Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 84 of 132
Found at i:24998075 original size:17 final size:17
Alignment explanation
Indices: 24998053--24998119 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
24998043 AGTAACACTA
24998053 AAATGCAATGACAATGG
1 AAATGCAATGACAATGG
*
24998070 AAATGCAATGACAATGA
1 AAATGCAATGACAATGG
*
24998087 AAATGTAATGACAAT-G
1 AAATGCAATGACAATGG
*
24998103 AGAATGCGATGACAATG
1 A-AATGCAATGACAATG
24998120 CATACTAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
16 1 0.02
17 42 0.98
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.19
Consensus pattern (17 bp):
AAATGCAATGACAATGG
Found at i:24998084 original size:6 final size:6
Alignment explanation
Indices: 24998054--24998119 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
24998044 GTAACACTAA
* *
24998054 AATG-C AATGAC AATGGA- AATG-C AATGAC AATGAA AATG-T AATGAC
1 AATGAC AATGAC AAT-GAC AATGAC AATGAC AATGAC AATGAC AATGAC
* *
24998099 AATGAG AATG-C GATGAC AATG
1 AATGAC AATGAC AATGAC AATG
24998120 CATACTAACA
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
5 16 0.33
6 30 0.62
7 2 0.04
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.20
Consensus pattern (6 bp):
AATGAC
Found at i:24998097 original size:34 final size:34
Alignment explanation
Indices: 24998052--24998119 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
24998042 CAGTAACACT
24998052 AAAATGCAATGACAATG-GAAATGCAATGACAATG
1 AAAATGCAATGACAATGAG-AATGCAATGACAATG
* *
24998086 AAAATGTAATGACAATGAGAATGCGATGACAATG
1 AAAATGCAATGACAATGAGAATGCAATGACAATG
24998120 CATACTAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 30 0.97
35 1 0.03
ACGTcount: A:0.49, C:0.10, G:0.22, T:0.19
Consensus pattern (34 bp):
AAAATGCAATGACAATGAGAATGCAATGACAATG
Found at i:24999281 original size:21 final size:21
Alignment explanation
Indices: 24999257--24999303 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
24999247 TGCAGATTAT
24999257 TGTGGCTACATCCGATTTTGA
1 TGTGGCTACATCCGATTTTGA
* * * *
24999278 TGTGGCTGCATCTGGTTTTGT
1 TGTGGCTACATCCGATTTTGA
24999299 TGTGG
1 TGTGG
24999304 ATGCATCTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.15, G:0.32, T:0.43
Consensus pattern (21 bp):
TGTGGCTACATCCGATTTTGA
Found at i:24999308 original size:21 final size:21
Alignment explanation
Indices: 24999272--24999312 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
24999262 CTACATCCGA
*
24999272 TTTTGATGTGGCTGCATCTGG
1 TTTTGATGTGGATGCATCTGG
*
24999293 TTTTGTTGTGGATGCATCTG
1 TTTTGATGTGGATGCATCTG
24999313 AGTCTGCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.12, G:0.32, T:0.46
Consensus pattern (21 bp):
TTTTGATGTGGATGCATCTGG
Found at i:25001826 original size:26 final size:26
Alignment explanation
Indices: 25001726--25001832 Score: 92
Period size: 26 Copynumber: 4.1 Consensus size: 26
25001716 AATTCTGGGC
* *
25001726 ACAATTCTAGACATGCTCATACAGTG
1 ACAATTCTAGACATGCTCATGCAGCG
* * * *
25001752 ACAACTGTGGACATGTTCATGCAGCG
1 ACAATTCTAGACATGCTCATGCAGCG
* * *
25001778 ATAATTCT-GAACAAGTTTC-TGCAGCG
1 ACAATTCTAG-ACATG-CTCATGCAGCG
*
25001804 ACAATTCTAGATATGCTCATGCAGCG
1 ACAATTCTAGACATGCTCATGCAGCG
25001830 ACA
1 ACA
25001833 TTAGTAGTAA
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
25 3 0.05
26 56 0.89
27 4 0.06
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (26 bp):
ACAATTCTAGACATGCTCATGCAGCG
Found at i:25005096 original size:10 final size:11
Alignment explanation
Indices: 25005067--25005101 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
25005057 TATGTGATAG
25005067 AGTGTTTTTGA
1 AGTGTTTTTGA
25005078 AGTGTTTTTGA
1 AGTGTTTTTGA
25005089 AGTGTTTTT-A
1 AGTGTTTTTGA
25005099 AGT
1 AGT
25005102 TGCCCAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (11 bp):
AGTGTTTTTGA
Found at i:25005711 original size:3 final size:3
Alignment explanation
Indices: 25005703--25006136 Score: 499
Period size: 3 Copynumber: 144.7 Consensus size: 3
25005693 ATTCTAAACC
*
25005703 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* **
25005751 ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ACC ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** ** **
25005799 ACC ATA ATA ATA ACC ATA ATA ATA ATA ATA ATA ATA ACC ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* **
25005847 ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA ACC ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** **
25005895 ATA ATA ATA ATA ACC ATA ATA ATA ATA ATA ATA ATA ATA ACC ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** ** **
25005943 ATA ATA ATA ACC ATA ACC ATA ATA ATA ATA ATA ATA ATA ATA ATA ACC
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** ** **
25005991 ATA ACC ATA ATA ATA ATA ATA ACC ATA ATA ATA ATA ACC ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
25006039 ATA ATA ATA ATA ATT AGA ATA ATA ACA ACA ACA ACA ACA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** * *
25006087 ATA ATA ATA ACC ATA ATA ATA ATA ATA ATT GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25006135 AT
1 AT
25006137 TTTAATTTGT
Statistics
Matches: 359, Mismatches: 72, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 359 1.00
ACGTcount: A:0.62, C:0.08, G:0.01, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:25012537 original size:13 final size:14
Alignment explanation
Indices: 25012511--25012538 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25012501 CTTTTTAGTC
25012511 AAAAAAGTATTTTT
1 AAAAAAGTATTTTT
25012525 AAAAAAGTATTTTT
1 AAAAAAGTATTTTT
25012539 TTCAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
AAAAAAGTATTTTT
Found at i:25012538 original size:15 final size:15
Alignment explanation
Indices: 25012511--25012553 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
25012501 CTTTTTAGTC
25012511 AAAAAAGTA-TTTTT
1 AAAAAAGTATTTTTT
25012525 AAAAAAGTATTTTTT
1 AAAAAAGTATTTTTT
**
25012540 TCAAAA-TATTTTTT
1 AAAAAAGTATTTTTT
25012554 TTGTGCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (15 bp):
AAAAAAGTATTTTTT
Found at i:25016585 original size:35 final size:34
Alignment explanation
Indices: 25016491--25016607 Score: 162
Period size: 34 Copynumber: 3.4 Consensus size: 34
25016481 CAAATAATAA
***
25016491 ATCAGAATGTCATATTACCAAAAACATATATCAG
1 ATCAGAATGTCATATTTTTAAAAACATATATCAG
* *
25016525 ATCAAAATGTCATATTTTTAAAAACACATATCAG
1 ATCAGAATGTCATATTTTTAAAAACATATATCAG
*
25016559 ATCAGAATGCCATATTTTTTAAAAACATATATCAG
1 ATCAGAATGTCATA-TTTTTAAAAACATATATCAG
*
25016594 ATTAGAATGTCATA
1 ATCAGAATGTCATA
25016608 CCAGATTAGA
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
34 41 0.57
35 31 0.43
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.32
Consensus pattern (34 bp):
ATCAGAATGTCATATTTTTAAAAACATATATCAG
Found at i:25022131 original size:29 final size:29
Alignment explanation
Indices: 25022098--25022158 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
25022088 AATAAGTAAG
* *
25022098 AAATATACATATATAATTAGTATATGTAT
1 AAATATACATATAAAATTAGTATATATAT
* * *
25022127 AAATATAGATATAAAATTTGTTTATATAT
1 AAATATACATATAAAATTAGTATATATAT
25022156 AAA
1 AAA
25022159 AAATTATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (29 bp):
AAATATACATATAAAATTAGTATATATAT
Found at i:25022286 original size:17 final size:17
Alignment explanation
Indices: 25022261--25022317 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
25022251 GTATAAAACC
*
25022261 ATATATATAAAAAATAT
1 ATATGTATAAAAAATAT
* *
25022278 ATATGTATAAAATATAC
1 ATATGTATAAAAAATAT
25022295 A-ATGTA-AAAAAGATAT
1 ATATGTATAAAAA-ATAT
*
25022311 GTATGTA
1 ATATGTA
25022318 AAAGTACCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 20 0.62
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (17 bp):
ATATGTATAAAAAATAT
Found at i:25028130 original size:38 final size:38
Alignment explanation
Indices: 25028082--25028159 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
25028072 ATGAGAATGT
25028082 ACCTCCAAAAGGCAAATGATCAACAAATAAACACTCTC
1 ACCTCCAAAAGGCAAATGATCAACAAATAAACACTCTC
* *
25028120 ACCTTCAAAAGGCAAATGATCAACAAATAAGCACTCTC
1 ACCTCCAAAAGGCAAATGATCAACAAATAAACACTCTC
25028158 AC
1 AC
25028160 ACAAAATTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.46, C:0.28, G:0.09, T:0.17
Consensus pattern (38 bp):
ACCTCCAAAAGGCAAATGATCAACAAATAAACACTCTC
Found at i:25042753 original size:24 final size:23
Alignment explanation
Indices: 25042724--25042772 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
25042714 GTCACCTTCT
* *
25042724 TCTTTGTGCTTCTTCTTCTTTTTA
1 TCTTTGCGCCTCTTCTT-TTTTTA
25042748 TCTTTGCGCCTCTTCTTTTTTTA
1 TCTTTGCGCCTCTTCTTTTTTTA
25042771 TC
1 TC
25042773 CGTCGAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.04, C:0.24, G:0.08, T:0.63
Consensus pattern (23 bp):
TCTTTGCGCCTCTTCTTTTTTTA
Found at i:25079918 original size:17 final size:18
Alignment explanation
Indices: 25079881--25079918 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25079871 GATTTTTCTT
* *
25079881 TTCCCTTTTCTTTCAATC
1 TTCCCTTTTCGTTCAACC
25079899 TTCCCTTTT-GTTCAACC
1 TTCCCTTTTCGTTCAACC
25079916 TTC
1 TTC
25079919 AAGCTTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.34, G:0.03, T:0.53
Consensus pattern (18 bp):
TTCCCTTTTCGTTCAACC
Found at i:25080442 original size:14 final size:15
Alignment explanation
Indices: 25080411--25080445 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
25080401 TTAAAAACCT
*
25080411 AACCAAACCCATTTG
1 AACCAAACCCAATTG
25080426 AACCAAA-CCAATTG
1 AACCAAACCCAATTG
25080440 AACCAA
1 AACCAA
25080446 GTCCAACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.49, C:0.31, G:0.06, T:0.14
Consensus pattern (15 bp):
AACCAAACCCAATTG
