Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 28
Found at i:221533 original size:33 final size:33
Alignment explanation
Indices: 221483--221572 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
221473 AAAAAGTACT
* *
221483 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
221516 ATTGCAACGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
221549 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
221573 GTTGCGATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:221543 original size:19 final size:19
Alignment explanation
Indices: 221483--221543 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 19
221473 AAAAAGTACT
*
221483 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
221502 ATTGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
221516 ATTGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
221535 ATCGCAACG
1 ATCGCAACG
221544 AGATAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:221590 original size:19 final size:19
Alignment explanation
Indices: 221568--221718 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
221558 CGAAATTAAA
221568 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
221587 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
221602 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
221620 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
221634 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
221653 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
221668 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
221686 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
221705 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
221719 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:221614 original size:33 final size:32
Alignment explanation
Indices: 221572--221698 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
221562 ATTAAATTCG
221572 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
221605 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
221638 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
221671 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
221699 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:221661 original size:66 final size:66
Alignment explanation
Indices: 221565--221697 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
221555 ACGCGAAATT
*
221565 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
221630 G
66 G
*
221631 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
221696 G
66 G
221697 A
1 A
221698 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:222530 original size:22 final size:22
Alignment explanation
Indices: 222502--222545 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
222492 ACACGATGTT
222502 CCAATGTTCCTGTAAATTTAAA
1 CCAATGTTCCTGTAAATTTAAA
222524 CCAATGTTCCTGTAAATTTAAA
1 CCAATGTTCCTGTAAATTTAAA
222546 TAAATAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
CCAATGTTCCTGTAAATTTAAA
Found at i:224012 original size:13 final size:13
Alignment explanation
Indices: 223994--224018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223984 CTTCGGAGTC
223994 TTTTTCTTCTTCT
1 TTTTTCTTCTTCT
224007 TTTTTCTTCTTC
1 TTTTTCTTCTTC
224019 AGGATTATAT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCTTCTTCT
Found at i:224226 original size:24 final size:24
Alignment explanation
Indices: 224192--224245 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
224182 CTGAAACATC
*
224192 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
224216 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
224240 ATCAAA
1 ATCAAA
224246 TTTCGAATAT
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:225060 original size:20 final size:21
Alignment explanation
Indices: 225035--225086 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
225025 TTTTCCTAAT
*
225035 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
225055 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
225076 TCGCAATGCGA
1 TCGCAATGCGA
225087 TACTAACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:225108 original size:20 final size:20
Alignment explanation
Indices: 225075--225148 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
225065 AATTTGGAAA
* *
225075 ATCGCAATGCGATACTAACT
1 ATCGCAACGAGATACTAACT
* **
225095 ATCGCAACGAGATAATACAAA
1 ATCGCAACGAGATACTA-ACT
* *
225116 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTAACT
*
225136 TTCGCAACGAGAT
1 ATCGCAACGAGAT
225149 TCTGAAAATC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATACTAACT
Found at i:225160 original size:20 final size:20
Alignment explanation
Indices: 225113--225162 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
225103 GAGATAATAC
225113 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
225133 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
225153 AAAATCGCAA
1 AAAATCGCAA
225163 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:225471 original size:20 final size:20
Alignment explanation
Indices: 225376--225463 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
225366 TAACGGGGAA
225376 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
225396 ATCGCAACGCGAAACTGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
225416 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
225436 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
225456 ATCGCAAC
1 ATCGCAAC
225464 TAGAAAATTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 4 0.07
20 45 0.83
21 5 0.09
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:225531 original size:19 final size:19
Alignment explanation
Indices: 225490--225557 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
225480 GAAATGAAAA
225490 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
225506 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
225523 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
225542 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
225558 TCGTTGGGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 28 0.62
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:225713 original size:14 final size:14
Alignment explanation
Indices: 225694--225730 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
225684 CATCAATTAA
225694 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
225708 ACAAATCATCTTTT
1 ACAAATCAACATTT
225722 ACAAATCAA
1 ACAAATCAA
225731 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:227637 original size:19 final size:20
Alignment explanation
Indices: 227585--227649 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
227575 ACTTAAAATT
*
227585 GCAACGCGAAAATGACTATC
1 GCAACGCGGAAATGACTATC
*
227605 GCAACGCGGAAATGGCTATC
1 GCAACGCGGAAATGACTATC
* **
227625 GCAATGC-GAAATGAAAATC
1 GCAACGCGGAAATGACTATC
227644 GCAACG
1 GCAACG
227650 ACAAAATCGC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 14 0.37
20 24 0.63
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.14
Consensus pattern (20 bp):
GCAACGCGGAAATGACTATC
Found at i:227657 original size:14 final size:14
Alignment explanation
Indices: 227638--227695 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
227628 ATGCGAAATG
227638 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
227652 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
227668 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
227684 AAAATCGCAACG
1 AAAATCGCAACG
227696 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:227680 original size:32 final size:33
Alignment explanation
Indices: 227622--227700 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
227612 GGAAATGGCT
227622 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
227655 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
227687 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
227701 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:227748 original size:14 final size:14
Alignment explanation
Indices: 227729--227785 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
227719 TTTCATTTCG
227729 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
227743 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
227759 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
227775 CGTTGCAATTT
1 CGTTGCGATTT
227786 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:227757 original size:32 final size:32
Alignment explanation
Indices: 227719--227801 Score: 148
Period size: 32 Copynumber: 2.6 Consensus size: 32
227709 GCATTACGAT
* *
227719 TTTCATTTCGCGTTGCGATTTTGTCGTTGCGA
1 TTTCATTTCGCATTGCGATTTTGTCGTTGCAA
227751 TTTCATTTCGCATTGCGATTTTGTCGTTGCAA
1 TTTCATTTCGCATTGCGATTTTGTCGTTGCAA
227783 TTTCATTTCGCATTGCGAT
1 TTTCATTTCGCATTGCGAT
227802 AGCCATTTCC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.47
Consensus pattern (32 bp):
TTTCATTTCGCATTGCGATTTTGTCGTTGCAA
Found at i:227839 original size:19 final size:19
Alignment explanation
Indices: 227785--227840 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
227775 CGTTGCAATT
*
227785 TCATTTCGCATTGCGATAG
1 TCATTTCGCGTTGCGATAG
*
227804 CCATTTCCCGCGTTGCGATAG
1 TCATTT--CGCGTTGCGATAG
*
227825 TCATTTCGTGTTGCGA
1 TCATTTCGCGTTGCGA
227841 AAGTAAACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 14 0.45
21 17 0.55
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:228336 original size:18 final size:18
Alignment explanation
Indices: 228310--228354 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
228300 GTCGATCAGA
*
228310 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
228328 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
228346 TGATGGCTC
1 TGATGGCTC
228355 CGAAGTGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:230009 original size:41 final size:41
