Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 22 of 295
Found at i:5936685 original size:21 final size:21
Alignment explanation
Indices: 5936656--5936715 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
5936646 TATTATATAT
*
5936656 AAAACAAAAGAAAGTA-AAAGA
1 AAAAGAAAAGAAA-TAGAAAGA
5936677 AAAAGAAAA-AGAATAGAAAGA
1 AAAAGAAAAGA-AATAGAAAGA
* *
5936698 AACAGAGAAGAAAT-GAAA
1 AAAAGAAAAGAAATAGAAA
5936716 CAGGGGAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 7 0.21
21 25 0.76
22 1 0.03
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.05
Consensus pattern (21 bp):
AAAAGAAAAGAAATAGAAAGA
Found at i:5936754 original size:14 final size:14
Alignment explanation
Indices: 5936656--5936762 Score: 56
Period size: 15 Copynumber: 7.3 Consensus size: 14
5936646 TATTATATAT
*
5936656 AAAACAAAAGAAAG
1 AAAAGAAAAGAAAG
*
5936670 TAAAAGAAAA-AGA-
1 -AAAAGAAAAGAAAG
*
5936683 AAAAGAATAGAAAG
1 AAAAGAAAAGAAAG
*
5936697 AAACAGAGAAGAAATG
1 AAA-AGAAAAGAAA-G
***
5936713 AAACAGGGGAGAAAG
1 AAA-AGAAAAGAAAG
*
5936728 AAGGAGAAAAAGAAAG
1 AA-AAG-AAAAGAAAG
*
5936744 GAAAGAAAAGAAAAG
1 AAAAGAAAAG-AAAG
5936759 AAAA
1 AAAA
5936763 AGGGGAAATA
Statistics
Matches: 70, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
12 8 0.11
13 2 0.03
14 10 0.14
15 30 0.43
16 20 0.29
ACGTcount: A:0.70, C:0.03, G:0.24, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:5936764 original size:21 final size:21
Alignment explanation
Indices: 5936723--5936765 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5936713 AAACAGGGGA
* *
5936723 GAAAGAAGGAGAAAAAGAAAG
1 GAAAGAAGAAGAAAAAAAAAG
5936744 GAAAGAA-AAGAAAAGAAAAAG
1 GAAAGAAGAAGAAAA-AAAAAG
5936765 G
1 G
5936766 GGAAATAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (21 bp):
GAAAGAAGAAGAAAAAAAAAG
Found at i:5939202 original size:23 final size:21
Alignment explanation
Indices: 5939144--5939196 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
5939134 ACGGAATGCC
5939144 CACACGGGCGTGGTAAGGGGA
1 CACACGGGCGTGGTAAGGGGA
5939165 CACACGGGCGTGGTAAGGGGA
1 CACACGGGCGTGGTAAGGGGA
5939186 CACACGGGCGT
1 CACACGGGCGT
5939197 ATGGTATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.45, T:0.09
Consensus pattern (21 bp):
CACACGGGCGTGGTAAGGGGA
Found at i:5939869 original size:8 final size:8
Alignment explanation
Indices: 5939853--5939884 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
5939843 TCTTCTCTAA
*
5939853 CTTTGTTT
1 CTTTATTT
5939861 CTTTATTT
1 CTTTATTT
5939869 CTTTATTT
1 CTTTATTT
5939877 CTTTATTT
1 CTTTATTT
5939885 AAATTATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.75
Consensus pattern (8 bp):
CTTTATTT
Found at i:5940573 original size:7 final size:7
Alignment explanation
Indices: 5940561--5940593 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
5940551 CTGTTATGGC
5940561 AGTTAGT
1 AGTTAGT
5940568 AGTTAGT
1 AGTTAGT
5940575 AGTTAG-
1 AGTTAGT
5940581 AGCTTAGT
1 AG-TTAGT
5940589 AGTTA
1 AGTTA
5940594 TGGTTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 2 0.08
7 20 0.83
8 2 0.08
ACGTcount: A:0.30, C:0.03, G:0.27, T:0.39
Consensus pattern (7 bp):
AGTTAGT
Found at i:5943197 original size:3 final size:3
Alignment explanation
Indices: 5943189--5943213 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5943179 TAATAAAATC
5943189 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
5943214 TTTTTGCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:5948877 original size:20 final size:21
Alignment explanation
Indices: 5948837--5948877 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5948827 AATAATTTTT
* *
5948837 AAAATTTTAAATTATTTATAA
1 AAAATTCTAAATTATTCATAA
5948858 AAAATTCTAAATT-TTCATAA
1 AAAATTCTAAATTATTCATAA
5948878 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATTCTAAATTATTCATAA
Found at i:5951157 original size:19 final size:19
Alignment explanation
Indices: 5951129--5951172 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5951119 CTCTGCTTTT
5951129 ATTAAAAATTAGAAAA-AA
1 ATTAAAAATTAGAAAATAA
*
5951147 ATTATAAAATTATAAAATAA
1 ATTA-AAAATTAGAAAATAA
5951167 A-TAAAA
1 ATTAAAA
5951173 GCTATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 13 0.57
20 3 0.13
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
ATTAAAAATTAGAAAATAA
Found at i:5951229 original size:9 final size:9
Alignment explanation
Indices: 5951209--5951386 Score: 105
Period size: 10 Copynumber: 18.7 Consensus size: 9
5951199 TAAAAAATTC
5951209 AATTATTAAA
1 AATTA-TAAA
5951219 AATTATAAA
1 AATTATAAA
5951228 AATTATAAA
1 AATTATAAA
5951237 AATTATAAAA
1 AATTAT-AAA
5951247 AATATATTAAA
1 AAT-TA-TAAA
*
5951258 AATTGT-AA
1 AATTATAAA
*
5951266 AATTTTATAA
1 AATTATA-AA
*
5951276 AATTGTAAAA
1 AATTAT-AAA
5951286 AATTA-AAA
1 AATTATAAA
*
5951294 AATATATAGA
1 AAT-TATAAA
*
5951304 AATATAAAAA
1 AAT-TATAAA
*
5951314 AATTATATA
1 AATTATAAA
5951323 AATT-TATAA
1 AATTATA-AA
* *
5951332 AGTCATGAGAA
1 AATTAT-A-AA
5951343 AATTATACAA
1 AATTATA-AA
5951353 AATGTA-AAGA
1 AAT-TATAA-A
5951363 AA-TATAAAA
1 AATTAT-AAA
5951372 AATTATAAA
1 AATTATAAA
*
5951381 AGTTAT
1 AATTAT
5951387 CGTTCCAAAA
Statistics
Matches: 135, Mismatches: 17, Indels: 33
0.73 0.09 0.18
Matches are distributed among these distances:
8 17 0.13
9 45 0.33
10 54 0.40
11 18 0.13
12 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (9 bp):
AATTATAAA
Found at i:5951571 original size:30 final size:30
Alignment explanation
Indices: 5951508--5951575 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
5951498 TAAGAGTCAT
* * **
5951508 TAATTTTTTTATGATTTTTATAAAATTTAA
1 TAATTTTTTCACGATTTTTATAAAAAATAA
5951538 TAATTTTTTCACGATTTTTATAAAAAA-ATA
1 TAATTTTTTCACGATTTTTATAAAAAATA-A
5951568 TAATTTTT
1 TAATTTTT
5951576 AATAAGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (30 bp):
TAATTTTTTCACGATTTTTATAAAAAATAA
Found at i:5951793 original size:91 final size:91
Alignment explanation
Indices: 5951658--5951823 Score: 228
Period size: 91 Copynumber: 1.8 Consensus size: 91
5951648 TTTAAAAAAA
* *
5951658 TTTGAGGGTCTTTTTTATACATTTTGAAAGTTCAAGCACCCAATTGAGTGA-AAAAAAGAAA-GC
1 TTTGAGGGCCTTTTTTATACATTTTGAAAGTTCAAGCACCCAATTGAGT-ACAAAAAAAAAATG-
5951721 AGGGGCTTAATTTTTTTTTTTGAAGAAG
64 AGGGGCTTAATTTTTTTTTTTGAAGAAG
* * ** *
5951749 TTTGAGGGCCTTTTTTATGCATTTTGAAAGTTTAAGTGCTCAATTGAGTACAAAAAAAAAATGAG
1 TTTGAGGGCCTTTTTTATACATTTTGAAAGTTCAAGCACCCAATTGAGTACAAAAAAAAAATGAG
*
5951814 TGGCTTAATT
66 GGGCTTAATT
5951824 GCTTTTTGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
90 1 0.02
91 63 0.97
92 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (91 bp):
TTTGAGGGCCTTTTTTATACATTTTGAAAGTTCAAGCACCCAATTGAGTACAAAAAAAAAATGAG
GGGCTTAATTTTTTTTTTTGAAGAAG
Found at i:5951830 original size:91 final size:91
Alignment explanation
Indices: 5951628--5951830 Score: 225
Period size: 91 Copynumber: 2.2 Consensus size: 91
5951618 TTTTAATAAG
* * * * *
5951628 AGCAGGGGCTTAAATAG--TTTTTTAAAAAAATTTGAGGGTCTTTTTTATACATTTTGAAAGTTC
1 AGCAGGGGCTT-AATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTTATACATTTTGAAAGTTC
*
5951691 AAGCACCCAATTGAGTGAAAAAAAGAA
65 AAGCACCCAATTGAGTGAAAAAAAAAA
** * *
5951718 AGCAGGGGCTTAATTTTTTTTTTTGAAGAAGTTTGAGGGCCTTTTTTATGCATTTTGAAAGTTTA
1 AGCAGGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTTATACATTTTGAAAGTTCA
** *
5951783 AGTGCTCAATTGAGT-ACAAAAAAAAA
66 AGCACCCAATTGAGTGA-AAAAAAAAA
*
5951809 ATG-AGTGGCTTAATTGCTTTTT
1 A-GCAGGGGCTTAATTGCTTTTT
5951831 GTTAAAAAAT
Statistics
Matches: 94, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
89 3 0.03
90 12 0.13
91 78 0.83
92 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37
Consensus pattern (91 bp):
AGCAGGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTTATACATTTTGAAAGTTCA
AGCACCCAATTGAGTGAAAAAAAAAA
Found at i:5955023 original size:17 final size:20
Alignment explanation
Indices: 5955001--5955037 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
5954991 AAATGATCAT
5955001 CTCTCA-TA-TTTT-TTTTC
1 CTCTCAGTACTTTTCTTTTC
5955018 CTCTCAGTACTTTTCTTTTC
1 CTCTCAGTACTTTTCTTTTC
5955038 TATCAAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 4 0.24