Found at i:25080506 original size:13 final size:14
Alignment explanation
Indices: 25080488--25080558 Score: 76
Period size: 13 Copynumber: 5.3 Consensus size: 14
25080478 GCCGTTGATC
*
25080488 GACTGTTGA-CTTT
1 GACTGTTGACCGTT
25080501 GACTGTTGACCGTT
1 GACTGTTGACCGTT
*
25080515 AACT-TTGACCGTT
1 GACTGTTGACCGTT
*
25080528 GACTGTTGA-CTTT
1 GACTGTTGACCGTT
* *
25080541 GACCGTTGATCGTT
1 GACTGTTGACCGTT
25080555 GACT
1 GACT
25080559 TTTTTTGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
13 32 0.67
14 16 0.33
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (14 bp):
GACTGTTGACCGTT
Found at i:25080509 original size:7 final size:7
Alignment explanation
Indices: 25080488--25080558 Score: 69
Period size: 7 Copynumber: 10.6 Consensus size: 7
25080478 GCCGTTGATC
25080488 GACTGTT
1 GACTGTT
25080495 GACT-TT
1 GACTGTT
25080501 GACTGTT
1 GACTGTT
*
25080508 GACCGTT
1 GACTGTT
*
25080515 AACT-TT
1 GACTGTT
*
25080521 GACCGTT
1 GACTGTT
25080528 GACTGTT
1 GACTGTT
25080535 GACT-TT
1 GACTGTT
*
25080541 GACCGTT
1 GACTGTT
25080548 GA-TCGTT
1 GACT-GTT
25080555 GACT
1 GACT
25080559 TTTTTTGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
6 15 0.29
7 35 0.69
8 1 0.02
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (7 bp):
GACTGTT
Found at i:25080521 original size:20 final size:20
Alignment explanation
Indices: 25080492--25080560 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
25080482 TTGATCGACT
*
25080492 GTTGACTTTGACTGTTGACC
1 GTTGACTTTGACCGTTGACC
* *
25080512 GTTAACTTTGACCGTTGACT
1 GTTGACTTTGACCGTTGACC
*
25080532 GTTGACTTTGACCGTTGATC
1 GTTGACTTTGACCGTTGACC
25080552 GTTGACTTT
1 GTTGACTTT
25080561 TTTTGAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GTTGACTTTGACCGTTGACC
Found at i:25081628 original size:3 final size:3
Alignment explanation
Indices: 25081620--25081664 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
25081610 AACATTATGG
* *
25081620 TTA TTA TTA TTTA TTA ATA TTA TTA TTA CTA TTA TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
25081665 TTGGAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:25089611 original size:12 final size:12
Alignment explanation
Indices: 25089594--25089624 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
25089584 GAAAAACAAG
25089594 AGGATGAAGAGA
1 AGGATGAAGAGA
*
25089606 AGGATGAAGTGA
1 AGGATGAAGAGA
25089618 AGGATGA
1 AGGATGA
25089625 CGAACACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (12 bp):
AGGATGAAGAGA
Found at i:25090083 original size:17 final size:17
Alignment explanation
Indices: 25090057--25090095 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
25090047 TTAGCATTCT
25090057 TGCA-TTTTATTGTGC-C
1 TGCATTTTTATTGT-CAC
25090073 TGCATTTTTATTGTCAC
1 TGCATTTTTATTGTCAC
25090090 TGCATT
1 TGCATT
25090096 CATTTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.51
Consensus pattern (17 bp):
TGCATTTTTATTGTCAC
Found at i:25090706 original size:20 final size:20
Alignment explanation
Indices: 25090674--25090713 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25090664 TCACTTGAAT
25090674 GAAAAAAATGAAAAAAAGAA
1 GAAAAAAATGAAAAAAAGAA
*
25090694 GAAAGAAAA-GAAAAAGAGAA
1 GAAA-AAAATGAAAAAAAGAA
25090714 TAAATTGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (20 bp):
GAAAAAAATGAAAAAAAGAA
Found at i:25092240 original size:13 final size:14
Alignment explanation
Indices: 25092212--25092240 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25092202 TTTCAATACA
25092212 CTGATATTTAACTT
1 CTGATATTTAACTT
25092226 CTGATATTT-ACTT
1 CTGATATTTAACTT
25092239 CT
1 CT
25092241 AATTGCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (14 bp):
CTGATATTTAACTT
Found at i:25095465 original size:21 final size:21
Alignment explanation
Indices: 25095439--25095482 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
25095429 CTCAGAACGA
25095439 TTATCAATATCCAATCTCTCG
1 TTATCAATATCCAATCTCTCG
25095460 TTATCAATATCCAATCTCTCG
1 TTATCAATATCCAATCTCTCG
25095481 TT
1 TT
25095483 CTGCACAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.41
Consensus pattern (21 bp):
TTATCAATATCCAATCTCTCG
Found at i:25095926 original size:18 final size:18
Alignment explanation
Indices: 25095895--25095929 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25095885 AAGTTCTCAA
**
25095895 CAGATGCAGTCACAATAC
1 CAGATGCACCCACAATAC
25095913 CAGATGCACCCACAATA
1 CAGATGCACCCACAATA
25095930 TTCATTGTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.31, G:0.14, T:0.14
Consensus pattern (18 bp):
CAGATGCACCCACAATAC
Found at i:25101488 original size:63 final size:64
Alignment explanation
Indices: 25101402--25101532 Score: 230
Period size: 63 Copynumber: 2.1 Consensus size: 64
25101392 GTGCTCAGGG
* *
25101402 ATGG-TGAGGAGATATTAGAGAATAAAGGCCCGATCAATGACATCTCCATTGAACGGATGACTC
1 ATGGCTGAGGAGATATTAGAGAATAAAGGCCCGATCAATGACATCTCCATTAAACAGATGACTC
25101465 ATGGCTGA-GAGATATTAGAGAATAAAGGCCCGATCAATGACATCTCCATTAAACAGATGACTC
1 ATGGCTGAGGAGATATTAGAGAATAAAGGCCCGATCAATGACATCTCCATTAAACAGATGACTC
25101528 ATGGC
1 ATGGC
25101533 CAGGAGACAC
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 62 0.95
64 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (64 bp):
ATGGCTGAGGAGATATTAGAGAATAAAGGCCCGATCAATGACATCTCCATTAAACAGATGACTC
Found at i:25102516 original size:25 final size:24
Alignment explanation
Indices: 25102467--25102516 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
25102457 TTGGTACGAC
* * *
25102467 GGATAAAAAGAGGAAAAGGCGCAA
1 GGATAAAAAGAAGAAAAAGCCCAA
25102491 GGATAAAAAGAAGAAAAAGCACCAA
1 GGATAAAAAGAAGAAAAAGC-CCAA
25102516 G
1 G
25102517 ACGAGGGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.58, C:0.10, G:0.28, T:0.04
Consensus pattern (24 bp):
GGATAAAAAGAAGAAAAAGCCCAA
Found at i:25123585 original size:79 final size:79
Alignment explanation
Indices: 25123453--25123816 Score: 514
Period size: 79 Copynumber: 4.6 Consensus size: 79
25123443 TGTTTAATTG
** * * * *
25123453 ACTAGAGCTGGGCTCACATTTGTTGTTTATCCGCTAGGCATTGGGTGCCAGGATTTGATGGACAT
1 ACTAGAGCTGGGCTCACATTTGCAGTTTATCCGCTAGGCACTAGGTGCTAGGATTTGACGGACAT
*
25123518 TGTTGGTTAATCCA
66 CGTTGGTTAATCCA
* * * * * * * *
25123532 ACTAGAGTTGGGCTCACATTTACGGTTTATCCACTAGGCACTGGGTACTAGGATTTGATGAACAT
1 ACTAGAGCTGGGCTCACATTTGCAGTTTATCCGCTAGGCACTAGGTGCTAGGATTTGACGGACAT
*
25123597 CATTGGTTAATCCA
66 CGTTGGTTAATCCA
***
25123611 ACTAGAGCTGGGCTCACATTTATGGTTTATCCGCTAGGCACTAGGTGCTAGGATTTGACGGACAT
1 ACTAGAGCTGGGCTCACATTTGCAGTTTATCCGCTAGGCACTAGGTGCTAGGATTTGACGGACAT
25123676 CGTTGGTTAATCCA
66 CGTTGGTTAATCCA
* *
25123690 ACTAGAGCTGGGCTCACATTTGCAGTTTATCCGCTAAGCACTAGGTGGC-AAGATTTGACGGACA
1 ACTAGAGCTGGGCTCACATTTGCAGTTTATCCGCTAGGCACTAGGT-GCTAGGATTTGACGGACA
*
25123754 TTGTTGGTTAATCCA
65 TCGTTGGTTAATCCA
25123769 ACTAGAGCTGGGCTCACATTTGCAGTTTATCCGCTAGGCACTAGGTGC
1 ACTAGAGCTGGGCTCACATTTGCAGTTTATCCGCTAGGCACTAGGTGC
25123817 CATACTGTCG
Statistics
Matches: 258, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
78 2 0.01
79 254 0.98
80 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (79 bp):
ACTAGAGCTGGGCTCACATTTGCAGTTTATCCGCTAGGCACTAGGTGCTAGGATTTGACGGACAT
CGTTGGTTAATCCA
Found at i:25128809 original size:79 final size:79
Alignment explanation
Indices: 25128693--25128890 Score: 272
Period size: 79 Copynumber: 2.5 Consensus size: 79
25128683 AGTTTAACTG
* * * * *
25128693 ACTAGAGCTGGGCTCAAATTTGCGGTTTATCCGCTAGGCACTGGGT-CCTAGGATTTGACGGACA
1 ACTAAAGCTGGGCTCACATTTGCGGTTTATCAGCTAGGCACTAGGTGCC-AGGATTTGACGAACA
*
25128757 TTGTTGGTTAATCCA
65 TCGTTGGTTAATCCA
* * * *
25128772 ACTAAAGTTGGGCTCACATTTACGGTTTATCTGCTAGGCACTAGGTGGCAGGATTTGACGAACAT
1 ACTAAAGCTGGGCTCACATTTGCGGTTTATCAGCTAGGCACTAGGTGCCAGGATTTGACGAACAT
25128837 CGTTGGTTAATCCA
66 CGTTGGTTAATCCA
* *
25128851 ACTAGAGCTGGGCTCACATTTGTGGTTTATCAGCTAGGCA
1 ACTAAAGCTGGGCTCACATTTGCGGTTTATCAGCTAGGCA
25128891 TTGGATGCCA
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
79 103 0.99
80 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (79 bp):
ACTAAAGCTGGGCTCACATTTGCGGTTTATCAGCTAGGCACTAGGTGCCAGGATTTGACGAACAT
CGTTGGTTAATCCA
Found at i:25130930 original size:16 final size:16
Alignment explanation
Indices: 25130909--25130942 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
25130899 AACTCCATTC
25130909 TTTAAAAGTTTATTTA
1 TTTAAAAGTTTATTTA
*
25130925 TTTAAATGTTTATTTA
1 TTTAAAAGTTTATTTA
25130941 TT
1 TT
25130943 ATTGCTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTAAAAGTTTATTTA
Found at i:25146326 original size:79 final size:79
Alignment explanation
Indices: 25146235--25146600 Score: 491
Period size: 79 Copynumber: 4.6 Consensus size: 79
25146225 AGTTTAATTG
* * * *
25146235 ACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTAGGAAATGGGTGCCAGGATTTGACAGACAT
1 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACGGACAT
25146300 CGTTGGTTAATCCA
66 CGTTGGTTAATCCA
* * *
25146314 ACTAGAGCTGGGCTCATATTTGTGGTTTA-CCAGCTAGGCACTGGGTGCCAGGATTTGACGAACA
1 ACTAGAGCTGGGCTCACATTTGCGGTTTATCC-GCTAGGCACTGGGTGCCAGGATTTGACGGACA
* *
25146378 TCTTTGGTTAATCTA
65 TCGTTGGTTAATCCA
* ** * * * *
25146393 GCTAGAGCTGGGCTCACATTTGCGGTTTATCTACTAGGCACTTGGCGCTAGGATTTGATGGACAT
1 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACGGACAT
25146458 CGTTGGTTAATCCA
66 CGTTGGTTAATCCA
* * * * * *
25146472 ACTAGAGCTGGGCTAACATTTGCGGTGTATCCACTAGGCACTAGGTGCTAGGATTTGGCGGACAT
1 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACGGACAT
** *
25146537 TATTGGTTAATCAA
66 CGTTGGTTAATCCA
25146551 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGCCA
1 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGCCA
25146601 TATTGTTGGT
Statistics
Matches: 248, Mismatches: 37, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