Alignment explanation
Indices: 229952--230040 Score: 160
Period size: 41 Copynumber: 2.1 Consensus size: 41
229942 TTTAGGTTTT
*
229952 AGGTTATGAGTTGCGATTACGGGATATACTGTGGATGGTTC
1 AGGTTCTGAGTTGCGATTACGGGATATACTGTGGATGGTTC
229993 AGGTTCTGAGTTGCGATTACGGGATATACTGTGGATGGTTC
1 AGGTTCTGAGTTGCGATTACGGGATATACTGTGGATGGTTC
230034 AGTGTTC
1 AG-GTTC
230041 CAATATATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 42 0.91
42 4 0.09
ACGTcount: A:0.20, C:0.11, G:0.34, T:0.35
Consensus pattern (41 bp):
AGGTTCTGAGTTGCGATTACGGGATATACTGTGGATGGTTC
Found at i:230218 original size:20 final size:20
Alignment explanation
Indices: 230112--230226 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
230102 AGCTTTGAAA
*
230112 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
230133 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
230153 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
230173 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
230194 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
230214 ATCGCATTGCGAT
1 ATCGCATTGCGAT
230227 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.06
20 47 0.61
21 23 0.30
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:230245 original size:41 final size:41
Alignment explanation
Indices: 230153--230247 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
230143 GAAAGTCAGA
* * * ** *
230153 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
*
230194 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
230236 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
230248 TTACTTATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:237317 original size:24 final size:24
Alignment explanation
Indices: 237290--237399 Score: 102
Period size: 24 Copynumber: 4.6 Consensus size: 24
237280 GTAAACGGAG
*
237290 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
237314 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
237338 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
237361 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
*
237385 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
237400 TAAAATATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 16 0.23
24 50 0.71
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:237321 original size:12 final size:12
Alignment explanation
Indices: 237294--237385 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
237284 ACGGAGATAT
* *
237294 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
237306 CAGAATTCATAT
1 CAGAATTCAGAA
237318 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
237330 CAGAATCCAGAT
1 CAGAATTCAGAA
237342 CAGAA-TCAGAA
1 CAGAATTCAGAA
237353 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
237367 C-GTA-TCAGAA
1 CAGAATTCAGAA
237377 CAGAATTCA
1 CAGAATTCA
237386 ATTCGGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:237373 original size:47 final size:48
Alignment explanation
Indices: 237292--237382 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
237282 AAACGGAGAT
*
237292 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
*
237340 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAAT
237383 TCAATTCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 30 0.77
48 6 0.15
49 3 0.08
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:239840 original size:18 final size:18
Alignment explanation
Indices: 239817--239862 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
239807 CAACGGTCAA
239817 CGGGTCGGGTAAACAGG-T
1 CGGGTCGGGTAAAC-GGTT
*
239835 CGGGTCGGGAAAACGGTT
1 CGGGTCGGGTAAACGGTT
239853 CGGGTCGGGT
1 CGGGTCGGGT
239863 TAGGTTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGTT
Found at i:241960 original size:24 final size:24
Alignment explanation
Indices: 241933--242004 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
241923 GTAAACGGAG
*
241933 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* * *
241957 ATATCAGATATCAGAACAAAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
241981 ATATCAG-AAGCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
242004 A
1 A
242005 GGTAACGTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 13 0.32
24 27 0.68
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:244475 original size:13 final size:13
Alignment explanation
Indices: 244457--244511 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
244447 GCCGGTCAAC
244457 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
244470 GGTCAACGGATCA
1 GGTCAACGGGTCG
*
244483 GGTCAACAGGTCG
1 GGTCAACGGGTCG
* *
244496 GGTAAATGGGTCG
1 GGTCAACGGGTCG
244509 GGT
1 GGT
244512 TGGGTTATGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.22, C:0.18, G:0.42, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:245460 original size:18 final size:18
Alignment explanation
Indices: 245437--245471 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
245427 CCTTTTGGCA
245437 CATTGTTGGTGACGATGC
1 CATTGTTGGTGACGATGC
245455 CATTGTTGGTGACGATG
1 CATTGTTGGTGACGATG
245472 ATAGATTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.34, T:0.34
Consensus pattern (18 bp):
CATTGTTGGTGACGATGC
Found at i:246105 original size:81 final size:81
Alignment explanation
Indices: 246003--246151 Score: 271
Period size: 81 Copynumber: 1.8 Consensus size: 81
245993 TTATAAAGAC
246003 TGGTGCGACCTTCTCAAGGACAGAAATAGAGCAGACCTCCTGAATGATCAATTAAAGTTCATGTG
1 TGGTGCGACCTTCTCAAGGACAGAAATAGAGCAGACCTCCTGAATGATCAATTAAAGTTCATGTG
246068 GACAATGCAACATCGA
66 GACAATGCAACATCGA
* * *
246084 TGGTGCGACCTTTTCATGGACAGAAATGGAGCAGACCTCCTGAATGATCAATTAAAGTTCATGTG
1 TGGTGCGACCTTCTCAAGGACAGAAATAGAGCAGACCTCCTGAATGATCAATTAAAGTTCATGTG
246149 GAC
66 GAC
246152 GGTGCCTATC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (81 bp):
TGGTGCGACCTTCTCAAGGACAGAAATAGAGCAGACCTCCTGAATGATCAATTAAAGTTCATGTG
GACAATGCAACATCGA
Found at i:249264 original size:31 final size:31
Alignment explanation
Indices: 249200--249267 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
249190 ATATTTAAAA
* *
249200 TATATTTTTAATATTTCTAATAATTTAATAT
1 TATATTTTTAATATTTATAATAATATAATAT
249231 TATACTTTTTAATA-TTATAATAATATACA-AT
1 TATA-TTTTTAATATTTATAATAATATA-ATAT
249262 TATATT
1 TATATT
249268 ATAATAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 21 0.64
32 10 0.30
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (31 bp):
TATATTTTTAATATTTATAATAATATAATAT
Found at i:249625 original size:24 final size:25
Alignment explanation
Indices: 249569--249628 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
249559 TATTTTAATA
*
249569 ATAATAAATAAATTATTTTAAAATTT
1 ATAATAAAT-AATTATATTAAAATTT
*
249595 -TCA-AAATAATTATATT-AAATTT
1 ATAATAAATAATTATATTAAAATTT
249617 ATAATAAATAAT
1 ATAATAAATAAT
249629 ATTATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 6 0.21
23 10 0.34
24 11 0.38
25 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATAATAAATAATTATATTAAAATTT
Found at i:249638 original size:28 final size:27
Alignment explanation
Indices: 249569--249645 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 27
249559 TATTTTAATA
*
249569 ATAATAAATAAATTATTT-TAAAATTT
1 ATAATAAATAAATTATTTATTAAATTT
*
249595 -TCA-AAAT-AATTA--TATTAAATTT
1 ATAATAAATAAATTATTTATTAAATTT
*
249617 ATAATAAATAATATTATTTATTATATTT
1 ATAATAAATAA-ATTATTTATTAAATTT
249645 A
1 A
249646 ATATTTCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
21 1 0.03
22 7 0.17
23 7 0.17
24 8 0.20
25 3 0.08
26 4 0.10
28 10 0.25
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
ATAATAAATAAATTATTTATTAAATTT
Found at i:249749 original size:18 final size:17
Alignment explanation
Indices: 249711--249747 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
249701 ACAACATCTT
249711 AAATCTGAATGACAAAA
1 AAATCTGAATGACAAAA
249728 AAATCTGAATGACAAAA
1 AAATCTGAATGACAAAA
249745 AAA
1 AAA
249748 ATTTATCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (17 bp):
AAATCTGAATGACAAAA
Found at i:260673 original size:207 final size:206
Alignment explanation
Indices: 260318--260719 Score: 646
Period size: 207 Copynumber: 1.9 Consensus size: 206
260308 GAATAGGAGT
*
260318 CATCACCATTCCCACACCAAAGATAACCATCAGCTTCATTCGAACCATCAGAGACATTACAAAGA
1 CATCACCATTCCCACACCAAAGATAACCATCAGCTTCATTCAAACCATCAGAGACATTACAAAGA
* *
260383 ATAGAGTTTAATTCCACCCATTCCTCTAACTCCCAATCCGCGAGATTCCTCCTCATTTGAATATC
66 ATAGAGTTTAATTCCACCCATTCCTCCAACTCCCAAGCCGCGAGATTCCTCCTCATTTGAATATC
260448 CCAACACCAACCCGATTGACTAGAATT-TCTGAAATCTGCTATTCTCCCCACTTTATTAACCGAA
131 CCAACACCAACCCGATTGACTAGAATTCT-TGAAATCTGCTATTCTCCCCACTTTATTAACC-AA
260512 AACACATAGGACC
194 AACACATAGGACC
* * * * *
260525 CATCACCATTTCCGCACCAAAGATAACTATCAGTTTCATTCAAACCATTAG-GAACATTACAAAG
1 CATCACCATTCCCACACCAAAGATAACCATCAGCTTCATTCAAACCATCAGAG-ACATTACAAAG
* * * *
260589 AATATAGTTTAATTCCACCCATTGCTCCAACTCCCAAGCCGCGAGATTCCTCCTTATTTTAATAT
65 AATAGAGTTTAATTCCACCCATTCCTCCAACTCCCAAGCCGCGAGATTCCTCCTCATTTGAATAT
*
260654 CCCAACACCAACCCGATTGACTAGAATTCTTGAAATCTGCTATTCTCCCCCCTTTATTAACCAAA
130 CCCAACACCAACCCGATTGACTAGAATTCTTGAAATCTGCTATTCTCCCCACTTTATTAACCAAA
260719 A
195 A
260720 GCGCATAAAT
Statistics
Matches: 180, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
206 5 0.03
207 174 0.97
208 1 0.01
ACGTcount: A:0.33, C:0.31, G:0.09, T:0.27
Consensus pattern (206 bp):
CATCACCATTCCCACACCAAAGATAACCATCAGCTTCATTCAAACCATCAGAGACATTACAAAGA
ATAGAGTTTAATTCCACCCATTCCTCCAACTCCCAAGCCGCGAGATTCCTCCTCATTTGAATATC
CCAACACCAACCCGATTGACTAGAATTCTTGAAATCTGCTATTCTCCCCACTTTATTAACCAAAA
CACATAGGACC
Found at i:261867 original size:36 final size:36
Alignment explanation
Indices: 261827--261908 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
261817 TCAGAACACA
* *
261827 AAGAAAAGAAAACAGAAGGTTCAACAAATATATTAC
1 AAGAAAAGAAAACAGAAGGTTAAACAAATAAATTAC
* *
261863 AAGAAAAGAAAGCAGAAGTTTAAACAAATAAATTAC
