Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002244.1 Hibiscus syriacus cultivar Beakdansim tig00004562_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: 122092
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2221 original size:19 final size:20
Alignment explanation
Indices: 2203--2238 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2193 TTTTTATATA
2203 ATTTTA-AT-ATTTATTTAT
1 ATTTTATATAATTTATTTAT
2221 ATTTTATATAATTTATTT
1 ATTTTATATAATTTATTT
2239 CATCTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.38
19 2 0.12
20 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTATATAATTTATTTAT
Found at i:2236 original size:20 final size:18
Alignment explanation
Indices: 2185--2238 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2175 ATTTTAAGAG
* *
2185 ATTTTCAATTTTTATATA-
1 ATTTT-AATATTTATTTAT
2203 ATTTTAATATTTATTTAT
1 ATTTTAATATTTATTTAT
2221 ATTTTATATAATTTATTT
1 ATTTTA-AT-ATTTATTT
2239 CATCTTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 10 0.32
18 11 0.35
19 2 0.06
20 8 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTAATATTTATTTAT
Found at i:10787 original size:32 final size:32
Alignment explanation
Indices: 10746--10808 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
10736 CCCAACATAT
10746 ACTCAAATTATACTTATCCTGTACTCATGTCC
1 ACTCAAATTATACTTATCCTGTACTCATGTCC
10778 ACTCAAATTATACTTATCCTGTACTCATGTC
1 ACTCAAATTATACTTATCCTGTACTCATGTC
10809 AGGGACGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (32 bp):
ACTCAAATTATACTTATCCTGTACTCATGTCC
Found at i:11629 original size:28 final size:29
Alignment explanation
Indices: 11575--11632 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
11565 AATTTGAACA
**
11575 TATAGAATTTTAAGGGAAAAATTTAAATT
1 TATAGAATTTTAAGGGAAAAAAATAAATT
11604 TATA-AATTTT-AGGGAATAAAAATAAATT
1 TATAGAATTTTAAGGGAA-AAAAATAAATT
11632 T
1 T
11633 TCAATAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.23
28 16 0.62
29 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (29 bp):
TATAGAATTTTAAGGGAAAAAAATAAATT
Found at i:19054 original size:13 final size:13
Alignment explanation
Indices: 19007--19065 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
18997 AATATTTTAT
*
19007 TAGGGTTAAAGT-
1 TAGGGTTAGAGTG
*
19019 TAGGATTTAGAGT-
1 TAGG-GTTAGAGTG
*
19032 TAGGGTTTAGGGTG
1 TAGGG-TTAGAGTG
*
19046 TAGGGTTAGAGTT
1 TAGGGTTAGAGTG
19059 TAGGGTT
1 TAGGGTT
19066 GAGGTAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 4 0.11
13 29 0.76
14 5 0.13
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (13 bp):
TAGGGTTAGAGTG
Found at i:20584 original size:7 final size:7
Alignment explanation
Indices: 20572--20603 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
20562 GTATTTGTTT
20572 GTGAATG
1 GTGAATG
20579 GTGAATG
1 GTGAATG
20586 GTGAATG
1 GTGAATG
20593 GTGAATG
1 GTGAATG
20600 GTGA
1 GTGA
20604 TCGTTTGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.44, T:0.28
Consensus pattern (7 bp):
GTGAATG
Found at i:22012 original size:40 final size:40
Alignment explanation
Indices: 21988--22083 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
21978 GCGAAAGTCA
* * *
21988 AATTCGCAACGCGAATAGTTAAATCGCAACGATAATATGT
1 AATTCACAACGCGAATAGGTAAATCGCAACGAGAATATGT
* *
22028 AATTCACAACGCGAATAGGTAAAGCGCAACGATAATATGT
1 AATTCACAACGCGAATAGGTAAATCGCAACGAGAATATGT
*
22068 AAATCACAACGCGAAT
1 AATTCACAACGCGAAT
22084 TCTCCAAACT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.21
Consensus pattern (40 bp):
AATTCACAACGCGAATAGGTAAATCGCAACGAGAATATGT
Found at i:22024 original size:20 final size:20
Alignment explanation
Indices: 21968--22083 Score: 94
Period size: 20 Copynumber: 5.8 Consensus size: 20
21958 ACAGGTTCCA
*
21968 AAATCGCAACGCGAA-AGTC
1 AAATCGCAACGCGAATAGTT
21987 AAATTCGCAACGCGAATAGTT
1 AAA-TCGCAACGCGAATAGTT
**
22008 AAATCGCAACGATAATA-TGT
1 AAATCGCAACGCGAATAGT-T
* * *
22028 AATTCACAACGCGAATAGGT
1 AAATCGCAACGCGAATAGTT
* **
22048 AAAGCGCAACGATAATA-TGT
1 AAATCGCAACGCGAATAGT-T
*
22068 AAATCACAACGCGAAT
1 AAATCGCAACGCGAAT
22084 TCTCCAAACT
Statistics
Matches: 74, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.05
20 64 0.86
21 6 0.08
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATAGTT
Found at i:22192 original size:84 final size:84
Alignment explanation
Indices: 22086--22254 Score: 266
Period size: 84 Copynumber: 2.0 Consensus size: 84
22076 ACGCGAATTC
*
22086 TCCAAACTCGCAACTCGAATTTCGCAACGCTAATTACCGATATAGGTAATTAGCGTTGCGAAAAC
1 TCCAAACTCACAACTCGAATTTCGCAACGCTAATTACCGATATAGGTAATTAGCGTTGCGAAAAC
* *
22151 AAAATTCGCGTTGCGGTTT
66 AAAATTCGCATTGCGCTTT
* * * *
22170 TCCAAATTCACAACTTGAATTTCTCAACGCTAATTACCGATATAGGTAATTAGCGTTGCGAAAAT
1 TCCAAACTCACAACTCGAATTTCGCAACGCTAATTACCGATATAGGTAATTAGCGTTGCGAAAAC
*
22235 GAAATTCGCATTGCGCTTT
66 AAAATTCGCATTGCGCTTT
22254 T
1 T
22255 GGAGAATCGC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (84 bp):
TCCAAACTCACAACTCGAATTTCGCAACGCTAATTACCGATATAGGTAATTAGCGTTGCGAAAAC
AAAATTCGCATTGCGCTTT
Found at i:23451 original size:17 final size:18
Alignment explanation
