Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014197.1 Kokia drynarioides strain JFW-HI SEQ_129230, 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: 282627
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:186118 original size:14 final size:14
Alignment explanation
Indices: 186080--186154 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 14
186070 AGTGTTTCAT
* *
186080 GTTTAAGGTTTAAG
1 GTTTAAAGTTTAGG
* *
186094 GTTTCATGTTTAGG
1 GTTTAAAGTTTAGG
*
186108 GTTTAAAGTTTTA-T
1 GTTTAAAG-TTTAGG
**
186122 GTTTAGGGTTTAGG
1 GTTTAAAGTTTAGG
* *
186136 GTTTAGAGTTTAGA
1 GTTTAAAGTTTAGG
186150 GTTTA
1 GTTTA
186155 TGGTTTAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
13 4 0.08
14 40 0.83
15 4 0.08
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.48
Consensus pattern (14 bp):
GTTTAAAGTTTAGG
Found at i:186132 original size:7 final size:7
Alignment explanation
Indices: 186122--186161 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
186112 AAAGTTTTAT
186122 GTTTAGG
1 GTTTAGG
186129 GTTTAGG
1 GTTTAGG
*
186136 GTTTAGA
1 GTTTAGG
*
186143 GTTTAGA
1 GTTTAGG
*
186150 GTTTATG
1 GTTTAGG
186157 GTTTA
1 GTTTA
186162 AAATCGAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:186139 original size:21 final size:21
Alignment explanation
Indices: 186065--186139 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
186055 CATCATATAT
*
186065 GGTTT-AGTGTTTCATGTTTAA
1 GGTTTAAG-GTTTCATGTTTAG
186086 GGTTTAAGGTTTCATGTTTAG
1 GGTTTAAGGTTTCATGTTTAG
* *
186107 GGTTTAAAGTTTTATGTTTAG
1 GGTTTAAGGTTTCATGTTTAG
*
186128 GGTTTAGGGTTT
1 GGTTTAAGGTTT
186140 AGAGTTTAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 46 0.96
22 2 0.04
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.51
Consensus pattern (21 bp):
GGTTTAAGGTTTCATGTTTAG
Found at i:186146 original size:21 final size:21
Alignment explanation
Indices: 186122--186161 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
186112 AAAGTTTTAT
*
186122 GTTTAGGGTTTAGGGTTTAGA
1 GTTTAGAGTTTAGGGTTTAGA
*
186143 GTTTAGAGTTTATGGTTTA
1 GTTTAGAGTTTAGGGTTTA
186162 AAATCGAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (21 bp):
GTTTAGAGTTTAGGGTTTAGA
Found at i:187466 original size:16 final size:16
Alignment explanation
Indices: 187436--187475 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
187426 TTGGAATTGG
187436 ATTTTTT-ATAAAAAT
1 ATTTTTTGATAAAAAT
*
187451 ATTTTTTGATAGAAAT
1 ATTTTTTGATAAAAAT
*
187467 TTTTTTTGA
1 ATTTTTTGA
187476 ACTAATTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
ATTTTTTGATAAAAAT
Found at i:194859 original size:48 final size:48
Alignment explanation
Indices: 194788--194896 Score: 159
Period size: 48 Copynumber: 2.3 Consensus size: 48
194778 AAGATTAGCT
194788 GAAGTTAATAAAAAGAAAATTGGGTTT-GTCATACAATAACAATGGGCA
1 GAAGTTAATAAAAAGAAAATTGGGTTTAG-CATACAATAACAATGGGCA
* * * *
194836 GAAGTTAATAAAATGAAAATTGGGTTTAGCATACAGTAACAGTGGGCC
1 GAAGTTAATAAAAAGAAAATTGGGTTTAGCATACAATAACAATGGGCA
194884 GAA-TTAATAAAAA
1 GAAGTTAATAAAAA
194897 TCCAAATTGC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
47 9 0.16
48 45 0.82
49 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (48 bp):
GAAGTTAATAAAAAGAAAATTGGGTTTAGCATACAATAACAATGGGCA
Found at i:194915 original size:48 final size:48
Alignment explanation
Indices: 194817--194929 Score: 120
Period size: 48 Copynumber: 2.4 Consensus size: 48
194807 TTGGGTTTGT
* * ** *
194817 CATACAATAACAATGGGCAGAAGTTAATAAAATGAAAATTGGGTTTAG
1 CATACAATAACAGTGGGCAGAAGTTAATAAAATCAAAATTGCATTAAG
* * *
194865 CATACAGTAACAGTGGGCCGAA-TTAATAAAAATCCAAATTGCATTAAG
1 CATACAATAACAGTGGGCAGAAGTTAAT-AAAATCAAAATTGCATTAAG
* *
194913 CATGCAACAACAGTGGG
1 CATACAATAACAGTGGG
194930 TAAGAATTAG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
47 5 0.09
48 48 0.91
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (48 bp):
CATACAATAACAGTGGGCAGAAGTTAATAAAATCAAAATTGCATTAAG
Found at i:198427 original size:18 final size:18
Alignment explanation
Indices: 198404--198440 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
198394 TTACGTACGC
198404 ATTCTAATCTTGTGTAGT
1 ATTCTAATCTTGTGTAGT
198422 ATTCTAATCTTGTGTAGT
1 ATTCTAATCTTGTGTAGT
198440 A
1 A
198441 GTTTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (18 bp):
ATTCTAATCTTGTGTAGT
Found at i:202230 original size:3 final size:3
Alignment explanation
Indices: 202216--202263 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
202206 GGCCCTTGAT
* *
202216 TTA TTA TCA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
202264 GAGTTTCATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:202590 original size:22 final size:20
Alignment explanation
Indices: 202562--202605 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
202552 TCCTTTCCAC
202562 TTACAAAAATAAAGGTTTTTTT
1 TTAC-AAAA-AAAGGTTTTTTT
*
202584 TTACAAAAAACGGTTTTTTT
1 TTACAAAAAAAGGTTTTTTT
202604 TT
1 TT
202606 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 4 0.19
22 4 0.19
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (20 bp):
TTACAAAAAAAGGTTTTTTT
Found at i:202746 original size:51 final size:49
Alignment explanation
Indices: 202679--203058 Score: 176
Period size: 51 Copynumber: 7.7 Consensus size: 49
202669 AGTGATTTTC
* *
202679 TTTAAAAAAAAGAGTTTATATTTTTACAAGTAAAATTCTGTTTTTTAGTTAT
1 TTTAAAGAAAA-AGTTTAAATTTTTA-AA-TAAAATTCTGTTTTTTAGTTAT
* * **
202731 TTTAAAGAAAAAGTTTAAATTTTTAAACAAAATTTTGATTTTTTTAACTAT
1 TTTAAAGAAAAAGTTTAAATTTTTAAATAAAATTCTG--TTTTTTAGTTAT
* * * * ** *
202782 TTCGAAA-TAAAATTTTAGATTTTTAAAT-AAATAGTG-ATTTTA--T-T
1 TT-TAAAGAAAAAGTTTAAATTTTTAAATAAAATTCTGTTTTTTAGTTAT
** * * *
202826 TAAAAAGAGAAAGTTTATATTTTTAAATATAAAAATCTGTTTTTTAGTTAT
1 TTTAAAGAAAAAGTTTAAATTTTT-AA-ATAAAATTCTGTTTTTTAGTTAT
* * * **
202877 TTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTTTAACT
1 TTTAAAGAAAAAGTTTAAATTTTTAAATAAAATTCTG-TTTTTTAGTT-A-T
* * * * * ** *
202929 ATTTCGAAA-TAAAAGTTTGAATTTTTAAGT-AAAGT-AGTGATTT--TCA-
1 -TTT--AAAGAAAAAGTTTAAATTTTTAAATAAAATTCTGTTTTTTAGTTAT
* * * * *
202975 -TTAAA-AAAAAGTTTAGATTTTTAAAAAATAAAAATATATTTTTTAGTGAT
1 TTTAAAGAAAAAGTTTAAATTTTT---AAATAAAATTCTGTTTTTTAGTTAT
*
203025 TTTAAAGAAAAAGTTTAAATTTTTAAACAAAATT
1 TTTAAAGAAAAAGTTTAAATTTTTAAATAAAATT
203059 TTAATTTTTC
Statistics
Matches: 244, Mismatches: 57, Indels: 57
0.68 0.16 0.16
Matches are distributed among these distances:
42 17 0.07
43 3 0.01
44 17 0.07
45 6 0.02
46 6 0.02
47 14 0.06
48 6 0.02
49 26 0.11
50 19 0.08
51 73 0.30
52 31 0.13
53 6 0.02
54 17 0.07
55 3 0.01
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (49 bp):
TTTAAAGAAAAAGTTTAAATTTTTAAATAAAATTCTGTTTTTTAGTTAT
Found at i:202805 original size:146 final size:144
Alignment explanation
Indices: 202619--203117 Score: 673
Period size: 146 Copynumber: 3.4 Consensus size: 144
202609 AAAAATAGCA
* * *
202619 TGATTTTTTTAAATAATTTCAAAATAAAAATTTTAATTTTTAAGAAAAATAGTGATTTTCTTTAA
1 TGATTTTTTTAACT-ATTTCGAAATAAAAATTTTGATTTTTAAGAAAAATAGTGATTTTCTTTAA
* *
202684 AAAAAAGAGTTTATATTTTTACAAGTAAAATTCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAA
65 AAAAAA-AGTTTATATTTTTA-AAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAA
202749 ATTTTTAAACAAAATTT
128 ATTTTTAAACAAAATTT
* *
202766 TGATTTTTTTAACTATTTCGAAAT-AAAATTTTAGATTTTTAA-ATAAATAGTGATTTTATTTAA
1 TGATTTTTTTAACTATTTCGAAATAAAAATTTT-GATTTTTAAGAAAAATAGTGATTTTCTTTAA
202829 AAAGAGAAAGTTTATATTTTTAAATATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTA
65 AAA-A-AAAGTTTATATTTTTAAA-ATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTA
*
202894 AATTTTTAAACAAAGTTT
127 AATTTTTAAACAAAATTT
* * * *
202912 TGATTTTTTTTTTAACTATTTCGAAAT-AAAAGTTTGAATTTTTAAGTAAAGTAGTGATTTTCAT
1 TGA---TTTTTTTAACTATTTCGAAATAAAAATTTTG-ATTTTTAAGAAAAATAGTGATTTTCTT