1 AAGAAAAGAAAACAGAAGGTTAAACAAATAAATTAC
261899 AAGAAAAGAA
1 AAGAAAAGAA
261909 GAAACTAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.62, C:0.09, G:0.15, T:0.15
Consensus pattern (36 bp):
AAGAAAAGAAAACAGAAGGTTAAACAAATAAATTAC
Found at i:265372 original size:14 final size:15
Alignment explanation
Indices: 265353--265381 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
265343 AATTTAAAGT
265353 ATTAAAA-AATTAAA
1 ATTAAAATAATTAAA
265367 ATTAAAATAATTAAA
1 ATTAAAATAATTAAA
265382 CCTAATTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAATTAAA
Found at i:266914 original size:2 final size:2
Alignment explanation
Indices: 266842--266897 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
266832 ACACACACAC
266842 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
266884 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
266898 TAATTTAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:267310 original size:27 final size:28
Alignment explanation
Indices: 267270--267323 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
267260 CATGTAAATA
267270 AAATTATATATTTT-TTAAAATAATTAT
1 AAATTATATATTTTATTAAAATAATTAT
*
267297 AAATTAT-TATTTTTATTAAATTAATTA
1 AAATTATATA-TTTTATTAAAATAATTA
267324 CAATTGATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 2 0.08
27 11 0.46
28 11 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AAATTATATATTTTATTAAAATAATTAT
Found at i:267336 original size:28 final size:27
Alignment explanation
Indices: 267270--267336 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
267260 CATGTAAATA
267270 AAATTAT-ATATTTTTTAAAATAATTAT
1 AAATTATCAT-TTTTTTAAAATAATTAT
* *
267297 AAATTATTATTTTTATTAAATTAATTA-
1 AAATTATCATTTTT-TTAAAATAATTAT
*
267324 CAATTGATCATTT
1 AAATT-ATCATTT
267337 CCACAGTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (27 bp):
AAATTATCATTTTTTTAAAATAATTAT
Found at i:269084 original size:21 final size:22
Alignment explanation
Indices: 269034--269094 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
269024 ATGAGATTTA
*
269034 TCCCGAAGGACCTGTGAATATG
1 TCCCGAAGGACCTATGAATATG
* **
269056 TCCTGAAGGACCTATGTGT-TG
1 TCCCGAAGGACCTATGAATATG
269077 TCCCGAAGGACCTATGAA
1 TCCCGAAGGACCTATGAA
269095 ACCCACGACT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (22 bp):
TCCCGAAGGACCTATGAATATG
Found at i:270772 original size:30 final size:31
Alignment explanation
Indices: 270687--270832 Score: 212
Period size: 31 Copynumber: 4.8 Consensus size: 31
270677 TCGAGGGTTA
*
270687 CTATGTTCTTCGGGACATACGGA-TG-TTA-
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
270715 CTATGTTCTTCGGGACATATGGACTGTTTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
270746 CTATGTTCTTCGGGACATAT-GACTGTTTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
*
270776 CTATGTTCTTCGGAACATATGGACTGTTTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
* *
270807 CTAGGTTCTTCGGAATC-TATGGACTG
1 CTATGTTCTTCGGGA-CATATGGACTG
270833 GTCCTTCGGG
Statistics
Matches: 110, Mismatches: 3, Indels: 7
0.92 0.03 0.06
Matches are distributed among these distances:
28 22 0.20
29 2 0.02
30 32 0.29
31 53 0.48
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
CTATGTTCTTCGGGACATATGGACTGTTTAC
Found at i:270795 original size:61 final size:59
Alignment explanation
Indices: 270687--270819 Score: 205
Period size: 61 Copynumber: 2.2 Consensus size: 59
270677 TCGAGGGTTA
*
270687 CTATGTTCTTCGGGACATACGGATGTTACTATGTTCTTCGGGACATATGGACTGTTTAC
1 CTATGTTCTTCGGGACATACGGATGTTACTATGTTCTTCGGAACATATGGACTGTTTAC
*
270746 CTATGTTCTTCGGGACATA-TGACTGTTTACCTATGTTCTTCGGAACATATGGACTGTTTAC
1 CTATGTTCTTCGGGACATACGGA-TG-TTA-CTATGTTCTTCGGAACATATGGACTGTTTAC
*
270807 CTAGGTTCTTCGG
1 CTATGTTCTTCGG
270820 AATCTATGGA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
58 2 0.03
59 21 0.31
60 3 0.04
61 42 0.62
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (59 bp):
CTATGTTCTTCGGGACATACGGATGTTACTATGTTCTTCGGAACATATGGACTGTTTAC
Found at i:275350 original size:31 final size:31
Alignment explanation
Indices: 275209--275362 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
275199 GGGTCGAGGG
*
275209 TTACCTATGTTCTTCGGGACATACGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
275240 TTACCTATGTTCTTCGGGACATACGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
275271 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
275302 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
275333 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
275363 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:279215 original size:6 final size:6
Alignment explanation
Indices: 279206--279231 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
279196 GATTTCTTCT
279206 TCTACC TCTACC TCTACC TCTACC TC
1 TCTACC TCTACC TCTACC TCTACC TC
279232 ATCCTCTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (6 bp):
TCTACC
Found at i:284133 original size:55 final size:55
Alignment explanation
Indices: 284096--284733 Score: 804
Period size: 55 Copynumber: 11.6 Consensus size: 55
284086 TCTTCAAATG
* * * * * **
284096 ACGGGTCTGCTCCCTATTCTTTCAGGGAGTATA-AGACTCGAATAATCTTCAGCAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATAAA
* * * * * *
284151 ATGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCGAACAATCTTCA-ATAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATA-AA
* * * * *
284206 ATGTGTCCGTTGTCTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAA
1 ACGGGTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
* * * * *
284261 ACGGGTCTGCTATCTATTTCTTCGGAGAGTATAGAACTCGAACAATCTTCGA-CAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTC-ATAAA
* *
284316 ACGAGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCGAACAATCTTCATAAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
284371 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
284426 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
*
284481 ACGGGTCCGCTCTCTATTCCTTCAGAGAATATAGAACTCGAACAATCTTCATAAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
* * * * * *
284536 ATGAGTCCGCTCTCTATTCCTCCAGAGAGTATAAAACTCAAACAATCTTTATAAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
** * *
284591 ATAGGACTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
* *
284646 ACAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
* *
284701 ACGTGTCTGCTC-CATATT-CTATCAGAGAGTATA
1 ACGGGTCCGCTCTC-TATTCCT-TCAGAGAGTATA
284734 TGACTCAAAC
Statistics
Matches: 523, Mismatches: 51, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
54 6 0.01
55 512 0.98
56 5 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (55 bp):
ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAA
Found at i:284811 original size:37 final size:37
Alignment explanation
Indices: 284752--284827 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
284742 ACTTCATAAA
* **
284752 ATGAGTTTGCTTCACTATTCTTCCGTGAAGGCTTATAG
1 ATGAGTTTGCTTCACTACTCTTCCAAGAAGGCTTA-AG
284790 ATGA-TTTGCTTCACTACTCTTCCAAGAAGGCTTAAG
1 ATGAGTTTGCTTCACTACTCTTCCAAGAAGGCTTAAG
284826 AT
1 AT
284828 TGACTTGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 4 0.11
37 27 0.77
38 4 0.11
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (37 bp):
ATGAGTTTGCTTCACTACTCTTCCAAGAAGGCTTAAG
Found at i:286139 original size:8 final size:8
Alignment explanation
Indices: 286104--286203 Score: 79
Period size: 8 Copynumber: 13.1 Consensus size: 8
286094 TTGAACCCCC
286104 TTTT-ATT
1 TTTTCATT
286111 TTTCTCTATT
1 TTT-TC-ATT
* *
286121 TTTTTAAT
1 TTTTCATT
286129 TTTTCATT
1 TTTTCATT
* *
286137 TTTCCCTT
1 TTTTCATT
*
286145 TCTTC-TT
1 TTTTCATT
*
286152 TCTT--TT
1 TTTTCATT
286158 TTTTCATT
1 TTTTCATT
286166 TTTTCATT
1 TTTTCATT
286174 TTTTCATT
1 TTTTCATT
286182 TTTT-A-T
1 TTTTCATT
286188 TTTTCATT
1 TTTTCATT
286196 TTTT-ATT
1 TTTTCATT
286203 T
1 T
286204 CTTCTTATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
6 10 0.13
7 15 0.19
8 45 0.58
9 1 0.01
10 6 0.08
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Found at i:286166 original size:29 final size:30
Alignment explanation
Indices: 286120--286221 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 30
286110 TTTTCTCTAT
*
286120 TTTTTTAATTTTTCATTTTTCCCTTTCTTC-
1 TTTTTT-ATTTTTCATTTTTCCATTTCTTCA
* *
286150 TTTCTTT-TTTTTCATTTTTTCATTTTTTCA
1 TTT-TTTATTTTTCATTTTTCCATTTCTTCA
*
286180 TTTTTTATTTTTCATTTTT-TATTTCTTCTTA
1 TTTTTTATTTTTCATTTTTCCATTTCTTC--A
286211 TTTTTTTATTT
1 -TTTTTTATTT
286222 ATTATTCAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
29 29 0.48
30 18 0.30
31 4 0.07
32 10 0.16
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTTTATTTTTCATTTTTCCATTTCTTCA
Found at i:286175 original size:6 final size:7
Alignment explanation
Indices: 286121--286203 Score: 62
Period size: 7 Copynumber: 11.4 Consensus size: 7
286111 TTTCTCTATT
*
286121 TTTTTAA
1 TTTTTCA
286128 TTTTTCA
1 TTTTTCA
*
286135 TTTTTCCC
1 TTTTT-CA
286143 TTTCTTC-
1 TTT-TTCA
*
286150 TTTCTT-T
1 TTT-TTCA
286157 TTTTTCA
1 TTTTTCA
286164 TTTTTTCA
1 -TTTTTCA
286172 TTTTTTCA
1 -TTTTTCA
*
286180 TTTTTTA
1 TTTTTCA
286187 TTTTTCA
1 TTTTTCA
*
286194 TTTTTTA
1 TTTTTCA
286201 TTT
1 TTT
286204 CTTCTTATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
6 2 0.03
7 41 0.63
8 20 0.31
9 2 0.03
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:286183 original size:14 final size:14
Alignment explanation
Indices: 286120--286203 Score: 82
Period size: 14 Copynumber: 5.7 Consensus size: 14
286110 TTTTCTCTAT
286120 TTTTTTAATTTTTCA
1 TTTTTT-ATTTTTCA
**
286135 TTTTTCCCTTTCTTC-
1 TTTTT-TATTT-TTCA
286150 TTTCTTT-TTTTTCA
1 TTT-TTTATTTTTCA
286164 TTTTTTCATTTTTTCA
1 TTTTTT-A-TTTTTCA
286180 TTTTTTATTTTTCA
1 TTTTTTATTTTTCA
286194 TTTTTTATTT
1 TTTTTTATTT
286204 CTTCTTATTT
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
