Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008194.1 Hibiscus syriacus cultivar Beakdansim tig00110813_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: 2426039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:2235563 original size:33 final size:33
Alignment explanation
Indices: 2235521--2235647 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
2235511 ACTAAAATCG
* *
2235521 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2235554 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
2235587 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2235620 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2235648 GGTCAATGAT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:2235594 original size:14 final size:14
Alignment explanation
Indices: 2235542--2235629 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
2235532 TCATTTCGCT
*
2235542 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
2235556 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
2235573 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
2235589 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
2235606 CATTGCGATTCTATCG
1 --TTGCGATTCTCTCG
2235622 TTGCGATT
1 TTGCGATT
2235630 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 13 0.22
19 12 0.20
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2238190 original size:24 final size:24
Alignment explanation
Indices: 2238156--2238209 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2238146 CTGAAACATC
* *
2238156 ATCAAAATCCGAGTATTGACTAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
2238180 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2238204 ATCAAA
1 ATCAAA
2238210 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2239236 original size:33 final size:33
Alignment explanation
Indices: 2239194--2239320 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
2239184 TCATTTGACC
*
2239194 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2239227 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2239260 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2239293 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2239321 CTATTTTAGT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2239367 original size:33 final size:33
Alignment explanation
Indices: 2239330--2239513 Score: 142
Period size: 33 Copynumber: 5.4 Consensus size: 33
2239320 GCTATTTTAG
*
2239330 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
*
2239363 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
* *
2239396 TTTCGCATTGCGATTTTCAT--TT-CGCA-TTGCGA
1 TTTCGCGTTGCGATTTTC-TCGTTGCG-ATTTTC-A
*
2239428 TTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TT-TCGCGTTGCGATTTTC---TCG--TTGCGATTTTCA
* * * * **
2239467 TTTCGCATTGCGATTCTATCGTTACGATAGTCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
*
2239500 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
2239514 CAGTCTGTTT
Statistics
Matches: 120, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
31 5 0.04
32 6 0.05
33 70 0.58
34 12 0.10
35 4 0.03
38 12 0.10
39 6 0.05
40 5 0.04
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
Found at i:2239373 original size:19 final size:19
Alignment explanation
Indices: 2239351--2239481 Score: 165
Period size: 19 Copynumber: 7.4 Consensus size: 19
2239341 GATTTTGTCG
*
2239351 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*
2239370 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2239384 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2239403 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2239422 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2239436 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2239455 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2239474 TTGCGATT
1 TTGCGATT
2239482 CTATCGTTAC
Statistics
Matches: 98, Mismatches: 4, Indels: 20
0.80 0.03 0.16
Matches are distributed among these distances:
14 12 0.12
16 14 0.14
17 14 0.14
19 58 0.59
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2239414 original size:52 final size:52
Alignment explanation
Indices: 2239351--2239494 Score: 261
Period size: 52 Copynumber: 2.8 Consensus size: 52
2239341 GATTTTGTCG
*
2239351 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
2239403 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
* *
2239455 TTGCGATTTTCATTTCGCATTGCGATTCTATCGTTACGAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGAT
2239495 AGTCAGTTTC
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 89 1.00
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:2241108 original size:42 final size:42
Alignment explanation
Indices: 2241053--2241145 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
2241043 CCTCTTCAAC
* *
2241053 GATGACAGTGGCCTCTTGAACG-GTGGGGGGAGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGG-GACTCTTGAGG
* *
2241095 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
2241137 GATGACAGG
1 GATGACAGG
2241146 TGAGTCGGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
42 39 0.87
43 6 0.13
ACGTcount: A:0.22, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:2241110 original size:21 final size:21
Alignment explanation
Indices: 2241084--2241141 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
2241074 GGTGGGGGGA
*
2241084 GACTCTTGAGGGATGATAGGG
1 GACTCTTGAGGGATGAGAGGG
* **
2241105 GCCTCTTGAACGATTG-GAGGG
1 GACTCTTGAGGGA-TGAGAGGG
2241126 GACTCTTGAGGGATGA
1 GACTCTTGAGGGATGA
2241142 CAGGTGAGTC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.22, C:0.14, G:0.40, T:0.24
Consensus pattern (21 bp):
GACTCTTGAGGGATGAGAGGG
Found at i:2241508 original size:20 final size:19
Alignment explanation
Indices: 2241483--2241534 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
2241473 AAGAATAGTT
2241483 TACTTTCGCAACACGAAACA
1 TACTTTCGCAACACGAAA-A
*
2241503 TACTTTCGCAACGCGAAAA
1 TACTTTCGCAACACGAAAA
*
2241522 TGACTATCGCAAC
1 T-ACTTTCGCAAC
2241535 GCGGAAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (19 bp):
TACTTTCGCAACACGAAAA
Found at i:2241535 original size:20 final size:19
Alignment explanation
Indices: 2241508--2241617 Score: 105
Period size: 19 Copynumber: 5.7 Consensus size: 19
2241498 AAACATACTT
**
2241508 TCGCAACGCGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
2241528 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
2241548 TCGCAATC-CGAAATGAAAA
1 TCGCAA-CGCGAAATGAAAA
**
2241567 TCGCATTGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
**
2241586 TCGCATTGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2241605 TCGCAACGCGAAA
1 TCGCAACGCGAAA
2241618 CACAAATCGC
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
19 53 0.67
20 24 0.30
21 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2241562 original size:19 final size:20
Alignment explanation
Indices: 2241508--2241553 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2241498 AAACATACTT
*
2241508 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2241528 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
2241548 TCGCAA
1 TCGCAA
2241554 TCCGAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2241569 original size:19 final size:19
Alignment explanation
Indices: 2241547--2241617 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
2241537 GGAAATGGCT
*
2241547 ATCGCAATCCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2241566 ATCGCATTGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2241585 ATCGCATTGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2241604 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2241618 CACAAATCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2241616 original size:38 final size:38
Alignment explanation
Indices: 2241527--2241634 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 38
2241517 GAAAATGACT
*** * *
2241527 ATCGCAACGCGGAAATGGCTATCGCAATCCGAAATGAAA
1 ATCGCAACGC-GAAATGAAAATCGCATTGCGAAATGAAA
**
2241566 ATCGCATTGCGAAATGAAAATCGCATTGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCATTGCGAAATGAAA
*
2241604 ATCGCAACGCGAAA-CACAAATCGCATTGCGA
1 ATCGCAACGCGAAATGA-AAATCGCATTGCGA
2241635 TTTTCATTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
37 1 0.02
38 49 0.84
39 8 0.14
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCATTGCGAAATGAAA
Found at i:2241634 original size:19 final size:19
Alignment explanation
Indices: 2241556--2241634 Score: 115
Period size: 19 Copynumber: 4.2 Consensus size: 19
2241546 TATCGCAATC
2241556 CGAAATGAAAATCGCATTG
1 CGAAATGAAAATCGCATTG
2241575 CGAAATGAAAATCGCATTG
1 CGAAATGAAAATCGCATTG
**
2241594 CGAAATGAAAATCGCAACG
1 CGAAATGAAAATCGCATTG
*
2241613 CGAAA-CACAAATCGCATTG
1 CGAAATGA-AAATCGCATTG
2241632 CGA
1 CGA
2241635 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
18 1 0.02
19 53 0.98
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.16
Consensus pattern (19 bp):