Indices: 23412--23453 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
23402 ATAATATCAT
23412 TAAT-AAAAATAAAAATA
1 TAATAAAAAATAAAAATA
* *
23429 TTATAAAAAATAAAATTA
1 TAATAAAAAATAAAAATA
23447 -AATAAAA
1 TAATAAAA
23454 TTGATATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAATAAAAAATAAAAATA
Found at i:27854 original size:177 final size:179
Alignment explanation
Indices: 27597--27950 Score: 522
Period size: 177 Copynumber: 2.0 Consensus size: 179
27587 AACTATTGAT
* *
27597 TCATTCGATTGTTAATGATTTAATGATCCAGTAAAAAAAAACAATGTTAAAAGTTTAGTGACAAA
1 TCATTCGATTGTTAATGATTTAATGATCCAATAAAAAAAAACAATATTAAAAGTTTAGTGACAAA
* * * *
27662 ATTGAAGCCTTTTAAAGTTCAATGACAAAATCAATACATAGACTAAGGTTCAATGACTAG-GGAG
66 ATTGAAGCATTTTAAAGTTCAATGACAAAATCAATAAATAGACTAAAGTACAATGACTAGCGG-G
* * *
27726 ATAATTTACTT-T-T-T-T-TATATAAATAATGTTCATCATAATTGATAG
130 ATAATTAACTTATATATATATATATAAATAACGTCCATCATAATTGATAG
*
27771 TCATTCGGTTGTTAATGATTTAATGATCCAATAACAAAAAAAGACAATATTAAAAGTTTAGTGAC
1 TCATTCGATTGTTAATGATTTAATGATCCAAT-A-AAAAAAA-ACAATATTAAAAGTTTAGTGAC
*
27836 AAAATTGAAGTATTTTAAAGTTCAATGACAAAATCAATAAATAGACTAAAGTACAATGACTAGCG
63 AAAATTGAAGCATTTTAAAGTTCAATGACAAAATCAATAAATAGACTAAAGTACAATGACTAGCG
*
27901 GGATAATTAACTTATATATATATATATATATAACGTCCATCATAATTGAT
128 GGATAATTAACTTATATATATATATATAAATAACGTCCATCATAATTGAT
27951 CGCAACACAA
Statistics
Matches: 159, Mismatches: 12, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
174 30 0.19
175 1 0.01
176 7 0.04
177 90 0.57
178 3 0.02
179 1 0.01
180 1 0.01
181 1 0.01
182 25 0.16
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (179 bp):
TCATTCGATTGTTAATGATTTAATGATCCAATAAAAAAAAACAATATTAAAAGTTTAGTGACAAA
ATTGAAGCATTTTAAAGTTCAATGACAAAATCAATAAATAGACTAAAGTACAATGACTAGCGGGA
TAATTAACTTATATATATATATATAAATAACGTCCATCATAATTGATAG
Found at i:28148 original size:22 final size:23
Alignment explanation
Indices: 28122--28178 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
28112 ACGTATAGAT
28122 TTATTTTAAAAAAAAT-AAAATA
1 TTATTTTAAAAAAAATAAAAATA
* **
28144 TTATTTTTAAAACATTTAAAAATA
1 TTA-TTTTAAAAAAAATAAAAATA
28168 TT-TTTTAAAAA
1 TTATTTTAAAAA
28179 TTTGGATGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 11 0.38
23 10 0.34
24 8 0.28
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TTATTTTAAAAAAAATAAAAATA
Found at i:28661 original size:13 final size:13
Alignment explanation
Indices: 28620--28661 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
28610 TGTAACAAAG
*
28620 AAAAGAAAA-AGA
1 AAAAGAAAATAAA
*
28632 AAAAGAAAATAAC
1 AAAAGAAAATAAA
*
28645 AAAAGAAAGTAAA
1 AAAAGAAAATAAA
28658 AAAA
1 AAAA
28662 TAACAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (13 bp):
AAAAGAAAATAAA
Found at i:28679 original size:21 final size:21
Alignment explanation
Indices: 28632--28680 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
28622 AAGAAAAAGA
*
28632 AAAAGAAAATAACAAAAGAAAG
1 AAAA-AAAATAACAAAAGAAAC
*
28654 TAAAAAAATAACAAAA-ATAAC
1 AAAAAAAATAACAAAAGA-AAC
28675 AAAAAA
1 AAAAAA
28681 TATATATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.83
22 3 0.13
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.08
Consensus pattern (21 bp):
AAAAAAAATAACAAAAGAAAC
Found at i:30897 original size:17 final size:16
Alignment explanation
Indices: 30862--30901 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
30852 ATTTCAATAA
*
30862 AAAATATAAAAAATCT
1 AAAATTTAAAAAATCT
*
30878 AAAATTTAAAATAATTT
1 AAAATTTAAAA-AATCT
30895 AAAATTT
1 AAAATTT
30902 TTAAGAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTTAAAAAATCT
Found at i:32402 original size:6 final size:6
Alignment explanation
Indices: 32391--32434 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
32381 TCAGGCGCCC
32391 GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GT
1 GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GT
32435 TCACTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.66, T:0.18
Consensus pattern (6 bp):
GTGGAG
Found at i:37065 original size:60 final size:58
Alignment explanation
Indices: 36992--37128 Score: 136
Period size: 59 Copynumber: 2.3 Consensus size: 58
36982 ATATAAAGGT
** *
36992 AAAG-TACACAAATGGTCATCTGATTATAG-GATACTGCTTTATTGAATC-ATTTGATTATTA
1 AAAGTTACA-AAATGGTCAT-TGACAATAGAGAT--TGCTTTATTGAATCTA-TTGACTATTA
* * * *
37052 AAAGTTACAAAATGATCCATTGACAATAGAGGTTGTTTTATTGAGTCTATTGACTATTA
1 AAAGTTACAAAATGGT-CATTGACAATAGAGATTGCTTTATTGAATCTATTGACTATTA
37111 AAAGTTACAAAATGGTCA
1 AAAGTTACAAAATGGTCA
37129 CTTGGCTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
58 2 0.03
59 36 0.55
60 18 0.28
61 9 0.14
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (58 bp):
AAAGTTACAAAATGGTCATTGACAATAGAGATTGCTTTATTGAATCTATTGACTATTA
Found at i:37606 original size:22 final size:22
Alignment explanation
Indices: 37536--37598 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
37526 ACAATCATTA
37536 GATGAACGTAAATGAATGAGAC
1 GATGAACGTAAATGAATGAGAC
37558 GATGAACGTAAATGAATGAGAC
1 GATGAACGTAAATGAATGAGAC
* *
37580 GATGAACGTATATAAATGA
1 GATGAACGTAAATGAATGA
37599 ATGAATGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.46, C:0.08, G:0.25, T:0.21
