Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000885.1 Hibiscus syriacus cultivar Beakdansim tig00001728_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: 1639497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:252152 original size:32 final size:31
Alignment explanation
Indices: 252095--252191 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 31
252085 AATAATAAAG
* *
252095 TATAGTTTTT-GAATATATTTTTGAAAAACA
1 TATAGTTTTTAGAAAAAATTTTTGAAAAACA
*
252125 TATAGTTTTTAGAAAACAATTTTTGAAAACATA
1 TATAGTTTTTAGAAAA-AATTTTTGAAAA-ACA
* *
252158 TATAGTTTTTA-AAAATGATTTTTGGAAAACA
1 TATAGTTTTTAGAAAA-AATTTTTGAAAAACA
252189 TAT
1 TAT
252192 TTTTCGAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.18
31 9 0.16
32 25 0.44
33 13 0.23
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.43
Consensus pattern (31 bp):
TATAGTTTTTAGAAAAAATTTTTGAAAAACA
Found at i:252166 original size:33 final size:32
Alignment explanation
Indices: 252095--252191 Score: 110
Period size: 33 Copynumber: 3.0 Consensus size: 32
252085 AATAATAAAG
* * *
252095 TATAGTTTTT-GAATATATTTTTGAAAA-ACA
1 TATAGTTTTTAGAAAAAATTTTTGAAAACATA
252125 TATAGTTTTTAGAAAACAATTTTTGAAAACATA
1 TATAGTTTTTAGAAAA-AATTTTTGAAAACATA
*
252158 TATAGTTTTTA-AAAATGATTTTTGGAAAACATA
1 TATAGTTTTTAGAAAA-AATTTTT-GAAAACATA
252191 T
1 T
252192 TTTTCGAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
30 10 0.17
31 4 0.07
32 21 0.36
33 23 0.40
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.43
Consensus pattern (32 bp):
TATAGTTTTTAGAAAAAATTTTTGAAAACATA
Found at i:259894 original size:15 final size:15
Alignment explanation
Indices: 259874--259905 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
259864 ACTAGTACTG
259874 CTCTACAATTCACGT
1 CTCTACAATTCACGT
259889 CTCTACAATTCACGT
1 CTCTACAATTCACGT
259904 CT
1 CT
259906 TAAGCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.34, G:0.06, T:0.34
Consensus pattern (15 bp):
CTCTACAATTCACGT
Found at i:265340 original size:22 final size:22
Alignment explanation
Indices: 265312--265356 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
265302 ACTACGCAAA
265312 GAACACATCATTTTTATTGTCG
1 GAACACATCATTTTTATTGTCG
265334 GAACACATCATTTTTATTGTCG
1 GAACACATCATTTTTATTGTCG
265356 G
1 G
265357 TTCGCCACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (22 bp):
GAACACATCATTTTTATTGTCG
Found at i:279816 original size:24 final size:24
Alignment explanation
Indices: 279785--279830 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
279775 GGTGGCCTTG
*
279785 ATGGAAGATGGTGTTGATGTTGAA
1 ATGGAAGATGGTGGTGATGTTGAA
279809 ATGGAAGATGGTGGTGATGTTG
1 ATGGAAGATGGTGGTGATGTTG
279831 TATCTCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.41, T:0.33
Consensus pattern (24 bp):
ATGGAAGATGGTGGTGATGTTGAA
Found at i:283215 original size:26 final size:26
Alignment explanation
Indices: 283163--283223 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
283153 ATGAAAAGGT
*
283163 AGAAGAAATGATTCAAGGAAAGGAAA
1 AGAAGAAATGATTCAAGGAAAGAAAA
* *
283189 AGAAGAAATGATTCAAGGTAATAAAA
1 AGAAGAAATGATTCAAGGAAAGAAAA
283215 AGAAAGAAA
1 AG-AAGAAA
283224 AGGTTGAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 25 0.81
27 6 0.19
ACGTcount: A:0.61, C:0.03, G:0.23, T:0.13
Consensus pattern (26 bp):
AGAAGAAATGATTCAAGGAAAGAAAA
Found at i:288040 original size:17 final size:17
Alignment explanation
Indices: 288018--288055 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
288008 AACTAATTCG
288018 GACCAACTCAAGTTGCA
1 GACCAACTCAAGTTGCA
288035 GACCAACTCAAGTTGCA
1 GACCAACTCAAGTTGCA
288052 GACC
1 GACC
288056 TAATTTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (17 bp):
GACCAACTCAAGTTGCA
Found at i:288163 original size:34 final size:35
Alignment explanation
Indices: 288104--288173 Score: 124
Period size: 34 Copynumber: 2.0 Consensus size: 35
288094 TATCGAAATC
288104 AAAATCTTTTTAAGTAATATCAAAAGATGCTTATT
1 AAAATCTTTTTAAGTAATATCAAAAGATGCTTATT
*
288139 AAAATCTTTTTAAGT-ATATCAAAAGCTGCTTATT
1 AAAATCTTTTTAAGTAATATCAAAAGATGCTTATT
288173 A
1 A
288174 CTTAAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 19 0.56
35 15 0.44
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (35 bp):
AAAATCTTTTTAAGTAATATCAAAAGATGCTTATT
Found at i:293792 original size:22 final size:22
Alignment explanation
Indices: 293764--293807 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
293754 CTTAAGTTAT
*
293764 ATCTTTATAAGTCAAATGACTA
1 ATCTTTATAAATCAAATGACTA
293786 ATCTTTATAAATCAAATGACTA
1 ATCTTTATAAATCAAATGACTA
293808 TTTTCTTTAA
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:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (22 bp):
ATCTTTATAAATCAAATGACTA
Found at i:293818 original size:22 final size:24
Alignment explanation
Indices: 293765--293818 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
293755 TTAAGTTATA
293765 TCTTTATAAGTCAAATGACTAATCT
1 TCTTTA-AAGTCAAATGACTAATCT
* *
293790 T-TATAAA-TCAAATGACT-ATTT
1 TCTTTAAAGTCAAATGACTAATCT
293811 TCTTTAAA
1 TCTTTAAA
293819 ACCTTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 4 0.16
22 15 0.60
23 2 0.08
24 3 0.12
25 1 0.04
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.43
Consensus pattern (24 bp):
TCTTTAAAGTCAAATGACTAATCT
Found at i:294427 original size:18 final size:18
Alignment explanation
Indices: 294396--294437 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
294386 ATTTGAATTT
*
294396 TACACTGAGTGTG-TCAA
1 TACACTGAGAGTGATCAA
294413 TACACTTGAGAGTGTATCAA
1 TACAC-TGAGAGTG-ATCAA
294433 TACAC
1 TACAC
294438 AACTGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
20 9 0.43
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (18 bp):
TACACTGAGAGTGATCAA
Found at i:295832 original size:22 final size:21
Alignment explanation
Indices: 295774--295833 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
295764 ACTAGTATTT
***
295774 AAAATATGTTTATATTTTAATA
1 AAAATAT-TTTATATACGAATA
*
295796 AAAATATTTCAATATACGAATA
1 AAAATATTT-TATATACGAATA
295818 AAAATATATTTATATA
1 AAAATAT-TTTATATA
295834 AATGTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (21 bp):
AAAATATTTTATATACGAATA
Found at i:295834 original size:16 final size:16
Alignment explanation
Indices: 295815--295848 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
295805 CAATATACGA
295815 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
295831 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
295847 AT
1 AT
295849 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:295922 original size:16 final size:18
Alignment explanation
Indices: 295890--295923 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
295880 TATTAATGTA
295890 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
295908 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
295924 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:296594 original size:130 final size:130
Alignment explanation
Indices: 296390--296637 Score: 388
Period size: 130 Copynumber: 1.9 Consensus size: 130
296380 AATTTTCTTC
* *
296390 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATAATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATAATGTGCTAACACATGTCAGAT
** *
296455 CCTGGTTAAATAATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATAATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * * *
296520 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCATAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATAATGTGCTAACACATGTCAGAT
* *
296585 CTTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATAATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
296638 TATATAAATA
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 106 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATAATGTGCTAACACATGTCAGAT
CCTAATTAAATAATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:297080 original size:35 final size:35
Alignment explanation
Indices: 297030--297105 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
297020 AATTGAATTT
* *
297030 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
297065 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
297100 AATTGA
1 AATTGA
297106 GGATTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:301484 original size:21 final size:21
Alignment explanation
Indices: 301438--301493 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
301428 GATTCTGACT
301438 ATCGCATTGCGA-TTTCCCAA
1 ATCGCATTGCGATTTTCCCAA
* *
301458 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGATTTTCCCAA
*
301480 ATCGCAATGCGATT
1 ATCGCATTGCGATT
301494 ACGTAAATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 21 0.70
22 8 0.27
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (21 bp):
ATCGCATTGCGATTTTCCCAA
Found at i:301502 original size:20 final size:21
Alignment explanation
Indices: 301477--301527 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
301467 GCGATTTTCC
301477 TAAATCGCAATGCG-ATTACG
1 TAAATCGCAATGCGAATTACG
*
301497 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAATTACG
*
301518 AAAATCGCAA
1 TAAATCGCAA
301528 CGAGATTCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (21 bp):
TAAATCGCAATGCGAATTACG
Found at i:301522 original size:21 final size:20
Alignment explanation
Indices: 301478--301527 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
301468 CGATTTTCCT
*
301478 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGA
*
301498 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCG-ATTACGA
