Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 41
Found at i:5659914 original size:60 final size:60
Alignment explanation
Indices: 5659839--5660537 Score: 1120
Period size: 60 Copynumber: 11.8 Consensus size: 60
5659829 TAATTTCATT
* *
5659839 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTAATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
5659898 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
5659958 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
5660018 ATTATTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
5660078 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
5660138 ATTACTAAATCATTAATATCAAATCATTAAATATTAAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATT-AATAATAATTTCATTATTACTAATC
** * *
5660199 ATTACTCTATCATTACTATAAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
5660259 ACTACTAAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
5660319 ATTACTAAATTATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
5660379 ATTACT-AATCATTACTATCAAATCATTAGAA-ATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTA-AATATTAATAATAATTTCATTATTACTAATC
*
5660438 ATTACT--ATCA--A--ATC---T--TTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
5660487 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTA
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTA
5660538 AATATTAATA
Statistics
Matches: 599, Mismatches: 26, Indels: 29
0.92 0.04 0.04
Matches are distributed among these distances:
48 2 0.00
49 37 0.06
51 5 0.01
53 1 0.00
54 3 0.01
55 3 0.01
56 1 0.00
58 5 0.01
59 61 0.10
60 426 0.71
61 55 0.09
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:5659984 original size:25 final size:24
Alignment explanation
Indices: 5659954--5660106 Score: 65
Period size: 25 Copynumber: 6.3 Consensus size: 24
5659944 CATTATTACT
5659954 AATCATTACTAAATCATTACTATCA
1 AATCATTACTAAATCATTA-TATCA
*
5659979 AATCA-T--TAAAT-ATTAATAACA
1 AATCATTACTAAATCATT-ATATCA
* *
5660000 ATTTCATTATTACTAATCATTAT-T-A
1 A-ATCATTACTA--AATCATTATATCA
5660025 AATCATTACTATCAAATCATTA-A--A
1 AATCATTAC--T-AAATCATTATATCA
* * * * *
5660049 AATTAATAATAATTTCATTAT-TACT
1 AATCATTACTAA-ATCATTATAT-CA
5660074 AATCATTACTAAATCATTACTATCA
1 AATCATTACTAAATCATTA-TATCA
5660099 AATCATTA
1 AATCATTA
5660107 AAAATTAATA
Statistics
Matches: 94, Mismatches: 15, Indels: 38
0.64 0.10 0.26
Matches are distributed among these distances:
21 10 0.11
22 16 0.17
23 1 0.01
24 20 0.21
25 36 0.38
26 2 0.02
27 6 0.06
28 3 0.03
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (24 bp):
AATCATTACTAAATCATTATATCA
Found at i:5660176 original size:15 final size:14
Alignment explanation
Indices: 5660143--5660176 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
5660133 TAATCATTAC
5660143 TAAATCATTAATAT
1 TAAATCATTAATAT
*
5660157 CAAATCATTAAATAT
1 TAAATCATT-AATAT
5660172 TAAAT
1 TAAAT
5660177 AATAATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATCATTAATAT
Found at i:5660236 original size:301 final size:299
Alignment explanation
Indices: 5659557--5660639 Score: 1459
Period size: 301 Copynumber: 3.7 Consensus size: 299
5659547 ATTACTATCA
* * * *
5659557 AATCATTACTAAATCATTACTATCAAATCATTAAATATT-AATAACAATTTCATTATTATTAATC
1 AATCATTACT-AATCATTAATATCAAATCATTAAATATTAAATAATAATTTAATTATTACTAATC
* *
5659621 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
65 ATTACTCAATCATTACTATAAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
* * *
5659686 TAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATTATTACT-AAT
130 TAAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATTATTACTAATCATTATTAAAT
5659750 CATTACTATCAAATCATTAAATAA-TAATAATAATTTC------A-T--T-ATTACTAATCATTA
195 CATTACTATCAAATCATTAAA-AATTAATAATAATTTCATTATTACTAATCATTACTAATCATTA
5659804 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
259 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
5659845 AATCA-T--T-A-C-----TATCAAATCATTAAAAATT-AATAATAATTTAATTATTACTAATCA
1 AATCATTACTAATCATTAATATCAAATCATTAAATATTAAATAATAATTTAATTATTACTAATCA
* *
5659899 TTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACT
66 TTACTCAATCATTACTATAAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACT
*
5659964 AAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTATTAAATC
131 AAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATTATTACTAATCATTATTAAATC
5660029 ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAC
196 ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT-AATCATTAC
*
5660094 TATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
260 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
5660134 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAAATAATAATTTCATTATTACTAATC
1 AATCATTACT-AATCATTAATATCAAATCATTAAATATTAAATAATAATTTAATTATTACTAATC
* *
5660199 ATTACTCTATCATTACTATAAAATCATTAAATATTAATAACAATTTCATTATTACTAATCACTAC
65 ATTACTCAATCATTACTATAAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
*
5660264 TAAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATTATTACTAATCATTACTAAAT
130 TAAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATTATTACTAATCATTATTAAAT
* *
5660329 TATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATCATTAC
195 CATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAATCATTAC
*
5660394 TATCAAATCATTAGAAATTAATAATAATTTCATTATTACT
260 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* * * * * * * *
5660434 AATCATTACT-ATCA--AATCTTTAAA-AATT-AATAATAATTTCATTATTACTAATCATTACTA
1 AATCATTACTAATCATTAAT-ATCAAATCATTAAATATTAA-ATAATAATT--TAATTATTACT-
* * * *
5660494 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTAAATATTAATAATAATTTTATT
61 AATCATT-A-CTC-AATCA-T---TACT-ATAA-AA--TCATTAAATATTAATAACAATTTCATT
* **
5660559 ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCAACATTAC
115 ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATTATTAC
5660624 TAATCATTATTAAATC
180 TAATCATTATTAAATC
5660640 TTATAAATAC
Statistics
Matches: 714, Mismatches: 40, Indels: 60
0.88 0.05 0.07
Matches are distributed among these distances:
277 165 0.23
278 37 0.05
282 1 0.00
283 1 0.00
284 1 0.00
285 2 0.00
287 2 0.00
288 11 0.02
289 53 0.07
290 1 0.00
292 1 0.00
294 1 0.00
295 8 0.01
296 12 0.02
297 4 0.01
298 13 0.02
299 7 0.01
300 76 0.11
301 204 0.29
302 4 0.01
303 1 0.00
306 3 0.00
307 4 0.01
308 2 0.00
310 100 0.14
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (299 bp):
AATCATTACTAATCATTAATATCAAATCATTAAATATTAAATAATAATTTAATTATTACTAATCA
TTACTCAATCATTACTATAAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACT
AAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATTATTACTAATCATTATTAAATC
ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAATCATTACT
ATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:5660368 original size:82 final size:82
Alignment explanation
Indices: 5660282--5660616 Score: 363
Period size: 82 Copynumber: 4.0 Consensus size: 82
5660272 TACTATCAAA
* * *
5660282 TCATTAAATATTAATAAAAATTTCATTATTACTAATCATTACTAAATTATTACTATCAAATCATT
1 TCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATT
5660347 AAATATTAATAATAATT
66 AAATATTAATAATAATT
* * * * * * * * * * ***
5660364 TCATT-ATTACTAATCATTACTAATCATTACTATCAAATCATTA-GAAATTAATAATAATTTCAT
1 TCATTAAATATTAAT-AATAAT-TTCATTATTA-CTAATCATTACTAAATCATTAAT-ATCAAAT
* * *
5660427 TATTACTAATCATTACT-ATCAA-A
62 CATTA--AAT-ATTAATAAT-AATT
* *
5660450 TCTTTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATT
1 TCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATT
5660515 AAATATTAATAATAATT
66 AAATATTAATAATAATT
* *
5660532 TCATTAAATATTAATAATAATTTTATTATTACTAATCATTACTAAATCATTACTATCAAATCATT
1 TCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATT
5660597 AAATATTAATAATAATT
66 AAATATTAATAATAATT
5660614 TCA
1 TCA
5660617 ACATTACTAA
Statistics
Matches: 202, Mismatches: 39, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
81 14 0.07
82 94 0.47
83 17 0.08
84 34 0.17
85 17 0.08
86 13 0.06
87 13 0.06
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (82 bp):
TCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATT
AAATATTAATAATAATT
Found at i:5660384 original size:10 final size:10
Alignment explanation
Indices: 5660369--5660395 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5660359 TAATTTCATT
5660369 ATTACTAATC
1 ATTACTAATC
5660379 ATTACTAATC
1 ATTACTAATC
5660389 ATTACTA
1 ATTACTA
5660396 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:5660494 original size:108 final size:110
Alignment explanation
Indices: 5660319--5660537 Score: 372
Period size: 108 Copynumber: 2.0 Consensus size: 110
5660309 ATTACTAATC
* *
5660319 ATTACTAAATTATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
5660384 T-AATCATTACTATCAAATCATTAGAA-ATTAATAATAATTTCATT
66 TAAATCATTAATATCAAATCATTA-AATATTAATAATAATTTCATT
*
5660428 ATTACT-AATCATTACTATCAAATCTTTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
5660492 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
5660537 A
1 A
5660538 AATATTAATA
Statistics
Matches: 104, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
108 58 0.56
109 46 0.44
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (110 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:5660535 original size:22 final size:22
Alignment explanation
Indices: 5660510--5660559 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
5660500 TAATATCAAA
5660510 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
5660532 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
*
5660554 TTATTA
1 TCATTA