Consensus pattern (22 bp):
GATGAACGTAAATGAATGAGAC
Found at i:42837 original size:156 final size:158
Alignment explanation
Indices: 42510--42881 Score: 545
Period size: 156 Copynumber: 2.4 Consensus size: 158
42500 TATTGTGGTA
**
42510 TATGAGCATGTGGTTCAAATTTGGTAAAAGATGGACTTAAAATAAATAATGAATTGAAGAAATAA
1 TATGAGCATGTGGTTCAAATTTGGTAAAAGATGGACTTAAAATAAAGGATGAATTGAAGAAATAA
* *
42575 GAAAAATATGAAATATTAAGGGACTAAATTGAAAAATAAAAAAATTATTATCGAAAAGAGGAATT
66 GAAAAATATGAAAAATTAAGGGACTAAATTGAAAAATAAAAAAATTATTAACGAAAAGAGGAATT
* *
42640 GAAAGTACATATGTATTCTACAATGGTT
131 GAAAATACATATGTATTCTACAATGATT
*
42668 TATGAGCATGTGGTTTAAATTTGGTAAAAGATGGACTTAAAATAAAGGATGAATTGAAGAAATAA
1 TATGAGCATGTGGTTCAAATTTGGTAAAAGATGGACTTAAAATAAAGGATGAATTGAAGAAATAA
* * *
42733 -AAAAATATGAAAAATTAA-GGACTAAATTGAAAAATAAAAAATTTGTTAAC-AAAATGAGGAGT
66 GAAAAATATGAAAAATTAAGGGACTAAATTGAAAAATAAAAAAATTATTAACGAAAA-GAGGAAT
* *
42795 TGAAAATACATATGTATTTTACGATGATT
130 TGAAAATACATATGTATTCTACAATGATT
* * * * *
42824 TATGAGCACGTGGTTCAAATTTGATAAAATACGGACTTAAAATGAAGGA-GAAATTGAA
1 TATGAGCATGTGGTTCAAATTTGGTAAAAGATGGACTTAAAATAAAGGATG-AATTGAA
42882 AGAATGTTGA
Statistics
Matches: 194, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
155 5 0.03
156 110 0.57
157 17 0.09
158 62 0.32
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (158 bp):
TATGAGCATGTGGTTCAAATTTGGTAAAAGATGGACTTAAAATAAAGGATGAATTGAAGAAATAA
GAAAAATATGAAAAATTAAGGGACTAAATTGAAAAATAAAAAAATTATTAACGAAAAGAGGAATT
GAAAATACATATGTATTCTACAATGATT
Found at i:48858 original size:16 final size:17
Alignment explanation
Indices: 48814--48869 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
48804 CTAAATTAGC
*
48814 TAAA-AATATTAAATAT
1 TAAATAATATTATATAT
48830 TAAAT-ATATTATATAT
1 TAAATAATATTATATAT
*
48846 TAAATAATA-TATATTT
1 TAAATAATATTATATAT
48862 TAAGATAA
1 TAA-ATAA
48870 AATCCATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 28 0.80
17 7 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATAATATTATATAT
Found at i:58640 original size:3 final size:3
Alignment explanation
Indices: 58632--58671 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
58622 TGCTCATGGC
* * *
58632 TCT TCT TCT TCT TCG TCG TCG TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
58672 ACTTTTATCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:59356 original size:20 final size:22
Alignment explanation
Indices: 59312--59356 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
59302 CCATGATCAC
*
59312 TTGACCATCGATAGATTTTATT
1 TTGACCATCGATAGATTTAATT
*
59334 TTGA-CATCGATCG-TTTAATT
1 TTGACCATCGATAGATTTAATT
59354 TTG
1 TTG
59357 TCAATCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (22 bp):
TTGACCATCGATAGATTTAATT
Found at i:63644 original size:20 final size:20
Alignment explanation
Indices: 63619--63711 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
63609 TTTTCCCAAT
63619 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
63639 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
63659 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
63680 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
63701 TCGCAATGCGA
1 TCGCAATGCGA
63712 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:63661 original size:41 final size:41
Alignment explanation
Indices: 63616--63711 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
63606 CGATTTTCCC
63616 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
63657 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
63698 AAATCGCAATGCGA
1 AATTCGCAATGCGA
63712 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:63665 original size:21 final size:20
Alignment explanation
Indices: 63619--63711 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
63609 TTTTCCCAAT
*
63619 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
63639 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
63659 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
63680 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
63701 TCGCAATGCGA
1 TCGCAATGCGA
63712 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:63725 original size:20 final size:20
Alignment explanation
Indices: 63700--63794 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
63690 AATTGGGAAA
*
63700 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
63720 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
63741 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
63761 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
63781 TTCGCAACGCGATA
1 ATCGCAACGCGATA
63795 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:63774 original size:41 final size:41
Alignment explanation
Indices: 63697--63774 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
63687 GCGAATTGGG
* * **
63697 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
63738 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
63775 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:65624 original size:18 final size:18
Alignment explanation
Indices: 65603--65647 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