301519 AAATCGCAA
1 AAATCGCAA
301528 CGAGATTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAATGCGATTACGA
Found at i:304981 original size:20 final size:19
Alignment explanation
Indices: 304953--305007 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
304943 CAATCATCTT
*
304953 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
304973 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
304992 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
305008 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:305017 original size:14 final size:14
Alignment explanation
Indices: 304998--305066 Score: 75
Period size: 14 Copynumber: 4.6 Consensus size: 14
304988 GCGAAATGAA
304998 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
305012 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
305031 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
305045 AATCGCAACGAGGG
1 AATCGCAACGAGAG
305059 AATCGCAA
1 AATCGCAA
305067 AGCGAAATGA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 31 0.66
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 10 0.21
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:305022 original size:33 final size:33
Alignment explanation
Indices: 304980--305052 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
304970 GGAAATGACT
304980 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
305013 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
305046 ATCGCAA
1 ATCGCAA
305053 CGAGGGAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:305036 original size:19 final size:19
Alignment explanation
Indices: 304960--305038 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
304950 CTTAATGTCT
* **
304960 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
304980 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
304999 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
305013 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
305032 ATCGCAA
1 ATCGCAA
305039 CGAGAGAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 24 0.49
20 9 0.18
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:305072 original size:47 final size:47
Alignment explanation
Indices: 304998--305087 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
304988 GCGAAATGAA
*
304998 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGAGAG
*
305045 AATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACG
1 AATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACG
305088 CAAATTTAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.44, C:0.20, G:0.26, T:0.10
Consensus pattern (47 bp):
AATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGAGAG
Found at i:305116 original size:19 final size:19
Alignment explanation
Indices: 305094--305130 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
305084 AACGCAAATT
305094 TAGTTTCGCGTTGCGATTA
1 TAGTTTCGCGTTGCGATTA
305113 TAGTTTCGCGTTGCGATT
1 TAGTTTCGCGTTGCGATT
305131 TTGTCGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (19 bp):
TAGTTTCGCGTTGCGATTA
Found at i:305144 original size:33 final size:33
Alignment explanation
Indices: 305102--305195 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
305092 TTTAGTTTCG
* *
305102 CGTTGCGATTAT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTATCA-TTTCGCGTTGCGATTCTCT
*
305135 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTATCATTTCGCGTTGCGATTCTCT
* *
305168 CGTTGTGAATT-TCATTTCGCATTGCGAT
1 CGTTGCG-ATTATCATTTCGCGTTGCGAT
305196 AGTCATTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
33 50 0.93
34 4 0.07
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTATCATTTCGCGTTGCGATTCTCT
Found at i:305159 original size:19 final size:18
Alignment explanation
Indices: 305092--305163 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
305082 GCAACGCAAA
305092 TTTAGTTTCGCGTTGCGAT
1 TTTA-TTTCGCGTTGCGAT
*
305111 TATAGTTTCGCGTTGCGA-
1 TTTA-TTTCGCGTTGCGAT
*
305129 TTT-TGT--CGTTGCGAT
1 TTTATTTCGCGTTGCGAT
305144 TTTCATTTCGCGTTGCGAT
1 TTT-ATTTCGCGTTGCGAT
305163 T
1 T
305164 CTCTCGTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 8 0.18
15 3 0.07
16 2 0.05
17 2 0.05
18 2 0.05
19 27 0.61
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (18 bp):
TTTATTTCGCGTTGCGAT
Found at i:305321 original size:14 final size:14
Alignment explanation
Indices: 305302--305338 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
305292 CATCAATTAA
305302 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
305316 ACAAATCATCTTTT
1 ACAAATCAACTTTT
305330 ACAAATCAA
1 ACAAATCAA
305339 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:306753 original size:21 final size:21
Alignment explanation
Indices: 306687--306753 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
306677 GTGAATCGGG
*
306687 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
306707 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
306729 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
306750 CTCT
1 CTCT
306754 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:306772 original size:42 final size:41
Alignment explanation
Indices: 306687--306808 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 41
306677 GTGAATCGGG
* * * *
306687 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
306729 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
306771 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAG
306809 ACGAGTCGAG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:307246 original size:19 final size:19
Alignment explanation
Indices: 307206--307365 Score: 106
Period size: 19 Copynumber: 8.8 Consensus size: 19
307196 TCTGGAACTT
*
307206 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
307227 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
* *
307246 AAAATCGCAAAGAGAGAATG
1 AAAATCGCAACGCGA-AATG
* *
307266 AAAATCGCAATGCGAAACG
1 AAAATCGCAACGCGAAATG
307285 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* * *
307299 AGAATCGCTACGTGAAATG
1 AAAATCGCAACGCGAAATG
307318 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
307332 AGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
*
307351 ATAATCGCAACGCGA
1 AAAATCGCAACGCGA
307366 TTATAGTTTC
Statistics
Matches: 109, Mismatches: 19, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
14 19 0.17
15 2 0.02
16 3 0.03
17 3 0.03
18 2 0.02
19 52 0.48
20 17 0.16
21 11 0.10
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:307267 original size:20 final size:20
Alignment explanation
Indices: 307242--307303 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
307232 CGCAACGCGA
307242 AATGAAAATCGCAAAGAGAG
1 AATGAAAATCGCAAAGAGAG
* *
307262 AATGAAAATCGCAATGCGA-
1 AATGAAAATCGCAAAGAGAG
* *
307281 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAAAGAGAG
307301 AAT
1 AAT
307304 CGCTACGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.52, C:0.15, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAAAGAGAG
Found at i:307321 original size:33 final size:33
Alignment explanation
Indices: 307230--307362 Score: 149
Period size: 33 Copynumber: 3.8 Consensus size: 33
307220 AAAAATGACT
*
307230 ATCGCAACGCGAAATGAAAATCGCAAAGAGAGAATGAAA
1 ATCGCAACGCGAAATGAAAATCGC-AA-CGAG-A-G--A
* *
307269 ATCGCAATGCGAAACGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
307302 ATCGCTACGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
307335 ATCGCAATGCGAAATGATAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
307363 CGATTATAGT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
33 54 0.65
35 1 0.01
36 1 0.01
37 3 0.04
38 2 0.02
39 22 0.27
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:307396 original size:20 final size:20
Alignment explanation
Indices: 307371--307458 Score: 120
Period size: 20 Copynumber: 4.8 Consensus size: 20
307361 CGCGATTATA
307371 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
307391 GTTTCGCGTTGCGA------
1 GTTTCGCGTTGCGATTTTTG
307405 --TTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
307423 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
307443 GTTTCGCGTTGCGATT
1 GTTTCGCGTTGCGATT
307459 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
12 12 0.20
20 48 0.80
ACGTcount: A:0.06, C:0.17, G:0.31, T:0.47
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTG
Found at i:307410 original size:12 final size:12
Alignment explanation
Indices: 307393--307418 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
307383 GATTTTTGGT
307393 TTCGCGTTGCGA
1 TTCGCGTTGCGA
307405 TTCGCGTTGCGA
1 TTCGCGTTGCGA
307417 TT
1 TT
307419 TTTGGTTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.31, T:0.38
Consensus pattern (12 bp):
TTCGCGTTGCGA
Found at i:307414 original size:32 final size:32
Alignment explanation
Indices: 307373--307438 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
307363 CGATTATAGT
307373 TTCGCGTTGCGATTTTTGGTTTCGCGTTGCGA
1 TTCGCGTTGCGATTTTTGGTTTCGCGTTGCGA
307405 TTCGCGTTGCGATTTTTGGTTTCGCGTTGCGA
1 TTCGCGTTGCGATTTTTGGTTTCGCGTTGCGA
307437 TT
1 TT
307439 TTTGGTTTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.06, C:0.18, G:0.30, T:0.45
Consensus pattern (32 bp):
TTCGCGTTGCGATTTTTGGTTTCGCGTTGCGA
Found at i:307439 original size:52 final size:53
Alignment explanation
Indices: 307371--307493 Score: 196
Period size: 52 Copynumber: 2.3 Consensus size: 53
307361 CGCGATTATA
* *
307371 GTTTCGCGTTGCGATTTTTGGTTTCGCGTTGCGA-T-TCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTGGTTTCGCGTTGCGATTCTCGCGTTGC-AATTTTC