5660560 TTACTAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TCATTAAATATTAATAATAATT
Found at i:5663418 original size:5 final size:5
Alignment explanation
Indices: 5663408--5663433 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5663398 TAAATCATTA
5663408 AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT A
5663434 CTATTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:5664792 original size:21 final size:21
Alignment explanation
Indices: 5664767--5664826 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
5664757 ACGCTGCAAT
5664767 CATGCAGCTATGGATGCAACG
1 CATGCAGCTATGGATGCAACG
5664788 CATGCAGCTATGGATGCAACG
1 CATGCAGCTATGGATGCAACG
* *
5664809 CATGCAACTACGGATGCA
1 CATGCAGCTATGGATGCA
5664827 GGAATCTCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CATGCAGCTATGGATGCAACG
Found at i:5665009 original size:29 final size:29
Alignment explanation
Indices: 5664967--5665055 Score: 151
Period size: 29 Copynumber: 3.0 Consensus size: 29
5664957 CCACAACTTG
5664967 GTCGCCGGGACTCCATGGCGACCTACCAT
1 GTCGCCGGGACTCCATGGCGACCTACCAT
* *
5664996 GTCGTCGGGACTCCATGGCGATCTACCAT
1 GTCGCCGGGACTCCATGGCGACCTACCAT
5665025 GTCGCCGGGACTCCATGGCGACCTACACAT
1 GTCGCCGGGACTCCATGGCGACCTAC-CAT
5665055 G
1 G
5665056 CACGATCTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 51 0.93
30 4 0.07
ACGTcount: A:0.18, C:0.35, G:0.28, T:0.19
Consensus pattern (29 bp):
GTCGCCGGGACTCCATGGCGACCTACCAT
Found at i:5665214 original size:29 final size:29
Alignment explanation
Indices: 5665181--5665247 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
5665171 CATGCATGAA
5665181 TCCTTGGTCGCCCCGAGTGCATGGCGACC
1 TCCTTGGTCGCCCCGAGTGCATGGCGACC
**** *
5665210 TCCTTGGTCGTTGGGCGTGCATGGCGACC
1 TCCTTGGTCGCCCCGAGTGCATGGCGACC
*
5665239 TCTTTGGTC
1 TCCTTGGTC
5665248 ACTGTACAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.07, C:0.31, G:0.33, T:0.28
Consensus pattern (29 bp):
TCCTTGGTCGCCCCGAGTGCATGGCGACC
Found at i:5671605 original size:229 final size:227
Alignment explanation
Indices: 5671205--5671653 Score: 785
Period size: 229 Copynumber: 2.0 Consensus size: 227
5671195 GTAAATTATC
* * *
5671205 TATCATTTTTATAAAAGTGTCCATACTTATTTCATTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
5671270 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
5671335 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAA-TT
5671399 GAAACATAAATTACATAACTTTCAAAAAAGTATA
195 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
5671433 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
5671498 TTAATATTGTTAAATTT-AAATGCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
65 TTAATATTGTTAAATTTAAAAT-CTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
*
5671562 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
5671627 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
5671654 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
228 44 0.21
229 164 0.78
230 3 0.01
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:5671742 original size:20 final size:19
Alignment explanation
Indices: 5671719--5671764 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
5671709 CGATATACCA
5671719 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
5671739 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
5671759 GGTAAA
1 GGTAAA
5671765 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:5671908 original size:20 final size:19
Alignment explanation
Indices: 5671885--5671931 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
5671875 CGATATAACA
*
5671885 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
5671905 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
5671925 GGTAAAA
1 GGTAAAA
5671932 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:5674277 original size:33 final size:33
Alignment explanation
Indices: 5674235--5674300 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
5674225 AAATAGATGG
*
5674235 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
5674268 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
5674301 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:5675697 original size:19 final size:19
Alignment explanation
Indices: 5675653--5675696 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
5675643 AATGTCGAGT
5675653 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
5675672 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
5675691 T-ATTTT
1 TAATTTT
5675697 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:5676524 original size:198 final size:198
Alignment explanation
Indices: 5675847--5677173 Score: 2473
Period size: 198 Copynumber: 6.7 Consensus size: 198
5675837 GTGCACCCAT
* *
5675847 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTTAATCTAAT
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
5675912 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
*
5675977 GTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCAATAAAGTGTCGATCCATAT
131 GTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCAATAAAGTGTCGATCCATAT
5676042 ATAA
195 ATAA
*
5676046 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATCTGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
5676111 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
*
5676176 GTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCAATAAAGTGTCGATCCATAT
131 GTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCAATAAAGTGTCGATCCATAT
5676241 ATAA
195 ATAA
*
5676245 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATCTGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
5676310 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
*
5676375 GTGTCGATATTTTTTTCCAGAATGAATT-AAAACAAGGTGCACCCATAAAGTGTCGATCCATATA
131 GTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCAATAAAGTGTCGATCCATATA
5676439 TAAA
196 T-AA
*
5676443 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTTAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
5676508 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
5676573 GTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCAATAAAGTGTCGATCCATATA
131 GTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCAATAAAGTGTCGATCCATATA
5676638 TAA
196 TAA
5676641 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
5676706 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
5676771 GTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACCAATAAAGTGTCGATCCATAT
131 GTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACCAATAAAGTGTCGATCCATAT
5676836 ATAA
195 ATAA
5676840 AAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
* *
5676904 CGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
5676969 GTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCAATAAAGTGTCGATCCATATA
131 GTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCAATAAAGTGTCGATCCATATA
5677034 TAA
196 TAA
*
5677037 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATCTGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
5677102 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATAT--TTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
5677165 GTGTCGATA
131 GTGTCGATA
5677174 CTAATTTAAA
Statistics
Matches: 1111, Mismatches: 13, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
196 12 0.01
197 116 0.10
198 531 0.48
199 452 0.41
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (198 bp):
AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAATATAGTTT
GTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCAATAAAGTGTCGATCCATATA
TAA
Found at i:5678651 original size:18 final size:18
Alignment explanation
Indices: 5678630--5678697 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
5678620 AGCGGTCGCA
5678630 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
5678648 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
5678669 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
5678690 GAAGATGA
1 GAAGATGA
5678698 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:5678654 original size:6 final size:6
Alignment explanation
Indices: 5678630--5678727 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
5678620 AGCGGTCGCA
* * * * * *
5678630 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
5678678 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
5678726 GA
1 GA
5678728 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:5678665 original size:3 final size:3
Alignment explanation
Indices: 5678645--5678731 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
5678635 TGAAGCTGAC
* * * * * ** *
5678645 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
5678693 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
5678732 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:5678680 original size:42 final size:42
Alignment explanation
Indices: 5678633--5678723 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
5678623 GGTCGCAGAA
*
5678633 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
5678675 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
5678717 GATGAAG
1 GATGAAG
5678724 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:5678731 original size:18 final size:18
Alignment explanation
Indices: 5678630--5678727 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
5678620 AGCGGTCGCA
* *
5678630 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
5678648 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
5678666 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
5678684 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
5678702 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