13 6 0.10
14 23 0.39
15 12 0.20
16 18 0.31
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTATTTTTCA
Found at i:286221 original size:8 final size:8
Alignment explanation
Indices: 286155--286221 Score: 59
Period size: 7 Copynumber: 8.4 Consensus size: 8
286145 TCTTCTTTCT
286155 TTTTTTTCA
1 TTTTTTT-A
*
286164 TTTTTTCA
1 TTTTTTTA
*
286172 TTTTTTCA
1 TTTTTTTA
286180 -TTTTTTA
1 TTTTTTTA
*
286187 -TTTTTCA
1 TTTTTTTA
286194 -TTTTTTA
1 TTTTTTTA
286201 TTTCTTCTTA
1 TTT-TT-TTA
286211 TTTTTTTA
1 TTTTTTTA
286219 TTT
1 TTT
286222 ATTATTCAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
7 18 0.35
8 17 0.33
9 10 0.20
10 6 0.12
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTTA
Found at i:293969 original size:18 final size:19
Alignment explanation
Indices: 293928--293974 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
293918 AATCTAAATA
293928 AAAAATAATTCACTTATTG
1 AAAAATAATTCACTTATTG
*
293947 AAAAATAGTTCACTTATTG
1 AAAAATAATTCACTTATTG
293966 AAAAATAAT
1 AAAAATAAT
293975 AAGATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (19 bp):
AAAAATAATTCACTTATTG
Found at i:294776 original size:18 final size:19
Alignment explanation
Indices: 294741--294784 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
294731 TATGATTTCA
*
294741 AAAATAAAAATTAGACTTT
1 AAAATAAAAATTAAACTTT
294760 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTTT
294778 ATAAATA
1 A-AAATA
294785 TCAAAAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATAAAAATTAAACTTT
Found at i:296752 original size:23 final size:24
Alignment explanation
Indices: 296700--296752 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
296690 TCCTGAATTG
*
296700 TTTACATTTAACACTATCATCATTTT
1 TTTACATTTAACACTATCATCA--TA
296726 TTTACATTTAACACTATCATCA-A
1 TTTACATTTAACACTATCATCATA
296749 TTTA
1 TTTA
296753 TGATGGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.15
26 22 0.85
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTACATTTAACACTATCATCATA
Found at i:296831 original size:29 final size:28
Alignment explanation
Indices: 296799--296861 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
296789 AGTGGAGCGT
296799 GAACCATAAACAATAATAGATGCCTAGTA
1 GAACCAT-AACAATAATAGATGCCTAGTA
* *
296828 GAACCCCTGACAATAATAGATGCCTAGTA
1 GAA-CCATAACAATAATAGATGCCTAGTA
296857 GAACC
1 GAACC
296862 CCTGAAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 2 0.06
29 26 0.84
30 3 0.10
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (28 bp):
GAACCATAACAATAATAGATGCCTAGTA
Found at i:296862 original size:29 final size:29
Alignment explanation
Indices: 296808--296866 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
296798 TGAACCATAA
296808 ACAATAATAGATGCCTAGTAGAACCCCTG
1 ACAATAATAGATGCCTAGTAGAACCCCTG
296837 ACAATAATAGATGCCTAGTAGAACCCCTG
1 ACAATAATAGATGCCTAGTAGAACCCCTG
296866 A
1 A
296867 AAACTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (29 bp):
ACAATAATAGATGCCTAGTAGAACCCCTG
Found at i:301311 original size:47 final size:47
Alignment explanation
Indices: 301240--301364 Score: 116
Period size: 45 Copynumber: 2.7 Consensus size: 47
301230 CCTAACCAAT
* * **
301240 ATGATATCT-ATCCCCATGCTTTGTTATTCACAAAA-AATTCTAACCGC
1 ATGATATCTAATTCGCATGC-TTGTTATTCA-AAAATAAACCTAACCGC
*
301287 ATGATATCTAATTCGCATGCTTG-T-TTGAAAAATAAACCTAACCGC
1 ATGATATCTAATTCGCATGCTTGTTATTCAAAAATAAACCTAACCGC
* * * *
301332 ATGATATCTAGTTCGTATGCAT-TTATTCGAAAA
1 ATGATATCTAATTCGCATGCTTGTTATTCAAAAA
301365 CGAAAATAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
44 4 0.06
45 33 0.52
46 7 0.11
47 12 0.19
48 8 0.12
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (47 bp):
ATGATATCTAATTCGCATGCTTGTTATTCAAAAATAAACCTAACCGC
Found at i:305379 original size:24 final size:23
Alignment explanation
Indices: 305330--305381 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
305320 AATTGTCACA
* **
305330 TAGAATTACACCGAAGTTCCGCG
1 TAGAATTACACCGAAGTGCCAAG
*
305353 TAGAATATGCACCGAAGTGCCAAG
1 TAGAAT-TACACCGAAGTGCCAAG
305377 TAGAA
1 TAGAA
305382 ATTGTCCCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (23 bp):
TAGAATTACACCGAAGTGCCAAG
Found at i:305439 original size:23 final size:23
Alignment explanation
Indices: 305412--305474 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
305402 AGTATTATCC
305412 CGAAGGACCGTGTAGAAATGTC-
1 CGAAGGACCGTGTAGAAATGTCT
** *
305434 CTGAAGGACCACGTAGAATTGTCT
1 C-GAAGGACCGTGTAGAAATGTCT
*
305458 CGAAAGACCGTGTAGAA
1 CGAAGGACCGTGTAGAA
305475 CCCTCGACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (23 bp):
CGAAGGACCGTGTAGAAATGTCT
Found at i:305467 original size:46 final size:47
Alignment explanation
Indices: 305376--305474 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 47
305366 GAAGTGCCAA
* * *
305376 GTAGAAATTGTCCCGAAAGACCATATAGTATTATCCCGAAGGACCGT
1 GTAGAAATTGTCCCGAAAGACCACATAGAATTATCCCGAAAGACCGT
* * * * *
305423 GTAGAAA-TGTCCTGAAGGACCACGTAGAATTGTCTCGAAAGACCGT
1 GTAGAAATTGTCCCGAAAGACCACATAGAATTATCCCGAAAGACCGT
305469 GTAGAA
1 GTAGAA
305475 CCCTCGACTC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 37 0.84
47 7 0.16
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.22
Consensus pattern (47 bp):
GTAGAAATTGTCCCGAAAGACCACATAGAATTATCCCGAAAGACCGT
Found at i:306036 original size:58 final size:58
Alignment explanation
Indices: 305972--306087 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
305962 TCATTCGGTA
305972 TCGGTACTGTTTTAAGGATTCATACAATTTTACCTTATGATATCGATACTGTTCTTCC
1 TCGGTACTGTTTTAAGGATTCATACAATTTTACCTTATGATATCGATACTGTTCTTCC
306030 TCGGTACTGTTTTAAGGATTCATACAATTTTACCTTATGATATCGATACTGTTCTTCC
1 TCGGTACTGTTTTAAGGATTCATACAATTTTACCTTATGATATCGATACTGTTCTTCC
306088 AATATCAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (58 bp):
TCGGTACTGTTTTAAGGATTCATACAATTTTACCTTATGATATCGATACTGTTCTTCC
Found at i:307037 original size:16 final size:16
Alignment explanation
Indices: 306981--307089 Score: 58
Period size: 16 Copynumber: 6.8 Consensus size: 16
306971 TCGGTTCAAA
**
306981 TTAATTTCTATTCGGG
1 TTAATTTCGGTTCGGG
**
306997 TTGTTTTCGGGTT-GGG
1 TTAATTTC-GGTTCGGG
*
307013 TTAAGTTCGGTTCGGG
1 TTAATTTCGGTTCGGG
* *
307029 TTACTTTCGGATCGGG
1 TTAATTTCGGTTCGGG
* * * *
307045 TTAAAATTCAGTTTGAG
1 TT-AATTTCGGTTCGGG
** * *
307062 TTTCTTTCAGTTCTGG
1 TTAATTTCGGTTCGGG
307078 TTAATTTCGGTT
1 TTAATTTCGGTT
307090 TCGGTTCGGG
Statistics
Matches: 65, Mismatches: 25, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
15 4 0.06
16 49 0.75
17 12 0.18
ACGTcount: A:0.15, C:0.12, G:0.27, T:0.47
Consensus pattern (16 bp):
TTAATTTCGGTTCGGG
Found at i:307114 original size:22 final size:22
Alignment explanation
Indices: 307066--307114 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
307056 TTTGAGTTTC
* *
307066 TTTCAGTTCTGGTTAATTTCGG
1 TTTCGGTTCGGGTTAATTTCGG
*
307088 TTTCGGTTCGGGTTAATTTTGG
1 TTTCGGTTCGGGTTAATTTCGG
307110 TTTCG
1 TTTCG
307115 CTAAATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.27, T:0.51
Consensus pattern (22 bp):
TTTCGGTTCGGGTTAATTTCGG
Found at i:311494 original size:185 final size:186
Alignment explanation
Indices: 311185--311561 Score: 699
Period size: 185 Copynumber: 2.0 Consensus size: 186
311175 AAAAAATCCT
311185 GAAATCATGAATTTAGAGATTATTGCACTTTCTGCTAGGAATTAATCTTAGTTTCAGTTTGATTG
1 GAAATCATGAATTTAGAGATTATTGCACTTTCTGCTAGGAATTAATCTTAGTTTCAGTTTGATTG
311250 AAGTAAAGAAGGAAAGCCAAAAAAATGTGTTTTTTTTCAAGCATATTAACACTTAATTAAGTGAT
66 AAGTAAAGAAGGAAAGCCAAAAAAATGTGTTTTTTTTCAAGCATATTAACACTTAATTAAGTGAT
311315 TAAA-T-TATATA-TCATTGGATATAG-AGACGATGATGGGGCATGCCATTGCTCA
131 TAAATTATATATATTCATTGGATATAGAAGACGATGATGGGGCATGCCATTGCTCA
311367 GAAATCATGAATTTAGAGAATTTATTTGCACTTTCTGCTAGGAATTAATCTTAGTTTCAGTTTGA
1 GAAATCATGAATTTAGAG-A-TTA-TTGCACTTTCTGCTAGGAATTAATCTTAGTTTCAGTTTGA
311432 TTGAAGTAAAGAAGGAAAGCCAAAAAAATGTGTTTTTTTTCAAGCATATTAACACTTAATTAAGT
63 TTGAAGTAAAGAAGGAAAGCCAAAAAAATGTGTTTTTTTTCAAGCATATTAACACTTAATTAAGT
311497 GATTAAATTATATATATTCATTGGATATAGAAGACGATGATGGGGCATGCCATTGCTCA
128 GATTAAATTATATATATTCATTGGATATAGAAGACGATGATGGGGCATGCCATTGCTCA
311556 GAAATC
1 GAAATC
311562 TCCGGTTGAG
Statistics
Matches: 188, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
182 18 0.10
183 1 0.01
184 3 0.02
185 112 0.60
186 1 0.01
187 6 0.03
188 13 0.07
189 34 0.18
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (186 bp):
GAAATCATGAATTTAGAGATTATTGCACTTTCTGCTAGGAATTAATCTTAGTTTCAGTTTGATTG
AAGTAAAGAAGGAAAGCCAAAAAAATGTGTTTTTTTTCAAGCATATTAACACTTAATTAAGTGAT
TAAATTATATATATTCATTGGATATAGAAGACGATGATGGGGCATGCCATTGCTCA
Found at i:313923 original size:10 final size:10
Alignment explanation
Indices: 313908--313946 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
313898 ATCGTTTAAT
313908 TTTATGTTCA
1 TTTATGTTCA
*
313918 TTTATGTTCG
1 TTTATGTTCA
* *
313928 TTTACGTTTA
1 TTTATGTTCA
313938 TTTATGTTC
1 TTTATGTTC
313947 GTTTGCGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.15, C:0.10, G:0.13, T:0.62
Consensus pattern (10 bp):
TTTATGTTCA
Found at i:313971 original size:20 final size:20
Alignment explanation
Indices: 313917--313964 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
313907 TTTTATGTTC
*
313917 ATTTATGTTCGTTTACGTTT
1 ATTTATGTTCGTTTGCGTTT
313937 ATTTATGTTCGTTTGCGTTT
1 ATTTATGTTCGTTTGCGTTT
313957 ATTTATGT
1 ATTTATGT
313965 CTGTTTGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.08, G:0.17, T:0.60
Consensus pattern (20 bp):
ATTTATGTTCGTTTGCGTTT
Found at i:322833 original size:199 final size:201
Alignment explanation
Indices: 322493--322894 Score: 781
Period size: 199 Copynumber: 2.0 Consensus size: 201
322483 AAAATAAAAT
322493 ATGTTTTGGGAACCCTAAATAAATTTTCGAATGATTCTTCTTACTAAATTAACGCAACAAAATTT
1 ATGTTTTGGGAACCCTAAATAAATTTTCGAATGATTCTTCTTACTAAATTAACGCAACAAAATTT
322558 ATTCTCTATGTTAAAAAAATATTCTGCATATATTCCTGAAATATTCATTTCACAGTCGTTAAACA