78 2 0.01
79 245 0.99
80 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (79 bp):
ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACGGACAT
CGTTGGTTAATCCA
Found at i:25155087 original size:17 final size:17
Alignment explanation
Indices: 25155073--25155111 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
25155063 TAATTGTCCT
25155073 TGCATTTTTATTGTCAC
1 TGCATTTTTATTGTCAC
* *
25155090 TGCATTTTTATTATCGC
1 TGCATTTTTATTGTCAC
25155107 TGCAT
1 TGCAT
25155112 CTACATTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (17 bp):
TGCATTTTTATTGTCAC
Found at i:25162857 original size:27 final size:26
Alignment explanation
Indices: 25162827--25162879 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
25162817 ATTAAAACCC
25162827 AAATTATTAATGAAAT-ATTTTATATTT
1 AAATTATTAA--AAATAATTTTATATTT
*
25162854 AAATTATTAAATATAATTTTATATTT
1 AAATTATTAAAAATAATTTTATATTT
25162880 TATTATTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 11 0.46
27 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AAATTATTAAAAATAATTTTATATTT
Found at i:25164764 original size:16 final size:17
Alignment explanation
Indices: 25164733--25164765 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25164723 CATTTTTATT
*
25164733 ACTTGCACATAAATAAA
1 ACTTGCACAGAAATAAA
25164750 ACTTG-ACAGAAATAAA
1 ACTTGCACAGAAATAAA
25164766 CTGATTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (17 bp):
ACTTGCACAGAAATAAA
Found at i:25168009 original size:12 final size:11
Alignment explanation
Indices: 25167982--25168015 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
25167972 AATTAGTTAG
*
25167982 TAAATAAAGAA
1 TAAATAAATAA
25167993 TAAATAAATAGA
1 TAAATAAATA-A
25168005 TAAATAAATAA
1 TAAATAAATAA
25168016 AATAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:25169718 original size:27 final size:26
Alignment explanation
Indices: 25169688--25169740 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
25169678 ATTAAAACCC
25169688 AAATTATTAATGAAAT-ATTTTATATTT
1 AAATTATTAA--AAATAATTTTATATTT
*
25169715 AAATTATTAAATATAATTTTATATTT
1 AAATTATTAAAAATAATTTTATATTT
25169741 TATTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 11 0.46
27 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AAATTATTAAAAATAATTTTATATTT
Found at i:25181732 original size:18 final size:18
Alignment explanation
Indices: 25181691--25181735 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
25181681 CATCACGATC
*
25181691 AGATGCAGTCACATACTT
1 AGATGCAGCCACATACTT
*
25181709 AGATGCAGCCACATGCTT
1 AGATGCAGCCACATACTT
25181727 -GTATGCAGC
1 AG-ATGCAGC
25181736 AACAACAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (18 bp):
AGATGCAGCCACATACTT
Found at i:25187924 original size:20 final size:22
Alignment explanation
Indices: 25187884--25187924 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
25187874 TAAGAAGAAA
25187884 AAGAAGATGAAAGAGAAGAAGAG
1 AAGAAGATGAAAGAG-AGAAGAG
25187907 AAGAAGA-GAAAGAG-GAAG
1 AAGAAGATGAAAGAGAGAAG
25187925 TTCCTATCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (22 bp):
AAGAAGATGAAAGAGAGAAGAG
Found at i:25217299 original size:20 final size:20
Alignment explanation
Indices: 25217274--25217313 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25217264 CGCCCACAGT
25217274 AAAGGAAGCAAAAGCAAAAA
1 AAAGGAAGCAAAAGCAAAAA
* *
25217294 AAAGGAGGGAAAAGCAAAAA
1 AAAGGAAGCAAAAGCAAAAA
25217314 TAGAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.07, G:0.25, T:0.00
Consensus pattern (20 bp):
AAAGGAAGCAAAAGCAAAAA
Found at i:25218259 original size:17 final size:17
Alignment explanation
Indices: 25218218--25218279 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
25218208 CATCGTATTC
25218218 CCATTGTCATTACATTT
1 CCATTGTCATTACATTT
** * *
25218235 TAAATGTCATTGCATTT
1 CCATTGTCATTACATTT
* *
25218252 GCATTGTCATTTCATTT
1 CCATTGTCATTACATTT
25218269 CCATTTGTCAT
1 CCA-TTGTCAT
25218280 GATATTTTAG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 28 0.80
18 7 0.20
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (17 bp):
CCATTGTCATTACATTT
Found at i:25218860 original size:14 final size:14
Alignment explanation
Indices: 25218841--25218874 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
25218831 TCAGTCACAT
*
25218841 AAAAAAAGAGAAGA
1 AAAAAAAGAAAAGA
25218855 AAAAAAAGAAAAGA
1 AAAAAAAGAAAAGA
25218869 AAAAAA
1 AAAAAA
25218875 TAAATGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAGA
Found at i:25219347 original size:26 final size:26
Alignment explanation
Indices: 25219318--25219393 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
25219308 TACTAATTTG
25219318 CTGCATGAGCATGTCAAGAATTGTCA
1 CTGCATGAGCATGTCAAGAATTGTCA
* * **
25219344 CTGCATGAGCATGTCTAGAATTATTG
1 CTGCATGAGCATGTCAAGAATTGTCA
* *
25219370 TTGCATGAGCATGTCAAAAATTGT
1 CTGCATGAGCATGTCAAGAATTGT
25219394 GCCCAGATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (26 bp):
CTGCATGAGCATGTCAAGAATTGTCA
Found at i:25220197 original size:22 final size:22
Alignment explanation
Indices: 25220169--25220211 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
25220159 TTCTGCTAAT
25220169 TATTCACGTTCGGAACCCCATC
1 TATTCACGTTCGGAACCCCATC
* *
25220191 TATTCACGTTGGGGACCCCAT
1 TATTCACGTTCGGAACCCCAT
25220212 TTAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.28
Consensus pattern (22 bp):
TATTCACGTTCGGAACCCCATC
Found at i:25236244 original size:25 final size:25
Alignment explanation
Indices: 25236207--25236376 Score: 180
Period size: 25 Copynumber: 6.8 Consensus size: 25
25236197 ATCATTGTCT
* * *
25236207 CAAAACCTGATAGGTAACACCGGCA
1 CAAAGCCTGATAGATAACACCGACA
*
25236232 CAAAGCCTAATAGATAACACCGACA
1 CAAAGCCTGATAGATAACACCGACA
* * ** *
25236257 AAAAGCCTAATAGATAACAATGATA
1 CAAAGCCTGATAGATAACACCGACA
*
25236282 AAAAGCCTGATAGATAACACC-AGCA
1 CAAAGCCTGATAGATAACACCGA-CA
*
25236307 CAAAGCTTGATAGATAACACCGACA
1 CAAAGCCTGATAGATAACACCGACA
* * *
25236332 AAAAGTCTGATAGATAACATCGACA
1 CAAAGCCTGATAGATAACACCGACA
* *
25236357 AAAAGCTTGATAGATAACAC
1 CAAAGCCTGATAGATAACAC
25236377 TGTTGCAAAG
Statistics
Matches: 122, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
24 1 0.01
25 120 0.98
26 1 0.01
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.16
Consensus pattern (25 bp):
CAAAGCCTGATAGATAACACCGACA
Found at i:25236386 original size:75 final size:75
Alignment explanation
Indices: 25236208--25236376 Score: 243
Period size: 75 Copynumber: 2.3 Consensus size: 75
25236198 TCATTGTCTC
* *
25236208 AAAA-CCTGATAGGTAACACCGGCACAAAGCCTAATAGATAACACCGACAAAAAGCCTAATAGAT
1 AAAAGCCTGATAGATAACACCAGCACAAAGCCTAATAGATAACACCGACAAAAAGCCTAATAGAT
*
25236272 AACAATGATA
66 AACAATGACA
* * * *
25236282 AAAAGCCTGATAGATAACACCAGCACAAAGCTTGATAGATAACACCGACAAAAAGTCTGATAGAT
1 AAAAGCCTGATAGATAACACCAGCACAAAGCCTAATAGATAACACCGACAAAAAGCCTAATAGAT
25236347 AAC-ATCGACA
66 AACAAT-GACA
*
25236357 AAAAGCTTGATAGATAACAC
1 AAAAGCCTGATAGATAACAC
25236377 TGTTGCAAAG
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
74 6 0.07
75 79 0.93
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.16
Consensus pattern (75 bp):
AAAAGCCTGATAGATAACACCAGCACAAAGCCTAATAGATAACACCGACAAAAAGCCTAATAGAT
AACAATGACA
Found at i:25242331 original size:25 final size:25
Alignment explanation
Indices: 25242297--25242558 Score: 235
Period size: 25 Copynumber: 10.5 Consensus size: 25
25242287 ATCATCGTCT
* *
25242297 CAAAACCTGATAGGTAACACCAGCA
1 CAAAGCCTGATAGATAACACCAGCA
25242322 CAAAGCCTGATAGATAACACC-GACA
1 CAAAGCCTGATAGATAACACCAG-CA
* * * * *
25242347 CAAAACTTGAAAGATAACACCGGTA
1 CAAAGCCTGATAGATAACACCAGCA
* *
25242372 AAAAGCCTGATAGATAACACCAGCT
1 CAAAGCCTGATAGATAACACCAGCA
* *
25242397 CAAAGCCTGATAAATAACACTAGCTA
1 CAAAGCCTGATAGATAACACCAGC-A
**
25242423 -AAAGCCTGATAGATAACACTGGCA
1 CAAAGCCTGATAGATAACACCAGCA
*
25242447 CAAAGCCTGATAGATAGCACC-GACA
1 CAAAGCCTGATAGATAACACCAG-CA
* * * * *
25242472 AAAAACCTCATAGATAAAACCGGCA
1 CAAAGCCTGATAGATAACACCAGCA
* * * *
25242497 AAAAGCTTAATAGATAACACCGGCA
1 CAAAGCCTGATAGATAACACCAGCA
* *
25242522 AAAAGCCTGATAGATAACACCTA-TA
1 CAAAGCCTGATAGATAACACC-AGCA
25242547 CAAAGCCTGATA
1 CAAAGCCTGATA
25242559 TTCTGTAACA
Statistics
Matches: 195, Mismatches: 35, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
24 3 0.02
25 190 0.97
26 2 0.01
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (25 bp):
CAAAGCCTGATAGATAACACCAGCA
Found at i:25242437 original size:75 final size:73
Alignment explanation
Indices: 25242298--25242558 Score: 267
Period size: 75 Copynumber: 3.5 Consensus size: 73
25242288 TCATCGTCTC
* * * *
25242298 AAAA-CCTGATAGGTAACACCAGCACAAAGCCTGATAGATAACACCGACACAAAACTTGAAAGAT
1 AAAAGCCTGATAGATAACACCAGCACAAAGCCTGATAGATAACACAG-CA-AAAGCTTGATAGAT
*
25242362 AACACCGGTA
64 AACACCGGCA
* * *
25242372 AAAAGCCTGATAGATAACACCAGCTCAAAGCCTGATAAATAACACTAGCTAAAAGCCTGATAGAT
1 AAAAGCCTGATAGATAACACCAGCACAAAGCCTGATAGATAACAC-AGC-AAAAGCTTGATAGAT
*
25242437 AACACTGGCA
64 AACACCGGCA
* * * * * * * *
25242447 CAAAGCCTGATAGATAGCACC-GACAAAAAACCTCATAGATAAAACCGGCAAAAAGCTTAATAGA
1 AAAAGCCTGATAGATAACACCAG-CACAAAGCCTGATAGATAACA-CAGC-AAAAGCTTGATAGA
25242511 TAACACCGGCA
63 TAACACCGGCA
*
25242522 AAAAGCCTGATAGATAACACCTA-TACAAAGCCTGATA
1 AAAAGCCTGATAGATAACACC-AGCACAAAGCCTGATA
25242559 TTCTGTAACA
Statistics
Matches: 152, Mismatches: 28, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
74 5 0.03
75 144 0.95
76 3 0.02
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.15
Consensus pattern (73 bp):
AAAAGCCTGATAGATAACACCAGCACAAAGCCTGATAGATAACACAGCAAAAGCTTGATAGATAA
CACCGGCA
Found at i:25255956 original size:13 final size:13
Alignment explanation
Indices: 25255938--25255962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25255928 AACTTTTACC