65593 TCCACTTCGT
*
65603 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
65621 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
65639 GAGCCATCA
1 GAGCCATCA
65648 TCTGATCGAC
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:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:66174 original size:19 final size:20
Alignment explanation
Indices: 66120--66186 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
66110 TAGTTTACTT
* *
66120 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
66140 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
66160 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
66179 TCGCAACG
1 TCGCAACG
66187 ACAAAAGCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:66197 original size:14 final size:14
Alignment explanation
Indices: 66175--66264 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
66165 ATGCGAAATG
66175 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
66189 AAAAGCGCAACGCGAA
1 AAAATCGCAA--CGAC
66205 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
66221 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
66237 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
66253 AAAATCGCAACG
1 AAAATCGCAACG
66265 CGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 29 0.47
16 16 0.26
18 17 0.27
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:66217 original size:32 final size:32
Alignment explanation
Indices: 66159--66269 Score: 195
Period size: 32 Copynumber: 3.4 Consensus size: 32
66149 GGAAATGGCT
*
66159 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
*
66192 AGCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
66224 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
66256 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
66270 CACAAATCGC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 61 0.81
33 14 0.19
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:66298 original size:19 final size:19
Alignment explanation
Indices: 66276--66429 Score: 105
Period size: 19 Copynumber: 8.6 Consensus size: 19
66266 GAAACACAAA
*
66276 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
66295 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
66311 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
66327 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
*
66343 T--CGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
66360 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
66379 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
66399 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
66419 TCGTGTTGCGA
1 TCGCGTTGCGA
66430 AAGTAAACTA
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 18 0.17
15 3 0.03
16 6 0.06
17 2 0.02
18 14 0.13
19 35 0.33
20 29 0.27
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:66317 original size:14 final size:14
Alignment explanation
Indices: 66298--66355 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
66288 TTTCATTTCG
66298 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
66312 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
66328 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
66344 CGTTGCAATTTT
1 CGTTGCGATTTT
66356 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:66362 original size:33 final size:33
Alignment explanation
Indices: 66281--66371 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
66271 ACAAATCGCA
66281 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
66314 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
66346 TTGCAATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
66372 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:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:66390 original size:20 final size:19
Alignment explanation
Indices: 66356--66410 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
66346 TTGCAATTTT
*
66356 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
66375 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
66395 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
66411 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:68297 original size:14 final size:14
Alignment explanation
Indices: 68278--68313 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
68268 ATTGTTTAAT
68278 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
68292 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
68306 TGATTTGT
1 TGATTTGT
68314 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:68439 original size:14 final size:15
Alignment explanation
Indices: 68420--68496 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
68410 CGAAATGGCT
68420 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
68434 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
68452 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
68471 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
68485 ATCGCAATGCGA
1 ATCGCAA-GCGA
68497 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:68452 original size:19 final size:19
