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 17 of 28
Found at i:3279844 original size:16 final size:17
Alignment explanation
Indices: 3279807--3279843 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3279797 GACTAACTTC
*
3279807 AAAATATTTTAGTATAA
1 AAAATATTTTAGAATAA
*
3279824 AAAATATTTTTGAATAA
1 AAAATATTTTAGAATAA
3279841 AAA
1 AAA
3279844 TTAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
AAAATATTTTAGAATAA
Found at i:3279903 original size:19 final size:19
Alignment explanation
Indices: 3279864--3279918 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
3279854 AAATCTTTAA
* *
3279864 ATTAAGTTAATAATCAATAT
1 ATTAAATTAA-AATAAATAT
* *
3279884 ATTAACTTCAAATAAATAT
1 ATTAAATTAAAATAAATAT
3279903 ATTAAATTAAAATAAA
1 ATTAAATTAAAATAAA
3279919 ATTAGTCCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (19 bp):
ATTAAATTAAAATAAATAT
Found at i:3284074 original size:25 final size:25
Alignment explanation
Indices: 3284046--3284114 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
3284036 AGAAATTCGA
3284046 AAACTTGACTAGACTCGAATTTTAT
1 AAACTTGACTAGACTCGAATTTTAT
* *
3284071 AAACTCGATTCA-ACTCGAATTTTAT
1 AAACTTGACT-AGACTCGAATTTTAT
*
3284096 AAA-TTCGACTTGACTCGAA
1 AAACTT-GACTAGACTCGAA
3284115 AAAAATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
24 1 0.03
25 34 0.94
26 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (25 bp):
AAACTTGACTAGACTCGAATTTTAT
Found at i:3284595 original size:11 final size:11
Alignment explanation
Indices: 3284579--3284641 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
3284569 AAAATTACAT
3284579 TATTAAAAATA
1 TATTAAAAATA
3284590 TATTAAAAATA
1 TATTAAAAATA
* ***
3284601 CATTATTGATA
1 TATTAAAAATA
3284612 -ATTATAAAAT-
1 TATTA-AAAATA
3284622 T-TTAAAAATA
1 TATTAAAAATA
*
3284632 AATTAAAAAT
1 TATTAAAAAT
3284642 TCTATAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
9 5 0.12
10 7 0.17
11 28 0.70
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:3284790 original size:21 final size:20
Alignment explanation
Indices: 3284752--3284824 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
3284742 GTAATGAACT
3284752 TAAACCCTAAAACC-TAAATCA
1 TAAACCCT-AAACCATAAA-CA
*
3284773 TAAACTCTAAACCATAAACCA
1 TAAACCCTAAACCATAAA-CA
* * * *
3284794 TGAATCCTAAACTATAAACC
1 TAAACCCTAAACCATAAACA
3284814 TAAACCCTAAA
1 TAAACCCTAAA
3284825 TCCGATTATG
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.51, C:0.27, G:0.01, T:0.21
Consensus pattern (20 bp):
TAAACCCTAAACCATAAACA
Found at i:3287278 original size:12 final size:12
Alignment explanation
Indices: 3287258--3287314 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
3287248 ATTGAGCTTG
3287258 AATCGAGCTCAA
1 AATCGAGCTCAA
* **
3287270 AACCGAGCT-TG
1 AATCGAGCTCAA
3287281 AATCGAGCTCAA
1 AATCGAGCTCAA
*
3287293 AATCGAGTTCAA
1 AATCGAGCTCAA
3287305 AATCGAGCTC
1 AATCGAGCTC
3287315 GAGTCTCGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
11 8 0.22
12 28 0.78
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (12 bp):
AATCGAGCTCAA
Found at i:3287278 original size:23 final size:23
Alignment explanation
Indices: 3287251--3287299 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
3287241 TTTACCTATT
3287251 GAGCTTGAATCGAGCTCAAAACC
1 GAGCTTGAATCGAGCTCAAAACC
*
3287274 GAGCTTGAATCGAGCTCAAAATC
1 GAGCTTGAATCGAGCTCAAAACC
3287297 GAG
1 GAG
3287300 TTCAAAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.18
Consensus pattern (23 bp):
GAGCTTGAATCGAGCTCAAAACC
Found at i:3289466 original size:14 final size:14
Alignment explanation
Indices: 3289419--3289464 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
3289409 CTTGTATATG
3289419 ATTTGTTTCCTTCT
1 ATTTGTTTCCTTCT
3289433 ATTTGTTTCCTTCT
1 ATTTGTTTCCTTCT
* *
3289447 TTTTTTTTCCTTCT
1 ATTTGTTTCCTTCT
3289461 ATTT
1 ATTT
3289465 TTAATTTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (14 bp):
ATTTGTTTCCTTCT
Found at i:3290700 original size:21 final size:21
Alignment explanation
Indices: 3290657--3290701 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3290647 GAAGTACCGT
* **
3290657 ATATATGTTCCAAAGGATTAC
1 ATATATGTCCCAAAGGACCAC
*
3290678 ATATATGTCCCGAAGGACCAC
1 ATATATGTCCCAAAGGACCAC
3290699 ATA
1 ATA
3290702 GAACCCTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (21 bp):
ATATATGTCCCAAAGGACCAC
Found at i:3292627 original size:9 final size:9
Alignment explanation
Indices: 3292607--3292639 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
3292597 TTAGGACTCA
3292607 ATTATA-AT
1 ATTATATAT
3292615 ATTATATAT
1 ATTATATAT
3292624 ATTATATAT
1 ATTATATAT
3292633 ATTATAT
1 ATTATAT
3292640 TATAGTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTATATAT
Found at i:3293053 original size:4 final size:4
Alignment explanation
Indices: 3293044--3293073 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3293034 ATAAATCATT
3293044 AATA AATA AATA AATA AAT- AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AAT
3293074 TTAATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:3293088 original size:27 final size:30
Alignment explanation
Indices: 3293057--3293121 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 30
3293047 AAATAAATAA
*
3293057 ATAAATAATAAAT-AAAT-TTAATTTAATT
1 ATAAATAATAAATAAAATCTTAAATTAATT
*
3293085 -TAAA-AAT-ATTAAAATCTTAAATTAATT
1 ATAAATAATAAATAAAATCTTAAATTAATT
3293112 ATAAATAATA
1 ATAAATAATA
3293122 TATTAGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
25 2 0.07
26 7 0.23
27 14 0.47
28 4 0.13
29 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (30 bp):
ATAAATAATAAATAAAATCTTAAATTAATT
Found at i:3293227 original size:7 final size:7
Alignment explanation
Indices: 3293215--3293240 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3293205 TATCATTAAC
3293215 TATAATA
1 TATAATA
3293222 TATAATA
1 TATAATA
3293229 TATAATA
1 TATAATA
3293236 TATAA
1 TATAA
3293241 AAAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TATAATA
Found at i:3294727 original size:31 final size:31
Alignment explanation
Indices: 3294614--3294717 Score: 172
Period size: 31 Copynumber: 3.3 Consensus size: 31
3294604 TTTTCAATAG
* *
3294614 TTTGATGGCTAAGATGAAAACGACACCTAAC
1 TTTGATGACTAAGATGAAAACGAAACCTAAC
*
3294645 TTTGATGACTAAGATGAAAAAGGAAACCTAAC
1 TTTGATGACTAAGATG-AAAACGAAACCTAAC
3294677 TTTGATGACTAAGATGAAAACGAAACCTAAC
1 TTTGATGACTAAGATGAAAACGAAACCTAAC
3294708 TTTGATGACT
1 TTTGATGACT
3294718 TGTTTGAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 39 0.57
32 29 0.43
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.25
Consensus pattern (31 bp):
TTTGATGACTAAGATGAAAACGAAACCTAAC
Found at i:3300372 original size:20 final size:20
Alignment explanation
Indices: 3300347--3300393 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3300337 GTCAAATTGA
*
3300347 CTATTTTGTCAAATGTTAAG
1 CTATTTTGTCAAACGTTAAG
3300367 CTATTTTGTCAAACGTTAAG
1 CTATTTTGTCAAACGTTAAG
3300387 CTATTTT
1 CTATTTT
3300394 CTTAGCATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (20 bp):
CTATTTTGTCAAACGTTAAG
Found at i:3301454 original size:122 final size:120
Alignment explanation
Indices: 3301247--3301470 Score: 369
Period size: 122 Copynumber: 1.9 Consensus size: 120
3301237 AAAAGAATGC
* * *
3301247 TCCTAGTAGATTTAAAGTTTATAATTTAAAAAATGAAAGAATAATAAACAACTTTATTTACCAAT
1 TCCTAATAGATCTAAAATTTATAATTTAAAAAATGAAAGAATAATAAACAACTTTATTTACCAAT
*
3301312 CAAATATATTTGTTCATAAAATGATAGGGACTTAAATCCACAAAGTTAAGAATAT
66 CAAATATATTTGCTCATAAAATGATAGGGACTTAAATCCACAAAGTTAAGAATAT
*
3301367 TCCTAATAGATCTAAAATTTATAA-TTAAAAAATGAAAGAATAAAAATAAACAACTTTATTTACG
1 TCCTAATAGATCTAAAATTTATAATTTAAAAAATGAAAGAAT---AATAAACAACTTTATTTACC
3301431 AATCAAATATATTTGCTCATAAAATGATAGGGACTTAAAT
63 AATCAAATATATTTGCTCATAAAATGATAGGGACTTAAAT
3301471 AGGCCTGTAA
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
119 17 0.18
120 21 0.22
122 58 0.60
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (120 bp):
TCCTAATAGATCTAAAATTTATAATTTAAAAAATGAAAGAATAATAAACAACTTTATTTACCAAT
CAAATATATTTGCTCATAAAATGATAGGGACTTAAATCCACAAAGTTAAGAATAT
Found at i:3301559 original size:16 final size:16
Alignment explanation
Indices: 3301538--3301570 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3301528 TAATAAATAA
*
3301538 ACGAACATAATCGAAC
1 ACGAACATAAACGAAC
3301554 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3301570 A
1 A
3301571 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3301693 original size:23 final size:23
Alignment explanation
Indices: 3301635--3301718 Score: 114
Period size: 23 Copynumber: 3.6 Consensus size: 23
3301625 TCATTTAATA
* * *
3301635 AATAAATGAACATAAACGAACAC
1 AATAAACGAACATAGACAAACAC
**
3301658 GAACGAACGAACATAGACAAACAC
1 -AATAAACGAACATAGACAAACAC
3301682 AATAAACGAACATAGACAAACAC
1 AATAAACGAACATAGACAAACAC
3301705 AATAAACGAACATA
1 AATAAACGAACATA
3301719 AACGAACAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 35 0.66
24 18 0.34
ACGTcount: A:0.60, C:0.20, G:0.11, T:0.10
Consensus pattern (23 bp):
AATAAACGAACATAGACAAACAC
Found at i:3301734 original size:23 final size:23
Alignment explanation
Indices: 3301642--3301734 Score: 98
Period size: 23 Copynumber: 4.0 Consensus size: 23
3301632 ATAAATAAAT
* *
3301642 GAACATAAACGAACACGAACGAAC
1 GAACATAAACAAACAC-AACAAAC
* *
3301666 GAACATAGACAAACACAATAAAC
1 GAACATAAACAAACACAACAAAC
* *
3301689 GAACATAGACAAACACAATAAAC
1 GAACATAAACAAACACAACAAAC
*
3301712 GAACATAAACGAACA-ACACAAAC
1 GAACATAAACAAACACA-ACAAAC
3301735 ACAAAAAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
22 1 0.02
23 46 0.75
24 14 0.23
ACGTcount: A:0.59, C:0.24, G:0.11, T:0.06
Consensus pattern (23 bp):
GAACATAAACAAACACAACAAAC
Found at i:3302011 original size:24 final size:25
Alignment explanation
Indices: 3301982--3302036 Score: 94
Period size: 24 Copynumber: 2.2 Consensus size: 25
3301972 GCCCTCTGTT
3301982 TGAACATAAATGAACGAACATA-AA
1 TGAACATAAATGAACGAACATATAA
3302006 TGAACATAAATGAACGAACATATAA
1 TGAACATAAATGAACGAACATATAA
3302031 TCGAAC
1 T-GAAC
3302037 GTTCACGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 22 0.76