25255938 ACTTTTACAATTT
1 ACTTTTACAATTT
25255951 ACTTTTACAATT
1 ACTTTTACAATT
25255963 AATCATCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (13 bp):
ACTTTTACAATTT
Found at i:25260088 original size:13 final size:14
Alignment explanation
Indices: 25260059--25260088 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
25260049 TTTAGTACAT
25260059 TGACATTTAACCTC
1 TGACATTTAACCTC
25260073 TGACATTTAA-CTC
1 TGACATTTAACCTC
25260086 TGA
1 TGA
25260089 TTGCGTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:25260119 original size:14 final size:14
Alignment explanation
Indices: 25260100--25260127 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25260090 TGCGTTGATA
25260100 GTAATTACATTGAC
1 GTAATTACATTGAC
25260114 GTAATTACATTGAC
1 GTAATTACATTGAC
25260128 ATCATTACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GTAATTACATTGAC
Found at i:25260134 original size:14 final size:14
Alignment explanation
Indices: 25260101--25260135 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
25260091 GCGTTGATAG
*
25260101 TAATTACATTGACG
1 TAATTACATTGACA
25260115 TAATTACATTGACA
1 TAATTACATTGACA
*
25260129 TCATTAC
1 TAATTAC
25260136 TCACATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (14 bp):
TAATTACATTGACA
Found at i:25263035 original size:51 final size:51
Alignment explanation
Indices: 25262956--25263293 Score: 489
Period size: 51 Copynumber: 6.6 Consensus size: 51
25262946 GCTATAAGCG
* *
25262956 AAAGGTCCGATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTACAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * *
25263007 AAGGGTCCGATGACTAAATTTCATCGTGAGCAAATGAATACTTTACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
25263058 AAAGGTCCGATGACTAAATATCATCGTGAGCAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
25263109 AAAGGTCCGATGACTAAGTGTCATCGTGAGCAAATAAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
25263160 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * **
25263211 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACAAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
25263262 AAAGGTCCGATGAC-AATATGTCATCGTGAGTA
1 AAAGGTCCGATGACTAA-GTGTCATCGTGAGTA
25263294 TTAAATGAAA
Statistics
Matches: 262, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
50 2 0.01
51 260 0.99
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:25275714 original size:24 final size:24
Alignment explanation
Indices: 25275682--25275736 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
25275672 TTTTAAGAGT
25275682 GTTTAAGTGAAGGGAATAGGTTTA
1 GTTTAAGTGAAGGGAATAGGTTTA
25275706 GTTTAAGTGAAGGGAATAGGTTTA
1 GTTTAAGTGAAGGGAATAGGTTTA
25275730 GTTTAAG
1 GTTTAAG
25275737 GGTTTAGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (24 bp):
GTTTAAGTGAAGGGAATAGGTTTA
Found at i:25276559 original size:24 final size:24
Alignment explanation
Indices: 25276529--25276574 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
25276519 AAAAATTGAT
25276529 AGTGCAAAAGTAAAATAAAATGTC
1 AGTGCAAAAGTAAAATAAAATGTC
* *
25276553 AGTGCAAATGTAATATAAAATG
1 AGTGCAAAAGTAAAATAAAATG
25276575 AATTGATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (24 bp):
AGTGCAAAAGTAAAATAAAATGTC
Found at i:25285984 original size:56 final size:56
Alignment explanation
Indices: 25285914--25286031 Score: 227
Period size: 56 Copynumber: 2.1 Consensus size: 56
25285904 CAAATATAAG
*
25285914 TATTTTAATTATCCTAGTACAATATAGACAAACATAATGAAATCATGCAAATTCCA
1 TATTTTAATTATCCTAGTACAATACAGACAAACATAATGAAATCATGCAAATTCCA
25285970 TATTTTAATTATCCTAGTACAATACAGACAAACATAATGAAATCATGCAAATTCCA
1 TATTTTAATTATCCTAGTACAATACAGACAAACATAATGAAATCATGCAAATTCCA
25286026 TATTTT
1 TATTTT
25286032 GGCTTGTAAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (56 bp):
TATTTTAATTATCCTAGTACAATACAGACAAACATAATGAAATCATGCAAATTCCA
Found at i:25294267 original size:12 final size:11
Alignment explanation
Indices: 25294250--25294283 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
25294240 TGAAGAGCAT
25294250 AAAATAAAAGAG
1 AAAATAAAAG-G
25294262 AAAATATAAAGG
1 AAAATA-AAAGG
25294274 AAAATAAAAG
1 AAAATAAAAG
25294284 CAAGATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 13 0.62
13 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (11 bp):
AAAATAAAAGG
Found at i:25302617 original size:24 final size:24
Alignment explanation
Indices: 25302570--25302628 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
25302560 AAAAGTAAGT
*
25302570 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATTA
25302593 TATATTATAATTTTTACTAAT-TTA
1 TATATTATAATTTTT-CTAATATTA
*
25302617 TATTTTAATAAT
1 TATATT-ATAAT
25302629 AATTATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 4 0.13
24 17 0.55
25 10 0.32
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATTA
Found at i:25302757 original size:58 final size:59
Alignment explanation
Indices: 25302593--25302757 Score: 194
Period size: 58 Copynumber: 2.8 Consensus size: 59
25302583 TCTAATATTA
* * * ** *
25302593 TATATTATAATTTTTACTAATTTATATTTTAATAATAATTATATTAAAACGTTATTAAAT
1 TATATTATTATTTTTATTAAATTATA-TTTAATAATAATTATATTAAAATATAATTAAAT
* *
25302653 TATATT-TTA-TTTTATTTAATTATATTTAATAATAATTATGTTAAAATATAATTAAAT
1 TATATTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
* *
25302710 TAT-TTATTATTTTTATTAAATTATGTTTAATAGTAATCT-TATTAAAAT
1 TATATTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAAT
25302758 TTCATAACAA
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
56 2 0.02
57 35 0.39
58 44 0.49
59 3 0.03
60 6 0.07
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (59 bp):
TATATTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
Found at i:25306225 original size:18 final size:19
Alignment explanation
Indices: 25306190--25306227 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
25306180 GGTATGGATA
* *
25306190 CATCAGGTTGCGTTGACAT
1 CATCAGGTTGCATCGACAT
25306209 CATC-GGTTGCATCGACAT
1 CATCAGGTTGCATCGACAT
25306227 C
1 C
25306228 GGCAGTTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (19 bp):
CATCAGGTTGCATCGACAT
Found at i:25308880 original size:258 final size:257
Alignment explanation
Indices: 25308423--25308934 Score: 970
Period size: 258 Copynumber: 2.0 Consensus size: 257
25308413 TAACAAGTAA
25308423 TTGTTGCTGGAATAAGGCACAATGAATGTCTTACCAAACTTGGCTTTTCTATTAAATCTAAGACT
1 TTGTTGCTGGAATAAGGCACAATGAATGTCTTACCAAACTTGGCTTTTCTATTAAATCTAAGACT
* *
25308488 TAAACATGCGCACTAACCACACCTTCCAGTGCTAGCAATGCAACATATTCAAGAACAAGTGGATT
66 TAAACATACGCACTAACCACACCGTCCAGTGCTAGCAATGCAACATATTCAAGAACAAGTGGATT
*
25308553 AAATTCCTTCAATCCCCAAGCAACTTCCGTTGTCTTGCTTGTTAATTTAATTTGTCGTTGCACCT
131 AAATTCCTTCAATCCCCAAGCAACTTCCGTTGTCTTGCTTGTTAATTCAATTTGTCGTTGCACCT
*
25308618 TCTAGTAATAGTGACTGCAATCACACTTCCGTGGTCAAAACAATTAAACCCAAAGATTAACAG
196 TCTAGTAATAGTGACTACAATCACACTTCCGTGGTCAAAACAATT-AACCCAAAGATTAACAG
25308681 TTGTTGCTGGAATAAGGCACAATGAATGTCTTACCAAACTTGGCTTTTCTATTAAATCTAAGACT
1 TTGTTGCTGGAATAAGGCACAATGAATGTCTTACCAAACTTGGCTTTTCTATTAAATCTAAGACT
25308746 TAAACATACGCACTAACCACACCGTCCAGTGCTAGCAATGCAACATATTCAAGAACAAGTGGATT
66 TAAACATACGCACTAACCACACCGTCCAGTGCTAGCAATGCAACATATTCAAGAACAAGTGGATT
25308811 AAATTCCTTCAATCCCCAAGCAACTTCCGTTGTCTTGCTTGTTAATTCAATTTGTCGTTGCACCT
131 AAATTCCTTCAATCCCCAAGCAACTTCCGTTGTCTTGCTTGTTAATTCAATTTGTCGTTGCACCT
*
25308876 TCTAGTAATAGTGACTACAATCACACTTCCGTGGTCAAAACAATTAACCTAAAGATTAA
196 TCTAGTAATAGTGACTACAATCACACTTCCGTGGTCAAAACAATTAACCCAAAGATTAA
25308935 TAGTAAAGGC
Statistics
Matches: 249, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
257 13 0.05
258 236 0.95
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (257 bp):
TTGTTGCTGGAATAAGGCACAATGAATGTCTTACCAAACTTGGCTTTTCTATTAAATCTAAGACT
TAAACATACGCACTAACCACACCGTCCAGTGCTAGCAATGCAACATATTCAAGAACAAGTGGATT
AAATTCCTTCAATCCCCAAGCAACTTCCGTTGTCTTGCTTGTTAATTCAATTTGTCGTTGCACCT
TCTAGTAATAGTGACTACAATCACACTTCCGTGGTCAAAACAATTAACCCAAAGATTAACAG
Found at i:25320787 original size:31 final size:31
Alignment explanation
Indices: 25320740--25320873 Score: 120
Period size: 31 Copynumber: 4.5 Consensus size: 31
25320730 TTTTTAAAAA
*
25320740 AAGTTTAGGTACCAAATTAGGAAAAAATATC
1 AAGTTTAGGTATCAAATTAGGAAAAAATATC
* ***
25320771 AAGTTTAAGTATCAAATTAGGTCCAAA-A--
1 AAGTTTAGGTATCAAATTAGGAAAAAATATC
* *
25320799 AAGTGTAGGTATCAAATTAAGAAAAAATATC
1 AAGTTTAGGTATCAAATTAGGAAAAAATATC
* * *
25320830 AAGTTCAGGTATTAAATT-GGATAAAA-A--
1 AAGTTTAGGTATCAAATTAGGAAAAAATATC
*
25320857 AAGTTTAGGTACCAAAT
1 AAGTTTAGGTATCAAAT
25320874 GTTATATTAA
Statistics
Matches: 81, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
27 14 0.17
28 21 0.26
29 2 0.02
30 7 0.09
31 37 0.46
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (31 bp):
AAGTTTAGGTATCAAATTAGGAAAAAATATC
Found at i:25320800 original size:59 final size:58
Alignment explanation
Indices: 25320734--25320873 Score: 192
Period size: 59 Copynumber: 2.4 Consensus size: 58
25320724 GAATTTTTTT
* *
25320734 TAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATATCAAGTTTAAGTATCAAATTAGG-
1 TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATATCAAGTTCAAGTATCAAATT-GGA
* * * * *
25320792 TCCAAAAAAGTGTAGGTATCAAATTAAGAAAAAATATCAAGTTCAGGTATTAAATTGGA
1 T-AAAAAAAGTTTAGGTACCAAATTAAGAAAAAATATCAAGTTCAAGTATCAAATTGGA
25320851 TAAAAAAAGTTTAGGTACCAAAT
1 TAAAAAAAGTTTAGGTACCAAAT
25320874 GTTATATTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 22 0.31
59 48 0.69
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (58 bp):
TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATATCAAGTTCAAGTATCAAATTGGA
Found at i:25323423 original size:56 final size:56
Alignment explanation
Indices: 25323281--25323423 Score: 187