Alignment explanation
Indices: 68430--68496 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
68420 ATCGCAACGA
68430 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
68449 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
68467 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
68481 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
68497 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:70073 original size:21 final size:21
Alignment explanation
Indices: 70007--70073 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
69997 GTGAATCGGG
*
70007 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
70027 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
70049 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
70070 CTCT
1 CTCT
70074 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:70092 original size:42 final size:41
Alignment explanation
Indices: 70007--70129 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
69997 GTGAATCGGG
* * * * *
70007 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
70049 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
70091 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
70130 CGAGTCGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:72244 original size:19 final size:19
Alignment explanation
Indices: 72127--72311 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
72117 TCTTTTGGTT
*
72127 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
72146 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
72166 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
72184 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
72200 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
72218 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
72233 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
72253 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
72272 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
72291 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
72310 GA
1 GA
72312 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:72265 original size:39 final size:38
Alignment explanation
Indices: 72127--72311 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
72117 TCTTTTGGTT
* *
72127 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
72166 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
72200 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
72233 GAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
*
72272 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
72310 GA
1 GA
72312 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
33 42 0.33
34 16 0.13
35 2 0.02
38 24 0.19
39 28 0.22
40 14 0.11
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:72341 original size:18 final size:19
Alignment explanation
Indices: 72307--72350 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
72297 AAAATCGCAA
*
72307 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
72326 TGCGATTTT-ATTTCGCGT
1 TGCGATTTTGATTTCGCGT
72344 TGCGATT
1 TGCGATT
72351 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:72988 original size:20 final size:20
Alignment explanation
Indices: 72903--72996 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
72893 CGCTAAGTAA
*
72903 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
72923 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
72943 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
72964 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
72984 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
72997 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:73015 original size:41 final size:41
Alignment explanation
Indices: 72985--73080 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
72975 ATAGTCAGTA
* * *
72985 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
73026 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
73067 TCGCATTGCGAATT
1 TCGCATTGCGAATT
73081 GGGAAAATCG
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:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:73029 original size:20 final size:20
Alignment explanation
Indices: 72985--73077 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
72975 ATAGTCAGTA
* **
72985 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
73006 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
73026 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
73047 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
73067 TCGCATTGCGA
1 TCGCATTGCGA
73078 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:76291 original size:2 final size:2
Alignment explanation
Indices: 76279--76321 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
76269 CTATGTGTTC
76279 AT AT A- 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
76320 AT
1 AT
76322 GCATATACGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:78507 original size:21 final size:21
Alignment explanation
Indices: 78459--78500 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