CGAAATGAAAATCGCATTG
Found at i:2241646 original size:19 final size:19
Alignment explanation
Indices: 2241624--2241758 Score: 146
Period size: 19 Copynumber: 7.6 Consensus size: 19
2241614 GAAACACAAA
2241624 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2241643 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2241659 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2241676 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2241695 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
2241714 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
2241730 TCG--TTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
2241747 TCGCATTGCGAT
1 TCGCATTGCGAT
2241759 AGCCATTTTC
Statistics
Matches: 99, Mismatches: 7, Indels: 20
0.79 0.06 0.16
Matches are distributed among these distances:
14 12 0.12
15 6 0.06
16 8 0.08
17 8 0.08
18 6 0.06
19 59 0.60
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2241671 original size:33 final size:33
Alignment explanation
Indices: 2241629--2241758 Score: 170
Period size: 33 Copynumber: 3.8 Consensus size: 33
2241619 ACAAATCGCA
2241629 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
2241662 TTGCGATTTTCATTTCGCAATGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA-TTT--TGTCG
* *
2241698 CAATGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
2241733 TTGCGATTTTAATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2241759 AGCCATTTTC
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
33 47 0.57
34 3 0.04
35 4 0.05
36 4 0.05
37 3 0.04
38 22 0.27
ACGTcount: A:0.15, C:0.18, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2241699 original size:71 final size:71
Alignment explanation
Indices: 2241624--2241758 Score: 234
Period size: 71 Copynumber: 1.9 Consensus size: 71
2241614 GAAACACAAA
* *
2241624 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCAATGCGATT
1 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTAATTTCGCAATGCGATT
2241689 TTCATT
66 TTCATT
* *
2241695 TCGCAATGCGATTTTCATTTCGCGTTGCGATTTTGTCGTTGCGATTTTAATTTCGCATTGCGAT
1 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTAATTTCGCAATGCGAT
2241759 AGCCATTTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (71 bp):
TCGCAATGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTAATTTCGCAATGCGATT
TTCATT
Found at i:2241794 original size:20 final size:20
Alignment explanation
Indices: 2241745--2241797 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2241735 GCGATTTTAA
*
2241745 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
2241765 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
2241785 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
2241798 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:2242339 original size:18 final size:18
Alignment explanation
Indices: 2242316--2242364 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
2242306 TGTCGTTGTG
2242316 GAGGTGTATAG-TCTGGGT
1 GAGGTG-ATAGCTCTGGGT
2242334 GAGGTGATAGCTCTGGGT
1 GAGGTGATAGCTCTGGGT
*
2242352 GAGGTGATGGCTC
1 GAGGTGATAGCTC
2242365 CCGAAGTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.16, C:0.10, G:0.45, T:0.29
Consensus pattern (18 bp):
GAGGTGATAGCTCTGGGT
Found at i:2243732 original size:20 final size:20
Alignment explanation
Indices: 2243685--2243742 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2243675 ATAGTTTCTA
* *
2243685 AAAATGAAAATCGCAACACG
1 AAAATGACAATCGCAACGCG
2243705 AAAATGACAATCGCAACGCG
1 AAAATGACAATCGCAACGCG
** *
2243725 AATTTGACTATCGCAACG
1 AAAATGACAATCGCAACG
2243743 AGAGAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAATGACAATCGCAACGCG
Found at i:2244023 original size:20 final size:21
Alignment explanation
Indices: 2243998--2244046 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2243988 TCTGAGAGAT
2243998 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
2244018 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
*
2244040 AGAGATG
1 GGAGATG
2244047 GGTGAGAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:2244032 original size:22 final size:22
Alignment explanation
Indices: 2244005--2244048 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2243995 GATGGAGATA
*
2244005 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
2244027 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
2244049 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:2244264 original size:20 final size:20
Alignment explanation
Indices: 2244235--2244298 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
2244225 GATTATGTAT
2244235 TATCTCGTTGCGAAAGTCAG
1 TATCTCGTTGCGAAAGTCAG
* *
2244255 TATCTAGTTGCGAAAGTAAG
1 TATCTCGTTGCGAAAGTCAG
* *
2244275 TATCGCGTTGCGAAAGTCAA
1 TATCTCGTTGCGAAAGTCAG
2244295 TATC
1 TATC
2244299 GCATTGCGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (20 bp):
TATCTCGTTGCGAAAGTCAG
Found at i:2244349 original size:20 final size:20
Alignment explanation
Indices: 2244242--2244348 Score: 92
Period size: 20 Copynumber: 5.3 Consensus size: 20
2244232 TATTATCTCG
*
2244242 TTGCGAAAGTCAGTATC-TA
1 TTGCGAAAGTCAGTATCGCA
* *
2244261 GTTGCGAAAGTAAGTATCGCG
1 -TTGCGAAAGTCAGTATCGCA
*
2244282 TTGCGAAAGTCAATATCGCA
1 TTGCGAAAGTCAGTATCGCA
** * *
2244302 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--AAGTCAGTATCGCA
*
2244323 TTGCGATAGTCAGTATCGCA
1 TTGCGAAAGTCAGTATCGCA
2244343 TTGCGA
1 TTGCGA
2244349 TTTTCCAAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.04
20 52 0.74
21 13 0.19
22 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (20 bp):
TTGCGAAAGTCAGTATCGCA
Found at i:2244352 original size:41 final size:41
Alignment explanation
Indices: 2244215--2244350 Score: 161
Period size: 41 Copynumber: 3.3 Consensus size: 41
2244205 CGCTTTGAAA
* *
2244215 ATCGTATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
2244256 ATC-TAGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAAT
1 ATCGCA-TTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* *
2244296 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
2244337 ATCGCATTGCGATT
1 ATCGCATTGCGATT
2244351 TTCCAAATTC
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
39 3 0.04
40 31 0.39
41 44 0.55
42 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:2244368 original size:41 final size:41
Alignment explanation
Indices: 2244275--2244370 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
2244265 CGAAAGTAAG
* ** *
2244275 TATCGCGTTGCGAAAGTCAATATCGCATTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAATATCGCATTGCGATTTTCAAA
*
2244316 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAA
1 TATCGCGTTGCGATAGTCAATATCGCATTGCGATTTT-CAAA
*
2244358 T-TCGCATTGCGAT
1 TATCGCGTTGCGAT
2244371 TTACTTATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAATATCGCATTGCGATTTTCAAA
Found at i:2244382 original size:20 final size:21
Alignment explanation
Indices: 2244338--2244385 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2244328 ATAGTCAGTA
*
2244338 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
2244359 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
2244379 TCGCATT
1 TCGCATT
2244386 ACGCATTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:2244414 original size:21 final size:21
Alignment explanation
Indices: 2244390--2244474 Score: 95
Period size: 21 Copynumber: 4.1 Consensus size: 21
2244380 CGCATTACGC
2244390 ATTGGTAAAATCGCAATGCGA
1 ATTGGTAAAATCGCAATGCGA
*
2244411 ATTGGGAAAATCGCAATGCGAA
1 ATTGGTAAAATCGCAATGCG-A
*
2244433 ATTGG-AAAATCGCATTGCG-
1 ATTGGTAAAATCGCAATGCGA
* *
2244452 A-TAGTAATAATCGCATTGCGA
1 ATTGGTAA-AATCGCAATGCGA
2244473 AT
1 AT
2244475 CTGGAAACTG
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
18 2 0.04
19 3 0.05
20 12 0.21
21 33 0.59
22 6 0.11
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (21 bp):
ATTGGTAAAATCGCAATGCGA
Found at i:2250486 original size:36 final size:36
Alignment explanation
Indices: 2250431--2250653 Score: 214
Period size: 36 Copynumber: 6.2 Consensus size: 36
2250421 TTATAGCCAG
* * *
2250431 CAGGCCGGCCAGACTCGGTACCATTGCTAGCACCAA
1 CAGGCCGTCCAGGCCCGGTACCATTGCTAGCACCAA
* *
2250467 TAGGCCGTCCAGGCCCGGTACCATTGCTAGCTCCAA
1 CAGGCCGTCCAGGCCCGGTACCATTGCTAGCACCAA
* * *
2250503 CAGGCCGTACAGGCCCGGTACCATTGCTAGCTCCAG
1 CAGGCCGTCCAGGCCCGGTACCATTGCTAGCACCAA
* * * * *
2250539 CATGCCGAT-TAGGGCCAGTACCACTGCTAGCACCAA
1 CAGGCCG-TCCAGGCCCGGTACCATTGCTAGCACCAA
* * ** * *
2250575 CAGGTCGACCAGGCCAAGTACCACTGCTAACACCAA
1 CAGGCCGTCCAGGCCCGGTACCATTGCTAGCACCAA
* *** *
2250611 CAGGTCGTCCAATTCCGGTACCATTGCTAGCACAAA
1 CAGGCCGTCCAGGCCCGGTACCATTGCTAGCACCAA
2250647 CAGGCCG
1 CAGGCCG
2250654 GCTAGACCCC
Statistics
Matches: 153, Mismatches: 32, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
36 152 0.99
37 1 0.01
ACGTcount: A:0.25, C:0.35, G:0.24, T:0.16
Consensus pattern (36 bp):
CAGGCCGTCCAGGCCCGGTACCATTGCTAGCACCAA
Found at i:2254073 original size:20 final size:20