20 5 0.29
ACGTcount: A:0.11, C:0.27, G:0.03, T:0.59
Consensus pattern (20 bp):
CTCTCAGTACTTTTCTTTTC
Found at i:5955438 original size:32 final size:33
Alignment explanation
Indices: 5955392--5955455 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
5955382 TTTTACTTGA
* *
5955392 TAAAGTGGAAAGAAAATTGGAATGATGAAAAAT
1 TAAAGTGGAAAGAAAATTAGAAGGATGAAAAAT
*
5955425 TAAAG-GGATAGAAAATTAGAAGGATGAAAAA
1 TAAAGTGGAAAGAAAATTAGAAGGATGAAAAA
5955456 CATAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (33 bp):
TAAAGTGGAAAGAAAATTAGAAGGATGAAAAAT
Found at i:5955455 original size:16 final size:16
Alignment explanation
Indices: 5955404--5955455 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5955394 AAGTGGAAAG
* *
5955404 AAAATTGGAATGATGA
1 AAAATTAGAAGGATGA
5955420 AAAATTA-AAGGGAT-A
1 AAAATTAGAA-GGATGA
5955435 GAAAATTAGAAGGATGA
1 -AAAATTAGAAGGATGA
5955452 AAAA
1 AAAA
5955456 CATAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 3 0.10
16 24 0.80
17 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (16 bp):
AAAATTAGAAGGATGA
Found at i:5957691 original size:16 final size:17
Alignment explanation
Indices: 5957672--5957706 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5957662 AAAAGTAAAT
*
5957672 AAAAGAAAA-ACGAGAG
1 AAAAGAAAACAAGAGAG
5957688 AAAAGAAAACAAGAGAG
1 AAAAGAAAACAAGAGAG
5957705 AA
1 AA
5957707 GTCTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.71, C:0.06, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAGAAAACAAGAGAG
Found at i:5958088 original size:30 final size:30
Alignment explanation
Indices: 5958054--5958112 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
5958044 CTTAACAAGA
5958054 AAATACCTCTAAAATAATAACAAAATTAAC
1 AAATACCTCTAAAATAATAACAAAATTAAC
*
5958084 AAATACCTTTAAAATAATAACAAAATTAA
1 AAATACCTCTAAAATAATAACAAAATTAA
5958113 TAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (30 bp):
AAATACCTCTAAAATAATAACAAAATTAAC
Found at i:5958627 original size:15 final size:17
Alignment explanation
Indices: 5958607--5958643 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5958597 AGGAAAATTA
5958607 TATTTTTC-A-TCTTTC
1 TATTTTTCTACTCTTTC
5958622 TATTTTTCTACTCTTTC
1 TATTTTTCTACTCTTTC
*
5958639 AATTT
1 TATTT
5958644 CCTATCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTTCTACTCTTTC
Found at i:5966156 original size:21 final size:21
Alignment explanation
Indices: 5966130--5966185 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
5966120 AATAGCGGTG
*
5966130 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
5966151 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
5966172 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
5966186 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:5966381 original size:29 final size:27
Alignment explanation
Indices: 5966355--5966431 Score: 118
Period size: 29 Copynumber: 2.8 Consensus size: 27
5966345 ATTCATTTAA
5966355 TAAAATACACTACATATATATATATTT
1 TAAAATACACTACATATATATATATTT
* *
5966382 TAAAATACACTACATATATTTTTTATTTT
1 TAAAATACACTACATATA-TATATA-TTT
5966411 TAAAATACACTACATATATAT
1 TAAAATACACTACATATATAT
5966432 TTTTTTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 18 0.40
28 6 0.13
29 21 0.47
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAAATACACTACATATATATATATTT
Found at i:5966391 original size:27 final size:28
Alignment explanation
Indices: 5966355--5966492 Score: 125
Period size: 33 Copynumber: 4.7 Consensus size: 28
5966345 ATTCATTTAA
5966355 TAAAATACACTACATATATATATA-TTT
1 TAAAATACACTACATATATATATATTTT
* *
5966382 TAAAATACACTACATATATTTTTTATTTT
1 TAAAATACACTACATATA-TATATATTTT
*
5966411 TAAAATACACTACATATATATTTTTTTTATTTT
1 TAAAATACACTACATATATA-----TATATTTT
* * *
5966444 TAAAATACACTACATGTATTTTTTTATTTT
1 TAAAATACACTACA--TATATATATATTTT
* *
5966474 TAAAATCCATTACATATAT
1 TAAAATACACTACATATAT
5966493 TTTTTTATTT
Statistics
Matches: 94, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
27 18 0.19
28 9 0.10
29 21 0.22
30 20 0.21
33 22 0.23
35 4 0.04
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.49
Consensus pattern (28 bp):
TAAAATACACTACATATATATATATTTT
Found at i:5966468 original size:30 final size:30
Alignment explanation
Indices: 5966355--5966509 Score: 210
Period size: 30 Copynumber: 5.2 Consensus size: 30
5966345 ATTCATTTAA
* *
5966355 TAAAATACACTACATATA--TATATA-TTT
1 TAAAATACACTACATATATTTTTTTATTTT
5966382 TAAAATACACTACATATA-TTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
5966411 TAAAATACACTACATATATATTTTTTTTATTTT
1 TAAAATACACTAC--ATATA-TTTTTTTATTTT
*
5966444 TAAAATACACTACATGTATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
* *
5966474 TAAAATCCATTACATATATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
5966504 TAAAAT
1 TAAAAT
5966510 TTTAAATACA
Statistics
Matches: 116, Mismatches: 6, Indels: 9
0.89 0.05 0.07
Matches are distributed among these distances:
27 18 0.16
28 4 0.03
29 16 0.14
30 45 0.39
31 9 0.08
33 24 0.21
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.51
Consensus pattern (30 bp):
TAAAATACACTACATATATTTTTTTATTTT
Found at i:5966649 original size:72 final size:65
Alignment explanation
Indices: 5966572--5966733 Score: 168
Period size: 67 Copynumber: 2.4 Consensus size: 65
5966562 CGTATCCTTC
*
5966572 TCCCATTTCCCATTCCCATGCAATACCCATTCCCATTTCCC-ATTCCACCGTGCCCTCCTCCCAT
1 TCCCATTTCCCATTCCCAT-C--T-CCCA-T-CCATTCCCCTATTCCACCGTGCCCTCCTCCCA-
5966636 TTCCCATT
59 TTCCCA-T
* * * * *
5966644 TCCCA-TTCCCATCTCCCCTCTTCCATCGATTCCCCTCTTCCACCGTTCCCTCCTCCCATTCCCA
1 TCCCATTTCCCAT-TCCCATCTCCCATCCATTCCCCTATTCCACCGTGCCCTCCTCCCATTCCCA
5966708 T
65 T
5966709 TCCCATTTCCCATTCCCAT-TCCCAT
1 TCCCATTTCCCATTCCCATCTCCCAT
5966734 TATCAACAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
64 5 0.06
65 11 0.14
66 20 0.25
67 21 0.27
68 3 0.04
69 1 0.01
71 8 0.10
72 10 0.13
ACGTcount: A:0.14, C:0.50, G:0.03, T:0.33
Consensus pattern (65 bp):
TCCCATTTCCCATTCCCATCTCCCATCCATTCCCCTATTCCACCGTGCCCTCCTCCCATTCCCAT
Found at i:5966663 original size:35 final size:34
Alignment explanation
Indices: 5966597--5966715 Score: 113
Period size: 35 Copynumber: 3.6 Consensus size: 34
5966587 CCATGCAATA
*
5966597 CCCATTCCCATTTCCCATTCCACCGTGCCCTCCT
1 CCCATTCCCATTTCCCATTCCACCGTCCCCTCCT
*
5966631 CCCATTTCCCATTTCCCATTCCCATC-TCCCCT-CT
1 CCCA-TTCCCATTTCCCATT-CCACCGTCCCCTCCT
* * * * *
5966665 TCCA-T-CGATTCCCCTCTTCCACCGTTCCCTCCT
1 CCCATTCCCATTTCCC-ATTCCACCGTCCCCTCCT
5966698 CCCATTCCCA-TTCCCATT
1 CCCATTCCCATTTCCCATT
5966716 TCCCATTCCC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
31 11 0.17
32 8 0.12
33 7 0.11
34 14 0.21
35 22 0.33
36 4 0.06
ACGTcount: A:0.12, C:0.52, G:0.03, T:0.33
Consensus pattern (34 bp):
CCCATTCCCATTTCCCATTCCACCGTCCCCTCCT
Found at i:5966708 original size:6 final size:6
Alignment explanation
Indices: 5966697--5966734 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
5966687 CGTTCCCTCC
5966697 TCCCAT TCCCAT TCCCATT TCCCAT TCCCAT TCCCAT T
1 TCCCAT TCCCAT TCCCA-T TCCCAT TCCCAT TCCCAT T
5966735 ATCAACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37
Consensus pattern (6 bp):
TCCCAT
Found at i:5966719 original size:19 final size:19
Alignment explanation
Indices: 5966697--5966734 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5966687 CGTTCCCTCC
5966697 TCCCATTCCCATTCCCATT
1 TCCCATTCCCATTCCCATT
5966716 TCCCATTCCCATTCCCATT
1 TCCCATTCCCATTCCCATT
5966735 ATCAACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37
Consensus pattern (19 bp):
TCCCATTCCCATTCCCATT
Found at i:5968693 original size:1 final size:1
Alignment explanation
Indices: 5968689--5968721 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
5968679 TTTTTCCCTC
*
5968689 TTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5968722 GATGGTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:5971397 original size:30 final size:30
Alignment explanation
Indices: 5971356--5971421 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
5971346 AAATTACACC
*
5971356 AACAATCACTCAACTTTGAG-AAAATAATAA