Period size: 56 Copynumber: 2.6 Consensus size: 56
25323271 CATACTTTTA
* * * **
25323281 AGAAAACACGAACAGGGTTTGCCTTAGGTCACAAGACTGGTTTGCACATGCTTATC
1 AGAAAACACGAACAGGGTTTGCCTTAGGTCGCAAGACCGATTCACACATGCTTATC
* * * * *
25323337 AGAAAACACGAACAAGGTCTGCTTTAGGTCGCAGGACCGATTCATACATGCTTATC
1 AGAAAACACGAACAGGGTTTGCCTTAGGTCGCAAGACCGATTCACACATGCTTATC
*
25323393 AGAAAACAAGAACAGGGTTTGCCTTAGGTCG
1 AGAAAACACGAACAGGGTTTGCCTTAGGTCG
25323424 TTAGACTGAT
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (56 bp):
AGAAAACACGAACAGGGTTTGCCTTAGGTCGCAAGACCGATTCACACATGCTTATC
Found at i:25325351 original size:17 final size:17
Alignment explanation
Indices: 25325301--25325363 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
25325291 TACATCTTTG
*
25325301 GCAGATAGTATAGCCTA
1 GCAGATAGTATAACCTA
* * *
25325318 GAAAAACAGTATAACCTA
1 G-CAGATAGTATAACCTA
* * *
25325336 GCGGATAGTATCACCTG
1 GCAGATAGTATAACCTA
25325353 GCAGATAGTAT
1 GCAGATAGTAT
25325364 TGCTGGCGAA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
17 21 0.62
18 13 0.38
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (17 bp):
GCAGATAGTATAACCTA
Found at i:25335447 original size:28 final size:28
Alignment explanation
Indices: 25335415--25335546 Score: 129
Period size: 28 Copynumber: 4.7 Consensus size: 28
25335405 TTTCTTTCCT
*
25335415 GAGGTTCGCCAAAAAGGCTTTCCTTTTA
1 GAGGTTCACCAAAAAGGCTTTCCTTTTA
* **
25335443 GAGGTTCACCACAAAGGCTTTCCTTACA
1 GAGGTTCACCAAAAAGGCTTTCCTTTTA
* * * * *
25335471 AAGGTTCGCCATAAATGTTTTCCTTTTA
1 GAGGTTCACCAAAAAGGCTTTCCTTTTA
* * *
25335499 GAGGTTTACTAAAAAGGTTTTCCTTTTA
1 GAGGTTCACCAAAAAGGCTTTCCTTTTA
* * *
25335527 GAGCTTCACCATAGAGGCTT
1 GAGGTTCACCAAAAAGGCTT
25335547 CCATTTTTTG
Statistics
Matches: 81, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 81 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (28 bp):
GAGGTTCACCAAAAAGGCTTTCCTTTTA
Found at i:25335476 original size:56 final size:56
Alignment explanation
Indices: 25335416--25335523 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
25335406 TTCTTTCCTG
*
25335416 AGGTTCGCCAAAAAGGCTTTCCTTTTAGAGGTTCACCACAAAGGCTTTCCTTACAA
1 AGGTTCGCCAAAAAGGCTTTCCTTTTAGAGGTTCACCAAAAAGGCTTTCCTTACAA
* * * * * *
25335472 AGGTTCGCCATAAATGTTTTCCTTTTAGAGGTTTACTAAAAAGGTTTTCCTT
1 AGGTTCGCCAAAAAGGCTTTCCTTTTAGAGGTTCACCAAAAAGGCTTTCCTT
25335524 TTAGAGCTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (56 bp):
AGGTTCGCCAAAAAGGCTTTCCTTTTAGAGGTTCACCAAAAAGGCTTTCCTTACAA
Found at i:25338541 original size:22 final size:22
Alignment explanation
Indices: 25338486--25338544 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
25338476 ATATAAACAT
* *
25338486 TCAATTATATTAGCATAATTAA
1 TCAATTATATTGGCATAATCAA
25338508 TCAATTATATTGGCATAATCAA
1 TCAATTATATTGGCATAATCAA
25338530 TCAATTATATTGGCA
1 TCAATTATATTGGCA
25338545 CAATACATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (22 bp):
TCAATTATATTGGCATAATCAA
Found at i:25342483 original size:15 final size:15
Alignment explanation
Indices: 25342463--25342491 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25342453 TGTAAAACCC
25342463 TAGTGCTAGAGGCCT
1 TAGTGCTAGAGGCCT
25342478 TAGTGCTAGAGGCC
1 TAGTGCTAGAGGCC
25342492 CTATTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (15 bp):
TAGTGCTAGAGGCCT
Found at i:25352731 original size:41 final size:41
Alignment explanation
Indices: 25352643--25352746 Score: 111
Period size: 41 Copynumber: 2.6 Consensus size: 41
25352633 AACATTTTTA
** * * * *
25352643 GGGGTTTGTCATGACGTAAACA-TTCTTTTTTATGACATAC
1 GGGGTTTGTCGCGACGTAGACATTTCTATCTCATGACATAC
*
25352683 GGGGTTTGTCGCGACGTAGACATTTCTATCTCATGACATAG
1 GGGGTTTGTCGCGACGTAGACATTTCTATCTCATGACATAC
* * *
25352724 GGGGTTTGTTGCAACATAGACAT
1 GGGGTTTGTCGCGACGTAGACAT
25352747 GCTATGTCGC
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
40 19 0.36
41 34 0.64
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (41 bp):
GGGGTTTGTCGCGACGTAGACATTTCTATCTCATGACATAC
Found at i:25355543 original size:22 final size:22
Alignment explanation
Indices: 25355501--25355542 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
25355491 ATTCACAAAT
25355501 TTTCTTACTCATACTTCTTTTG
1 TTTCTTACTCATACTTCTTTTG
**
25355523 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATACTTCTTTT
25355543 TCTTTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.21, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTCTTACTCATACTTCTTTTG
Found at i:25360721 original size:12 final size:13
Alignment explanation
Indices: 25360694--25360742 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
25360684 AAATAAAATG
*
25360694 AAAACGAAA-ACG
1 AAAACGAAATACA
25360706 AAAACGAAATACA
1 AAAACGAAATACA
*
25360719 AAATACAAAATACA
1 AAA-ACGAAATACA
25360733 AAATACGAAA
1 AAA-ACGAAA
25360743 AATAATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
12 9 0.28
13 5 0.16
14 18 0.56
ACGTcount: A:0.69, C:0.14, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAACGAAATACA
Found at i:25360724 original size:7 final size:7
Alignment explanation
Indices: 25360712--25360743 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
25360702 AACGAAAACG
25360712 AAATACA
1 AAATACA
25360719 AAATACA
1 AAATACA
25360726 AAATACA
1 AAATACA
25360733 AAATACGA
1 AAATAC-A
25360741 AAA
1 AAA
25360744 ATAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.72, C:0.12, G:0.03, T:0.12
Consensus pattern (7 bp):
AAATACA
Found at i:25364046 original size:18 final size:21
Alignment explanation
Indices: 25364020--25364060 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
25364010 CAATTAAAAT
*
25364020 TAAAAAAA-ATAAACTAATAA
1 TAAAAAAATATAGACTAATAA
25364040 TAAAAAAATATAGACTAATAA
1 TAAAAAAATATAGACTAATAA
25364061 AATTTAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAAAAAATATAGACTAATAA
Found at i:25382984 original size:41 final size:40
Alignment explanation
Indices: 25382880--25383123 Score: 308
Period size: 41 Copynumber: 5.9 Consensus size: 40
25382870 GGTGTATAAA
* * * * *
25382880 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATA-TGAAT
* *
25382921 AAATGGAATACTCATGTCTCGAGATGTGAATGAGACTATGAAT
1 -AA-GGAAGACTCATGTCTCGAGATGAGAATGAGA-TATGAAT
*
25382964 AAGGAAGACTCATGTCTCGAGCTGAGAATGAGATATGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATATGAAT
25383004 AAGGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGA-TATGAAT
* * *
25383045 AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGA-TATGAAT
* *
25383086 AAGGAAGACCCATGTCTCGAGATGAGGATGAGAATATG
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAG-ATATG
25383124 GTTAAAGGAA
Statistics
Matches: 179, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
40 39 0.22
41 104 0.58
42 5 0.03
43 30 0.17
44 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (40 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATATGAAT
Found at i:25383036 original size:81 final size:81
Alignment explanation
Indices: 25382880--25383123 Score: 326
Period size: 81 Copynumber: 3.0 Consensus size: 81
25382870 GGTGTATAAA
* * * * * *
25382880 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATGGAATACTCATGTCTCGAGA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATA-TGAAT-AA-GGAAGACTCATGTCTCGAGA
*
25382945 TGTGAATGAGACTATGAAT
63 TGAGAATGAGACTATGAAT
*
25382964 AAGGAAGACTCATGTCTCGAGCTGAGAATGAGATATGAATAAGGAAGACTCATGTCTCGAGATGA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATATGAATAAGGAAGACTCATGTCTCGAGATGA
25383029 GAATGAGACTATGAAT
66 GAATGAGACTATGAAT
* * * *
25383045 AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACCCATGTCTCGAGATG
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGA-TATGAATAAGGAAGACTCATGTCTCGAGATG
* *
25383110 AGGATGAGAATATG
65 AGAATGAGACTATG
25383124 GTTAAAGGAA
Statistics
Matches: 145, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
81 68 0.47
82 42 0.29
83 4 0.03
84 31 0.21
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (81 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATATGAATAAGGAAGACTCATGTCTCGAGATGA
GAATGAGACTATGAAT
Found at i:25383100 original size:122 final size:125
Alignment explanation
Indices: 25382880--25383123 Score: 325
Period size: 122 Copynumber: 2.0 Consensus size: 125
25382870 GGTGTATAAA
* * * * * *
25382880 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATGGAATACTCATGTCTCGAGA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGAATAAATGGAAGACTCATGTCTCGAAA
* * *
25382945 TGTGAATGAGACTATGAATAAGGAAGACTCATGTCTCGAGCTGAGAATGAG-ATATGAAT
66 TGAGAATGAGACTATGAATAAGGAAGACCCATGTCTCGAGATGAGAATGAGAATATGAAT
*
25383004 AAGGAAGACTCATGTCTCGAGATGAGAATGAG-ACTATGAAT-AA-GGAAGACTCATGTCTCGAA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGAAAT-TGAATAAATGGAAGACTCATGTCTCGAA
* * * *
25383066 ATGAGAATGAGATTTTGATTAAGGAAGACCCATGTCTCGAGATGAGGATGAGAATATG
65 ATGAGAATGAGACTATGAATAAGGAAGACCCATGTCTCGAGATGAGAATGAGAATATG
25383124 GTTAAAGGAA
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
122 62 0.60
123 9 0.09
124 33 0.32
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (125 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGAATAAATGGAAGACTCATGTCTCGAAA
TGAGAATGAGACTATGAATAAGGAAGACCCATGTCTCGAGATGAGAATGAGAATATGAAT
Found at i:25400248 original size:16 final size:16
Alignment explanation
Indices: 25400227--25400260 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25400217 AGGTTCTTCT
25400227 CTTCTTACCTCTTTTC
1 CTTCTTACCTCTTTTC
* *
25400243 CTTCTTATCTTTTTTC
1 CTTCTTACCTCTTTTC
25400259 CT
1 CT
25400261 CTTCTGCCTC
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:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTCTTACCTCTTTTC
Found at i:25411805 original size:24 final size:24
Alignment explanation