78449 TAACCTAAAA
* *
78459 TAATATATTTATTAAAAATAT
1 TAATTTATTTAATAAAAATAT
*
78480 TACTTTATTTAATAAAAATAT
1 TAATTTATTTAATAAAAATAT
78501 AGATTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTTATTTAATAAAAATAT
Found at i:78546 original size:2 final size:2
Alignment explanation
Indices: 78539--78567 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
78529 TTATTGCAAT
78539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
78568 GGATATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:80348 original size:2 final size:2
Alignment explanation
Indices: 80341--80371 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
80331 TTTCTCTAAT
80341 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
80372 TCTTTTTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:89792 original size:21 final size:21
Alignment explanation
Indices: 89746--89792 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
89736 TTAAGGATTT
* *
89746 GAAATTTAGATATTGTTACGA
1 GAAATTTAGATATTGGTACAA
*
89767 TAAATTTAGATATTGAGTA-AA
1 GAAATTTAGATATTG-GTACAA
89788 GAAAT
1 GAAAT
89793 AAGATAGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (21 bp):
GAAATTTAGATATTGGTACAA
Found at i:93222 original size:20 final size:20
Alignment explanation
Indices: 93184--93224 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
93174 TTCCGAAAAT
*
93184 TATTTCTTTAAAAAGATTTA
1 TATTTCTTTAAAAAAATTTA
93204 TATTT-TTTAAAAATAATTTA
1 TATTTCTTTAAAAA-AATTTA
93224 T
1 T
93225 GGACACGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TATTTCTTTAAAAAAATTTA
Found at i:93625 original size:22 final size:23
Alignment explanation
Indices: 93600--93646 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
93590 CTAAATACAT
93600 TATTATAACACTAAAAATA-TAA
1 TATTATAACACTAAAAATATTAA
* * *
93622 TATTATATCATTAAAATTATTAA
1 TATTATAACACTAAAAATATTAA
93645 TA
1 TA
93647 AATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (23 bp):
TATTATAACACTAAAAATATTAA
Found at i:96696 original size:31 final size:31
Alignment explanation
Indices: 96661--96738 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
96651 GTTTTAAAAA
* *
96661 TAACAAATTGGTCACTAATATTATCGATTTG
1 TAACAAAATGGTCACTAACATTATCGATTTG
*
96692 TAACAAAATGGTCACCAACATTATCGATTTG
1 TAACAAAATGGTCACTAACATTATCGATTTG
*
96723 TAACAAAATAGTCACT
1 TAACAAAATGGTCACT
96739 CGTTATCTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (31 bp):
TAACAAAATGGTCACTAACATTATCGATTTG
Found at i:97287 original size:85 final size:85
Alignment explanation
Indices: 97183--97368 Score: 345
Period size: 85 Copynumber: 2.2 Consensus size: 85
97173 AATACATGAG
*
97183 TATTTAAAAGCATATATTCAATTAATTTTAATATAAAAAAATAATGCATTTGGGTTGGTTTTTAT
1 TATTTAAAA--ATACATTCAATTAATTTTAATATAAAAAAATAATGCATTTGGGTTGGTTTTTAT
97248 TTTGTAAGGGAGGTGGCTAAAA
64 TTTGTAAGGGAGGTGGCTAAAA
97270 TATTTAAAAATACATTCAATTAATTTTAATATAAAAAAATAATGCATTTGGGTTGGTTTTTATTT
1 TATTTAAAAATACATTCAATTAATTTTAATATAAAAAAATAATGCATTTGGGTTGGTTTTTATTT
97335 TGTAAGGGAGGTGGCTAAAA
66 TGTAAGGGAGGTGGCTAAAA
97355 TATTTAAAAATACA
1 TATTTAAAAATACA
97369 ACTATATTCG
Statistics
Matches: 98, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
85 89 0.91
87 9 0.09
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (85 bp):
TATTTAAAAATACATTCAATTAATTTTAATATAAAAAAATAATGCATTTGGGTTGGTTTTTATTT
TGTAAGGGAGGTGGCTAAAA
Found at i:98629 original size:16 final size:16
Alignment explanation
Indices: 98608--98641 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
98598 TATATTTGAT
98608 ATATTATTTTAATATA
1 ATATTATTTTAATATA
98624 ATATTATTTTAATATA
1 ATATTATTTTAATATA
98640 AT
1 AT
98642 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTATTTTAATATA
Found at i:98658 original size:39 final size:39
Alignment explanation
Indices: 98571--98662 Score: 91
Period size: 39 Copynumber: 2.4 Consensus size: 39
98561 AATTCTCTAG
* * *
98571 ATAATTTTAATATAATTTTATTTTTAATATATTTGATATA
1 ATAA-TTTAATATAATATTATTTTTAATATATTTGAAAAA
* *
98611 TTATTTTAATATAATATTA-TTTTAATATAATTAT-AAAAA
1 ATAATTTAATATAATATTATTTTTAATAT-ATT-TGAAAAA
98650 ATAATTTAA-ATAA
1 ATAATTTAATATAA
98663 AAATATTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
38 13 0.30
39 27 0.63
40 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (39 bp):
ATAATTTAATATAATATTATTTTTAATATATTTGAAAAA
Found at i:102806 original size:53 final size:52
Alignment explanation
Indices: 102722--102879 Score: 298
Period size: 53 Copynumber: 3.0 Consensus size: 52
102712 TACGTTCGGG
102722 AGGATTATGAATAGTTAAGTATGGGATTAGAATATCTTTGATATTAGAAGGA
1 AGGATTATGAATAGTTAAGTATGGGATTAGAATATCTTTGATATTAGAAGGA
102774 AGGATTATGAATAGTTCAAGTATGGGATTAGAATATCTTTGATATTAGAAGGA
1 AGGATTATGAATAGTT-AAGTATGGGATTAGAATATCTTTGATATTAGAAGGA
102827 AGGATTATGAATAGTTTAAGTATGGGATTAGAATATCTTTGATATTAGAAGGA
1 AGGATTATGAATAG-TTAAGTATGGGATTAGAATATCTTTGATATTAGAAGGA
102880 TTTAATTATT
Statistics
Matches: 104, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
52 16 0.15
53 86 0.83
54 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (52 bp):
AGGATTATGAATAGTTAAGTATGGGATTAGAATATCTTTGATATTAGAAGGA