1 AACAGTCACTCAA-TTTGAGAAAAATAATAA
*
5971386 AACAGTCACTCAATTTTAGAAAAATAATAA
1 AACAGTCACTCAATTTGAGAAAAATAATAA
5971416 AACAGT
1 AACAGT
5971422 TACCCACTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.24
Consensus pattern (30 bp):
AACAGTCACTCAATTTGAGAAAAATAATAA
Found at i:5972323 original size:3 final size:3
Alignment explanation
Indices: 5972309--5972338 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5972299 GTATCTCCAT
5972309 TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5972339 ACTGCCCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:5972531 original size:29 final size:28
Alignment explanation
Indices: 5972476--5972555 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
5972466 TTGTTATTTT
* **
5972476 TTTTCTAAAGTTTAGTGATTGAGTTGTAA
1 TTTTC-AAAGTTAAGTGGCTGAGTTGTAA
* *
5972505 CTTTTCAAAGTTAAGTGGCTGATTTGTTA
1 -TTTTCAAAGTTAAGTGGCTGAGTTGTAA
5972534 TTTTACACAAAGTTAAGTGGCT
1 TTTT---CAAAGTTAAGTGGCT
5972556 AATGGTGTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
28 4 0.10
29 18 0.43
30 5 0.12
31 15 0.36
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.44
Consensus pattern (28 bp):
TTTTCAAAGTTAAGTGGCTGAGTTGTAA
Found at i:5972570 original size:31 final size:31
Alignment explanation
Indices: 5972510--5972570 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
5972500 TGTAACTTTT
* * *
5972510 CAAAGTTAAGTGGCTGATTTGTTATTTTACA
1 CAAAGTTAAGTGGCTAATGTGTTACTTTACA
5972541 CAAAGTTAAGTGGCTAATG-GTGTACTTTAC
1 CAAAGTTAAGTGGCTAATGTGT-TACTTTAC
5972571 CTTTTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (31 bp):
CAAAGTTAAGTGGCTAATGTGTTACTTTACA
Found at i:5972616 original size:20 final size:19
Alignment explanation
Indices: 5972593--5972630 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5972583 TCTTTTAACA
5972593 TTATCATATTTCTCTCAAAT
1 TTATCATA-TTCTCTCAAAT
*
5972613 TTATCTTATTCTCTCAAA
1 TTATCATATTCTCTCAAA
5972631 CACCCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATCATATTCTCTCAAAT
Found at i:5975203 original size:14 final size:14
Alignment explanation
Indices: 5975186--5975218 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5975176 TTATGATTAG
5975186 GGATTTATAGATGA
1 GGATTTATAGATGA
*
5975200 GGATTTATAGGTGA
1 GGATTTATAGATGA
5975214 GGATT
1 GGATT
5975219 AGGCCTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (14 bp):
GGATTTATAGATGA
Found at i:5984112 original size:22 final size:21
Alignment explanation
Indices: 5984069--5984109 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5984059 TTTTAGATAT
*
5984069 TTTAGAATTTTTAACAATTTG
1 TTTAGAAATTTTAACAATTTG
5984090 TTTAGAAGATTTTAA-AATTT
1 TTTAGAA-ATTTTAACAATTT
5984110 TGTACTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTAGAAATTTTAACAATTTG
Found at i:5991428 original size:20 final size:19
Alignment explanation
Indices: 5991389--5991439 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 19
5991379 TTTTTATACA
5991389 TATTTTGAATTTTAAAATT
1 TATTTTGAATTTTAAAATT
*
5991408 TATTTTGAATATTTGAAATT
1 TATTTTGAAT-TTTAAAATT
5991428 TATTTTGAATTT
1 TATTTTGAATTT
5991440 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
TATTTTGAATTTTAAAATT
Found at i:5991438 original size:11 final size:12
Alignment explanation
Indices: 5991397--5991451 Score: 57
Period size: 11 Copynumber: 5.0 Consensus size: 12
5991387 CATATTTTGA
*
5991397 ATTTTAAAATTT
1 ATTTTGAAATTT
5991409 ATTTTG-AA--T
1 ATTTTGAAATTT
5991418 A-TTTGAAATTT
1 ATTTTGAAATTT
5991429 ATTTTG-AATTT
1 ATTTTGAAATTT
*
5991440 ATTTTGTAATTT
1 ATTTTGAAATTT
5991452 TTGTTGAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
8 4 0.11
9 4 0.11
11 15 0.41
12 14 0.38
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (12 bp):
ATTTTGAAATTT
Found at i:5995351 original size:12 final size:12
Alignment explanation
Indices: 5995336--5995362 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5995326 ATTATATAAC
5995336 AAATATATTTAT
1 AAATATATTTAT
5995348 AAATATATTTAT
1 AAATATATTTAT
5995360 AAA
1 AAA
5995363 GGTTGGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATATATTTAT
Found at i:5996454 original size:17 final size:17
Alignment explanation
Indices: 5996416--5996454 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5996406 ATCTTGAATT
*
5996416 TTTTTAAAATTTCTTAA
1 TTTTTAAAATTTCTAAA
5996433 TTTTTAAAATTT-TAAA
1 TTTTTAAAATTTCTAAA
5996449 TATTTT
1 T-TTTT
5996455 TGAATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTAAAATTTCTAAA
Found at i:5996857 original size:5 final size:5
Alignment explanation
Indices: 5996847--5996871 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5996837 TATTTAATTG
5996847 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
5996872 GTTCTTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:5997919 original size:27 final size:27
Alignment explanation
Indices: 5997888--5997943 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5997878 GAGGTTGGGC
5997888 CAAGTCGGGCTAAAGAGGAACTAGAGG
1 CAAGTCGGGCTAAAGAGGAACTAGAGG
5997915 CAAGTCGGGCTAAAGAGGAACTAGAGG
1 CAAGTCGGGCTAAAGAGGAACTAGAGG
5997942 CA
1 CA
5997944 GATGAATTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.36, T:0.11
Consensus pattern (27 bp):
CAAGTCGGGCTAAAGAGGAACTAGAGG
Found at i:6006079 original size:25 final size:24
Alignment explanation
Indices: 6006030--6006082 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
6006020 AATAATACTA
*
6006030 ATAT-TACATAAAGATATACTTAT
1 ATATATACATAAAGATATACTCAT
6006053 ATATATACATTAAAGATATA-TGCAT
1 ATATATACA-TAAAGATATACT-CAT
6006078 ATATA
1 ATATA
6006083 ATAAAATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 4 0.15
24 5 0.19
25 17 0.65
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.38
Consensus pattern (24 bp):
ATATATACATAAAGATATACTCAT
Found at i:6006168 original size:18 final size:19
Alignment explanation
Indices: 6006137--6006176 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
6006127 TAAAATAGAG
* *
6006137 ATAATAATATACATAATAT
1 ATAATAATACACATAACAT
6006156 ATAA-AATACACATAACAT
1 ATAATAATACACATAACAT
6006174 ATA
1 ATA
6006177 CTTACATAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAATAATACACATAACAT
Found at i:6006559 original size:13 final size:13
Alignment explanation
Indices: 6006541--6006598 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
6006531 ATATATATAC
*
6006541 GTATATAATAAGA
1 GTATATAATAATA
*
6006554 GTATATATTAATA
1 GTATATAATAATA
6006567 -TATAATAATAATA
1 GTAT-ATAATAATA
*
6006580 GTATAATATTAATA
1 GTAT-ATAATAATA
*
6006594 ATATA
1 GTATA
6006599 AAAATAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
12 3 0.08
13 20 0.53
14 15 0.39
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (13 bp):
GTATATAATAATA
Found at i:6006594 original size:23 final size:26
Alignment explanation
Indices: 6006545--6006605 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
6006535 ATATACGTAT
6006545 ATAATAAGAGTATATATTAATATATA
1 ATAATAAGAGTATATATTAATATATA
*
6006571 ATAATAATAGTATAATATTAATAATATA
1 ATAATAAGAGTAT-ATATTAAT-ATATA
*
6006599 AAAATAA
1 ATAATAA
6006606 AAAGAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 12 0.39
27 8 0.26
28 11 0.35
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (26 bp):
ATAATAAGAGTATATATTAATATATA
Found at i:6009272 original size:21 final size:21
Alignment explanation
Indices: 6009248--6009316 Score: 120
Period size: 21 Copynumber: 3.3 Consensus size: 21
6009238 GTCGTATTTT
6009248 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTATC
6009269 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTATC
* *
6009290 AGGCACCTCGTGTGTCGTTTT
1 AGGCACCTCGTGTGTCGTATC
6009311 AGGCAC
1 AGGCAC
6009317 TTTATGTGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.14, C:0.28, G:0.29, T:0.29
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTATC
Found at i:6009324 original size:21 final size:21
Alignment explanation
Indices: 6009248--6009330 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 21
6009238 GTCGTATTTT
*
6009248 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTTTC
*
6009269 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTTTC
*
6009290 AGGCACCTCGTGTGTCGTTTT
1 AGGCACCTCGTGTGTCGTTTC
* **
6009311 AGGCACTTTATGTGTCGTTT
1 AGGCACCTCGTGTGTCGTTT
6009331 ACTGATCAGG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.13, C:0.24, G:0.28, T:0.35
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTTTC
Found at i:6009325 original size:42 final size:43
Alignment explanation
Indices: 6009222--6009328 Score: 144
Period size: 42 Copynumber: 2.5 Consensus size: 43
6009212 GGCTTTACTG
*
6009222 ATCAGGCACTTTATGTGTCGTATTTTAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGTA-TTCAGGCACCTCGTGTGTCGT
* **
6009266 ATCAGGCACCTCGTGTGTCGTA-TCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGTATTCAGGCACCTCGTGTGTCGT
* *
6009308 TTTAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
6009329 TTACTGATCA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 35 0.65
44 19 0.35
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.36
Consensus pattern (43 bp):
ATCAGGCACTTTATGTGTCGTATTCAGGCACCTCGTGTGTCGT
Found at i:6017865 original size:16 final size:16
Alignment explanation
Indices: 6017842--6017891 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
6017832 GAAATTGATC
6017842 TAAACTTAAAATAACT
1 TAAACTTAAAATAACT
* *
6017858 TGAACTTAATATTAACT
1 TAAACTTAA-AATAACT
*
6017875 CAAAC-TAAAATAACT
1 TAAACTTAAAATAACT
6017890 TA
1 TA
6017892 CTTTAAAACA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 7 0.26
16 11 0.41
17 9 0.33
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (16 bp):
TAAACTTAAAATAACT
Found at i:6020598 original size:41 final size:41
Alignment explanation
Indices: 6020541--6020621 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
6020531 ACAAAAATGA
6020541 TTGTTTTTATACTTTACCCTTTTAACTTTACCTAAATTTAT
1 TTGTTTTTATACTTTACCCTTTTAACTTTACCTAAATTTAT
6020582 TTGTTTTTATACTTTACCCTTTTAACTTTACCTAAATTTA
1 TTGTTTTTATACTTTACCCTTTTAACTTTACCTAAATTTA
6020622 GACATTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.25, C:0.17, G:0.02, T:0.56
Consensus pattern (41 bp):
TTGTTTTTATACTTTACCCTTTTAACTTTACCTAAATTTAT
Found at i:6021701 original size:13 final size:14
Alignment explanation
Indices: 6021661--6021701 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
6021651 TTAATTCAGT
6021661 TTGAAATCAAATAA
1 TTGAAATCAAATAA
6021675 TT--AATCAAATTAA
1 TTGAAATCAAA-TAA
6021688 TTGAAAT-AAATAA
1 TTGAAATCAAATAA
6021701 T
1 T
6021702 ATATATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 7 0.29
13 9 0.38
14 5 0.21
15 3 0.12
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (14 bp):
TTGAAATCAAATAA
Found at i:6032542 original size:18 final size:18
Alignment explanation
Indices: 6032521--6032558 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6032511 TTCAATGTAA
*
6032521 TTAAAT-ATGTATTTATAT
1 TTAAATAATATATTT-TAT
6032539 TTAAATAATATATTTTAT
1 TTAAATAATATATTTTAT
6032557 TT
1 TT
6032559 TATTTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTAAATAATATATTTTAT
Found at i:6032710 original size:22 final size:21
Alignment explanation
Indices: 6032666--6032719 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
6032656 TGAAAAAAAT
*
6032666 AATATTAGTATTTTAATTATA
1 AATATTAGTATTATAATTATA
6032687 AATATATAG-ATTATAATTTATA
1 AATAT-TAGTATTATAA-TTATA
6032709 AATATTTAGTA
1 AATA-TTAGTA
6032720 ATAAATGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 11 0.39
22 15 0.54
23 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (21 bp):
AATATTAGTATTATAATTATA
Found at i:6033488 original size:20 final size:20
Alignment explanation
Indices: 6033463--6033500 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6033453 TAAATTTTAA
6033463 AAAATTATAAAATTATTATT
1 AAAATTATAAAATTATTATT
* *
6033483 AAAATTATTAATTTATTA
1 AAAATTATAAAATTATTA
6033501 GAATTATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATTATAAAATTATTATT
Found at i:6033850 original size:31 final size:31
Alignment explanation
Indices: 6033782--6033850 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
6033772 TAAGAAAATT
* *
6033782 AATAGTGTAATGACTTAAATAAAAACATTTA
1 AATAGTTTAATGAATTAAATAAAAACATTTA
* * *
6033813 AATAGTTTAGTGAATTAAATAAGAACTTTTA
1 AATAGTTTAATGAATTAAATAAAAACATTTA
6033844 AATAGTT
1 AATAGTT
6033851 CAATAACCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (31 bp):
AATAGTTTAATGAATTAAATAAAAACATTTA
Found at i:6034678 original size:4 final size:4
Alignment explanation
Indices: 6034669--6034697 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
6034659 AGCAAACGTG
6034669 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
6034698 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:6041931 original size:4 final size:4
Alignment explanation
Indices: 6041922--6041950 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
6041912 AGCAAACGTG
6041922 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
6041951 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:6044301 original size:16 final size:15
Alignment explanation
Indices: 6044280--6044328 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
6044270 ATAAAAACTG
6044280 AAATTAACAAATTTAA
1 AAATTAACAAA-TTAA
*
6044296 AAATTATAAAAATT-A
1 AAATTA-ACAAATTAA
6044311 AAATTAATCAAATTAA
1 AAATTAA-CAAATTAA
6044327 AA
1 AA
6044329 TATAGATACC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 1 0.04
15 12 0.43
16 11 0.39
17 4 0.14
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATTAACAAATTAA
Found at i:6044304 original size:31 final size:31
Alignment explanation
Indices: 6044264--6044328 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
6044254 AAAAAATAAT
*
6044264 AAAAGTATAAAAACTGAAATTAA-CAAATTTA
1 AAAAGTATAAAAACTAAAATTAATCAAA-TTA
* *
6044295 AAAATTATAAAAATTAAAATTAATCAAATTA
1 AAAAGTATAAAAACTAAAATTAATCAAATTA
6044326 AAA
1 AAA
6044329 TATAGATACC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (31 bp):
AAAAGTATAAAAACTAAAATTAATCAAATTA
Found at i:6044900 original size:15 final size:15
Alignment explanation
Indices: 6044880--6044918 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
6044870 ATTTACAAAT
*
6044880 TAAAAAATAATTATA
1 TAAAAAATAATAATA
*
6044895 TTAAAAATAATAATA
1 TAAAAAATAATAATA
6044910 TAAAAAATA
1 TAAAAAATA
6044919 TTCAATAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAAATAATAATA
Found at i:6044984 original size:26 final size:28
Alignment explanation
Indices: 6044942--6045006 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
6044932 TTGTCAAAAT
*
6044942 TTAAAA-AAAATTATAAATAT-TTTTAA
1 TTAAAATAAAATTATAAATATATTATAA
*
6044968 -TAAAATAAAATTTTAAATATATTATAA
1 TTAAAATAAAATTATAAATATATTATAA
*
6044995 TTAAATTAAAAT
1 TTAAAATAAAAT
6045007 AATTTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 5 0.15
26 13 0.39
27 5 0.15
28 10 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TTAAAATAAAATTATAAATATATTATAA
Found at i:6052886 original size:3 final size:3
Alignment explanation
Indices: 6052878--6052902 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6052868 TTTAAAAATA
6052878 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
6052903 TTAACTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:6057725 original size:20 final size:19
Alignment explanation
Indices: 6057687--6057731 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
6057677 ATAAAGTTGT
* *
6057687 ATAAAAAAAATATTTAAGG
1 ATAAAAAAAAAATTAAAGG
6057706 ATAAAAAAGAAAATTAAAGG
1 ATAAAAAA-AAAATTAAAGG
*
6057726 TTAAAA
1 ATAAAA
6057732 TGTTGCTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (19 bp):
ATAAAAAAAAAATTAAAGG
Found at i:6058489 original size:15 final size:15
Alignment explanation
Indices: 6058469--6058501 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6058459 TTCAAAAAAT
6058469 TATACAGAGATTTGA
1 TATACAGAGATTTGA
6058484 TATACAGAGATTTGA
1 TATACAGAGATTTGA
6058499 TAT
1 TAT
6058502 TGCGAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (15 bp):
TATACAGAGATTTGA
Found at i:6059136 original size:27 final size:26
Alignment explanation
Indices: 6059088--6059140 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