Indices: 25411776--25411833 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
25411766 ATAAACATAT
25411776 ATGCAAGATAGAATATAGCAAGGC
1 ATGCAAGATAGAATATAGCAAGGC
*
25411800 ATGCAAGATAGAATATAGCATGGC
1 ATGCAAGATAGAATATAGCAAGGC
25411824 ATGCAAGATA
1 ATGCAAGATA
25411834 ATTCCCCCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.19
Consensus pattern (24 bp):
ATGCAAGATAGAATATAGCAAGGC
Found at i:25420207 original size:10 final size:10
Alignment explanation
Indices: 25420189--25420232 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
25420179 GGTATAGAGT
*
25420189 TAAACTGAAA
1 TAAAATGAAA
25420199 TAAAATGAAAA
1 TAAAATG-AAA
25420210 TAAAAT-AAA
1 TAAAATGAAA
*
25420219 TAAAGTGAAA
1 TAAAATGAAA
25420229 TAAA
1 TAAA
25420233 TCTTGATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 8 0.27
10 13 0.43
11 9 0.30
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.20
Consensus pattern (10 bp):
TAAAATGAAA
Found at i:25437311 original size:22 final size:23
Alignment explanation
Indices: 25437269--25437320 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 23
25437259 AATAATCGTT
25437269 ATATATATATTTACACTTATAAA
1 ATATATATATTTACACTTATAAA
*
25437292 ATATAT-TATTT-CA-TTATATA
1 ATATATATATTTACACTTATAAA
25437312 ATACTATAT
1 ATA-TATAT
25437321 CACATACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.35
21 5 0.19
22 6 0.23
23 6 0.23
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATATATTTACACTTATAAA
Found at i:25441133 original size:21 final size:21
Alignment explanation
Indices: 25441109--25441183 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
25441099 GAAATTTAAA
*
25441109 ACAAACATAATGATGAGAGTT
1 ACAAACATAATGAGGAGAGTT
*
25441130 ACAAA-ACTTATGAGGAGAGTT
1 ACAAACA-TAATGAGGAGAGTT
* *
25441151 ACAAACATTATAAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
25441172 ACAAACATAATG
1 ACAAACATAATG
25441184 TTTTGTAGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 1 0.02
21 45 0.96
22 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.23
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:25442500 original size:30 final size:29
Alignment explanation
Indices: 25442456--25442527 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 29
25442446 ATGTTAACAA
25442456 GACACCCCCACATTTTCAAGTGGTTCTAG
1 GACACCCCCACATTTTCAAGTGGTTCTAG
25442485 GACACCCCTCACATTTTCAAGTGGTTCTAG
1 GACACCCC-CACATTTTCAAGTGGTTCTAG
25442515 GACACCCCCACAT
1 GACACCCCCACAT
25442528 GTTCTGTGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 13 0.31
30 29 0.69
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (29 bp):
GACACCCCCACATTTTCAAGTGGTTCTAG
Found at i:25445771 original size:29 final size:29
Alignment explanation
Indices: 25445725--25446053 Score: 169
Period size: 29 Copynumber: 11.3 Consensus size: 29
25445715 GATTAAATGC
* ** *
25445725 AATTTTTGGATACCCGAGGGCAAAATAGT
1 AATTTTTGGACATTCGAGGGCAAAATGGT
** *
25445754 AATTTTTGGAGGTTCGAGGTCAAAAATGGT
1 AATTTTTGGACATTCGAGGGC-AAAATGGT
* * *
25445784 -ATTTTTGGACATTTGGGGGTAAAATGGT
1 AATTTTTGGACATTCGAGGGCAAAATGGT
* * *
25445812 AATTTTTGGAAATT-TAGGGGTC-GAATGGT
1 AATTTTTGGACATTCGA-GGG-CAAAATGGT
* * * *
25445841 AATTTTTGAAAAATT-TAGGGTAAAATGGT
1 AATTTTTG-GACATTCGAGGGCAAAATGGT
* *
25445870 AATTTTTAGACATTC-ATGGGTAAAATGGT
1 AATTTTTGGACATTCGA-GGGCAAAATGGT
* *
25445899 AATTTTTGGAAAGTT-TAGGGTCAAAATGG-
1 AATTTTTGGACA-TTCGAGGG-CAAAATGGT
* *
25445928 AATTTTTGGAAATT-TAGGCGCAAAATGGT
1 AATTTTTGGACATTCGAGG-GCAAAATGGT
* * * *
25445957 AATTTTTAGAAAGTTTGAGGTCAAAAATGG-
1 AATTTTTGGACA-TTCGAGGGC-AAAATGGT
* * *
25445987 AATTTTTGGA-AGTTTGGGGGTAAAATGGT
1 AATTTTTGGACA-TTCGAGGGCAAAATGGT
* * *
25446016 AATTTTTGGAAAGTT-TAGGGGAAAAT-GT
1 AATTTTTGGACA-TTCGAGGGCAAAATGGT
25446044 AATTTTTGGA
1 AATTTTTGGA
25446054 AAGTTTAGGG
Statistics
Matches: 246, Mismatches: 36, Indels: 37
0.77 0.11 0.12
Matches are distributed among these distances:
28 46 0.19
29 150 0.61
30 40 0.16
31 10 0.04
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
AATTTTTGGACATTCGAGGGCAAAATGGT
Found at i:25446073 original size:30 final size:30
Alignment explanation
Indices: 25445776--25446173 Score: 375
Period size: 29 Copynumber: 13.6 Consensus size: 30
25445766 TTCGAGGTCA
* *
25445776 AAAATGGT-ATTTTTGGACA-TTTGGGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGGT
25445804 AAAATGGTAATTTTTGGAAA-TTTAGGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGGT
** * *
25445833 CGAATGGTAATTTTTGAAAAATTTA-GGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGGT
* * * *
25445862 AAAATGGTAATTTTTAGACA-TTCATGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGGT
25445891 AAAATGGTAATTTTTGGAAAGTTTA-GGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGGT
* *
25445920 CAAAATGG-AATTTTTGGAAA-TTTAGGCGC
1 -AAAATGGTAATTTTTGGAAAGTTTAGGGGT
* *
25445949 AAAATGGTAATTTTTAGAAAGTTT-GAGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGGT
*
25445978 CAAAAATGG-AATTTTTGG-AAGTTTGGGGGT
1 --AAAATGGTAATTTTTGGAAAGTTTAGGGGT
25446008 AAAATGGTAATTTTTGGAAAGTTTAGGGG-
1 AAAATGGTAATTTTTGGAAAGTTTAGGGGT
25446037 AAAAT-GTAATTTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGGT
25446066 AAAAAT-GTAATTTTTGGAAAGTTT-GGAGGT
1 -AAAATGGTAATTTTTGGAAAGTTTAGG-GGT
* * *
25446096 CAAAAT-ATAATTTTTGTAAAGTTT-GGAGGCA
1 -AAAATGGTAATTTTTGGAAAGTTTAGG-GG-T
** **
25446127 AAAAT-GTAATTTTTAAAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGGT
*
25446156 CAAAAT-ATAATTTTTGGA
1 -AAAATGGTAATTTTTGGA
25446174 TAGCTTAAGG
Statistics
Matches: 316, Mismatches: 35, Indels: 36
0.82 0.09 0.09
Matches are distributed among these distances:
28 52 0.16
29 129 0.41
30 126 0.40
31 9 0.03
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAAGTTTAGGGGT
Found at i:25446197 original size:7 final size:7
Alignment explanation
Indices: 25446185--25446220 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
25446175 AGCTTAAGGA
25446185 CCTAAAC
1 CCTAAAC
25446192 CCTAAAC
1 CCTAAAC
*
25446199 CTTAAAC
1 CCTAAAC
25446206 CCTAAAC
1 CCTAAAC
25446213 CCTAAAC
1 CCTAAAC
25446220 C
1 C
25446221 ATCCCTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (7 bp):
CCTAAAC
Found at i:25447325 original size:17 final size:17
Alignment explanation
Indices: 25447305--25447382 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
25447295 TATTAATTTT
*
25447305 AATTTAAAATATATTCA
1 AATTTAAAATAAATTCA
* *
25447322 AATTTAAAGTAAATTTA
1 AATTTAAAATAAATTCA
* * * *
25447339 AACTCAAAATGAATTTA
1 AATTTAAAATAAATTCA
25447356 AATTTAAAAATAAATTCA
1 AATTT-AAAATAAATTCA
25447374 AATTTAAAA
1 AATTTAAAA
25447383 ATTAAAAGTC
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
17 34 0.69
18 15 0.31
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:25448051 original size:86 final size:86
Alignment explanation
Indices: 25447903--25448110 Score: 308
Period size: 86 Copynumber: 2.4 Consensus size: 86
25447893 TAGCTTCATT
* * * * *
25447903 AATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGTAACACTTGTTTCAATTCGCTTCT
1 AATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTGACCGCAACACTTGTTTCAATCCGCTTCT
**
25447968 CTATATCTCATTAGGAAGACG
66 CTATATCTCAACAGGAAGACG
* * *
25447989 AATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTGACCGCATCACTTGTTTCAATCCGCTTCT
1 AATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTGACCGCAACACTTGTTTCAATCCGCTTCT
25448054 CTATATCTCAACAGGAAGACG
66 CTATATCTCAACAGGAAGACG
* *
25448075 AATTTGGTCTGCTTTTCAGTATCTCATCAGGAAGCT
1 AATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCT
25448111 AGCCATTTTA
Statistics
Matches: 108, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 108 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (86 bp):
AATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTGACCGCAACACTTGTTTCAATCCGCTTCT
CTATATCTCAACAGGAAGACG
Found at i:25448225 original size:295 final size:295
Alignment explanation
Indices: 25447695--25448319 Score: 892
Period size: 295 Copynumber: 2.1 Consensus size: 295
25447685 GGTGTTATTG
* * * **
25447695 ATTTGGTCTACTTCTCATTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTCTC
1 ATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGACCGCATCACTTGTTTCAATCCACTTCTC
* * * * * * *
25447760 TGTGTCTCATCAAGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTACCCGCTTT
66 TATATCTCAACAAGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAGGAAGCTACCCACTTT
* * *
25447825 ATTGCTTCGACCTGCTTCTCAGTATCTCATCATGAAGCTGGGGTTCGAAGATTCGCTCACTTTGA
131 ATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCACTTAGA
* *
25447890 GCCTAGCTTCATTAATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGTAACACTTGTT
196 GCCTAGCTTCATTAATTTGGTCTTCTTCTCAGTACCTCATCAGAAAGATGACCGCAACACTTGTT
* *
25447955 TCAATTCGCTTCTCTATATCTCATTAGGAAGACGA
261 TCAATCCGCTTCTCTATATCTCATCAGGAAGACGA
* * *
25447990 ATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTGACCGCATCACTTGTTTCAATCCGCTTCTC
1 ATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGACCGCATCACTTGTTTCAATCCACTTCTC
* * * * * *
25448055 TATATCTCAACAGGAAGACGAATTTGG-TCTGCTTTTCAGTATCTCATCAGGAAGCTAGCCATTT
66 TATATCTCAACAAGAAGACGAATCTGGTTC-ACTTCTCAGTATCTCATCAGGAAGCTACCCACTT
*
25448119 TATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTAG
130 TATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCACTTAG
* * * * *
25448184 AGCTTGGCTTCATTGATTTGGTCTTCTTCTCAGTACCTCATCAGAAAGATGATCGCATCACTTGT
195 AGCCTAGCTTCATTAATTTGGTCTTCTTCTCAGTACCTCATCAGAAAGATGACCGCAACACTTGT
* *
25448249 TTCAATCCGCTTCTCTGTATCTTATCAGGAAGACGA
260 TTCAATCCGCTTCTCTATATCTCATCAGGAAGACGA
* *
25448285 ATTTGGTTCGCTTCTCAGTATCTCATCAAGAAGCT
1 ATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCT
25448320 AACCATTTTA