25 3 0.10
26 4 0.14
ACGTcount: A:0.55, C:0.15, G:0.13, T:0.18
Consensus pattern (25 bp):
TGAACATAAATGAACGAACATATAA
Found at i:3302036 original size:16 final size:14
Alignment explanation
Indices: 3301983--3302037 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
3301973 CCCTCTGTTT
3301983 GAACATAAATGAAC
1 GAACATAAATGAAC
3301997 GAACATAAAT----
1 GAACATAAATGAAC
3302007 GAACATAAATGAAC
1 GAACATAAATGAAC
3302021 GAACATATAATCGAAC
1 GAACATA-AAT-GAAC
3302037 G
1 G
3302038 TTCACGAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.29
14 17 0.49
15 3 0.09
16 5 0.14
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.16
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:3306589 original size:18 final size:19
Alignment explanation
Indices: 3306559--3306603 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
3306549 TCTATTTTGC
3306559 TTTTATTTCATTTTATCAT-
1 TTTTATTTCATTTT-TCATA
*
3306578 TTTTATTT-ATTTTTTATA
1 TTTTATTTCATTTTTCATA
3306596 TTTTATTT
1 TTTTATTT
3306604 TGAATTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 3 0.12
18 13 0.54
19 8 0.33
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATTTCATTTTTCATA
Found at i:3313122 original size:27 final size:27
Alignment explanation
Indices: 3313091--3313228 Score: 125
Period size: 27 Copynumber: 5.1 Consensus size: 27
3313081 GAAGATGAAG
* *
3313091 AAATGAGAGAGAAAAATAAAAAGTTAC
1 AAATGAGAGAGAAAAAGAAAAAGTTAA
*
3313118 AAATGAAAGAGAAAAAGAAAAAGTTAA
1 AAATGAGAGAGAAAAAGAAAAAGTTAA
** ***
3313145 AAATGAGAGAGAAATGGCTGAAGTTAA
1 AAATGAGAGAGAAAAAGAAAAAGTTAA
* * **
3313172 AAATGAAAGAG-AAATGACTGAAGTTAA
1 AAATGAGAGAGAAAAAGA-AAAAGTTAA
* **
3313199 AAATGAAAGAGAAATGGAAAAAGTTAA
1 AAATGAGAGAGAAAAAGAAAAAGTTAA
3313226 AAA
1 AAA
3313229 AACAATTGAG
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
26 3 0.03
27 85 0.92
28 4 0.04
ACGTcount: A:0.61, C:0.02, G:0.22, T:0.15
Consensus pattern (27 bp):
AAATGAGAGAGAAAAAGAAAAAGTTAA
Found at i:3313223 original size:54 final size:54
Alignment explanation
Indices: 3313108--3313228 Score: 154
Period size: 54 Copynumber: 2.2 Consensus size: 54
3313098 AGAGAAAAAT
* *
3313108 AAAAAGTTACAAATGAAAGAGAAAAAGAAAAAGTTAAAAATGAGAGAGAAATGG
1 AAAAAGTTAAAAATGAAAGAGAAAAAGAAAAAGTTAAAAATGAAAGAGAAATGG
*** * **
3313162 CTGAAGTTAAAAATGAAAGAG-AAATGACTGAAGTTAAAAATGAAAGAGAAATGG
1 AAAAAGTTAAAAATGAAAGAGAAAAAGA-AAAAGTTAAAAATGAAAGAGAAATGG
3313216 AAAAAGTTAAAAA
1 AAAAAGTTAAAAA
3313229 AACAATTGAG
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 5 0.09
54 50 0.91
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.16
Consensus pattern (54 bp):
AAAAAGTTAAAAATGAAAGAGAAAAAGAAAAAGTTAAAAATGAAAGAGAAATGG
Found at i:3328690 original size:39 final size:39
Alignment explanation
Indices: 3328647--3328761 Score: 140
Period size: 39 Copynumber: 2.9 Consensus size: 39
3328637 CATAAAGAAA
* *
3328647 ATAATTCCTAAGGTGAGGATGACGAGTGCAATAAAGGCG
1 ATAATGCCTAAGGTGAGGATGACGAGTGCAATAAAGGCC
* *
3328686 ATAATGCCTAAGGTGAGGATGAGGAGTACAATAAAGGCC
1 ATAATGCCTAAGGTGAGGATGACGAGTGCAATAAAGGCC
* * * ** *
3328725 ATACTGCCTAAGGCGAGGTTGATAAATGCAATAAAGG
1 ATAATGCCTAAGGTGAGGATGACGAGTGCAATAAAGG
3328762 TGGCTGTGCC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (39 bp):
ATAATGCCTAAGGTGAGGATGACGAGTGCAATAAAGGCC
Found at i:3330639 original size:116 final size:115
Alignment explanation
Indices: 3330428--3330748 Score: 367
Period size: 116 Copynumber: 2.8 Consensus size: 115
3330418 AAAAAGATAG
* * * * *
3330428 ACCAAACATTTCCCATGGAAGAGTTCCTAATGAGAAGAAGTCATCCGAAT-AGGGAGAAAAAGTT
1 ACCAAA-ATTT-CCATGAAAGGGTTCATAATGAGAAGAAATCATCC-AATGAGGGAGAAGAAGTT
* *
3330492 CCTGATGAGAAGAACTTGTTCAACCTTGGTTCATCCATCACAAAAGGAGATGA
63 CCTAATGAGAAGAACTTGTTCAACCCTGGTTCATCCATCACAAAAGGAGATGA
3330545 ACCAAAATTTCCAGTGAAAGGGTTCATAATGAGAAGAAATCATCCAATGAGGGAGAAGAAGTTCC
1 ACCAAAATTTCCA-TGAAAGGGTTCATAATGAGAAGAAATCATCCAATGAGGGAGAAGAAGTTCC
* ** * *
3330610 TAATGAGAAGAACTTGTTCAACCCTGGTTCGTTTATCACAGAAGGGGATGA
65 TAATGAGAAGAACTTGTTCAACCCTGGTTCATCCATCACAAAAGGAGATGA
* * * * * * ** *
3330661 ATCAACATTTCCAAT-AGATGGGTTCATAATGCGAAGAACTCGTTTAATGAGGGAGAAGAAGCTC
1 ACCAAAATTTCC-ATGA-AAGGGTTCATAATGAGAAGAAATCATCCAATGAGGGAGAAGAAGTTC
* *
3330725 CTAATAAGAAGAACTTGTCCAACC
64 CTAATGAGAAGAACTTGTTCAACC
3330749 TTGACTCATA
Statistics
Matches: 177, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
115 7 0.04
116 163 0.92
117 7 0.04
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (115 bp):
ACCAAAATTTCCATGAAAGGGTTCATAATGAGAAGAAATCATCCAATGAGGGAGAAGAAGTTCCT
AATGAGAAGAACTTGTTCAACCCTGGTTCATCCATCACAAAAGGAGATGA
Found at i:3331008 original size:37 final size:36
Alignment explanation
Indices: 3330884--3331065 Score: 190
Period size: 36 Copynumber: 5.1 Consensus size: 36
3330874 TTCACTCAAT
* *
3330884 ATTTTATATCACTTGAGATTGTTTTTCTTAAAACAT
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* * * *
3330920 ATTTTATCTCACGTAAGATTGTTTTTCTCAAAATAA
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* *
3330956 ATTTCATCTCTCTTGAGATTGTTTTTCTCT-AAACAAA
1 ATTTTATCTCACTTGAGATTGTTTTTCT-TAAAAC-AA
* *
3330993 ATTTTATTTCGCTTGAGATTGTTTTTCTTAAAACAA
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* * * * *
3331029 GTTTTGTCTCCCATGAGA-T-TTTTTCTCAAAACAA
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
3331063 ATT
1 ATT
3331066 GTGTCACTTA
Statistics
Matches: 121, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
34 16 0.13
35 1 0.01
36 73 0.60
37 31 0.26
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (36 bp):
ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:3331046 original size:73 final size:73
Alignment explanation
Indices: 3330897--3331063 Score: 180
Period size: 73 Copynumber: 2.3 Consensus size: 73
3330887 TTATATCACT
* *
3330897 TGAGATTGTTTTTCT-TAAA-ACATATTTTATCTCACGTAAGATTGTTTTTCTCAAAATAAATTT
1 TGAGATTGTTTTTCTCTAAACA-AAATTTTATCTCACGTAAGATTGTTTTTCTCAAAACAAATTT
* *
3330960 CATCTCTCT
65 CATCTCCCA
* * * * * * *
3330969 TGAGATTGTTTTTCTCTAAACAAAATTTTATTTCGCTTGAGATTGTTTTTCTTAAAACAAGTTTT
1 TGAGATTGTTTTTCTCTAAACAAAATTTTATCTCACGTAAGATTGTTTTTCTCAAAACAAATTTC
*
3331034 GTCTCCCA
66 ATCTCCCA
*
3331042 TGAGA-T-TTTTTCTCAAAACAAA
1 TGAGATTGTTTTTCTCTAAACAAA
3331064 TTGTGTCACT
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
71 15 0.19
72 16 0.20
73 48 0.60
74 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (73 bp):
TGAGATTGTTTTTCTCTAAACAAAATTTTATCTCACGTAAGATTGTTTTTCTCAAAACAAATTTC
ATCTCCCA
Found at i:3333716 original size:21 final size:21
Alignment explanation
Indices: 3333692--3333739 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
3333682 TATAGTCCTT
3333692 AGCTACTCTCCAACTAATGTC
1 AGCTACTCTCCAACTAATGTC
*
3333713 AGCTACTTTCCAACTAATGTC
1 AGCTACTCTCCAACTAATGTC
3333734 AGCTAC
1 AGCTAC
3333740 CCTTGAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.29
Consensus pattern (21 bp):
AGCTACTCTCCAACTAATGTC
Found at i:3335756 original size:60 final size:60
Alignment explanation
Indices: 3335663--3335785 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
3335653 TCAATTTCCA
3335663 CATAGTGCTACAATTCAACTAAGTTAGCAATGTCAATATTTAACCAAATAATAACCTTAT
1 CATAGTGCTACAATTCAACTAAGTTAGCAATGTCAATATTTAACCAAATAATAACCTTAT
3335723 CATAGTGCTACAATTCAACTAAGTTAGCAATGTCAATATTTAACCAAATAATAACCTTAT
1 CATAGTGCTACAATTCAACTAAGTTAGCAATGTCAATATTTAACCAAATAATAACCTTAT
3335783 CAT
1 CAT
3335786 TGTTGTTTCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (60 bp):
CATAGTGCTACAATTCAACTAAGTTAGCAATGTCAATATTTAACCAAATAATAACCTTAT
Found at i:3350240 original size:19 final size:18
Alignment explanation
Indices: 3350207--3350250 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
3350197 ATTATAGTGT
3350207 AATATTAAAAATTTAATA
1 AATATTAAAAATTTAATA
*
3350225 AATATCTAAAATTTTAATA
1 AATAT-TAAAAATTTAATA
*
3350244 GATATTA
1 AATATTA
3350251 GACTTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
AATATTAAAAATTTAATA
Found at i:3351609 original size:2 final size:2
Alignment explanation
Indices: 3351604--3351646 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3351594 AAAAAAGTAT
3351604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3351646 T
1 T
3351647 GTTAATAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3352332 original size:25 final size:25
Alignment explanation
Indices: 3352298--3352355 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
3352288 CAAACTATAC
*
3352298 CGTTTTTCTCGAATATGTGTCCAAA
1 CGTTTTTCTCGAATATGTGTACAAA
3352323 CGTTTTTCTCGAATATGTGTACAAA
1 CGTTTTTCTCGAATATGTGTACAAA
3352348 CGTTTTTC
1 CGTTTTTC
3352356 GATTCTTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (25 bp):
CGTTTTTCTCGAATATGTGTACAAA
Found at i:3352839 original size:19 final size:19
Alignment explanation
Indices: 3352802--3352838 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3352792 GGGAGGTGAT
3352802 TTTAATATATATATATATA
1 TTTAATATATATATATATA
3352821 TTTAATATA-ATATA-ATA
1 TTTAATATATATATATATA
3352838 T
1 T
3352839 AATAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAATATATATATATATA
Found at i:3359572 original size:24 final size:24
Alignment explanation
Indices: 3359500--3359577 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
3359490 GAATGTTTTA
*
3359500 TCTGAT-TTTCGATTTGAATTATGT
1 TCTGATATTT-GATATGAATTATGT
** * *
3359524 TCTGATACCTGAAATGGATTATGT
1 TCTGATATTTGATATGAATTATGT
* *
3359548 TCTGATATTTGATCTGAATTCTGT
1 TCTGATATTTGATATGAATTATGT
*
3359572 TTTGAT
1 TCTGAT
3359578 TTCTGGTATC
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (24 bp):
TCTGATATTTGATATGAATTATGT
Found at i:3362744 original size:30 final size:29
Alignment explanation
Indices: 3362704--3362935 Score: 139
Period size: 30 Copynumber: 7.6 Consensus size: 29
3362694 TATGGTATGT
*
3362704 AATAAAAATAAAATATATTTTATAATTTAA
1 AATAAAAATAAAATATATTTT-TAAGTTAA
* * *
3362734 AATAAGAATAAAGTATATTTTTAAGTGAA
1 AATAAAAATAAAATATATTTTTAAGTTAA
* *
3362763 GATAAGAATAAAATATATTTTTATA-TTAA
1 AATAAAAATAAAATATATTTTTA-AGTTAA
* * * *
3362792 ATTAATAATAAAATAGTTAAATATAATATAATTTAA