6059078 TTTCATCTCC
**
6059088 ATCTTGATCATCATTACAATCAATCAA
1 ATCTTGATCATCACCACAATC-ATCAA
6059115 ATCTTGATCATCACCATC-ATCATCAA
1 ATCTTGATCATCACCA-CAATCATCAA
6059141 GAAATTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 17 0.74
28 1 0.04
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (26 bp):
ATCTTGATCATCACCACAATCATCAA
Found at i:6060023 original size:25 final size:25
Alignment explanation
Indices: 6059973--6060023 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
6059963 TTTAAAATGT
* * *
6059973 AAAATAATAATAATTAAAAATTAGA
1 AAAATAAAAATAATGAAAAATAAGA
6059998 AAAATAAAAAT-ATGAAAATATAAGA
1 AAAATAAAAATAATGAAAA-ATAAGA
6060023 A
1 A
6060024 TTTTTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (25 bp):
AAAATAAAAATAATGAAAAATAAGA
Found at i:6060158 original size:19 final size:19
Alignment explanation
Indices: 6060134--6060170 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6060124 CAAAAGTTTG
*
6060134 GTTTTTTTTTTCAATTTTC
1 GTTTTTTTTATCAATTTTC
6060153 GTTTTTTTTATCAATTTT
1 GTTTTTTTTATCAATTTT
6060171 AAATTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.73
Consensus pattern (19 bp):
GTTTTTTTTATCAATTTTC
Found at i:6060907 original size:25 final size:23
Alignment explanation
Indices: 6060870--6060917 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
6060860 AATTTTTTAA
* *
6060870 AAAATTTAGATTTTTTTTAAATAT
1 AAAATTTA-AATTTTTATAAATAT
6060894 AAAATTTGAAATTTTTATAAATAT
1 AAAATTT-AAATTTTTATAAATAT
6060918 TTTGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (23 bp):
AAAATTTAAATTTTTATAAATAT
Found at i:6060925 original size:19 final size:20
Alignment explanation
Indices: 6060898--6060953 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
6060888 AAATATAAAA
*
6060898 TTTGAAATTTTTATAAA-TAT
1 TTTG-AATTTTTAAAAATTAT
6060918 TTTGAA-TTTTAAAAATTAT
1 TTTGAATTTTTAAAAATTAT
6060937 TTTGAATTTTTGAAAAA
1 TTTGAATTTTT-AAAAA
6060954 AAATTGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.25
19 11 0.34
20 8 0.25
21 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTGAATTTTTAAAAATTAT
Found at i:6063738 original size:28 final size:28
Alignment explanation
Indices: 6063704--6063762 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
6063694 AATTATTTTT
*
6063704 AAATAA-TTTTAATGATTTTAAATTTTAA
1 AAATAATTTTTAA-AATTTTAAATTTTAA
6063732 AAATAATTTTTAAAATTTTAAATTTTAA
1 AAATAATTTTTAAAATTTTAAATTTTAA
6063760 AAA
1 AAA
6063763 ACTAATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AAATAATTTTTAAAATTTTAAATTTTAA
Found at i:6063741 original size:39 final size:35
Alignment explanation
Indices: 6063666--6063760 Score: 97
Period size: 35 Copynumber: 2.7 Consensus size: 35
6063656 TTTAATTAAT
* *
6063666 TTTTTAAAATTTTAAA---AAATATTTAAAAAATTA
1 TTTTTAAAATTTTAAATTTTAA-ATTTAAAAAATAA
*
6063699 TTTTTAAATAATTTTAATGATTTTAAATTTTAAAAATAA
1 TTTTT-AA-AATTTTAA--ATTTTAAATTTAAAAAATAA
6063738 TTTTTAAAATTTTAAATTTTAAA
1 TTTTTAAAATTTTAAATTTTAAA
6063761 AAACTAATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
33 5 0.10
34 2 0.04
35 16 0.31
37 9 0.17
38 2 0.04
39 16 0.31
40 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
TTTTTAAAATTTTAAATTTTAAATTTAAAAAATAA
Found at i:6066555 original size:24 final size:24
Alignment explanation
Indices: 6066524--6066572 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
6066514 ATACTTAACT
6066524 AAAACTTCAAATCATTAAAAAAGA
1 AAAACTTCAAATCATTAAAAAAGA
6066548 AAAACTTCAAATCATTAAAAAAGA
1 AAAACTTCAAATCATTAAAAAAGA
6066572 A
1 A
6066573 GTTTAAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.63, C:0.12, G:0.04, T:0.20
Consensus pattern (24 bp):
AAAACTTCAAATCATTAAAAAAGA
Found at i:6072271 original size:27 final size:27
Alignment explanation
Indices: 6072229--6072280 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
6072219 ATCTAAATCA
*
6072229 TCCAACACTTGTGTTTCGC-CACCAAAG
1 TCCAACACTTGAGTTTC-CTCACCAAAG
6072256 TCCAACACTTGAGTTTCCTCACCAA
1 TCCAACACTTGAGTTTCCTCACCAA
6072281 GGTTTAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (27 bp):
TCCAACACTTGAGTTTCCTCACCAAAG
Found at i:6078953 original size:43 final size:43
Alignment explanation
Indices: 6078900--6079007 Score: 103
Period size: 45 Copynumber: 2.4 Consensus size: 43
6078890 GCATTTCGCT
* * *
6078900 TGCTAGGCTCGAGGCCCGATA-TCAT-TTCACCGGCTTTATAGCC
1 TGCTAAGCTCGAGGCCCGATAGT-ATCTT-ACCGACGTTATAGCC
* *
6078943 TGCTAAGCTCGAAAGCCCGAATAGTATCTTACCGACGTTATAGTC
1 TGCTAAGCTCG-AGGCCCG-ATAGTATCTTACCGACGTTATAGCC
*
6078988 TGCTAAGCTCAAAGGCCCGA
1 TGCTAAGCTC-GAGGCCCGA
6079008 ATAATCAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
43 10 0.19
44 7 0.13
45 33 0.62
46 3 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (43 bp):
TGCTAAGCTCGAGGCCCGATAGTATCTTACCGACGTTATAGCC
Found at i:6079384 original size:43 final size:43
Alignment explanation
Indices: 6079336--6079492 Score: 296
Period size: 43 Copynumber: 3.7 Consensus size: 43
6079326 CCGGCATTAC
*
6079336 GCCTGCTAGGCATGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
6079379 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
6079422 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACAAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
6079465 GCCTGCTAGGCACGAAGGCCCGAATACA
1 GCCTGCTAGGCACGAAGGCCCGAATACA
6079493 ATACCAACAC
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 112 1.00
ACGTcount: A:0.31, C:0.34, G:0.25, T:0.10
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:6079551 original size:38 final size:38
Alignment explanation
Indices: 6079509--6079606 Score: 133
Period size: 38 Copynumber: 2.5 Consensus size: 38
6079499 ACACTAGGCT
*
6079509 TGCGGGATTTATCCCGGATATAATACCAGCACGAAGCC
1 TGCGGGATTTAACCCGGATATAATACCAGCACGAAGCC
**
6079547 TGCGGGATTTAACCCGGATATTTTACCAGCACGAAGCC
1 TGCGGGATTTAACCCGGATATAATACCAGCACGAAGCC
* *
6079585 TGTGGGTCTTTAAGCCCGGATA
1 TGCGGG-ATTTAA-CCCGGATA
6079607 CACATCAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
38 40 0.75
39 5 0.09
40 8 0.15
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (38 bp):
TGCGGGATTTAACCCGGATATAATACCAGCACGAAGCC
Found at i:6084731 original size:21 final size:21
Alignment explanation
Indices: 6084705--6084755 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
6084695 ATAAAAGTTA
6084705 TAAAAATTAGT-AAATTTTAAT
1 TAAAAATTAGTAAAATTTT-AT
*
6084726 TAAAAA-TATTAAAATTTTAT
1 TAAAAATTAGTAAAATTTTAT
6084746 TAAAAATTAG
1 TAAAAATTAG
6084756 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TAAAAATTAGTAAAATTTTAT
Found at i:6084781 original size:19 final size:19
Alignment explanation
Indices: 6084757--6084842 Score: 77
Period size: 19 Copynumber: 4.4 Consensus size: 19
6084747 AAAAATTAGA
*
6084757 ATAAAAAATTATAAAAACC
1 ATAAAAAATTATAAAAATC
* *
6084776 ATAAAAGAA-TAAAAAAATT
1 ATAAAA-AATTATAAAAATC
**
6084795 ATAAAATTTTATAAAAATC
1 ATAAAAAATTATAAAAATC
6084814 ATAAAAAAATTA-ATAAAATGC
1 AT-AAAAAATTATA-AAAAT-C
6084835 ATAAAAAA
1 ATAAAAAA
6084843 AACTCTTTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
19 30 0.57
20 20 0.38
21 3 0.06
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (19 bp):
ATAAAAAATTATAAAAATC
Found at i:6084800 original size:9 final size:9
Alignment explanation
Indices: 6084671--6084820 Score: 54
Period size: 9 Copynumber: 15.6 Consensus size: 9
6084661 ATGCGGCAAA
6084671 AAAAATTAT
1 AAAAATTAT
*
6084680 AATAA--AT
1 AAAAATTAT
*
6084687 AAAAATAAAT
1 AAAAAT-TAT
*
6084697 AAAAGTTAT
1 AAAAATTAT
6084706 AAAAATTAGT
1 AAAAATTA-T
**
6084716 AAATTTTAATT
1 AAAAATT-A-T
6084727 AAAAA-TATT
1 AAAAATTA-T
*
6084736 AAAATTTTATT
1 AAAA-ATTA-T
6084747 AAAAATTAGAAT
1 AAAAATT---AT
6084759 AAAAAATTAT
1 -AAAAATTAT
**
6084769 AAAAACCAT
1 AAAAATTAT
* *
6084778 AAAAGAATAA
1 AAAA-ATTAT
6084788 AAAAATTAT
1 AAAAATTAT
*
6084797 AAAATTTTAT
1 AAAA-ATTAT
*
6084807 AAAAATCAT
1 AAAAATTAT
6084816 AAAAA
1 AAAAA
6084821 AATTAATAAA
Statistics
Matches: 106, Mismatches: 22, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
7 6 0.06
9 46 0.43
10 32 0.30
11 13 0.12
12 1 0.01
13 8 0.08
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:6084831 original size:59 final size:61