*
307423 GTTTCGCGTTGCGATTTTTGGTTTCGCGTTGCGATTCTCTCGTTGCAATTTTC
1 GTTTCGCGTTGCGATTTTTGGTTTCGCGTTGCGATTCTCGCGTTGCAATTTTC
307476 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
307494 CATTCTCTCG
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
52 34 0.52
53 24 0.36
54 8 0.12
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.47
Consensus pattern (53 bp):
GTTTCGCGTTGCGATTTTTGGTTTCGCGTTGCGATTCTCGCGTTGCAATTTTC
Found at i:307507 original size:20 final size:20
Alignment explanation
Indices: 307456--307517 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
307446 TCGCGTTGCG
*
307456 ATTCTCTCGTTGCAATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
307476 GTT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
307495 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
307515 ATT
1 ATT
307518 TCAACCAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.11, C:0.23, G:0.16, T:0.50
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:307835 original size:187 final size:184
Alignment explanation
Indices: 307610--307984 Score: 576
Period size: 187 Copynumber: 2.0 Consensus size: 184
307600 ATGGATTGCA
* * *
307610 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATATACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATATTAAAGAATACACAGT
*
307674 TTAGCAGAATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAGAC-AAAGACAAATA
66 TTAGCAGAATTGGCAGCAAACGAACAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATA
307738 CTAACTTCACAGTGTTAAAGAACACACAATTTAGCAGAATTGGCAGCAACCGAA-AAAT
130 CTAACTTCACAGTGTT-AA-AA-A-ACAATTTAGCAGAATTGGCAGCAACCGAATAAAT
* *
307796 TTACTTTCAACGAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATATTAAAGAATACACAGT
* * *
307861 TTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGATAAATAC
66 TTAGCAGAATTGGCAGCAAACGAACAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAATAC
* * *
307926 TAACTTCACAGTGTTAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATAAAT
131 TAACTTCACAGTGTTAAAAAACAATTTAGCAGAATTGGCAGCAACCGAATAAAT
307980 TTACT
1 TTACT
307985 AAGCAATCTA
Statistics
Matches: 174, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
183 27 0.16
184 10 0.06
185 1 0.01
186 24 0.14
187 112 0.64
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (184 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATATTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAAACGAACAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAATAC
TAACTTCACAGTGTTAAAAAACAATTTAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:307840 original size:93 final size:94
Alignment explanation
Indices: 307610--307984 Score: 575
Period size: 93 Copynumber: 4.1 Consensus size: 94
307600 ATGGATTGCA
* * *
307610 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATATACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
307674 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAATAAAT
* * *
307703 TTACTTTCAACCAAAAGACAAGACAAAGACAAATACTAACTTCACAGTGTTAAAGAACACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
307768 TTAGCAGAATTGGCAGCAACCGAA-AAAT
66 TTAGCAGAATTGGCAGCAACCGAATAAAT
* *
307796 TTACTTTCAACGAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
307861 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAATAAAT
* *
307890 TTAC-TTCAACCAAAAGACAAAACAAAAGATAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
*
307950 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAATAAAT
307980 TTACT
1 TTACT
307985 AAGCAATCTA
Statistics
Matches: 261, Mismatches: 17, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
90 41 0.16
93 110 0.42
94 110 0.42
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:309697 original size:20 final size:20
Alignment explanation
Indices: 309672--309714 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
309662 TTTTGGTTGA
309672 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
309692 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
309712 AAT
1 AAT
309715 CGCAACGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:309787 original size:33 final size:33
Alignment explanation
Indices: 309739--309819 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
309729 AAAATCGTAA
** *
309739 TGCGATTTTGGTTTCGCGTTGGGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
309772 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
309805 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
309820 TCTCATTGCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:309822 original size:21 final size:20
Alignment explanation
Indices: 309803--309874 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
309793 CGATTCTCTC
309803 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
* ** *
309823 CATTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
309844 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
309864 GTTGCGATTTT
1 GTTGCGATTTT
309875 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:310438 original size:21 final size:20
Alignment explanation
Indices: 310405--310501 Score: 95
Period size: 21 Copynumber: 4.7 Consensus size: 20
310395 GGCGCTATGT
*
310405 AAATCGCATTGCGAATTAGG
1 AAATCGCAATGCGAATTAGG
* *
310425 AAACTCGCAATGCGATTTACG
1 AAA-TCGCAATGCGAATTAGG
* * *
310446 TATTCGCATTGCGAATTAGG
1 AAATCGCAATGCGAATTAGG
* *
310466 AAAATCGCAACGCGAATTTGGG
1 -AAATCGCAATGCGAA-TTAGG
310488 AAATCGCAATGCGA
1 AAATCGCAATGCGA
310502 TAGTCAGAAT
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
20 17 0.28
21 39 0.65
22 4 0.07
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (20 bp):
AAATCGCAATGCGAATTAGG
Found at i:316386 original size:20 final size:20
Alignment explanation
Indices: 316363--316406 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
316353 TGCTTTCAAC
316363 TTTTCTTGC-TTTTCTTTTCT
1 TTTTCTT-CTTTTTCTTTTCT
*
316383 TTTTCTTCTTTTTGTTTTCT
1 TTTTCTTCTTTTTCTTTTCT
316403 TTTT
1 TTTT
316407 TTGAGTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTTCTTCTTTTTCTTTTCT
Found at i:339706 original size:36 final size:36
Alignment explanation
Indices: 339652--339724 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 36
339642 TAGCCGGGAG
*
339652 TAGCAGTGATCAGGTAGTCCTTGATAACCCCAAGTT
1 TAGCAGTGATCAGGTAGTCCTCGATAACCCCAAGTT
339688 TAGCAGTGATC-GGCTAGTCCTCGATAACCCCAAGTT
1 TAGCAGTGATCAGG-TAGTCCTCGATAACCCCAAGTT
339724 T
1 T
339725 CCGCAGCGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 2 0.06
36 33 0.94
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (36 bp):
TAGCAGTGATCAGGTAGTCCTCGATAACCCCAAGTT
Found at i:347358 original size:21 final size:20
Alignment explanation
Indices: 347326--347365 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
347316 ATATATCTAT
347326 TTTTGTTATCATTTCCAATA
1 TTTTGTTATCATTTCCAATA
* *
347346 TTTTGATTGTCATTTTCAAT
1 TTTTG-TTATCATTTCCAAT
347366 TTTGAAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTGTTATCATTTCCAATA
Found at i:347446 original size:51 final size:54
Alignment explanation
Indices: 347370--347481 Score: 187
Period size: 54 Copynumber: 2.1 Consensus size: 54
347360 TTCAATTTTG
*
347370 AAATGAAAACCTAAAAAGAAT-AAAAA-AAA-ATTAATTGGATTTAAGTTAAAA
1 AAATGAAAACCTAAAAAGAATAAAAAACAAACATTAATGGGATTTAAGTTAAAA
347421 AAATGAAAACCTAAAAAGAATAAAAAACAAACATTAATGGGATTTAAGTTAAAA
1 AAATGAAAACCTAAAAAGAATAAAAAACAAACATTAATGGGATTTAAGTTAAAA
347475 AAA-GAAA
1 AAATGAAA
347482 TATTTCATTA
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
51 21 0.37
52 5 0.09
53 7 0.12
54 24 0.42
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (54 bp):
AAATGAAAACCTAAAAAGAATAAAAAACAAACATTAATGGGATTTAAGTTAAAA
Found at i:347584 original size:45 final size:45
Alignment explanation
Indices: 347520--347610 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
347510 CTACAAAGAA
347520 TGTTTTTGTTGTTGTAACAAATGTTGTAGAAATTACATATTAATT
1 TGTTTTTGTTGTTGTAACAAATGTTGTAGAAATTACATATTAATT
347565 TGTTTTTGTTGTTGTAACAAATGTTGTAGAAATTACATATTAATT
1 TGTTTTTGTTGTTGTAACAAATGTTGTAGAAATTACATATTAATT
347610 T
1 T
347611 TATTTTATGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.49
Consensus pattern (45 bp):
TGTTTTTGTTGTTGTAACAAATGTTGTAGAAATTACATATTAATT
Found at i:351717 original size:11 final size:10
Alignment explanation
Indices: 351692--351725 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
351682 TAGTTGCCAA
351692 CTTATTTTCC
1 CTTATTTTCC
351702 CTTATTTTCAC
1 CTTATTTTC-C
351713 CTTATTTTCC
1 CTTATTTTCC
351723 CTT
1 CTT
351726 GGTTAAGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (10 bp):
CTTATTTTCC
Found at i:362977 original size:11 final size:11
Alignment explanation
Indices: 362963--363000 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
362953 TGAAGCTTGA
362963 GATTTGAGCTC
1 GATTTGAGCTC
362974 GA-TTGAAGCTC
1 GATTTG-AGCTC
362985 GATTTTGAGCTC
1 GA-TTTGAGCTC
362997 GATT
1 GATT
363001 CAATCTCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 3 0.12
11 11 0.46
12 7 0.29
13 3 0.12
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (11 bp):
GATTTGAGCTC
Found at i:362995 original size:23 final size:24
Alignment explanation
Indices: 362944--363000 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
362934 AAAAAATCAA
*
362944 GAGCTCGATTGAAGCTTGAGATTT
1 GAGCTCGATTGAAGCTCGAGATTT
*
362968 GAGCTCGATTGAAGCTCGA-TTTT
1 GAGCTCGATTGAAGCTCGAGATTT
362991 GAGCTCGATT
1 GAGCTCGATT
363001 CAATCTCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (24 bp):
GAGCTCGATTGAAGCTCGAGATTT
Found at i:364308 original size:22 final size:21