66 ATTCTCTATGTTAAAAAAATATTCTGCATATATTCCTGAAATATTCATTTCACAGTCGTTAAACA
322623 CCGGAGAATATTGATTTTTTC-ATGATCTAAC-AAAACTCGAATAGAATGATGTGAATTACTCGC
131 CCGGAGAATATTGATTTTTTCAATGATCTAACAAAAACTCGAATAGAATGATGTGAATTACTCGC
322686 ATTAGA
196 ATTAGA
322692 ATGTTTTGGGAACCCTAAATAAATTTTCGAATGATTCTTCTTACTAAATTAACGCAACAAAATTT
1 ATGTTTTGGGAACCCTAAATAAATTTTCGAATGATTCTTCTTACTAAATTAACGCAACAAAATTT
322757 ATTCTCTATGTTAAAAAAATATTCTGCATATATTCCTGAAATATTCATTTCACAGTCGTTAAACA
66 ATTCTCTATGTTAAAAAAATATTCTGCATATATTCCTGAAATATTCATTTCACAGTCGTTAAACA
322822 CCGGAGAATATTGATTTTTTCATATGATCTAACAAAAACTCGAATAGAATGATGTGAATTACTCG
131 CCGGAGAATATTGATTTTTTCA-ATGATCTAACAAAAACTCGAATAGAATGATGTGAATTACTCG
322887 CATTAGA
195 CATTAGA
322894 A
1 A
322895 GACCAGATTC
Statistics
Matches: 200, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
199 151 0.75
201 10 0.05
202 39 0.19
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (201 bp):
ATGTTTTGGGAACCCTAAATAAATTTTCGAATGATTCTTCTTACTAAATTAACGCAACAAAATTT
ATTCTCTATGTTAAAAAAATATTCTGCATATATTCCTGAAATATTCATTTCACAGTCGTTAAACA
CCGGAGAATATTGATTTTTTCAATGATCTAACAAAAACTCGAATAGAATGATGTGAATTACTCGC
ATTAGA
Found at i:329015 original size:10 final size:10
Alignment explanation
Indices: 329000--329074 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
328990 CATTTAATAA
329000 ATAAACGAAC
1 ATAAACGAAC
329010 ATAAACGAAC
1 ATAAACGAAC
329020 ----ACGAAC
1 ATAAACGAAC
329026 ATAAACGAAC
1 ATAAACGAAC
** *
329036 ACGAAC-ATAA
1 ATAAACGA-AC
329046 ATGAACACGAAC
1 AT-AA-ACGAAC
*
329058 ATAAACAAAC
1 ATAAACGAAC
329068 ATAAACG
1 ATAAACG
329075 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 33 0.67
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:329025 original size:16 final size:16
Alignment explanation
Indices: 329004--329068 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
328994 TAATAAATAA
329004 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
329020 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
329036 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
329052 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
329068 A
1 A
329069 TAAACGTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:329836 original size:14 final size:14
Alignment explanation
Indices: 329819--329874 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
329809 AATGAACATA
329819 AACGAACATAATCG
1 AACGAACATAATCG
329833 AACGAACAT-A---
1 AACGAACATAATCG
* *
329843 AACAAACATAACCG
1 AACGAACATAATCG
329857 AACGAACATAATCG
1 AACGAACATAATCG
329871 AACG
1 AACG
329875 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:329839 original size:24 final size:24
Alignment explanation
Indices: 329799--329873 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
329789 GATTGAGTTA
*
329799 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
329823 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
329847 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
329871 AAC
1 AAC
329874 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:330427 original size:13 final size:15
Alignment explanation
Indices: 330399--330444 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
330389 AAAATAATTA
330399 AAATATTAATTTTAT
1 AAATATTAATTTTAT
330414 AAATATT-A-TTTAT
1 AAATATTAATTTTAT
* * *
330427 AATTTTTATTTTTAT
1 AAATATTAATTTTAT
330442 AAA
1 AAA
330445 ATAAATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 10 0.40
14 1 0.04
15 14 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATATTAATTTTAT
Found at i:332203 original size:22 final size:22
Alignment explanation
Indices: 332160--332203 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
332150 TCGCGGTAGG
* *
332160 ATTTTTCTAGTCAGTTCCTTGC
1 ATTTTTCTAATCAGTTCATTGC
*
332182 ATTTTTCTAATCAGTTTATTGC
1 ATTTTTCTAATCAGTTCATTGC
332204 TGGATTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.52
Consensus pattern (22 bp):
ATTTTTCTAATCAGTTCATTGC
Found at i:332957 original size:36 final size:36
Alignment explanation
Indices: 332915--332990 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
332905 TTATAGCTAA
*
332915 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
332951 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
332987 AAAA
1 AAAA
332991 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:335454 original size:14 final size:14
Alignment explanation
Indices: 335435--335463 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
335425 CCACGGTGCT
335435 CCCGGAATCCTGCG
1 CCCGGAATCCTGCG
335449 CCCGGAATCCTGCG
1 CCCGGAATCCTGCG
335463 C
1 C
335464 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.45, G:0.28, T:0.14
Consensus pattern (14 bp):
CCCGGAATCCTGCG
Found at i:335927 original size:36 final size:36
Alignment explanation
Indices: 335885--335960 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
335875 TTATAGCTAA
*
335885 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
335921 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
335957 AAAA
1 AAAA
335961 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:338328 original size:3 final size:3
Alignment explanation
Indices: 338320--338347 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
338310 GAATTGAGTT
338320 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
338348 AAAGGTTTCT
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:341926 original size:55 final size:56
Alignment explanation
Indices: 341863--342125 Score: 263
Period size: 55 Copynumber: 4.8 Consensus size: 56
341853 CTTCAAATGG
* * ***
341863 CGGGTCTGCTCCCTATTCTTTCAGGGAGTATAAG-ACTCAAACAATCTTCGGCAAA
1 CGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGAACTCGAACAATCTTCATAAAA
* * *
341918 CGTGTCTGCTCCCTATTCAGTCAGGGAGTATAAG-ACTTGAACAATCTTCAATAAAA
1 CGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGAACTCGAACAATCTTC-ATAAAA
* * * *
341974 CGGGT-TCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGGAA-AATCTTCA-ATAAT
1 CGGGTCT-GCTCCCTATTCATTCAGGGAGTATAAGAACTC-GAACAATCTTCATA-AAA
*
342029 CGGGTCCGCTCCCTATTCATTCAGGGAGTAT-AGAACTCGAACAATCTTCATAAAA
1 CGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGAACTCGAACAATCTTCATAAAA
* * * * * *
342084 CGTGTCCGCTCTCTATTCCTTTAGAGAGTAT-AGAACTCGAAC
1 CGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGAACTCGAAC
342126 CTCATAAAAT
Statistics
Matches: 175, Mismatches: 25, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
54 4 0.02
55 130 0.74
56 38 0.22
57 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (56 bp):
CGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGAACTCGAACAATCTTCATAAAA
Found at i:342021 original size:111 final size:111
Alignment explanation
Indices: 341863--342124 Score: 325
Period size: 111 Copynumber: 2.4 Consensus size: 111
341853 CTTCAAATGG
* * * * ** * *
341863 CGGGTCTGCTCCCTATTCTTTCAGGGAGTATA-AGACTC-AAACAATCTTCGGCAAACGTGTCTG
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAACAATCTTCAACAAACGGGTCCG
*
341926 CTCCCTATTCAGTCAGGGAGTATA-AGACTTGAACAATCTTCAATAAAA
65 CTCCCTATTCAGTCAGGGAGTATAGA-ACTCGAACAATCTTC-ATAAAA
* * * *
341974 CGGGTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAA-AATCTTCAATAATCGGGTCCGC
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAACAATCTTCAACAAACGGGTCCGC
*
342038 TCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAAA
66 TCCCTATTCAGTCAGGGAGTATAGAACTCGAACAATCTTCATAAAA
* *
342084 CGTGTCCGCTCTCTATTCCTTTAGAGAGTATAGAACTCGAA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA
342125 CCTCATAAAA
Statistics
Matches: 130, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
110 43 0.33
111 83 0.64
112 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (111 bp):
CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAACAATCTTCAACAAACGGGTCCGC
TCCCTATTCAGTCAGGGAGTATAGAACTCGAACAATCTTCATAAAA
Found at i:342183 original size:37 final size:38
Alignment explanation
Indices: 342132--342205 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
342122 GAACCTCATA
342132 AAATGTGTCTGCTTCACTAATCTTCCGTGAAGGCTTAC
1 AAATGTGTCTGCTTCACTAATCTTCCGTGAAGGCTTAC
* *
342170 AAATG-GTTTGCTTCACTACTCTTCCGTGAAGGCTTA
1 AAATGTGTCTGCTTCACTAATCTTCCGTGAAGGCTTA
342206 AGATTGACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 29 0.85
38 5 0.15
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (38 bp):
AAATGTGTCTGCTTCACTAATCTTCCGTGAAGGCTTAC
Found at i:343511 original size:24 final size:23
Alignment explanation
Indices: 343484--343549 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 23
343474 TTCTATCTTT
*
343484 TTTTTTTTCTTTCTTTCATTTTCA
1 TTTTTTTTCATT-TTTCATTTTCA
343508 ---TTTTTCATTTTTCATTTTTCA
1 TTTTTTTTCATTTTTCA-TTTTCA
343529 TTTTTTTTCATTTTTCATTTT
1 TTTTTTTTCATTTTTCATTTT
343550 TTTTATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
20 5 0.14
21 14 0.38
23 4 0.11
24 14 0.38
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTTTTCATTTTTCATTTTCA
Found at i:343514 original size:7 final size:7
Alignment explanation
Indices: 343487--343550 Score: 76
Period size: 7 Copynumber: 8.7 Consensus size: 7
343477 TATCTTTTTT
*
343487 TTTTTCT
1 TTTTTCA
343494 TTCTTTCA
1 TT-TTTCA
343502 -TTTTCA
1 TTTTTCA
343508 TTTTTCA
1 TTTTTCA
343515 TTTTTCA
1 TTTTTCA
343522 TTTTTCA
1 TTTTTCA
343529 TTTTTTTTCA
1 ---TTTTTCA
343539 TTTTTCA
1 TTTTTCA
343546 TTTTT
1 TTTTT
343551 TTTATTTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
6 5 0.10
7 35 0.69
8 4 0.08
10 7 0.14
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:343537 original size:10 final size:10
Alignment explanation
Indices: 343522--343570 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
343512 TCATTTTTCA
343522 TTTTTCATTT
1 TTTTTCATTT
343532 TTTTTCA---
1 TTTTTCATTT
343539 TTTTTCATTT
1 TTTTTCATTT
343549 TTTTT-ATTT
1 TTTTTCATTT