1 AATAAAAATAAAATA--T--AT-T--TTTAAGTTAA
* * *
3362828 AATATTTTAAAT--AATATATTTTTAAGTGAT
1 AATA---AAAATAAAATATATTTTTAAGTTAA
* * *
3362858 GATAAAGATAAAATATATATTTTTTA-TTAA
1 AATAAAAAT-AAA-ATATATTTTTAAGTTAA
* *
3362888 AATAAAAATAATATATATTTAATAAGTTAA
1 AATAAAAATAAAATATATTT-TTAAGTTAA
3362918 AATAAAAATAAAATATAT
1 AATAAAAATAAAATATAT
3362936 ATGTAAGATA
Statistics
Matches: 154, Mismatches: 30, Indels: 36
0.70 0.14 0.16
Matches are distributed among these distances:
27 3 0.02
28 8 0.05
29 46 0.30
30 60 0.39
31 12 0.08
32 1 0.01
33 4 0.03
34 1 0.01
35 2 0.01
36 10 0.06
37 4 0.03
39 3 0.02
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (29 bp):
AATAAAAATAAAATATATTTTTAAGTTAA
Found at i:3362779 original size:29 final size:29
Alignment explanation
Indices: 3362704--3362785 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
3362694 TATGGTATGT
* * *
3362704 AATAAAAATAAAATATATTTTATAATTTAA
1 AATAAGAATAAAATATATTTT-TAAGTGAA
*
3362734 AATAAGAATAAAGTATATTTTTAAGTGAA
1 AATAAGAATAAAATATATTTTTAAGTGAA
*
3362763 GATAAGAATAAAATATATTTTTA
1 AATAAGAATAAAATATATTTTTA
3362786 TATTAAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 27 0.59
30 19 0.41
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (29 bp):
AATAAGAATAAAATATATTTTTAAGTGAA
Found at i:3362801 original size:29 final size:29
Alignment explanation
Indices: 3362704--3362806 Score: 104
Period size: 29 Copynumber: 3.5 Consensus size: 29
3362694 TATGGTATGT
* *
3362704 AATAAAAATAAAATATA-TTTTATAATTTAA
1 AATAAGAATAAAATATATTTTTAT-AGTT-A
* *
3362734 AATAAGAATAAAGTATATTTTTA-AGTGA
1 AATAAGAATAAAATATATTTTTATAGTTA
3362762 AGATAAGAATAAAATATATTTTTATA-TTA
1 A-ATAAGAATAAAATATATTTTTATAGTTA
*
3362791 AATTAATAATAAAATA
1 AA-TAAGAATAAAATA
3362807 GTTAAATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
28 3 0.05
29 38 0.61
30 16 0.26
31 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (29 bp):
AATAAGAATAAAATATATTTTTATAGTTA
Found at i:3362823 original size:26 final size:24
Alignment explanation
Indices: 3362794--3362845 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
3362784 TATATTAAAT
3362794 TAATAATAAAATAGTTAAATATAATA
1 TAAT-ATAAAATAGTTAAA-ATAATA
* * *
3362820 TAATTTAAAATATTTTAAATAATA
1 TAATATAAAATAGTTAAAATAATA
3362844 TA
1 TA
3362846 TTTTTAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
25 11 0.48
26 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TAATATAAAATAGTTAAAATAATA
Found at i:3363569 original size:2 final size:2
Alignment explanation
Indices: 3363562--3363610 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3363552 TAATAAGTTC
3363562 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
3363604 AT AT AT A
1 AT AT AT A
3363611 ATTCAATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3364580 original size:137 final size:139
Alignment explanation
Indices: 3364344--3364640 Score: 338
Period size: 138 Copynumber: 2.1 Consensus size: 139
3364334 GTCCTAAAAA
* * * *
3364344 AATAATTTTAAAATTTTATTAATAAGTTCATATATATATATATATATAATTCAATTTATTTTATT
1 AATAATTTTAAAATTTTACTAATAAGTTCATATATAGATATACATATAAATCAATTTATTTTATT
* * *
3364409 AAAATATATAATAAATTATTTGATAAATTTAATAATAATTTATATATATAATCAT-TA-AATTAT
66 --AATATATAATAAATTATTTGA-AAAATT-A-AATAATTTATATATACAATCATCAACAATTAT
*
3364472 TTTTTAACTGATGT
126 TTTTTAACTGAAGT
** *
3364486 AATAATTTTAATTTTTTTACTAATAA-TT-ATATATAGATATACATTTAAATCAATTTATTTTTA
1 AATAATTTTAA-AATTTTACTAATAAGTTCATATATAGATATACATATAAATCAATTTA-TTTTA
* *
3364549 TT-ATATAT-AT-AATTATTTTAAAAATTAAATAATTTATATATACAATCATCGAACTAATTTTT
64 TTAATATATAATAAATTATTTGAAAAATTAAATAATTTATATATACAATCATC-AAC-AATTATT
*
3364611 TTTTAACTTAAGT
127 TTTTAACTGAAGT
3364624 AATAATTTTAAAATTTT
1 AATAATTTTAAAATTTT
3364641 TATTAATGTT
Statistics
Matches: 133, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
134 21 0.16
135 1 0.01
136 6 0.05
137 13 0.10
138 30 0.23
139 6 0.05
141 25 0.19
142 20 0.15
143 11 0.08
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (139 bp):
AATAATTTTAAAATTTTACTAATAAGTTCATATATAGATATACATATAAATCAATTTATTTTATT
AATATATAATAAATTATTTGAAAAATTAAATAATTTATATATACAATCATCAACAATTATTTTTT
AACTGAAGT
Found at i:3364585 original size:21 final size:21
Alignment explanation
Indices: 3364530--3364585 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
3364520 AGATATACAT
* **
3364530 TTAAATCAATTTATTTTTATTA
1 TTAAAT-AATTTATTTTAAAAA
*
3364552 TATATATAA-TTATTTTAAAAA
1 T-TAAATAATTTATTTTAAAAA
3364573 TTAAATAATTTAT
1 TTAAATAATTTAT
3364586 ATATACAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
20 6 0.22
21 14 0.52
22 3 0.11
23 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAAATAATTTATTTTAAAAA
Found at i:3371695 original size:23 final size:23
Alignment explanation
Indices: 3371664--3371716 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
3371654 TCCCGAAGGA
3371664 CCACATAGGTTTGCACCAAAGTG
1 CCACATAGGTTTGCACCAAAGTG
* *
3371687 TCACATAGGTTTGCACCGAAGTG
1 CCACATAGGTTTGCACCAAAGTG
3371710 CCACATA
1 CCACATA
3371717 TTTGTCCCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CCACATAGGTTTGCACCAAAGTG
Found at i:3371726 original size:21 final size:22
Alignment explanation
Indices: 3371702--3371759 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
3371692 TAGGTTTGCA
*
3371702 CCGAAGTG-CCACATATTTGTC
1 CCGAAGTGACCACATAATTGTC
3371723 CCGAA-TGACCACATAATTGTC
1 CCGAAGTGACCACATAATTGTC
*
3371744 CCAAAG-GACCACATAA
1 CCGAAGTGACCACATAA
3371760 AACCCTCGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (22 bp):
CCGAAGTGACCACATAATTGTC
Found at i:3372325 original size:22 final size:20
Alignment explanation
Indices: 3372300--3372351 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
3372290 TACCTCTCCA
*
3372300 GTATCGATACTTCTCTTCAAGG
1 GTATCGATAC-TCTCCTCAA-G
*
3372322 GTATCAATAC-CTCCTCAAG
1 GTATCGATACTCTCCTCAAG
*
3372341 GTACCGATACT
1 GTATCGATACT
3372352 GATTTGGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.36
20 7 0.28
22 9 0.36
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (20 bp):
GTATCGATACTCTCCTCAAG
Found at i:3372449 original size:42 final size:42
Alignment explanation
Indices: 3372402--3372503 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
3372392 TACCATCCCC
* *
3372402 CTGGTATCAATACTACCCACACAGCATCAATACCCTCTTCAA
1 CTGGTATCGATACTACCCACACAACATCAATACCCTCTTCAA
* * *
3372444 CTGGTATCGATACTACCTACACAATATCGATACCCTCTTCAA
1 CTGGTATCGATACTACCCACACAACATCAATACCCTCTTCAA
3372486 CTGGTATCGATACTACCC
1 CTGGTATCGATACTACCC
3372504 TTAATAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.30, C:0.33, G:0.10, T:0.26
Consensus pattern (42 bp):
CTGGTATCGATACTACCCACACAACATCAATACCCTCTTCAA
Found at i:3372496 original size:22 final size:22
Alignment explanation
Indices: 3372431--3372498 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
3372421 CACAGCATCA
3372431 ATACCCTCTTCAACTGGTATCG
1 ATACCCTCTTCAACTGGTATCG
* * **
3372453 ATACTAC-CTAC-AC-AATATCG
1 ATAC-CCTCTTCAACTGGTATCG
3372473 ATACCCTCTTCAACTGGTATCG
1 ATACCCTCTTCAACTGGTATCG
3372495 ATAC
1 ATAC
3372499 TACCCTTAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 12 0.35
21 4 0.12
22 16 0.47
23 1 0.03
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.29
Consensus pattern (22 bp):
ATACCCTCTTCAACTGGTATCG
Found at i:3376363 original size:13 final size:13
Alignment explanation
Indices: 3376345--3376377 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
3376335 CTCATTTTAA
3376345 GTTGGCAATCCAC
1 GTTGGCAATCCAC
3376358 GTTGGCAATCCAC
1 GTTGGCAATCCAC
3376371 GTTGGCA
1 GTTGGCA
3376378 TGATAATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (13 bp):
GTTGGCAATCCAC
Found at i:3378569 original size:21 final size:21
Alignment explanation
Indices: 3378543--3378592 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3378533 TACCGAAGTG
3378543 CCACATAATTATCCCAAAAGA
1 CCACATAATTATCCCAAAAGA
*
3378564 CCACATAATTATCCCGAAAGA
1 CCACATAATTATCCCAAAAGA
3378585 CCACATAA
1 CCACATAA
3378593 AACCCTCGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.46, C:0.30, G:0.06, T:0.18
Consensus pattern (21 bp):
CCACATAATTATCCCAAAAGA
Found at i:3379290 original size:42 final size:42
Alignment explanation
Indices: 3379238--3379336 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
3379228 CCATCCCCTA
* *
3379238 GTATCGATACTACCCACACAGTATCGATACCCTCTTCAATTG
1 GTATCGATACTACCCACACAATATCGATACCCTCTTCAACTG
* *
3379280 GTATCGATACTACCTACACAATATCGATACGCTCTTCAACTG
1 GTATCGATACTACCCACACAATATCGATACCCTCTTCAACTG
3379322 GTATCGATACTACCC
1 GTATCGATACTACCC
3379337 TTAATAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.28
Consensus pattern (42 bp):
GTATCGATACTACCCACACAATATCGATACCCTCTTCAACTG
Found at i:3379329 original size:22 final size:22
Alignment explanation
Indices: 3379258--3379331 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
3379248 TACCCACACA
* *
3379258 GTATCGATACCCTCTTCAATTG
1 GTATCGATACACTCTTCAACTG
* *
3379280 GTATCGATACTAC-CTAC-AC-A
1 GTATCGATAC-ACTCTTCAACTG
* *
3379300 ATATCGATACGCTCTTCAACTG
1 GTATCGATACACTCTTCAACTG
3379322 GTATCGATAC
1 GTATCGATAC
3379332 TACCCTTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 1 0.03
20 12 0.31
21 3 0.08
22 22 0.56
23 1 0.03
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (22 bp):
GTATCGATACACTCTTCAACTG
Found at i:3386066 original size:45 final size:45
Alignment explanation
Indices: 3385908--3387038 Score: 618
Period size: 45 Copynumber: 25.7 Consensus size: 45
3385898 GAAGCTTCAA
* * * * *
3385908 CTTGACTACATCGTGAAGAGGAGTCAGTCTTTCA--A-TGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * * *
3385950 CTTGACTTTCTCCTAAAGAGAAGTCAATCCTTCA--A-TGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * *
3385992 CTTGACTT-CTCGTGGAGAGAAGTTAATCTTTCAGTATGGTCATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * *
3386036 CTTGACTTCCTCGTGAAGGGGATTCAATCTTTCA--A-TGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
*
3386078 CTTAACTTCCTCGTGAAGA-ATAGTCAATCTTTCA--A-TGAT-ATT
1 CTTGACTTCCTCGTGAAGAGA-AGTCAATCTTTCAGTATTG-TCATT
* * *