Found at i:106365 original size:291 final size:290
Alignment explanation
Indices: 105840--106397 Score: 791
Period size: 291 Copynumber: 1.9 Consensus size: 290
105830 CCGAAAATTC
* *
105840 GAGCTGCTAATGGCGTTCGAGACATATTAGTTTCTCCTCTACTACCATTGGCATTGAAAATCTAG
1 GAGCTGCTAATGGCGTTCGAGACAAATTAGTTTCTCCTCTACTACCATAGGCATTGAAAATCTAG
* * * * *
105905 CACAGATAAGTTGAATTTTAAACTTGTTGAGTGTGCTGATATATGCATAACTGGAATTTGATACT
66 CACAGACAAGTTGAATCTTAAACTTGCTGAATGTGCTGATATATGCATAACTGGAATTGGATACT
** * * * *
105970 TTGAGCTGCCAATGGTGTTTGAAGATGATTAGTTTCTTTGCTACTGTCTGGTGTCGCTTTAGCAT
131 AGGAGCAGCCAATAGTGTTTGAAGATGATCAGTTTCTTTGCTACTGTCTGGTGTAGCTTTAGCAT
* * * *
106035 TGAAAATTTAGCAATGACGAGCGAATTGAATCTTAAAACTTGTCGATCGTGCTCGACTTATACAT
196 TGAAAATCTAGCAATGACGACCGAATTGAATCATAAAACTTGTCGATCGTGCTCCACTTATACAT
106100 AATTGGAACCTGAAACTAATCTGAAACTTT
261 AATTGGAACCTGAAACTAATCTGAAACTTT
*
106130 GAGCTGCTAATGGCGTTCGAGA-AGAATTAGTTTCTTCC-CTGCTACCATAGGCATTGAAAATCT
1 GAGCTGCTAATGGCGTTCGAGACA-AATTAGTTTC-TCCTCTACTACCATAGGCATTGAAAATCT
** * *
106193 AGCA-ATGACGGGTTGAATCTTAAACTTGCTGAATGTGCTTGATTTGTGCATAACTTGG-ATTGG
64 AGCACA-GACAAGTTGAATCTTAAACTTGCTGAATGTGC-TGATATATGCATAAC-TGGAATTGG
* *
106256 ATACTAGGAGCAGCTAATAGTGTTTGAAGATGATCAGTTTCTTTGCTGCTGTCTGGTGTAGCTTT
126 ATACTAGGAGCAGCCAATAGTGTTTGAAGATGATCAGTTTCTTTGCTACTGTCTGGTGTAGCTTT
** * *
106321 AGCATTGAAAATCTAGCAATGACGACCGGGTTGAATCATAAAACTTGTCGGTCGTGCTCCAGTTA
191 AGCATTGAAAATCTAGCAATGACGACCGAATTGAATCATAAAACTTGTCGATCGTGCTCCACTTA
106386 TACATAATTGGA
256 TACATAATTGGA
106398 GTCAGAAACT
Statistics
Matches: 235, Mismatches: 28, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
289 2 0.01
290 84 0.36
291 146 0.62
292 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (290 bp):
GAGCTGCTAATGGCGTTCGAGACAAATTAGTTTCTCCTCTACTACCATAGGCATTGAAAATCTAG
CACAGACAAGTTGAATCTTAAACTTGCTGAATGTGCTGATATATGCATAACTGGAATTGGATACT
AGGAGCAGCCAATAGTGTTTGAAGATGATCAGTTTCTTTGCTACTGTCTGGTGTAGCTTTAGCAT
TGAAAATCTAGCAATGACGACCGAATTGAATCATAAAACTTGTCGATCGTGCTCCACTTATACAT
AATTGGAACCTGAAACTAATCTGAAACTTT
Found at i:110527 original size:29 final size:29
Alignment explanation
Indices: 110491--110601 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
110481 CTTTGGTTCC
*
110491 GTTTAGTGCCTAATATTTATTTCGTTCTA
1 GTTTAGTGCCTAACATTTATTTCGTTCTA
110520 GTTTAGTGCCTAACATTTATTTCGTTCTA
1 GTTTAGTGCCTAACATTTATTTCGTTCTA
110549 GTTTAGTGCCTAACATTTATTTCGTTCTA
1 GTTTAGTGCCTAACATTTATTTCGTTCTA
* *
110578 GTTTAGTGTCTAACGTTTCATTTC
1 GTTTAGTGCCTAACATTT-ATTTC
110602 ATAACTCAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 73 0.94
30 5 0.06
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.50
Consensus pattern (29 bp):
GTTTAGTGCCTAACATTTATTTCGTTCTA
Found at i:112635 original size:3 final size:3
Alignment explanation
Indices: 112627--112653 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
112617 TGCCCGCTGC
112627 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
112654 CGGAGGAACT
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:118081 original size:298 final size:302
Alignment explanation
Indices: 117245--118347 Score: 1134
Period size: 297 Copynumber: 3.7 Consensus size: 302
117235 TCTCTCATAT
* * ** *
117245 GTGGTAACATTGAAATCCCATGTTCTCATCGGTTATTTCACATCATTTCAAGATATATTATCCAT
1 GTGGTAACATTGAAATTCCATGTTCTCTTCGGTTATTTCACATCATTTCCGGATATATTATTCAT
* * * * * * *
117310 TCATT-GCCCTCACACACACACACTGACGACTTC-AAGGCACGTGGAG-ATCCTAACAACCAATA
66 TTATTGGCCCT---TCACACACACTAACGACTTCAAAGCCACGTAGAGCTTCCTAACAACTAATA
* * *** * *
117372 AAAATCAAGGATTCTAAATACGGACAGGTGAAACGGTTCCAAGGCAATCAAAACATACGAC-AAA
128 AAAATCAAGGATTCTAAATACGAACAGGTTAGGTGATTCCAAGGCAATCAAAACATACGACTAAG
* * * * * * *
117436 AG-AGCACATGTATCATACAAGTAATGTTCAAAGATAGTAGTTAGATCTTTTAGGACACGGGTTT
193 GGCAGCACA-GTTTCATACAAATAACGTTTAAAGATAGTAGTTACATCTTTTAGGACACGAGTTT
*
117500 TCTGGAAAAGAGAAAATGAACC-ACCACCA-AAAGATCTCT-CCCAT
257 TCTGGAAAAGAGAAAATG-ACCAACCACCAGAAAGATCTCTCCCCAC
** * * * *
117544 GTGGTAACATCAAAATTCCACGTTCTCTTTGGTTATTTGACATCATTTTCGG-TATATTATTCAT
1 GTGGTAACATTGAAATTCCATGTTCTCTTCGGTTATTTCACATCATTTCCGGATATATTATTCAT
* * * * *
117608 TTATTGTCCTTTCACACACTCCAACGACTTCAAAGCCACGTAGAGCTTCC-AA-AAAT-ATACTA
66 TTATTGGCCCTTCACACACACTAACGACTTCAAAGCCACGTAGAGCTTCCTAACAACTAATA--A
* *
117670 AAATCAAGGATTCTAAATAC--ACAGGTTA--TGCATTCCAAGGCAATCGAAAAAATACGACAAA
129 AAATCAAGGATTCTAAATACGAACAGGTTAGGTG-ATTCCAAGGCAATC-AAAACATACGAC-TA
** * * * *
117731 AGGGCA-CACA-TGCCATACAAGTAACGTATAAAGATCGCAGTTACGATCTTTTAGGACACGAGT
191 AGGGCAGCACAGTTTCATACAAATAACGTTTAAAGATAGTAGTTAC-ATCTTTTAGGACACGAGT
117794 TTTCTGGAAAAGAGAAAATGACCAACCACCAGAAAGATCTCTCCCCCAC
255 TTTCTGGAAAAGAGAAAATGACCAACCACCAGAAAGATCTCT-CCCCAC
* * *
117843 GTGGT-A-ATTGAAATTTCATGTTCTCTTCGGCTATTTCACATCAATTCCGGATATATTATTCAT
1 GTGGTAACATTGAAATTCCATGTTCTCTTCGGTTATTTCACATCATTTCCGGATATATTATTCAT
* * *
117906 TTATTGGCCCTTCACACACACTGAC-ACTTCAAAACCATGTAGA-CTTCCTAACAACTAATAAAA
66 TTATTGGCCCTTCACACACACTAACGACTTCAAAGCCACGTAGAGCTTCCTAACAACTAATAAAA
* * * * *
117969 GTCGAGGATTCTAAATATGAAAAGGTTAGGTGATTCCAAGGCAATCAAAACATATGACTAAGGG-