Alignment explanation
Indices: 2254031--2254072 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2254021 TTATTTTAGA
2254031 TTTACTTTTTAATAATAATT
1 TTTACTTTTTAATAATAATT
2254051 TTTACTTTTTAATAAT-ATT
1 TTTACTTTTTAATAATAATT
2254070 TTT
1 TTT
2254073 TTTGTGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTACTTTTTAATAATAATT
Found at i:2257449 original size:64 final size:63
Alignment explanation
Indices: 2257380--2257603 Score: 206
Period size: 64 Copynumber: 3.5 Consensus size: 63
2257370 TTATATGAAT
* *
2257380 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTATTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCACCCA--TTAATAATAAA-ACATCGAATGCAA-T
2257443 C-
62 CG
* * *
2257444 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
** ** * ** *
2257508 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAACAATAATACTACATCGAATACCTTTG
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
* *
2257572 ATGCACCGATGCATCA-GTAGTGCATCGATGCA
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCA
2257604 TACCTTCATT
Statistics
Matches: 135, Mismatches: 19, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
63 3 0.02
64 124 0.92
65 6 0.04
66 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCACCCATTAATAATAAAACATCGAATGCAATCG
Found at i:2257930 original size:12 final size:12
Alignment explanation
Indices: 2257913--2257959 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
2257903 ATATATGTTC
2257913 ATGTGATATGAT
1 ATGTGATATGAT
2257925 ATGTGATATGAT
1 ATGTGATATGAT
*
2257937 ATGTGATATGAC
1 ATGTGATATGAT
*
2257949 ATGTAATATGA
1 ATGTGATATGA
2257960 GAACATGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.38
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:2258122 original size:15 final size:15
Alignment explanation
Indices: 2258104--2258150 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
2258094 GAGGGTATAA
2258104 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2258119 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2258134 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2258149 TA
1 TA
2258151 ATGGTCCTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.32, T:0.34
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:2264394 original size:64 final size:63
Alignment explanation
Indices: 2264325--2264548 Score: 206
Period size: 64 Copynumber: 3.5 Consensus size: 63
2264315 TTATATGAAT
* *
2264325 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTATTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCACCCA--TTAATAATAAA-ACATCGAATGCAA-T
2264388 C-
62 CG
* * *
2264389 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
** ** * ** *
2264453 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAACAATAATACTACATCGAATACCTTTG
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
* *
2264517 ATGCACCGATGCATCA-GTAGTGCATCGATGCA
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCA
2264549 TACCTTCATT
Statistics
Matches: 135, Mismatches: 19, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
63 3 0.02
64 124 0.92
65 6 0.04
66 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCACCCATTAATAATAAAACATCGAATGCAATCG
Found at i:2264875 original size:12 final size:12
Alignment explanation
Indices: 2264857--2264892 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2264847 TATATATGTT
2264857 CATGTGATATGA
1 CATGTGATATGA
*
2264869 TATGTGATATGA
1 CATGTGATATGA
*
2264881 CATGTAATATGA
1 CATGTGATATGA
2264893 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:2265055 original size:15 final size:15
Alignment explanation
Indices: 2265037--2265083 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
2265027 GAGGGTATAA
2265037 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2265052 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2265067 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2265082 TA
1 TA
2265084 ATGGTCCTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.32, T:0.34
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:2268132 original size:14 final size:13
Alignment explanation
Indices: 2268106--2268135 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
2268096 TGTGCCGTCA
2268106 TTTCTTTTTTTTC
1 TTTCTTTTTTTTC
2268119 TTTCTTTCTTTTTC
1 TTTCTTT-TTTTTC
2268133 TTT
1 TTT
2268136 TTTAATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:2268339 original size:11 final size:13
Alignment explanation
Indices: 2268315--2268343 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2268305 AATATTTTTC
2268315 AATAATTTTATAT
1 AATAATTTTATAT
2268328 AATAATTTTATA-
1 AATAATTTTATAT
2268340 AATA
1 AATA
2268344 TAATCTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATAATTTTATAT
Found at i:2273729 original size:42 final size:42
Alignment explanation
Indices: 2273682--2273769 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
2273672 CAAATGTGTA
* * * *
2273682 TTTGTTTCACTTACTTCGTTTTTTGAAAAATATTTTTTCA-TG
1 TTTGTTTCACGTAATTCATTTTTTAAAAAATA-TTTTTCAGTG
* *
2273724 TTTGTTTTACGTAATTTATTTTTTAAAAAATATTTTTCAGTG
1 TTTGTTTCACGTAATTCATTTTTTAAAAAATATTTTTCAGTG
2273766 TTTG
1 TTTG
2273770 GTTAGAGGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 7 0.18
42 32 0.82
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (42 bp):
TTTGTTTCACGTAATTCATTTTTTAAAAAATATTTTTCAGTG
Found at i:2274022 original size:17 final size:17
Alignment explanation
Indices: 2274000--2274038 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2273990 AATATTTTTT
2274000 TAATATTTCTAATAATA
1 TAATATTTCTAATAATA
* *
2274017 TAATATTTTTAATATTA
1 TAATATTTCTAATAATA
2274034 TAATA
1 TAATA
2274039 AAATAATCAA
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATATTTCTAATAATA
Found at i:2274074 original size:23 final size:23
Alignment explanation
Indices: 2274009--2274078 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
2273999 TTAATATTTC
* *
2274009 TAATAATATAATATTTTTAATATTA
1 TAATAATATAACA-TATT-ATATTA
*
2274034 TAATAAAATAATCA-ATTATATTA
1 TAATAATATAA-CATATTATATTA
*
2274057 TAATAATATAAGATATTATATT
1 TAATAATATAACATATTATATT
2274079 TTTATTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 24 0.63
24 2 0.05
25 10 0.26
26 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
TAATAATATAACATATTATATTA
Found at i:2274107 original size:29 final size:29
Alignment explanation
Indices: 2274019--2274101 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 29
2274009 TAATAATATA
* *
2274019 ATATTTTTAATATTAT-A-ATAAAATAAT
1 ATATTTTTATTATAATAATATAAAATAAT
* * *
2274046 CA-A-TTATATTATAATAATATAAGATATT
1 -ATATTTTTATTATAATAATATAAAATAAT
*
2274074 ATATTTTTATTTTAATAATATAAAATAA
1 ATATTTTTATTATAATAATATAAAATAA
2274102 ATTATTAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
26 9 0.21
27 3 0.07
28 10 0.24
29 20 0.48
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
ATATTTTTATTATAATAATATAAAATAAT
Found at i:2274198 original size:27 final size:27
Alignment explanation
Indices: 2274118--2274203 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
2274108 AATAAAATTT
* *
2274118 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
2274145 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
2274172 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
2274201 ATA
1 ATA
2274204 ATATAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:2274397 original size:22 final size:25
Alignment explanation
Indices: 2274372--2274428 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
2274362 AAATAATATT
2274372 TAATAAT-TTAA-TATTT-TAA-AAA
1 TAATAATATTAAGT-TTTATAATAAA
2274394 TAATAATATTAAGTTTTATAATAAA
1 TAATAATATTAAGTTTTATAATAAA
*
2274419 TAATATTATT
1 TAATAATATT
2274429 TATTATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.23
23 7 0.23
24 4 0.13
25 12 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TAATAATATTAAGTTTTATAATAAA
Found at i:2274442 original size:22 final size:22
Alignment explanation
Indices: 2274371--2274426 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2274361 AAAATAATAT
* *
2274371 TTAATAAT-TTAATATTTTAAAA
1 TTAATAATATTAA-GTTTTATAA
*
2274393 ATAATAATATTAAGTTTTATAA
1 TTAATAATATTAAGTTTTATAA
*
2274415 TAAATAATATTA
1 TTAATAATATTA
2274427 TTTATTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TTAATAATATTAAGTTTTATAA
Found at i:2275236 original size:24 final size:24
Alignment explanation
Indices: 2275198--2275258 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
2275188 GGCTTCAACT
*
2275198 TTCCATCAAAGGAGGGAAAGTGAA
1 TTCCATCAAATGAGGGAAAGTGAA
*
2275222 TTCGATCAAATGAGGGAAAGTGAA
1 TTCCATCAAATGAGGGAAAGTGAA
*
2275246 TTCCATCCAATGA
1 TTCCATCAAATGA
2275259 TGAATGGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (24 bp):
TTCCATCAAATGAGGGAAAGTGAA
Found at i:2275832 original size:260 final size:250
Alignment explanation
Indices: 2275341--2275908 Score: 793
Period size: 260 Copynumber: 2.2 Consensus size: 250
2275331 CTTATTCATA
* * *