Statistics
Matches: 289, Mismatches: 40, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
294 2 0.01
295 287 0.99
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (295 bp):
ATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGACCGCATCACTTGTTTCAATCCACTTCTC
TATATCTCAACAAGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAGGAAGCTACCCACTTT
ATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCACTTAGA
GCCTAGCTTCATTAATTTGGTCTTCTTCTCAGTACCTCATCAGAAAGATGACCGCAACACTTGTT
TCAATCCGCTTCTCTATATCTCATCAGGAAGACGA
Found at i:25449066 original size:209 final size:209
Alignment explanation
Indices: 25447990--25449008 Score: 1669
Period size: 209 Copynumber: 4.9 Consensus size: 209
25447980 AGGAAGACGA
** * * *
25447990 ATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTGACCGCATCACTTGTTTCAATCCGCTTCTC
1 ATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTC
* * * * *
25448055 TATATCTCAACAGGAAGACGAATTTGGTCTGCTTTTCAGTATCTCATCAGGAAGCTAGCCATTTT
66 TGTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTT
* *
25448120 ATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTAGA
131 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCACTTAGA
25448185 GCTTGGCTTCATTG
196 GCTTGGCTTCATTG
* *
25448199 ATTTGGTCTTCTTCTCAGTACCTCATCAGAAAGATGATCGCATCACTTGTTTCAATCCGCTTCTC
1 ATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTC
* * *
25448264 TGTATCTTATCAGGAAGACGAATTTGGTTCGCTTCTCAGTATCTCATCAAGAAGCTAACCATTTT
66 TGTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTT
* * *
25448329 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTTAAAGATTTGCTCACTTGGA
131 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCACTTAGA
25448394 GCTTGGCTTCATTG
196 GCTTGGCTTCATTG
*
25448408 ATTTGGTCTTCTTCTCAATACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTC
1 ATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTC
* *
25448473 TATATCTCATCAAGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTT
66 TGTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTT
25448538 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCACTTAGA
131 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCACTTAGA
25448603 GCTTGGCTTCATTG
196 GCTTGGCTTCATTG
* *
25448617 ATTTGGTCTTCTTCTCAATACCTCATCAGGAAGATGATCGCATCACTTGTTTCAATCCGCTTCTC
1 ATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTC
* * *
25448682 TGTATCTCTTCAAGAAGACTAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTT
66 TGTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTT
*
25448747 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCACTTGGA
131 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCACTTAGA
25448812 GCTTGGCTTCATTG
196 GCTTGGCTTCATTG
* * * *
25448826 ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAAATGACCGTATCACTTGTTTTAATCCGCTTCTC
1 ATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTC
* * *
25448891 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGAAAGCTAACCATTTT
66 TGTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTT
* * * * *
25448956 ATTGCTTCGAACTGCTTCTCAGTATCTTATAAAGAAGCTGGGGTTCGAAGATT
131 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATT
25449009 CACTCATTTT
Statistics
Matches: 757, Mismatches: 53, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
209 757 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (209 bp):
ATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTC
TGTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTT
ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCACTTAGA
GCTTGGCTTCATTG
Found at i:25457599 original size:29 final size:30
Alignment explanation
Indices: 25457567--25457668 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 30
25457557 TTTTGGGGGC
* ** *
25457567 AAAATAGTAATTTTTGGAGGTTCGAGGTTA
1 AAAATGGTAATTTTTGGACATTCGAGGGTA
*
25457597 AAAATGGT-ATTTTTGGACATTCGGGGGT-
1 AAAATGGTAATTTTTGGACATTCGAGGGTA
* *
25457625 AAAATGGTAATTTTTGGAAATT-AAGGGGTA
1 AAAATGGTAATTTTTGGACATTCGA-GGGTA
*
25457655 TAAATGG-AATTTTT
1 AAAATGGTAATTTTT
25457669 AGAAATTTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
28 8 0.13
29 39 0.65
30 13 0.22
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.37
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGACATTCGAGGGTA
Found at i:25457673 original size:29 final size:29
Alignment explanation
Indices: 25457597--25457808 Score: 131
Period size: 29 Copynumber: 7.5 Consensus size: 29
25457587 TTCGAGGTTA
* * **
25457597 AAAATGGT-ATTTTTGGACATTCGGGGGT
1 AAAATGGTAATTTTTAGAAATTAAGGGGT
*
25457625 AAAATGGTAATTTTTGGAAATTAAGGGGT
1 AAAATGGTAATTTTTAGAAATTAAGGGGT
**
25457654 ATAAATGG-AATTTTTAGAAATTTGGGGGT
1 A-AAATGGTAATTTTTAGAAATTAAGGGGT
** * * * *
25457683 CGAATGGTAA----AACAAAAT-CGGGGT
1 AAAATGGTAATTTTTAGAAATTAAGGGGT
* *
25457707 AAAATGGTAATTTTTGGACATTCAA--GGT
1 AAAATGGTAATTTTTAGAAATT-AAGGGGT
* * *
25457735 AAAATGGTAATTTTTGGAAAGTTTAGGGGCA
1 AAAATGGTAATTTTTAGAAA-TTAAGGGG-T
*
25457766 AAAAT-GTAATTTTTAGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTAGAAA-TTAAGGGGT
25457795 AAAAT-GTAATTTTT
1 AAAATGGTAATTTTT
25457809 GTAAAGTTTG
Statistics
Matches: 146, Mismatches: 25, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
24 13 0.09
25 5 0.03
28 39 0.27
29 54 0.37
30 30 0.21
31 5 0.03
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTAGAAATTAAGGGGT
Found at i:25457777 original size:30 final size:30
Alignment explanation
Indices: 25457735--25457876 Score: 164
Period size: 30 Copynumber: 4.7 Consensus size: 30
25457725 CATTCAAGGT
25457735 AAAATGGTAATTTTTGGAAAGTTTAGGGGCA
1 AAAAT-GTAATTTTTGGAAAGTTTAGGGGCA
* *
25457766 AAAATGTAATTTTTAGAAAGTTTAGGGG-T
1 AAAATGTAATTTTTGGAAAGTTTAGGGGCA
*
25457795 AAAATGTAATTTTTGTAAAGTTT-GGAGGTC-
1 AAAATGTAATTTTTGGAAAGTTTAGG-GG-CA
* * *
25457825 AAAATATAATTTTTGTAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAAGTTTAGGGGCA
* *
25457855 AAAATGTAGTTTTTAGAAAGTT
1 AAAATGTAATTTTTGGAAAGTT
25457877 CGACGGTCAA
Statistics
Matches: 96, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.02
29 23 0.24
30 64 0.67
31 7 0.07
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTTAGGGGCA
Found at i:25457859 original size:60 final size:58
Alignment explanation
Indices: 25457732--25457911 Score: 206
Period size: 60 Copynumber: 3.0 Consensus size: 58
25457722 GGACATTCAA
*
25457732 GGTAAAATGGTAATTTTTGGAAAGTTTAGG-GG-CAAAAATGTAATTTTTAGAAAGTTTAGG
1 GGTAAAAT-GTAATTTTT-GAAAGTTT-GGAGGTC-AAAATATAATTTTTAGAAAGTTTAGG
25457792 GGTAAAATGTAATTTTTGTAAAGTTTGGAGGTCAAAATATAATTTTT-GTAAAGTTTAGG
1 GGTAAAATGTAATTTTTG-AAAGTTTGGAGGTCAAAATATAATTTTTAG-AAAGTTTAGG
* * * *
25457851 GGTAAAAATGTAGTTTTTAGAAAG-TTCGACGGTCAAAATATAATTTTTAGATAGTTGAGG
1 GGT-AAAATGTAATTTTT-GAAAGTTTGGA-GGTCAAAATATAATTTTTAGAAAGTTTAGG
25457911 G
1 G
25457912 ACCTATTGGG
Statistics
Matches: 107, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
58 4 0.04
59 48 0.45
60 53 0.50
61 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (58 bp):
GGTAAAATGTAATTTTTGAAAGTTTGGAGGTCAAAATATAATTTTTAGAAAGTTTAGG
Found at i:25457889 original size:30 final size:30
Alignment explanation
Indices: 25457735--25457911 Score: 159
Period size: 30 Copynumber: 5.9 Consensus size: 30
25457725 CATTCAAGGT
* *
25457735 AAAATGGTAATTTTTGGAAAGTTTAGGGG-C
1 AAAAT-GTAATTTTTAGAAAGTTGAGGGGTC
*
25457765 AAAAATGTAATTTTTAGAAAGTTTAGGGGT-
1 -AAAATGTAATTTTTAGAAAGTTGAGGGGTC
*
25457795 AAAATGTAATTTTT-GTAAAGTTTG-GAGGTC
1 AAAATGTAATTTTTAG-AAAG-TTGAGGGGTC
* * *
25457825 AAAATATAATTTTT-GTAAAGTTTAGGGGTA
1 AAAATGTAATTTTTAG-AAAGTTGAGGGGTC
* *
25457855 AAAATGTAGTTTTTAGAAAGTTCGA-CGGTC
1 AAAATGTAATTTTTAGAAAGTT-GAGGGGTC
* *
25457885 AAAATATAATTTTTAGATAGTTGAGGG
1 AAAATGTAATTTTTAGAAAGTTGAGGG
25457912 ACCTATTGGG
Statistics
Matches: 122, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
28 1 0.01
29 26 0.21
30 88 0.72
31 7 0.06
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTAGAAAGTTGAGGGGTC
Found at i:25461076 original size:13 final size:13
Alignment explanation
Indices: 25461058--25461095 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
25461048 CAATTTATTC
25461058 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
25461071 TTCTTTCTTTT-TT
1 TTCTTT-TTTTCTT
25461084 TTCATTTTTTTC
1 TTC-TTTTTTTC
25461096 AAGTGACTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:25461084 original size:18 final size:18
Alignment explanation
Indices: 25461061--25461095 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25461051 TTTATTCTTC
25461061 TTTTTTTC-TTTTCTTTCT
1 TTTTTTTCATTTT-TTTCT
25461079 TTTTTTTCATTTTTTTC
1 TTTTTTTCATTTTTTTC
25461096 AAGTGACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTCATTTTTTTCT
Found at i:25461716 original size:17 final size:16
Alignment explanation
Indices: 25461686--25461729 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
25461676 AAGCTAAAAG
*
25461686 GAATGCAGTGACAATTA
1 GAATGCA-TGACAATAA
*
25461703 TAATGCATGCACAATAA
1 GAATGCATG-ACAATAA
25461720 GAATGCATGA
1 GAATGCATGA
25461730 AAACTAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (16 bp):
GAATGCATGACAATAA
Found at i:25469709 original size:23 final size:23
Alignment explanation
Indices: 25469631--25469737 Score: 101
Period size: 23 Copynumber: 4.5 Consensus size: 23
25469621 CGAAGTACTT
25469631 AACAGTAAGCACAC-AAGTGCTGAGGA
1 AACAGTAAGCACACAAAGTGC----GA
* *
25469657 AACAGTAAGCACACATAGTG-TA
1 AACAGTAAGCACACAAAGTGCGA
* * *
25469679 ATCCAGTAGGCACACACAGTGCGA
1 A-ACAGTAAGCACACAAAGTGCGA
*
25469703 AATAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
25469726 AACAGTAAGCAC
1 AACAGTAAGCAC
25469738 GCTAGCGTTC
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
22 2 0.03
23 45 0.67