5678720 GAAGATGA
1 GAAGATGA
5678728 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:5680511 original size:184 final size:184
Alignment explanation
Indices: 5680202--5681057 Score: 1642
Period size: 184 Copynumber: 4.7 Consensus size: 184
5680192 CTTTCAACAT
**
5680202 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
5680267 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
5680332 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
5680386 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGT-TTAATGAGCGAAT
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTT-ATGCGCGAAT
5680450 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAA
65 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAA
5680515 AAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
130 AAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
5680570 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
5680635 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
5680700 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
5680754 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
5680819 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
5680884 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
5680938 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
5681003 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
5681058 CCATTTAAAA
Statistics
Matches: 663, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
183 2 0.00
184 659 0.99
185 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:5681894 original size:23 final size:23
Alignment explanation
Indices: 5681863--5681926 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
5681853 ATAGGTAAAC
*
5681863 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
5681886 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
5681909 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5681927 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:5681933 original size:23 final size:23
Alignment explanation
Indices: 5681863--5681935 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
5681853 ATAGGTAAAC
* **
5681863 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
5681886 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
5681909 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
5681932 ATAT
1 ATAT
5681936 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:5682325 original size:23 final size:23
Alignment explanation
Indices: 5682294--5682357 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
5682284 ATAGGTAAAC
*
5682294 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
5682317 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
5682340 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5682358 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:5682364 original size:23 final size:23
Alignment explanation
Indices: 5682294--5682366 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
5682284 ATAGGTAAAC
* **
5682294 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
5682317 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
5682340 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
5682363 ATAT
1 ATAT
5682367 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:5682595 original size:431 final size:431
Alignment explanation
Indices: 5681788--5682787 Score: 1964
Period size: 431 Copynumber: 2.3 Consensus size: 431
5681778 TACTTTGACA
* *
5681788 AAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGGATGGACACTTTCAATAAA
1 AAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
5681853 ATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
66 ATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
5681918 AATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
131 AATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
5681983 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
196 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
5682048 GCGTCTAATGATTTATTTTTTACGTTACAGTATATATTATTATTAAATTAAAAATTCTAAATAAT
261 GCGTCTAATGATTTATTTTTTACGTTACAGTATATATTATTATTAAATTAAAAATTCTAAATAAT
*
5682113 ATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTG
326 ATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATAAAATTATTAAATCAATATTG
5682178 TAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACAT
391 TAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACAT
5682219 AAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
1 AAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
5682284 ATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
66 ATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
5682349 AATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
131 AATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
5682414 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
196 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
*
5682479 GCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAATTCTAAATAAT
261 GCGTCTAATGATTTATTTTTTACGTTACAGTATATATTATTATTAAATTAAAAATTCTAAATAAT
5682544 ATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATAAAATTATTAAATCAATATTG
326 ATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATAAAATTATTAAATCAATATTG
5682609 TAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACAT
391 TAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACAT
5682650 AAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
1 AAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
5682715 ATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
66 ATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
5682780 AATAGGTA
131 AATAGGTA
5682788 TCTATCTCGC
Statistics
Matches: 565, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
431 565 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (431 bp):
AAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
ATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
AATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
GCGTCTAATGATTTATTTTTTACGTTACAGTATATATTATTATTAAATTAAAAATTCTAAATAAT
ATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATAAAATTATTAAATCAATATTG
TAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACAT
Found at i:5682788 original size:23 final size:23
Alignment explanation
Indices: 5682725--5682789 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
5682715 ATAGGTAAAC
* *
5682725 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
5682748 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
5682771 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
5682790 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:5683014 original size:18 final size:18
Alignment explanation
Indices: 5682993--5683029 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5682983 GTAATTGGAG
5682993 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5683011 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5683029 T
1 T
5683030 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5683037 original size:24 final size:24
Alignment explanation
Indices: 5682985--5683031 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5682975 TTTCATATGT
* *
5682985 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
5683009 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
5683032 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:5690344 original size:17 final size:17
Alignment explanation
Indices: 5690322--5690377 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
5690312 AACGATCAAC
5690322 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
5690339 GGTCAACGATCGGGTCG
1 GGTCAACGGTCGGGTCG
5690356 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
5690373 GGTCA
1 GGTCA
5690378 GACCGGTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:5697620 original size:22 final size:22
Alignment explanation
Indices: 5697592--5697641 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
5697582 CGGTCAACGA
5697592 TCGGGTCGGGTCAACGGTCGGG
1 TCGGGTCGGGTCAACGGTCGGG
5697614 TCGGGTCGGGTCAACGGTCGGG
1 TCGGGTCGGGTCAACGGTCGGG
5697636 TCGGGT
1 TCGGGT
5697642 TAGACCGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.22, G:0.50, T:0.20
Consensus pattern (22 bp):
TCGGGTCGGGTCAACGGTCGGG
Found at i:5697641 original size:17 final size:17
Alignment explanation
Indices: 5697583--5697620 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5697573 AACGGTCAAC
5697583 GGTCAACGATCGGGTCG
1 GGTCAACGATCGGGTCG
*
5697600 GGTCAACGGTCGGGTCG
1 GGTCAACGATCGGGTCG
5697617 GGTC
1 GGTC
5697621 GGGTCAACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGATCGGGTCG
Found at i:5697688 original size:19 final size:19
Alignment explanation
Indices: 5697639--5697680 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
5697629 GGTCGGGTCG
5697639 GGTT-AGACCGGTAAAATC
1 GGTTCAGACCGGTAAAATC
*
5697657 GGTTCAGACCGGTCAAATC
1 GGTTCAGACCGGTAAAATC
5697676 GGTTC
1 GGTTC
5697681 GAACCGGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (19 bp):
GGTTCAGACCGGTAAAATC
Found at i:5697704 original size:19 final size:20
Alignment explanation
Indices: 5697682--5697728 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
5697672 AATCGGTTCG
5697682 AACCGGTTG-AAACCGGTCA
1 AACCGGTTGAAAACCGGTCA
*
5697701 AACCGGTTGAAAACCGGTTA
1 AACCGGTTGAAAACCGGTCA
5697721 AACCGGTT
1 AACCGGTT
5697729 TCCAGCAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (20 bp):
AACCGGTTGAAAACCGGTCA
Found at i:5697723 original size:29 final size:29
Alignment explanation