Alignment explanation
Indices: 364263--364303 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
364253 TTTTAAAATT
*
364263 TTTCCCATCTAAATATATTAA
1 TTTCACATCTAAATATATTAA
364284 TTTCACAT-TAAATATATTAA
1 TTTCACATCTAAATATATTAA
364304 CATTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTCACATCTAAATATATTAA
Found at i:364493 original size:29 final size:29
Alignment explanation
Indices: 364418--364483 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
364408 TAAAGTACAT
364418 AAATAGTCTCATGGCTATTAAAAGTTATA
1 AAATAGTCTCATGGCTATTAAAAGTTATA
364447 AAATAGTCTCATGGCTATTAAAAGTTATA
1 AAATAGTCTCATGGCTATTAAAAGTTATA
364476 AAATAGTC
1 AAATAGTC
364484 CAATGACTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
AAATAGTCTCATGGCTATTAAAAGTTATA
Found at i:365304 original size:14 final size:14
Alignment explanation
Indices: 365270--365319 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
365260 CACATAATTG
*
365270 GGTTTAGGGTTTAA
1 GGTTTAGGGATTAA
**
365284 GACTTAGGGATTAA
1 GGTTTAGGGATTAA
*
365298 GGTTTAGGGATTAG
1 GGTTTAGGGATTAA
365312 GGTTTAGG
1 GGTTTAGG
365320 TTTCATTACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.24, C:0.02, G:0.38, T:0.36
Consensus pattern (14 bp):
GGTTTAGGGATTAA
Found at i:366373 original size:6 final size:6
Alignment explanation
Indices: 366362--366386 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
366352 TCGTCTCGGC
366362 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
366387 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:366591 original size:25 final size:24
Alignment explanation
Indices: 366569--366618 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
366559 AATTAAACAG
366569 TTTTTTCCTAATTAAACAAAAACGT
1 TTTTTTCCTAATTAAA-AAAAACGT
*
366594 TTTTTTCCTAATTTAAAAAAACGT
1 TTTTTTCCTAATTAAAAAAAACGT
366618 T
1 T
366619 AAGATATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (24 bp):
TTTTTTCCTAATTAAAAAAAACGT
Found at i:366595 original size:24 final size:23
Alignment explanation
Indices: 366563--366618 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 23
366553 ACCAAAAATT
366563 AAACAGTTTTTTCCTAATTAAACAA
1 AAAC-GTTTTTTCCTAATTAAA-AA
*
366588 AAACGTTTTTTTCCTAATTTAAAA
1 AAACG-TTTTTTCCTAATTAAAAA
366612 AAACGTT
1 AAACGTT
366619 AAGATATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 2 0.07
24 8 0.28
25 19 0.66
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.39
Consensus pattern (23 bp):
AAACGTTTTTTCCTAATTAAAAA
Found at i:373776 original size:33 final size:33
Alignment explanation
Indices: 373719--373817 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 33
373709 CTCATATGCA
* * *
373719 AAGTTGGTCACCCTACCAAAGATGATTTTTTCAAT
1 AAGTTGGCCA-CCAACC-AAGATGAATTTTTCAAT
*
373754 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAGATGAATTTTTCAAT
* *
373787 AAGTTAGCTACCAACCAAGATGAATTTTTCA
1 AAGTTGGCCACCAACCAAGATGAATTTTTCA
373818 CTTACCAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 43 0.75
34 5 0.09
35 9 0.16
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAGATGAATTTTTCAAT
Found at i:374055 original size:96 final size:93
Alignment explanation
Indices: 373894--374082 Score: 335
Period size: 96 Copynumber: 2.0 Consensus size: 93
373884 ACTCAACTTC
373894 TTAAACTCCCCAAATTTGATGTTGCCTCTAATTGTGCACAAGCGTGACACACCCGAAGGTGTTCA
1 TTAAACTCCCCAAATTTGATGTTGCCTCTAATTGTGCACAAGCGTGACACACCCGAAGGTGTTCA
373959 TAATTTCAGGATGTTAATCAAGTTCAAA
66 TAATTTCAGGATGTTAATCAAGTTCAAA
373987 TTAAACTCCCCAAATTTGATGTTGTGCCTCTAA-TGTGCTCACAAGCGTGACACACCCGAAGGTG
1 TTAAACTCCCCAAATTTGATG-T-TGCCTCTAATTGTG--CACAAGCGTGACACACCCGAAGGTG
374051 TTCATAATTTCAGGATGTTAATCAAGTTCAAA
62 TTCATAATTTCAGGATGTTAATCAAGTTCAAA
374083 CTATGATTGA
Statistics
Matches: 92, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
93 21 0.23
94 5 0.05
95 9 0.10
96 57 0.62
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (93 bp):
TTAAACTCCCCAAATTTGATGTTGCCTCTAATTGTGCACAAGCGTGACACACCCGAAGGTGTTCA
TAATTTCAGGATGTTAATCAAGTTCAAA
Found at i:377209 original size:89 final size:88
Alignment explanation
Indices: 377039--377211 Score: 283
Period size: 88 Copynumber: 2.0 Consensus size: 88
377029 TAATCCCGAA
* * *
377039 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAATAATAAATCCATAATATGATTA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAATAATAAAACCATAATATGATTA
*
377104 GGGTAACTTGGATATAAAATGAT
66 GGGTAACTTAGATATAAAATGAT
*
377127 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTG-AATAATAAAACCATAATATGATT
*
377192 AGGGTAACTTAGCTATAAAA
65 AGGGTAACTTAGATATAAAA
377212 GGGTGTGTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 39 0.50
89 39 0.50
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (88 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAATAATAAAACCATAATATGATTA
GGGTAACTTAGATATAAAATGAT
Found at i:383884 original size:87 final size:88
Alignment explanation
Indices: 383771--383940 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 88
383761 ATCCGAATAT
* *
383771 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTAATATGATTAGG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
383836 GTAAC-TGGATATAAAAGTATTA
66 GTAACTTGGATATAAAAGTATTA
383858 TTAAATTCTAATTAATT-AATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
383922 GGTAACTTGGCTATAAAAG
65 GGTAACTTGGATATAAAAG
383941 GGTATGTTAG
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
87 59 0.76
88 19 0.24
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAAAGTATTA
Found at i:386716 original size:33 final size:33
Alignment explanation
Indices: 386654--386752 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
386644 CCCATATGCA
** *
386654 AAGTTGGCCACTTACCAAATATGAATTTTCCAAT
1 AAGTTGGCCACCAACC-AAGATGAATTTTCCAAT
*
386688 AAGTTGGCCACCAACTAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
386721 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
386753 CTTGCCAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 47 0.78
34 13 0.22
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
Found at i:388705 original size:21 final size:21
Alignment explanation
Indices: 388667--388706 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
388657 TCTGTTGAAA
***
388667 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTGCAGAGTATG
388688 CTCCACCTGTTGCAGAGTA
1 CTCCACCTGTTGCAGAGTA
388707 CTACTTATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.33
Consensus pattern (21 bp):
CTCCACCTGTTGCAGAGTATG
Found at i:401496 original size:22 final size:22
Alignment explanation
Indices: 401452--401496 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
401442 AATTAGTTTC
* *
401452 AAAATTTTAAGACATCCTAATT
1 AAAATTTTAAAACATCATAATT
*
401474 AAAATTTTAAAACATCATTATT
1 AAAATTTTAAAACATCATAATT
401496 A
1 A
401497 TATCGATCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATTTTAAAACATCATAATT
Found at i:414671 original size:37 final size:37
Alignment explanation
Indices: 414573--414690 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 37
414563 ATGTTGTCAT
* * * *
414573 TTGAGATTATTTCTCTCGAAACAAAATGTCATCTCGC
1 TTGAGATAATTTCTCTCAAAACAAAATTTCGTCTCGC
* * * *
414610 TAGAGATAGCTTT-TCTTGAAAAACAAAATTTTGTCTCGC
1 TTGAGATA-ATTTCTC-T-CAAAACAAAATTTCGTCTCGC
*
414649 TTGAGATAATTTCTCTCAAAAC-AAATTTCGTCTCAC
1 TTGAGATAATTTCTCTCAAAACAAAATTTCGTCTCGC
414685 TTGAGA
1 TTGAGA
414691 CATTTTTTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 9
0.74 0.15 0.10
Matches are distributed among these distances:
36 18 0.28
37 13 0.20
38 8 0.12
39 25 0.39
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (37 bp):
TTGAGATAATTTCTCTCAAAACAAAATTTCGTCTCGC
Found at i:414826 original size:67 final size:65
Alignment explanation
Indices: 414743--414938 Score: 311
Period size: 67 Copynumber: 2.9 Consensus size: 65
414733 TAAAATTTAT
* *
414743 AATCTTTGAGAATGTTTCTCTTGAAACAAATTTTGTCTCCATTGAGACAATTTCTCTTGAAACAC
1 AATCTTTGAGTATGTTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAC
414808 AA
65 -A
*
414810 AATCTTTGAGTTTGTTTCCTTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAC
1 AATCTTTGAGTATGTTTCC-TTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAC
414875 A
65 A
*
414876 AATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
1 AATCTTTGAGTATGTTT-CCTTGAAACAAA-TTTTGTCTCCCTTGAGACAATTTCTCTTGAAA
414939 TAAATCCCTA
Statistics
Matches: 121, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
66 28 0.23
67 93 0.77
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (65 bp):
AATCTTTGAGTATGTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACA
Found at i:414854 original size:21 final size:21
Alignment explanation
Indices: 414820--414859 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
414810 AATCTTTGAG
* *
414820 TTTGTTTCCTTTGAAACAAAT
1 TTTGTCTCCCTTGAAACAAAT
*
414841 TTTGTCTCCCTTGAGACAA
1 TTTGTCTCCCTTGAAACAA
414860 TTTCTCTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (21 bp):
TTTGTCTCCCTTGAAACAAAT
Found at i:415281 original size:134 final size:131
Alignment explanation
Indices: 414942--415295 Score: 392
Period size: 131 Copynumber: 2.7 Consensus size: 131
414932 CTTGAAATAA
* * * * *
414942 ATCCCTAAAGATGGCCA-GTCGTCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCC
1 ATCCCTAAAGATAGACATGTCGTCCTCATCGCGTAGGAACCGTGTCATCCACCGACCAGATCTCA
* * *
415006 TCATCACGTAGGAGTCGTGTCACCCCATGATAACTAGCCATCCTAATCATGTAGGAACCGTGTTA
66 TCATCACGTAGGAGACGTGTCA-CCCATGATAACCAGCCATCCTAATCATGTAAGAACCGTGTTA
415071 TC
130 TC
* * * **