2275341 TATTAAATAAAAAT-ATTTTTTTATTATTTCGGGTCAG--GTTTCTAATTCATATATTCGGGTCA
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGTCGTTTCTAATTCATATATTCAGGTCA
*
2275403 GGTGAAACTTTATTTTGATCGGGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTCGGGTCGAG
66 GGTGAAACTTTATTTTGATCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGGGTCGAG
* * * *
2275468 TTCGGGTTTAGGATGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGA
131 TTCGGGTTTAGGATAAAAAAGACCCAACCCAAAAATATATATAATTTTACCTTATATATTTAGGA
* *
2275533 ATAATTACAATAATACATCTCTATATATAATTTTTTTCAATTAAGTCATTGTTTT
196 ATAATTACAATAATACACCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTT
*
2275588 TATTGAATAAAAATAATTTTTTTATTATTTTGGGTCGGTCGAATTTCTAATTCATATATTCAGGT
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGTCG--TTTCTAATTCATATATTCAGGT
* *
2275653 CGGGTAGGGTGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTC-
64 C----A-GGTGAAACTTTATTTTGATCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCG
* * * *
2275717 GGTCGGGTTCGGGTTTAGGGTAAAAAACCGGACCTAACCCAAAAAATATATATAATTTTATCTTA
124 GGTCGAGTTCGGGTTTAGGATAAAAAA---GACCCAACCC-AAAAATATATATAATTTTACCTTA
* *
2275782 TATATTTAGGAGTAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGTTT
185 TATATTTAGGAATAATTACAATAATACACCTCTATATATAATTTTTTTCAATTAAGTCAATGTTT
2275847 T
250 T
* *
2275848 TATTGAATAAAATTAATTTTTTTATTATTTCGTGTCGTGTCGGGTTTCTAATTCATATATT
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCG-GTC--GTTTCTAATTCATATATT
2275909 GAATAAAAAT
Statistics
Matches: 282, Mismatches: 22, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
247 13 0.05
248 21 0.07
250 1 0.00
252 22 0.08
256 25 0.09
257 54 0.19
259 7 0.02
260 118 0.42
261 20 0.07
263 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (250 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGTCGTTTCTAATTCATATATTCAGGTCA
GGTGAAACTTTATTTTGATCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGGGTCGAG
TTCGGGTTTAGGATAAAAAAGACCCAACCCAAAAATATATATAATTTTACCTTATATATTTAGGA
ATAATTACAATAATACACCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTT
Found at i:2278689 original size:2 final size:2
Alignment explanation
Indices: 2278682--2278717 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2278672 TTCATCTTTA
2278682 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
2278718 TAAGTTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2278896 original size:18 final size:18
Alignment explanation
Indices: 2278870--2278919 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
2278860 AGAATGTTTA
* *
2278870 TGAAAGAATTGTAATCTG
1 TGAAGGAATTGGAATCTG
2278888 TGAAGGAATTGGAATCTG
1 TGAAGGAATTGGAATCTG
2278906 T--AGGAATTGGAATC
1 TGAAGGAATTGGAATC
2278920 CAATTCTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 13 0.43
18 17 0.57
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (18 bp):
TGAAGGAATTGGAATCTG
Found at i:2278912 original size:16 final size:17
Alignment explanation
Indices: 2278875--2278919 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
2278865 GTTTATGAAA
*
2278875 GAATTGTAATCTGTGAAG
1 GAATTGGAATCTGT-AAG
2278893 GAATTGGAATCTGT-AG
1 GAATTGGAATCTGTAAG
2278909 GAATTGGAATC
1 GAATTGGAATC
2278920 CAATTCTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.50
18 13 0.50
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (17 bp):
GAATTGGAATCTGTAAG
Found at i:2278959 original size:44 final size:44
Alignment explanation
Indices: 2278909--2279034 Score: 216
Period size: 44 Copynumber: 2.9 Consensus size: 44
2278899 GAATCTGTAG
* *
2278909 GAATTGGAATCCAATTCTATATTCTGTTTCGTTGGCAGGAAATA
1 GAATTGGAATCCAATTCCATATTCTGTTTGGTTGGCAGGAAATA
*
2278953 GAATTGGAATCCAATTCCATATTATGTTTGGTTGGCAGGAAATA
1 GAATTGGAATCCAATTCCATATTCTGTTTGGTTGGCAGGAAATA
*
2278997 GAATTGGAATCCAATTCCATATTCTGTTTGGTTCGCAG
1 GAATTGGAATCCAATTCCATATTCTGTTTGGTTGGCAG
2279035 ACATGTCAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 77 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (44 bp):
GAATTGGAATCCAATTCCATATTCTGTTTGGTTGGCAGGAAATA
Found at i:2279613 original size:26 final size:28
Alignment explanation
Indices: 2279559--2279618 Score: 106
Period size: 26 Copynumber: 2.2 Consensus size: 28
2279549 ACCCGACCTA
2279559 ACCCGAATATCACACTTAAAAAAACCCG
1 ACCCGAATATCACACTTAAAAAAACCCG
2279587 ACCCGAATATCACAC-T-AAAAAACCCG
1 ACCCGAATATCACACTTAAAAAAACCCG
2279613 ACCCGA
1 ACCCGA
2279619 CCCAAACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 16 0.50
27 1 0.03
28 15 0.47
ACGTcount: A:0.45, C:0.35, G:0.08, T:0.12
Consensus pattern (28 bp):
ACCCGAATATCACACTTAAAAAAACCCG
Found at i:2280103 original size:247 final size:246
Alignment explanation
Indices: 2279738--2280215 Score: 714
Period size: 248 Copynumber: 1.9 Consensus size: 246
2279728 ACTTAATCCG
* *
2279738 ACCCGACCCGACTCTACCCGAATATCACACTTAAAAAACCCGACAGACCCGAACAAAATAAAGTT
1 ACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGAC--ACCCGAAAAAAATAAAGTT
*
2279803 TCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCGACCCGAAATAATAAAAAA-TAT
64 TCAT----CCCGACCCGAATATATAAATTAGAAATCCGACCCGACCCGAAATAATAAAAAATTAT
**
2279867 TTTTATTTAATAAAAACAATGACTTAATCCGTCCCGACCTGAATTATATATATTTTCGGGTCGG-
125 TTTTATTTAATAAAAACAATGACTTAATCCAACCCGACCTGAATTATATATATTTTCGGGTCGGT
* * *
2279931 TCTGGTTTTTTTCACCCTAAACCTGAACTCGACCCGACCCGAATATCACACTTAAAAA
190 TC-GATTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAA
*
2279989 ACCCGACCCGATTCGACCCGAATATCACACTTAAAAAACCCGAC-CCC-AAAAAAATAAAGTTTC
1 ACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACACCCGAAAAAAATAAAGTTTC
*
2280052 AT-CCGACCCGAATATATAAATTAGAAATCCAACCCGACCCGACCTGAAATAATAAAAAATTATT
66 ATCCCGACCCGAATATATAAATTAGAAAT-----CCGACCCGACCCGAAATAATAAAAAATTATT
2280116 TTTATTTAATAAAAACAATGACTTAATCCAACCCGACCTGAATTATATATATTTTCGGGTCGGTT
126 TTTATTTAATAAAAACAATGACTTAATCCAACCCGACCTGAATTATATATATTTTCGGGTCGGTT
*
2280181 CGATTTTTTTCACCCTAAACCCGAACCCGATCCGA
191 CGATTTTTTTCACCCTAAACCCGAACCCGACCCGA
2280216 ATATATGAAT
Statistics
Matches: 209, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
242 25 0.12
247 42 0.20
248 98 0.47
249 2 0.01
251 42 0.20
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25
Consensus pattern (246 bp):
ACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACACCCGAAAAAAATAAAGTTTC
ATCCCGACCCGAATATATAAATTAGAAATCCGACCCGACCCGAAATAATAAAAAATTATTTTTAT
TTAATAAAAACAATGACTTAATCCAACCCGACCTGAATTATATATATTTTCGGGTCGGTTCGATT
TTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAA
Found at i:2280645 original size:20 final size:21
Alignment explanation
Indices: 2280620--2280671 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2280610 TTTTCCCAAT
*
2280620 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2280640 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2280661 TCGCAATGCGA
1 TCGCAATGCGA
2280672 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2280685 original size:20 final size:20
Alignment explanation
Indices: 2280660--2280794 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
2280650 AATTGGGAAA
2280660 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
2280680 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2280700 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
2280721 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
2280741 TTCGAAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
2280761 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
2280781 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
2280795 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.68
21 24 0.26
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2280704 original size:61 final size:61
Alignment explanation
Indices: 2280657--2280788 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
2280647 GCGAATTGGG
* * * * * *
2280657 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGAAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
2280718 AAAATCGCAACGAGATACTGACTTTCGAAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGAAACGCGATACTGACTATCGCAACGCGATAATAC
*
2280779 ATAATCGCAA
1 AAAATCGCAA
2280789 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGAAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:2280990 original size:22 final size:22
Alignment explanation
Indices: 2280962--2281005 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2280952 CACTCTCTCA
2280962 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2280984 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2281006 TATCTTCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2281322 original size:20 final size:20
Alignment explanation
Indices: 2281268--2281326 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2281258 GCGATTCTCT
**
2281268 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
2281288 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
2281308 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