Indices: 5697664--5697727 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
5697654 ATCGGTTCAG
*
5697664 ACCGGTCAAATCGGTTCGAACCGGTTGAA
1 ACCGGTCAAACCGGTTCGAACCGGTTGAA
5697693 ACCGGTCAAACCGGTT-GAAAACCGGTT-AA
1 ACCGGTCAAACCGGTTCG--AACCGGTTGAA
5697722 ACCGGT
1 ACCGGT
5697728 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 1 0.03
29 23 0.72
30 8 0.25
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.19
Consensus pattern (29 bp):
ACCGGTCAAACCGGTTCGAACCGGTTGAA
Found at i:5697728 original size:9 final size:9
Alignment explanation
Indices: 5697639--5697728 Score: 63
Period size: 9 Copynumber: 9.4 Consensus size: 9
5697629 GGTCGGGTCG
*
5697639 GGTTAGACC
1 GGTTAAACC
* *
5697648 GGTAAAATC
1 GGTTAAACC
*
5697657 GGTTCAGACC
1 GGTT-AAACC
* *
5697667 GGTCAAATC
1 GGTTAAACC
*
5697676 GGTTCGAACC
1 GGTT-AAACC
5697686 GGTTGAAACC
1 GGTT-AAACC
*
5697696 GGTCAAACC
1 GGTTAAACC
5697705 GGTTGAAAACC
1 GGTT--AAACC
5697716 GGTTAAACC
1 GGTTAAACC
5697725 GGTT
1 GGTT
5697729 TCCAGCAGCC
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
9 32 0.52
10 20 0.33
11 9 0.15
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (9 bp):
GGTTAAACC
Found at i:5715050 original size:6 final size:6
Alignment explanation
Indices: 5715039--5715114 Score: 134
Period size: 6 Copynumber: 12.7 Consensus size: 6
5715029 AAAAGAAAGG
* *
5715039 GCATAT GCATAT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
1 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
5715087 GCATGT GCATGT GCATGT GCATGT GCAT
1 GCATGT GCATGT GCATGT GCATGT GCAT
5715115 TGCTATTTCT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (6 bp):
GCATGT
Found at i:5717586 original size:15 final size:15
Alignment explanation
Indices: 5717566--5717599 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5717556 CTCTGGTGGT
5717566 TCAGCAGGAGAAGCA
1 TCAGCAGGAGAAGCA
*
5717581 TCAGCAGGAGGAGCA
1 TCAGCAGGAGAAGCA
5717596 TCAG
1 TCAG
5717600 GCAAATGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.21, G:0.35, T:0.09
Consensus pattern (15 bp):
TCAGCAGGAGAAGCA
Found at i:5720398 original size:50 final size:50
Alignment explanation
Indices: 5720343--5720468 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
5720333 ATAGCAGGAA
* * *
5720343 AGCGCGCCCCCTGAACCGCGCTATATGCAGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCTTGAACCGCGCTATACGCAGATCTGGCGCCACGTGGGTAT
** * **
5720393 AGCGCGCCCCTTGCCCCGCGATATACGGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCTTGAACCGCGCTATACGCAGATCTGGCGCCACGTGGGTAT
* * *
5720443 AGTGCGCCCCTTGATCTGCGCTATAC
1 AGCGCGCCCCTTGAACCGCGCTATAC
5720469 CTGGATATCT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.16, C:0.33, G:0.29, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCTTGAACCGCGCTATACGCAGATCTGGCGCCACGTGGGTAT
Found at i:5720946 original size:111 final size:111
Alignment explanation
Indices: 5720771--5720973 Score: 388
Period size: 111 Copynumber: 1.8 Consensus size: 111
5720761 CATTTTGCTG
* *
5720771 ATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGTTGATTTATTTA
1 ATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGATTCATTTA
5720836 ATGCATGATTATTAGATTAAGAATTAAATATCTCGACACCTTACTA
66 ATGCATGATTATTAGATTAAGAATTAAATATCTCGACACCTTACTA
5720882 ATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGATTCATTTA
1 ATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGATTCATTTA
5720947 ATGCATGATTATTAGATTAAGAATTAA
66 ATGCATGATTATTAGATTAAGAATTAA
5720974 TTTTTGTAAT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 90 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.44
Consensus pattern (111 bp):
ATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGATTCATTTA
ATGCATGATTATTAGATTAAGAATTAAATATCTCGACACCTTACTA
Found at i:5722506 original size:18 final size:18
Alignment explanation
Indices: 5722479--5722518 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5722469 CCAGCAGCCA
*
5722479 CCGCAGCCATATATGATG
1 CCGCAACCATATATGATG
5722497 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
5722515 CCGC
1 CCGC
5722519 CATCGCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:5729796 original size:19 final size:19
Alignment explanation
Indices: 5729772--5729809 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5729762 AAATTTTCTC
5729772 TGCTTAATGTTTTAAGCTT
1 TGCTTAATGTTTTAAGCTT
5729791 TGCTTAATGTTTTAAGCTT
1 TGCTTAATGTTTTAAGCTT
5729810 ATATAAGCTT
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:0.21, C:0.11, G:0.16, T:0.53
Consensus pattern (19 bp):
TGCTTAATGTTTTAAGCTT
Found at i:5731956 original size:43 final size:43
Alignment explanation
Indices: 5731855--5732102 Score: 157
Period size: 43 Copynumber: 5.8 Consensus size: 43
5731845 AGGTGAAGAG
* *
5731855 ATATAGCGACGTTTTTGGAACAAACGCCTCAAAATG-TCA-ATAT
1 ATATAGCGACATTTTTGGAACAAACGCCACAAAA-GAT-ATATAT
*** *
5731898 ATATAGCGGTTTTTTTGGAACAAACGCCGCAAAAGATATATAT
1 ATATAGCGACATTTTTGGAACAAACGCCACAAAAGATATATAT
* * * * * ** *
5731941 TTATAGCGACATTTTT-TAACAAATGTCACAAAAGGTCGAGAT
1 ATATAGCGACATTTTTGGAACAAACGCCACAAAAGATATATAT
* * *
5731983 ATATAGCGACGTTTTTTGGATACAAACGCTACAAACA-ATCTATAT
1 ATATAGCGAC-ATTTTTGGA-ACAAACGCCACAAA-AGATATATAT
* * * * * ** **
5732028 CTATAGCGGCATTTTT-TAACAAATGTCGTAAAAGAT-TAGGT
1 ATATAGCGACATTTTTGGAACAAACGCCACAAAAGATATATAT
*
5732069 ATATAGCGACGTTTTTGGATACAAACGCCACAAA
1 ATATAGCGACATTTTTGGA-ACAAACGCCACAAA
5732103 TTATCTAAAA
Statistics
Matches: 152, Mismatches: 44, Indels: 18
0.71 0.21 0.08
Matches are distributed among these distances:
41 17 0.11
42 41 0.27
43 63 0.41
44 6 0.04
45 24 0.16
46 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (43 bp):
ATATAGCGACATTTTTGGAACAAACGCCACAAAAGATATATAT
Found at i:5731974 original size:42 final size:42
Alignment explanation
Indices: 5731927--5732084 Score: 124
Period size: 42 Copynumber: 3.7 Consensus size: 42
5731917 ACAAACGCCG
* *
5731927 CAAAAGATATATATTTATAGCGACATTTTTTAACAAATGTCA
1 CAAAAGATCTATATATATAGCGACATTTTTTAACAAATGTCA
* * * * *
5731969 CAAAAGGTCGAGATATATAGCGACGTTTTTTGGATACAAACG-CTA
1 CAAAAGATCTATATATATAGCGACATTTTTT--A-ACAAATGTC-A
* * *
5732014 CAAACA-ATCTATATCTATAGCGGCATTTTTTAACAAATGTCG
1 CAAA-AGATCTATATATATAGCGACATTTTTTAACAAATGTCA
* ** *
5732056 TAAAAGAT-TAGGTATATAGCGACGTTTTT
1 CAAAAGATCTATATATATAGCGACATTTTT
5732085 GGATACAAAC
Statistics
Matches: 88, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
41 17 0.19
42 36 0.41
43 2 0.02
44 2 0.02
45 30 0.34
46 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (42 bp):
CAAAAGATCTATATATATAGCGACATTTTTTAACAAATGTCA
Found at i:5732010 original size:87 final size:86
Alignment explanation
Indices: 5731896--5732102 Score: 262
Period size: 87 Copynumber: 2.4 Consensus size: 86
5731886 AAATGTCAAT
* *
5731896 ATATATAGCG--GTTTTTTTGGA-ACAAACGCCGCAAA-AGATATATATTTATAGCGACATTTTT
1 ATATATAGCGACG-TTTTTTGGATACAAACGCCACAAACA-ATATATATCTATAGCGACATTTTT
*
5731957 TAACAAATGTCACAAAAGGTCGAG
64 TAACAAATGTCACAAAAGAT-GAG
* * *
5731981 ATATATAGCGACGTTTTTTGGATACAAACGCTACAAACAATCTATATCTATAGCGGCATTTTTTA
1 ATATATAGCGACGTTTTTTGGATACAAACGCCACAAACAATATATATCTATAGCGACATTTTTTA
** *
5732046 ACAAATGTCGTAAAAGATTAG
66 ACAAATGTCACAAAAGATGAG
*
5732067 GTATATAGCGACG-TTTTTGGATACAAACGCCACAAA
1 ATATATAGCGACGTTTTTTGGATACAAACGCCACAAA
5732103 TTATCTAAAA
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
85 32 0.30
86 23 0.21
87 51 0.48
88 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (86 bp):
ATATATAGCGACGTTTTTTGGATACAAACGCCACAAACAATATATATCTATAGCGACATTTTTTA
ACAAATGTCACAAAAGATGAG
Found at i:5744780 original size:22 final size:22
Alignment explanation
Indices: 5744753--5744803 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
5744743 CGAGCTACAA
5744753 ATTATTAGGTATATTTGTTGAT
1 ATTATTAGGTATATTTGTTGAT
5744775 ATTATTAGGTATATTTGTTGAT
1 ATTATTAGGTATATTTGTTGAT
5744797 ATTATTA
1 ATTATTA
5744804 AAGAAGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (22 bp):
ATTATTAGGTATATTTGTTGAT
Found at i:5746311 original size:22 final size:22
Alignment explanation
Indices: 5746283--5746324 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5746273 CGTCGTCCGG
5746283 TTCTTCCGATCGATCAGACCGA
1 TTCTTCCGATCGATCAGACCGA
*
5746305 TTCTTCCGATCGATTAGACC
1 TTCTTCCGATCGATCAGACC
5746325 AGTTCGATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (22 bp):
TTCTTCCGATCGATCAGACCGA
Found at i:5753164 original size:51 final size:51
Alignment explanation
Indices: 5753083--5753287 Score: 293
Period size: 51 Copynumber: 4.0 Consensus size: 51
5753073 ACTTTTTATC
** * * *
5753083 ATTTTATTTTATTTTAATTTAGTCACTGTTTATTTTTGATTTAACTAATGTT
1 ATTTTATTTTA-TGCAATTTAGTCACTGTTTATTTTTAATTTAGCTACTGTT
* * *
5753135 ATTTTGTTTTATGCAATTTAGTCATTGTTTATTTTTAATTTAGCTATTGTT
1 ATTTTATTTTATGCAATTTAGTCACTGTTTATTTTTAATTTAGCTACTGTT
* * *
5753186 ATTTTATTTTATGCAATTTAGTTATTGTTTATTTCTAATTTAGCTACTGTT
1 ATTTTATTTTATGCAATTTAGTCACTGTTTATTTTTAATTTAGCTACTGTT
*
5753237 ATTTTATTTTATGCAATTTAGTCACTGTTTATTTTTGATTTAGCTACTGTT
1 ATTTTATTTTATGCAATTTAGTCACTGTTTATTTTTAATTTAGCTACTGTT
5753288 TTATCTTGTT
Statistics
Matches: 138, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
51 128 0.93
52 10 0.07
ACGTcount: A:0.23, C:0.07, G:0.10, T:0.60
Consensus pattern (51 bp):
ATTTTATTTTATGCAATTTAGTCACTGTTTATTTTTAATTTAGCTACTGTT
Found at i:5753189 original size:21 final size:22
Alignment explanation
Indices: 5753149--5753190 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5753139 TGTTTTATGC
5753149 AATTTAGTCATTGTTTATTTTT
1 AATTTAGTCATTGTTTATTTTT
5753171 AATTTAG-CTATTG-TTATTTT
1 AATTTAGTC-ATTGTTTATTTT