* * * *
202976 T-AAAAAAAAGTTTAGATTTTTAAAAAATAAAAATATATTTTTTAGTGATTTTAAAGAAAAAGTT
62 TAAAAAAAAAGTTTATATTTTT--AAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTT
203040 TAAATTTTTAAACAAAATTT
125 TAAATTTTTAAACAAAATTT
* * * *
203060 TAATTTTTCTAACTATTTCGAAATAAAAATTTTGATTTTGAAGTAAAATAGTGATTTT
1 TGATTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGAAAAATAGTGATTTT
203118 GTTTTAATCA
Statistics
Matches: 316, Mismatches: 24, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
145 74 0.23
146 98 0.31
147 29 0.09
148 58 0.18
149 43 0.14
150 14 0.04
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (144 bp):
TGATTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGAAAAATAGTGATTTTCTTTAAA
AAAAAAGTTTATATTTTTAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATT
TTTAAACAAAATTT
Found at i:204839 original size:23 final size:20
Alignment explanation
Indices: 204813--204862 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
204803 TTTTTTTTAG
204813 TATTTGTGCATATTAGATTTATT
1 TATTTGTGC--ATTA-ATTTATT
*
204836 TATTCGTGCATTAATTTATT
1 TATTTGTGCATTAATTTATT
*
204856 TAATTGT
1 TATTTGT
204863 CTAATGTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 4 0.17
23 8 0.33
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (20 bp):
TATTTGTGCATTAATTTATT
Found at i:216439 original size:42 final size:42
Alignment explanation
Indices: 216373--216782 Score: 364
Period size: 42 Copynumber: 10.3 Consensus size: 42
216363 AAGGAAAGAA
* *
216373 TTCATTGCATTTAGAGGTCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
216415 TTCATTGCATTTAAAGGCCCAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * *
216457 TTCATTACATTTAAAGACTCAGGTGTGGAGGTCTATATACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
216499 TTCATTGCATTTAGAGGCTCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
216541 TTCATCGCATTTAGAGGCCCATGTGTGGAGG-----TT-C--
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
216575 ATC--T-CATTTAGAGGCCTAGGAGTGGAGGT-C----A---
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
216606 -TC--T-CATTTAGAGGCCTAGGAGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
216644 TTCATCGCATTTAGAGACCTAGGTGTGAAGTTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** * * * *
216686 TTCATCCCATTTAGAGGCCCAAGTATGGAAG-CTCATTTACTG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
*
216728 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
216770 TTCATTGCATTTA
1 TTCATTGCATTTA
216783 TTTCTTCATT
Statistics
Matches: 306, Mismatches: 45, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
30 28 0.09
31 22 0.07
34 2 0.01
35 1 0.00
36 1 0.00
37 2 0.01
39 2 0.01
41 1 0.00
42 246 0.80
43 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:216609 original size:30 final size:30
Alignment explanation
Indices: 216542--216634 Score: 141
Period size: 30 Copynumber: 3.1 Consensus size: 30
216532 CATTTACTTT
* * * *
216542 TCATCGCATTTAGAGGCCCATGTGTGGAGG
1 TCATCTCATTTAGAGGCCTAGGAGTGGAGG
216572 TTCATCTCATTTAGAGGCCTAGGAGTGGAGG
1 -TCATCTCATTTAGAGGCCTAGGAGTGGAGG
216603 TCATCTCATTTAGAGGCCTAGGAGTGGAGG
1 TCATCTCATTTAGAGGCCTAGGAGTGGAGG
216633 TC
1 TC
216635 CATTTACTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 32 0.55
31 26 0.45
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (30 bp):
TCATCTCATTTAGAGGCCTAGGAGTGGAGG
Found at i:216757 original size:187 final size:187
Alignment explanation
Indices: 216422--216759 Score: 464
Period size: 187 Copynumber: 1.8 Consensus size: 187
216412 CTTTTCATTG
* * *
216422 CATTTAAAGGCCCAGGTGTAGAGGTCCATTTACTTTTCATTACATTTAAAGACTCAGGTGTGGAG
1 CATTTAAAGGCCCAGGAGTAGAGGTCCATTTACTTTTCATCACATTTAAAGACTCAGGTGTGAAG
* ** * * * *
216487 GTCTATATACTTTTCATTGCATTTAGAGGCTCAAGTGTGGAGGTCCATTTACTTTTCATCGCATT
66 GTCCATATACTTTTCATCCCATTTAGAGGCCCAAGTATGGAGCTCCATTTACTGTTCATCGCATT
*
216552 TAGAGGCCCATGTGTGGAGGTTCATCTCATTTAGAGGCCTAGGAGTGGAGGTCATCT
131 TAGAGGCCCAGGTGTGGAGGTTCATCTCATTTAGAGGCCTAGGAGTGGAGGTCATCT
* * * * *
216609 CATTTAGAGGCCTAGGAGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGAC-CTAGGTGTGAA
1 CATTTAAAGGCCCAGGAGTAGAGGTCCATTTACTTTTCATCACATTTAAAGACTC-AGGTGTGAA
* * *
216673 GTTCCATTTACTTTTCATCCCATTTAGAGGCCCAAGTATGGAAGCT-CATTTACTGTTCATTGCA
65 GGTCCATATACTTTTCATCCCATTTAGAGGCCCAAGTATGG-AGCTCCATTTACTGTTCATCGCA
*
216737 TTTAGAGGCCTAGGTGTGGAGGT
129 TTTAGAGGCCCAGGTGTGGAGGT
216760 CCATTTACTT
Statistics
Matches: 129, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
186 1 0.01
187 125 0.97
188 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (187 bp):
CATTTAAAGGCCCAGGAGTAGAGGTCCATTTACTTTTCATCACATTTAAAGACTCAGGTGTGAAG
GTCCATATACTTTTCATCCCATTTAGAGGCCCAAGTATGGAGCTCCATTTACTGTTCATCGCATT
TAGAGGCCCAGGTGTGGAGGTTCATCTCATTTAGAGGCCTAGGAGTGGAGGTCATCT
Found at i:216782 original size:16 final size:17
Alignment explanation
Indices: 216761--216793 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
216751 TGTGGAGGTC
216761 CATTTACTT-TTCATTG
1 CATTTACTTCTTCATTG
*
216777 CATTTATTTCTTCATTG
1 CATTTACTTCTTCATTG
216794 TATATGAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.58
Consensus pattern (17 bp):
CATTTACTTCTTCATTG
Found at i:217230 original size:3 final size:3
Alignment explanation
Indices: 217222--217251 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
217212 AAGGGCCCAA
217222 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
217252 TTAGGGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:218084 original size:146 final size:147
Alignment explanation
Indices: 217678--218329 Score: 856
Period size: 146 Copynumber: 4.4 Consensus size: 147
217668 GATTTTGGAA
* * * *
217678 AAAGTATTGA-TTTTTTTAAATAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATT
1 AAAGTTTTGATTTTTTTTAACT-ATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGAAT
* * * * *
217742 TTCTTTAAAAAAGAGAAAGTTTATATTTTTAAATATTAAAATCTGTTTTTTAGTTATTTTAAAGA
65 TTCTTTTAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATTTATTTTTTAG-TATTTTAAA-A
217807 AAAAGTTTAAATTTTTAAAC
128 AAAAGTTTAAATTTTTAAAC
* * *
217827 AAATTTTTTATTTTTTTTAACTATTTCGAAATAAAAG-TTTGAATTTGTAAGTAAAATAGT-AAT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTTG-ATTTTTAAGTAAAATAGTGAAT
* *
217890 TT-TTTTAAAAAGAGACAGTTTATA-TTTTAAAAATAAAAATATATTTTTTAGTATTTTAAAGAA
65 TTCTTTTAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATTTATTTTTTAGTATTTTAAA-AA
*
217953 AAAGTTTAAA-TTTTAAAT
129 AAAGTTTAAATTTTTAAAC
*
217971 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTTGAGTTTTAAGTAAAATAGTGAATT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGAATT
* *
218036 TCTTTTAAAAAGAGAAAGTTTATATTTTTAAAAATAAAATTTTATTTTTTATTTATTTT--AAAA
66 TCTTTTAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATTTATTTTTTA-GTATTTTAAAAAA
*
218099 AAGTTTAAATTTTTAATC
130 AAGTTTAAATTTTTAAAC
* * * *
218117 AAAGTGTTGATTTTTTTTAACTATTTCGAAATAAAAG-TTTGAATTTTTAAGTAAAGTAATGATT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTTG-ATTTTTAAGTAAAATAGTGAAT
* * *
218181 TTC-ATTAAAAAGGAAAGAAATTTTAGATTTTTAAAAAATAAAAATTTATTTTTTAGTGATTTTA
65 TTCTTTTAAAAA-G--AGAAAGTTTATATTTTT-AAAAATAAAAATTTATTTTTTAGT-ATTTTA
218245 AAAAAAAGTTTAAATTTTTAAAC
125 AAAAAAAGTTTAAATTTTTAAAC
* * * *
218268 AAAATTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTTTATTTTGAAGTAAAGTAGTGA
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGA
218330 TTTTGTTTGA
Statistics
Matches: 446, Mismatches: 40, Indels: 32
0.86 0.08 0.06
Matches are distributed among these distances:
144 58 0.13
145 54 0.12
146 109 0.24
147 44 0.10
148 30 0.07
149 64 0.14
150 10 0.02
151 74 0.17
152 3 0.01
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.46
Consensus pattern (147 bp):
AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGAATT
TCTTTTAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATTTATTTTTTAGTATTTTAAAAAAA
AGTTTAAATTTTTAAAC
Found at i:218085 original size:22 final size:23
Alignment explanation
Indices: 218033--218085 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
218023 AAAATAGTGA
218033 ATTTCTTTTAAAAAGAGAAAGTTT
1 ATTT-TTTTAAAAAGAGAAAGTTT
* * *
218057 ATATTTTTAAAAATA-AAATTTT
1 ATTTTTTTAAAAAGAGAAAGTTT
218079 ATTTTTT
1 ATTTTTT
218086 ATTTATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 12 0.48
23 10 0.40
24 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (23 bp):
ATTTTTTTAAAAAGAGAAAGTTT
Found at i:218086 original size:21 final size:23
Alignment explanation
Indices: 218038--218086 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
218028 AGTGAATTTC
218038 TTTTAAAAAGAGAAAGTTTATAT
1 TTTTAAAAAGAGAAAGTTTATAT
* *
218061 TTTTAAAAATA-AAATTTTAT-T
1 TTTTAAAAAGAGAAAGTTTATAT
218082 TTTTA
1 TTTTA
218087 TTTATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.25
22 8 0.33
23 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (23 bp):
TTTTAAAAAGAGAAAGTTTATAT
Found at i:219592 original size:73 final size:72
Alignment explanation
Indices: 219515--219682 Score: 185
Period size: 73 Copynumber: 2.3 Consensus size: 72
219505 GATTTCTTAA
* * *
219515 AACAGTATATTCACACGGTCTGGCACACGCTCGTGTGCCCAGG-CAATGTAACTCTCTGTTTTTG
1 AACAGTATACTCACACGGTCTGGCACACGCTCGTGTACCCAGGTC-ATGTAACTCACTGTTTTTG
*
219579 ATTTCATCC
65 AATTC-TCC
* * * * * *
219588 AACAGTATGCCCATACGGTTTGGCACACGCTCGTGTATCCAGGTCGTGTAACTCACTGTTTTTGA
1 AACAGTATACTCACACGGTCTGGCACACGCTCGTGTACCCAGGTCATGTAACTCACTGTTTTTGA
**
219653 ATTCTTG
66 ATTCTCC
*
219660 AGACAGTATAGTCACACGGTCTG
1 A-ACAGTATACTCACACGGTCTG
219683 ACTCACGACC
Statistics
Matches: 76, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
72 2 0.03
73 73 0.96
74 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (72 bp):
AACAGTATACTCACACGGTCTGGCACACGCTCGTGTACCCAGGTCATGTAACTCACTGTTTTTGA
ATTCTCC
Found at i:223397 original size:2 final size:2
Alignment explanation
Indices: 223390--223419 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
223380 GAAAAGGTAA
223390 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
223420 GGGGAGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:223786 original size:15 final size:15
Alignment explanation
Indices: 223761--223810 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
223751 AAATTTTAAC
223761 ATTTTTCTAATATTTA
1 ATTTTT-TAATATTTA
**
223777 ATTTTTTAATAACT-
1 ATTTTTTAATATTTA
*
223791 ATTTTTTAACATTTA
1 ATTTTTTAATATTTA
223806 ATTTT
1 ATTTT
223811 GAGTAAACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 11 0.39
15 11 0.39
16 6 0.21
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTTAATATTTA
Found at i:224595 original size:17 final size:17
Alignment explanation
Indices: 224573--224637 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
224563 CAAACTCATT
224573 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
*
224590 TTAAATTTGTTTTCAA-A
1 TTAAATTTATTTT-AAGA
* *
224607 TTTAAATTTAATTTAAGT
1 -TTAAATTTATTTTAAGA
224625 TTAAATTTATTTT
1 TTAAATTTATTTT
224638 TAAACTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 27 0.68
18 13 0.32
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:224611 original size:35 final size:35
Alignment explanation
Indices: 224572--224653 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
224562 CCAAACTCAT
*
224572 TTTAAATTTATTTTAAGATTAAATTTGTTTTCAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTCAAA
* * *
224607 TTTAAATTTAATTTAAGTTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTCAAA
* *
224642 CTTAAAATTATT
1 TTTAAATTTATT
224654 ATAAATTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAATTTATTTTCAAA
Found at i:224663 original size:17 final size:16
Alignment explanation
Indices: 224604--224666 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
224594 ATTTGTTTTC
*
224604 AAATTTAAATTTAATTT
1 AAATTTAAAATT-ATTT
* *
224621 AAGTTTAAATTTATTTTT
1 AAATTTAAAATTA--TTT
*
224639 AAACTTAAAATTATTAT
1 AAATTTAAAATTATT-T
224656 AAATTTAAAAT
1 AAATTTAAAAT
224667 AAATAAAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 3 0.08
17 22 0.58
18 13 0.34
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
AAATTTAAAATTATTT
Found at i:224663 original size:35 final size:35
Alignment explanation
Indices: 224590--224664 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
224580 TATTTTAAGA
* * * *
224590 TTAAATTTGTTTTCAAATTTAAATTTAATTTAAGT
1 TTAAATTTATTTTCAAACTTAAAATTAATTTAAAT
*
224625 TTAAATTTATTTTTAAACTTAAAATT-ATTATAAAT
1 TTAAATTTATTTTCAAACTTAAAATTAATT-TAAAT
224660 TTAAA
1 TTAAA
224665 ATAAATAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (35 bp):
TTAAATTTATTTTCAAACTTAAAATTAATTTAAAT
Found at i:226537 original size:29 final size:29
Alignment explanation
Indices: 226486--226774 Score: 198
Period size: 29 Copynumber: 9.8 Consensus size: 29
226476 CTGGAGGTCA
*
226486 CTAAACTGTCC-AAAATTATATTTTGACCC
1 CTAAACT-TCCAAAAATTACATTTTGACCC
* *
226515 CTAAACTTCCAAAATTTACATTTTCACCC
1 CTAAACTTCCAAAAATTACATTTTGACCC
* * *
226544 CTGAACTTCCAAAAATTCCATTTTTTGACAC
1 CTAAACTTCCAAAAATTACA--TTTTGACCC
* * *
226575 CGAAACTTCCAAAAAATACATTTTTA-CC
1 CTAAACTTCCAAAAATTACATTTTGACCC
* *
226603 CTCGAACTTCCAAAAATTCCATTTTGA-CC
1 CT-AAACTTCCAAAAATTACATTTTGACCC
* *
226632 TTAAAACTTCCAAAAATTACATTTTTACCTC
1 CT-AAACTTCCAAAAATTACATTTTGACC-C
* * * *
226663 C-GAACTTTCAAAAATCT-CGATTTTAACCA
1 CTAAACTTCCAAAAAT-TAC-ATTTTGACCC
* **
226692 CGAAAC-TCTTGAAAATTACCATTTT-A-CC
1 CTAAACTTC-CAAAAATTA-CATTTTGACCC
* *
226720 CTAAACTTCCAAAAATTCCACTTTTGACCT
1 CTAAACTTCCAAAAATTACA-TTTTGACCC
* *
226750 CGAAACTTTCAAAAATTACCATTTT
1 CTAAACTTCCAAAAATTA-CATTTT
226775 TCCCCCGGAT
Statistics
Matches: 201, Mismatches: 42, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
27 2 0.01
28 21 0.10
29 108 0.54
30 43 0.21
31 27 0.13
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
CTAAACTTCCAAAAATTACATTTTGACCC
Found at i:226567 original size:58 final size:57
Alignment explanation
Indices: 226505--226897 Score: 323
Period size: 58 Copynumber: 6.7 Consensus size: 57
226495 CCAAAATTAT
* *
226505 ATTTTGACCCCTAAACTTCCAAAATTTA-CATTTTCACCCCTGAACTTCCAAAAATTCC
1 ATTTTGACCCCGAAACTTCCAAAAATTACCATTTT-ACCCC-GAACTTCCAAAAATTCC
* *
226563 ATTTTTTGACACCGAAACTTCCAAAAAATA-CATTTTTACCCTCGAACTTCCAAAAATTCC
1 A--TTTTGACCCCGAAACTTCCAAAAATTACCA-TTTTACCC-CGAACTTCCAAAAATTCC
*** * *
226623 ATTTTGACCTTAAAACTTCCAAAAATTA-CATTTTTACCTCCGAACTTTCAAAAATCTCG
1 ATTTTGACCCCGAAACTTCCAAAAATTACCA-TTTTACC-CCGAACTTCCAAAAAT-TCC
* * ** **
226682 ATTTTAACCACGAAAC-TCTTGAAAATTACCATTTTACCCTAAACTTCCAAAAATTCC
1 ATTTTGACCCCGAAACTTC-CAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCC
* * * * *
226739 ACTTTTGACCTCGAAACTTTCAAAAATTACCATTTTTCCCCCGGA-TGTCCAAAAATTCA
1 A-TTTTGACCCCGAAACTTCCAAAAATTACCA-TTTTACCCCGAACT-TCCAAAAATTCC
* * * * *
226798 ATTTTTAACCCTGATACTTTCAAAAATTACCCTTTTACCCCGAA-TGTCCAAAAATTCC
1 A-TTTTGACCCCGAAACTTCCAAAAATTACCATTTTACCCCGAACT-TCCAAAAATTCC
* * **
226856 ATTTTTGATCTCG-ATTTTCCTAAAAATTACCATTTTACCCCG
1 A-TTTTGACCCCGAAACTTCC-AAAAATTACCATTTTACCCCG
226898 GATGTCTAAA
Statistics
Matches: 273, Mismatches: 49, Indels: 26
0.78 0.14 0.07
Matches are distributed among these distances:
57 6 0.02
58 138 0.51
59 75 0.27
60 49 0.18
61 5 0.02
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (57 bp):
ATTTTGACCCCGAAACTTCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCC
Found at i:226764 original size:117 final size:116
Alignment explanation
Indices: 226505--226912 Score: 356
Period size: 117 Copynumber: 3.5 Consensus size: 116
226495 CCAAAATTAT
* * * *
226505 ATTTTGACCCCTAAACTTCCAAAATTTA-CA-TTTTCACCCCTGAACT-TCCAAAAATTCCATTT
