064 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
109085 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
109105 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:109134 original size:20 final size:20
Alignment explanation
Indices: 109111--109156 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
109101 CAACGCGAAT
109111 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCG
* *
109131 TTGCGA-ATTAGCGATCGCG
1 TTGCGATAATAGAGATCGCG
109150 TTGCGAT
1 TTGCGAT
109157 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCG
Found at i:115040 original size:23 final size:22
Alignment explanation
Indices: 114996--115040 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
114986 AATGCCAGAG
*
114996 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
115018 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
115041 AAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:116110 original size:31 final size:31
Alignment explanation
Indices: 116041--116115 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
116031 ATGGACATGT
* *
116041 ACATATGGATAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGTATACCTAGGTTCTAAGGA
** *
116072 ACATATGGACAGTATACCTAGGTTCTTCGGG
1 ACATATGGACAGTATACCTAGGTTCTAAGGA
*
116103 ACCTATGGACAGT
1 ACATATGGACAGT
116116 TGCCGAGGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (31 bp):
ACATATGGACAGTATACCTAGGTTCTAAGGA
Found at i:116152 original size:30 final size:30
Alignment explanation
Indices: 116102--116174 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
116092 GGTTCTTCGG
* * * *
116102 GACCTATGGACAGTTGCCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCCTTAT
*
116132 GACCTCTGGATAGTTACCGAGGTTCCTTAT
1 GACCTCTGGATAGTTACCGAGGATCCTTAT
116162 GACCTCTGGATAG
1 GACCTCTGGATAG
116175 GTCATTCGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCCTTAT
Found at i:119527 original size:21 final size:21
Alignment explanation
Indices: 119501--119545 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
119491 AATTTCTGGG
* *
119501 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
119522 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
119543 CAA
1 CAA
119546 ACGAACATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:119618 original size:23 final size:22
Alignment explanation
Indices: 119574--119618 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
119564 AATGCCAGAG
*
119574 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
119596 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
119619 AAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:120659 original size:31 final size:31
Alignment explanation
Indices: 120589--120712 Score: 135
Period size: 31 Copynumber: 4.0 Consensus size: 31
120579 GTCGAGGGTT
* *
120589 TACCTATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTTCGGGACATATGGACAGT-A
*
120620 TTACCTATG-TCTTTCGGGACATATGGATAGTA
1 -TACCTATGTTC-TTCGGGACATATGGACAGTA
** *
120652 TACCTATGTTCTAAGGAACATATGGACAGTA
1 TACCTATGTTCTTCGGGACATATGGACAGTA
* *
120683 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTTCGGGACATATGGACAGT
120713 TGCCGAGGAT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
31 51 0.66
32 25 0.32
33 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTTCGGGACATATGGACAGTA
Found at i:127927 original size:25 final size:25
Alignment explanation
Indices: 127899--127950 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
127889 AGAATAGGAC
*
127899 TTGTTTTGTAATGTCTTAGTTCTTA
1 TTGTCTTGTAATGTCTTAGTTCTTA
127924 TTGTCTTGTAATGTCTTAGTTCTTA
1 TTGTCTTGTAATGTCTTAGTTCTTA
127949 TT
1 TT
127951 TTCGATTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.60
Consensus pattern (25 bp):
TTGTCTTGTAATGTCTTAGTTCTTA
Found at i:130245 original size:17 final size:17
Alignment explanation
Indices: 130218--130256 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
130208 AAATTACAAT
130218 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
130234 TAATTATAAATAATATC
1 TAATTATAAATAATATC
130251 TAATTA
1 TAATTA
130257 ATTTGATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:133192 original size:12 final size:12
Alignment explanation
Indices: 133171--133217 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
133161 TTTAACTAAA
133171 ATAGAGATAGAT
1 ATAGAGATAGAT
*
133183 ATAGATATAGAT
1 ATAGAGATAGAT
* *
133195 ATAGAGATAAAG
1 ATAGAGATAGAT
*
133207 ATAAAGATAGA
1 ATAGAGATAGA
133218 AGTCCTATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.23
Consensus pattern (12 bp):
ATAGAGATAGAT
Found at i:138033 original size:42 final size:43
Alignment explanation
Indices: 137960--138048 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 43
137950 TAGGCGAGAC
* * *
137960 ATAC-TTTTATATTAAAAAGTTGTGTTGTAATATATCTAGTAG
1 ATACTTTTTATACTAAAAAGTTATGTTATAATATATCTAGTAG
* * *
138002 ATACTTTTTATACTAAAATGTTAT-TTATAATATATCTATTAT
1 ATACTTTTTATACTAAAAAGTTATGTTATAATATATCTAGTAG
138044 ATACT
1 ATACT
138049 GGTTCACTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
42 24 0.60
43 16 0.40
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (43 bp):
ATACTTTTTATACTAAAAAGTTATGTTATAATATATCTAGTAG
Done.