5753191 ATTTTATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.62
Consensus pattern (22 bp):
AATTTAGTCATTGTTTATTTTT
Found at i:5753191 original size:26 final size:26
Alignment explanation
Indices: 5753162--5753246 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 26
5753152 TTAGTCATTG
5753162 TTTATTTTTAATTTAGCTATTGTTAT
1 TTTATTTTTAATTTAGCTATTGTTAT
*
5753188 TTTATTTTATGCAATTTAGTTATTG----
1 TTTATTTT-T--AATTTAGCTATTGTTAT
* *
5753213 TTTATTTCTAATTTAGCTACTGTTAT
1 TTTATTTTTAATTTAGCTATTGTTAT
5753239 TTTATTTT
1 TTTATTTT
5753247 ATGCAATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
22 11 0.23
24 1 0.02
25 7 0.15
26 15 0.32
27 1 0.02
29 12 0.26
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.64
Consensus pattern (26 bp):
TTTATTTTTAATTTAGCTATTGTTAT
Found at i:5753211 original size:29 final size:30
Alignment explanation
Indices: 5753133--5753219 Score: 68
Period size: 29 Copynumber: 3.2 Consensus size: 30
5753123 TTAACTAATG
* *
5753133 TTATTTTGTTTTATGCAATTTAGTCATTG-
1 TTATTTTATTTTATGCAATTTAGTTATTGT
*
5753162 ----TTTATTTT-T--AATTTAGCTATTGT
1 TTATTTTATTTTATGCAATTTAGTTATTGT
5753185 TAT-TT-TATTTTATGCAATTTAGTTATTGT
1 T-TATTTTATTTTATGCAATTTAGTTATTGT
5753214 TTATTT
1 TTATTT
5753220 CTAATTTAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 19
0.66 0.06 0.28
Matches are distributed among these distances:
22 11 0.25
24 1 0.02
25 7 0.16
26 6 0.14
27 2 0.05
28 1 0.02
29 16 0.36
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (30 bp):
TTATTTTATTTTATGCAATTTAGTTATTGT
Found at i:5757826 original size:2 final size:2
Alignment explanation
Indices: 5757819--5757866 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5757809 ATGCATCCAA
5757819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5757861 AT AT AT
1 AT AT AT
5757867 TTACCTATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5758229 original size:82 final size:82
Alignment explanation
Indices: 5758126--5758395 Score: 292
Period size: 82 Copynumber: 3.3 Consensus size: 82
5758116 GTTTTTTGAC
* * * * *
5758126 AAACGCCGTGATATCCAAATATATAGTGGCGTTTTTGTGCAAACGCCACTAAAAACGTGTACTTT
1 AAACACCGTAATATCCAAATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAACGCGTACTTT
5758191 AGTGGCATTTATGTAAA
66 AGTGGCATTTATGTAAA
* * * **** * * *
5758208 AAACACCGTAATATCTAAATATATAGCGGTGTTTTCACAAAAACGTCGCTAAAATCACGTACTTT
1 AAACACCGTAATATCCAAATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAACGCGTACTTT
*
5758273 AGTGGCATTT-T-TAGAC
66 AGTGGCATTTATGTA-AA
** * * * *
5758289 AAACGTCGTGATATCCAAATATATAATGGCGTTTTTGTGTAAACGCCGCTAAAAACGCGTAATTT
1 AAACACCGTAATATCCAAATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAACGCGTACTTT
*
5758354 AGTGGTATTTATGTAAA
66 AGTGGCATTTATGTAAA
* *
5758371 AAACACCGCAATATCCGAATATATA
1 AAACACCGTAATATCCAAATATATA
5758396 TAAAAACGCG
Statistics
Matches: 146, Mismatches: 39, Indels: 6
0.76 0.20 0.03
Matches are distributed among these distances:
80 2 0.01
81 60 0.41
82 82 0.56
83 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (82 bp):
AAACACCGTAATATCCAAATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAACGCGTACTTT
AGTGGCATTTATGTAAA
Found at i:5758339 original size:81 final size:81
Alignment explanation
Indices: 5758117--5758363 Score: 271
Period size: 81 Copynumber: 3.0 Consensus size: 81
5758107 TGTAGCGGCG
* * *
5758117 TTTTTTGACAAACGCCGTGATATCCAAATATATAGTGGCGTTTTTGTGCAAACGCCACTAAAAAC
1 TTTTTAGACAAACGCCGTGATATCCAAATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAAC
*
5758182 GTGTACTTTAGTGGCA
66 GCGTACTTTAGTGGCA
* * * * * * **** *
5758198 TTTATGTA-AAAAACACCGTAATATCTAAATATATAGCGGTGTTTTCACAAAAACGTCGCTAAAA
1 TTT-T-TAGACAAACGCCGTGATATCCAAATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAA
* *
5758262 TCACGTACTTTAGTGGCA
64 ACGCGTACTTTAGTGGCA
* * *
5758280 TTTTTAGACAAACGTCGTGATATCCAAATATATAATGGCGTTTTTGTGTAAACGCCGCTAAAAAC
1 TTTTTAGACAAACGCCGTGATATCCAAATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAAC
* *
5758345 GCGTAATTTAGTGGTA
66 GCGTACTTTAGTGGCA
5758361 TTT
1 TTT
5758364 ATGTAAAAAA
Statistics
Matches: 128, Mismatches: 35, Indels: 6
0.76 0.21 0.04
Matches are distributed among these distances:
80 2 0.02
81 63 0.49
82 62 0.48
83 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (81 bp):
TTTTTAGACAAACGCCGTGATATCCAAATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAAC
GCGTACTTTAGTGGCA
Found at i:5758734 original size:33 final size:31
Alignment explanation
Indices: 5758673--5758734 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
5758663 CACTAACTAT
** *
5758673 TATTCTTGCGTCAATCTTCTCGACGCTGCCG
1 TATTCTTGCGTCAATAGTCTCGAAGCTGCCG
5758704 TATTCTTGCCGTCAAGTAGTCTCGAAGCTGC
1 TATTCTTG-CGTCAA-TAGTCTCGAAGCTGC
5758735 TGTCACCGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 8 0.31
32 6 0.23
33 12 0.46
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (31 bp):
TATTCTTGCGTCAATAGTCTCGAAGCTGCCG
Found at i:5761353 original size:104 final size:104
Alignment explanation
Indices: 5761209--5761420 Score: 388
Period size: 104 Copynumber: 2.0 Consensus size: 104
5761199 TAACTAAGGA
*
5761209 TATATAACCTCTGAGTTACTTTATTTTCTTTGTTTACTTCATTTGAAATGCGCGTTTTTTGTGCT
1 TATATAACCTCTGAGTTACTTTATTTCCTTTGTTTACTTCATTTGAAATGCGCGTTTTTTGTGCT
*
5761274 GCTCTTTAACTGAAACAATGAGGTATATAAGAGAAGATT
66 GCTCTTTAACTGAAACAATGAGGTATATAAAAGAAGATT
*
5761313 TATATATCCTCTGAGTTACTTTATTTCCTTTGTTTACTTCATTTGAAATGCGCGTTTTTTGTGCT
1 TATATAACCTCTGAGTTACTTTATTTCCTTTGTTTACTTCATTTGAAATGCGCGTTTTTTGTGCT
*
5761378 GCTCTTTAATTGAAACAATGAGGTATATAAAAGAAGATT
66 GCTCTTTAACTGAAACAATGAGGTATATAAAAGAAGATT
5761417 TATA
1 TATA
5761421 AACTCGATCA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (104 bp):
TATATAACCTCTGAGTTACTTTATTTCCTTTGTTTACTTCATTTGAAATGCGCGTTTTTTGTGCT
GCTCTTTAACTGAAACAATGAGGTATATAAAAGAAGATT
Found at i:5762439 original size:43 final size:43
Alignment explanation
Indices: 5762389--5762696 Score: 379
Period size: 43 Copynumber: 7.2 Consensus size: 43
5762379 ACGGTCATTA
* * *
5762389 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCT-AACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTCGACCTATT
* * * *
5762432 GTGGCGTTTGTTTCAAAAACGTCGCTATAGATCT-GACAT-TT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATT
* * * *
5762473 ACGGCGTTTGTTCCAAAAATGCCGCTATAGATATCGATCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATT
*
5762516 GCGGCATTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATT
* * *
5762559 GCGGCGTTTGTCCCAAAAACGTCGCTATAGATCTCAACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATT
* * *
5762602 ACGGCGTTTGTCCCAAAAATGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATT
* * *
5762645 TCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACATATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATT
* *
5762688 ACGGTGTTT
1 GCGGCGTTT
5762697 TTTGTTCACA
Statistics
Matches: 231, Mismatches: 32, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
41 30 0.13
42 26 0.11
43 175 0.76
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATT
Found at i:5762655 original size:129 final size:127
Alignment explanation
Indices: 5762389--5762696 Score: 429
Period size: 129 Copynumber: 2.4 Consensus size: 127
5762379 ACGGTCATTA
* * * * **
5762389 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCT-AACCTTTTGTGGCGTTTGTTTCAAAAACG
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCCAAAAACG
* * *
5762453 TCGCTATAGATCTGACATTTACGGCGTTTGTTCCAAAAATGCCGCTATAGATATCGATCTATT
65 TCGCTATAGATCTAACATTTACGGCGTTTGTCCCAAAAATGCCGCTATAGATATCGACCTATT
*
5762516 GCGGCATTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCCAAAAACGT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCCAAAAACGT
* *
5762581 CGCTATAGATCTCAACCTATTACGGCGTTTGTCCCAAAAATGCCGCTATAGATCTCGACCTATT
66 CGCTATAGATCT-AACAT-TTACGGCGTTTGTCCCAAAAATGCCGCTATAGATATCGACCTATT
* * * * *
5762645 TCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACATATTACGGTGTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTT
5762697 TTTGTTCACA
Statistics
Matches: 160, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
126 22 0.14
127 47 0.29
128 3 0.02
129 88 0.55
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (127 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCCAAAAACGT
CGCTATAGATCTAACATTTACGGCGTTTGTCCCAAAAATGCCGCTATAGATATCGACCTATT
Found at i:5763453 original size:30 final size:29
Alignment explanation
Indices: 5763400--5763458 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
5763390 TGTAAACATA
* *
5763400 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
5763430 TCACATATACATGTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
5763459 GTAAATTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:5765032 original size:23 final size:23
Alignment explanation
Indices: 5764973--5765039 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
5764963 CGTATAAATA
*
5764973 CACCGAAGTGCCACGTAAAATTG
1 CACCGAAGTGCCATGTAAAATTG
*
5764996 CACCGAAGTGCCATGTAGAATTG
1 CACCGAAGTGCCATGTAAAATTG
*
5765019 CACCGAAGTGCCATATAAAAT
1 CACCGAAGTGCCATGTAAAAT
5765040 GTCCCTAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (23 bp):
CACCGAAGTGCCATGTAAAATTG
Found at i:5781598 original size:36 final size:36
Alignment explanation
Indices: 5781548--5781623 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
5781538 GCCTTAGGTC
* * *
5781548 CATAAGGAATTACCAGCTTGATCGGTGCTGAACCTG
1 CATAAGGAAATACCAGCTTGATCGGAGCTGAACCTA
5781584 CATAAGGAAATACCAGCTTGATCGGAGCTGAACCTA
1 CATAAGGAAATACCAGCTTGATCGGAGCTGAACCTA
5781620 CATA
1 CATA
5781624 CTCCAGAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (36 bp):