*
343558 TTTTTCCTTT
1 TTTTTCATTT
343568 TTT
1 TTT
343571 ATTTCTCCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
7 7 0.21
9 9 0.26
10 18 0.53
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:343550 original size:24 final size:24
Alignment explanation
Indices: 343508--343574 Score: 89
Period size: 26 Copynumber: 2.7 Consensus size: 24
343498 TTCATTTTCA
343508 TTTTTCATTTTTCATTTTTCATTT
1 TTTTTCATTTTTCATTTTTCATTT
*
343532 TTTTTCATTTTTCATTTTTTTTATTT
1 TTTTTCATTTTTCA--TTTTTCATTT
* *
343558 TTTTTCCTTTTTTATTT
1 TTTTTCATTTTTCATTT
343575 CTCCTTCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 17 0.45
26 21 0.55
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTCATTTTTCATTTTTCATTT
Found at i:343560 original size:17 final size:17
Alignment explanation
Indices: 343502--343559 Score: 88
Period size: 17 Copynumber: 3.6 Consensus size: 17
343492 CTTTCTTTCA
343502 TTTTCATTTTTCA---T
1 TTTTCATTTTTCATTTT
343516 TTTTCATTTTTCATTTT
1 TTTTCATTTTTCATTTT
343533 TTTTCATTTTTCATTTT
1 TTTTCATTTTTCATTTT
343550 TTTT-ATTTTT
1 TTTTCATTTTT
343560 TTTCCTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
14 13 0.32
16 6 0.15
17 22 0.54
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCATTTTTCATTTT
Found at i:353338 original size:45 final size:45
Alignment explanation
Indices: 353227--353371 Score: 200
Period size: 45 Copynumber: 3.1 Consensus size: 45
353217 TGTTATCCAC
* * *
353227 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
1 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCTTATTC-G
* *
353274 AAAAACAAACCTAACCGCATGATATCTAGTTCGCATGCTTGTTCG
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTATTCG
*
353319 AAAAATAAACCTAACCGCATGATATCTAGTTCGCAAGCATTTATTCG
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC--TTATTCG
353366 AAAAAT
1 AAAAAT
353372 GAAAATAAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
45 36 0.40
46 33 0.37
47 20 0.22
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (45 bp):
AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTATTCG
Found at i:355287 original size:191 final size:189
Alignment explanation
Indices: 354965--355346 Score: 746
Period size: 191 Copynumber: 2.0 Consensus size: 189
354955 TGACCTAAAA
354965 TATAAAAACAAAATCATAGCATGCTAAACTATAAATTAAAAAAGTATATATATATATACATAAAT
1 TATAAAAACAAAATCATAGCATGCTAAACTATAAATTAAAAAAGTATATATATATATACATAAAT
355030 ATAATGACTAAATTCAAATACACATAAAATTAAACATACTAATTAAGAATTAAAACAAAGAATTA
66 ATAATGACTAAATTCAAATACACATAAAATTAAACATACTAATTAAGAATTAAAACAAAGAATTA
355095 AAGAAAAACAAACATAAATATAATGGACTTAAGCCTAAAATAAAAGTATGGTGATATGG
131 AAGAAAAACAAACATAAATATAATGGACTTAAGCCTAAAATAAAAGTATGGTGATATGG
355154 TATAAAAACAAAATCATAGCATGCTAAACTATAAATTAAAAAAGTATATATATATATATACATAA
1 TATAAAAACAAAATCATAGCATGCTAAACTATAAATTAAAAAAG--TATATATATATATACATAA
355219 ATATAATGACTAAATTCAAATACACATAAAATTAAACATACTAATTAAGAATTAAAACAAAGAAT
64 ATATAATGACTAAATTCAAATACACATAAAATTAAACATACTAATTAAGAATTAAAACAAAGAAT
355284 TAAAGAAAAACAAACATAAATATAATGGACTTAAGCCTAAAATAAAAGTATGGTGATATGG
129 TAAAGAAAAACAAACATAAATATAATGGACTTAAGCCTAAAATAAAAGTATGGTGATATGG
355345 TA
1 TA
355347 CATACATGCA
Statistics
Matches: 191, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
189 44 0.23
191 147 0.77
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.26
Consensus pattern (189 bp):
TATAAAAACAAAATCATAGCATGCTAAACTATAAATTAAAAAAGTATATATATATATACATAAAT
ATAATGACTAAATTCAAATACACATAAAATTAAACATACTAATTAAGAATTAAAACAAAGAATTA
AAGAAAAACAAACATAAATATAATGGACTTAAGCCTAAAATAAAAGTATGGTGATATGG
Found at i:369637 original size:19 final size:19
Alignment explanation
Indices: 369613--369652 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
369603 AGGCGACCCA
*
369613 TTTTTACGATTTTCTTTAT
1 TTTTTACGATTTTATTTAT
**
369632 TTTTTATTATTTTATTTAT
1 TTTTTACGATTTTATTTAT
369651 TT
1 TT
369653 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTTACGATTTTATTTAT
Found at i:369667 original size:19 final size:20
Alignment explanation
Indices: 369621--369667 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
369611 CATTTTTACG
*
369621 ATTTTC-TTTATTTTTTATT
1 ATTTTCATTTATTTATTATT
369640 ATTTT-ATTTATTTATT-TT
1 ATTTTCATTTATTTATTATT
369658 ATTTTCATTT
1 ATTTTCATTT
369668 TTAGGAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTTCATTTATTTATTATT
Found at i:371285 original size:18 final size:17
Alignment explanation
Indices: 371257--371313 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 17
371247 GGGATTATTC
371257 TTAGGATTTTATTTTCT
1 TTAGGATTTTATTTTCT
* *
371274 TTAGGTATTTTATTCTCA
1 TTAGG-ATTTTATTTTCT
371292 TTAGGAATTTTATTTTCT
1 TTAGG-ATTTTATTTTCT
371310 TTAG
1 TTAG
371314 CTTTTCTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 5 0.15
18 29 0.85
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (17 bp):
TTAGGATTTTATTTTCT
Found at i:380568 original size:36 final size:36
Alignment explanation
Indices: 380520--380612 Score: 177
Period size: 36 Copynumber: 2.6 Consensus size: 36
380510 AATATTCTAA
380520 TGGACCAGAGAATCGGTTTGACAACAGTCTTGGCAG
1 TGGACCAGAGAATCGGTTTGACAACAGTCTTGGCAG
*
380556 TGGACCAAAGAATCGGTTTGACAACAGTCTTGGCAG
1 TGGACCAGAGAATCGGTTTGACAACAGTCTTGGCAG
380592 TGGACCAGAGAATCGGTTTGA
1 TGGACCAGAGAATCGGTTTGA
380613 GCTTAGGTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (36 bp):
TGGACCAGAGAATCGGTTTGACAACAGTCTTGGCAG
Found at i:391247 original size:130 final size:130
Alignment explanation
Indices: 391014--391276 Score: 517
Period size: 130 Copynumber: 2.0 Consensus size: 130
391004 AGCTTCAGCC
*
391014 GATGGACGAGTTCGTGACCCCTCCTTCCAGCCCTGTTCATTTCCTGGATGCTAAGTCAAAATAGT
1 GATGGACGAGTTCGTGACCCCTCCTTCCAGCCCTGTTCATTTCCTGGATGCTAAGTCAAAAGAGT
391079 CAGAGGGTTCAACATCATGGATTTCGTGGATGAGAGGGACTCGTGGTGGCCAGTTAAGTGATAGT
66 CAGAGGGTTCAACATCATGGATTTCGTGGATGAGAGGGACTCGTGGTGGCCAGTTAAGTGATAGT
391144 GATGGACGAGTTCGTGACCCCTCCTTCCAGCCCTGTTCATTTCCTGGATGCTAAGTCAAAAGAGT
1 GATGGACGAGTTCGTGACCCCTCCTTCCAGCCCTGTTCATTTCCTGGATGCTAAGTCAAAAGAGT
391209 CAGAGGGTTCAACATCATGGATTTCGTGGATGAGAGGGACTCGTGGTGGCCAGTTAAGTGATAGT
66 CAGAGGGTTCAACATCATGGATTTCGTGGATGAGAGGGACTCGTGGTGGCCAGTTAAGTGATAGT
391274 GAT
1 GAT
391277 AGTAATCGAT
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 132 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (130 bp):
GATGGACGAGTTCGTGACCCCTCCTTCCAGCCCTGTTCATTTCCTGGATGCTAAGTCAAAAGAGT
CAGAGGGTTCAACATCATGGATTTCGTGGATGAGAGGGACTCGTGGTGGCCAGTTAAGTGATAGT
Found at i:412046 original size:25 final size:25
Alignment explanation
Indices: 412018--412098 Score: 64
Period size: 25 Copynumber: 3.4 Consensus size: 25
412008 AAAAAATAAC
412018 ATTTTAGGTAGCACACAATATTAAT
1 ATTTTAGGTAGCACACAATATTAAT
* * *
412043 ATTTTCGTTAG-A-A-AA-A-AAAT
1 ATTTTAGGTAGCACACAATATTAAT
* * *
412063 ATTTTAGATAGCCCACAATATTAAC
1 ATTTTAGGTAGCACACAATATTAAT
*
412088 ATTTTTGGTAG
1 ATTTTAGGTAG
412099 AAAAAATAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
20 12 0.29
21 1 0.02
22 3 0.07
23 3 0.07
24 2 0.05
25 20 0.49
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (25 bp):
ATTTTAGGTAGCACACAATATTAAT
Found at i:412104 original size:46 final size:46
Alignment explanation
Indices: 412004--412119 Score: 162
Period size: 45 Copynumber: 2.5 Consensus size: 46
411994 CTAATTTCCA
* * *
412004 GTAGAAAAAATAACATTTTAGGTAGCACACAATATTAATATTTTCG
1 GTAGAAAAAATAATATTTTAGATAGCACACAATATTAACATTTTCG
* * *
412050 TTAGAAAAAA-AATATTTTAGATAGCCCACAATATTAACATTTTTG
1 GTAGAAAAAATAATATTTTAGATAGCACACAATATTAACATTTTCG
*
412095 GTAGAAAAAATAATGTTTTAGATAG
1 GTAGAAAAAATAATATTTTAGATAG
412120 TATTTTACCG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 39 0.64
46 22 0.36
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.34
Consensus pattern (46 bp):
GTAGAAAAAATAATATTTTAGATAGCACACAATATTAACATTTTCG
Found at i:417467 original size:82 final size:83
Alignment explanation
Indices: 417316--417468 Score: 231
Period size: 82 Copynumber: 1.9 Consensus size: 83
417306 GTGCGATATA
* *
417316 ATTTATTTTTTATATTATTTATTAATTTAAAATTTTATTTTTTAACTCATTAGGTGAGGCCGATG
1 ATTTATTTTTTATATTATTTATTAATTTAAAATTTTAATTTTTAACTCATTAGGTGAGGCCGATA
417381 TAATTTATTTATTAATTC
66 TAATTTATTTATTAATTC
* *
417399 ATTTATTTTTGTAT-TTTTTTATTAATTT-AAATTTTAATTTTTAACTCATTAGGTGAGTG-GGA
1 ATTTATTTTT-TATATTATTTATTAATTTAAAATTTTAATTTTTAACTCATTAGGTGAG-GCCGA
417461 TATAATTT
64 TATAATTT
417469 GAGTAATAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
82 37 0.58
83 24 0.38
84 3 0.05
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (83 bp):
ATTTATTTTTTATATTATTTATTAATTTAAAATTTTAATTTTTAACTCATTAGGTGAGGCCGATA
TAATTTATTTATTAATTC
Found at i:429135 original size:18 final size:17
Alignment explanation
Indices: 429114--429243 Score: 67
Period size: 18 Copynumber: 7.7 Consensus size: 17
429104 CGATATTTTA
429114 AAATAAATTAATCTATAC
1 AAATAAATTAAT-TATAC
429132 AAATAAATT-ATT-TA-
1 AAATAAATTAATTATAC
*
429146 AAATAAATCAATTCATAC
1 AAATAAATTAATT-ATAC
* * * *
429164 TAATAAATTATTTAAAAT
1 AAATAAATTAATT-ATAC
* * *
429182 AAATCAATCCATATTTTA-
1 AAATAAAT-TA-ATTATAC
*
429200 AAATAAATCAATTCATAC
1 AAATAAATTAATT-ATAC
*
429218 TAATAAATT-ATT-TA-
1 AAATAAATTAATTATAC
429232 AAATAAATTAAT
1 AAATAAATTAAT
429244 CCATATTTTA
Statistics
Matches: 85, Mismatches: 18, Indels: 21
0.69 0.15 0.17
Matches are distributed among these distances:
14 16 0.19
15 9 0.11
16 4 0.05
17 11 0.13
18 41 0.48
19 2 0.02
20 2 0.02
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATAAATTAATTATAC
Found at i:429149 original size:32 final size:33
Alignment explanation
Indices: 429110--429248 Score: 137
Period size: 32 Copynumber: 4.7 Consensus size: 33
429100 CAATCGATAT
*
429110 TTTAAAATAAATTAATCT-ATACAAATAAATTA
1 TTTAAAATAAATCAATCTCATACAAATAAATTA
*
429142 TTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCTCATACAAATAAATTA
429174 TTTAAAATAAATCAA--TC---C--AT--A-T-