3386120 CTTCAC-TCCTTCGTGAAGAGAAGTCAATCTCTCAGTATGGTCATT
1 CTTGACTTCC-TCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * *
3386165 CTCGACTTCCTCGTGAAGAGGAGTCAATCTTTCA--A-TGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * ** * * * *
3386207 CATCACTCCCTTAT-AAAAGAAGTCAATATTTCAATATGGTCATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * *
3386251 CTTGTCTTCCTCGTGAAGAGGAA-TCAATATTTCA--A-TGTTATT
1 CTTGACTTCCTCGTGAAGA-GAAGTCAATCTTTCAGTATTGTCATT
* * *
3386293 CATGACTTCCTCGTGAAGATG-AGTCAATCTTTTAGTATTTTCACTT
1 CTTGACTTCCTCGTGAAGA-GAAGTCAATCTTTCAGTATTGTCA-TT
* * *
3386339 -TTGACTTTCTCGTGAAGAGAAGTCAATGTTTCAATATTGTCATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * *
3386383 CTTAACTTTCTCGTGAAGAGAAGCTC-ATCTTTCAGTATTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAG-TCAATCTTTCAGTATTGTCATT
* * * *
3386428 ATTGACTTTCTCATGAAGAGAGGTCAATCTTTCAGTATTGTCACTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCA-TT
* * * * *
3386474 -TTGACTTTCTCATAAAGAGAAGTAAATCTTTCAATATTGTCATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * * * * *
3386518 CTTGACTTTCTTGTGAAGAGAAGTCCATCTATCTGTAATGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* *
3386563 CTTAACTT--T-G-GAAGAGAAGTCAATCTTTCAATATTGTCATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * * *
3386604 CTTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGA-TGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGT-ATTGTCATT
* * * * * * *** *
3386649 CTTGATTTTCTCATGAAAAGAAGTCAACCTTTTAGTGGCGTCGTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * * *
3386694 CTTGACTTTCTCATGAAGAGACGTCAACCTTT-AGTGA-TGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGT-ATTGTCATT
* * * * * * ** *
3386738 CTTGACTTTCTCATAAAGAGAATTCAACCTTTTAGTGGTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * * * * * * *
3386783 TTTAACTTTCTCGTGAAGAGAAATCAACCTTTTAGTGTGGGT-GTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTAT-TGTCATT
* * * * **
3386828 CTTGACTTTCTCGTCAAGAGAATTCAACCTTTTTGTGA-TG-CTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGT-ATTGTC-ATT
* * ** * * ** **
3386873 CTTGATTTTCTCACGAAGAAGAA-TCAACCTTTTAGTGGTGTTTTT
1 CTTGACTTCCTCGTGAAG-AGAAGTCAATCTTTCAGTATTGTCATT
* * * * * *
3386918 CTT-ACTTTCTTGTGAAGATAAGTCAACCTTTTAGTGA-TGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGT-ATTGTCATT
* * * * ** *
3386962 CTTGAGTTTCTCATGAAGAGAAGTCAA-CATTTTAGTGGTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATC-TTTCAGTATTGTCATT
** * *
3387007 CTTGACTTTTTCATGAAGAGAATTCAATCTTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTT
3387039 TAGTGTAGTT
Statistics
Matches: 878, Mismatches: 160, Indels: 99
0.77 0.14 0.09
Matches are distributed among these distances:
41 72 0.08
42 154 0.18
43 12 0.01
44 107 0.12
45 513 0.58
46 20 0.02
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (45 bp):
CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
Found at i:3386311 original size:128 final size:126
Alignment explanation
Indices: 3385918--3386547 Score: 470
Period size: 128 Copynumber: 4.8 Consensus size: 126
3385908 CTTGACTACA
* * * * *
3385918 TCGTGAAGAGGAGTCAGTCTTTCAATGTTATTCTTGACTTTCTCCTAAAGAGAAGTCAATCCTTC
1 TCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTTCCTCATAAA-AGAAGTCAATCTTTC
* * *
3385983 AATGTTATTCTTGACTT-CTCGTGGAGAGAAGTTAATCTTTCAGTATGGTCATTCTTGACTTCC
65 AATGGTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAG-ATGGTCATTC-TGACTTCC
* * * *
3386046 TCGTGAAGGGGATTCAATCTTTCAATGTTATTCTTAACTTCCTCGTGAAGAA-TAGTCAATCTTT
1 TCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTTCCTCAT-AA-AAGAAGTCAATCTTT
* * *
3386110 CAATGATATTCTTCAC-TCCTTCGTGAAGAGAAGTCAATCTCTCAGTATGGTCATTCTCGACTTC
64 CAATGGTATTCTTGACTTCC-TCGTGAAGAGAAGTCAATCTTTCAG-ATGGTCATTCT-GACTTC
3386174 C
126 C
* * * * *
3386175 TCGTGAAGAGGAGTCAATCTTTCAATGTTATTCATCACTCCCTTATAAAAGAAGTCAATATTTCA
1 TCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTTCCTCATAAAAGAAGTCAATCTTTC-
* * *
3386240 ATATGGTCATTCTTGTCTTCCTCGTGAAGAGGAA-TCAATATTTCA-AT-GTTATTCATGACTTC
65 A-ATGGT-ATTCTTGACTTCCTCGTGAAGA-GAAGTCAATCTTTCAGATGGTCATTC-TGACTTC
3386302 C
126 C
* * * * * * * *
3386303 TCGTGAAGATGAGTCAATCTTTTAGTATTTTCACTT-TTGACTTTCTCGTGAAGAGAAGTCAATG
1 TCGTGAAGAGGAGTCAATCTTTCA--ATGTT-A-TTCTTAACTTCCTCAT-AAAAGAAGTCAATC
* * * * * *
3386367 TTTCAATATTGTCATTCTTAACTTTCTCGTGAAGAGAAGCTC-ATCTTTCAGTATTGTTATTATT
61 TTTC-A-ATGGT-ATTCTTGACTTCCTCGTGAAGAGAAG-TCAATCTTTCAG-ATGGTCATT-CT
*
3386431 GACTTTC
120 GACTTCC
* * * * *
3386438 TCATGAAGA-GAGGTCAATCTTTCAGTATTGTCACTT-TTGACTTTCTCATAAAGAGAAGTAAAT
1 TCGTGAAGAGGA-GTCAATCTTTCA--A-TGTTA-TTCTTAACTTCCTCATAAA-AGAAGTCAAT
* * * *
3386501 CTTTCAATATTGTCATTCTTGACTTTCTTGTGAAGAGAAGTCCATCT
60 CTTTC-A-ATGGT-ATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
3386548 ATCTGTAATG
Statistics
Matches: 419, Mismatches: 56, Indels: 47
0.80 0.11 0.09
Matches are distributed among these distances:
127 3 0.01
128 114 0.27
129 86 0.21
130 9 0.02
131 36 0.09
132 58 0.14
133 2 0.00
134 8 0.02
135 101 0.24
136 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (126 bp):
TCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTTCCTCATAAAAGAAGTCAATCTTTCA
ATGGTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGATGGTCATTCTGACTTCC
Found at i:3386603 original size:86 final size:87
Alignment explanation
Indices: 3385918--3386630 Score: 414
Period size: 86 Copynumber: 8.2 Consensus size: 87
3385908 CTTGACTACA
* * * * ** *
3385918 TCGTGAAGAGGAGTCAGTCT-T-TCAATGTTATTCTTGACTTTCTCCTAAAGAGAAGTCAATCCT
1 TCGTGAAGAGAAGTCAATCTATCTTAATGTTATTCTTAAC-TTCT-CGGAAGAGAAGTCAATCTT
*
3385981 TC-A-A-TGTTATTCTTGAC-TTC
64 TCAATATTGTCATTCTTGACTTTC
* * * * * * * * *
3386001 TCGTGGAGAGAAGTTAATCTTTCAGT-ATGGTCATTCTTGACTTCCTCGTGAAGGGGATTCAATC
1 TCGTGAAGAGAAGTCAATCTATC-TTAAT-GTTATTCTTAACTT-CTCG-GAAGAGAAGTCAATC
* * *
3386065 TTTC-A-A-TGTTATTCTTAACTTCC
62 TTTCAATATTGTCATTCTTGACTTTC
* * * *
3386088 TCGTGAAGA-ATAGTCAATCT-T-TCAATGATATTCTTCACTCCTTCGTGAAGAGAAGTCAATCT
1 TCGTGAAGAGA-AGTCAATCTATCTTAATGTTATTCTTAACTTC-TCG-GAAGAGAAGTCAATCT
* * * * *
3386150 CTCAGTATGGTCATTCTCGACTTCC
63 TTCAATATTGTCATTCTTGACTTTC
* * * * * *** * *
3386175 TCGTGAAGAGGAGTCAATCT-T-TCAATGTTATTCATCACTCCCTTATAAAAGAAGTCAATATTT
1 TCGTGAAGAGAAGTCAATCTATCTTAATGTTATTCTTAACT-TCTCGGAAGAGAAGTCAATCTTT
* * *
3386238 CAATATGGTCATTCTTGTCTTCC
65 CAATATTGTCATTCTTGACTTTC
* *
3386261 TCGTGAAGAGGAA-TCAA--TAT-TTCAATGTTATTCATGACTTCCTCGTGAAGATG-AGTCAAT
1 TCGTGAAGA-GAAGTCAATCTATCTT-AATGTTATTCTTAACTT-CTCG-GAAGA-GAAGTCAAT
* * *
3386321 CTTTTAGTATTTTCACTT-TTGACTTTC
61 CTTTCAATATTGTCA-TTCTTGACTTTC
* * * * *
3386348 TCGTGAAGAGAAGTCAATGTTTCAATATTGTCATTCTTAACTTTCTCGTGAAGAGAAGCTC-ATC
1 TCGTGAAGAGAAGTCAATCTATC-TTAATGTTATTCTTAAC-TTCTCG-GAAGAGAAG-TCAATC
* * *
3386412 TTTCAGTATTGTTATTATTGACTTTC
62 TTTCAATATTGTCATTCTTGACTTTC
* * * * * * * ** *
3386438 TCATGAAGAGAGGTCAATCTTTCAGTATTGTCACTT-TTGACTTTCTCATAAAGAGAAGTAAATC
1 TCGTGAAGAGAAGTCAATCTATC-TTAATGTTA-TTCTTAAC-TTCTC-GGAAGAGAAGTCAATC
3386502 TTTCAATATTGTCATTCTTGACTTTC
62 TTTCAATATTGTCATTCTTGACTTTC
* *
3386528 TTGTGAAGAGAAGTCCATCTATCTGTAATGTTATTCTTAACTT-T-GGAAGAGAAGTCAATCTTT
1 TCGTGAAGAGAAGTCAATCTATCT-TAATGTTATTCTTAACTTCTCGGAAGAGAAGTCAATCTTT
3386591 CAATATTGTCATTCTTGACTTTC
65 CAATATTGTCATTCTTGACTTTC
*
3386614 TCGTGAAAAGAAGTCAA
1 TCGTGAAGAGAAGTCAA
3386631 CCTTTTAGTG
Statistics
Matches: 500, Mismatches: 94, Indels: 69
0.75 0.14 0.10
Matches are distributed among these distances:
83 17 0.03
84 31 0.06
85 9 0.02
86 164 0.33
87 109 0.22
88 6 0.01
89 10 0.02
90 147 0.29
91 7 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (87 bp):
TCGTGAAGAGAAGTCAATCTATCTTAATGTTATTCTTAACTTCTCGGAAGAGAAGTCAATCTTTC
AATATTGTCATTCTTGACTTTC
Found at i:3386814 original size:179 final size:177
Alignment explanation
Indices: 3386574--3387043 Score: 518
Period size: 179 Copynumber: 2.6 Consensus size: 177
3386564 TTAACTTTGG
* * * * * *
3386574 AAGAGAAGTCAATCTTTCAAT-ATTGTCATTCTTGACTTTCTCGTGAAAAGAAGTCAACCTTTTA
1 AAGAGAAGTCAACCTTTTAGTGA-TGTTATTCTTAACTTTCTCGTGAAGAGAAGTCAACCTTTTA
* * *
3386638 GTGATGTTATTCTTGATTTTCTCATGAAAAGAAGTCAACCTTTTAGTG-GCGTCGTTCTTGACTT
65 GTG-TGTTATTCTTGATTTTCTCATGAAGAGAATTCAACCTTTTAGTGAGC-T-ATTCTTGACTT
* *
3386702 TCTCATGAAG-AGACGTCAACC-TTTAGTGATGTTATTCTTGACTTTCTCATA
127 TCTCACGAAGAAGA-ATCAACCTTTTAGTGATGTTATTCTT-ACTTTCTCATA
* * * *
3386753 AAGAGAATTCAACCTTTTAGTGGTGTTATTTTTAACTTTCTCGTGAAGAGAAATCAACCTTTTAG
1 AAGAGAAGTCAACCTTTTAGTGATGTTATTCTTAACTTTCTCGTGAAGAGAAGTCAACCTTTTAG
* * * * * * *
3386818 TGTGGGTGTTCTTGACTTTCTCGTCAAGAGAATTCAACCTTTTTGTGATGCTATTCTTGATTTTC
66 TGT-GTTATTCTTGATTTTCTCATGAAGAGAATTCAACCTTTTAGTGA-GCTATTCTTGACTTTC
* * ** *
3386883 TCACGAAGAAGAATCAACCTTTTAGTGGTGTTTTTCTTACTTTCTTGTG
129 TCACGAAGAAGAATCAACCTTTTAGTGATGTTATTCTTACTTTCTCATA
* * * * *
3386932 AAGATAAGTCAACCTTTTAGTGATGTTATTCTTGAGTTTCTCATGAAGAGAAGTCAACATTTTAG
1 AAGAGAAGTCAACCTTTTAGTGATGTTATTCTTAACTTTCTCGTGAAGAGAAGTCAACCTTTTAG
*
3386997 TGGTGTTATTCTTGACTTTT-TCATGAAGAGAATTCAATCTTTTAGTG
66 T-GTGTTATTCTTGA-TTTTCTCATGAAGAGAATTCAACCTTTTAGTG
3387044 TAGTTTTTCT
Statistics
Matches: 240, Mismatches: 43, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
178 1 0.00
179 212 0.88
180 25 0.10
181 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (177 bp):
AAGAGAAGTCAACCTTTTAGTGATGTTATTCTTAACTTTCTCGTGAAGAGAAGTCAACCTTTTAG
TGTGTTATTCTTGATTTTCTCATGAAGAGAATTCAACCTTTTAGTGAGCTATTCTTGACTTTCTC
ACGAAGAAGAATCAACCTTTTAGTGATGTTATTCTTACTTTCTCATA
Found at i:3387050 original size:134 final size:133
Alignment explanation
Indices: 3386381--3387054 Score: 564
Period size: 134 Copynumber: 5.0 Consensus size: 133
3386371 AATATTGTCA
* * * * *
3386381 TTCTTAACTTTCTCGTGAAGAGAAGCTC-ATCTTTCAGTATTGTTATTATTGACTTTCTCATGAA
1 TTCTTAACTTTCTCGTGAAGAGAAG-TCAACCTTTTAGT-GTGTTGTTCTTGACTTTCTCATGAA
* * * * * * * * *
3386445 GAGAGGTCAATCTTTCAGT-ATTGTCACTT-TTGACTTTCTCATAAAGAGAAGTAAATCTTTCAA
64 GAGAAGTCAA-CTTTTAGTGA-TGTTA-TTCTTGACTTTCTCATGAAGAGAATTCAACCTTTTAG
** **
3386508 TATTGTCA
126 TGGTGTTT
* * * * * * * * *