CATAAGGAAATACCAGCTTGATCGGAGCTGAACCTA
Found at i:5782613 original size:26 final size:26
Alignment explanation
Indices: 5782577--5782641 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
5782567 TTCGAGATTG
*
5782577 ATTTATTCATTTCAGAGCTT-GAGAGT
1 ATTTAGTCATTTCAGAGCTTGGAG-GT
* *
5782603 ATTTAGTCATTCCAGGGCTTGGAGGT
1 ATTTAGTCATTTCAGAGCTTGGAGGT
*
5782629 ATTTGGGTCATTT
1 ATTT-AGTCATTT
5782642 TACACTTCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 23 0.72
27 9 0.28
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.42
Consensus pattern (26 bp):
ATTTAGTCATTTCAGAGCTTGGAGGT
Found at i:5782677 original size:27 final size:27
Alignment explanation
Indices: 5782626--5782687 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
5782616 AGGGCTTGGA
* *
5782626 GGTATTTGGGTCATTTTACACTTCAGG
1 GGTATTTTGGTCATTTTACACTTCAAG
*
5782653 GGTATTTTGGTCATTTTATGA-TTCAAG
1 GGTATTTTGGTCATTTTA-CACTTCAAG
5782680 GGTATTTT
1 GGTATTTT
5782688 ATTCATTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (27 bp):
GGTATTTTGGTCATTTTACACTTCAAG
Found at i:5793691 original size:14 final size:14
Alignment explanation
Indices: 5793672--5793700 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5793662 AGCACCCTTA
5793672 TTTTTATGAAGTCT
1 TTTTTATGAAGTCT
5793686 TTTTTATGAAGTCT
1 TTTTTATGAAGTCT
5793700 T
1 T
5793701 ACTCGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (14 bp):
TTTTTATGAAGTCT
Found at i:5795523 original size:23 final size:24
Alignment explanation
Indices: 5795492--5795546 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
5795482 CTTGTTTTTT
5795492 TATTATTATTCAAATTTGGT-ATTG
1 TATT-TTATTCAAATTTGGTCATTG
***
5795516 TATTTTATTTTTATTTGGTCATTG
1 TATTTTATTCAAATTTGGTCATTG
5795540 -ATTTTAT
1 TATTTTAT
5795547 GTTACTATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.24, C:0.04, G:0.11, T:0.62
Consensus pattern (24 bp):
TATTTTATTCAAATTTGGTCATTG
Found at i:5796723 original size:47 final size:48
Alignment explanation
Indices: 5796653--5796744 Score: 159
Period size: 47 Copynumber: 1.9 Consensus size: 48
5796643 TGTATCTCCC
5796653 GCTTTTGTCCAGGGGTGACCGCTATTGATTACCAAAATAAATCAATAT
1 GCTTTTGTCCAGGGGTGACCGCTATTGATTACCAAAATAAATCAATAT
* *
5796701 GCTTTT-TCCCGGGGTGACCGCTATTGATTCCCAAAATAAATCAA
1 GCTTTTGTCCAGGGGTGACCGCTATTGATTACCAAAATAAATCAA
5796745 CACCTTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
47 36 0.86
48 6 0.14
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (48 bp):
GCTTTTGTCCAGGGGTGACCGCTATTGATTACCAAAATAAATCAATAT
Found at i:5797320 original size:46 final size:45
Alignment explanation
Indices: 5797264--5797369 Score: 144
Period size: 45 Copynumber: 2.3 Consensus size: 45
5797254 TGCACATACC
*
5797264 ATGCACCGATGCACTGAGGA-T-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACT-AGGACTATTT-TG-AAACATCGAATGCATTTG
**
5797310 ATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCATTTG
1 ATGCATCGATGCACTAGGACTATTTTGAAACATCGAATGCATTTG
5797355 ATGCATCGATGCACT
1 ATGCATCGATGCACT
5797370 CTTAGTGCAC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
45 35 0.64
46 17 0.31
47 3 0.05
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTAGGACTATTTTGAAACATCGAATGCATTTG
Found at i:5799306 original size:22 final size:21
Alignment explanation
Indices: 5799282--5799321 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5799272 GAGAAATTGT
5799282 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
5799303 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
5799322 AAATAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:5805730 original size:65 final size:64
Alignment explanation
Indices: 5805661--5805840 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 64
5805651 AATTAAATTG
* *
5805661 AACATCGAATGCATTTCATGCATCGATGCACATATCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACATATCATGCACCGATGCACTCAGGATATTT-TG-
5805725 A
64 A
* ** * * *
5805726 AACATCGAATGCATTTGATACATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATATCATGCACCGATGCACTCAGGATATTTTGA
* * *
5805790 AACATCGAATGCACTTGATGCATCGATGCAC-TCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACATATCA-TGCACCGATGCACT
5805841 AAGGGTCCAA
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
63 2 0.02
64 42 0.43
65 48 0.49
66 5 0.05
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACATATCATGCACCGATGCACTCAGGATATTTTGA
Found at i:5805820 original size:17 final size:19
Alignment explanation
Indices: 5805792--5805840 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5805782 TATTTTGAAA
5805792 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
5805810 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
5805829 CACCGATGCACT
1 CATCGATGCACT
5805841 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:5817242 original size:20 final size:20
Alignment explanation
Indices: 5817217--5817267 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
5817207 ATCCTATTCT
5817217 CTGATAATCTTTTATTCTCA
1 CTGATAATCTTTTATTCTCA
5817237 CTGATAATCTTTTATTCTCA
1 CTGATAATCTTTTATTCTCA
*
5817257 CTGGTAATCTT
1 CTGATAATCTT
5817268 ACATTCCGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.49
Consensus pattern (20 bp):
CTGATAATCTTTTATTCTCA
Found at i:5817273 original size:20 final size:20
Alignment explanation
Indices: 5817217--5817273 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
5817207 ATCCTATTCT
**
5817217 CTGATAATCTTTTATTCTCA
1 CTGATAATCTTACATTCTCA
**
5817237 CTGATAATCTTTTATTCTCA
1 CTGATAATCTTACATTCTCA
*
5817257 CTGGTAATCTTACATTC
1 CTGATAATCTTACATTC
5817274 CGTGAACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.47
Consensus pattern (20 bp):
CTGATAATCTTACATTCTCA
Found at i:5820287 original size:24 final size:23
Alignment explanation
Indices: 5820217--5820281 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 23
5820207 CAATCTTATA
*
5820217 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * *
5820240 CGACACTTCGGTGTAAATTCTACG
1 TGGCACTTCGGTG-CAATTCTACG
5820264 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
5820282 TATACGAGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 14 0.41
24 20 0.59
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:5821476 original size:46 final size:45
Alignment explanation
Indices: 5821374--5821479 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
5821364 GTGCACTAAG
* * * *
5821374 AGTGCATTGATACATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* * *
5821419 AGTACATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
5821465 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
5821480 GGTATATACA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 26 0.51
46 22 0.43
47 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:5821525 original size:65 final size:65
Alignment explanation
Indices: 5821421--5821580 Score: 284
Period size: 65 Copynumber: 2.5 Consensus size: 65
5821411 ATAGCCAGAG
*
5821421 TACATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTATA
1 TACATCGATGCATGAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTATA
* *
5821486 TACATCGATGCATGAAATCCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTATG
1 TACATCGATGCATGAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTATA
*
5821551 TGCATCGATGCATGAAATGCATTCGATGTT
1 TACATCGATGCATGAAATGCATTCGATGTT
5821581 CAATTTAATT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 90 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (65 bp):
TACATCGATGCATGAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTATA
Found at i:5822249 original size:2 final size:2
Alignment explanation
Indices: 5822242--5822269 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5822232 ACCAAAACAA
5822242 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
5822270 TAAGTTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5823946 original size:24 final size:24
Alignment explanation
Indices: 5823919--5823968 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
5823909 GTTTGTAATC
5823919 ATCAAACAATCAATGCCCGATAAA
1 ATCAAACAATCAATGCCCGATAAA
5823943 ATCAAACAATCAATGCCCGATAAA
1 ATCAAACAATCAATGCCCGATAAA
5823967 AT
1 AT
5823969 GTTCATCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.24, G:0.08, T:0.18
Consensus pattern (24 bp):
ATCAAACAATCAATGCCCGATAAA
Found at i:5824315 original size:23 final size:22
Alignment explanation
Indices: 5824285--5824360 Score: 100
Period size: 21 Copynumber: 3.5 Consensus size: 22
5824275 GGCCTTGTGC
5824285 ATCGATGCACATTCAAGGCGTGT
1 ATCGATGCACATTCAAGG-GTGT
* *
5824308 ATCGATGCACCTTC-ATGGTGT
1 ATCGATGCACATTCAAGGGTGT
*
5824329 ATCGATGCACATTCAAGGATGT
1 ATCGATGCACATTCAAGGGTGT
*
5824351 ATTGATGCAC
1 ATCGATGCAC
5824361 TGTTAGGTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 17 0.37
22 16 0.35
23 13 0.28
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (22 bp):
ATCGATGCACATTCAAGGGTGT
Found at i:5824330 original size:21 final size:20
Alignment explanation
Indices: 5824285--5824379 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 20
5824275 GGCCTTGTGC
5824285 ATCGATGCACATTCAAGGCGTGT
1 ATCGATGCACATTC-A-G-GTGT
*
5824308 ATCGATGCACCTTCATGGTGT
1 ATCGATGCACATTCA-GGTGT
5824329 ATCGATGCACATTCAAGGATGT
1 ATCGATGCACATTC-AGG-TGT
* *
5824351 ATTGATGCAC-TGTTAGGTGT
1 ATCGATGCACAT-TCAGGTGT
5824371 ATCGATGCA
1 ATCGATGCA
5824380 TGAAGCACAA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
20 11 0.17
21 23 0.37
22 16 0.25
23 13 0.21
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATCGATGCACATTCAGGTGT
Found at i:5824340 original size:44 final size:42
Alignment explanation