1 ATTTTGACCTCGAAACTTCCAAAAATTACCATTTTTC-CCCC-GAA-TGTCCAAAAATT-CAATT
* * *
226567 TTTGACACC-GAAACTTCCAAAAAATA-CATTTTTACCCTCGAACTTCCAAAAATTCC
62 TTTAAC-CCTGAAACTTTCAAAAATTACCA-TTTTACCCT-GAACTTCCAAAAATTCC
** * * *
226623 ATTTTGACCTTAAAACTTCCAAAAATTA-CATTTTTACCTCCGAACT-TTCAAAAATCTCGA-TT
1 ATTTTGACCTCGAAACTTCCAAAAATTACCATTTTT-CCCCCGAA-TGTCCAAAAAT-TCAATTT
* *
226685 TTAACCAC-GAAACTCTT-GAAAATTACCATTTTACCCTAAACTTCCAAAAATTCC
63 TTAACC-CTGAAACT-TTCAAAAATTACCATTTTACCCTGAACTTCCAAAAATTCC
* *
226739 ACTTTTGACCTCGAAACTTTCAAAAATTACCATTTTTCCCCCGGATGTCCAAAAATTCAATTTTT
1 A-TTTTGACCTCGAAACTTCCAAAAATTACCATTTTTCCCCCGAATGTCCAAAAATTCAATTTTT
* * *
226804 AACCCTGATACTTTCAAAAATTACCCTTTTACCCCGAA-TGTCCAAAAATTCC
65 AACCCTGAAACTTTCAAAAATTACCATTTTACCCTGAACT-TCCAAAAATTCC
* ** * * *
226856 ATTTTTGATCTCG-ATTTTCCTAAAAATTACCA-TTTTACCCCGGATGTCTAAAAATTC
1 A-TTTTGACCTCGAAACTTCC-AAAAATTACCATTTTTCCCCCGAATGTCCAAAAATTC
226913 CGTTTTTTAT
Statistics
Matches: 244, Mismatches: 32, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
116 53 0.22
117 132 0.54
118 50 0.20
119 8 0.03
120 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (116 bp):
ATTTTGACCTCGAAACTTCCAAAAATTACCATTTTTCCCCCGAATGTCCAAAAATTCAATTTTTA
ACCCTGAAACTTTCAAAAATTACCATTTTACCCTGAACTTCCAAAAATTCC
Found at i:226774 original size:88 final size:87
Alignment explanation
Indices: 226518--226774 Score: 242
Period size: 87 Copynumber: 2.9 Consensus size: 87
226508 TTGACCCCTA
* *
226518 AACTTCCAAAATTTA-CATTTTCACCCCTGAACTTCCAAAAATTCCATTTTTTGACAC-CGAAAC
1 AACTTCCAAAAATTACCATTTTCA-CCCTAAACTTCCAAAAATTCCA--TTTTGAC-CTCGAAAC
* * * *
226581 TTCCAAAAAATA-CATTTTTACCCTCG
62 TTTCAAAAATTACCA-TTTTAACCACG
* * * *
226607 AACTTCCAAAAATT-CCATTTTGACCTTAAAACTTCCAAAAATTACATTTTTACCTCCG-AACTT
1 AACTTCCAAAAATTACCATTTTCACCCT-AAACTTCCAAAAATTCCATTTTGACCT-CGAAACTT
*
226670 TCAAAAATCT-CGATTTTAACCACG
64 TCAAAAAT-TACCATTTTAACCACG
**
226694 AAAC-TCTTGAAAATTACCATTTT-ACCCTAAACTTCCAAAAATTCCACTTTTGACCTCGAAACT
1 -AACTTC-CAAAAATTACCATTTTCACCCTAAACTTCCAAAAATTCCA-TTTTGACCTCGAAACT
226757 TTCAAAAATTACCATTTT
63 TTCAAAAATTACCATTTT
226775 TCCCCCGGAT
Statistics
Matches: 139, Mismatches: 17, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
86 1 0.01
87 48 0.35
88 47 0.34
89 43 0.31
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.33
Consensus pattern (87 bp):
AACTTCCAAAAATTACCATTTTCACCCTAAACTTCCAAAAATTCCATTTTGACCTCGAAACTTTC
AAAAATTACCATTTTAACCACG
Found at i:226791 original size:29 final size:28
Alignment explanation
Indices: 226759--226919 Score: 112
Period size: 28 Copynumber: 5.6 Consensus size: 28
226749 TCGAAACTTT
*
226759 CAAAAATTACCATTTTTCCCCCGGATGTC
1 CAAAAATT-CCATTTTTACCCCGGATGTC
* * * * *
226788 CAAAAATTCAATTTTTAACCCTGATACTTT
1 CAAAAATTCCATTTTTACCCCGGAT--GTC
* *
226818 CAAAAATTACC-CTTTTACCCCGAATGTC
1 CAAAAATT-CCATTTTTACCCCGGATGTC
* * *
226846 CAAAAATTCCATTTTTGATCTC-GATTTTC
1 CAAAAATTCCATTTTT-ACCCCGGA-TGTC
226875 CTAAAAATTACCA-TTTTACCCCGGATGTC
1 C-AAAAATT-CCATTTTTACCCCGGATGTC
* *
226904 TAAAAATTCCGTTTTT
1 CAAAAATTCCATTTTT
226920 TATCCCATTT
Statistics
Matches: 99, Mismatches: 23, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
27 4 0.04
28 38 0.38
29 21 0.21
30 32 0.32
31 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (28 bp):
CAAAAATTCCATTTTTACCCCGGATGTC
Found at i:226817 original size:59 final size:58
Alignment explanation
Indices: 226551--227012 Score: 290
Period size: 58 Copynumber: 7.9 Consensus size: 58
226541 CCCCTGAACT
* * * *
226551 TCCAAAAATTCCATTTTTTGACAC-CGAAACTTCCAAAAAATA-CATTTTTACCCTCGAACT-
1 TCCAAAAATTCCA-TTTTTGAC-CTCGATACTTTCAAAAATTACCA-TTTTACCC-CGGA-TG
** * * *
226611 TCCAAAAATTCCA-TTTTGACCTTAAAACTTCCAAAAATTA-CATTTTTACCTCCGAACT-
1 TCCAAAAATTCCATTTTTGACCTCGATACTTTCAAAAATTACCA-TTTTACC-CCGGA-TG
* * * * * * ***
226669 TTCAAAAATCTCGA-TTTTAACCACGAAACTCTT-GAAAATTACCATTTTACCCTAAACT-
1 TCCAAAAAT-TCCATTTTTGACCTCGATACT-TTCAAAAATTACCATTTTACCCCGGA-TG
* * *
226727 TCCAAAAATTCCACTTTTGACCTCGAAACTTTCAAAAATTACCATTTTTCCCCCGGATG
1 TCCAAAAATTCCATTTTTGACCTCGATACTTTCAAAAATTACCA-TTTTACCCCGGATG
* * * *
226786 TCCAAAAATTCAATTTTTAACC-CTGATACTTTCAAAAATTACCCTTTTACCCCGAATG
1 TCCAAAAATTCCATTTTTGACCTC-GATACTTTCAAAAATTACCATTTTACCCCGGATG
*
226844 TCCAAAAATTCCATTTTTGATCTCGAT--TTTCCTAAAAATTACCATTTTACCCCGGATG
1 TCCAAAAATTCCATTTTTGACCTCGATACTTT-C-AAAAATTACCATTTTACCCCGGATG
* * * ** * * * *
226902 TCTAAAAATTCCGTTTTTTATCC-C-ATTTTTTTAAAAGTTACCTTTTTACCCCCGAGTG
1 TCCAAAAATTCCATTTTTGA-CCTCGATACTTTCAAAAATTACCATTTTACCCCGGA-TG
* * * *
226960 TCTAAAAATTCCATTTTT-AGCCTCGA-ACTTTCCCAAAATTATCGTTTTACCCC
1 TCCAAAAATTCCATTTTTGA-CCTCGATACTTT-CAAAAATTACCATTTTACCCC
227013 AAAGTCCAAA
Statistics
Matches: 331, Mismatches: 51, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
56 3 0.01
57 32 0.10
58 183 0.55
59 97 0.29
60 16 0.05
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTGACCTCGATACTTTCAAAAATTACCATTTTACCCCGGATG
Found at i:226976 original size:29 final size:28
Alignment explanation
Indices: 226760--226978 Score: 112
Period size: 29 Copynumber: 7.6 Consensus size: 28
226750 CGAAACTTTC
* *
226760 AAAAATTACCATTTTTCCCCCGGATGTCC
1 AAAAATTACCATTTTTACCCC-GATGTCT
* * * *
226789 AAAAATT-CAATTTTTAACCCTGATACTTT
1 AAAAATTACCATTTTT-ACCCCGAT-GTCT
* *
226818 CAAAAATTACC-CTTTTACCCCGAATGTCC
1 -AAAAATTACCATTTTTACCCCG-ATGTCT
* * *
226847 AAAAATT-CCATTTTTGATCTCGATTTTCCT
1 AAAAATTACCATTTTT-ACCCCGA-TGT-CT
226877 AAAAATTACCA-TTTTACCCCGGATGTCT
1 AAAAATTACCATTTTTACCCC-GATGTCT
* * * *
226905 AAAAATT-CCGTTTTTTATCCC-ATTTTTTT
1 AAAAATTACC-ATTTTTACCCCGA--TGTCT
*
226934 AAAAGTTACC-TTTTTACCCCCGAGTGTCT
1 AAAAATTACCATTTTTA-CCCCGA-TGTCT
226963 AAAAATT-CCATTTTTA
1 AAAAATTACCATTTTTA
226979 GCCTCGAACT
Statistics
Matches: 141, Mismatches: 30, Indels: 38
0.67 0.14 0.18
Matches are distributed among these distances:
27 5 0.04
28 39 0.28
29 63 0.45
30 30 0.21
31 4 0.03
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (28 bp):
AAAAATTACCATTTTTACCCCGATGTCT
Found at i:227008 original size:116 final size:115
Alignment explanation
Indices: 226521--227012 Score: 355
Period size: 117 Copynumber: 4.2 Consensus size: 115
226511 ACCCCTAAAC
* * * * * *
226521 TTCCAAAATTTA-CATTTTCACCCCTGAACT-TCCAAAAATTCCATTTTTTGACACCGAAACTTC
1 TTCCAAAAATTACCATTTT-ACCCC-GGA-TGTCCAAAAATT-CAATTTTTAAC-CCGATACTTT
* ** **
226584 CAAAAAATACATTTTTACCCTCGAACT-TCCAAAAATTCCA-TTTTGACCTTAAAAC-
61 CAAAAATTACCCTTTTACCC-CGAA-TGTCCAAAAATTCCATTTTTGACC-TCGAACT
* * * *
226639 TTCCAAAAATTA-CATTTTTACCTCCGAACT-TTCAAAAATCTCGA-TTTTAACCACGAAACTCT
1 TTCCAAAAATTACCA-TTTTACC-CCGGA-TGTCCAAAAAT-TCAATTTTTAACC-CGATACT-T
* * ** *
226701 T-GAAAATTACCATTTTACCCTAAACT-TCCAAAAATTCCACTTTTGACCTCGAAACT
60 TCAAAAATTACCCTTTTACCCCGAA-TGTCCAAAAATTCCATTTTTGACCTCG-AACT
*
226757 TT-CAAAAATTACCATTTTTCCCCCGGATGTCCAAAAATTCAATTTTTAACCCTGATACTTTCAA
1 TTCCAAAAATTACCA-TTTTACCCCGGATGTCCAAAAATTCAATTTTTAACCC-GATACTTTCAA
* *
226821 AAATTACCCTTTTACCCCGAATGTCCAAAAATTCCATTTTTGATCTCG-ATT
64 AAATTACCCTTTTACCCCGAATGTCCAAAAATTCCATTTTTGACCTCGAACT
* ** * ** *
226872 TTCCTAAAAATTACCATTTTACCCCGGATGTCTAAAAATTCCGTTTTTTATCCC-ATTTTTTTAA
1 TTCC-AAAAATTACCATTTTACCCCGGATGTCCAAAAATT-CAATTTTTAACCCGATACTTTCAA
* * * *
226936 AAGTTACCTTTTTACCCCCGAGTGTCTAAAAATTCCATTTTT-AGCCTCGAACT
64 AAATTACCCTTTTA-CCCCGAATGTCCAAAAATTCCATTTTTGA-CCTCGAACT
* * *
226989 TTCCCAAAATTATCGTTTTACCCC
1 TTCCAAAAATTACCATTTTACCCC
227013 AAAGTCCAAA
Statistics
Matches: 311, Mismatches: 43, Indels: 42
0.79 0.11 0.11
Matches are distributed among these distances:
115 24 0.08
116 96 0.31
117 142 0.46
118 42 0.14
119 7 0.02
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (115 bp):
TTCCAAAAATTACCATTTTACCCCGGATGTCCAAAAATTCAATTTTTAACCCGATACTTTCAAAA