3386516 TTCTTGACTTTCTTGTGAAGAGAAGTCCATCTATCT-GTAATGTTATTCTTAAC-TT-T--GGAA
1 TTCTTAACTTTCTCGTGAAGAGAAGTCAACCT-TTTAGT-GTGTTGTTCTTGACTTTCTCATGAA
* * * * * *
3386576 GAGAAGTCAATCTTTCAAT-ATTGTCATTCTTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGT
64 GAGAAGTCAA-CTTTTAGTGA-TGTTATTCTTGACTTTCTCATGAAGAGAATTCAACCTTTTAGT
* *
3386640 GATGTTA
127 GGTGTTT
* * * * * *
3386647 TTCTTGATTTTCTCATGAAAAGAAGTCAACCTTTTAGTGGCGTCGTTCTTGACTTTCTCATGAAG
1 TTCTTAACTTTCTCGTGAAGAGAAGTCAACCTTTTAGT-GTGTTGTTCTTGACTTTCTCATGAAG
* * *
3386712 AGACGTCAACCTTTAGTGATGTTATTCTTGACTTTCTCATAAAGAGAATTCAACCTTTTAGTGGT
65 AGAAGTCAACTTTTAGTGATGTTATTCTTGACTTTCTCATGAAGAGAATTCAACCTTTTAGTGGT
3386777 GTTAT
130 GTT-T
* * * *
3386782 TT-TTAACTTTCTCGTGAAGAGAAATCAACCTTTTAGTGTGGGTGTTCTTGACTTTCTCGTCAAG
1 TTCTTAACTTTCTCGTGAAGAGAAGTCAACCTTTTAGTGT-GTTGTTCTTGACTTTCTCATGAAG
* * * * *
3386846 AGAATTCAACCTTTTTGTGATGCTATTCTTGATTTTCTCACGAAGAAGAA-TCAACCTTTTAGTG
65 AGAAGTCAA-CTTTTAGTGATGTTATTCTTGACTTTCTCATGAAG-AGAATTCAACCTTTTAGTG
3386910 GTGTTT
128 GTGTTT
* * * *
3386916 TTCTT-ACTTTCTTGTGAAGATAAGTCAACCTTTTAGTGATGTTATTCTTGAGTTTCTCATGAAG
1 TTCTTAACTTTCTCGTGAAGAGAAGTCAACCTTTTAGTG-TGTTGTTCTTGACTTTCTCATGAAG
* * *
3386980 AGAAGTCAACATTTTAGTGGTGTTATTCTTGACTTTTTCATGAAGAGAATTCAATCTTTTAGT-G
65 AGAAGTCAAC-TTTTAGTGATGTTATTCTTGACTTTCTCATGAAGAGAATTCAACCTTTTAGTGG
3387044 TAGTTT
129 T-GTTT
3387050 TTCTT
1 TTCTT
3387055 TTAGTGTGGT
Statistics
Matches: 442, Mismatches: 79, Indels: 37
0.79 0.14 0.07
Matches are distributed among these distances:
130 4 0.01
131 96 0.22
132 2 0.00
133 10 0.02
134 218 0.49
135 107 0.24
136 5 0.01
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (133 bp):
TTCTTAACTTTCTCGTGAAGAGAAGTCAACCTTTTAGTGTGTTGTTCTTGACTTTCTCATGAAGA
GAAGTCAACTTTTAGTGATGTTATTCTTGACTTTCTCATGAAGAGAATTCAACCTTTTAGTGGTG
TTT
Found at i:3387056 original size:17 final size:17
Alignment explanation
Indices: 3387034--3387071 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
3387024 GAGAATTCAA
3387034 TCTTTTAGTGTAGTTTT
1 TCTTTTAGTGTAGTTTT
*
3387051 TCTTTTAGTGTGGTTTT
1 TCTTTTAGTGTAGTTTT
3387068 TCTT
1 TCTT
3387072 AAATTTCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.66
Consensus pattern (17 bp):
TCTTTTAGTGTAGTTTT
Found at i:3388232 original size:2 final size:2
Alignment explanation
Indices: 3388225--3388278 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
3388215 TTAAATAGTA
* *
3388225 AT AT AT AT -T AT -T AT -T AT AC AA 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
3388264 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
3388279 AGTTGAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3388913 original size:2 final size:2
Alignment explanation
Indices: 3388906--3388938 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3388896 ATGGATTTTC
3388906 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3388939 AAAGAGGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3390525 original size:19 final size:17
Alignment explanation
Indices: 3390489--3390521 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3390479 ATTTGTCTTC
*
3390489 TACAAAGAGTTCTGTTA
1 TACAAAAAGTTCTGTTA
3390506 TACAAAAAGTTCTGTT
1 TACAAAAAGTTCTGTT
3390522 TTATGTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (17 bp):
TACAAAAAGTTCTGTTA
Found at i:3392899 original size:41 final size:41
Alignment explanation
Indices: 3392842--3392923 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
3392832 GTGTCCGTTG
3392842 CAAGTTTTTTATGCACCTCAGATGTGCTCGGCCACCACCCA
1 CAAGTTTTTTATGCACCTCAGATGTGCTCGGCCACCACCCA
3392883 CAAGTTTTTTATGCACCTCAGATGTGCTCGGCCACCACCCA
1 CAAGTTTTTTATGCACCTCAGATGTGCTCGGCCACCACCCA
3392924 TTATTGAGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.34, G:0.17, T:0.27
Consensus pattern (41 bp):
CAAGTTTTTTATGCACCTCAGATGTGCTCGGCCACCACCCA
Found at i:3397889 original size:14 final size:14
Alignment explanation
Indices: 3397871--3397922 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
3397861 TTGATAATAT
* *
3397871 GTTCATTTATTTTT
1 GTTCATTTATATTC
* *
3397885 GTTCATATATGTTC
1 GTTCATTTATATTC
* *
3397899 GTTCGTTTATATGC
1 GTTCATTTATATTC
3397913 GTTCATTTAT
1 GTTCATTTAT
3397923 GTTTAGTCCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.17, C:0.12, G:0.13, T:0.58
Consensus pattern (14 bp):
GTTCATTTATATTC
Found at i:3398137 original size:3 final size:3
Alignment explanation
Indices: 3398129--3398178 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
3398119 TTTTATATTA
3398129 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3398177 AA
1 AA
3398179 ATTTCATGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3406608 original size:3 final size:3
Alignment explanation
Indices: 3406561--3406592 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3406551 TTTTATATTA
3406561 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3406593 ATGTCATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3408299 original size:13 final size:13
Alignment explanation
Indices: 3408283--3408309 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3408273 GTCACTTTTA
3408283 ATTTTTTAAAAAT
1 ATTTTTTAAAAAT
3408296 ATTTTTTAAAAAT
1 ATTTTTTAAAAAT
3408309 A
1 A
3408310 CTTATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTTTAAAAAT
Found at i:3409154 original size:18 final size:18
Alignment explanation
Indices: 3409133--3409194 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
3409123 TTCTATTTTA
3409133 ATTTTAATTATTGTTAAT
1 ATTTTAATTATTGTTAAT
* *
3409151 ATTTTATTTATT-TAAAT
1 ATTTTAATTATTGTTAAT
* * *
3409168 -TTTTTAGTATTAGTTTAT
1 ATTTTAATTATT-GTTAAT
3409186 ATTTTAATT
1 ATTTTAATT
3409195 TCTATAATAT
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
16 8 0.25
17 4 0.12
18 14 0.44
19 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
ATTTTAATTATTGTTAAT
Found at i:3411075 original size:3 final size:3
Alignment explanation
Indices: 3411067--3411129 Score: 90
Period size: 3 Copynumber: 21.0 Consensus size: 3
3411057 TATCTGCTCC
* * * *
3411067 TGA TGA TGA TGA TGA TGA TAA TGA TAA TGA TGA TGG TGG TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
3411115 TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA
3411130 GTGTGAGGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:3411387 original size:25 final size:24
Alignment explanation
Indices: 3411315--3411388 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
3411305 ATTACTTAAT
*
3411315 TTATTTTGTTTTTTTAATTTTTTTA
1 TTATTTAGTTTTTTTAA-TTTTTTA
* * * *
3411340 TTACTTAATTGTTTGAATGTTTTTA
1 TTATTTAGTTTTTTTAAT-TTTTTA
3411365 TTATTTAGTGTTTTTTAATTTTTT
1 TTATTTAGT-TTTTTTAATTTTTT
3411389 TGTATCGTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
24 1 0.03
25 30 0.79
26 7 0.18
ACGTcount: A:0.19, C:0.01, G:0.08, T:0.72
Consensus pattern (24 bp):
TTATTTAGTTTTTTTAATTTTTTA
Found at i:3419756 original size:45 final size:45
Alignment explanation
Indices: 3419662--3419779 Score: 159
Period size: 45 Copynumber: 2.6 Consensus size: 45
3419652 GTAAGCATGC
* *
3419662 AAATAAGTTTACGAGCTTATGG-AATAATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGTAATAATGACAAGTATATGGGTA
* *
3419706 AAATAAGCTTACGAGCTTATGGTACA-AATGACAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGTA-ATAATGACAAGTATATGGGTA
*
3419751 AAATAAGCTTACAAGCTTATGGTTAATAA
1 AAATAAGCTTACGAGCTTATGG-TAATAA
3419780 ATGGTAAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
44 21 0.32
45 39 0.60
46 5 0.08
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGTAATAATGACAAGTATATGGGTA
Found at i:3422520 original size:32 final size:31
Alignment explanation
Indices: 3422473--3422535 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 31
3422463 CAGCATCTTG
*
3422473 TTTGAACTTGTTTTTGAACTTTCTCATATTT
1 TTTGAACTTGCTTTTGAACTTTCTCATATTT
3422504 TTTGTAACTTGCTTTTGAACTTTCTCATATTT
1 TTTG-AACTTGCTTTTGAACTTTCTCATATTT
3422536 CTTTTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 4 0.13
32 26 0.87
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (31 bp):
TTTGAACTTGCTTTTGAACTTTCTCATATTT
Found at i:3424716 original size:142 final size:142
Alignment explanation
Indices: 3424460--3424744 Score: 561
Period size: 142 Copynumber: 2.0 Consensus size: 142
3424450 AGGTCATCTT
3424460 TCATTTAGAGGAAATTTACACCACAACTTAAGTCGATAAAAACTCTGTGTCAACAAACACCTCTC
1 TCATTTAGAGGAAATTTACACCACAACTTAAGTCGATAAAAACTCTGTGTCAACAAACACCTCTC
3424525 CAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAAGATATTGAACTCGAAAGCAATGCAATT
66 CAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAAGATATTGAACTCGAAAGCAATGCAATT
3424590 TTGGATTTCAAC
131 TTGGATTTCAAC
*
3424602 TCATTTAGAGGAAATTTACACCACAACTTAAGTCGATAAAAACTGTGTGTCAACAAACACCTCTC
1 TCATTTAGAGGAAATTTACACCACAACTTAAGTCGATAAAAACTCTGTGTCAACAAACACCTCTC
3424667 CAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAAGATATTGAACTCGAAAGCAATGCAATT
66 CAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAAGATATTGAACTCGAAAGCAATGCAATT
3424732 TTGGATTTCAAC
131 TTGGATTTCAAC
3424744 T
1 T
3424745 TCACAACGAA
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (142 bp):
TCATTTAGAGGAAATTTACACCACAACTTAAGTCGATAAAAACTCTGTGTCAACAAACACCTCTC
CAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAAGATATTGAACTCGAAAGCAATGCAATT
TTGGATTTCAAC
Found at i:3425136 original size:85 final size:85
Alignment explanation
Indices: 3424900--3425234 Score: 329
Period size: 85 Copynumber: 4.0 Consensus size: 85
3424890 TCCCAGCCTA
* * ** *
3424900 TTACAGTACAGCTCAAGGCGAGAAGGGCTATCTGTCAGTAAAAACCTTCGAGTTCGATTCCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
* ** *
3424965 AGCTCAAGGGCA-GCCGAAT
66 AGCTCAAGGACATATCAAAT
* * * * * * * *
3424984 TTATAGCATATCTCAAGGCGAGATGGGTTATATGTTAAC--AAACCTTTGAGTTTGATTACATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
3425047 AGCTCAAGGACATATCAAAT
66 AGCTCAAGGACATATCAAAT
* * * * *
3425067 TTACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACCAAAACATTCGGGTTTGATTACATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
3425132 AGCTCAAGGGA-ATATCAAAT