Indices: 5824259--5824379 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 42
5824249 AAAACCTGAT
* ** *
5824259 GGATGTATCGATGCA-TGGCCTTGTGCATCGATGCACATTCAA
1 GGATGTATCGATGCACT-GTCAGGTGTATCGATGCACATTCAA
*
5824301 GGCGTGTATCGATGCACCT-TCATGGTGTATCGATGCACATTCAA
1 GG-ATGTATCGATGCA-CTGTCA-GGTGTATCGATGCACATTCAA
* *
5824345 GGATGTATTGATGCACTGTTAGGTGTATCGATGCA
1 GGATGTATCGATGCACTGTCAGGTGTATCGATGCA
5824380 TGAAGCACAA
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
42 18 0.27
43 26 0.39
44 21 0.32
45 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (42 bp):
GGATGTATCGATGCACTGTCAGGTGTATCGATGCACATTCAA
Found at i:5830245 original size:18 final size:18
Alignment explanation
Indices: 5830218--5830264 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
5830208 GCATGGCTGG
5830218 TGCA-TCGATGTATCAAA
1 TGCATTCGATGTATCAAA
5830235 TGCATTCGATGTATCAAA
1 TGCATTCGATGTATCAAA
5830253 TGCATTCGATGT
1 TGCATTCGATGT
5830265 TTTCATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (18 bp):
TGCATTCGATGTATCAAA
Found at i:5830304 original size:83 final size:82
Alignment explanation
Indices: 5830154--5830333 Score: 217
Period size: 83 Copynumber: 2.2 Consensus size: 82
5830144 GAACTAAGAG
* * *
5830154 TGCA-TCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGACTCGATGCATGGCTGG
1 TGCATTCGATGTATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGACTCGATGCATGGCTGG
*
5830218 TGCATCGATGTATCAAA
66 TGCATCGATGCATCAAA
* *
5830235 TGCATTCGATGTATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTG-CATCGATGCATGG-
1 TGCATTCGATGTATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGAC-TCGATGCATGGC
* *
5830297 TATGTGCATCGATGCATGAAA
63 T-GGTGCATCGATGCATCAAA
5830318 TGCATTCGATGT-TCAA
1 TGCATTCGATGTATCAA
5830334 TTTAATTCAT
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
81 4 0.05
82 28 0.33
83 51 0.59
84 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (82 bp):
TGCATTCGATGTATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGACTCGATGCATGGCTGG
TGCATCGATGCATCAAA
Found at i:5831389 original size:22 final size:22
Alignment explanation
Indices: 5831364--5831424 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
5831354 TTAAGGACAG
*
5831364 TAAATCGGACTTGTTAAAGAAA
1 TAAATCAGACTTGTTAAAGAAA
5831386 TAAATCAGACTTGTTAAAGAAA
1 TAAATCAGACTTGTTAAAGAAA
5831408 TAAATCAGACTTGTTAA
1 TAAATCAGACTTGTTAA
5831425 TTACATGAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.30
Consensus pattern (22 bp):
TAAATCAGACTTGTTAAAGAAA
Found at i:5834885 original size:24 final size:22
Alignment explanation
Indices: 5834845--5834921 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
5834835 ATGCAATTAA
5834845 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
5834864 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
5834887 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
5834908 TGCATCGATGCACT
1 TGCATCGATGCACT
5834922 TCAAGGGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:5836537 original size:23 final size:23
Alignment explanation
Indices: 5836511--5836569 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
5836501 TGGCACTTTA
5836511 GTGCATTTCTACGCGGCACTACG
1 GTGCATTTCTACGCGGCACTACG
* * * *
5836534 GTGCAATTCTATGTGGCACTTCG
1 GTGCATTTCTACGCGGCACTACG
* *
5836557 GGGCATTTATACG
1 GTGCATTTCTACG
5836570 AGCTGTGGTG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.31
Consensus pattern (23 bp):
GTGCATTTCTACGCGGCACTACG
Found at i:5840526 original size:13 final size:13
Alignment explanation
Indices: 5840508--5840541 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5840498 AATATAAGTT
5840508 TATATATAAACTA
1 TATATATAAACTA
5840521 TATATATAAACTA
1 TATATATAAACTA
*
5840534 TATTTATA
1 TATATATA
5840542 TTATAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:5840528 original size:15 final size:15
Alignment explanation
Indices: 5840508--5840568 Score: 72
Period size: 15 Copynumber: 4.0 Consensus size: 15
5840498 AATATAAGTT
5840508 TATATATAAAC--TA
1 TATATATAAACTATA
5840521 TATATATAAACTATA
1 TATATATAAACTATA
5840536 TTTATATTATAAACTATA
1 --TATA-TATAAACTATA
*
5840554 TATGTATAAACTATA
1 TATATATAAACTATA
5840569 AAAATATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
13 11 0.26
15 13 0.31
16 3 0.07
17 4 0.10
18 11 0.26
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:5840562 original size:33 final size:30
Alignment explanation
Indices: 5840506--5840568 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 30
5840496 ATAATATAAG
5840506 TTTATATATAAACTATATATATAAACTATA
1 TTTATATATAAACTATATATATAAACTATA
5840536 TTTATATTATAAACTATATATGTATAAACTATA
1 TTTATA-TATAAACTATATA--TATAAACTATA
5840569 AAAATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 6 0.20
31 13 0.43
33 11 0.37
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (30 bp):
TTTATATATAAACTATATATATAAACTATA
Found at i:5840622 original size:2 final size:2
Alignment explanation
Indices: 5840617--5840655 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5840607 AGTGTGTGTG
5840617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5840656 TCAAAGTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5840994 original size:4 final size:4
Alignment explanation
Indices: 5840987--5841055 Score: 57
Period size: 4 Copynumber: 17.2 Consensus size: 4
5840977 TCTATATATA
* * * * *
5840987 TGTG TGTG TGTG TGTG CGTG TGTG TGTG CGTG TGTG CGTG CGTG CGTG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
* * * *
5841035 CGTG TATG CGTG TGCG TGTG T
1 TGTG TGTG TGTG TGTG TGTG T
5841056 AAACTATATA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.01, C:0.12, G:0.48, T:0.39
Consensus pattern (4 bp):
TGTG
Found at i:5841007 original size:12 final size:12
Alignment explanation
Indices: 5840987--5841030 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
5840977 TCTATATATA
*
5840987 TGTGTGTGTGTG
1 TGTGCGTGTGTG
5840999 TGTGCGTGTGTG
1 TGTGCGTGTGTG
5841011 TGTGCGTGTGTG
1 TGTGCGTGTGTG
*
5841023 CGTGCGTG
1 TGTGCGTG
5841031 CGTGCGTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.00, C:0.09, G:0.50, T:0.41
Consensus pattern (12 bp):
TGTGCGTGTGTG
Found at i:5841046 original size:12 final size:12
Alignment explanation
Indices: 5840992--5841038 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
5840982 ATATATGTGT
*
5840992 GTGTGTGTGTGC
1 GTGTGTGCGTGC
*
5841004 GTGTGTGTGTGC
1 GTGTGTGCGTGC
5841016 GTGTGTGCGTGC
1 GTGTGTGCGTGC
*
5841028 GTGCGTGCGTG
1 GTGTGTGCGTG
5841039 TATGCGTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.00, C:0.13, G:0.51, T:0.36
Consensus pattern (12 bp):
GTGTGTGCGTGC
Found at i:5841197 original size:66 final size:65
Alignment explanation
Indices: 5841054--5841205 Score: 150
Period size: 68 Copynumber: 2.3 Consensus size: 65
5841044 GTGTGCGTGT
* * * * *
5841054 GTAAACTATATAA--AATATATAGTTTATAAATTATAATTTATATTAATATAGTATATATATGTA
1 GTAAACTATATAAGTAATATATAGATTATAAATTATAATATATATTAATATAGAAAATATATGCA
* *
5841117 TGTATAACTAATATAAGTAATCTATAGATTATATATATATATATATATATT-ATATAGAAAATAC
1 -GTA-AACT-ATATAAGTAATATATAGATTATAAAT-TATA-ATATATATTAATATAGAAAATA-
5841181 TATGCA
60 TATGCA
5841187 -TAAACTATATAAAGTAATA
1 GTAAACTATAT-AAGTAATA
5841206 AAATTATAGT
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
64 3 0.04
65 4 0.06
66 10 0.14
67 11 0.15
68 17 0.24
69 14 0.19
70 13 0.18
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.41
Consensus pattern (65 bp):
GTAAACTATATAAGTAATATATAGATTATAAATTATAATATATATTAATATAGAAAATATATGCA
Found at i:5841337 original size:19 final size:19
Alignment explanation
Indices: 5841313--5841349 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5841303 CATGTATAGT
5841313 ATATATAAACTACATATAC
1 ATATATAAACTACATATAC
* *
5841332 ATATATAACCTATATATA
1 ATATATAAACTACATATA
5841350 TAAACAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATATAAACTACATATAC
Found at i:5841452 original size:7 final size:7
Alignment explanation
Indices: 5841442--5841502 Score: 61
Period size: 7 Copynumber: 8.7 Consensus size: 7
5841432 ATAGAAACCC
5841442 TAAACTA
1 TAAACTA
*
5841449 TAAACCA
1 TAAACTA
*
5841456 TAAACTT
1 TAAACTA
*
5841463 TAAACCA
1 TAAACTA
*
5841470 TAAACTT
1 TAAACTA
*
5841477 TAAACCA
1 TAAACTA
5841484 TAAAC-A
1 TAAACTA
5841490 CTAAACTA
1 -TAAACTA
5841498 TAAAC
1 TAAAC
5841503 CCTAATATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
6 1 0.02
7 41 0.95
8 1 0.02
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAACTA
Found at i:5841460 original size:21 final size:20
Alignment explanation
Indices: 5841436--5841507 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
5841426 AGGTTTATAG
*
5841436 AAACCCTAAACTATAAACCAT
1 AAACCCTAAAC-ATAAACTAT
** *
5841457 AAACTTTAAACCATAAACTTT
1 AAACCCTAAA-CATAAACTAT
*
5841478 AAACCATAAACACTAAACTAT
1 AAACCCTAAACA-TAAACTAT
5841499 AAACCCTAA
1 AAACCCTAA
5841508 TATAAATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.05
21 38 0.93
22 1 0.02
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (20 bp):
AAACCCTAAACATAAACTAT
Found at i:5841507 original size:14 final size:14
Alignment explanation
Indices: 5841436--5841502 Score: 89
Period size: 14 Copynumber: 4.8 Consensus size: 14
5841426 AGGTTTATAG
* *
5841436 AAACCCTAAACTAT
1 AAACCATAAACTTT
5841450 AAACCATAAACTTT
1 AAACCATAAACTTT
5841464 AAACCATAAACTTT
1 AAACCATAAACTTT
**
5841478 AAACCATAAACACT
1 AAACCATAAACTTT
*
5841492 AAACTATAAAC
1 AAACCATAAAC
5841503 CCTAATATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 48 1.00
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (14 bp):
AAACCATAAACTTT
Found at i:5841988 original size:14 final size:14