415073 ATCCCTAAAGATAGA-ATGTCATCCTCATCACGTAAGAATTGTGTCATCCACCGACCAGAGT-TC
1 ATCCCTAAAGATAGACATGTCGTCCTCATCGCGTAGGAACCGTGTCATCCACCGACCAGA-TCTC
* * * * *
415136 TTCATCACGTAGGAGACGTGTCACCTATAGATAACCAGTCATCCTCATCGTGTAAGAACCGTGTT
65 ATCATCACGTAGGAGACGTGTCACCCAT-GATAACCAGCCATCCTAATCATGTAAGAACCGTGTT
415201 ATCACC
129 AT---C
* * * * * *
415207 ATCTCTAAAGAT-GACATGTCGTCCTCATTGCATAGGAACCATGTCATCCACCGACTATATCTCA
1 ATCCCTAAAGATAGACATGTCGTCCTCATCGCGTAGGAACCGTGTCATCCACCGACCAGATCTCA
* *
415271 TCATCACGTAGAAGCCGTGTCACCC
66 TCATCACGTAGGAGACGTGTCACCC
415296 TTTGATGACC
Statistics
Matches: 183, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
130 5 0.03
131 105 0.57
133 3 0.02
134 70 0.38
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (131 bp):
ATCCCTAAAGATAGACATGTCGTCCTCATCGCGTAGGAACCGTGTCATCCACCGACCAGATCTCA
TCATCACGTAGGAGACGTGTCACCCATGATAACCAGCCATCCTAATCATGTAAGAACCGTGTTAT
C
Found at i:415535 original size:15 final size:16
Alignment explanation
Indices: 415487--415535 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
415477 GTCTAAAAAA
415487 TATTATTAA-TTATAT
1 TATTATTAATTTATAT
*
415502 TATTATTATTCTTATTAT
1 TATTATTAAT-TTA-TAT
415520 TATT-TTAATTTATAT
1 TATTATTAATTTATAT
415535 T
1 T
415536 TTACATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 12 0.41
16 3 0.10
17 7 0.24
18 7 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATTAATTTATAT
Found at i:417953 original size:25 final size:22
Alignment explanation
Indices: 417925--417986 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
417915 CAAATCACCA
417925 TTTTTCAAAATAAAAGTCATAATTG
1 TTTTT-AAAATAAAA-T-ATAATTG
* *
417950 TTTTTTAAAATAATATTTAATTG
1 -TTTTTAAAATAAAATATAATTG
417973 TTTTTAAAA-AAAAT
1 TTTTTAAAATAAAAT
417987 GGTTATGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 4 0.12
22 9 0.27
23 6 0.18
24 1 0.03
25 8 0.24
26 5 0.15
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (22 bp):
TTTTTAAAATAAAATATAATTG
Found at i:418172 original size:31 final size:31
Alignment explanation
Indices: 418133--418200 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
418123 GGTCTGATTA
* *
418133 GGTACTTGAACTTGACTTATTGGTTCAAACTT
1 GGTACTTGAACTTCACTTATTGGTCCAAA-TT
*
418165 -GTACTTGAACTTCACTTTTTGGTCCAAATT
1 GGTACTTGAACTTCACTTATTGGTCCAAATT
418195 GGTACT
1 GGTACT
418201 AATGATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (31 bp):
GGTACTTGAACTTCACTTATTGGTCCAAATT
Found at i:418321 original size:152 final size:148
Alignment explanation
Indices: 418129--418412 Score: 435
Period size: 152 Copynumber: 1.9 Consensus size: 148
418119 TTTAGGTCTG
**
418129 ATTAGGTACTTGAACTTGACTTATTGGTTCAAACTTGTACTTGAACTTCACTTTTTGGTCCAAAT
1 ATTAGGTACTTGAACTTGACTTATTGGTTCAAACCGGTACTTGAACTTCACTTTTTGGTCCAAAT
* *
418194 TGGTACTAATGATAAATGACTTATTTGAAT-AAACTAGAACCATGAAGTCAAGTTCAGGTACCAA
66 TGGTACCAATGATAAATGACTTATTTGAATCAAA-TAGAACAATGAAGTCAAGTTCAGGTACCAA
418258 TTTGGCACGTTTTGGTCCA
130 TTTGGCACGTTTTGGTCCA
*
418277 ATTAGGTATTTGAACTTGACTTAGTTATTGGTTCAAACCGGTACTTGAACTTCACTTTTTGGTCC
1 ATTAGGTACTTGAACTTGAC----TTATTGGTTCAAACCGGTACTTGAACTTCACTTTTTGGTCC
* * * *
418342 AAATTGGTACCAATGGTAGATGACTTATTTGAATCAAATTGAACAATGAAGTCAAGTTCATGTAC
62 AAATTGGTACCAATGATAAATGACTTATTTGAATCAAATAGAACAATGAAGTCAAGTTCAGGTAC
418407 CAATTT
127 CAATTT
418413 AAACCTAAAA
Statistics
Matches: 122, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
148 19 0.16
152 100 0.82
153 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (148 bp):
ATTAGGTACTTGAACTTGACTTATTGGTTCAAACCGGTACTTGAACTTCACTTTTTGGTCCAAAT
TGGTACCAATGATAAATGACTTATTTGAATCAAATAGAACAATGAAGTCAAGTTCAGGTACCAAT
TTGGCACGTTTTGGTCCA
Found at i:421825 original size:36 final size:36
Alignment explanation
Indices: 421785--421973 Score: 283
Period size: 36 Copynumber: 5.3 Consensus size: 36
421775 AAGTTTGCAT
*
421785 CGATTGAAGTCGAACGGAGGGAAGCATCGGCACTTC
1 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
** * *
421821 CGATTCAAGTCGAACGGAATGAAGCAACAGCACTTC
1 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
421857 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
1 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
* * *
421893 CGATTTAAGT-GAACGGAAGGAACCATCGGCACTTC
1 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
421928 CGATTCAAGTCGAACGG-GAGGAAGCATCGGCACTTC
1 CGATTCAAGTCGAACGGAG-GGAAGCATCGGCACTTC
421964 CGATTCAAGT
1 CGATTCAAGT
421974 GTTCATCTTT
Statistics
Matches: 136, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
35 32 0.24
36 104 0.76
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (36 bp):
CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
Found at i:421951 original size:71 final size:71
Alignment explanation
Indices: 421785--421974 Score: 301
Period size: 71 Copynumber: 2.7 Consensus size: 71
421775 AAGTTTGCAT
* * *
421785 CGATTGAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAATGAAGCAACA
1 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTCAAGT-GAACGGAAGGAACCAACA
421850 GCACTTC
65 GCACTTC
* * *
421857 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTTAAGTGAACGGAAGGAACCATCGG
1 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTCAAGTGAACGGAAGGAACCAACAG
421922 CACTTC
66 CACTTC
421928 CGATTCAAGTCGAACGG-GAGGAAGCATCGGCACTTCCGATTCAAGTG
1 CGATTCAAGTCGAACGGAG-GGAAGCATCGGCACTTCCGATTCAAGTG
421975 TTCATCTTTT
Statistics
Matches: 110, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
70 1 0.01
71 65 0.59
72 44 0.40
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (71 bp):
CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTCAAGTGAACGGAAGGAACCAACAG
CACTTC
Found at i:425142 original size:33 final size:33
Alignment explanation
Indices: 425100--425165 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
425090 TCTTTCCTTG
425100 CTTTTCTACAATTTAAAATCTCATTTTTAAGGT
1 CTTTTCTACAATTTAAAATCTCATTTTTAAGGT
425133 CTTTTCTACAATTTAAAATCTCATTTTTAAGGT
1 CTTTTCTACAATTTAAAATCTCATTTTTAAGGT
425166 TAATTGGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.48
Consensus pattern (33 bp):
CTTTTCTACAATTTAAAATCTCATTTTTAAGGT
Found at i:437994 original size:2 final size:2
Alignment explanation
Indices: 437987--438027 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
437977 ATTAATAATC
437987 TA TA TA TA TA 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 TA TA TA TA TA T
438028 GAAACTACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:448171 original size:45 final size:46
Alignment explanation
Indices: 448083--448173 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
448073 TTGAAAAATC
* * *
448083 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTACATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
448129 CTGAGTACATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTACATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
448174 TTCGATGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.52
46 20 0.48
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (46 bp):
CTGAGTACATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:448218 original size:20 final size:20
Alignment explanation
Indices: 448193--448230 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
448183 TAAAAAATTA
448193 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
448213 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
448231 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:454841 original size:22 final size:21
Alignment explanation
Indices: 454799--454838 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
454789 GAGTTTATTT
*
454799 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
454820 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
454839 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:456908 original size:45 final size:46
Alignment explanation
Indices: 456820--456910 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
456810 TTGAAAAAGC
* *
456820 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
456866 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
456911 TTCGATGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:459487 original size:15 final size:15
Alignment explanation
Indices: 459464--459494 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
459454 CATGTATTTT
*
459464 AATATAAAAAATAAA
1 AATAAAAAAAATAAA
459479 AATAAAAAAAATAAA
1 AATAAAAAAAATAAA
459494 A
1 A
459495 GAGGAGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAAAAAAATAAA
Found at i:467913 original size:23 final size:22
Alignment explanation
Indices: 467859--467920 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
467849 AGCTCATATA
*
467859 AATGCACCGAAGTGCCACATAG
1 AATGCACCGTAGTGCCACATAG
*
467881 AATGCACCGTAGTGCCACGTAG
1 AATGCACCGTAGTGCCACATAG
467903 AATTGCACCGTAGTGCCA
1 AA-TGCACCGTAGTGCCA
467921 TATAATAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 22 0.59
23 15 0.41
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (22 bp):
AATGCACCGTAGTGCCACATAG
Found at i:468152 original size:100 final size:100
Alignment explanation
Indices: 467936--468248 Score: 497
Period size: 100 Copynumber: 3.1 Consensus size: 100
467926 TAATGTTCAT
* * *
467936 AAGGACCACATATCATTCCTTAAG-A--ATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
467998 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCC--AGAA-ACACATATGTCCCG
* *
468036 AAGAACCATATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
468101 GACTTCACACATGTTCCAGAAACACATATGTCCCG
66 GACTTCACACATGTTCCAGAAACACATATGTCCCG