1 TTTAAAATAAATCAATCTCATACAAATAAATTA
*
429196 TTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCTCATACAAATAAATTA
*
429228 TTTAAAATAAATTAATC-CATA
1 TTTAAAATAAATCAATCTCATA
429249 TTTTAAAATA
Statistics
Matches: 92, Mismatches: 3, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
22 15 0.16
23 3 0.03
24 1 0.01
26 3 0.03
28 3 0.03
30 1 0.01
31 4 0.04
32 62 0.67
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (33 bp):
TTTAAAATAAATCAATCTCATACAAATAAATTA
Found at i:429200 original size:22 final size:22
Alignment explanation
Indices: 429174--429216 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
429164 TAATAAATTA
429174 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
429196 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
429217 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:429200 original size:54 final size:54
Alignment explanation
Indices: 428996--429810 Score: 323
Period size: 54 Copynumber: 15.5 Consensus size: 54
428986 AATCCATATA
*
428996 ATACATAAT-AATTATTTAAAATAAATCAATCCATATTTTAAAAT-AATTAATTC
1 ATAC-TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
* * **
429049 ATA-TAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAA-TC
1 ATACTAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATTC
* * * * *
429105 GATATTTTAAAATAAATTAATCT-ATACAAATAAAT---TA-TTTAAAATAAATCAATTC
1 -ATA--CT--AATAAATT-ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
429160 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
1 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
* *
429214 ATACTAATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATTAATTC
1 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
*
429268 ATACTAAT-AATTATTTAAAA-AAATCAAT-C-TA-TAT-AAAT-AAT-AA-TC
1 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
* ** * *
429313 AT-C-CAT--A-T-TTT-AAATAAATCAATCCATACAATAAATAATAAATCAATCC
1 ATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAA-AATAAATCAATTC
** * * * * *
429362 ATTTTTAAAATAAATCAATCTATACT-AAT-AAT---TA-TTTAAAAT-AATC-ATCC
1 A-TACT--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
* * * * *
429412 ATATTTAAATAAATCAATTATACT-AAT--AT---TA-TTTAAAAT-AATCAATCCATAC
1 ATA-CT-AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT---T-C
* *
429464 AACTAAATAATAATAATTATTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAATTA
1 -A-T-ACTAAT-A-AATTATTTAAAATAAATCAATC----C--AT--A-T-TTTAAAATAAATCA
*
429529 ATCC
51 ATTC
429533 ATAC-AAT-AA--A--T--AATAAATCAATCCATATTTTAAAATAAAT-AA-TC
1 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
* *
429577 TATACAAAT-AATTATTTAAAATAAATCAATTCATACTAATATATTATTTAAAAT-AATCAATCC
1 -ATACTAATAAATTATTTAAAATAAATCAA-TC---C----ATA-T-TTTAAAATAAATCAATTC
* *
429640 ATAC-AACT--A-CA--T--AAT-AAT-AATCCATA-TTTAAAATAAATC-ATCC
1 ATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
* *
429683 ATAC---TAAATTATTTAAAATAAATCAATCTATATTTT-AAATAAATCAATCC
1 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
*
429733 ATACTAATAAATTATTT--AATAAATCAATCCATATTTTAAAATAAATCAATCC
1 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
429785 ATACTAATAAATTATTTAAAATAAAT
1 ATACTAATAAATTATTTAAAATAAAT
429811 TATTTCAAAA
Statistics
Matches: 602, Mismatches: 52, Indels: 215
0.69 0.06 0.25
Matches are distributed among these distances:
39 3 0.00
40 12 0.02
41 2 0.00
42 4 0.01
43 19 0.03
44 6 0.01
45 12 0.02
46 25 0.04
47 26 0.04
48 23 0.04
49 32 0.05
50 42 0.07
51 28 0.05
52 78 0.13
53 38 0.06
54 105 0.17
55 24 0.04
56 26 0.04
57 8 0.01
58 7 0.01
59 6 0.01
60 8 0.01
61 7 0.01
62 34 0.06
63 4 0.01
65 3 0.00
66 1 0.00
67 2 0.00
68 1 0.00
69 2 0.00
72 8 0.01
73 6 0.01
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
Found at i:429204 original size:86 final size:86
Alignment explanation
Indices: 428996--429248 Score: 332
Period size: 86 Copynumber: 3.0 Consensus size: 86
428986 AATCCATATA
428996 ATACATAAT-AATTATTTAAAATAAATCAATCCATATTTTAAAAT-AATTAATTCATA-TAATAA
1 ATAC-TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATTAATTCATACTAATAA
429058 ATTATTTAAAATAAATCAA-TC
65 ATTATTTAAAATAAATCAATTC
* * *
429079 TATAC-AACTACA--A--T--AATAAATCAATCGATATTTTAAAATAAATTAA-TCTATACAAAT
1 -ATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATTAATTC-ATACTAAT
429136 AAATTATTTAAAATAAATCAATTC
63 AAATTATTTAAAATAAATCAATTC
*
429160 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAA
1 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATTAATTCATACTAATAAA
* *
429225 TTATTTAAAATAAATTAATCC
66 TTATTTAAAATAAATCAATTC
429246 ATA
1 ATA
429249 TTTTAAAATA
Statistics
Matches: 146, Mismatches: 9, Indels: 26
0.81 0.05 0.14
Matches are distributed among these distances:
78 26 0.18
79 9 0.06
80 32 0.22
81 4 0.03
82 4 0.03
83 1 0.01
84 6 0.04
86 62 0.42
87 2 0.01
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (86 bp):
ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATTAATTCATACTAATAAA
TTATTTAAAATAAATCAATTC
Found at i:429225 original size:22 final size:22
Alignment explanation
Indices: 429176--429224 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
429166 ATAAATTATT
**
429176 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
429198 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
429221 TAAA
1 TAAA
429225 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:429243 original size:22 final size:22
Alignment explanation
Indices: 429218--429265 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
429208 CAATTCATAC
429218 TAATAAAT-TATTTAAAATAAAT
1 TAATAAATAT-TTTAAAATAAAT
**
429240 TAATCCATATTTTAAAATAAAT
1 TAATAAATATTTTAAAATAAAT
429262 TAAT
1 TAAT
429266 TCATACTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAAATATTTTAAAATAAAT
Found at i:429270 original size:22 final size:22
Alignment explanation
Indices: 429228--429270 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
429218 TAATAAATTA
429228 TTTAAAATAAATTAATCCATAT
1 TTTAAAATAAATTAATCCATAT
*
429250 TTTAAAATAAATTAATTCATA
1 TTTAAAATAAATTAATCCATA
429271 CTAATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATAAATTAATCCATAT
Found at i:429326 original size:40 final size:41
Alignment explanation
Indices: 429281--429393 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 41
429271 CTAATAATTA
429281 TTTAAAAAAATCAATCTATATAAATAAT-AATC-ATCCATAT
1 TTTAAAAAAATCAATCTATATAAATAATAAATCAATCCAT-T
* *
429321 TTTAAATAAATCAATCCATACAATAAATAATAAATCAATCCATT
1 TTTAAAAAAATCAAT-C-TA-TATAAATAATAAATCAATCCATT
429365 TTTAAAATAAATCAATCTATACT-AATAAT
1 TTTAAAA-AAATCAATCTATA-TAAATAAT
429394 TATTTAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
40 14 0.23
41 1 0.02
42 9 0.15
43 12 0.19
44 12 0.19
45 14 0.23
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (41 bp):
TTTAAAAAAATCAATCTATATAAATAATAAATCAATCCATT
Found at i:429339 original size:21 final size:21
Alignment explanation
Indices: 429309--429381 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
429299 TATAAATAAT
429309 AATC-ATCCATATTTTAAATA
1 AATCAATCCATATTTTAAATA
* **
429329 AATCAATCCATACAATAAATAATA
1 AATCAATCCAT--ATTTTA-AATA
429353 AATCAATCCAT-TTTTAAAATA
1 AATCAATCCATATTTT-AAATA
429374 AATCAATC
1 AATCAATC
429382 TATACTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
20 4 0.10
21 19 0.45
22 1 0.02
23 3 0.07
24 15 0.36
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (21 bp):
AATCAATCCATATTTTAAATA
Found at i:429512 original size:41 final size:39
Alignment explanation
Indices: 429435--429548 Score: 120
Period size: 32 Copynumber: 3.1 Consensus size: 39
429425 TCAATTATAC
429435 TAATATTATTTAAAATAATCAATCCATACAACTAAATAA
1 TAATATTATTTAAAATAATCAATCCATACAACTAAATAA
*
429474 TAATAATTATTTAAAATAAATCAATCGAT---AC----TAA
1 TAAT-ATTATTTAAAAT-AATCAATCCATACAACTAAATAA
*
429508 TAA-ATTATTTAAAATAAATTAATCCATACAA-TAAATAA
1 TAATATTATTTAAAAT-AATCAATCCATACAACTAAATAA
429546 TAA
1 TAA
429549 ATCAATCCAT
Statistics
Matches: 63, Mismatches: 3, Indels: 19
0.74 0.04 0.22
Matches are distributed among these distances:
32 22 0.35
34 6 0.10
35 1 0.02
38 8 0.13
39 4 0.06
40 12 0.19
41 10 0.16
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (39 bp):
TAATATTATTTAAAATAATCAATCCATACAACTAAATAA
Found at i:429537 original size:73 final size:74
Alignment explanation
Indices: 429413--429617 Score: 264
Period size: 76 Copynumber: 2.8 Consensus size: 74
429403 TAATCATCCA
429413 TATTT-AAATAAATCAAT-TATACTAAT-ATTATTTAAAAT-AATCAATCCATACAACTAAATAA
1 TATTTAAAATAAATCAATCTATACTAATAATTATTTAAAATAAATCAATCCATACAA-TAAATAA
429474 T-AAT-AAT-
65 TAAATCAATC
* *
429481 TATTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAATTAATCCATACAATAAATAA
1 TATTTAAAATAAATCAATCTATACTAAT-AATTATTTAAAATAAATCAATCCATACAATAAATAA
429546 TAAATCAATCC
65 TAAATCAAT-C
* *
429557 ATATTTTAAAATAAAT-AATCTATACAAATAATTATTTAAAATAAATCAATTCATACTAATA
1 -TA-TTTAAAATAAATCAATCTATACTAATAATTATTTAAAATAAATCAATCCATAC-AATA
429618 TATTATTTAA
Statistics
Matches: 119, Mismatches: 6, Indels: 15
0.85 0.04 0.11
Matches are distributed among these distances:
68 5 0.04
69 12 0.10
70 8 0.07
72 20 0.17
73 17 0.14
74 3 0.03
76 25 0.21
77 17 0.14
78 12 0.10
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (74 bp):
TATTTAAAATAAATCAATCTATACTAATAATTATTTAAAATAAATCAATCCATACAATAAATAAT
AAATCAATC
Found at i:429541 original size:118 final size:113
Alignment explanation
Indices: 429250--429765 Score: 362
Period size: 108 Copynumber: 4.5 Consensus size: 113
429240 TAATCCATAT
* * * * *
429250 TTTAAAATAAATTAATTCATACTAATAATTATTTAAAAAAATCAATCTATATAA-ATAATAATCA
1 TTTAAAATAAATCAATTCATACTAATAATTATTTAAAATAATCAATCCATACAATA-AATAATTA
* *
429314 T-C-CATAT-TTTAAATAAATCAATCCATACAA-TAAATAATAAATCAATCCATT
65 TACTAATATATTTAAAT-AATCAATCCATACAACTAAATAAT-AAT-AAT---TA
*
429365 TTTAAAATAAATCAA-TCTATACTAATAATTATTTAAAATAATC-ATCCATATTTAAATAAATCA