131 ATCAAGGATTCTAAATACGAACAGGTTAGGTGATTCCAAGGCAATCAAAACATACGACTAAGGGC
* * * *
118033 AGCA-AGTTTCATACAAATGACGTTTAAAGATAGTAATTATCTTCTTTTAGGGCACGAGTTTTCT
196 AGCACAGTTTCATACAAATAACGTTTAAAGATAGTAGTTA-CATCTTTTAGGACACGAGTTTTCT
* * * *
118097 GGAAAAGAG-GAATG---AACCACCAGCAAGATCCCTCTCCAC
260 GGAAAAGAGAAAATGACCAACCACCAGAAAGATCTCTCCCCAC
* * ** *
118136 GTGGTAACATTGAAATTCCATCTTCTTTTCGGTTGCTTCACATCATTTCCGGATATATTACTCAT
1 GTGGTAACATTGAAATTCCATGTTCTCTTCGGTTATTTCACATCATTTCCGGATATATTATTCAT
* * * * * * *
118201 CTATTGGCCTTTCACACGCATTAACGGCTTCAAAGTCACGCAGAGCTTCCTAACAACTAATAAAA
66 TTATTGGCCCTTCACACACACTAACGACTTCAAAGCCACGTAGAGCTTCCTAACAACTAATAAAA
* * * *
118266 ATCAAGGATTCTAAATACGAGCATGTTAGGAGATTACAAGGCAATCAAAACATAC-AGCTAAGGG
131 ATCAAGGATTCTAAATACGAACAGGTTAGGTGATTCCAAGGCAATCAAAACATACGA-CTAAGGG
118330 CAG-AC-GTTTCATACAAAT
195 CAGCACAGTTTCATACAAAT
118348 GAAACGAACC
Statistics
Matches: 667, Mismatches: 104, Indels: 68
0.79 0.12 0.08
Matches are distributed among these distances:
293 11 0.02
294 31 0.05
295 119 0.18
296 81 0.12
297 215 0.32
298 119 0.18
299 75 0.11
300 14 0.02
301 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (302 bp):
GTGGTAACATTGAAATTCCATGTTCTCTTCGGTTATTTCACATCATTTCCGGATATATTATTCAT
TTATTGGCCCTTCACACACACTAACGACTTCAAAGCCACGTAGAGCTTCCTAACAACTAATAAAA
ATCAAGGATTCTAAATACGAACAGGTTAGGTGATTCCAAGGCAATCAAAACATACGACTAAGGGC
AGCACAGTTTCATACAAATAACGTTTAAAGATAGTAGTTACATCTTTTAGGACACGAGTTTTCTG
GAAAAGAGAAAATGACCAACCACCAGAAAGATCTCTCCCCAC
Found at i:120382 original size:2 final size:2
Alignment explanation
Indices: 120375--120414 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
120365 GCAGAGCATT
120375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
120415 TCAATAAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:120819 original size:20 final size:20
Alignment explanation
Indices: 120794--120886 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
120784 TTTTCCCAAT
120794 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
120814 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
120834 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
120855 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
120876 TCGCAATGCGA
1 TCGCAATGCGA
120887 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:120836 original size:41 final size:41
Alignment explanation
Indices: 120791--120886 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
120781 CGATTTTCCC
120791 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
120832 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
120873 AAATCGCAATGCGA
1 AATTCGCAATGCGA
120887 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:120840 original size:21 final size:20
Alignment explanation
Indices: 120794--120886 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
120784 TTTTCCCAAT
*
120794 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
120814 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
120834 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
120855 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
120876 TCGCAATGCGA
1 TCGCAATGCGA
120887 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:120899 original size:41 final size:41
Alignment explanation
Indices: 120813--120946 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
120803 GAATAAGTAA
* * *
120813 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
120854 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * * * * *
120895 ATCGCAATGCGATAAT--AAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
120935 TTCGCAACGCGA
1 ATCGCAACGCGA
120947 TACTGACTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
40 34 0.43
41 43 0.54
42 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:120900 original size:20 final size:20
Alignment explanation
Indices: 120875--120968 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
120865 AATTGGGAAA
*
120875 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
120895 ATCGCAATGCGATAATAAAA
1 ATCGCAACGCGATACTGACT
* *
120915 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
120935 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
120955 TTCGCAACGCGATA
1 ATCGCAACGCGATA
120969 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:120929 original size:40 final size:40
Alignment explanation
Indices: 120872--120948 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
120862 GCGAATTGGG
* * *
120872 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATA
* *
120912 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
120949 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (40 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATA
Found at i:121181 original size:22 final size:22
Alignment explanation
Indices: 121154--121197 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
121144 CACTCTCTCA
121154 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
121176 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
121198 TATCTAAATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Done.