Alignment explanation
Indices: 5841957--5841991 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5841947 TCATAAAACC
5841957 TAAACCCTAAATAT
1 TAAACCCTAAATAT
5841971 TAAACCCTAAACTA-
1 TAAACCCTAAA-TAT
5841985 TAAACCC
1 TAAACCC
5841992 CAAGTAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 18 0.90
15 2 0.10
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAATAT
Found at i:5841988 original size:21 final size:21
Alignment explanation
Indices: 5841927--5841982 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
5841917 TTATAGAAAC
*
5841927 CATACACCCTAAACCCTAAAT
1 CATAAACCCTAAACCCTAAAT
*
5841948 CATAAAACCTAAACCCTAAAT
1 CATAAACCCTAAACCCTAAAT
5841969 -ATTAAACCCTAAAC
1 CA-TAAACCCTAAAC
5841983 TATAAACCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (21 bp):
CATAAACCCTAAACCCTAAAT
Found at i:5842582 original size:37 final size:39
Alignment explanation
Indices: 5842503--5842583 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 39
5842493 TAACAATTTG
* *
5842503 TAAAATATTTATATATTTTCTTTAAAAAATTTAAATTCA
1 TAAAATATTTATATATTTTCTTTAAAAAATTGAAAATCA
*
5842542 TAAAAT-TTATATATATTTT-TTTACAAAATTGAAAAT-A
1 TAAAATATT-TATATATTTTCTTTAAAAAATTGAAAATCA
5842579 TAAAA
1 TAAAA
5842584 AGGTTTAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 6 0.16
38 16 0.42
39 16 0.42
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (39 bp):
TAAAATATTTATATATTTTCTTTAAAAAATTGAAAATCA
Found at i:5843508 original size:23 final size:24
Alignment explanation
Indices: 5843478--5843523 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
5843468 TTATTTTTTG
5843478 TATAAATTAAACTATA-TAATTTA
1 TATAAATTAAACTATATTAATTTA
*
5843501 TATAAATTAAAGTATATTAATTT
1 TATAAATTAAACTATATTAATTT
5843524 TCCTTTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TATAAATTAAACTATATTAATTTA
Found at i:5843814 original size:16 final size:16
Alignment explanation
Indices: 5843793--5843843 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
5843783 CTGATCATTT
5843793 ACATGTCAGGTTAAAA
1 ACATGTCAGGTTAAAA
* *
5843809 ACATGTTAGATTAAAA
1 ACATGTCAGGTTAAAA
*
5843825 ACATGTCAGGTTGAAA
1 ACATGTCAGGTTAAAA
5843841 ACA
1 ACA
5843844 GGTCGGGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (16 bp):
ACATGTCAGGTTAAAA
Found at i:5844428 original size:24 final size:25
Alignment explanation
Indices: 5844375--5844428 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
5844365 TATAAAATTC
*
5844375 AATAATTAAATTAAAAAATTAAAAG
1 AATAATTAAATTAAAAAAGTAAAAG
* *
5844400 TATAA-TAAA-TAAAATAAGTAAGAG
1 AATAATTAAATTAAAA-AAGTAAAAG
5844424 AATAA
1 AATAA
5844429 AATTTAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 5 0.21
24 15 0.62
25 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (25 bp):
AATAATTAAATTAAAAAAGTAAAAG
Found at i:5846027 original size:24 final size:24
Alignment explanation
Indices: 5846000--5846059 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
5845990 TATTTGGTGT
5846000 TAAAATTATTAAAAAATTTGAGCA
1 TAAAATTATTAAAAAATTTGAGCA
* *
5846024 TAAAATTATTAAACACTTTGAGCA
1 TAAAATTATTAAAAAATTTGAGCA
5846048 TAAAATTATTAA
1 TAAAATTATTAA
5846060 TCACAATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.35
Consensus pattern (24 bp):
TAAAATTATTAAAAAATTTGAGCA
Found at i:5849314 original size:34 final size:34
Alignment explanation
Indices: 5849267--5849371 Score: 122
Period size: 34 Copynumber: 3.1 Consensus size: 34
5849257 TATTAATTAA
* *
5849267 CCTGAATTCCATAAGATACAAAATGCACTCAAAC
1 CCTGAATTACATAAGATACAAAATACACTCAAAC
* * *
5849301 CCTGAATTACATAAGATACACATTACACTCTAAC
1 CCTGAATTACATAAGATACAAAATACACTCAAAC
* * *
5849335 CCTGAAATACATAAGATACACATTACACT-ATAAC
1 CCTGAATTACATAAGATACAAAATACACTCA-AAC
5849369 CCT
1 CCT
5849372 CCTTGATTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.43, C:0.27, G:0.07, T:0.24
Consensus pattern (34 bp):
CCTGAATTACATAAGATACAAAATACACTCAAAC
Found at i:5861722 original size:23 final size:23
Alignment explanation
Indices: 5861692--5861750 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
5861682 CATTATTATA
5861692 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
5861715 TGGCACTACGATGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
5861738 CGGCACTTCGGTG
1 TGGCACTACGGTG
5861751 TATTTATACG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:5862047 original size:15 final size:13
Alignment explanation
Indices: 5862012--5862049 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
5862002 TAATTTGATG
5862012 ATAATGAT-ATAA
1 ATAATGATAATAA
5862024 ATAATGATAATAA
1 ATAATGATAATAA
5862037 TATATATGATAAT
1 -ATA-ATGATAAT
5862050 GCTAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 3 0.13
15 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (13 bp):
ATAATGATAATAA
Found at i:5864484 original size:13 final size:13
Alignment explanation
Indices: 5864466--5864510 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
5864456 TTAAATGATA
*
5864466 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
5864479 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
5864492 AAACAACTACAAT
1 AAAAAACTACAAT
5864505 AAAAAA
1 AAAAAA
5864511 GTATTAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.69, C:0.13, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:5864523 original size:26 final size:25
Alignment explanation
Indices: 5864463--5864536 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
5864453 GTATTAAATG
*
5864463 ATAAAAAAATTACAATAAAAAAGTCCA
1 ATAAACAAA-TACAATAAAAAAGT-CA
*
5864490 ATAAACAACTACAATAAAAAAGT-A
1 ATAAACAAATACAATAAAAAAGTCA
* *
5864514 TTAAATACAAATATAATAAAAAA
1 AT-AA-ACAAATACAATAAAAAA
5864537 AACAAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.05
25 2 0.05
26 29 0.73
27 7 0.17
ACGTcount: A:0.68, C:0.09, G:0.03, T:0.20
Consensus pattern (25 bp):
ATAAACAAATACAATAAAAAAGTCA
Found at i:5867176 original size:20 final size:19
Alignment explanation
Indices: 5867151--5867198 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
5867141 TACCTTAAAC
**
5867151 AGAGAATATAAGAGTATTTG
1 AGAGAAT-TAAGAGTAACTG
5867171 AGAGAAGTTAAGAGTAACTG
1 AGAGAA-TTAAGAGTAACTG
5867191 AGAGAATT
1 AGAGAATT
5867199 TGGTGTGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 22 0.88
21 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.27, T:0.25
Consensus pattern (19 bp):
AGAGAATTAAGAGTAACTG
Found at i:5868112 original size:19 final size:19
Alignment explanation
Indices: 5868088--5868165 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 19
5868078 TTAATTTTCC
5868088 TTTTCCTCTCTTTCCTCTT
1 TTTTCCTCTCTTTCCTCTT
*
5868107 TTTTCCT-TCTTTTCTTTTCTT
1 TTTTCCTCTC-TTTC--CTCTT
* *
5868128 TTTT-CTCTTTTTCCCCTT
1 TTTTCCTCTCTTTCCTCTT
* * *
5868146 TCTCCCTCTTTTTCCTCTT
1 TTTTCCTCTCTTTCCTCTT
5868165 T
1 T
5868166 CTAACTTTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
18 7 0.15
19 25 0.53
20 6 0.13
21 9 0.19
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTCCTCTCTTTCCTCTT
Found at i:5871602 original size:12 final size:12
Alignment explanation
Indices: 5871585--5871609 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5871575 TGCAATGTCG
5871585 TATTTGCAAGTT
1 TATTTGCAAGTT
5871597 TATTTGCAAGTT
1 TATTTGCAAGTT
5871609 T
1 T
5871610 GAGCTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TATTTGCAAGTT
Found at i:5872498 original size:7 final size:7
Alignment explanation
Indices: 5872490--5872543 Score: 72
Period size: 7 Copynumber: 7.4 Consensus size: 7
5872480 CACTCTTTTC
*
5872490 CTCTTTC
1 CTCTTTA
5872497 CTCTTTA
1 CTCTTTA
5872504 CTCTTTA
1 CTCTTTA
5872511 CTCTTTA
1 CTCTTTA
5872518 CTCTTTA
1 CTCTTTA
*
5872525 CTCCTTTG
1 CT-CTTTA
5872533 CTCCTTTA
1 CT-CTTTA
5872541 CTC
1 CTC
5872544 CGCTCTAGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
7 30 0.70
8 13 0.30
ACGTcount: A:0.09, C:0.35, G:0.02, T:0.54
Consensus pattern (7 bp):
CTCTTTA
Found at i:5873248 original size:17 final size:19
Alignment explanation
Indices: 5873213--5873250 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5873203 CTTTCCACAC
5873213 TAATTTTATTATATTTACA
1 TAATTTTATTATATTTACA
5873232 TAATTTTATT-T-TTTACA
1 TAATTTTATTATATTTACA
5873249 TA
1 TA
5873251 TCAATATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TAATTTTATTATATTTACA
Found at i:5881766 original size:39 final size:39
Alignment explanation
Indices: 5881723--5881800 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
5881713 TGGCGTTGTC
5881723 TGTCTGGGTTTAGTTAACCTTGTGAAGCTTCCCTTCTTT
1 TGTCTGGGTTTAGTTAACCTTGTGAAGCTTCCCTTCTTT
5881762 TGTCTGGGTTTAGTTAACCTTGTGAAGCTTCCCTTCTTT
1 TGTCTGGGTTTAGTTAACCTTGTGAAGCTTCCCTTCTTT
5881801 CTTTCTGATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (39 bp):
TGTCTGGGTTTAGTTAACCTTGTGAAGCTTCCCTTCTTT
Found at i:5885053 original size:38 final size:36
Alignment explanation
Indices: 5884977--5885053 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
5884967 TTTTTATATT
*
5884977 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
5885013 TTTAATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAA-AAAATTATATAAATATTAT-CAA
5885051 TTT
1 TTT
5885054 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 5 0.14
37 21 0.60
38 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:5885235 original size:20 final size:20
Alignment explanation
Indices: 5885199--5885236 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5885189 ATCCTATTCC
**
5885199 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
5885219 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
5885237 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Done.