468136 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
468201 GACTTCACACATGTTCCAAAGAATACATATGTCCCG
66 GACTTCACACATGTTCCAGA-AACACATATGTCCCG
468237 AAGGACCACATA
1 AAGGACCACATA
468249 GACCCTCGAC
Statistics
Matches: 199, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
100 117 0.59
101 31 0.16
103 51 0.26
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (100 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAGAAACACATATGTCCCG
Found at i:469318 original size:20 final size:20
Alignment explanation
Indices: 469295--469332 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
469285 TATTCAATAA
* *
469295 TTTATTATCATATCATATGG
1 TTTATCATCATAACATATGG
469315 TTTATCATCATAACATAT
1 TTTATCATCATAACATAT
469333 CACACATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTATCATCATAACATATGG
Found at i:469782 original size:21 final size:21
Alignment explanation
Indices: 469758--469798 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
469748 TTTTGTTCGT
* *
469758 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
469779 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
469799 TTGCCCAGAA
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:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:471027 original size:13 final size:13
Alignment explanation
Indices: 471009--471035 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
470999 AATCATATTT
471009 CCTTTCATGTTCA
1 CCTTTCATGTTCA
471022 CCTTTCATGTTCA
1 CCTTTCATGTTCA
471035 C
1 C
471036 ATACTCTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.44
Consensus pattern (13 bp):
CCTTTCATGTTCA
Found at i:476714 original size:18 final size:17
Alignment explanation
Indices: 476674--476715 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
476664 ACAAAATACA
476674 ACATTCCCAGTAATCTT
1 ACATTCCCAGTAATCTT
*
476691 --ATTCCCTGGTAATCTT
1 ACATTCCC-AGTAATCTT
476707 ACATTCCCA
1 ACATTCCCA
476716 CTAGAGATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 6
0.71 0.07 0.21
Matches are distributed among these distances:
15 6 0.30
16 8 0.40
18 6 0.30
ACGTcount: A:0.26, C:0.31, G:0.07, T:0.36
Consensus pattern (17 bp):
ACATTCCCAGTAATCTT
Found at i:476980 original size:21 final size:20
Alignment explanation
Indices: 476935--476980 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
476925 CGGTCATCCA
476935 ATTTTTAAACCCCAGACCGG
1 ATTTTTAAACCCCAGACCGG
476955 ATTTTTAAACCCCAGACCGG
1 ATTTTTAAACCCCAGACCGG
476975 ATTTTT
1 ATTTTT
476981 TTCCGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
ATTTTTAAACCCCAGACCGG
Found at i:477227 original size:20 final size:20
Alignment explanation
Indices: 477199--477243 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
477189 TGCACCTCTA
*
477199 ATTCCCACTGGTAATCTTAC
1 ATTCTCACTGGTAATCTTAC
*
477219 ATTCTCACTGGTAATTTTAC
1 ATTCTCACTGGTAATCTTAC
477239 ATTCT
1 ATTCT
477244 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (20 bp):
ATTCTCACTGGTAATCTTAC
Found at i:483088 original size:2 final size:2
Alignment explanation
Indices: 483083--483111 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
483073 TTTATTTTAT
483083 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
483112 TAAAATTTGC
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:494928 original size:20 final size:20
Alignment explanation
Indices: 494899--494941 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
494889 ATTTCACCAC
*
494899 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
494919 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
494939 ATG
1 ATG
494942 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:495775 original size:302 final size:303
Alignment explanation
Indices: 495203--495807 Score: 1104
Period size: 302 Copynumber: 2.0 Consensus size: 303
495193 CTTCGAACCA
*
495203 TTTTTAAGTGGAGGTGAAAGCGACGCCTTCGTGAGAATTTATTCTCCACATAGGCCTAGTAAGTA
1 TTTTTAAGTGGAGGTGAAAGCGACGCCTTCGTGAGAATTTATTCTCCACATAGGCCTAGCAAGTA
495268 ACCTTCGGGATTCATATACCTTATGTCTTCGTGTGAATTTATTCACCGCACAGACATAAGGGAAT
66 ACCTTCGGGATTCATATACCTTATGTCTTCGTGTGAATTTATTCACCGCACAGACATAAGGGAAT
*
495333 GTATCCTCTCGAGTTTAACTTAGTCCACATGAGCTTCTAAAAGGCTTAGGACTAAGGGTATGGCA
131 GCATCCTCTCGAGTTTAACTTAGTCCACATGAGCTTCTAAAAGGCTTAGGACTAAGGGTATGGCA
* * *
495398 AGCCCAAGGGGGTACCAGCAAGGAGAACTCATGTACCTTCTTTAGAACCTAAACCGGGAGACTAG
196 AGCCCAAGGGGGCACCAGCAAGGAGAACTCAGGTACCTTCTTTAGAACCTAAACCGGGAGACTAC
*
495463 AAGGAATTAGAGCCCACCCCAAAACCTTATTTCAAACCCTAGG
261 AAGGAATTAGAGCCCACCCCAAAACCTCATTTCAAACCCTAGG
*
495506 TTTTTAAGTGGAGGTGAAA-CGACGTCTTCGTGAGAATTTATTCTCCACATAGGCCTAGCAAGTA
1 TTTTTAAGTGGAGGTGAAAGCGACGCCTTCGTGAGAATTTATTCTCCACATAGGCCTAGCAAGTA
495570 ACCTTCGGGATTCATATACCTTATGTCTTCGTGTGAATTTATTCACCGCACAGACATAAGGGAAT
66 ACCTTCGGGATTCATATACCTTATGTCTTCGTGTGAATTTATTCACCGCACAGACATAAGGGAAT
* *
495635 GCATCCTCTCGAGTTTAACTTAGTCCACATGAGCTTCTAATAGGCTTAGGACTAAGGGTCTGGCA
131 GCATCCTCTCGAGTTTAACTTAGTCCACATGAGCTTCTAAAAGGCTTAGGACTAAGGGTATGGCA
* *
495700 AGCCCAAGGGGGCACCAGCAAGGAGAACTCGGGTACCTTCTTTAGAAGCTAAACCGGGAGACTAC
196 AGCCCAAGGGGGCACCAGCAAGGAGAACTCAGGTACCTTCTTTAGAACCTAAACCGGGAGACTAC
495765 AAGGAATTAGAGCCCACCCCAAAACCTCATTTCAAACCCTAGG
261 AAGGAATTAGAGCCCACCCCAAAACCTCATTTCAAACCCTAGG
495808 ATGCTTTGAG
Statistics
Matches: 291, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
302 272 0.93
303 19 0.07
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (303 bp):
TTTTTAAGTGGAGGTGAAAGCGACGCCTTCGTGAGAATTTATTCTCCACATAGGCCTAGCAAGTA
ACCTTCGGGATTCATATACCTTATGTCTTCGTGTGAATTTATTCACCGCACAGACATAAGGGAAT
GCATCCTCTCGAGTTTAACTTAGTCCACATGAGCTTCTAAAAGGCTTAGGACTAAGGGTATGGCA
AGCCCAAGGGGGCACCAGCAAGGAGAACTCAGGTACCTTCTTTAGAACCTAAACCGGGAGACTAC
AAGGAATTAGAGCCCACCCCAAAACCTCATTTCAAACCCTAGG
Found at i:496453 original size:12 final size:12
Alignment explanation
Indices: 496436--496472 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
496426 TATTATTCAC
496436 TGCTACAGTAAT
1 TGCTACAGTAAT
* *
496448 TGCTACAATAAC
1 TGCTACAGTAAT
496460 TGCTACAGTAAT
1 TGCTACAGTAAT
496472 T
1 T
496473 TCAGCCAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (12 bp):
TGCTACAGTAAT
Found at i:496916 original size:45 final size:44
Alignment explanation
Indices: 496860--497074 Score: 270
Period size: 45 Copynumber: 4.8 Consensus size: 44
496850 TATAAAATTT
* * *
496860 CTTATCATTTATCCTATAAGCTCGTAAGCTTATTCTACCAATATA
1 CTTACCATTTAT-CTATAAGCTCGTAAGCTTATTTTACCAATACA
* *
496905 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTA-TCTATAAGCTCGTAAGCTTATTTTACCAATACA
* *
496950 CTTACCATTTATTTCATAAGTTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTTATCT-ATAAGCTCGTAAGCTTATTTTACCAATACA
* *
496995 CTTACCATTTATTTCATAAGCTCGTAAGCATATTTTACCAATACA
1 CTTACCATTTATCT-ATAAGCTCGTAAGCTTATTTTACCAATACA
** *
497040 CTTGTCA-TTATTCTATAAGCTCGTAAACTTATTTT
1 CTTACCATTTA-TCTATAAGCTCGTAAGCTTATTTT
497075 CATGTTTACC
Statistics
Matches: 153, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
44 23 0.15
45 129 0.84
46 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (44 bp):
CTTACCATTTATCTATAAGCTCGTAAGCTTATTTTACCAATACA
Found at i:497018 original size:90 final size:89
Alignment explanation
Indices: 496868--497074 Score: 299
Period size: 90 Copynumber: 2.3 Consensus size: 89
496858 TTCTTATCAT
* * *
496868 TTATCCTATAAGCTCGTAAGCTTATTCTACCAATATACTTACCATTTATTCCATAAGCTCGTAAG
1 TTATTCTATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTTATTCCATAAGCTCGTAAG
* *
496933 CTTATTTTACCAATATACTTACCA
66 CATATTTTACCAATACACTTACCA
* *
496957 TTTATT-TCATAAGTTCGTAAGCTTATTTTACCAATACACTTACCATTTATTTCATAAGCTCGTA
1 -TTATTCT-ATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTTATTCCATAAGCTCGTA
**
497021 AGCATATTTTACCAATACACTTGTCA
64 AGCATATTTTACCAATACACTTACCA
*
497047 TTATTCTATAAGCTCGTAAACTTATTTT
1 TTATTCTATAAGCTCGTAAGCTTATTTT
497075 CATGTTTACC
Statistics
Matches: 104, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
89 25 0.24
90 79 0.76
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (89 bp):
TTATTCTATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTTATTCCATAAGCTCGTAAG
CATATTTTACCAATACACTTACCA
Found at i:503650 original size:85 final size:84
Alignment explanation
Indices: 503404--503832 Score: 570
Period size: 85 Copynumber: 5.0 Consensus size: 84
503394 TACAATATAG
* * *
503404 CTCAAGGCGAGAAGGGCTATTTGTCAACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGG
* * *
503469 CAAATCAAATATACATCATAA
65 C-ATTCAAATTTACAGCATAA
* *
503490 CTCAAGGTGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTATATTCAGCTCAAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGG
503555 CATATCAAATTTACAGCATAA
65 CAT-TCAAATTTACAGCATAA
* *
503576 CTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTCGATTACATTCAGCTTAAAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
* * *
503641 ACTTTAAATTCACAGCTTAA
66 A-TTCAAATTTACAGCATAA
* * * *
503661 CCCAAGGCGAGAAGGGTTATCTATCAATAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
* * * *
503726 ACATCAAATTCACAGCTTAG
66 A-TTCAAATTTACAGCATAA
* * *
503746 CTCAAGGTGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTTCATTCAGCTCAAGGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
*
503811 ATGTCAAATTTACAACATAA
66 AT-TCAAATTTACAGCATAA
503831 CT
1 CT
503833 TAAGTTAAGA
Statistics
Matches: 304, Mismatches: 36, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
85 201 0.66
86 103 0.34
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (84 bp):
CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
ATTCAAATTTACAGCATAA
Found at i:504645 original size:21 final size:21