66 AGCTCAA-GGACATATCAAAT
* * * ** * * *
3425152 TTACAGCATAACTTAAGTCGAGAAAAGTTATCTGTCAACAAAAA-CTGTCAAGTTCGATTTCATT
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCT-TCGAGTTCGATTACATT
* *
3425216 CAGCTCGATGACATATCAA
65 CAGCTCAAGGACATATCAA
3425235 CCGCATGGTA
Statistics
Matches: 203, Mismatches: 42, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
82 32 0.16
83 36 0.18
84 32 0.16
85 100 0.49
86 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (85 bp):
TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
AGCTCAAGGACATATCAAAT
Found at i:3427325 original size:14 final size:15
Alignment explanation
Indices: 3427292--3427328 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3427282 AATATTTTTT
3427292 TATTT-TTTATTTCA
1 TATTTATTTATTTCA
3427306 TATTTATTTATTT-A
1 TATTTATTTATTTCA
*
3427320 TTTTTATTT
1 TATTTATTT
3427329 TTGCAATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTATTTATTTCA
Found at i:3436986 original size:66 final size:66
Alignment explanation
Indices: 3436815--3437106 Score: 368
Period size: 66 Copynumber: 4.4 Consensus size: 66
3436805 ATATTGTATT
* * * * * **
3436815 GATCGCTCTATGTGACTCGGGTACCTTTGTGGTGCATGAGGTGGAATGATAATTGAATACTATAC
1 GATCACTCAATGTGACTCGTGTACCTTTGTGGTACATGAGGTGGAGTGATAATTGAATACTGCAC
3436880 AA
66 -A
* * * * *
3436882 GATCACTCAATGTGACTTGTGTACCTTTATAGTGCATGAGGTGGAGTGATAATTGAATACTGCAT
1 GATCACTCAATGTGACTCGTGTACCTTTGTGGTACATGAGGTGGAGTGATAATTGAATACTGCAC
3436947 A
66 A
* **
3436948 GATCACTCAATGTGACTCGTGTACCTTTGTGGTACATGATGTGGAGTGATAATTGAATACTTTAC
1 GATCACTCAATGTGACTCGTGTACCTTTGTGGTACATGAGGTGGAGTGATAATTGAATACTGCAC
3437013 A
66 A
** * * * * *
3437014 GATCACTTGATGTGACTCATGTACCTTTGTGGTACACGAGGTGTAGTGATAATTGAATATTGTAC
1 GATCACTCAATGTGACTCGTGTACCTTTGTGGTACATGAGGTGGAGTGATAATTGAATACTGCAC
3437079 A
66 A
*
3437080 GATCACTCGATGTGACTCGTGTACCTT
1 GATCACTCAATGTGACTCGTGTACCTT
3437107 AGGATACCTT
Statistics
Matches: 197, Mismatches: 28, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
66 142 0.72
67 55 0.28
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (66 bp):
GATCACTCAATGTGACTCGTGTACCTTTGTGGTACATGAGGTGGAGTGATAATTGAATACTGCAC
A
Found at i:3437083 original size:132 final size:133
Alignment explanation
Indices: 3436793--3437106 Score: 414
Period size: 132 Copynumber: 2.4 Consensus size: 133
3436783 CATGAGATAA
* * * * * * *
3436793 AGTGATTACTGAATATTGTATTGATCGCTCTATGTGACTCGGGTACCTTTGTGGTGCATGAGGTG
1 AGTGATAATTGAATATTGTATAGATCACTCAATGTGACTCGTGTACCTTTGTGGTACATGAGGTG
** * *
3436858 GAATGATAATTGAATACTATACAAGATCACTCAATGTGACTTGTGTACCTTTATAGTGCATGAGG
66 GAATGATAATTGAATACTATACAAGATCACTCAATGTGACTCATGTACCTTTATAGTACACGAGG
3436923 TGG
131 TGG
* * *
3436926 AGTGATAATTGAATACTGCATAGATCACTCAATGTGACTCGTGTACCTTTGTGGTACATGATGTG
1 AGTGATAATTGAATATTGTATAGATCACTCAATGTGACTCGTGTACCTTTGTGGTACATGAGGTG
* * ** * *
3436991 GAGTGATAATTGAATACTTTAC-AGATCACTTGATGTGACTCATGTACCTTTGTGGTACACGAGG
66 GAATGATAATTGAATACTATACAAGATCACTCAATGTGACTCATGTACCTTTATAGTACACGAGG
*
3437055 TGT
131 TGG
* *
3437058 AGTGATAATTGAATATTGTACAGATCACTCGATGTGACTCGTGTACCTT
1 AGTGATAATTGAATATTGTATAGATCACTCAATGTGACTCGTGTACCTT
3437107 AGGATACCTT
Statistics
Matches: 156, Mismatches: 25, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
132 81 0.52
133 75 0.48
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (133 bp):
AGTGATAATTGAATATTGTATAGATCACTCAATGTGACTCGTGTACCTTTGTGGTACATGAGGTG
GAATGATAATTGAATACTATACAAGATCACTCAATGTGACTCATGTACCTTTATAGTACACGAGG
TGG
Found at i:3437274 original size:17 final size:18
Alignment explanation
Indices: 3437252--3437285 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3437242 TGAAATTTAA
3437252 GATACAATACAC-TAAAT
1 GATACAATACACATAAAT
3437269 GATACAATACACATAAA
1 GATACAATACACATAAA
3437286 ATAGTACAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.56, C:0.18, G:0.06, T:0.21
Consensus pattern (18 bp):
GATACAATACACATAAAT
Found at i:3438982 original size:17 final size:17
Alignment explanation
Indices: 3438960--3438999 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3438950 CGCGGGTAGA
3438960 TATTTTCCAGAAATTTT
1 TATTTTCCAGAAATTTT
**
3438977 TATTTTTTAGAAATTTT
1 TATTTTCCAGAAATTTT
*
3438994 GATTTT
1 TATTTT
3439000 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (17 bp):
TATTTTCCAGAAATTTT
Found at i:3439003 original size:18 final size:17
Alignment explanation
Indices: 3438968--3439001 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3438958 GATATTTTCC
*
3438968 AGAAATTTTTATTTTTT
1 AGAAATTTTGATTTTTT
3438985 AGAAATTTTGATTTTTT
1 AGAAATTTTGATTTTTT
3439002 TAATTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
AGAAATTTTGATTTTTT
Found at i:3442669 original size:13 final size:13
Alignment explanation
Indices: 3442651--3442692 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3442641 ACCGGTCATA
3442651 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
3442664 ACCCGACCCATTG
1 ACCCGACCCGTTG
**
3442677 ACTTGACCCGTTG
1 ACCCGACCCGTTG
3442690 ACC
1 ACC
3442693 GTTGCCCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.19, C:0.43, G:0.19, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:3445026 original size:24 final size:24
Alignment explanation
Indices: 3444999--3445110 Score: 154
Period size: 24 Copynumber: 4.7 Consensus size: 24
3444989 ATTTGATTTA
3444999 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
3445023 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
* *
3445047 TGATCTGATACTTGACTTGGATTA
1 TGATCTGATACTTGACATGGATTC
* * *
3445071 TGATCTGTTACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTC
*
3445095 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
3445111 GTGAACTATG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 77 0.97
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:3452494 original size:19 final size:19
Alignment explanation
Indices: 3452470--3452523 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
3452460 AAGCTATTTT
3452470 GTGCATCGATACACCCATA
1 GTGCATCGATACACCCATA
3452489 GTGCATCGATACACCCATA
1 GTGCATCGATACACCCATA
3452508 GTGCATCGATACACCC
1 GTGCATCGATACACCC
3452524 CTAAAGGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (19 bp):
GTGCATCGATACACCCATA
Found at i:3453457 original size:22 final size:22
Alignment explanation
Indices: 3453432--3453476 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3453422 GAGTCGAGGG
*
3453432 ATATACAGTGGTCCTTCGGGAC
1 ATATACAGTGGTCCTTCGAGAC
3453454 ATATACAGTGGTCCTTCGAGAC
1 ATATACAGTGGTCCTTCGAGAC
3453476 A
1 A
3453477 AATTTCACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (22 bp):
ATATACAGTGGTCCTTCGAGAC
Found at i:3457670 original size:12 final size:12
Alignment explanation
Indices: 3457624--3457706 Score: 62
Period size: 13 Copynumber: 6.8 Consensus size: 12
3457614 ATTGGAGTGC
3457624 AAAAAG-AAAGA
1 AAAAAGAAAAGA
*
3457635 AAAAGACAAAAGA
1 AAAA-AGAAAAGA
* *
3457648 AGAGA-AAAAGA
1 AAAAAGAAAAGA
*
3457659 TAAAAGAAAAGA
1 AAAAAGAAAAGA
* *
3457671 AAAAATCAAAAAA
1 AAAAA-GAAAAGA
3457684 GAAAAAGAAAAAGA
1 -AAAAAG-AAAAGA
3457698 AAAAAGAAA
1 AAAAAGAAA
3457707 GCAAGCCAAG
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
11 12 0.22
12 15 0.27
13 18 0.33
14 10 0.18
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:3457688 original size:6 final size:6
Alignment explanation
Indices: 3457630--3457706 Score: 68
Period size: 6 Copynumber: 12.2 Consensus size: 6
3457620 GTGCAAAAAG
* *
3457630 AAAGAA AAAGACA AAAG-A AGAGAA AAAGATA AAAG-A AAAGAAA AAATCAAA
1 AAAGAA AAAGA-A AAAGAA AAAGAA AAAGA-A AAAGAA AAAG-AA AAA--GAA
3457681 AAAGAA AAAGAA AAAGAAA AAAGAA A
1 AAAGAA AAAGAA AAAG-AA AAAGAA A
3457707 GCAAGCCAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
5 9 0.15
6 25 0.42
7 20 0.34
8 5 0.08
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:3457700 original size:18 final size:18
Alignment explanation
Indices: 3457625--3457706 Score: 87
Period size: 18 Copynumber: 4.4 Consensus size: 18
3457615 TTGGAGTGCA
3457625 AAAAG-AAAGAAAAAGAC
1 AAAAGAAAAGAAAAAGAC
* *
3457642 AAAAGAAGAGAAAAAGAT
1 AAAAGAAAAGAAAAAGAC
3457660 AAAAGAAAAGAAAAA-ATC
1 AAAAGAAAAGAAAAAGA-C
*
3457678 AAAAAAGAAAAAGAAAAAGAA
1 --AAAAG-AAAAGAAAAAGAC
3457699 AAAAGAAA
1 AAAAGAAA
3457707 GCAAGCCAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
17 6 0.11
18 27 0.50
19 5 0.09
20 5 0.09
21 10 0.19
22 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAGAC
Found at i:3457705 original size:7 final size:7
Alignment explanation
Indices: 3457630--3457706 Score: 63
Period size: 7 Copynumber: 11.0 Consensus size: 7
3457620 GTGCAAAAAG
3457630 AAAGAAA
1 AAAGAAA
*
3457637 AAGACAAA
1 AA-AGAAA
3457645 AGAAGAGAA
1 A-AAGA-AA
*
3457654 AAAGATA
1 AAAGAAA
3457661 AAAG--A
1 AAAGAAA
3457666 AAAGAAA
1 AAAGAAA
*
3457673 AAATCAAA
1 AAA-GAAA
3457681 AAAG-AA
1 AAAGAAA
3457687 AAAG-AA
1 AAAGAAA
3457693 AAAGAAA
1 AAAGAAA
3457700 AAAGAAA
1 AAAGAAA
3457707 GCAAGCCAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
5 5 0.09
6 12 0.21
7 20 0.34
8 17 0.29
9 4 0.07
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:3463257 original size:22 final size:22
Alignment explanation
Indices: 3463229--3463288 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
3463219 GAGTCGAGGG
3463229 ATATACAGTGGTCCTTCAGGAC
1 ATATACAGTGGTCCTTCAGGAC
* *
3463251 ATATACAGTGGTCATTCGGGAC
1 ATATACAGTGGTCCTTCAGGAC
*
3463273 ATA-AGCATTGGTCCTT
1 ATATA-CAGTGGTCCTT
3463289 TGAGACAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (22 bp):
ATATACAGTGGTCCTTCAGGAC
Found at i:3475567 original size:45 final size:45
Alignment explanation
Indices: 3475482--3475567 Score: 100
Period size: 45 Copynumber: 1.9 Consensus size: 45
3475472 AAGAAAAAGA
** * *
3475482 AAATGGGGGATCAAGATGAAAATTCGAAAAGGGTGTCTTGAAACC
1 AAATGGGGGATCAAGATGAAAACCCGAAAAGGGCGACTTGAAACC
** * *
3475527 AAATGGGGTCTCAAGTTGAAAACCCGCAAAGGGCGACTTGA
1 AAATGGGGGATCAAGATGAAAACCCGAAAAGGGCGACTTGA
3475568 GTATCATTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.29, T:0.19
Consensus pattern (45 bp):