ATTACCCTTTTACCCCGAATGTCCAAAAATTCCATTTTTGACCTCGAACT
Found at i:232580 original size:13 final size:13
Alignment explanation
Indices: 232555--232588 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
232545 TTCGATGAAT
232555 AAAAGAA-AAGAA
1 AAAAGAAGAAGAA
232567 AAAAGAAGAAGAA
1 AAAAGAAGAAGAA
*
232580 AAAAAAAGA
1 AAAAGAAGA
232589 GAGGTCGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAGAA
Found at i:234030 original size:49 final size:49
Alignment explanation
Indices: 233977--234274 Score: 232
Period size: 49 Copynumber: 6.1 Consensus size: 49
233967 TGTACCTCAG
* * *
233977 AGACATGACGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGCGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGA
* * * *
234026 AGACATGAAGGGAAAGATCTAAGTCACAACGACGGATCTAGTACCACGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGA
* * * * * * *
234075 AGACA-CAAGAGAAAGGTTTAAGTCGCAATGGCGGA-CCTAGTACCTC-A
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCC-AGTACCACGA
* *
234122 GAGACATAAAGGGAAAGATCT-AGACCGCAACGGCGGATCCAGTACCACAA
1 -AGACATGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGA
* * * * * *
234172 AGATACA-AAAGGGAAAGGTTTAAGTCGCAACGGCAGA-CC-GTGAACCTCAGA
1 AG--ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGT--ACCAC-GA
* * * * *
234223 AGACAAGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCATGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGA
234272 AGA
1 AGA
234275 TTTGAAGAGG
Statistics
Matches: 197, Mismatches: 37, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
47 2 0.01
48 39 0.20
49 87 0.44
50 57 0.29
51 10 0.05
52 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.27, T:0.13
Consensus pattern (49 bp):
AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGA
Found at i:234128 original size:97 final size:100
Alignment explanation
Indices: 233996--234268 Score: 292
Period size: 97 Copynumber: 2.8 Consensus size: 100
233986 GGGAAAGATC
* * *
233996 TAAGCCGCAATGGCGGATCC-AGTACCGC-GAAGACATGAAGGGAAAGATCTAAG-TCACAACGA
1 TAAGTCGCAATGGCGGA-CCTAGTACCTCAGAAGACATGAAGGGAAAGATCTAAGACCACAACGA
* * *
234058 CGGATCTAGTACCACGAAG-ACACAAGAGAAAGGTT
65 CGGATCCAGTACCACAAAGAACAAAAGAGAAAGGTT
* * *
234093 TAAGTCGCAATGGCGGACCTAGTACCTCAG-AGACATAAAGGGAAAGATCT-AGACCGCAACGGC
1 TAAGTCGCAATGGCGGACCTAGTACCTCAGAAGACATGAAGGGAAAGATCTAAGACCACAACGAC
*
234156 GGATCCAGTACCACAAAGATACAAAAGGGAAAGGTT
66 GGATCCAGTACCACAAAGA-ACAAAAGAGAAAGGTT
* * * * * ** *
234192 TAAGTCGCAACGGCAGACCGT-GAACCTCAGAAGACAAGAAGGGAAAGATTTAAG-CCGTAACGG
1 TAAGTCGCAATGGCGGACC-TAGTACCTCAGAAGACATGAAGGGAAAGATCTAAGACCACAACGA
*
234255 CGAATCCAGTACCA
65 CGGATCCAGTACCA
234269 TGAAGATTTG
Statistics
Matches: 150, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
96 4 0.03
97 65 0.43
98 1 0.01
99 39 0.26
100 39 0.26
101 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (100 bp):
TAAGTCGCAATGGCGGACCTAGTACCTCAGAAGACATGAAGGGAAAGATCTAAGACCACAACGAC
GGATCCAGTACCACAAAGAACAAAAGAGAAAGGTT
Found at i:234230 original size:146 final size:145
Alignment explanation
Indices: 233943--234210 Score: 324
Period size: 146 Copynumber: 1.8 Consensus size: 145
233933 GAAAGGGAAG
* * * *
233943 GGTTTAAGTCACAACGGCAAACCTTGTACCTCAGAGACATGACGGGAAAGATCTAAGCCGCAATG
1 GGTTTAAGTCACAACGGCAAACCTAGTACCTCAGAGACATAAAGGGAAAGATCTAAGCCGCAACG
* * * * * *
234008 GCGGATCCAGTACCGCGAAGACATGAAGGGAAAGATCTAAGTCACAACGACGGATCTAGTACCAC
66 GCGGATCCAGTACCACAAAGACATAAAGGGAAAGATCTAAGTCACAACGACAGACCTAGAACCAC
234073 GAAGACACAAGAGAAA
131 GAAGA-ACAAGAGAAA
* * **
234089 GGTTTAAGTCGCAATGGCGGACCTAGTACCTCAGAGACATAAAGGGAAAGATCT-AGACCGCAAC
1 GGTTTAAGTCACAACGGCAAACCTAGTACCTCAGAGACATAAAGGGAAAGATCTAAG-CCGCAAC
* * * *
234153 GGCGGATCCAGTACCACAAAGATACA-AAAGGGAAAGGTTTAAGTCGCAACGGCAGACC
65 GGCGGATCCAGTACCACAAAG--ACATAAAGGGAAAGATCTAAGTCACAACGACAGACC
234211 GTGAACCTCA
Statistics
Matches: 102, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
145 2 0.02
146 72 0.71
147 25 0.25
148 3 0.03
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (145 bp):
GGTTTAAGTCACAACGGCAAACCTAGTACCTCAGAGACATAAAGGGAAAGATCTAAGCCGCAACG
GCGGATCCAGTACCACAAAGACATAAAGGGAAAGATCTAAGTCACAACGACAGACCTAGAACCAC
GAAGAACAAGAGAAA
Found at i:234275 original size:100 final size:100
Alignment explanation
Indices: 234024--234275 Score: 300
Period size: 100 Copynumber: 2.5 Consensus size: 100
234014 CCAGTACCGC
* * * * * *
234024 GAAGACATGAAGGGAAAGATCTAAGTCACAACGACGGATCTAGTACCACGAAG--ACACAAGAGA
1 GAAGACAAGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGAGA
* * *
234087 AAGGTTTAAGTCGCAATGGCGGACCTAGTACCTCA
66 AAGGTTTAAGTCGCAACGGCAGACCTAGAACCTCA
* *
234122 G-AGACATA-AAGGGAAAGATCT-AGACCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGG
1 GAAGACA-AGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGA
234184 GAAAGGTTTAAGTCGCAACGGCAGACCGT-GAACCTCA
64 GAAAGGTTTAAGTCGCAACGGCAGACC-TAGAACCTCA
* * * *
234221 GAAGACAAGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCATGAAGAT
1 GAAGACAAGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGAT
234276 TTGAAGAGGA
Statistics
Matches: 130, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
96 2 0.02
97 41 0.32
98 1 0.01
99 40 0.31
100 44 0.34
101 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (100 bp):
GAAGACAAGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGAGA
AAGGTTTAAGTCGCAACGGCAGACCTAGAACCTCA
Found at i:234572 original size:101 final size:101
Alignment explanation
Indices: 234396--234577 Score: 292
Period size: 101 Copynumber: 1.8 Consensus size: 101
234386 GATCAAAACT
* * * *
234396 ACAATGGCAAGTCTCTATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAGCTTTAACATCAATTC
1 ACAATAGCAAGTCTCTATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAACTTCAACATCAAATC
234461 CTATCCTCTTAAAGTTGCAGTAAAGTCGGATTAAAA
66 CTATCCTCTTAAAGTTGCAGTAAAGTCGGATTAAAA
* *
234497 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAACTTCAACATCAAATC
1 ACAATAGCAAGTCTCTATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAACTTCAACATCAAATC
* *
234562 TTATCTTCTTAAAGTT
66 CTATCCTCTTAAAGTT
234578 ACAGCGAAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 73 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (101 bp):
ACAATAGCAAGTCTCTATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAACTTCAACATCAAATC
CTATCCTCTTAAAGTTGCAGTAAAGTCGGATTAAAA
Found at i:234577 original size:51 final size:50
Alignment explanation
Indices: 234411--234577 Score: 124
Period size: 51 Copynumber: 3.3 Consensus size: 50
234401 GGCAAGTCTC
* * * * * *
234411 TATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAGCTTTAACATCAATTCC
1 TATCTCT-TAAAGTTGTAGTAAGAGCAAGATGAAACTTCAACATCAAATCT
* * * ** * * *
234462 TATCCTCTTAAAGTTGCAGTAA-AGTC-GGATTAAA-AACAATAGCAAGTCTT
1 TAT-CTCTTAAAGTTGTAGTAAGAG-CAAGATGAAACTTCAACATCAAATC-T
*
234512 TATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAACTTCAACATCAAATCT
1 TATCTCT-TAAAGTTGTAGTAAGAGCAAGATGAAACTTCAACATCAAATCT
234563 TATCTTCTTAAAGTT
1 TATC-TCTTAAAGTT
234578 ACAGCGAAGT
Statistics
Matches: 85, Mismatches: 23, Indels: 16
0.69 0.19 0.13
Matches are distributed among these distances:
49 12 0.14
50 23 0.27
51 34 0.40
52 16 0.19
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (50 bp):
TATCTCTTAAAGTTGTAGTAAGAGCAAGATGAAACTTCAACATCAAATCT
Found at i:234597 original size:101 final size:100
Alignment explanation
Indices: 234396--234605 Score: 285
Period size: 101 Copynumber: 2.1 Consensus size: 100
234386 GATCAAAACT
* * * *
234396 ACAATGGCAAGTCTCTATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAGCTTTAACATCAATTC
1 ACAATAGCAAGTCTCTATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAACTTCAACATCAAATC
* * *
234461 CTATCCTCTTAAAGTTGCAGTAAAGTCGGATTAAAA