2281327 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2281517 original size:25 final size:24
Alignment explanation
Indices: 2281463--2281517 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2281453 TGTTTATTAT
* *
2281463 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2281487 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2281513 TGTTT
1 TGTTT
2281518 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2282667 original size:18 final size:18
Alignment explanation
Indices: 2282646--2282690 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2282636 TCCACTTCGG
*
2282646 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2282664 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2282682 GAGCCATCA
1 GAGCCATCA
2282691 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2283303 original size:14 final size:14
Alignment explanation
Indices: 2283284--2283337 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
2283274 TTTCGCATTA
2283284 CGATTTTGTCGTTG
1 CGATTTTGTCGTTG
*
2283298 CGATTTTCATTTCGCATTG
1 CGA-TTT--TGTCG--TTG
2283317 CGATTTTGTCGTTG
1 CGATTTTGTCGTTG
2283331 CGATTTT
1 CGATTTT
2283338 TATTTCGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 6 0.18
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (14 bp):
CGATTTTGTCGTTG
Found at i:2283311 original size:33 final size:33
Alignment explanation
Indices: 2283261--2283353 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
2283251 TTGTGTTTCG
*
2283261 CGTTGCGA-TTTCATTTCGCATTACGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
2283293 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
*
2283326 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2283354 AGCCATTTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 8 0.14
33 50 0.86
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:2283319 original size:19 final size:17
Alignment explanation
Indices: 2283256--2283353 Score: 73
Period size: 18 Copynumber: 5.8 Consensus size: 17
2283246 GCGATTTGTG
*
2283256 TTTCGCGTTGCGATTTCA
1 TTTCGCATTGCGATTT-A
*
2283274 TTTCGCATTACGATTT-
1 TTTCGCATTGCGATTTA
*
2283290 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGA-TTT-A
2283307 TTTCGCATTGCGATTT-
1 TTTCGCATTGCGATTTA
*
2283323 TGTCG--TTGCGATTTTTA
1 TTTCGCATTGCGA--TTTA
2283340 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
2283354 AGCCATTTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 21
0.69 0.08 0.23
Matches are distributed among these distances:
14 11 0.17
15 3 0.05
16 11 0.17
17 9 0.14
18 17 0.27
19 12 0.19
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.48
Consensus pattern (17 bp):
TTTCGCATTGCGATTTA
Found at i:2283365 original size:20 final size:20
Alignment explanation
Indices: 2283340--2283393 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2283330 GCGATTTTTA
*
2283340 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
2283360 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
2283380 TTTTGCGTTGCGAT
1 TTTCGCGTTGCGAT
2283394 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:2283856 original size:42 final size:42
Alignment explanation
Indices: 2283759--2283847 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
2283749 GACTCACCTG
* * *
2283759 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
* * *
2283801 TCCTCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
2283843 TCATC
1 TCATC
2283848 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.44, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
Found at i:2285282 original size:14 final size:14
Alignment explanation
Indices: 2285263--2285298 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2285253 ATTGTTTAAT
2285263 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2285277 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2285291 TGATTTGT
1 TGATTTGT
2285299 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2285447 original size:19 final size:18
Alignment explanation
Indices: 2285425--2285469 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 18
2285415 GAAAATGGCT
2285425 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAA-GAAA
2285444 ATCGCAA--C--AAGAAA
1 ATCGCAATGCGAAAGAAA
2285458 ATCGCAATGCGA
1 ATCGCAATGCGA
2285470 TTTTCATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 9
0.71 0.00 0.29
Matches are distributed among these distances:
14 11 0.50
15 2 0.09
16 1 0.05
17 1 0.05
19 7 0.32
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (18 bp):
ATCGCAATGCGAAAGAAA
Found at i:2285513 original size:20 final size:20
Alignment explanation
Indices: 2285488--2285563 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
2285478 TCGCATTGCG
*
2285488 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
2285508 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
2285529 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
2285548 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
2285564 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:2285521 original size:34 final size:34
Alignment explanation
Indices: 2285476--2285579 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
2285466 GCGATTTTCA
*
2285476 TTTCGCATTGCGATTTTCTAGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
*
2285510 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC---T--AGTTGCGATAGCCAT
* **
2285550 TTTCGCGTTGCGATTTCCCCGTTGCGATAG
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAG
2285580 TCAAATGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 21 0.36
35 5 0.09
38 1 0.02
39 4 0.07
40 27 0.47
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
Found at i:2285802 original size:20 final size:20
Alignment explanation
Indices: 2285777--2285868 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
2285767 TTGAAGATGA
2285777 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
2285797 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
2285817 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
2285838 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
2285858 TTGCGATTTTC
1 TTGCGATTTTC
2285869 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:2285897 original size:20 final size:21
Alignment explanation
Indices: 2285853--2285904 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2285843 ATAGTCAGTA
*
2285853 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
2285874 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
2285894 TCGCATTGCGA
1 TCGCATTGCGA
2285905 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:2286120 original size:12 final size:12
Alignment explanation
Indices: 2286101--2286134 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2286091 CTCTCCGGCG
2286101 ACATCCGTTCCT
1 ACATCCGTTCCT
*
2286113 ATATCCGTTCCT
1 ACATCCGTTCCT
2286125 ACATCC-TTCC
1 ACATCCGTTCC
2286135 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:2286716 original size:24 final size:24
Alignment explanation
Indices: 2286689--2286742 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2286679 GTATTCGAAA
*
2286689 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
2286713 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
2286737 TTTGAT
1 TTTGAT
2286743 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:2286925 original size:3 final size:3
Alignment explanation
Indices: 2286917--2286961 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
2286907 ATATAATCCT
* * *
2286917 GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2286962 AAAGTCCCCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2286934 original size:12 final size:12
Alignment explanation
Indices: 2286917--2286965 Score: 98
Period size: 12 Copynumber: 4.1 Consensus size: 12
2286907 ATATAATCCT
2286917 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2286929 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2286941 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2286953 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2286965 G
1 G
2286966 TCCCCGAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2289298 original size:33 final size:33
Alignment explanation
Indices: 2289256--2289380 Score: 189
Period size: 33 Copynumber: 3.8 Consensus size: 33
2289246 GGAAATTACT
2289256 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
***
2289289 ATCGCAATGCGAAATGAAAATCGCAACTCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2289321 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2289355 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2289381 TGCGAATTTA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2289363 original size:66 final size:66
Alignment explanation
Indices: 2289257--2289380 Score: 239
Period size: 66 Copynumber: 1.9 Consensus size: 66
2289247 GAAATTACTA
2289257 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACTCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACTCTAAT
2289322 T
66 T
*
2289323 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
2289381 TGCGAATTTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACTCTAAT
T
Found at i:2289397 original size:19 final size:19
Alignment explanation
Indices: 2289256--2289386 Score: 96
Period size: 19 Copynumber: 7.7 Consensus size: 19
2289246 GGAAATTACT
2289256 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2289275 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2289289 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2289308 ATCGCAACT-C----T-AAT
1 ATCGCAA-TGCGAAATGAAA
*
2289322 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
2289341 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
2289355 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2289374 ATCGCAATGCGAA
1 ATCGCAATGCGAA
2289387 TTTAATTTCG
Statistics
Matches: 85, Mismatches: 10, Indels: 34
0.66 0.08 0.26
Matches are distributed among these distances:
13 1 0.01
14 28 0.33
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 41 0.48
20 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2289564 original size:14 final size:14
Alignment explanation
Indices: 2289545--2289581 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2289535 CATCAATTAA
2289545 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2289559 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2289573 ACAAATCAA
1 ACAAATCAA
2289582 TTAAACAATA
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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2290986 original size:42 final size:41
Alignment explanation
Indices: 2290927--2291132 Score: 173
Period size: 42 Copynumber: 4.9 Consensus size: 41
2290917 GTGAATCGGG
* *
2290927 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
2290969 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
2291011 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
2291053 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
2291095 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
2291133 GCGAGTCGGG
Statistics
Matches: 128, Mismatches: 28, Indels: 16
0.74 0.16 0.09
Matches are distributed among these distances:
41 9 0.07
42 108 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:2291068 original size:84 final size:84
Alignment explanation
Indices: 2290957--2291132 Score: 352
Period size: 84 Copynumber: 2.1 Consensus size: 84
2290947 CCTCTTCAAC
2290957 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
2291022 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
2291041 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
2291106 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
2291125 GATGACAG
1 GATGACAG
2291133 GCGAGTCGGG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 92 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:2291077 original size:21 final size:21
Alignment explanation
Indices: 2290927--2291077 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
2290917 GTGAATCGGG
*
2290927 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2290947 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2290969 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** *
2290990 CTCTCG-A-GGAATGATAGGGGC
1 CTCTTGAACGG--TGGGAGGGGA
* * * *
2291011 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * *
2291032 CTCTTG-AGGGATGACAGTGGC
1 CTCTTGAACGG-TGGGAGGGGA
2291053 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2291074 CTCT
1 CTCT
2291078 CGAGGAATGA
Statistics
Matches: 86, Mismatches: 37, Indels: 14
0.63 0.27 0.10
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 74 0.86
22 6 0.07
23 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2291526 original size:91 final size:93
Alignment explanation
Indices: 2291351--2291535 Score: 306
Period size: 91 Copynumber: 2.0 Consensus size: 93
2291341 ATTTCAAACT
2291351 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAACACACAATTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAACACACAATTTAGC
2291416 AGAATTGGCAGCAACCGAATAAATTTAC
66 AGAATTGGCAGCAACCGAATAAATTTAC
*
2291444 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AA-TA-A-ACAATTTA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAGAACACACAATTTA
*
2291505 GCAGTATTGGCAGCAACCGAATAAATTTAC
64 GCAGAATTGGCAGCAACCGAATAAATTTAC
2291535 T
1 T
2291536 AAGTAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 38 0.43
92 1 0.01
93 20 0.23
94 2 0.02
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.21
Consensus pattern (93 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAACACACAATTTAGC
AGAATTGGCAGCAACCGAATAAATTTAC
Found at i:2293290 original size:14 final size:14
Alignment explanation
Indices: 2293271--2293326 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2293261 GGAAATGACT
2293271 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2293285 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
2293302 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
2293318 ATCGCAACG
1 ATCGCAACG
2293327 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2293304 original size:33 final size:33
Alignment explanation
Indices: 2293247--2293343 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
2293237 ACGAGATAAT
*
2293247 GAGAATCGCAATGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
2293281 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
2293314 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
2293344 TGCGATTTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 47 0.78
34 13 0.22
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:2293341 original size:19 final size:19
Alignment explanation
Indices: 2293222--2293348 Score: 85
Period size: 20 Copynumber: 7.1 Consensus size: 19
2293212 TCTTTTGGTT
* *
2293222 GAAATGAAAATCGCAACGA
1 GAAATGAGAATCGCAACGC
*
2293241 GATAATGAGAATCGCAATGC
1 GA-AATGAGAATCGCAACGC
**
2293261 GGAAATGACTATCGCAA--C
1 -GAAATGAGAATCGCAACGC
2293279 G--A-GAGAATCGCAACGC
1 GAAATGAGAATCGCAACGC
**
2293295 GAAATGACTATCGCAA--C
1 GAAATGAGAATCGCAACGC
2293312 G--A-GAGAATCGCAACGC
1 GAAATGAGAATCGCAACGC
* *
2293328 GAAATGAAAATCGCAATGC
1 GAAATGAGAATCGCAACGC
2293347 GA
1 GA
2293349 TTTTGGTTTC
Statistics
Matches: 83, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
14 18 0.22
15 2 0.02
16 4 0.05
17 3 0.04
18 3 0.04
19 25 0.30
20 26 0.31
21 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAGAATCGCAACGC
Found at i:2293377 original size:19 final size:19
Alignment explanation
Indices: 2293344--2293388 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2293334 AAAATCGCAA
*
2293344 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
2293363 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
2293382 TGCGATT
1 TGCGATT
2293389 CTCTCGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:2293978 original size:20 final size:20
Alignment explanation
Indices: 2293930--2293969 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2293920 GCGCTATGTA
2293930 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2293950 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2293970 TATCTCGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2294019 original size:20 final size:20
Alignment explanation
Indices: 2293990--2294043 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2293980 GATTTTGTAT
2293990 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
2294010 TATCGTATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2294030 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2294044 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2294154 original size:21 final size:21
Alignment explanation
Indices: 2294114--2294154 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2294104 ACTGTAGACC
**
2294114 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
2294135 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
2294155 GCGAATTTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:2302674 original size:11 final size:11
Alignment explanation
Indices: 2302658--2302688 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2302648 ATGGAAGATG
2302658 GTAAATAAACA
1 GTAAATAAACA
2302669 GTAAATAAACA
1 GTAAATAAACA
*
2302680 GCAAATAAA
1 GTAAATAAA
2302689 ATGAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (11 bp):
GTAAATAAACA
Found at i:2308909 original size:22 final size:24
Alignment explanation
Indices: 2308858--2308909 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
2308848 GATTCCTCTG
*
2308858 TGGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGGAATCAGTTCCCCTTCA
**
2308882 -AAGGGGGAATCAGTT-CCC-TCA
1 TGGGGGGGAATCAGTTCCCCTTCA
2308903 TGGGGGG
1 TGGGGGG
2308910 ATCGATTCCC
Statistics
Matches: 22, Mismatches: 5, Indels: 4
0.71 0.16 0.13
Matches are distributed among these distances:
21 3 0.14
22 7 0.32
23 12 0.55
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (24 bp):