AAATGGGGGATCAAGATGAAAACCCGAAAAGGGCGACTTGAAACC
Found at i:3477113 original size:134 final size:132
Alignment explanation
Indices: 3476836--3477367 Score: 629
Period size: 134 Copynumber: 4.0 Consensus size: 132
3476826 CTGGTTTTCC
* * * *
3476836 CCTAAAGAGTAGCGGA-ACAGATTCTTCTTCTTTTAGATTTGGTCTTCTTGAAAAGCAGCGAAGC
1 CCTAAAGAGTAGTGGAGA-AGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGC
* * * * *
3476900 AAATCAAGTTC-ATTCAATCTTTCCTGAAGAGCAGCGAAGTGAATCAAAATTTTCTCAAGTCTGG
65 AAATCAAATTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGAATCAAAATTTTCTCGAGTCTGA
3476964 CTT
130 CTT
3476967 CCCCTAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAG
1 --CCTAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAG
* * *
3477032 CAAATCAAATTTGATTTAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTTTCTCGAGTCTG
64 CAAATCAAATTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGAATCAAAATTTTCTCGAGTCTG
3477097 ACTT
129 ACTT
* * * * * * * *
3477101 CCTGTAAAGAGTAATGGAGCAGATTCTTCTTCTTTCATATTTAGTTTTCTTGAAGAACAGCAAAG
1 CC--TAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAG
* * * * *** *
3477166 CAAATCACATTCGATTTAATCTTCCCTGAAAAGCAACGAAGTGAATAAAAAAAAAAT-TCGAGTA
64 CAAATCAAATTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGAAT--CAAAATTTTCTCGAGTC
3477230 TGACCTCT
127 TGA-CT-T
* * * *
3477238 CCTAAAAAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTTCTGAAGAGCAGAGAAGCA
1 CCTAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCA
* * * *
3477303 AATCACATTCAATTCAATCTTCCCTGAAGAGCAGCGAAGTGGATCAAAAATTTTCTCGAGTCTGA
66 AATCAAATTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGAATC-AAAATTTTCTCGAGTCTGA
3477368 TCTCCCCTAG
Statistics
Matches: 340, Mismatches: 49, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
132 2 0.01
133 67 0.20
134 151 0.44
135 110 0.32
136 7 0.02
137 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (132 bp):
CCTAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCA
AATCAAATTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGAATCAAAATTTTCTCGAGTCTGAC
TT
Found at i:3477291 original size:269 final size:268
Alignment explanation
Indices: 3476838--3477367 Score: 717
Period size: 269 Copynumber: 2.0 Consensus size: 268
3476828 GGTTTTCCCC
* * * *
3476838 TAAAGAGTAGCGGAACAGATTCTTCTTCTTTTAGATTTGGTCTTCTTGAAAAGCAGCGAAGCAAA
1 TAAAGAGTAACGGAACAGATTCTTCTTCTTTCAGATTTAGTCTTCTTGAAAAGCAGCAAAGCAAA
* * * * *** * * *
3476903 TCAAGTTCATTCAATCTTTCCTGAAGAGCAGCGAAGTGAATCAAAATTTTCTCAAGTCTGGCTTC
66 TCAAGTTCATTCAATCTTCCCTGAAAAGCAACGAAGTGAATAAAAAAAATCTCAAGTATGACCTC
* *
3476968 CCCTAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGC
131 CCCTAAAAAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGAGAAGC
** *
3477033 AAATCAAATTTGATTTAATCTTCCCTGAAGAGCAACGAAGTGGATC-AAAATTTTCTCGAGTCTG
196 AAATCAAATTCAATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAAATTTTCTCGAGTCTG
3477097 ACTTCCTG
261 ACTTCCTG
* * * *
3477105 TAAAGAGTAATGGAGCAGATTCTTCTTCTTTCATATTTAGTTTTCTTGAAGAA-CAGCAAAGCAA
1 TAAAGAGTAACGGAACAGATTCTTCTTCTTTCAGATTTAGTCTTCTTGAA-AAGCAGCAAAGCAA
* *
3477169 ATCACA-TTCGATTTAATCTTCCCTGAAAAGCAACGAAGTGAATAAAAAAAAAAT-TCGAGTATG
65 ATCA-AGTTC-ATTCAATCTTCCCTGAAAAGCAACGAAGTGAAT--AAAAAAAATCTCAAGTATG
* * *
3477232 ACCTCTCCTAAAAAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTTCTGAAGAGCAGA
126 ACCTCCCCTAAAAAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGA
* *
3477297 GAAGCAAATCACATTCAATTCAATCTTCCCTGAAGAGCAGCGAAGTGGATCAAAAATTTTCTCGA
191 GAAGCAAATCAAATTCAATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAAATTTTCTCGA
3477362 GTCTGA
256 GTCTGA
3477368 TCTCCCCTAG
Statistics
Matches: 227, Mismatches: 30, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
267 60 0.26
268 32 0.14
269 111 0.49
270 24 0.11
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (268 bp):
TAAAGAGTAACGGAACAGATTCTTCTTCTTTCAGATTTAGTCTTCTTGAAAAGCAGCAAAGCAAA
TCAAGTTCATTCAATCTTCCCTGAAAAGCAACGAAGTGAATAAAAAAAATCTCAAGTATGACCTC
CCCTAAAAAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGAGAAGC
AAATCAAATTCAATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAAATTTTCTCGAGTCTG
ACTTCCTG
Found at i:3477806 original size:2 final size:2
Alignment explanation
Indices: 3477799--3477830 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3477789 AAGTAATCAA
3477799 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
3477831 TTATTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3479074 original size:21 final size:20
Alignment explanation
Indices: 3479048--3479094 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
3479038 GAACGCTGGA
3479048 AACCGGTTTTGACCGGTTTTG
1 AACCGGTTTTGACCGG-TTTG
3479069 AACCGGTTTTGACCGGTTTG
1 AACCGGTTTTGACCGGTTTG
3479089 -ACCGGT
1 AACCGGT
3479095 CACGACCCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
21 16 0.62
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.34
Consensus pattern (20 bp):
AACCGGTTTTGACCGGTTTG
Found at i:3479075 original size:11 final size:10
Alignment explanation
Indices: 3479049--3479094 Score: 76
Period size: 10 Copynumber: 4.6 Consensus size: 10
3479039 AACGCTGGAA
3479049 ACCGGTTTTG
1 ACCGGTTTTG
3479059 ACCGGTTTTG
1 ACCGGTTTTG
3479069 AACCGGTTTTG
1 -ACCGGTTTTG
3479080 ACCGG-TTTG
1 ACCGGTTTTG
3479089 ACCGGT
1 ACCGGT
3479095 CACGACCCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.26
10 15 0.44
11 10 0.29
ACGTcount: A:0.13, C:0.22, G:0.30, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:3479139 original size:36 final size:36
Alignment explanation
Indices: 3479099--3479168 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
3479089 ACCGGTCACG
3479099 ACCCGACCCCATCGACCCGACCCGA-CCGTTGACCCA
1 ACCCGA-CCCATCGACCCGACCCGACCCGTTGACCCA
** *
3479135 ACCCGACCTGTTGACCCGACCCGACCCGTTGACC
1 ACCCGACCCATCGACCCGACCCGACCCGTTGACC
3479169 GGTGCTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.20, C:0.50, G:0.19, T:0.11
Consensus pattern (36 bp):
ACCCGACCCATCGACCCGACCCGACCCGTTGACCCA
Found at i:3479149 original size:18 final size:17
Alignment explanation
Indices: 3479112--3479168 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 17
3479102 CGACCCCATC
3479112 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
3479129 GACCCAACCCGACCTGTT
1 GACCCGACCCGACC-GTT
3479147 GACCCGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
3479165 GACC
1 GACC
3479169 GGTGCTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 13 0.36
18 21 0.58
19 2 0.06
ACGTcount: A:0.19, C:0.47, G:0.21, T:0.12
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:3479230 original size:29 final size:29
Alignment explanation
Indices: 3479198--3479265 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
3479188 ATTTGGTTTT
*
3479198 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
* * * *
3479227 GGTGCTATATTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
3479256 GGTGCTATTT
1 GGTGCTATTT
3479266 GTGTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.29, C:0.06, G:0.25, T:0.40
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCAAAAAG
Found at i:3479999 original size:24 final size:24
Alignment explanation
Indices: 3479967--3480035 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
3479957 ATAGTTTATC
*
3479967 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * *
3479991 TGATATTTGACCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
3480015 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
3480036 TTTTGTACTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:3486320 original size:17 final size:18
Alignment explanation
Indices: 3486289--3486330 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
3486279 TGACCGGTCA
3486289 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
3486307 CGACCCGA-CCGTTGACC
1 CGACCCGACCCGTTGACC
3486324 CGACCCG
1 CGACCCG
3486331 TTGATCGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.17, C:0.50, G:0.24, T:0.10
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:3486325 original size:12 final size:13
Alignment explanation
Indices: 3486290--3486334 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
3486280 GACCGGTCAC
3486290 GACCCGACCCGTT
1 GACCCGACCCGTT
3486303 GACCCGACCCGACCGTT
1 GACCCGA--C--CCGTT
3486320 GACCCGACCCGTT
1 GACCCGACCCGTT
3486333 GA
1 GA
3486335 TCGGTGCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 14 0.50
15 2 0.07
17 12 0.43
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3486398 original size:29 final size:29
Alignment explanation
Indices: 3486337--3486433 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
3486327 CCCGTTGATC
*****
3486337 GGTGCTATTTTGGGAATTAATTTGGTTTT
1 GGTGCTATTTTGGGAATTAATTTGAAAAG
*
3486366 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGGAATTAATTTGAAAAG
* * * * *
3486395 GGTGTTATATTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTTGAAAAG
3486424 GGTGCTATTT
1 GGTGCTATTT
3486434 GTGTAAAATG
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.44
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTTGAAAAG
Found at i:3487169 original size:24 final size:24
Alignment explanation
Indices: 3487137--3487205 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
3487127 ATAGTTTATC
*
3487137 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * *
3487161 TGATATTTGACCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
3487185 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
3487206 TTTTGTACTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:3487871 original size:8 final size:8
Alignment explanation
Indices: 3487857--3487898 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
3487847 GCAAAAACAT
3487857 AAAAGAAA
1 AAAAGAAA
*
3487865 AACAGAAA
1 AAAAGAAA
3487873 AAAAG---
1 AAAAGAAA
3487878 AAAAGAAA
1 AAAAGAAA
3487886 AAAAGAAA
1 AAAAGAAA
3487894 AAAAG
1 AAAAG
3487899 GATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
5 5 0.17
8 24 0.83
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:3487881 original size:21 final size:21