66 CTATCCTCTTAAAGTTACAGCAAAGTCGGAAT-AAA
* *
234497 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAACTTCAACATCAAATC
1 ACAATAGCAAGTCTCTATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAACTTCAACATCAAATC
* * * *
234562 TTATCTTCTTAAAGTTACAGCGAAGTTGGAATAAA
66 CTATCCTCTTAAAGTTACAGCAAAGTCGGAATAAA
*
234597 ACTATAGCA
1 ACAATAGCA
234606 TCGGATCCCA
Statistics
Matches: 95, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 11 0.12
101 84 0.88
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (100 bp):
ACAATAGCAAGTCTCTATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAACTTCAACATCAAATC
CTATCCTCTTAAAGTTACAGCAAAGTCGGAATAAA
Found at i:234713 original size:39 final size:39
Alignment explanation
Indices: 234659--234872 Score: 209
Period size: 39 Copynumber: 5.5 Consensus size: 39
234649 CTACATCGTT
234659 AACCAATCTCTTACCCCGAGCTTGGGGCAGATCATCATC
1 AACCAATCTCTTACCCCGAGCTTGGGGCAGATCATCATC
* *
234698 AACCAATCCCTTACCCCGAGCTTGGGGCAGAT--TGAAGTC
1 AACCAATCTCTTACCCCGAGCTTGGGGCAGATCAT-CA-TC
**** *
234737 ATTTGATCTTTTACCCCGAGCTTGGGGCAGATCATCATC
1 AACCAATCTCTTACCCCGAGCTTGGGGCAGATCATCATC
* ** * * *
234776 AACCAATCTCTTACCCCAAGCCAGAGGCAGATTA-CAGCC
1 AACCAATCTCTTACCCCGAGCTTGGGGCAGATCATCA-TC
** * *
234815 ATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCGTC
1 AACCAATCTCTTACCCCGAGCTTGGGGCAGATCATCATC
* *
234854 AACCAAACTCCTACCCCGA
1 AACCAATCTCTTACCCCGA
234873 TCACAGGACA
Statistics
Matches: 134, Mismatches: 35, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
37 1 0.01
38 3 0.02
39 127 0.95
40 2 0.01
41 1 0.01
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.23
Consensus pattern (39 bp):
AACCAATCTCTTACCCCGAGCTTGGGGCAGATCATCATC
Found at i:234805 original size:78 final size:78
Alignment explanation
Indices: 234664--234870 Score: 299
Period size: 78 Copynumber: 2.7 Consensus size: 78
234654 TCGTTAACCA
* * ** *
234664 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCCCTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCAAGCCAGAGGCAGA
* *
234729 TTGA-AGTCATTTG
66 TT-ACAGCCATTCG
*
234742 ATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCAAGCCAGAGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCAAGCCAGAGGCAGA
234807 TTACAGCCATTCG
66 TTACAGCCATTCG
* * *
234820 ATCTCTTACCCCGAGCTTGGGGCAGATCATCGTCAACCAAACTCCTACCCC
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCC
234871 GATCACAGGA
Statistics
Matches: 116, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
77 1 0.01
78 115 0.99
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.24
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCAAGCCAGAGGCAGA
TTACAGCCATTCG
Found at i:235485 original size:206 final size:206
Alignment explanation
Indices: 234955--235965 Score: 1501
Period size: 206 Copynumber: 4.9 Consensus size: 206
234945 CAACTCAAAG
* * *
234955 GTGAGCAAATCTTCGAATCCCAACTTCCTGATGAGATATTGAGAAGCGGGTCGAAGCAATAAAAT
1 GTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAAT
* *
235020 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGAGGAGATACAGAGAA
66 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
* * *
235085 GCGGATTGAAACAAATGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAAC
131 GCGGATTGAAACAAACGACGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
235150 CCACG-TCGAT
196 CCACGCTCGAT
* * *
235160 GTGAGCAAATCTTCGAATCCCAACTTCCTGATAAGATACTGAGAAGCGGGTCGAAGCAATAAAAT
1 GTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAAT
* *
235225 GGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAA
66 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
235290 GCGGATTGAAACAAACGACGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
131 GCGGATTGAAACAAACGACGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
*
235355 CCATGCTCGAT
196 CCACGCTCGAT
* * *
235366 GTGAGTAAATCTTTGAATCACAGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAAT
1 GTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAAT
* **
235431 AGTTAGCTTCCTGATGAGATACTGAGAAGCAGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
66 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
* * * *
235496 GCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAAAAGAAGACCAAATCAAAG
131 GCGGATTGAAACAAACGACGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
**
235561 CCGTGCTCGAT
196 CCACGCTCGAT
235572 GTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAAT
1 GTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAAT
* * *
235637 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCTTCTTTCTGATGTGATACAGAGAA
66 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
* * *
235702 GCGGATTGAAAAAAACGACG-TAGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAA
131 GCGGATTGAAACAAACGACGCGA-TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA
235766 CCCACGCTCGAT
195 CCCACGCTCGAT
* *
235778 GTGAGCAAATCTTCGAA-CCCTTGCTTCCTAATGAGATACTGAGAAGC-AGGTCGAAGCAATAAA
1 GTGAGCAAATCTTCGAATCCC-AGCTTCCTGATGAGATACTGAGAAGCGA-GTCGAAGCAATAAA
* * * * * * * *
235841 GTGGTTAGCTCCCTGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACATAGAG
64 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAG
* ** ** * * *
235906 AAGTGGATCAAAACAAGTGATGC-AGTCACCTTCCTGATGAGATATTGAGAAGAAGACCAA
129 AAGCGGATTGAAACAAACGACGCGA-TCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
235966 GTGAATGAAA
Statistics
Matches: 736, Mismatches: 65, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
205 196 0.27
206 540 0.73
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (206 bp):
GTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAAT
GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
GCGGATTGAAACAAACGACGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
CCACGCTCGAT
Found at i:236322 original size:17 final size:18
Alignment explanation
Indices: 236299--236443 Score: 151
Period size: 17 Copynumber: 8.3 Consensus size: 18
236289 CCAAACTCAT
236299 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
* *
236317 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGA
*
236334 TTTAAATTTATTTCAA-A
1 TTTAAATTTATTTTAAGA
*
236351 TTTAAATTTAATTTAAG-
1 TTTAAATTTATTTTAAGA
*
236368 TTAAAATTTATTTTCAA-A
1 TTTAAATTTATTTT-AAGA
*
236386 TTTAAATTTAATTTAAG-
1 TTTAAATTTATTTTAAGA
236403 TTTAAATTTATTTTCAA-A
1 TTTAAATTTATTTT-AAGA
* *
236421 TTTAAAATTATTATAA-A
1 TTTAAATTTATTTTAAGA
236438 TTTAAA
1 TTTAAA
236444 ATAAATAAAG
Statistics
Matches: 107, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
17 66 0.62
18 41 0.38
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:236338 original size:35 final size:34
Alignment explanation
Indices: 236299--236443 Score: 168
Period size: 35 Copynumber: 4.2 Consensus size: 34
236289 CCAAACTCAT
** *
236299 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTT-AAG
*
236334 TTTAAATTTATTTCAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
*
236368 TTAAAATTTATTTTCAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTT-AAATTTAAATTTAATTTAAG
* *
236403 TTTAAATTTATTTTCAAATTTAAAATT-ATTATAAA
1 TTTAAATTTATTTT-AAATTTAAATTTAATT-TAAG
236438 TTTAAA
1 TTTAAA
236444 ATAAATAAAG
Statistics
Matches: 98, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
34 18 0.18
35 80 0.82
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
Found at i:236353 original size:7 final size:6
Alignment explanation
Indices: 236331--236443 Score: 80
Period size: 6 Copynumber: 19.5 Consensus size: 6
236321 ATTTGTTTTA
* *
236331 AAATTT AAATTT --ATTT CAAATTT AAATTT -AATTT AAGTTA AAATTT
1 AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT
* * *
236377 -ATTTT CAAATTT AAATTT -AATTT AAGTTT AAATTT -ATTTT CAAATTT
1 AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT
*
236424 AAAATT --ATTAT AAATTT AAA