Alignment explanation
Indices: 6084727--6084840 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 61
6084717 AATTTTAATT
*
6084727 AAAAATATTAAAATTTTATTAAAAATTAGAATAAAAAATTATAAAAACCATAAAAGAATAA
1 AAAAATATTAAAATTTTATTAAAAATCAGAATAAAAAATTATAAAAACCATAAAAGAATAA
* **
6084788 AAAAAT-TATAAAATTTTA-TAAAAATCA-TA-AAAAAATTAATAAAATGCATAAAA
1 AAAAATAT-TAAAATTTTATTAAAAATCAGAATAAAAAATT-ATAAAAACCATAAAA
6084841 AAAACTCTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
58 8 0.17
59 14 0.30
60 9 0.19
61 16 0.34
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.28
Consensus pattern (61 bp):
AAAAATATTAAAATTTTATTAAAAATCAGAATAAAAAATTATAAAAACCATAAAAGAATAA
Found at i:6084839 original size:30 final size:27
Alignment explanation
Indices: 6084759--6084842 Score: 87
Period size: 30 Copynumber: 2.9 Consensus size: 27
6084749 AAATTAGAAT
*
6084759 AAAAAATTATAAAAACCATAAAAGAATA
1 AAAAAATTATAAAATCCATAAAA-AATA
**
6084787 AAAAAATTATAAAATTTTATAAAAATCATA
1 AAAAAATTATAAAA-TCCATAAAAA--ATA
*
6084817 AAAAAATTAATAAAATGCATAAAAAA
1 AAAAAATT-ATAAAATCCATAAAAAA
6084843 AACTCTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
28 16 0.34
29 6 0.13
30 19 0.40
31 6 0.13
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (27 bp):
AAAAAATTATAAAATCCATAAAAAATA
Found at i:6092747 original size:15 final size:15
Alignment explanation
Indices: 6092724--6092761 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
6092714 TTTATATTAC
6092724 AAAATATTTATTATT
1 AAAATATTTATTATT
*
6092739 AATATATTTATTATT
1 AAAATATTTATTATT
6092754 AAAATATT
1 AAAATATT
6092762 AATATTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:6092871 original size:27 final size:27
Alignment explanation
Indices: 6092841--6092908 Score: 66
Period size: 30 Copynumber: 2.4 Consensus size: 27
6092831 ACAAAAATTG
*
6092841 AAATATTAAATATTTTATTAAATTAAT
1 AAATATTAAATATTTTATTAAATGAAT
* * *
6092868 AAATTTTATTAATAATTTTATTACATGACT
1 AAATATTA--AAT-ATTTTATTAAATGAAT
6092898 AAATA-TAAATA
1 AAATATTAAATA
6092909 ATTAAATATG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
26 1 0.03
27 10 0.30
29 5 0.15
30 17 0.52
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (27 bp):
AAATATTAAATATTTTATTAAATGAAT
Found at i:6092886 original size:12 final size:13
Alignment explanation
Indices: 6092862--6092890 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6092852 ATTTTATTAA
6092862 ATTAATAAATTTT
1 ATTAATAAATTTT
6092875 ATTAAT-AATTTT
1 ATTAATAAATTTT
6092887 ATTA
1 ATTA
6092891 CATGACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTAATAAATTTT
Found at i:6092901 original size:30 final size:30
Alignment explanation
Indices: 6092844--6092901 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
6092834 AAAATTGAAA
*
6092844 TATTAAATATTTTATTAAATTAATAAATTT
1 TATTAAATATTTTATTAAATGAATAAATTT
* *
6092874 TATT-AATAATTTTATTACATGACTAAAT
1 TATTAAAT-ATTTTATTAAATGAATAAAT
6092902 ATAAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (30 bp):
TATTAAATATTTTATTAAATGAATAAATTT
Found at i:6103393 original size:29 final size:30
Alignment explanation
Indices: 6103334--6103402 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 30
6103324 ATTAAATCTA
*
6103334 AAATTTTAAAATTTAAAAAGTAATAAAATT
1 AAATTTTAAAATATAAAAAGTAATAAAATT
6103364 AAATTCTTAAAA-ATAAAAA-TAA-AACAATT
1 AAATT-TTAAAATATAAAAAGTAATAA-AATT
6103393 AAATTTTAAA
1 AAATTTTAAA
6103403 TGTACGGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 7 0.19
29 12 0.33
30 11 0.31
31 6 0.17
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (30 bp):
AAATTTTAAAATATAAAAAGTAATAAAATT
Found at i:6110567 original size:13 final size:13
Alignment explanation
Indices: 6110551--6110592 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
6110541 TTTTGATTTA
6110551 AAGTTTAGGGTTC
1 AAGTTTAGGGTTC
*
6110564 AAGTTT-GAGTTTC
1 AAGTTTAG-GGTTC
*
6110577 TAGTTTAGGGTTC
1 AAGTTTAGGGTTC
6110590 AAG
1 AAG
6110593 ATTCTTGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 1 0.04
13 21 0.91
14 1 0.04
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.40
Consensus pattern (13 bp):
AAGTTTAGGGTTC
Found at i:6114961 original size:41 final size:41
Alignment explanation
Indices: 6114904--6114991 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
6114894 GCAAAAATTG
*
6114904 TAAAATACAGAGCTTTAGCGACGCTTTTGATAAAACGCAGC
1 TAAAAGACAGAGCTTTAGCGACGCTTTTGATAAAACGCAGC
* * *
6114945 TAAAAGACAGAGCTTTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAGACAGAGCTTTAGCGACGCTTTTGATAAAACGCAGC
6114986 TAAAAG
1 TAAAAG
6114992 TCATATAACT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (41 bp):
TAAAAGACAGAGCTTTAGCGACGCTTTTGATAAAACGCAGC
Found at i:6115636 original size:24 final size:24
Alignment explanation
Indices: 6115609--6115657 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
6115599 CGTATATTTA
*
6115609 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
6115633 TTAAAAGTCTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
6115657 T
1 T
6115658 GTTATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
TTAAAAGTCTATATAAAAATTAAT
Found at i:6115756 original size:7 final size:7
Alignment explanation
Indices: 6115702--6115842 Score: 52
Period size: 7 Copynumber: 19.9 Consensus size: 7
6115692 TTTTTATTAA
6115702 GGTTTAT
1 GGTTTAT
*
6115709 GGATTAT
1 GGTTTAT
*
6115716 GGATTAT
1 GGTTTAT
6115723 GGGTTTAT
1 -GGTTTAT
*
6115731 GGATTAT
1 GGTTTAT
* *
6115738 GATTTAC
1 GGTTTAT
*
6115745 AGTTTAT
1 GGTTTAT
*
6115752 GGTTTAA
1 GGTTTAT
* **
6115759 GGGTTGG
1 GGTTTAT
*
6115766 GGTTTAA
1 GGTTTAT
6115773 GGTTTA-
1 GGTTTAT
*
6115779 GGTGTTAG
1 GGT-TTAT
*
6115787 GGGTTAT
1 GGTTTAT
*
6115794 GGGTTAT
1 GGTTTAT
* *
6115801 GGGTTACG
1 GGTTTA-T
*
6115809 GGTTTAA
1 GGTTTAT
*
6115816 GGGTTAT
1 GGTTTAT
6115823 -GTTGTAT
1 GGTT-TAT
* *
6115830 GATTTAG
1 GGTTTAT
6115837 GGTTTA
1 GGTTTA
6115843 AGGGATAAAA
Statistics
Matches: 100, Mismatches: 28, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
6 5 0.05
7 80 0.80
8 15 0.15
ACGTcount: A:0.20, C:0.01, G:0.35, T:0.44
Consensus pattern (7 bp):
GGTTTAT
Found at i:6115770 original size:21 final size:22
Alignment explanation
Indices: 6115746--6115814 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 22
6115736 ATGATTTACA
6115746 GTTTATGGTTTAAGGGTT-GGG
1 GTTTATGGTTTAAGGGTTAGGG
*
6115767 GTTTAAGGTTT-AGGTGTTAGGG
1 GTTTATGGTTTAAGG-GTTAGGG
* * *
6115789 G-TTATGGGTTATGGGTTACGG
1 GTTTATGGTTTAAGGGTTAGGG
6115810 GTTTA
1 GTTTA
6115815 AGGGTTATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 3 0.08
21 27 0.69
22 9 0.23
ACGTcount: A:0.16, C:0.01, G:0.41, T:0.42
Consensus pattern (22 bp):
GTTTATGGTTTAAGGGTTAGGG
Found at i:6116216 original size:22 final size:21
Alignment explanation
Indices: 6116174--6116231 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
6116164 AATTTTTAAA
*
6116174 AAAAATTATTTAAAATTAATAT
1 AAAAATTA-TAAAAATTAATAT
6116196 AAAAGA-TATAAAAATTCAATAT
1 AAAA-ATTATAAAAATT-AATAT
6116218 AAAAATTATAAAAA
1 AAAAATTATAAAAA
6116232 AGTCAAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.25
22 23 0.72
23 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAATTATAAAAATTAATAT
Found at i:6116273 original size:40 final size:40
Alignment explanation
Indices: 6116229--6116351 Score: 167
Period size: 40 Copynumber: 3.1 Consensus size: 40
6116219 AAAATTATAA
* * *
6116229 AAAAGTCAAACATTAGCGGCGTTTATGATAAAAATGCCGC
1 AAAAGACAAACAATAGCGGCGTTTATGATAAAAACGCCGC
*
6116269 AAAAGACAAGCAATAGCGGCGTTTAT-ATAAAAACGCCGC
1 AAAAGACAAACAATAGCGGCGTTTATGATAAAAACGCCGC
* * * *
6116308 AAAAGGCAATCAATAGCAGCGTTTATGATACAAACGCCGC
1 AAAAGACAAACAATAGCGGCGTTTATGATAAAAACGCCGC
6116348 AAAA
1 AAAA
6116352 AGTAATTTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 35 0.47
40 39 0.53
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (40 bp):
AAAAGACAAACAATAGCGGCGTTTATGATAAAAACGCCGC
Found at i:6116310 original size:39 final size:40
Alignment explanation
Indices: 6116242--6116351 Score: 168
Period size: 39 Copynumber: 2.8 Consensus size: 40
6116232 AGTCAAACAT
*