1 TTTAAAATAAATCAATTC-ATACTAATAATTATTTAAAATAATCAATCCATA---CAATAAAT-A
429428 ATTATACTAATATTATTTAAAATAATCAATCCATACAACTAAATAATAATAATTA
61 ATTATACTAATA-TATTT-AAATAATCAATCCATACAACTAAATAATAATAATTA
*
429483 TTTAAAATAAATCAA-TCGATACTAATAAATTATTTAAAATAAATTAATCCATACAATAAATAA-
1 TTTAAAATAAATCAATTC-ATACTAAT-AATTATTTAAAAT-AATCAATCCATACAATAAATAAT
* * *
429546 TA-AATCAATCCATATTTTAA-AAT-AA---ATA-ATCT--ATACA-AATAATTA
63 TATACT-AAT--ATATTTAAATAATCAATCCATACAACTAAATA-ATAATAATTA
*
429591 TTTAAAATAAATCAATTCATACTAATATATTATTTAAAATAATCAATCCATACAACTACATAA-T
1 TTTAAAATAAATCAATTCATACTAATA-ATTATTTAAAATAATCAATCCATACAA-TAAATAATT
*
429655 A-A-TAATCCATATTTAAAATAAATC-ATCCATACTAAATTATTTAA-AATAAATCAATCTATA
64 ATACTAAT--ATATTT-AAAT-AATCAATCCATAC--AACTA---AATAAT-AAT-AA--T-TA
* * *
429715 TTTTAAATAAATCAATCCATACTAATAAATTATTTAATA-AATCAATCCATA
1 TTTAAAATAAATCAATTCATACTAAT-AATTATTTAAAATAATCAATCCATA
429766 TTTTAAAATA
Statistics
Matches: 336, Mismatches: 21, Indels: 80
0.77 0.05 0.18
Matches are distributed among these distances:
106 11 0.03
107 18 0.05
108 55 0.16
109 7 0.02
110 3 0.01
111 3 0.01
112 3 0.01
114 10 0.03
115 45 0.13
116 7 0.02
117 12 0.04
118 41 0.12
119 15 0.04
120 10 0.03
121 13 0.04
122 21 0.06
123 25 0.07
124 36 0.11
125 1 0.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (113 bp):
TTTAAAATAAATCAATTCATACTAATAATTATTTAAAATAATCAATCCATACAATAAATAATTAT
ACTAATATATTTAAATAATCAATCCATACAACTAAATAATAATAATTA
Found at i:429633 original size:180 final size:171
Alignment explanation
Indices: 429140--429808 Score: 559
Period size: 176 Copynumber: 3.8 Consensus size: 171
429130 ACAAATAAAT
* * * * *
429140 TATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATA
1 TATTTAAAATAAATC-ATCCATAC---TAAATTATTTAAAATAAATCAATCTACA-ATAAAAATA
* * * * * *
429205 AATCAATTCATACTAATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATTAATTCAT
61 AATCAATCCATACTAATAAATAATCT--AACAAATCAAT-C-TA-TTTAAAATAAATCAATTCAT
* * *
429270 ACTAATA-ATTATTTAAAAAAATCAAT-C-TA-TA-TAAATAATAATCATCC
121 ACTAATATATTATTTAAAATAATCAATCCATACAACTAAATAATAATAAT-C
* * *** *
429317 ATATTTTAAATAAATCAATCCATAC--AA-TA---AATAATAAATCAATCCATTTTTAAAATAAA
1 -TATTTAAAATAAATC-ATCCATACTAAATTATTTAA-AATAAATCAATCTACAATAAAAATAAA
* * * *
429376 TCAATCTATACTAAT-AATTATTTAAAATAATC-ATCCATATTT-AAATAAATCAATT-ATACT-
63 TCAATCCATACTAATAAATAATCTAACA-AATCAAT-C-TATTTAAAATAAATCAATTCATACTA
429436 A-ATATTATTTAAAATAATCAATCCATACAACTAAATAATAATAAT-
125 ATATATTATTTAAAATAATCAATCCATACAACTAAATAATAATAATC
* *
429481 TATTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAATTAATCCATACAATAAATAA
1 TATTTAAAATAAATC-ATCCATAC---TAAATTATTTAAAATAAATCAAT-C-TACAATAAA-AA
*
429546 TAAATCAATCCATATTTTAAAATAAATAATCTATACAAAT-AAT-TATTTAAAATAAATCAATTC
59 TAAATCAATCCATA--CT--AATAAATAATCTA-ACAAATCAATCTATTTAAAATAAATCAATTC
*
429609 ATACTAATATATTATTTAAAATAATCAATCCATACAACTACATAATAATAATCC
119 ATACTAATATATTATTTAAAATAATCAATCCATACAACTAAATAATAATAAT-C
* * **
429663 ATATTTAAAATAAATCATCCATACTAAATTATTTAAAATAAATCAATCTATATTTTAAATAAATC
1 -TATTTAAAATAAATCATCCATACTAAATTATTTAAAATAAATCAATCTACAATAAAAATAAATC
* * * *
429728 AATCCATACTAATAAATTATTTAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
65 AATCCATACTAATAAATAATCTAACAAATCAAT-C-TA-TTTAAAATAAATCAATTCATACTAAT
*
429793 AAATTATTTAAAATAA
127 ATATTATTTAAAATAA
429809 ATTATTTCAA
Statistics
Matches: 416, Mismatches: 37, Indels: 78
0.78 0.07 0.15
Matches are distributed among these distances:
161 1 0.00
162 19 0.05
163 28 0.07
164 14 0.03
165 4 0.01
166 23 0.06
167 3 0.01
168 10 0.02
169 28 0.07
170 15 0.04
171 15 0.04
172 19 0.05
173 6 0.01
174 16 0.04
175 2 0.00
176 62 0.15
177 18 0.04
178 31 0.07
179 35 0.08
180 45 0.11
182 7 0.02
183 15 0.04
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (171 bp):
TATTTAAAATAAATCATCCATACTAAATTATTTAAAATAAATCAATCTACAATAAAAATAAATCA
ATCCATACTAATAAATAATCTAACAAATCAATCTATTTAAAATAAATCAATTCATACTAATATAT
TATTTAAAATAATCAATCCATACAACTAAATAATAATAATC
Found at i:429643 original size:31 final size:31
Alignment explanation
Indices: 429561--429645 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
429551 CAATCCATAT
*
429561 TTTAAAATAAAT-AATCTATACAAATAATTA
1 TTTAAAATAAATCAATCCATACAAATAATTA
* *
429591 TTTAAAATAAATCAATTCATACTAATATATTA
1 TTTAAAATAAATCAATCCATACAAATA-ATTA
429623 TTTAAAAT-AATCAATCCATACAA
1 TTTAAAATAAATCAATCCATACAA
429646 CTACATAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
30 12 0.25
31 24 0.50
32 12 0.25
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACAAATAATTA
Found at i:429716 original size:21 final size:21
Alignment explanation
Indices: 429692--429731 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
429682 CATACTAAAT
429692 TATTTAAAATAAATCAATCTA
1 TATTTAAAATAAATCAATCTA
*
429713 TATTTTAAATAAATCAATC
1 TATTTAAAATAAATCAATC
429732 CATACTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCTA
Found at i:429754 original size:30 final size:30
Alignment explanation
Indices: 429720--429803 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 30
429710 CTATATTTTA
429720 AATAAATCAATCCATACTAATAAATTATTT
1 AATAAATCAATCCATACTAATAAATTATTT
*
429750 AATAAATCAATCCATA-T--T---TTA--A
1 AATAAATCAATCCATACTAATAAATTATTT
429772 AATAAATCAATCCATACTAATAAATTATTT
1 AATAAATCAATCCATACTAATAAATTATTT
429802 AA
1 AA
429804 AATAAATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
22 16 0.36
23 1 0.02
24 3 0.07
25 1 0.02
27 1 0.02
28 3 0.07
29 1 0.02
30 18 0.41
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (30 bp):
AATAAATCAATCCATACTAATAAATTATTT
Found at i:429792 original size:52 final size:52
Alignment explanation
Indices: 429651--429833 Score: 230
Period size: 52 Copynumber: 3.7 Consensus size: 52
429641 TACAACTACA
429651 TAAT-AAT-AATCCATA-TTTAAAATAAATC-ATCCATAC---TAAATTATT
1 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
*
429696 TAAAATAAATCAATCTATATTTT-AAATAAATCAATCCATACTAATAAATTATT
1 T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
429749 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
1 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
* *
429801 T-A-AAATAAAT---TATTTCAAAATAAATCAATCCAT
1 TAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
429834 TTTTAATAAT
Statistics
Matches: 124, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
45 1 0.01
47 25 0.20
48 3 0.02
49 16 0.13
50 18 0.15
51 20 0.16
52 31 0.25
53 10 0.08
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.37
Consensus pattern (52 bp):
TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
Found at i:429796 original size:22 final size:22
Alignment explanation
Indices: 429750--429795 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
429740 TAAATTATTT
**
429750 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATAATAA
429772 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATA-TAATAA
429795 A
1 A
429796 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAAATCAATCCATATAATAA
Found at i:429822 original size:15 final size:15
Alignment explanation
Indices: 429790--429947 Score: 189
Period size: 15 Copynumber: 10.5 Consensus size: 15
429780 AATCCATACT
429790 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
*
429804 AATAAATTATTTCAA
1 AATAAATTATTTTAA
*
429819 AATAAATCAATCCATTTT-T
1 AATAAAT---T--ATTTTAA
*
429838 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
429853 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
429868 AATAAATTATTTTAT
1 AATAAATTATTTTAA
429883 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
429898 AAT-AATTATTTTAC
1 AATAAATTATTTTAA
429912 AATAAATT-TTTTAA
1 AATAAATTATTTTAA
429926 AATAAATTATTTTAA
1 AATAAATTATTTTAA
429941 AATAAAT
1 AATAAAT
429948 AACCTTATTA
Statistics
Matches: 125, Mismatches: 10, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
14 40 0.32
15 73 0.58
16 1 0.01
18 1 0.01
19 6 0.05
20 4 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:429822 original size:29 final size:29
Alignment explanation
Indices: 429790--429947 Score: 174
Period size: 29 Copynumber: 5.2 Consensus size: 29
429780 AATCCATACT
*
429790 AATAAATTATTTAAAATAAATTATTTCAA
1 AATAAATTATTTAAAATAAATTATTTTAA
** *
429819 AATAAATCAATCCATTTTTAATAATTTATTTTAA
1 AATAAAT---T--ATTTAAAATAAATTATTTTAA
* *
429853 AATAAATTATTTTATAATAAATTATTTTAT
1 AATAAATTA-TTTAAAATAAATTATTTTAA
*
429883 AATAAATTATTTTAAAAT-AATTATTTTAC
1 AATAAATTA-TTTAAAATAAATTATTTTAA
*
429912 AATAAATTTTTTAAAATAAATTATTTTAA
1 AATAAATTATTTAAAATAAATTATTTTAA
429941 AATAAAT
1 AATAAAT
429948 AACCTTATTA
Statistics
Matches: 111, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
28 8 0.07
29 43 0.39
30 34 0.31
31 1 0.01
32 1 0.01
34 24 0.22
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATAAATTATTTAAAATAAATTATTTTAA
Found at i:430318 original size:11 final size:11
Alignment explanation
Indices: 430302--430495 Score: 156
Period size: 11 Copynumber: 16.6 Consensus size: 11
430292 AATATTTAAG
430302 AGCTCGATTCA
1 AGCTCGATTCA
*
430313 AGCTCGAGACTCA
1 AGCTC--GATTCA
*
430326 AGCTCGATTAA
1 AGCTCGATTCA
**
430337 AGCTCGATTTTG
1 AGCTCGA-TTCA
*
430349 AGCTCGATTGAAA
1 AGCTCGATT--CA
* *
430362 AACTCGATGCA
1 AGCTCGATTCA
*
430373 AGCTCGATTGAGA
1 AGCTCGATT--CA
*
430386 AGCTCGATTAAAA
1 AGCTCGATT--CA
*
430399 AGCTCGATTTTA
1 AGCTCGA-TTCA
*
430411 AGCTCGATTTTA
1 AGCTCGA-TTCA
430423 AGCTCGATTCA
1 AGCTCGATTCA
*
430434 AGCTCGTTTCA
1 AGCTCGATTCA
430445 AGCTCGATTCA
1 AGCTCGATTCA
*
430456 AGCTCGTTTCA
1 AGCTCGATTCA
430467 AGCTCGATTCA
1 AGCTCGATTCA
430478 AGCTC-ATTTCA
1 AGCTCGA-TTCA
430489 AGCTCGA
1 AGCTCGA
430496 AAACGAGTTA
Statistics
Matches: 152, Mismatches: 21, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
10 1 0.01
11 83 0.55
12 30 0.20
13 36 0.24
14 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (11 bp):
AGCTCGATTCA
Done.