24 2 0.03
26 14 0.21
27 4 0.06
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:25473667 original size:18 final size:18
Alignment explanation
Indices: 25473636--25473680 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
25473626 TATAAAAAAT
25473636 ATAAAT-AT-AATTTAAA
1 ATAAATAATAAATTTAAA
* *
25473652 TTTAATAATAAATTTAAA
1 ATAAATAATAAATTTAAA
25473670 ATAAATAATAA
1 ATAAATAATAA
25473681 GTATACTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.17
17 2 0.09
18 17 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATAATAAATTTAAA
Found at i:25474050 original size:21 final size:21
Alignment explanation
Indices: 25474026--25474100 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
25474016 GAAATTTAAA
*
25474026 ACAAACATAATGATAAGAGTT
1 ACAAACATAATGAGAAGAGTT
*
25474047 ACAAA-ACTTATGAGGAA-AGTT
1 ACAAACA-TAATGA-GAAGAGTT
* * *
25474068 ACAAACATTATGAGGAGAATT
1 ACAAACATAATGAGAAGAGTT
25474089 ACAAACATAATG
1 ACAAACATAATG
25474101 TTTTGTAGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.23
Consensus pattern (21 bp):
ACAAACATAATGAGAAGAGTT
Found at i:25476123 original size:3 final size:3
Alignment explanation
Indices: 25476115--25476142 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25476105 ATAAGCGATG
25476115 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
25476143 TGGTAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:25477082 original size:14 final size:13
Alignment explanation
Indices: 25477063--25477101 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
25477053 ATAGTAGTAC
25477063 ATTATATATTACTT
1 ATTATATATTA-TT
25477077 ATTATATATTATT
1 ATTATATATTATT
25477090 ATT-TATTATTAT
1 ATTATA-TATTAT
25477102 ACTAGTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.08
13 11 0.46
14 11 0.46
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATATATTATT
Found at i:25477300 original size:16 final size:16
Alignment explanation
Indices: 25477279--25477332 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
25477269 ATAATCTATA
25477279 ATATAATAATAGTTAT
1 ATATAATAATAGTTAT
*
25477295 ATATAATAGTAGTATATT
1 ATATAATAATAGT-TA-T
** *
25477313 ATATGCTAATAATTAT
1 ATATAATAATAGTTAT
25477329 ATAT
1 ATAT
25477333 TTTTGTCTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 17 0.55
17 4 0.13
18 10 0.32
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (16 bp):
ATATAATAATAGTTAT
Found at i:25483415 original size:17 final size:16
Alignment explanation
Indices: 25483386--25483421 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
25483376 AATAACTGGC
25483386 AATAAAAATAAAAATA
1 AATAAAAATAAAAATA
*
25483402 AATAAAACATAAAACTA
1 AATAAAA-ATAAAAATA
25483419 AAT
1 AAT
25483422 GAAATCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
AATAAAAATAAAAATA
Found at i:25483561 original size:30 final size:30
Alignment explanation
Indices: 25483506--25483598 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
25483496 AAAAAAAGGT
* *
25483506 ACATGGCCATGT-GTCAGGCCATGTGAGCC
1 ACATGGCCATGTGGCCAGACCATGTGAGCC
* *
25483535 ACATGG-CAGTGTGGCTAGATCATGTGAGCC
1 ACATGGCCA-TGTGGCCAGACCATGTGAGCC
* * *
25483565 ACACGGCCATTTGGCCAGGCCATGTGAGCC
1 ACATGGCCATGTGGCCAGACCATGTGAGCC
25483595 ACAT
1 ACAT
25483599 AATCGTGTGA
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 2 0.04
29 9 0.18
30 38 0.75
31 2 0.04
ACGTcount: A:0.23, C:0.27, G:0.30, T:0.20
Consensus pattern (30 bp):
ACATGGCCATGTGGCCAGACCATGTGAGCC
Found at i:25486061 original size:23 final size:23
Alignment explanation
Indices: 25486035--25486099 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 23
25486025 GCACATGAAT
25486035 ATATGAGAGCCCTTTTATGGGAC
1 ATATGAGAGCCCTTTTATGGGAC
* *
25486058 ATATGAGAACCC-TTTATGGGAT
1 ATATGAGAGCCCTTTTATGGGAC
* * *
25486080 GTATGAAAGCCCTTTAATGG
1 ATATGAGAGCCCTTTTATGG
25486100 CGGTAAAGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (23 bp):
ATATGAGAGCCCTTTTATGGGAC
Found at i:25486499 original size:17 final size:18
Alignment explanation
Indices: 25486463--25486500 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25486453 ATTACTATTA
* *
25486463 TTAAATATGTTTTTTAAT
1 TTAAATATATTTTATAAT
25486481 TTAAATATATTTTAT-AT
1 TTAAATATATTTTATAAT
25486498 TTA
1 TTA
25486501 TCTTGAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TTAAATATATTTTATAAT
Found at i:25487430 original size:16 final size:17
Alignment explanation
Indices: 25487399--25487432 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25487389 CTGAATATAT
*
25487399 AAAATTTAAACATAAAA
1 AAAATCTAAACATAAAA
25487416 AAAATCTAAAC-TAAAA
1 AAAATCTAAACATAAAA
25487432 A
1 A
25487433 GAGTTAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATCTAAACATAAAA
Found at i:25496410 original size:18 final size:17
Alignment explanation
Indices: 25496383--25496421 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
25496373 ATTTTTTTTC
25496383 TTTT-TCATTTTCTTCCT
1 TTTTCTCATTTT-TTCCT
*
25496400 TTTTCTCATTTTTTTCT
1 TTTTCTCATTTTTTCCT
25496417 TTTTC
1 TTTTC
25496422 AAGTGATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTCTCATTTTTTCCT
Found at i:25496710 original size:41 final size:41
Alignment explanation
Indices: 25496654--25496737 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
25496644 TTGGTAAGTT
*
25496654 AGTTCAAGATCCAAAGAGTGATACTATCCATTTTTTATTGA
1 AGTTCAAGATCCAAAGAGTGATACTATCCATTTATTATTGA
25496695 AGTTCAAGATCCAAAGAGTGATACTATCCATTTATTATTGA
1 AGTTCAAGATCCAAAGAGTGATACTATCCATTTATTATTGA
25496736 AG
1 AG
25496738 CAATTCCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (41 bp):
AGTTCAAGATCCAAAGAGTGATACTATCCATTTATTATTGA
Found at i:25498652 original size:12 final size:14
Alignment explanation
Indices: 25498625--25498656 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
25498615 AAGATAACAA
25498625 GTAAAAGTGAAAAT
1 GTAAAAGTGAAAAT
25498639 GTAAAAG-G-AAAT
1 GTAAAAGTGAAAAT
25498651 GTAAAA
1 GTAAAA
25498657 TACGTTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (14 bp):
GTAAAAGTGAAAAT
Found at i:25503894 original size:18 final size:18
Alignment explanation
Indices: 25503871--25503907 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25503861 ACTACTTATT
* *
25503871 ACTTGTACGACCGTGTAC
1 ACTTGTACAACAGTGTAC
25503889 ACTTGTACAACAGTGTAC
1 ACTTGTACAACAGTGTAC
25503907 A
1 A
25503908 TTTGCATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (18 bp):
ACTTGTACAACAGTGTAC
Found at i:25507930 original size:21 final size:21
Alignment explanation
Indices: 25507906--25507954 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
25507896 TGTTGTCAAA
*
25507906 ACATAGTTTATGTATGTCGCG
1 ACATAGTTTATGTATGTCACG
*
25507927 ACATAGTTTATGTATGTCATG
1 ACATAGTTTATGTATGTCACG
25507948 ACATAGT
1 ACATAGT
25507955 GATTAACTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (21 bp):
ACATAGTTTATGTATGTCACG
Found at i:25511330 original size:21 final size:19
Alignment explanation
Indices: 25511298--25511336 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
25511288 AAACACAATT
25511298 AAATATTAATAAAATAAAC
1 AAATATTAATAAAATAAAC
25511317 AAATAATTAAATAAAATAAA
1 AAAT-ATT-AATAAAATAAA
25511337 AACTGACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 3 0.17
21 11 0.61
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATATTAATAAAATAAAC
Found at i:25514114 original size:28 final size:28
Alignment explanation
Indices: 25514062--25514209 Score: 149
Period size: 28 Copynumber: 5.3 Consensus size: 28
25514052 ATTCGAGGCA
* * * *
25514062 AGCTATAAACAGGTGAAATCTCTACCCG
1 AGCTATAAATAGATCAAAGCTCTACCCG
* *
25514090 AGCTATAAAT-GATTCAAAGCACTACGCG
1 AGCTATAAATAGA-TCAAAGCTCTACCCG
25514118 AGCTAT-AATAGATCAAAGCTCTACCCG
1 AGCTATAAATAGATCAAAGCTCTACCCG
*
25514145 AGCTATAAGT-GAATCAAAGCTCTACCCG
1 AGCTATAAATAG-ATCAAAGCTCTACCCG
* * * * *
25514173 AACTGTAAATGGATCAAAGCTCTACTCA
1 AGCTATAAATAGATCAAAGCTCTACCCG
25514201 AGCTATAAA
1 AGCTATAAA
25514210 CAGAGTATCG
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
27 24 0.24
28 74 0.75
29 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (28 bp):
AGCTATAAATAGATCAAAGCTCTACCCG
Found at i:25514147 original size:55 final size:56
Alignment explanation
Indices: 25514081--25514209 Score: 170
Period size: 55 Copynumber: 2.3 Consensus size: 56
25514071 CAGGTGAAAT
* * *
25514081 CTCTACCCGAGCTATAAATGATTCAAAGCACTACGCGAGCTAT-AATAGATCAAAG
1 CTCTACCCGAGCTATAAATGAATCAAAGCACTACCCGAACTATAAATAGATCAAAG
* * * *
25514136 CTCTACCCGAGCTATAAGTGAATCAAAGCTCTACCCGAACTGTAAATGGATCAAAG
1 CTCTACCCGAGCTATAAATGAATCAAAGCACTACCCGAACTATAAATAGATCAAAG
* *
25514192 CTCTACTCAAGCTATAAA
1 CTCTACCCGAGCTATAAA
25514210 CAGAGTATCG
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
55 37 0.59
56 26 0.41
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (56 bp):
CTCTACCCGAGCTATAAATGAATCAAAGCACTACCCGAACTATAAATAGATCAAAG
Found at i:25522154 original size:21 final size:21
Alignment explanation
Indices: 25522106--25522163 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
25522096 CATTGACGAG
25522106 TGTTGT-GACTGCATCTAATTC
1 TGTTGTGGA-TGCATCTAATTC
*
25522127 TGGTGTGGATGCATCTAGATT-
1 TGTTGTGGATGCATCTA-ATTC
*
25522148 TGTTGTGTATGCATCT
1 TGTTGTGGATGCATCT
25522164 GAGCGTACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (21 bp):
TGTTGTGGATGCATCTAATTC
Found at i:25541604 original size:19 final size:19
Alignment explanation
Indices: 25541580--25541617 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
25541570 TCCTAATGCT
*
25541580 ATCACACCTCCAAACTTAA
1 ATCACACCCCCAAACTTAA
25541599 ATCACACCCCCAAACTTAA
1 ATCACACCCCCAAACTTAA
25541618 GTTTTTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.18
Consensus pattern (19 bp):
ATCACACCCCCAAACTTAA
Done.