6116242 TAGCGGCGTTTATGATAAAAATGCCGCAAAAGACAAGCAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
* *
6116282 TAGCGGCGTTTAT-ATAAAAACGCCGCAAAAGGCAATCAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
* *
6116321 TAGCAGCGTTTATGATACAAACGCCGCAAAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAA
6116352 AGTAATTTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.55
40 29 0.45
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (40 bp):
TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
Found at i:6116537 original size:20 final size:19
Alignment explanation
Indices: 6116516--6116553 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6116506 TATTTCTCTC
*
6116516 CCCCGATTCCCTTTTCTTT
1 CCCCAATTCCCTTTTCTTT
6116535 -CCCAATTCCCTTTTCTTT
1 CCCCAATTCCCTTTTCTTT
6116553 C
1 C
6116554 TCAGCCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.42, G:0.03, T:0.47
Consensus pattern (19 bp):
CCCCAATTCCCTTTTCTTT
Found at i:6119391 original size:33 final size:33
Alignment explanation
Indices: 6119340--6119406 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
6119330 ATCCTTTGGA
*
6119340 TCTCTTTGCTACTAGTTCCAATGCGTATCTTCT
1 TCTCATTGCTACTAGTTCCAATGCGTATCTTCT
* *
6119373 TCTCATTGCTACTGGTTCCAATGCGTATGTTCT
1 TCTCATTGCTACTAGTTCCAATGCGTATCTTCT
6119406 T
1 T
6119407 AAGTATGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.15, C:0.25, G:0.15, T:0.45
Consensus pattern (33 bp):
TCTCATTGCTACTAGTTCCAATGCGTATCTTCT
Found at i:6119932 original size:225 final size:233
Alignment explanation
Indices: 6119431--6120090 Score: 1039
Period size: 225 Copynumber: 2.8 Consensus size: 233
6119421 ATGAACTAAT
* *
6119431 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACTTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACATT
*
6119496 TTTTTAAATATTTTAAAGATTAAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 TTTTTAAATATTTTAAAGATT--CA--ATATAGGCT---AA-CTGACGGGTTGCCTTATATCGAG
*
6119561 TTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
123 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
6119626 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
188 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
*
6119672 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAGCATT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACATT
*
6119737 TTTTTAAATATTTTAAAGATTC-A-A-A-G-T-A-T-ACGGGTTGCCTTATATCGAGCTGTAACA
66 TTTTTAAATATTTTAAAGATTCAATATAGGCTAACTGACGGGTTGCCTTATATCGAGCTGTAAGA
6119794 TATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGAC
131 TATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGAC
6119859 TTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 TTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
*
6119897 TTTATTACCATGTAGCTTGCTTGTCGATTAAAATTACAACAATAGCTGACCTTCTCTCCAACATT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACATT
6119962 TTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACTTGACGGGTTGCCTTATATCGAG
66 TTTTTAAATATTTTAAAGATTC--A--ATATAGGCT---AAC-TGACGGGTTGCCTTATATCGAG
* *
6120027 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACATATGATGAATATTAAAAAATT
123 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATT
6120091 ACTATATTCA
Statistics
Matches: 392, Mismatches: 11, Indels: 32
0.90 0.03 0.07
Matches are distributed among these distances:
225 214 0.55
226 1 0.00
228 1 0.00
230 1 0.00
231 1 0.00
232 2 0.01
233 2 0.01
234 2 0.01
235 1 0.00
236 1 0.00
238 1 0.00
240 1 0.00
241 164 0.42
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (233 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACATT
TTTTTAAATATTTTAAAGATTCAATATAGGCTAACTGACGGGTTGCCTTATATCGAGCTGTAAGA
TATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGAC
TTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:6120246 original size:9 final size:9
Alignment explanation
Indices: 6120210--6120328 Score: 103
Period size: 9 Copynumber: 12.6 Consensus size: 9
6120200 ATTGATCATT
*
6120210 ACTTAAATA
1 ACTTACATA
*
6120219 AATTACATA
1 ACTTACATA
* *
6120228 ACTCATATA
1 ACTTACATA
6120237 ACTTACATA
1 ACTTACATA
*
6120246 ATTTACATAACA
1 ACTTACAT---A
6120258 ACTTACATA
1 ACTTACATA
*
6120267 ACTCACATA
1 ACTTACATA
6120276 ACTTACATA
1 ACTTACATA
*
6120285 ATTTACATA
1 ACTTACATA
*
6120294 ACTCACATA
1 ACTTACATA
*
6120303 ACGTACATAACA
1 ACTTACAT---A
6120315 ACTTACATA
1 ACTTACATA
6120324 ACTTA
1 ACTTA
6120329 ACTAATACAT
Statistics
Matches: 87, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
9 71 0.82
12 16 0.18
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:6120277 original size:39 final size:39
Alignment explanation
Indices: 6120221--6120295 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
6120211 CTTAAATAAA
*
6120221 TTACATAACTCATATAACTTACATAATTTACATAACAAC
1 TTACATAACTCACATAACTTACATAATTTACATAACAAC
6120260 TTACATAACTCACATAACTTACATAATTTACATAAC
1 TTACATAACTCACATAACTTACATAATTTACATAAC
6120296 TCACATAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (39 bp):
TTACATAACTCACATAACTTACATAATTTACATAACAAC
Found at i:6120310 original size:57 final size:57
Alignment explanation
Indices: 6120216--6120326 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
6120206 CATTACTTAA
* * **
6120216 ATAAATTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTCAC
1 ATAAATTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTCAC
* * *
6120273 ATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ATAAATTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
6120327 TAACTAATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.31
Consensus pattern (57 bp):
ATAAATTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTCAC
Found at i:6120324 original size:39 final size:37
Alignment explanation
Indices: 6120223--6120313 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 37
6120213 TAAATAAATT
* *
6120223 ACATAACTCATATAACTTACATAATTTACATAACAACTT
1 ACATAACTCACATAACTTACATAATTTACAT-A-AACTC
6120262 ACATAACTCACATAACTTACATAATTTACAT-AACTC
1 ACATAACTCACATAACTTACATAATTTACATAAACTC
6120298 ACATAACGT-ACATAAC
1 ACATAAC-TCACATAAC
6120314 AACTTACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
36 18 0.37
37 1 0.02
39 30 0.61
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (37 bp):
ACATAACTCACATAACTTACATAATTTACATAAACTC
Found at i:6123383 original size:40 final size:41
Alignment explanation
Indices: 6123328--6123430 Score: 145
Period size: 41 Copynumber: 2.5 Consensus size: 41
6123318 TACCGACGTT
* *
6123328 TTTTGTTAAAACGCCGCTAAAAA-TAGAGAAATAACGGCGC
1 TTTTGGTAAAACGCCGCTAAAAACCAGAGAAATAACGGCGC
* * *
6123368 TTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAAACCAGAGAAATAACGGCGC
*
6123409 TTTTGGTAAAACACCGCTAAAA
1 TTTTGGTAAAACGCCGCTAAAA
6123431 GTCATATAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
40 22 0.39
41 34 0.61
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (41 bp):
TTTTGGTAAAACGCCGCTAAAAACCAGAGAAATAACGGCGC
Found at i:6124009 original size:32 final size:32
Alignment explanation
Indices: 6123953--6124015 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
6123943 TGAGTTACTA
* *
6123953 TTTTAAGGTTTAGGGATTATGGTTTAAGTGTG
1 TTTTAAGGGTTAGGGATTAAGGTTTAAGTGTG
* * *
6123985 TTTTAAGGGTTGGGGTTTAAGGTTTAGGTGT
1 TTTTAAGGGTTAGGGATTAAGGTTTAAGTGT
6124016 TAGGGGTTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (32 bp):
TTTTAAGGGTTAGGGATTAAGGTTTAAGTGTG
Found at i:6124018 original size:7 final size:7
Alignment explanation
Indices: 6124008--6124038 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
6123998 GGTTTAAGGT
*
6124008 TTAGGTG
1 TTAGGGG
6124015 TTAGGGG
1 TTAGGGG
6124022 TTAGGGG
1 TTAGGGG
6124029 TTAGGGG
1 TTAGGGG
6124036 TTA
1 TTA
6124039 AGAGTTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.35
Consensus pattern (7 bp):
TTAGGGG
Found at i:6124076 original size:14 final size:14
Alignment explanation
Indices: 6124053--6124110 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
6124043 TTAAGTGTTC
6124053 ATGATTTAGGGTTT
1 ATGATTTAGGGTTT
* * *
6124067 ATGTTTTAGGATCT
1 ATGATTTAGGGTTT
* *
6124081 ATGGTTTAGGGATT