1 AAATTT AAATT-T AAATTT AAA
236444 ATAAATAAAG
Statistics
Matches: 83, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
4 6 0.07
5 19 0.23
6 43 0.52
7 15 0.18
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:236366 original size:52 final size:52
Alignment explanation
Indices: 236299--236443 Score: 163
Period size: 52 Copynumber: 2.8 Consensus size: 52
236289 CCAAACTCAT
* *
236299 TTTAAATTTATTTTAAGATT-AAATTTGTTTTAAAATTTAAATTT-ATTTCAAA
1 TTTAAATTTAATTTAAG-TTAAAATTTATTTTAAAATTTAAATTTAATTT-AAA
* *
236351 TTTAAATTTAATTTAAGTTAAAATTTATTTTCAAATTTAAATTTAATTTAAG
1 TTTAAATTTAATTTAAGTTAAAATTTATTTTAAAATTTAAATTTAATTTAAA
* * *
236403 TTTAAATTTATTTTCAAATTTAAAA-TTATTAT-AAATTTAAA
1 TTTAAATTTAATTT--AAGTTAAAATTTATTTTAAAATTTAAA
236444 ATAAATAAAG
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
51 2 0.02
52 62 0.76
53 10 0.12
54 8 0.10
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGTTAAAATTTATTTTAAAATTTAAATTTAATTTAAA
Found at i:236421 original size:12 final size:11
Alignment explanation
Indices: 236332--236425 Score: 77
Period size: 11 Copynumber: 8.2 Consensus size: 11
236322 TTTGTTTTAA
236332 AATTTAAATTT
1 AATTTAAATTT
236343 -ATTTCAAATTT
1 AATTT-AAATTT
236354 AAATTT-AATTT
1 -AATTTAAATTT
*
236365 AAGTTAAAATTT
1 AA-TTTAAATTT
*
236377 ATTTTCAAATTT
1 AATTT-AAATTT
236389 AAATTT-AATTT
1 -AATTTAAATTT
236400 AAGTTTAAATTT
1 AA-TTTAAATTT
*
236412 ATTTTCAAATTT
1 AATTT-AAATTT
236424 AA
1 AA
236426 AATTATTATA
Statistics
Matches: 67, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
10 8 0.12
11 26 0.39
12 25 0.37
13 8 0.12
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:238333 original size:29 final size:29
Alignment explanation
Indices: 238282--238620 Score: 230
Period size: 29 Copynumber: 11.6 Consensus size: 29
238272 AGAGGTCCCT
* *
238282 AAACTGTCCAGAAATTATA-TTTTGACCCC
1 AAACT-TCCAAAAATTACATTTTTGACCCC
*
238311 AAACTTCCAAAAATTACATTTTT-ATCCTC
1 AAACTTCCAAAAATTACATTTTTGA-CCCC
* * *
238340 GAACTTCC-AAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTACATTTTTGACC-CC
*
238369 AAACTTCCAAAAATTACA-TTTTCACCCCC
1 AAACTTCCAAAAATTACATTTTTGA-CCCC
* * * *
238398 AAACTTTCAAAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTACATTTTTGACC-CC
*
238428 AAACTTCTAAAAATTACATTTTT-ACCCC
1 AAACTTCCAAAAATTACATTTTTGACCCC
* * ** **
238456 TGAACTTTCAAAAATCTTGA-TTTTGACCTTG
1 -AAACTTCCAAAAAT-TACATTTTTGACC-CC
* *
238487 AAACTCCCAAAAATTATATTTTT-ACCTCC
1 AAACTTCCAAAAATTACATTTTTGACC-CC
* *
238516 GAACTTCCAAAAATTCCATTTTTGACCCC
1 AAACTTCCAAAAATTACATTTTTGACCCC
* *
238545 AAAACTTCC-AAAATTACCA-ATTTGCCCCC
1 -AAACTTCCAAAAATTA-CATTTTTGACCCC
* * * *
238574 GAA-TGTCCAAAAATTTCATTTTTAACCCTG
1 AAACT-TCCAAAAATTACATTTTTGACCC-C
*
238604 AAACTTTCAAAAATTAC
1 AAACTTCCAAAAATTAC
238621 CCTTTTACCC
Statistics
Matches: 239, Mismatches: 50, Indels: 41
0.72 0.15 0.12
Matches are distributed among these distances:
27 1 0.00
28 35 0.15
29 122 0.51
30 80 0.33
31 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTGACCCC
Found at i:238440 original size:59 final size:59
Alignment explanation
Indices: 238301--238655 Score: 348
Period size: 59 Copynumber: 6.1 Consensus size: 59
238291 AGAAATTATA
* * * *
238301 TTTTGACC-CCAAACTTCCAAAAATTACATTTTTATCCTCGAAC-TTCCAAAATTCCAT
1 TTTTGACCTCGAAACTTCCAAAAATTACATTTTTACCCCCGAACTTTCAAAAATTCCAT
* *
238358 TTTTGACCTCGAAACTTCCAAAAATTACATTTTCACCCCCAAACTTTCAAAAATTCCAT
1 TTTTGACCTCGAAACTTCCAAAAATTACATTTTTACCCCCGAACTTTCAAAAATTCCAT
* * * **
238417 TTTTAACCTCGAAACTTCTAAAAATTACATTTTTACCCCTGAACTTTCAAAAATCTTGA-
1 TTTTGACCTCGAAACTTCCAAAAATTACATTTTTACCCCCGAACTTTCAAAAAT-TCCAT
* * * * *
238476 TTTTGACCTTGAAACTCCCAAAAATTATATTTTTACCTCCGAACTTCCAAAAATTCCAT
1 TTTTGACCTCGAAACTTCCAAAAATTACATTTTTACCCCCGAACTTTCAAAAATTCCAT
* * * * * *
238535 TTTTGACCCCAAAACTTCC-AAAATTACCA-ATTTGCCCCCGAA-TGTCCAAAAATTTCAT
1 TTTTGACCTCGAAACTTCCAAAAATTA-CATTTTTACCCCCGAACT-TTCAAAAATTCCAT
* * ** ** *
238593 TTTTAACC-CTGAAACTTTCAAAAATTACCCTTTTACCCTTGAA-TGTCCAAAAATTCCAT
1 TTTTGACCTC-GAAACTTCCAAAAATTACATTTTTACCCCCGAACT-TTCAAAAATTCCAT
238652 TTTT
1 TTTT
238656 ATCCCGATTT
Statistics
Matches: 248, Mismatches: 41, Indels: 16
0.81 0.13 0.05
Matches are distributed among these distances:
57 10 0.04
58 77 0.31
59 159 0.64
60 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (59 bp):
TTTTGACCTCGAAACTTCCAAAAATTACATTTTTACCCCCGAACTTTCAAAAATTCCAT
Found at i:238643 original size:29 final size:28
Alignment explanation
Indices: 238554--238705 Score: 105
Period size: 29 Copynumber: 5.2 Consensus size: 28
238544 CAAAACTTCC
** *
238554 AAAATTACCAATTTGCCCCCGAATGTCCA
1 AAAATTACC-ATTTTACCCTGAATGTCCA
* *
238583 AAAATT-TCATTTTTAACCCTGAAACT-TTCA
1 AAAATTACCA-TTTT-ACCCTG-AA-TGTCCA
*
238613 AAAATTACCCTTTTACCCTTGAATGTCCA
1 AAAATTACCATTTTACCC-TGAATGTCCA
* *
238642 AAAATT-CCATTTTTATCCC-GATTTTCCTA
1 AAAATTACCA-TTTTA-CCCTGAATGTCC-A
*
238671 AAAATTACCATTTTACCCCTGGATGTCCA
1 AAAATTACCATTTTA-CCCTGAATGTCCA
238700 AAAATT
1 AAAATT
238706 TTGTTTTTGA
Statistics
Matches: 96, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
27 1 0.01
28 13 0.14
29 52 0.54
30 28 0.29
31 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTGAATGTCCA
Found at i:238656 original size:59 final size:59
Alignment explanation
Indices: 238311--238827 Score: 288
Period size: 59 Copynumber: 8.9 Consensus size: 59
238301 TTTTGACCCC
* * * *
238311 AAACTTCCAAAAATTA-CATTTTTATCCTCGAACTTCC-AAAATTCCATTTTTGA-CCTCG
1 AAACTTTCAAAAATTACCA-TTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCT-G
* * *
238369 AAACTTCCAAAAATTA-CATTTTCACCCCCAAACTTTCAAAAATTCCATTTTTAA-CCTCG
1 AAACTTTCAAAAATTACCATTTT-ACCCCCGAACTTCCAAAAATTCCATTTTTAACCCT-G
* * ** * *
238428 AAAC-TTCTAAAAATTA-CATTTTTACCCCTGAACTTTCAAAAATCTTGA-TTTTGACCTTG
1 AAACTTTC-AAAAATTACCA-TTTTACCCCCGAACTTCCAAAAAT-TCCATTTTTAACCCTG
** * * * **
238487 AAACTCCCAAAAATTA-TATTTTTACCTCCGAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTTCAAAAATTACCA-TTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCTG
* * * *
238546 AAAC-TTCCAAAATTACCAATTTGCCCCCGAA-TGTCCAAAAATTTCATTTTTAACCCTG
1 AAACTTTCAAAAATTACCATTTTACCCCCGAACT-TCCAAAAATTCCATTTTTAACCCTG
* ** *
238604 AAACTTTCAAAAATTACCCTTTTACCCTTGAA-TGTCCAAAAATTCCATTTTTATCCC-G
1 AAACTTTCAAAAATTACCATTTTACCCCCGAACT-TCCAAAAATTCCATTTTTAACCCTG
* * * *** *
238662 --ATTTTCCTAAAAATTACCATTTTACCCCTGGA-TGTCCAAAAATTTTGTTTTTGATCCC-G
1 AAACTTT-C-AAAAATTACCATTTTACCCCCGAACT-TCCAAAAATTCCATTTTT-AACCCTG
** * * * ** * *
238721 --TTTTTTAAAAGTTACCGTTTTACCCCCG-GGTGTCTAAAAATTCCATTTTTAACCC-C
1 AAACTTTCAAAAATTACCATTTTACCCCCGAACT-TCCAAAAATTCCATTTTTAACCCTG
* * **
238777 AAACTTTCCCAAAATTACCATTTTGCCCCC-AAAGTCC-AAAATTACCATTTT
1 AAACTTT-CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATT-CCATTTT
238828 GCCTCCCCGG
Statistics
Matches: 367, Mismatches: 72, Indels: 40
0.77 0.15 0.08
Matches are distributed among these distances:
56 8 0.02
57 47 0.13
58 126 0.34
59 177 0.48
60 9 0.02
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (59 bp):
AAACTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCTG
Found at i:238697 original size:58 final size:57
Alignment explanation
Indices: 238506--238827 Score: 215
Period size: 58 Copynumber: 5.6 Consensus size: 57
238496 AAAATTATAT
* * * ** *
238506 TTTTACCTCCGAACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTC-CAAAATTACCA
1 TTTTACCCCCGAA-TGTCCAAAAATTCCATTTTT-ATCCC-GATTTTCTAAAAATTACCA
* * * * * *
238564 ATTTGCCCCCGAATGTCCAAAAATTTCATTTTTAACCCTGAAACTTTC-AAAAATTACCC
1 TTTTACCCCCGAATGTCCAAAAATTCCATTTTTATCCC-G--ATTTTCTAAAAATTACCA
**
238623 TTTTACCCTTGAATGTCCAAAAATTCCATTTTTATCCCGATTTTCCTAAAAATTACCA
1 TTTTACCCCCGAATGTCCAAAAATTCCATTTTTATCCCGATTTT-CTAAAAATTACCA
* * *** * * *