Alignment explanation
Indices: 504605--504645 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
504595 TTCGTCTGTA
* * *
504605 TTTTTATTTATTTATTTTATT
1 TTTTTATATATATATATTATT
504626 TTTTTATATATATATATTAT
1 TTTTTATATATATATATTAT
504646 ATAATTTGCA
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTATATATATATATTATT
Found at i:504743 original size:36 final size:36
Alignment explanation
Indices: 504635--505019 Score: 195
Period size: 36 Copynumber: 10.5 Consensus size: 36
504625 TTTTTTATAT
* ** ** ** *
504635 ATATATATTATATAATTTGCAAATGATTTTTTAAAT
1 ATATATATTATATAGTTTTTAAAACATTTTGGAAAC
* *
504671 ATATATAATATATAGTTTTTGAAAGCATTTTGGAAAC
1 ATATATATTATATAGTTTTT-AAAACATTTTGGAAAC
*
504708 ATATATATTATATAGTTCTTAAAACATTTTGGAAAC
1 ATATATATTATATAGTTTTTAAAACATTTTGGAAAC
* * ** * *
504744 ATATATATATATATA-TATATATATATATATATATATATATATAT
1 ATATATAT-TATATAGT-T-T-T-TA-A-A-ACAT-TTTGGAAAC
*
504788 ATATATATATATATAGTTTTTATAAAACATTTTGAAAAC
1 ATATATAT-TATATAG-TTTT-TAAAACATTTTGGAAAC
* * * * *
504827 TTGTATAATATATAGTTTTTAAAACATTTTGAATATAT
1 ATATATATTATATAGTTTTTAAAACATTTTGGA-A-AC
504865 ATATATATAATATATAGTTTTTAAAACATTTT-GAAA-
1 ATATATAT--TATATAGTTTTTAAAACATTTTGGAAAC
* * * *
504901 A-ATTTA-T-TATAGTTTTGAAATCATTTT-GAAAT
1 ATATATATTATATAGTTTTTAAAACATTTTGGAAAC
* * * *
504933 TTATATA-TATATAGTTTTAAAAAAAGCATTTTGAAAAA
1 ATATATATTATATAGTTTT--TAAAA-CATTTTGGAAAC
*
504971 ATATATA-TAT-TATTTTTTAAAACATTTT-GAAAGC
1 ATATATATTATATAGTTTTTAAAACATTTTGGAAA-C
505005 -TATA-A-TATATAGTTT
1 ATATATATTATATAGTTT
505020 GAAAACTTTT
Statistics
Matches: 276, Mismatches: 48, Indels: 53
0.73 0.13 0.14
Matches are distributed among these distances:
31 22 0.08
32 5 0.02
33 17 0.06
34 15 0.05
35 8 0.03
36 58 0.21
37 54 0.20
38 26 0.09
39 11 0.04
40 27 0.10
41 2 0.01
42 2 0.01
43 7 0.03
44 20 0.07
45 1 0.00
46 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (36 bp):
ATATATATTATATAGTTTTTAAAACATTTTGGAAAC
Found at i:504751 original size:2 final size:2
Alignment explanation
Indices: 504744--504802 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
504734 TTTTGGAAAC
504744 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
504786 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
504803 GTTTTTATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:504838 original size:40 final size:39
Alignment explanation
Indices: 504784--505058 Score: 185
Period size: 31 Copynumber: 7.6 Consensus size: 39
504774 ATATATATAT
504784 ATATATATATATATATATAGTTTTTATAAAACATTTTGAAA
1 ATATATATATATATATATAG-TTTT-TAAAACATTTTGAAA
* * *
504825 A-CT-TGTATA-ATATATAGTTTTTAAAACATTTTGAAT
1 ATATATATATATATATATAGTTTTTAAAACATTTTGAAA
504861 ATATATATATATAATATATAGTTTTTAAAACATTTTG--A
1 ATATATATATAT-ATATATAGTTTTTAAAACATTTTGAAA
* *
504899 A-A-A-AT-T-TAT-TATAGTTTTGAAATCATTTTG--A
1 ATATATATATATATATATAGTTTTTAAAACATTTTGAAA
*
504930 A-AT-T-TATATATATATAGTTTTAAAAAAAGCATTTTGAAA
1 ATATATATATATATATATAGTTTT--TAAAA-CATTTTGAAA
504969 A-A-ATATATATAT-TAT--TTTTTAAAACATTTTG---
1 ATATATATATATATATATAGTTTTTAAAACATTTTGAAA
** * * *
505000 A-A-AGCTATA-ATATATAG-TTTGAAAACTTTTTTTAAA
1 ATATATATATATATATATAGTTTTTAAAAC-ATTTTGAAA
505036 AT-TATATATATATATATAGTTTT
1 ATATATATATATATATATAGTTTT
505059 AAATTATTTT
Statistics
Matches: 189, Mismatches: 18, Indels: 56
0.72 0.07 0.21
Matches are distributed among these distances:
30 2 0.01
31 33 0.17
32 11 0.06
33 8 0.04
34 17 0.09
35 6 0.03
36 20 0.11
37 22 0.12
38 22 0.12
39 15 0.08
40 32 0.17
41 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (39 bp):
ATATATATATATATATATAGTTTTTAAAACATTTTGAAA
Found at i:504839 original size:119 final size:114
Alignment explanation
Indices: 504669--504880 Score: 307
Period size: 119 Copynumber: 1.8 Consensus size: 114
504659 GATTTTTTAA
* * *
504669 ATATATATAATATATAGTTTTTGAAAGCATTTTGGAAACATATATATTATATAGTTCTTAAAACA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATAATATATAGTTCTTAAAACA
504734 TTTTGGAAACATATATATATATATATATATATATATATATATATATATATAT
66 TTTT-G-AACATATATATATATA-ATATATATATATATATATATATATATAT
* * * *
504786 ATATATATATATATATAGTTTTTATAAAACATTTTGAAAACTTGTATAATATATAGTTTTTAAAA
1 ATATATATA-ATATATAGTTTTT-GAAAACATTTTGAAAACATATATAATATATAGTTCTTAAAA
*
504851 CATTTTGAATATATATATATATAATATATA
64 CATTTTGAACATATATATATATAATATATA
504881 GTTTTTAAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
116 7 0.08
117 24 0.28
118 14 0.16
119 40 0.47
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (114 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATAATATATAGTTCTTAAAACA
TTTTGAACATATATATATATAATATATATATATATATATATATATATAT
Found at i:504916 original size:71 final size:73
Alignment explanation
Indices: 504780--505001 Score: 244
Period size: 71 Copynumber: 3.0 Consensus size: 73
504770 ATATATATAT
*
504780 ATATATATATATATATATATATAGTTTTTATAAAACATTTTGAAAACTTGTATAATATATAGTTT
1 ATATATATATATATA-ATATATAG-TTTTATAAAACATTTTGAAAA-AT-T-T-ATATATAGTTT
504845 TTAAAACATTTTGA
60 TTAAAACATTTTGA
* *
504859 ATATATATATATATAATATATAGTTTT-TAAAACATTTTGAAAAATTTAT-TATAGTTTTGAAAT
1 ATATATATATATATAATATATAGTTTTATAAAACATTTTGAAAAATTTATATATAGTTTTTAAAA
504922 CATTTTG-
66 CATTTTGA
* * *
504929 A-A-AT-T-TATAT-ATATATAGTTTTAAAAAAAGCATTTTGAAAAAATATATATATTATTTTTT
1 ATATATATATATATAATATATAGTTTT-ATAAAA-CATTTTG-AAAAATTTATATA-TAGTTTTT
504989 AAAACATTTTGA
62 AAAACATTTTGA
505001 A
1 A
505002 AGCTATAATA
Statistics
Matches: 128, Mismatches: 8, Indels: 21
0.82 0.05 0.13
Matches are distributed among these distances:
65 12 0.09
66 5 0.04
67 5 0.04
68 9 0.07
69 10 0.08
70 3 0.02
71 35 0.27
72 3 0.02
73 1 0.01
74 1 0.01
75 1 0.01
76 16 0.12
77 4 0.03
78 8 0.06
79 15 0.12
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (73 bp):
ATATATATATATATAATATATAGTTTTATAAAACATTTTGAAAAATTTATATATAGTTTTTAAAA
CATTTTGA
Found at i:505013 original size:34 final size:33
Alignment explanation
Indices: 504869--505019 Score: 116
Period size: 34 Copynumber: 4.5 Consensus size: 33
504859 ATATATATAT
504869 ATATAATATA-TAGTTTTTAAAACATTTTGAAA
1 ATATAATATATTAGTTTTTAAAACATTTTGAAA
* * *
504901 A-AT-TTAT-TATAGTTTTGAAATCATTTTG-AA
1 ATATAATATAT-TAGTTTTTAAAACATTTTGAAA
* *
504931 ATTTATATATATATAGTTTTAAAAAAAGCATTTTGAAA
1 ATATA-ATATAT-TAGTTTT--TAAAA-CATTTTGAAA
* *
504969 AAATATATATATTATTTTTTAAAACATTTTGAAA
1 ATATA-ATATATTAGTTTTTAAAACATTTTGAAA
*
505003 GCTATAATATA-TAGTTT
1 -ATATAATATATTAGTTT
505020 GAAAACTTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
30 6 0.06
31 20 0.21
32 1 0.01
33 8 0.09
34 24 0.26
35 7 0.07
36 3 0.03
37 13 0.14
38 12 0.13
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (33 bp):
ATATAATATATTAGTTTTTAAAACATTTTGAAA
Found at i:505041 original size:104 final size:105
Alignment explanation
Indices: 504811--505049 Score: 267
Period size: 104 Copynumber: 2.3 Consensus size: 105
504801 TAGTTTTTAT
* *
504811 AAAACATTTTGAAAACTTGTATAATATATAGTTTTTAAAACATTTTGAATATATATATATATAAT
1 AAAACATTTTGAAAA-TTATAT-ATATATAGTTTTAAAAACATTTTGAATATATATATATATAAT
*
504876 ATATAGTTTTTAAAACATTTTGAAAAATTTATTATAGTTTTG
64 ATATAGTTTTTAAAACATTTTGAAAAATTAATTATAGTTTTG
* *
504918 AAATCATTTTGAAATTTATATATATATAGTTTTAAAAAAAGCATTTTGAA-A-A-A-ATATAT-A
1 AAAACATTTTGAAAATTATATATATATAGTTTT--AAAAA-CATTTTGAATATATATATATATAA
* **
504978 TAT-TATTTTTTAAAACATTTTGAAAGCTATAATATATAG-TTTG
63 TATATAGTTTTTAAAACATTTTGAAAAAT-TAAT-TATAGTTTTG
* *
505021 AAAACTTTTTTTAAAATTATATATATATA
1 AAAAC-ATTTTGAAAATTATATATATATA
505050 TATAGTTTTA
Statistics
Matches: 114, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
102 22 0.19
103 15 0.13
104 31 0.27
105 13 0.11
106 6 0.05
107 18 0.16
108 9 0.08
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (105 bp):
AAAACATTTTGAAAATTATATATATATAGTTTTAAAAACATTTTGAATATATATATATATAATAT
ATAGTTTTTAAAACATTTTGAAAAATTAATTATAGTTTTG
Found at i:505081 original size:39 final size:37
Alignment explanation
Indices: 505005--505081 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 37
504995 TTTTGAAAGC
*
505005 TATAATATATAGTTTGAAAACTTTTTTTAAAATTATA
1 TATAATATATAGTTTGAAAACTTTTTTTAAAAATATA
*
505042 TATATATATATAGTTTTAAATTA-TTTTTTTAAAAATATA
1 TATA-ATATATAGTTTGAAA--ACTTTTTTTAAAAATATA
505081 T
1 T
505082 TTTATTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 4 0.11
38 14 0.40
39 16 0.46
40 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (37 bp):
TATAATATATAGTTTGAAAACTTTTTTTAAAAATATA
Found at i:506145 original size:22 final size:21
Alignment explanation
Indices: 506097--506145 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
506087 TTTTCTACTT
506097 TTTTTTACTTTATTTATTTTA
1 TTTTTTACTTTATTTATTTTA
* *
506118 TGTTTTTATTTTATTTTTATTTA
1 T-TTTTTACTTTATTTAT-TTTA
506141 TTTTT
1 TTTTT
506146 CTTCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.75
23 5 0.21
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTTACTTTATTTATTTTA
Found at i:506157 original size:28 final size:27
Alignment explanation
Indices: 506086--506157 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
506076 AATCTACCAT
*
506086 TTTTTCTACTTTTTTTTACTTTATTTA
1 TTTTTCTTCTTTTTTTTACTTTATTTA
* * *
506113 TTTTATGTT-TTTATTTTATTTTTATTTA
1 TTTT-TCTTCTTTTTTTTA-CTTTATTTA
506141 TTTTTCTTCTTTTTTTT
1 TTTTTCTTCTTTTTTTT
506158 TAAAATCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
27 15 0.42
28 21 0.58
ACGTcount: A:0.12, C:0.07, G:0.01, T:0.79
Consensus pattern (27 bp):
TTTTTCTTCTTTTTTTTACTTTATTTA
Found at i:512053 original size:16 final size:16
Alignment explanation
Indices: 512008--512076 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