TGGGGGGGAATCAGTTCCCCTTCA
Found at i:2321990 original size:61 final size:61
Alignment explanation
Indices: 2321835--2321995 Score: 268
Period size: 61 Copynumber: 2.6 Consensus size: 61
2321825 GTGCAGGTTT
* *
2321835 ATGTCCGGATTAGCACTATAGCGTAAGCTTAGTATAGATGGTGGGCACAACCTTATGTGTA
1 ATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGTGGTGGGCACAACCTTATGTGTA
*
2321896 ATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGTGGTGGGCACGACCTTATGTGTA
1 ATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGTGGTGGGCACAACCTTATGTGTA
* * *
2321957 TTGTCCGGATTAGCACTATGGCGTAAGCTTAGTGCAGGT
1 ATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGT
2321996 TTAGCACTAT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 94 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (61 bp):
ATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGTGGTGGGCACAACCTTATGTGTA
Found at i:2322223 original size:51 final size:48
Alignment explanation
Indices: 2322119--2322252 Score: 139
Period size: 48 Copynumber: 2.7 Consensus size: 48
2322109 GTAACCATGC
* *
2322119 AAATAAGCTTATGAGCTTACGGAA-TAATGGCAAGTATATTGAAAAAAATA
1 AAATAAGCTTATGAGCTTATGGAATTAATGGTAAGTATATTG---AAAATA
* **
2322169 ATAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTA-A
1 A-AATAAGCTTATGAGCTTATGGAA-TT-AATGGTAAGTATATTGAAAATA
*
2322218 AAATAAGCTTATGAGCTTATGGGATTAATGGTAAG
1 AAATAAGCTTATGAGCTTATGGAATTAATGGTAAG
2322253 AAATTTTATA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
46 9 0.12
47 2 0.03
48 22 0.30
49 2 0.03
50 2 0.03
51 22 0.30
53 1 0.01
54 14 0.19
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (48 bp):
AAATAAGCTTATGAGCTTATGGAATTAATGGTAAGTATATTGAAAATA
Found at i:2326425 original size:24 final size:24
Alignment explanation
Indices: 2326389--2326460 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
2326379 GAAGATGAAG
*
2326389 AAATGAGAGAGAAAAGTAAAAGTA
1 AAATGAAAGAGAAAAGTAAAAGTA
* *
2326413 AAATGAAATAGAAAAGTTAAAG--
1 AAATGAAAGAGAAAAGTAAAAGTA
*
2326435 -AA-GAAAGAGAAAAGAAAAAGTTA
1 AAATGAAAGAGAAAAGTAAAAG-TA
2326458 AAA
1 AAA
2326461 ATTTGAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 15 0.39
21 2 0.05
24 21 0.55
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (24 bp):
AAATGAAAGAGAAAAGTAAAAGTA
Found at i:2339161 original size:23 final size:23
Alignment explanation
Indices: 2339117--2339165 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2339107 ATAAAGAACC
*
2339117 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
2339140 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
2339163 AAA
1 AAA
2339166 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:2345298 original size:23 final size:23
Alignment explanation
Indices: 2345272--2345320 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2345262 ATAAAGAACC
*
2345272 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
2345295 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
2345318 AAA
1 AAA
2345321 CCAATCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:2348148 original size:13 final size:13
Alignment explanation
Indices: 2348130--2348188 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
2348120 AATATATATC
*
2348130 AAATTAAACATTA
1 AAATTAAAAATTA
2348143 AAATTAAAAATT-
1 AAATTAAAAATTA
2348155 AAA-TAAAAATGTA
1 AAATTAAAAAT-TA
* *
2348168 AATACTAAAAA-TC
1 AA-ATTAAAAATTA
2348181 AAATTAAA
1 AAATTAAA
2348189 TATCAATGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 7 0.18
12 9 0.23
13 16 0.41
14 1 0.03
15 6 0.15
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (13 bp):
AAATTAAAAATTA
Found at i:2348614 original size:2 final size:2
Alignment explanation
Indices: 2348607--2348656 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2348597 ATATCTACCA
2348607 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
2348649 AT AT AT AT
1 AT AT AT AT
2348657 CGTGATCTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2360609 original size:14 final size:14
Alignment explanation
Indices: 2360590--2360617 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2360580 GTAACTTCTG
2360590 AAATGTTATATGAT
1 AAATGTTATATGAT
2360604 AAATGTTATATGAT
1 AAATGTTATATGAT
2360618 TGATGGAATT
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:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
AAATGTTATATGAT
Found at i:2361091 original size:31 final size:31
Alignment explanation
Indices: 2360971--2361095 Score: 160
Period size: 31 Copynumber: 4.0 Consensus size: 31
2360961 AGAGTCGAGG
* *
2360971 GTTTACCTATGTTCTTTGGGATATATGGAAT
1 GTTTACCTATGTTCTTCGGGATATATGGACT
*
2361002 GTTTACCTATGTTCTTCGGGATATATAGACT
1 GTTTACCTATGTTCTTCGGGATATATGGACT
* * *
2361033 ATTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGATATATGGACT
* * * *
2361064 GTTTACCTAGGTTCTTCAGAATCTATGGACT
1 GTTTACCTATGTTCTTCGGGATATATGGACT
2361095 G
1 G
2361096 GTCTTTCGGG
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 80 1.00
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGATATATGGACT
Found at i:2361845 original size:22 final size:21
Alignment explanation
Indices: 2361802--2361845 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
2361792 GTACTATAGT
*
2361802 AGGGTATTAGTACCCTGTAGC
1 AGGGTATTAGTACCCTGAAGC
2361823 AGGGTATT-GATACCCCTGAAGC
1 AGGGTATTAG-TA-CCCTGAAGC
2361845 A
1 A
2361846 ATCTGGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 10 0.50
22 9 0.45
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (21 bp):
AGGGTATTAGTACCCTGAAGC
Found at i:2363499 original size:18 final size:18
Alignment explanation
Indices: 2363476--2363567 Score: 121
Period size: 18 Copynumber: 4.9 Consensus size: 18
2363466 GTTCTTAAGG
*
2363476 AGTGGTCCTTCGGTACAT
1 AGTGGTCCTTCGGGACAT
* *
2363494 AGTGGTCCGTCGGGATAAAT
1 AGTGGTCCTTCGGG--ACAT
*
2363514 CAGTGGTCCTTCGGGATAT
1 -AGTGGTCCTTCGGGACAT
2363533 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
2363551 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
2363568 AATATACAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
18 46 0.71
19 3 0.05
20 3 0.05
21 13 0.20
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2363535 original size:39 final size:36
Alignment explanation
Indices: 2363476--2363567 Score: 121
Period size: 39 Copynumber: 2.5 Consensus size: 36
2363466 GTTCTTAAGG
*
2363476 AGTGGTCCTTCGGTACATAGTGGTCCGTCGGGATAAAT
1 AGTGGTCCTTCGGGACATAGTGGTCCGTCGGG--AAAT
* * *
2363514 CAGTGGTCCTTCGGGATATAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACATAGTGGTCCGTCGGGAAAT
2363551 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
2363568 AATATACAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 16 0.33
37 3 0.06
39 29 0.60
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.28
Consensus pattern (36 bp):
AGTGGTCCTTCGGGACATAGTGGTCCGTCGGGAAAT
Found at i:2363996 original size:21 final size:21
Alignment explanation
Indices: 2363970--2364009 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2363960 TTAATTAAGG
2363970 AAAAGG-TATATAGATAAGTAT
1 AAAAGGATAT-TAGATAAGTAT
2363991 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAGATAAGT
2364010 GGTGCAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAGATAAGTAT
Found at i:2368888 original size:22 final size:21
Alignment explanation
Indices: 2368863--2368903 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2368853 ATTAATTAAG
*
2368863 AAAAAGGTATATAGATAAGTAT
1 AAAAAGATAT-TAGATAAGTAT
*
2368885 AAAATGATATTAGATAAGT
1 AAAAAGATATTAGATAAGT
2368904 GGTGCAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (21 bp):
AAAAAGATATTAGATAAGTAT
Found at i:2370695 original size:16 final size:16
Alignment explanation
Indices: 2370671--2370701 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2370661 CATTTCTGAG
2370671 TCATGCATTAAAATAT
1 TCATGCATTAAAATAT
*
2370687 TCATTCATTAAAATA
1 TCATGCATTAAAATA
2370702 ATGATAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (16 bp):
TCATGCATTAAAATAT
Found at i:2374035 original size:36 final size:36
Alignment explanation
Indices: 2373992--2374190 Score: 123
Period size: 36 Copynumber: 5.3 Consensus size: 36
2373982 AGAGGATTTA
*
2373992 TCTCACTTGAGATTGTTTTTCTTAAAACAGACTTTG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTG
* * * * *
2374028 TCTCACTTGAGACTGTTTTACTCGAAAAAAAACATTTCA
1 TCTCACTTGAGATTGTTTTTCT-TAAAACAAAC-TTT-G
* * ** *
2374067 TTTGACTCAAGATTGTTTTTCTTAAAACAAAATTTG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTG
** ** * *
2374103 TCTCACTTGAGACAGTTTTTACTCGAAACAAGAAGATTTA
1 TCTCACTTGAGATTGTTTTT-CTTAAAAC-A-AA-CTTTG
* **
2374143 TTTCACTCAAGATTGTTTTTCTTAAAACAATA-TTTG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAA-ACTTTG
2374179 TCT-AGCTTGAGA
1 TCTCA-CTTGAGA
2374191 CGGTTTTCAC
Statistics
Matches: 118, Mismatches: 36, Indels: 18
0.69 0.21 0.10
Matches are distributed among these distances:
35 1 0.01
36 44 0.37
37 17 0.14
38 13 0.11
39 24 0.20