Alignment explanation
Indices: 3487857--3487898 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3487847 GCAAAAACAT
*
3487857 AAAAGAAAAACAGAAAAAAAG
1 AAAAGAAAAAAAGAAAAAAAG
3487878 AAAAGAAAAAAAGAAAAAAAG
1 AAAAGAAAAAAAGAAAAAAAG
3487899 GATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAAGAAAAAAAG
Found at i:3487887 original size:13 final size:13
Alignment explanation
Indices: 3487868--3487894 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3487858 AAAGAAAAAC
3487868 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
3487881 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
3487894 A
1 A
3487895 AAAGGATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:3492507 original size:3 final size:3
Alignment explanation
Indices: 3492501--3492547 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3492491 ATTAAAAATA
3492501 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3492548 ATTATTCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3492713 original size:16 final size:16
Alignment explanation
Indices: 3492663--3492713 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
3492653 TTCAGTTTGA
*
3492663 TTACTTTCGATTC-AG
1 TTACTTTTGATTCGAG
*
3492678 TTTACTTTTGGTTCGAG
1 -TTACTTTTGATTCGAG
3492695 TTACTTTTGATTCGAG
1 TTACTTTTGATTCGAG
3492711 TTA
1 TTA
3492714 ATTTCAGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 29 0.94
17 2 0.06
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.51
Consensus pattern (16 bp):
TTACTTTTGATTCGAG
Found at i:3503854 original size:21 final size:21
Alignment explanation
Indices: 3503825--3503867 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3503815 TTGATGGCGT
*
3503825 AGCAACGAATGTGAAATCTGA
1 AGCAACGAATGCGAAATCTGA
*
3503846 AGCAGCGAATGCGAAATCTGA
1 AGCAACGAATGCGAAATCTGA
3503867 A
1 A
3503868 TCTGCATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16
Consensus pattern (21 bp):
AGCAACGAATGCGAAATCTGA
Found at i:3509976 original size:11 final size:11
Alignment explanation
Indices: 3509960--3509985 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3509950 TTTTTTTTTC
3509960 AAAAAAACAAA
1 AAAAAAACAAA
3509971 AAAAAAACAAA
1 AAAAAAACAAA
3509982 AAAA
1 AAAA
3509986 GGCAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:3509995 original size:12 final size:11
Alignment explanation
Indices: 3509979--3510017 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
3509969 AAAAAAAAAC
3509979 AAAAAAAGGCA
1 AAAAAAAGGCA
3509990 AGAAAAAAGGC-
1 A-AAAAAAGGCA
*
3510001 AAAAAAAGCCA
1 AAAAAAAGGCA
3510012 AAAAAA
1 AAAAAA
3510018 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 8 0.32
11 8 0.32
12 9 0.36
ACGTcount: A:0.74, C:0.10, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAGGCA
Found at i:3510018 original size:10 final size:10
Alignment explanation
Indices: 3509959--3510024 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
3509949 ATTTTTTTTT
3509959 CAAAAAAA-C
1 CAAAAAAAGC
* **
3509968 AAAAAAAAAA
1 CAAAAAAAGC
3509978 CAAAAAAAGGC
1 CAAAAAAA-GC
* *
3509989 AAGAAAAAAGG
1 CA-AAAAAAGC
3510000 CAAAAAAAGC
1 CAAAAAAAGC
3510010 CAAAAAAAGC
1 CAAAAAAAGC
3510020 CAAAA
1 CAAAA
3510025 TTTCAAAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
9 7 0.16
10 29 0.64
11 3 0.07
12 6 0.13
ACGTcount: A:0.76, C:0.14, G:0.11, T:0.00
Consensus pattern (10 bp):
CAAAAAAAGC
Found at i:3520672 original size:24 final size:24
Alignment explanation
Indices: 3520604--3520750 Score: 102
Period size: 24 Copynumber: 5.9 Consensus size: 24
3520594 TTTAATATCA
*
3520604 TTTTAATAAAAATTATATTTATTAATAA
1 TTTTAAT-AAAATTATA-TTA-T-ATAT
*
3520632 TTTTAATAAAATAATATTATATAT
1 TTTTAATAAAATTATATTATATAT
* *
3520656 TTTTGATATAATTATATTATAATAT
1 TTTTAATAAAATTATATTAT-ATAT
* *
3520681 TTTTAAT--AA-TATATAATAAAT
1 TTTTAATAAAATTATATTATATAT
* *
3520702 TATTAATAAAATTAATTTTATATAT
1 TTTTAATAAAATT-ATATTATATAT
* *
3520727 TAATTTCATAAAAATAATATTATA
1 T--TTTAAT-AAAATTATATTATA
3520751 AAATTATTAA
Statistics
Matches: 95, Mismatches: 16, Indels: 17
0.74 0.12 0.13
Matches are distributed among these distances:
21 9 0.09
22 7 0.07
23 4 0.04
24 21 0.22
25 20 0.21
26 3 0.03
27 19 0.20
28 12 0.13
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (24 bp):
TTTTAATAAAATTATATTATATAT
Found at i:3520886 original size:40 final size:39
Alignment explanation
Indices: 3520798--3520940 Score: 136
Period size: 43 Copynumber: 3.6 Consensus size: 39
3520788 TAAAATGTAA
* * **
3520798 TATAATAT-TT-TTATTTTAATATTATATTTTTTAATATT
1 TATAATATATTATTATTTTAATA-AATAATTAATAATATT
*
3520836 T-TAATGATATTATTATTTTAATAAGTAATTAATAATATT
1 TATAAT-ATATTATTATTTTAATAAATAATTAATAATATT
3520875 TAATAATATATTATTCTTATTTTAATAAATAATTAAT-ATAATT
1 T-ATAATATATTA---TTATTTTAATAAATAATTAATAAT-ATT
3520918 TATAATA-ATT-TTATTTTAATAAA
1 TATAATATATTATTATTTTAATAAA
3520941 ATATAATAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
37 17 0.19
38 3 0.03
39 14 0.16
40 17 0.19
41 7 0.08
42 8 0.09
43 24 0.27
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (39 bp):
TATAATATATTATTATTTTAATAAATAATTAATAATATT
Found at i:3520901 original size:22 final size:22
Alignment explanation
Indices: 3520843--3520925 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
3520833 ATTTTAATGA
3520843 TATTATTATTTTAATAAGTAAT
1 TATTATTATTTTAATAAGTAAT
* *
3520865 TAATAATA-TTTAATAA-TATAT
1 TATTATTATTTTAATAAGTA-AT
* *
3520886 TATTCTTATTTTAATAAATAAT
1 TATTATTATTTTAATAAGTAAT
* *
3520908 TAATATAATTTATAATAA
1 TATTATTATTT-TAATAA
3520926 TTTTATTTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 2 0.04
21 15 0.31
22 24 0.49
23 8 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (22 bp):
TATTATTATTTTAATAAGTAAT
Found at i:3521046 original size:24 final size:25
Alignment explanation
Indices: 3521017--3521079 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 25
3521007 TAAATAATAT
3521017 TAAATAAATTATTTTAATATTCTAA
1 TAAATAAATTATTTTAATATTCTAA
* *
3521042 -AAAT-AA-TATTATTAATTTTTTAA
1 TAAATAAATTATT-TTAATATTCTAA
3521065 TAAATAATATTATTT
1 TAAATAA-ATTATTT
3521080 ATTGTATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
22 4 0.13
23 12 0.39
24 8 0.26
25 1 0.03
26 2 0.06
27 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TAAATAAATTATTTTAATATTCTAA
Found at i:3521229 original size:14 final size:14
Alignment explanation
Indices: 3521210--3521240 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3521200 AATGAATTAT
3521210 AAAATTCATTTTAC
1 AAAATTCATTTTAC
*
3521224 AAAATTCATTTTTC
1 AAAATTCATTTTAC
3521238 AAA
1 AAA
3521241 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATTCATTTTAC
Found at i:3521626 original size:31 final size:31
Alignment explanation
Indices: 3521588--3521654 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
3521578 TTTTATTAAT
*
3521588 TTTAATAATTATTTTATAACAATTCGATAAG
1 TTTAATAATTATTTTATAACAATTCGAAAAG
* * *
3521619 TTTAATAATTATTTTGTAATAATTTGAAAAG
1 TTTAATAATTATTTTATAACAATTCGAAAAG
3521650 TTTAA
1 TTTAA
3521655 CCATCAGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (31 bp):
TTTAATAATTATTTTATAACAATTCGAAAAG
Found at i:3522583 original size:32 final size:32
Alignment explanation
Indices: 3522530--3522616 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
3522520 GTTCCTTAGA
*
3522530 ACATAGGT-A-TATTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTA-TGTCCATATGTCCCAAAAG
* *
3522561 ACGTAGGTAATTCTGTCCATATGTCCCAAAAG
1 ACATAGGTAATTATGTCCATATGTCCCAAAAG
3522593 ACATAGGTAATTATGTCCATATGT
1 ACATAGGTAATTATGTCCATATGT
3522617 TCCGTAGAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 7 0.14
32 41 0.84
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (32 bp):
ACATAGGTAATTATGTCCATATGTCCCAAAAG
Found at i:3522629 original size:32 final size:32
Alignment explanation
Indices: 3522495--3522634 Score: 121
Period size: 32 Copynumber: 4.4 Consensus size: 32
3522485 ATAGGTCCTG
* *
3522495 AAGAACCTAGGTAA--ACTGTCCATATGTTCCT
1 AAGAACATAGGTAATTA-TGTCCATATGTTCCA
* *
3522526 TAGAACATAGGT-A-TATTGTCCATATGTCTCAA
1 AAGAACATAGGTAATTA-TGTCCATATGT-TCCA
* * *
3522558 AAG-ACGTAGGTAATTCTGTCCATATGTCCCA
1 AAGAACATAGGTAATTATGTCCATATGTTCCA
*
3522589 AA-AGACATAGGTAATTATGTCCATATGTTCCG
1 AAGA-ACATAGGTAATTATGTCCATATGTTCCA
*
3522621 TAGAACATAGGTAA
1 AAGAACATAGGTAA
3522635 ACCCTCGACT
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
30 1 0.01
31 33 0.38
32 51 0.59
33 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (32 bp):
AAGAACATAGGTAATTATGTCCATATGTTCCA
Found at i:3523615 original size:64 final size:63
Alignment explanation
Indices: 3523547--3523668 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 63
3523537 TGCACTATCC
* * *
3523547 ATGCATCGGTACACAAATTACATTCGATGTTTTCATTT-TAAGGGAGTGCATCGATACACTCCTT
1 ATGCATCGATACACAAATTACATTCGAT-ATTT-ATTTATAAGAGAGTGCATCGATACACTCCTT
* * * **
3523611 ATGCATCGATGCACTAATTGCATTCGATATTTATTTATTTGAGAGTGCATCGATACAC
1 ATGCATCGATACACAAATTACATTCGATATTTATTTATAAGAGAGTGCATCGATACAC
3523669 ATTGAAGATG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 4 0.08
63 21 0.43
64 24 0.49
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (63 bp):
ATGCATCGATACACAAATTACATTCGATATTTATTTATAAGAGAGTGCATCGATACACTCCTT
Found at i:3526792 original size:32 final size:32
Alignment explanation
Indices: 3526642--3526797 Score: 153
Period size: 32 Copynumber: 4.9 Consensus size: 32
3526632 ACCTCGAAAA
* * *
3526642 CTGTCCATA-GGTCCTGAAGAACCTAGGTAAGT
1 CTGTCCATATGTTCC-GAAGAACATAGGTAATT
**
3526674 -TGTCCATATGTTCCTTAGAACATAGGT-ATAT
1 CTGTCCATATGTTCCGAAGAACATAGGTAAT-T
**
3526705 -TGTCCATATGTCTCAAAAG-ACATAGGTAATT
1 CTGTCCATATGT-TCCGAAGAACATAGGTAATT
*
3526736 CTGTCCATATGTCCCGAA-ATACATAGGTAATT
1 CTGTCCATATGTTCCGAAGA-ACATAGGTAATT
*
3526768 CTGTCCATATGTTCCGTAGAACATAGGTAA
1 CTGTCCATATGTTCCGAAGAACATAGGTAA
3526798 ACCTTCGACT
Statistics
Matches: 103, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
30 1 0.01
31 42 0.41
32 59 0.57
33 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (32 bp):
CTGTCCATATGTTCCGAAGAACATAGGTAATT
Done.