238681 TTTTACCCCTGGATGTCCAAAAATTTTGTTTTTGATCCCG-TTTTTTAAAAGTTACCG
1 TTTTACCCCCGAATGTCCAAAAATTCCATTTTT-ATCCCGATTTTCTAAAAATTACCA
** * * * * **
238738 TTTTACCCCCGGGTGTCTAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCA
1 TTTTACCCCCGAATGTCCAAAAATTCCATTTTT-ATCCC-GATTTTCTAAAAATTACCA
* *
238797 TTTTGCCCCC-AAAGTCC-AAAATTACCATTTT
1 TTTTACCCCCGAATGTCCAAAAATT-CCATTTT
238828 GCCTCCCCGG
Statistics
Matches: 208, Mismatches: 47, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
56 4 0.02
57 53 0.25
58 80 0.38
59 71 0.34
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (57 bp):
TTTTACCCCCGAATGTCCAAAAATTCCATTTTTATCCCGATTTTCTAAAAATTACCA
Found at i:240623 original size:3 final size:3
Alignment explanation
Indices: 240615--240639 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
240605 AGGGTTGGCT
240615 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
240640 AAGAAGAAGA
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:240785 original size:31 final size:31
Alignment explanation
Indices: 240715--240852 Score: 84
Period size: 31 Copynumber: 4.5 Consensus size: 31
240705 AATATAATAT
* * * *
240715 TTGGTACTTGAACTTAACA-TTTTTTTACTAAT
1 TTGGTACTTAAACTTGACACTTTTTCT--TAAG
*
240747 TTAGTACTTAAACTTGACACTTTTTCTTAAG
1 TTGGTACTTAAACTTGACACTTTTTCTTAAG
* ******** *
240778 TTGGTACTTAATCTTTTGGGGGGTTC--AAT
1 TTGGTACTTAAACTTGACACTTTTTCTTAAG
*
240807 TTGGTACTTAAACTTGACTCTTTTTCTTAAG
1 TTGGTACTTAAACTTGACACTTTTTCTTAAG
*
240838 TTGGTACTTCAACTT
1 TTGGTACTTAAACTT
240853 TTGGGGTGAT
Statistics
Matches: 76, Mismatches: 27, Indels: 7
0.69 0.25 0.06
Matches are distributed among these distances:
29 19 0.25
31 35 0.46
32 16 0.21
33 6 0.08
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACTTTTTCTTAAG
Found at i:240818 original size:60 final size:61
Alignment explanation
Indices: 240744--240885 Score: 198
Period size: 60 Copynumber: 2.3 Consensus size: 61
240734 TTTTTTTACT
* *
240744 AATTTAGTACTTAAACTTGACACTTTTTCTTAAGTTGGTACTT-AATCTTTTGGGG-GGTTC
1 AATTTGGTACTTAAACTTGACACTTTTTCTTAAGTTGGTACTTCAA-CTTTTGGGGTGATTC
* *
240804 AATTTGGTACTTAAACTTGACTCTTTTTCTTAAGTTGGTACTTCAACTTTTGGGGTGATTG
1 AATTTGGTACTTAAACTTGACACTTTTTCTTAAGTTGGTACTTCAACTTTTGGGGTGATTC
* * *
240865 AATTTGATACCTGAACTTGAC
1 AATTTGGTACTTAAACTTGAC
240886 TTTTTTTTTC
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
60 50 0.68
61 23 0.32
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (61 bp):
AATTTGGTACTTAAACTTGACACTTTTTCTTAAGTTGGTACTTCAACTTTTGGGGTGATTC
Found at i:241082 original size:4 final size:4
Alignment explanation
Indices: 241075--241100 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
241065 AATTTTAATC
241075 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
241101 GAGAATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:241391 original size:31 final size:32
Alignment explanation
Indices: 241334--241401 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 32
241324 TTTAGGTTCT
* * *
241334 AAATTAAAATATATATATCAAGTTCAGATATC
1 AAATTAAAATAAAAATATCAAATTCAGATATC
*
241366 AAATTAAAA-AAAAATATCAAATTCAGGTATC
1 AAATTAAAATAAAAATATCAAATTCAGATATC
241397 AAATT
1 AAATT
241402 TTATATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 23 0.72
32 9 0.28
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (32 bp):
AAATTAAAATAAAAATATCAAATTCAGATATC
Found at i:241860 original size:13 final size:13
Alignment explanation
Indices: 241844--241868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
241834 ATTATTACCA
241844 AAAAAATAAAAAT
1 AAAAAATAAAAAT
241857 AAAAAATAAAAA
1 AAAAAATAAAAA
241869 CTCTACTGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:257800 original size:2 final size:2
Alignment explanation
Indices: 257793--257824 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
257783 GGGTAATGGA
257793 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
257825 GATGATGGAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:261073 original size:32 final size:32
Alignment explanation
Indices: 261032--261093 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
261022 CAACCTAATC
261032 GTTACATGCAATTTTCCCATTTAGAACACCAT
1 GTTACATGCAATTTTCCCATTTAGAACACCAT
261064 GTTACATGCAATTTTCCCATTTAGAACACC
1 GTTACATGCAATTTTCCCATTTAGAACACC
261094 GAATAGGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.34
Consensus pattern (32 bp):
GTTACATGCAATTTTCCCATTTAGAACACCAT
Found at i:263427 original size:17 final size:17
Alignment explanation
Indices: 263387--263437 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
263377 ACCCAAAAAC
*
263387 CTTCATCACCTTCATCTT
1 CTTCATCATCTTC-TCTT
*
263405 CATCATCATCTTCTCTT
1 CTTCATCATCTTCTCTT
263422 CTTCATCATCTTCTCT
1 CTTCATCATCTTCTCT
263438 AAACGTGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 19 0.63
18 11 0.37
ACGTcount: A:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (17 bp):
CTTCATCATCTTCTCTT
Found at i:265093 original size:19 final size:19
Alignment explanation
Indices: 265069--265108 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
265059 ATTATGTTCC
265069 TTTAGCTATTTGCATGCCA
1 TTTAGCTATTTGCATGCCA
265088 TTTAGCTATTTGCATGCCA
1 TTTAGCTATTTGCATGCCA
265107 TT
1 TT
265109 ATAGACTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (19 bp):
TTTAGCTATTTGCATGCCA
Found at i:270104 original size:8 final size:8
Alignment explanation
Indices: 270061--270105 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
270051 TTTCTTGGAC
270061 AAAAATAA
1 AAAAATAA
*
270069 ATAAATAA
1 AAAAATAA
270077 ATAAAATAGA
1 A-AAAATA-A
*
270087 GAAAATAA
1 AAAAATAA
270095 AAAAATAA
1 AAAAATAA
270103 AAA
1 AAA
270106 TAATTGGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 19 0.61
9 11 0.35
10 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:273419 original size:19 final size:19
Alignment explanation
Indices: 273395--273437 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
273385 AAACATAAAT
273395 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
273414 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
273433 TAAAT
1 TAAAT
273438 CCTAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:277843 original size:57 final size:58
Alignment explanation
Indices: 277755--277885 Score: 185
Period size: 57 Copynumber: 2.3 Consensus size: 58
277745 AAACCCATCA
* * **
277755 ATAAACTAAACTCAAATATTTTTAAACCCAAATATAAT-TTCATTCTTAAAAAACATTC
1 ATAAATTAAACTCAAATATTTTTAAACCCAAATATAATATT-ATTATTAAAAAACACCC
* *
277813 ATAAATTAAAC-CAATTATTTTTAAACCCAAATATAATATTATTATTATAAAACACCC
1 ATAAATTAAACTCAAATATTTTTAAACCCAAATATAATATTATTATTAAAAAACACCC
277870 ATAAATTAAACTCAAA
1 ATAAATTAAACTCAAA
277886 ATCAATTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
57 49 0.77
58 15 0.23
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (58 bp):
ATAAATTAAACTCAAATATTTTTAAACCCAAATATAATATTATTATTAAAAAACACCC
Found at i:277960 original size:24 final size:24
Alignment explanation
Indices: 277928--277978 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
277918 TTAAACCCCC
277928 CCCATTTAGTCGAAGAGGCTGAAA
1 CCCATTTAGTCGAAGAGGCTGAAA
*
277952 CCCATTTAGTTGAAGAGGCTGAAA
1 CCCATTTAGTCGAAGAGGCTGAAA
277976 CCC
1 CCC
277979 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (24 bp):
CCCATTTAGTCGAAGAGGCTGAAA
Found at i:278459 original size:34 final size:34
Alignment explanation
Indices: 278406--278481 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
278396 TTTGTTTTGT
* *
278406 TTTGTACTGTAATACCCAAAGCTGAATTTTAGTA
1 TTTGAACTGCAATACCCAAAGCTGAATTTTAGTA
278440 TTTGAACTGCAATACCCAAAGCTGAATTTTAGTA
1 TTTGAACTGCAATACCCAAAGCTGAATTTTAGTA
278474 TTTGAACT
1 TTTGAACT
278482 AGTAGCTATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (34 bp):
TTTGAACTGCAATACCCAAAGCTGAATTTTAGTA
Done.