40 19 0.16
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (36 bp):
TCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTG
Found at i:2374161 original size:40 final size:38
Alignment explanation
Indices: 2374043--2374162 Score: 100
Period size: 40 Copynumber: 3.1 Consensus size: 38
2374033 CTTGAGACTG
* *
2374043 TTTTACTCGAAAAAAAACATTTCATTTGACTCAAGATTGT
1 TTTTACTCGAAACAAAA-ATTT-ATTTCACTCAAGATTGT
** * * ** **
2374083 TTTT-CTTAAAAC-AAAATTTGTCTCACTTGAGACAGT
1 TTTTACTCGAAACAAAAATTTATTTCACTCAAGATTGT
2374119 TTTTACTCGAAACAAGAAGATTTATTTCACTCAAGATTGT
1 TTTTACTCGAAACAA-AA-ATTTATTTCACTCAAGATTGT
2374159 TTTT
1 TTTT
2374163 CTTAAAACAA
Statistics
Matches: 58, Mismatches: 18, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
36 14 0.24
37 10 0.17
38 4 0.07
39 7 0.12
40 23 0.40
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (38 bp):
TTTTACTCGAAACAAAAATTTATTTCACTCAAGATTGT
Found at i:2374169 original size:76 final size:76
Alignment explanation
Indices: 2374001--2374238 Score: 306
Period size: 76 Copynumber: 3.1 Consensus size: 76
2373991 ATCTCACTTG
* * * * *
2374001 AGATTGTTTTTCTTAAAACAGACTTTGTCTCACTTGAGACTG-TTTTACTCGAAAAAAAACATTT
1 AGATTGTTTTTCTTAAAACAAAATTTGTCTCACTTGAGACAGTTTTTACTCGAAAAAGAAGATTT
*
2374065 CATTTGACTCA
66 CATTTCACTCA
2374076 AGATTGTTTTTCTTAAAACAAAATTTGTCTCACTTGAGACAGTTTTTACTCGAAACAAGAAGATT
1 AGATTGTTTTTCTTAAAACAAAATTTGTCTCACTTGAGACAGTTTTTACTCGAAA-AAGAAGATT
2374141 T-ATTTCACTCA
65 TCATTTCACTCA
* * * *
2374152 AGATTGTTTTTCTTAAAACAATATTTGTCT-AGCTTGAGACGGTTTTCACTCG--AAAGAAGGCC
1 AGATTGTTTTTCTTAAAACAAAATTTGTCTCA-CTTGAGACAGTTTTTACTCGAAAAAGAA-G-A
2374214 TTTCATTTCACTCA
63 TTTCATTTCACTCA
*
2374228 AGATTATTTTT
1 AGATTGTTTTT
2374239 AAAGAAGATT
Statistics
Matches: 146, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
73 5 0.03
74 2 0.01
75 43 0.29
76 88 0.60
77 8 0.05
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAAATTTGTCTCACTTGAGACAGTTTTTACTCGAAAAAGAAGATTT
CATTTCACTCA
Found at i:2374372 original size:38 final size:39
Alignment explanation
Indices: 2374241--2374380 Score: 192
Period size: 39 Copynumber: 3.6 Consensus size: 39
2374231 TTATTTTTAA
* *
2374241 AGAAGATTTTATCTCACTAGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * *
2374280 ATAAGATTTTATTTCGCTTGAGATAGTTTTCTTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
2374319 AAAAGATTTTATCTCGCTTGAAATAGTTTCCCTCG-AAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
2374357 AGAAGATTTTATCTCGCTTGAGAT
1 AGAAGATTTTATCTCGCTTGAGAT
2374381 CAATGTTTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 25 0.29
39 61 0.71
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:2375199 original size:17 final size:17
Alignment explanation
Indices: 2375173--2375224 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
2375163 TAAATAAAAA
2375173 AAGTATATAATTGATAC
1 AAGTATATAATTGATAC
*
2375190 AAGTAAATAA---A-A-
1 AAGTATATAATTGATAC
2375202 AAGTATATAATTGATAC
1 AAGTATATAATTGATAC
2375219 AAGTAT
1 AAGTAT
2375225 CAATCATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
12 9 0.32
13 1 0.04
14 1 0.04
15 1 0.04
16 1 0.04
17 15 0.54
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.31
Consensus pattern (17 bp):
AAGTATATAATTGATAC
Found at i:2375208 original size:29 final size:30
Alignment explanation
Indices: 2375163--2375223 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
2375153 ATCAGAAAAC
2375163 TAAATAAAAAAAGTATATAATTGATACAAG
1 TAAATAAAAAAAGTATATAATTGATACAAG
2375193 TAAAT-AAAAAAGTATATAATTGATACAAG
1 TAAATAAAAAAAGTATATAATTGATACAAG
2375222 TA
1 TA
2375224 TCAATCATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (30 bp):
TAAATAAAAAAAGTATATAATTGATACAAG
Found at i:2375529 original size:39 final size:39
Alignment explanation
Indices: 2375475--2375768 Score: 400
Period size: 39 Copynumber: 7.6 Consensus size: 39
2375465 TGATAACCAT
2375475 GCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTC
1 GCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTC
*
2375514 GCTTGAGATAGTTTCCCTCGAAACAAAAGATTTT-TCTC
1 GCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTC
*
2375552 GCTTGAGATAGTTTCCCTCGAAACATAAGATTTTATCTC
1 GCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTC
*
2375591 GCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTC
1 GCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTC
* * *
2375630 ACTTGAGATAATTACCCTCGAAACAGAAGATTTTATCTC
1 GCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTC
* *
2375669 GCTTGAGATAGTTTCTCTCGAAACAGAA-AGTTTTGTCTC
1 GCTTGAGATAGTTTCCCTCGAAACAGAAGA-TTTTATCTC
* * * *
2375708 CCTTGAGAAAGTTTCCCTTGAAACA-AA-A-TTTGTCTC
1 GCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTC
* * * *
2375744 CCTTGAGACAGTTTCTCTTGAAACA
1 GCTTGAGATAGTTTCCCTCGAAACA
2375769 TAAACTTTGA
Statistics
Matches: 234, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
36 31 0.13
38 41 0.18
39 162 0.69
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (39 bp):
GCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTC
Found at i:2375832 original size:36 final size:35
Alignment explanation
Indices: 2375788--2375869 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 35
2375778 AAAACATTTC
* *
2375788 CCTTGAAACGAATTTTATCTCACTTGAGATAGTTTT
1 CCTTGAAACAAATTTTATCTCACTTGAGACAG-TTT
* *
2375824 CCTTGAAACAAATTTTGTCTCAGTTGAGACAGTTT
1 CCTTGAAACAAATTTTATCTCACTTGAGACAGTTT
2375859 CTCTTGAAACA
1 C-CTTGAAACA
2375870 TAAACTTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 4 0.10
36 37 0.90
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (35 bp):
CCTTGAAACAAATTTTATCTCACTTGAGACAGTTT
Found at i:2375889 original size:101 final size:101
Alignment explanation
Indices: 2375699--2375897 Score: 317
Period size: 101 Copynumber: 2.0 Consensus size: 101
2375689 AAACAGAAAG
* * *
2375699 TTTTGTCTCCCTTGAGAAAGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTTATCTCACTTGAGAAAGTTTCCCTTGAAACAAAATTTGTCTCACTTGAGACAGTTTCTCTTG
2375764 AAACATAAACTTTGAAAACATTTCCCTTGAAACGAA
66 AAACATAAACTTTGAAAACATTTCCCTTGAAACGAA
* * * *
2375800 TTTTATCTCACTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCAGTTGAGACAGTTTCTCTTG
1 TTTTATCTCACTTGAGAAAGTTTCCCTTGAAACAAAATTTGTCTCACTTGAGACAGTTTCTCTTG
**
2375865 AAACATAAACTTTGAAAATGTTTCCCTTGAAAC
66 AAACATAAACTTTGAAAACATTTCCCTTGAAAC
2375898 ACAAAATATT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (101 bp):
TTTTATCTCACTTGAGAAAGTTTCCCTTGAAACAAAATTTGTCTCACTTGAGACAGTTTCTCTTG
AAACATAAACTTTGAAAACATTTCCCTTGAAACGAA
Found at i:2375968 original size:30 final size:30
Alignment explanation
Indices: 2375933--2376082 Score: 138
Period size: 30 Copynumber: 4.8 Consensus size: 30
2375923 TGGAACGAGT
* * *
2375933 TTTGAGACAGTTTCCCTTGAAACACCCACA
1 TTTGAGATAGTTTCCCTTGAAACACCAACC
* ****
2375963 TTTGAGATTGTTTCCCTTGAAACATGTTTTGTCTC
1 TTTGAGATAGTTTCCCTTGAAACA----CCAAC-C
*
2375998 TCTTGAGATAGTTTCTCTTGAAACACCAACC
1 T-TTGAGATAGTTTCCCTTGAAACACCAACC
* *
2376029 TTTGAGACAGTTTCTCTTGAAACACCAACC
1 TTTGAGATAGTTTCCCTTGAAACACCAACC
*
2376059 TTTGAGATTGTTTCCCTTGAAACA
1 TTTGAGATAGTTTCCCTTGAAACA
2376083 AATTTCGTCT
Statistics
Matches: 97, Mismatches: 17, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
30 71 0.73
31 2 0.02
32 1 0.01
34 1 0.01
35 1 0.01
36 21 0.22
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (30 bp):
TTTGAGATAGTTTCCCTTGAAACACCAACC
Found at i:2376088 original size:16 final size:17
Alignment explanation
Indices: 2376069--2376120 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
2376059 TTTGAGATTG
2376069 TTTCCCTTGAAACAAAT
1 TTTCCCTTGAAACAAAT
*
2376086 TTCGTCTCGCTTGAGAC-AAT
1 TT--TC-C-CTTGAAACAAAT
2376106 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
2376121 GAAATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
16 7 0.25
17 4 0.14
18 2 0.07
19 2 0.07
20 6 0.21
21 7 0.25
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.35
Consensus pattern (17 bp):
TTTCCCTTGAAACAAAT
Found at i:2376099 original size:96 final size:97
Alignment explanation
Indices: 2375933--2376119 Score: 277
Period size: 96 Copynumber: 1.9 Consensus size: 97
2375923 TGGAACGAGT
* ** *
2375933 TTTGAGACAGTTTCCCTTGAAACACCCACATTTGAGATTGTTTCCCTTGAAACATGTTTTGTCTC
1 TTTGAGACAGTTTCCCTTGAAACACCAACATTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTC
* * *
2375998 TCTTGAGA-TAGTTTCTCTTGAAACACCAACC
66 GCTTGAGACAAGTTTCCCTTGAAACACCAACC
* *
2376029 TTTGAGACAGTTTCTCTTGAAACACCAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTC
1 TTTGAGACAGTTTCCCTTGAAACACCAACATTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTC
*
2376094 GCTTGAGACAATTTTCCCTTGAAACA
66 GCTTGAGACAAGTTTCCCTTGAAACA
2376120 AGAAATTTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
96 66 0.82
97 14 0.17
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (97 bp):
TTTGAGACAGTTTCCCTTGAAACACCAACATTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTC
GCTTGAGACAAGTTTCCCTTGAAACACCAACC
Done.