511998 TGTTTCTATT
*
512008 TTTTTTGTGTTTTTTG
1 TTTTGTGTGTTTTTTG
**
512024 TTTACT-T-TTCTTTTG
1 TTTTGTGTGTT-TTTTG
*
512039 TTTTGTGTGTTTTTTT
1 TTTTGTGTGTTTTTTG
*
512055 TTTTGTTTGCTTTTTT-
1 TTTTGTGTG-TTTTTTG
512071 TTTTGT
1 TTTTGT
512077 TTTGTGTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
14 2 0.05
15 10 0.23
16 23 0.53
17 8 0.19
ACGTcount: A:0.01, C:0.04, G:0.14, T:0.80
Consensus pattern (16 bp):
TTTTGTGTGTTTTTTG
Found at i:512080 original size:17 final size:16
Alignment explanation
Indices: 512034--512078 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
512024 TTTACTTTTC
* * *
512034 TTTTGTTTTGTGTGTT
1 TTTTTTTTTGTTTGCT
512050 TTTTTTTTTGTTTGCT
1 TTTTTTTTTGTTTGCT
512066 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
512079 TGTGTTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTGTTTGCT
Found at i:518590 original size:25 final size:25
Alignment explanation
Indices: 518562--518611 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
518552 TTTAGCACCA
518562 TATCACTACATGTTTATGCTCCAGT
1 TATCACTACATGTTTATGCTCCAGT
* *
518587 TATCACTATATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTCCAGT
518612 ACCCCTGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (25 bp):
TATCACTACATGTTTATGCTCCAGT
Found at i:521102 original size:8 final size:9
Alignment explanation
Indices: 521070--521118 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
521060 AATTTGAATT
521070 TTAAAAACA
1 TTAAAAACA
521079 TTTAACAAACA
1 -TTAA-AAACA
521090 TTAAAAA-A
1 TTAAAAACA
521098 TTAAAAAACA
1 TT-AAAAACA
521108 TTAAAAA-A
1 TTAAAAACA
521116 TTA
1 TTA
521119 CATAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.19
9 13 0.36
10 11 0.31
11 5 0.14
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (9 bp):
TTAAAAACA
Found at i:521106 original size:18 final size:18
Alignment explanation
Indices: 521070--521118 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 18
521060 AATTTGAATT
*
521070 TTAAAAACATTTAACAAACA
1 TTAAAAA-A-TTAAAAAACA
521090 TTAAAAAATTAAAAAACA
1 TTAAAAAATTAAAAAACA
521108 TTAAAAAATTA
1 TTAAAAAATTA
521119 CATAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 20 0.71
19 1 0.04
20 7 0.25
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (18 bp):
TTAAAAAATTAAAAAACA
Found at i:521559 original size:21 final size:21
Alignment explanation
Indices: 521535--521605 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
521525 GGTATCATAA
*
521535 AACCCTGTGGGCTAGGAATAT
1 AACCCTGTGGGCTAGGAATGT
* ** * *
521556 AACCTTACGGGCTGGGTATGT
1 AACCCTGTGGGCTAGGAATGT
*
521577 ACCCCGTGTGGGCTAGGAATGT
1 AACCC-TGTGGGCTAGGAATGT
521599 AACCCTG
1 AACCCTG
521606 CGGTGGTTGC
Statistics
Matches: 36, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
21 20 0.56
22 16 0.44
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.24
Consensus pattern (21 bp):
AACCCTGTGGGCTAGGAATGT
Found at i:521650 original size:42 final size:41
Alignment explanation
Indices: 521600--521686 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 41
521590 TAGGAATGTA
* * *
521600 ACCCTGCGGTGGTTGCATATGAA-TTGTTGGGCTGGGCATAT
1 ACCCTGCGGAGGTGGCATATGAACTAG-TGGGCTGGGCATAT
*
521641 ACCCATGCGGAGGTGGCATCTGAACTAGTGGGCTGGGCATAT
1 ACCC-TGCGGAGGTGGCATATGAACTAGTGGGCTGGGCATAT
521683 ACCC
1 ACCC
521687 CTTTGGGCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.25
Consensus pattern (41 bp):
ACCCTGCGGAGGTGGCATATGAACTAGTGGGCTGGGCATAT
Found at i:522980 original size:59 final size:59
Alignment explanation
Indices: 522882--523526 Score: 1001
Period size: 59 Copynumber: 11.0 Consensus size: 59
522872 TTCCATACGT
* ** *
522882 AAATTCATACACTTAATATGATTTCCTT-CTCATTTTAGCACACTTAGTGCTCTATCTAG
1 AAATTCATACATTTAATATGATTTCCTTAC-CATTTTAGCACACAAAGTGCTCTATCTGG
* * * * * * *
522941 AAA-TCTATACACTTACTATGATTTCCTTATCATTTTAGCACCCGAAGTGCCCTGTCTGG
1 AAATTC-ATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
523000 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
1 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
* *
523059 AAATTCTTACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATTTGG
1 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
*
523118 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACAC-AAGTGCTCTATCTGA
1 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
* *
523176 AAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACACAAAGTGCTCTATCTGG
1 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
*
523235 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATTTGG
1 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
* *
523294 AAATTCATACATTTGATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTAG
1 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
* * *
523353 AAATTTATACACTTAATATGATTTCCTTATCATTTTAGCACACAAAGTGCTCTATCTGG
1 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
* * *
523412 AAATTCATACATTTAATATGATTTCTTTACTATTTTAACACACAAAGTGCTCTATCTGG
1 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
* *
523471 AAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACAC-AAGTGCTCTATCT
1 AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCT
523527 AGTAATCACC
Statistics
Matches: 537, Mismatches: 45, Indels: 9
0.91 0.08 0.02
Matches are distributed among these distances:
58 69 0.13
59 466 0.87
60 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (59 bp):
AAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGG
Found at i:523415 original size:294 final size:294
Alignment explanation
Indices: 522882--523533 Score: 1058
Period size: 294 Copynumber: 2.2 Consensus size: 294
522872 TTCCATACGT
* *
522882 AAATTCATACACTTAATATGATTTCCTTCTCATTTTAGCACACTTAGTGCTCTATCTAGAAATCT
1 AAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACAC-AAGTGCTCTATCTAGAAATCT
* * * * *
522947 ATACACTTACTATGATTTCCTTATCATTTTAGCACCCGAAGTGCCCTGTCTGGAAATTCATACAT
65 ATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACAT
* *
523012 TTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGGAAATTCTTACATTTAATA
130 TTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTAGAAATTCTTACACTTAATA
*
523077 TGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATTTGGAAATTCATACATTTAATATGATTT
195 TGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGGAAATTCATACATTTAATATGATTT
*
523142 CCTTACCATTTTAGCACAC-AAGTGCTCTATCTGA
260 CCTTACCATTTTAACACACAAAGTGCTCTATCTGA
*
523176 AAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACACAAAGTGCTCTATCTGGAAAT-T
1 AAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACAC-AAGTGCTCTATCTAGAAATCT
* * *
523240 CATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATTTGGAAATTCATACA
65 -ATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACA
*
523305 TTTGATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTAGAAATT-TATACACTTAA
129 TTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTAGAAATTCT-TACACTTAA
*
523369 TATGATTTCCTTATCATTTTAGCACACAAAGTGCTCTATCTGGAAATTCATACATTTAATATGAT
193 TATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGGAAATTCATACATTTAATATGAT
* * *
523434 TTCTTTACTATTTTAACACACAAAGTGCTCTATCTGG
258 TTCCTTACCATTTTAACACACAAAGTGCTCTATCTGA
*
523471 AAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACACAAGTGCTCTATCTAGTAATC
1 AAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACACAAGTGCTCTATCTAGAAATC
523534 ACCATACATA
Statistics
Matches: 331, Mismatches: 23, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
293 2 0.01
294 272 0.82
295 57 0.17
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.38
Consensus pattern (294 bp):
AAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACACAAGTGCTCTATCTAGAAATCTA
TACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACATT
TAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTAGAAATTCTTACACTTAATAT
GATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGGAAATTCATACATTTAATATGATTTC
CTTACCATTTTAACACACAAAGTGCTCTATCTGA
Found at i:523920 original size:19 final size:19
Alignment explanation
Indices: 523883--523930 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
523873 TTCTATACTA
* **
523883 TGGTACCGATACCCCTTTT
1 TGGTATCGATACCAATTTT
523902 TGGTATCGATACCAATTTT
1 TGGTATCGATACCAATTTT
*
523921 AGGT-TCGATA
1 TGGTATCGATA
523931 TTGTCTGGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (19 bp):
TGGTATCGATACCAATTTT
Found at i:523973 original size:17 final size:19
Alignment explanation
Indices: 523936--524008 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 19
523926 CGATATTGTC
523936 TGGTATCGATACCTTTACCA
1 TGGTATCGATACC-TTACCA
* *
523956 TGGTATCGATACTACCATACTA
1 TGGTATCG--A-TACCTTACCA
523978 TGGTATCGATACCCCTTACCA
1 TGGTATCGATA--CCTTACCA
523999 --GTATCGATAC
1 TGGTATCGATAC
524009 TACCATACCG
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
17 1 0.02
19 11 0.25
20 9 0.20
21 6 0.14
22 13 0.30
23 4 0.09
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (19 bp):
TGGTATCGATACCTTACCA
Found at i:523983 original size:22 final size:22
Alignment explanation
Indices: 523951--524017 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
523941 TCGATACCTT
523951 TACCATGGTATCGATACTACCA
1 TACCATGGTATCGATACTACCA
* * *
523973 TACTATGGTATCGATAC-CCCT
1 TACCATGGTATCGATACTACCA
523994 TACCA--GTATCGATACTACCA
1 TACCATGGTATCGATACTACCA
524014 TACC
1 TACC
524018 GATACCCTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 10 0.26
20 6 0.16
21 6 0.16
22 16 0.42
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (22 bp):
TACCATGGTATCGATACTACCA
Done.