1 ATGATTTAGGGTTT
*
6124095 AGGAATTTAGGGTTT
1 ATG-ATTTAGGGTTT
6124110 A
1 A
6124111 AATTAATTAG
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
14 23 0.70
15 10 0.30
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.45
Consensus pattern (14 bp):
ATGATTTAGGGTTT
Found at i:6129334 original size:19 final size:19
Alignment explanation
Indices: 6129312--6129352 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6129302 TTTATTGATA
6129312 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
6129330 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
6129349 TTTT
1 TTTT
6129353 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:6132834 original size:33 final size:33
Alignment explanation
Indices: 6132797--6132874 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 33
6132787 AATTAATGTC
* * *
6132797 TTTGGTTGTATTTTTTATGTTAAATTTGCTGTT
1 TTTGGTTGCATTTTTTATATTAAATTTGCTGTA
* * *
6132830 TTTGGCTGCA--TTTTATATTATATTTGTTGTA
1 TTTGGTTGCATTTTTTATATTAAATTTGCTGTA
*
6132861 TTTGGTTGGATTTT
1 TTTGGTTGCATTTT
6132875 AATGTAGGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
31 25 0.71
33 10 0.29
ACGTcount: A:0.15, C:0.04, G:0.19, T:0.62
Consensus pattern (33 bp):
TTTGGTTGCATTTTTTATATTAAATTTGCTGTA
Found at i:6132855 original size:31 final size:31
Alignment explanation
Indices: 6132809--6132875 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
6132799 TGGTTGTATT
* *
6132809 TTTTATGTTAAATTTGCTGTTTTTGGCTGCA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
* * * *
6132840 TTTTATATTATATTTGTTGTATTTGGTTGGA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
6132871 TTTTA
1 TTTTA
6132876 ATGTAGGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.60
Consensus pattern (31 bp):
TTTTATATTAAATTTGCTGTATTTGGCTGCA
Found at i:6133022 original size:43 final size:43
Alignment explanation
Indices: 6132961--6133152 Score: 330
Period size: 43 Copynumber: 4.5 Consensus size: 43
6132951 GCCGCTAAAA
*
6132961 GCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCC
1 GCTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCCACAAACGCC
* * *
6133004 GCTAAAAGCCTTGACCTTTTGCGGCGTTTTTTCCACGAACGCC
1 GCTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCCACAAACGCC
*
6133047 GCTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCAACAAACGCC
1 GCTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCCACAAACGCC
6133090 GCTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCCACAAACGCC
1 GCTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCCACAAACGCC
*
6133133 GCTAAAAGCCTTAACCTTTA
1 GCTAAAAGCCTTGACCTTTA
6133153 ACGAGGTTCT
Statistics
Matches: 139, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 139 1.00
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (43 bp):
GCTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCCACAAACGCC
Found at i:6137900 original size:19 final size:19
Alignment explanation
Indices: 6137839--6137900 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
6137829 TTTTATAATT
*
6137839 TAAAATTTAATAATTAAT-
1 TAAAATTTAATAATAAATA
* *
6137857 T-AAATTTATTAAAAAATA
1 TAAAATTTAATAATAAATA
**
6137875 TTTAATTTAATAATAAATA
1 TAAAATTTAATAATAAATA
6137894 TAAAATT
1 TAAAATT
6137901 ATACACTATT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
17 13 0.38
18 2 0.06
19 19 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATTTAATAATAAATA
Found at i:6146055 original size:17 final size:18
Alignment explanation
Indices: 6146033--6146078 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
6146023 TTAGGCCCGA
6146033 TTTTAATATTAAA-TTAT
1 TTTTAATATTAAATTTAT
**
6146050 TTTTAA-AAAAAATTTAT
1 TTTTAATATTAAATTTAT
*
6146067 TTTTAATTTTAA
1 TTTTAATATTAA
6146079 GTAACTTTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
16 4 0.18
17 16 0.73
18 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATATTAAATTTAT
Found at i:6146293 original size:19 final size:20
Alignment explanation
Indices: 6146271--6146309 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
6146261 CTTATTTTTT
6146271 TATTTGTTTTT-TGTTTTAA
1 TATTTGTTTTTATGTTTTAA
6146290 TATTTGTTTTTATGTTTTAA
1 TATTTGTTTTTATGTTTTAA
6146310 ATATATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TATTTGTTTTTATGTTTTAA
Found at i:6146327 original size:25 final size:23
Alignment explanation
Indices: 6146289--6146335 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
6146279 TTTTGTTTTA
*
6146289 ATATTTGTTTTTATGTTTTAAAT
1 ATATTTGTTTTTATATTTTAAAT
6146312 ATATTTGATTTATTATATTTTAAA
1 ATATTTG-TTT-TTATATTTTAAA
6146336 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 3 0.14
25 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (23 bp):
ATATTTGTTTTTATATTTTAAAT
Found at i:6148807 original size:25 final size:23
Alignment explanation
Indices: 6148765--6148810 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
6148755 TTTTTTTTAA
*
6148765 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
6148788 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
6148811 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:6149542 original size:10 final size:10
Alignment explanation
Indices: 6149527--6149551 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6149517 TAATGAAAGT
6149527 TTAAACAAAA
1 TTAAACAAAA
6149537 TTAAACAAAA
1 TTAAACAAAA
6149547 TTAAA
1 TTAAA
6149552 GAACGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (10 bp):
TTAAACAAAA
Found at i:6150417 original size:41 final size:41
Alignment explanation
Indices: 6150345--6150427 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
6150335 TTCGGGCTCC
*
6150345 GTGCCTAGCAGGCTTTGTGCCGGTTTATTATATCAAGCTTT
1 GTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAAGCTTT
* * * *
6150386 GTGCTTAGCAGGCTTTGTGCTGGTGTGTTATATCAGGCTTT
1 GTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAAGCTTT
6150427 G
1 G
6150428 AGCGTAGTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.14, C:0.17, G:0.29, T:0.40
Consensus pattern (41 bp):
GTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAAGCTTT
Found at i:6151730 original size:20 final size:21
Alignment explanation
Indices: 6151707--6151749 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6151697 ATAAATGTGT
*
6151707 ATTTTG-ATGTTTGATGATAG
1 ATTTTGAATGCTTGATGATAG
*
6151727 ATTTTGAATGCTTGTTGATAG
1 ATTTTGAATGCTTGATGATAG
6151748 AT
1 AT
6151750 AAACAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (21 bp):
ATTTTGAATGCTTGATGATAG
Found at i:6152397 original size:48 final size:48
Alignment explanation
Indices: 6152321--6152430 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
6152311 ATACATTGAG
* * * *
6152321 TTGGCTTCGGGCCATGATATTAGCACTTCGGGTGCAAGTTATAC-TAAT
1 TTGGCTTTGGGCCACGATATTAGCACTTCGGATACAAGTTA-ACTTAAT
* * *
6152369 TTGGCTTTGGGCCACGATATTAGTACTTCGGATATAAGTTACCTTAAT
1 TTGGCTTTGGGCCACGATATTAGCACTTCGGATACAAGTTAACTTAAT
*
6152417 TTGGCTTTGAGCCA
1 TTGGCTTTGGGCCA
6152431 TGGTATAGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (48 bp):
TTGGCTTTGGGCCACGATATTAGCACTTCGGATACAAGTTAACTTAAT
Found at i:6154424 original size:26 final size:26
Alignment explanation
Indices: 6154393--6154500 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
6154383 TGAAATGCCC
*
6154393 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
6154419 ATCATGGAGCATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
6154445 ATCATGGAATATTTACTTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
6154471 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
6154497 ATCA
1 ATCA
6154501 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:6155146 original size:33 final size:33
Alignment explanation
Indices: 6155109--6155172 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
6155099 AAATATATGC
6155109 CTAATGATACTATATTGTGTGCCATATGAGTGT
1 CTAATGATACTATATTGTGTGCCATATGAGTGT
6155142 CTAATGATACTATATTGTGTGCCATATGAGT
1 CTAATGATACTATATTGTGTGCCATATGAGT
6155173 TGTGTAGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.39
Consensus pattern (33 bp):
CTAATGATACTATATTGTGTGCCATATGAGTGT
Done.